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I recently read this beautiful paper by Fredrik Nederberg from the IBM Almaden Research Center and A*STAR Institute of Bioengineeringtitled “Biodegradable nanostructures with selective lysis of microbial membranes” (http://www.nature.com/nchem/journal/v3/n5/full/nchem.1012.html)
This paper gained a lot of attention as it merged as an innovation in nanotechnology and antibacterial therapeutics and therefore I have decided to introduce it here to the audience.
“Bacteria are increasingly resistant to conventional antibiotics and, as a result, macromolecular peptide-based antimicrobial agents are now receiving a significant level of attention. Most conventional antibiotics (such as ciprofloxacin, doxycycline and ceftazidime) do not physically damage the cell wall, but penetrate into the target microorganism and act on specific targets (for example, causing the breakage of double-stranded DNA due to inhibition of DNA gyrase, blockage of cell division and triggering of intrinsic autolysins). Bacterial morphology is preserved and, as a consequence, the bacteria can easily develop resistance. In contrast, many cationic peptides (for example, magainins, alamethicin, protegrins and defensins) do not have a specific target in the microbes, and instead interact with the microbial membranes through an electrostatic interaction, causing damage to the membranes by forming pores in them3. It is the physical nature of this action that prevents the microbes from developing resistance to the peptides. Indeed, it has been proven that cationic antimicrobial peptides can overcome bacterial resistance”.
“Most antimicrobial peptides have cationic and amphiphilic features, and their antimicrobial activities largely depend on the formation of facially amphiphilic a-helical or b-sheet-like tubular structures when interacting with negatively charged cell walls, followed by diffusion through the cell walls and insertion into the lipophilic domain of the cell membrane after recruiting additional
peptide monomers. The disintegration of the cell membrane eventually leads to cell death. Over the last two decades, efforts have been made to design peptides with a variety of structures, but there has been limited success in clinical settings, and only a few cationic synthetic peptides have entered phase III clinical trials. This is largely due to the cytotoxicity (for example, haemolysis) resulting from their cationic nature, their short half-lives in vivo (they are labile to proteases) and their high manufacturing costs”
A number of cationic polymers thatmimic the facially amphiphilic structure and antimicrobial functionalities of peptides have been proposed as a better approach, because they can be prepared more easily and their synthesis can be more readily scaled up compared with peptides.
The authors Yang, Hedrick and their co-workers have developed a polymer-based peptide alternative which avoids all of these problems. The polymer incorporates three key components: a non-polar hydrophobic head and tail, which drives the polymer to self-assemble into a nanoparticle; a positively charged block that selectively interacts with the bacterial cell membrane; and a carbonate backbone that slowly breaks down inside the cell, ensuring good biocompatibility. “The starting materials of our synthesis are inexpensive, and the synthesis of the antimicrobial nanoparticles is simple and can be scaled up easily for future clinical application.
“Polycarbonates are attractive biomaterials because of their biocompatibility, biodegradability, low inherent toxicity and tunable mechanical properties”
In general, Preclinical results confirm that the nanoparticles can efficiently kill fungi and multidrug-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE), even at low concentrations. The nanoparticles also showed insignificant activity against red blood cells, and no significant toxicity was observed during the in vivo studies in mice, even at concentrations well above their effective dose.
In more specific, the authors evaluated the minimal inhibitory concentrations (MICs) of the polymers against Gram-positive bacteria such as Bacillus subtilis, Enterococcus faecalis, Staphylococcus aureus and methicillin-resistant S. aureus (MRSA), and the fungus Cryptococcus neoformans. MIC is an important parameter commonly used to evaluate the activity of new antimicrobial agents, and is generally defined as the minimum concentration of an antimicrobial agent at which no visible growth of microbes is observed
Some of the MIC were evaluated against conventional antimicrobial agents that are used in clinical settings to treat infections caused by these microbes, such as vancomycin for S. aureus, MRSA and E. faecalis, and amphotericin B for C. neoformans. When compared with these conventional antimicrobial agents, the polymers demonstrated comparable antimicrobial activities against all the microbes except for E. faecalis. This is important, because vancomycin-resistant E. faecalis, and S. aureus, as well as amphotericin B-resistant C. neoformans have been reported, and the resistant strains of these microbes are not susceptible to conventional antimicrobial agents. This suggests that there is an urgent need to develop safe and efficient macromolecular antimicrobial agents.
The hypothesis was that the cationic micelles can interact easily with the negatively charged cell wall by means of an electrostatic interaction, and the steric hindrance imposed by the mass of micelles in the cell wall and the hydrogen-binding/electrostatic interaction between the cationic micelle and the cell wall may inhibit cell wall synthesis and/or damage the cell wall, resulting in cell lysis. In addition, the micelles may easily permeate the cytoplasmic membrane of the organisms due to the relatively large volume of the micelle, destabilizing the membrane as a result of electroporation and/or the sinking raft model, leading to cell death.
Haemolysis is a major harmful side effect of many cationic antimicrobial peptides and polymers. The haemolysis of mouse red blood cells was evaluated after incubation with polymers 1 and 3 at various concentrations. Although the polymers disrupt microbial walls/membranes efficiently, they do not damage red blood cell membranes.
Toxicity tests in vivo showed that the micelles do not cause significant acute damage to liver and kidney functions, nor do they interfere with the electrolyte balance in the blood. Importantly, these parameters remain unchanged, even at 14 days post-injection.
In addition, no mouse treated with the polymer died, and no colour change was observed in the serum samples and urine of the mice treated with the polymer when compared with the control group. These findings demonstrate that the polymer did not induce significant toxicity to the mice during the period of testing. Nonetheless, preclinical studies should be conducted in the future to further evaluate potential long-term toxicity of the antimicrobial polymers before clinical applications.
In summary, the authors have designed and synthesized novel biodegradable, cationic and amphiphilic polycarbonates that can easily self-assemble into cationic micellar nanoparticles by direct dissolution in water. The cationic nanoparticles formed from the polymers, with optimal compositions, can efficiently kill Gram positive bacteria, MRSA and fungi, even at low concentrations. Importantly, they have no significant haemolytic activity over a wide range of concentrations, and cause no obvious acute toxicity to the major organs and the electrolyte balance in the blood of mice at a concentration well above the MICs. These antimicrobial polycarbonate nanoparticles could be promising as antimicrobial drugs for the decolonization of MRSA and for the treatment of various infectious diseases, including MRSA associated infections.
The data presented by the authors is very promising and open a new door to antimicrobial therapy. Several questions and new avenues comes in minds:
Can these polymers be proven for there efficiency in specific disease animal models?
Can these NPs or similar approach can be applied to gram-negative bacteria?
Can these polycarbonate affect massive biofilms?!
Looking forward to reading more news and results from this research group.
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:
Size
Th1/Th2 stimulation
Adjuvent properties
Internalization/phagocytic uptake
Hapten properties
Particle clearance
Charge
Toxicity to immune cells
Binding plasma proteins
Particle clearance
Immune cell stimulation
Hydrophobicity
Interaction with plasma proteins
Internalization/phagocytic uptake
Immune cell stimulation
Particle clearance
Targeting
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.
Conclusions:
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.
Ref.
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
Advances in Separations Technology for the “OMICs” and Clarification of Therapeutic Targets
Curator, Reporter, EAW: Larry H Bernstein, MD, FCAP
Article 1.5 Advances in Separations Technology for the “OMICs” and Clarification of Therapeutic Targets
This discussion is a continuation of an earlier piece on the technologic framework for , proteomics, nutrigenomics, and translational medicine. The last decade has seen the emergence of a genomic science that is changing the trajectory of biological sciences and medicine. It has not resolved all of our problems by any means, but it has begun to redraw the map, which began with the elucidation of major metabolic pathways in the first half of the 20th century, was then captured by the transformation of genetics with the discovery of the “Watson-Crick Model”, and then later was recharged with the discovery of the Toll-like receptor and the drawing of “signaling pathways”. What we have seen in an unraveling of protein-genome interactions, small peptide regulators, and dynamic changes in pathway dominance, bloackage, and reentry, depending on genetic, dietary, and environmental conditions, mostly expressed in what we refer to as “oxidative stress”.
Unraveling the multitude of nutrigenomic, proteomic, and metabolomic patterns that arise from the ingestion of foods or their bioactive food components will not be simple but is likely to provide insights into a tailored approach to diet and health. The use of new and innovative technologies, such as microarrays, RNA interference, and nanotechnologies, will provide needed insights into molecular targets for specific bioactive food components and how they harmonize to influence individual phenotypes. A challenging aspect of omic technologies is the refined analysis of quantitative dynamics in biological systems.
In recent years, nutrition research has moved from classical epidemiology and physiology to molecular biology and genetics. The new era of nutrition research translates empirical knowledge to evidence-based molecular science. Following this trend, Nutrigenomics has emerged as a novel and multidisciplinary research field in nutritional science that aims to elucidate how diet can influence human health. It is already well known that bioactive food compounds can interact with genes affecting transcription factors, protein expression and metabolite production. The study of these complex interactions requires the development of advanced analytical approaches combined with bioinformatics. The Institute of Medicine recently convened a workshop to review the state of the various domains of nutritional genomics research and policy and to provide guidance for further development and translation of this knowledge into nutrition practice and policy. Nutritional genomics holds the promise to revolutionize both clinical and public health nutrition practice and facilitate the establishment of
genome-informed nutrient and food-based dietary guidelines for disease prevention and healthful aging,
individualized medical nutrition therapy for disease management, and
better targeted public health nutrition interventions (including micronutrient fortification and supplementation) that maximize benefit and minimize adverse outcomes within genetically diverse human populations.
For metabolomics, gas and liquid chromatography coupled to mass spectrometry are well suited for coping with high sample numbers in reliable measurement times with respect to both technical accuracy and the identification and quantitation of small-molecular-weight metabolites. This potential is a prerequisite for the analysis of dynamic systems. Thus, metabolomics is a key technology for systems biology. The bioavailability of bioactive food constituents as well as dose-effect correlations are key information to understand the impact of food on defined health outcomes. Both strongly depend on appropriate analytical tools to identify and quantify minute amounts of individual compounds in highly complex matrices–food or biological fluids–and to monitor molecular changes in the body in a highly specific and sensitive manner. Based on these requirements, mass spectrometry has become the analytical method of choice with broad applications throughout all areas of nutrition research.
Dynamic Construct of the –Omics
Metabolomics is a term that encompasses several types of analyses, including
metabolic fingerprinting, which measures a subset of the whole profile with little differentiation or quantitation of metabolites;
metabolic profiling, the quantitative study of a group of metabolites, known or unknown, within or associated with a particular metabolic pathway; and
target isotope-based analysis, which focuses on a particular segment of the metabolome by analyzing only a few selected metabolites that comprise a specific biochemical pathway.
Any unifying concept of the metabolome was incomplete or debatable in the first 30 years of the 20th century. It was only known that insulin is anabolic and that insulin deficiency (or resistance) would have consequences in the point of entry into the citric acid cycle, which generates 28-32 ATPs. In fat catabolism, triglycerides are hydrolyzed to break them into fatty acids and glycerol. In the liver the glycerol can be converted into glucose via dihydroxyacetone phosphate and glyceraldehyde-3-phosphate by way of gluconeogenesis. In the case of this cycle there is a tie in with both catabolism and anabolism.
For bypass of the Pyruvate Kinase reaction of Glycolysis, cleavage of 2 ~P bonds is required. The free energy change associated with cleavage of one ~P bond of ATP is insufficient to drive synthesis of phosphoenolpyruvate (PEP), since PEP has a higher negative DG of phosphate hydrolysis than ATP. The two enzymes that catalyze the reactions for bypass of the Pyruvate Kinase reaction are the following:
Pyruvate Carboxylase (Gluconeogenesis) catalyzes pyruvate + HCO3- + ATP — oxaloacetate + ADP + Pi
PEP Carboxykinase (Gluconeogenesis) catalyzes: oxaloacetate + GTP —- phosphoenolpyruvate + GDP + CO2
Many high throughput methods have been employed to get some insight into the whole process and several examples of successful research. Proteomics and metabolomics need to encompass large numbers of experiments and linked data. Due to the nature of the proteins, as well as due to the properties of various metabolites, experimental approaches require the use of comprehensive high throughput methods and a sufficiency of analysed tissue or body fluids.
An important and revolutionary aspect of ‘The 2010 Project’ is that it implicitly endorses the allocation of resources to attempts to assign function to genes that have no known function. This represents a significant departure from the common practice of defining and justifying a scientific goal based on the biological phenomena. The rationale for endorsing this radical change is that for the first time it is feasible to envision a whole-systems approach to gene and protein function. I shall not discuss the emerging field of bioinformatics that makes this possible. In this review, the end-of-the line “detector will be considered having been covered. The entire focus proceeds to a discussion of separation methods. Separation methods have always been tricky, time consuming, and a multiple step process that depended on using anionic and cationic resins as intermediate steps in bulk separation, and then molecular size separation. Therapeutic Targets will be identified as they are seen.
Affinity Chromatography The rapid development of biotechnology and biomedicine requires more reliable and efficient separation technologies for the isolation and purification of biopolymers such as therapeutic proteins, antibodies, enzymes and nucleic acids. In particular, monoclonal antibodies are centrally important as therapeutics for the treatment of cancer and other diseases, leading to recombinant monoclonal antibodies that dominate today’s biopharmaceutical pipeline. The large-scale production of therapeutic biopolymers requires
a manufacturing process that delivers reliability and in high-yield, as well as
an effective purification process affording extremely pure products.
Because of its high selectivity, affinity chromatography has been used extensively to isolate a variety of biopolymers. The retention of solutes is based on specific, reversible interactions found in biological systems, such as the binding of an enzyme with an inhibitor or an antibody with an antigen. These interactions are exploited in affinity chromatography by immobilizing an affinity ligand onto a support, and using this as a stationary phase. Non-porous particles having an average diameter of 2.1 mm were prepared by co-polymerization of styrene, methyl methacrylate and glycidyl methacrylate, which was abbreviated as P(S–MMA–GMA). The particles were mechanically stable due to the presence of benzene rings in the backbone of polymer chains, and could withstand high pressures when a column packed with these particles was operated in the HPLC mode.
The polymer particles were advantaged by immobilization of ligands via the epoxy groups on the particle surface that were introduced by one of the monomers, glycidyl methacrylate. As a model system, Cibacron Blue 3G-A was covalently immobilized onto the non-porous copolymer beads. The dye-immobilized P(S–MMA–GMA) particles were slurry packed into a 1.0 cm30.46 cm I.D. column. This affinity column was effective for the separation of turkey egg white lysozyme from a protein mixture. The bound lysozyme could be eluted to yield a sharp peak by using a phosphate buffer containing 1 M NaCl. For a sample containing up to 8 mg of lysozyme, the retained portion of proteins could be completely eluted without any slit peak. Due to the use of a shorter column, the analysis time was shorter in comparison with other affinity systems reported in the literature. The retention time could be reduced significantly by increasing the flow-rate, while the capacity factor remained at the same level. CH Chen, WC Lee. Affinity chromatography of proteins on non-porous copolymerized particles of styrene, methyl methacrylate and glycidyl methacrylate. Journal of Chromatography A 2001; 921: 31–37.
Affinity separation membranes, consisting of electrospun nanofibers, have been developed recently. Affinity ligands are attached to the surface of the constituent fibers, offering a potential solution to some of the problems of traditional, column-based, affinity chromatography. Electrospun fibers are good candidates for use in affinity separation because of their
unique characteristics of high surface area to volume ratio, resulting in
high ligand loading, and
their large porosity, resulting in
high throughput operation.
A number of polymers have been used for electrospun fiber mesh-based affinity membrane separations including poly (ether-urethane-urea), cellulose, poly(ethylene terephthalate, polysulphone, and polyacrlonitrile. Typically, very thin electrospun fiber meshes are produced by electrostatically collecting negatively charged fibers on a collector electrode. These very thin 2D electrospun fiber mesh mats provide excellent solution permeability as compared to 3D column packed with affinity beads. M Miyauchi, J Miao, TJ Simmons, JS Dordick and RJ Linhardt. Flexible Electrospun Cellulose Fibers as an Affinity Packing Material for the Separation of Bovine Serum Albumin. J Chromatograph Separat Techniq 2011; 2:2 http://dx.doi.org/10.4172/2157-7064.1000110
Dye Affinity Chromatography Biomimetic Dyes Affinity adsorbents based on immobilized triazine dyes offer important advantages circumventing many of the problems associated with biological ligands. The main drawback of dyes is their moderate selectivity for proteins. Rational attempts to tackle this problem are realized through the biomimetic dye concept according to which new dyes, the biomimetic dyes, are designed to mimic natural ligands. Biomimetic dyes are expected to exhibit increased affinity and purifying ability for the targeted proteins.
Biocomputing offers a powerful approach to biomimetic ligand design. The successful exploitation of contemporary computational techniques in molecular design requires the knowledge of the three-dimensional structure of the target protein, or at least, the amino acid sequence of the target protein and the three-dimensional structure of a highly homologous protein. From such information one can then design, on a graphics workstation,
the model of the protein and also
a number of suitable synthetic ligands which mimic natural biological ligands of the protein.
There are several examples of enzyme purifications
Interactions between Cibacron Blue F3GA (CB F3GA), as a model of triazine dye, and 2-hydroxypropyl-b-cyclodextrin (HP-b-CD), as a model of cyclodextrin, were investigated by monitoring the spectral shift that accompanies the binding phenomena. Matrix analysis of the difference spectral titration of CB F3GA with HP-b-CD revealed only two absorbing species, indicating a host–guest ratio of 1:1. The dissociation constant for this HP-b-CD–CB F3GA complex, K , was found d to be 0.43 mM. The data for HP-b-CD forming inclusion complexes with CB F3GA were used to develop the concept of competitive elution by inclusion complexes in dye-affinity chromatography. When this concept was applied to the elution of L-lactate dehydrogenase from a CB F3GA affinity matrix, it was shown to be an effective elution strategy. It provided a 15-fold purification factor with 89% recovery and sharp elution profile (0.8 column volumes for 80% recovery), which is as good as that obtained by specific elution with NADH (16-fold, 78% recovery and 1.8 column volumes). In addition, the new elution strategy showed a better purification factor and sharper elution profile than traditional non-specific. JA Lopez-Mas, SA Streitenberger, F Garcıa-Carmona, AA Sanchez-Ferrer. Cyclodextrin biospecific-like displacement in dye-affinity chromatography. Journal of Chromatography A 2001; 911: 47–53.
Affinity chromatography uses biospecific binding usually between an antibody and an antigen, an enzyme and a substrate or other pairs of key-lock type of matching molecules. Due to its high selectivity, it is able to purify proteins and other macromolecules from very dilute solutions. In this work, a general rate model for affinity chromatography was used for scale-up studies. Parameters for the model were estimated from existing correlations, or from experimental results obtained on a small column with the same packing material. As anexample, Affi-Gel with 4.5mol cm−3 Cibacron Blue F-3GA as immobilized ligands covalently attached to cross-linked 6% agarose was used for column packing. Cibacron Blue F-3GA was also used as a soluble ligand in the elution stage. Satisfactory scale-up predictions were obtained for a 98.2 ml column and a 501 ml column based on a few experimental data obtained on a 7.85 ml small column. T. Gu, K.-H. Hsu and M.-J. Syu, “Scale-Up of Affinity Chromatography for Purification of Enzymes and Other Proteins.” Enzyme and Microbial Technology 2003; 33:433-437.
Affinity Column with AAAA as a Model Sense Ligand The degeneracy of antisense peptides was studied by high-performance affinity chromatography. A model sense peptide (AAAA) and its antisense peptides (CGGG, GGGG, RGGG, SGGG) were designed and synthesized according to the degeneracy of genetic codes. An affinity column with AAAA as the ligand was prepared. The affinity chromatographic behaviors of antisense peptides on the column were evaluated. The results indicated that model antisense peptides have clear retention on the immobilized AAAA affinity column. RGGG showed the strongest affinity interaction. R Zhao, X Yu, H Liu, L Zhai, S Xiong, et al. Study on the degeneracy of antisense peptides using affinity chromatography. Journal of Chromatography A 2001; 913: 421–428.
Frontal AC for Biomolecular Interactions Frontal affinity chromatography is a method for quantitative analysis of biomolecular interactions. We reinforced it by incorporating various merits of a contemporary liquid chromatography system. As a model study, the interaction between an immobilized Caenorhabditis elegans galectin (LEC-6) and fluorescently labeled oligosaccharides (pyridylaminated sugars) was analyzed. LEC-6 was coupled to N-hydroxysuccinimide-activated Sepharose 4 Fast Flow (100 mm diameter), and packed into a miniature column (e.g., 1034.0 mm, 0.126 ml). The volume of the elution front (V) determined graphically for each sample was compared with that obtained in the presence of an excess amount of hapten saccharide, lactose (V ); and the dissociation constant, K , was calculated according to the literature. This system also proved to be useful for an inverse confirmation; that is, application of galectins to an immobilized glycan column (in the present case, asialofetuin was immobilized on Sepharose 4 Fast Flow), and the elution profiles were monitored by fluorescence based on tryptophan. The newly constructed system proved to be extremely versatile. It enabled rapid (analysis time 12 min/ cycle) and sensitive (20 nM for pyridylaminated derivatives, and 1 mg/ml for protein) analyses of lectin–carbohydrate interactions. J Hirabayashi, Y Arata, K Kasai. Reinforcement of frontal affinity chromatography for effective analysis of lectin–oligosaccharide interactions. Journal of Chromatography A 2000; 890:261–271.
Immobilized Metal Ion Affinity New immobilized metal ion affinity chromatography (IMAC) matrices containing a high concentration of metal–chelate moieties and completely coated with inert flexible and hydrophilic dextrans are here proposed to improve the purification of polyhistidine (poly-His) tagged proteins. The purification of an interesting recombinant multimeric enzyme (a thermoresistant b-galactosidase from Thermus sp. strain T2) has been used to check the performance of these new chromatographic media.
IMAC supports with a high concentration (and surface density) of metal chelate groups promote a rapid adsorption of poly-His tagged proteins during IMAC. However, these supports also favor the promotion of undesirable multi-punctual adsorptions and problems may arise for the simple and effective purification of poly-His tagged proteins. For example, desorption of the pure enzyme from the support may become quite difficult (e.g., it is not fully desorbed from the support even using 200 mM of imidazole).
The coating of these IMAC supports with dextrans greatly reduces these undesired multi-point adsorptions. However, this dextran coating of chromatographic matrices seems to allow the formation of strong one-point adsorptions that involve small areas of the protein and support surface, but the dextran coating seems to have dramatic effects for the prevention of weak or strong multipoint interactions that should involve a high geometrical congruence between the enzyme and the support surface. C Mateo , G Fernandez-Lorente , BCC Pessela , A Vian, et al. Affinity chromatography of polyhistidine tagged enzymes. New dextran-coated immobilized metal ion affinity chromatography matrices for prevention of undesired multipoint adsorptions. Journal of Chromatography A 2001; 915:97–106. The underlying principle of immobilized metal ion affinity chromatography (IMAC) of proteins is the coordination between the electron donor groupings on a protein surface (histidine, tryptophan, cysteine) and chelated (iminodiacetate; IDA) transition metal ions [IDA-M(II)]. This principle of immobilized metal ion affinity (IMA) has been presented by now in some detail. The practice of IMAC in the purification of proteins has had its empirical phase. There is now a need, from the body of data, to establish somewhat more detailed ground rules that would allow for the use of IMAC in a more predictive manner. Immobilized metal ion affinity chromatography (IMAC) has been explored as a probe into the topography of histidyl residues of a protein molecule. An evaluation of the chromatographic behavior of selected model proteins-
thioredoxin
ubiquitin
calmodulin
lysozyme
cytochrome c
myoglobin
on immobilized transition metal ions
Co2+
Ni2+
Cu2+
Zn2
-allows establishment of the following facets of the histidyl side chain distribution:
either interior or surface;
when localized on the surface, accessible or unaccessible for coordination;
single or multiple;
When multiple, either distant or vicinal.
Moreover, proteins displaying single histidyl side chains on their surfaces may, in some instances, be resolved by IMAC; apparently, the microenvironments of histidyl residues are sufficiently diverse to result in different affinities for the immobilized metal ions. IMAC, previously introduced as an approach to the fractionation of proteins, has become also, upon closer examination, a facile probe into the topography of histidyl residues. This is possible because of the inherent versatility of IMAC; an appropriate metal ion (M2+) can be selected to suit the analytical purpose and a particular chromatographic protocol can be applied (isocratic pH, falling pH, and imidazole elution). We now report that IMAC may be exploited as an analytical tool in addition to its use as a protein purification technique. IMAC can be used to ascertain several facets of the status of a histidyl residue(s) in a protein molecule:
localization (interior vs. surface)
coordination potential as defined by the steric accessibility and the state of protonation
A novel, two-step preparative technique is described for the purification of authentic recombinant human prolactin (rhPRL) secreted into the periplasm of transformed Escherichia coli cells. The first step is based on immobilized metal ion affinity chromatography of periplasmic extract, using Ni(II) as a relatively specific ligand for hPRL in this system. It gives superior resolution and yield than established ion-exchange chromatography. Size-exclusion chromatography is used for further purification to .99.5% purity. The methodology is reproducible, leading to 77% recovery. Identity and purity of the rhPRL were demonstrated using sodium dodecylsulphate–polyacrylamide electrophoresis, isoelectric focusing, mass spectrometry (matrix-assisted laser desorption ionization time-of-flight), radioimmunoassay, RP-HPLC and high-performance size-exclusion chromatography. In the Nb2 bioassay, the hormone showed a bioactivity of 40.9 IU/mg.
Adenosine Affinity Ligand for Glutamine Synthase Glutamine synthetase has been purified from both procaryotic and eucaryotic sources using various types of affinity chromatography. For example, ADP-agarose has been used to purify glutamine synthetase from photosynthetic bacteria, while the related “Blue” chromatography media (e.g. Affigel Blue) have been used to purify glutamine synthetases from a variety of sources. In addition, 2’,5’-ADPSepharose 4B has been used to purify glutamine synthetase from procaryotes, plants and insects. However, this latter affinity ligand resembles NADP more than ADP, particularly with respect to the position of the phosphate moieties. This is reflected in the more general use of this affinity ligand in the purification of NADPH-dependent enzymes. In the present report, we characterize the ability of glutamine synthetase to be purified by three different adenosine-affinity ligands: 5’-ADP-agarose (an ADP analogue), 2’,5’-ADP-Sepharose 4B (an NADP analogue) and 3’,5’-ADP-agarose (a cyclic AMP analogue). We report conditions for the successful purification of insect flight muscle glutamine synthetase using each of these three different affinity ligands. The enzyme bound most strongly to the
ADP analogue (S-ADP-agarose),
followed by the NADPH analogue (2’,5’-ADP-Sepharose 4B), and least strongly to
the cyclic AMP analogue (3’J’-ADP-agarose).
In all cases, binding was strongest in the presence of Mn2+ when compared to Mg”. These results suggest that the binding of glutamine synthetase to adenosine-affinity media is related to the participation of Mn. ADP in the y-glutamyl transferase reaction that is catalyzed by glutamine synthetase. M Dowton, IR Kennedy. Purification of glutamine synthetase by adenosine-affinity chromatography. Journal of Chromatography A 1994; 664: 280-283
Aptamer Based Stationary Phase An anti-adenosine aptamer was evaluated as a stationary phase in packed capillary liquid chromatography. Using an 21 aqueous mobile phase containing 20 mM Mg , adenosine was strongly retained on the column. A gradient of increasing 21 Ni (to 18 mM), which is presumed to complex with nitrogen atoms in adenosine involved in binding to the aptamer, eluted adenosine in a narrow zone. The adenosine assay, which required no sample preparation, was used on microdialysis samples. Total analysis times were short so samples could be injected every 5 min. Q Deng, CJ Watson, RT Kennedy. Aptamer affinity chromatography for rapid assay of adenosine in microdialysis samples collected in vivo. Journal of Chromatography A 2003; 1005:123–130.
We will realize the full power of proteomics only when we can measure and compare the proteomes of many individuals to identify biomarkers of human health and disease and track the blood-based proteome of an individual over time. Because the human proteome contains an estimated 20,000 proteins – plus splicing and post-translational variants – that span a concentration range of ,12 logs, identifying and quantifying valid biomarkers is a great technical challenge. Proteomic measurements demand
extreme sensitivity
specificity
dynamic range
accurate quantification.
We describe a new class of DNA-based aptamers enabled by a versatile chemistry technology that endows nucleotides with protein-like functional groups. These modifications greatly expand the repertoire of targets accessible to aptamers. The resulting technology provides efficient, large-scale selection of exquisite protein-binding reagents selected specifically for use in highly multiplexed proteomics arrays. Aptamers are a class of nucleic acid-based molecules discovered twenty years ago, and have since been employed in diverse applications including
therapeutics
catalysis
proteomics
Aptamers are short single-stranded oligonucleotides, which fold into diverse and intricate molecular structures that bind with high affinity and specificity to
proteins
peptides
small molecules.
Aptamers are selected in vitro from enormously large libraries of randomized sequences by the process of Systematic Evolution of Ligands by EXponential enrichment (SELEX). A SELEX library with 40 random sequence positions has 440 (,1024) possible combinations and a typical selection screens 1014–1015 unique molecules. This is on the order of 105 times larger than standard peptide or protein combinatorial molecular libraries.
The interrogation of proteomes (‘‘proteomics’’) in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology and medicine. We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 mL of serum or plasma).
Our current assay measures 813 proteins with low limits of detection (1 pM median), 7 logs of overall dynamic range (,100 fM–1 mM), and 5% median coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding signature of DNA aptamer concentrations, which is quantified on a DNA microarray.
Our assay takes advantage of the dual nature of aptamers as both folded protein-binding entities with defined shapes and unique nucleotide sequences recognizable by specific hybridization probes.
This is a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine. L Gold, D Ayers, J Bertino, Christopher Bock, et al. Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery. PlosONE 2010; 5 (12): e15004
Biomarker Discovery, Diagnostics, and Therapeutics Progression from health to disease is accompanied by complex changes in protein expression in both the circulation and affected tissues. Large-scale comparative interrogation of the human proteome can offer insights into disease biology as well as lead to
the discovery of new biomarkers for diagnostics
new targets for therapeutics
can identify patients most likely to benefit from treatment.
Although genomic studies provide an increasingly sharper understanding of basic biological and pathobiological processes, they ultimately only offer a prediction of relative disease risk, whereas proteins offer an immediate assessment of “real-time” health and disease status. We have recently developed a new proteomic technology, based on modified aptamers, for biomarker discovery that is capable of simultaneously measuring more than a thousand proteins from small volumes of biological samples such as plasma, tissues, or cells. Our technology is enabled by SOMAmers (Slow Off-rate Modified Aptamers), a new class of protein binding reagents that contain chemically modified nucleotides that greatly expand the physicochemical diversity of nucleic acid-based ligands. Such modifications introduce functional groups that are absent in natural nucleic acids but are often found in protein-protein, small molecule-protein, and antibody-antigen interactions. The use of these modifications expands the range of possible targets for SELEX (Systematic Evolution of Ligands by EXponential Enrichment), results in improved binding properties, and facilitates selection of SOMAmers with slow dissociation rates. Our assay works by transforming protein concentrations in a mixture into a corresponding DNA signature, which is then quantified on current commercial DNA microarray platforms. In essence, we take advantage of the dual nature of SOMAmers as
both folded binding entities with defined shapes and
unique nucleic acid sequences recognizable by specific hybridization probes.
Aptamers and Smart Drug delivery Targeting In this review, the strategies for using functional nucleic acids in creating smart drug delivery devices will be explained, as their has been very recent progress in controlled drug release based on molecular gating achieved with aptamers. Aptamers are functional nucleic acid sequences which can bind specific targets. An artificial combinatorial methodology can identify aptamer sequences for any target molecule, from ions to whole cells. Drug delivery systems seek to increase efficacy and reduce side-effects by concentrating the therapeutic agents at specific disease sites in the body. This is generally achieved by specific targeting of inactivated drug molecules. Aptamers which can bind to various cancer cell types selectively and with high affinity have been exploited in a variety of drug delivery systems for therapeutic purposes. Recent progress in selection of cell-specific aptamers has provided new opportunities in targeted drug delivery. Especially functionalization of nanoparticles with such aptamers has drawn major attention in the biosensor and biomedical areas.
Nucleic acids are recognized as attractive building materials in nanomachines because of their unique molecular recognition properties and structural features. An active controlled delivery of drugs once targeted to a disease site is a major research challenge. Stimuli-responsive gating is one way of achieving controlled release of nanoparticle cargoes. Recent reports incorporate the structural properties of aptamers in controlled release systems of drug delivering nanoparticles.
Nanoparticle-encapsulated drug delivery aims to deliver the active therapeutic ingredients to the disease site in stable compartments in order to reduce premature release. This ensures that the effects of drug are maximized and the side effects are reduced. An encapsulated nanoparticle system requires a specific targeting mechanism and at the same time the retention of drugs inside the container should be high. The balance between specificity of targeting and the extent of premature leakage determines the success of a given delivery system.
Nanotechnology research approaches in drug delivery include a wide variety of nanomaterials ranging from soft hydrogels to solid polymeric particles. Large surface area, high drug loading efficiency and potential combination with other organic/inorganic materials are the main properties of hollow nanostructures that are attractive for biomedical applications.
Packaging of small-molecule drugs
improves their availability
compatibility
reduces toxicity
Controlling the drug release profile is the main challenge in drug delivery development when the drug is to be successfully targeted to a specific site. Stimuli-responsive materials have been created by using biological, physical and chemical properties of materials for heat-activated, light-activated or pH-activated delivery. Nucleic acids are utilized to construct rationally designed nanostructures at molecular levels for nanotechnology applications. Integration of the properties of nucleic acids can offer many opportunities for drug delivery systems, including stimuli-responsive nanogates for nanocarriers and molecular sensors. Favorable drug release kinetics can be achieved at the target sites by aptamer-based capping systems.
Activity Based Profiling Powerful strategies for the gel-free analysis of proteomes have emerged, including isotope-coded affinity tagging (ICAT) for quantitative proteomics and multidimensional protein identification technology (MudPIT) for comprehensive proteomics, both of which utilize liquid chromatography (LC) and MS for protein separation and detection, respectively. Nonetheless, these methods, like 2DE-MS, still focus on measuring changes in protein abundance and, therefore, provide only an indirect estimate of dynamics in protein function. Indeed, several important forms of post-translational regulation, including protein–protein and protein–small-molecule interactions, may elude detection by abundance-based proteomic methods. To facilitate the analysis of protein function, several proteomic methods have been introduced to characterize the activity of proteins on a global scale. These include large-scale yeast two-hybrid screens and epitope tagging immunoprecipitation experiments, which aim to construct comprehensive maps of protein–protein interactions, and protein microarrays, which aim to provide an assay platform for the rapid assessment of protein activities. A chemical proteomic strategy referred to as activity-based protein profiling (ABPP) has emerged that utilizes active site-directed probes to profile the functional state of enzyme families directly in complex proteomes.
Recent advances in genomic and proteomic technologies have begun to address the challenge of assigning molecular and cellular functions to the numerous protein products encoded by prokaryotic and eukaryotic genomes. In particular, chemical strategies for proteome analysis have emerged that enable profiling of protein activity on a global scale. Herein, we highlight these chemical proteomic methods and their application to the discovery and characterization of disease-related enzyme activities.
Cells with fundamental metabolic alterations commonly arise during tumorigenesis, and it is these types of changes that help to establish a biochemical foundation for disease progression and malignancy. A seminal example of this was discovered in the 1920s when Otto Warburg found that cancer cells consume higher levels of glucose and secrete most of the glucose carbon as lactate rather than oxidizing it completely. Since then, studies by multiple groups have uncovered a diverse array of metabolic changes in cancer, including alterations in
glycolytic pathways
the citric acid cycle
glutaminolysis
lipogenesis
lipolysis
proteolysis
These in turn modulate the levels of cellular building blocks
lipids, nucleic acids and amino acids,
cellular energetics,
oncogenic signaling molecules
the extracellular environment to confer protumorigenic and malignant properties.
Despite these advances, our current understanding of cancer metabolism is far from complete and would probably benefit from experimental strategies that are capable of profiling enzymatic pathways on a global scale. To this end, conventional genomic and proteomic methods, which comparatively quantify the expression levels of transcripts and proteins, respectively, have yielded many useful insights. These platforms are, however, limited in their capacity to identify changes in protein activity that are caused by posttranslational mechanisms.
Annotating biochemical pathways in cancer is further complicated by the potential for enzymes to carry out distinct metabolic activities in tumor cells that might not be mirrored in normal physiology. In addition, a substantial proportion of the human proteome remains functionally uncharacterized, and it is likely that at least some of these poorly understood proteins also have roles in tumorigenesis. These challenges require new proteomic technologies that can accelerate the assignment of protein function in complex biological systems, such as cancer cells and tumors.
Metabolomics has emerged as a powerful approach for investigating enzyme function in living systems. Metabolomic experiments in the context of enzyme studies typically start with
the extraction of metabolites from control and enzyme-disrupted biological systems,
followed by metabolite detection and comparative data analysis.
For example, lipophilic metabolites can be enriched from cells or tissues by organic extraction. Mass spectrometry (MS) has become a primary analytical method for surveying metabolites in complex biological samples, with upfront separation accomplished by liquid chromatography (LC–MS) or gas chromatography (GC–MS). MS experiments can be carried out using
targeted or untargeted approaches,
depending on whether the objective is
to profile and quantitate known metabolites or
to broadly scan for metabolites across a large mass range, respectively.
As metabolomic experiments generate a large amount of data, powerful software tools are needed for identification and quantitation of ions in LC–MS data sets (see the figure; the mass to charge ratio (m/z) is indicated). One such program is XCMS95, which
aligns,
quantifies and
statistically ranks ions that are altered between two sets of metabolomic data.
This program can be used to rapidly identify metabolomic signatures of various disease states or to assess metabolic networks that are regulated by an enzyme using pharmacological or genetic tools that modulate enzyme function. Additional databases assist in metabolite structural characterization, such as HMDB96,97, METLIN98,99 and LIPID MAPS100. In this Review, we discuss one such proteomic platform, termed activity based protein profiling (ABPP), and its implementation in the discovery and functional characterization of deregulated enzymatic pathways in cancer. We discuss the evidence that, when coupled with other large scale profiling methods, such as metabolomics and proteomics, ABPP can provide a compelling, systems level understanding of biochemical networks that are important for the development and progression of cancer.
Large-scale profiling methods have uncovered numerous gene and protein expression changes that correlate with tumorigenesis. However, determining the relevance of these expression changes and which biochemical pathways they affect has been hindered by our incomplete understanding of the proteome and its myriad functions and modes of regulation. Activity-based profiling platforms enable both the discovery of cancer-relevant enzymes and selective pharmacological probes to perturb and characterize these proteins in tumour cells. When integrated with other large-scale profiling methods, activity-based proteomics can provide insight into the metabolic and signaling pathways that support cancer pathogenesis and illuminate new strategies for disease diagnosis and treatment.
Representative activity-based probes and their application to cancer research
enzyme class applications in cancer
Serine hydrolases increased KIAA1363 and MAGL
aggressive human cancer lines
uPA and tPA serine protease aggressive cancers
RBBP9 activity in pancreatic carcinoma
Metalloproteinases neprilysin activity in melanoma cell lines
Cysteine proteases cathepsin cysteine protease in pancreatic islet tumours
Kinases Inhibitor selectivity profiling of kinase inhibitors
Caspases visualization of apoptosis in colon tumour-bearing mice treated with Apomab
Deubiquitylases Identified increased carboxy-terminal hydrolase UCHL3 and UCH37 activity in HPV cervical carcinomas
Cytochrome P450s Identified the aromatase inhibitor anastrazole as an inducer of CYP1A2
Serine hydrolases KIaa1363 and MaGL regulate lipid metabolic pathways that support cancer pathogenesis. Activity-based protein profiling (ABPP) identified
KIAA1363 and
monoacylglycerol (MAG) lipase (MAGL)
as being increased in aggressive human cancer cells from multiple tumour types. Pharmacological and/or RNA interference ablation of KIAA1363 and MAGL coupled with metabolomic analysis revealed specific roles for KIAA1363 and MAGL in cancer metabolism. Disruption of KIAA1363 by the small-molecule inhibitor AS115 lowered monoalkylglycerol ether (MAGE), alkyl lysophosphatidic acid (alkyl LPA) and alkyl lysophosphatidyl choline (alkyl LPC) levels in cancer cells. Disruption of MAGL by the small-molecule inhibitor JZL184 raised MAG levels and reduced free fatty acid, lysophosphatidic acid (LPA) and prostaglandin E2 (PGE2) levels in cancer cells. Disruption of KIAA1363 and MAGL leads to impairments in cancer cell aggressiveness and tumour growth, PAF, platelet-activating factor.
At a glance
• Activity-based protein profiling (ABPP) facilitates the discovery of deregulated enzymes in cancer. • Competitive ABPP yields selective inhibitors for functional characterization of cancer enzymes. • ABPP can be integrated with metabolomics to map deregulated enzymatic pathways in cancer. • ABPP can be integrated with other proteomic methods to map proteolytic pathways in cancer. • ABPP probes can be used to image tumour development in living animals.
Activity-based protein profiling (ABPP), the use of active site-directed chemical probes to monitor enzyme function in complex biological systems, is emerging as a powerful post-genomic technology. ABPP probes have been developed for several enzyme classes and have been used to inventory enzyme activities en masse for a range of (patho)physiological processes.
ABPP uses active site–directed, small molecule–based covalent probes to report on the functional state of enzyme activities directly in native biological systems. ABPP probes are designed or selected to target a subset of the proteome based on shared principles of binding and/or reactivity and have been successfully developed for many enzyme classes, including
serine
cysteine,
aspartyl
metallo hydrolases
kinases
glycosidases
histone deacetylases and
oxidoreductases.
These probes have been shown to selectively label active enzymes but not their inactive precursor (zymogen) or inhibitor-bound forms, thus allowing researchers to capture functional information that is beyond the scope of standard proteomic methods. By presenting specific examples, we show here that ABPP provides researchers with a distinctive set of chemical tools to embark on the assignment of functions to many of the uncharacterized enzymes that populate eukaryotic and prokaryotic proteomes.
Vinyl-methylester UL from HSV-1 Deubiquitinating enzyme (DUB)
Aryl 2-deoxy-2-fluoro glycoside Cfx from C. fimi Glycosidase (β-1-4-glycanase) Fluorophosphonate SAE Serine hydrolase
Examples of enzymes assigned to specific mechanistic classes by ABPP
ABPP can also be implemented as a direct assay for inhibitor discovery, allowing researchers to develop potent and selective pharmacological probes for uncharacterized enzymes.
Examples of enzymes assigned to specific mechanistic classes by ABPP.
Probe Leu-Asp-αCA probe selectively labeled Upβ
Substrate the endogenous Upβ substrate, N-carbamoyl-β-alanine
Substrate mimicry of an ABPP probe.
Multidimensional profiling strategy for the annotation of the cancer-related enzyme KIAA1363. ABPP using fluorophosphonate probes identified KIAA1363 as a highly elevated enzyme activity in aggressive cancer cells. Competitive ABPP was then used to develop a selective KIAA1363 inhibitor (AS115). Metabolomic analysis of cancer cells treated with AS115 determined a role for this enzyme in the regulation of MAGE lipids in cancer cells. Biochemical studies confirmed that KIAA1363 acts as 2-acetyl MAGE hydrolase in a metabolic network that bridges the platelet activating factor and lysophosphatidic acid classes of signaling lipids. Assignment of enzyme mechanism by ABPP
There are multiple levels of annotation for enzymes. The most basic level is assignment to a specific mechanistic class based on the general chemical reaction catalyzed by the enzyme (for example, hydrolase, kinase, oxidoreductase and others). Additional annotation involves determining the endogenous substrates and products for the enzyme. Finally, complete annotation requires an understanding of how the specific chemical transformation(s) catalyzed by an enzyme integrate into larger metabolic and signaling pathways to influence cell physiology and behavior.
Many of the predicted enzymes uncovered by genome sequencing projects can be assigned to a mechanistic class or ascribed a putative biochemical function based on sequence homology to well-characterized enzymes. But some enzymes have insufficient sequence relatedness for class assignment or have a function different from that predicted by sequence comparisons. ABPP has facilitated class annotation for several such uncharacterized enzymes.
A principal goal of modern biomedical research is to discover, assemble, and experimentally manipulate molecular pathways in cells and organisms to reveal new disease mechanisms.
Toward this end, complete genome sequences for numerous bacteria and higher organisms, including humans, have laid the fundamental groundwork for understanding the molecular basis of life in its many forms. However, the information content of DNA sequences is limited and, on its own, cannot describe most physiological and pathological processes.
Unlike oligonucleotides, proteins are a very diverse group of biomolecules that display a wide range of chemical and biophysical features, including
membrane-binding,
hetero/homo-oligomerization, and
posttranslational modification.
The biochemical complexity intrinsic to protein science intimates that several complementary analytical strategies will be needed to achieve the ultimate goal of proteomics – a comprehensive characterization of the expression, modification state, interaction map, and activity of all proteins in cells and tissues.
A powerful LC-MS strategy for proteomics involves the use of isotope-coded affinity tags (ICAT). This approach enables the comparison of protein expression in proteomes by treating samples with isotopically distinct forms of a chemical labeling reagent. ICAT methods provide superior resolving power compared to gel-based methods and improve access to membrane-associated proteins. More recently, isotope-free MS methods for quantitative proteomics have emerged.
Reverse protein microarrays have also been described in which proteomes themselves are arrayed and the antibodies used for detection in a format analogous to Western blotting. In addition to increasing the throughput of proteomic experiments by integrating the protein separation and detection steps, microarrays consume much less material than conventional proteomic methods. Still, the general application of microarrays for proteomics is currently limited by the availability of high-quality capture reagents (e.g., antibodies, aptamers, etc).
These approaches, by measuring protein abundance provide, like genomics, only an indirect assessment of protein activity and may fail to detect important posttranslational events that regulate protein function, such as protein–protein or protein–small-molecule interactions. To address these limitations, complementary strategies for the functional analysis of proteins have been introduced. Prominent among these functional proteomic efforts is the use of chemistry for the design of active site-directed probes that measure enzyme activity in samples of high biological complexity.
Many post-translational modes of enzyme regulation share a common mechanistic foundation – they perturb the active site such that catalytic power and/or substrate recognition is impaired. Accordingly, it was hypothesized that chemical probes capable of reporting on the integrity of enzyme active sites directly in cells and tissues might serve as effective functional proteomic tools. These activity based protein profiling (ABPP) probes consist of at least two general elements:
a reactive group for binding and covalently modifying the active sites of many members of a given enzyme class or classes
a reporter tag for the detection, enrichment, and identification of probe-labeled proteins
ABPP probes have been successfully developed for more than a dozen enzyme classes, including
all major classes of proteases
kinases
phosphatases
glycosidases
GSTs
oxidoreductases.
Post-translational regulation of enzyme activity. Many enzymes are produced as inactive precursors, or zymogens, which require proteolytic processing for activation. Enzyme activity can be further regulated by interactions with endogenous protein inhibitors. The field of proteomics aims to develop and apply technologies for the characterization of protein function on a global scale. Toward this end, synthetic chemistry has played a major role by providing new reagents to profile segments of the proteome based on activity rather than abundance. Small molecule probes for activity-based protein profiling have been created for more than a dozen enzyme classes and used to discover several enzyme activities elevated in disease states. These innovations have inspired complementary advancements in analytical chemistry, where new platforms have been introduced to augment the information content achievable in chemical proteomics experiments. Here, we will review these analytical platforms and discuss how they have exploited the versatility of chemical probes to gain unprecedented insights into the function of proteins in biological samples of high complexity.
Advanced analytical platforms utilize a range of separation and detection strategies, including LC-MS, CELIF, and antibody microarrays, to achieve an unprecedented breadth and depth of proteome coverage in ABPP investigations. The complementary strengths and weaknesses of each of these methods suggest that the selection of an appropriate analytical platform should be guided by the specific experimental question being addressed. SA Sieber and BF Cravatt. Analytical platforms for activity-based protein profiling – exploiting the versatility of chemistry for functional proteomics. Chem. Commun. 2006, 2311–2319. http://www.rsc.org/chemcomm
Diagnostic Therapeutics in Activity Based Probes Activity-based chemical proteomics-an emerging field involving a combination of organic synthesis, biochemistry, cell biology, biophysics and bioinformatics-allows the detection, visualisation and activity quantification of whole families or selected sub-sets of proteases based upon their substrate specificity. This approach can be applied for drug target/lead identification and validation, the fundamentals of drug discovery. The activity-based probes discussed in this review contain three key features;
a ‘warhead’ (binds irreversibly but selectively to the active site),
a ‘tag’ (allowing enzyme ‘handling’, with a combination of fluorescent, affinity and/or radio labels),
a linker region between warhead and tag.
From the design and synthesis of the linker arise some of the latest developments discussed here; not only can the physical properties (e.g., solubility, localisation) of the probe be tuned, but the inclusion of a cleavable moiety allows selective removal of tagged enzyme from affinity beads etc. Heal WP, Wickramasinghe SR, Tate EW. Activity based chemical proteomics: profiling proteases as drug targets. Curr Drug Discov Technol 2008; 5(3):200-12. PMID: 18690889
The genomic revolution has created a wealth of information regarding the fundamental genetic code that defines the inner workings of a cell. However, it has become clear that analyzing genome sequences alone will not lead to new therapies to fight human disease. Rather, an understanding of protein function within the context of complex cellular networks will be required to facilitate the discovery of novel drug targets and, subsequently, new therapies directed against them. The past ten years has seen a dramatic increase in technologies that allow large-scale, systems-based methods for analysis of global biological processes and disease states.
In the field of proteomics, several well-established methods persist as a means to resolve and analyze complex mixtures of proteins derived from cells and tissues. However, the resolving power of these methods is often challenged by the diverse and dynamic nature of the proteome. The field of activity-based proteomics, or chemical proteomics, has been established in an attempt to focus proteomic efforts on subsets of physiologically important protein targets. This new approach to proteomics is centered around the use of small molecules termed activity-based probes (ABPs) as a means to tag, enrich, and isolate, distinct sets of proteins based on their enzymatic activity. Berger AB, Vitorino PM, Bogyo M. Activity-based protein profiling: applications to biomarker discovery, in vivo imaging and drug discovery. Am J Pharmacogenomics. 2004;4(6):371-81.
Recent advances in global genomic and proteomic methods have led to a greater understanding of how genes and proteins function in complex networks within a cell. One of the major limitations in these methodologies is their inability to provide information on the dynamic, post-translational regulation of enzymatic proteins. In particular proteases are often synthesized as inactive zymogens that need to be activated in order to carry out specific biological processes. Thus, methods that allow direct monitoring of protease activity in the context of a living cell or whole animal will be required to begin to understand the systems-wide functional roles of proteases. In this review, we discuss the development and applications of activity based probes (ABPs) to study proteases and their role in pathological processes. Specifically we focus on application of this technique for biomarker discovery, in vivo imaging and drug screening.
Proteases, in particular, are known for their multilayered post-translational activity regulation that can lead to a significant difference between protease abundance levels and their enzyme activity. To address these issues, the field of activity-based proteomics has been established in order to characterize protein activity and monitor the functional regulation of enzymes in complex proteomes.
As a result of the recent enormous technological progress, experimental structure determination has become an integral part of the development of drugs against disease-related target proteins. The post-translational modification of proteins is an important regulatory process in living organisms; one such example is lytic processing by peptidases. Many different peptidases represent disease targets and are being used in structure-based drug design approaches. The development of drugs such as aliskiren and tipranavir, which inhibit renin and HIV protease, respectively, testifies to the success of this approach.
Presenilin is the catalytic component of γ-secretase, a complex aspartyl protease and a founding member of intramembrane-cleaving proteases. γ-Secretase is involved in the pathogenesis of Alzheimer’s disease and a top target for therapeutic intervention. However, the protease complex processes a variety of transmembrane substrates, including the Notch receptor, raising concerns about toxicity. Nevertheless, γ-secretase inhibitors and modulators have been identified that allow Notch processing and signaling to continue, and promising compounds are entering clinical trials.
Molecular and biochemical studies offer a model for how this protease hydrolyzes transmembrane domains in the confines of the lipid bilayer. Progress has also been made toward structure elucidation of presenilin and the γ-secretase complex by electron microscopy as well as by studying cysteine-mutant presenilins. The signal peptide peptidase (SPP) family of proteases are distantly related to presenilins. However, the SPPs work as single polypeptides without the need for cofactors and otherwise appear to be simple model systems for presenilin in the γ-secretase complex.
Critical clues to the identity of γ-secretase included: (1) Genes encoding the multi-pass membrane proteins presenilin-1 and presenilin-2 are, like APP, associated with familial, early-onset Alzheimer’s disease. The disease-causing missense mutations were found to alter how γ-secretase cuts APP, leading to increased proportions of longer, more aggregation-prone forms of Aβ. (2) Knockout of presenilin genes eliminates γ-secretase cleavage of APP. (3) Peptidomimetics that inhibit γ-secretase contain moieties typically found in aspartyl protease inhibitors. These findings led to the identification of two conserved transmembrane aspartates in the multi-pass presenilins that are critical for γ-secretase cleavage of APP, evidence that presenilins are aspartyl proteases. Presenilin is endoproteolytically cleaved into two polypeptides, an N-terminal fragment (NTF) and a C-terminal fragment (CTF), the formation of which is
regulated
metabolically stable
part of a high-molecular weight complex
suggesting that the NTF-CTF heterodimer is the biologically active form. NTF and CTF each contribute one of the essential and conserved aspartates, and transition-state analogue inhibitors of γ-secretase, compounds designed to interact with the active site of the protease, bind directly to presenilin NTF and CTF. Presenilins are also required for Notch signaling (Levitan and Greenwald, 1995), a pathway essential for cell differentiation during development and beyond.
The highly conserved role of γ-secretase in Notch signalling and its importance in development led to genetic screens in Caenorhabditis elegans that identified three other integral membrane proteins besides presenilin that modify Notch signaling. Designed inhibitors have proven to be useful tools in understanding the mechanism of γ-secretase and substrate recognition – affinity labelling with transition-state analogue inhibitors showed binding at the interface between the presenilin NTF and CTF subunits, consistent with the active site residing at this interface, with each presenilin subunit contributing one of the essential aspartates. The concept of presenilin as the catalytic component for γ-secretase was considerably strengthened when
signal peptide peptidase (SPP) was found to be a similar intramembrane aspartyl protease
SPP is exploited by the hepatitis C virus for the maturation of its core protein, suggesting that this protease may be a suitable target for antiviral therapy
SPP was identified by affinity labeling with a peptidomimetic inhibitor, and the protein sequence displayed similarities with presenilin.
SPP contains two conserved aspartates, each predicted to lie in the middle of a transmembrane domain, and the aspartate-containing sequences resemble those found in presenilins.
SPP appears to be less complicated than γ-secretase.
Expression of human SPP in yeast reconstituted the protease activity, suggesting that the protein has activity on its own and does not require other mammalian protein cofactors.
Aspartyl I-CLiPs are found in all forms of life and play essential roles in biology and disease. How these enzymes carry out hydrolysis in the membrane is a fascinating question that is not entirely resolved, but evidence suggests an initial substrate docking site and a lateral gate into a pore where water and the active site aspartates reside. Designed inhibitors have been critical in elucidating these mechanisms, but inhibitors targeting γ-secretase for the treatment of Alzheimer’s disease must avoid interfering with Notch signaling.
MS Wolfe. Structure, Mechanism and Inhibition of γ-Secretase and Presenilin-Like Proteases. Biol Chem. 2010 August; 391(8): 839–847. doi: 10.1515/BC.2010.086. PMCID: PMC2997569. NIHMSID: NIHMS254540 Study Suggests Expanding the Genetic Alphabet May Be Easier than Previously Thought Genomics Monday, June 4, 2012 A new study led by scientists at The Scripps Research Institute suggests that the replication process for DNA—the genetic instructions for living organisms that is composed of four bases (C, G, A and T)—is more open to unnatural letters than had previously been thought.
An expanded “DNA alphabet” could carry more information than natural DNA, potentially coding for a much wider range of molecules and enabling a variety of powerful applications, from precise molecular probes and nanomachines to useful new life forms. The new study, which appears in the June 3, 2012 issue of Nature Chemical Biology, solves the mystery of how a previously identified pair of artificial DNA bases can go through the DNA replication process almost as efficiently as the four natural bases. “We now know that the efficient replication of our unnatural base pair isn’t a fluke, and also that the replication process is more flexible than had been assumed,” said Floyd E. Romesberg, principal developer of the new DNA bases.
Adding to the DNA Alphabet Romesberg and his lab have been trying to find a way to extend the DNA alphabet since the late 1990s. In 2008, they developed the efficiently replicating bases NaM and 5SICS, which come together as a complementary base pair within the DNA helix, much as, in normal DNA, the base adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G).
The following year, Romesberg and colleagues showed that NaM and 5SICS could be efficiently transcribed into RNA. But these bases’ lack the ability to form the hydrogen bonds that join natural base pairs in DNA. Such bonds had been thought to be an absolute requirement for successful DNA replication‑—a process in which a large enzyme, DNA polymerase, moves along a single, unwrapped DNA strand and stitches together the opposing strand, one complementary base at a time.
An early structural study of a very similar base pair in double-helix DNA added to Romesberg’s concerns. The data strongly suggested that NaM and 5SICS do not even approximate the edge-to-edge geometry of natural base pairs—termed the Watson-Crick geometry, after the co-discoverers of the DNA double-helix. Instead, they join in a looser, overlapping, “intercalated” fashion. “Their pairing resembles a ‘mispair,’ such as two identical bases together, which normally wouldn’t be recognized as a valid base pair by the DNA polymerase.” Yet in test after test, the NaM-5SICS pair was efficiently replicable.
Edge to Edge The NaM-5SICS pair maintain an abnormal, intercalated structure within double-helix DNA—but remarkably adopt the normal, edge-to-edge, “Watson-Crick” positioning when gripped by the polymerase during the crucial moments of DNA replication. “The DNA polymerase apparently induces this unnatural base pair to form a structure that’s virtually indistinguishable from that of a natural base pair.” NaM and 5SICS, lacking hydrogen bonds, are held together in the DNA double-helix by “hydrophobic” forces, which cause certain molecular structures to be repelled by water molecules, and thus to cling together in a watery medium. “It’s very possible that these hydrophobic forces have characteristics that enable the flexibility and thus the replicability of the NaM-5SICS base pair.”
An Arbitrary Choice? The finding suggests that NaM-5SICS and potentially other, hydrophobically bound base pairs could some day be used to extend the DNA alphabet. It also hints that Evolution’s choice of the existing four-letter DNA alphabet—on this planet—may have been somewhat arbitrary. “It seems that life could have been based on many other genetic systems.” Source: The Scripps Research Institute
DNA damage response (DDR) network
Eukaryotic cells have evolved an intricate system to resolve DNA damage to prevent its transmission to daughter cells. This system, collectively known as the DNA damage response (DDR) network, includes many proteins that detect DNA damage, promote repair, and coordinate progression through the cell cycle. Because defects in this network can lead to cancer, this network constitutes a barrier against tumorigenesis. The modular BRCA1 carboxyl-terminal (BRCT) domain is frequently present in proteins involved in the DDR, can exist either as an individual domain or as tandem domains (tBRCT), and can bind phosphorylated peptides. We performed a systematic analysis of protein-protein interactions involving tBRCT in the DDR.
We identified 23 proteins containing conserved BRCT domains and generated a human protein-protein interaction network for seven proteins with tBRCT. This study also revealed previously unknown components in DNA damage signaling, such as COMMD1 and the target of rapamycin complex mTORC2. Additionally, integration of tBRCT domain interactions with DDR phosphoprotein studies and analysis of kinase-substrate interactions revealed signaling subnetworks that may aid in understanding the involvement of tBRCT in disease and DNA repair.
Mitochondria have various essential functions in metabolism and in determining cell fate during apoptosis. In addition, mitochondria are also important nodes in a number of signaling pathways. For example, mitochondria can modulate signals transmitted by second messengers such as calcium. Because mitochondria are also major sources of reactive oxygen species (ROS), they can contribute to redox signaling—for example, by the production of ROS such as hydrogen peroxide that can reversibly modify cysteine residues and thus the activity of target proteins. Mitochondrial ROS production is thought to play a role in hypoxia signaling by stabilizing the oxygen-sensitive transcription factor hypoxia-inducible factor–1α. New evidence has extended the mechanism of mitochondrial redox signaling in cellular responses to hypoxia in interesting and unexpected ways. Hypoxia altered the microtubule-dependent transport of mitochondria so that the organelles accumulated in the perinuclear region, where they increased the intranuclear concentration of ROS. The increased ROS in turn enhanced the expression of hypoxia-sensitive genes such as VEGF (vascular endothelial growth factor) not by reversibly oxidizing a protein, but by oxidizing DNA sequences in the hypoxia response element of the VEGF promoter. This paper and other recent work suggest a new twist on mitochondrial signaling: that the redistribution of mitochondria within the cell can be a component of regulatory pathways.
A challenge in the treatment of lung cancer is the lack of early diagnostics. Here, we describe the application of monoclonal antibody proteomics for discovery of a panel of biomarkers for early detection (stage I) of non-small cell lung cancer (NSCLC). We produced large monoclonal antibody libraries directed against the natural form of protein antigens present in the plasma of NSCLC patients. Plasma biomarkers associated with the presence of lung cancer were detected via high throughput ELISA. Differential profiling of plasma proteomes of four clinical cohorts, totaling 301 patients with lung cancer and 235 healthy controls, identified 13 lung cancer-associated (p < 0.05) monoclonal antibodies. The monoclonal antibodies recognize five different cognate proteins identified using immunoprecipitation followed by mass spectrometry. Four of the five antigens were present in non-small cell lung cancer cells in situ.
The recent advances of “molecular and medical imaging” as an integrated discipline in academic medical centers has set the stage for an evolutionary leap in diagnostic imaging and therapy. Molecular imaging is not a substitute for the traditional process of image formation and interpretation, but is intended to improve diagnostic accuracy and sensitivity.
Medical imaging technologies allow for the rapid diagnosis and evaluation of a wide range of pathologies. In order to increase their sensitivity and utility, many imaging technologies such as CT and MRI rely on intravenously administered contrast agents. While the current generation of contrast agents has enabled rapid diagnosis, they still suffer from many undesirable drawbacks including a lack of tissue specificity and systemic toxicity issues. Through advances made in nanotechnology and materials science, researchers are now creating a new generation of contrast agents that overcome many of these challenges, and are capable of providing more sensitive and specific information (1)
Magnetic resonance imaging (MRI) contrast enhancement for molecular imaging takes advantage of superb and tunable magnetic properties of engineered magnetic nanoparticles, while a range of surface chemistry offered by nanoparticles provides multifunctional capabilities for image-directed drug delivery. In parallel with the fast growing research in nanotechnology and nanomedicine, the continuous advance of MRI technology and the rapid expansion of MRI applications in the clinical environment further promote the research in this area.
It is well known that magnetic nanoparticles, distributed in a magnetic field, create extremely large microscopic field gradients. These microscopic field gradients cause substantial diphase and shortening of longitudinal relaxation time (T1) and transverse relaxation time (T2 and T2*) of nearby nuclei, e.g., proton in the case of most MRI applications. The magnitudes of MRI contrast enhancement over clinically approved conventional gadolinium chelate contrast agents combined with functionalities of biomarker specific targeting enable the early detection of diseases at the molecular and cellular levels with engineered magnetic nanoparticles. While the effort in developing new engineered magnetic nanoparticles and constructs with new chemistry, synthesis, and functionalization approaches continues to grow, the importance of specific material designs and proper selection of imaging methods have been increasingly recognized (2)
Earlier investigations have shown that the MRI contrast enhancement by magnetic nanoparticles is highly related to their composition, size, surface properties, and the degree of aggregation in the biological environment.
Therefore, understanding the relationships between these intrinsic parameters and relaxivities of nuclei under influence of magnetic nanoparticles can provide critical information for predicting the properties of engineered magnetic nanoparticles and enhancing their performance in the MRI based theranostic applications. On the other hand, new contrast mechanisms and imaging strategies can be applied based on the novel properties of engineered magnetic nanoparticles. The most common MRI sequences, such as the spin echo (SE) or fast spin echo (FSE) imaging and gradient echo (GRE), have been widely used for imaging of magnetic nanoparticles due to their common availabilities on commercial MRI scanners. In order to minimize the artificial effect of contrast agents and provide a promising tool to quantify the amount of imaging probe and drug delivery vehicles in specific sites, some special MRI methods, such as have been developed recently to take maximum advantage of engineered magnetic NPs
off-resonance saturation (ORS) imaging
ultrashort echo time (UTE) imaging
Because one of the major limitations of MRI is its relative low sensitivity, the strategies of combining MRI with other highly sensitive, but less anatomically informative imaging modalities such as positron emission tomography (PET) and NIRF imaging, are extensively investigated. The complementary strengths from different imaging methods can be realized by using engineered magnetic nanoparticles via surface modifications and functionalizations. In order to combine optical or nuclear with MR for multimodal imaging, optical dyes and radio-isotope labeled tracer molecules are conjugated onto the moiety of magnetic nanoparticles
Since most functionalities assembled by magnetic nanoparticles are accomplished by the surface modifications, the chemical and physical properties of nanoparticle surface as well as surface coating materials have considerable effects on the function and ability of MRI contrast enhancement of the nanoparticle core.
The longitudinal and transverse relaxivities, Ri (i=1, 2), defined as the relaxation rate per unit concentration (e.g., millimole per liter) of magnetic ions, reflects the efficiency of contrast enhancement by the magnetic nanoparticles as MRI contrast agents. In general, the relaxivities are determined, but not limited, by three key aspects of the magnetic nanoparticles:
Chemical composition,
Size of the particle or construct and the degree of their aggregation
Surface properties that can be manipulated by the modification and functionalization.
(It is also recognized that the shape of the nanoparticles can affect the relaxivities and contrast enhancement. However these shaped particles typically have increased sizes, which may limit their in vivo applications. Nevertheless, these novel magnetic nanomaterials are increasingly attractive and currently under investigation for their applications in MRI and image-directed drug delivery).
Composition Effect: The composition of magnetic nanoparticles can significantly affect the contrast enhancing capability of nanoparticles because it dominates the magnetic moment at the atomic level. For instance, the magnetic moments of the iron oxide nanoparticles, mostly used nanoparticulate T2 weighted MRI contrast agents, can be changed by incorporating other metal ions into the iron oxide. The composition of magnetic nanoparticles can significantly affect the contrast enhancing capability of nanoparticles because it dominates the magnetic moment at the atomic level. For instance, the magnetic moments of the iron oxide nanoparticles, mostly used nanoparticulate T2 weighted MRI contrast agents, can be changed by incorporating other metal ions into the iron oxide.
Size Effect: The dependence of relaxation rates on the particle size has been widely studied both theoretically and experimentally. Generally the accelerated diphase, often described by the R2* in magnetically inhomogeneous environment induced by magnetic nanoparticles, is predicted into two different regimes. For the relatively small nanoparticles, proton diffusion between particles is much faster than the resonance frequency shift. This resulted in the relative independence of T2 on echo time. The values for R2 and R2*are predicted to be identical. This process is called “motional averaging regime” (MAR). It has been well demonstrated that the saturation magnetization Ms increases with the particle size. A linear relationship is predicted between Ms1/3 and d-1. Therefore, the capability of MRI signal enhancement by nanoparticles correlates directly with the particle size.
Surface Effect: MRI contrast comes from the signal difference between water molecules residing in different environments that are under the effect of magnetic nanoparticles. Because the interactions between water and the magnetic nanoparticles occur primarily on the surface of the nanoparticles, surface properties of magnetic nanoparticles play important roles in their magnetic properties and the efficiency of MRI contrast enhancement. As most biocompatible magnetic nanoparticles developed for in vivo applications need to be stabilized and functionalized with coating materials, the coating moieties can affect the relaxation of water molecules in various forms, such as diffusion, hydration and hydrogen binding.
The early investigation carried at by Duan et al suggested that hydrophilic surface coating contributes greatly to the resulted MRI contrast effect. Their study examined the proton relaxivities of iron oxide nanocrystals coated by copolymers with different levels of hydrophilicity including: poly(maleic acid) and octadecene (PMO), poly(ethylene glycol) grated polyethylenimine (PEG-g-PEI), and hyperbranched polyethylenimine (PEI). It was found that proton relaxivities of those IONPs depend on the surface hydrophilicity and coating thickness in addition to the coordination chemistry of inner capping ligands and the particle size.
The thickness of surface coating materials also contributed to the relaxivity and contrast effect of the magnetic nanoparticles. Generally, the measured T2 relaxation time increases as molecular weight of PEG increases.
In Summary
Much progress has taken place in the theranostic applications of engineered magnetic nanoparticles, especially in MR imaging technologies and nanomaterials development. As the feasibilities of magnetic nanoparticles for molecular imaging and drug delivery have been demonstrated by a great number of studies in the past decade, MRI guiding and monitoring techniques are desired to improve the disease specific diagnosis and efficacy of therapeutics. Continuous effort and development are expected to be focused on further improvement of the sensitivity and quantifications of magnetic nanoparticles in vivo for theranostics in future.
The new design and preparation of magnetic nanoparticles need to carefully consider the parameters determining the relaxivities of the nanoconstructs. Sensitive and reliable MRI methods have to be established for the quantitative detection of magnetic nanoparticles. The new generations of magnetic nanoparticles will be made not only based on the new chemistry and biological applications, but also with combined knowledge of contrast mechanisms and MRI technologies and capabilities. As new magnetic nanoparticles are available for theranostic applications, it is anticipated that new contrast mechanism and MR imaging strategies can be developed based on the novel properties of engineered magnetic nanoparticles.
English: Schematic sketch showing the transport types at the blood-brain barrier. Deutsch: Schematische Darstellung der Transportmechanismen an der Blut-Hirn-Schranke. Français : Schéma des types de transport à travers la barrière hémato-encéphalique (Photo credit: Wikipedia)
Larry H Bernstein, MD Reporter
Provided without comment. Quite interesting.
novel protease resistant peptide shuttles able to cross the blood-brain barrier (BBB) by binding to a specific brain receptor
Description
A Catalan Research Institute based in Barcelona (Spain) has identified novel protease resistant peptide shuttles able to cross the blood-brain barrier (BBB) by binding to a specific brain receptor. These shuttles are a powerful alternative to carry a wide variety of small and large molecules as cargos. This represents a novel opportunity to develop new delivery carriers able to cross actively a range of biological barriers.
New and innovative aspects
These compounds are novel drug delivery carriers that provide a non-invasive, non-antigenic, stable and receptor-specific way to transport drugs across the Blood-Brain Barrier and into the Central Nervous System.
These compounds show high permeability, biocompatibility, good solubility in water and resistance to proteases.
Specifications
The treatment of most neurological disorders has not been fully addressed mainly because of the neuroprotective role of the blood-brain barrier (BBB) that hinders the delivery of many diagnostic and therapeutic agents into the brain. Consequently, therapeutic molecules and genes that might otherwise be effective in diagnosis and therapy do not cross the BBB in adequate amounts: 98% of compounds smaller than 400Da and 100% of larger ones do not reach further drug development stages.
Most central nervous system (CNS) diseases, however, are complex disorders with difficult molecular targets that require larger, safer and more selective drugs. As a result, brain tumors, neurodegenerative diseases such as Parkinson’s and Alzheimer’s, and central nervous system (CNS) diseases such as schizophrenia are not successfully treated. Therefore, finding an efficient CNS delivery system is one of the major challenges in neurological treatment and one our technology can potentially overcome.
One of the best approaches for drug delivery to the brain is the use of endogenous transport mechanisms, such as receptor-mediated transcystosis. Peptides are biocompatible molecules able to transport cargos (i.e. therapeutic compounds) to specific tissues such as the brain. However, one of the main limitations of peptides as therapeutic agents is their low stability in plasma.
The use of non-natural amino acids in peptidic sequences can circumvent this problem because they are resistant to human serum proteases. Using this approach, we obtained several modified peptides. Two of them were selected based on their protease resistance and transport capacity across the blood-brain barrier, using a specific endogenous receptor. Both peptides showed enhanced membrane permeability in vitro in comparison to standard peptides and even greater stability in plasma (over 24h).
Main advantages of its use
Novel delivery technology that provides a non-invasive, non-antigenic, permeable, stable, soluble and receptor-specific way to transport drugs across the BBB and into the CNS.
This technology may ultimately allow the delivery of therapeutic agents, even large ones, across the BBB and other biological barriers, thus increasing the effectiveness of existing or new drugs.
Potential of application in a wide number of fields and in transport through various biological barriers.
Applications
Biotechnological and Pharmaceutical companies specialized in drug discovery, drug delivery, neurological disorders, tools to cross the Blood-brain barrier. The final aim is to increase the efficiency of existing molecules for the treatment of neurological disorders.
Molecule and treatment design, drug manufacture, treatment of neurological disorders, drug delivery across the blood-brain barrier (BBB).
Intellectual property status
This invention is protected by a priority application in Spain and we plan to apply for a PCT in due time.
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.
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.
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
Title: Building a DSS: choice of polymers and drugs
Category: Nanotechnology and drug delivery
During the last 40 years, controlled drug delivery has become one of the most challenging and rapidly advancing scientific areas. Delivery systems can offer numerous advantages compared to conventional dosage forms. This coalition of polymeric science and pharmaceutical science led to the innovation in the design and development of drug delivery systems (DDS). Some of the challenges of most drug delivery systems include poor bioavailability, in vivo stability, solubility, intestinal absorption, sustained and targeted delivery to site of action, therapeutic effectiveness, side effects and patient compliance as well as plasma fluctuations of drugs which either fall below the minimum effective concentrations or exceed the safe therapeutic concentrations.
The purpose of these polymers in such system is to increase the delivery effectiveness of drugs to pathological cells by protecting them from degradation in the physiological environment, localize the drug to the desired site and be non-toxic. (1,3,4 ).
Grund S and colleagues nicely outlined the history of polymer-based drug delivery system, the types of polymers and drug combinations (1).
Classification:
– Origin (synthetic, natural or both)
– Chemical nature (polyester, polyanhydride etc)
– Backbone stability (biodegradable or not)
– Water solubility (hydrophilic, hydrophobic) and Electrical charges
Although intertwined, delivery systems can be generally grouped as:
– Biodegradable drug delivery systems
– Diffusion controlled drug delivery system
– Responsive drug delivery system (thermo, pH, enzymatic)
These DDS systems among others are differentiated on the basis of the mechanism controlling the release of the drug from the polymers (1,2).
Biodegradable polymers disintegrate into biocompatible compounds when exposed to chemicals (like water), enzymes or microbial which leaves the incorporated drug behind. The drug molecule present in the DDS is released due to the process of erosion. Moreover, the degradation of the polymers involves breakdown of polymers and reduction by the Kreb’s cycle to carbon dioxide and water. Furthermore, biodegradable polymers can be manipulated by the addition of functional/liable groups such as: esters, amine, urea, anhydride, carbonates etc to the backbone. Here are some examples to the most common biodegradable polymers; polyesters, polyacrylic acids, polyanhydride, polyurea etc
Diffusion controlled-polymer systems involve the dispersion of the therapeutic molecule within the polymer shell. The sustained release of the drug from this system is driven by diffusion through the pores or between the polymer chains. Drug: Progestasert (intra-uterine), Nicoderm (transdermal)
Responsive drug delivery systems release the drug in a more controlled manner which can be stimulated by the surrounding such as temperature, solvent, pH and/or concentration. Poly (N-isopropylacrylamide) is a well known example for a thermo-responsive polymer. Poly (ethylene glycol), poly lactic acid etc are known to be used for their thermogelling system. Drug: Atridox.
A different way to approach drug delivery system is:
– Temporal controlled
– Distribution controlled
In temporal control DDS, the aim is to deliver the drug a specific time during the treatment and controlled release over extended duration is highly beneficial for drugs that are rapidly metabolized and eliminated from the body after administration (2)
in distribution controlled DDS, the aim is to the deliver the drug to a specific site in the body. This delivery system is highly beneficial when natural distribution encounter body cells and cause major side effects that prohibit further treatment ( i.e chemotherapy) or when natural distribution can’t be facilitated using the regular systemic system (i.e passing the BBB and reaching brain tumors)
The choice of drugs imposed various restrictions on the type of the delivery system employed.
For example, a drug that is to be released over an extended period in a patient’s stomach where the pH is acidic and environmental conditions fluctuate widely will require a controlled release system very different from that of a drug that is to be delivered in a pulsatile manner within the blood system.
It is also very important to understand the fate of the polymer after the drug has been released, such as polymers that naturally excreted from the body (kidneys), removed after the drug release (patch or and insert) or extract through the GI track, are acceptable in medical application.
Four physicochemical properties of polymers can affect the opsonisation process and determine the degree of RES clearance (1):
Charge
Molecular size
Shape
Hydrophobicity/lipophilicity
In summary
Polymer science has become the motor for the development of new drug delivery systems in the past decades and requires an increasingly intensive cooperation between chemists, technologists and biologists.
“Over the years, especially induced by the introduction of micro- and nanosized carriers, they have changed their profile to parenteral drug applications and are now capable of offering advanced, more sophisticated and multifunctional approaches such as stealth effects and drug targeting for medicines. Combination therapy applying multiple types of drugs concurrently with one single drug delivery system will lead to more effective therapeutics and a more convenient application for the patients”
Novel, tailored polymers with more complicated and complex structures and functions may influence many related scientific and regulatory fields. However, several questions regarding regulatory approval of polymer-based carriers are still pending, and the establishment of new guidelines and policies especially adapted to nanosized polymer materials and their unique properties is still in the beginning. New criteria to determine identity, purity, and stability of the materials during manufacturing and storage have to be
defined and confirmed by new validated analytical methods.
Muhammad T, Nur Z, Piletska E.V, Yimit O and Piletsky S.A.Rational design of molecularly imprinted polymer: the choice of cross-linker. Analyst. 2012 Jun 7;137(11):2623-8. Epub 2012 Apr 26. http://pubs.rsc.org/en/content/articlelanding/2012/AN/C2AN35228
Kaparissides C, Alexandridou S, Kotti K and Chaitidou S. Recent Advances in Novel Drug Delivery Systems. Journal on nanotechnology online. March 2006. http://www.azonano.com/article.aspx?ArticleID=1538
Key words: polymers, drug delivery system, materials, nanotechnology
This post is in the second part of the reviews that focuses on the current status of drug delivery to bone and the issues facing this field. The first part can be accessed here
Annual treatment costs for musculoskeletal diseases in the US are roughly 7.7% (~ $849 billion) of total gross domestic product. Such disorders are the main cause of physical disability in US. Almost half of all chronic conditions in people can be attributed to bone and joint disorders. In addition there is increasing ageing population and associated increases in osteoporosis and other diseases, rising incidences of degenerative intervertebral disk diseases and numbers of revision orthopedic arthroplasty surgeries, and increases in spinal fusions. All these factors contribute towards the increasing requirement of bone regeneration and reconstruction methods and products. Delivery of therapeutic grade products to bone has various challenges. Parenteral administration limits the efficient delivery of drugs to the required site of injury and local delivery methods are often expensive and invasive. The theme issue of Advance Drug Delivery reviews focuses on the current status of drug delivery to bone and the issues facing this field. Here is the second part of these reviews and research articles.
An aging population in the developing world has led to an increase in musculoskeletal diseases such as osteoporosis and bone metastases. Left untreated many bone diseases cause debilitating pain and in the case of cancer, death. Many potential drugs are effective in treating diseases but result in side effects preventing their efficacy in the clinic. Bone, however, provides a unique environment of inorganic solids, which can be exploited in order to effectively target drugs to diseased tissue. By integration of bone targeting moieties to drug-carrying water-soluble polymers, the payload to diseased area can be increased while side effects decreased. The realization of clinically relevant bone targeted polymer therapeutics depends on (1) understanding bone targeting moiety interactions, (2) development of controlled drug delivery systems, as well as (3) understanding drug interactions. The latter makes it possible to develop bone targeted synergistic drug delivery systems.
Rheumatoid arthritis (RA) is a chronic autoimmune disease that is considered to be one of the major public health problems worldwide. The development of therapies that target tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and co-stimulatory pathways that regulate the immune system have revolutionized the care of patients with RA. Despite these advances, many patients continue to experience symptomatic and functional impairment. To address this issue, more recent therapies that have been developed are designed to target intracellular signaling pathways involved in immunoregulation. Though this approach has been encouraging, there have been major challenges with respect to off-target organ side effects and systemic toxicities related to the widespread distribution of these signaling pathways in multiple cell types and tissues. These limitations have led to an increasing interest in the development of strategies for the macromolecularization of anti-rheumatic drugs, which could target them to the inflamed joints. This approach enhances the efficacy of the therapeutic agent with respect to synovial inflammation, while markedly reducing non-target organ adverse side effects. In this manuscript, we provide a comprehensive overview of the rational design and optimization of macromolecular prodrugs for treatment of RA. The superior and the sustained efficacy of the prodrug may be partially attributed to their Extravasation through Leaky Vasculature and subsequent Inflammatory cell-mediated Sequestration (ELVIS) in the arthritic joints. This biologic process provides a plausible mechanism, by which macromolecular prodrugs preferentially target arthritic joints and illustrates the potential benefits of applying this therapeutic strategy to the treatment of other inflammatory diseases.
Peptides are attractive as novel therapeutic reagents, since they are flexible in adopting and mimicking the local structural features of proteins. Versatile capabilities to perform organic synthetic manipulations are another unique feature of peptides compared to protein-based medicines, such as antibodies. On the other hand, a disadvantage of using a peptide for a therapeutic purpose is its low stability and/or high level of aggregation. During the past two decades, numerous peptides were developed for the treatment of bone diseases, and some peptides have already been used for local applications to repair bone defects in the clinic. However, very few peptides have the ability to form bone themselves. We herein summarize the effects of the therapeutic peptides on bone loss and/or local bone defects, including the results from basic studies. We also herein describe some possible methods for overcoming the obstacles associated with using therapeutic peptide candidates.
Biomaterial scaffolds have been extensively used to deliver growth factors to induce new bone formation. The pharmacokinetics of growth factor delivery has been a critical regulator of their clinical success. This review will focus on the surface interactions that control the non-covalent incorporation of growth factors into scaffolds and the mechanisms that control growth factor release from clinically relevant biomaterials. We will focus on the delivery of recombinant human bone morphogenetic protein-2 from materials currently used in the clinical practice, but also suggest how general mechanisms that control growth factor incorporation and release delineated with this growth factor could extend to other systems. A better understanding of the changing mechanisms that control growth factor release during the different stages of preclinical development could instruct the development of future scaffolds for currently untreatable injuries and diseases.
Complications in treatment of large bone defects using bone grafting still remain. Our understanding of the endogenous bone regeneration cascade has inspired the exploration of a wide variety of growth factors (GFs) in an effort to mimic the natural signaling that controls bone healing. Biomaterial-based delivery of single exogenous GFs has shown therapeutic efficacy, and this likely relates to its ability to recruit and promote replication of cells involved in tissue development and the healing process. However, as the natural bone healing cascade involves the action of multiple factors, each acting in a specific spatiotemporal pattern, strategies aiming to mimic the critical aspects of this process will likely benefit from the usage of multiple therapeutic agents. This article reviews the current status of approaches to deliver single GFs, as well as ongoing efforts to develop sophisticated delivery platforms to deliver multiple lineage-directing morphogens (multiple GFs) during bone healing.
Over the past several decades, recombinant human bone morphogenetic proteins (rhBMPs) have been the most extensively studied and widely used osteoinductive agents for clinical bone repair. Since rhBMP-2 and rhBMP-7 were cleared by the U.S. Food and Drug Administration for certain clinical uses, millions of patients worldwide have been treated with rhBMPs for various musculoskeletal disorders. Current clinical applications include treatment of long bone fracture non-unions, spinal surgeries, and oral maxillofacial surgeries. Considering the growing number of recent publications related to clincal research of rhBMPs, there exists enormous promise for these proteins to be used in bone regenerative medicine. The authors take this opportunity to review the rhBMP literature paying specific attention to the current applications of rhBMPs in bone repair and spine surgery. The prospective future of rhBMPs delivered in combination with tissue engineered scaffolds is also reviewed.
The controlled delivery of growth factors and cells within biomaterial carriers can enhance and accelerate functional bone formation. The carrier system can be designed with pre-programmed release kinetics to deliver bioactive molecules in a localized, spatiotemporal manner most similar to the natural wound healing process. The carrier can also act as an extracellular matrix-mimicking substrate for promoting osteoprogenitor cellular infiltration and proliferation for integrative tissue repair. This review discusses the role of various regenerative factors involved in bone healing and their appropriate combinations with different delivery systems for augmenting bone regeneration. The general requirements of protein, cell and gene therapy are described, with elaboration on how the selection of materials, configurations and processing affects growth factor and cell delivery and regenerative efficacy in both in vitroand in vivoapplications for bone tissue engineering.
Reconstruction of complex craniofacial deformities is a clinical challenge in situations of injury, congenital defects or disease. The use of cell-based therapies represents one of the most advanced methods for enhancing the regenerative response for craniofacial wound healing. Both somatic and stem cells have been adopted in the treatment of complex osseous defects and advances have been made in finding the most adequate scaffold for the delivery of cell therapies in human regenerative medicine. As an example of such approaches for clinical application for craniofacial regeneration, Ixmyelocel-T or bone repair cells are a source of bone marrow derived stem and progenitor cells. They are produced through the use of single pass perfusion bioreactors for CD90+ mesenchymal stem cells and CD14+ monocyte/macrophage progenitor cells. The application of ixmyelocel-T has shown potential in the regeneration of muscular, vascular, nervous and osseous tissue. The purpose of this manuscript is to highlight cell therapies used to repair bony and soft tissue defects in the oral and craniofacial complex. The field at this point remains at an early stage, however this review will provide insights into the progress being made using cell therapies for eventual development into clinical practice.
Bone formation and regeneration therapies continue to require optimization and improvement because many skeletal disorders remain undertreated. Clinical solutions to nonunion fractures and osteoporotic vertebral compression fractures, for example, remain suboptimal and better therapeutic approaches must be created. The widespread use of recombinant human bone morphogenetic proteins (rhBMPs) for spine fusion was recently questioned by a series of reports in a special issue of The Spine Journal, which elucidated the side effects and complications of direct rhBMP treatments. Gene therapy – both direct (in vivo) and cell-mediated (ex vivo) – has long been studied extensively to provide much needed improvements in bone regeneration. In this article, we review recent advances in gene therapy research whose aims are in vivo or ex vivo bone regeneration or formation. We examine appropriate vectors, safety issues, and rates of bone formation. The use of animal models and their relevance for translation of research results to the clinical setting are also discussed in order to provide the reader with a critical view. Finally, we elucidate the main challenges and hurdles faced by gene therapy aimed at bone regeneration as well as expected future trends in this field.
Gene delivery to bone is useful both as an experimental tool and as a potential therapeutic strategy. Among its advantages over protein delivery are the potential for directed, sustained and regulated expression of authentically processed, nascent proteins. Although no clinical trials have been initiated, there is a substantial pre-clinical literature documenting the successful transfer of genes to bone, and their intraosseous expression. Recombinant vectors derived from adenovirus, retrovirus and lentivirus, as well as non-viral vectors, have been used for this purpose. Both ex vivoand in vivostrategies, including gene-activated matrices, have been explored. Ex vivodelivery has often employed mesenchymal stem cells (MSCs), partly because of their ability to differentiate into osteoblasts. MSCs also have the potential to home to bone after systemic administration, which could serve as a useful way to deliver transgenes in a disseminated fashion for the treatment of diseases affecting the whole skeleton, such as osteoporosis orosteogenesis imperfecta. Local delivery of osteogenic transgenes, particularly those encoding bone morphogenetic proteins, has shown great promise in a number of applications where it is necessary to regenerate bone. These include healing large segmental defects in long bones and the cranium, as well as spinal fusion and treating avascular necrosis.
RNA interference (RNAi) is a sequence-specific post-transcriptional gene silencing technique developed with dramatically increasing utility for both scientific and therapeutic purposes. Short interfering RNA (siRNA) is currently exploited to regulate protein expression relevant to many therapeutic applications, and commonly used as a tool for elucidating disease-associated genes. Osteoporosis and their associated osteoporotic fragility fractures in both men and women are rapidly becoming a global healthcare crisis as average life expectancy increases worldwide. New therapeutics are needed for this increasing patient population. This review describes the diversity of molecular targets suitable for RNAi-based gene knock down in osteoclasts to control osteoclast-mediated excessive bone resorption. We identify strategies for developing targeted siRNA delivery and efficient gene silencing, and describe opportunities and challenges of introducing siRNA as a therapeutic approach to hard and connective tissue disorders.
Nanotechnology is simply defined as the technology to manipulate the matter on the atomic and/or molecular scale. It is generalized to materials, devices and structures with dimensions sizes at the nanoscale of 1 to 1000 nanometers (nm) (1,2).
Nanotachnology can be applied to many fields including sensors, biomaterials for tissue engineering, and nanostructures or 3D materials for molecular imaging and drug delivery among others. In medicine, nanotechnology is essentially a multidisciplinary field of physics, organic and polymer chemistry as well as molecular biology, pharmacology and engineering. These fields team up together to design a better and most opt treatment option for a disease using “the right drug, the right vehicle and the right route of administration”. In pharmaceutical industries, a new molecular entity (NME) that demonstrates potent biological activity but poor water solubility, or a very short circulating halflife, will likely face significant development challenges or be deemed undevelopable. There is always a degree of compromise, and such tradeoffs may inevitably result in the production of less-ideal drugs. However, with the emerging trends and recent advances in nanotechnology, it has become increasingly possible to address some of the shortcomings associated with potential NMEs. By using nanoscale delivery vehicles, the pharmacological properties (e.g., solubility and circulating half-life) of such NMEs can be drastically improved, essentially leading to the discovery of optimally safe and effective drug candidates. (3,4).
This is just one example which demonstrates the degree to which nanotechnology may revolutionize the rules and possibilities of drug discovery and change the landscape of pharmaceutical industries. (5)
Nanomedicine is facing many challenges in overcoming biological barriers, arrival and accumulation at the target site, therefore advances in nanoparticle engineering, as well as advances in understanding the importance of nanoparticle characteristics such as size, shape and surface properties for biological interactions, are necessary to create new opportunities for the development of nanoparticles for therapeutic applications (6).
Compared to conventional drug delivery, the first generation nanosystems provide a number of advantages. In particular, they can enhance the therapeutic activity by prolonging drug half-life, improving solubility of hydrophobic drugs, reducing potential immunogenicity, and/or releasing drugs in a sustained or stimuli-triggered fashion. Thus, the toxic side effects of drugs can be reduced, as well as the administration frequency. In addition, nanoscale particles can passively accumulate in specific tissues (e.g., tumors) through the enhanced permeability and retention (EPR) effect. Beyond these clinically efficacious nanosystems, nanotechnology has been utilized to enable new therapies and to develop next generation nanosystems for “smart” drug delivery (such as gene theraphy).
In summary; there are several factors that need to be included for a rational nanocarrier design:
– Protect the drug from premature degradation
– Protect the drug from premature interaction with biological environment
– Enhance the absorption of the drug into the selected tissue-site
– Improve intracellular drug penetration
– Improve and control the drug pharmacokinetics and distribution profile.
Moreover there are several other factors that need to be taken into consideration to effectively influence the clinical translation of the drug delivery system (DDS) i.e materials that are biodegradable and biocompatible, easily functionalized, exhibit high differential uptake efficiency etc.(7-9).
In the next few chapters, we will try to address some of these factors as well as some examples that succeeded in the clinical setting as well as those who failed.
Sengupta, S. et al. Temporal targeting of tumour cells and neovasculature with a nanoscale delivery system. Nature 436, 568–572 (2005) http://www.ncbi.nlm.nih.gov/pubmed/16049491
Nanocarriers as an emerging platform for cancer therapy. Dan Peer1†, Jeffrey M. Karp2,3†, Seungpyo Hong4†, Omid C. Farokhzad5, Rimona Margalit6 and Robert Langer3,4*. nature nanotechnology 2007 | vol 2 751-760. http://www.nature.com/nnano/journal/v2/n12/abs/nnano.2007.387.html
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