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Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors.
Cowen SD, Russell D, Dakin LA, Chen H, Larsen NA, Godin R, Throner S, Zheng X, Molina A, Wu J, Cheung T, Howard T, Garcia-Arenas R, Keen N, Pendleton CS, Pietenpol JA, Ferguson AD
(2016) J Med Chem 59: 11079-11097
MeSH Terms: Cell Line, Tumor, Cell Proliferation, Dose-Response Relationship, Drug, Drug Design, Enzyme Inhibitors, HCT116 Cells, Histone-Lysine N-Methyltransferase, Humans, Molecular Structure, Structure-Activity Relationship
Show Abstract · Added April 9, 2017
Protein lysine methyltransferases (KMTs) have emerged as important regulators of epigenetic signaling. These enzymes catalyze the transfer of donor methyl groups from the cofactor S-adenosylmethionine to specific acceptor lysine residues on histones, leading to changes in chromatin structure and transcriptional regulation. These enzymes also methylate an array of nonhistone proteins, suggesting additional mechanisms by which they influence cellular physiology. SMYD2 is reported to be an oncogenic methyltransferase that represses the functional activity of the tumor suppressor proteins p53 and RB. HTS screening led to identification of five distinct substrate-competitive chemical series. Determination of liganded crystal structures of SMYD2 contributed significantly to "hit-to-lead" design efforts, culminating in the creation of potent and selective inhibitors that were used to understand the functional consequences of SMYD2 inhibition. Taken together, these results have broad implications for inhibitor design against KMTs and clearly demonstrate the potential for developing novel therapies against these enzymes.
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10 MeSH Terms
Diverse Effects on M Signaling and Adverse Effect Liability within a Series of M Ago-PAMs.
Rook JM, Abe M, Cho HP, Nance KD, Luscombe VB, Adams JJ, Dickerson JW, Remke DH, Garcia-Barrantes PM, Engers DW, Engers JL, Chang S, Foster JJ, Blobaum AL, Niswender CM, Jones CK, Conn PJ, Lindsley CW
(2017) ACS Chem Neurosci 8: 866-883
MeSH Terms: Allosteric Regulation, Animals, Drug Discovery, Humans, Mice, Muscarinic Agonists, Rats, Receptor, Muscarinic M1, Structure-Activity Relationship
Show Abstract · Added April 6, 2017
Both historical clinical and recent preclinical data suggest that the M muscarinic acetylcholine receptor is an exciting target for the treatment of Alzheimer's disease and the cognitive and negative symptom clusters in schizophrenia; however, early drug discovery efforts targeting the orthosteric binding site have failed to afford selective M activation. Efforts then shifted to focus on selective activation of M via either allosteric agonists or positive allosteric modulators (PAMs). While M PAMs have robust efficacy in rodent models, some chemotypes can induce cholinergic adverse effects (AEs) that could limit their clinical utility. Here, we report studies aimed at understanding the subtle structural and pharmacological nuances that differentiate efficacy from adverse effect liability within an indole-based series of M ago-PAMs. Our data demonstrate that closely related M PAMs can display striking differences in their in vivo activities, especially their propensities to induce adverse effects. We report the discovery of a novel PAM in this series that is devoid of observable adverse effect liability. Interestingly, the molecular pharmacology profile of this novel PAM is similar to that of a representative M PAM that induces severe AEs. For instance, both compounds are potent ago-PAMs that demonstrate significant interaction with the orthosteric site (either bitopic or negative cooperativity). However, there are subtle differences in efficacies of the compounds at potentiating M responses, agonist potencies, and abilities to induce receptor internalization. While these differences may contribute to the differential in vivo profiles of these compounds, the in vitro differences are relatively subtle and highlight the complexities of allosteric modulators and the need to focus on in vivo phenotypic screening to identify safe and effective M PAMs.
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Challenges in the development of an M PAM in vivo tool compound: The discovery of VU0467154 and unexpected DMPK profiles of close analogs.
Wood MR, Noetzel MJ, Poslusney MS, Melancon BJ, Tarr JC, Lamsal A, Chang S, Luscombe VB, Weiner RL, Cho HP, Bubser M, Jones CK, Niswender CM, Wood MW, Engers DW, Brandon NJ, Duggan ME, Conn PJ, Bridges TM, Lindsley CW
(2017) Bioorg Med Chem Lett 27: 171-175
MeSH Terms: Animals, Humans, Ligands, Nucleoside Transport Proteins, Pyridazines, Rats, Sprague-Dawley, Receptor, Muscarinic M4, Structure-Activity Relationship, Thiophenes
Show Abstract · Added April 6, 2017
This letter describes the chemical optimization of a novel series of M positive allosteric modulators (PAMs) based on a 5-amino-thieno[2,3-c]pyridazine core, developed via iterative parallel synthesis, and culminating in the highly utilized rodent in vivo tool compound, VU0467154 (5). This is the first report of the optimization campaign (SAR and DMPK profiling) that led to the discovery of VU0467154, and details all of the challenges faced in allosteric modulator programs (steep SAR, species differences in PAM pharmacology and subtle structural changes affecting CNS penetration).
Copyright © 2016 Elsevier Ltd. All rights reserved.
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9 MeSH Terms
Structural Insights into Reovirus σ1 Interactions with Two Neutralizing Antibodies.
Dietrich MH, Ogden KM, Katen SP, Reiss K, Sutherland DM, Carnahan RH, Goff M, Cooper T, Dermody TS, Stehle T
(2017) J Virol 91:
MeSH Terms: Amino Acid Sequence, Animals, Antibodies, Neutralizing, Antibodies, Viral, Binding Sites, CHO Cells, Cell Line, Cricetulus, Hemagglutinin Glycoproteins, Influenza Virus, Immunoglobulin Fab Fragments, Mice, Molecular Docking Simulation, Molecular Dynamics Simulation, Neutralization Tests, Protein Binding, Protein Conformation, Protein Interaction Domains and Motifs, Reoviridae, Structure-Activity Relationship, Viral Proteins, Virus Replication
Show Abstract · Added April 26, 2017
Reovirus attachment protein σ1 engages glycan receptors and junctional adhesion molecule-A (JAM-A) and is thought to undergo a conformational change during the proteolytic disassembly of virions to infectious subvirion particles (ISVPs) that accompanies cell entry. The σ1 protein is also the primary target of neutralizing antibodies. Here, we present a structural and functional characterization of two neutralizing antibodies that target σ1 of serotype 1 (T1) and serotype 3 (T3) reoviruses. The crystal structures revealed that each antibody engages its cognate σ1 protein within the head domain via epitopes distinct from the JAM-A-binding site. Surface plasmon resonance and cell-binding assays indicated that both antibodies likely interfere with JAM-A engagement by steric hindrance. To define the interplay between the carbohydrate receptor and antibody binding, we conducted hemagglutination inhibition assays using virions and ISVPs. The glycan-binding site of T1 σ1 is located in the head domain and is partly occluded by the bound Fab in the crystal structure. The T1-specific antibody inhibited hemagglutination by virions and ISVPs, probably via direct interference with glycan engagement. In contrast to T1 σ1, the carbohydrate-binding site of T3 σ1 is located in the tail domain, distal to the antibody epitope. The T3-specific antibody inhibited hemagglutination by T3 virions but not ISVPs, indicating that the antibody- and glycan-binding sites in σ1 are in closer spatial proximity on virions than on ISVPs. Our results provide direct evidence for a structural rearrangement of σ1 during virion-to-ISVP conversion and contribute new information about the mechanisms of antibody-mediated neutralization of reovirus.
IMPORTANCE - Virus attachment proteins mediate binding to host cell receptors, serve critical functions in cell and tissue tropism, and are often targeted by the neutralizing antibody response. The structural investigation of antibody-antigen complexes can provide valuable information for understanding the molecular basis of virus neutralization. Studies with enveloped viruses, such as HIV and influenza virus, have helped to define sites of vulnerability and guide vaccination strategies. By comparison, less is known about antibody binding to nonenveloped viruses. Here, we structurally investigated two neutralizing antibodies that bind the attachment protein σ1 of reovirus. Furthermore, we characterized the neutralization efficiency, the binding affinity for σ1, and the effect of the antibodies on reovirus receptor engagement. Our analysis defines reovirus interactions with two neutralizing antibodies, allows us to propose a mechanism by which they block virus infection, and provides evidence for a conformational change in the σ1 protein during viral cell entry.
Copyright © 2017 American Society for Microbiology.
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21 MeSH Terms
A Deep Hydrophobic Binding Cavity is the Main Interaction for Different Y R Antagonists.
Burkert K, Zellmann T, Meier R, Kaiser A, Stichel J, Meiler J, Mittapalli GK, Roberts E, Beck-Sickinger AG
(2017) ChemMedChem 12: 75-85
MeSH Terms: Animals, Arginine, Benzazepines, Binding Sites, COS Cells, Cells, Cultured, Chlorocebus aethiops, Dose-Response Relationship, Drug, HEK293 Cells, Humans, Hydrophobic and Hydrophilic Interactions, Molecular Docking Simulation, Molecular Structure, Receptors, Neuropeptide Y, Structure-Activity Relationship
Show Abstract · Added April 8, 2017
The neuropeptide Y receptor (Y R) is involved in various pathophysiological processes such as epilepsy, mood disorders, angiogenesis, and tumor growth. Therefore, the Y R is an interesting target for drug development. A detailed understanding of the binding pocket could facilitate the development of highly selective antagonists to study the role of Y R in vitro and in vivo. In this study, several residues crucial to the interaction of BIIE0246 and SF-11 derivatives with Y R were investigated by signal transduction assays. Using the experimental results as constraints, the antagonists were docked into a comparative structural model of the Y R. Despite differences in size and structure, all three antagonists display a similar binding site, including a deep hydrophobic cavity formed by transmembrane helices (TM) 4, 5, and 6, as well as a hydrophobic patch at the top of TM2 and 7. Additionally, we suggest that the antagonists block Q , a position that has been shown to be crucial for binding of the amidated C terminus of NPY and thus for receptor activation.
© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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15 MeSH Terms
C-terminal motif of human neuropeptide Y receptor determines internalization and arrestin recruitment.
Wanka L, Babilon S, Burkert K, Mörl K, Gurevich VV, Beck-Sickinger AG
(2017) Cell Signal 29: 233-239
MeSH Terms: Amino Acid Motifs, Amino Acid Sequence, Amino Acids, Animals, COS Cells, Chlorocebus aethiops, Endocytosis, HEK293 Cells, Humans, Mutant Proteins, Receptors, Neuropeptide Y, Reproducibility of Results, Sequence Alignment, Sequence Deletion, Structure-Activity Relationship, beta-Arrestin 2
Show Abstract · Added March 14, 2018
The human neuropeptide Y receptor is a rhodopsin-like G protein-coupled receptor (GPCR), which contributes to anorexigenic signals. Thus, this receptor is a highly interesting target for metabolic diseases. As GPCR internalization and trafficking affect receptor signaling and vice versa, we aimed to investigate the molecular mechanism of hYR desensitization and endocytosis. The role of distinct segments of the hYR carboxyl terminus was investigated by fluorescence microscopy, binding assays, inositol turnover experiments and bioluminescence resonance energy transfer assays to examine the internalization behavior of hYR and its interaction with arrestin-3. Based on results of C-terminal deletion mutants and substitution of single amino acids, the motif EESEHLPLSTVHTEVSKGS was identified, with glutamate, threonine and serine residues playing key roles, based on site-directed mutagenesis. Thus, we identified the internalization motif for the human neuropeptide Y receptor, which regulates arrestin-3 recruitment and receptor endocytosis.
Copyright © 2016 Elsevier Inc. All rights reserved.
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16 MeSH Terms
Optimization of the choline transporter (CHT) inhibitor ML352: Development of VU6001221, an improved in vivo tool compound.
Bertron JL, Ennis EA, Tarr CJ, Wright J, Dickerson JW, Locuson CW, Blobaum AL, Rook JM, Blakely RD, Lindsley CW
(2016) Bioorg Med Chem Lett 26: 4637-4640
MeSH Terms: Animals, Benzamides, Dose-Response Relationship, Drug, Half-Life, Inhibitory Concentration 50, Isoxazoles, Membrane Transport Proteins, Oxazoles, Piperidines, Rats, Structure-Activity Relationship
Show Abstract · Added March 21, 2018
This Letter describes the further lead optimization of the CHT inhibitor probe, ML352 (VU0476201), and the development of VU6001221, an improved in vivo tool. A multi-dimensional optimization effort encountered steep SAR, and ultimately, subtle tuning of the electronics of the central phenyl core provided VU6001221, a CHT inhibitor with comparable potency for choline uptake inhibition as ML352, yet improved PK and CNS penetration. Moreover, VU6001221 enabled evaluation, for the first time, of a CHT inhibitor in a standard preclinical rodent cognition model, novel object recognition (NOR). We observed VU6001221 to elicit a dose-responsive increase in NOR, raising the possibility of agonism of synaptic α7 nicotinic ACh receptors by elevated extracellular choline, that if confirmed would represent a novel molecular strategy to enhance cognition.
Copyright © 2016 Elsevier Ltd. All rights reserved.
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Discovery of N-((1-(4-(3-(3-((6,7-Dimethoxyquinolin-3-yl)oxy)phenyl)ureido)-2-(trifluoromethyl)phenyl)piperidin-4-yl)methyl)propionamide (CHMFL-KIT-8140) as a Highly Potent Type II Inhibitor Capable of Inhibiting the T670I "Gatekeeper" Mutant of cKIT Kinase.
Li B, Wang A, Liu J, Qi Z, Liu X, Yu K, Wu H, Chen C, Hu C, Wang W, Wu J, Hu Z, Ye L, Zou F, Liu F, Wang B, Wang L, Ren T, Zhang S, Bai M, Zhang S, Liu J, Liu Q
(2016) J Med Chem 59: 8456-72
MeSH Terms: Amides, Animals, Cell Line, Tumor, Female, Gastrointestinal Neoplasms, Gastrointestinal Stromal Tumors, Gastrointestinal Tract, Halogenation, Humans, Methylation, Mice, Mice, Nude, Models, Molecular, Mutation, Protein Kinase Inhibitors, Proto-Oncogene Proteins c-kit, Rats, Sprague-Dawley, Structure-Activity Relationship
Show Abstract · Added April 2, 2019
cKIT kinase inhibitors, e.g., imatinib, could induce drug-acquired mutations such as cKIT T670I that rendered drug resistance after chronic treatment. Through a type II kinase inhibitor design approach we discovered a highly potent type II cKIT kinase inhibitor compound 35 (CHMFL-KIT-8140), which potently inhibited both cKIT wt (IC50 = 33 nM) and cKIT gatekeeper T670I mutant (IC50 = 99 nM). Compound 35 displayed strong antiproliferative effect against GISTs cancer cell lines GIST-T1 (cKIT wt, GI50 = 4 nM) and GIST-5R (cKIT T670I, GI50 = 26 nM). In the cellular context it strongly inhibited c-KIT mediated signaling pathways and induced apoptosis. In the BaF3-TEL-cKIT-T670I isogenic cell inoculated xenograft mouse model, 35 exhibited dose dependent tumor growth suppression efficacy and 100 mg/kg dosage provided 47.7% tumor growth inhibition (TGI) without obvious toxicity. We believe compound 35 would be a good pharmacological tool for exploration of the cKIT-T670I mutant mediated pathology in GISTs.
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Structure/Function Analysis of Recurrent Mutations in SETD2 Protein Reveals a Critical and Conserved Role for a SET Domain Residue in Maintaining Protein Stability and Histone H3 Lys-36 Trimethylation.
Hacker KE, Fahey CC, Shinsky SA, Chiang YJ, DiFiore JV, Jha DK, Vo AH, Shavit JA, Davis IJ, Strahl BD, Rathmell WK
(2016) J Biol Chem 291: 21283-21295
MeSH Terms: Enzyme Stability, Histone-Lysine N-Methyltransferase, Histones, Humans, Methylation, Methyltransferases, Mutation, Neoplasm Proteins, Neoplasms, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Structure-Activity Relationship
Show Abstract · Added October 30, 2019
The yeast Set2 histone methyltransferase is a critical enzyme that plays a number of key roles in gene transcription and DNA repair. Recently, the human homologue, SETD2, was found to be recurrently mutated in a significant percentage of renal cell carcinomas, raising the possibility that the activity of SETD2 is tumor-suppressive. Using budding yeast and human cell line model systems, we examined the functional significance of two evolutionarily conserved residues in SETD2 that are recurrently mutated in human cancers. Whereas one of these mutations (R2510H), located in the Set2 Rpb1 interaction domain, did not result in an observable defect in SETD2 enzymatic function, a second mutation in the catalytic domain of this enzyme (R1625C) resulted in a complete loss of histone H3 Lys-36 trimethylation (H3K36me3). This mutant showed unchanged thermal stability as compared with the wild type protein but diminished binding to the histone H3 tail. Surprisingly, mutation of the conserved residue in Set2 (R195C) similarly resulted in a complete loss of H3K36me3 but did not affect dimethylated histone H3 Lys-36 (H3K36me2) or functions associated with H3K36me2 in yeast. Collectively, these data imply a critical role for Arg-1625 in maintaining the protein interaction with H3 and specific H3K36me3 function of this enzyme, which is conserved from yeast to humans. They also may provide a refined biochemical explanation for how H3K36me3 loss leads to genomic instability and cancer.
© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
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Ligand-based virtual screen for the discovery of novel M5 inhibitor chemotypes.
Geanes AR, Cho HP, Nance KD, McGowan KM, Conn PJ, Jones CK, Meiler J, Lindsley CW
(2016) Bioorg Med Chem Lett 26: 4487-4491
MeSH Terms: Animals, CHO Cells, Cricetulus, Drug Discovery, Humans, Ligands, Muscarinic Antagonists, Quantitative Structure-Activity Relationship, Receptor, Muscarinic M5
Show Abstract · Added April 6, 2017
This Letter describes a ligand-based virtual screening campaign utilizing SAR data around the M5 NAMs, ML375 and VU6000181. Both QSAR and shape scores were employed to virtually screen a 98,000-member compound library. Neither approach alone proved productive, but a consensus score of the two models identified a novel scaffold which proved to be a modestly selective, but weak inhibitor (VU0549108) of the M5 mAChR (M5 IC50=6.2μM, M1-4 IC50s>10μM) based on an unusual 8-((1,3,5-trimethyl-1H-pyrazol-4-yl)sulfonyl)-1-oxa-4-thia-8-azaspiro[4,5]decane scaffold. [(3)H]-NMS binding studies showed that VU0549108 interacts with the orthosteric site (Ki of 2.7μM), but it is not clear if this is negative cooperativity or orthosteric binding. Interestingly, analogs synthesized around VU0549108 proved weak, and SAR was very steep. However, this campaign validated the approach and warranted further expansion to identify additional novel chemotypes.
Copyright © 2016 Elsevier Ltd. All rights reserved.
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