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Fabitha K, Chandrakanth M, Pramod RN, Arya CG, Li Y, Banothu J. Recent Developments in the Synthesis of Indole‐Pyrazole Hybrids. ChemistrySelect 2022. [DOI: 10.1002/slct.202201064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- K. Fabitha
- Department of Chemistry National Institute of Technology Calicut Kozhikode 673601 Kerala India
| | - Munugala Chandrakanth
- Department of Chemistry National Institute of Technology Calicut Kozhikode 673601 Kerala India
| | - Rakendu N. Pramod
- Department of Chemistry National Institute of Technology Calicut Kozhikode 673601 Kerala India
| | - C. G. Arya
- Department of Chemistry National Institute of Technology Calicut Kozhikode 673601 Kerala India
| | - Yupeng Li
- Masonic Cancer Center and Department of Medicinal Chemistry University of Minnesota Minneapolis Minnesota 55455 United States
| | - Janardhan Banothu
- Department of Chemistry National Institute of Technology Calicut Kozhikode 673601 Kerala India
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2
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Kоbylinska L, Khylyuk D, Subtelna I, Kitsera M, Lesyk R. In silico identification and biochemical validation of plausible molecular targets of 4-thiazolidinone derivative Les-3833 as a potential anticancer agent. UKRAINIAN BIOCHEMICAL JOURNAL 2021. [DOI: 10.15407/ubj93.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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3
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Hong WP, Shin I, Lim HN. Recent Advances in One-Pot Modular Synthesis of 2-Quinolones. Molecules 2020; 25:E5450. [PMID: 33233747 PMCID: PMC7699938 DOI: 10.3390/molecules25225450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022] Open
Abstract
It is known that 2-quinolones are broadly applicable chemical structures in medicinal and agrochemical research as well as various functional materials. A number of current publications about their synthesis and their applications emphasize the importance of these small molecules. The early synthetic chemistry originated from the same principle of the classical Friedländer and Knorr procedures for the preparation of quinolines. The analogous processes were developed by applying new synthetic tools such as novel catalysts, the microwave irradiation method, etc., whereas recent innovations in new bond forming reactions have allowed for novel strategies to construct the core structures of 2-quinolones beyond the bond disconnections based on two classical reactions. Over the last few decades, some reviews on structure-based, catalyst-based, and bioactivity-based studies have been released. In this focused review, we extensively surveyed recent examples of one-pot reactions, particularly in view of modular approaches. Thus, the contents are categorized as three major sections (two-, three-, and four-component reactions) according to the number of reagents that ultimately compose atoms of the core structures of 2-quinolones. The collected synthetic methods are discussed from the perspectives of strategy, efficiency, selectivity, and reaction mechanism.
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Affiliation(s)
- Wan Pyo Hong
- School of Advanced Materials and Chemical Engineering, Daegu Catholic University, 13-13, Hayang-ro, Hayang-eup, Gyeongsan-si, Gyeongbuk 38430, Korea;
| | - Inji Shin
- Department of Fine Chemistry, Seoul National University of Science and Technology, 232 Gongneung-ro, Nowon-gu, Seoul 01811, Korea
| | - Hee Nam Lim
- Eco-Friendly New Materials Research Center, Therapeutics&Biotechnology Division, 141, Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea
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4
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Roos K, Wu C, Damm W, Reboul M, Stevenson JM, Lu C, Dahlgren MK, Mondal S, Chen W, Wang L, Abel R, Friesner RA, Harder ED. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. J Chem Theory Comput 2019; 15:1863-1874. [PMID: 30768902 DOI: 10.1021/acs.jctc.8b01026] [Citation(s) in RCA: 619] [Impact Index Per Article: 123.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Katarina Roos
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Chuanjie Wu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wolfgang Damm
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Mark Reboul
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - James M. Stevenson
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Chao Lu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Markus K. Dahlgren
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Sayan Mondal
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wei Chen
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Robert Abel
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A. Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Edward D. Harder
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
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5
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Yamamoto Y. Recent Advances in Transition-Metal-Catalyzed Synthesis of 3- and/or 4-Aryl-2(1H)-Quinolones. HETEROCYCLES 2019. [DOI: 10.3987/rev-19-914] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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6
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Malvacio I, Cuzzolin A, Sturlese M, Vera DMA, Moyano EL, Moro S. Synthesis and preliminary structure-activity relationship study of 2-aryl-2H-pyrazolo[4,3-c]quinolin-3-ones as potential checkpoint kinase 1 (Chk1) inhibitors. J Enzyme Inhib Med Chem 2017; 33:171-183. [PMID: 29210298 PMCID: PMC6010083 DOI: 10.1080/14756366.2017.1404592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The serine-threonine checkpoint kinase 1 (Chk1) plays a critical role in the cell cycle arrest in response to DNA damage. In the last decade, Chk1 inhibitors have emerged as a novel therapeutic strategy to potentiate the anti-tumour efficacy of cytotoxic chemotherapeutic agents. In the search for new Chk1 inhibitors, a congeneric series of 2-aryl-2 H-pyrazolo[4,3-c]quinolin-3-one (PQ) was evaluated by in-vitro and in-silico approaches for the first time. A total of 30 PQ structures were synthesised in good to excellent yields using conventional or microwave heating, highlighting that 14 of them are new chemical entities. Noteworthy, in this preliminary study two compounds 4e2 and 4h2 have shown a modest but significant reduction in the basal activity of the Chk1 kinase. Starting from these preliminary results, we have designed the second generation of analogous in this class and further studies are in progress in our laboratories.
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Affiliation(s)
- Ivana Malvacio
- a Department of Organic Chemistry, INFIQC, School of Chemical Sciences , National University of Cordoba , Cordoba , Argentina.,b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - Alberto Cuzzolin
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - Mattia Sturlese
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - D Mariano A Vera
- c Department of Chemistry, QUIAMM-INBIOTEC, School of Exact and Natural Sciences , National University of Mar del Plata , Mar del Plata , Buenos Aires , Argentina
| | - E Laura Moyano
- a Department of Organic Chemistry, INFIQC, School of Chemical Sciences , National University of Cordoba , Cordoba , Argentina
| | - Stefano Moro
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
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7
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Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J Chem Theory Comput 2015; 12:281-96. [PMID: 26584231 DOI: 10.1021/acs.jctc.5b00864] [Citation(s) in RCA: 2020] [Impact Index Per Article: 224.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addition of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chemical space, OPLS3 employs over an order of magnitude more reference data and associated parameter types relative to other commonly used small molecule force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small molecule conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a number of proteins. Together, the improvements made to both the small molecule and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.
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Affiliation(s)
- Edward Harder
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wolfgang Damm
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jon Maple
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Chuanjie Wu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Mark Reboul
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jin Yu Xiang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Dmitry Lupyan
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Markus K Dahlgren
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jennifer L Knight
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Joseph W Kaus
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - David S Cerutti
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Goran Krilov
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Robert Abel
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
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8
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Cuzzolin A, Sturlese M, Malvacio I, Ciancetta A, Moro S. DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations. Molecules 2015; 20:9977-93. [PMID: 26035098 PMCID: PMC6272630 DOI: 10.3390/molecules20069977] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/05/2015] [Accepted: 05/21/2015] [Indexed: 11/17/2022] Open
Abstract
Virtual screening (VS) is a computational methodology that streamlines the drug discovery process by reducing costs and required resources through the in silico identification of potential drug candidates. Structure-based VS (SBVS) exploits knowledge about the three-dimensional (3D) structure of protein targets and uses the docking methodology as search engine for novel hits. The success of a SBVS campaign strongly depends upon the accuracy of the docking protocol used to select the candidates from large chemical libraries. The identification of suitable protocols is therefore a crucial step in the setup of SBVS experiments. Carrying out extensive benchmark studies, however, is usually a tangled task that requires users' proficiency in handling different file formats and philosophies at the basis of the plethora of existing software packages. We present here DockBench 1.0, a platform available free of charge that eases the pipeline by automating the entire procedure, from docking benchmark to VS setups. In its current implementation, DockBench 1.0 handles seven docking software packages and offers the possibility to test up to seventeen different protocols. The main features of our platform are presented here and the results of the benchmark study of human Checkpoint kinase 1 (hChk1) are discussed as validation test.
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Affiliation(s)
- Alberto Cuzzolin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova 35131, Italy.
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova 35131, Italy.
| | - Ivana Malvacio
- INFIQC-Organic Chemistry Department, School of Chemical Sciences, National University of Cordoba, Cordoba, CP 5000, Argentine.
| | - Antonella Ciancetta
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova 35131, Italy.
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova 35131, Italy.
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9
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Discovery of the 1,7-diazacarbazole class of inhibitors of checkpoint kinase 1. Bioorg Med Chem Lett 2014; 24:5704-5709. [PMID: 25453805 DOI: 10.1016/j.bmcl.2014.10.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/10/2014] [Accepted: 10/17/2014] [Indexed: 11/22/2022]
Abstract
Checkpoint kinase 1 (ChK1) is activated in response to DNA damage, acting to temporarily block cell cycle progression and allow for DNA repair. It is envisaged that inhibition of ChK1 will sensitize tumor cells to treatment with DNA-damaging therapies, and may enhance the therapeutic window. High throughput screening identified carboxylate-containing diarylpyrazines as a prominent hit series, but with limited biochemical potency and no cellular activity. Through a series of SAR investigations and X-ray crystallographic analysis the critical role of polar contacts with conserved waters in the kinase back pocket was established. Structure-based design, guided by in silico modeling, transformed the series to better satisfy these contacts and the novel 1,7-diazacarbazole class of inhibitors was discovered. Here we present the genesis of this novel series and the identification of GNE-783, a potent, selective and orally bioavailable inhibitor of ChK1.
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10
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Desaphy J, Rognan D. sc-PDB-Frag: A Database of Protein–Ligand Interaction Patterns for Bioisosteric Replacements. J Chem Inf Model 2014; 54:1908-18. [DOI: 10.1021/ci500282c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jérémy Desaphy
- Laboratory for Therapeutical
Innovation,
UMR 7200 Université de Strasbourg/CNRS, MEDALIS Drug Discovery
Center, F-67400 Illkirch, France
| | - Didier Rognan
- Laboratory for Therapeutical
Innovation,
UMR 7200 Université de Strasbourg/CNRS, MEDALIS Drug Discovery
Center, F-67400 Illkirch, France
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11
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O’Brien NJ, Brzozowski M, Wilson DJ, Deady LW, Abbott BM. Synthesis and biological evaluation of substituted 3-anilino-quinolin-2(1H)-ones as PDK1 inhibitors. Bioorg Med Chem 2014; 22:3781-90. [DOI: 10.1016/j.bmc.2014.04.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
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12
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Bruneau A, Brion JD, Messaoudi S, Alami M. A general Pd/Cu-catalyzed C–H heteroarylation of 3-bromoquinolin-2(1H)-ones. Org Biomol Chem 2014; 12:8533-41. [DOI: 10.1039/c4ob01610f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Pd(OAc)2/CuI system effectively catalyzes the coupling of 3-bromoquinolin-2(1H)-ones with a series of azoles to give 3-(heteroaryl)quinolin-2(1H)-ones in good yields.
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Affiliation(s)
- Alexandre Bruneau
- Univ Paris-Sud
- CNRS
- BioCIS-UMR 8076
- Laboratoire de Chimie Thérapeutique
- Equipe Labellisée Ligue Contre le Cancer
| | - Jean-Daniel Brion
- Univ Paris-Sud
- CNRS
- BioCIS-UMR 8076
- Laboratoire de Chimie Thérapeutique
- Equipe Labellisée Ligue Contre le Cancer
| | - Samir Messaoudi
- Univ Paris-Sud
- CNRS
- BioCIS-UMR 8076
- Laboratoire de Chimie Thérapeutique
- Equipe Labellisée Ligue Contre le Cancer
| | - Mouad Alami
- Univ Paris-Sud
- CNRS
- BioCIS-UMR 8076
- Laboratoire de Chimie Thérapeutique
- Equipe Labellisée Ligue Contre le Cancer
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13
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Lancelot N, Piotto M, Theret I, Lesur B, Hennig P. Applications of NMR screening techniques to the pharmaceutical target Checkpoint kinase 1. J Pharm Biomed Anal 2013; 93:125-35. [PMID: 24280017 DOI: 10.1016/j.jpba.2013.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 10/17/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022]
Abstract
Ligand screening techniques based on NMR spectroscopy are not as sensitive as other commonly used methods like fluorescence, radiolabeling and surface plasmon resonance. However, using modern NMR instrumentation, they can achieve reliable screening under near physiological condition using as little as 4.6 nmol of receptor and 100 nmol of ligand. Additionally, these NMR methods can also provide valuable and specific information on the ligand under investigation such as the dissociation constant KD, the binding epitope and most importantly some structural information on the actual conformation in the bound state. In this manuscript, we describe the use of NMR based screening techniques ("Saturation Transfer Difference" (STD) and "Water Ligand Observed via Gradient SpectroscopY" (WaterLOGSY)) to detect small therapeutic molecules that interact with the DNA damage checkpoint enzyme Checkpoint kinase 1 (Chk1). After the identification of the most potent ligand, we used specific NMR experiments to perform the epitope mapping of this ligand ("Group epitope mapping-STD" (GEM-STD), "Difference of Inversion REcovery rate with and without Target IrradiatiON" (DIRECTION)) and to characterize its bound conformation ("Transferred-Nuclear Overhauser Effect SpectroscopY" (tr-NOESY), "Transferred-Rotating frame Overhauser Effect SpectroscopY" (tr-ROESY)). Finally, we used molecular docking procedures to position the ligand within the active site of Chk1. On the experimental level, a comparison between NMR studies performed in a 90%H2O/10%D2O buffer and a 100% D2O buffer is also presented and discussed.
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Affiliation(s)
- N Lancelot
- Institut de Recherches Servier, Analytical and Physical Chemistry Department, 11 rue des Moulineaux, 92150 Suresnes, France.
| | - M Piotto
- Bruker BioSpin, Laboratoire d'applications RMN, 34 rue de l'industrie, 67166 Wissembourg, France.
| | - I Theret
- Institut de Recherches Servier, Chimie Partenariats et Modélisation Moléculaire, 125 Chemin de Ronde, 78290 Croissy-Sur-Seine, France
| | - B Lesur
- Institut de Recherches Servier, Chimie Partenariats et Modélisation Moléculaire, 125 Chemin de Ronde, 78290 Croissy-Sur-Seine, France
| | - P Hennig
- Institut de Recherches Servier, Analytical and Physical Chemistry Department, 11 rue des Moulineaux, 92150 Suresnes, France
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14
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Ambre PK, Pissurlenkar RRS, Coutinho EC, Iyer RP. Identification of new checkpoint kinase-1 (Chk1) inhibitors by docking, 3D-QSAR, and pharmacophore-modeling methods. CAN J CHEM 2012. [DOI: 10.1139/v2012-047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Inhibition of checkpoint kinase-1 (Chk1) by small molecules is of great therapeutic interest in the field of oncology and for understanding cell-cycle regulations. This paper presents a model with elements from docking, pharmacophore mapping, the 3D-QSAR approaches CoMFA, CoMSIA and CoRIA, and virtual screening to identify novel hits against Chk1. Docking, 3D-QSAR (CoRIA, CoMFA and CoMSIA), and pharmacophore studies delineate crucial site points on the Chk1 inhibitors, which can be modified to improve activity. The docking analysis showed residues in the proximity of the ligands that are involved in ligand–receptor interactions, whereas CoRIA models were able to derive the magnitude of these interactions that impact the activity. The ligand-based 3D-QSAR methods (CoMFA and CoMSIA) highlight key areas on the molecules that are beneficial and (or) detrimental for activity. The docking studies and 3D-QSAR models are in excellent agreement in terms of binding-site interactions. The pharmacophore hypotheses validated using sensitivity, selectivity, and specificity parameters is a four-point model, characterized by a hydrogen-bond acceptor (A), hydrogen-bond donor (D), and two hydrophobes (H). This map was used to screen a database of 2.7 million druglike compounds, which were pruned to a small set of potential inhibitors by CoRIA, CoMFA, and CoMSIA models with predicted activity in the range of 8.5–10.5 log units.
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Affiliation(s)
- Premlata K. Ambre
- Molecular Simulations Group, Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (East), Mumbai 400 098 India
| | - Raghuvir R. S. Pissurlenkar
- Molecular Simulations Group, Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (East), Mumbai 400 098 India
| | - Evans C. Coutinho
- Molecular Simulations Group, Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (East), Mumbai 400 098 India
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15
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Dudkin VY, Wang C, Arrington KL, Fraley ME, Hartman GD, Stirdivant SM, Drakas RA, Rickert K, Walsh ES, Hamilton K, Buser CA, Hardwick J, Tao W, Beck SC, Mao X, Lobell RB, Sepp-Lorenzino L. Pyridyl aminothiazoles as potent Chk1 inhibitors: Optimization of cellular activity. Bioorg Med Chem Lett 2012; 22:2613-9. [DOI: 10.1016/j.bmcl.2012.01.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/26/2012] [Accepted: 01/30/2012] [Indexed: 11/26/2022]
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16
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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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17
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Structural requirements of pyrimidine, thienopyridine and ureido thiophene carboxamide-based inhibitors of the checkpoint kinase 1: QSAR, docking, molecular dynamics analysis. J Mol Model 2012; 18:3227-42. [DOI: 10.1007/s00894-011-1321-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 11/23/2011] [Indexed: 11/27/2022]
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18
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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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19
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Abstract
Over the last decade, polar surface area (PSA) has become a ubiquitous term in medicinal and computational chemistry circles. This article charts the development of the increasingly efficient methods for the calculation of PSA before illustrating its usefulness through selected examples drawn from the medicinal chemistry literature. Consideration of PSA is shown to assist in the improvement of cellular potency, intestinal absorption and blood-brain barrier permeation or restriction to the peripheral circulation.
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20
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Lainchbury M, Collins I. Checkpoint kinase inhibitors: a patent review (2009 - 2010). Expert Opin Ther Pat 2011; 21:1191-210. [PMID: 21599421 DOI: 10.1517/13543776.2011.586632] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Cells that suffer DNA damage activate the checkpoint kinases CHK1 and CHK2, which signal to initiate repair processes, limit cell-cycle progression and prevent cell replication, until the damaged DNA is repaired. Due to their potential application as novel anticancer therapies, inhibitors of CHK1 and CHK2 have become the focus of numerous drug discovery projects. AREAS COVERED This patent review examines the chemical structures and biological activities of recently reported CHK1 and CHK2 inhibitors. The chemical abstract and patent databases SciFinder and esp@cenet were used to locate patent applications that were published between September 2008 and December 2010, claiming chemical structures for use as CHK1 or CHK2 inhibitors. EXPERT OPINION This is an exciting time for checkpoint kinase inhibitors, with several currently in Phase I or II clinical trials. Many of the CHK1 inhibitors contained within this patent review have shown preclinical efficacy in combination with DNA-damaging chemotherapies. CHK1 inhibitors have recently been demonstrated to be efficacious as single agents in preclinical models of tumors with constitutive activation of CHK1 or high intrinsic DNA damage due to replication stress. The level of newly published patent applications covering CHK1 and CHK2 inhibitors remains high and a diverse range of scaffolds has been claimed.
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Affiliation(s)
- Michael Lainchbury
- The Institute of Cancer Research, Cancer Research UK Cancer Therapeutics Unit, Haddow Laboratories, Sutton, Surrey, UK.
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21
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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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22
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Ackermann L, Barfüßer S, Potukuchi H. Copper-CatalyzedN-Arylation/Hydroamin(d)ation Domino Synthesis of Indoles and its Application to the Preparation of a Chek1/KDR Kinase Inhibitor Pharmacophore. Adv Synth Catal 2009. [DOI: 10.1002/adsc.200900004] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Jake Slavish P, Jiang Q, Cui X, Morris SW, Webb TR. Design and synthesis of a novel tyrosine kinase inhibitor template. Bioorg Med Chem 2009; 17:3308-16. [PMID: 19362847 DOI: 10.1016/j.bmc.2009.03.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 03/18/2009] [Accepted: 03/21/2009] [Indexed: 11/25/2022]
Abstract
We report the design and synthesis of an insulin receptor kinase family-targeted inhibitor template using the inhibitor conformation observed in an IGF1R/inhibitor co-crystal complex by application of a novel molecular design approach that we have recently published. The synthesis of the template involves a one pot Opatz cyclization reaction that provides a versatile indole ester in good yields. We also developed the required chemistry to elaborate this template with additional substituents and have used this chemistry to prepare some initial compounds that show selective inhibition of anaplastic lymphoma kinase (ALK).
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Affiliation(s)
- P Jake Slavish
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105-3678, United States
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24
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Development of thioquinazolinones, allosteric Chk1 kinase inhibitors. Bioorg Med Chem Lett 2009; 19:1240-4. [DOI: 10.1016/j.bmcl.2008.12.076] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 12/16/2008] [Accepted: 12/17/2008] [Indexed: 11/19/2022]
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25
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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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26
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Garbaccio RM, Huang S, Tasber ES, Fraley ME, Yan Y, Munshi S, Ikuta M, Kuo L, Kreatsoulas C, Stirdivant S, Drakas B, Rickert K, Walsh ES, Hamilton KA, Buser CA, Hardwick J, Mao X, Beck SC, Abrams MT, Tao W, Lobell R, Sepp-Lorenzino L, Hartman GD. Synthesis and evaluation of substituted benzoisoquinolinones as potent inhibitors of Chk1 kinase. Bioorg Med Chem Lett 2007; 17:6280-5. [PMID: 17900896 DOI: 10.1016/j.bmcl.2007.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 08/28/2007] [Accepted: 09/04/2007] [Indexed: 11/23/2022]
Abstract
From HTS lead 1, a novel benzoisoquinolinone class of ATP-competitive Chk1 inhibitors was devised and synthesized via a photochemical route. Using X-ray crystallography as a guide, potency was rapidly enhanced through the installation of a tethered basic amine designed to interact with an acidic residue (Glu91) in the enzyme pocket. Further SAR was explored at the solvent front and near to the H1 pocket and resulted in the discovery of low MW, sub-nanomolar inhibitors of Chk1.
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Affiliation(s)
- Robert M Garbaccio
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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27
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Brnardic EJ, Garbaccio RM, Fraley ME, Tasber ES, Steen JT, Arrington KL, Dudkin VY, Hartman GD, Stirdivant SM, Drakas BA, Rickert K, Walsh ES, Hamilton K, Buser CA, Hardwick J, Tao W, Beck SC, Mao X, Lobell RB, Sepp-Lorenzino L, Yan Y, Ikuta M, Munshi SK, Kuo LC, Kreatsoulas C. Optimization of a pyrazoloquinolinone class of Chk1 kinase inhibitors. Bioorg Med Chem Lett 2007; 17:5989-94. [PMID: 17804227 DOI: 10.1016/j.bmcl.2007.07.051] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 07/03/2007] [Accepted: 07/17/2007] [Indexed: 11/19/2022]
Abstract
The development of 2,5-dihydro-4H-pyrazolo[4,3-c]quinolin-4-ones as inhibitors of Chk1 kinase is described. Introduction of a fused ring at the C7/C8 positions of the pyrazoloquinolinone provided an increase in potency while guidance from overlapping inhibitor bound Chk1 X-ray crystal structures contributed to the discovery of a potent and solubilizing propyl amine moiety in compound 52 (Chk1 IC(50)=3.1 nM).
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Affiliation(s)
- Edward J Brnardic
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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28
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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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