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Kageji H, Momose T, Ebisawa M, Nakazawa Y, Okada H, Togashi N, Nagamoto Y, Obuchi W, Yasumatsu I, Kihara K, Hiramoto K, Minami M, Kasanuki N, Isoyama T, Naito H, Tanaka N. Discovery of a potent, selective, and orally available EGFR C797S mutant inhibitor (DS06652923) with in vivo antitumor activity. Bioorg Med Chem 2024; 111:117862. [PMID: 39111073 DOI: 10.1016/j.bmc.2024.117862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/24/2024]
Abstract
The C797S mutation is one of the major factors behind resistance to the third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs). Herein, we describe the discovery of DS06652923, a novel, potent, and orally available EGFR-triple-mutant inhibitor. Through scaffold hopping from the previously reported nicotinamide derivative, a novel biaryl scaffold was obtained. The potency was successfully enhanced by the introduction of basic substituents based on analysis of the docking study results. In addition, the difluoromethoxy group on the pyrazole ring improved the kinase selectivity by inducing steric clash with the other kinases. The most optimized compound, DS06652923, achieved tumor regression in the Ba/F3 allograft model upon its oral administration.
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Affiliation(s)
- Hideaki Kageji
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.
| | - Takayuki Momose
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Masayuki Ebisawa
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Yusuke Nakazawa
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Hiroyuki Okada
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Noriko Togashi
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Yasuhito Nagamoto
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Wataru Obuchi
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Isao Yasumatsu
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Kawori Kihara
- Daiichi Sankyo Co., Ltd., 2716-1 Chiyodamachi, Oaza Akaiwa, Aza Kurakake, Oura, Gunma 370-0503, Japan
| | - Kumiko Hiramoto
- Daiichi Sankyo Co., Ltd., 2716-1 Chiyodamachi, Oaza Akaiwa, Aza Kurakake, Oura, Gunma 370-0503, Japan
| | - Megumi Minami
- Daiichi Sankyo Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Naomi Kasanuki
- Daiichi Sankyo Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Takeshi Isoyama
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Hiroyuki Naito
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Naoki Tanaka
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
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Taniguchi T, Yasumatsu I, Inagaki H, Baba D, Toyota A, Kaneta Y, Odagiri T, Momose T, Kawai J, Imaoka T, Nakayama K. Optimization of Novel Pyrido-pyridazinone Derivatives as FER Tyrosine Kinase Inhibitors, Leading to the Potent DS08701581. ACS Med Chem Lett 2024; 15:1010-1016. [PMID: 39015278 PMCID: PMC11247628 DOI: 10.1021/acsmedchemlett.4c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/20/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
Previously, we reported the new pyrido-pyridazinone template as a feline sarcoma-related (FER) tyrosine kinase inhibitor. Representative compound 1 (DS21360717) showed strong enzyme inhibitory activity (IC50 = 0.5 nM), however, its antitumor effect was insufficient, probably due to poor solubility and resultant low bioavailability (BA). In addition, the kinase selectivity was inadequate, which may result in certain safety risks. Here, we focused on derivatization of the unoptimized C-5 position to obtain promising FER inhibitors possessing strong antitumor effects and improved selectivity, referring to their X-ray crystal structure and the docking model with FES proto-oncogene tyrosine kinase as an FER surrogate. While establishing the synthetic route of the pyrido-pyridazinone scaffold, we obtained a desired compound via our derivatization. Our optimized compound 17c (DS08701581) showed the highest class cell-free and cell activities in this template, good oral BA, and improved kinase selectivity, resulting in significant tumor growth inhibition in the Ba/F3-FER tumor model without body weight loss.
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Affiliation(s)
- Toru Taniguchi
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Isao Yasumatsu
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Hiroaki Inagaki
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Daichi Baba
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Akiko Toyota
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Yasuyuki Kaneta
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Takashi Odagiri
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Takayuki Momose
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Junya Kawai
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Tomoki Imaoka
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Kiyoshi Nakayama
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
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Kurup S, Gesinski D, Assaad K, Reynolds A. Design, synthesis, and evaluation of dual EGFR/AURKB inhibitors as anticancer agents for non-small cell lung cancer. Bioorg Med Chem Lett 2024; 100:129612. [PMID: 38199330 PMCID: PMC10951975 DOI: 10.1016/j.bmcl.2024.129612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/20/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
The epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are first-line agents for mutant EGFR-positive (mEGFR+) NSCLC. However, secondary resistant mutations develop following therapy that prevent EGFR-TKI binding. The EGFR-TKIs are rendered ineffective in NSCLC expressing EGFR resistant mutations (rmEGFR+). Mutations in Kirsten rat sarcoma virus protein (mKRAS) support persistent signaling downstream of EGFR regardless of EGFR-TKI earlier in the signaling cascade. The EGFR-TKIs are ineffective in mKRAS+ NSCLC. Thus, newer anticancer agents are needed for rmEGFR+ and mKRAS+ NSCLC. Aurora kinase B (AURKB) is a mitosis related kinase that is overexpressed in NSCLC and supports cancer cell proliferation and survival. Literature reports have suggested that AURKB inhibitors if given concurrently with an EGFR-TKI could overcome EGFR-TKI resistance in mKRAS+ NSCLC and rmEGFR + NSCLC, and showed improved anticancer effects compared to current single-targeted EGFR-TKIs. Molecular modeling was used to identify similarities between the kinase pockets of EGFR and AURKB. An overlap was observed for the inactive conformation of EGFR and the active conformation of AURKB. Compounds 3-7 were synthesized as dual EGFR/AURKB inhibitors for mKRAS+ and rmEGFR+ NSCLC. Compounds 5, 6 and 7 were identified as dual EGFR/AURKB inhibitors. Compound 5 demonstrated modest micromolar inhibition of rmEGFR+ NSCLC. All investigated compounds showed moderate inhibition of mKRAS+ NSCLC cells. Compound 7 demonstrated single-digit micromolar inhibition of mKRAS+ NSCLC.
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Affiliation(s)
- Sonali Kurup
- College of Pharmacy, Ferris State University, United States.
| | - Dayna Gesinski
- College of Pharmacy, Ferris State University, United States
| | - Kaitlin Assaad
- College of Pharmacy, Ferris State University, United States
| | - Aidan Reynolds
- College of Pharmacy, Ferris State University, United States
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Ong WJG, Kirubakaran P, Karanicolas J. Poor Generalization by Current Deep Learning Models for Predicting Binding Affinities of Kinase Inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.556234. [PMID: 37732243 PMCID: PMC10508770 DOI: 10.1101/2023.09.04.556234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The extreme surge of interest over the past decade surrounding the use of neural networks has inspired many groups to deploy them for predicting binding affinities of drug-like molecules to their receptors. A model that can accurately make such predictions has the potential to screen large chemical libraries and help streamline the drug discovery process. However, despite reports of models that accurately predict quantitative inhibition using protein kinase sequences and inhibitors' SMILES strings, it is still unclear whether these models can generalize to previously unseen data. Here, we build a Convolutional Neural Network (CNN) analogous to those previously reported and evaluate the model over four datasets commonly used for inhibitor/kinase predictions. We find that the model performs comparably to those previously reported, provided that the individual data points are randomly split between the training set and the test set. However, model performance is dramatically deteriorated when all data for a given inhibitor is placed together in the same training/testing fold, implying that information leakage underlies the models' performance. Through comparison to simple models in which the SMILES strings are tokenized, or in which test set predictions are simply copied from the closest training set data points, we demonstrate that there is essentially no generalization whatsoever in this model. In other words, the model has not learned anything about molecular interactions, and does not provide any benefit over much simpler and more transparent models. These observations strongly point to the need for richer structure-based encodings, to obtain useful prospective predictions of not-yet-synthesized candidate inhibitors.
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Affiliation(s)
- Wern Juin Gabriel Ong
- Cancer Signaling & Microenvironment Program, Fox Chase Cancer Center, Philadelphia, PA 19111
- Bowdoin College, Brunswick, ME 04011
| | - Palani Kirubakaran
- Cancer Signaling & Microenvironment Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - John Karanicolas
- Cancer Signaling & Microenvironment Program, Fox Chase Cancer Center, Philadelphia, PA 19111
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Lv G, Shi Q, Zhang T, Li J, Long Y, Zhang W, Choudhry N, Yang K, Li H, Kalashova J, Yang C, Zhou X, Reddy MC, Anantoju KK, Zhang S, Zhang J, Allen TD, Liu H, Nimishetti N, Yang D. Integrating a phenotypic screening with a structural simplification strategy to identify 4-phenoxy-quinoline derivatives to potently disrupt the mitotic localization of Aurora kinase B. Bioorg Med Chem 2023; 80:117173. [PMID: 36696874 DOI: 10.1016/j.bmc.2023.117173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023]
Abstract
We combined a mechanism-informed phenotypic screening (MIPS) assay with a structural simplification strategy to guide the discovery of compounds that disrupt the localization of the mitotic regulator, Aurora kinase B (AURKB), rather than inhibiting its catalytic activity. An initial hit 4-(4-methylthiophen-2-yl)-N-(4-(quinolin-4-yloxy)phenyl)phthalazin-1-amine was identified after screening an in-house library of small molecules and phenocopied the loss of function mutations in AURKB without inhibiting its catalytic activity. We isolated this hit compound activity to its 4-phenoxy-quinoline moiety. The fragment was further optimized into a class of new chemical entities that potently disrupt the mitotic localization of AURKB at low nanomolar concentrations and consequently elicit severe growth inhibition in diverse human cancer cell lines. A lead compound, N-(3-methoxy-5-(6-methoxyquinolin-4-yl)oxy)phenyl)acetamide possessed desirable pharmacokinetic properties such as AUC0-∞: 227.15 [ng∙h/mL/(mg/kg)]; Cmax: 3378.52 ng/mL T1/2: 3.52 h; and F%: 42 % and produced the AURKB-inhibitory phenotypes in a mouse xenograft model. A lead compound is a powerful tool for interrogating the regulation of AURKB and has the potential to be further developed as a first-in-class oncology therapeutic.
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Affiliation(s)
- Gang Lv
- Chengdu Anticancer Bioscience, Chengdu 610000, China; J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China.
| | - Qiong Shi
- J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China
| | - Ting Zhang
- Chengdu Anticancer Bioscience, Chengdu 610000, China; J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China
| | - Jinhua Li
- Chengdu Anticancer Bioscience, Chengdu 610000, China; J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China
| | - Yan Long
- Chengdu Anticancer Bioscience, Chengdu 610000, China; J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China
| | - Wenhui Zhang
- Chengdu Anticancer Bioscience, Chengdu 610000, China
| | - Namrta Choudhry
- Chengdu Anticancer Bioscience, Chengdu 610000, China; J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China
| | - Kevin Yang
- Chengdu Anticancer Bioscience, Chengdu 610000, China; Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA
| | - Hongmei Li
- Chengdu Anticancer Bioscience, Chengdu 610000, China; J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China
| | - Julia Kalashova
- Chengdu Anticancer Bioscience, Chengdu 610000, China; J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China
| | - Chenglu Yang
- Chengdu Anticancer Bioscience, Chengdu 610000, China; J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China
| | - Xiaohu Zhou
- Chengdu Anticancer Bioscience, Chengdu 610000, China
| | | | | | - Shenqiu Zhang
- J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China
| | - Jing Zhang
- J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China
| | | | - Hong Liu
- Anticancer Bioscience (US), South San Francisco, CA 94080, USA
| | - Naganna Nimishetti
- Chengdu Anticancer Bioscience, Chengdu 610000, China; J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China.
| | - Dun Yang
- Chengdu Anticancer Bioscience, Chengdu 610000, China; J. Michael Bishop Institute of Cancer Research, Chengdu 610000, China.
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6
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Wells C, Liang Y, Pulliam TL, Lin C, Awad D, Eduful B, O’Byrne S, Hossain MA, Catta-Preta CMC, Ramos PZ, Gileadi O, Gileadi C, Couñago RM, Stork B, Langendorf CG, Nay K, Oakhill JS, Mukherjee D, Racioppi L, Means AR, York B, McDonnell DP, Scott JW, Frigo DE, Drewry DH. SGC-CAMKK2-1: A Chemical Probe for CAMKK2. Cells 2023; 12:287. [PMID: 36672221 PMCID: PMC9856672 DOI: 10.3390/cells12020287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
The serine/threonine protein kinase calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) plays critical roles in a range of biological processes. Despite its importance, only a handful of inhibitors of CAMKK2 have been disclosed. Having a selective small molecule tool to interrogate this kinase will help demonstrate that CAMKK2 inhibition can be therapeutically beneficial. Herein, we disclose SGC-CAMKK2-1, a selective chemical probe that targets CAMKK2.
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Affiliation(s)
- Carrow Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yi Liang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas L. Pulliam
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chenchu Lin
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dominik Awad
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Benjamin Eduful
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sean O’Byrne
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolina Moura Costa Catta-Preta
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Opher Gileadi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Carina Gileadi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Brittany Stork
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Kevin Nay
- St Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia
| | | | - Debarati Mukherjee
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Luigi Racioppi
- Department of Medicine, Division of Hematological Malignancies and Cellular Therapy, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Anthony R. Means
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donald P. McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - John W. Scott
- St Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC 3052, Australia
| | - Daniel E. Frigo
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX 77204, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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7
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Gizzio J, Thakur A, Haldane A, Levy RM. Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases. eLife 2022; 11:83368. [PMID: 36562610 PMCID: PMC9822262 DOI: 10.7554/elife.83368] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022] Open
Abstract
Inactive conformations of protein kinase catalytic domains where the DFG motif has a "DFG-out" orientation and the activation loop is folded present a druggable binding pocket that is targeted by FDA-approved 'type-II inhibitors' in the treatment of cancers. Tyrosine kinases (TKs) typically show strong binding affinity with a wide spectrum of type-II inhibitors while serine/threonine kinases (STKs) usually bind more weakly which we suggest here is due to differences in the folded to extended conformational equilibrium of the activation loop between TKs vs. STKs. To investigate this, we use sequence covariation analysis with a Potts Hamiltonian statistical energy model to guide absolute binding free-energy molecular dynamics simulations of 74 protein-ligand complexes. Using the calculated binding free energies together with experimental values, we estimated free-energy costs for the large-scale (~17-20 Å) conformational change of the activation loop by an indirect approach, circumventing the very challenging problem of simulating the conformational change directly. We also used the Potts statistical potential to thread large sequence ensembles over active and inactive kinase states. The structure-based and sequence-based analyses are consistent; together they suggest TKs evolved to have free-energy penalties for the classical 'folded activation loop' DFG-out conformation relative to the active conformation, that is, on average, 4-6 kcal/mol smaller than the corresponding values for STKs. Potts statistical energy analysis suggests a molecular basis for this observation, wherein the activation loops of TKs are more weakly 'anchored' against the catalytic loop motif in the active conformation and form more stable substrate-mimicking interactions in the inactive conformation. These results provide insights into the molecular basis for the divergent functional properties of TKs and STKs, and have pharmacological implications for the target selectivity of type-II inhibitors.
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Affiliation(s)
- Joan Gizzio
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, United States.,Department of Chemistry, Temple University, Philadelphia, United States
| | - Abhishek Thakur
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, United States.,Department of Chemistry, Temple University, Philadelphia, United States
| | - Allan Haldane
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, United States.,Department of Physics, Temple University, Philadelphia, United States
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, United States.,Department of Chemistry, Temple University, Philadelphia, United States
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8
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Jaiswal E, Globisch C, Jain A. Knowledge-driven design and optimization of potent symmetric anticancer molecules: A case study on PKM2 activators. Comput Biol Med 2022; 151:106313. [PMID: 36450217 DOI: 10.1016/j.compbiomed.2022.106313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/18/2022] [Accepted: 11/13/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Pyruvate kinase M2 (PKM2) is preferentially expressed as a low-activity dimer over the active tetramer in proliferating tumor cells, resulting in metabolic reprogramming to achieve high energy requirements and nutrient uptake. This leads to a shift from the normal glycolytic pathway causing tumor cells to proliferate uncontrollably. This study utilizes knowledge-based drug discovery to determine the critical features from experimentally known PKM2 activators and design compounds that would significantly confer a stable structural and functional edge over the known compounds which are still at the preclinical stage. METHODS Conscientious molecular modeling studies were carried out and critical structural features were identified and validated from the knowledge of experimentally known PKM2 activators to confer high-binding affinities. A virtual library of 200 palindromic and non-palindromic activators was designed based on these identified critical features to target a distinct activator binding-site. This binding would favor specific dimer-dimer association and subsequent protein tetramerization. The resultant compounds strongly correlated with identified structural features and binding affinities which further strengthened our findings. The designed activators were then subjected to pharmacokinetic profiling and toxicity prediction, followed by free-binding energy calculations and MD simulations. RESULTS All the virtually designed activators comprising the identified critical features were observed to confer high-binding affinities ranging from -9.1 to -15.0 kcal/mol to the receptor protein. The designed activators also demonstrated optimum pharmacokinetic and toxicity profiles. CONCLUSION The best activators selected for MD simulations studies were conclusively observed to stabilize the required tetrameric conformation suggesting that these activators could potentially target PKM2 tetramerization that might restore the normal glycolytic pathway and suppress tumor progression.
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Affiliation(s)
- Eshika Jaiswal
- Department of Bioengineering and Biotechnology, Birla Institute of Technology Mesra, Ranchi, 835215, Jharkhand, India
| | | | - Alok Jain
- Department of Bioengineering and Biotechnology, Birla Institute of Technology Mesra, Ranchi, 835215, Jharkhand, India.
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9
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Arter C, Trask L, Ward S, Yeoh S, Bayliss R. Structural features of the protein kinase domain and targeted binding by small-molecule inhibitors. J Biol Chem 2022; 298:102247. [PMID: 35830914 PMCID: PMC9382423 DOI: 10.1016/j.jbc.2022.102247] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are key components in cellular signaling pathways as they carry out the phosphorylation of proteins, primarily on Ser, Thr, and Tyr residues. The catalytic activity of protein kinases is regulated, and they can be thought of as molecular switches that are controlled through protein-protein interactions and post-translational modifications. Protein kinases exhibit diverse structural mechanisms of regulation and have been fascinating subjects for structural biologists from the first crystal structure of a protein kinase over 30 years ago, to recent insights into kinase assemblies enabled by the breakthroughs in cryo-EM. Protein kinases are high-priority targets for drug discovery in oncology and other disease settings, and kinase inhibitors have transformed the outcomes of specific groups of patients. Most kinase inhibitors are ATP competitive, deriving potency by occupying the deep hydrophobic pocket at the heart of the kinase domain. Selectivity of inhibitors depends on exploiting differences between the amino acids that line the ATP site and exploring the surrounding pockets that are present in inactive states of the kinase. More recently, allosteric pockets outside the ATP site are being targeted to achieve high selectivity and to overcome resistance to current therapeutics. Here, we review the key regulatory features of the protein kinase family, describe the different types of kinase inhibitors, and highlight examples where the understanding of kinase regulatory mechanisms has gone hand in hand with the development of inhibitors.
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Affiliation(s)
- Chris Arter
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Engineering and Physical Sciences, School of Chemistry, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Luke Trask
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Engineering and Physical Sciences, School of Chemistry, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sarah Ward
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Engineering and Physical Sciences, School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Sharon Yeoh
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.
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10
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Andrianov GV, Ong WJG, Serebriiskii I, Karanicolas J. Efficient Hit-to-Lead Searching of Kinase Inhibitor Chemical Space via Computational Fragment Merging. J Chem Inf Model 2021; 61:5967-5987. [PMID: 34762402 PMCID: PMC8865965 DOI: 10.1021/acs.jcim.1c00630] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In early-stage drug discovery, the hit-to-lead optimization (or "hit expansion") stage entails starting from a newly identified active compound and improving its potency or other properties. Traditionally, this process relies on synthesizing and evaluating a series of analogues to build up structure-activity relationships. Here, we describe a computational strategy focused on kinase inhibitors, intended to expedite the process of identifying analogues with improved potency. Our protocol begins from an inhibitor of the target kinase and generalizes the synthetic route used to access it. By searching for commercially available replacements for the individual building blocks used to make the parent inhibitor, we compile an enumerated library of compounds that can be accessed using the same chemical transformations; these huge libraries can exceed many millions─or billions─of compounds. Because the resulting libraries are much too large for explicit virtual screening, we instead consider alternate approaches to identify the top-scoring compounds. We find that contributions from individual substituents are well described by a pairwise additivity approximation, provided that the corresponding fragments position their shared core in precisely the same way relative to the binding site. This key insight allows us to determine which fragments are suitable for merging into single new compounds and which are not. Further, the use of pairwise approximation allows interaction energies to be assigned to each compound in the library without the need for any further structure-based modeling: interaction energies instead can be reliably estimated from the energies of the component fragments, and the reduced computational requirements allow for flexible energy minimizations that allow the kinase to respond to each substitution. We demonstrate this protocol using libraries built from six representative kinase inhibitors drawn from the literature, which target five different kinases: CDK9, CHK1, CDK2, EGFRT790M, and ACK1. In each example, the enumerated library includes additional analogues reported by the original study to have activity, and these analogues are successfully prioritized within the library. We envision that the insights from this work can facilitate the rapid assembly and screening of increasingly large libraries for focused hit-to-lead optimization. To enable adoption of these methods and to encourage further analyses, we disseminate the computational tools needed to deploy this protocol.
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Affiliation(s)
- Grigorii V. Andrianov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111-2497,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia, 420008
| | - Wern Juin Gabriel Ong
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111-2497,Bowdoin College, Brunswick, ME 04011
| | - Ilya Serebriiskii
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111-2497,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia, 420008
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111-2497,To whom correspondence should be addressed. , 215-728-7067
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11
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Inhibition of protein kinases by proton pump inhibitors: computational screening and in vitro evaluation. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02812-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Eduful B, O’Byrne SN, Temme L, Asquith CR, Liang Y, Picado A, Pilotte JR, Hossain MA, Wells CI, Zuercher WJ, Catta-Preta CMC, Zonzini Ramos P, Santiago AD, Couñago RM, Langendorf CG, Nay K, Oakhill JS, Pulliam TL, Lin C, Awad D, Willson TM, Frigo DE, Scott JW, Drewry DH. Hinge Binder Scaffold Hopping Identifies Potent Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2) Inhibitor Chemotypes. J Med Chem 2021; 64:10849-10877. [PMID: 34264658 PMCID: PMC8365604 DOI: 10.1021/acs.jmedchem.0c02274] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Indexed: 12/18/2022]
Abstract
CAMKK2 is a serine/threonine kinase and an activator of AMPK whose dysregulation is linked with multiple diseases. Unfortunately, STO-609, the tool inhibitor commonly used to probe CAMKK2 signaling, has limitations. To identify promising scaffolds as starting points for the development of high-quality CAMKK2 chemical probes, we utilized a hinge-binding scaffold hopping strategy to design new CAMKK2 inhibitors. Starting from the potent but promiscuous disubstituted 7-azaindole GSK650934, a total of 32 compounds, composed of single-ring, 5,6-, and 6,6-fused heteroaromatic cores, were synthesized. The compound set was specifically designed to probe interactions with the kinase hinge-binding residues. Compared to GSK650394 and STO-609, 13 compounds displayed similar or better CAMKK2 inhibitory potency in vitro, while compounds 13g and 45 had improved selectivity for CAMKK2 across the kinome. Our systematic survey of hinge-binding chemotypes identified several potent and selective inhibitors of CAMKK2 to serve as starting points for medicinal chemistry programs.
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Affiliation(s)
- Benjamin
J. Eduful
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sean N. O’Byrne
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Louisa Temme
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Christopher R.
M. Asquith
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department
of Pharmacology, School of Medicine, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yi Liang
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alfredo Picado
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joseph R. Pilotte
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mohammad Anwar Hossain
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Carrow I. Wells
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William J. Zuercher
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Carolina M. C. Catta-Preta
- Centro
de Química Medicinal (CQMED), Centro de Biologia Molecular
e Engenharia Genética (CBMEG), Universidade
Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-875, Brazil
- Structural
Genomics Consortium, Departamento de Genética e Evolução,
Instituto de Biologia, UNICAMP, Campinas, São Paulo 13083-886, Brazil
| | - Priscila Zonzini Ramos
- Centro
de Química Medicinal (CQMED), Centro de Biologia Molecular
e Engenharia Genética (CBMEG), Universidade
Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-875, Brazil
- Structural
Genomics Consortium, Departamento de Genética e Evolução,
Instituto de Biologia, UNICAMP, Campinas, São Paulo 13083-886, Brazil
| | - André de
S. Santiago
- Centro
de Química Medicinal (CQMED), Centro de Biologia Molecular
e Engenharia Genética (CBMEG), Universidade
Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-875, Brazil
- Structural
Genomics Consortium, Departamento de Genética e Evolução,
Instituto de Biologia, UNICAMP, Campinas, São Paulo 13083-886, Brazil
| | - Rafael M. Couñago
- Centro
de Química Medicinal (CQMED), Centro de Biologia Molecular
e Engenharia Genética (CBMEG), Universidade
Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-875, Brazil
- Structural
Genomics Consortium, Departamento de Genética e Evolução,
Instituto de Biologia, UNICAMP, Campinas, São Paulo 13083-886, Brazil
| | - Christopher G. Langendorf
- St
Vincent’s Institute and Department of Medicine, The University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Australia
| | - Kévin Nay
- St
Vincent’s Institute and Department of Medicine, The University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Australia
- Mary MacKillop
Institute for Health Research, Australian
Catholic University, 215 Spring Street, Melbourne 3000, Australia
| | - Jonathan S. Oakhill
- St
Vincent’s Institute and Department of Medicine, The University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Australia
- Mary MacKillop
Institute for Health Research, Australian
Catholic University, 215 Spring Street, Melbourne 3000, Australia
| | - Thomas L. Pulliam
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- Center
for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas 77204, United States
- Department
of Biology and Biochemistry, University
of Houston, Houston, Texas 77204, United
States
| | - Chenchu Lin
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- The University of Texas MD Anderson Cancer Center UTHealth
Graduate
School of Biomedical Sciences, Houston, Texas 77030, United States
| | - Dominik Awad
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- The University of Texas MD Anderson Cancer Center UTHealth
Graduate
School of Biomedical Sciences, Houston, Texas 77030, United States
| | - Timothy M. Willson
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel E. Frigo
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- Center
for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas 77204, United States
- Department
of Biology and Biochemistry, University
of Houston, Houston, Texas 77204, United
States
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- The Methodist Hospital Research Institute, Houston, Texas 77030, United States
| | - John W. Scott
- St
Vincent’s Institute and Department of Medicine, The University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Australia
- Mary MacKillop
Institute for Health Research, Australian
Catholic University, 215 Spring Street, Melbourne 3000, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, Parkville 3052, Australia
| | - David H. Drewry
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger Comprehensive Cancer Center,
UNC Eshelman School of
Pharmacy, University of North Carolina at
Chapel Hill, Chapel Hill, North Carolina 27599, United States
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13
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Wlodarchak N, Feltenberger JB, Ye Z, Beczkiewicz J, Procknow R, Yan G, King TM, Golden JE, Striker R. Engineering Selectivity for Reduced Toxicity of Bacterial Kinase Inhibitors Using Structure-Guided Medicinal Chemistry. ACS Med Chem Lett 2021; 12:228-235. [PMID: 35035774 PMCID: PMC8757511 DOI: 10.1021/acsmedchemlett.0c00580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/08/2021] [Indexed: 01/15/2023] Open
Abstract
![]()
Tuberculosis is a
major global public health concern, and new drugs
are needed to combat both the typical form and the increasingly common
drug-resistant form of this disease. The essential tuberculosis kinase
PknB is an attractive drug development target because of its central
importance in several critical signaling cascades. A major hurdle
in kinase inhibitor development is the reduction of toxicity due to
nonspecific kinase activity in host cells. Here a novel class of PknB
inhibitors was developed from hit aminopyrimidine 1 (GW779439X),
which was originally designed for human CDK4 but failed to progress
clinically because of high toxicity and low specificity. Replacing
the pyrazolopyridazine headgroup of the original hit with substituted
pyridine or phenyl headgroups resulted in a reduction of Cdk activity
and a 3-fold improvement in specificity over the human kinome while
maintaining PknB activity. This also resulted in improved microbiological
activity and reduced toxicity in THP-1 cells and zebrafish.
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Affiliation(s)
- Nathan Wlodarchak
- William S. Middleton Veterans Hospital, 2500 Overlook Terrace, Madison, Wisconsin 53705, United States.,Department of Medicine, University of Wisconsin-Madison, 1550 Linden Drive, Madison, Wisconsin 53706, United States
| | - John B Feltenberger
- University of Wisconsin-Madison Medicinal Chemistry Center, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Zhengqing Ye
- University of Wisconsin-Madison Medicinal Chemistry Center, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Jeffrey Beczkiewicz
- Department of Medicine, University of Wisconsin-Madison, 1550 Linden Drive, Madison, Wisconsin 53706, United States
| | - Rebecca Procknow
- Department of Medicine, University of Wisconsin-Madison, 1550 Linden Drive, Madison, Wisconsin 53706, United States
| | - Gang Yan
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Troy M King
- Department of Medicine, University of Wisconsin-Madison, 1550 Linden Drive, Madison, Wisconsin 53706, United States
| | - Jennifer E Golden
- University of Wisconsin-Madison Medicinal Chemistry Center, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States.,Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Rob Striker
- William S. Middleton Veterans Hospital, 2500 Overlook Terrace, Madison, Wisconsin 53705, United States.,Department of Medicine, University of Wisconsin-Madison, 1550 Linden Drive, Madison, Wisconsin 53706, United States
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14
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Munni YA, Ali MC, Selsi NJ, Sultana M, Hossen M, Bipasha TH, Rahman M, Uddin MN, Hosen SMZ, Dash R. Molecular simulation studies to reveal the binding mechanisms of shikonin derivatives inhibiting VEGFR-2 kinase. Comput Biol Chem 2020; 90:107414. [PMID: 33191109 DOI: 10.1016/j.compbiolchem.2020.107414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/17/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022]
Abstract
Traditional vascular endothelial growth factor receptor 2 (VEGFR-2) inhibitors can manage angiogenesis; however, severe toxicity and resistance limit their long-term applications in clinical therapy. Shikonin (SHK) and its derivatives could be promising to inhibit the VEGFR-2 mediated angiogenesis, as they are reported to bind in the catalytic kinase domain with low affinity. However, the detailed molecular insights and binding dynamics of these natural inhibitors are unknown, which is crucial for potential SHK based lead design. Therefore, the present study employed molecular modeling and simulations techniques to get insight into the binding behaviors of SHK and its two derivates, β-hydroxyisovalerylshikonin (β-HIVS) and acetylshikonin (ACS). Here the intermolecular interactions between protein and ligands were studied by induced fit docking approach, which were further evaluated by treating QM/MM (quantum mechanics/molecular mechanics) and molecular dynamics (MD) simulation. The result showed that the naphthazarin ring of the SHK derivates is vital for strong binding to the catalytic domain; however, the binding stability can be modulated by the side chain modification. Because of having electrostatic potential, this ring makes essential interactions with the DFG (Asp1046 and Phe1047) motif and also allows interacting with the allosteric binding site. Taken together, the studies will advance our knowledge and scope for the development of new selective VEGFR-2 inhibitors based on SHK and its analogs.
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Affiliation(s)
- Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
| | - Md Chayan Ali
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh.
| | - Nusrat Jahan Selsi
- Department of Pharmacy, University of Science & Technology, Chittagong, 4202, Bangladesh.
| | - Marium Sultana
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Md Hossen
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Tanjiba Harun Bipasha
- Department of Pharmacy, University of Science & Technology, Chittagong, 4202, Bangladesh.
| | - Mahbubur Rahman
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Md Nazim Uddin
- Department of Pharmacy, Southern University Bangladesh, Chittagong, 4000, Bangladesh.
| | - S M Zahid Hosen
- Pancreatic Research Group, South Western Sydney Clinical School, University of New South Wales, and Ingham Institute for Applied Medical Research, Liverpool, NSW, 2170, Australia.
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
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15
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O’Byrne SN, Eduful BJ, Willson TM, Drewry DH. Concise, gram-scale synthesis of furo[2,3- b]pyridines with functional handles for chemoselective cross-coupling. Tetrahedron Lett 2020; 61:152353. [PMID: 33012852 PMCID: PMC7526865 DOI: 10.1016/j.tetlet.2020.152353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A concise 4-step synthesis of furo[2,3-b]pyridines, with handles in the 3- and 5-positions for palladium mediated cross-coupling reactions, is described. The synthetic route has been optimized, with only one step requiring purification by column chromatography. The route is amenable to scale-up, and was successfully executed on a multi-gram scale. Furopyridines are of growing interest in medicinal chemistry, and this route should enable easy access to the core for structure-activity relationship (SAR) studies.
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Affiliation(s)
- Sean N. O’Byrne
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin J. Eduful
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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16
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Zheng Z, Borbulevych OY, Liu H, Deng J, Martin RI, Westerhoff LM. MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment. J Chem Inf Model 2020; 60:5437-5456. [PMID: 32791826 PMCID: PMC7781189 DOI: 10.1021/acs.jcim.0c00618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
For decades, the
complicated energy surfaces found in macromolecular
protein:ligand structures, which require large amounts of computational
time and resources for energy state sampling, have been an inherent
obstacle to fast, routine free energy estimation in industrial drug
discovery efforts. Beginning in 2013, the Merz research group addressed
this cost with the introduction of a novel sampling methodology termed
“Movable Type” (MT). Using numerical integration methods,
the MT method reduces the computational expense for energy state sampling
by independently calculating each atomic partition function from an
initial molecular conformation in order to estimate the molecular
free energy using ensembles of the atomic partition functions. In
this work, we report a software package, the DivCon Discovery Suite
with the MovableType module from QuantumBio Inc., that performs this
MT free energy estimation protocol in a fast, fully encapsulated manner.
We discuss the computational procedures and improvements to the original
work, and we detail the corresponding settings for this software package.
Finally, we introduce two validation benchmarks to evaluate the overall
robustness of the method against a broad range of protein:ligand structural
cases. With these publicly available benchmarks, we show that the
method can use a variety of input types and parameters and exhibits
comparable predictability whether the method is presented with “expensive”
X-ray structures or “inexpensively docked” theoretical
models. We also explore some next steps for the method. The MovableType
software is available at http://www.quantumbioinc.com/
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Affiliation(s)
- Zheng Zheng
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Oleg Y Borbulevych
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
| | - Hao Liu
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Jianpeng Deng
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Roger I Martin
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
| | - Lance M Westerhoff
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
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17
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Mahindra A, Janha O, Mapesa K, Sanchez-Azqueta A, Alam MM, Amambua-Ngwa A, Nwakanma DC, Tobin AB, Jamieson AG. Development of Potent PfCLK3 Inhibitors Based on TCMDC-135051 as a New Class of Antimalarials. J Med Chem 2020; 63:9300-9315. [PMID: 32787140 PMCID: PMC7497403 DOI: 10.1021/acs.jmedchem.0c00451] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Indexed: 12/20/2022]
Abstract
The protein kinase PfCLK3 plays a critical role in the regulation of malarial parasite RNA splicing and is essential for the survival of blood stage Plasmodium falciparum. We recently validated PfCLK3 as a drug target in malaria that offers prophylactic, transmission blocking, and curative potential. Herein, we describe the synthesis of our initial hit TCMDC-135051 (1) and efforts to establish a structure-activity relationship with a 7-azaindole-based series. A total of 14 analogues were assessed in a time-resolved fluorescence energy transfer assay against the full-length recombinant protein kinase PfCLK3, and 11 analogues were further assessed in asexual 3D7 (chloroquine-sensitive) strains of P. falciparum parasites. SAR relating to rings A and B was established. These data together with analysis of activity against parasites collected from patients in the field suggest that TCMDC-135051 (1) is a promising lead compound for the development of new antimalarials with a novel mechanism of action targeting PfCLK3.
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Affiliation(s)
- Amit Mahindra
- School
of Chemistry, University of Glasgow, Joseph Black Building, University
Avenue, Glasgow G12 8QQ, U.K.
| | - Omar Janha
- Centre
for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, University of Glasgow, Davidson Building, Glasgow G12 8QQ, U.K.
| | - Kopano Mapesa
- School
of Chemistry, University of Glasgow, Joseph Black Building, University
Avenue, Glasgow G12 8QQ, U.K.
| | - Ana Sanchez-Azqueta
- Centre
for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, University of Glasgow, Davidson Building, Glasgow G12 8QQ, U.K.
| | - Mahmood M. Alam
- Wellcome
Centre for Integrative Parasitology and Centre for Translational Pharmacology,
Institute of Infection Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, U.K.
| | - Alfred Amambua-Ngwa
- MRC
Unit The Gambia at LSHTM, Atlantic Boulevard,
Fajara, P. O. Box 273, Banjul, The Gambia
| | - Davis C. Nwakanma
- MRC
Unit The Gambia at LSHTM, Atlantic Boulevard,
Fajara, P. O. Box 273, Banjul, The Gambia
| | - Andrew B. Tobin
- Centre
for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, University of Glasgow, Davidson Building, Glasgow G12 8QQ, U.K.
| | - Andrew G. Jamieson
- School
of Chemistry, University of Glasgow, Joseph Black Building, University
Avenue, Glasgow G12 8QQ, U.K.
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18
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Liu K, Kokubo H. Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations. J Comput Aided Mol Des 2020; 34:1195-1205. [DOI: 10.1007/s10822-020-00340-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 08/21/2020] [Indexed: 01/18/2023]
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19
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Vásquez AF, Reyes Muñoz A, Duitama J, González Barrios A. Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products. J Biomol Struct Dyn 2020; 39:3285-3299. [DOI: 10.1080/07391102.2020.1763839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrés Felipe Vásquez
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Reyes Muñoz
- Grupo de Biología Computacional Ecología Microbiana (BCEM), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
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20
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Brys R, Gibson K, Poljak T, Van Der Plas S, Amantini D. Discovery and development of ASK1 inhibitors. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:101-179. [PMID: 32362327 DOI: 10.1016/bs.pmch.2020.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aberrant activation of mitogen-activated protein kinases (MAPKs) like c-Jun N-terminal kinase (JNK) and p38 is an event involved in the pathophysiology of numerous human diseases. The apoptosis signal-regulating kinase 1 (ASK1) is an upstream target that gets activated only under pathological conditions and as such is a promising target for therapeutic intervention. In the first part of this review the molecular mechanisms leading to ASK1 activation and regulation will be described as well as the evidences supporting a pathogenic role for ASK1 in human disease. In the second part, an update on drug discovery efforts towards the discovery and development of ASK1-targeting therapies will be provided.
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Affiliation(s)
| | - Karl Gibson
- Sandexis Medicinal Chemistry Ltd, Innovation House Discovery ParkSandwich, Kent, United Kingdom
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21
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Dash R, Arifuzzaman M, Mitra S, Abdul Hannan M, Absar N, Hosen SMZ. Unveiling the Structural Insights into the Selective Inhibition of Protein Kinase D1. Curr Pharm Des 2020; 25:1059-1074. [PMID: 31131745 DOI: 10.2174/1381612825666190527095510] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 05/14/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Although protein kinase D1 (PKD1) has been proved to be an efficient target for anticancer drug development, lack of structural details and substrate binding mechanisms are the main obstacles for the development of selective inhibitors with therapeutic benefits. OBJECTIVE The present study described the in silico dynamics behaviors of PKD1 in binding with selective and non-selective inhibitors and revealed the critical binding site residues for the selective kinase inhibition. METHODS Here, the three dimensional model of PKD1 was initially constructed by homology modeling along with binding site characterization to explore the non-conserved residues. Subsequently, two known inhibitors were docked to the catalytic site and the detailed ligand binding mechanisms and post binding dyanmics were investigated by molecular dynamics simulation and binding free energy calculations. RESULTS According to the binding site analysis, PKD1 serves several non-conserved residues in the G-loop, hinge and catalytic subunits. Among them, the residues including Leu662, His663, and Asp665 from hinge region made polar interactions with selective PKD1 inhibitor in docking simulation, which were further validated by the molecular dynamics simulation. Both inhibitors strongly influenced the structural dynamics of PKD1 and their computed binding free energies were in accordance with experimental bioactivity data. CONCLUSION The identified non-conserved residues likely to play critical role on molecular reorganization and inhibitor selectivity. Taken together, this study explained the molecular basis of PKD1 specific inhibition, which may help to design new selective inhibitors for better therapies to overcome cancer and PKD1 dysregulated disorders.
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Affiliation(s)
- Raju Dash
- Department of Biochemistry and Biotechnology, University of Science and Technology, Chittagong-4202, Bangladesh.,Molecular Modeling and Drug Design Laboratory, Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research, Chittagong-4220, Bangladesh.,Department of Anatomy, Dongguk University Graduate School of Medicine, Gyeongju 38066, Korea
| | - Md Arifuzzaman
- College of Pharmacy, Yeungnam University, Gyeongsan-38541, Korea
| | - Sarmistha Mitra
- Plasma Bioscience Research Center, Plasma-bio display, Kwangwoon University, Seoul, 01897, Korea
| | - Md Abdul Hannan
- Department of Anatomy, Dongguk University Graduate School of Medicine, Gyeongju 38066, Korea.,Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Nurul Absar
- Department of Biochemistry and Biotechnology, University of Science and Technology, Chittagong-4202, Bangladesh
| | - S M Zahid Hosen
- Molecular Modeling and Drug Design Laboratory, Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research, Chittagong-4220, Bangladesh
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22
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O’Byrne SN, Scott JW, Pilotte JR, Santiago ADS, Langendorf CG, Oakhill JS, Eduful BJ, Couñago RM, Wells CI, Zuercher WJ, Willson TM, Drewry DH. In Depth Analysis of Kinase Cross Screening Data to Identify CAMKK2 Inhibitory Scaffolds. Molecules 2020; 25:E325. [PMID: 31941153 PMCID: PMC7024175 DOI: 10.3390/molecules25020325] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/25/2022] Open
Abstract
The calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) activates CAMK1, CAMK4, AMPK, and AKT, leading to numerous physiological responses. The deregulation of CAMKK2 is linked to several diseases, suggesting the utility of CAMKK2 inhibitors for oncological, metabolic and inflammatory indications. In this work, we demonstrate that STO-609, frequently described as a selective inhibitor for CAMKK2, potently inhibits a significant number of other kinases. Through an analysis of literature and public databases, we have identified other potent CAMKK2 inhibitors and verified their activities in differential scanning fluorimetry and enzyme inhibition assays. These inhibitors are potential starting points for the development of selective CAMKK2 inhibitors and will lead to tools that delineate the roles of this kinase in disease biology.
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Affiliation(s)
- Sean N. O’Byrne
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.N.O.); (J.R.P.); (B.J.E.); (C.I.W.); (W.J.Z.); (T.M.W.)
| | - John W. Scott
- St Vincent’s Institute and Department of Medicine, The University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Australia; (J.W.S.); (C.G.L.); (J.S.O.)
- Mary MacKillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne 3000, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, Parkville 3052, Australia
| | - Joseph R. Pilotte
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.N.O.); (J.R.P.); (B.J.E.); (C.I.W.); (W.J.Z.); (T.M.W.)
| | - André da S. Santiago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas SP 13083-875, Brazil; (A.d.S.S.); (R.M.C.)
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas SP 13083-886, Brazil
| | - Christopher G. Langendorf
- St Vincent’s Institute and Department of Medicine, The University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Australia; (J.W.S.); (C.G.L.); (J.S.O.)
| | - Jonathan S. Oakhill
- St Vincent’s Institute and Department of Medicine, The University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Australia; (J.W.S.); (C.G.L.); (J.S.O.)
- Mary MacKillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne 3000, Australia
| | - Benjamin J. Eduful
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.N.O.); (J.R.P.); (B.J.E.); (C.I.W.); (W.J.Z.); (T.M.W.)
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas SP 13083-875, Brazil; (A.d.S.S.); (R.M.C.)
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas SP 13083-886, Brazil
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.N.O.); (J.R.P.); (B.J.E.); (C.I.W.); (W.J.Z.); (T.M.W.)
| | - William J. Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.N.O.); (J.R.P.); (B.J.E.); (C.I.W.); (W.J.Z.); (T.M.W.)
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.N.O.); (J.R.P.); (B.J.E.); (C.I.W.); (W.J.Z.); (T.M.W.)
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.N.O.); (J.R.P.); (B.J.E.); (C.I.W.); (W.J.Z.); (T.M.W.)
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23
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Belasri K, Fülöp F, Szatmári I. Solvent-Free C-3 Coupling of Azaindoles with Cyclic Imines. Molecules 2019; 24:molecules24193578. [PMID: 31590280 PMCID: PMC6803843 DOI: 10.3390/molecules24193578] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/26/2019] [Accepted: 10/02/2019] [Indexed: 12/17/2022] Open
Abstract
By direct coupling 7-azaindole and cyclic imines, such as 3,4-dihydroisoquinoline, 6,7-dihydrothieno[3,2-c]pyridine, 3,4-dihydro-β-carboline, and 4,5-dihydro-3H-benz[c]azepine, new 3-substituted 7-azaindole derivatives have been synthesized. The reaction was extended to 4-azaindoles and 6-azaindoles, as electron-rich aromatic compounds. The lowest reactivity was observed in the case of C-3 substitution of 5-azaindole. In this case, the aza-Friedel-Crafts reaction took place by using 10 mol % of p-toluenesulfonic acid (p-TSA) as the catalyst. The role of the acid catalyst can be explained by the different pKa values of the azaindoles. All reactions were performed in solvent-free conditions by using both classical heating and microwave irradiation. In all cases, microwave heating proved to be more convenient to synthesize new C-3-substituted azaindole derivatives.
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Affiliation(s)
- Khadija Belasri
- Institute of Pharmaceutical Chemistry and MTA-SZTE Stereochemistry Research Group, University of Szeged, H-6720 Szeged, Hungary.
- Institute of Pharmaceutical Chemistry, Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary.
| | - Ferenc Fülöp
- Institute of Pharmaceutical Chemistry and MTA-SZTE Stereochemistry Research Group, University of Szeged, H-6720 Szeged, Hungary.
- Institute of Pharmaceutical Chemistry, Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary.
| | - István Szatmári
- Institute of Pharmaceutical Chemistry and MTA-SZTE Stereochemistry Research Group, University of Szeged, H-6720 Szeged, Hungary.
- Institute of Pharmaceutical Chemistry, Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary.
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24
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Ding HW, Wang S, Qin XC, Wang J, Song HR, Zhao QC, Song SJ. Design, synthesis, and biological evaluation of some novel 4-aminoquinazolines as Pan-PI3K inhibitors. Bioorg Med Chem 2019; 27:2729-2740. [DOI: 10.1016/j.bmc.2019.04.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 04/09/2019] [Accepted: 04/16/2019] [Indexed: 02/08/2023]
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25
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Structure-based identification of potent VEGFR-2 inhibitors from in vivo metabolites of a herbal ingredient. J Mol Model 2019; 25:98. [PMID: 30904971 DOI: 10.1007/s00894-019-3979-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/05/2019] [Indexed: 12/22/2022]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2) is one of the regulatory elements of angiogenesis that is expressed highly in various diseases and is also essential for solid tumor growth. The present study was aimed at identifying potent inhibitors of VEGFR-2 by considering herbal secondary metabolites; as natural molecules are less toxic than synthetic derivatives. A structure-based virtual screening protocol consisting of molecular docking, MM-GBSA and ADME/T analysis was initially used to screen a library of in vivo metabolites of the herbal ingredient. Using a fixed cutoff value, four potent virtual hits were identified from molecular docking, ADME/T and binding affinity calculations, which were considered further for molecular dynamics (MD) simulation to broadly describe the binding mechanisms to VEGFR-2. The results suggested that these molecules have high affinity for the catalytic region of VEGFR-2, and form strong hydrophobic and polar interactions with the amino acids involved in the binding site of ATP and linker regions of the catalytic site. Subsequently, the stability of the docked complexes and binding mechanisms were evaluated by MD simulations, and the energy of binding was calculated through MM-PBSA analysis. The results uncovered two virtual hits, designated ZINC14762520 and ZINC36470466, as VEGFR-2 inhibitors, and suggested that they bind to kinase domain in an ATP-competitive manner. These virtual hits will offer a suitable starting point for the further design of their various analogs, allowing a rational search for more effective inhibitors in the future. Graphical abstract.
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26
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Paul A, Edwards J, Pepper C, Mackay S. Inhibitory-κB Kinase (IKK) α and Nuclear Factor-κB (NFκB)-Inducing Kinase (NIK) as Anti-Cancer Drug Targets. Cells 2018; 7:E176. [PMID: 30347849 PMCID: PMC6210445 DOI: 10.3390/cells7100176] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 12/23/2022] Open
Abstract
The cellular kinases inhibitory-κB kinase (IKK) α and Nuclear Factor-κB (NF-κB)-inducing kinase (NIK) are well recognised as key central regulators and drivers of the non-canonical NF-κB cascade and as such dictate the initiation and development of defined transcriptional responses associated with the liberation of p52-RelB and p52-p52 NF-κB dimer complexes. Whilst these kinases and downstream NF-κB complexes transduce pro-inflammatory and growth stimulating signals that contribute to major cellular processes, they also play a key role in the pathogenesis of a number of inflammatory-based conditions and diverse cancer types, which for the latter may be a result of background mutational status. IKKα and NIK, therefore, represent attractive targets for pharmacological intervention. Here, specifically in the cancer setting, we reflect on the potential pathophysiological role(s) of each of these kinases, their associated downstream signalling outcomes and the stimulatory and mutational mechanisms leading to their increased activation. We also consider the downstream coordination of transcriptional events and phenotypic outcomes illustrative of key cancer 'Hallmarks' that are now increasingly perceived to be due to the coordinated recruitment of both NF-κB-dependent as well as NF-κB⁻independent signalling. Furthermore, as these kinases regulate the transition from hormone-dependent to hormone-independent growth in defined tumour subsets, potential tumour reactivation and major cytokine and chemokine species that may have significant bearing upon tumour-stromal communication and tumour microenvironment it reiterates their potential to be drug targets. Therefore, with the emergence of small molecule kinase inhibitors targeting each of these kinases, we consider medicinal chemistry efforts to date and those evolving that may contribute to the development of viable pharmacological intervention strategies to target a variety of tumour types.
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Affiliation(s)
- Andrew Paul
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161 Cathedral Street, University of Strathclyde, Glasgow G4 0NR, UK.
| | - Joanne Edwards
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK.
| | - Christopher Pepper
- Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK.
| | - Simon Mackay
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161 Cathedral Street, University of Strathclyde, Glasgow G4 0NR, UK.
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27
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Raheel A, Imtiaz-ud-Din, Taj MB, Tahir MN, Al-Shakban M. Synthesis, Structures, and Molecular Docking of Some Bioactive Benzamide Derivatives as Ionic Solids. RUSS J GEN CHEM+ 2018. [DOI: 10.1134/s1070363218070253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Irie T, Sawa M. 7-Azaindole: A Versatile Scaffold for Developing Kinase Inhibitors. Chem Pharm Bull (Tokyo) 2018; 66:29-36. [DOI: 10.1248/cpb.c17-00380] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Masaaki Sawa
- Research and Development, Carna Biosciences, Inc
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29
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Rational approach to highly potent and selective apoptosis signal-regulating kinase 1 (ASK1) inhibitors. Eur J Med Chem 2017; 145:606-621. [PMID: 29348070 DOI: 10.1016/j.ejmech.2017.12.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 11/21/2022]
Abstract
Many diseases are believed to be driven by pathological levels of reactive oxygen species (ROS) and oxidative stress has long been recognized as a driver for inflammatory disorders. Apoptosis signal-regulating kinase 1 (ASK1) has been reported to be activated by intracellular ROS and its inhibition leads to a down regulation of p38-and JNK-dependent signaling. Consequently, ASK1 inhibitors may have the potential to treat clinically important inflammatory pathologies including renal, pulmonary and liver diseases. Analysis of the ASK1 ATP-binding site suggested that Gln756, an amino acid that rarely occurs at the GK+2 position, offered opportunities for achieving kinase selectivity for ASK1 which was applied to the design of a parallel medicinal chemistry library that afforded inhibitors of ASK1 with nanomolar potency and excellent kinome selectivity. A focused optimization strategy utilizing structure-based design resulted in the identification of ASK1 inhibitors with low nanomolar potency in a cellular assay, high selectivity when tested against kinase and broad pharmacology screening panels, and attractive physicochemical properties. The compounds we describe are attractive tool compounds to inform the therapeutic potential of ASK1 inhibition.
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30
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Jiang MN, Zhou XP, Sun DR, Gao H, Zheng QC, Zhang HX, Liang D. 2D-QSAR study, molecular docking, and molecular dynamics simulation studies of interaction mechanism between inhibitors and transforming growth factor-beta receptor I (ALK5). J Biomol Struct Dyn 2017; 36:3705-3717. [PMID: 29064324 DOI: 10.1080/07391102.2017.1396256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Transforming growth factor type 1 receptor (ALK5) is kinase associated with a wide variety of pathological processes, and inhibition of ALK5 is a good strategy to treat many kinds of cancer and fibrotic diseases. Recently, a series of compounds have been synthesized as ALK5 inhibitors. However, the study of their selectivity against other potential targets remains elusive. In this research, a data-set of ALK5 inhibitors were collected and studied based on the combination of 2D-QSAR, molecular docking and molecular dynamics simulation. The quality of QSAR models were assessed statistically by F, R2, and R2ADJ, proved to be credible. The cross-validations for the models (q2LOO = 0.571 and 0.629, respectively) showed their robustness, while the external validations (r2test = 0.703 and 0.764, respectively) showed their predictive power. Besides, the predicted binding free energy results calculated by MM/GBSA method were in accordance with the experimental data, and the van der Waals energy term was the factor that had the most significant impact on ligand binding. What is more, several important residues were found to significantly affect the binding affinity. Finally, based on our analyses above, a proposed series of molecules were designed.
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Key Words
- , Molecular Mechanics/Generalized Born Surface Area
- , general Amber force field
- , leave-one-out
- , molecular dynamics
- , partial least square analysis
- , particle mesh Ewald
- , quantitative structure–activity relationship
- , root-mean-square deviation
- , root-mean-square fluctuation
- , transforming growth factor beta
- , transforming growth factor beta type I receptor
- 2D-QSAR
- ALK5
- MM/GBSA calculation
- molecular dynamics simulation
- small molecule inhibitor
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Affiliation(s)
- Meng-Nan Jiang
- a School of Pharmaceutical Sciences , Jilin University , Changchun , People's Republic of China
| | - Xiao-Ping Zhou
- a School of Pharmaceutical Sciences , Jilin University , Changchun , People's Republic of China
| | - Dong-Ru Sun
- b Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun , People's Republic of China
| | - Huan Gao
- a School of Pharmaceutical Sciences , Jilin University , Changchun , People's Republic of China
| | - Qing-Chuan Zheng
- b Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun , People's Republic of China
| | - Hong-Xing Zhang
- a School of Pharmaceutical Sciences , Jilin University , Changchun , People's Republic of China.,b Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun , People's Republic of China
| | - Di Liang
- a School of Pharmaceutical Sciences , Jilin University , Changchun , People's Republic of China.,b Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun , People's Republic of China
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31
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Wang Y, Sun Y, Cao R, Liu D, Xie Y, Li L, Qi X, Huang N. In Silico Identification of a Novel Hinge-Binding Scaffold for Kinase Inhibitor Discovery. J Med Chem 2017; 60:8552-8564. [PMID: 28945083 DOI: 10.1021/acs.jmedchem.7b01075] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To explore novel kinase hinge-binding scaffolds, we carried out structure-based virtual screening against p38α MAPK as a model system. With the assistance of developed kinase-specific structural filters, we identify a novel lead compound that selectively inhibits a panel of kinases with threonine as the gatekeeper residue, including BTK and LCK. These kinases play important roles in lymphocyte activation, which encouraged us to design novel kinase inhibitors as drug candidates for ameliorating inflammatory diseases and cancers. Therefore, we chemically modified our substituted triazole-class lead compound to improve the binding affinity and selectivity via a "minimal decoration" strategy, which resulted in potent and selective kinase inhibitors against LCK (18 nM) and BTK (8 nM). Subsequent crystallographic experiments validated our design. These rationally designed compounds exhibit potent on-target inhibition against BTK in B cells or LCK in T cells, respectively. Our work demonstrates that structure-based virtual screening can be applied to facilitate the development of novel chemical entities in crowded chemical space in the field of kinase inhibitor discovery.
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Affiliation(s)
- Yanli Wang
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yuze Sun
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ran Cao
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Dan Liu
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yuting Xie
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Li Li
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Xiangbing Qi
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Niu Huang
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
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32
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Anthony NG, Baiget J, Berretta G, Boyd M, Breen D, Edwards J, Gamble C, Gray AI, Harvey AL, Hatziieremia S, Ho KH, Huggan JK, Lang S, Llona-Minguez S, Luo JL, McIntosh K, Paul A, Plevin RJ, Robertson MN, Scott R, Suckling CJ, Sutcliffe OB, Young LC, Mackay SP. Inhibitory Kappa B Kinase α (IKKα) Inhibitors That Recapitulate Their Selectivity in Cells against Isoform-Related Biomarkers. J Med Chem 2017; 60:7043-7066. [PMID: 28737909 PMCID: PMC5578373 DOI: 10.1021/acs.jmedchem.7b00484] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Indexed: 01/01/2023]
Abstract
IKKβ plays a central role in the canonical NF-kB pathway, which has been extensively characterized. The role of IKKα in the noncanonical NF-kB pathway, and indeed in the canonical pathway as a complex with IKKβ, is less well understood. One major reason for this is the absence of chemical tools designed as selective inhibitors for IKKα over IKKβ. Herein, we report for the first time a series of novel, potent, and selective inhibitors of IKKα. We demonstrate effective target engagement and selectivity with IKKα in U2OS cells through inhibition of IKKα-driven p100 phosphorylation in the noncanonical NF-kB pathway without affecting IKKβ-dependent IKappa-Bα loss in the canonical pathway. These compounds represent the first chemical tools that can be used to further characterize the role of IKKα in cellular signaling, to dissect this from IKKβ and to validate it in its own right as a target in inflammatory diseases.
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Affiliation(s)
- Nahoum G. Anthony
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Jessica Baiget
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Giacomo Berretta
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Marie Boyd
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - David Breen
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Joanne Edwards
- Wolfson Wohl Cancer Research Centre, Institute
of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, Scotland, United Kingdom
| | - Carly Gamble
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Alexander I. Gray
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Alan L. Harvey
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Sophia Hatziieremia
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Ka Ho Ho
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Judith K. Huggan
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Stuart Lang
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Sabin Llona-Minguez
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Jia Lin Luo
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Kathryn McIntosh
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Andrew Paul
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Robin J. Plevin
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Murray N. Robertson
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Rebecca Scott
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Colin J. Suckling
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Oliver B. Sutcliffe
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Louise C. Young
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Simon P. Mackay
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
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Discovery of novel furanone derivatives as potent Cdc7 kinase inhibitors. Eur J Med Chem 2017; 130:406-418. [PMID: 28279847 DOI: 10.1016/j.ejmech.2017.02.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/09/2017] [Accepted: 02/11/2017] [Indexed: 11/24/2022]
Abstract
Cdc7 is a serine-threonine kinase and plays a conserved and important role in DNA replication, and it has been recognized as a potential anticancer target. Herein, we report the design, synthesis and structure-activity relationship of novel furanone derivatives as Cdc7 kinase inhibitors. Compound 13 was identified as a strong inhibitor of Cdc7 with an IC50 value of 0.6 nM in the presence of 1 mM ATP and showed excellent kinase selectivity. In addition, it exhibited slow off-rate characteristics, which may offer advantages over known Cdc7 inhibitors in its potential to yield prolonged inhibitory effects in vivo. Compound 13 potently inhibited Cdc7 activity in cancer cells, and effectively induced cell death.
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34
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Lawhorn BG, Philp J, Graves AP, Holt DA, Gatto GJ, Kallander LS. Substituent Effects on Drug–Receptor H-bond Interactions: Correlations Useful for the Design of Kinase Inhibitors. J Med Chem 2016; 59:10629-10641. [DOI: 10.1021/acs.jmedchem.6b01342] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Brian G. Lawhorn
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joanne Philp
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Alan P. Graves
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Dennis A. Holt
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Gregory J. Gatto
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Lara S. Kallander
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
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35
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2-Methyl-4/5-nitroimidazole derivatives potentiated against sexually transmitted Trichomonas: Design, synthesis, biology and 3D-QSAR study. Eur J Med Chem 2016; 124:820-839. [PMID: 27643640 DOI: 10.1016/j.ejmech.2016.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 12/13/2022]
Abstract
Trichomoniasis is the most prevalent, non-viral sexually transmitted diseases (STD) caused by amitochondriate protozoan Trichomonas vaginalis. Increased resistance of T. vaginalis to the marketed drug Metronidazole necessitates the development of newer chemical entities. A library of sixty 2-methyl-4/5-nitroimidazole derivatives was synthesized via nucleophilic ring opening reaction of epoxide and the efficacies against drug-susceptible and -resistant Trichomonas vaginalis were evaluated. All the molecules except two were found to be active against both susceptible and resistant strains with MICs ranging 8.55-336.70 μM and 28.80-1445.08 μM, respectively. Most of the compounds were remarkably more effective than the standard Metronidazole. This study analyzes the in vitro and in vivo activities of the new 5-nitroimidazoles, which were found to be safe against human cervical HeLa cells with good selectivity index. The exploration of SAR by the synthesis of four different prototypes and 3D-QSAR study has shown the importance of prototype 1 over other prototypes.
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36
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5-Substituted 3-chlorokenpaullone derivatives are potent inhibitors of Trypanosoma brucei bloodstream forms. Bioorg Med Chem 2016; 24:3790-800. [DOI: 10.1016/j.bmc.2016.06.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/09/2016] [Accepted: 06/11/2016] [Indexed: 01/31/2023]
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37
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Sun D, Yang Y, Lyu J, Zhou W, Song W, Zhao Z, Chen Z, Xu Y, Li H. Discovery and Rational Design of Pteridin-7(8H)-one-Based Inhibitors Targeting FMS-like Tyrosine Kinase 3 (FLT3) and Its Mutants. J Med Chem 2016; 59:6187-200. [PMID: 27266526 DOI: 10.1021/acs.jmedchem.6b00374] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
FLT3 has been validated as a therapeutic target for the treatment of acute myeloid leukemia (AML). In this paper, we describe for the first time, pteridin-7(8H)-one as a scaffold for potent FLT3 inhibitors derived from structural optimizations on irreversible EGFR inhibitors. The representative inhibitor (31) demonstrates single-digit nanomolar inhibition against FLT3 and subnanomolar KD for drug-resistance FLT3 mutants. In profiling of the in vitro tumor cell lines, it shows good selectivity against AML cells harboring FLT3-ITD mutations over other leukemia and solid tumor cell lines. The mechanism of action study illustrates that pteridin-7(8H)-one derivatives suppress the phosphorylation of FLT3 and its downstream pathways, thereby inducing G0/G1 cell cycle arrest and apoptosis in AML cells. In in vivo studies, 31 significantly suppresses the tumor growth in MV4-11 xenograft model. Overall, we provide a structurally distinct chemical scaffold with which to develop FLT3 mutants-selective inhibitors for AML treatment.
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Affiliation(s)
- Deheng Sun
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology , Shanghai 200237, China
| | - Yu Yang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology , Shanghai 200237, China
| | - Jiankun Lyu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology , Shanghai 200237, China
| | - Wei Zhou
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology , Shanghai 200237, China
| | - Wenlin Song
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology , Shanghai 200237, China
| | - Zhenjiang Zhao
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology , Shanghai 200237, China
| | - Zhuo Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology , Shanghai 200237, China
| | - Yufang Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology , Shanghai 200237, China
| | - Honglin Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology , Shanghai 200237, China
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38
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Koroleva EV, Ignatovich ZI, Sinyutich YV, Gusak KN. Aminopyrimidine derivatives as protein kinases inhibitors. Molecular design, synthesis, and biologic activity. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1070428016020019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Shah S, Lee C, Choi H, Gautam J, Jang H, Kim GJ, Lee YJ, Chaudhary CL, Park SW, Nam TG, Kim JA, Jeong BS. 5-Hydroxy-7-azaindolin-2-one, a novel hybrid of pyridinol and sunitinib: design, synthesis and cytotoxicity against cancer cells. Org Biomol Chem 2016; 14:4829-4841. [DOI: 10.1039/c6ob00406g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Synthesis of a series of hybrid compounds of pyridinol and sunitinib and their cytotoxicity against human cancer cell lines and improved safety windows are described.
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40
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Goldberg FW, Daunt P, Pearson SE, Greenwood R, Grist M, Debreczeni JÉ. Identification and optimisation of a series of N-(4-anilino-2-pyridyl)acetamide activin receptor-like kinase 1 (ALK1) inhibitors. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00039h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A probe compound is described to inhibit ALK1, a target of interest for oncology due to its connection to angiogenesis.
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41
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Kinase hinge binding scaffolds and their hydrogen bond patterns. Bioorg Med Chem 2015; 23:6520-7. [DOI: 10.1016/j.bmc.2015.08.006] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/24/2015] [Accepted: 08/08/2015] [Indexed: 11/20/2022]
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42
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Wu CF, Efferth T. Miltirone Induces G2/M Cell Cycle Arrest and Apoptosis in CCRF-CEM Acute Lymphoblastic Leukemia Cells. JOURNAL OF NATURAL PRODUCTS 2015; 78:1339-1347. [PMID: 26035463 DOI: 10.1021/acs.jnatprod.5b00158] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Miltirone (1) is a diterpene quinone extracted from a well-known Chinese traditional herb (Salvia miltiorrhiza). We investigated the cytotoxic effects of miltirone toward sensitive and multidrug-resistant acute lymphoblastic leukemia cell lines. Miltirone inhibited multidrug-resistant P-glycoprotein (P-gp)-overexpressing CEM/ADR5000 cells better than drug-sensitive CCRF-CEM wild-type cells, a phenomenon termed collateral sensitivity. Flow cytometric analyses revealed that miltirone induced G2/M arrest and apoptosis. Furthermore, miltirone stimulated reactive oxygen species (ROS) generation and mitochondrial membrane potential (MMP) disruption, which in turn induced DNA damage and activation of caspases and poly ADP-ribose polymerase (PARP). Downregulation of CCNB1 (cyclin B1) and CDC2 mRNA and upregulation of CDKN1A (p21) mRNA were in accord with miltirone-induced G2/M arrest. Moreover, miltirone decreased cell adherence to fibronectin. Molecular docking revealed that miltirone bound to the ATP-binding site of IKK-β. In conclusion, miltirone was collateral sensitive in multidrug-resistant P-gp-overexpressing cells, induced G2/M arrest, and triggered apoptosis via ROS-generated breakdown of MMP and DNA damage. Therefore, miltirone may be a promising candidate for cancer chemotherapy.
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Affiliation(s)
- Ching-Fen Wu
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz 55128, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz 55128, Germany
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43
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Lim SM, Xie T, Westover KD, Ficarro SB, Tae HS, Gurbani D, Sim T, Marto JA, Jänne PA, Crews CM, Gray NS. Development of small molecules targeting the pseudokinase Her3. Bioorg Med Chem Lett 2015; 25:3382-9. [PMID: 26094118 DOI: 10.1016/j.bmcl.2015.04.103] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/22/2015] [Accepted: 04/30/2015] [Indexed: 01/21/2023]
Abstract
Her3 is a member of the human epidermal growth factor receptor (EGFR) tyrosine kinase family, and it is often either overexpressed or deregulated in many types of human cancer. Her3 has not been the subject of small-molecule inhibitor development because it is a pseudokinase and does not possess appreciable kinase activity. We recently reported on the development of the first selective irreversible Her3 ligand (TX1-85-1) that forms a covalent bond with cysteine 721 which is unique to Her3 among all kinases. We also developed a bi-functional compound (TX2-121-1) containing a hydrophobic adamantane moiety and the same warhead of TX1-85-1 that is capable of inhibiting Her3-dependent signaling and growth. Here we report on the structure-based medicinal chemistry effort that resulted in the discovery of these two compounds.
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Affiliation(s)
- Sang Min Lim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ting Xie
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Scott B Ficarro
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Hyun Seop Tae
- Departments of Chemistry, Pharmacology, and Molecular, Cellular and Development Biology, Yale University, New Haven, CT 06511, USA
| | - Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Taebo Sim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Jarrod A Marto
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Craig M Crews
- Departments of Chemistry, Pharmacology, and Molecular, Cellular and Development Biology, Yale University, New Haven, CT 06511, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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44
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Möbitz H. The ABC of protein kinase conformations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1555-66. [PMID: 25839999 DOI: 10.1016/j.bbapap.2015.03.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/18/2015] [Accepted: 03/24/2015] [Indexed: 02/06/2023]
Abstract
Due to their involvement in human diseases, protein kinases are an important therapeutic target class. Conformation is a key concept for understanding how functional activity, inhibition and sequence are linked. We assemble and annotate the mammalian structural kinome from the Protein Data Bank on the basis of a universal residue nomenclature. We identify a torsion angle around the Gly of the DFG-motif whose sharp distribution profile corresponds to three eclipsed conformations. This allows the definition a small set of clusters whose distribution shows a bias for the active conformation. A common rationale links the active and inactive state: stabilization of the active conformation, as well as inactivation by displacement of helix-αC or the DFG-motif is governed by the interaction between helix-αC and the DFG motif. In particular, the conformation of the DFG-motif is tightly correlated with the propensity of helix-αC displacement. Our analysis reveals detailed mechanisms for the displacement of helix-αC and the DFG and improves our understanding of the role of individual residues. By pooling conformations from the whole structural kinome, the energetic contributions of sequence and extrinsic factors can be estimated in free energy analyses. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.
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Affiliation(s)
- Henrik Möbitz
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland.
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45
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Ravichandran S, Luke BT, Collins JR. Can structural features of kinase receptors provide clues on selectivity and inhibition? A molecular modeling study. J Mol Graph Model 2015; 57:36-48. [PMID: 25635590 PMCID: PMC4361267 DOI: 10.1016/j.jmgm.2014.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Cancer is a complex disease resulting from the uncontrolled proliferation of cell signaling events. Protein kinases have been identified as central molecules that participate overwhelmingly in oncogenic events, thus becoming key targets for anticancer drugs. A majority of studies converged on the idea that ligand-binding pockets of kinases retain clues to the inhibiting abilities and cross-reacting tendencies of inhibitor drugs. Even though these ideas are critical for drug discovery, validating them using experiments is not only difficult, but also in some cases infeasible. To overcome these limitations and to test these ideas at the molecular level, we present here the results of receptor-focused in-silico docking of nine marketed drugs to 19 different wild-type and mutated kinases chosen from a wide range of families. This investigation highlights the need for using relevant models to explain the correct inhibition trends and the results are used to make predictions that might be able to influence future experiments. Our simulation studies are able to correctly predict the primary targets for each drug studied in majority of cases and our results agree with the existing findings. Our study shows that the conformations a given receptor acquires during kinase activation, and their micro-environment, defines the ligand partners. Type II drugs display high compatibility and selectivity for DFG-out kinase conformations. On the other hand Type I drugs are less selective and show binding preferences for both the open and closed forms of selected kinases. Using this receptor-focused approach, it is possible to capture the observed fold change in binding affinities between the wild-type and disease-centric mutations in ABL kinase for Imatinib and the second-generation ABL drugs. The effects of mutation are also investigated for two other systems, EGFR and B-Raf. Finally, by including pathway information in the design it is possible to model kinase inhibitors with potentially fewer side-effects.
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Affiliation(s)
- Sarangan Ravichandran
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research (FNLCR), P.O. Box B, Frederick, MD 21702, USA.
| | - Brian T Luke
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research (FNLCR), P.O. Box B, Frederick, MD 21702, USA
| | - Jack R Collins
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research (FNLCR), P.O. Box B, Frederick, MD 21702, USA
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46
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Abstract
Fragment-based drug design has become an important strategy for drug design and development over the last decade. It has been used with particular success in the development of kinase inhibitors, which are one of the most widely explored classes of drug targets today. The application of fragment-based methods to discovering and optimizing kinase inhibitors can be a complicated and daunting task; however, a general process has emerged that has been highly fruitful. Here a practical outline of the fragment process used in kinase inhibitor design and development is laid out with specific examples. A guide to the overall process from initial discovery through fragment screening, including the difficulties in detection, to the computational methods available for use in optimization of the discovered fragments is reported.
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Affiliation(s)
- Jon A Erickson
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, 46285, USA,
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47
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Sikorska J, Codutti L, Skjærven L, Elshorst B, Saez-Ameneiro R, Angelini A, Monecke P, Carlomagno T. Identification of new hit scaffolds by INPHARMA-guided virtual screening. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00116a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
INPHARMA, an NMR-based method that determines ligand binding poses, allows finding novel scaffolds as inhibitors of a target protein.
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Affiliation(s)
- Justyna Sikorska
- EMBL
- Structural and Computational Biology Unit
- D-69117 Heidelberg
- Germany
| | - Luca Codutti
- EMBL
- Structural and Computational Biology Unit
- D-69117 Heidelberg
- Germany
| | - Lars Skjærven
- EMBL
- Structural and Computational Biology Unit
- D-69117 Heidelberg
- Germany
| | - Bettina Elshorst
- Sanofi-Aventis Deutschland GmbH
- R&D LGCR/Structure, Design & Informatics
- D-65926 Frankfurt am Main
- Germany
| | | | - Andrea Angelini
- EMBL
- Structural and Computational Biology Unit
- D-69117 Heidelberg
- Germany
| | - Peter Monecke
- Sanofi-Aventis Deutschland GmbH
- R&D LGCR/Structure, Design & Informatics
- D-65926 Frankfurt am Main
- Germany
| | - Teresa Carlomagno
- EMBL
- Structural and Computational Biology Unit
- D-69117 Heidelberg
- Germany
- Helmholtz Zentrum für Infektionsforschung
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48
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Badrinarayan P, Sastry GN. Specificity rendering 'hot-spots' for aurora kinase inhibitor design: the role of non-covalent interactions and conformational transitions. PLoS One 2014; 9:e113773. [PMID: 25485544 PMCID: PMC4259475 DOI: 10.1371/journal.pone.0113773] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/29/2014] [Indexed: 11/19/2022] Open
Abstract
The present study examines the conformational transitions occurring among the major structural motifs of Aurora kinase (AK) concomitant with the DFG-flip and deciphers the role of non-covalent interactions in rendering specificity. Multiple sequence alignment, docking and structural analysis of a repertoire of 56 crystal structures of AK from Protein Data Bank (PDB) has been carried out. The crystal structures were systematically categorized based on the conformational disposition of the DFG-loop [in (DI) 42, out (DO) 5 and out-up (DOU) 9], G-loop [extended (GE) 53 and folded (GF) 3] and αC-helix [in (CI) 42 and out (CO) 14]. The overlapping subsets on categorization show the inter-dependency among structural motifs. Therefore, the four distinct possibilities a) 2W1C (DI, CI, GE) b) 3E5A (DI, CI, GF) c) 3DJ6 (DI, CO, GF) d) 3UNZ (DOU, CO, GF) along with their co-crystals and apo-forms were subjected to molecular dynamics simulations of 40 ns each to evaluate the variations of individual residues and their impact on forming interactions. The non-covalent interactions formed by the 157 AK co-crystals with different regions of the binding site were initially studied with the docked complexes and structure interaction fingerprints. The frequency of the most prominent interactions was gauged in the AK inhibitors from PDB and the four representative conformations during 40 ns. Based on this study, seven major non-covalent interactions and their complementary sites in AK capable of rendering specificity have been prioritized for the design of different classes of inhibitors.
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Affiliation(s)
- Preethi Badrinarayan
- Molecular Modeling Group, Organic Chemical Sciences, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad- 500 607, India
| | - G. Narahari Sastry
- Molecular Modeling Group, Organic Chemical Sciences, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad- 500 607, India
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49
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Duan Y, Chen L, Chen Y, Fan XG. c-Src binds to the cancer drug Ruxolitinib with an active conformation. PLoS One 2014; 9:e106225. [PMID: 25197973 PMCID: PMC4157781 DOI: 10.1371/journal.pone.0106225] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 07/28/2014] [Indexed: 01/17/2023] Open
Abstract
The cancer drug Ruxolitinib is a potent janus kinase inhibitor approved for the treatment of the myeloproliferative neoplasms. In addition, Ruxolitinib has weak inhibitory activity against a panel of other kinases, including Src kinase. There is no structural information of Ruxolitinib binding to any kinase. In this paper, we determined the crystal structure of c-Src kinase domain in complex of Ruxolitinib at a resolution of 2.26 Å. C-Src kinase domain adopts the DFG-in active conformation upon Ruxolitinib binding, indicating Ruxolitinib is a type I inhibitor for c-Src. Ruxolitinib forms two hydrogen bonds with Met341, a water-mediated hydrogen bond with Thr338, and a number of van der Waals contacts with c-Src. Ruxolitinib was then docked into the ligand-binding pocket of a previously solved JAK1 structure. From the docking result, Ruxolitinib also binds JAK1 as a type I inhibitor, with more interactions and a higher shape complementarity with the ligand-binding pocket of JAK1 compared to that of c-Src. Since Ruxolitinib is a relatively small inhibitor and there is sizeable cavity between Ruxolitinib and c-Src ligand-binding pocket, we propose to modify Ruxolitinib to develop more potent inhibitors to c-Src.
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Affiliation(s)
- Yankun Duan
- Department of Infectious Diseases & Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan, China
| | - Lin Chen
- Department of Infectious Diseases & Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan, China
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Yongheng Chen
- Department of Infectious Diseases & Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan, China
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (YC); (X-gF)
| | - Xue-gong Fan
- Department of Infectious Diseases & Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan, China
- * E-mail: (YC); (X-gF)
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Wang HC, Jagtap AD, Chang PT, Liu JR, Liu CP, Tseng HW, Chen GS, Chern JW. Bioisosteric replacement of an acylureido moiety attached to an indolin-2-one scaffold with a malonamido or a 2/4-pyridinoylamido moiety produces a selectively potent Aurora-B inhibitor. Eur J Med Chem 2014; 84:312-34. [PMID: 25036791 DOI: 10.1016/j.ejmech.2014.07.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 12/23/2022]
Abstract
Bioisosteric replacement of acylureido moiety in 6-acylureido-3-pyrrolylmethylidene-2-oxoindoline derivatives resulted in a series of malonamido derivatives with indolin-2-one scaffold (11-14). Further conformational restrictions of the malonamido moiety led to 2-oxo-1,2-dihydropyridine (21-25) or a 4-oxo-1,4-dihydropyridine derivatives (31-36). 4-Oxo-1,4-dihydropyridine derivatives were more potent Aurora B inhibitors than their 2-oxo-1,2-dihydropyridine counterparts and demonstrated cytotoxicities against A549 and HepG2 cells in the submicromolar range. In A549 cells, 31h decreased phosphorylation of histone H3, triggered polyploidy, induced expression of pro-apoptotic Fas and FasL with subsequent activation of caspase 8, resulting into apoptosis. In a Huh7-xenograft mouse model, 31h demonstrated potent in vivo efficacy with a daily dose of 5 mg/kg.
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Affiliation(s)
- Hsiao-Chun Wang
- School of Pharmacy and Center for Innovative Therapeutics Discovery, National Taiwan University, No. 33, LinSen South Road, Taipei 10051, Taiwan
| | - Ajit Dhananjay Jagtap
- School of Pharmacy and Center for Innovative Therapeutics Discovery, National Taiwan University, No. 33, LinSen South Road, Taipei 10051, Taiwan
| | - Pei-Teh Chang
- School of Pharmacy and Center for Innovative Therapeutics Discovery, National Taiwan University, No. 33, LinSen South Road, Taipei 10051, Taiwan
| | - Jia-Rong Liu
- School of Pharmacy and Center for Innovative Therapeutics Discovery, National Taiwan University, No. 33, LinSen South Road, Taipei 10051, Taiwan
| | - Chih-Peng Liu
- Biomedical Engineering Research Laboratories, Industrial Technology Research Institute, No. 321, Section 2, Guangfu Road, Hsinchu 30011, Taiwan
| | - Hsiang-Wen Tseng
- Biomedical Engineering Research Laboratories, Industrial Technology Research Institute, No. 321, Section 2, Guangfu Road, Hsinchu 30011, Taiwan
| | - Grace Shiahuy Chen
- Department of Applied Chemistry, Providence University, No. 200, Section 7, Taiwan Boulevard, Taichung 43301, Taiwan.
| | - Ji-Wang Chern
- School of Pharmacy and Center for Innovative Therapeutics Discovery, National Taiwan University, No. 33, LinSen South Road, Taipei 10051, Taiwan; Department of Life Science, College of Life Science, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.
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