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Zeng J, Tao Y, Giese TJ, York DM. QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. J Chem Theory Comput 2023; 19:1261-1275. [PMID: 36696673 PMCID: PMC9992268 DOI: 10.1021/acs.jctc.2c01172] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report QDπ-v1.0 for modeling the internal energy of drug molecules containing H, C, N, and O atoms. The QDπ model is in the form of a quantum mechanical/machine learning potential correction (QM/Δ-MLP) that uses a fast third-order self-consistent density-functional tight-binding (DFTB3/3OB) model that is corrected to a quantitatively high-level of accuracy through a deep-learning potential (DeepPot-SE). The model has the advantage that it is able to properly treat electrostatic interactions and handle changes in charge/protonation states. The model is trained against reference data computed at the ωB97X/6-31G* level (as in the ANI-1x data set) and compared to several other approximate semiempirical and machine learning potentials (ANI-1x, ANI-2x, DFTB3, MNDO/d, AM1, PM6, GFN1-xTB, and GFN2-xTB). The QDπ model is demonstrated to be accurate for a wide range of intra- and intermolecular interactions (despite its intended use as an internal energy model) and has shown to perform exceptionally well for relative protonation/deprotonation energies and tautomers. An example application to model reactions involved in RNA strand cleavage catalyzed by protein and nucleic acid enzymes illustrates QDπ has average errors less than 0.5 kcal/mol, whereas the other models compared have errors over an order of magnitude greater. Taken together, this makes QDπ highly attractive as a potential force field model for drug discovery.
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Affiliation(s)
- Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yujun Tao
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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Moukhliss Y, Koubi Y, Alaqarbeh M, Muzzammel Rehman H, Maghat H, Sbai A, Bouachrine M, Lakhlifi T. Computational and Retrosynthetic Investigation of Isoxazole‐Bearing Chalcones as Antioxidant Activate Compounds. ChemistrySelect 2023. [DOI: 10.1002/slct.202203908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- Youness Moukhliss
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | - Yassine Koubi
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | | | | | - Hamid Maghat
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
- EST Khenifra Sultan Moulay Slimane University Beni Mellal Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
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Dutkiewicz Z. Computational methods for calculation of protein-ligand binding affinities in structure-based drug design. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2020-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
Drug design is an expensive and time-consuming process. Any method that allows reducing the time the costs of the drug development project can have great practical value for the pharmaceutical industry. In structure-based drug design, affinity prediction methods are of great importance. The majority of methods used to predict binding free energy in protein-ligand complexes use molecular mechanics methods. However, many limitations of these methods in describing interactions exist. An attempt to go beyond these limits is the application of quantum-mechanical description for all or only part of the analyzed system. However, the extensive use of quantum mechanical (QM) approaches in drug discovery is still a demanding challenge. This chapter briefly reviews selected methods used to calculate protein-ligand binding affinity applied in virtual screening (VS), rescoring of docked poses, and lead optimization stage, including QM methods based on molecular simulations.
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Affiliation(s)
- Zbigniew Dutkiewicz
- Department of Chemical Technology of Drugs , Poznan University of Medical Sciences , ul. Grunwaldzka 6 , 60-780 Poznań , Poznan , 60-780, Poland
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Rocha-Santos A, Chaves EJ, Grillo IB, de Freitas AS, Araújo DAM, Rocha GB. Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors. ACS OMEGA 2021; 6:8764-8777. [PMID: 33842748 PMCID: PMC8027999 DOI: 10.1021/acsomega.0c02588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/30/2020] [Indexed: 05/03/2023]
Abstract
In this work, we performed a study to assess the interactions between the ricin toxin A (RTA) subunit of ricin and some of its inhibitors using modern semiempirical quantum chemistry and ONIOM quantum mechanics/molecular mechanics (QM/MM) methods. Two approaches were followed (calculation of binding enthalpies, ΔH bind, and reactivity quantum chemical descriptors) and compared with the respective half-maximal inhibitory concentration (IC50) experimental data, to gain insight into RTA inhibitors and verify which quantum chemical method would better describe RTA-ligand interactions. The geometries for all RTA-ligand complexes were obtained after running classical molecular dynamics simulations in aqueous media. We found that single-point energy calculations of ΔH bind with the PM6-DH+, PM6-D3H4, and PM7 semiempirical methods and ONIOM QM/MM presented a good correlation with the IC50 data. We also observed, however, that the correlation decreased significantly when we calculated ΔH bind after full-atom geometry optimization with all semiempirical methods. Based on the results from reactivity descriptors calculations for the cases studied, we noted that both types of interactions, molecular overlap and electrostatic interactions, play significant roles in the overall affinity of these ligands for the RTA binding pocket.
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Affiliation(s)
- Acassio Rocha-Santos
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Elton José
Ferreira Chaves
- Department
of Biotechnology, Federal University of
Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Igor Barden Grillo
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Amanara Souza de Freitas
- Department
of Chemical Engineering, Federal University
of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | | | - Gerd Bruno Rocha
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
- . Phone/Fax: +55-83-3216-7437
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Abstract
INTRODUCTION Molecular docking has been consolidated as one of the most important methods in the molecular modeling field. It has been recognized as a prominent tool in the study of protein-ligand complexes, to describe intermolecular interactions, to accurately predict poses of multiple ligands, to discover novel promising bioactive compounds. Molecular docking methods have evolved in terms of their accuracy and reliability; but there are pending issues to solve for improving the connection between the docking results and the experimental evidence. AREAS COVERED In this article, the author reviews very recent innovative molecular docking applications with special emphasis on reverse docking, treatment of protein flexibility, the use of experimental data to guide the selection of docking poses, the application of Quantum mechanics(QM) in docking, and covalent docking. EXPERT OPINION There are several issues being worked on in recent years that will lead to important breakthroughs in molecular docking methods in the near future These developments are related to more efficient exploration of large datasets and receptor conformations, advances in electronic description, and the use of structural information for guiding the selection of results.
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Affiliation(s)
- Julio Caballero
- Departamento De Bioinformática, Centro De Bioinformática, Simulación Y Modelado (CBSM), Facultad De Ingeniería, Universidad De Talca, Talca, Chile
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Hassanzadeh P. Towards the quantum-enabled technologies for development of drugs or delivery systems. J Control Release 2020; 324:260-279. [DOI: 10.1016/j.jconrel.2020.04.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022]
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Singh RK, Najmi AK. Novel Therapeutic Potential of Mitogen-Activated Protein Kinase Activated Protein Kinase 2 (MK2) in Chronic Airway Inflammatory Disorders. Curr Drug Targets 2020; 20:367-379. [PMID: 30112991 DOI: 10.2174/1389450119666180816121323] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/17/2018] [Accepted: 08/09/2018] [Indexed: 02/04/2023]
Abstract
OBJECTIVE The primary focus of this review is to highlight the current and emerging proinflammatory role of MK2 kinase signaling in p38MAPK pathway and to provide a detailed evaluation on the prospects of MK2 inhibition with special emphasis on the etiology of chronic inflammatory airway diseases, such as asthma, idiopathic pulmonary fibrosis, lung cancer, acute lung injury and acute respiratory distress syndrome. BACKGROUND MK2 belongs to serine-threonine kinase family and is activated directly by stress and inflammatory signal through p38MAPK phosphorylation in diverse inflammatory conditions through the Toll-like receptor signaling pathway. MK2 has been thought to be a critical factor involved in the regulation of synthesis and release of pro-inflammatory (TNF-α, IL-6 and IL-1β, etc.) proteins. Targeted inhibition of MK2 kinase has been shown to significantly reduce the production and release of these cytokine molecules. Therefore, MK2 has been identified as an effective strategy (alternative to p38MAPK) to block this pro-inflammatory signaling pathway. RESULTS The inhibition of MK2 may lead to similar or better efficacy as that of p38 inhibitors, and interestingly avoids the systemic toxicity shown by the p38 inhibitors. Thus, MK2 has been the focus of intense interdisciplinary research and its specific inhibition can be a novel and potential therapeutic strategy for the treatment of chronic airway inflammatory diseases. CONCLUSION Promising advancement in understanding and rigorous exploration of the role of MK2 kinase in inflammatory processes may contribute to the development of newer and safer therapy for the treatment of chronic airway inflammatory diseases in the future.
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Affiliation(s)
- Rakesh Kumar Singh
- School of Pharmaceutical Sciences, Apeejay Stya University, Sohna, Gurgaon-122013, India.,Department of Pharmacology, Faculty of Pharmacy, Jamia Hamdard, New Delhi-110062, India
| | - Abul Kalam Najmi
- Department of Pharmacology, Faculty of Pharmacy, Jamia Hamdard, New Delhi-110062, India
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Pratama MRF, Poerwono H, Siswodihardjo S. Molecular docking of novel 5-O-benzoylpinostrobin derivatives as wild type and L858R/T790M/V948R mutant EGFR inhibitor. J Basic Clin Physiol Pharmacol 2019; 30:/j/jbcpp.ahead-of-print/jbcpp-2019-0301/jbcpp-2019-0301.xml. [PMID: 31855568 DOI: 10.1515/jbcpp-2019-0301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
Abstract
Background Previous studies have shown that 5-O-benzoylpinostrobin derivatives is a potential anti-breast cancer, with the highest potential being the HER2 inhibitors, is a protein's member of the epidermal growth factor receptor (EGFR) family. Overexpression of EGFR itself is known to be one of the causes of other cancer, including non-small cell lung cancer (NSCLC). Thus, it is possible that 5-O-benzoylpinostrobin derivatives can also inhibit the overexpression of EGFR in NSCLC. In the case of NSCLC, mutations of EGFR are often found in several amino acids, such as L858R, T790M, and V948R. This study aimed to determine the potential of 5-O-benzoylpinostrobin derivatives as an inhibitor of wild type and L858R/T790M/V948R-mutant EGFR. Methods Docking was performed using AutoDock Vina 1.1.2 on both wild type and L858R/T790M/V948R-mutant EGFR. Parameters observed, consisted of free energy of binding (ΔG) and amino acid interactions of each ligand. Results Docking results showed that all 5-O-benzoylpinostrobin derivatives showed a lower ΔG for both wild type and L858R/T790M/V948R-mutant EGFR, with the lowest ΔG shown by 4-methyl-5-O-benzoylpinostrobin and 4-trifluoromethyl-5-O-benzoylpinostrobin. Both the ligands have the similarity of interacting amino acids compared to reference ligands between 76.47 and 88.24%. Specifically, the ΔG of all test ligands was lower in mutant EGFR than in the wild type, which indicates the potential of the ligand as EGFR inhibitors where a mutation to EGFR occurs. Conclusions These results confirm that 5-O-benzoylpinostrobin derivatives have the potential to inhibit EGFR in both wild type and L858R/T790M/V948R-mutant.
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Affiliation(s)
- Mohammad Rizki Fadhil Pratama
- Universitas Airlangga, Doctoral Program of Pharmaceutical Science, Faculty of Pharmacy, Kampus C UNAIR Jl Dr Ir H Soekarno Mulyorejo Surabaya, East Java, Indonesia
| | - Hadi Poerwono
- Universitas Airlangga, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kampus C UNAIR Jl Dr Ir H Soekarno Mulyorejo Surabaya, East Java, Indonesia
| | - Siswandono Siswodihardjo
- Universitas Airlangga, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kampus C UNAIR Jl Dr Ir H Soekarno Mulyorejo Surabaya, East Java, Indonesia
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Synthesis of dispiro[1-benzothiophene-2,3'-pyrrolidine-2',3”-indoline]-2”,3-diones in cycloaddition reaction. Chem Heterocycl Compd (N Y) 2019. [DOI: 10.1007/s10593-019-02575-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Li J, Fu A, Zhang L. An Overview of Scoring Functions Used for Protein-Ligand Interactions in Molecular Docking. Interdiscip Sci 2019; 11:320-328. [PMID: 30877639 DOI: 10.1007/s12539-019-00327-w] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 02/06/2019] [Accepted: 03/06/2019] [Indexed: 12/17/2022]
Abstract
Currently, molecular docking is becoming a key tool in drug discovery and molecular modeling applications. The reliability of molecular docking depends on the accuracy of the adopted scoring function, which can guide and determine the ligand poses when thousands of possible poses of ligand are generated. The scoring function can be used to determine the binding mode and site of a ligand, predict binding affinity and identify the potential drug leads for a given protein target. Despite intensive research over the years, accurate and rapid prediction of protein-ligand interactions is still a challenge in molecular docking. For this reason, this study reviews four basic types of scoring functions, physics-based, empirical, knowledge-based, and machine learning-based scoring functions, based on an up-to-date classification scheme. We not only discuss the foundations of the four types scoring functions, suitable application areas and shortcomings, but also discuss challenges and potential future study directions.
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Affiliation(s)
- Jin Li
- College of Computer and Information Science, Southwest University, Chongqing, 400715, China.,School of Medical Information and Engineering, Southwest Medical University, Luzhou, 646000, China
| | - Ailing Fu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Le Zhang
- College of Computer and Information Science, Southwest University, Chongqing, 400715, China. .,College of Computer Science, Sichuan University, Chengdu, 610065, China. .,Medical Big Data Center, Sichuan University, Chengdu, 610065, China. .,Zdmedical, Information Polytron Technologies Inc Chongqing, Chongqing, 401320, China.
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Toma C, Gadaleta D, Roncaglioni A, Toropov A, Toropova A, Marzo M, Benfenati E. QSAR Development for Plasma Protein Binding: Influence of the Ionization State. Pharm Res 2018; 36:28. [PMID: 30591975 PMCID: PMC6308215 DOI: 10.1007/s11095-018-2561-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/17/2018] [Indexed: 01/05/2023]
Abstract
Purpose This study explored several strategies to improve the performance of literature QSAR models for plasma protein binding (PPB), such as a suitable endpoint transformation, a correct representation of chemicals, more consistency in the dataset, and a reliable definition of the applicability domain. Methods We retrieved human fraction unbound (Fu) data for 670 compounds from the literature and carefully checked them for consistency. Descriptors were calculated taking account of the ionization state of molecules at physiological pH (7.4), in order to better estimate the affinity of molecules to blood proteins. We used different algorithms and chemical descriptors to explore the most suitable strategy for modeling the endpoint. SMILES (simplified molecular input line entry system)-based string descriptors were also tested with the CORAL software (CORelation And Logic). We did an outlier analysis to establish the models to use (or not to use) in case of well recognized families. Results Internal validation of the selected models returned Q2 values close to 0.60. External validation also gave r2 values always greater than 0.60. The CORAL descriptor based model for √fu was the best, with r2 0.74 in external validation. Conclusions Performance in prediction confirmed the robustness of all the derived models and their suitability for real-life purposes, i.e. screening chemicals for their ADMET profiling. Optimization of descriptors can be useful in order to obtain the correct results with a ionized molecule. Electronic supplementary material The online version of this article (10.1007/s11095-018-2561-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cosimo Toma
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via la Masa 19, 20156, Milano, Italy.
| | - Domenico Gadaleta
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via la Masa 19, 20156, Milano, Italy
| | - Alessandra Roncaglioni
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via la Masa 19, 20156, Milano, Italy
| | - Andrey Toropov
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via la Masa 19, 20156, Milano, Italy
| | - Alla Toropova
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via la Masa 19, 20156, Milano, Italy
| | - Marco Marzo
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via la Masa 19, 20156, Milano, Italy
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via la Masa 19, 20156, Milano, Italy
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Singh RK, Najmi AK, Dastidar SG. Biological functions and role of mitogen-activated protein kinase activated protein kinase 2 (MK2) in inflammatory diseases. Pharmacol Rep 2017; 69:746-756. [DOI: 10.1016/j.pharep.2017.03.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/19/2017] [Accepted: 03/31/2017] [Indexed: 10/19/2022]
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Boyaala R, Touzani R, Guerchais V, Soulé JF, Doucet H. Synthesis of 2-(fluorinated aryl)pyridine derivatives via palladium-catalyzed C H bond arylation of fluorobenzenes using 2-halopyridines as aryl sources. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.06.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Adeniyi AA, Soliman MES. Implementing QM in docking calculations: is it a waste of computational time? Drug Discov Today 2017; 22:1216-1223. [PMID: 28689054 DOI: 10.1016/j.drudis.2017.06.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/25/2017] [Accepted: 06/29/2017] [Indexed: 12/14/2022]
Abstract
The greatest challenge in molecular docking (MD) is the deficiency of scoring functions (SFs), which limits their reliability. SFs are too simplified to represent the true features of the complex free energy of protein-ligand interactions. Investigations of docking functions have traded accuracy for speed through the use of approximations and simplifications. Consequently, there has been an increase in the popularity of quantum-mechanical (QM)-based methods as reference points for the development of fast, reliable, valuable, yet inexpensive, tools. As we discuss here, one significant QM-based parameter used to predict docking is the accuracy of atomic partial charges, which is strongly related to the accuracy of the SF prediction.
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Affiliation(s)
- Adebayo A Adeniyi
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa.
| | - Mahmoud E S Soliman
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa.
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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Bobovská A, Tvaroška I, Kóňa J. Using DFT methodology for more reliable predictive models: Design of inhibitors of Golgi α-Mannosidase II. J Mol Graph Model 2016; 66:47-57. [PMID: 27035259 DOI: 10.1016/j.jmgm.2016.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 11/28/2022]
Abstract
Human Golgi α-mannosidase II (GMII), a zinc ion co-factor dependent glycoside hydrolase (E.C.3.2.1.114), is a pharmaceutical target for the design of inhibitors with anti-cancer activity. The discovery of an effective inhibitor is complicated by the fact that all known potent inhibitors of GMII are involved in unwanted co-inhibition with lysosomal α-mannosidase (LMan, E.C.3.2.1.24), a relative to GMII. Routine empirical QSAR models for both GMII and LMan did not work with a required accuracy. Therefore, we have developed a fast computational protocol to build predictive models combining interaction energy descriptors from an empirical docking scoring function (Glide-Schrödinger), Linear Interaction Energy (LIE) method, and quantum mechanical density functional theory (QM-DFT) calculations. The QSAR models were built and validated with a library of structurally diverse GMII and LMan inhibitors and non-active compounds. A critical role of QM-DFT descriptors for the more accurate prediction abilities of the models is demonstrated. The predictive ability of the models was significantly improved when going from the empirical docking scoring function to mixed empirical-QM-DFT QSAR models (Q(2)=0.78-0.86 when cross-validation procedures were carried out; and R(2)=0.81-0.83 for a testing set). The average error for the predicted ΔGbind decreased to 0.8-1.1kcalmol(-1). Also, 76-80% of non-active compounds were successfully filtered out from GMII and LMan inhibitors. The QSAR models with the fragmented QM-DFT descriptors may find a useful application in structure-based drug design where pure empirical and force field methods reached their limits and where quantum mechanics effects are critical for ligand-receptor interactions. The optimized models will apply in lead optimization processes for GMII drug developments.
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Affiliation(s)
- Adela Bobovská
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic; Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, Ilkovičova 6, 842 15 Bratislava, Slovak Republic.
| | - Igor Tvaroška
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic.
| | - Juraj Kóňa
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic.
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Fiore M, Forli S, Manetti F. Targeting Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MAPKAPK2, MK2): Medicinal Chemistry Efforts To Lead Small Molecule Inhibitors to Clinical Trials. J Med Chem 2015; 59:3609-34. [PMID: 26502061 DOI: 10.1021/acs.jmedchem.5b01457] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The p38/MAPK-activated kinase 2 (MK2) pathway is involved in a series of pathological conditions (inflammation diseases and metastasis) and in the resistance mechanism to antitumor agents. None of the p38 inhibitors entered advanced clinical trials because of their unwanted systemic side effects. For this reason, MK2 was identified as an alternative target to block the pathway but avoiding the side effects of p38 inhibition. However, ATP-competitive MK2 inhibitors suffered from low solubility, poor cell permeability, and scarce kinase selectivity. Fortunately, non-ATP-competitive inhibitors of MK2 have been already discovered that allowed circumventing the selectivity issue. These compounds showed the additional advantage to be effective at lower concentrations in comparison to the ATP-competitive inhibitors. Therefore, although the significant difficulties encountered during the development of these inhibitors, MK2 is still considered as an attractive target to treat inflammation and related diseases to prevent tumor metastasis and to increase tumor sensitivity to chemotherapeutics.
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Affiliation(s)
- Mario Fiore
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Fabrizio Manetti
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
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Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. J Mol Recognit 2015; 28:581-604. [PMID: 25808539 DOI: 10.1002/jmr.2471] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
Abstract
Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.
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Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jessica Holien
- ACRF Rational Drug Discovery Centre and Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia.,Department of Surgery Austin Health, University of Melbourne, Melbourne, Victoria, 3084, Australia.,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, 3004, Australia.,School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia, 6845, Australia
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Chaskar P, Zoete V, Röhrig UF. Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function. J Chem Inf Model 2014; 54:3137-52. [DOI: 10.1021/ci5004152] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prasad Chaskar
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
| | - Ute F. Röhrig
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
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Juneja H, Panchbhai D, Sheikh J, Ingle V, Hadda TB. Synthesis, antibacterial screening, and POM analyses of novel bis-isoxazolyl/pyrazolyl-1,3-diols. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0755-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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POM analyses for antimicrobial evaluation of thienopyrimidinones derivatives: a rapid method for drug design. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0614-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Mucs D, Bryce RA. The application of quantum mechanics in structure-based drug design. Expert Opin Drug Discov 2013; 8:263-76. [DOI: 10.1517/17460441.2013.752812] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Natesan S, Balaz S. Rigorous incorporation of tautomers, ionization species, and different binding modes into ligand-based and receptor-based 3D-QSAR methods. Curr Pharm Des 2013; 19:4316-22. [PMID: 23170882 PMCID: PMC3778504 DOI: 10.2174/1381612811319230013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 11/19/2012] [Indexed: 11/22/2022]
Abstract
Speciation of drug candidates and receptors caused by ionization, tautomerism, and/or covalent hydration complicates ligandand receptor-based predictions of binding affinities by 3-dimensional structure-activity relationships (3D-QSAR). The speciation problem is exacerbated by tendency of tautomers to bind in multiple conformations or orientations (modes) in the same binding site. New forms of the 3D-QSAR correlation equations, capable of capturing this complexity, can be developed using the time hierarchy of all steps that lie behind the monitored biological process - binding, enzyme inhibition or receptor activity. In most cases, reversible interconversions of individual ligand and receptor species can be treated as quickly established equilibria because they are finished in a small fraction of the exposure time that is used to determine biological effects. The speciation equilibria are satisfactorily approximated by invariant fractions of individual ligand and receptor species for buffered experimental or in vivo conditions. For such situations, the observed drug-receptor association constant of a ligand is expressed as the sum of products, for each ligand and receptor species pair, of the association microconstant and the fractions of involved species. For multiple binding modes, each microconstant is expressed as the sum of microconstants of individual modes. This master equation leads to new 3D-QSAR correlation equations integrating the results of all molecular simulations or calculations, which are run for each ligand-receptor species pair separately. The multispecies, multimode 3D-QSAR approach is illustrated by a ligand-based correlation of transthyretin binding of thyroxine analogs and by a receptor-based correlation of inhibition of MK2 by benzothiophenes and pyrrolopyrimidines.
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Affiliation(s)
- Senthil Natesan
- Albany College of Pharmacy and Health Sciences, Vermont Campus, Colchester, VT 05446
| | - Stefan Balaz
- Albany College of Pharmacy and Health Sciences, Vermont Campus, Colchester, VT 05446
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Abstract
Antibiotic treatment may fail to protect individuals, if not started early enough, after infection with Bacillus anthracis, due to the continuing activity of toxins that the bacterium produces. Stable and easily stored inhibitors of the edema factor toxin (EF), an adenylyl cyclase, could save lives in the event of an outbreak, due to natural causes or a bioweapon attack. The toxin’s basic activity is to convert ATP to cAMP, and it is thus in principle a simple phosphatase, which means that many mammalian enzymes, including intracellular adenylcyclases, may have a similar activity. While nucleotide based inhibitors, similar to its natural substrate, ATP, were identified early, these compounds had low activity and specificity for EF. We used a combined structural and computational approach to choose small organic molecules in large, web-based compound libraries that would, based on docking scores, bind to residues within the substrate binding pocket of EF. A family of fluorenone-based inhibitors was identified that inhibited the release of cAMP from cells treated with EF. The lead inhibitor was also shown to inhibit the diarrhea caused by enterotoxigenic E. coli (ETEC) in a murine model, perhaps by serving as a quorum sensor. These inhibitors are now being tested for their ability to inhibit Anthrax infection in animal models and may have use against other pathogens that produce toxins similar to EF, such as Bordetella pertussis or Vibrio cholera.
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Ullmann RT, Andrade SLA, Ullmann GM. Thermodynamics of transport through the ammonium transporter Amt-1 investigated with free energy calculations. J Phys Chem B 2012; 116:9690-703. [PMID: 22804733 DOI: 10.1021/jp305440f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Amt-1 from Archaeoglobus fulgidus (AfAmt-1) belongs to the Amt/Rh family of ammonium/ammonia transporting membrane proteins. The transport mode and the precise microscopic permeation mechanism utilized by these proteins are intensely debated. Open questions concern the identity of the transported substrate (ammonia and/or ammonium) and whether the transport is passive or active. To address these questions, we studied the overall thermodynamics of the different transport modes as a function of the environmental conditions. Then, we investigated the thermodynamics of the underlying microscopic transport mechanisms with free energy calculations within a continuum electrostatics model. The formalism developed for this purpose is of general utility in the calculation of binding free energies for ligands with multiple protonation forms or other binding forms. The results of our calculations are compared to the available experimental and theoretical data on Amt/Rh proteins and discussed in light of the current knowledge on the physiological conditions experienced by microorganisms and plants. We found that microscopic models of electroneutral and electrogenic transport modes are in principle thermodynamically viable. However, only the electrogenic variants have a net thermodynamic driving force under the physiological conditions experienced by microorganisms and plants. Thus, the transport mechanism of AfAmt-1 is most likely electrogenic.
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Affiliation(s)
- R Thomas Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany.
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