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Wang S, Sun X, Cui W, Yuan S. MM/PB(GB)SA benchmarks on soluble proteins and membrane proteins. Front Pharmacol 2022; 13:1018351. [PMID: 36532746 PMCID: PMC9751045 DOI: 10.3389/fphar.2022.1018351] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/17/2022] [Indexed: 08/27/2023] Open
Abstract
Predicting protein-ligand binding free energy rapidly and accurately remains a challenging question in modern drug discovery. Molecular mechanics/Poisson-Boltzmann (Generalized Born) surface area (MM/PB(GB)SA) has emerged as an essential tool for accelerating cost-efficient binding free energy calculation. This study presents benchmarks with three membrane-bound protein systems and six soluble protein systems. Different parameters were sampled for different benchmarks to explore the highest accuracy. These include ligand charges, protein force fields, extra points, GB models, nonpolar optimization methods, internal dielectric constants and membrane dielectric constants. Comparisons of accuracy were made between MM/PB(GB)SA, docking and free energy perturbation (FEP). The results reveal a competitive performance between MM/PB(GB)SA and FEP. In summary, MM/PB(GB)SA is a powerful approach to predict ligand binding free energy rapidly and accurately. Parameters of MM/PB(GB)SA calculations, such as the GB models and membrane dielectric constants, need to be optimized for different systems. This method can be served as a powerful tool for drug design.
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Affiliation(s)
- Shiyu Wang
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- College of Chemical Science, University of Chinese Academy of Sciences, Beijing, China
- AlphaMol-SIAT Joint Laboratory, Shenzhen, China
| | - Xiaolin Sun
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- AlphaMol-SIAT Joint Laboratory, Shenzhen, China
| | - Wenqiang Cui
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- AlphaMol-SIAT Joint Laboratory, Shenzhen, China
| | - Shuguang Yuan
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- AlphaMol-SIAT Joint Laboratory, Shenzhen, China
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
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Sammeta VR, Norris JD, Artham S, Torrice CD, Byemerwa J, Joiner C, Fanning SW, McDonnell DP, Willson TM. A New Chemotype of Chemically Tractable Nonsteroidal Estrogens Based on a Thieno[2,3- d]pyrimidine Core. ACS Med Chem Lett 2022; 13:1151-1158. [DOI: 10.1021/acsmedchemlett.2c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Vamshikrishna Reddy Sammeta
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - John D. Norris
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Sandeep Artham
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Chad D. Torrice
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Jovita Byemerwa
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Carstyn Joiner
- Department of Cancer Biology, Loyola University of Chicago Stritch School of Medicine, Maywood, Illinois 60611, United States
| | - Sean W. Fanning
- Department of Cancer Biology, Loyola University of Chicago Stritch School of Medicine, Maywood, Illinois 60611, United States
| | - Donald P. McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Timothy M. Willson
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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Feng FF, Li JK, Liu XY, Zhang FG, Cheung CW, Ma JA. General Synthesis of Tri-Carbo-Substituted N2-Aryl-1,2,3-triazoles via Cu-Catalyzed Annulation of Azirines with Aryldiazonium Salts. J Org Chem 2020; 85:10872-10883. [PMID: 32691600 DOI: 10.1021/acs.joc.0c01433] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The general synthesis of fully substituted N2-aryl-1,2,3-triazoles is hitherto challenging compared with that of the N1-aryl counterparts. Herein, we describe a Cu-catalyzed annulation reaction of azirines and aryldiazonium salts. This regiospecific method allows access to a broad spectrum of tri-carbo N2-aryl-1,2,3-triazoles substituted with diverse aryl and alkyl moieties. Its utility is highlighted by the synthesis of several triazole precursors applicable in drug discovery, as well as novel chiral binaphthyl ligands bearing triazole moieties.
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Affiliation(s)
- Fang-Fang Feng
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Centre of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China
| | - Jun-Kuan Li
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Centre of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China
| | - Xuan-Yu Liu
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Centre of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China
| | - 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 Centre of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, P. R. of 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 Centre of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, P. R. of 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 Centre of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, P. R. of China
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Abstract
Estimating the range of three-dimensional structures (conformations) that are available to a molecule is a key component of computer-aided drug design. Quantum mechanical simulation offers improved accuracy over forcefield methods, but at a high computational cost. The question is whether this increased cost can be justified in a context in which high-throughput analysis of large numbers of molecules is often key. This chapter discusses the application of quantum mechanics to conformational searching, with a focus on three key challenges: (1) the generation of ensembles that include a good approximation to a molecule's bioactive conformation at as prominent a ranking as possible; (2) rational analysis and modification of a pre-established bioactive conformation in terms of its energetics; and (3) approximation of real solution-phase conformational ensembles in tandem with NMR data. The impact of QM on the high-throughput application (1) is debatable, meaning that for the moment its primary application is still lower-throughput applications such as (2) and (3). The optimal choice of QM method is also discussed. Rigorous benchmarking suggests that DFT methods are only acceptable when used with large basis sets, but a trickle of papers continue to obtain useful results with relatively low-cost methods, leading to a dilemma that the literature has yet to fully resolve.
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Li ZH, Jiang ZJ, Shao QL, Qin JJ, Shu QF, Lu WH, Su WK. One-Pot Cascade Heterocyclization of γ- and β-Ketomalononitriles to 2,4-Dichloro-Substituted Pyrano[2,3- d]pyrimidines and Furo[2,3- d]pyrimidines Mediated by Triphosgene and Triphenylphosphine Oxide. J Org Chem 2018; 83:6423-6431. [PMID: 29779383 DOI: 10.1021/acs.joc.8b00669] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A one-pot cascade heterocyclization strategy has been developed for the synthesis of 2,4-dichloro-substituted pyrano[2,3- d]pyrimidines and furo[2,3- d]pyrimidines from linear γ- and β-ketomalononitriles using triphosgene and triphenylphosphine oxide. The reaction afforded synthetic useful products with moderate to good yields, bypassing the conventional harsh conditions of chlorination. The mechanistic study revealed that the reaction proceeded with a non-isocyanate route, and the second step may conduct in a triphenylphosphine oxide-catalyzed manner.
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Affiliation(s)
- Zhen-Hua Li
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, College of Pharmaceutical Sciences , Zhejiang University of Technology , Hangzhou 310014 , People's Republic of China
| | - Zhi-Jiang Jiang
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals , Zhejiang University of Technology , Hangzhou 310014 , People's Republic of China
| | - Qiao-Ling Shao
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals , Zhejiang University of Technology , Hangzhou 310014 , People's Republic of China
| | - Jin-Jing Qin
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, College of Pharmaceutical Sciences , Zhejiang University of Technology , Hangzhou 310014 , People's Republic of China
| | - Qiang-Feng Shu
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, College of Pharmaceutical Sciences , Zhejiang University of Technology , Hangzhou 310014 , People's Republic of China
| | - Wen-Hao Lu
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, College of Pharmaceutical Sciences , Zhejiang University of Technology , Hangzhou 310014 , People's Republic of China
| | - Wei-Ke Su
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals , Zhejiang University of Technology , Hangzhou 310014 , People's Republic of China
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Li C, Lu X, Yang Y, Yang S, Zhang L. Ionic liquid promoted synthesis of heterocycle-fused pyrimidine-2,4(1H,3H)-diones utilising CO2. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.05.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Heifetz A, Chudyk EI, Gleave L, Aldeghi M, Cherezov V, Fedorov DG, Biggin PC, Bodkin MJ. The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR–Ligand Interactions. J Chem Inf Model 2015; 56:159-72. [PMID: 26642258 DOI: 10.1021/acs.jcim.5b00644] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Our interpretation of ligand-protein interactions is often informed by high-resolution structures, which represent the cornerstone of structure-based drug design. However, visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum Mechanics approaches are often too computationally expensive, but one method, Fragment Molecular Orbital (FMO), offers an excellent compromise and has the potential to reveal key interactions that would otherwise be hard to detect. To illustrate this, we have applied the FMO method to 18 Class A GPCR-ligand crystal structures, representing different branches of the GPCR genome. Our work reveals key interactions that are often omitted from structure-based descriptions, including hydrophobic interactions, nonclassical hydrogen bonds, and the involvement of backbone atoms. This approach provides a more comprehensive picture of receptor-ligand interactions than is currently used and should prove useful for evaluation of the chemical nature of ligand binding and to support structure-based drug design.
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Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Ewa I. Chudyk
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Laura Gleave
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Matteo Aldeghi
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Vadim Cherezov
- Department
of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, United States
- Laboratory
for Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Dmitri G. Fedorov
- NMRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Philip C. Biggin
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Mike J. Bodkin
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
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8
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Recent trends in orexin research—2010 to 2015. Bioorg Med Chem Lett 2015; 25:2875-87. [DOI: 10.1016/j.bmcl.2015.05.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/08/2015] [Accepted: 05/09/2015] [Indexed: 12/31/2022]
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