Gennadiy Poda

The CEBPA gene is mutated in 9% of patients with acute myeloid leukemia (AML). Selective expression of a short (30-kDa) CCAAT-enhancer binding protein-α (C/EBPα) translational isoform, termed p30, represents the most common type of CEBPA mutation in AML. The molecular mechanisms underlying p30-mediated transformation remain incompletely understood. We show that C/EBPα p30, but not the normal p42 isoform, preferentially interacts with Wdr5, a key component of SET/MLL (SET-domain/mixed-lineage leukemia) histone-methyltransferase complexes. Accordingly, p30-bound genomic regions were enriched for MLL-dependent H3K4me3 marks. The p30-dependent increase in self-renewal and inhibition of myeloid differentiation required Wdr5, as downregulation of the latter inhibited proliferation and restored differentiation in p30-dependent AML models. OICR-9429 is a new small-molecule antagonist of the Wdr5-MLL interaction. This compound selectively inhibited proliferation and induced differentiation i...

Transdermal therapy receives increasing attention as an attractive alternative to traditional drug delivery. Unfortunately the exact algorithm of transdermal permeation that could guide medicinal chemists towards delivery optimization at an early stage of the drug design process still remains to be decoded. This paper discusses some major hurdles on the way to full understanding of Quantitative Structure-Activity Relationships (QSAR) of skin permeation. From the statistical perspective, a recently published combined data set is found to be inappropriate with respect to the distribution of major molecular descriptors, and therefore should be approached cautiously as a source for QSAR model training and in modelling of occupational and environmental skin exposures.

Endoplasmic reticulum (ER) stress activates the unfolded protein response and its dysfunction is linked to multiple diseases. The stress transducer IRE1α is a transmembrane kinase endoribonuclease (RNase) that cleaves mRNA substrates to re-establish ER homeostasis. Aromatic ring systems containing hydroxy-aldehyde moieties, termed hydroxy aryl aldehydes (HAA), selectively inhibit IRE1α RNase and thus represent a novel chemical series for therapeutic To whom correspondence should be addressed: John Patterson, jpatterson@mankindcorp.com, 661-775-5317, Frank Sicheri, sicheri@lunenfeld.ca, 416-586-8471. *these authors contributed equally to this work Author contributions M.S. and M.T. performed the co-structure determinations. N.D., M.T., L.L., and M.C. performed in vitro enzymatic assays and direct inhibitor binding measurements. D.C., N.T., and K.L. performed biophysical analyses and/or generated reagents. I.K. collected synchrotron diffraction data. D.U., R.A., G.P., M.P. and B.W che...

Background Aberrant kallikrein activity is observed in a number of inflammatory dermatoses. Up-regulation of kallikrein-5 (KLK5) activity leads to uncontrolled skin desquamation and cleavage of proteinase-activated receptor-2 (PAR2), causing the release of pro-inflammatory cytokines and disruption of epidermal barrier function. This study aimed to identify KLK5-specific small molecule inhibitors which can serve as the foundation of a novel therapeutic for inflammatory skin disorders. Methods Five chemical libraries (13,569 compounds total) were screened against recombinant KLK5 using a fluorogenic enzymatic assay. Secondary validation was performed on the top 22 primary hits. All hits were docked in the KLK5 crystal structure to rationalize their potential interactions with the protein. Results A naturally occurring compound derived from the wood of Caesalpinia sappan (Brazilin) was identified as a novel KLK5 inhibitor (IC50: 20 μM, Ki: 6.4 μM). Docking suggests that the phenolic mo...

Multiple myeloma (MM) is one of the most common hematological malignancies, but current therapeutic options are limited to high-dose chemotherapy or high-risk stem-cell transplantation. In a kinome-wide RNAi study by Tiedemann and colleagues (2010), the G-protein coupled receptor kinase GRK6 was identified as a critical kinase required for survival of MM cells. This study also suggests that MM cells, but not other cell types, are dependent on GRK6; and that gene silencing by shRNA or siRNA of GRK6, but not other members of the GRK family, results in decreased survival. Through gene silencing techniques, we determined that a functional GRK6 kinase domain is required for survival of MM cells. These findings helped validate that the kinase domain of GRK6 is a promising target for MM, and therefore encouraged us to embark on an effort to identify potent small molecule kinase inhibitors of GRK6. Toward that end, by screening a focused kinase-directed library of small molecule inhibitors, compounds with moderate potency against GRK6 in biochemical assays were identified. Through this exercise, we discovered that two structurally distinct aminopyrazoles AZ-960 and ASC-082 had modest inhibition of GRK6. By combining structural features of these hits and further optimization we identified the quinazoline analogue OICR9945, a potent GRK6 inhibitor with good selectivity against a panel of diverse kinases and anti-proliferative activity against MM cell lines. Herein, we describe the design, synthesis and early pharmacological characterization of OICR9945 along with structure activity relationships (SAR) of this series against GRK6 and other kinases. Citation Format: David Uehling, Babu Joseph, Carly Griffin, Ratheesh Subramaniam, Ayome Abibi, Richard Marcellus, Michael Prakesch, Gennadiy Poda, Methvin Isaac, Chungyee Leung-Hagesteijn, Rodger Tiedemann, Rima Al-awar. Design, synthesis, and characterization of 4-aminopyrazole quinazolines as potent inhibitors of G protein-coupled receptor kinase GRK6 for the potential treatment of multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2377.

Evaluation of the ALOGPS, ACD Labs LogD, and PALLAS PrologD suites to calculate the log D distribution coefficient resulted in high root-mean-squared error (RMSE) of 1.0-1.5 log for two in-house Pfizer's log D data sets of 17,861 and 640 compounds. Inaccuracy in log P prediction was the limiting factor for the overall log D estimation by these algorithms. The self-learning feature of the ALOGPS (LIBRARY mode) remarkably improved the accuracy in log D prediction, and an rmse of 0.64-0.65 was calculated for both data sets.

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Inositol-requiring enzyme 1 (IRE1) is a key player in endoplasmic reticulum (ER) stress conditions. IRE1 is a highly conserved ER-membrane protein activated by the unfolded protein response (UPR) or other ER-stressors, such as hypoxia and glucose deprivation. Stress causes IRE1 to undergo oligomerization and autophosphorylation, which triggers nonconventional splicing of XBP-1 mRNA by its cytosolic endonuclease domain. The resulting spliced XBP-1 protein (XBP-1s) is a transcription factor that serves to increase the protein folding capacity and ultimately restore homeostasis of the ER. Thus, sustained IRE1 activity promotes cell survival and inhibition of IRE1 may be a potential therapeutic target for diseases associated with chronic ER-stress, such as neurodegenerative disorders, diabetes, and cancer. Proper RNase function of IRE1 is dependent upon autophosphorylation of the kinase domain. We therefore screened a library of 380 known kinase inhibitors, consisting of tool compounds and compounds already in clinical use, for those with activity against the human IRE1 kinase domain. As a result, a number of compounds were found that potently inhibit phosphorylation of a biotin-STK peptide substrate in the presence of human IRE1 (IC50 < 1 μM), as determined by HTRF (homogeneous time-resolved fluorescence). The lead compounds were then screened in cell-based assays. Several ATP-mimetic compounds with diverse chemotypes were found to inhibit expression of XBP-1s in human cancer cells under pharmacologically-induced acute ER-stress. Furthermore, transcriptional targets of XBP-1s and phosphorylation of IRE1 were also negatively affected by these compounds. Interestingly one compound in particular, a known ROCK1 (Rho-associated coiled-coil containing protein kinase 1) inhibitor (OICR000287A), was significantly more toxic to cells under acute ER-stress than to unstressed cells. This study suggests that development of ATP-competitive inhibitors of human IRE1 is a promising therapeutic strategy for ER-stress related diseases including myeloma, pancreatic and other secretory cancers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4989. doi:1538-7445.AM2012-4989

Publisher Summary This chapter describes methods to develop opioid G protein-coupled receptors (GPCR) structural models for use in molecular docking and drug design. They are characterized by seven alpha helical transmembrane (TM) domains connected by three intracellular and three extracellular loops. The extracellular (EL) N-terminus and the intracellular (IL) C-terminus are both targets for posttranslational glycosylation. Although, the widespread cloning of GPCRs and the determination of high-resolution X-ray data on rhodopsin has greatly advanced this field over the last decade, significant challenges still remain in the development of molecular models for predicting ligand binding and selectivity, function, and the structural basis to signal transduction. The models reported are developed with a primary focus on ligand binding and recognition. To some extent, current models could be viewed as “averaged” structures as a wide range of data are accounted for in the model building. As more receptor-type specific data is available, however, these models will continue to evolve to capture individual conformational preferences for the receptors leading to more reliable automated docking and virtual screens. It also reviews that one of the main applications of GPCR model building is the rationalization and development of structure-based concepts of ligand recognition. It focuses on the automated docking of naloxone and naltrexone-derived ligands. The chapter concludes that virtual screening across diverse ligand databases may be out of the reach of current model resolutions; there is little doubt that the application will be expanded as more experimental and structural data on GPCRs becomes available and integrated into structural models of ligand-receptor recognition.

Tissue kallikreins are a family of fifteen secreted serine proteases encoded by the largest protease gene cluster in the human genome. In the past decade, substantial progress has been made in characterizing the natural substrates, endogenous inhibitors and in vivo functions of kallikreins, and studies have delineated important pathophysiological roles for these proteases in a variety of tissues. Thus, kallikreins are now considered attractive targets for the development of novel therapeutics for airway, cardiovascular, tooth, brain, skin and neoplastic diseases. In this Review, we discuss recent advances in our understanding of the physiological functions and pathological implications of kallikrein proteases, and highlight progress in the identification of kallikrein inhibitors, which together are bringing us closer to therapeutically targeting kallikreins in selected disease settings.

The comparative study of the ability of three compounds (indomethacin, agent BW 755 C and arachidonate hydroxamic acid) to inhibit the activity of preparations of soya bean lipoxygenase and to block leukotriene C4 biosynthesis in human leukocytes recorded by reversed phase liquid chromatography was performed. It was shown that irrespectively of purification degree soya bean lipoxygenase is a sufficiently adequate object for primary testing of inhibitors of biosynthesis of leukotrienes with the given type of action. Compounds with IC50 less than or equal to 1.10(-6) mol/l might be considered promising for the further investigation.

The data bearing witness to realization of the cytostatic activity of alkylating agents by means of interaction with cell membrane receptors was obtained. Alkylating agents block receptors of the polyphosphoinositol system. It is shown that chloralkylamines inhibiting sites coincide with M-++cholinomimetics and alpha-adrenergic receptors, inhibitors of H-histamine receptors, cyclo- and lypoxigenase inhibitors. Such likeness is determined by identical structures of the molecule active part, and quantum-chemical calculations.

ABSTRACT The effect of the synthetic thrombin substrate (TAME) and three compounds exerting an opposite effect on Ca-PPI and AdC (caffeine, atropine and meta-tolyl derivative of mechlorethamine (TDM)) on hormone-like and catalytic functions of thrombin was studied. It is shown that both TAME and other drugs under test block effectively the thrombin-induced platelet aggregation, as well as protect the active site of the enzyme from denaturation by dithiothreitol. The same compounds inhibit thrombin in thrombin-fibrinogen reaction and platelet 12-lipoxygenase. These data suggest identity of thrombin moieties which determine its enzymatic and hormone-like activities.

Artificial neural networks were used to analyze and predict the human immunodeficiency virus type 1 reverse transcriptase inhibitors. The training and control sets included 44 molecules (most of them are well-known substances such as AZT, dde, etc.). The activities of the molecules were taken from literature. Topological indices were calculated and used as molecular parameters. The four most informative parameters were chosen and applied to predict activities of both new and control molecules. We used a network pruning algorithm and network ensembles to obtain the final classifier. Increasing of neural network generalization of the new data was observed, when using the aforementioned methods. The prognosis of new molecules revealed one molecule as possibly very active. It was confirmed by further biological tests.

Bent but not broken: cyclic oligoprolines are accessed in a reaction that effectively bends rigid oligoproline peptides (see scheme; TBDMS=tert-butyldimethylsilyl). The stitching is accomplished during macrocyclization enabled by aziridine aldehydes and isocyanides. Molecular modeling studies suggest that electrostatic attraction between the termini of the linear peptide is pivotal for macrocyclization. The macrocycles were studied by circular dichroism with a polyproline II structure being observed in larger macrocycles.

A series of 4-(N,N-diarylamino)piperidines are synthesized and evaluated for high affinity binding and selectivity to the delta-opioid receptor using a combination of 3D-QSAR and molecular docking techniques. Based on experimental ligand binding data to both mu- and delta- opioid receptors, CoMFA fields are generated and applied to identify potential ligand modifications to further optimize lead compounds. Molecular docking experiments to the delta-receptor are also reported that explain the CoMFA trends predicted as well as the differential binding and selectivity displayed by various compounds in the series. An analysis of the binding site model proposed indicates the piperidines take advantage of 3 key sites or binding domains within the delta-receptor. These include an aromatic pocket (approximately 1/3 into the receptor cavity), an aspartic acid residue (which serves as a docking point for the piperidinyl cationic amine) and a hydrophobic pocket at the extracellular boundary of...

Based on a set of compounds possessing hypolipidemic activity, it was demonstrated that evolutionary algorithms can be successfully used to compile an informative set of molecular parameters. The parameter sets selected using the method of potential functions allowed correct prediction of the activity of test molecules.