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Abstract
In classical medicinal chemistry, nitrile groups were commonly considered as bioisosteres of carbonyl, hydroxyl and carboxyl groups, as well as halogen atoms. However, there is a lack of in-depth understanding about the structural and energetic characteristics of nitrile groups in protein–ligand interactions. Here, we have surveyed the Protein Data Bank and ChEMBL databases with the goal of characterizing such protein–ligand interactions for nitrile-containing compounds. We discuss the versatile roles of nitrile groups in improving binding affinities, and give special attention to examples of displacing and mimicking binding-site waters by nitrile groups. We expect that this review article will further inspire medicinal chemists to exploit nitrile groups rationally in structure-based drug design.
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2
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Kitamura S, Morisseau C, Harris TR, Inceoglu B, Hammock BD. Occurrence of urea-based soluble epoxide hydrolase inhibitors from the plants in the order Brassicales. PLoS One 2017; 12:e0176571. [PMID: 28472063 PMCID: PMC5417501 DOI: 10.1371/journal.pone.0176571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 04/12/2017] [Indexed: 01/08/2023] Open
Abstract
Recently, dibenzylurea-based potent soluble epoxide hydrolase (sEH) inhibitors were identified in Pentadiplandra brazzeana, a plant in the order Brassicales. In an effort to generalize the concept, we hypothesized that plants that produce benzyl glucosinolates and corresponding isothiocyanates also produce these dibenzylurea derivatives. Our overall aim here was to examine the occurrence of urea derivatives in Brassicales, hoping to find biologically active urea derivatives from plants. First, plants in the order Brassicales were analyzed for the presence of 1, 3-dibenzylurea (compound 1), showing that three additional plants in the order Brassicales produce the urea derivatives. Based on the hypothesis, three dibenzylurea derivatives with sEH inhibitory activity were isolated from maca (Lepidium meyenii) roots. Topical application of one of the identified compounds (compound 3, human sEH IC50 = 222 nM) effectively reduced pain in rat inflammatory pain model, and this compound was bioavailable after oral administration in mice. The biosynthetic pathway of these urea derivatives was investigated using papaya (Carica papaya) seed as a model system. Finally, a small collection of plants from the Brassicales order was grown, collected, extracted and screened for sEH inhibitory activity. Results show that several plants of the Brassicales order could be potential sources of urea-based sEH inhibitors.
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Affiliation(s)
- Seiya Kitamura
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, California, United States of America
| | - Christophe Morisseau
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, California, United States of America
| | - Todd R. Harris
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, California, United States of America
| | - Bora Inceoglu
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, California, United States of America
| | - Bruce D. Hammock
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, California, United States of America
- * E-mail:
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3
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Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods. J Chem Theory Comput 2015; 10:3207-20. [PMID: 26588291 DOI: 10.1021/ct500189s] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Accurate and efficient affinity calculations are critical to enhancing the contribution of in silico modeling during the lead optimization phase of a drug discovery campaign. Here, we present a large-scale study of the efficacy of data fusion strategies to leverage results from end-point MM/GBSA calculations in multiple receptors to identify potent inhibitors among an ensemble of congeneric ligands. The retrospective analysis of 13 congeneric ligand series curated from publicly available data across seven biological targets demonstrates that in 90% of the individual receptor structures MM/GBSA scores successfully identify subsets of inhibitors that are more potent than a random selection, and data fusion strategies that combine MM/GBSA scores from each of the receptors significantly increase the robustness of the predictions. Among nine different data fusion metrics based on consensus scores or receptor rankings, the SumZScore (i.e., converting MM/GBSA scores into standardized Z-Scores within a receptor and computing the sum of the Z-Scores for a given ligand across the ensemble of receptors) is found to be a robust and physically meaningful metric for combining results across multiple receptors. Perhaps most surprisingly, even with relatively low to modest overall correlations between SumZScore and experimental binding affinities, SumZScore tends to reliably prioritize subsets of inhibitors that are at least as potent as those that are prioritized from a "best" single receptor identified from known compounds within the congeneric series.
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Affiliation(s)
- Jennifer L Knight
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Goran Krilov
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Kenneth W Borrelli
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Joshua Williams
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - John R Gunn
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Alec Clowes
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Luciano Cheng
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Richard A Friesner
- Columbia University , Department of Chemistry, 3000 Broadway, MC 3110, New York, New York 10027, United States
| | - Robert Abel
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
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4
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Dolezal M, Zitko J. Pyrazine derivatives: a patent review (June 2012 – present). Expert Opin Ther Pat 2014; 25:33-47. [DOI: 10.1517/13543776.2014.982533] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Martin Dolezal
- 1Charles University in Prague, Faculty of Pharmacy in Hradec Kralove, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Jan Zitko
- 2Charles University in Prague, Faculty of Pharmacy in Hradec Kralove, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
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Lv M, Ma S, Tian Y, Zhang X, Lv W, Zhai H. Computational studies on the binding mechanism between triazolone inhibitors and Chk1 by molecular docking and molecular dynamics. MOLECULAR BIOSYSTEMS 2014; 11:275-86. [PMID: 25372494 DOI: 10.1039/c4mb00449c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chk1, a serine/threonine protein kinase that participates in transducing DNA damage signals, is an attractive target due to its involvement in tumor initiation and progression. As a novel Chk1 inhibitor, the triazolone's bioactivity mechanism is not clear. In this study, we carried out an integrated computational study that combines molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations to identify the key factors necessary for the bioactivities. With the aim of discerning the structural features that affect the inhibitory activity of triazolones, MK-8776, a Chk1 inhibitor that reached the clinical stage, was also used as a reference for simulations. A comparative analysis of the triazolone inhibitors at the molecular level offers valuable insight into the structural and energetic properties. A general feature is that all the studied inhibitors bind in the pocket characterized by residues Leu14, Val22, Ala35, Glu84, Tyr85, Cys86, and Leu136 of Chk1. Moreover, introducing hydrophobic groups into triazolone inhibitors is favorable for binding to Chk1, which is corroborated by residue Leu136 with a relatively large difference in the contribution between MK-8776 and five triazolones to the total binding free energies. A hydrogen bond between the polar hydrogen atoms at R1 and Cys86 can facilitate proper placement of the inhibitor in the binding pocket of Chk1 that favors binding. However, the introduction of hydrophilic groups into the R2 position diminishes binding affinity. The information provided by this research is of benefit for further rational design of novel promising inhibitors of Chk1.
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Affiliation(s)
- Min Lv
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, Gansu Province, People's Republic of China.
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6
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King C, Diaz H, Barnard D, Barda D, Clawson D, Blosser W, Cox K, Guo S, Marshall M. Characterization and preclinical development of LY2603618: a selective and potent Chk1 inhibitor. Invest New Drugs 2013; 32:213-26. [PMID: 24114124 DOI: 10.1007/s10637-013-0036-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 09/30/2013] [Indexed: 12/27/2022]
Abstract
Interference with DNA damage checkpoints has been demonstrated preclinically to be a highly effective means of increasing the cytotoxicity of a number of DNA-damaging cancer therapies. Cell cycle arrest at these checkpoints protects injured cells from apoptotic cell death until DNA damage can be repaired. In the absence of functioning DNA damage checkpoints, cells with damaged DNA may proceed into premature mitosis followed by cell death. A key protein kinase involved in activating and maintaining the S and G2/M checkpoints is Chk1. Pharmacological inhibition of Chk1 in the absence of p53 functionality leads to abrogation of DNA damage checkpoints and has been shown preclinically to enhance the activity of many standard of care chemotherapeutic agents. LY2603618 is a potent and selective small molecule inhibitor of Chk1 protein kinase activity in vitro (IC(50) = 7 nM) and the first selective Chk1 inhibitor to enter clinical cancer trials. Treatment of cells with LY2603618 produced a cellular phenotype similar to that reported for depletion of Chk1 by RNAi. Inhibition of intracellular Chk1 by LY2603618 results in impaired DNA synthesis, elevated H2A.X phosphorylation indicative of DNA damage and premature entry into mitosis. When HeLa cells were exposed to doxorubicin to induce a G2/M checkpoint arrest, subsequent treatment with LY2603618 released the checkpoint, resulting in cells entering into metaphase with poorly condensed chromosomes. Consistent with abrogation of the Chk1 and p53-dependent G2/M checkpoint, mutant TP53 HT-29 colon cancer cells were more sensitive to gemcitabine when also treated with LY2603618, while wild-type TP53 HCT116 cells were not sensitized by LY2603618 to gemcitabine. Treatment of Calu-6 human mutant TP53 lung cancer cell xenografts with gemcitabine resulted in a stimulation of Chk1 kinase activity that was inhibited by co-administration of LY2603618. By all criteria, LY2603618 is a highly effective inhibitor of multiple aspects of Chk1 biology.
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Affiliation(s)
- Constance King
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, 46285, USA
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7
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Mane M, Balaskar R, Gavade S, Pabrekar P, Mane D. An efficient and greener protocol towards synthesis of unsymmetrical N,N′-biphenyl urea. ARAB J CHEM 2013. [DOI: 10.1016/j.arabjc.2011.01.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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8
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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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9
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Zhao L, Liu Y, Hu S, Zhang H. 3D-QSAR study of Chk1 kinase inhibitors based on docking. J Mol Model 2012; 18:3669-94. [DOI: 10.1007/s00894-012-1363-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 01/17/2012] [Indexed: 11/24/2022]
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10
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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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11
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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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12
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Mane MS, Balaskar RS, Gavade SN, Pabrekar PN, Shingare MS, Mane DV. Regiospecific oxidation of an alkyl group of aromatic amine to carbonyl group by DDQ in aq. medium. CHINESE CHEM LETT 2011. [DOI: 10.1016/j.cclet.2011.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Seebeck B, Wagener M, Rarey M. From Activity Cliffs to Target-Specific Scoring Models and Pharmacophore Hypotheses. ChemMedChem 2011; 6:1630-9, 1533. [DOI: 10.1002/cmdc.201100179] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 05/27/2011] [Indexed: 11/06/2022]
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14
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Hong PC, Chen LJ, Lai TY, Yang HY, Chiang SJ, Lu YY, Tsai PK, Hsu HY, Wei WY, Liao CB. Synthesis of selenophene derivatives as novel CHK1 inhibitors. Bioorg Med Chem Lett 2010; 20:5065-8. [DOI: 10.1016/j.bmcl.2010.07.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 07/07/2010] [Accepted: 07/09/2010] [Indexed: 10/19/2022]
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15
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Chen JJ, Liu TL, Yang LJ, Li LL, Wei YQ, Yang SY. Pharmacophore modeling and virtual screening studies of checkpoint kinase 1 inhibitors. Chem Pharm Bull (Tokyo) 2009; 57:704-9. [PMID: 19571415 DOI: 10.1248/cpb.57.704] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this study, chemical feature-based 3-dimensional (3D) pharmacophore models of Checkpoint kinase 1 (Chk1) inhibitors were developed based on the known inhibitors of Chk1. The best pharmacophore model Hypo1 was characterized by the best correlation coefficient (0.9577), and the lowest root mean square deviation (0.8871). Hypo1 consists of one hydrogen-bond acceptor, one hydrogen-bond donor, and two hydrophobic features, as well as one excluded volume. This pharmacophore model was further validated by both test set and cross validation methods. A comparison analysis of Hypo1 with chemical features in the active site of Chk1 indicates that the pharmacophore model Hypo1 can correctly reflect the interactions between Chk1 and its ligands. Then Hypo1 was used to screen chemical databases, including Specs and Chinese Nature Product Database (CNPD) for potential lead compounds. The hit compounds were subsequently subjected to filtering by Lipinski's rule of five and docking study to refine the retrieved hits. Finally some of the most potent (estimated) compounds were selected from the final refined hits and suggested for further experimental investigation.
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Affiliation(s)
- Jin-Juan Chen
- State Key Laboratory of Biotherapy, West China Hospital, West China School of Pharmacy, Sichuan University
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16
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Wang Y, Ji P, Liu J, Broaddus RR, Xue F, Zhang W. Centrosome-associated regulators of the G(2)/M checkpoint as targets for cancer therapy. Mol Cancer 2009; 8:8. [PMID: 19216791 PMCID: PMC2657106 DOI: 10.1186/1476-4598-8-8] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 02/13/2009] [Indexed: 01/04/2023] Open
Abstract
In eukaryotic cells, control mechanisms have developed that restrain cell-cycle transitions in response to stress. These regulatory pathways are termed cell-cycle checkpoints. The G(2)/M checkpoint prevents cells from entering mitosis when DNA is damaged in order to afford these cells an opportunity to repair the damaged DNA before propagating genetic defects to the daughter cells. If the damage is irreparable, checkpoint signaling might activate pathways that lead to apoptosis. Since alteration of cell-cycle control is a hallmark of tumorigenesis, cell-cycle regulators represent potential targets for therapy. The centrosome has recently come into focus as a critical cellular organelle that integrates G(2)/M checkpoint control and repairs signals in response to DNA damage. A growing number of G(2)/M checkpoint regulators have been found in the centrosome, suggesting that centrosome has an important role in G(2)/M checkpoint function. In this review, we discuss centrosome-associated regulators of the G(2)/M checkpoint, the dysregulation of this checkpoint in cancer, and potential candidate targets for cancer therapy.
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Affiliation(s)
- Yingmei Wang
- Tianjin General Hospital, Tianjin Medical University, Tianjin, PR China.
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17
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Janetka JW, Ashwell S. Checkpoint kinase inhibitors: a review of the patent literature. Expert Opin Ther Pat 2009; 19:165-97. [DOI: 10.1517/13543770802653622] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Asakawa K, Noguchi N, Takashima S, Nakada M. Preparation of a new chiral building block containing a benzylic quaternary stereogenic center and a formal total synthesis of (−)-physostigmine. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.09.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Chaturvedi D, Mishra N, Mishra V. A High Yielding, One-pot Synthesis of Substituted Ureas from the Corresponding Amines Using Mitsunobu’s Reagent. MONATSHEFTE FUR CHEMIE 2008. [DOI: 10.1007/s00706-007-0776-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Li G, Tao ZF, Tong Y, Przytulinska MK, Kovar P, Merta P, Chen Z, Zhang H, Sowin T, Rosenberg SH, Lin NH. Synthesis and in-vitro biological activity of macrocyclic urea Chk1 inhibitors. Bioorg Med Chem Lett 2007; 17:6499-504. [DOI: 10.1016/j.bmcl.2007.09.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Revised: 09/24/2007] [Accepted: 09/26/2007] [Indexed: 11/27/2022]
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21
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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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22
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Tao ZF, Li G, Tong Y, Stewart KD, Chen Z, Bui MH, Merta P, Park C, Kovar P, Zhang H, Sham HL, Rosenberg SH, Sowin TJ, Lin NH. Discovery of 4′-(1,4-dihydro-indeno[1,2-c]pyrazol-3-yl)-benzonitriles and 4′-(1,4-dihydro-indeno[1,2-c]pyrazol-3-yl)-pyridine-2′-carbonitriles as potent checkpoint kinase 1 (Chk1) inhibitors. Bioorg Med Chem Lett 2007; 17:5944-51. [PMID: 17827013 DOI: 10.1016/j.bmcl.2007.07.102] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 07/20/2007] [Accepted: 07/23/2007] [Indexed: 10/22/2022]
Abstract
An extensive structure-activity relationship study of the 3-position of a series of tricyclic pyrazole-based Chk1 inhibitors is described. As a result, 4'-(1,4-dihydro-indeno[1,2-c]pyrazol-3-yl)-benzonitriles (4) and 4'-(1,4-dihydro-indeno[1,2-c]pyrazol-3-yl)-pyridine-2'-carbonitriles (29) emerged as new lead series. Compared with the original lead compound 2, these new leads fully retain the biological activity in both enzymatic inhibition and cell-based assays. More importantly, the new leads 4 and 29 exhibit favorable physicochemical properties such as lower molecular weight, lower Clog P, and the absence of a hydroxyl group. Furthermore, structure-activity relationship studies were performed at the 6- and 7-positions of 4, which led to the identification of ideal Chk1 inhibitors 49, 50, 51, and 55. These compounds not only potently inhibit Chk1 in an enzymatic assay but also significantly potentiate the cytotoxicity of DNA-damaging agents in cell-based assays while they show little single agent activity. A cell cycle analysis by FACS confirmed that these Chk1 inhibitors efficiently abrogate the G2/M and S checkpoints induced by DNA-damaging agent. The current work paved the way to the identification of several potent Chk1 inhibitors with good pharmacokinetics that are suitable for in vivo study with oral dosing.
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Affiliation(s)
- Zhi-Fu Tao
- Cancer Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA.
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23
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Tao ZF, Li G, Tong Y, Chen Z, Merta P, Kovar P, Zhang H, Rosenberg SH, Sham HL, Sowin TJ, Lin NH. Synthesis and biological evaluation of 4'-(6,7-disubstituted-2,4-dihydro-indeno[1,2-c]pyrazol-3-yl)-biphenyl-4-ol as potent Chk1 inhibitors. Bioorg Med Chem Lett 2007; 17:4308-15. [PMID: 17544271 DOI: 10.1016/j.bmcl.2007.05.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 05/04/2007] [Accepted: 05/09/2007] [Indexed: 10/23/2022]
Abstract
A new series of potent tricyclic pyrazole-based Chk1 inhibitors are described. Analogues disubstituted on the 6- and 7-positions show improved Chk1 inhibition potency compared with analogues with a single substituent on either the 6- or 7-position. Based on the lead compound 4'-(6,7-dimethoxy-2,4-dihydro-indeno[1,2-c]pyrazol-3-yl)-biphenyl-4-ol (2), detailed SAR studies on the 6- and 7-positions were performed. 3'-morpholin-4'-yl-propoxy, pyridin-4'-ylmethoxy, pyridin-3'-ylmethoxy, 2'-(5''-ethyl-pyridin-2''-yl)-ethoxy, pyridin-2'-ylethoxy, (6'-methyl-pyridin-2'-yl)-propoxyethoxy, 2',3'-dihydroxyl-1'-yl-propoxy, and tetrahydro-furan-3'-yloxy have been identified as the best groups on the 6-position when the 7-position is substituted with methoxyl group. Pyridin-2'-ylmethoxy and pyridin-3'-ylmethoxy have been identified as the best substituents at the 7-position while the 6-position bearing methoxyl group. These compounds significantly potentiate the cytotoxicity of DNA-damaging antitumor agents in a cell-based assay and efficiently abrogate the doxorubicin-induced G2/M and the camptothecin-induced S checkpoints, suggesting that their potent biological activities are mechanism-based through Chk1 inhibition.
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Affiliation(s)
- Zhi-Fu Tao
- Cancer Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA.
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24
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Tong Y, Claiborne A, Stewart KD, Park C, Kovar P, Chen Z, Credo RB, Gu WZ, Gwaltney SL, Judge RA, Zhang H, Rosenberg SH, Sham HL, Sowin TJ, Lin NH. Discovery of 1,4-dihydroindeno[1,2-c]pyrazoles as a novel class of potent and selective checkpoint kinase 1 inhibitors. Bioorg Med Chem 2007; 15:2759-67. [PMID: 17287122 DOI: 10.1016/j.bmc.2007.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 01/11/2007] [Indexed: 11/22/2022]
Abstract
A new class of checkpoint kinase 1 (CHK-1) inhibitors bearing a 1,4-dihydroindeno[1,2-c]pyrazole core was developed after initial hits from high throughput screening. The efficient hit-to-lead process was facilitated by X-ray crystallography and led to potent inhibitors (<10nM) against CHK-1. X-ray co-crystal structures of bound inhibitors demonstrated that two sub-series of this class of compounds, exemplified by 21 and 41, exhibit distinctive hydrogen bonding patterns in the specificity pocket of the active site. Two compounds, 41 and 43, were capable of potentiating doxorubicin and camptothecin, both DNA-damaging agents, in cell proliferation assays (MTS and soft agar assays) and abrogating G2/M checkpoint in a mechanism-based FACS assay.
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Affiliation(s)
- Yunsong Tong
- Cancer Research, Global Pharmaceutical R&D, Abbott Laboratories, Abbott Park, IL 60064, USA.
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25
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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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