1
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Wilson BAP, Li N, Martinez Fiesco JA, Dalilian M, Wang D, Smith EA, Wamiru A, Shah R, Goncharova EI, Beutler JA, Grkovic T, Zhang P, O’Keefe BR. Biochemical Discovery, Intracellular Evaluation, and Crystallographic Characterization of Synthetic and Natural Product Adenosine 3',5'-Cyclic Monophosphate-Dependent Protein Kinase A (PKA) Inhibitors. ACS Pharmacol Transl Sci 2023; 6:633-650. [PMID: 37082750 PMCID: PMC10111623 DOI: 10.1021/acsptsci.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Indexed: 04/22/2023]
Abstract
The recent demonstration that adenosine 3',5'-cyclic monophosphate (cAMP)-dependent protein kinase A (PKA) plays an oncogenic role in a number of important cancers has led to a renaissance in drug development interest targeting this kinase. We therefore have established a suite of biochemical, cell-based, and structural biology assays for identifying and evaluating new pharmacophores for PKA inhibition. This discovery process started with a 384-well high-throughput screen of more than 200,000 substances, including fractionated natural product extracts. Identified active compounds were further prioritized in biochemical, biophysical, and cell-based assays. Priority lead compounds were assessed in detail to fully characterize several previously unrecognized PKA pharmacophores including the generation of new X-ray crystallography structures demonstrating unique interactions between PKA and bound inhibitor molecules.
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Affiliation(s)
- Brice A. P. Wilson
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ning Li
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Juliana A. Martinez Fiesco
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Masoumeh Dalilian
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Dongdong Wang
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Emily A. Smith
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Antony Wamiru
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Rohan Shah
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ekaterina I. Goncharova
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Advanced
Biomedical Computational Science, Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - John A. Beutler
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Tanja Grkovic
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Natural
Products Branch, Developmental Therapeutics Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702, United States
| | - Ping Zhang
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Barry R. O’Keefe
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Natural
Products Branch, Developmental Therapeutics Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702, United States
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2
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Puch-Giner I, Molina A, Municoy M, Pérez C, Guallar V. Recent PELE Developments and Applications in Drug Discovery Campaigns. Int J Mol Sci 2022; 23:ijms232416090. [PMID: 36555731 PMCID: PMC9788188 DOI: 10.3390/ijms232416090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Computer simulation techniques are gaining a central role in molecular pharmacology. Due to several factors, including the significant improvements of traditional molecular modelling, the irruption of machine learning methods, the massive data generation, or the unlimited computational resources through cloud computing, the future of pharmacology seems to go hand in hand with in silico predictions. In this review, we summarize our recent efforts in such a direction, centered on the unconventional Monte Carlo PELE software and on its coupling with machine learning techniques. We also provide new data on combining two recent new techniques, aquaPELE capable of exhaustive water sampling and fragPELE, for fragment growing.
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Affiliation(s)
- Ignasi Puch-Giner
- Barcelona Supercomputing Center, Plaça d’Eusebi Güell, 1-3, 08034 Barcelona, Spain
| | - Alexis Molina
- Nostrum Biodiscovery S.L., Av. de Josep Tarradellas, 8-10, 3-2, 08029 Barcelona, Spain
| | - Martí Municoy
- Barcelona Supercomputing Center, Plaça d’Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Nostrum Biodiscovery S.L., Av. de Josep Tarradellas, 8-10, 3-2, 08029 Barcelona, Spain
| | - Carles Pérez
- Nostrum Biodiscovery S.L., Av. de Josep Tarradellas, 8-10, 3-2, 08029 Barcelona, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center, Plaça d’Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Nostrum Biodiscovery S.L., Av. de Josep Tarradellas, 8-10, 3-2, 08029 Barcelona, Spain
- Correspondence:
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3
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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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4
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Tong L, Song P, Jiang K, Xu L, Jin T, Wang P, Hu X, Fang S, Gao A, Zhou Y, Liu T, Li J, Hu Y. Discovery of (R)-5-((5-(1-methyl-1H-pyrazol-4-yl)-4-(methylamino)pyrimidin-2-yl)amino)-3-(piperidin-3-yloxy)picolinonitrile, a novel CHK1 inhibitor for hematologic malignancies. Eur J Med Chem 2019; 173:44-62. [DOI: 10.1016/j.ejmech.2019.03.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 11/17/2022]
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5
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Lindel T. Chemistry and Biology of the Pyrrole–Imidazole Alkaloids. THE ALKALOIDS: CHEMISTRY AND BIOLOGY 2017; 77:117-219. [DOI: 10.1016/bs.alkal.2016.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Yan W, Wang X, Dai Y, Zhao B, Yang X, Fan J, Gao Y, Meng F, Wang Y, Luo C, Ai J, Geng M, Duan W. Discovery of 3-(5'-Substituted)-Benzimidazole-5-(1-(3,5-dichloropyridin-4-yl)ethoxy)-1H-indazoles as Potent Fibroblast Growth Factor Receptor Inhibitors: Design, Synthesis, and Biological Evaluation. J Med Chem 2016; 59:6690-708. [PMID: 27348537 DOI: 10.1021/acs.jmedchem.6b00056] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fibroblast growth factor receptor (FGFR) represents an attractive oncology target for cancer therapy in view of its critical role in promoting cancer formation and progression, as well as causing resistance to approved therapies. In this article, we describe the identification of the potent pan-FGFR inhibitor (R)-21c (FGFR1-4 IC50 values of 0.9, 2.0, 2.0, and 6.1 nM, respectively). Compound (R)-21c exhibited excellent in vitro inhibitory activity against a panel of FGFR-amplified cell lines. Western blot analysis demonstrated that (R)-21c suppressed FGF/FGFR and downstream signaling pathways at nanomolar concentrations. Moreover, (R)-21c provided nearly complete inhibition of tumor growth (96.9% TGI) in NCI-H1581 (FGFR1-amplified) xenograft mice model at the dose of 10 mg/kg/qd via oral administration.
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Affiliation(s)
- Wei Yan
- School of Pharmacy, East China University of Science & Technology , 130 Mei Long Road, Shanghai 200237, P. R. China
| | - Xinyi Wang
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences , Beijing 100049, P. R. China
| | - Yang Dai
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Bin Zhao
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Xinying Yang
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Jun Fan
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Yinglei Gao
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Fanwang Meng
- Department of Chemistry, College of Sciences, Shanghai University , 99 Shang Da Road, Shanghai 200444, P. R. China.,Drug Discovery & Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Yuming Wang
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Cheng Luo
- Drug Discovery & Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Jing Ai
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Meiyu Geng
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Wenhu Duan
- School of Pharmacy, East China University of Science & Technology , 130 Mei Long Road, Shanghai 200237, P. R. China.,Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
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7
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Identification of novel inhibitors of human Chk1 using pharmacophore-based virtual screening and their evaluation as potential anti-cancer agents. J Comput Aided Mol Des 2014; 28:1247-56. [DOI: 10.1007/s10822-014-9800-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 10/03/2014] [Indexed: 12/22/2022]
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8
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Halavaty AS, Anderson SM, Wawrzak Z, Kudritska M, Skarina T, Anderson WF, Savchenko A. Type III effector NleH2 from Escherichia coli O157:H7 str. Sakai features an atypical protein kinase domain. Biochemistry 2014; 53:2433-5. [PMID: 24712300 DOI: 10.1021/bi500016j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The crystal structure of a C-terminal domain of enterohemorrhagic Escherichia coli type III effector NleH2 has been determined to 2.6 Å resolution. The structure resembles those of protein kinases featuring the catalytic, activation, and glycine-rich loop motifs and ATP-binding site. The position of helix αC and the lack of a conserved arginine within an equivalent HRD motif suggested that the NleH2 kinase domain's active conformation might not require phosphorylation. The activation segment markedly contributed to the dimerization interface of NleH2, which can also accommodate the NleH1-NleH2 heterodimer. The C-terminal PDZ-binding motif of NleH2 provided bases for interaction with host proteins.
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Affiliation(s)
- Andrei S Halavaty
- Center for Structural Genomics of Infectious Diseases (CSGID), Molecular Pharmacology and Biological Chemistry, Northwestern University , Chicago, Illinois 60611, United States
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9
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Crocetti L, Schepetkin IA, Cilibrizzi A, Graziano A, Vergelli C, Giomi D, Khlebnikov AI, Quinn MT, Giovannoni MP. Optimization of N-benzoylindazole derivatives as inhibitors of human neutrophil elastase. J Med Chem 2013; 56:6259-72. [PMID: 23844670 DOI: 10.1021/jm400742j] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human neutrophil elastase (HNE) is an important therapeutic target for treatment of pulmonary diseases. Previously, we identified novel N-benzoylindazole derivatives as potent, competitive, and pseudoirreversible HNE inhibitors. Here, we report further development of these inhibitors with improved potency, protease selectivity, and stability compared to our previous leads. Introduction of a variety of substituents at position 5 of the indazole resulted in the potent inhibitor 20f (IC50 ∼10 nM) and modifications at position 3 resulted the most potent compound in this series, the 3-CN derivative 5b (IC50 = 7 nM); both derivatives demonstrated good stability and specificity for HNE versus other serine proteases. Molecular docking of selected N-benzoylindazoles into the HNE binding domain suggested that inhibitory activity depended on geometry of the ligand-enzyme complexes. Indeed, the ability of a ligand to form a Michaelis complex and favorable conditions for proton transfer between Hys57, Asp102, and Ser195 both affected activity.
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Affiliation(s)
- Letizia Crocetti
- NEUROFARBA, Sezione di Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
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10
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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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11
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Lainchbury M, Matthews TP, McHardy T, Boxall KJ, Walton MI, Eve PD, Hayes A, Valenti MR, de Haven Brandon AK, Box G, Aherne GW, Reader JC, Raynaud FI, Eccles SA, Garrett MD, Collins I. Discovery of 3-alkoxyamino-5-(pyridin-2-ylamino)pyrazine-2-carbonitriles as selective, orally bioavailable CHK1 inhibitors. J Med Chem 2012; 55:10229-40. [PMID: 23082860 PMCID: PMC3506129 DOI: 10.1021/jm3012933] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Inhibitors of checkpoint kinase 1 (CHK1) are of current
interest
as potential antitumor agents, but the most advanced inhibitor series
reported to date are not orally bioavailable. A novel series of potent
and orally bioavailable 3-alkoxyamino-5-(pyridin-2-ylamino)pyrazine-2-carbonitrile
CHK1 inhibitors was generated by hybridization of two lead scaffolds
derived from fragment-based drug design and optimized for CHK1 potency
and high selectivity using a cell-based assay cascade. Efficient in
vivo pharmacokinetic assessment was used to identify compounds with
prolonged exposure following oral dosing. The optimized compound (CCT244747)
was a potent and highly selective CHK1 inhibitor, which modulated
the DNA damage response pathway in human tumor xenografts and showed
antitumor activity in combination with genotoxic chemotherapies and
as a single agent.
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Affiliation(s)
- Michael Lainchbury
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG U. K
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12
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X-ray crystallographic structure-based design of selective thienopyrazole inhibitors for interleukin-2-inducible tyrosine kinase. Bioorg Med Chem Lett 2012; 22:3296-300. [DOI: 10.1016/j.bmcl.2012.03.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/02/2012] [Accepted: 03/05/2012] [Indexed: 11/22/2022]
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13
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Dudkin VY, Rickert K, Kreatsoulas C, Wang C, Arrington KL, Fraley ME, Hartman GD, Yan Y, Ikuta M, Stirdivant SM, Drakas RA, Walsh ES, Hamilton K, Buser CA, Lobell RB, Sepp-Lorenzino L. Pyridyl aminothiazoles as potent inhibitors of Chk1 with slow dissociation rates. Bioorg Med Chem Lett 2012; 22:2609-12. [PMID: 22374217 DOI: 10.1016/j.bmcl.2012.01.110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/26/2012] [Accepted: 01/30/2012] [Indexed: 11/25/2022]
Abstract
Pyridyl aminothiazoles comprise a novel class of ATP-competitive Chk1 inhibitors with excellent inhibitory potential. Modification of the core with ethylenediamine amides provides compounds with low picomolar potency and very high residence times. Investigation of binding parameters of such compounds using X-ray crystallography and molecular dynamics simulations revealed multiple hydrogen bonds to the enzyme backbone as well as stabilization of the conserved water molecules network in the hydrophobic binding region.
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Affiliation(s)
- Vadim Y Dudkin
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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14
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Li Y, Kim DJ, Ma W, Lubet RA, Bode AM, Dong Z. Discovery of novel checkpoint kinase 1 inhibitors by virtual screening based on multiple crystal structures. J Chem Inf Model 2011; 51:2904-14. [PMID: 21955044 PMCID: PMC3244973 DOI: 10.1021/ci200257b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Incorporating receptor flexibility is considered crucial for improvement of docking-based virtual screening. With an abundance of crystallographic structures freely available, docking with multiple crystal structures is believed to be a practical approach to cope with protein flexibility. Here we describe a successful application of the docking of multiple structures to discover novel and potent Chk1 inhibitors. Forty-six Chk1 structures were first compared in single structure docking by predicting the binding mode and recovering known ligands. Combinations of different protein structures were then compared by recovery of known ligands and an optimal ensemble of Chk1 structures were selected. The chosen structures were used in the virtual screening of over 60 000 diverse compounds for Chk1 inhibitors. Six novel compounds ranked at the top of the hits list were tested experimentally, and two of these compounds inhibited Chk1 activity-the best with an IC(50) value of 9.6 μM. Further study indicated that achieving a better enrichment and identifying more diverse compounds was more likely using multiple structures than using only a single structure even when protein structures were randomly selected. Taking into account conformational energy difference did not help to improve enrichment in the top ranked list.
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Affiliation(s)
- Yan Li
- The Hormel Institute, University of Minnesota, Austin, MN
| | - Dong Joon Kim
- The Hormel Institute, University of Minnesota, Austin, MN
| | - Weiya Ma
- The Hormel Institute, University of Minnesota, Austin, MN
| | | | - Ann M. Bode
- The Hormel Institute, University of Minnesota, Austin, MN
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, MN
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15
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Reader JC, Matthews TP, Klair S, Cheung KMJ, Scanlon J, Proisy N, Addison G, Ellard J, Piton N, Taylor S, Cherry M, Fisher M, Boxall K, Burns S, Walton MI, Westwood IM, Hayes A, Eve P, Valenti M, de Haven Brandon A, Box G, van Montfort RLM, Williams DH, Aherne GW, Raynaud FI, Eccles SA, Garrett MD, Collins I. Structure-guided evolution of potent and selective CHK1 inhibitors through scaffold morphing. J Med Chem 2011; 54:8328-42. [PMID: 22111927 PMCID: PMC3241339 DOI: 10.1021/jm2007326] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Pyrazolopyridine inhibitors with low micromolar potency
for CHK1
and good selectivity against CHK2 were previously identified by fragment-based
screening. The optimization of the pyrazolopyridines to a series of
potent and CHK1-selective isoquinolines demonstrates how fragment-growing
and scaffold morphing strategies arising from a structure-based understanding
of CHK1 inhibitor binding can be combined to successfully progress
fragment-derived hit matter to compounds with activity in vivo. The
challenges of improving CHK1 potency and selectivity, addressing synthetic
tractability, and achieving novelty in the crowded kinase inhibitor
chemical space were tackled by multiple scaffold morphing steps, which
progressed through tricyclic pyrimido[2,3-b]azaindoles
to N-(pyrazin-2-yl)pyrimidin-4-amines and ultimately
to imidazo[4,5-c]pyridines and isoquinolines. A potent
and highly selective isoquinoline CHK1 inhibitor (SAR-020106) was
identified, which potentiated the efficacies of irinotecan and gemcitabine
in SW620 human colon carcinoma xenografts in nude mice.
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Affiliation(s)
- John C Reader
- Cancer Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
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16
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Lountos GT, Jobson AG, Tropea JE, Self CR, Zhang G, Pommier Y, Shoemaker RH, Waugh DS. X-ray structures of checkpoint kinase 2 in complex with inhibitors that target its gatekeeper-dependent hydrophobic pocket. FEBS Lett 2011; 585:3245-9. [PMID: 21907711 PMCID: PMC3195894 DOI: 10.1016/j.febslet.2011.08.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/11/2011] [Accepted: 08/29/2011] [Indexed: 12/01/2022]
Abstract
The serine/threonine checkpoint kinase 2 (Chk2) is an attractive molecular target for the development of small molecule inhibitors to treat cancer. Here, we report the rational design of Chk2 inhibitors that target the gatekeeper-dependent hydrophobic pocket located behind the adenine-binding region of the ATP-binding site. These compounds exhibit IC(50) values in the low nanomolar range and are highly selective for Chk2 over Chk1. X-ray crystallography was used to determine the structures of the inhibitors in complex with the catalytic kinase domain of Chk2 to verify their modes of binding.
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Affiliation(s)
- George T. Lountos
- Basic Science Program, SAIC-Frederick, Frederick, MD 21702-1201, USA
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA
| | - Andrew G. Jobson
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph E. Tropea
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA
| | | | - Guangtao Zhang
- Provid Pharmaceuticals, Monmouth Junction, NJ 08852, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert H. Shoemaker
- Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA
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17
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Lountos GT, Jobson AG, Tropea JE, Self CR, Zhang G, Pommier Y, Shoemaker RH, Waugh DS. Structural characterization of inhibitor complexes with checkpoint kinase 2 (Chk2), a drug target for cancer therapy. J Struct Biol 2011; 176:292-301. [PMID: 21963792 DOI: 10.1016/j.jsb.2011.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 09/14/2011] [Accepted: 09/19/2011] [Indexed: 01/08/2023]
Abstract
Chk2 (checkpoint kinase 2) is a serine/threonine kinase that participates in a series of signaling networks responsible for maintaining genomic integrity and responding to DNA damage. The development of selective Chk2 inhibitors has recently attracted much interest as a means of sensitizing cancer cells to current DNA-damaging agents used in the treatment of cancer. Additionally, selective Chk2 inhibitors may reduce p53-mediated apoptosis in normal tissues, thereby helping to mitigate adverse side effects from chemotherapy and radiation. Thus far, relatively few selective inhibitors of Chk2 have been described and none have yet progressed into clinical trials. Here, we report crystal structures of the catalytic domain of Chk2 in complex with a novel series of potent and selective small molecule inhibitors. These compounds exhibit nanomolar potencies and are selective for Chk2 over Chk1. The structures reported here elucidate the binding modes of these inhibitors to Chk2 and provide information that can be exploited for the structure-assisted design of novel chemotherapeutics.
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Affiliation(s)
- George T Lountos
- Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA
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18
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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19
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1172] [Impact Index Per Article: 90.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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20
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Insight into analysis of interactions of GW9508 to wild-type and H86F and H137F GPR40: A combined QM/MM study and pharmacophore modeling. J Mol Graph Model 2011; 29:818-25. [DOI: 10.1016/j.jmgm.2011.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/13/2011] [Accepted: 01/13/2011] [Indexed: 02/06/2023]
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21
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Duschek A, Kirsch SF. 2-Iodoxybenzoic Acid-A Simple Oxidant with a Dazzling Array of Potential Applications. Angew Chem Int Ed Engl 2011; 50:1524-52. [DOI: 10.1002/anie.201000873] [Citation(s) in RCA: 205] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Indexed: 12/26/2022]
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22
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Duschek A, Kirsch SF. 2-Iodoxybenzoesäure - ein einfaches Oxidationsmittel mit einer Vielfalt an Anwendungsmöglichkeiten. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201000873] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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23
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Abstract
PGVL Hub is a Pfizer internal desktop tool for chemical library and singleton design. In this chapter, we give a short introduction to PGVL Hub, the core workflow it supports, and the rich design capabilities it provides. By re-creating two legacy targeted libraries against the human checkpoint kinase 1 (Chk1) as a showcase, we illustrate how PGVL Hub could be used to help library designers carry out the steps in library design and realize design objectives such as SAR expansion and improvement in both kinase selectivity and compound aqueous solubility. Finally we share several tips about library design and usage of PGVL Hub.
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Affiliation(s)
- Zhengwei Peng
- Pfizer Global Research and Development, La Jolla Laboratories, San Diego, CA, USA.
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24
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Affiliation(s)
- Caterina Bissantz
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
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25
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Design and evaluation of 3,6-di(hetero)aryl imidazo[1,2-a]pyrazines as inhibitors of checkpoint and other kinases. Bioorg Med Chem Lett 2010; 20:4045-9. [PMID: 20561787 DOI: 10.1016/j.bmcl.2010.05.096] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 05/21/2010] [Accepted: 05/22/2010] [Indexed: 11/23/2022]
Abstract
A range of 3,6-di(hetero)arylimidazo[1,2-a]pyrazine ATP-competitive inhibitors of CHK1 were developed by scaffold hopping from a weakly active screening hit. Efficient synthetic routes for parallel synthesis were developed to prepare analogues with improved potency and ligand efficiency against CHK1. Kinase profiling showed that the imidazo[1,2-a]pyrazines could inhibit other kinases, including CHK2 and ABL, with equivalent or better potency depending on the pendant substitution. These 3,6-di(hetero)aryl imidazo[1,2-a]pyrazines appear to represent a general kinase inhibitor scaffold.
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26
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Amirthaganesan S, Aridoss G, Park KS, Lim KT, Jeong YT. Synthesis, Spectral and Antimicrobial Studies of Some N(2)-Substituted Tetrahydroindazoles. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.5.1135] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Ajmani S, Agrawal A, Kulkarni SA. A comprehensive structure-activity analysis of protein kinase B-alpha (Akt1) inhibitors. J Mol Graph Model 2010; 28:683-94. [PMID: 20153226 DOI: 10.1016/j.jmgm.2010.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 01/12/2010] [Accepted: 01/16/2010] [Indexed: 11/29/2022]
Abstract
Protein kinase B (PKB, also known as Akt) belongs to the AGC subfamily of the protein kinase superfamily. Akt1 has been reported as a central player in regulation of metabolism, cell survival, motility, transcription and cell-cycle progression, among the signalling proteins that respond to a large variety of signals. In this study an attempt was made to understand structural requirements for Akt1 inhibition using conventional QSAR, k-nearest neighbour QSAR and novel GQSAR methods. With this intention, a wide variety of structurally diverse Akt1 inhibitors were collected from various literature reports. The conventional QSAR analyses revealed the key role of Baumann's alignment independent topological descriptors along with other descriptors such as the number of hydrogen bond acceptors, hydrogen bond donors, rotatable bonds and aromatic oxygen (SaaOcount) along with molecular branching (chi3Cluster), alkene carbon atom type (SdsCHE-index) in governing activity variation. Further, the GQSAR analyses show that chemical variations like presence of hetero-aromatic ring, flexibility, polar surface area and fragment length present in the hinge binding fragment (in the present case fragment D) are highly influential for achieving highly potent Akt1 inhibitors. In addition, this study resulted in a k-nearest neighbour classification model with three descriptors suggesting the key role of oxygen (SssOE-index) and aromatic carbon (SaaCHE-index and SaasCE-index) atoms electro-topological environment that differentiate molecules binding to Akt1 kinase or PH domain. The developed models are interpretable, with good statistical and predictive significance, and can be used for guiding ligand modification for the development of potential new Akt1 inhibitors.
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Affiliation(s)
- Subhash Ajmani
- NovaLead Pharma Pvt. Ltd., Pride Purple Coronet, 1st floor, S No. 287, Baner Road, Pune 411045, India.
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28
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Chen XM, Lu T, Lu S, Li HF, Yuan HL, Ran T, Liu HC, Chen YD. Structure-based and shape-complemented pharmacophore modeling for the discovery of novel checkpoint kinase 1 inhibitors. J Mol Model 2009; 16:1195-204. [DOI: 10.1007/s00894-009-0630-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 11/18/2009] [Indexed: 02/04/2023]
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29
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Matthews TP, Klair S, Burns S, Boxall K, Cherry M, Fisher M, Westwood IM, Walton MI, McHardy T, Cheung KMJ, Van Montfort R, Williams D, Aherne GW, Garrett MD, Reader J, Collins I. Identification of inhibitors of checkpoint kinase 1 through template screening. J Med Chem 2009; 52:4810-9. [PMID: 19572549 DOI: 10.1021/jm900314j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Checkpoint kinase 1 (CHK1) is an oncology target of significant current interest. Inhibition of CHK1 abrogates DNA damage-induced cell cycle checkpoints and sensitizes p53 deficient cancer cells to genotoxic therapies. Using template screening, a fragment-based approach to small molecule hit generation, we have identified multiple CHK1 inhibitor scaffolds suitable for further optimization. The sequential combination of in silico low molecular weight template selection, a high concentration biochemical assay and hit validation through protein-ligand X-ray crystallography provided 13 template hits from an initial in silico screening library of ca. 15000 compounds. The use of appropriate counter-screening to rule out nonspecific aggregation by test compounds was essential for optimum performance of the high concentration bioassay. One low molecular weight, weakly active purine template hit was progressed by iterative structure-based design to give submicromolar pyrazolopyridines with good ligand efficiency and appropriate CHK1-mediated cellular activity in HT29 colon cancer cells.
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Affiliation(s)
- Thomas P Matthews
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
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30
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Lountos GT, Tropea JE, Zhang D, Jobson AG, Pommier Y, Shoemaker RH, Waugh DS. Crystal structure of checkpoint kinase 2 in complex with NSC 109555, a potent and selective inhibitor. Protein Sci 2009; 18:92-100. [PMID: 19177354 DOI: 10.1002/pro.16] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Checkpoint kinase 2 (Chk2), a ser/thr kinase involved in the ATM-Chk2 checkpoint pathway, is activated by genomic instability and DNA damage and results in either arrest of the cell cycle to allow DNA repair to occur or apoptosis if the DNA damage is severe. Drugs that specifically target Chk2 could be beneficial when administered in combination with current DNA-damaging agents used in cancer therapy. Recently, a novel inhibitor of Chk2, NSC 109555, was identified that exhibited high potency (IC(50) = 240 nM) and selectivity. This compound represents a new chemotype and lead for the development of novel Chk2 inhibitors that could be used as therapeutic agents for the treatment of cancer. To facilitate the discovery of new analogs of NSC 109555 with even greater potency and selectivity, we have solved the crystal structure of this inhibitor in complex with the catalytic domain of Chk2. The structure confirms that the compound is an ATP-competitive inhibitor, as the electron density clearly reveals that it occupies the ATP-binding pocket. However, the mode of inhibition differs from that of the previously studied structure of Chk2 in complex with debromohymenialdisine, a compound that inhibits both Chk1 and Chk2. A unique hydrophobic pocket in Chk2, located very close to the bound inhibitor, presents an opportunity for the rational design of compounds with higher binding affinity and greater selectivity.
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Affiliation(s)
- George T Lountos
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, P. O. Box B, Frederick, Maryland 21702-1201, USA
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31
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Parmentier JG, Portevin B, Golsteyn RM, Pierré A, Hickman J, Gloanec P, De Nanteuil G. Synthesis and CHK1 inhibitory potency of Hymenialdisine analogues. Bioorg Med Chem Lett 2009; 19:841-4. [DOI: 10.1016/j.bmcl.2008.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 11/28/2008] [Accepted: 12/02/2008] [Indexed: 10/21/2022]
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32
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Kinnings SL, Jackson RM. Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family. J Chem Inf Model 2009; 49:318-29. [DOI: 10.1021/ci800289y] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sarah L. Kinnings
- Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Richard M. Jackson
- Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
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33
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2-(6-Phenyl-1H-indazol-3-yl)-1H-benzo[d]imidazoles: design and synthesis of a potent and isoform selective PKC-zeta inhibitor. Bioorg Med Chem Lett 2008; 19:908-11. [PMID: 19097791 DOI: 10.1016/j.bmcl.2008.11.105] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 11/24/2008] [Accepted: 11/26/2008] [Indexed: 11/22/2022]
Abstract
The inhibition of PKC-zeta has been proposed to be a potential drug target for immune and inflammatory diseases. A series of 2-(6-phenyl-1H indazol-3-yl)-1H-benzo[d]imidazoles with initial high crossover to CDK-2 has been optimized to afford potent and selective inhibitors of protein kinase c-zeta (PKC-zeta). The determination of the crystal structures of key inhibitor:CDK-2 complexes informed the design and analysis of the series. The most selective and potent analog was identified by variation of the aryl substituent at the 6-position of the indazole template to give a 4-NH(2) derivative. The analog displays good selectivity over other PKC isoforms (alpha, betaII, gamma, delta, epsilon, mu, theta, eta and iota/lambda) and CDK-2, however it displays marginal selectivity against a panel of other kinases (37 profiled).
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34
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Ghose AK, Herbertz T, Pippin DA, Salvino JM, Mallamo JP. Knowledge based prediction of ligand binding modes and rational inhibitor design for kinase drug discovery. J Med Chem 2008; 51:5149-71. [PMID: 18710211 DOI: 10.1021/jm800475y] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Arup K Ghose
- Department of Medicinal Chemistry, Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania 19380, USA.
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35
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Affiliation(s)
- Andreas Schmidt
- Clausthal University of Technology, Institute of Organic Chemistry, Leibnizstrasse 6, 38678 Clausthal‐Zellerfeld, Germany, Fax: +49‐5323‐722858
| | - Ariane Beutler
- Clausthal University of Technology, Institute of Organic Chemistry, Leibnizstrasse 6, 38678 Clausthal‐Zellerfeld, Germany, Fax: +49‐5323‐722858
| | - Bohdan Snovydovych
- Clausthal University of Technology, Institute of Organic Chemistry, Leibnizstrasse 6, 38678 Clausthal‐Zellerfeld, Germany, Fax: +49‐5323‐722858
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36
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Xiang Y, Caron PY, Lillie BM, Vaidyanathan R. Sulfur Contamination Due to Quenching of Halogenation Reactions with Sodium Thiosulfate: Resolution of Process Problems via Improved Quench Protocols. Org Process Res Dev 2008. [DOI: 10.1021/op700227p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yanqiao Xiang
- Development Science and Technology, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, U.S.A
| | - Pierre-Yves Caron
- Development Science and Technology, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, U.S.A
| | - Brett M. Lillie
- Development Science and Technology, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, U.S.A
| | - Rajappa Vaidyanathan
- Development Science and Technology, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, U.S.A
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37
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Affiliation(s)
- Kenneth L Arrington
- Department of Medicinal Chemistry, Merck Research Laboratories, P.O. Box 4, Sumneytown Pike, West Point, PA 19486, USA
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38
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Claramunt RM, López C, Pérez-Medina C, Pinilla E, Torres MR, Elguero J. Synthesis and structural study of tetrahydroindazolones. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.09.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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39
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Conchon E, Aboab B, Golsteyn RM, Cruzalegui F, Edmonds T, Léonce S, Pfeiffer B, Prudhomme M. Synthesis, in vitro antiproliferative activities, and Chk1 inhibitory properties of indolylpyrazolones and indolylpyridazinedione. Eur J Med Chem 2006; 41:1470-7. [PMID: 16996169 DOI: 10.1016/j.ejmech.2006.06.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Accepted: 06/22/2006] [Indexed: 11/30/2022]
Abstract
The synthesis of 5-indolylpyrazol-3-one, 4-indolylpyrazol-3-one and 4-indolyl-pyridazin-3,6-dione is reported. Their Chk1 inhibitory properties have been evaluated and their in vitro antiproliferative activities toward three tumor cell lines: murine leukemia L1210, human colon carcinoma HT29 and HCT116 have been determined. 4-Indolyl-pyridazin-3,6-dione is inactive against Chk1 and exhibits weak cytotoxicities toward the tumor cell lines tested. The IC(50) values toward Chk1 of the two indolylpyrazolones are identical and are in the micromolar range, but the cytotoxicities of 4-indolylpyrazol-3-one are significantly stronger than those of 5-indolylpyrazol-3-one. Since 4-indolylpyrazol-3-one and 5-indolylpyrazol-3-one can present several conformers and tautomeric forms, molecular modelling in the ATP binding site of Chk1 has been carried out to investigate which form could induce the best stabilization in the active site of the enzyme. To get an insight into the kinase selectivity of these compounds, their inhibitory activities toward Src kinase were evaluated.
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Affiliation(s)
- Elisabeth Conchon
- Laboratoire SEESIB, Université Blaise Pascal, UMR 6504 du CNRS, 63177 Aubière Cedex, France
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40
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Ivanova NV, Sviridov SI, Stepanov AE. Parallel solution-phase synthesis of substituted 2-(1,2,4-triazol-3-yl)benzimidazoles. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.09.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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41
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Huang S, Garbaccio RM, Fraley ME, Steen J, Kreatsoulas C, Hartman G, Stirdivant S, Drakas B, Rickert K, Walsh E, Hamilton K, Buser CA, Hardwick J, Mao X, Abrams M, Beck S, Tao W, Lobell R, Sepp-Lorenzino L, Yan Y, Ikuta M, Murphy JZ, Sardana V, Munshi S, Kuo L, Reilly M, Mahan E. Development of 6-substituted indolylquinolinones as potent Chek1 kinase inhibitors. Bioorg Med Chem Lett 2006; 16:5907-12. [PMID: 16990002 DOI: 10.1016/j.bmcl.2006.08.053] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Revised: 08/09/2006] [Accepted: 08/09/2006] [Indexed: 11/24/2022]
Abstract
Through a comparison of X-ray co-crystallographic data for 1 and 2 in the Chek1 active site, it was hypothesized that the affinity of the indolylquinolinone series (2) for Chek1 kinase would be improved via C6 substitution into the hydrophobic region I (HI) pocket. An efficient route to 6-bromo-3-indolyl-quinolinone (9) was developed, and this series was rapidly optimized for potency by modification at C6. A general trend was observed among these low nanomolar Chek1 inhibitors that compounds with multiple basic amines, or elevated polar surface area (PSA) exhibited poor cell potency. Minimization of these parameters (basic amines, PSA) resulted in Chek1 inhibitors with improved cell potency, and preliminary pharmacokinetic data are presented for several of these compounds.
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Affiliation(s)
- Shaei Huang
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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42
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3-(Indol-2-yl)indazoles as Chek1 kinase inhibitors: Optimization of potency and selectivity via substitution at C6. Bioorg Med Chem Lett 2006; 16:6049-53. [PMID: 16978863 DOI: 10.1016/j.bmcl.2006.08.118] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 08/29/2006] [Accepted: 08/29/2006] [Indexed: 10/24/2022]
Abstract
The development of 3-(indol-2-yl)indazoles as inhibitors of Chek1 kinase is described. Introduction of amides and heteroaryl groups at the C6 position of the indazole ring system provided sufficient Chek1 potency and selectivity over Cdk7 to permit escape from DNA damage-induced arrest in a cellular assay. Enzyme potency against Chek1 was optimized by the incorporation of a hydroxymethyl triazole moiety in compound 21 (Chek1 IC(50)=0.30nM) that was shown by X-ray crystallography to displace one of three highly conserved water molecules in the HI region of the ATP-binding cleft.
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