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Sulimov A, Ilin I, Kutov D, Shikhaliev K, Shcherbakov D, Pyankov O, Stolpovskaya N, Medvedeva S, Sulimov V. New Chemicals Suppressing SARS-CoV-2 Replication in Cell Culture. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27175732. [PMID: 36080498 PMCID: PMC9457583 DOI: 10.3390/molecules27175732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Candidates to being inhibitors of the main protease (Mpro) of SARS-CoV-2 were selected from the database of Voronezh State University using molecular modeling. The database contained approximately 19,000 compounds represented by more than 41,000 ligand conformers. These ligands were docked into Mpro using the SOL docking program. For one thousand ligands with best values of the SOL score, the protein–ligand binding enthalpy was calculated by the PM7 quantum-chemical method with the COSMO solvent model. Using the SOL score and the calculated protein–ligand binding enthalpies, eighteen compounds were selected for the experiments. Several of these inhibitors suppressed the replication of the coronavirus in cell culture, and we used the best three among them in the search for chemical analogs. Selection among analogs using the same procedure followed by experiments led to identification of seven inhibitors of the SARS-CoV-2 replication in cell culture with EC50 values at the micromolar level. The identified inhibitors belong to three chemical classes. The three inhibitors, 4,4-dimethyldithioquinoline derivatives, inhibit SARS-CoV-2 replication in Vero E6 cell culture just as effectively as the best published non-covalent inhibitors, and show low cytotoxicity. These results open up a possibility to develop antiviral drugs against the SARS-CoV-2 coronavirus.
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Affiliation(s)
- Alexey Sulimov
- Dimonta Ltd., 15 Nagornaya Str., Bldg 8, 117186 Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Leninskie Gory, 1, Building 4, 119234 Moscow, Russia
| | - Ivan Ilin
- Dimonta Ltd., 15 Nagornaya Str., Bldg 8, 117186 Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Leninskie Gory, 1, Building 4, 119234 Moscow, Russia
| | - Danil Kutov
- Dimonta Ltd., 15 Nagornaya Str., Bldg 8, 117186 Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Leninskie Gory, 1, Building 4, 119234 Moscow, Russia
- Correspondence: (D.K.); (V.S.)
| | - Khidmet Shikhaliev
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya Sq., 394018 Voronezh, Russia
| | - Dmitriy Shcherbakov
- State Research Centre of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia
| | - Oleg Pyankov
- State Research Centre of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia
| | - Nadezhda Stolpovskaya
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya Sq., 394018 Voronezh, Russia
| | - Svetlana Medvedeva
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya Sq., 394018 Voronezh, Russia
| | - Vladimir Sulimov
- Dimonta Ltd., 15 Nagornaya Str., Bldg 8, 117186 Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Leninskie Gory, 1, Building 4, 119234 Moscow, Russia
- Correspondence: (D.K.); (V.S.)
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Tashchilova A, Podoplelova N, Sulimov A, Kutov D, Ilin I, Panteleev M, Shikhaliev K, Medvedeva S, Novichikhina N, Potapov A, Sulimov V. New Blood Coagulation Factor XIIa Inhibitors: Molecular Modeling, Synthesis, and Experimental Confirmation. Molecules 2022; 27:molecules27041234. [PMID: 35209023 PMCID: PMC8876603 DOI: 10.3390/molecules27041234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/02/2022] Open
Abstract
In the modern world, complications caused by disorders in the blood coagulation system are found in almost all areas of medicine. Thus, the development of new, more advanced drugs that can prevent pathological conditions without disrupting normal hemostasis is an urgent task. The blood coagulation factor XIIa is one of the most promising therapeutic targets for the development of anticoagulants based on its inhibitors. The initial stage of drug development is directly related to computational methods of searching for a lead compound. In this study, docking followed by quantum chemical calculations was used to search for noncovalent low-molecular-weight factor XIIa inhibitors in a focused library of druglike compounds. As a result of the study, four low-molecular-weight compounds were experimentally confirmed as factor XIIa inhibitors. Selectivity testing revealed that two of the identified factor XIIa inhibitors were selective over the coagulation factors Xa and XIa.
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Affiliation(s)
- Anna Tashchilova
- Dimonta, Ltd., 117186 Moscow, Russia; (A.T.); (A.S.); (I.I.)
- Research Computing Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Nadezhda Podoplelova
- Russian Children’s Clinical Hospital of the Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 119571 Moscow, Russia; (N.P.); (M.P.)
- Center for Theoretical Problems of Physicochemical Pharmakology, 119991 Moscow, Russia
| | - Alexey Sulimov
- Dimonta, Ltd., 117186 Moscow, Russia; (A.T.); (A.S.); (I.I.)
- Research Computing Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Danil Kutov
- Dimonta, Ltd., 117186 Moscow, Russia; (A.T.); (A.S.); (I.I.)
- Research Computing Center, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence: (D.K.); (V.S.)
| | - Ivan Ilin
- Dimonta, Ltd., 117186 Moscow, Russia; (A.T.); (A.S.); (I.I.)
- Research Computing Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Mikhail Panteleev
- Russian Children’s Clinical Hospital of the Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 119571 Moscow, Russia; (N.P.); (M.P.)
- Center for Theoretical Problems of Physicochemical Pharmakology, 119991 Moscow, Russia
| | - Khidmet Shikhaliev
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018 Voronezh, Russia; (K.S.); (S.M.); (N.N.); (A.P.)
| | - Svetlana Medvedeva
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018 Voronezh, Russia; (K.S.); (S.M.); (N.N.); (A.P.)
| | - Nadezhda Novichikhina
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018 Voronezh, Russia; (K.S.); (S.M.); (N.N.); (A.P.)
| | - Andrey Potapov
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018 Voronezh, Russia; (K.S.); (S.M.); (N.N.); (A.P.)
| | - Vladimir Sulimov
- Dimonta, Ltd., 117186 Moscow, Russia; (A.T.); (A.S.); (I.I.)
- Research Computing Center, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence: (D.K.); (V.S.)
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Kumar AA, Buckley BJ, Ranson M. The Urokinase Plasminogen Activation System in Pancreatic Cancer: Prospective Diagnostic and Therapeutic Targets. Biomolecules 2022; 12:152. [PMID: 35204653 PMCID: PMC8961517 DOI: 10.3390/biom12020152] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 02/07/2023] Open
Abstract
Pancreatic cancer is a highly aggressive malignancy that features high recurrence rates and the poorest prognosis of all solid cancers. The urokinase plasminogen activation system (uPAS) is strongly implicated in the pathophysiology and clinical outcomes of patients with pancreatic ductal adenocarcinoma (PDAC), which accounts for more than 90% of all pancreatic cancers. Overexpression of the urokinase-type plasminogen activator (uPA) or its cell surface receptor uPAR is a key step in the acquisition of a metastatic phenotype via multiple mechanisms, including the increased activation of cell surface localised plasminogen which generates the serine protease plasmin. This triggers multiple downstream processes that promote tumour cell migration and invasion. Increasing clinical evidence shows that the overexpression of uPA, uPAR, or of both is strongly associated with worse clinicopathological features and poor prognosis in PDAC patients. This review provides an overview of the current understanding of the uPAS in the pathogenesis and progression of pancreatic cancer, with a focus on PDAC, and summarises the substantial body of evidence that supports the role of uPAS components, including plasminogen receptors, in this disease. The review further outlines the clinical utility of uPAS components as prospective diagnostic and prognostic biomarkers for PDAC, as well as a rationale for the development of novel uPAS-targeted therapeutics.
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Affiliation(s)
- Ashna A. Kumar
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; (A.A.K.); (B.J.B.)
- School of Chemistry and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Benjamin J. Buckley
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; (A.A.K.); (B.J.B.)
- School of Chemistry and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Marie Ranson
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; (A.A.K.); (B.J.B.)
- School of Chemistry and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
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Sevillano N, Bohn MF, Zimanyi M, Chen Y, Petzold C, Gupta S, Ralston CY, Craik CS. Structure of an affinity-matured inhibitory recombinant fab against urokinase plasminogen activator reveals basis of potency and specificity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140562. [PMID: 33221341 DOI: 10.1016/j.bbapap.2020.140562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 10/16/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
Affinity maturation of U33, a recombinant Fab inhibitor of uPA, was used to improve the affinity and the inhibitory effect compared to the parental Fab. Arginine scanning of the six CDR loops of U33 was done to identify initial binding determinants since uPA prefers arginine in its primary substrate binding pocket. Two CDR loops were selected to create an engineered affinity maturation library of U33 that was diversified around ArgL91 (CDR L3) and ArgH52 (CDR H2). Biopanning of the randomized U33 library under stringent conditions resulted in eight Fabs with improved binding properties. One of the most potent inhibitors, AB2, exhibited a 13-fold decrease in IC50 when compared to U33 largely due to a decrease in its off rate. To identify contributions of interfacial residues that might undergo structural rearrangement upon interface formation we used X-ray footprinting and mass spectrometry (XFMS). Four residues showed a pronounced decrease in solvent accessibility, and their clustering suggests that AB2 targets the active site and also engages residues in an adjacent pocket unique to human uPA. The 2.9 Å resolution crystal structure of AB2-bound to uPA shows a binding mode in which the CDR L1 loop inserts into the active site cleft and acts as a determinant of inhibition. The selectivity determinant of this binding mode is unlike previously identified inhibitory Fabs against uPA related serine proteases, MTSP-1, HGFA and FXIa. CDRs H2 and L3 loops aid in interface formation and provide critical salt-bridges to remodel loops surrounding the active site of uPA providing specificity and further evidence that antibodies can be potent and selective inhibitors of proteolytic enzymes.
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Affiliation(s)
- N Sevillano
- Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94158, United States of America
| | - M F Bohn
- Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94158, United States of America
| | - M Zimanyi
- Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94158, United States of America
| | - Y Chen
- Molecular Biophysics and Integrated Bioimaging, Environmental Genomics and Systems Biology, and Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - C Petzold
- Molecular Biophysics and Integrated Bioimaging, Environmental Genomics and Systems Biology, and Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - S Gupta
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - C Y Ralston
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - C S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94158, United States of America.
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Synthesis, Docking, and In Vitro Anticoagulant Activity Assay of Hybrid Derivatives of Pyrrolo[3,2,1- ij]Quinolin-2(1 H)-one as New Inhibitors of Factor Xa and Factor XIa. Molecules 2020; 25:molecules25081889. [PMID: 32325823 PMCID: PMC7222003 DOI: 10.3390/molecules25081889] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 12/04/2022] Open
Abstract
Coagulation factor Xa and factor XIa are proven to be convenient and crucial protein targets for treatment for thrombotic disorders and thereby their inhibitors can serve as effective anticoagulant drugs. In the present work, we focused on the structure–activity relationships of derivatives of pyrrolo[3,2,1-ij]quinolin-2(1H)-one and an evaluation of their activity against factor Xa and factor XIa. For this, docking-guided synthesis of nine compounds based on pyrrolo[3,2,1-ij]quinolin-2(1H)-one was carried out. For the synthesis of new hybrid hydropyrrolo[3,2,1-ij]quinolin-2(1H)-one derivatives, we used convenient structural modification of both the tetrahydro- and dihydroquinoline moiety by varying the substituents at the C6,8,9 positions. In vitro testing revealed that four derivatives were able to inhibit both coagulation factors and three compounds were selective factor XIa inhibitors. An IC50 value of 3.68 μM for was found for the best factor Xa inhibitor and 2 μM for the best factor XIa inhibitor.
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Sulimov VB, Kutov DC, Sulimov AV. Advances in Docking. Curr Med Chem 2020; 26:7555-7580. [PMID: 30182836 DOI: 10.2174/0929867325666180904115000] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Design of small molecules which are able to bind to the protein responsible for a disease is the key step of the entire process of the new medicine discovery. Atomistic computer modeling can significantly improve effectiveness of such design. The accurate calculation of the free energy of binding a small molecule (a ligand) to the target protein is the most important problem of such modeling. Docking is one of the most popular molecular modeling methods for finding ligand binding poses in the target protein and calculating the protein-ligand binding energy. This energy is used for finding the most active compounds for the given target protein. This short review aims to give a concise description of distinctive features of docking programs focusing on computation methods and approximations influencing their accuracy. METHODS This review is based on the peer-reviewed research literature including author's own publications. The main features of several representative docking programs are briefly described focusing on their characteristics influencing docking accuracy: force fields, energy calculations, solvent models, algorithms of the best ligand pose search, global and local optimizations, ligand and target protein flexibility, and the simplifications made for the docking accelerating. Apart from other recent reviews focused mainly on the performance of different docking programs, in this work, an attempt is made to extract the most important functional characteristics defining the docking accuracy. Also a roadmap for increasing the docking accuracy is proposed. This is based on the new generation of docking programs which have been realized recently. These programs and respective new global optimization algorithms are described shortly. RESULTS Several popular conventional docking programs are considered. Their search of the best ligand pose is based explicitly or implicitly on the global optimization problem. Several algorithms are used to solve this problem, and among them, the heuristic genetic algorithm is distinguished by its popularity and an elaborate design. All conventional docking programs for their acceleration use the preliminary calculated grids of protein-ligand interaction potentials or preferable points of protein and ligand conjugation. These approaches and commonly used fitting parameters restrict strongly the docking accuracy. Solvent is considered in exceedingly simplified approaches in the course of the global optimization and the search for the best ligand poses. More accurate approaches on the base of implicit solvent models are used frequently for more careful binding energy calculations after docking. The new generation of docking programs are developed recently. They find the spectrum of low energy minima of a protein-ligand complex including the global minimum. These programs should be more accurate because they do not use a preliminary calculated grid of protein-ligand interaction potentials and other simplifications, the energy of any conformation of the molecular system is calculated in the frame of a given force field and there are no fitting parameters. A new docking algorithm is developed and fulfilled specially for the new docking programs. This algorithm allows docking a flexible ligand into a flexible protein with several dozen mobile atoms on the base of the global energy minimum search. Such docking results in improving the accuracy of ligand positioning in the docking process. The adequate choice of the method of molecular energy calculations also results in the better docking positioning accuracy. An advancement in the application of quantum chemistry methods to docking and scoring is revealed. CONCLUSION The findings of this review confirm the great demand in docking programs for discovery of new medicine substances with the help of molecular modeling. New trends in docking programs design are revealed. These trends are focused on the increase of the docking accuracy at the expense of more accurate molecular energy calculations without any fitting parameters, including quantum-chemical methods and implicit solvent models, and by using new global optimization algorithms which make it possible to treat flexibility of ligands and mobility of protein atoms simultaneously. Finally, it is shown that all the necessary prerequisites for increasing the docking accuracy can be accomplished in practice.
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Affiliation(s)
- Vladimir B Sulimov
- Dimonta, Ltd., Nagornaya Street 15, Building 8, 117186 Moscow, Russian Federation.,Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, 119991 Moscow, Russian Federation
| | - Danil C Kutov
- Dimonta, Ltd., Nagornaya Street 15, Building 8, 117186 Moscow, Russian Federation.,Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, 119991 Moscow, Russian Federation
| | - Alexey V Sulimov
- Dimonta, Ltd., Nagornaya Street 15, Building 8, 117186 Moscow, Russian Federation.,Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, 119991 Moscow, Russian Federation
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Morais PA, Maia FF, Solis-Calero C, Caetano EWS, Freire VN, Carvalho HF. The urokinase plasminogen activator binding to its receptor: a quantum biochemistry description within an in/homogeneous dielectric function framework with application to uPA–uPAR peptide inhibitors. Phys Chem Chem Phys 2020; 22:3570-3583. [DOI: 10.1039/c9cp06530j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DFT calculations using the MFCC fragment-based model considering a spatial-dependent dielectric function based on the Poisson–Boltzmann approximation were performed to describe the uPA–uPAR interactions.
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Affiliation(s)
- Pablo A. Morais
- Instituto Federal de Educação
- Ciência e Tecnologia do Ceará
- Campus Horizonte
- Horizonte
- Brazil
| | - Francisco Franciné Maia
- Departamento de Ciências Naturais
- Matemática e Estatística
- Universidade Federal Rural do Semi-Árido
- Mossoró
- Brazil
| | - Christian Solis-Calero
- Departamento de Biologia Estrutural e Funcional
- Instituto de Biologia
- Universidade Estadual de Campinas
- Campinas
- Brazil
| | | | | | - Hernandes F. Carvalho
- Departamento de Biologia Estrutural e Funcional
- Instituto de Biologia
- Universidade Estadual de Campinas
- Campinas
- Brazil
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Agarwal H, Shanmugam VK. Anti-inflammatory activity screening of Kalanchoe pinnata methanol extract and its validation using a computational simulation approach. INFORMATICS IN MEDICINE UNLOCKED 2019. [DOI: 10.1016/j.imu.2019.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking. Russ Chem Bull 2018. [DOI: 10.1007/s11172-017-1966-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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11
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New generation of docking programs: Supercomputer validation of force fields and quantum-chemical methods for docking. J Mol Graph Model 2017; 78:139-147. [DOI: 10.1016/j.jmgm.2017.10.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/19/2022]
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Lopes MD, Oliveira FM, Coelho IEV, Passos MJF, Alves CC, Taranto AG, Júnior MC, Santos LL, Fonseca CT, Villar JAFP, Lopes DO. Epitopes rationally selected through computational analyses induce T‐cell proliferation in mice and are recognized by serum from individuals infected with
Schistosoma mansoni. Biotechnol Prog 2017; 33:804-814. [DOI: 10.1002/btpr.2463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/03/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Marcelo D. Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del‐Rei, Rua Sebastião Gonçalves CoelhoDivinópolis MG Brasil
| | - Flávio M. Oliveira
- Laboratório de Biologia Molecular, Universidade Federal de São João del‐Rei, Rua Sebastião Gonçalves CoelhoDivinópolis MG Brasil
| | - Ivan E. V. Coelho
- Laboratório de Química Farmacêutica, Universidade Federal de São João del‐ReiDivinópolis MGBrasil
| | - Maria J. F. Passos
- Laboratório de Síntese Orgânica e Nanoestruturas, Universidade Federal de São João del‐ReiDivinópolis MG Brasil
| | - Clarice C. Alves
- Grupo de Pesquisa em Biologia Parasitária e Imunologia, Centro de Pesquisas René Rachou, Fundação Oswaldo CruzBelo Horizonte MG30190‐002 Brasil
| | - Alex G. Taranto
- Laboratório de Química Farmacêutica, Universidade Federal de São João del‐ReiDivinópolis MGBrasil
| | - Moacyr C. Júnior
- Laboratório de Química Farmacêutica, Universidade Federal de São João del‐ReiDivinópolis MGBrasil
| | - Luciana L. Santos
- Laboratório de Biologia Molecular, Universidade Federal de São João del‐Rei, Rua Sebastião Gonçalves CoelhoDivinópolis MG Brasil
| | - Cristina T. Fonseca
- Grupo de Pesquisa em Biologia Parasitária e Imunologia, Centro de Pesquisas René Rachou, Fundação Oswaldo CruzBelo Horizonte MG30190‐002 Brasil
| | - José A. F. P. Villar
- Laboratório de Síntese Orgânica e Nanoestruturas, Universidade Federal de São João del‐ReiDivinópolis MG Brasil
| | - Débora O. Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del‐Rei, Rua Sebastião Gonçalves CoelhoDivinópolis MG Brasil
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Sulimov AV, Zheltkov DA, Oferkin IV, Kutov DC, Katkova EV, Tyrtyshnikov EE, Sulimov VB. Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms. Comput Struct Biotechnol J 2017; 15:275-285. [PMID: 28377797 PMCID: PMC5367798 DOI: 10.1016/j.csbj.2017.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/28/2017] [Indexed: 11/28/2022] Open
Abstract
We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters. The conformation space of the system coordinates is formed by translations and rotations of the ligand as a whole, by the ligand torsions and also by Cartesian coordinates of the selected target protein atoms. Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally. The algorithm is realized in the novel parallel docking SOL-P program and results of its performance for a set of 30 protein-ligand complexes are presented. Dependence of the docking positioning accuracy is investigated as a function of parameters of the docking algorithm and the number of protein moveable atoms. It is shown that mobility of the protein atoms improves docking positioning accuracy. The SOL-P program is able to perform docking of a flexible ligand into the active site of the target protein with several dozens of protein moveable atoms: the native crystallized ligand pose is correctly found as the global energy minimum in the search space with 157 dimensions using 4700 CPU ∗ h at the Lomonosov supercomputer.
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Affiliation(s)
- Alexey V Sulimov
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
| | - Dmitry A Zheltkov
- Faculty of Computational Mathematics and Cybernetics of Lomonosov Moscow State University, Leninskie Gory 1, Bldg. 52, Moscow 119992, Russia
| | - Igor V Oferkin
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia
| | - Danil C Kutov
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
| | - Ekaterina V Katkova
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
| | - Eugene E Tyrtyshnikov
- Faculty of Computational Mathematics and Cybernetics of Lomonosov Moscow State University, Leninskie Gory 1, Bldg. 52, Moscow 119992, Russia; Institute of Numerical Mathematics of Russian Academy of Sciences, Gubkin Street 8, Moscow, 119333, Russia
| | - Vladimir B Sulimov
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
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Sulimov AV, Kutov DC, Katkova EV, Sulimov VB. Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7. Adv Bioinformatics 2017; 2017:7167691. [PMID: 28191015 PMCID: PMC5278191 DOI: 10.1155/2017/7167691] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/19/2016] [Accepted: 12/22/2016] [Indexed: 12/11/2022] Open
Abstract
Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.
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Affiliation(s)
- A. V. Sulimov
- Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia
- Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia
| | - D. C. Kutov
- Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia
- Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia
| | - E. V. Katkova
- Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia
- Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia
| | - V. B. Sulimov
- Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia
- Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia
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Katkova EV, Onufriev AV, Aguilar B, Sulimov VB. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding. J Mol Graph Model 2016; 72:70-80. [PMID: 28064081 DOI: 10.1016/j.jmgm.2016.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/07/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022]
Abstract
In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field. The following implicit solvent (water) models considered here are: PCM (Polarized Continuum Model implemented in DISOLV and MCBHSOLV programs), GB (Generalized Born method implemented in DISOLV program, S-GB, and GBNSR6 stand-alone version), COSMO (COnductor-like Screening Model implemented in the DISOLV program and the MOPAC package) and the Poisson-Boltzmann model (implemented in the APBS program). Different parameterizations of the molecules were examined: we compared MMFF94 force field, Amber12 force field and the quantum-chemical semi-empirical PM7 method implemented in the MOPAC package. For small molecules, all of the implicit solvent models tested here yield high correlation coefficients (0.87-0.93) between the calculated solvation energies and the experimental values of hydration energies. For small molecules high correlation (0.82-0.97) with the explicit solvent energies is seen as well. On the other hand, estimated protein solvation energies and protein-ligand binding desolvation energies show substantial discrepancy (up to 10kcal/mol) with the explicit solvent reference. The correlation of polar protein solvation energies and protein-ligand desolvation energies with the corresponding explicit solvent results is 0.65-0.99 and 0.76-0.96 respectively, though this difference in correlations is caused more by different parameterization and less by methods and indicates the need for further improvement of implicit solvent models parameterization. Within the same parameterization, various implicit methods give practically the same correlation with results obtained in explicit solvent model for ligands and proteins: e.g. correlation values of polar ligand solvation energies and the corresponding energies in the frame of explicit solvent were 0.953-0.966 for the APBS program, the GBNSR6 program and all models used in the DISOLV program. The DISOLV program proved to be on a par with the other used programs in the case of proteins and ligands solvation energy calculation. However, the solution of the Poisson-Boltzmann equation (APBS program) and Generalized Born method (implemented in the GBNSR6 program) proved to be the most accurate in calculating the desolvation energies of complexes.
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Affiliation(s)
- E V Katkova
- Dimonta, Ltd., Nagornaya Street 15, Bldg 8, Moscow, 117186, Russia; Research Computer Center, Lomonosov Moscow State University, Leninskie Gory 1,Bldg 4, Moscow, 119992, Russia.
| | - A V Onufriev
- Departments of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, USA
| | - B Aguilar
- Institute for Systems Biology, Seattle, WA, USA
| | - V B Sulimov
- Dimonta, Ltd., Nagornaya Street 15, Bldg 8, Moscow, 117186, Russia; Research Computer Center, Lomonosov Moscow State University, Leninskie Gory 1,Bldg 4, Moscow, 119992, Russia
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16
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van Dam PA, Coelho A, Rolfo C. Is there a role for urokinase-type plasminogen activator inhibitors as maintenance therapy in patients with ovarian cancer? Eur J Surg Oncol 2016; 43:252-257. [PMID: 27345498 DOI: 10.1016/j.ejso.2016.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/27/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022] Open
Abstract
There is abundant evidence that the urokinase-type plasminogen activator (uPA), its inhibitors PAI-1 and PAI-2 (plasminogen activator inhibitor type-1 and type-2) and its cells surface receptor (uPA-R, CD87) play a fundamental role in tumor invasion and metastasis and are of significant prognostic significance for many tumor types. We performed a systematic Med-line search on uPA, PAI, uPA-R and (epithelial) ovarian cancer (EOC). The majority of malignant EOC specimens show moderate to strong immunostating of tumor and stromal cells. Overexpression of u-PA and PAI-1 can be found in more the 75% of primary ovarian carcinomas, in most metastatic EOC samples and all examined epithelial ovarian cancer cell lines. uPA overexpression in primary specimens was significantly associated with tumor stage, grade, residual disease status after cytoreductive surgery, and poor clinical outcome. This may be explained by increased chemoresistance, a lower resectability and more aggressive tumor biology and tumor dissemination in patients with high uPA and PAI-1. Several therapeutical approaches aimed at inhibiting the uPA/uPAR functions have shown to possess anti-tumor effects in vitro and in animal models. When treating a patient with advanced ovarian cancer it may to be assumed that inhibiting the progression of established (micro) metastases may be more therapeutically relevant than trying to destroy all tumor cells which is not possible in most cases with current systemic treatment modalities. Taking into account the role of uPA and PAI in cell detachment, formation of new stroma, tumor cell reimplantation and metastasis uPA inhibition should be further investigated as maintenance treatment in patients with advanced EOC.
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Affiliation(s)
- P A van Dam
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Antwerp University Hospital, Edegem, B2650, Belgium; Centre of Oncologic Research (CORE), Antwerp University, Edegem, B2650, Belgium.
| | - A Coelho
- Centre of Oncologic Research (CORE), Antwerp University, Edegem, B2650, Belgium; Phase I-Early Trials Unit, Antwerp University Hospital, Edegem, Belgium
| | - C Rolfo
- Centre of Oncologic Research (CORE), Antwerp University, Edegem, B2650, Belgium; Phase I-Early Trials Unit, Antwerp University Hospital, Edegem, Belgium
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Carlson HA, Smith RD, Damm-Ganamet KL, Stuckey JA, Ahmed A, Convery MA, Somers DO, Kranz M, Elkins PA, Cui G, Peishoff CE, Lambert MH, Dunbar JB. CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. J Chem Inf Model 2016; 56:1063-77. [PMID: 27149958 DOI: 10.1021/acs.jcim.5b00523] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 2014 CSAR Benchmark Exercise was the last community-wide exercise that was conducted by the group at the University of Michigan, Ann Arbor. For this event, GlaxoSmithKline (GSK) donated unpublished crystal structures and affinity data from in-house projects. Three targets were used: tRNA (m1G37) methyltransferase (TrmD), Spleen Tyrosine Kinase (SYK), and Factor Xa (FXa). A particularly strong feature of the GSK data is its large size, which lends greater statistical significance to comparisons between different methods. In Phase 1 of the CSAR 2014 Exercise, participants were given several protein-ligand complexes and asked to identify the one near-native pose from among 200 decoys provided by CSAR. Though decoys were requested by the community, we found that they complicated our analysis. We could not discern whether poor predictions were failures of the chosen method or an incompatibility between the participant's method and the setup protocol we used. This problem is inherent to decoys, and we strongly advise against their use. In Phase 2, participants had to dock and rank/score a set of small molecules given only the SMILES strings of the ligands and a protein structure with a different ligand bound. Overall, docking was a success for most participants, much better in Phase 2 than in Phase 1. However, scoring was a greater challenge. No particular approach to docking and scoring had an edge, and successful methods included empirical, knowledge-based, machine-learning, shape-fitting, and even those with solvation and entropy terms. Several groups were successful in ranking TrmD and/or SYK, but ranking FXa ligands was intractable for all participants. Methods that were able to dock well across all submitted systems include MDock,1 Glide-XP,2 PLANTS,3 Wilma,4 Gold,5 SMINA,6 Glide-XP2/PELE,7 FlexX,8 and MedusaDock.9 In fact, the submission based on Glide-XP2/PELE7 cross-docked all ligands to many crystal structures, and it was particularly impressive to see success across an ensemble of protein structures for multiple targets. For scoring/ranking, submissions that showed statistically significant achievement include MDock1 using ITScore1,10 with a flexible-ligand term,11 SMINA6 using Autodock-Vina,12,13 FlexX8 using HYDE,14 and Glide-XP2 using XP DockScore2 with and without ROCS15 shape similarity.16 Of course, these results are for only three protein targets, and many more systems need to be investigated to truly identify which approaches are more successful than others. Furthermore, our exercise is not a competition.
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Affiliation(s)
- Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Richard D Smith
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Kelly L Damm-Ganamet
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Jeanne A Stuckey
- Center for Structural Biology, University of Michigan , 3358E Life Sciences Institute, 210 Washtenaw Ave., Ann Arbor, Michigan 48109-2216, United States
| | - Aqeel Ahmed
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Maire A Convery
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Donald O Somers
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Michael Kranz
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Patricia A Elkins
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Guanglei Cui
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Catherine E Peishoff
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Millard H Lambert
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - James B Dunbar
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
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Yilmazer ND, Korth M. Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods. Int J Mol Sci 2016; 17:ijms17050742. [PMID: 27196893 PMCID: PMC4881564 DOI: 10.3390/ijms17050742] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/18/2016] [Accepted: 05/03/2016] [Indexed: 11/16/2022] Open
Abstract
We review the first successes and failures of a “new wave” of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of “enhanced”, dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.
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Affiliation(s)
- Nusret Duygu Yilmazer
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany.
| | - Martin Korth
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany.
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Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima. Adv Bioinformatics 2015; 2015:126858. [PMID: 26693223 PMCID: PMC4674582 DOI: 10.1155/2015/126858] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/28/2015] [Accepted: 11/04/2015] [Indexed: 12/19/2022] Open
Abstract
The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.
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Application of Molecular Modeling to Development of New Factor Xa Inhibitors. BIOMED RESEARCH INTERNATIONAL 2015; 2015:120802. [PMID: 26484350 PMCID: PMC4592935 DOI: 10.1155/2015/120802] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 08/12/2015] [Accepted: 08/20/2015] [Indexed: 12/30/2022]
Abstract
In consequence of the key role of factor Xa in the clotting cascade and absence of its activity in the processes that do not affect coagulation, this protein is an attractive target for development of new blood coagulation inhibitors. Factor Xa is more effective and convenient target for creation of anticoagulants than thrombin, inhibition of which may cause some side effects. This study is aimed at finding new inhibitors of factor Xa by molecular computer modeling including docking SOL and postdocking optimization DISCORE programs. After validation of molecular modeling methods on well-known factor Xa inhibitors the virtual screening of NCI Diversity and Voronezh State University databases of ready-made low molecular weight species has been carried out. Seventeen compounds selected on the basis of modeling results have been tested experimentally in vitro. It has been found that 12 of them showed activity against factor Xa (IC50 = 1.8-40 μM). Based on analysis of the results, the new original compound was synthesized and experimentally verified. It shows activity against factor Xa with IC50 value of 0.7 μM.
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