Posts Tagged ‘Chemistry’

Targeting Untargetable Proto-Oncogenes

Curators: Larry H. Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

The following is a summary of a just published cancer research paper that describes the discovery of targetting proteins previously thought to be untargetable.

Getting Around “Undruggable” Proto-Oncogenes

Patricia Fitzpatrick Dimond, Ph.D.
The Notch1 protein and BET bromodomains are among the targets researchers are investigating. [© iQoncept – Fotolia.com]
    While multiple human cancers are associated with oncogene amplification,
  • epigenetic targets causing amplification such as transcription factors were once considered “undruggable,” or
  • unlikely to be modulated with a small molecule drug.
Generally, these proteins lack surface involutions suitable for high-affinity binding by small molecules. But by thinking outside the “loop” or the usual structures required for drug targets, investigators have been making headway in targeting the formerly untargetable.
    Multiple human cancers are associated with c-Myc gene amplification including lung carcinoma breast carcinoma, colon carcinoma, and neuroblastoma. The protogene also plays a key role in cell cycle regulation, metabolism, apoptosis, differentiation, cell adhesion, as well as in tumorigenesis, and participates in regulating hematopoietic homeostasis. Its gene product functions as a transcription regulator, part of
an extensive network of interacting factors regulating the expression, it has been estimated, of more than 15 percent of all human genes.
    While Myc oncogene family members, for example, act as key drivers in human cancers,
  • they have been considered undruggable as
  • they encode transcription factors and carry out essential functions in proliferative tissues,
  • suggesting that their inhibition could cause severe side effects.
And from a chemist’s point of view, these proteins’ surfaces are not amenable to binding drugs. In an online dialog posted on the NCI’s website in October of 2010, an investigator noted, “We don’t know how to interfere with these factors or their activities in clinical settings because, in general,
  • we lack the means to inhibit proteins that are not enzymes.”
    But by preventing key protein-protein interactions that enable the actions of these transcriptional drivers, scientists are drugging the formerly undruggable.

To Drug the Undruggable Target

    One such approach published  in Nature in 2009 by a team of Harvard scientists who was reported that they had successfully targeted a “master” protein, Notch1, which had been considered “untouchable” by conventional drugs. The protein is a
  • key transcription factor regulating genes involved in cell growth and survival but
  • like other transcription factors has proven an elusive drug target due to its structure.
The scientists said they had designed
  • a synthetic, cell-permeable alpha-helical peptide, SAHM1,
  • which could target a critical protein-protein interface in the notch transactivation complex.
The drug molecule enters cells and interferes with a protein-protein interaction essential for the transmission of cell growth signals via the Notch pathway.
    The researchers tested the drug using cells from patients with T-cell acute lymphoblastic leukemia (T-ALL) and a mouse model of the disease. The Notch1 gene is mutated in half of patients with T-ALL and
  • produces an inappropriately active Notch1 protein.
Activated Notch signaling has been seen in several other cancers including lung, ovarian, and pancreatic cancer, and melanoma.
    “We’ve drugged a so-called undruggable target,” said Gregory L. Verdine, Ph.D., Erving professor of chemistry at Harvard University. “This study validates the notion that you can target a transcription factor
  • by choosing a new class of molecules, namely stapled peptides.”

He added that, because the molecular logic of these proteins is similar to Notch1’s,

  • this strategy might work for other transcription factors as well.

Targeting BET

    Another emerging approach to drugging the undruggable is to target the bromo and extra C-terminal domain (BET) family of bromodomains that are
  • involved in binding epigenetic “marks” on histone proteins.
Four members of this 47-protein family interact with chromatin including histone acetylases and nucleosome remodeling complexes. Bromodomain proteins act as chromatin “readers” to recruit chromatin-regulating enzymes, including
  • “writers” and “erasers” of histone modification, to target promoters and to regulate gene expression.
As mentioned in a previous GEN article, epigenetic control systems generally involve three types of proteins:
  1. “writers”,   Writers attach chemical marks, such as methyl groups (to DNA) or acetyl groups (to the histone proteins that DNA wraps around)
  2. “readers”,  Readers bind to these marks, thereby influencing gene expression
  3. “erasers.”  Erasers remove the marks
    While investigators have considered that the precise function of the so-called BET bromodomain remains incompletely defined,
  • proteins containing this domain have become another epigenetic target for drug development companies.
  • these domains may allow researchers a way to get at oncogenic targets that were once thought undruggable including the proto-oncogene Myc.
    Small molecule inhibition of BET protein bromodomains also selectively suppresses other genes such as Bcl-2 that have important roles in cancer, as well as some NF-κB-dependent genes that have roles in both cancer and inflammation. Small molecule inhibition of BET bromodomains
  • leads to selective killing of tumor cells across a range of hematologic malignancies and in subsets of solid tumors.
In particular, the bromodomain protein, BRD4, has been identified recently as a therapeutic target in acute myeloid leukemia, multiple myeloma, Burkitt’s lymphoma, human nuclear protein in testis (NUT) midline carcinoma, colon cancer, and inflammatory disease;
  • its loss is a prognostic signature for metastatic breast cancer.
    BRD4 also contributes to regulation of both cell cycle and transcription of oncogenes, HIV, and human papilloma virus (HPV). Despite its role in a broad range of biological processes, the precise molecular mechanism of BRD4 function, until very recently, remained unknown.
    In 2010, investigators reported in Nature that they had identified a cell-permeable small molecule that bound competitively to bromodomains, or acetyl-lysine recognition motifs. Competitive binding by the small molecule JQ1, the investigators reported,
  • displaces the BRD4 fusion oncoprotein from chromatin,
  • prompting squamous differentiation and
  • specific antiproliferative effects in BRD4-dependent cell lines and patient-derived xenograft models.
    The authors say that these data established proof-of-concept for targeting protein–protein interactions of epigenetic readers, and could provide a versatile
  • chemical scaffold for the development of chemical probes more broadly throughout the bromodomain family.
    More recently, writing in the Journal of Medicinal Chemistry, investigators at GlaxoSmithKline reported that they had successfully optimized
a class of benzodiazepines as BET bromodomain inhibitors, apparently without any prior knowledge of identified molecular targets.
Significant medicinal chemistry provided the bromodomain inhibitor, I-BET762 or GSK525762, which is currently in a Phase I clinical trial for the treatment of NUT midline carcinoma, a rare but lethal form of cancer, and other cancers.

 Casting a Wide Net

    Constellation Pharmaceuticals of Cambridge, MA, announced that it has initiated a Phase I clinical trial of CPI-0610, a novel small molecule BET protein bromodomain inhibitor, in patients with previously treated and progressive lymphomas. This first-in-human trial is currently open at Sarah Cannon Research Institute in Nashville, Tennessee, and at the John Theurer Cancer Center in Hackensack, New Jersey. Additional study sites in the U.S. will join the trial over the next several months. Studies of CPI-0610 are also planned in patients with multiple myeloma and in patients with acute leukemia or myelodysplastic syndrome.
    Constellation’s CMO, Michael Cooper, M.D. told GEN that “small molecule inhibitors of BET protein bromodomains have demonstrated broad activity against hematologic malignancies in preclinical models. And this activity can be achieved in vivo with levels of compound exposure that are well tolerated. While we are encouraged by these observations, what really makes the area interesting is
  • the novel mechanism by which BET protein bromodomain inhibitors elicit their biologic effects.
  • They disrupt the interaction of BET proteins with acetylated lysine residues on histones and thereby
  • suppress the transcription of key cancer-related genes such as MYC, BCL-2, and a subset of NF-κB-dependent genes.
These genes have in the past been difficult to target with small molecules. In light of the breadth of the activity in preclinical models of hematologic malignancies and the important genes that are targeted, we intend to cast a wide net across hematologic malignancies in the clinic.”
    Robert Sims, Ph.D., and senior director of biology at Constellation explained that BET protein bromodomain inhibition is only of several areas of interest for the company. “The BET proteins constitute one class of epigenetic targets, namely
  • molecules that recognize patterns in chromatin architecture and
  • either enhance or suppress gene transcription.
Constellation’s approach to epigenetics also includes programs in the enzymes that modify the architecture of chromatin, for example by the
  • methylation or demethylation of histone proteins (writers and erasers, respectively).
Even though our first drug candidate is directed against a set of reader proteins, we are also looking at inhibitors of the writer protein, EZH2, which is mutated in some types of non-Hodgkin lymphoma and overexpressed in many malignancies.”
    In January 2012, Constellation and Genentech announced collaboration based on the science of epigenetics and chromatin biology to discover and develop innovative treatments for cancer and other diseases. Each company will each commit a significant portion of their research and development efforts to the advancement of programs under the collaboration, and each party will have the right to retain exclusive rights to programs emerging from the collaboration.
    And more biotech giants can be expected to enter the field of epigenetics as smaller companies advance into the clinic with this novel approach to controlling gene expression gone wrong in cancer cells.
Patricia Fitzpatrick Dimond, Ph.D. (pdimond@genengnews.com), is technical editor at Genetic Engineering & Biotechnology News
Employing Metabolomics in Cell Culture and Bioprocessing: Gaining greater predictability, control and quality
Challenges in developing and producing biotherapeutics are numerous and dynamic, including various market drivers and industry responses. Finding effective measures to support a foundation of control, predictability, and quality have been a concern and have paved the way to seeking out and applying newer technologies such as metabolomics successfully to bioprocessing. This webinar will first navigate through the landscape and challenges in developing and producing biotherapeutics. The journey continues with a walk through of the rationale for why metabolomics is a key tool for addressing critical bioprocessing needs followed by specific case studies and examples of how a functional metabolomic approach has been applied.
There are many relevant applications for functional metabolomics in bioprocessing starting with process development that include being able to: boost titer or productivity, improve product quality, enhance viability, or optimize defined media. The technology has be employed in biomarker discovery applications for the following purposes: to identify predictors of lactate consumption, to assess product quality, to predict indicative biomarkers of bioreactor performance or identify ideal clones. Lastly, functional metabolomics has been applied to enrich DOE experiments and troubleshooting for: historical deviation, process transfer, scale-up issues, disposable concerns, and lot or performance changes.

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Curator/Reporter Aviral Vatsa PhD, MBBS

Based on: A review by (Wink et al., 2011)

This post is in continuation to Part 1 by the same title.

In part one I covered the basics of role of redox chemistry in immune reactions, the phagosome cauldron, and how bacteria bacteria, virus and parasites trigger the complex pathway of NO production and its downstream effects. While we move further in this post, the previous post can be accessed here.


Regulation of the redox immunomodulators—NO/RNS and ROS

In addition to eradicating pathogens, NO/RNS and ROS and their chemical interactions act as effective immunomodulators that regulate many cellular metabolic pathways and tissue repair and proinflammatory pathways. Figure 3 shows these pathways.

Figure 3. Schematic overview of interactive connections between NO and ROS-mediated metabolic pathways. Credit: (Wink et al., 2011)

Regulation of iNOS enzyme activity is critical to NO production. Factors such as the availability of arginine, BH4, NADPH, and superoxide affect iNOS activity and thus NO production. In the absence of arginine and BH4 iNOS becomes a O2_/H2O2 generator (Vásquez-Vivar et al., 1999). Hence metabolic pathways that control arginine and BH4 play a role in determining the NO/superoxide balance. Arginine levels in cells depend on various factors such as type of uptake mechanisms that determine its spatial presence in various compartments and enzymatic systems. As shown in Fig3 Arginine is the sole substrate for iNOS and arginase. Arginase is another key enzyme in immunemodulation. AG is also regulated by NOS and NOX activities. NOHA, a product of NOS, inhibits AG, and O2–increases AG activity. Importantly, high AG activity is associated with elevated ROS and low NO fluxes. NO antagonises NOX2 assembly that in turn leads to reduction in O2_ production. NO also inhibits COX2 activity thus reducing ROS production. Thus, as NO levels decline, oxidative mechanisms increase. Oxidative and nitrosative stress can also decrease intracellular GSH (reduced form) levels, resulting in a reduced antioxidant capability of the cell.

Immune-associated redox pathways regulate other important metabolic cell functions that have the potential for widespread impact on cells, organs, and organisms. These pathways, such as mediated via methionine and polyamines, are critical for DNA stabilization, cell proliferation, and membrane channel activity, all of which are also involved in immune-mediated repair processes.

NO levels dictate the immune signaling pathway

NO/RNS and ROS actively control innate and adaptive immune signaling by participating in induction, maintenance, and/or termination of proinflammatory and anti-inflammatory signaling. As in pathogen eradication, the temporal and spatial concentration profiles of NO are key factors in determining immune-mediated processes.

Brune and coworkers (Messmer et al., 1994) first demonstrated that p53 expression was associated with the concentrations of NO that led to apoptosis in macrophages. Subsequent studies linked NO concentration profiles with expression of other key signaling proteins such as HIF-1α and Akt-P (Ridnour et al., 2008; Thomas et al., 2008). Various levels of NO concentrations trigger different pathways and expectedly this concentration-dependent profile varies with distance from the NO source.NO is highly diffucible and this characteristic can result in 1000 fold reduction in concentration within one cell length distance travelled from the source of production. Time course studies have also shown alteration in effects of same levels of NO over time e.g. NO-mediated ERK-P levels initially increased rapidly on exposure to NO donors and then decreased with continued NO exposure (Thomas et al., 2004), however HIF-1α levels remained high as long as NO levels were elevated. Thus some of the important factors that play critical role in NO effects are: distance from source, NO concentrations, duration of exposure, bioavailability of NO, and production/absence of other redox molecules.

Figure and legend credits: (Wink et al., 2011)

Fig 4: The effect of steady-state flux of NO on signal transduction mechanisms.

This diagram represents the level of sustained NO that is required to activate specific pathways in tumor cells. Similar effects have been seen on endothelial cells. These data were generated by treating tumor or endothelial cells with the NO donor DETANO (NOC-18) for 24 h and then measuring the appropriate outcome measures (for example, p53 activation). Various concentrations of DETANO that correspond to cellular levels of NO are: 40–60 μM DETANO = 50 nM NO; 80–120 μM DETANO = 100 nM NO; 500 μM DETANO = 400 nM NO; and 1 mM DETANO = 1 μM NO. The diagram represents the effect of diffusion of NO with distance from the point source (an activated murine macrophage producing iNOS) in vitro (Petri dish) generating 1 μM NO or more. Thus, reactants or cells located at a specific distance from the point source (i.e., iNOS, represented by star) would be exposed to a level of NO that governs a specific subset of physiological or pathophysiological reactions. The x-axis represents the different zone of NO-mediated events that is experienced at a specific distance from a source iNOS producing >1 μM. Note: Akt activation is regulated by NO at two different sites and by two different concentration levels of NO.

Species-specific NO production

The relationship of NO and immunoregulation has been established on the basis of studies on tumor cell lines or rodent macrophages, which are readily available sources of NO. However in humans the levels of protein expression for NOS enzymes and the immune induction required for such levels of expression are quite different than in rodents (Weinberg, 1998). This difference is most likely due to the human iNOS promotor rather than the activity of iNOS itself. There is a significant mismatch between the promoters of humans and rodents and that is likely to account for the notable differences in the regulation of gene induction between them. The combined data on rodent versus human NO and O2– production strongly suggest that in general, ROS production is a predominant feature of activated human macrophages, neutrophils, and monocytes, and the equivalent murine immune cells generate a combination of O2– and NO and in some cases, favor NO production. These differences may be crucial to understanding how immune responses are regulated in a species-specific manner. This is particularly useful, as pathogen challenges change constantly.

The next post in this series will cover the following topics:

The impact of NO signaling on an innate immune response—classical activation

NO and proinflammatory genes

NO and regulation of anti-inflammatory pathways

NO impact on adaptive immunity—immunosuppression and tissue-restoration response

NO and revascularization

Acute versus chronic inflammatory disease


1. Wink, D. A. et al. Nitric oxide and redox mechanisms in the immune response. J Leukoc Biol 89, 873–891 (2011).

2. Vásquez-Vivar, J. et al. Tetrahydrobiopterin-dependent inhibition of superoxide generation from neuronal nitric oxide synthase. J. Biol. Chem. 274, 26736–26742 (1999).

3. Messmer, U. K., Ankarcrona, M., Nicotera, P. & Brüne, B. p53 expression in nitric oxide-induced apoptosis. FEBS Lett. 355, 23–26 (1994).

4. Ridnour, L. A. et al. Molecular mechanisms for discrete nitric oxide levels in cancer. Nitric Oxide 19, 73–76 (2008).

5. Thomas, D. D. et al. The chemical biology of nitric oxide: implications in cellular signaling. Free Radic. Biol. Med. 45, 18–31 (2008).

6. Thomas, D. D. et al. Hypoxic inducible factor 1alpha, extracellular signal-regulated kinase, and p53 are regulated by distinct threshold concentrations of nitric oxide. Proc. Natl. Acad. Sci. U.S.A. 101, 8894–8899 (2004).

7. Weinberg, J. B. Nitric oxide production and nitric oxide synthase type 2 expression by human mononuclear phagocytes: a review. Mol. Med. 4, 557–591 (1998).

Further reading on NO:

Nitric Oxide in bone metabolism July 16, 2012

Author: Aviral Vatsa PhD, MBBS


Nitric Oxide production in Systemic sclerosis July 25, 2012

Curator: Aviral Vatsa, PhD, MBBS


Nitric Oxide Signalling Pathways August 22, 2012 by

Curator/ Author: Aviral Vatsa, PhD, MBBS


Nitric Oxide: a short historic perspective August 5, 2012

Author/Curator: Aviral Vatsa PhD, MBBS


Nitric Oxide: Chemistry and function August 10, 2012

Curator/Author: Aviral Vatsa PhD, MBBS


Nitric Oxide and Platelet Aggregation August 16, 2012 by

Author: Dr. Venkat S. Karra, Ph.D.


The rationale and use of inhaled NO in Pulmonary Artery Hypertension and Right Sided Heart Failure August 20, 2012

Author: Larry Bernstein, MD


Nitric Oxide: The Nobel Prize in Physiology or Medicine 1998 Robert F. Furchgott, Louis J. Ignarro, Ferid Murad August 16, 2012

Reporter: Aviva Lev-Ari, PhD, RN


Coronary Artery Disease – Medical Devices Solutions: From First-In-Man Stent Implantation, via Medical Ethical Dilemmas to Drug Eluting Stents August 13, 2012

Author: Aviva Lev-Ari, PhD, RN


Nano-particles as Synthetic Platelets to Stop Internal Bleeding Resulting from Trauma

August 22, 2012

Reported by: Dr. V. S. Karra, Ph.D.


Cardiovascular Disease (CVD) and the Role of agent alternatives in endothelial Nitric Oxide Synthase (eNOS) Activation and Nitric Oxide Production July 19, 2012

Curator and Research Study Originator: Aviva Lev-Ari, PhD, RN


Macrovascular Disease – Therapeutic Potential of cEPCs: Reduction Methods for CV Risk

July 2, 2012

An Investigation of the Potential of circulating Endothelial Progenitor Cells (cEPCs) as a Therapeutic Target for Pharmacological Therapy Design for Cardiovascular Risk Reduction: A New Multimarker Biomarker Discovery

Curator: Aviva Lev-Ari, PhD, RN


Bone remodelling in a nutshell June 22, 2012

Author: Aviral Vatsa, Ph.D., MBBS


Targeted delivery of therapeutics to bone and connective tissues: current status and challenges- Part, September  

Author: Aviral Vatsa, PhD, September 23, 2012


Calcium dependent NOS induction by sex hormones: Estrogen

Curator: S. Saha, PhD, October 3, 2012


Nitric Oxide and Platelet Aggregation,

Author V. Karra, PhD, August 16, 2012


Bystolic’s generic Nebivolol – positive effect on circulating Endothelial Progenitor Cells endogenous augmentation

Curator: Aviva Lev-Ari, PhD, July 16, 2012


Endothelin Receptors in Cardiovascular Diseases: The Role of eNOS Stimulation

Author: Aviva Lev-Ari, PhD, 10/4/2012


Inhibition of ET-1, ETA and ETA-ETB, Induction of NO production, stimulation of eNOS and Treatment Regime with PPAR-gamma agonists (TZD): cEPCs Endogenous Augmentation for Cardiovascular Risk Reduction – A Bibliography

Curator: Aviva Lev-Ari, 10/4/2012.


Nitric Oxide Nutritional remedies for hypertension and atherosclerosis. It’s 12 am: do you know where your electrons are?

Author and Reporter: Meg Baker, 10/7/2012.


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Immunoreactivity of Nanoparticles

Author: Tilda Barliya PhD

As nanotechnology progresses from research and development to commercialization and use, it is likely that manufactured nanomaterials and nanoproducts will be released into the environment.

Adverse effects of nanoparticles on human health depend on individual factors such as genetics and existing disease, as well as exposure, and nanoparticle chemistry, size, shape, agglomeration state, and electromagnetic properties. Animal and human studies show that inhaled nanoparticles are lessefficiently removed than larger particles by the macrophage clearance mechanisms in the lung,causing lung damage, and that nanoparticles can translocate through the circulatory, lymphatic, and nervous systems to many tissues and organs, including the brain.

The key to understanding the toxicity of nanoparticles is that their minute size, smaller than cells and cellular organelles, allows them to penetrate these basic biological structures, disrupting their normal function. Examples of toxic effects include tissue inflammation, and altered cellular redox balance toward oxidation, causing abnormal function or cell death. http://arxiv.org/ftp/arxiv/papers/0801/0801.3280.pdf

Some NPs happen to be toxic to biological systems, others are relatively benign, while others confer health benefits. As current knowledge of the toxicology of ‘bulk’ materials may not suffice in reliably predicting toxic forms of nanoparticles, ongoing and expanded study of ‘nanotoxicity’ will be necessary. For nanotechnologies with clearly associated health risks, intelligent design of materials and devices is needed to derive the benefits of these new technologies while limiting adverse health impacts.

Human skin, lungs, and the gastro-intestinal tract are in constant contact with the environment. While the skin is generally an effective barrier to foreign substances, the lungs and gastro-intestinal tract are more vulnerable. These three ways are the most likely points of entry for natural or anthropogenic nanoparticles. Injections and implants are other possible routes of exposure, primarily limited to engineered materials. Due to their small size, nanoparticles can translocate from these entry portals into the circulatory and lymphatic systems, and ultimately to body tissues and organs. Some nanoparticles, depending on their composition and size, can produce irreversible damage to cells by oxidative stress or/and organelle injury.

Are they biocompatible? Do the nanoparticles enter the lymphatic and circulatory systems? If not, do they accumulate in the skin and what are the long-term effects of accumulation? Do they produce inflammation? If they enter the lymphatic and circulatory system, is the amount significant? What are the long-term effects of this uptake? Related to the beneficial antioxidant properties of some nanomaterials, long-term effect need to be studied, in addition to the short-term antioxidant effect. What is the long-

term fate of these nanoparticles? Are they stored in the skin? Do they enter circulation? What happens when the nanoparticles undergo chemical reactions and lose their antioxidant properties?

For a full view of the questions needed to be addressed please visit. http://bdds.fudan.edu.cn/…/fdfa2aa9-df2b-4c9f-a2a5-a33ee29acb76.pdf

The answers to some of these questions are known, and will be presented in the chapter dedicated to nanoparticles toxicity, however most of the remaining questions still remain unanswered.

The immunostimulatory properties of nanoparticles discussed here include their antigenicity, adjuvant properties, inflammatory responses and the mechanisms through which nanoparticles are recognized by the immune system. Since this is a very complicated mechanism , the factors affecting the immune response are summaried here:


  • Th1/Th2 stimulation
  • Adjuvent properties
  • Internalization/phagocytic uptake
  • Hapten properties
  • Particle clearance


  • Toxicity to immune cells
  • Binding plasma proteins
  • Particle clearance
  • Immune cell stimulation


  • Interaction with plasma proteins
  • Internalization/phagocytic uptake
  • Immune cell stimulation
  • Particle clearance


  • Immunogenicity

For example: In general, cationic (positively-charged) particles are more likely to induce inflammatory reactions than anionic (negativelycharged) and neutral species. For example, anionic generation- 4.5 PAMAM dendrimers did not cause human leukocytes (white blood cells) to secrete cytokines53 but cationic liposomes induced secretion of cytokines such as TNF, IL-12 and IFNγ. Systemic administration of another cationic nanoliposome alone or in combination with bacterial DNA did not induce cytokine production but increased the expression of DC surface markers, CD80/CD86, which are important in the inflammatory response.

Trace impurities within the nanomaterial formulation can also frequently induce an inflammatory response. Early studies suggest that carbon nanotubes induce inflammatory reactions, but a more recent study shows that they don’t when they are purified.

Another consideration in the inflammatory response is maintaining the Th1/Th2 response — the inflammatory reaction.  triggered by Th cells that direct and activate other immune cells such as B and T cells and macrophages to secrete different cytokines. This response is important for protecting against cancer cells and pathogens and to avoid hypersensitivity (undesirable and exaggerated immune response) reactions. Several studies have addressed the influence of nanoparticles on Th1 and Th2 responses. Large (>1 μm) industrialized particles induced the Th1 response, whereas smaller ones (<500 nm) were associated with Th2.

In contrast, some small engineered nanoparticles such as 500 nm PLGA, 270 nm PLGA65, 80 nm and 100 nm nanoemulsions, 95 nm and 112 nm PEG–PHDA nanoparticles, and 123 nm dendrosome induced the Th1 response, while 5mn 5th generation PAMAM dendrimers didn’t cause overall inflammatory reaction in vivo but weakly induced Th2 cytokine production.

Therefore, more structure–activity relationship studies are required to understand how size, surface modification and charge of engineered particles influence the Th1/Th2 balance

Particle stimulation of adaptive (acquired) immunity has also been described. For example, small (<100 nm) polystyrene particles promoted CD8 and CD4 T-cell responses and were associated with higher antibody levels than larger (>500 nm) particles. Understanding the mechanisms requires further investigation, and is important for nanovaccine formulation development.

Phagosome-mediated processing and presentation of nanoparticles may differ from that of ‘canonical’ antigens. Certain biodegradable nanoparticles can be taken up through conventional pathogen-specific routes and can stimulate inflammatory reactions just like pathogens

More mechanistic studies are required to understand how the immune system manages non-biodegradable components of nanoparticles (for example, metallic cores). Many questions remain regarding processing of multi-component and multi functional nanoparticles. Are the individual components (the coating, core, and so on) stable inside the phagosome or do they separate? Are the biodegradable and non-biodegradable components processed together or individually?

Immunotoxicological analysis of new molecular entities is not a straightforward process, and there is no universal guide for immunotoxicity.


The mechanism of cellular uptake of nanoparticles and the biodistribution depend on the physico-chemical properties of the particles and in particular on their surface characteristics. Moreover, as particles are mainly recognized and engulfed by immune cells special attention should be paid to nano–immuno interactions. It is also important to use primary cells for testing of the biocompatibility of nanoparticles, as they are closer to the in vivo situation when compared to transformed cell lines.

Understanding the unique characteristics of engineered nanomaterials and their interactions with biological systems is key to the safe implementation of these materials in novel biomedical diagnostics and therapeutics.

The main challenge in immunological studies of nanomaterials is choosing an experimental approach that is free of falsepositive or false-negative readouts. The majority of the standard immunotoxicological methods are applicable to nanomaterials. However, as nanoparticles represent physically and chemically diverse materials, the classical methods cannot always be applied without modification, and novel approaches may be required. For example, many nanoparticles absorb in the UV–Vis range and some particles may catalyse enzyme reactions or quench fluorescent dyes commonly used as detection reagents in various end-point or kinetic assays. These and other methodological

challenges in preclinical evaluation of nanoparticles are reviewed in detail elsewhere.

Both ‘classical’ and novel imunotoxicological assessments of nanomaterials clearly need a scrupulous stepwise validation, standardization, and demonstration of their physiological relevance.

Industry, academics, and federal agencies are now collaborating to identify critical parameters in nanoparticles characterization and to establish acceptance criteria for nanomaterial-specific assays.


1.Cristina Buzea, Ivan. I. Pacheco Blandino, and Kevin Robbie. Nanomaterials and nanoparticles:Sources and toxicity. Biointerphases vol. 2, issue 4 (2007) pages MR17 – MR172 http://arxiv.org/ftp/arxiv/papers/0801/0801.3280.pdf

2. Marina A. Dobrovolskaia* and Scott E. McNeil. Immunological properties of engineered nanomaterials. Nature Nanotechnology 2007; 2; 469-479.  http:// bdds.fudan.edu.cn/…/fdfa2aa9-df2b-4c9f-a2a5-a33ee29acb76.pdf

3.  Kunzmanna A,  Anderssonb B, Thurnherrc T, Krugc H, Scheyniusb A,  Fadeel B. Toxicology of engineered nanomaterials: Focus on biocompatibility, biodistribution and biodegradation. Biochimica et Biophysica Acta (BBA) – General Subjects. Volume 1810, Issue 3, March 2011, Pages 361–373 http://www.sciencedirect.com/science/article/pii/S0304416510001145

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Curator and Reporter: Aviral Vatsa PhD, MBBS

Based on: A review by Wink et al., 2011

This is the first part of a two part post

Nitric oxide (NO), reactive nitrogen species (RNS) and reactive oxygen species (ROS) perform dual roles as immunotoxins and immunomodulators. An incoming immune signal initiates NO and ROS production both for tackling the pathogens and modulating the downstream immune response via complex signaling pathways. The complexity of these interactions is a reflection of involvement of redox chemistry in biological setting (fig. 1)

Fig 1. Image credit: (Wink et al., 2011)

Previous studies have highlighted the role of NO in immunity. It was shown that macrophages released a substance that had antitumor and antipathogen activity and required arginine for its production (Hibbs et al., 1987, 1988). Hibbs and coworkers further strengthened the connection between immunity and NO by demonstrating that IL2 mediated immune activation increased NO levels in patients and promoted tumor eradication in mice (Hibbs et al., 1992; Yim et al., 1995).

In 1980s a number of authors showed the direct evidence that macrophages made nitrite, nitrates and nitrosamines. It was also shown that NO generated by macrophages could kill leukemia cells (Stuehr and Nathan, 1989). Collectively these studies along with others demonstrated the important role NO plays in immunity and lay the path for further research in understanding the role of redox molecules in immunity.

NO is produced by different forms of nitric oxide synthase (NOS) enzymes such as eNOS (endothelial), iNOS (inducible) and nNOS (neuronal). The constitutive forms of eNOS generally produce NO in short bursts and in calcium dependent manner. The inducible form produces NO for longer durations and is calcium independent. In immunity, iNOS plays a vital role. NO production by iNOS can occur over a wide range of concentrations from as little as nM to as much as µM. This wide range of NO concentrations provide iNOS with a unique flexibility to be functionally effective in various conditions and micro-environements and thus provide different temporal and concentration profiles of NO, that can be highly efficient in dealing with immune challenges.

Redox reactions in immune responses

NO/RNS and ROS are two categories of molecules that bring about immune regulation and ‘killing’ of pathogens. These molecules can perform independently or in combination with each other. NO reacts directly with transition metals in heme or cobalamine, with non-heme iron, or with reactive radicals (Wink and Mitchell, 1998). The last reactivity also imparts it a powerful antioxidant capability. NO can thus act directly as a powerful antioxidant and prevent injury initiated by ROS (Wink et al., 1999). On the other hand, NO does not react directly with thiols or other nucleophiles but requires activation with superoxide to generate RNS. The RNS species then cause nitrosative and oxidative stress (Wink and Mitchell, 1998).

The variety of functions achieved by NO can be understood if one looks at certain chemical concepts. NO and NO2 are lipophilic and thus can migrate through cells, thus widening potential target profiles. ONOO-, a RNS, reacts rapidly with CO2 that shortens its half life to <10 ms. The anionic form and short half life limits its mobility across membranes. When NO levels are higher than superoxide levels, the CO2-OONOintermediate is converted to NO2 and N2O3 and changes the redox profile from an oxidative to a nitrosative microenvironment. The interaction of NO and ROS determines the bioavailability of NO and proximity of RNS generation to superoxide source, thus defining a reaction profile. The ROS also consumes NO to generate NO2 and N2O3 as well as nitrite in certain locations. The combination of these reactions in different micro-environments provides a vast repertoire of reaction profiles for NO/RNS and ROS entities.

The Phagosome ‘cauldron’

The phagosome provides an ‘isolated’ environment for the cell to carry out foreign body ‘destruction’. ROS, NO and RNS interact to bring about redox reactions. The concentration of NO in a phagosome can depend on the kind of NOS in the vicinity and its activity and other localised cellular factors. NO and is metabolites such as nitrites and nitrates along with ROS combine forces to kill pathogens in the acidic environment of the phagosome as depicted in the figure 2 below.

Fig 2. The NO chemistry of the phagosome. (image credit: (Wink et al., 2011)

This diagram depicts the different nitrogen oxide and ROS chemistry that can occur within the phagosome to fight pathogens. The presence of NOX2 in the phagosomes serves two purposes: one is to focus the nitrite accumulation through scavenging mechanisms, and the second provides peroxide as a source of ROS or FA generation. The nitrite (NO2−) formed in the acidic environment provides nitrosative stress with NO/NO2/N2O3. The combined acidic nature and the ability to form multiple RNS and ROS within the acidic environment of the phagosome provide the immune response with multiple chemical options with which it can combat bacteria.


There are various ways in which NO combines forces with other molecules to bring about bacterial killing. Here are few examples

E.coli: It appears to be resistant to individual action of NO/RNS and H2O2 /ROS. However, when combined together, H2O2 plus NO mediate a dramatic, three-log increase in cytotoxicity, as opposed to 50% killing by NO alone or H2O2 alone. This indicates that these bacteria are highly susceptible to their synergistic action.

Staphylococcus: The combined presence of NO and peroxide in staphylococcal infections imparts protective effect. However, when these bacteria are first exposed to peroxide and then to NO there is increased toxicity. Hence a sequential exposure to superoxide/ROS and then NO is a potent tool in eradicating staphylococcal bacteria.

Mycobacterium tuberculosis: These bacterium are sensitive to NO and RNS, but in this case, NO2 is the toxic species. A phagosome microenvironment consisting of ROS combined with acidic nitrite generates NO2/N2O3/NO, which is essential for pathogen eradication by the alveolar macrophage. Overall, NO has a dual function; it participates directly in killing an organism, and/or it disarms a pathway used by that organism to elude other immune responses.


Many human parasites have demonstrated the initiation of the immune response via the induction of iNOS, that then leads to expulsion of the parasite. The parasites include Plasmodia(malaria), Leishmania(leishmaniasis), and Toxoplasma(toxoplasmosis). Severe cases of malaria have been related with increased production of NO. High levels of NO production are however protective in these cases as NO was shown to kill the parasites (Rockett et al., 1991; Gyan et al., 1994). Leishmania is an intracellualr parasite that resides in the mamalian macrophages. NO upregulation via iNOS induction is the primary pathway involved in containing its infestation. A critical aspect of NO metabolism is that NOHA inhibits AG activity, thereby limiting the growth of parasites and bacteria including Leishmania, Trypanosoma, Schistosoma, HelicobacterMycobacterium, and Salmonella, and is distinct from the effects of RNS. Toxoplasma gondii is also an intracellular parasite that elicits NO mediated response. INOS knockout mice have shown more severe inflammatory lesions in the CNS that their wild type counterparts, in response to toxoplasma exposure. This indicates the CNS preventative role of iNOS in toxoplasmosis (Silva et al., 2009).


Viral replication can be checked by increased production of NO by induction of iNOS (HIV-1, coxsackievirus, influenza A and B, rhino virus, CMV, vaccinia virus, ectromelia virus, human herpesvirus-1, and human parainfluenza virus type 3) (Xu et al., 2006). NO can reduce viral load, reduce latency and reduce viral replication. One of the main mechanisms as to how NO participates in viral eradication involves the nitrosation of critical cysteines within key proteins required for viral infection, transcription, and maturation stages. For example, viral proteases or even the host caspases that contain cysteines in their active site are involved in the maturation of the virus. The nitrosative stress environment produced by iNOS may serve to protect against some viruses by inhibiting viral infectivity, replication, and maturation.

To be continued in part 2 …


Gyan, B., Troye-Blomberg, M., Perlmann, P., Björkman, A., 1994. Human monocytes cultured with and without interferon-gamma inhibit Plasmodium falciparum parasite growth in vitro via secretion of reactive nitrogen intermediates. Parasite Immunol. 16, 371–3

Hibbs, J.B., Jr, Taintor, R.R., Vavrin, Z., 1987. Macrophage cytotoxicity: role for L-arginine deiminase and imino nitrogen oxidation to nitrite. Science 235, 473–476.

Hibbs, J.B., Jr, Taintor, R.R., Vavrin, Z., Rachlin, E.M., 1988. Nitric oxide: a cytotoxic activated macrophage effector molecule. Biochem. Biophys. Res. Commun. 157, 87–94.

Hibbs, J.B., Jr, Westenfelder, C., Taintor, R., Vavrin, Z., Kablitz, C., Baranowski, R.L., Ward, J.H., Menlove, R.L., McMurry, M.P., Kushner, J.P., 1992. Evidence for cytokine-inducible nitric oxide synthesis from L-arginine in patients receiving interleu

Rockett, K.A., Awburn, M.M., Cowden, W.B., Clark, I.A., 1991. Killing of Plasmodium falciparum in vitro by nitric oxide derivatives. Infect Immun 59, 3280–3283.

Stuehr, D.J., Nathan, C.F., 1989. Nitric oxide. A macrophage product responsible for cytostasis and respiratory inhibition in tumor target cells. J. Exp. Med. 169, 1543–1555.

Wink, D.A., Hines, H.B., Cheng, R.Y.S., Switzer, C.H., Flores-Santana, W., Vitek, M.P., Ridnour, L.A., Colton, C.A., 2011. Nitric oxide and redox mechanisms in the immune response. J Leukoc Biol 89, 873–891.

Wink, D.A., Mitchell, J.B., 1998. Chemical biology of nitric oxide: Insights into regulatory, cytotoxic, and cytoprotective mechanisms of nitric oxide. Free Radic. Biol. Med. 25, 434–456.

Wink, D.A., Vodovotz, Y., Grisham, M.B., DeGraff, W., Cook, J.C., Pacelli, R., Krishna, M., Mitchell, J.B., 1999. Antioxidant effects of nitric oxide. Meth. Enzymol. 301, 413–424.

Xu, W., Zheng, S., Dweik, R.A., Erzurum, S.C., 2006. Role of epithelial nitric oxide in airway viral infection. Free Radic. Biol. Med. 41, 19–28.

Yim, C.Y., McGregor, J.R., Kwon, O.D., Bastian, N.R., Rees, M., Mori, M., Hibbs, J.B., Jr, Samlowski, W.E., 1995. Nitric oxide synthesis contributes to IL-2-induced antitumor responses against intraperitoneal Meth A tumor. J. Immunol. 155, 4382–4390.

Further reading on NO:

Nitric Oxide in bone metabolism July 16, 2012

Author: Aviral Vatsa PhD, MBBS


Nitric Oxide production in Systemic sclerosis July 25, 2012

Curator: Aviral Vatsa, PhD, MBBS


Nitric Oxide Signalling Pathways August 22, 2012 by

Curator/ Author: Aviral Vatsa, PhD, MBBS


Nitric Oxide: a short historic perspective August 5, 2012

Author/Curator: Aviral Vatsa PhD, MBBS


Nitric Oxide: Chemistry and function August 10, 2012

Curator/Author: Aviral Vatsa PhD, MBBS


Nitric Oxide and Platelet Aggregation August 16, 2012 by

Author: Dr. Venkat S. Karra, Ph.D.


The rationale and use of inhaled NO in Pulmonary Artery Hypertension and Right Sided Heart Failure August 20, 2012

Author: Larry Bernstein, MD


Nitric Oxide: The Nobel Prize in Physiology or Medicine 1998 Robert F. Furchgott, Louis J. Ignarro, Ferid Murad August 16, 2012

Reporter: Aviva Lev-Ari, PhD, RN


Coronary Artery Disease – Medical Devices Solutions: From First-In-Man Stent Implantation, via Medical Ethical Dilemmas to Drug Eluting Stents August 13, 2012

Author: Aviva Lev-Ari, PhD, RN


Nano-particles as Synthetic Platelets to Stop Internal Bleeding Resulting from Trauma

August 22, 2012

Reported by: Dr. V. S. Karra, Ph.D.


Cardiovascular Disease (CVD) and the Role of agent alternatives in endothelial Nitric Oxide Synthase (eNOS) Activation and Nitric Oxide Production July 19, 2012

Curator and Research Study Originator: Aviva Lev-Ari, PhD, RN


Macrovascular Disease – Therapeutic Potential of cEPCs: Reduction Methods for CV Risk

July 2, 2012

An Investigation of the Potential of circulating Endothelial Progenitor Cells (cEPCs) as a Therapeutic Target for Pharmacological Therapy Design for Cardiovascular Risk Reduction: A New Multimarker Biomarker Discovery

Curator: Aviva Lev-Ari, PhD, RN


Bone remodelling in a nutshell June 22, 2012

Author: Aviral Vatsa, Ph.D., MBBS


Targeted delivery of therapeutics to bone and connective tissues: current status and challenges- Part, September  

Author: Aviral Vatsa, PhD, September 23, 2012


Calcium dependent NOS induction by sex hormones: Estrogen

Curator: S. Saha, PhD, October 3, 2012


Nitric Oxide and Platelet Aggregation,

Author V. Karra, PhD, August 16, 2012


Bystolic’s generic Nebivolol – positive effect on circulating Endothelial Progenitor Cells endogenous augmentation

Curator: Aviva Lev-Ari, PhD, July 16, 2012


Endothelin Receptors in Cardiovascular Diseases: The Role of eNOS Stimulation

Author: Aviva Lev-Ari, PhD, 10/4/2012


Inhibition of ET-1, ETA and ETA-ETB, Induction of NO production, stimulation of eNOS and Treatment Regime with PPAR-gamma agonists (TZD): cEPCs Endogenous Augmentation for Cardiovascular Risk Reduction – A Bibliography

Curator: Aviva Lev-Ari, 10/4/2012.


Nitric Oxide Nutritional remedies for hypertension and atherosclerosis. It’s 12 am: do you know where your electrons are?

Author and Reporter: Meg Baker, 10/7/2012.



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Author: Tilda Barliya PhD

Title: Factors affecting the PK of the nanocarrier.

Category: Nanotechnology in drug delivery

A plethora of new products are emerging as potential therapeutic agents. This calls for detailed studies of their unique pharmacologic characteristics and mechanisms of action in humans. This review written by Caron WP et al (Zamboni’s group) provides a major overview of the factors that affect the pharmacokinetics (PK) and pharmacodynamics (PD) of nanoparticle carries in preclinical models and patients (1). I will use this article as the main source as it was so nicely written yet many other references are added within.

The disposition of carrier-mediated agents (CMAs) is dependent on the carrier and not on the parent drug, until the drug is released from the carrier into the system and includes encapsulated (the drug within or bound to the carrier), released (the active drug that gets released from the carrier), and sum total (encapsulated drug plus released drug).

After the drug has been released from its carrier, it is pharmacologically active and subjected to the same routes of metabolism and clearance (CL) as the non-carrier form of the drug (1,2).

In theory, the PK disposition of the drug after it is released from the carrier should be the same as after administration of the small-molecule or standard formulations. Therefore, the pharmacology and PK of CMAs are complex and call for comprehensive analytical studies to assess the disposition of encapsulated and released forms of the drug in plasma and tumor.

Interindividual variability in drug exposure, represented by area under the plasma concentration– time curve (AUC) of the encapsulated drug and several factor can potentially affect it:

  • Physical characteristics of the CMA (size, charge, surface modification). Figure 1
  • Host-associated characteristics such as gender and age as well as the host mononuclear phagocyte system (MPS), which is a collective term for the immune cells.

F3.large.jpg (1280×843)

Figure 1 here (=figure 3 in the original paper. ref 1) : Nanoparticle clearance and biocompatibility are dependent on various factors including physical characteristics of the carrier as well as physiologic parameters such as the mononuclear phagocyte system (MPS) (reticuloendothelial system (RES)) recognition and enhanced permeability and retention (EPR) effect. There are qualitative relationships between the independent variables, namely, particle size, particle zeta-potential (surface charge), and solubility, and the dependent variable, namely, biocompatibility. Biocompatibility, or extent of exposure (area under the plasma concentration–time curve), includes the route of uptake and clearance (shown in green as the EPR effect and renal and biliary clearance), cytotoxicity (shown in red, can represent either efficacy or toxicities/ adverse events in anticancer treatment), and MPS/RES recognition (shown in blue).

The effect on the immune cells is divided into two categories:  (i) responses to nanoparticles that are specifically modified to stimulate the immune system (e.g., vaccine carriers) and (ii) undesirable interactions and/or side-effects.

Immune cells that participate in nanoparticle uptake are circulating monocytes, platelets, leukocytes, and dendritic cells in the bloodstream (3,4).  In addition, nanoparticles can be taken up in tissues by phagocytes, e.g., by Kupffer cells in the liver, by dendritic cells in the lymph nodes, by B cells in the spleen, and by macrophages

Uptake mechanisms may occur through different pathways and can often be facilitated by the adsorption of opsonins to the nanoparticle surface

Physical characteristics:

  • Particle size: In one study of liposomes, particles that had a hydrodynamic diameter between 100 and 200 nm had a fourfold higher rate of uptake in tumors than particles <50 nm or >300 nm.
  • Surface modification: Conjugated PEG polymer onto the surface- is known to minimize opsonization and thus subsequent decreased rate of MPS uptake overall plasma exposures of drugs contained within PEGylated liposomes were six fold higher than those contained within non-PEGylated liposomes
  • Surface charge: Uncharged liposomes have lower CLs than either positively or negatively charged liposomes (probably due to reduced opsonization by MPS. rate of CL from blood was significantly higher for negatively charged particles than for uncharged particles

It can be summarized as for their rate of clearance from highest (left) to lowest (right) as:

positive>negative> neutral

Note: PEGylation can alter the alter this rate significantly for example,

Levchenko et al. showed that the negative charge on liposomes can be shielded with this physical alteration, leading to a significantly reduced rate of liver uptake and consequent prolongation of their presence in circulating blood (5).

Host characteristics

  • Age: In some cases, age-related effects on the PK of some PEGylated liposomal agents have been reported, where in younger male patients (<60) there was a higher rate of clearance of two different agents (Doxil and CDK602) compared to older patients (>60). In other words, in older age, the CL rate was lower and therefore higher AUC/dose. No relation to age was observed for female patients, in the same study.

Alterations in the PK and PD of CMAs may involve accerelated decline in immune system functioning, specifically the association between aging and the functioning of monocytes (6). In theory, there is a loss of MPS activity or function in elderly patients, and this decreases the CL of CMAs by the MPS, leading to increased drug exposures and toxicity in elderly patients. In terms of efficacy, greater age was inversely proportional to progression-free survival; however, no correlation was found between age and overall survival.

  •  Gender: In similar study to the one presented above, female patients had overall lower CL of DOXIL, IHL-305 and CDK602 compared to male patients of the same age.

The basis for the gender-related differences in the PK and PD of CMAs is unclear. It has been hypothesized that some of the differences may be attributed to the effects of sex hormones such as testosterone and estrogen on immune cell function.

Delivery of CMAs Into Tumor

Major advances in the understanding of tumor biology have led to the discovery of targeted agents that can deliver drugs to the desired site while minimizing exposure in normal tissues, thereby minimizing the associated adverse effects. Whereas conventional drugs encounter numerous obstacles en route to their target, CMAs can take advantage of a tumor’s leaky vasculature to extravasate into tissue, via the enhanced permeability and retention effect (EPR).

Note: The extend of the EPR effect is highly debated since although passive targeting through the EPR effect has been a key concept in delivering CMAs to tumors, it does not ensure uniform delivery to all regions of tumor. Furthermore, not all tumors exhibit an EPR effect, and the permeability of vessels may not be the same across any single tumor.

Active targeting may overcome these limitations. The CMAs can be enabled to bind to specific cells in a tumor by using surface attached ligands that are capable of recognizing and binding to cells of interest.

Antibody-mediated targeting has been the method of choice, other targeting strategies using nucleic acids, carbohydrates, peptides, aptamers, vitamins, and other agents are also being evaluated.

Other major points that can affect the PK disposition

  • The linearity and nonlinearity of the CLs of a drug (might be associated with the dose like with S-CKD602)(7).
  • Drug-drug interaction (single agent vs combination)
  • Body composition (Body surface area, body weight)

There are a multitude of properties of CMAs that differ from those of the active small-molecule drugs they contain. These differences lead to significant variability in the PK and PD of carrier- mediated drugs. It has been shown that physical properties, the MPS, the presence of tumors in the liver, EPRs, drug–drug interactions, age, and gender all contribute in varying degrees to the PK disposition and PD end points of CMAs in patients.

Areas of research that can aid in an understanding of how these agents should be used and how we may predict their actions in patients include pharmacogenomics, cellular function (probing the MPS), more sensitive and accurate analytical PK methods, and identification of the optimal preclinical (animal and in vitro) models.


1. W P Caron, G Song, P Kumar, S Rawal and W C Zamboni.Interpatient PK and PD variability of carrier-mediated anticancer agent.  Clinical Pharmacology and Therapeutics 2012 91, 802-812 http://www.nature.com/clpt/journal/vaop/ncurrent/full/clpt201212a.html

2. Zamboni, W.C. Liposomal, nanoparticle, and conjugated formulations of anticancer agents. Clin. Cancer Res. 11, 8230–8234 (2005).



3. Dobrovolskaia, M.A., Aggarwal, P., Hall, J.B. & McNeil, S.E. Preclinical studies to understand nanoparticle interaction with the immune system and its potential effects on nanoparticle biodistribution. Mol. Pharm. 5, 487–495 (2008). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613572/

4. Dobrovolskaia, M.A. & McNeil, S.E. Immunological properties of engineered nanomaterials. Nat. Nanotechnol. 2, 469–478 (2007). http://www.ncbi.nlm.nih.gov/pubmed/18654343

5. Levchenko, T.S., Rammohan, R., Lukyanov, A.N., Whiteman, K.R. & Torchilin, V.P. Liposome clearance in mice: the effect of a separate and combined presence of surface charge and polymer coating. Int. J. Pharm. 240, 95–102 (2002). http://www.ncbi.nlm.nih.gov/pubmed/12062505

6. Lloberas, J. & Celada, A. Effect of aging on macrophage function. Exp. Gerontol. 37, 1325–1331 (2002). http://www.ncbi.nlm.nih.gov/pubmed/12559402

7. Zamboni, W.C. et al. Pharmacokinetic study of pegylated liposomal CKD-602 (S-CKD602) in patients with advanced malignancies. Clin. Pharmacol. Ther. 86, 519–526 (2009). http://www.nature.com/clpt/journal/v86/n5/abs/clpt2009141a.html

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SDS-PAGE with Taq DNA Polymerase. SDS-PAGE is ...

SDS-PAGE with Taq DNA Polymerase. SDS-PAGE is an useful technique to separate proteins according to their electrophoretic mobility. (Photo credit: Wikipedia)

Proteomics and Biomarker Discovery

Reporter: Larry H. Bernstein, MD, FCAP



Advanced Proteomic Technologies for Cancer Biomarker Discovery

Sze Chuen Cesar Wong; Charles Ming Lok Chan; Brigette Buig Yue Ma; Money Yan Yee Lam; Gigi Ching Gee Choi; Thomas Chi Chuen Au; Andrew Sai Kit Chan; Anthony Tak Cheung Chan

Published: 06/10/2009

This report is extracted from the article above with editing and shortening as much as possible for the reader, and updated from LCGCNA Aug 12,  2012; 8

Part I


This review will focus on four state-of-the-art proteomic technologies, namely 2D difference gel electrophoresis, MALDI imaging mass spectrometry, electron transfer dissociation mass spectrometry and reverse-phase protein array. The major advancements these techniques have brought about biomarker discovery will be presented in this review. The wide dynamic range of protein abundance, standardization of protocols and validation of cancer biomarkers, and a 5-year view of potential solutions to such problems is discussed.

English: Public domain image from cancer.gov h...

English: Public domain image from cancer.gov http://visualsonline.cancer.gov/details.cf?imageid=3483. TECAN Genesis 2000 robot preparing Ciphergen SELDI-TOF protein chips for proteomic  analysis. (Photo credit: Wikipedia)


A common method used for isolating and identifying cancer biomarkers involves the use of serum or tissue protein identification. Unfortunately, currently used tumor markers have low sensitivities and specificities.[2] Therefore, the development of novel tumor markers might be helpful in improving cancer diagnosis, prognosis and treatment.

The rapid development of proteomic technologies during the past 10 years has brought about a massive increase in the discovery of novel cancer biomarkers. Such biomarkers may have broad applications, such as for the detection of the presence of a disease, monitoring of disease clearance and/or progression, monitoring of treatment response and demonstration of drug targeting of a particular pathway and/or target. In general, proteomic approaches begin with the collection of biological specimens representing two different physiological conditions, cancer patients and reference subjects. Proteins or peptides are extracted and separated, and the protein or peptide profiles are compared against each other in order to detect differentially expressed proteins. Commonly, quantitative proteomics is mainly performed by protein separation using either 2DE- or liquid chromatography (LC)-based methods coupled with protein identification using mass spectrometry (MS). Limitations include inability to obtain protein profiles directly from tissue sections for correlation with tissue morphology, limited ability to analyze post-translational modifications (PTMs) and low capacity for high-throughput validation of identified markers. Progress in proteomic technologies has led to the development of 2D DIGE, MALDI imaging MS (IMS), electron transfer dissociation (ETD) MS, and reverse-phase protein array (RPA).

2D Difference Gel Electrophoresis

The 2DE method has been one of the mainstream technologies used for proteomic investigations.[3,4] In this method, proteins are separated in the first dimension according to charge by isoelectric focusing, followed by separation in the second dimension according to molecular weight, using polyacrylamide gel electrophoresis. The gels are then stained to visualize separated protein spots,[5] separating up to 1000 protein spots in a single experiment and  protein spots are then excised and identified using mass spectrometry (MS).[6,7]

We previously used a 2DE approach to compare the proteomic profiles to identify differentially expressed proteins that may be involved in the development of nasopharyngeal cancer, [8]   as well as proteins that were responsive to treatment with the chemotherapeutic agent 5-fluorouracil (5FU) in the colorectal cancer SW480 cell line. Briefly, cell lysates from SW480 cells that were either treated with 5FU or were controls were separated using 2DE. After staining and analysis of the gels, differentially expressed protein spots were excised and identified using MS. The upregulation of heat-shock protein (Hsp)-27 and peroxiredoxin 6 and the downregulation of Hsp-70 were successfully validated by immunohistochemical (IHC) staining of SW480 cells.[9]

The 2D DIGE method improved the 2DE technique. Figure 1 shows how two different protein samples (e.g., control and disease) and, optionally, one reference sample (e.g., control and disease pooled together) are labeled with one of three spectrally different fluorophores: cyanine (Cy)2, 3 or 5. They have the same charge, similar molecular weight and distinct fluorescent properties, allowing their discrimination during fluorometric scanning.[10-12]  The minimal dye causes minimal change in the electrophoretic mobility pattern of the protein, whereas the saturation dye labels all available cysteine residues but causes a shift in electrophoretic mobility labeled proteins.[13]  The same pooled reference sample used for all gels within an experiment is an internal reference for normalization and spot matching.[12] The gel is scanned at three different wavelengths yielding images for each of the different samples, and variation between gels is minimized and difficulties are reduced in correctly matching of protein spots across different gels.[10,11]  Significant advantages of the DIGE technology includes a dynamic range of over four orders of magnitude and full compatibility with MS.  However, careful validations of identified markers using alternative techniques are still needed.

In a study that compared three commonly used DIGE analysis software packages, Kang et al. concluded that although the three softwares performed satisfactorily with minimal user intervention, significant improvements in the accuracy of analysis could be achieved .[14] Moreover, it was suggested that results concerning the magnitude of differential expression between protein spots after statistical analysis by such softwares must be examined with care.[14]

Figure 1.  Procedures for performing a 2D DIGE experiment. CY: Cyanine; DIGE: Differential in gel electrophoresis.

The choice of appropriate statistical methods for the analysis of DIGE data has to be considered. Statistical methodological error can be addressed by the use of statistical methods that apply a false-discovery rate (FDR) for the determination of significance. In this method, q-values are calculated for all protein spots. The q-value of each spot corresponds to the expected proportion of false-positives incurred by a change in expression level of that protein spot found to be significant.

Despite the ease of use and enabling the researcher to select an appropriate FDR according to study requirements, this approach was found to be only applicable to DIGE experiments using a two-dye labeling scheme, as a three-dye labeling approach violated the assumption of data independence required for statistical analysis.[16] Other statistical tests that have been applied for the analysis of DIGE results include significance analysis of microarrays,[7] principal components analysis[17,18] and partial least squares discriminant analysis.[18,19] Detailed discussions of the different statistical approaches applicable to proteomic research are beyond the scope of this review and readers may refer to[18,20] for further reading.

Using 2D DIGE, Yu et al. successfully identified biomarkers that were associated with pancreatic cancer.[21] In the study, 24 upregulated and 17 downregulated proteins were identified by MS. Among those proteins, upregulation of apolipoprotein E, α-1-antichymotrypsin and inter-α-trypsin inhibitor were confirmed by western blot analysis. Furthermore, the association of those three proteins with pancreatic cancer was successfully validated in another series of 20 serum samples from pancreatic cancer patients. Using a similar approach, Huang et al. identified and confirmed the upregulation of transferrin in the sera of patients with breast cancer.[22] When Sun et al. compared the proteomic profiles between malignant and adjacent benign tissue samples from patients with hepatocellular carcinoma, they proved 2D DIGE is not limited to serum or plasma samples.[23] In their study, overexpression of Hsp70/Hsp90-organizing protein and heterogenous nuclear ribonucleoproteins C1 and C2 were identified by 2D DIGE coupled with MS analysis, and the findings were successfully validated by both western blotting and IHC staining. Next, Kondo et al. applied 2D DIGE to laser-microdissected cells from fresh patient tissues.[13] Using this protocol, a 1-mm area of an 8-12-µm-thick tissue section was shown to be sufficient. These examples demonstrate the high sensitivity and broad applicability of 2D DIGE for proteomic investigations using various types of patient samples and provide evidence that 2D DIGE is a powerful technique for biomarker discovery.

MALDI Imaging Mass Spectrometry

A deeper understanding of the complex biochemical processes occurring within tumor cells and tissues requires a knowledge of the spatial and temporal expression of individual proteins. Currently, such information is mainly obtained by IHC staining for specific proteins in patient tissues.[8,24,25] Nevertheless, IHC has limited use in high-throughput proteomic biomarker discovery because only a few proteins can be immunostained simultaneously. MALDI IMS allows researchers to analyze proteomic expression profiles directly from patient tissue sections.[26-28] The protocol begins with mounting a tissue section onto a sample plate (Figure 2). MALDI matrix is then applied onto the tissue sample, which is analyzed by MALDI MS in order to obtain mass spectra from predefined locations across the entire patient tissue section. The mass spectrum from each location is a complete proteomic profile for that particular area. All acquired mass spectra from the entire tissue are then compiled to create a 2D map for that tissue sample. This map could then be compared with those from other tissue samples to identify changes in protein or peptide expression or comparisons of the maps from different areas within the same tissue section could be performed. This technology  importantly allows the high-throughput discovery of novel protein markers. In addition, correlations between protein expression and tissue histology can also be studied easily.

Most studies using MALDI IMS have been performed on frozen tissue sections ranging from 5 to 20 µm in thickness.[26,27,29] After sectioning, a MALDI matrix is applied either by automated spraying or spotting. The matrix of choice is usually α-cyano-4-hydroxy-cinnamic acid for peptides and sinapinic acid (3,5-dimethoxy-4-hydroxycinnamic acid) for proteins.

Figure 2.  Procedures for MALDI imaging. IMS: Imaging mass spectrometry; MS: Mass spectrometry.

Spotting allows the precise application of matrix to areas of interest and minimizes the diffusion of analyte material across the sample, although the imaging resolution achieved by spotting is lower (~150 µm). A laser beam is then fired towards the area of interest on the tissue section to generate protein ions for analysis by a mass analyzer.[29] Among the different mass analyzers, TOF analyzers are the most commonly used owing to their high sensitivity, broad mass range and suitability for detection of ions generated by MALDI. Use of other mass analyzers such as TOF-TOF, quadrupole TOF (QTOF), ion traps (ITs) and Fourier transform-ion cyclotron resonance (FT-ICR) have also been reported in other studies.[30-33]

After obtaining the mass spectra, statistical analysis needs to be performed to identify statistically significant features that could have potential use as biomarkers. But before such analyses can be applied, there has to be background-noise subtraction, spectral normalization and spectral alignment.[34,35,34] Statistical methods used to identify significant differences in peak intensity are symbolic discriminant analysis and principal component analysis. Symbolic discriminant analysis determines discriminatory features and builds functions based on such features for distinguishing samples according to their classification.[36,37] Using this approach, Lemaire et al. found a putative proteomic biomarker from ovarian cancer tissues by MALDI IMS that was later identified to be the Reg-α protein, a member of the proteasome activator 11S.[37] This result was later successfully validated by western blot (protein expression found in 88.8% carcinoma cases vs 18.7% benign disease) and IHC (protein expression found in 63.6% carcinoma tissues vs 16.6% benign tissues).[37] On the other hand, principal component analysis reduces data complexity by transforming data based on peak intensities to information based on data variance, termed ‘principal components’, resulting in a list of significant peaks (principal components) ordered by decreasing variance.[35,38,39] Neither symbolic discriminant analysis or principal component analysis is capable of performing unsupervised classification. This aim requires the use of other methods such as hierarchical clustering.[39,40] In this method identified peaks are clustered as nodes in a pair-wise manner according to similarity until a dendogram is obtained, providing information as to the degree of association of all peak masses in a hierarchical fashion. Peaks that are capable of differentiating between different histological/pathological features could then be chosen for further validation of their value as tumor markers.[39]

In MALDI IMS, protein identification cannot be performed with confidence solely on the molecular weight. However, Groseclose et al. have developed a method using in situ digestion of proteins directly on tissue section.[41] They first used MALDI IMS to obtain a map of the protein and peptide spectra, then spotted a consecutive section of the same tissue sample with trypsin for protein digestion, and then spotted matrix solution onto the digested spots and the resulting peptides are identified directly from the tissue by MS/MS. This modification increases the confidence in protein identification. The time required for MALDI IMS analysis per tissue section is as follows: tissue sectioning, mounting and matrix application: 4-8 h; MALDI image acquisition: 1-2 days; spectral analysis: 1-2 h.[33,39]

Recently, in situ enzymatic digestion has been successfully applied for improving the retrieval of peptides directly from formalin-fixed, paraffin-embedded FFPE tissue samples.[27] Such development has greatly facilitated the application of MALDI IMS in FFPE tissues.[26,42] In fact, Stauber et al. identified the downregulation of ubiquitin, transelongation factor 1, hexokinase and neurofilament M from FFPE brain tissues of rat models of Parkinson disease using this modified technique.[42] The success of performing proteomic profiling using MALDI IMS directly on FFPE tissues opens up great possibility for using archival patient materials in high-throughput biomarker discovery. Novel cancer biomarkers identified using MALDI IMS still require validation by other techniques such as IHC.

Electron Transfer Dissociation MS

Post-translational modifications play important roles in the structure and function of proteins such as protein folding, protein localization, regulation of protein activity and mediation of protein-protein interaction. Two common forms of PTM that have been implicated in cancer development are phosphorylation and glycosylation. Previously, phosphoproteomic studies have led to the identification of novel tyrosine kinase substrates in breast cancer,[43] discovery of novel therapeutic targets for brain cancer[44] and increased understanding of signaling pathways involved in lung cancer formation.[45,46] Conversely, the identification of abnormally glycosylated proteins, such as mucins, has provided novel biomarkers and therapeutic targets for ovarian cancer.[47]

The study of PTM begins with digesting the target protein using enzymes such as trypsin,   introducing the fragments into MS for determination of the sites and types of modification and, at the same time, identification of the protein. The analysis is conventionally carried out using collision-induced dissociation (CID) MS, where peptides are collided with a neutral gas for cleavage of peptide bonds to produce b- and y-type ions (Figure 3). A complete series of peptides differing in length by one amino acid is produced, leading to identification of the protein by peptide-sequence determination. However, for phosphopeptides, the presence of phosphate groups would compete with the peptide backbone as the preferred cleavage site. The end result is a reduced set of peptide fragments, which hinders protein identification, and the exact location of the phosphate group on the peptide cannot be determined accurately when there are more than one possible phosphorylation sites.[48,49]

Figure 3.  Peptide bond-cleavage site for a-, b-, c-, x-, y– and z-type ions.

Electron transfer dissociation is a recently developed dissociation technique for the analysis of peptides by MS, utilizing radiofrequency quadrupole ion traps such as 2D linear IT, spherical IT and Orbitrap™ (Thermo Fisher Scientific Inc., MA, USA) mass analyzers.[48,49] In this technology, peptides are fragmented by transfer of electrons from anions to induce cleavage of Cα-N bonds along the peptide backbone, hence producing c- and z-type ions (Figure 3). In contrast to CID, ETD preserves the localization of labile PTM and also provides peptide-sequence information.[48] But ETD fails to fragment peptide bonds adjacent to proline, which are readily cleaved by CID.[50] A study that compared the performance of CID with that of ETD found that only 12% of the identified peptides were commonly detected between the two techniques. A study reported that CID successfully identified more peptides with charge states of +2 and below, whereas ETD was found to be better at identifying peptide ions with charge states of greater than +2.[51] Therefore, it is suggested that CID and ETD should be used together to complement each other.[52]  Han et al. successfully differentiated the isobaric amino acids isoleucine and leucine from one another by performing CID on the resulting z-ions after ETD. The presence of isoleucine residue was then confirmed by the detection of a specific 29-Da loss from the peptide.[53]  A clear advantage of using ETD for the analysis of phosphopeptides is a near complete series of c- and z-ions without loss of phosphoric acid,[48] greatly facilitating the determination of the phosphorylation sites and the identification of phosphopeptides. Recently, an analysis of yeast phosphoproteome using ETD successfully identified 1252 phosphorylation sites on 629 proteins, whose expression levels ranged from less than 50 to 1,200,000 copies per cell.[54] In another study using ETD, a total of 1435 phosphorylation sites were identified from human embryonic kidney 293T cells, of which 1141 (80%) were previously unidentified. Finally, a study by Molina et al. successfully identified 80% of the known phosphorylation sites in more than 1000 yeast phosphopeptides in one single study using a combination of ETD and CID.[55] In addition, ETD could be applied to investigate other forms of PTM, such as N-linked glycosylations.[56,57] N-linked glycans contain a common core with branched structures. These can be processed by stepwise addition or removal of monosaccharide residues linked by glycosidic bonds, producing highly varied forms of N-linked glycan structures.[58-60] A weakness of analyzing glycopeptides using CID is that cleavage of glycosidic bonds occurs with little peptide backbone fragmentation, so that only the glycan structure is available.[61]  Hogan et al. used CID and ETD together to overcome this problem determining the glycan structure and glycosylation site.[61] ICID was initially used for cleavage of glycosidic bonds that allowed the entire glycan structure to be inferred from the CID spectrum alone. ETD was later performed to dissociate the same peptide that resulted in a contiguous series of fragment ions with no loss of glycan molecules, allowing the identification of both the site of glycosylation and the identity of the glycoprotein.[61] Readers are strongly encouraged to refer to[49] and.[62] In a comprehensive comparison of CID versus ETD for the identification of peptides without PTMs, CID was found to identify 50% more peptides than ETD (3518 by CID vs 2235 by ETD), but ETD provided somewhat better sequence coverage (67% for CID vs 82% for ETD). It turns out that ETD produced more uniformly fragmented ions with intensities that were five- to ten-times lower than those produced by CID.[55] Finally, the best sequence coverage of up to 92% was achieved when consecutive CID and ETD were performed.[55]

This increase in sequence coverage using the combined approach is needed for studies requiring de novo peptide identifications. As such, this strategy is particularly suited for studies involved in the discovery, identification and characterization of novel peptides or proteins and their PTMs for biomarker use. A prerequisite of this technique is that the biological samples under investigation must undergo some form of fractionation before they are amenable to analysis by ETD or CID. This is achieved by the use of LC techniques, such as reverse-phase, strong cation exchange or strong anion exchange chromatography, and serves to reduce the complexity and wide dynamic range of protein-expression levels commonly found in biological specimens. Given the important roles of PTM in the function and activity of proteins, this technology paves the way for exploring the intricate cellular activities within a cancer cell.


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    •• Excellent review on the application of MALDI imaging MS for studying biological systems.
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Advanced Proteomic Technologies for Cancer Biomarker Discovery

Part II

Reverse-phase Protein Array

One of the goals of proteomics is to identify protein changes associated with the development of diseases such as cancer.  Even with the rapid development of proteomic technologies during the past few years, analysis of patient samples is still a challenge. Difficulties arise from the fact that[63,64]:

  • Proteomic patterns differ among cell types;
  • Protein expression changes occur over time;
  • Proteins have a broad dynamic range of expression levels spanning several orders of magnitude;
  • Proteins can be present in multiple forms, such as polymorphisms and splice variants;
  • Traditional proteomic methods require relatively large amounts of protein
  • Many proteomic technologies cannot be used to study protein-protein interactions.

The principle of RPA is simple and involves the spotting of patient samples in an array format onto a nitrocellulose support (Figure 4). Hundreds of patient specimens can be spotted onto an array, allowing a comparison of a large number of samples at once.[65] Each array is incubated with one particular antibody, and signal intensity proportional to the amount of analyte in the sample spot is generated.[66] Signal detection is commonly performed by fluorescence, chemiluminescence or colorimetric methods. The results are quantified by scanning and analyzed by softwares such as P-SCAN and ProteinScan, which can be downloaded from[84] for free.[67,68]

Figure 4.  Principle of reverse-phase protein array.

Main advantages of RPA technology include[69-71]:

  • Various types of biological samples can be used;
  • The possibility of investigating PTMs;
  • Protein-protein interactions can be studied;
  • Labeling of patient samples with fluorescent dyes (e.g., 2D DIGE) or mass tags (e.g., isotope-coded affinity tag [ICAT]) are not required;
  • Any samples spotted as a dilution allows quantifying in the linear range of detection;
  • Quantitative measurement of any protein is possible compared to reference standards of known amounts on the same array.

It has been shown that RPA is extremely sensitive as it is capable of detecting up to zeptomole (1 x 10-21 mole) levels of target proteins with less than 10% variance. The analysis of few cell signaling events is known.[65,70,71] The assay sensitivity depends on antibody affinity, which depends upon antigen-antibody pairs.[68] Of course, only known proteins with available antibodies can be identified. Therefore, this method is more suitable for biomarker screening or validation than discovery of novel proteins. To assist researchers in selecting suitable antibodies, two open antibody databases show their western blot results using cell lysates.[72,73,85,86]

One application of RPA is to investigate the signaling pathways in human cancers. Zha et al. compared the survival signaling events between Bcl 2-positive and -negative lymphomas and found that survival signals, independent of Bcl 2 expression, were detected in follicular lymphoma and confirmed by validation with IHC.[71] In another study, patient-specific signaling pathways have been identified in breast cancers using RPA. Bayesian clustering of a set of 54 subjects successfully separated normal subjects from cancer patients based on an epithelial signaling signature. Principal component analysis was capable of distinguishing normal from cancer patient samples by using a signature composed of a panel of kinase substrates.[69] Differences in cell signaling between patient-matched primary and metastatic lesions have also been found using RPA. In the study, six patient-matched primary ovarian tumors probed with antibodies against signaling proteins, and the signaling profiles differed significantly between primary and metastatic tumors and upregulation of phosphor c-kit was capable of distinguishing five of the six metastatic tumors from the primary lesions.[70] These findings suggest that treatment strategies may need to target signaling events among disseminated tumor cells.

Reverse-phase protein array has also been used to validate mathematical models of cellular pathways. The p53-Mdm2 feedback loop is one of the most well-studied cellular-feedback mechanisms.[74] Normally, p53 activates transcription and expression of Mdm2, which, in turn, suppresses p53 activity. This negative-feedback loop ensures the low-level expression of p53 under normal conditions. Mathematical models have previously been used to investigate this negative-feedback loop.[67] Ramalingam et al. has shown, by using RPA, that part of the mechanism of the p53-Mdm2 feedback loop can be explained by current mathematical models.[75]

Another important application of RPA is for the identification of cancer specific antigens.  Using this method serum from 14 lung cancer patients, colon cancer patients and normal subjects were incubated and eight fractions of the cell lysate were recognized by the sera from four patients, while none of the sera from normal individuals was positive.[76] This study demonstrates the diagnostic potential of identifying cancer antigens that induce immune response in cancer patients by using RPA.

Expert Commentary and Five-year View

The development of 2D DIGE in the past few years has provided researchers with a more accurate method for relative quantification of proteins substantially reducing the number of replicates required for 2D gels and increased its applicability for high-throughput biomarker discovery. MALDI MS has immensely facilitated the direct discovery of biomarkers from patient tissue. Even though archival patient tissue samples are a potential source of materials for tumor marker research, high-throughput techniques for biomarker discovery using such samples has been problematic. With the development of MALDI IMS, investigators can now perform studies that aim to discover novel biomarkers directly from tissue sections and are able to correlate their expression with the histopathological changes of tumors. Previously, investigation into the sites of protein PTM has been difficult since MS-dissociation techniques, such as CID, would lead to preferential loss of PTM, but the use of ETD as a complementary peptide ion-dissociation method has allowed researchers to investigate the precise location and structure of the PTM, and to identify peptide sequence with higher confidence.

The rapid technological improvements in proteomic technologies will identify potential biomarkers for clinical use. Independent validation studies using clinical specimens must be performed before such markers can be applied clinically,. In this regard, RPA has added a potential for high-throughput screening or validation of newly found markers. Using this technique, it will be possible for researchers to quantitatively measure and validate novel markers on hundreds of patient samples simultaneously.

A big problem for proteomic researchers iincludes the abundance of proteins in biological samples. This could be partially solved by depletion of abundant proteins or by fractionation of protein samples according to characteristics. It is envisaged that, in the future, proteomic technologies will be developed to a stage that is capable of analyzing complex protein mixtures without preparatory fractionation. Such progress has recently been achieved in LC-MS, where the use of a high-field, asymmetric waveform, ion-mobility spectrometry device as an interface to an IT MS resulted in a more than fivefold increase in dynamic range without increasing the length of the LC-MS analysis.[77]

Another area that needs improvement is the standardization of protocols for patient-sample collection because results were found to be inconsistent among various studies using MS.[78] It is also considered that part of the reason for this inconsistency is due to the differences in sample-collection or sample-handling procedures.[78,79] The Human Proteome Organization previously published its findings on pre-analytical factors that affect plasma proteomic patterns and provides suggestions for sample handling.[80,81] In addition to the pre-analytical stages, it is imperative to stress that consistent and strict adherence to predefined procedures or standards, from sample collection, sample processing, experimentation, data analysis through to result validation, are of utmost importance to minimize variations and achieve consistent and reproducible results.

Any newly identified potential biomarker must also be validated using an independent cohort of patients in order to establish its clinical value, but the translation of results from the laboratory to the clinic has been slow. Consequently, it has been suggested that quantitative MS could be used for the detection of proteins.[82] The increasing availability of MS facilities to researchers worldwide will facilitate the detection, measurement and validation of protein biomarkers using quantitative MS techniques. Even after validation of such results in the laboratory, diagnostic tests will need to be developed for the marker and large-scale clinical trials would also have to be performed to confirm the results.  All these efforts require cooperation of personnel from various disciplines, such as scientists, medical professionals, pharmaceutical companies and governments. Finally, it is hoped that, through improved understanding of the protein expression as cancer progresses will lead to the discovery and development of useful cancer biomarkers for patient diagnosis, prognosis, monitoring and treatment.

Key Issues

  • 2DE coupled with mass spectrometry has been the main workhorse for the proteomic discovery of novel biomarkers in the past 10 years, and the development of 2D difference gel electrophoresis has substantially improved the quantification accuracy of 2DE.
  • MALDI imaging mass spectrometry has allowed the identification of novel proteomic features directly from patient tissue section for correlation with histopathological changes.
  • Electron transfer dissociation mass spectrometry has opened up the possibility of identifying the structure and localization of the post-translational modification and the peptide/protein.
  • Reverse-phase protein array is a powerful tool for the high-throughput validation of novel biomarkers across hundreds of patient samples simultaneously.


63.  States DJ, Omenn GS, Blackwell TW et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol. 24(3),333-338 (2006).

64. Wulfkuhle JD, Edmiston KH, Liotta LA, Petricoin EF 3rd. Technology insight: pharmacoproteomics for cancer – promises of patient-tailored medicine using protein microarrays. Nat. Clin. Pract. Oncol. 3(5),256-268 (2006).

•• Excellent review on the clinical application of reverse-phase protein array.

65. Tibes R, Qiu Y, Lu Y et al. Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol. Cancer Ther. 5(10),2512-2521 (2006).

66. LaBaer J, Ramachandran N. Protein microarrays as tools for functional proteomics. Curr. Opin. Chem. Biol. 9(1),14-19 (2005).

67. Ramalingam S, Honkanen P, Young L et al. Quantitative assessment of the p53-Mdm2 feedback loop using protein lysate microarrays. Cancer Res. 67(13),6247-6252 (2007).

68. Nishizuka S, Ramalingam S, Spurrier B et al. Quantitative protein network monitoring in response to DNA damage. J. Proteome Res. 7(2),803-808 (2008).

69. Petricoin EF 3rd, Bichsel VE, Calvert VS et al. Mapping molecular networks using proteomics: a vision for patient-tailored combination therapy. J. Clin. Oncol. 23(15),3614-3621 (2005).

70. Sheehan KM, Calvert VS, Kay EW et al. Use of reverse-phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell Proteomics 4(4),346-355 (2005).

71. Zha H, Raffled M, Charboneau L et al. Similarities of prosurvival signals in Bcl 2-positive and Bcl 2-negative follicular lymphomas identified by reverse phase protein microarray. Lab. Invest. 84(2),235-244 (2004).

72. Major SM, Nishizuka S, Morita D et al. AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies. BMC Bioinformatics 7,192 (2006).

73. Spurrier B, Washburn FL, Asin S, Ramalingam S, Nishizuka S. Antibody screening database for protein kinetic modeling. Proteomics 7(18),3259-3263 (2007).

74. Ciliberto A, Novak B, Tyson JJ. Steady states and oscillations in the p53/Mdm2 network. Cell Cycle 4(3),488-493 (2005).

75. Ma L, Wagner J, Rice JJ, Hu W, Levine AJ, Stolovitzky GA. A plausible model for the digital response of p53 to DNA damage. Proc. Natl Acad. Sci. USA 102(40),14266-14271 (2005).

76. Madoz-Gurpide J, Kuick R, Wang H, Misek DE, Hanash SM. Integral protein microarrays for the identification of lung cancer antigens in sera that induce a humoral immune response. Mol. Cell. Proteomics 7(2),268-281 (2007).

77. Canterbury JD, Yi X, Hoopmann MR, MacCoss MJ. Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics. Anal. Chem. 80(18),6888-6897 (2008).

78. Coombes KR, Morris JS, Hu J, Edmonson SR, Baggerly KA. Serum proteomics – a young technology begins to mature. Nat. Biotechnol. 23(3),291-292 (2005).

78. Hortin GL. Can mass spectrometric protein profiling meet desired standards of clinical laboratory practice? Clin. Chem. 51(1),3-5 (2005).

79. Omenn GS, States DJ, Adamski M et al. Overview of the HUPO plasma proteome project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 5(13),3226-3245 (2005).

80. Rai AJ, Gelfrand CA, Haywood BC et al. HUPO plasma proteome project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5(13),3262-3277 (2005).

• Concise report on several pre-analytical factors that impact the results of plasma proteomic profiling.

81. Mann M. Can proteomics retire the western blot? J. Proteome Res. 7(8),3065 (2008).

Update from LC/GC North America.

Solutions for Separation Scientists. Aug 2012; 30(8).

30 years of LCGC


The key advances in separation science is covered in five areas of the discipline:

  1. sample preparation
  2. gas chromatography(GC) columns
  3. GC instrumentation
  4. liquid cheomatography (LC) columns
  5. LC instrumentation

In the first, there is automated sample preparation in kit form (QuEChERS). A short list of automated sample preparation techniques includes: supercritical fluid extraction (SFE), microwave extraction, automated solvent extraction (ASE), and solid phase extraction (SPE). A panel of experts views the bast basic method of extraction is SPE, and one uses solid phase microextraction with direct immersion and static headspace extraction, along with liquid-liquid extraction.[2] In GC incremental improvements have been made with ionic liquids, multidimentional GC, and fast GC. LC has advanced dramatically with ultra-high pressure LC and superficially porous particles. LC-MS has become standard equipment routinely used in many labs.[1]

Biomarkers have to be detected in a background of 104-106 other components of comparable concentration that also partition with the stationary phase. The partition coefficients of many species are similar, or identical to the biomarker target. The issue is how to select and resolve fewer than 100 biomarkers from a milieu of 1 million components in a complex mixture. The novel idea is to target structure instead of general properties of molecules.[3] How might this work?  A single substrate, metabolite, hormone, or toxin is identified in milliseconds by specific protein receptors. The combinatorial chemistry community has shown that synthetic polynucleotides (aptamers) can be found and amplified that have selectivities approaching antibodies.This is a method well know for years as affinity chromatography. A distinct problem has been the natural process of post translational modification (PTMs), which may create isoforms by addition of a single phosphate ester to be found in the proverbial soup.

1. Bush L. Separation Science: Past, Present and Future. LCGC NA 2012; 30(8):620.

2.McNally ME. Analysis of the State of the Art: Sample Preparation. LCGC NA 2012; 30(8):648-651.

2. Regnier FE. Plates vs Selectivity: An Emerging Issue with Complex Samples.  LCGC NA 2012; 30(8):622.

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Curator/Author: Aviral Vatsa PhD, MBBS

Nitric oxide is one of the smallest molecules involved in physiological functions in the body. It is a diatom and thus seeks formation of chemical bonds with its targets rather than structure-function configuration of say protein receptors. Nitric oxide can exert its effects principally by two ways:

  • Direct
  • Indirect

Direct actions, as the name suggests, result from direct chemical interaction of NO with its targets e.g. with metal complexes, radical species. These actions occur at relatively low NO concentrations (<200 nM)

Indirect actions result from the effects of reactive nitrogen species (RNS) such as NO2 and N2O3. These reactive species are formed by the interaction of NO with superoxide or molecular oxygen. RNS are generally formed at relatively high NO concentrations (>400 nM)

Credits: Nitric Oxide: Biology and Pathobiology By Louis J. Ignarro

Credits: Nitric Oxide: Biology and Pathobiology By Louis J. Ignarro

Although it can be tempting for scientists to believe that RNS will always have deleterious effects and NO will have anabolic effects, this is not entirely true as certain RNS mediated actions mediate important signalling steps e.g. thiol oxidation and nitrosation of proteins mediate cell proliferation and survival, and apoptosis respectively. As depicted in the figure above, NO concentration determines the action it exerts on different proteins. This is highlighted in the following examples from different studies:

  • Cells subjected to NO concentration between 10-30 nM were associated with cGMP dependent phosphorylation of ERK
  • Cells subjected to NO concentration between 30-60 nM were associated with Akt phosphorylation
  • Concentration nearing 100 nM resulted in stabilisation of hypoxia inducible factor-1
  • At nearly 400 nM NO, p53 can be modulated
  • >1μM NO, it nhibits mitochondrial respiration

Besides the concentration, duration of NO exposure also determines how proteins respond to NO. Hence proteins can be ‘immediate’ responders or ‘delayed’ responders. The response can be either ‘transient’ (short lived) or ‘sustained’ (prolonged). Different proteins fall into these different categories. These are not rigid categories rather a functional ‘classification’.

Endogenously generated NO concentration ranges from 2 nM as in endothelial cell to >1 μM in a fully activated macrophage. This wide range, along with the unique chemical reactivity of NO offers immense versatility to the physiological effects that it can exert in different cellular milieu in the body.

In addition to the concentration-dependent effects, other factors that determine the local cellular/tissue milieu add to the complexities involved with signal transduction undertaken by NO. These factors are

  • rate of NO production
  • diffusion distance
  • rates of consumption
  • reactivity of RNS with molecular targets.

These kinetic determinants play vital role in physiological functions and disease states.

Although it is not possible to detail the modes of modulation of biological functions by NO in a short post, but I hope the post gives a taste of the intricacies involved with NO functions and that there are various parameters that determine the exact role of NO in a biological milieu.







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Curator: Aviva Lev-Ari, PhD, RN

For IP and Legal aspects of Biosimilars, go to:

Biosimilars: Intellectual Property Creation and Protection by Pioneer and by Biosimilar Manufacturers


For CMC and Regulatory Affairs of Biosimilars, go to:

Biosimilars: CMC Issues and Regulatory Requirements


The patent provisions of the Biosimilar Act, 2009 establish demanding and time-sensitive disclosure requirements. ObamaCare upheld by the Supreme Court is a victory for future development of pathways for biosimilar regulatory approval and eventually biosimilar generic drugs.

With the upheld ObamaCare, critical parts of the PPACA constitutional, and with it the BPCIA giving the FDA authority to approve biosimilars.

Had the PPACA been stricken in part or in its entirety, it would have presented obstacles to the BPCIA surviving in its present form. The US government has been critical of the 12-year data exclusivity period for Pioneer Innovators, calling for it to be shortened to 7 years (12 years is favorable to Pioneer Innovators and less favorable for Biosimilar manufacturers). The upheld ObamaCare, PPACA and BPCIA, constitutional, has prevented a multiyear delay in biosimilar approval. Thus, it was the best scenario for the biologics industry.

Thus, projection of Sales for Biosmilars as % of top 100 U.S. Pharmaceutical will receive a special meaning and an expected enhanced market share for 2012 year end and beyond 2012.

Biosimilars are occupying the Following ranking in the U.S. Pharmacuetical Sales – 2012: Top 100 Drugs for Q1 2012 by Sales: 10, 11, 12 13, 15, 24, 27, 29, 33, 35, 39, 57, 58, 62, 65, 70,  72, 74, 90, 98, 99. In addition the following biosimilars did not make the Top 100 list:

Biosimilar Drugs by US Sales – not included in the Top 100 Drug List 

Recombinate $2.9 1998 — Antihemophilic Factor VIII (Recombinant) by Baxter 5.7 Billion in 2012

Cerezyme $1.5 1994 —  Gaucher disease and Fabrazyme for Fabry disease by Genzyme 200 millions in sales

TYSABRI(R) (natalizumab) revenues were $280 million, in-line with the second quarter of 2011 by Elan and Biogen

NovoSeven $1.4 1999 —  Anti-fibrinolytics by Novo Nordisk – $1.5Billion

Synagis $1.3 1998 — Generic Name:  palivizumab     Anti-virals by AstraZeneca  $570 millions

Humulin $1.1 1992 Insulin Human by Eli Lilly $ 1.2 Billion

Kogenate FS $1.1 1993 — octocog alfa    Anti-fibrinolytics By Bayer $1.4 billion

U.S. Pharmacuetical Sales – 2012: Top 100 Drugs for Q1 2012 by Sales – Small Molecule Drugs (in green) and Biosimilars (in red)

The following is a list of the top 100 pharmaceutical drugs by retail sales in 2012, listed by U.S. sales value and drug name. Last updated: July 2012 (updated quarterly)


Rank Drug

Sales ($000)

1 PlavixBristol-Myers Squibb Company



2 NexiumAstraZeneca Pharmaceuticals



3 AbilifyOtsuka Pharmaceutical Co.



4 SingulairMerck & Co., Inc.



5 SeroquelAstraZeneca Pharmaceuticals



6 Advair DiskusGlaxoSmithKline



7 CrestorAstraZeneca Pharmaceuticals



8 CymbaltaEli Lilly and Company



9 atorvastatinGeneric Drug



10 HumiraAbbott Laboratories




11 RemicadeCentocor Ortho Biotech, Inc




12 EnbrelAmgen Inc.




13 NeulastaAmgen Inc.




14 LipitorPfizer Inc



15 RituxanGenentech, Inc




16 CopaxoneTeva Pharmaceuticals



17 AtriplaGilead Sciences, Inc.



18 OxyContin



19 SpirivaBoehringer Ingelheim Pharmaceuticals, Inc



20 AvastinGenentech, Inc



21 ActosTakeda Pharmaceuticals North America, Inc



22 JanuviaMerck & Co., Inc.



23 TruvadaGilead Sciences, Inc.



24 LantusSanofi-Aventis



25 DiovanNovartis Corporation



26 LexaproForest Pharmaceuticals, Inc



27 EpogenAmgen Inc.




28 LyricaPfizer Inc



29 Lantus SolostarSanofi-Aventis




30 enoxaparinGeneric Drug



31 EloxatinSanofi-Aventis



32 CelebrexPfizer Inc



33 HerceptinGenentech, Inc




34 Diovan HCTNovartis Corporation



35 LucentisGenentech, Inc




36 SynagisMedImmune, Inc



37 NamendaForest Pharmaceuticals, Inc



38 GleevecNovartis Corporation



39 AvonexBiogen Idec




40 VyvanseShire US Inc



41 olanzapineGeneric Drug



42 IncivekVertex Pharmaceuticals



43 One Touch Ultra



44 SuboxoneReckitt Benckiser Pharmaceuticals Inc.



45 methylphenidateGeneric Drug



46 ZetiaMerck & Co., Inc.



47 AndroGelAbbott Laboratories



48 ProvigilCephalon, Inc.



49 LidodermEndo Pharmaceuticals



50 TriCorAbbott Laboratories



51 SymbicortAstraZeneca Pharmaceuticals



52 CombiventBoehringer Ingelheim Pharmaceuticals, Inc



53 ProAir HFATeva Pharmaceuticals



54 Seroquel XRAstraZeneca Pharmaceuticals



55 amphetamine/dextroamphetamineGeneric Drug



56 NasonexMerck & Co., Inc.



57 NovologNovo Nordisk Inc.




58 ProcritJanssen Pharmaceuticals, Inc




59 AlimtaEli Lilly and Company



60 ViagraPfizer Inc



61 GeodonPfizer Inc



62 Rebif




63 budesonideGeneric Drug



64 NiaspanAbbott Laboratories



65 HumalogEli Lilly and Company




66 Flovent HFAGlaxoSmithKline



67 LovazaGlaxoSmithKline



68 LevemirNovo Nordisk Inc.



69 Adderall XRShire US Inc



70 NeupogenAmgen Inc.




71 ReyatazBristol-Myers Squibb Company



72 AranespAmgen Inc.




73 metoprololGeneric Drug



74 NovoLog FlexPenNovo Nordisk Inc.




75 VytorinMerck & Co., Inc.



76 JanumetMerck & Co., Inc.



77 IsentressMerck & Co., Inc.



78 escitalopramGeneric Drug



79 CialisEli Lilly and Company



80 AciphexEisai Corporation



81 PradaxaBoehringer Ingelheim Pharmaceuticals, Inc



82 SolodynMedicis Pharmaceutical Corporation



83 fentanylGeneric Drug



84 ZyprexaEli Lilly and Company



85 VelcadeTakeda Pharmaceuticals North America, Inc



86 RestasisAllergan, Inc



87 LunestaSunovion Pharmaceuticals Inc.



88 acetaminophen/hydrocodoneGeneric Drug



89 PrezistaJanssen Pharmaceuticals, Inc



90 PegasysGenentech, Inc




91 ZyvoxPfizer Inc



92 Prevnar 13Wyeth



93 LovenoxSanofi-Aventis



94 BenicarDaiichi Sankyo



95 VESIcareAstellas Pharma US



96 Ventolin HFAGlaxoSmithKline



97 OrenciaBristol-Myers Squibb Company



98 BetaseronBayer Healthcare Pharmaceuticals




99 ErbituxBristol-Myers Squibb Company




100 DexilantTakeda Pharmaceuticals North America, Inc



Source: IMS Health (Midas).

Biosimilars Drugs by US Sales – not included in the Top 100 Drug List 

Recombinate $2.9 1998 — Antihemophilic Factor VIII (Recombinant) by Baxter 5.7 Billion in 2012

Cerezyme $1.5 1994 —  Gaucher disease and Fabrazyme for Fabry disease by Genzyme 200 millions in sales

TYSABRI(R) (natalizumab) revenues were $280 million, in-line with the second quarter of 2011 by Elan and Biogen

NovoSeven $1.4 1999 —  Anti-fibrinolytics by Novo Nordisk – $1.5Billion

Synagis $1.3 1998 — Generic Name:  palivizumab     Anti-virals by AstraZeneca  $570 millions

Humulin $1.1 1992 Insulin Human by Eli Lilly $ 1.2 Billion

Kogenate FS $1.1 1993 — octocog alfa    Anti-fibrinolytics By Bayer $1.4 billion

2011 US Sales vs. 2008 US Sales (in Billions) for Top Selling Biologics

Source for 2008 Sales


Source for 20011, Q1 2012 Sales


Drug Name,  2008 Sales, Year approved , Indication

[i.e. Drug Name Enbrel,  2008 Sales $8.0B, Year approved 1998 , Indication RA]

Enbrel $8.0 1998 — RA, psoriatic arthritis, or ankylosing spondylitis indication

Q1 2012 12 (1) $890,135 1.92% 823 -4.63%
Q4 2011 11 (1) $873,343 1.67% 863 1.77%
Q3 2011 12 (1) $858,997 1.27% 848 -2.97%
Q2 2011 13 (2) $848,230 3.77% 874 3.19%
Q1 2011 11 $817,401 847


Remicade $7.9 1998 — RA & Chron’s Disease

Q1 2012 11 (2) $899,453 10.04% 1,556 10.04%
Q4 2011 13 (3) $817,365 -7.02% 1,414 -9.82%
Q3 2011 10 $879,054 1.52% 1,568 1.03%
Q2 2011 10 (2) $865,903 7.61% 1,552 7.11%
Q1 2011 12 $804,699 1,449


Humira $7.3 2002  — treat rheumatoid arthritis, juvenile idiopathic arthritis, psoriatic arthritis, ankylosing spondylitis, and plaque psoriasis

Q1 2012 10 $928,124 2.50% 546 -2.85%
Q4 2011 10 (1) $905,527 3.18% 562 2.55%
Q3 2011 11 (3) $877,641 3.95% 548 3.01%
Q2 2011 14 $844,296 6.32% 532 2.31%
Q1 2011 14 $794,076 520


Rituxan $7.3 1997 — cancer medicines to treat non-Hodgkin’s lymphoma or chronic lymphocytic leukemia.

Q1 2012 15 (1) $756,875 -1.91% 547 -0.91%
Q4 2011 14 (2) $771,622 6.96% 552 4.74%
Q3 2011 16 $721,408 -1.77% 527 -1.86%
Q2 2011 16 (4) $734,378 7.26% 537 5.09%
Q1 2011 20 $684,666


Second Quarter 2012 Highlights: RITUXAN(R) (rituximab) revenues from our unconsolidated joint business arrangement were $285 million for the quarter, an increase of 31% year-over-year. As previously disclosed, during the second quarter of 2011 our share of RITUXAN revenues from unconsolidated joint business was reduced by approximately $50 million to reflect our share of damages and interest that might be awarded in relation to an intermediate decision in Genentech, Inc.’s ongoing arbitration with Hoechst GmbH


Herceptin $5.7 1998 —  treat metastatic breast cancer that has progressed after treatment with other chemotherapy

Q1 2012 33 $425,687 -0.06% 155
Q4 2011 33 (2) $425,931 7.61% 155 4.73%
Q3 2011 31 (1) $395,804 -0.64% 148 -0.67%
Q2 2011 32 (4) $398,348 3.62% 149 1.36%
Q1 2011 36 $384,428 147


Lantus $5.1 2000 — long-acting form of the hormone insulin.

Q1 2012 29 (5) $448,388 9.81% 3,737 7.32%
Q4 2011 34 $408,336 8.54% 3,482 7.07%
Q3 2011 34 (2) $376,208 4.53% 3,252 6.00%
Q2 2011 36 (5) $359,907 7.80% 3,068 8.30%
Q1 2011 41 $333,878 2,833


Epogen/Procrit $5.1 1989Anemia, low RBC

Worldwide, sales of the two drugs – sold under the brand names Epogen, Procrit and Aranesp – exceeded $9 billion in 2005 for Amgen and Johnson & Johnson, their makers.  Johnson & Johnson, which sells epoetin under the brand names Procrit in the United States and Eprex everywhere else, reported sales of $2.4 billion in the first nine months of 2006, down slightly from 2005.

Amgen Recalls Anemia Medications for Glass Fragments09/24/2010 – Drug-makers Amgen (AMGN) and Johnson & Johnson (JNJ) are voluntarily recalling two brandsof an injectable anemia medication because vials containing the drug may have tiny glass flakes. The drug, Epoetin alfa, is marketed under the brand names Epogen and Procrit.Known as lamellae, the glass fragments are created by the interaction of the drug with glass vials during storage, Amgen said in a statement announcing the recall. The recall is being conducted in cooperation with the Food and Drug Administration, Amgen said.

Latest study shows anemia drugs Epogen, Aranesp and Procrit cause strokes, says FDA

Posted on January 7, 2010

Anemia drugs sold by Amgen and Johnson & Johnson have been reported to cause strokes when prescribed in high doses, according to an article from the FDA, recently published in the The New England Journal of Medicine. The law firm of Aylstock, Witkin, Kreis & Overholtz is investigating the FDA’s recent announcement.

The FDA commentary said the latest study and previous studies “raise major concerns” about the use of these drugs to treat anemia caused by kidney disease. The drugs are also used to treat anemia caused by chemotherapy. Studies over the past several years have revealed a link between the drugs and heart attacks, strokes, and other problems.

Amgen’s anemia drugs include Epogen and Aranesp. Johnson & Johnson sells anemia drug Procrit, which is produced by Amgen. The drugs are designed to raise red blood cell levels, to promote delivery of oxygen to body tissues.


Epogen / Procrit / Aranesp: The July 2012 News Report Which Tells Story Of Big Pharma Profits Over Patient Safety And Drug Efficacy

Once The FDA Started Paying Attention The Writing On The Wall Became Apparent, Albeit Too Late For Some

(Posted by  at DrugInjuryWatch.com)

This lengthy and well-presented news report, “Anemia drugs made billions, but at what cost?”, written by Peter Whoriskey and published July 19, 2012 by The Washington Post (free registration required), is a must-read for anyone with a concern or interest in how larger pharmaceutical companies might put corporate profits ahead of patient safety and drug efficacy.

Here is an excerpt from this Washington Post article which will give you a sense of what went on that, in hindsight, is so disturbing:

For years, a trio of anemia drugs known as Epogen, Procrit and Aranesp ranked among the best-selling prescription drugs in the United States, generating more than $8 billion a year for two companies, Amgen and Johnson & Johnson. Even compared with other pharmaceutical successes, they were superstars. For several years, Epogen ranked as the single costliest medicine under Medicare: U.S. taxpayers put up as much as $3 billion a year for the drugs.

The trouble, as a growing body of research has shown, is that for about two decades, the benefits of the drug — including “life satisfaction and happiness” according to the FDA-approved label — were wildly overstated, and potentially lethal side effects, such as cancer and strokes, were overlooked.

Last year, Medicare researchers issued an 84-page study declaring that among most kidney patients, the original and largest market for the drugs, there was no solid evidence that they made people feel better, improved their survival or had any “clinical benefit” besides elevating a statistic for red blood cell count.

As for some of the key events which led up to this revelation of sorts, we start with a June 24, 2011 FDA press release, “FDA modifies dosing recommendations for Erythropoiesis-Stimulating Agents — Cites increased risk of cardiovascular events when used to treat chronic kidney disease”, which included the following:

The U.S. Food and Drug Administration today recommended more conservative dosing guidelines for Erythropoiesis-Stimulating Agents (ESAs) when used to treat anemia in patients with chronic kidney disease (CKD) because of the increased risks of cardiovascular events such as stroke, thrombosis, and death….

Procrit —  (epoetin alfa) is a man-made form of a protein that helps your body produce red blood cells

Q1 2012 58 (3) $264,190 -2.13% 295 -4.22%
Q4 2011 55 (2) $269,937 3.58% 308 3.01%
Q3 2011 53 (12) $260,610 -21.61% 299 -21.32%
Q2 2011 41 (7) $332,466 7.04% 380 5.56%
Q1 2011 48 $310,606 360


Epogen —  (epoetin alfa) is a man-made form of a protein that helps your body produce red blood cells

Q1 2012 27 (7) $489,570 -24.54% 555 -17.04%
Q4 2011 20 (2) $648,794 4.67% 669 3.40%
Q3 2011 22 (2) $619,828 -13.96% 647 -18.41%
Q2 2011 20 (1) $720,376 3.32% 793 4.48%
Q1 2011 19 $697,224 759


Neulasta $4.2 2002 — used to prevent neutropenia, a lack of certain white blood cells caused by receiving chemotherapy. stimulates the bone marrow and promotes the growth of white blood cells called neutrophils

Q1 2012 13 (1) $849,971 3.33% 331 1.53%
Q4 2011 12 (2) $822,578 4.59% 326 3.49%
Q3 2011 14 (1) $786,464 -3.86% 315 -5.69%
Q2 2011 15 $818,068 4.04% 334 3.41%
Q1 2011 15 $786,288 323


Novolog $3.7 2000 —  Insulin aspart is a fast-acting form of insulin. NovoLog is used to treat type 1 (insulin-dependent) diabetes in adults and children who are at least 2 years old. It is usually given together with a long-acting insulin.

Q1 2012 57 (6) $266,305 5.67% 2,980 3.72%
Q4 2011 63 (3) $252,015 0.97% 2,873 -0.48%
Q3 2011 60 (1) $249,591 -0.96% 2,887 -2.66%
Q2 2011 61 (5) $252,010 3.16% 2,966 -0.70%
Q1 2011 66 $244,297 2,987


Erbitux $3.6 2004 — used to treat cancers of the colon and rectum. It is also used to treat head and neck cancer.

Q1 2012 99 (2) $171,513 2.30% 266 3.91%
Q4 2011 97 (7) $167,657 -0.15% 256 0.79%
Q3 2011 90 (3) $167,909 -2.48% 254 -1.93%
Q2 2011 93 (2) $172,185 -0.89% 259 -0.38%
Q1 2011 95 $173,735 260


Aranesp $3.2 2001 — Anemia, low RBC,  (darbepoetin alfa) is a man-made form of a protein that helps your body produce red blood cells. 

Q1 2012 72 (6) $231,643 -5.86% 293 -7.86%
Q4 2011 66 (15) $246,056 -6.07% 318 -3.64%
Q3 2011 51 (3) $261,967 -10.25% 330 -11.29%
Q2 2011 48 (3) $291,873 -1.03% 372 -1.33%
Q1 2011 51 $294,912 377


The article reports on the decline of worldwide sales of Aranesp drug from Thousand Oaks, California-based Amgen Inc. as of the second quarter of 2007. According to Amgen, the 10% decrease of Aranesp worldwide sales was due to the reimbursement issues related to the anemia drug and the drop of U.S. demand for drug, in which the U.S. Aranesp reported sales in the second quarter of 2007 was only $578 million from $713 million in 2006.


1/24/2011, Amgen boosts prices to offset Aranesp sales

Amgen is hiking prices to make up for the shrinking sales volume of its anemia drug Aranesp. Bloomberg reports that Amgen raised the price tag on Aranesp itself by 4.4 percent, but also marked up the white-blood-cell-boosting meds Neulasta and Neupogen by 2.9 percent.


Recombinate $2.9 1998 — Antihemophilic Factor VIII (Recombinant)

BioScience core franchises include: Hemophilia, Biotherapeutics, BioSurgery and Vaccines. BioScience products represent approximately 45 percent of Baxter’s annual sales, totaling $5.7 billion in 2010.

2007 Outlook – Sales within Baxter’s BioScience business totaled $1.2 billion, an increase of 18 percent from the same period last year. This growth was driven by record sales of ADVATE, Antihemophilic Factor (Recombinant), Plasma/Albumin Free Method (rAHF-PFM) for the treatment of hemophilia A, antibody therapy products, including GAMMAGARD LIQUID(TM) [Immune Globulin Intravenous (Human)] (IVIG) 10% Solution for the treatment of primary immunodeficiencies, specialty plasma therapeutics and biosurgery products. Medication Delivery sales increased 7 percent to $1.0 billion, with increased sales of infusion systems, intraveneous solutions and parenteral nutrition products, along with accelerated growth in the company’s drug delivery business. Renal sales increased 6 percent to $537 million reflecting accelerating gains in peritoneal dialysis patients globally.

Lucentis $2.7 2006 intraocular injection. (ranibizumab injection) is a recombinant humanized IgG1 kappa isotype monoclonal antibody fragment designed for intraocular use. Ranibizumab binds to and inhibits the biologic activity of human vascular endothelial growth factor A (VEGF-A).

Date Range Sales Rank Sales ($000) Units (000)
Q1 2012 35 (5) $409,547 -6.89% 224 -5.88%
Q4 2011 30 (2) $439,867 2.44% 238 2.59%
Q3 2011 28 (2) $429,393 1.13% 232 0.87%
Q2 2011 30 (3) $424,611 0.95% 230 1.32%
Q1 2011 33 $420,635 227



Lucentis brought in $1.7 billion for Roche last year, according to data compiled by Bloomberg.Alimera Sciences Inc. (ALIM), based in Alpharetta, Georgia, and Psivida Corp. (PSDV) also are developing a diabetic macular edema treatment known as Iluvien. The FDA has twice rejected Iluvien, most recently in November.

The FDA pooled results from two Roche clinical trials and found 39 percent of patients who used the 0.3 milligram dose were able to read three additional lines of letters on an eye chart after two years compared to 41 percent who had the same effect on the 0.5 milligram dose, according to an FDA staff report released July 24.

Genentech recommended approval of the 0.3 milligram dose in its application to the FDA since there isn’t evidence of additional benefit of the higher dose, Terence Hurley, a spokesman for the company, said in an e-mail.

Patients who received the monthly injection also were significantly more likely than those who received fake doses of the drug to achieve 20/40 vision, enough eyesight to drive.


Avonex $2.6 1996 —  Multiple Sclerosis, a form of protein called beta interferon that occurs naturally in the body. Interferons help the body fight viral infections. Avonex is used to treat patients with relapsing forms of multiple sclerosis to slow the accumulation of physical disability. This medication will not cure MS, it will only decrease the frequency of relapse symptoms.

Q1 2012 39 (1) $388,623 2.22% 130 -3.70%
Q4 2011 38 (5) $380,189 0.19% 135 -2.17%
Q3 2011 33 $379,457 -0.05% 138 -1.43%
Q2 2011 33 (4) $379,639 2.45% 140 -1.41%
Q1 2011 37 $370,570 142


Second-quarter net income surged 34 percent to $386.8 million, or $1.61 a share, from $288 million, or $1.18, a year earlier, the Weston, Massachusetts-based company said today in a statement. Earnings excluding some items of $1.82 topped by 26 cents the average of 21 analysts’ estimates (BIIB) compiled by Bloomberg. Revenue beat estimates by about $90 million.

Biogen said profit this year is expected to be more than $6.20 a share, 5 cents higher than its May 1 forecast (BIIB). The company has been increasing sales of Avonex, Rituxan and Tysabri, another MS therapy, while developing new medicines to introduce to the market.


AVONEX(R) (interferon beta-1a) revenues increased 16% year-over-year to $762 million.

Novolin $2.5 1991  —  Novolin R (insulin regular) is a short-acting form of human insulin, Diabetes, Type 1 Type 2

Date Range Sales Rank Sales ($000) Units (000)
Q1 2012 74 (2) $227,228 8.96% 2,489 13.81%
Q4 2011 76 (4) $208,552 10.19% 2,187 6.73%
Q3 2011 80 (6) $189,267 4.15% 2,049 4.92%
Q2 2011 86 (7) $181,733 3.71% 1,953 29.60%
Q1 2011 93 $175,235 1,507
Novo Nordisk launches iPhone app Posted 17th September 2010, 15:11:54
An iPhone app has been launched by Novo Nordisk in the US which lets healthcare staff check dosage guidelines for diabetes patients.

Novo Dose provides product-specific data for the company’s insulin analog agents Levemir (insulin detemir), NovoLog (insulin aspart) and NovoLog Mix (insulin aspart protamine/insulin aspart injectable).

Combined sales of the three medications increased by 24% last year, feeding a double-digit growth in Novo Nordisk sales and profits.

Novo Dose, the second diabetes app created by the industry, tells professionals when and how to dose the drugs, how to titrate and provides information on the blood glucose goals of patients.

Commenting on the new technology, Anup Kumar Sabharwal, an endocrinologist at the University of Miami Clinics’ Diabetes Research Institute, said: “This is where modern medicine is headed.”

Humalog $2.2 1996  Humalog is used to treat type 1 (insulin-dependent) diabetes in adults. Insulin lispro is a fast-acting form of insulin. It is usually given together with another long-acting insulin. It works by lowering levels of glucose in the blood. Humalog is also used together with oral (taken by mouth) medications to treat type 2 (non insulin-dependent) diabetes in adults.

Q1 2012 65 $244,587 -2.70% 2,570 -3.85%
Q4 2011 65 (2) $251,367 3.78% 2,673 2.81%
Q3 2011 63 (4) $242,208 -0.75% 2,600 -1.78%
Q2 2011 67 (5) $244,050 4.83% 2,647 1.15%
Q1 2011 72 $232,809 2,617


Pegasys $2.0 2002 — (peginterferon alfa-2a) is made from human proteins that help the body fight viral infections. Pegasys is used to treat chronic hepatitis B or C. It is often used together with another medication called ribavirin (Copegus, Rebetol, RibaPak, Ribasphere, RibaTab).

Q1 2012 90 (1) $181,693 3.92% 87 3.57%
Q4 2011 91 () $174,833 84


Rebif $1.7 2002 — (interferon beta-1a) is a protein identical to one found in the body. Interferon beta-1a is made from human proteins. Interferons help the body fight viral infections. Rebif is used to treat relapsing multiple sclerosis (MS). This medication will not cure MS, it will only decrease the frequency of relapse symptoms.

Q1 2012 62 (1) $258,088 -0.21% 540 -9.09%
Q4 2011 61 (7) $258,643 0.43% 594 -0.34%
Q3 2011 54 (5) $257,535 1.48% 596 -1.49%
Q2 2011 59 (2) $253,780 0.25% 605 -0.66%
Q1 2011 61 $253,143 609


Cerezyme $1.5 1994 —  Gaucher disease and Fabrazyme for Fabry disease.

Last year Genzyme was forced to temporarily close its manufacturing plant in Boston due to a viral contamination. The interruption lead to shortages of two key drugs: Cerezyme for Gaucher disease and Fabrazyme for Fabry disease.

That crisis sent the company’s stock price plummeting from nearly $84 in 2008 to a low earlier this year of $45.39. Sanofi’s offer to acquire the company for $18.5 billion, or $69 a share — along with a 14 percent rise in the NYSE Arca Biotech Index since late July — have helped the shares rebound.

But Genzyme is now on a mission to prove to shareholders that it is worth more than Sanofi is offering, and executives told investors on a conference call that the third quarter marks the beginning of its financial turnaround.

Third-quarter sales of Cerezyme, the company’s top drug, rose to $179.8 million from $93.6 million a year earlier, beating analysts’ average forecast of $175 million.

“In the third quarter we saw our financial recovery start to take effect, and we expect that this will accelerate during the fourth quarter as Cerezyme patients are able to return to normal dosing levels and we begin to increase shipments of Fabrazyme,” Genzyme CEO Henri Termeer said in a statement.

Cerezyme is the principal drug for Gaucher patients. In the first quarter of 2012 Genzyme (now part of Sanofi (SNY))reported Cerezyme sales of 149 million euros (approx. $194 million), up 5.8% from the same quarter of the previous year. The other supplier Shire (SHPGY) reported $72 million in Vpriv sales, up 22%. There is now a third supplier, Pfizer (PFE), teamed up with the Israeli company Protalix Biotherapeutics (PLX), whose product was approved by the FDA in May 2012. Elelyso (taliglucerase alfa) is now available in the US.
Product Cerezyme
2009 2010 2011
 Total 793 720 885
 Ann. Growth Total -9% 23%


Tysabri $1.4 2004 — Multiple Sclerosis by Elan and Biogen

Global in-market sales of TYSABRI in the second quarter of 2012 were $395 million, an increase of 2% over the second quarter of 2011. The total was comprised of $211 million in U.S. sales and $184 million in sales outside the U.S.

TYSABRI(R) (natalizumab) revenues were $280 million, in-line with the second quarter of 2011.

Elan derives its revenue almost exclusively from Tysabri and it reported total sales for the three months to June 30 of $288 million, up 6 percent on a year ago once sales from its since-divested drug delivery business are omitted.

That compared to the $299 million forecast by four analysts surveyed by Reuters and was driven by in-market sales of Tysabri that rose 2 percent year-on-year to $395 million, also shy of the $419 million expected by analysts.

Biogen, which detailed the sales numbers when it reported second quarter results on Tuesday, attributed the softer-than-expected Tysabri sales to a dispute with the Italian government over pricing.

The number of patients on Tysabri rose 4 percent to 69,100, maintaining Elan and Biogen’s 10 to 12 percent share of the MS drug market in the face of competition from Swiss drugmaker Novartis AG’s Gilenya treatment, the first multiple sclerosis pill to come on the market.

The average addition of 185 new patients per week was the highest quarterly run-rate since the fourth quarter of 2009.


NovoSeven $1.4 1999 —  Anti-fibrinolytics by Novo Nordisk —

Generic Name:   eptacog alfa
Product NovoSeven
2009 2010 2011
 Total 1,324 1,431 1,559
 Ann. Growth Total 8% 9%


Synagis $1.3 1998 — Generic Name:  palivizumab     Anti-virals by AstraZeneca

Product Synagis
2009 2010 2011
 Total 1,042 906 570
 Ann. Growth Total -13% -37%


Neupogen $1.3 1991 —  (filgrastim) is a man-made form of a protein that stimulates the growth of whiteblood cells in your body. White blood cells help your body fight against infection. Neupogen is used to treat neutropenia, a lack of certain white blood cells caused by cancer,bone marrow transplant, receiving chemotherapy, or by other conditions.

Q1 2012 70 $238,427 0.06% 170 -2.86%
Q4 2011 70 (5) $238,289 0.16% 175 10.76%
Q3 2011 65 (5) $237,915 0.69% 158 0.64%
Q2 2011 70 (4) $236,294 2.51% 157 0.64%
Q1 2011 74 $230,515 156


Betaseron $1.2 1993 — (interferon) is made from human proteins. Interferons help the body fight viral infections. Betaseron is used to treat relapsing multiple sclerosis (MS). Betaseron will not cure MS, it will only decrease the frequency of relapse symptoms.

Q1 2012 98 (1) $172,143 2.93% 67 -10.67%
Q4 2011 99 (12) $167,236 -3.76% 75 -5.06%
Q3 2011 87 (2) $173,769 -2.89% 79 -2.47%
Q2 2011 89 (4) $178,938 -2.17% 81 -7.95%
Q1 2011 85 $182,908 88


Humulin $1.1 1992 Insulin Human by Eli Lilly 

Product Humulin R
2009 2010 2011
 Total 1,022 1,089 1,249
 Ann. Growth Total 7% 15%


Kogenate FS $1.1 1993 — octocog alfa    Anti-fibrinolytics By Bayer

Product Kogenate
2009 2010 2011
 Total 1,238 1,332 1,496
 Ann. Growth Total 8% 12%



Biosimilars are defined as biological products similar, but not identical, to the reference biological products that are submitted for separate marketing approval following patent expiration of the reference biological products. As one of the ICH members, the US needs to catch up with the EU and Japan as those two countries have already issued regulatory guidelines for biosimilars.

Once Congress establishes a legal framework, FDA is expected to set up a biosimilar approval pathway which will be similar to those in the EU and Japan and harmonized under ICH. The biosimilar will need a full CMC development package plus demonstration of comparable quality attributes and comparable efficacy and safety to the innovator’s product. Table 5 provides a comparison summary between small-molecule generics and biosimilars. It will take a much bigger effort to develop a biosimilar than a generic drug. Automatic substitution between the innovator product and a biosimilar is not appropriate as a biosimilar is not a generic version of the innovator product and is approved based on comparability to the innovator product.



Read Full Post »

Biosimilars: CMC Issues and Regulatory Requirements

Reporter: Aviva Lev-Ari, PhD, RN

Updated on 6/30/2015

Biosimilars in the US: How much can we learn from Europe?


Updated on 2/10/2014

Cambridge Healthtech    Institute’s Fifth  Annual Biotherapeutics Analytical Summit
Hyatt Regency    Baltimore | Baltimore,  MD | BiotherapeuticsAnalyticalSummit.com


The    Science and  Regulation of Process Changes for Biologics (Comparability)
Thursday,  March 27, 2014 | 5:30 – 8:30 PM | More Information 


Manufacturing changes can impact on quality     attributes of biologics, and may affect efficacy and/or safety of the product.   For that reason, a thorough comparability exercise is required, to assess the   impact of the change and whether CMC data alone will suffice to support the     change. This interactive short course will consider comparability exercises     during development, as well as post-approval, addressing regulatory and     technical requirements. This should provide the attendee with the knowledge on   how to prepare a comparability package for discussion with regulatory  agencies,   towards acceptance of the proposed change to the process/product.  Attendees   will  be contacted before the event and asked about topics on which  they would   like to  focus.

Topics covered     include:

  • Ways that manufacturing changes can impact    on quality attributes
  • Features of a thorough comparability exercise
  • Critical evaluation of quality data
  • The comparability exercise during development
  • Post-approval comparability, ICH Q5E, Comparability Protocols (US) and Change Management Protocols (EU)
  • Regulatory requirements in the EU and US: guidelines, their interpretation and application
  • Discussion with Q&A

Course    Instructors:
Christopher J. Holloway, Ph.D., Group     Director, Regulatory Affairs &  CSO, ERA Consulting Group        
Kazumi Kobayashi, Ph.D., Director, Bioprocess Development, Biogen Idec,    Inc.       
Marjorie Shapiro, Ph.D., Chief, Laboratory of Molecular and Developmental  Immunology, Division of Monoclonal Antibodies,            FDA/CDER

Comparability and Developability conference program at Biotherapeutics Analytical Summit.

The third track of the Biotherapeutics Analytical    Summit focuses on the practical application of analytical characterization for    Comparability, Biosimilarity and Development purposes. It covers case studies    with a variety of products and a range of analytical technologies. We have    invited the FDA and regulatory experts to advise and to discuss regulatory    challenges being experienced by the industry. This conference also covers the    link between the process and analytical technologies for innovator products and   for biosimilars.




From: Biotherapeutics Analytical Summit Short Course <lauran@healthtech.com>
Date: Mon, 10 Feb 2014 12:40:59 -0500
To: <avivalev-ari@alum.berkeley.edu>
Subject: The Science and Regulation of Process Changes for Biologics (Comparability)

Comparability: The Final Frontier of Protein Therapies

The rapid expansion of protein therapeutics has crossed into all major disease classes (cancer, metabolic disease, inflammatory disease, infectious disease, immune disorders, etc.).  Due to the lengthy learning curve and high cost of developing these complex products, the development of therapies has been traditionally limited to highly specialized companies.  As protein therapeutics become more mainstream, these products are finding new applications in disease treatment and commercial application beyond the range of the traditional biotech companies.  Unfortunately, the expansion of medical applications for these therapies is outpacing the rate of innovation in product development and, as a result, market availability is becoming constrained by the ability to characterize and control product characteristics.

The Future Opportunity:

The key to most effectively and efficiently developing a biopharmaceutical or biologic to marketing approval is to have a clear understanding of the unique properties of proteins and to use that knowledge to design appropriate manufacturing processes, preclinical pharmacology-toxicology and clinical programs.  It is essential in dealing with complex comparability issues related to the types of manufacturing processes or changes in manufacturing to understand the scientific reasons for requiring a demonstration of comparability and the relationships between bioanalytical differences or changes in a protein and potential alterations in protein functionality in terms of specificity, potency, pharmacological activity, pharmacokinetics, toxicity and ultimately clinical safety and efficacy.  This understanding requires in depth knowledge of protein chemistry, manufacturing processes, pharmacology, immunology and toxicology that comes with extensive training and experience.  The same scientific and regulatory expertise and experience that is required for a successful demonstration of comparability is also applicable to the development of a biosimilar. This type of experience and expertise should prove invaluable as the expansion in the area of protein therapies continues and the development of biosimilars grows in the coming years.

How to Get There from Here:

Product developers can begin today to capitalize on this opportunity.   A number of technology advancements are being explored that will enhance our understanding of relationships between process, product, and clinical safety and efficacy.   One must think through how to integrate the future product comparability into early stage product development.  For new product development, these issues will include more in-depth analysis of the product structure and relationship of various structural features to function andin vivo activity, increased knowledge about the effect of process conditions on the types and mix of final product variants, and careful choice of in vitro binding and functional assays that clearly relate to the proposed mechanism of action of the product and can often also be used as a potency assays.  New technologies are being developed for these assays, and appropriate in vitro functional assays as relates to pharmacological mechanism of action can be very useful for demonstrating comparability.

A careful determination of appropriate animal models of disease for demonstration of proof-of-concept pharmacology is also important early in development. Identification of appropriate biomarkers of efficacy or safety should also be examined in these early animal models for future use in clinical development as well as demonstration of comparability.  The discovery of appropriate biomarkers can sometimes be carried over to the clinic and used in clinical trials with the appropriate validation.  Finally, as the safety database for the various classes of biopharmaceuticals and biologics expands, the understanding of safety issues associated with each of these various product classes will make it easier to more efficiently demonstrate comparability as well as to develop biosimilar products.

For developers who are trying to bridge comparability on products that lack a complete process/product history due to legacy issues or as in the case for biosimilar development, companies must think about the pharmacology of the product as relates to the proposed indication of either the previous iteration of the product or the innovator product, depending on whether this is a comparability issue or development of a biosimilar. It is the pharmacological activity of a given protein product that determines the efficacy and to a great extent the toxicity of the product.   The pharmacological activity of a product is driven by protein structure, mix of product variants, binding kinetics, dose, dosing regimen, route of administration, and final product formulation, among others.

As the development of biopharmaceuticals and biologics continues to expand, more and more information accrues on potential safety issues related to each of the various product classes, and this information will also prove quite useful to demonstration of comparability and development of biosimilars.

Biologics Consulting Group can assist developers in designing and implementing each of their comparability programs with the greatest chance of rapid regulatory approval.  Our staff has both FDA and industry experience, with a track record of success in helping academic institutions, start-ups, and established biotech and pharma companies.  Our direct knowledge and contemporary experience with all possible regulatory pathways – and every associated nuance — and can provide the requisite preclinical, clinical, quality, analytical, and manufacturing support to increase your chances for success.

Contributors: T. CarrierD. BarngroverJ. JessopV. NarbutJ. HumphriesB. FraserR. WolffN. RitterL. Winberry 



For IP and Legal aspects of Biosimilars, go to:

Biosimilars: Intellectual Property Creation and Protection by Pioneer and by Biosimilar Manufacturers


For Financial Aspects of Biosimilars, go to:

Biosimilars: Financials 2012 vs. 2008


Tr e n d s  i n  B i o / P h a r m a c e u t i c a l I n d u s t r y , 1 9 -26

Special Report on Biosimilars

About the Author: Dr. Bao-Lu has over 18 years of experience in product development, CMC regulatory, manufacturing management and quality oversight. He is currently the Director of Manufacturing and Process Development at Sangamo BioSciences. In this role, he oversees outsourced GMP production and testing of Sangamo’s gene therapy products and is responsible for the release and disposition of final drug product. He also provides CMC regulatory support and manages the in-house quality system by maintaining GMP database and implementing quality SOPs. Previously, Bao-Lu served as an Associate Director of Formulation at Xencor and Chiron and a Formulation Scientist at Amgen. Bao-Lu graduated with a BS degree from Fudan University and was selected as one of the forty chemistry students in the first year CGP Doering program. Bao-Lu earned his Ph.D. in Chemistry from University of Oregon and performed postdoctoral research in Biology at Massachusetts Institute of Technology.


CMC Issues and Regulatory Requirements for Biosimilars


Chemistry, Manufacturing and Controls (CMC), preclinical and clinical are three critical pieces in biosimilars development. Unlike a small-molecule generic drug, which is approved based on “sameness” to the innovator’s drug; a biosimilar is approved based on high similarity to the original approved biologic drug. This is because biologics are large and complex molecules. Many functional-, safety- and efficacy-related characteristics of a biologic depend on its manufacturing process. A biosimilars manufacturer won’t be able to exactly replicate the innovator’s process. The traditional abbreviated pathway for generic drug approval through the Hatch- Waxman Act of 1984 doesn’t apply for biosimilars as drugs and biologics are regulated under different laws. New laws and regulations are needed for biosimilars approval in the US. The EU has issued biosimilars guidelines based on comparative testing against the reference biologic drug (the original approved biologic). A full scale CMC development is required including expression system, culture, purification, formulation, analytics and packaging. The manufacturing process needs to be developed and optimized using state-of-the-art technologies. Minor differences in structure and impurity profiles are acceptable but should be justified. Abbreviated clinical testing is required to evaluate surrogate markers for efficacy and demonstrate no immunogenic response to the product.

We anticipate the package for a biosimilars approval in the US will be similar to that in the EU and contain a full quality dossier with a comparability program including detailed product characterization comparison and reduced preclinical and clinical requirements.

Biosimilars Become Inevitable

 Biologics developed through biotechnology constitute an essential part of the pipeline for medicines available to patients today. Biologic drugs are quite expensive and many of them are top-selling medicines (see Table 1). Since they come at extremely high prices to consumers, some patients may not be able to afford the use of biologics as the best-available treatments to their conditions. The patent protection on a large number of biologics has expired since 2001. These off-patent biologics include Neupogen, Novolin, Protropin, Activase, Epogen or Procrit, Nutropin, Humatrope, Avonex, Intron A, and Humulin. Traditionally, when a drug patent expires, a generic drug will be quickly developed and marketed. Similarly, generic version of off-patent biologic drugs (also referred to biosimilars or follow-on biologics or biogenerics) represents an extraordinary opportunity to companies that want to seize the potentially great commercial rewards in this unexploited territory. Biosimilars not only benefit the biosimilar manufacturers but also can save patients, and insurance companies, substantial cost and allow patients to gain access to more affordable biologics resulting in market expansion. The government can use biosimilars to reduce healthcare costs. Therefore, development and marketing of bosimilars are supported by both manufacturers and consumers.

Differences between Generic Drugs and Biosimilars

Enacted in 1984, the US Drug Price Competition and Patent Term Restoration Act, informally known as the “Hatch-Waxman Act of 1984” standardized US procedures for an abbreviated pathway for the approval of small-molecule generic drugs. The generic drug approval

is based on “sameness”. In comparison to the innovator’s drug, a generic drug is a product that has the same active ingredient, identical in dose, strength, route of administration, safety, efficacy, and intended use. For approval, the generic companies can go through the Abbreviated

New Drug Application (ANDA) process with reduced requirement in comparison to approval for a new drug entity. The generic drugs need to show bioequivalence to the innovator drugs typically based on pharmacokinetic parameters such as the rate of absorption or bioavailability in 24 to 36 healthy volunteers. No large clinical trials for safety and efficacy are required. The generic companies can rely on the FDA’s previous findings of safety and effectiveness of the innovator’s drugs.

However, the abbreviated pathway for generic drugs legally doesn’t apply to biologics as small-molecule drugs and biologics are regulated under different laws and approved through different pathways in the US (Table 2). Small-molecule drugs are regulated under the Food, Drug and Cosmetic Act (FD&C) and require submission of a New Drug Application (NDA) to FDA for drug review and approval. Biologics are regulated under the Public Health Service Act (PHS) and require submission of a Biologic License Application (BLA) to FDA for review and approval. The Hatch-Waxman Act of 1984 doesn’t apply for biosimilars. New laws are needed to establish a pathway for biosimilar approval.

There are some crucial differences between biologics and small-molecule drugs (Table 3). Small-molecule drugs are made from chemical synthesis. They are not sensitive to process changes. The final product of a small-molecule drug can be fully characterized. The developmentand production of generic drugs are relatively straightforward. Biologics are made from living organisms so that its functional-, efficacy- and safety-related properties depend on its manufacturing and processing conditions. They are sensitive to process changes. Even minor modifications of the manufacturing process can cause variations in important properties of a biological product. Thus it is believed that a biologic product is defined by its manufacturing process. Biologics are 100- or 1,000-fold larger than small-molecule drugs, possess sophisticated three-dimensional structures, and contain mixtures of protein isoforms. A biological product is a heterogeneous mixture and the current analytical methods cannot characterize these complex molecules sufficiently to confirm structural equivalence with the reference biologics.

Laws and Regulatory Pathways for Drug Approval in the US

Law/Application           Small-molecule            Drug Biologics                     

Law                     Food, Drug and Cosmetic Act (FD&C)             Public Health Service Act (PHS)

Drug application                 New Drug Application (NDA)   Biologic License Application (BLA)

Generic application   Abbreviated New Drug   Application(ANDA)   No pathway yet

 Immunogenicity Poses a Concern

One of the major complications that biologics can produce is immunogenicity as therapeutic proteins are inherently immunogenic [2]. Immunogenicity is related to biologics structure and formulation and is dependent on dose, route of administration and frequency of administration.

Clinical implications of immunogenicity are not always predictable. Formation of antibodies can result in harmless clinical effect or produce significant adverse events or severe disease. Examples are provided below. The Eprex (Erythropoietin, EPO) has been marketed by Johnson & Johnson (J&J) in the European Union (EU) countries for 10 years with no noticeable

Differences between small-molecule drugs and biologics

Product characteristics

Small-molecule generics Small, simple molecule

(Molecular weight: 100-1,000 Da)

Biosimilars   Large, complex molecules, Higher order structures, Post-translational, modifications

(Molecular weight: 15,000-150,000 Da)


Small-molecule generics Produced by chemical synthesis

Biosimilars  Produced in living organisms

Analytical testing

Small-molecule  Well-defined chemical structure, all its various components in the finished drug can be determined

Biosimilars  Heterogeneous mixture, difficult to characterize, some of the components of a finished biologic may be unknown

Process dependence

Small-molecule   Not sensitive to manufacturing process changes. The finished product can be analyzed to establish the sameness.

Biosimilars   Sensitive to minor changes in manufacturing process. The product is defined by the process

Identity and purity

Small-molecule Often meeting pharmacopeia or other standards of identity (e.g., minimums for purity and potency)

Biosimilars   Most have no pharmacopeia monographs

immunogenicity issues prior to 1998. When J&J made a change in the Eprex formulation by replacing human serum albumin (HAS) with polysobate 80 and glycine in response to the

request from European health authorities, some patients developed pure red-cell aplasia (PRCA), a severe form of anemia. Eprex induced antibodies neutralize all the exogenous rHuEPO and cross-react with endogenous erythropoietic proteins. As a result, serum EPO is undetectable

and erythropoiesis becomes ineffective. Upon investigation, J&J found that polysorbate 80 might have caused uncoated rubber stoppers in single-use Eprex syringes to leach plasticizers, which stimulated an immune response that resulted in PRCA. Replacing with Teflon coated stoppers resulted in 90% decrease in PRCA by 2003 [3,4]. The effect of neutralizing antibodies has not always resulted in serious clinical consequences. Three interferon beta products, Betaseron, Rebif and Avonex, are marketed by three different companies. These products induce neutralizing antibodies in multiple sclerosis patients from 5 to 50% after one year treatment. Although these antibodies might be associated with loss of efficacy of treatment resulting in some patients to withdraw from the treatment, it seems no other severe adverse effects were detected [5,6].

Regulatory Landscape

The US, the EU and Japan are the three cornerstonemembers of the International Conference on Harmonization (ICH), which intends to harmonize the regulatory requirements for drug or biologic approval in these three regions. With the other two members, the EU and Japan, already have established biosimilar approval procedures (see below), the US lags behind in the biosimilar race. There are no formal approval pathways for biosimilars in the US. Congress needs to establish a legal framework in order for FDA to develop guidelines. Legislation has been under discussion in Congress since 2007. The legislative debate is centered on patient safety and preserving incentives to innovate with introduction of biosimilars. Two bills introduced in March 2009 deserve attentions [7,8]. The Waxman bill (H.R. 1427) proposes 5 years of market exclusivity to the innovator companies and requires no clinical trials for biosimilar development. The Eshoo bill (H.R. 1548) proposes 12 years of market exclusivity to the innovator companies and requires clinical trials for biosimilar development. Obama administration appears to favor a 7-year market exclusivity [9]. Once a legal framework is established for biosimilars, the FDA will likely take a conservative approach using the comparability as an approval principle. Clinical proof of efficacy and safety will be required, probably in reduced scale.

In the EU, the European Medicines Agency (EMEA) issued regulatory guidelines for approving biosimilars in 2005 (Figure 1) [10-16]. These include two general guidelines for quality issues [11] and non-clinical and clinical issues [12] and four class-specific annexes for specific data requirements for Granulocyte-Colony Stimulating factor (G-CSF) [13], Insulin [14], Growth hormone [15] and Erythropoietin [16]. In addition, a concept paper on interferon alpha [17] is also available. So far, there are eleven biosimilar products which received market authorization in the EU and they are biosimilar versions of human growth hormone, Epoetin and filgrastim. It is estimated six to eight years on average for a biosimilar to be developed [18].

The EMEA treats a biosimilar medicine as a medicine which is similar to a biological medicine that has already been authorized (the “biological reference medicine”) in the EU, The active substance of a biosimilar medicine is similar to the one of the biological reference medicine.

A biosimilar and the biological reference medicine are used in general at the same dose to treat the same disease. A biosimilar and the biological reference medicine are not automatically interchangeable because biosimilar and biological reference medicine are only similar but not identical. A physician or a qualified healthcare professional should make the decision to treat a patient with a reference or a biosimilar medicine. Since the biosimilar may contain different inactive ingredients, the name, appearance and packaging of a biosimilar medicine differ to those of the biological reference medicine. In addition, a pharmacovigilance plan must be in place for post-marketing safety monitoring.

Japan’s Ministry of Health, Labor and Welfare (MHLW) issued guidelines for follow-on proteins or biosimilars approval in March 2009. The first biosimilar, Sandoz’ growth hormone Somatropin, was approved in June 2009. The MHLW’s guidelines consider biosimilars drugs which are equivalent and homogeneous to the original biopharmaceuticals in terms of quality, efficacy and safety. Biosimilars are also requested to be developed with updated technologies and knowledge. Biosimilars need to demonstrate enough similarity to guarantee the safety and efficacy instead of absolute identity to the original biologics. Biosimilars’ regulatory approval applications will be categorized separately from conventional generic drugs. In general, the applications should be submitted, as the new drug applications, with data from clinical trials, manufacturing methods, long-term stability and information on overseas use. The MHLW will assess the data on absorption, distribution, metabolism and excretion (ADME) on a case-by-case basis. The applications do not need to provide data on accessory pharmacology, safety pharmacology and genotoxicity.

Biosmilars are already thriving in Eastern Europe and Asia, where regulatory and intellectual property (IP) standards for biosimilars are more liberal. Biosimilars developed in these regions are primarily sold domestically. These markets are considered less controlled. The quality of the biosimilars may not be in full compliance with ICH guidelines although they are often developed through comparative quality testing and clinical trials against the biologics which are already approved in Western countries

CMC Development

The CMC requirements for biosimilars in the EU are those described in the ICH Common Technical Document (CTD) Quality Module 3 with supplemental information demonstrating comparability or similarity on quality attributes to the reference medicine product.

Since the US is a member of ICH and encourages submission using CTD format, once the legal framework for approving biosimilars is established in the US, the CMC development will be similar to those in the EU.

Biosimilar manufacturers will have no access to the manufacturing process and product specifications of the innovator’s products because these are proprietary knowledges. To develop a biosimilar, a biosimilar manufacturer will need to first identify a marketed biologic product to serve as the reference biologic product. Then a detailed characterization of the reference biologic product will be performed. The information obtained from the characterization of the reference biologic product will be utilized to direct the process development of the biosimilar product and comparative testing to demonstrate bioequivalence between the biosimilar product and the reference biologic product. A biosimilar will be manufactured from a completely new process, which may be based on different host/vector system with different process steps, facilities and equipment.

A flow chart for a typical work flow from production to drug use is shown in Figure 2. The CMC development starts with establishment of the expression system. A cell-line will be selected among bacterial, yeast and mammalian host strains and then the correct DNA sequence will be inserted. Elaborate cell-screening and selection methods are then used to establish a master cell bank. Extensive characterization on the master cell bank needs to be carried out to provide microbiological purity or sterility and identity [19].

Bulk protein production involves developing robust and scalable fermentation and purification processes. The goals for fermentation are to increase the expression level and efficiency without compromising the correct amino acid sequence and post translational modification. Achieving high expression requires optimizing culture medium and growth conditions, and efficient extraction and recovery procedures. Correct amino acid sequence and post translati0nal modification will need to be verified.

Cell Bank



Drug Substance



Drug Product



Typical flow chart for a biologics from production to drug use, above

Solubilization and refolding of insoluble proteins are sometimes necessary for proteins which have tendency to aggregate under the processing condition. Differences in the cell bank and production processes may create impurities that are different from the innovator’s product. The purification process needs to remove impurities such as host-cell proteins, DNA, medium constituents, viruses and metabolic by-products as much as possible. It is important for biosimilar manufacturers to accept appropriate yield losses to achieve high purity, because any increase in yield at the expense of purity is unacceptable and can have clinical consequences.

The final product is produced by going through formulation, sterile filtration and fill/finish into the final containers. Selection of formulation components starts from basic buffer species for proper pH control and salt for isotonicity adjustment. Surfactants may be needed to prevent proteins from being absorbed onto container surface or water-air interface or other hydrophobic surfaces. Stabilizers are required to inhibit aggregation, oxidation, deamidation and other degradations. The container and closure system can be glass vials, rubber stoppers and aluminum seals or pre-filled syringes or IV bags. The container and closure integrity needs to be verified by sterility or dyeleak test.

Biologics are not pure substances. They are heterogeneous mixtures. Each batch of a biologic product for clinical or commercial use needs to be produced in compliance with current Good Manufacturing Practice (cGMP) and is typically tested by a panel of assays to ensure the product meets pre-defined specifications for quality, purity, potency, strength, identity and safety. The product purity is often measured by multiple assays, which measure different product related variants (biologically active) or product related impurities (biologically inactive). Biologics are parenteral drugs and filled into the final containers through the aseptic process so that microbiological control is critical. It is advisable to set up product specifications for a biosimilar within the variation of the reference biologic product. Product characterization can be performed on selected batches for primary sequence, high order structures, isoform profiles, heterogeneity, product variants and impurities and process impurity profiles. Physicochemical characterization tests include IEF, CE, HIC, LCMS, carbohydrate analysis, N & C terminal sequencing, amino acid analysis, analytical ultracentrifugation, CD and DSC [20,21]. Biologics are highly sensitive to environmental influences during storage, shipment and handling. Temperature excursion, movement, and exposure to UV light can lead to protein degradation. Product expiry needs to be based on the real time stability data. Stability program should also include accelerated or stress studies to gain insight of the degradation profiles. In-use stability studies are carried out to verify shipping conditions or handling procedures cause no detrimental effect to the drug product.

 Comparability Demonstration

 A comparability exercise based on the ICH guideline [22] needs to be performed to demonstrate that the biosimilar product and the reference biologic product have similar profiles with respect to product quality, safety, and efficacy. This is accomplished by comparative testing of the biosimilar product and the reference biologic product to demonstrate they have comparable molecular structure, in vitro and in vivo biological activities, pre-clinical safety and pharmacokinetics, and safety and efficacy in human patients. Comparison of quality attributes between the biosimilar and the reference biologic product employs physicochemical

Product release assays for biologics

Type                         Assays

Quality              Appearance, particulates, pH, osmolality

Purity                 SDS-PAGE, SEC-HPLC, IEX-HPLC, RP-HPLC

Potency             In vitro or in vivo bioactivity assays

Strength             Protein concentration by A280

Identity               Western blot, peptide mapping, isoelectric focusing

Safety                  Endotoxin, sterility, residual DNA, host cell proteins

and biological characterization. Comparability on physical properties, amino acid sequence, high order structures, post-translationally modified forms are evaluated by physicochemical tests. In vitro receptor-binding or cell-based (binding) assays or even the in vivo potency studies in animals need to be performed to demonstrate comparable activity despite they are often imprecise. Levels of product related impurities (aggregates, oxidized forms, deamidated forms) and process related impurities and contaminants (host cell proteins, residual genomic DNA, reagents, downstream impurities) need to be assessed and quantified. Stability profiles of the biosimilar product and the reference biologic product also need to be studies by placing the products under stressed conditions. The rate of degradation and degradation profiles (oxidation, deamidation, aggregation and other degradation reactions) will be compared. If unknown degradation species are detected, they need to be studied to determine if they affect safety and efficacy. If differences on product purities and stability profiles are present between the biosimilar product and the reference biologic product, these differences need to be justified using scientific knowledge or preclinical or clinical studies. Changes in the impurity profile should be justified as well.

The demonstration of comparability in quality attributes does not necessarily mean that the biosimilars and the reference biologics are identical, but that they are highly similar. In many cases, the relationship between specific quality attributes and safety and efficacy has not been fully established. For example, physicochemical characterization cannot easily predict immunogenicity and slight changes in manufacturing processes or product composition can give rise to unpredicted changes in safety and efficacy. Changes in bioavailability, pharmacokinetics, bioactivity bioactivity, and immunogenicity are the main risks associated with the manufacturing of biosimilars. In vivo studies should be designed to measure the pharmacokinetics and pharmacodynamics relevant to clinical studies. Such in vivo studies should be designed to detect response differences between the biosimilar and the reference biologic not just responses per se. In vivo studies of the biosimilar’s safety in animals may be used to research any concerns into the safety of the biosimilar in human patients. Although extensive clinical testing is not necessary for biosimilars, some degree of clinical testing is needed to establish therapeutic comparability on efficacy and safety between the biosimilar and the reference biologic product [23,24]. This includes using surrogate markers of specific biologic activity as endpoints for demonstrating efficacy, and showing that patients didn’t develop immunogenic responses to the product. In general, the approval of biosimilars will be based on the demonstration of comparable efficacy and safety to an innovator reference product in a relevant patient population. Clinical data requirement for each individual product will be different and will be determined on a case-by-case basis.

Small-molecule Generics versus Biosimilars


  • Approval based on “sameness”


  • Approval based on “high similarity”


  • Replicate the innovator’s process and product and perform a bioavailability study demonstrating similar pharmacokinetic properties


  • Full CMC development with comparative testing, conduct substantial clinical trials for efficacy and safety including immunogenicity


  • Abbreviated registration procedures in Europe and US


  • Regulatory pathway is defined in EU on “Comparability” status, no pathway yet in US under BLA


  • Therapeutically equivalent, thus interchangeable


  • Lack of automatic substitutability


  • $1 to $5 million to develop


  • $100-$200 million to develop


  • Brand-to-generic competition


  • Brand-to-Brand competition


The patent provisions of the Biosimilar Act, 2009 establish demanding and time-sensitive disclosure requirements. ObamaCare upheld by the Supreme Court is a victory for future development of pathways for biosimilar regulatory approvaland eventually biosimilar generic drugs.

Biosimilars are defined as biological products similar, but not identical, to the reference biological products that are submitted for separate marketing approval following patent expiration of the reference biological products. As one of the ICH members, the US needs to catch up with the EU and Japan as those two countries have already issued regulatory guidelines for biosimilars. 2009 and 2012 represent milestones in the regulatory provisions for biosimilars in the US.

Once Congress establishes a legal framework, FDA is expected to set up a biosimilar approval pathway which will be similar to those in the EU and Japan and harmonized under ICH. The biosimilar will need a full CMC development package plus demonstration of comparable quality attributes and comparable efficacy and safety to the innovator’s product. Table 5 provides a comparison summary between small-molecule generics and biosimilars. It will take a much bigger effort to develop a biosimilar than a generic drug. Automatic substitution between the innovator product and a biosimilar is not appropriate as a biosimilar is not a generic version of the innovator product and is approved based on comparability to the innovator product.


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