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Mai NT, Lan NT, Vu TY, Duong PTM, Tung NT, Phung HTT. Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations. J Mol Graph Model 2020; 100:107648. [PMID: 32653524 DOI: 10.1016/j.jmgm.2020.107648] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/29/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Checkpoint kinase 1 (CHK1) is a serine/threonine-protein kinase that is involved in cell cycle regulation in eukaryotes. Inhibition of CHK1 is thus considered as a promising approach in cancer therapy. In this study, the fast pulling of ligand (FPL) process was applied to predict the relative binding affinities of CHK1 inhibitors using non-equilibrium molecular dynamics (MD) simulations. The work of external harmonic forces to pull the ligand out of the binding cavity strongly correlated with the experimental binding affinity of CHK1 inhibitors with the correlation coefficient of R = -0.88 and an overall root mean square error (RMSE) of 0.99 kcal/mol. The data indicate that the FPL method is highly accurate in predicting the relative binding free energies of CHK1 inhibitors with an affordable CPU time. A new set of molecules were designed based on the molecular modeling of interactions between the known inhibitor and CHK1 as inhibitory candidates. Molecular docking and FPL results exhibited that the binding affinities of developed ligands were similar to the known inhibitor in interaction with the catalytic site of CHK1, producing very potential CHK1 inhibitors of that the inhibitory activities should be further evaluated in vitro.
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Affiliation(s)
- Nguyen Thi Mai
- Laboratory of Theoretical and Computational Biophysics, Ho Chi Minh City, Viet Nam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Ngo Thi Lan
- Institute of Materials Science & Graduate University of Science and Technology, Academy of Science and Technology, Hanoi, Viet Nam
| | - Thien Y Vu
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Phuong Thi Mai Duong
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Nguyen Thanh Tung
- Institute of Materials Science & Graduate University of Science and Technology, Academy of Science and Technology, Hanoi, Viet Nam.
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam.
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Yang B, Vasbinder MM, Hird AW, Su Q, Wang H, Yu Y, Toader D, Lyne PD, Read JA, Breed J, Ioannidis S, Deng C, Grondine M, DeGrace N, Whitston D, Brassil P, Janetka JW. Adventures in Scaffold Morphing: Discovery of Fused Ring Heterocyclic Checkpoint Kinase 1 (CHK1) Inhibitors. J Med Chem 2018; 61:1061-1073. [DOI: 10.1021/acs.jmedchem.7b01490] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bin Yang
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Melissa M. Vasbinder
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Alexander W. Hird
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Qibin Su
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Haixia Wang
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Yan Yu
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Dorin Toader
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Paul D. Lyne
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jon A. Read
- Discovery
Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science
Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Jason Breed
- Discovery
Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science
Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Stephanos Ioannidis
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Chun Deng
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Michael Grondine
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Nancy DeGrace
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - David Whitston
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Patrick Brassil
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - James W. Janetka
- Oncology
Chemistry, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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Gomha SM, Abdulla MM, Abou-Seri SM. Identification of novel aminothiazole and aminothiadiazole conjugated cyanopyridines as selective CHK1 inhibitors. Eur J Med Chem 2015; 92:459-70. [PMID: 25594740 DOI: 10.1016/j.ejmech.2015.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/08/2014] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
Abstract
Inhibitors of checkpoint kinase 1 (CHK1) are of current interest as potential anti-tumor agents. Novel series of cyanopyridyl-aminothiadiazoles (synthesized from reaction of 1-(3-cyano-4,6-diphenylpyridin-2-yl)-3-phenylthiourea (14) with hydrazonoyl halides) and cyanopyridyl-aminothiazolyl-thiadiazoles (synthesized from treatment of 14 with ethyl chloroacetate followed by reaction of the obtained cyanopyridyl-aminothiazole with hydrazonoyl halides) were synthesized and evaluated for their CHK1 inhibitory potential using a cell-based assay cascade. The tested compounds exhibited a potent and selective CHK1 inhibitory activity at nanomolar levels that reflected their ability to abrogate cell cycle arrest and potentiate the cytotoxic effect of the genotoxic drug gemcitabine in colon cancer cells. Molecular modeling simulation revealed that, the most active compound 28a docked well into the enzyme active site and their complex is stabilized by a key H-bonding with the backbone amide of Cys-87 as well as multiple favorable hydrophobic interactions with different hydrophobic binding regions of the enzyme.
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Affiliation(s)
- Sobhi M Gomha
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt.
| | | | - Sahar M Abou-Seri
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Egypt
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Beno BR, Yeung KS, Bartberger MD, Pennington LD, Meanwell NA. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J Med Chem 2015; 58:4383-438. [DOI: 10.1021/jm501853m] [Citation(s) in RCA: 468] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Brett R. Beno
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Michael D. Bartberger
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Lewis D. Pennington
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
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Balupuri A, Balasubramanian PK, Gadhe CG, Cho SJ. Docking-based 3D-QSAR study of pyridyl aminothiazole derivatives as checkpoint kinase 1 inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:651-671. [PMID: 24911214 DOI: 10.1080/1062936x.2014.923040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Checkpoint kinase 1 (Chk1) is a promising target for the design of novel anticancer agents. In the present work, molecular docking simulations and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed on pyridyl aminothiazole derivatives as Chk1 inhibitors. AutoDock was used to determine the probable binding conformations of all the compounds inside the active site of Chk1. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were developed based on the docking conformations and alignments. The CoMFA model produced statistically significant results with a cross-validated correlation coefficient (q2) of 0.608 and a coefficient of determination (r2) of 0.972. The reliable CoMSIA model with q2 of 0.662 and r2 of 0.970 was obtained from the combination of steric, electrostatic and hydrogen bond acceptor fields. The predictive power of the models were assessed using an external test set of 14 compounds and showed reasonable external predictabilities (r(2)pred) of 0.668 and 0.641 for CoMFA and CoMSIA models, respectively. The models were further evaluated by leave-ten-out cross-validation, bootstrapping and progressive scrambling analyses. The study provides valuable information about the key structural elements that are required in the rational design of potential drug candidates of this class of Chk1 inhibitors.
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Affiliation(s)
- A Balupuri
- a Department of Bio-New Drug Development, College of Medicine , Chosun University , Gwangju 501-759 , Republic of Korea
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Matthews TP, Jones AM, Collins I. Structure-based design, discovery and development of checkpoint kinase inhibitors as potential anticancer therapies. Expert Opin Drug Discov 2013; 8:621-40. [PMID: 23594139 DOI: 10.1517/17460441.2013.788496] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Checkpoint kinase (CHK) inhibitors offer the promise of enhancing the effectiveness of widely prescribed cancer chemotherapies and radiotherapy by inhibiting the DNA damage response, as well as the potential for single agent efficacy. AREAS COVERED This article surveys structural insights into the checkpoint kinases CHK1 and CHK2 that have been exploited to enhance the selectivity and potency of small molecule inhibitors. Furthermore, the authors review the use of mechanistic cellular assays to guide the optimisation of inhibitors. Finally, the authors discuss the status of the current clinical candidates and emerging new clinical contexts for CHK1 and CHK2 inhibitors, including the prospects for single agent efficacy. EXPERT OPINION Protein-bound water molecules play key roles in structural features that can be targeted to gain high selectivity for either enzyme. The results of early phase clinical trials of checkpoint inhibitors have been mixed, but significant progress has been made in testing the combination of CHK1 inhibitors with genotoxic chemotherapy. Second-generation CHK1 inhibitors are likely to benefit from increased selectivity and oral bioavailability. While the optimum therapeutic context for CHK2 inhibition remains unclear, the emergence of single agent preclinical efficacy for CHK1 inhibitors in specific tumour types exhibiting constitutive replication stress represents exciting progress in exploring the therapeutic potential of these agents.
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Affiliation(s)
- Thomas P Matthews
- Institute of Cancer Research, Cancer Research UK Cancer Therapeutics Unit, London SM2 5NG, UK
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Yurttaş L, Özkay Y, Akalın-Çiftçi G, Ulusoylar-Yıldırım Ş. Synthesis and anticancer activity evaluation of N-[4-(2-methylthiazol-4-yl)phenyl]acetamide derivatives containing (benz)azole moiety. J Enzyme Inhib Med Chem 2013; 29:175-84. [PMID: 23391122 DOI: 10.3109/14756366.2013.763253] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A new class of novel thiazole-(benz)azole derivatives was synthesized to investigate their anticancer activity. The structure of the compounds was confirmed by IR, (1)H-NMR, and MS spectral data and elemental analyses. Anticancer effect of the compounds was evaluated against A549 and C6 tumor cell lines. MTT, analysis of DNA synthesis, acridine orange/ethidium bromide staining method and analysis of caspase-3 activation assays were performed for anticancer activity investigations. Compounds 6f and 6g, which carry 5-chloro and 5-methylbenzimidazole groups showed significant anticancer activity. Potential of these compounds to direct tumor cells to apoptotic pathway, which is a precondition of anticancer action, was also observed.
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