Partial List of Publications

Journal Articles and Book Chapters

 

http://www.biopredict.com/Pics_for_Publications/Cover_pic_crop.bmpThe Design and Preliminary Structure Activity Relationship Studies of Benzotriazines as Potent Inhibitors of Abl and Abl-T315I Enzymes, Cao et.al. Bioorganic & Medicinal Chemistry Letters 17 (2007) 5812-5818; article and journal cover (Targegen and BioPredict).

Abstract: We describe the design, synthesis and structure–activity relationship studies in optimizing a series of benzotriazine compounds as potent inhibitors of both Abl and Abl-T315I enzymes. The design includes targeting of an acid functional residue on the aC-helix that is available only upon kinase activation. This designed interaction provides an advantage in overcoming the challenges arising from the T315I mutation of Abl and transforms poor (ca. 10 microM) inhibitors into those with low nM potency.

 

 

 

 

 

http://www.biopredict.com/Pics_for_Publications/PI3K_JMB_pic.bmpDiscovery of 3,3'-(2,4-Diaminopteridine-6,7-diyl)diphenol as an Isozyme-Selective Inhibitor of PI3K for the Treatment of Ischemia Reperfusion Injury Associated with Myocardial Infarction.  Palanki et. al.  Journal of Medicinal Chemistry 50 (2007) 4279-4294 (Targegen and BioPredict). 

Abstract: In studies aimed toward identifying effective and safe inhibitors of kinase signaling cascades that underlie ischemia/reperfusion (I/R) injury, we synthesized a series of pteridines and pyridopyrazines. The design strategy was inspired by the examination of naturally occurring PI3K inhibitors such as wortmannin and quercetin, and building a pharmacophore-based model used for optimization. Structural modifications led to hybrid molecules which incorporated aminopyrimidine and aminopyridine moieties with ATP mimetic characteristics into the pharmacophore motifs to modulate kinase affinity and selectivity. Elaborations involving substitutions of the 2 and 4 positions of the pyrimidine or pyridine ring and the 6 and 7 positions of the central pyrazine ring resulted in in Vivo activity profiles which identified potent inhibitors of vascular endothelial growth factor (VEGF) induced vascular leakage. Pathway analysis identified diaminopteridinediphenol as a potent and selective phosphatidylinositol-3-kinase (PI3K) inhibitor. The structure-activity relationship studies of various analogues of diaminopteridine-diphenol-based on biochemical assays resulted in potent inhibitors of PI3K.

 

 

Targeting Drug Resistant Mutations Using Novel Binding Interactions – Lessons Learned from Abl-T315I and their Implications in Drug Design (book chapter). Noronha et. al., Frontiers in Drug Design and Discovery Volume 3, Bentham Science, 2007; ISBN: 90-77527-03-6. (Targegen and BioPredict). 

Abstract: Tyrosine kinases regulate various biological processes including cell proliferation, migration, differentiation and survival. Src and Abl are cellular tyrosine kinases that play roles in cellular function, including proliferation and growth. Both are usually under tight regulatory control in normal cells. Disruption in certain regulatory mechanisms results in the activation of Src mediated pathways, which have been implicated in cancers, stroke, myocardial infarction, and bone disorders. The formation of the Philadelphia chromosome results in the production of the fusion protein Bcr-Abl with a constitutively active Abl kinase portion, causative for chronic myelogenous leukemia (CML). Gleevec (Imatinib) targeting the Abl ATP site is the current standard of care for treating CML. Drug resistance to treatment with Gleevec in 50-90% of cases arises due to mutations mostly clustered around the Gleevec binding site. Since all known inhibitors of Src that bind at the ATP site are also inhibitors of Abl, several Src and Abl inhibitors are being intensely studied as they target many of the Abl mutations seen in Gleevec resistance, potentially due to differential binding modes. Sprycel, a highly potent Src and Abl inhibitor was advanced and has now been approved for the treatment of Gleevec resistant CML. None of these inhibitors target the particularly challenging mutation of the gatekeeper residue, the T315I mutation. The gatekeeper residue sits at the entrance to the hydrophobic pocket – a region proximal to the hinge and one that several classes of ATP site binding inhibitors exploit since it serves to enhance both potency and selectivity. We describe a novel conceptual design used to obtain potent inhibitors targeting the active form of Src. This powerful concept was further applied to design inhibitors targeting the Abl-T315I mutant. The approach targets an acid functional group on the alphaC-helix located deep within this hydrophobic pocket and that is available only after kinase activation. This designed interaction provides a “magic bullet” in overcoming the steric clashes arising from the Ile-315, and changes poor (ca. 10 mM) inhibitors into those with low nM potency. Targeting the active state of the kinase via this unique and relatively unexplored portion of the active kinase, the Glu on the aC-helix, has implications for targeting disease states with upregulated or constitutively activated kinase pathways.

 

 

http://www.biopredict.com/Pics_for_Publications/BMCL_2006.bmpDiscovery and preliminary structure activity relationship studies of novel benzotriazine based compounds as src inhibitors, Noronha et.al., Bioorganic & Medicinal Chemistry Letters. 2006, 16: 5546–5550. (Targegen and BioPredict)

Abstract: We report the discovery and preliminary SAR studies of a series of structurally novel benzotriazine core based small molecules as inhibitors of Src kinase. To the best of our knowledge, benzotriazine template based compounds have not been reported as kinase inhibitors. The 3-(2-(1-pyrrolidinyl)ethoxy)phenyl analogue (43) was identified as one of the most potent inhibitors of Src kinase.

 

 

 

 

 

 

http://www.biopredict.com/Pics_for_Publications/BMCL_2007.bmpDiscovery of [7-(2,6-dichlorophenyl)-5-methylbenzo[1,2,4]triazin-3-yl]-[4-(2-pyrrolidin-1-ylethoxy)phenyl]amine—a potent, orally active src kinase inhibitor with anti-tumor activity in preclinical assays, Noronha et.al., Bioorganic Medicinal Chemistry Letters.  2007 Feb, 17(3):602-608 (Targegen and BioPredict)

Abstract: We describe the identification of [7-(2,6-dichlorophenyl)-5-methylbenzo [1,2,4]triazin-3-yl]-[4-(2-pyrrolidin-1-ylethoxy)phenyl]amine (3), a potent, orally active Src inhibitor with desirable PK properties, demonstrated activity in human tumor cell lines and in animal models of tumor growth.

 

 

 

http://www.biopredict.com/Pics_for_Publications/PNAS.bmpPhosphoinositide 3-kinase (gamma}/(delta) inhibition limits infarct size after myocardial ischemia/reperfusion injury, Doukas et.al., Proc Natl Acad Sci U S A. 2006 Dec 15; 17172449 (Targegen and BioPredict) 

Abstract: Although phosphoinositide 3-kinases (PI3Ks) play beneficial pro-cell survival roles during tissue ischemia, some isoforms (gamma and delta) paradoxically contribute to the inflammation that damages these same tissues upon reperfusion. We therefore considered the possibility that selectively inhibiting proinflammatory PI3K isoforms during the reperfusion phase could ultimately limit overall tissue damage seen in ischemia/reperfusion injuries such as myocardial infarction. Panreactive and isoform-restricted PI3K inhibitors were identified by screening a novel chemical family; molecular modeling studies attributed isoform specificity based on rotational freedom of substituent groups. One compound (TG100-115) identified as a selective PI3K gamma/delta inhibitor potently inhibited edema and inflammation in response to multiple mediators known to participate in myocardial infarction, including vascular endothelial growth factor and platelet-activating factor; by contrast, endothelial cell mitogenesis, a repair process important to tissue survival after ischemic damage, was not disrupted. In rigorous animal MI models, TG100-115 provided potent cardioprotection, reducing infarct development and preserving myocardial function. Importantly, this was achieved when dosing well after myocardial reperfusion (up to 3 h after), the same time period when patients are most accessible for therapeutic intervention. In conclusion, by targeting pathologic events occurring relatively late in myocardial damage, we have identified a potential means of addressing an elusive clinical goal: meaningful cardioprotection in the postreperfusion time period.

 

Development of prodrug 4-chloro-3-(5-methyl-3-{[4-(2-pyrrolidin-1 ylethoxy)phenyl]amino}- 1,2,4-benzotriazin-7-yl)phenyl benzoate (TG100801): a topically administered therapeutic candidate in clinical trials for the treatment of age-related macular degeneration.  Palanki MS, Akiyama H, Campochiaro P, Cao J, Chow C, Dellamary L, Doukas J, Fine R, Gritzen C, Hood J, Hu S, Kachi S, Kang X, Klebansky, B, Kousba A, Lohse D, Mak C, Martin M, McPherson A, Pathak V, Renick J, Soll R, Umeda N, Yee S, Yokoi K, Zeng B, Zhu H, Noronha G., J Med Chem. 2008 Mar 27;51(6):1546-59. 

Abstract: Age-related macular degeneration (AMD) is one of the leading causes of loss of vision in the industrialized world. Attenuating the VEGF signal in the eye to treat AMD has been validated clinically. A large body of evidence suggests that inhibitors targeting the VEGFR pathway may be effective for the treatment of AMD. Recent studies using Src/YES knockout mice suggest that along with VEGF, Src and YES play a crucial role in vascular leak and might be useful in treating edema associated with AMD. Therefore, we have developed several potent benzotriazine inhibitors designed to target VEGFr2, Src, and YES. One of the most potent compounds is 4-chloro-3-{5-methyl-3-[4-(2-pyrrolidin-1-yl-ethoxy)phenylamino]benzo[1,2,4]triazin-7-yl}phenol (5), a dual inhibitor of both VEGFr2 and the Src family (Src and YES) kinases. Several ester analogues of 5 were prepared as prodrugs to improve the concentration of 5 at the back of the eye after topical administration. The thermal stability of these esters was studied, and it was found that benzoyl and substituted benzoyl esters of 5 showed good thermal stability. The hydrolysis rates of these prodrugs were studied to analyze their ability to undergo conversion to 5 in vivo so that appropriate concentrations of 5 are available in the back-of-the-eye tissues. From these studies, we identified 4-chloro-3-(5-methyl-3-{[4-(2-pyrrolidin-1-ylethoxy)phenyl]amino}-1,2,4-benzotriazin-7-yl)phenyl benzoate ( 12), a topically administered prodrug delivered as an eye drop that is readily converted to the active compound 5 in the eye. This topically delivered compound exhibited excellent ocular pharmacokinetics and poor systemic circulation and showed good efficacy in the laser induced choroidal neovascularization model. On the basis of its superior profile, compound 12 was advanced. It is currently in a clinical trial as a first in class, VEGFr2 targeting, topically applied compound for the treatment of AMD.

 

Inhibitors of ABL and the ABL-T315I Mutation, Noronha G, Cao J, Chow C, Dneprovskaia E, Fine R, Hood J, Kang X, Klebansky B, Lohse D, Mak C, McPherson A, Palanki M, Pathak V, Renick J, Soll R, and Zeng B, Current Topics in Medicinal Chemistry Volume 8, Number 10, 2008. 

Abstract:  Chronic myelogenous leukemia (CML) is a hematological stem cell disorder caused by increased and unregulated growth of myeloid cells in the bone marrow, and the accumulation of excessive white blood cells. Abelson tyrosine kinase (ABL) is a non-receptor tyrosine kinase involved in cell growth and proliferation and is usually under tight control. However, 95% of CML patients have the ABL gene from chromosome 9 fused with the breakpoint cluster (BCR) gene from chromosome 22, resulting in a short chromosome known as the Philadelphia chromosome. This Philadelphia chromosome is responsible for the production of BCR-ABL, a constitutively active tyrosine kinase that causes uncontrolled cellular proliferation. An ABL inhibitor, imatinib, was approved by the FDA for the treatment of CML, and is currently used as first line therapy. However, a high percentage of clinical relapse has been observed due to long term treatment with imatinib. A majority of these relapsed patients have several point mutations at and around the ATP binding pocket of the ABL kinase domain in BCR-ABL. In order to address the resistance of mutated BCR-ABL to imatinib, 2nd generation inhibitors such as Dasatinib, and nilotinib were developed. These compounds were approved for the treatment of CML patients who are resistant to imatinib. All of the BCR-ABL mutants are inhibited by the 2nd generation inhibitors with the exception of the T315I mutant. Several 3rd generation inhibitors such as AP24534, VX-680 (MK-0457), PHA- 739358, PPY-A, XL-228, SGX-70393, FTY720 and TG101113 are being developed to target the T315I mutation. The early results from these compounds are encouraging and it is anticipated that physicians will have additional drugs at their disposal for the treatment of patients with the mutated BCR-ABL-T315I. The success of these inhibitors has greater implication not only in CML, but also in other diseases driven by kinases where the mutated gatekeeper residue plays a major role.

 

 

Molecular mechanism for the umami taste synergism.  Zhang F, Klebansky B, Fine RM, Xu H, Pronin A, Liu H, Tachdjian C, Li X. Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20930-4.  

Abstract: Umami is one of the 5 basic taste qualities. The umami taste of L-glutamate can be drastically enhanced by 5' ribonucleotides and the synergy is a hallmark of this taste quality. The umami taste receptor is a heteromeric complex of two class C G-protein-coupled receptors, T1R1 and T1R3. Here we elucidate the molecular mechanism of the synergy using chimeric T1R receptors, site-directed mutagenesis, and molecular modeling. We propose a cooperative ligand-binding model involving the Venus flytrap domain of T1R1, where L-glutamate binds close to the hinge region, and 5' ribonucleotides bind to an adjacent site close to the opening of the flytrap to further stabilize the closed conformation. This unique mechanism may apply to other class C G-protein-coupled receptors.

 

 

 

 Molecular mechanism of the sweet taste enhancers. Zhang F, Klebansky B, Fine R, Liu H, Xu H, Servant G, Zoller M, Tachdjian C, Li X.   Proc Natl Acad Sci U S A.  2010 Mar 9;107(10):4752-7. 

Abstract:  Positive allosteric modulators of the human sweet taste receptor have been developed as a new way of reducing dietary sugar intake. Besides their potential health benefit, the sweet taste enhancers are also valuable tool molecules to study the general mechanism of positive allosteric modulations of T1R taste receptors. Using chimeric receptors, mutagenesis, and molecular modeling, we reveal how these sweet enhancers work at the molecular level. Our data argue that the sweet enhancers follow a similar mechanism as the natural umami taste enhancer molecules. Whereas the sweeteners bind to the hinge region and induce the closure of the Venus flytrap domain of T1R2, the enhancers bind close to the opening and further stabilize the closed and active conformation of the receptor.

 

 

 

A novel steroidal inhibitor of estrogen-related receptor alpha (ERR alpha).  Duellman SJ, Calaoagan JM, Sato BG, Fine R, Klebansky B, Chao WR, Hobbs P, Collins N, Sambucetti L, Laderoute KR. A  Biochem Pharmacol. 2010 Sep 15;80(6):819-26.

Abstract: The orphan nuclear receptor estrogen-related receptor α (ERRα) has been implicated in the development of various human malignancies, including breast, prostate, ovary, and colon cancer. ERRα, bound to a co-activator protein (e.g., peroxisome proliferator receptor γ co-activator-1α, PGC-1α), regulates cellular energy metabolism by activating transcription of genes involved in various metabolic processes, such as mitochondrial genesis, oxidative phosphorylation, and fatty acid oxidation. Accumulating evidence suggests that ERRα is a novel target for solid tumor therapy, conceivably through effects on the regulation of tumor cell energy metabolism associated with energy stress within solid tumor microenvironments. This report describes a novel steroidal antiestrogen (SR16388) that binds selectively to ERRα, but not to ERRβ or ERRγ, as determined using a time-resolved fluorescence resonance energy transfer assay. SR16388 potently inhibits ERRα's transcriptional activity in reporter gene assays, and prevents endogenous PGC-1α and ERRα from being recruited to the promoters or enhancers of target genes. Representative in vivo results show that SR16388 inhibited the growth of human prostate tumor xenografts in nude mice as a single agent at 30 mg/kg given once daily and 100 mg/kg given once weekly. In a combination study, SR16388 (10 mg/kg, once daily) and paclitaxel (7.5 mg/kg, twice weekly) inhibited the growth of prostate tumor xenografts in nude mice by 61% compared to untreated xenograft tumors. SR16388 also inhibited the proliferation of diverse human tumor cell lines after a 24-h exposure to the compound. SR16388 thus has utility both as an experimental antitumor agent and as a chemical probe of ERRα biology.

 

 

https://ars.els-cdn.com/content/image/1-s2.0-S0960894X10014770-gr1.smlDiamino-1,2,4 triazole derivatives are selective inhibitors of TYK2 and JAK1 over JAK2 and JAK3. Malericha,J., Lama, J.Hart, B., Fine, R., Klebansky, B., Tanga, M., and D’Andreaa, Bioorg Med Chem Lett. 2010 Dec 15;20(24):7454-7.

Abstract:   Tyrosine kinase 2 (TYK2) is required for signaling of interleukin-23 (IL-23), which plays a key role in rheumatoid arthritis. Presented is the design and synthesis of 1,2,4-triazoles, and the evaluation of their inhibitory activity against the Janus associated kinases TYK2 and JAKs 1-3.

 

 

 

 

A high-throughput fluorescence polarization assay for inhibitors of gyrase B.  Glaser BT, Malerich JP, Duellman SJ, Fong J, Hutson C, Fine RM, Klebansky B, Tang MJ, Madrid PB.. J Biomol Screen. 2011 Feb;16(2):230-8. 

Abstract:  DNA gyrase, a type II topoisomerase that introduces negative supercoils into DNA, is a validated antibacterial drug target. The holoenzyme is composed of 2 subunits, gyrase A (GyrA) and gyrase B (GyrB), which form a functional A(2)B(2) heterotetramer required for bacterial viability. A novel fluorescence polarization (FP) assay has been developed and optimized to detect inhibitors that bind to the adenosine triphosphate (ATP) binding domain of GyrB. Guided by the crystal structure of the natural product novobiocin bound to GyrB, a novel novobiocin-Texas Red probe (Novo-TRX) was designed and synthesized for use in a high-throughput FP assay. The binding kinetics of the interaction of Novo-TRX with GyrB from Francisella tularensis has been characterized, as well as the effect of common buffer additives on the interaction. The assay was developed into a 21-µL, 384-well assay format and has been validated for use in high-throughput screening against a collection of Food and Drug Administration-approved compounds. The assay performed with an average Z' factor of 0.80 and was able to identify GyrB inhibitors from a screening library.

 

 

Meeting Presentations and Posters


Earlier than 2007:

Probabilistic Pharmacophore Matching (Klebansky et. al.)

Drug Discovery Targeting the GHKL Superfamily - HSP90, DNA Gyrase, Histidine Kinases (Kang et. al.)

Validation of novel binding interaction for tyrosine kinases via crystal structures of low nM Src inhibitors  (Pathak et. al.)

A New Binding Mode for Inhibitors of Src Reminiscent of Gleevec in Abl (Renick et. al.)

Src Inhibitors with Sub nM VEGFR2 Activity – Discovery and SAR (Dneprovskaia et. al.)

Design, Synthesis and SAR of Inhibitors Targeting the T315-ABL Mutation (Cao et. al.)

Optimization of a novel Src Inhibitor Series to Obtain sub-nM Compounds (Mak et. al.)

Structure Based Design of novel, Single-Digit nM Benzotriazine Src Inhibitors (McPherson et. al.)

Strategies Involved in the Construction of Novel Benzotriazine Inhibitors or SRC (Zeng et. al.)

Datamining Results of Docking-Based Virtual Screens (Fine, et. al.)

Probabilistic Pharmacophore Matching for Structure-Based Virtual Screening (Klebansky et. al.)

 

2007 and later:

Back-of-the-eye exposure following topical administration--insight into ocular transport (Dellamary et.al.) Poster for American Association of Pharmaceutical Scientists (AAPS), November 11-15, 2007, San Diego, CA. (Targegen and BioPredict). 

Abstract - The dependence of physicochemical properties of drug substances on back-of-the-eye tissue exposure was evaluated following topical instillation.  Sixteen amine-based drug substances across multiple structural classes were formulated and topically administered to C57/Bl6 mice.  All drug substances were formulated at 10 mg/mL in a 1%HPMC/0.2%tyloxapol vehicle; a 10 µL dose volume was utilized.  The resulting tissue concentrations were determined at 2 hours post administration via LC/MS/MS.  Quantitative structure activity relationships (QSAR) were established for sclera/choroid tissue concentrations following topical instillation.  Back-of-the-eye tissue exposure best correlated with physicochemical parameters that describe molecular size, i.e., the Vander Waals volume, PSA and logD.  The results of this investigation suggest that molecular diffusion is the main driving force in the delivery to the back of the eye following topical administration.

Synthetic strategies towards the construction of novel ABL-T315I, (Zeng et.al.), Presentation for American Chemical Society 41st Western Regional Meeting, October 9-13, 2007, San Diego. (Targegen and BioPredict)

Abstract - Although Gleevec has been a remarkable success for the treatment of CML, a significant number of patients develop drug resistance. The T315I (gatekeeper) mutation stands out among the >40 clinically identified mutations because it shows the highest prevalence (>20%), and maintains resistance to all recently developed BCR-ABL inhibitors (Tasigna, Sprycel) that target all other known mutations. Using molecular modeling, we have identified elements in Imatinib and Dasatinib that prevent effective binding to the ABL-T315I mutant and have developed and optimized a series of ATP-competitive ABL-T315I inhibitors. We will present the design elements that provide potency against the T315I mutant along with our synthetic strategies that utilized modular and convergent, microwave-facilitated couplings in a 3-step sequence.

Strategies involved in the construction of two series of novel potent inhibitors of ABL-T315I, (Zeng et. al.), Poster for American Chemical Society (ACS) National Meeting, August 19-23, 2007, Boston, MA. (Targegen and BioPredict)

Abstract - Although Gleevec has been a remarkable success for treatment of CML, a significant number of patients develop drug resistance. It is estimated that 50-90% of resistance is drug related and due to mutations that alter the affinity of Gleevec to the mutated enzyme. The T315I (gatekeeper) mutation stands out among the >40 clinically identified mutations because it shows highest prevalence (>20%), and maintains resistance to all recently developed BCRABL inhibitors (Tasigna, Sprycel) that target most other mutations. Using molecular modeling, we have developed two series of novel ABL-T315I inhibitors to target the ABL-T315I mutant both in enzyme and cell-based assays. We will present the synthetic strategies that enabled optimizations of nM inhibitors of ABL-T315I in both series.

Design and SAR of thiazole-based inhibitors for the ABL-T3151 (Chow et.al.), Poster for American Chemical Society (ACS) National Meeting, August 19-23, 2007, Boston, MA. (Targegen and BioPredict).

Abstract - Imatinib, a BCR-ABL tyrosine kinase inhibitor, is the standard of care for patients with chronic myelogenous leukemia (CML).  Unfortunately, refractory response due to Imatinib treatment arises because of point mutations within the ABL kinase domain of BCR-ABL. These mutations interfere with Imatinib binding. Specifically, the T315I mutation accounts for about 15 percent of cases in which CML patients develop resistance to Imatinib. The T315I mutation also shows resistance to Dasatinib, a newer drug that has demonstrated effectiveness in Imatinib resistant patients by targeting all the clinically relevant mutants except the T315I mutant. Using molecular modeling, we have identified elements in Imatinib and Dasatinib that prevent effective binding to the ABL-T315I mutant. We have developed and optimized a series of ABLT315I inhibitors to mediate the deficiency found in Dasatinib. We will present design elements that provide potency against the T315I mutant along with our optimization strategy.

Design and SAR of pyrimidine-based inhibitors targeting the ABL-T315I mutation (Dneprovskaia et.al.). Poster for American Chemical Society (ACS) National Meeting, August 19-23, 2007, Boston, MA.(Targegen and BioPredict).

Abstract - Imatinib, a BCR-ABL kinase inhibitor, is the standard of care for patients with chronic myelogenous leukemia. Mutations in the ABL kinase domain of the BCR-ABL protein result in interference with imatinib binding. Resistance to imatinib treatment leads to 50-90% of relapses of the disease. The T315I mutation accounts for 10-20 % of all observed mutations and is resistant to all approved and clinically advanced kinase inhibitors. TargeGen has designed and synthesized a new series of compounds based on a pyrimidine template by exploiting a unique binding interaction with Glu286 of the αC helix deep within the hydrophobic pocket. Optimization efforts guided by molecular modeling resulted in compounds with low nM ABL and ABL-T315I activity. Here we present the design and SAR of inhibitors with low nM activity against the ABL-T315I.

Development of novel and potent inhibitors of JAK2:  structure activity relationship studies for optimization of JAK2 potency while minimizing JAK3 activity, McPherson et. al. Poster at American Chemical Society National Spring Meeting, March 25-29, 2007, Chicago, IL. (Targegen and BioPredict).

Abstract - Somatic mutations such as JAK2(V617F) result in constitutive activation of JAK-STAT signaling that commonly characterizes myeloproliferative disorders (MPDs). Aberrant JAK-STAT signaling is therefore a potential therapeutic target in various MPDs including polycythemia vera (PV), agnogenic myeloid metaplasia (AMM), and essential thrombocythemia (ET). JAK2 inhibitors may find therapeutic utility in these and other myeloid disease states in which the JAK2 pathway is involved. These therapeutic agents must maintain a high degree of selectivity and minimal side effects in such chronic disease states, as these patient groups will likely be on lifetime therapy. The closely related JAK3 is a known target for immunosuppression to eliminate transplant rejection, and as such, it is important to develop JAK2 inhibitors that minimize JAK3 activity. Presented herein is a series of potent JAK2 inhibitors that have been designed to deselect JAK3 activity.

A novel series of low nM JAK2 selective inhibitors exhibit potent in vitro activities with favorable preclinical properties, (Mak et.al.), Poster at American Chemical Society (ACS) National Spring Meeting, March 25-29, 2007, Chicago, IL. (Targegen and BioPredict).

Abstract - The Janus Kinases (JAKs) play pivotal roles in intracellular cytokine signaling. Acquisition of somatic mutations, such as JAK2(V617F), results in constitutive activation of JAK-STAT signaling, which is associated with the pathogenesis of various myeloproliferative disorders (MPD). JAK2(V617F) is widely distributed in MPDs including a majority (>95%) of polycythemia vera (PV) cases, and approximately half of the patients with either essential thrombocythaemia (ET) or agnogenic myeloid metaplasia (AMM). Therefore, JAK2 inhibitors may be potential therapeutics in MPD, where aberrant JAK-STAT pathway is involved.  TargeGen has designed a new class of pyrimidine-based inhibitors that potently and selectively target JAK2. Details of a lead sub-series optimized for biochemical activity and selectivity, cellular potency in JAK(V617F) driven cells, and further characterization of selected compounds, both in vitro and in vivo, will be presented.

Design, syntheses and SAR of low nM inhibitors targeting JAK2. (Cao et.al.), Poster at American Chemical Society (ACS) National Spring Meeting, March 25-29, 2007, Chicago. IL. (Targegen and BioPredict).

Abstract - Janus kinase 2 (JAK2) is a cytoplasmic tyrosine kinase of the JAK family, and plays an integral role in cytokine signaling. somatic mutations in JAK2 and in the associated receptor kinases, play a critical role in keeping the JAK2 pathway constitutively active, and are associated with the pathogenesis of myeloproliferative disorders (MPDs). JAK2 pathway dysregulation gives proliferative and survival advantages to hematopoietic precursors. Therefore, JAK2 inhibitors may find therapeutic utility in myeloid disease states in which the JAK2 pathway is involved. Using structure-based drug design in conjunction with molecular modeling utilizing a homology model of JAK2 based on the known crystal structure of JAK3, a new series of JAK2 inhibitors has been designed and optimized. The design, synthesis, and SAR efforts for this new pyrimidine series that led to single-digit nM inhibitors of JAK2 will be discussed.

Development of isoform-specific PI3K inhibitors: reduction of myocardial infarction using a γ/δ inhibitor with potent anti-inflammatory activities (Doukas et.al.). Poster at Keystone Conference:  PI3-Kinase Signaling Pathways in Disease, February 15-20, 2007, Santa Fe NM. (Targegen and BioPredict).

Abstract - We review the preclinical development of TG100-115, a PI3K (phosphoinositide 3-kinase) gamma/delta isoform-specific inhibitor currently in clinical trials for the reduction of acute MI (myocardial infarction). An overview is presented outlining the pathogenesis of acute MI and the rationale for clinical use of PI3K gamma/delta-specific inhibitors in this indication. TG100-115's broad anti-inflammatory activities are described, as well as its ability to discriminate between cellular signaling pathways downstream of receptor tyrosine kinase ligands such as vascular endothelial growth factor. Finally, we review TG100-115's potent cardioprotective activities as revealed in rigorous animal models of acute MI, and, based on these data, this compound's potential for clinical utility.

Novel selective low nM JAK2 inhibitors with favorable preclinical properties (Mak, C. et.al.), Poster at American Association for Cancer Research (AACR) Annual Meeting, February 4-7, 2007, San Diego, CA. (Targegen and BioPredict).

Abstract - The Janus Kinases (JAKs) play pivotal roles in intracellular cytokine signaling. Acquisition of somatic mutations, such as JAK2(V617F), results in constitutive activation of JAK-STAT signaling, which is associated with the pathogenesis of various myeloproliferative disorders (MPD). JAK2(V617F) is widely distributed in MPDs including a majority (>95%) of polycythemia vera (PV) cases, and approximately half of the patients with either essential thrombocythaemia (ET) or agnogenic myeloid metaplasia (AMM). Therefore, JAK2 inhibitors may be potential therapeutics in MPD, where aberrant JAK-STAT pathway is involved.  TargeGen has designed a new class of pyrimidine-based inhibitors that potently and selectively target JAK2. Details of a lead sub-series optimized for biochemical activity and selectivity, cellular potency in JAK(V617F) driven cells, and further characterization of selected compounds, both in vitro and in vivo, will be presented.

A general strategy for designing kinase inhibitors by structure-based drug design targeting the active conformation -- lessons learned from Src and Abl-T3151 (Palanki et.al.), Poster at 8th Winter Conference of Medicinal and Bioorganic Chemistry, January 21-15, 2007, Steamboat Springs, CO. (Targegen and BioPredict). 

Abstract - Src is the prototype member of the Src-family of tyrosine kinases.  The Src family of tyrosine kinases comprises Src, Yes, Fyn, Hck, Blk, Brk, Frk, Srm, Lck, and Yrk.   Src is implicated in a number of disease states including myocardial infarction, stroke, osteoporosis, neurodegeneration, metastases and tumor progression particularly those of breast, metastatic colorectal, ovarian and pancreatic cancers.  Inhibitors of Src have broad potential utility in these disease states.  We report a strategy that takes advantage of the active form of Src for designing potent inhibitors.  Specifically, we leveraged a key interaction in active Src by designing inhibitors that interact with an untapped region deep within the hydrophobic pocket available only upon kinase activation.   The strategy is quite powerful as we have subsequently used it to target Bcr-Abl via an interaction with a similarly conserved residue deep within the hydrophobic pocket, as well as the Gleevec, Tasigna, and Sprycel resistant T315I mutant of Bcr-Abl.  Details of this strategy along with key modeling, crystallographic and enzymatic data across various inhibitor series, and implications for kinase inhibitor design will be discussed.

 

Using Binding Kinetics to Guide Docking. Klebansky, B. and Fine, R. Poster at Keystone Conference: Computer-Aided Drug Design, April 2010.

 

Abstract - The kinetics of peptide or long ligand binding to a protein is analyzed and the principles learned are applied to docking procedures.  Our main conjecture is that if the binding path of complex ligands travels through the succession of small entropic barriers then the path can be traversed in a reasonably short time.  In cases examined, there are identifiable ligand fragments that bind to the protein first, overcoming an initial translational and rotational entropy barrier.  Initial-binding fragments lower configurational entropy barriers by being internally rigid, by targeting rigid portions of the protein binding site, and by exploiting relatively high fragment binding free energy.   With the initial fragment bound the rest of the ligand fragments have significantly smaller configurational entropy barriers to overcome and, in many cases, a conformational change of the protein active site critical to ligand binding is promoted by initial fragment binding.

 

 

PUBLISHED PATENTS:

 

2018   Flavor compositions and pet food products containing the same, US20180168208A1.

2018   Screening methods using canine t2r receptors and pet food products and compositions identified using the same, EP3329275A1.

2017   Methods for identifying modulators of gpr92, WO2017181008A1.

2017   Methods for identifying modulators of calcium-sensing receptors, US20170356907A1.

2017   Compounds that modulate calcium-sensing receptor activity for modulating kokumi taste and pet food products containing the same, WO2017181062A1.

2008   Pyridylpiperazines and aminonicotinamides and their use as therapeutic agents, US7390813.

2004   Nicotinamide derivatives and their use as therapeutic agents. EP1763350.

2003   RXR activating molecules, US098184.

2003   Bicyclic heterocycles for the treatment of diabetes and other diseases, US84391.

1985   Computing device for calculating energy and pairwise central forces of particle
           interactions, US796870.