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Posts Tagged ‘NOTCH1’


Targeting Untargetable Proto-Oncogenes

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

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

Getting Around “Undruggable” Proto-Oncogenes

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

To Drug the Undruggable Target

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

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

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

Targeting BET

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

 Casting a Wide Net

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

Acute lymphoblastic leukemia (ALL), a malignant disorder of lymphoid progenitor cells, affects both children and adults,
with peak prevalence between the ages of 2 and 5 years (2). Acute lymphocytic leukemia (ALL) is a heterogeneous disease, both in terms of its pathology and the populations that it affects. Disease pathogenesis involves a number of deregulated pathways controlling cell proliferation, differentiation, and survival that are important determinants of treatment response (3). Approximately 5200 new cases of ALL are estimated to have occurred in the United States in 2007 and survival varies with age and disease biology (3). Although five-year survival rates for ALL approach 90 percent with available chemotherapy treatments, the harmful side effects of the drugs, including secondary cancers and fertility, cognitive, hearing, and developmental problems, present significant concern for survivors and their families.

Biological and Clinical Prognostic Factors in ALL: Setting the Stage for Risk-Adapted Therapy

Of the many variables that influence prognosis the genetic subsets, initial white blood cell count (WBC), age at diagnosis, and early treatment response are the most important.

Childhood Acute Lymphoblastic Leukemia

Pathobiology

Acute lymphoblastic leukaemia is thought to originate  from various important genetic lesions in blood-progenitor  cells that are committed to differentiate in the T-cell or B-cell pathway, including mutations that impart the  capacity for unlimited self-renewal and those that lead to  precise stage-specific developmental arrest. In some  cases, the first mutation along the multistep pathway to  overt acute lymphoblastic leukaemia might arise in a  haemopoietic stem cell possessing multilineage developmental capacity.

The dominant theme of contemporary research in pathobiology of acute lymphoblastic leukaemia is to understand the outcomes of frequently arising genetic lesions, in terms of their effects on cell proliferation, differentiation, and survival, and then to devise selectively targeted treatments against the altered gene products to which the leukaemic clones have become addicted (2).

Table 1.

Prognostic factors used in pediatric and adult clinical trials

The Table  illustrates the different prognostic factors in children and adults that may be used for risk stratification in current clinical trials (3).

Genetics

  • Chromosomal translocations that activate specifi c genes
    are a defi ning characteristic of human leukaemias and
    of acute lymphoblastic leukaemia in particular.
  • About 25% of cases of B-cell precursor acute lymphoblastic leukaemia, the most frequent form of acute leukaemia in children, harbour the TEL-AML1 fusion gene—generated by the t(12;21)(p13;q22) chromosomal translocation.

The presence of the TEL-AML1 fusion
protein in B-cell progenitors seems to lead to disordered
early B-lineage lymphocyte development, a hallmark of
leukaemic lymphoblasts.

Analysis of TEL-AML1-induced cord blood cells suggests that the fusion gene serves as a first-hit mutation by endowing the preleukemic cell with altered self-renewal and survival properties.

  • In adults, the most frequent chromosomal translocation  is t(9;22), or the Philadelphia chromosome, which causes  fusion of the BCR signalling protein to the ABL  non-receptor tyrosine kinase, resulting in constitutive  tyrosine kinase activity and complex interactions of this  fusion protein with many other transforming elements.  BCR-ABL off ers an attractive therapeutic  target, and imatinib mesilate, a small-molecule inhibitor  of the ABL kinase, has proven effective against leukaemias that express BCR-ABL
  • More than 50% of cases of T-cell acute lymphoblastic  leukaemia have activating mutations that involve  NOTCH1. NOTCH1, which translocates to the nucleus and regulates by transcription a diverse set of responder genes, including the MYC oncogene.  The precise  mechanisms by which aberrant NOTCH signalling (due  to mutational activation) causes T-cell acute lymphoblastic  leukaemia are still unclear but probably entail constitutive  expression of oncogenic responder genes, such as MYC,  and cooperation with other signalling pathways (pre-TCR  [T-cell receptor for antigen] and RAS, for example).  Interference with NOTCH signalling by small-molecule  inhibition of γ-secretase activity has the potential to induce remission of T-cell acute lymphoblastic  leukemia.

Additionally A recent discussion has aimed to reveal the genetic origin of the disease (1). Several of these genes, including ARID5B, IKZF1, and CEBPE, have been implicated in processes such as hematopoietic differentiation and development of ALL. These gene obviously adds up to a number of other gene mutations and translocation already discovered and are associated with disease progression (2)  “The fact that alterations in these genes lead to ALL raises the question of what would happen if we restore these pathways in ALL and also make them possible exciting therapeutic targets as well.”

Nanotechnology and therapeutic

Dr. Rajasekaran, director and head of the Membrane Biology Laboratory University of Delaware,  says that there are currently seven or eight drugs that are used for chemotherapy to treat leukemia in children. They are all toxic and do their job by killing rapidly dividing cells. these drugs don’t differentiate cancer cells from other healthy cells. “The good news is that these drugs are 80 to 90 percent effective in curing leukemia. The bad news is that many chemotherapeutic treatments cause severe side effects, especially in children.  In preclinical models of leukemia, Dr. Rajasekaran research team have created NP  with an average diameter of 110 nm were assembled from an amphiphilic block copolymer of poly(ethylene glycol) (PEG) and poly(ε-caprolactone) (PCL) bearing pendant cyclic ketals (ECT2). The researches have been encapsulated with dexamethasone as one third of the typical dose, with good treatment results and no discernible side effects.In addition, the mice that received the drugs delivered via nanoparticles survived longer than those that received the drug administered in the traditional way (4).

In another preclinical study Uckun F et al  developed nanoparticle (NP) constructs of WHI-P131. WHI-P131 (CAS 202475-60-3) is a dual-function inhibitor of JAK3 tyrosine kinase that demonstrated potent in vivo anti-inflammatory and anti-leukemic activity in several preclinical animal models (5). Notably, WHI-P131-NP was capable of causing apoptotic death in primary leukemia cells from chemotherapy-resistant acute lymphoblastic leukemia (ALL) as well as chronic lymphocytic leukemia (CLL) patients. WHI-P131-NP was also active in the RS4;11 SCID mouse xenograft model of chemotherapy-resistant B-lineage ALL. The life table analysis showed that WHI-P131-NP was more effective than WHI-P131 (P = 0.01), vincristine (P<0.0001), or vehicle (P<0.0001). These experimental results demonstrate that the nanotechnology-enabled delivery of WHI-P131 shows therapeutic potential against leukemias with constitutive activation of the JAK3-STAT3/STAT5 molecular target (5).

Summary:

Acute Lymphoblastic Leukemia (ALL) is a pediatric type of cancer that affects adults to lesser degree. The current rate of cure if 80% in  children whereas in adults only 30-40% will survive. Much of the success is due to understanding the mechanisms that lead to the development and progression of cancer. Several gene mutations and gene-translocation have already been identified,  and targeting them enabled some of the major success in curing these kids.

Thus far, nanotechnology has been  mainly focusing on solid tumors affecting adults. Not much attention is been made on childhood cancer in general and hematopoietic types per se. Two examples of preclinical studies have been discussed above and although they show promise in treatment and reduction of side effects, yet  additional research is needed to evaluated their effect in human clinical trials.

Ref:

1. The Genetic Origin of Childhood Acute Lymphoblastic Leukemia (ALL).  Reported by Aviva Lev-Ari, PhD, RN. March 20, 2013 https://pharmaceuticalintelligence.com/2013/03/20/the-genetic-origin-of-childhood-acute-lymphoblastic-leukemia-all/

2. Ching-Hon Pui, Leslie L Robison, A Thomas Look. Acute lymphoblastic leukaemia. Lancet 2008; 371: 1030–43.

http://www.med.upenn.edu/timm/documents/PuiLookLancetLeukemiareview.pdf

3. Wendy Stock. Adolescents and Young Adults with Acute Lymphoblastic Leukemia. Hematology December 4, 2010 vol. 2010 no. 1 21-29. http://asheducationbook.hematologylibrary.org/content/2010/1/21.full

4. Vinu Krishnan,  Xian Xu,, Sonali P. BarweXiaowei YangKirk CzymmekScott A. WaldmanRobert W. MasonXinqiao Jia, and Ayyappan K. Rajasekaran. Dexamethasone-Loaded Block Copolymer Nanoparticles Induce Leukemia Cell Death and Enhance Therapeutic Efficacy: A Novel Application in Pediatric Nanomedicine. Mol. Pharmaceutics 2012 ahead of print.

http://pubs.acs.org/doi/abs/10.1021/mp300350e?prevSearch=Rajasekaran&searchHistoryKey=

5. Uckun FMDibirdik IQazi SYiv S. Therapeutic nanoparticle constructs of a JAK3 tyrosine kinase inhibitor against human B-lineage ALL cells. Arzneimittelforschung 2010; 60(4): 210-217.

http://www.ncbi.nlm.nih.gov/pubmed/20486472

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