1
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Papadourakis M, Sinenka H, Matricon P, Hénin J, Brannigan G, Pérez-Benito L, Pande V, van Vlijmen H, de Graaf C, Deflorian F, Tresadern G, Cecchini M, Cournia Z. Alchemical Free Energy Calculations on Membrane-Associated Proteins. J Chem Theory Comput 2023; 19:7437-7458. [PMID: 37902715 PMCID: PMC11017255 DOI: 10.1021/acs.jctc.3c00365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 10/31/2023]
Abstract
Membrane proteins have diverse functions within cells and are well-established drug targets. The advances in membrane protein structural biology have revealed drug and lipid binding sites on membrane proteins, while computational methods such as molecular simulations can resolve the thermodynamic basis of these interactions. Particularly, alchemical free energy calculations have shown promise in the calculation of reliable and reproducible binding free energies of protein-ligand and protein-lipid complexes in membrane-associated systems. In this review, we present an overview of representative alchemical free energy studies on G-protein-coupled receptors, ion channels, transporters as well as protein-lipid interactions, with emphasis on best practices and critical aspects of running these simulations. Additionally, we analyze challenges and successes when running alchemical free energy calculations on membrane-associated proteins. Finally, we highlight the value of alchemical free energy calculations calculations in drug discovery and their applicability in the pharmaceutical industry.
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Affiliation(s)
- Michail Papadourakis
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Hryhory Sinenka
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Pierre Matricon
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Jérôme Hénin
- Laboratoire
de Biochimie Théorique UPR 9080, CNRS and Université Paris Cité, 75005 Paris, France
| | - Grace Brannigan
- Center
for Computational and Integrative Biology, Rutgers University−Camden, Camden, New Jersey 08103, United States of America
- Department
of Physics, Rutgers University−Camden, Camden, New Jersey 08102, United States
of America
| | - Laura Pérez-Benito
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Vineet Pande
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Herman van Vlijmen
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Chris de Graaf
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Francesca Deflorian
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Gary Tresadern
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marco Cecchini
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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2
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Perissinotti L, Guo J, Kudaibergenova M, Lees-Miller J, Ol'khovich M, Sharapova A, Perlovich GL, Muruve DA, Gerull B, Noskov SY, Duff HJ. The Pore-Lipid Interface: Role of Amino-Acid Determinants of Lipophilic Access by Ivabradine to the hERG1 Pore Domain. Mol Pharmacol 2019; 96:259-271. [PMID: 31182542 DOI: 10.1124/mol.118.115642] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/28/2019] [Indexed: 12/14/2022] Open
Abstract
Abnormal cardiac electrical activity is a common side effect caused by unintended block of the promiscuous drug target human ether-à-go-go-related gene (hERG1), the pore-forming domain of the delayed rectifier K+ channel in the heart. hERG1 block leads to a prolongation of the QT interval, a phase of the cardiac cycle that underlies myocyte repolarization detectable on the electrocardiogram. Even newly released drugs such as heart-rate lowering agent ivabradine block the rapid delayed rectifier current IKr, prolong action potential duration, and induce potentially lethal arrhythmia known as torsades de pointes. In this study, we describe a critical drug-binding pocket located at the lateral pore surface facing the cellular membrane. Mutations of the conserved M651 residue alter ivabradine-induced block but not by the common hERG1 blocker dofetilide. As revealed by molecular dynamics simulations, binding of ivabradine to a lipophilic pore access site is coupled to a state-dependent reorientation of aromatic residues F557 and F656 in the S5 and S6 helices. We show that the M651 mutation impedes state-dependent dynamics of F557 and F656 aromatic cassettes at the protein-lipid interface, which has a potential to disrupt drug-induced block of the channel. This fundamentally new mechanism coupling the channel dynamics and small-molecule access from the membrane into the hERG1 intracavitary site provides a simple rationale for the well established state-dependence of drug blockade. SIGNIFICANCE STATEMENT: The drug interference with the function of the cardiac hERG channels represents one of the major sources of drug-induced heart disturbances. We found a novel and a critical drug-binding pocket adjacent to a lipid-facing surface of the hERG1 channel, which furthers our molecular understanding of drug-induced QT syndrome.
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Affiliation(s)
- Laura Perissinotti
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Jiqing Guo
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Meruyert Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - James Lees-Miller
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Marina Ol'khovich
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Angelica Sharapova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - German L Perlovich
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Daniel A Muruve
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Brenda Gerull
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Henry J Duff
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
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3
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Ngo VA, Fanning JK, Noskov SY. Comparative Analysis of Protein Hydration from MD simulations with Additive and Polarizable Force Fields. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800106] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Van A. Ngo
- Department of Biological SciencesCentre for Molecular Simulation and Biochemistry Research ClusterUniversity of Calgary Calgary Alberta T2N 1N4 Canada
| | - John Keenan Fanning
- Department of Biological SciencesCentre for Molecular Simulation and Biochemistry Research ClusterUniversity of Calgary Calgary Alberta T2N 1N4 Canada
| | - Sergei Yu Noskov
- Department of Biological SciencesCentre for Molecular Simulation and Biochemistry Research ClusterUniversity of Calgary Calgary Alberta T2N 1N4 Canada
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4
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Williams-Noonan BJ, Yuriev E, Chalmers DK. Free Energy Methods in Drug Design: Prospects of “Alchemical Perturbation” in Medicinal Chemistry. J Med Chem 2017; 61:638-649. [DOI: 10.1021/acs.jmedchem.7b00681] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Billy J. Williams-Noonan
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - David K. Chalmers
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
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5
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Lai PK, Kaznessis YN. Free Energy Calculations of Microcin J25 Variants Binding to the FhuA Receptor. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00417] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pin-Kuang Lai
- Department of Chemical Engineering
and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Yiannis N. Kaznessis
- Department of Chemical Engineering
and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
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6
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Zhekova H, Zhao C, Schnetkamp PPM, Noskov SY. Characterization of the Cation Binding Sites in the NCKX2 Na +/Ca 2+-K + Exchanger. Biochemistry 2016; 55:6445-6455. [PMID: 27805378 DOI: 10.1021/acs.biochem.6b00591] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
NCKX1-5 are proteins involved in K+-dependent Na+/Ca2+ exchange in various signal tissues. Here we present a homology model of NCKX2 based on the crystal structure of the NCX_Mj transporter found in Methanoccocus jannaschii. Molecular dynamics simulations were performed on the resultant wild-type NCKX2 model and two mutants (D548N and D575N) loaded with either four Na+ ions or one Ca2+ ion and one K+ ion, in line with the experimentally observed transport stoichiometry. The selectivity of the active site in wild-type NCKX2 for Na+, K+, and Li+ and the electrostatic interactions of the positive Na+ ions in the negatively charged active site of wild-type NCKX2 and the two mutants were evaluated from free energy perturbation calculations. For validation of the homology model, our computational results were compared to available experimental data obtained from numerous prior functional studies. The NCKX2 homology model is in good agreement with the discussed experimental data and provides valuable insights into the structure of the active site, which is lined with acidic and polar residues. The binding of the potassium and calcium ions is accomplished via Asp 575 and 548, respectively. Mutation of these residues to Asn alters the functionality of NCKX2 because of the elimination of the favorable carboxylate-cation interactions. The knowledge obtained from the NCKX2 model can be transferred to other isoforms of the NCKX family: newly discovered pathological mutations in NCKX4 and NCKX5 affect residues that are involved in ion binding and/or transport according to our homology model.
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Affiliation(s)
- Hristina Zhekova
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary , Calgary, AB, Canada T2N 1N4
| | - Chunfeng Zhao
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary , Calgary, AB, Canada T2N 1N4
| | - Paul P M Schnetkamp
- Department of Physiology & Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary , Calgary, AB T2N 4N1, Canada
| | - Sergei Yu Noskov
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary , Calgary, AB, Canada T2N 1N4
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7
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Zhang JL, Zheng QC, Yu LY, Li ZQ, Zhang HX. Effect of External Electric Field on Substrate Transport of a Secondary Active Transporter. J Chem Inf Model 2016; 56:1539-46. [PMID: 27472561 DOI: 10.1021/acs.jcim.6b00212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Substrate transport across a membrane accomplished by a secondary active transporter (SAT) is essential to the normal physiological function of living cells. In the present research, a series of all-atom molecular dynamics (MD) simulations under different electric field (EF) strengths was performed to investigate the effect of an external EF on the substrate transport of an SAT. The results show that EF both affects the interaction between substrate and related protein's residues by changing their conformations and tunes the timeline of the transport event, which collectively reduces the height of energy barrier for substrate transport and results in the appearance of two intermediate conformations under the existence of an external EF. Our work spotlights the crucial influence of external EFs on the substrate transport of SATs and could provide a more penetrating understanding of the substrate transport mechanism of SATs.
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Affiliation(s)
- Ji-Long Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University , Changchun 130021, Jilin, People's Republic of China.,Department of Chemistry and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Qing-Chuan Zheng
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
| | - Li-Ying Yu
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
| | - Zheng-Qiang Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University , Changchun 130021, Jilin, People's Republic of China
| | - Hong-Xing Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
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8
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Miranda WE, Ngo VA, Valiente PA, Noskov SY. Improved QM/MM Linear-Interaction Energy Model for Substrate Recognition in Zinc-Containing Metalloenzymes. J Phys Chem B 2016; 120:7824-35. [PMID: 27448039 DOI: 10.1021/acs.jpcb.6b05628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the essential challenges in the description of receptor-drug interactions in the presence of various polyvalent cations (such as zinc, magnesium, or iron) is the accurate assessment of the electronic effects due to cofactor binding. The effects can range from partial electronic polarization of the proximal atoms in a receptor and bound substrate to long-range effects related to partial charge transfer and electronic delocalization effects between the cofactor and the drug. Here, we examine the role of the explicit account for electronic effects for a panel of small-molecule inhibitors binding to the zinc-aminopeptidase PfA-M1, an essential target for antimalarial drug development. Our study on PfA-M1:inhibitor interactions at the QM level reveals that the partial charge and proton transfer due to bound zinc ion are important mechanisms in the inhibitors' recognition and catalysis. The combination of classical MD simulations with a posteriori QM/MM corrections with novel DFTB parameters for the zinc cation and the linear-interaction energy (LIE) approach offers by far the most accurate estimates for the PfA-M1:inhibitor binding affinities, opening the door for future inhibitor design.
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Affiliation(s)
- Williams E Miranda
- Computational Biology and Biomolecular Dynamics Laboratory, Center for Protein Studies, Faculty of Biology, University of Havana , Havana, Cuba.,Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary , 2500 University Drive, BI-449, Calgary, Alberta T2N 1N4, Canada
| | - Van A Ngo
- Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary , 2500 University Drive, BI-449, Calgary, Alberta T2N 1N4, Canada
| | - Pedro A Valiente
- Computational Biology and Biomolecular Dynamics Laboratory, Center for Protein Studies, Faculty of Biology, University of Havana , Havana, Cuba
| | - Sergei Yu Noskov
- Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary , 2500 University Drive, BI-449, Calgary, Alberta T2N 1N4, Canada
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9
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Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC. Accurate calculation of the absolute free energy of binding for drug molecules. Chem Sci 2016; 7:207-218. [PMID: 26798447 PMCID: PMC4700411 DOI: 10.1039/c5sc02678d] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/24/2015] [Indexed: 12/13/2022] Open
Abstract
Accurate prediction of binding affinities has been a central goal of computational chemistry for decades, yet remains elusive. Despite good progress, the required accuracy for use in a drug-discovery context has not been consistently achieved for drug-like molecules. Here, we perform absolute free energy calculations based on a thermodynamic cycle for a set of diverse inhibitors binding to bromodomain-containing protein 4 (BRD4) and demonstrate that a mean absolute error of 0.6 kcal mol-1 can be achieved. We also show a similar level of accuracy (1.0 kcal mol-1) can be achieved in pseudo prospective approach. Bromodomains are epigenetic mark readers that recognize acetylation motifs and regulate gene transcription, and are currently being investigated as therapeutic targets for cancer and inflammation. The unprecedented accuracy offers the exciting prospect that the binding free energy of drug-like compounds can be predicted for pharmacologically relevant targets.
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Affiliation(s)
- Matteo Aldeghi
- Structural Bioinformatics and Computational Biochemistry , Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; ; Tel: +44 (0)1865 613305
| | - Alexander Heifetz
- Evotec (U.K.) Ltd , 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , UK
| | - Michael J Bodkin
- Evotec (U.K.) Ltd , 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , UK
| | - Stefan Knapp
- Structural Genomics Consortium , Nuffield Department of Clinical Medicine , University of Oxford , Old Road Campus Research Building, Roosevelt Drive , Oxford OX3 7DQ , UK ; Target Discovery Institute , Nuffield Department of Clinical Medicine , University of Oxford , Roosevelt Drive , Oxford OX3 7BN , UK
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry , Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; ; Tel: +44 (0)1865 613305
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10
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Miranda WE, Noskov SY, Valiente PA. Improving the LIE Method for Binding Free Energy Calculations of Protein–Ligand Complexes. J Chem Inf Model 2015; 55:1867-77. [DOI: 10.1021/acs.jcim.5b00012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Williams E. Miranda
- Computational
Biology and Biomolecular Dynamics Laboratory, Center for Protein Studies,
Faculty of Biology, University of Havana, Havana, Cuba
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Pedro A. Valiente
- Computational
Biology and Biomolecular Dynamics Laboratory, Center for Protein Studies,
Faculty of Biology, University of Havana, Havana, Cuba
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11
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Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J Membr Biol 2015; 248:611-40. [PMID: 26063070 PMCID: PMC4515176 DOI: 10.1007/s00232-015-9802-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/26/2015] [Indexed: 01/05/2023]
Abstract
Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
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Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Toby W. Allen
- School of Applied Sciences & Health Innovations Research Institute, RMIT University, GPO Box 2476, Melbourne, Vic, 3001, Australia; and Department of Chemistry, University of California, Davis. Davis, CA 95616, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Daniel Baum
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Grace Brannigan
- Center for Computational and Integrative Biology and Department of Physics, Rutgers University-Camden, Camden, NJ, USA
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Lucie Delemotte
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Coral del Val
- Department of Artificial Intelligence, University of Granada, E-18071 Granada, Spain
| | - Ran Friedman
- Linnæus University, Department of Chemistry and Biomedical Sciences & Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| | - Paraskevi Gkeka
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Hans-Christian Hege
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, IBPC and CNRS, Paris, France
| | - Marina A. Kasimova
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Michael L. Klein
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Syma Khalid
- Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - M. Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, and Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Norbert Lindow
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Mahua Roy
- Department of Chemistry, University of California, Irvine
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Mounir Tarek
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- CNRS, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
| | - Florentina Tofoleanu
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Sinisa Urban
- Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, 725 N. Wolfe Street, 507 Preclinical Teaching Building, Baltimore, MD 21205, USA
| | - David J. Wales
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeremy C. Smith
- Oak Ridge National Laboratory, PO BOX 2008 MS6309, Oak Ridge, TN 37831-6309, USA
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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12
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Kang H, Klauda JB. Molecular dynamics simulations of palmitoyloleoylphosphatidylglycerol bilayers. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.926548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Noskov SY, Rostovtseva TK, Bezrukov SM. ATP transport through VDAC and the VDAC-tubulin complex probed by equilibrium and nonequilibrium MD simulations. Biochemistry 2013; 52:9246-56. [PMID: 24245503 PMCID: PMC7259721 DOI: 10.1021/bi4011495] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Voltage-dependent anion channel (VDAC), the major channel of the mitochondrial outer membrane, serves as a principal pathway for ATP, ADP, and other respiratory substrates across this membrane. Using umbrella-sampling simulations, we established the thermodynamic and kinetic components governing ATP transport across the VDAC1 channel. We found that there are several low-affinity binding sites for ATP along the translocation pathway and that the main barrier for ATP transport is located around the center of the channel and is formed predominantly by residues in the N-terminus. The binding affinity of ATP to an open channel was found to be in the millimolar to micromolar range. However, we show that this weak binding increases the ATP translocation probability by about 10-fold compared with the VDAC pore in which attractive interactions were artificially removed. Recently, it was found that free dimeric tubulin induces a highly efficient, reversible blockage of VDAC reconstituted into planar lipid membranes. It was proposed that by blocking VDAC permeability for ATP/ADP and other mitochondrial respiratory substrates tubulin controls mitochondrial respiration. Using the Rosetta protein-protein docking algorithm, we established a tentative structure of the VDAC-tubulin complex. An extensive set of equilibrium and nonequilibrium (under applied electric field) molecular dynamics (MD) simulations was used to establish the conductance of the open and blocked channel. It was found that the presence of the unstructured C-terminal tail of tubulin in the VDAC pore decreases its conductance by more than 40% and switches its selectivity from anionic to cationic. The subsequent 1D potential of mean force (PMF) computations for the VDAC-tubulin complex show that the state renders ATP transport virtually impossible. A number of residues pivotal for tubulin binding to the channel were identified that help to clarify the molecular details of VDAC-tubulin interaction and to provide new insight into the mechanism of the control of mitochondria respiration by VDAC.
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Affiliation(s)
- Sergei Yu. Noskov
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Tatiana K. Rostovtseva
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Sergey M. Bezrukov
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
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14
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Gkeka P, Eleftheratos S, Kolocouris A, Cournia Z. Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore. J Chem Theory Comput 2013; 9:1272-81. [DOI: 10.1021/ct300899n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paraskevi Gkeka
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou,
11527 Athens, Greece
| | - Stelios Eleftheratos
- Faculty
of Pharmacy, Department of Pharmaceutical
Chemistry, University of Athens, Panepistimioupolis-Zografou,
15771 Athens, Greece
| | - Antonios Kolocouris
- Faculty
of Pharmacy, Department of Pharmaceutical
Chemistry, University of Athens, Panepistimioupolis-Zografou,
15771 Athens, Greece
| | - Zoe Cournia
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou,
11527 Athens, Greece
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15
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Merchant BA, Madura JD. Insights from molecular dynamics: the binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters. J Mol Graph Model 2012; 38:1-12. [PMID: 23079638 DOI: 10.1016/j.jmgm.2012.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 04/30/2012] [Accepted: 05/04/2012] [Indexed: 11/18/2022]
Abstract
The dopamine transporter (DAT) facilitates the regulation of synaptic neurotransmitter levels. As a target for therapeutic and illicit psycho-stimulant drugs like antidepressants and cocaine, DAT has been studied intensively. Despite a wealth of mutational and physiological data regarding DAT, the structure remains unsolved and details of the transport mechanism, binding sites and conformational changes remain debated. A bacterial homolog of DAT, the leucine transporter (LeuT(Aa)) has been used as a template and framework for modeling and understanding DAT. Free energy profiles obtained from Multi-Configuration Thermodynamic Integration simulations allowed us to correctly identify the primary and secondary binding pockets of LeuT(Aa). A comparison of free energy profiles for dopamine and cocaine in DAT suggests that the binding site of cocaine is located in a secondary pocket, not the primary substrate site. Two recurring primary pathways for intracellular substrate release from the primary pocket are identified in both transporters using the Random Acceleration Molecular Dynamics method. One pathway appears to follow transmembranes (TMs) 1a and 6b while the other pathway follows along TMs 6b and 8. Interestingly, we observe that a single sodium ion is co-transported with leucine during both simulation types.
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Affiliation(s)
- Bonnie A Merchant
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, USA
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16
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Chaput L, Sanejouand YH, Balloumi A, Tran V, Graber M. Contribution of both catalytic constant and Michaelis constant to CALB enantioselectivity: Use of FEP calculations for prediction studies. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2011.11.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Zdravkovic I, Zhao C, Lev B, Cuervo JE, Noskov SY. Atomistic models of ion and solute transport by the sodium-dependent secondary active transporters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:337-47. [PMID: 22138368 DOI: 10.1016/j.bbamem.2011.10.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 10/24/2011] [Accepted: 10/25/2011] [Indexed: 12/19/2022]
Abstract
The recent determination of high-resolution crystal structures of several transporters offers unprecedented insights into the structural mechanisms behind secondary transport. These proteins utilize the facilitated diffusion of the ions down their electrochemical gradients to transport the substrate against its concentration gradient. The structural studies revealed striking similarities in the structural organization of ion and solute binding sites and a well-conserved inverted-repeat topology between proteins from several gene families. In this paper we will overview recent atomistic simulations applied to study the mechanisms of selective binding of ion and substrate in LeuT, Glt, vSGLT and hSERT as well as its consequences for the transporter conformational dynamics. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Igor Zdravkovic
- Institute for Biocomplexity and Informatics (IBI), University of Calgary, 2500 University Drive, Calgary, Canada, T2N 1N4
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18
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Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U. Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration. J Am Chem Soc 2011; 133:13081-92. [DOI: 10.1021/ja202972m] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel Genheden
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Paulius Mikulskis
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - LiHong Hu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Pär Söderhjelm
- Department of Chemistry and Applied Biosciences—Computational Science, ETH Zürich, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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19
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Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol 2011; 21:150-60. [PMID: 21349700 DOI: 10.1016/j.sbi.2011.01.011] [Citation(s) in RCA: 395] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 01/25/2011] [Accepted: 01/27/2011] [Indexed: 11/23/2022]
Abstract
Improved rational drug design methods are needed to lower the cost and increase the success rate of drug discovery and development. Alchemical binding free energy calculations, one potential tool for rational design, have progressed rapidly over the past decade, but still fall short of providing robust tools for pharmaceutical engineering. Recent studies, especially on model receptor systems, have clarified many of the challenges that must be overcome for robust predictions of binding affinity to be useful in rational design. In this review, inspired by a recent joint academic/industry meeting organized by the authors, we discuss these challenges and suggest a number of promising approaches for overcoming them.
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20
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Zhao C, Noskov SY. The Role of Local Hydration and Hydrogen-Bonding Dynamics in Ion and Solute Release from Ion-Coupled Secondary Transporters. Biochemistry 2011; 50:1848-56. [DOI: 10.1021/bi101454f] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Chunfeng Zhao
- Institute for Biocomplexity and Informatics and Department of Biological Sciences, University of Calgary, 2500 University Drive, BI558, Calgary, Alberta, Canada T2N 1N4
| | - Sergei Yu. Noskov
- Institute for Biocomplexity and Informatics and Department of Biological Sciences, University of Calgary, 2500 University Drive, BI558, Calgary, Alberta, Canada T2N 1N4
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21
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Evidence for a third sodium-binding site in glutamate transporters suggests an ion/substrate coupling model. Proc Natl Acad Sci U S A 2010; 107:13912-7. [PMID: 20634426 DOI: 10.1073/pnas.1006289107] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Excitatory amino acid transporters (EAATs) remove glutamate from synapses. They maintain an efficient synaptic transmission and prevent glutamate from reaching neurotoxic levels. Glutamate transporters couple the uptake of one glutamate to the cotransport of three sodium ions and one proton and the countertransport of one potassium ion. The molecular mechanism for this coupled uptake of glutamate and its co- and counter-transported ions is not known. In a crystal structure of the bacterial glutamate transporter homolog, GltPh, only two cations are bound to the transporter, and there is no indication of the location of the third sodium site. In experiments using voltage clamp fluorometry and simulations based on molecular dynamics combined with grand canonical Monte Carlo and free energy simulations performed on different isoforms of GltPh as well on a homology model of EAAT3, we sought to locate the third sodium-binding site in EAAT3. Both experiments and computer simulations suggest that T370 and N451 (T314 and N401 in GltPh) form part of the third sodium-binding site. Interestingly, the sodium bound at T370 forms part of the binding site for the amino acid substrate, perhaps explaining both the strict coupling of sodium transport to uptake of glutamate and the ion selectivity of the affinity for the transported amino acid in EAATs.
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