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Long L, Zhang H, Zhou Z, Duan L, Fan D, Wang R, Xu S, Qiao D, Zhu W. Pyrrole-containing hybrids as potential anticancer agents: An insight into current developments and structure-activity relationships. Eur J Med Chem 2024; 273:116470. [PMID: 38762915 DOI: 10.1016/j.ejmech.2024.116470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024]
Abstract
Cancer poses a significant threat to human health. Therefore, it is urgent to develop potent anti-cancer drugs with excellent inhibitory activity and no toxic side effects. Pyrrole and its derivatives are privileged heterocyclic compounds with significant diverse pharmacological effects. These compounds can target various aspects of cancer cells and have been applied in clinical settings or are undergoing clinical trials. As a result, pyrrole has emerged as a promising drug scaffold and has been further probed to get novel entities for the treatment of cancer. This article reviews recent research progress on anti-cancer drugs containing pyrrole. It focuses on the mechanism of action, biological activity, and structure-activity relationships of pyrrole derivatives, aiming to assist in designing and synthesizing innovative pyrrole-based anti-cancer compounds.
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Affiliation(s)
- Li Long
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Han Zhang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - ZhiHui Zhou
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Lei Duan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Dang Fan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Ran Wang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Shan Xu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China.
| | - Dan Qiao
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China.
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China.
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McCone JAJ, Teesdale-Spittle PH, Flanagan JU, Harvey JE. A Structure-Activity Investigation of the Fungal Metabolite (-)-TAN-2483B: Inhibition of Bruton's Tyrosine Kinase. Chemistry 2024; 30:e202401051. [PMID: 38629656 DOI: 10.1002/chem.202401051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Indexed: 06/01/2024]
Abstract
The natural product (-)-TAN-2483B is a fungal secondary metabolite which displays promising anti-cancer and immunomodulatory activity. Our previous syntheses of (-)-TAN-2483B and sidechain analogues uncovered inhibitory activity against Bruton's tyrosine kinase (Btk), an established drug target for various leukaemia and immunological diseases. A structure-based computational study using ensemble docking and molecular dynamics was performed to determine plausible binding modes for (-)-TAN-2483B and analogues in the Btk binding site. These hypotheses guided the design of new analogues which were synthesised and their inhibitory activities determined, providing insights into the structural determinants of the furopyranone scaffold that confer both activity and selectivity for Btk. These findings offer new perspectives for generating optimised (-)-TAN-2483B-based kinase inhibitors for the treatment of leukaemia and immunological diseases.
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Affiliation(s)
- Jordan A J McCone
- School of Chemical and Physical Sciences, Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Paul H Teesdale-Spittle
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- School of Biological Sciences, Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Jack U Flanagan
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Joanne E Harvey
- School of Chemical and Physical Sciences, Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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3
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Wang X, Yun Y, Chen L, Guo S, Niu B, Fang J, Yuan Q, Shen J, Xie X, Wang K. A novel approach to exploit Small-Molecule glucagon-like Peptide-1 receptor agonists with high potency. Bioorg Med Chem 2024; 107:117761. [PMID: 38795571 DOI: 10.1016/j.bmc.2024.117761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/28/2024]
Abstract
Small-molecule glucagon-like peptide-1 receptor (GLP-1R) agonists are recognized as promising therapeutics for type 2 diabetes mellitus (T2DM) and obesity. Danuglipron, an investigational small-molecule agonist, has demonstrated high efficacy in clinical trials. However, further development of danuglipron is challenged by a high rate of gastrointestinal adverse events. While these effects may be target-related, it is plausible that the carboxylic acid group present in danuglipron may also play a role in these outcomes by affecting the pharmacokinetic properties and dosing regimen of danuglipron, as well as by exerting direct gastrointestinal irritation. Therefore, this study aims to replace the problematic carboxylic acid group by exploring the internal binding cavity of danuglipron bound to GLP-1R using a water molecule displacement strategy. A series of novel triazole-containing compounds have been designed and synthesized during the structure-activity relationship (SAR) study. These efforts resulted in the discovery of compound 2j with high potency (EC50 = 0.065 nM). Moreover, docking simulations revealed that compound 2j directly interacts with the residue Glu387 within the internal cavity of GLP-1R, effectively displacing the structural water previously bound to Glu387. Subsequent in vitro and in vivo experiments demonstrated that compound 2j had comparable efficacy to danuglipron in enhancing insulin secretion and improving glycemic control. Collectively, this study offers a practicable approach for the discovery of novel small-molecule GLP-1R agonists based on danuglipron, and compound 2j may serve as a lead compound to further exploit the unoccupied internal cavity of danuglipron's binding pocket.
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Affiliation(s)
- Xiaoyan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, No. 555 Zu Chong Zhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Ying Yun
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Lili Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, No. 555 Zu Chong Zhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Shimeng Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, No. 555 Zu Chong Zhi Road, Shanghai, 201203, China
| | - Buying Niu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, No. 555 Zu Chong Zhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Jiahui Fang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, No. 555 Zu Chong Zhi Road, Shanghai, 201203, China
| | - Qianting Yuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, No. 555 Zu Chong Zhi Road, Shanghai, 201203, China
| | - Jianhua Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, No. 555 Zu Chong Zhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Xin Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, No. 555 Zu Chong Zhi Road, Shanghai, 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, China.
| | - Kai Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, No. 555 Zu Chong Zhi Road, Shanghai, 201203, China.
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4
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Mousavi H, Rimaz M, Zeynizadeh B. Practical Three-Component Regioselective Synthesis of Drug-Like 3-Aryl(or heteroaryl)-5,6-dihydrobenzo[ h]cinnolines as Potential Non-Covalent Multi-Targeting Inhibitors To Combat Neurodegenerative Diseases. ACS Chem Neurosci 2024; 15:1828-1881. [PMID: 38647433 DOI: 10.1021/acschemneuro.4c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Neurodegenerative diseases (NDs) are one of the prominent health challenges facing contemporary society, and many efforts have been made to overcome and (or) control it. In this research paper, we described a practical one-pot two-step three-component reaction between 3,4-dihydronaphthalen-1(2H)-one (1), aryl(or heteroaryl)glyoxal monohydrates (2a-h), and hydrazine monohydrate (NH2NH2•H2O) for the regioselective preparation of some 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnoline derivatives (3a-h). After synthesis and characterization of the mentioned cinnolines (3a-h), the in silico multi-targeting inhibitory properties of these heterocyclic scaffolds have been investigated upon various Homo sapiens-type enzymes, including hMAO-A, hMAO-B, hAChE, hBChE, hBACE-1, hBACE-2, hNQO-1, hNQO-2, hnNOS, hiNOS, hPARP-1, hPARP-2, hLRRK-2(G2019S), hGSK-3β, hp38α MAPK, hJNK-3, hOGA, hNMDA receptor, hnSMase-2, hIDO-1, hCOMT, hLIMK-1, hLIMK-2, hRIPK-1, hUCH-L1, hPARK-7, and hDHODH, which have confirmed their functions and roles in the neurodegenerative diseases (NDs), based on molecular docking studies, and the obtained results were compared with a wide range of approved drugs and well-known (with IC50, EC50, etc.) compounds. In addition, in silico ADMET prediction analysis was performed to examine the prospective drug properties of the synthesized heterocyclic compounds (3a-h). The obtained results from the molecular docking studies and ADMET-related data demonstrated that these series of 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines (3a-h), especially hit ones, can really be turned into the potent core of new drugs for the treatment of neurodegenerative diseases (NDs), and/or due to the having some reactionable locations, they are able to have further organic reactions (such as cross-coupling reactions), and expansion of these compounds (for example, with using other types of aryl(or heteroaryl)glyoxal monohydrates) makes a new avenue for designing novel and efficient drugs for this purpose.
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Affiliation(s)
- Hossein Mousavi
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran 19395-3697, Iran
| | - Behzad Zeynizadeh
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
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Ross GA, Lu C, Scarabelli G, Albanese SK, Houang E, Abel R, Harder ED, Wang L. The maximal and current accuracy of rigorous protein-ligand binding free energy calculations. Commun Chem 2023; 6:222. [PMID: 37838760 PMCID: PMC10576784 DOI: 10.1038/s42004-023-01019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
Computational techniques can speed up the identification of hits and accelerate the development of candidate molecules for drug discovery. Among techniques for predicting relative binding affinities, the most consistently accurate is free energy perturbation (FEP), a class of rigorous physics-based methods. However, uncertainty remains about how accurate FEP is and can ever be. Here, we present what we believe to be the largest publicly available dataset of proteins and congeneric series of small molecules, and assess the accuracy of the leading FEP workflow. To ascertain the limit of achievable accuracy, we also survey the reproducibility of experimental relative affinity measurements. We find a wide variability in experimental accuracy and a correspondence between binding and functional assays. When careful preparation of protein and ligand structures is undertaken, FEP can achieve accuracy comparable to experimental reproducibility. Throughout, we highlight reliable protocols that can help maximize the accuracy of FEP in prospective studies.
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Affiliation(s)
- Gregory A Ross
- Schrödinger Inc, New York, NY, USA.
- Isomorphic Labs, London, UK.
| | - Chao Lu
- Schrödinger Inc, New York, NY, USA
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6
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Gracia Carmona O, Gillhofer M, Tomasiak L, De Ruiter A, Oostenbrink C. Accelerated Enveloping Distribution Sampling to Probe the Presence of Water Molecules. J Chem Theory Comput 2023. [PMID: 37167545 DOI: 10.1021/acs.jctc.3c00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Determining the presence of water molecules at protein-ligand interfaces is still a challenging task in free-energy calculations. The inappropriate placement of water molecules results in the stabilization of wrong conformational orientations of the ligand. With classical alchemical perturbation methods, such as thermodynamic integration (TI), it is essential to know the amount of water molecules in the active site of the respective ligands. However, the resolution of the crystal structure and the correct assignment of the electron density do not always lead to a clear placement of water molecules. In this work, we apply the one-step perturbation method named accelerated enveloping distribution sampling (AEDS) to determine the presence of water molecules in the active site by probing them in a fast and straightforward way. Based on these results, we combined the AEDS method with standard TI to calculate accurate binding free energies in the presence of buried water molecules. The main idea is to perturb the water molecules with AEDS such that they are allowed to alternate between regular water molecules and non-interacting dummy particles while treating the ligand with TI over an alchemical pathway. We demonstrate the use of AEDS to probe the presence of water molecules for six different test systems. For one of these, previous calculations showed difficulties to reproduce the experimental binding free energies, and here, we use the combined TI-AEDS approach to tackle these issues.
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Affiliation(s)
- Oriol Gracia Carmona
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Michael Gillhofer
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Lisa Tomasiak
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Anita De Ruiter
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
- Christian Doppler Laboratory for Molecular Informatics in the Biosciences, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
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7
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Meanwell NA. The pyridazine heterocycle in molecular recognition and drug discovery. Med Chem Res 2023; 32:1-69. [PMID: 37362319 PMCID: PMC10015555 DOI: 10.1007/s00044-023-03035-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/06/2023] [Indexed: 03/17/2023]
Abstract
The pyridazine ring is endowed with unique physicochemical properties, characterized by weak basicity, a high dipole moment that subtends π-π stacking interactions and robust, dual hydrogen-bonding capacity that can be of importance in drug-target interactions. These properties contribute to unique applications in molecular recognition while the inherent polarity, low cytochrome P450 inhibitory effects and potential to reduce interaction of a molecule with the cardiac hERG potassium channel add additional value in drug discovery and development. The recent approvals of the gonadotropin-releasing hormone receptor antagonist relugolix (24) and the allosteric tyrosine kinase 2 inhibitor deucravacitinib (25) represent the first examples of FDA-approved drugs that incorporate a pyridazine ring. In this review, the properties of the pyridazine ring are summarized in comparison to the other azines and its potential in drug discovery is illustrated through vignettes that explore applications that take advantage of the inherent physicochemical properties as an approach to solving challenges associated with candidate optimization. Graphical Abstract
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8
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Walsh L, Erlanson DA, de Esch IJP, Jahnke W, Woodhead A, Wren E. Fragment-to-Lead Medicinal Chemistry Publications in 2021. J Med Chem 2023; 66:1137-1156. [PMID: 36622056 DOI: 10.1021/acs.jmedchem.2c01827] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This Perspective is the seventh in an annual series that summarizes successful Fragment-to-Lead (F2L) case studies published in a given year. A tabulated summary of relevant articles published in 2021 is provided, and features such as target class, screening methods, and ligand efficiency are discussed, both for the 2021 examples and for the combined examples over the years 2015-2021. In addition, trends and new developments in the field are summarized. In particular, the use of structural information in fragment-based drug discovery is discussed.
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Affiliation(s)
- Louise Walsh
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Blvd., South San Francisco, California 94080, United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Andrew Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Ella Wren
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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9
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Ge Y, Baumann HM, Mobley DL. Absolute Binding Free Energy Calculations for Buried Water Molecules. J Chem Theory Comput 2022; 18:6482-6499. [PMID: 36197451 PMCID: PMC9873352 DOI: 10.1021/acs.jctc.2c00658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Water often plays a key role in mediating protein-ligand interactions. Understanding contributions from active-site water molecules to binding thermodynamics of a ligand is important in predicting binding free energies for ligand optimization. In this work, we tested a non-equilibrium switching method for absolute binding free energy calculations on water molecules in binding sites of 13 systems. We discuss the lessons we learned about identified issues that affected our calculations and ways to address them. This work fits with our larger focus on how to do accurate ligand binding free energy calculations when water rearrangements are very slow, such as rearrangements due to ligand modification (as in relative free energy calculations) or ligand binding (as in absolute free energy calculations). The method studied in this work can potentially be used to account for limited water sampling via providing endpoint corrections to free energy calculations using our calculated binding free energy of water.
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Affiliation(s)
- Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, California92697, United States
| | - Hannah M Baumann
- Department of Pharmaceutical Sciences, University of California, Irvine, California92697, United States
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, California92697, United States
- Department of Chemistry, University of California, Irvine, California92697, United States
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10
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Screening assays for tyrosine kinase inhibitors:A review. J Pharm Biomed Anal 2022; 223:115166. [DOI: 10.1016/j.jpba.2022.115166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
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11
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Li N, Zhang X, Fan X. Synthesis of pyrazolidinone fused cinnolines via the cascade reactions of 1-phenylpyrazolidinones with vinylene carbonate. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.153984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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12
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Sun SL, Wu SH, Kang JB, Ma YY, Chen L, Cao P, Chang L, Ding N, Xue X, Li NG, Shi ZH. Medicinal Chemistry Strategies for the Development of Bruton's Tyrosine Kinase Inhibitors against Resistance. J Med Chem 2022; 65:7415-7437. [PMID: 35594541 DOI: 10.1021/acs.jmedchem.2c00030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Despite significant efficacy, one of the major limitations of small-molecule Bruton's tyrosine kinase (BTK) agents is the presence of clinically acquired resistance, which remains a major clinical challenge. This Perspective focuses on medicinal chemistry strategies for the development of BTK small-molecule inhibitors against resistance, including the structure-based design of BTK inhibitors targeting point mutations, e.g., (i) developing noncovalent inhibitors from covalent inhibitors, (ii) avoiding steric hindrance from mutated residues, (iii) making interactions with the mutated residue, (iv) modifying the solvent-accessible region, and (v) developing new scaffolds. Additionally, a comparative analysis of multi-inhibitions of BTK is presented based on cross-comparisons between 2916 unique BTK ligands and 283 other kinases that cover 7108 dual/multiple inhibitions. Finally, targeting the BTK allosteric site and uding proteolysis-targeting chimera (PROTAC) as two potential strategies are addressed briefly, while also illustrating the possibilities and challenges to find novel ligands of BTK.
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Affiliation(s)
- Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shi-Han Wu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ji-Bo Kang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yi-Yuan Ma
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lu Chen
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Peng Cao
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, China
| | - Liang Chang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhi-Hao Shi
- Department of Organic Chemistry, China Pharmaceutical University, Nanjing 211198, China
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13
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Lal Gupta P, Carlson HA. Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth. J Chem Theory Comput 2022; 18:3829-3844. [PMID: 35533286 DOI: 10.1021/acs.jctc.1c01054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In drug design, chemical groups are sequentially added to improve a weak-binding fragment into a tight-binding lead molecule. Often, the direction to make these additions is unclear, and there are numerous chemical modifications to choose. Lead development can be guided by crystal structures of the fragment-bound protein, but this alone is unable to capture structural changes like closing or opening of the binding site and any side-chain movements. Accounting for adaptation of the site requires a dynamic approach. Here, we use molecular dynamics calculations of small organic solvents with protein-fragment pairs to reveal the nearest "hot spots". These close hot spots show the direction to make appropriate additions and suggest types of chemical modifications that could improve binding affinity. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that is well established for finding binding "hot spots" in active sites and allosteric sites of proteins. We simulated 20 fragment-bound and apo forms of key pharmaceutical targets to map out hot spots for potential lead space. Furthermore, we analyzed whether the presence of a fragment facilitates the probes' binding in the lead space, a type of binding cooperativity. To the best of our knowledge, this is the first use of cosolvent MD conducted with bound inhibitors in the simulation. Our work provides a general framework to extract molecular features of binding sites to choose chemical groups for growing lead molecules. Of the 20 systems, 17 systems were well mapped by MixMD. For the three not-mapped systems, two had lead growth out into solution away from the protein, and the third had very small modifications which indicated no nearby hot spots. Therefore, our lack of mapping in three systems was appropriate given the experimental data (true-negative cases). The simulations are run for very short time scales, making this method tractable for use in the pharmaceutical industry.
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Affiliation(s)
- Pancham Lal Gupta
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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14
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Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL. Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques. J Chem Theory Comput 2022; 18:1359-1381. [PMID: 35148093 PMCID: PMC9241631 DOI: 10.1021/acs.jctc.1c00590] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Water often plays a key role in protein structure, molecular recognition, and mediating protein-ligand interactions. Thus, free energy calculations must adequately sample water motions, which often proves challenging in typical MD simulation time scales. Thus, the accuracy of methods relying on MD simulations ends up limited by slow water sampling. Particularly, as a ligand is removed or modified, bulk water may not have time to fill or rearrange in the binding site. In this work, we focus on several molecular dynamics (MD) simulation-based methods attempting to help rehydrate buried water sites: BLUES, using nonequilibrium candidate Monte Carlo (NCMC); grand, using grand canonical Monte Carlo (GCMC); and normal MD. We assess the accuracy and efficiency of these methods in rehydrating target water sites. We selected a range of systems with varying numbers of waters in the binding site, as well as those where water occupancy is coupled to the identity or binding mode of the ligand. We analyzed the rehydration of buried water sites in binding pockets using both clustering of trajectories and direct analysis of electron density maps. Our results suggest both BLUES and grand enhance water sampling relative to normal MD and grand is more robust than BLUES, but also that water sampling remains a major challenge for all of the methods tested. The lessons we learned for these methods and systems are discussed.
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Affiliation(s)
- Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - David C Wych
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Marley L Samways
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Michael E Wall
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, California 92697, United States
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15
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Zhang Z, Li J, Chen H, Huang J, Song X, Tu ZC, Zhang Z, Peng L, Zhou Y, Ding K. Design, Synthesis, and Biological Evaluation of 2-Formyl Tetrahydronaphthyridine Urea Derivatives as New Selective Covalently Reversible FGFR4 Inhibitors. J Med Chem 2022; 65:3249-3265. [PMID: 35119278 DOI: 10.1021/acs.jmedchem.1c01816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aberrant FGF19/FGFR4 signaling is an oncogenic driver force for the development of human hepatocellular carcinoma (HCC). A series of 2-formyl tetrahydronaphthyridine urea derivatives were designed and synthesized as new covalently reversible inhibitors of FGFR4. The representative compound 9ka exhibited an IC50 value of 5.4 nM against FGFR4 and demonstrated extraordinary kinome selectivity. Compound 9ka also exhibited good oral pharmacokinetic properties with an AUC(0-t) value of 38 950.06 h·ng/mL, a T1/2 value of 3.06 h, and an oral bioavailability of 50.97%, at an oral dose of 25 mg/kg in Sprague-Dawley (SD) rats. Furthermore, compound 9ka induced significant tumor regressions in a xenograft mouse model of Hep3B2.1-7 HCC cell line without an obvious sign of toxicity upon 30 mg/kg oral administration. Compound 9ka may serve as a promising lead compound for further anticancer drug development.
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Affiliation(s)
- Zhen Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, College of Pharmacy, Jinan University, # 855 Xingye Avenue, Guangzhou 510632, China
| | - Jie Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, College of Pharmacy, Jinan University, # 855 Xingye Avenue, Guangzhou 510632, China
| | - Hao Chen
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, College of Pharmacy, Jinan University, # 855 Xingye Avenue, Guangzhou 510632, China
| | - Jing Huang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, College of Pharmacy, Jinan University, # 855 Xingye Avenue, Guangzhou 510632, China
| | | | - Zheng-Chao Tu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, College of Pharmacy, Jinan University, # 855 Xingye Avenue, Guangzhou 510632, China.,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, # 160 Kaiyuan Avenue, Guangzhou 510530, China
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, College of Pharmacy, Jinan University, # 855 Xingye Avenue, Guangzhou 510632, China
| | - Lijie Peng
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, College of Pharmacy, Jinan University, # 855 Xingye Avenue, Guangzhou 510632, China
| | - Yang Zhou
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, College of Pharmacy, Jinan University, # 855 Xingye Avenue, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, College of Pharmacy, Jinan University, # 855 Xingye Avenue, Guangzhou 510632, China.,The First Affiliated Hospital, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.,State Key Laboratory of Bioorganic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, # 345 Lingling Road, Shanghai 200032, China
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16
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Ganesh PSKP, Muthuraja P, Gopinath P. Hydrazine-Directed Rh(III) Catalyzed (4+2) Annulation with Sulfoxonium Ylides: Synthesis and Photophysical Properties of Dihydrocinnolines. Chem Commun (Camb) 2022; 58:4211-4214. [DOI: 10.1039/d1cc06353g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We herein report hydrazine-directed, Rh(III) catalyzed (4+2) annulation of N-alkyl aryl hydrazines with sulfoxonium ylides as a safe carbene precursor. The reaction shows excellent functional group tolerance with broad substrate...
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17
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Ahmadi S, Lotfi S, Afshari S, Kumar P, Ghasemi E. CORAL: Monte Carlo based global QSAR modelling of Bruton tyrosine kinase inhibitors using hybrid descriptors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:1013-1031. [PMID: 34875951 DOI: 10.1080/1062936x.2021.2003429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Global QSAR modelling was performed to predict the pIC50 values of 233 diverse heterocyclic compounds as BTK inhibitors with the Monte Carlo algorithm of CORAL software using the DCW hybrid descriptors extracted from SMILES notations of molecules. The dataset of 233 BTK inhibitors was randomly split into training, invisible training, calibration and validation sets. The index of ideality of correlation was also applied to build and judge the predictability of the QSAR models. Eight global QSAR models based on the hybrid optimal descriptor using two target functions, i.e. TF1 (WIIC = 0) and TF2 (WIIC = 0.2) have been constructed. The statistical parameters of QSAR models computed by TF2 are more reliable and robust and were used to predict the pIC50 values. The model constructed for split 4 via TF2 is regarded as the best model and the numerical values of r2Train, r2Valid, Q2Train and Q2Valid are equal to 0.7981, 0.7429, 0.7898 and 0.6784, respectively. By internal and external validation techniques, the predictability and reliability of the designed models have been assessed. The structural attributes responsible for the increase and decrease of pIC50 of BTK inhibitors were also identified.
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Affiliation(s)
- S Ahmadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - S Lotfi
- Department of Chemistry, Payame Noor University (PNU), Tehran, Iran
| | - S Afshari
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - P Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, Haryana, India
| | - E Ghasemi
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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18
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Lin C, Huang W, Huang Y, Dhole S, Sun C. Rhodium‐Catalyzed [4+2] Annulation of N‐Aryl Pyrazolones with Diazo Compounds To Access Pyrazolone‐Fused Cinnolines. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Chih‐Yu Lin
- Department of Applied Chemistry National Chiao-Tung University 1001 Ta-Hseuh Road Hsinchu 300-10, ROC Taiwan
| | - Wan‐Wen Huang
- Department of Applied Chemistry National Chiao-Tung University 1001 Ta-Hseuh Road Hsinchu 300-10, ROC Taiwan
| | - Ying‐Ti Huang
- Department of Applied Chemistry National Chiao-Tung University 1001 Ta-Hseuh Road Hsinchu 300-10, ROC Taiwan
| | - Sandip Dhole
- Amar Chemistry Pvt. Ltd. G1 A, Ackruti Corporate Park Mumbai 400078 India
| | - Chung‐Ming Sun
- Department of Applied Chemistry National Chiao-Tung University 1001 Ta-Hseuh Road Hsinchu 300-10, ROC Taiwan
- Department of Medicinal and Applied Chemistry Kaohsiung Medical University Kaohsiung 807-08, ROC Taiwan
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19
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Sabat M, Dougan DR, Knight B, Lawson JD, Scorah N, Smith CR, Taylor ER, Vu P, Wyrick C, Wang H, Balakrishna D, Hixon M, Madakamutil L, McConn D. Discovery of the Bruton's Tyrosine Kinase Inhibitor Clinical Candidate TAK-020 ( S)-5-(1-((1-Acryloylpyrrolidin-3-yl)oxy)isoquinolin-3-yl)-2,4-dihydro-3 H-1,2,4-triazol-3-one, by Fragment-Based Drug Design. J Med Chem 2021; 64:12893-12902. [PMID: 34448571 DOI: 10.1021/acs.jmedchem.1c01026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This publication details the successful use of FBDD (fragment-based drug discovery) principles in the invention of a novel covalent Bruton's tyrosine kinase inhibitor, which ultimately became the Takeda Pharmaceuticals clinical candidate TAK-020. Described herein are the discovery of the fragment 5-phenyl-2,4-dihydro-3H-1,2,4-triazol-3-one, the subsequent optimization of this hit molecule to the candidate, and synthesis and performance in pharmacodynamic and efficacy models along with direct biophysical comparison of TAK-020 with other clinical-level assets and the marketed drug Ibrutinib.
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Affiliation(s)
- Mark Sabat
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Douglas R Dougan
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Beverly Knight
- Pfizer, 10777 Science Center Dr., San Diego, California 92121, United States
| | - J David Lawson
- Mirati Therapeutics, Inc., 9393 Towne Centre Dr. #200, San Diego, California 92121, United States
| | - Nicholas Scorah
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Christopher R Smith
- Mirati Therapeutics, Inc., 9393 Towne Centre Dr. #200, San Diego, California 92121, United States
| | - Ewan R Taylor
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Phong Vu
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Corey Wyrick
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Haixia Wang
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Deepika Balakrishna
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Mark Hixon
- VeriSIM Life, 1 Sansome Street Suite 3500, San Francisco, California 94104, United States
| | - Loui Madakamutil
- Invivoscribe Therapeutics, Inc., 10222 Barnes Canyon Rd., Bldg. 1, San Diego, California 92121, United States
| | - Donavon McConn
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
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20
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Recent Advances in BTK Inhibitors for the Treatment of Inflammatory and Autoimmune Diseases. Molecules 2021; 26:molecules26164907. [PMID: 34443496 PMCID: PMC8399599 DOI: 10.3390/molecules26164907] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
Bruton’s tyrosine kinase (BTK) plays a crucial role in B-cell receptor and Fc receptor signaling pathways. BTK is also involved in the regulation of Toll-like receptors and chemokine receptors. Given the central role of BTK in immunity, BTK inhibition represents a promising therapeutic approach for the treatment of inflammatory and autoimmune diseases. Great efforts have been made in developing BTK inhibitors for potential clinical applications in inflammatory and autoimmune diseases. This review covers the recent development of BTK inhibitors at preclinical and clinical stages in treating these diseases. Individual examples of three types of inhibitors, namely covalent irreversible inhibitors, covalent reversible inhibitors, and non-covalent reversible inhibitors, are discussed with a focus on their structure, bioactivity and selectivity. Contrary to expectations, reversible BTK inhibitors have not yielded a significant breakthrough so far. The development of covalent, irreversible BTK inhibitors has progressed more rapidly. Many candidates entered different stages of clinical trials; tolebrutinib and evobrutinib are undergoing phase 3 clinical evaluation. Rilzabrutinib, a covalent reversible BTK inhibitor, is now in phase 3 clinical trials and also offers a promising future. An analysis of the protein–inhibitor interactions based on published co-crystal structures provides useful clues for the rational design of safe and effective small-molecule BTK inhibitors.
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21
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Liu J, Chen C, Wang D, Zhang J, Zhang T. Emerging small-molecule inhibitors of the Bruton's tyrosine kinase (BTK): Current development. Eur J Med Chem 2021; 217:113329. [PMID: 33740548 DOI: 10.1016/j.ejmech.2021.113329] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/12/2021] [Accepted: 02/21/2021] [Indexed: 12/29/2022]
Abstract
Therapy based on Bruton's tyrosine kinase (BTK) inhibitors one of the major treatment options currently recommended for lymphoma patients. The first generation of BTK inhibitor, Ibrutinib, achieved remarkable progress in the treatment of B-cell malignancies, but still has problems with drug-resistance or off-target induced serious side effects. Therefore, numerous new BTK inhibitors were developed to address this unmet medical need. In parallel, the effect of BTK inhibitors against immune-related diseases has been evaluated in clinical trials. This review summarizes recent progress in the research and development of BTK inhibitors, with a focus on structural characteristics and structure-activity relationships. The structure-refinement process of representative pharmacophores as well as their effects on binding affinity, biological activity and pharmacokinetics profiles were analyzed. The advantages and disadvantages of reversible/irreversible BTK inhibitors and their potential implications were discussed to provide a reference for the rational design and development of novel potent BTK inhibitors.
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Affiliation(s)
- Jiakuo Liu
- Pharmaceutical Department, PLA Strategic Support Force Medical Center, No.9 Anxiangbeili Road, Chaoyang District, Beijing, 100101, PR China
| | - Chengjuan Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China
| | - Dongmei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China
| | - Jie Zhang
- Pharmaceutical Department, PLA Strategic Support Force Medical Center, No.9 Anxiangbeili Road, Chaoyang District, Beijing, 100101, PR China.
| | - Tiantai Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China.
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22
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Xie Z, Yang X, Duan Y, Han J, Liao C. Small-Molecule Kinase Inhibitors for the Treatment of Nononcologic Diseases. J Med Chem 2021; 64:1283-1345. [PMID: 33481605 DOI: 10.1021/acs.jmedchem.0c01511] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Great successes have been achieved in developing small-molecule kinase inhibitors as anticancer therapeutic agents. However, kinase deregulation plays essential roles not only in cancer but also in almost all major disease areas. Accumulating evidence has revealed that kinases are promising drug targets for different diseases, including cancer, autoimmune diseases, inflammatory diseases, cardiovascular diseases, central nervous system disorders, viral infections, and malaria. Indeed, the first small-molecule kinase inhibitor for treatment of a nononcologic disease was approved in 2011 by the U.S. FDA. To date, 10 such inhibitors have been approved, and more are in clinical trials for applications other than cancer. This Perspective discusses a number of kinases and their small-molecule inhibitors for the treatment of diseases in nononcologic therapeutic fields. The opportunities and challenges in developing such inhibitors are also highlighted.
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Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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23
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Ben-Shalom IY, Lin Z, Radak BK, Lin C, Sherman W, Gilson MK. Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations. J Chem Theory Comput 2020; 16:7883-7894. [PMID: 33206520 PMCID: PMC7725968 DOI: 10.1021/acs.jctc.0c00785] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rigorous binding free energy methods in drug discovery are growing in popularity because of a combination of methodological advances, improvements in computer hardware, and workflow automation. These calculations typically use molecular dynamics (MD) to sample from the Boltzmann distribution of conformational states. However, when part or all of the binding sites is inaccessible to the bulk solvent, the time needed for water molecules to equilibrate between bulk solvent and the binding site can be well beyond what is practical with standard MD. This sampling limitation is problematic in relative binding free energy calculations, which compute the reversible work of converting ligand 1 to ligand 2 within the binding site. Thus, if ligand 1 is smaller and/or more polar than ligand 2, the perturbation may allow additional water molecules to occupy a region of the binding site. However, this change in hydration may not be captured by standard MD simulations and may therefore lead to errors in the computed free energy. We recently developed a hybrid Monte Carlo/MD (MC/MD) method, which speeds up the equilibration of water between bulk solvent and buried cavities, while sampling from the intended distribution of states. Here, we report on the use of this approach in the context of alchemical binding free energy calculations. We find that using MC/MD markedly improves the accuracy of the calculations and also reduces hysteresis between the forward and reverse perturbations, relative to matched calculations using only MD with or without the crystallographic water molecules. The present method is available for use in AMBER simulation software.
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Affiliation(s)
- Ido Y Ben-Shalom
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 92093 La Jolla, California, United States
| | - Zhixiong Lin
- Silicon Therapeutics LLC, Boston, Massachusetts 02110, United States
| | - Brian K Radak
- Silicon Therapeutics LLC, Boston, Massachusetts 02110, United States
| | - Charles Lin
- Silicon Therapeutics LLC, Boston, Massachusetts 02110, United States
| | - Woody Sherman
- Silicon Therapeutics LLC, Boston, Massachusetts 02110, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 92093 La Jolla, California, United States
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24
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Municoy M, Roda S, Soler D, Soutullo A, Guallar V. aquaPELE: A Monte Carlo-Based Algorithm to Sample the Effects of Buried Water Molecules in Proteins. J Chem Theory Comput 2020; 16:7655-7670. [PMID: 33201691 DOI: 10.1021/acs.jctc.0c00925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Water is frequently found inside proteins, carrying out important roles in catalytic reactions or molecular recognition tasks. Therefore, computational models that aim to study protein-ligand interactions usually have to include water effects through explicit or implicit approaches to obtain reliable results. While full explicit models might be too computationally daunting for some applications, implicit models are normally faster but omit some of the most important contributions of water. This is the case of our in-house software, called protein energy landscape exploration (PELE), which uses implicit models to speed up conformational explorations as much as possible; the lack of explicit water sampling, however, limits its model. In this work, we confront this problem with the development of aquaPELE. It is a new algorithm that extends the exploration capabilities while keeping efficiency as it employs a mixed implicit/explicit approach to also take into account the effects of buried water molecules. With an additional Monte Carlo (MC) routine, a set of explicit water molecules is perturbed inside protein cavities and their effects are dynamically adjusted to the current state of the system. As a result, this implementation can be used to predict the principal hydration sites or the rearrangement and displacement of conserved water molecules upon the binding of a ligand. We benchmarked this new tool focusing on estimating ligand binding modes and hydration sites in cavities with important interfacial water molecules, according to crystallographic structures. Results suggest that aquaPELE sets a fast and reliable alternative for molecular recognition studies in systems with a strong water-dependency.
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Affiliation(s)
- Martí Municoy
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | - Sergi Roda
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | - Daniel Soler
- Nostrum Biodiscovery, Jordi Girona 29, Nexus II D128, 08034 Barcelona, Spain
| | - Alberto Soutullo
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
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25
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Zhang F, Chen Z, Cheung CW, Ma J. Aryl Diazonium
Salt‐Triggered
Cyclization and Cycloaddition Reactions: Past, Present, and Future. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000270] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Fa‐Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University Tianjin 300072 China
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University Binhai New City Fuzhou 350207 Fujian China
| | - Zhen Chen
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University Tianjin 300072 China
| | - Chi Wai Cheung
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University Tianjin 300072 China
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University Binhai New City Fuzhou 350207 Fujian China
| | - Jun‐An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University Tianjin 300072 China
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University Binhai New City Fuzhou 350207 Fujian China
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26
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Bommagani MB, Mokenapelli S, Yerrabelli JR, Boda SK, Chitneni PR. Novel 4-(1H-1,2,3-triazol-4-yl)methoxy)cinnolines as potent antibacterial agents: Synthesis and molecular docking study. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1728333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Mohan Babu Bommagani
- Natural Products Laboratory, Department of Chemistry, Osmania University, Hyderabad, Telangana, India
| | - Sudhakar Mokenapelli
- Natural Products Laboratory, Department of Chemistry, Osmania University, Hyderabad, Telangana, India
| | | | - Sathish Kumar Boda
- Natural Products Laboratory, Department of Chemistry, Osmania University, Hyderabad, Telangana, India
| | - Prasad Rao Chitneni
- Natural Products Laboratory, Department of Chemistry, Osmania University, Hyderabad, Telangana, India
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27
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Ma W, Wang Y, Chu D, Yan H. 4D-QSAR and MIA-QSAR study on the Bruton's tyrosine kinase (Btk) inhibitors. J Mol Graph Model 2019; 92:357-362. [DOI: 10.1016/j.jmgm.2019.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/11/2019] [Accepted: 08/11/2019] [Indexed: 01/14/2023]
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28
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Maurer M, Oostenbrink C. Water in protein hydration and ligand recognition. J Mol Recognit 2019; 32:e2810. [PMID: 31456282 PMCID: PMC6899928 DOI: 10.1002/jmr.2810] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/16/2022]
Abstract
This review describes selected basics of water in biomolecular recognition. We focus on a qualitative understanding of the most important physical aspects, how these change in magnitude between bulk water and protein environment, and how the roles that water plays for proteins arise from them. These roles include mechanical support, thermal coupling, dielectric screening, mass and charge transport, and the competition with a ligand for the occupation of a binding site. The presence or absence of water has ramifications that range from the thermodynamic binding signature of a single ligand up to cellular survival. The large inhomogeneity in water density, polarity and mobility around a solute is hard to assess in experiment. This is a source of many difficulties in the solvation of protein models and computational studies that attempt to elucidate or predict ligand recognition. The influence of water in a protein binding site on the experimental enthalpic and entropic signature of ligand binding is still a point of much debate. The strong water‐water interaction in enthalpic terms is counteracted by a water molecule's high mobility in entropic terms. The complete arrest of a water molecule's mobility sets a limit on the entropic contribution of a water displacement process, while the solvent environment sets limits on ligand reactivity.
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Affiliation(s)
- Manuela Maurer
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
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29
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Yao X, Sun X, Jin S, Yang L, Xu H, Rao Y. Discovery of 4-Aminoquinoline-3-carboxamide Derivatives as Potent Reversible Bruton’s Tyrosine Kinase Inhibitors for the Treatment of Rheumatoid Arthritis. J Med Chem 2019; 62:6561-6574. [DOI: 10.1021/acs.jmedchem.9b00329] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xia Yao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China
| | - Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, P. R. China
| | - Shuyu Jin
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Ling Yang
- R&D Institute, Chia Tai Tianqing Pharmaceutical Group Co., LTD, Nanjing 210023, P. R. China
| | - Hongjiang Xu
- R&D Institute, Chia Tai Tianqing Pharmaceutical Group Co., LTD, Nanjing 210023, P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China
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30
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Szumilak M, Stanczak A. Cinnoline Scaffold-A Molecular Heart of Medicinal Chemistry? Molecules 2019; 24:molecules24122271. [PMID: 31216762 PMCID: PMC6631947 DOI: 10.3390/molecules24122271] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 12/18/2022] Open
Abstract
The cinnoline nucleus is a very important bicyclic heterocycle that is used as the structural subunit of many compounds with interesting pharmaceutical properties. Cinnoline derivatives exhibit broad spectrum of pharmacological activities such as antibacterial, antifungal, antimalarial, anti-inflammatory, analgesic, anxiolytic and antitumor activities. Some of them are under evaluation in clinical trials. In the present review, we have compiled studies focused on the biological properties of cinnoline derivatives conducted by many research groups worldwide between 2005 and 2019. Comprehensive and target oriented information clearly indicate that the development of cinnoline based molecules constitute a significant contribution to the identification of lead compounds with optimized pharmacodynamic and pharmacokinetic properties.
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Affiliation(s)
- Marta Szumilak
- Department of Hospital Pharmacy, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland.
| | - Andrzej Stanczak
- Department of Applied Pharmacy, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland.
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31
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Sharma A, Thelma BK. Pharmacophore modeling and virtual screening in search of novel Bruton's tyrosine kinase inhibitors. J Mol Model 2019; 25:179. [PMID: 31172362 DOI: 10.1007/s00894-019-4047-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/23/2019] [Indexed: 12/11/2022]
Abstract
Bruton's tyrosine kinase (BTK) is a known drug target for B cell malignancies and autoimmune diseases like rheumatoid arthritis. Consequently, efforts to develop BTK inhibitors have gained momentum in the last decade, resulting in a number of potential inhibitory molecules. However, to date, there are only two FDA approved drugs for B cell malignancies (Ibrutinib and Acalabrutinib), thus continued efforts are warranted. A large number of molecular scaffolds with potential BTK inhibitory activity are already available from these studies, and therefore we employed a ligand-based approach towards computer-aided drug design to develop a pharmacophore model for BTK inhibitors. Using over 400 molecules with known half maximal inhibitory concentrations (IC50) for BTK, a four-point pharmacophore hypothesis was derived, with two aromatic rings (R), one hydrogen bond acceptor (A) and one hydrogen bond donor (D). Screening of two small-molecule databases against this pharmacophore returned 620 hits with matching chemical features. Docking these against the ATP-binding site of the BTK kinase domain through a virtual screening workflow yielded 30 hits from which ultimately two natural compounds (two best scoring poses for each) were prioritized. Molecular dynamics simulations of these four docked complexes confirmed the stability of protein-ligand binding over a 200 ns time period, and thus their suitability for lead molecule development with further optimization and experimental testing. Of note, the pharmacophore model developed in this study would also be further useful for de novo drug design and virtual screening efforts on a larger scale. Graphical abstract Pharmacophore modeling and virtual screening in search of novel Bruton's tyrosine kinase inhibitors.
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Affiliation(s)
- Aditya Sharma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India.
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32
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Colombano G, Caldwell JJ, Matthews TP, Bhatia C, Joshi A, McHardy T, Mok NY, Newbatt Y, Pickard L, Strover J, Hedayat S, Walton MI, Myers SM, Jones AM, Saville H, McAndrew C, Burke R, Eccles SA, Davies FE, Bayliss R, Collins I. Binding to an Unusual Inactive Kinase Conformation by Highly Selective Inhibitors of Inositol-Requiring Enzyme 1α Kinase-Endoribonuclease. J Med Chem 2019; 62:2447-2465. [PMID: 30779566 PMCID: PMC6437697 DOI: 10.1021/acs.jmedchem.8b01721] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Indexed: 12/19/2022]
Abstract
A series of imidazo[1,2- b]pyridazin-8-amine kinase inhibitors were discovered to allosterically inhibit the endoribonuclease function of the dual kinase-endoribonuclease inositol-requiring enzyme 1α (IRE1α), a key component of the unfolded protein response in mammalian cells and a potential drug target in multiple human diseases. Inhibitor optimization gave compounds with high kinome selectivity that prevented endoplasmic reticulum stress-induced IRE1α oligomerization and phosphorylation, and inhibited endoribonuclease activity in human cells. X-ray crystallography showed the inhibitors to bind to a previously unreported and unusually disordered conformation of the IRE1α kinase domain that would be incompatible with back-to-back dimerization of the IRE1α protein and activation of the endoribonuclease function. These findings increase the repertoire of known IRE1α protein conformations and can guide the discovery of highly selective ligands for the IRE1α kinase site that allosterically inhibit the endoribonuclease.
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Affiliation(s)
- Giampiero Colombano
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - John J. Caldwell
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Thomas P. Matthews
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Chitra Bhatia
- Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - Amar Joshi
- Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - Tatiana McHardy
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Ngai Yi Mok
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Yvette Newbatt
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Lisa Pickard
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Jade Strover
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Somaieh Hedayat
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Michael I. Walton
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Stephanie M. Myers
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Alan M. Jones
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Harry Saville
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Craig McAndrew
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Suzanne A. Eccles
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Faith E. Davies
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Richard Bayliss
- Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
- School
of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Ian Collins
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
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33
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Wahl J, Smieško M. Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules. J Chem Inf Model 2019; 59:754-765. [DOI: 10.1021/acs.jcim.8b00826] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Joel Wahl
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
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34
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Xiang Y, Wang C, Ding Q, Peng Y. Diazo Compounds: Versatile Synthons for the Synthesis of Nitrogen Heterocycles via
Transition Metal-Catalyzed Cascade C-H Activation/Carbene Insertion/Annulation Reactions. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800960] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yunyu Xiang
- Key Laboratory of Small Functional Organic Molecule, Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry; Jiangxi Normal University; Nanchang, Jiangxi 330022 People's Republic of China
| | - Cong Wang
- Key Laboratory of Small Functional Organic Molecule, Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry; Jiangxi Normal University; Nanchang, Jiangxi 330022 People's Republic of China
| | - Qiuping Ding
- Key Laboratory of Small Functional Organic Molecule, Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry; Jiangxi Normal University; Nanchang, Jiangxi 330022 People's Republic of China
| | - Yiyuan Peng
- Key Laboratory of Small Functional Organic Molecule, Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry; Jiangxi Normal University; Nanchang, Jiangxi 330022 People's Republic of China
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35
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Li R, Du Y, Shen J. Molecular modelling studies on cinnoline-based BTK inhibitors using docking and structure-based 3D-QSAR. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:847-873. [PMID: 30280589 DOI: 10.1080/1062936x.2018.1518927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
BTK inhibitors have been proved as an effective target for B-cell malignancies. Ibrutinib is the most advanced irreversible BTK inhibitor for treating mantle cell lymphoma/chronic lymphocytic leukaemia but with existing drug resistance and adverse effects. To design novel effective and safety reversible BTK inhibitors, 115 newly cinnoline analogues were selected to perform molecular docking and 3D-QSAR study because of the main scaffold similarity to Ibrutinib. Both established CoMFA and CoMSIA models obtained high predictive and satisfactory value. CoMFA/CoMSIA contour maps demonstrated that bulky substitutions are preferred at R1 and R3 positions, and introducing hydrophilic and negative electrostatic substitutions at R1 positions is important for improving BTK inhibitory activities. These results will be useful to provide clues for rationally designing novel and high potency BTK inhibitors.
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Affiliation(s)
- R Li
- a School of Chemistry and Pharmaceutical Engineering , Qilu University of Technology (Shandong Academy of Sciences) , Jinan , China
| | - Y Du
- a School of Chemistry and Pharmaceutical Engineering , Qilu University of Technology (Shandong Academy of Sciences) , Jinan , China
| | - J Shen
- b State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai , China
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36
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Zhang SG, Liang CG, Zhang WH. Recent Advances in Indazole-Containing Derivatives: Synthesis and Biological Perspectives. Molecules 2018; 23:E2783. [PMID: 30373212 PMCID: PMC6278422 DOI: 10.3390/molecules23112783] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 10/14/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023] Open
Abstract
Indazole-containing derivatives represent one of the most important heterocycles in drug molecules. Diversely substituted indazole derivatives bear a variety of functional groups and display versatile biological activities; hence, they have gained considerable attention in the field of medicinal chemistry. This review aims to summarize the recent advances in various methods for the synthesis of indazole derivatives. The current developments in the biological activities of indazole-based compounds are also presented.
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Affiliation(s)
- Shu-Guang Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chao-Gen Liang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wei-Hua Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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37
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Design and synthesis of novel 6-hydroxy-4-methoxy-3-methylbenzofuran-7-carboxamide derivatives as potent Mnks inhibitors by fragment-based drug design. Bioorg Med Chem 2018; 26:4602-4614. [DOI: 10.1016/j.bmc.2018.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 11/19/2022]
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38
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Drwal MN, Bret G, Perez C, Jacquemard C, Desaphy J, Kellenberger E. Structural Insights on Fragment Binding Mode Conservation. J Med Chem 2018; 61:5963-5973. [PMID: 29906118 DOI: 10.1021/acs.jmedchem.8b00256] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Aiming at a deep understanding of fragment binding to ligandable targets, we performed a large scale analysis of the Protein Data Bank. Binding modes of 1832 drug-like ligands and 1079 fragments to 235 proteins were compared. We observed that the binding modes of fragments and their drug-like superstructures binding to the same protein are mostly conserved, thereby providing experimental evidence for the preservation of fragment binding modes during molecular growing. Furthermore, small chemical changes in the fragment are tolerated without alteration of the fragment binding mode. The exceptions to this observation generally involve conformational variability of the molecules. Our data analysis also suggests that, provided enough fragments have been crystallized within a protein, good interaction coverage of the binding pocket is achieved. Last, we extended our study to 126 crystallization additives and discuss in which cases they provide information relevant to structure-based drug design.
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Affiliation(s)
- Malgorzata N Drwal
- Laboratoire d'Innovation Thérapeutique , UMR7200, Université de Strasbourg , 74 Route du Rhin , 67401 Illkirch , France
| | - Guillaume Bret
- Laboratoire d'Innovation Thérapeutique , UMR7200, Université de Strasbourg , 74 Route du Rhin , 67401 Illkirch , France
| | - Carlos Perez
- Eli Lilly Research Laboratories , Avenida de la Industria, 30 , 28108 Alcobendas , Madrid , Spain
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique , UMR7200, Université de Strasbourg , 74 Route du Rhin , 67401 Illkirch , France
| | - Jérémy Desaphy
- Lilly Research Laboratories, Eli Lilly and Company , Lilly Corporate Center , Indianapolis , Indiana 46285 , United States
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique , UMR7200, Université de Strasbourg , 74 Route du Rhin , 67401 Illkirch , France
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39
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Bryan MC, Rajapaksa NS. Kinase Inhibitors for the Treatment of Immunological Disorders: Recent Advances. J Med Chem 2018; 61:9030-9058. [DOI: 10.1021/acs.jmedchem.8b00667] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Marian C. Bryan
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Naomi S. Rajapaksa
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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40
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Wahl J, Smieško M. Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations. ChemMedChem 2018; 13:1325-1335. [DOI: 10.1002/cmdc.201800093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/07/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Joel Wahl
- Molecular Modeling, Department of Pharmaceutical Sciences; University of Basel; Klingelbergstrasse 50 4056 Basel Switzerland
| | - Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences; University of Basel; Klingelbergstrasse 50 4056 Basel Switzerland
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41
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Zhang Z, Zhang D, Liu Y, Yang D, Ran F, Wang ML, Zhao G. Targeting Bruton's tyrosine kinase for the treatment of B cell associated malignancies and autoimmune diseases: Preclinical and clinical developments of small molecule inhibitors. Arch Pharm (Weinheim) 2018; 351:e1700369. [DOI: 10.1002/ardp.201700369] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Zhen Zhang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Daoguang Zhang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Yang Liu
- The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Dezhi Yang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Fansheng Ran
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Michael L. Wang
- The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Guisen Zhao
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
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42
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Xue Y, Song P, Song Z, Wang A, Tong L, Geng M, Ding J, Liu Q, Sun L, Xie H, Zhang A. Discovery of 4,7-Diamino-5-(4-phenoxyphenyl)-6-methylene-pyrimido[5,4-b]pyrrolizines as Novel Bruton’s Tyrosine Kinase Inhibitors. J Med Chem 2018; 61:4608-4627. [DOI: 10.1021/acs.jmedchem.8b00441] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yu Xue
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Peiran Song
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | | | - Aoli Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | | | - Meiyu Geng
- College of Pharmacy, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jian Ding
- College of Pharmacy, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qingsong Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Liping Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Hua Xie
- College of Pharmacy, University of Chinese Academy of Sciences, Shanghai, China
| | - Ao Zhang
- College of Pharmacy, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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43
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Young RJ, Leeson PD. Mapping the Efficiency and Physicochemical Trajectories of Successful Optimizations. J Med Chem 2018; 61:6421-6467. [DOI: 10.1021/acs.jmedchem.8b00180] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Robert J. Young
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul D. Leeson
- Paul Leeson Consulting Ltd., The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K
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44
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Crawford JJ, Johnson AR, Misner DL, Belmont LD, Castanedo G, Choy R, Coraggio M, Dong L, Eigenbrot C, Erickson R, Ghilardi N, Hau J, Katewa A, Kohli PB, Lee W, Lubach JW, McKenzie BS, Ortwine DF, Schutt L, Tay S, Wei B, Reif K, Liu L, Wong H, Young WB. Discovery of GDC-0853: A Potent, Selective, and Noncovalent Bruton's Tyrosine Kinase Inhibitor in Early Clinical Development. J Med Chem 2018; 61:2227-2245. [PMID: 29457982 DOI: 10.1021/acs.jmedchem.7b01712] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bruton's tyrosine kinase (Btk) is a nonreceptor cytoplasmic tyrosine kinase involved in B-cell and myeloid cell activation, downstream of B-cell and Fcγ receptors, respectively. Preclinical studies have indicated that inhibition of Btk activity might offer a potential therapy in autoimmune diseases such as rheumatoid arthritis and systemic lupus erythematosus. Here we disclose the discovery and preclinical characterization of a potent, selective, and noncovalent Btk inhibitor currently in clinical development. GDC-0853 (29) suppresses B cell- and myeloid cell-mediated components of disease and demonstrates dose-dependent activity in an in vivo rat model of inflammatory arthritis. It demonstrates highly favorable safety, pharmacokinetic (PK), and pharmacodynamic (PD) profiles in preclinical and Phase 2 studies ongoing in patients with rheumatoid arthritis, lupus, and chronic spontaneous urticaria. On the basis of its potency, selectivity, long target residence time, and noncovalent mode of inhibition, 29 has the potential to be a best-in-class Btk inhibitor for a wide range of immunological indications.
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Affiliation(s)
- James J Crawford
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Adam R Johnson
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Dinah L Misner
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Lisa D Belmont
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Georgette Castanedo
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Regina Choy
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Melis Coraggio
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Liming Dong
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Charles Eigenbrot
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Rebecca Erickson
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Nico Ghilardi
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jonathan Hau
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Arna Katewa
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Pawan Bir Kohli
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Wendy Lee
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Joseph W Lubach
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Brent S McKenzie
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Daniel F Ortwine
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Leah Schutt
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Suzanne Tay
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - BinQing Wei
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Karin Reif
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Lichuan Liu
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Harvey Wong
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Wendy B Young
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
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45
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Design, synthesis and biological evaluation of 7 H -pyrrolo[2,3- d ]pyrimidin-4-amine derivatives as selective Btk inhibitors with improved pharmacokinetic properties for the treatment of rheumatoid arthritis. Eur J Med Chem 2018; 145:96-112. [DOI: 10.1016/j.ejmech.2017.12.079] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/22/2017] [Accepted: 12/22/2017] [Indexed: 12/18/2022]
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46
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Kumar A, Tiwari DK, Sridhar B, Likhar PR. Unprecedented synthesis of 1,2,3-triazolo-cinnolinone via Sonogashira coupling and intramolecular cyclization. Org Biomol Chem 2018; 16:4840-4848. [DOI: 10.1039/c8ob01152d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An unprecedented copper mediated one-pot sequential synthesis of 1,2,3-triazolo cinnolinone derivatives from 2-halo-phenyl triazoles and terminal alkynes has been reported.
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Affiliation(s)
- Avnish Kumar
- Department of Catalysis & Fine Chemicals
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Academy of Scientific & Innovative Research (AcSIR)
| | - Dharmendra Kumar Tiwari
- Department of Organic Synthesis and Process Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
| | - Balasubramanian Sridhar
- X-Ray Crystallography Center CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
| | - Pravin R. Likhar
- Department of Catalysis & Fine Chemicals
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Academy of Scientific & Innovative Research (AcSIR)
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47
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Wells CI, Kapadia NR, Couñago RM, Drewry DH. In depth analysis of kinase cross screening data to identify chemical starting points for inhibition of the Nek family of kinases. MEDCHEMCOMM 2018; 9:44-66. [PMID: 30108900 PMCID: PMC6071746 DOI: 10.1039/c7md00510e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/01/2017] [Indexed: 01/11/2023]
Abstract
Potent, selective, and cell active small molecule kinase inhibitors are useful tools to help unravel the complexities of kinase signaling. As the biological functions of individual kinases become better understood, they can become targets of drug discovery efforts. The small molecules used to shed light on function can also then serve as chemical starting points in these drug discovery efforts. The Nek family of kinases has received very little attention, as judged by number of citations in PubMed, yet they appear to play many key roles and have been implicated in disease. Here we present our work to identify high quality chemical starting points that have emerged due to the increased incidence of broad kinome screening. We anticipate that this analysis will allow the community to progress towards the generation of chemical probes and eventually drugs that target members of the Nek family.
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Affiliation(s)
- C I Wells
- Structural Genomics Consortium , Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , NC , 27599 USA .
| | - N R Kapadia
- Structural Genomics Consortium , Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , NC , 27599 USA .
| | - R M Couñago
- Structural Genomics Consortium , Universidade Estadual de Campinas - UNICAMP , Campinas , SP , 13083 Brazil
| | - D H Drewry
- Structural Genomics Consortium , Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , NC , 27599 USA .
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48
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He L, Li D, Zhang C, Bai P, Chen L. Discovery of (R)-5-(benzo[d][1,3]dioxol-5-yl)-7-((1-(vinylsulfonyl)pyrrolidin-2-yl)methyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (B6) as a potent Bmx inhibitor for the treatment of NSCLC. Bioorg Med Chem Lett 2017; 27:4171-4175. [PMID: 28734581 DOI: 10.1016/j.bmcl.2017.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/28/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023]
Abstract
Described as a Btk inhibitor, ibrutinib also potently inhibits Bmx and EGFR, two good targets for lung cancer. Owing to its high CLogP (4.07) and low aqueous solubility (<0.01mg/ml), resulting in unfavorable bioavailability, ibrutinib requires high dosages to achieve good clinical response in the treatment of non-small cell lung cancer (NSCLC). In our effort to improve the CLogP of ibrutinib by structural optimization led to the discovery of a potent anti-cancer agent B6, with beneficial physicochemical parameters (CLogP=2.56, solubility in water≈0.1mg/ml) meeting the principles of oral drugs. B6 exhibited anti-proliferation activities against EGFR-expressing cells, especially the mutant ones, such as H1975 (L858R/T790M, IC50=0.92±0.19μM) and HCC827 (Del119 IC50=0.014±0.01μM). Moreover, B6 significantly slowed down H1975 tumor growth with anti-tumor rate of 73.9% (p<0.01). Enzyme potencies assay demonstrated B6 moderately selectively inhibited Bmx (IC50=35.7±0.1nM) over other kinases. So, as a potent Bmx inhibitor, B6 has the potential to be an efficacious treatment for NSCLC with acquired drug resistance.
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Affiliation(s)
- Linhong He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, PR China
| | - Da Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, PR China
| | - Chufeng Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, PR China
| | - Peng Bai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, PR China
| | - Lijuan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, PR China.
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49
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Zhang Q, Zhang L, Yu J, Li H, He S, Tang W, Zuo J, Lu W. Discovery of new BTK inhibitors with B cell suppression activity bearing a 4,6-substituted thieno[3,2-d]pyrimidine scaffold. RSC Adv 2017. [DOI: 10.1039/c7ra04261b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Seventeen compounds with 4,6-substituted thieno[3,2-d]pyrimidine scaffold were prepared as new Bruton's tyrosine kinase inhibitors. Compound 8 exhibits anti-BTK activity, immunosuppressive activity, enzymatic selectivity and low toxicity.
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Affiliation(s)
- Qiumeng Zhang
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- P. R. China
| | - Luyao Zhang
- Laboratory of Immunopharmacology
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
- P. R. China
| | - Jie Yu
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- P. R. China
| | - Heng Li
- Laboratory of Immunopharmacology
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
- P. R. China
| | - Shijun He
- Laboratory of Immunopharmacology
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
- P. R. China
| | - Wei Tang
- Laboratory of Immunopharmacology
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
- P. R. China
| | - Jianping Zuo
- Laboratory of Immunopharmacology
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
- P. R. China
| | - Wei Lu
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- P. R. China
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50
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Johnson CN, Erlanson DA, Murray CW, Rees DC. Fragment-to-Lead Medicinal Chemistry Publications in 2015. J Med Chem 2016; 60:89-99. [PMID: 27739691 DOI: 10.1021/acs.jmedchem.6b01123] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fragment-based drug discovery (FBDD) is now well-established as a technology for generating new chemical leads and drugs. This Miniperspective provides a tabulated overview of the fragment-to-lead literature published in the year 2015, together with a commentary on trends observed across the FBDD field during this time. It is hoped that this tabulated summary will provide a useful point of reference for both FBDD practitioners and the wider medicinal chemistry community.
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Affiliation(s)
- Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 409 Illinois Street, San Francisco, California 94158, United States
| | - Christopher W Murray
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - David C Rees
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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