1
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Afshinpour M, Mahdiuni H. Arginine transportation mechanism through cationic amino acid transporter 1: insights from molecular dynamics studies. J Biomol Struct Dyn 2023; 41:13580-13594. [PMID: 36762692 DOI: 10.1080/07391102.2023.2175374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/28/2023] [Indexed: 02/11/2023]
Abstract
Metabolic and signaling mechanisms in mammalian cells are facilitated by the transportation of L-arginine (Arg) across the plasma membrane through cationic amino acid transporter (CAT) proteins. Due to a lack of argininosuccinate synthase (ASS) activity in various tumor cells such as acute myeloid leukemia, acute lymphocytic leukemia, and chronic lymphocytic leukemia, these tumor entities are arginine-auxotrophic and therefore depend on the uptake of the amino acid arginine. Cationic amino acid transporter-1 (CAT-1) is the leading arginine importer expressed in the aforementioned tumor entities. Hence, in the present study, to investigate the transportation mechanism of arginine in CAT-1, we performed molecular dynamics (MD) simulation methods on the modeled human CAT-1. The MM-PBSA approach was conducted to determine the critical residues interacting with arginine within the corresponding binding site of CAT-1. In addition, we found out that the water molecules have the leading role in forming the transportation channel within CAT-1. The conductive structure of CAT-1 was formed only when the water molecules were continuously distributed across the channel. Steered molecular dynamics (SMD) simulation approach showed various energy barriers against arginine transportation through CAT-1, especially while crossing the bottlenecks of the related channel. These findings at the molecular level might shed light on identifying the crucial amino acids in the binding of arginine to eukaryotic CATs and also provide fundamental insights into the arginine transportation mechanisms through CAT-1. Understanding the transportation mechanism of arginine is essential to developing CAT-1 blockers, which can be potential medications for some types of cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maral Afshinpour
- Bioinformatics Lab., Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
| | - Hamid Mahdiuni
- Bioinformatics Lab., Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
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2
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Chang Y, Hawkins BA, Du JJ, Groundwater PW, Hibbs DE, Lai F. A Guide to In Silico Drug Design. Pharmaceutics 2022; 15:pharmaceutics15010049. [PMID: 36678678 PMCID: PMC9867171 DOI: 10.3390/pharmaceutics15010049] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as in silico structure prediction, refinement, modelling and target validation, that are commonly used in this area.
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Affiliation(s)
- Yiqun Chang
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Bryson A. Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jonathan J. Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W. Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David E. Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence:
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3
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Blazhynska M, Goulard Coderc de Lacam E, Chen H, Roux B, Chipot C. Hazardous Shortcuts in Standard Binding Free Energy Calculations. J Phys Chem Lett 2022; 13:6250-6258. [PMID: 35771686 DOI: 10.1021/acs.jpclett.2c01490] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Calculating the standard binding free energies of protein-protein and protein-ligand complexes from atomistic molecular dynamics simulations in explicit solvent is a problem of central importance in computational biophysics. A rigorous strategy for carrying out such calculations is the so-called "geometrical route". In this method, two molecular objects are progressively separated from one another in the presence of orientational and conformational restraints serving to control the change in configurational entropy that accompanies the dissociation process, thereby allowing the computations to converge within simulations of affordable length. Although the geometrical route provides a rigorous theoretical framework, a tantalizing computational shortcut consists of simply leaving out such orientational and conformational degrees of freedom during the separation process. Here the accuracy and convergence of the two approaches are critically compared in the case of two protein-ligand complexes (Abl kinase-SH3:p41 and MDM2-p53:NVP-CGM097) and three protein-protein complexes (pig insulin dimer, SARS-CoV-2 spike RBD:ACE2, and CheA kinase-P2:CheY). The results of the simulations that strictly follow the geometrical route match the experimental standard binding free energies within chemical accuracy. In contrast, simulations bereft of geometrical restraints converge more poorly, yielding inconsistent results that are at variance with the experimental measurements. Furthermore, the orientational and positional time correlation functions of the protein in the unrestrained simulations decay over several microseconds, a time scale that is far longer than the typical simulation times of the geometrical route, which explains why those simulations fail to sample the relevant degrees of freedom during the separation process of the complexes.
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Affiliation(s)
- Marharyta Blazhynska
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche 7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France
| | - Emma Goulard Coderc de Lacam
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche 7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France
| | - Haochuan Chen
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche 7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, W225, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche 7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, W225, Chicago, Illinois 60637, United States
- Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Shinobu A, Re S, Sugita Y. Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics. Front Mol Biosci 2022; 9:878830. [PMID: 35573746 PMCID: PMC9099257 DOI: 10.3389/fmolb.2022.878830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular dynamics (MD) simulations are increasingly used to study various biological processes such as protein folding, conformational changes, and ligand binding. These processes generally involve slow dynamics that occur on the millisecond or longer timescale, which are difficult to simulate by conventional atomistic MD. Recently, we applied a two-dimensional (2D) replica-exchange MD (REMD) method, which combines the generalized replica exchange with solute tempering (gREST) with the replica-exchange umbrella sampling (REUS) in kinase-inhibitor binding simulations, and successfully observed multiple ligand binding/unbinding events. To efficiently apply the gREST/REUS method to other kinase-inhibitor systems, we establish modified, practical protocols with non-trivial simulation parameter tuning. The current gREST/REUS simulation protocols are tested for three kinase-inhibitor systems: c-Src kinase with PP1, c-Src kinase with Dasatinib, and c-Abl kinase with Imatinib. We optimized the definition of kinase-ligand distance as a collective variable (CV), the solute temperatures in gREST, and replica distributions and umbrella forces in the REUS simulations. Also, the initial structures of each replica in the 2D replica space were prepared carefully by pulling each ligand from and toward the protein binding sites for keeping stable kinase conformations. These optimizations were carried out individually in multiple short MD simulations. The current gREST/REUS simulation protocol ensures good random walks in 2D replica spaces, which are required for enhanced sampling of inhibitor dynamics around a target kinase.
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Affiliation(s)
- Ai Shinobu
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Suyong Re
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Ibaraki, Japan
| | - Yuji Sugita
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
- RIKEN Center for Computational Science, Kobe, Japan
- *Correspondence: Yuji Sugita,
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5
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Taka E, Yilmaz SZ, Golcuk M, Kilinc C, Aktas U, Yildiz A, Gur M. Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor. J Phys Chem B 2021; 125:5537-5548. [PMID: 33979162 PMCID: PMC8130525 DOI: 10.1021/acs.jpcb.1c02048] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/23/2021] [Indexed: 12/22/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects human cells by binding its spike (S) glycoproteins to angiotensin-converting enzyme 2 (ACE2) receptors and causes the coronavirus disease 2019 (COVID-19). Therapeutic approaches to prevent SARS-CoV-2 infection are mostly focused on blocking S-ACE2 binding, but critical residues that stabilize this interaction are not well understood. By performing all-atom molecular dynamics (MD) simulations, we identified an extended network of salt bridges, hydrophobic and electrostatic interactions, and hydrogen bonds between the receptor-binding domain (RBD) of the S protein and ACE2. Mutagenesis of these residues on the RBD was not sufficient to destabilize binding but reduced the average work to unbind the S protein from ACE2. In particular, the hydrophobic end of RBD serves as the main anchor site and is the last to unbind from ACE2 under force. We propose that blocking the hydrophobic surface of RBD via neutralizing antibodies could prove to be an effective strategy to inhibit S-ACE2 interactions.
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Affiliation(s)
- Elhan Taka
- Department of Mechanical Engineering,
Istanbul Technical University (ITU), 34437 Istanbul,
Turkey
| | - Sema Z. Yilmaz
- Department of Mechanical Engineering,
Istanbul Technical University (ITU), 34437 Istanbul,
Turkey
| | - Mert Golcuk
- Department of Mechanical Engineering,
Istanbul Technical University (ITU), 34437 Istanbul,
Turkey
| | - Ceren Kilinc
- Department of Mechanical Engineering,
Istanbul Technical University (ITU), 34437 Istanbul,
Turkey
| | - Umut Aktas
- Department of Mechanical Engineering,
Istanbul Technical University (ITU), 34437 Istanbul,
Turkey
| | - Ahmet Yildiz
- Physics Department, University of
California, Berkeley, California 94720-3220, United
States
- Department of Molecular and Cellular Biology,
University of California, Berkeley, California 94720-3220,
United States
| | - Mert Gur
- Department of Mechanical Engineering,
Istanbul Technical University (ITU), 34437 Istanbul,
Turkey
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6
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Narayan B, Buchete NV, Elber R. Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning. J Phys Chem B 2021; 125:5706-5715. [PMID: 33930271 DOI: 10.1021/acs.jpcb.1c00264] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gleevec (a.k.a., imatinib) is an important anticancer (e.g., chronic myeloid leukemia) chemotherapeutic drug due to its inhibitory interaction with the Abl kinase. Here, we use atomically detailed simulations within the Milestoning framework to study the molecular dissociation mechanism of Gleevec from Abl kinase. We compute the dissociation free energy profile, the mean first passage time for unbinding, and explore the transition state ensemble of conformations. The milestones form a multidimensional network with average connectivity of about 2.93, which is significantly higher than the connectivity for a one-dimensional reaction coordinate. The free energy barrier for Gleevec dissociation is estimated to be ∼10 kcal/mol, and the exit time is ∼55 ms. We examined the transition state conformations using both, the committor and transition function. We show that near the transition state the highly conserved salt bridge K217 and E286 is transiently broken. Together with the calculated free energy profile, these calculations can advance the understanding of the molecular interaction mechanisms between Gleevec and Abl kinase and play a role in future drug design and optimization studies.
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Affiliation(s)
- Brajesh Narayan
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.,Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nicolae-Viorel Buchete
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.,Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ron Elber
- Oden Institute for Computational Engineering and Science, Department of Chemistry, University of Texas at Austin, Austin Texas 78712, United States
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7
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Paul F, Thomas T, Roux B. Diversity of Long-Lived Intermediates along the Binding Pathway of Imatinib to Abl Kinase Revealed by MD Simulations. J Chem Theory Comput 2020; 16:7852-7865. [PMID: 33147951 DOI: 10.1021/acs.jctc.0c00739] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Imatinib, a drug used for the treatment of chronic myeloid leukemia and other cancers, works by blocking the catalytic site of pathological constitutively active Abl kinase. While the binding pose is known from X-ray crystallography, the different steps leading to the formation of the complex are not well understood. The results from extensive molecular dynamics simulations show that imatinib can primarily exit the known crystallographic binding pose through the cleft of the binding site or by sliding under the αC helix. Once displaced from the crystallographic binding pose, imatinib becomes trapped in intermediate states. These intermediates are characterized by a high diversity of ligand orientations and conformations, and relaxation timescales within this region may exceed 3-4 ms. Analysis indicates that the metastable intermediate states should be spectroscopically indistinguishable from the crystallographic binding pose, in agreement with tryptophan stopped-flow fluorescence experiments.
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Affiliation(s)
- Fabian Paul
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Trayder Thomas
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
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8
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Baradaran M, Jalali A, Naderi Soorki M, Jokar M, Galehdari H. Three New Scorpion Chloride Channel Toxins as Potential Anti-Cancer Drugs: Computational Prediction of The Interactions With Hmmp-2 by Docking and Steered Molecular Dynamics Simulations. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2019; 18:720-734. [PMID: 31531056 PMCID: PMC6706747 DOI: 10.22037/ijpr.2019.1100659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Scorpion venom is a rich source of toxins which have great potential to develop new therapeutic agents. Scorpion chloride channel toxins (ClTxs), such as Chlorotoxin selectively inhibit human Matrix Methaloproteinase-2 (hMMP-2). The inhibitors of hMMP-2 have potential use in cancer therapy. Three new ClTxs, meuCl14, meuCl15 and meuCl16, derived from the venom transcriptome of Iranian scorpion, M. eupeus (Buthidea family), show high sequence identity (71.4%) with Chlorotoxin. Here, 3-D homology model of new ClTxs were constructed. The models were optimized by Molecular Dynamics simulation based on MDFF (molecular dynamics flexible fitting) method. New ClTxs indicate the presence of CSαβ folding of other scorpion toxins. A docking followed by steered molecular dynamics (SMD) simulations to investigate the interactions of meuCl14, meuCl15, and meuCl16 with hMMP-2 was applied. The current study creates a correlation between the unbinding force and the inhibition activities of meuCl14, meuCl15 and meuCl16 to shed some insights as to which toxin may be used as a drug deliverer. To this aim, SMD simulations using Constant Force Pulling method were carried out. The SMD provided useful details related to the changes of electrostatic, van de Waals (vdW), and hydrogen-bonding (H-bonding) interactions between ligands and receptor during the pathway of unbinding. According to SMD results, the interaction of hMMP-2 with meuCl14 is more stable. In addition, Arginine residue was found to contribute significantly in interaction of ClTxs with hMMP-2. All in all, the present study is a dynamical approach whose results are capable of being implemented in structure-based drug design.
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Affiliation(s)
- Masoumeh Baradaran
- Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Amir Jalali
- Department of Toxicology, School of Pharmacy and Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Pharmacology and Toxicology, School of Pharmacy, Guilan University of Medical Sciences, Rasht, Iran
| | - Maryam Naderi Soorki
- Genetics Department, Sciences Faculty, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mahmoud Jokar
- Cotton Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran
| | - Hamid Galehdari
- Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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9
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Molecular Modeling of ALK L1198F and/or G1202R Mutations to Determine Differential Crizotinib Sensitivity. Sci Rep 2019; 9:11390. [PMID: 31388026 PMCID: PMC6684801 DOI: 10.1038/s41598-019-46825-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/17/2019] [Indexed: 01/29/2023] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase that has been recognized as a therapeutic target for EML4-ALK fusion-positive nonsmall cell lung cancer (NSCLC) treatment using type I kinase inhibitors such as crizotinib to take over the ATP binding site. According to Shaw’s measurements, ALK carrying G1202R mutation shows reduced response to crizotinib (IC50 = 382 nM vs. IC50 = 20 nM for wild-type), whereas L1198F mutant is more responsive (IC50 = 0.4 nM). Interestingly, the double mutant L1198F/G1202R maintains a similar response (IC50 = 31 nM) to the wild-type. Herein we conducted molecular modeling simulations to elucidate the varied crizotinib sensitivities in three mutants carrying L1198F and/or G1202R. Both L1198 and G1202 are near the ATP pocket. Mutation G1202R causes steric hindrance that blocks crizotinib accessibility, which greatly reduces efficacy, whereas mutation L1198F enlarges the binding pocket entrance and hydrophobically interacts with crizotinib to enhance sensitivity. With respect to the double mutant L1198F/G1202R, F1198 indirectly pulls R1202 away from the binding entrance and consequently alleviates the steric obstacle introduced by R1202. These results demonstrated how the mutated residues tune the crizotinib response and may assist kinase inhibitor development especially for ALK G1202R, analogous to the ROS1 G2302R and MET G1163R mutations that are also resistant to crizotinib treatment in NSCLC.
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10
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Do PC, Lee EH, Le L. Steered Molecular Dynamics Simulation in Rational Drug Design. J Chem Inf Model 2018; 58:1473-1482. [DOI: 10.1021/acs.jcim.8b00261] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Phuc-Chau Do
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Eric H. Lee
- Department of Medicine and Division of Hematology and Oncology, Loma Linda University Medical Center, Loma Linda, California 92350, United States
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
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11
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You W, Chang CEA. Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors. J Chem Inf Model 2018; 58:968-981. [PMID: 29620886 PMCID: PMC5975198 DOI: 10.1021/acs.jcim.7b00640] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding the governing factors of fast or slow inhibitor binding/unbinding assists in developing drugs with preferred kinetic properties. For inhibitors with the same binding affinity targeting different binding sites of the same protein, the kinetic behavior can profoundly differ. In this study, we investigated unbinding kinetics and mechanisms of fast (type-I) and slow (type-II/III) binders of p38α mitogen-activated protein kinase, where the crystal structures showed that type-I and type-II/III inhibitors bind to pockets with different conformations of the Asp-Phe-Gly (DFG) motif. The work used methods that combine conventional molecular dynamics (MD), accelerated molecular dynamics (AMD) simulations, and the newly developed pathway search guided by internal motions (PSIM) method to find dissociation pathways. The study focuses on revealing key interactions and molecular rearrangements that hinder ligand dissociation by using umbrella sampling and post-MD processing to examine changes in free energy during ligand unbinding. As anticipated, the initial dissociation steps all require breaking interactions that appeared in crystal structures of the bound complexes. Interestingly, for type-I inhibitors such as SB2, p38α keeps barrier-free conformational fluctuation in the ligand-bound complex and during ligand dissociation. In contrast, with a type-II/III inhibitor such as BIRB796, with the rearrangements of p38α in its bound state, ligand unbinding features energetically unfavorable protein-ligand concerted movement. Our results also show that the type-II/III inhibitors preferred dissociation pathways through the allosteric channel, which is consistent with an existing publication. The study suggests that the level of required protein rearrangement is one major determining factor of drug binding kinetics in p38α systems, providing useful information for development of inhibitors.
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Affiliation(s)
- Wanli You
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Chia-en A. Chang
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
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12
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Nguyen MK, Jaillet L, Redon S. ART-RRT: As-Rigid-As-Possible exploration of ligand unbinding pathways. J Comput Chem 2018; 39:665-678. [DOI: 10.1002/jcc.25132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/30/2017] [Accepted: 11/20/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Minh Khoa Nguyen
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK; 38000 Grenoble France
| | - Léonard Jaillet
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK; 38000 Grenoble France
| | - Stéphane Redon
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK; 38000 Grenoble France
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13
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Liang D, Chen Q, Guo Y, Zhang T, Guo W. Insight into resistance mechanisms of AZD4547 and E3810 to FGFR1 gatekeeper mutation via theoretical study. DRUG DESIGN DEVELOPMENT AND THERAPY 2017; 11:451-461. [PMID: 28255231 PMCID: PMC5322841 DOI: 10.2147/dddt.s129991] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Inhibitors targeting the amplification of the fibroblast growth factor receptor 1 (FGFR1) have found success in the treatment of FGFR1-positive squamous cell lung and breast cancers. A secondary mutation of gatekeeper residue (V561M) in the binding site has been linked to the acquired resistance. Recently, two well-known small molecule inhibitors of FGFR1, AZD4547 and E3810, reported that the V561M mutation confers significant resistance to E3810, while retaining affinity for AZD4547. FGFR1 is widely investigated as potential therapeutic target, while there are few computational studies made to understand the resistance mechanisms about FGFR1 V561M gatekeeper mutation. In this study, molecular docking, classical molecular dynamics simulations, molecular mechanics/generalized born surface area (MM/GBSA) free energy calculations, and umbrella sampling (US) simulations were carried out to make clear the principle of the binding preference of AZD4547 and E3810 toward FGFR1 V561M gatekeeper mutation. The results provided by MM/GBSA reveal that AZD4547 has similar binding affinity to both FGFR1WT and FGFR1V561M, whereas E3810 has much higher binding affinity to FGFR1WT than to FGFR1V561M. Comparison of individual energy terms indicates that the major variation of E3810 between FGFR1WT and FGFR1V561M are van der Waals interactions. In addition, US simulations prove that the potential of mean force (PMF) profile of AZD4547 toward FGFR1WT and FGFR1V561M has similar PMF depth. However, the PMF profile of E3810 toward FGFR1WT and FGFR1V561M has much higher PMF depth, suggesting that E3810 is more easily dissociated from FGFR1V561M than from FGFR1WT. The results not only show the drug-resistance determinants of FGFR1 gatekeeper mutation but also provide valuable implications and provide vital clues for the development of new inhibitors to combat drug resistance.
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Affiliation(s)
| | - Qiaowan Chen
- Department of Obstetrics, Affiliated Hospital of Jining Medical University, Jining, Shandong
| | - Yujin Guo
- Pharmacy Department, Jining First People's Hospital
| | - Ting Zhang
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University
| | - Wentao Guo
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
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14
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A theoretical model of the interaction between phosphates in the ATP molecule and guanidinium systems. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2012-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Abstract
Interest in the application of molecular dynamics (MD) simulations has increased in the field of protein kinase (PK) drug discovery. PKs belong to an important drug target class because they are directly involved in a number of diseases, including cancer. MD methods simulate dynamic biological and chemical events at an atomic level. This information can be combined with other in silico and experimental methods to efficiently target selected receptors. In this review, we present common and advanced methods of MD simulations and we focus on the recent applications of MD-based methodologies that provided significant insights into the elucidation of biological mechanisms involving PKs and into the discovery of novel kinase inhibitors.
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16
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Kong X, Sun H, Pan P, Tian S, Li D, Li Y, Hou T. Molecular principle of the cyclin-dependent kinase selectivity of 4-(thiazol-5-yl)-2-(phenylamino) pyrimidine-5-carbonitrile derivatives revealed by molecular modeling studies. Phys Chem Chem Phys 2016; 18:2034-46. [DOI: 10.1039/c5cp05622e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to the high sequence identity of the binding pockets of cyclin-dependent kinases (CDKs), designing highly selective inhibitors towards a specific CDK member remains a big challenge.
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Affiliation(s)
- Xiaotian Kong
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
- College of Pharmaceutical Sciences
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Dan Li
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Tingjun Hou
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
- College of Pharmaceutical Sciences
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17
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Molecular Modeling and Its Applications in Protein Engineering. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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18
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Lovera S, Morando M, Pucheta-Martinez E, Martinez-Torrecuadrada JL, Saladino G, Gervasio FL. Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics. PLoS Comput Biol 2015; 11:e1004578. [PMID: 26606374 PMCID: PMC4659586 DOI: 10.1371/journal.pcbi.1004578] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/01/2015] [Indexed: 11/18/2022] Open
Abstract
Due to its inhibition of the Abl kinase domain in the BCR-ABL fusion protein, imatinib is strikingly effective in the initial stage of chronic myeloid leukemia with more than 90% of the patients showing complete remission. However, as in the case of most targeted anti-cancer therapies, the emergence of drug resistance is a serious concern. Several drug-resistant mutations affecting the catalytic domain of Abl and other tyrosine kinases are now known. But, despite their importance and the adverse effect that they have on the prognosis of the cancer patients harboring them, the molecular mechanism of these mutations is still debated. Here by using long molecular dynamics simulations and large-scale free energy calculations complemented by in vitro mutagenesis and microcalorimetry experiments, we model the effect of several widespread drug-resistant mutations of Abl. By comparing the conformational free energy landscape of the mutants with those of the wild-type tyrosine kinases we clarify their mode of action. It involves significant and complex changes in the inactive-to-active dynamics and entropy/enthalpy balance of two functional elements: the activation-loop and the conserved DFG motif. What is more the T315I gatekeeper mutant has a significant impact on the binding mechanism itself and on the binding kinetics.
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MESH Headings
- Computational Biology
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/physiology
- Fusion Proteins, bcr-abl/chemistry
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Humans
- Imatinib Mesylate/chemistry
- Imatinib Mesylate/metabolism
- Imatinib Mesylate/pharmacology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive
- Molecular Dynamics Simulation
- Mutagenesis, Site-Directed
- Thermodynamics
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Affiliation(s)
- Silvia Lovera
- Department of Chemistry, University College London, London, United Kingdom
| | - Maria Morando
- Center of Technological Development in Health, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | | | | | - Giorgio Saladino
- Department of Chemistry, University College London, London, United Kingdom
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- * E-mail: (GS); (FLG)
| | - Francesco L. Gervasio
- Department of Chemistry, University College London, London, United Kingdom
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- * E-mail: (GS); (FLG)
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19
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Kang CM, Liu DQ, Wang XY, Yu RL, Lv YT. The unbinding studies of vascular endothelial growth factor receptor-2 protein tyrosine kinase type II inhibitors. J Mol Graph Model 2015; 59:130-5. [PMID: 25989626 DOI: 10.1016/j.jmgm.2015.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 01/16/2023]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2) tyrosine kinase has two conformations, active and inactive conformations. Type II inhibitors bind to inactive conformation. It has two possible binding/unbinding paths. To explore the unbinding path of inhibitor 01-435 that was generated by fragment build in the binding pocket of VEGFR-2, molecular dynamics (MD) simulation was performed on the crystal structure of VEGFR-2 in complex with 01-435, then steered molecular dynamics (SMD) simulation was executed on the crystal structure of VEGFR-2 in complex with 01-435. Pull force, van der Waals and electrostatic interaction along the two paths were calculated by using SMD simulation. The SMD simulation results indicate that the more favorable path for inhibitor dissociation is along with the traditional ATP-channel rather than the allosteric-pocket-channel, which is mainly due to the less electrostatic interaction that the ligand suffers during dissociation process along the traditional ATP-channel.
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Affiliation(s)
- Cong-min Kang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Dong-qing Liu
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xin-ying Wang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Ri-lei Yu
- School of Pharmacy, Ocean University of China, Qingdao 266003, PR China
| | - Ying-tao Lv
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China.
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20
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Sun H, Tian S, Zhou S, Li Y, Li D, Xu L, Shen M, Pan P, Hou T. Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations. Sci Rep 2015; 5:8457. [PMID: 25678308 PMCID: PMC4326958 DOI: 10.1038/srep08457] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/13/2015] [Indexed: 11/12/2022] Open
Abstract
How does a type II inhibitor bind to/unbind from a kinase target is still a confusing question because the small molecule occupies both the ATP pocket and the allosteric pocket of the kinase binding site. Here, by using enhanced sampling simulations (umbrella sampling, US) and two-end-state free energy calculations (MM/GSBA), we systemically studied the dissociation processes of two distinct small molecules escaping from the binding pocket of p38 MAP kinase through the allosteric channel and the ATP channel. The results show that the unbinding pathways along the allosteric channel have much lower PMF depths than those along the ATP channel, suggesting that the allosteric channel is more favorable for the dissociations of the two inhibitors and thereby supporting the general understanding that the largest channel of a target is usually the entry/exit pathway for the binding/dissociation of small molecules. Interestingly, the MM/GBSA approach yielded similar PMF profiles compared with those based on US, a much time consuming approach, indicating that for a general study, such as detecting the important transition state of a ligand binding/unbinding process, MM/GBSA may be a feasible choice.
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Affiliation(s)
- Huiyong Sun
- 1] Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China [2] College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Shunye Zhou
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Lei Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Mingyun Shen
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tingjun Hou
- 1] Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China [2] College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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21
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Hu Y, Liu H. Case study on temperature-accelerated molecular dynamics simulation of ligand dissociation: inducer dissociation from the Lac repressor protein. J Phys Chem A 2014; 118:9272-9. [PMID: 24941022 DOI: 10.1021/jp503856h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied ligand dissociation from the inducer-binding domain of the Lac repressor protein using temperature-accelerated molecular dynamics (TAMD) simulations. With TAMD, ligand dissociation could be observed within relatively short simulation time. This allowed many dissociation trajectories to be sampled. Under the adiabatic approximation of TAMD, all but one degree of freedom of the system were sampled from usual canonical ensembles at room temperature. Thus, meaningful statistical analyses could be carried out on the trajectories. A systematic approach was proposed to analyze possible correlations between ligand dissociation and fluctuations of various protein conformational coordinates. These analyses employed relative entropies, allowing both linear and nonlinear correlations to be considered. Applying the simulation and analysis methods to the inducer binding domain of the Lac repressor protein, we found that ligand dissociation from this protein correlated mainly with fluctuations of side-chain conformations of a few residues that surround the binding pocket. In addition, the two binding sites of the dimeric protein were dynamically coupled: occupation of one site by an inducer molecule could significantly reduce or slow down conformational dynamics around the other binding pocket.
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Affiliation(s)
- Yue Hu
- School of Life Sciences, ‡Hefei National Laboratory for Physical Sciences at the Microscales, and §Hefei Institutes of Physical Science, Chinese Academy of Sciences, University of Science and Technology of China , 96 Jinzhai Road, Hefei, Anhui 230026, China
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22
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Johnston JM, Filizola M. Beyond standard molecular dynamics: investigating the molecular mechanisms of G protein-coupled receptors with enhanced molecular dynamics methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:95-125. [PMID: 24158803 PMCID: PMC4074508 DOI: 10.1007/978-94-007-7423-0_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field.
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Affiliation(s)
- Jennifer M. Johnston
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Marta Filizola
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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23
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Agius R, Torchala M, Moal IH, Fernández-Recio J, Bates PA. Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization. PLoS Comput Biol 2013; 9:e1003216. [PMID: 24039569 PMCID: PMC3764008 DOI: 10.1371/journal.pcbi.1003216] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 07/25/2013] [Indexed: 12/21/2022] Open
Abstract
Predicting the effects of mutations on the kinetic rate constants of protein-protein interactions is central to both the modeling of complex diseases and the design of effective peptide drug inhibitors. However, while most studies have concentrated on the determination of association rate constants, dissociation rates have received less attention. In this work we take a novel approach by relating the changes in dissociation rates upon mutation to the energetics and architecture of hotspots and hotregions, by performing alanine scans pre- and post-mutation. From these scans, we design a set of descriptors that capture the change in hotspot energy and distribution. The method is benchmarked on 713 kinetically characterized mutations from the SKEMPI database. Our investigations show that, with the use of hotspot descriptors, energies from single-point alanine mutations may be used for the estimation of off-rate mutations to any residue type and also multi-point mutations. A number of machine learning models are built from a combination of molecular and hotspot descriptors, with the best models achieving a Pearson's Correlation Coefficient of 0.79 with experimental off-rates and a Matthew's Correlation Coefficient of 0.6 in the detection of rare stabilizing mutations. Using specialized feature selection models we identify descriptors that are highly specific and, conversely, broadly important to predicting the effects of different classes of mutations, interface regions and complexes. Our results also indicate that the distribution of the critical stability regions across protein-protein interfaces is a function of complex size more strongly than interface area. In addition, mutations at the rim are critical for the stability of small complexes, but consistently harder to characterize. The relationship between hotregion size and the dissociation rate is also investigated and, using hotspot descriptors which model cooperative effects within hotregions, we show how the contribution of hotregions of different sizes, changes under different cooperative effects.
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Affiliation(s)
- Rudi Agius
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
| | - Mieczyslaw Torchala
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
| | - Iain H. Moal
- Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Juan Fernández-Recio
- Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Paul A. Bates
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
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24
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Sun H, Li Y, Li D, Hou T. Insight into crizotinib resistance mechanisms caused by three mutations in ALK tyrosine kinase using free energy calculation approaches. J Chem Inf Model 2013; 53:2376-89. [PMID: 23952683 DOI: 10.1021/ci400188q] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As a safe and efficacious drug, crizotinib was approved by the U.S. Food and Drug Administration (FDA) in 2011 for the treatment of advanced fusion-type nonsmall-cell lung cancer. Although high response ratio was detected from the patients treated with crizotinib, the cancer has eventually conferred resistance to crizotinib. Several drug resistance mutations have been found in the anaplastic lymphoma kinase (ALK) tyrosine kinase domain as the target for crizotinib, but the drug resistance mechanisms remain unclear. Therefore, in this study, the adaptive biasing force (ABF) method and two-end-state free energy calculation approaches were employed to elucidate the resistance mechanisms of crizotinib induced by the mutations L1152R, G1202R, and S1206Y. The ABF simulation results suggest that the reaction coordinates for the unbinding processes of crizotinib from the binding pockets of the mutated ALKs is different from that of the wild type ALK. The potentials of mean force for the crizotinib unbinding and the binding free energies predicted by the two-end-state free energy calculations are consistent with the experimental data. Our results indicate that the three mutations weaken the binding affinity of crizotinib obviously and lead to drug resistance. The free energy decomposition analysis illustrates the importance of the loss of two important H-bonds in the L1152R and S1206Y mutants on drug resistance. The entropy analysis shows that the entropy term plays a critical role in the substantial change of the conformational entropies of G1202R and L1152R. Our results reveal the mechanisms of drug resistance and provide vital clues for the development of new inhibitors to combat drug resistance.
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Affiliation(s)
- Huiyong Sun
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University , Suzhou, Jiangsu 215123, China
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25
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Kalyaanamoorthy S, Chen YPP. Modelling and enhanced molecular dynamics to steer structure-based drug discovery. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 114:123-36. [PMID: 23827463 DOI: 10.1016/j.pbiomolbio.2013.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/31/2013] [Accepted: 06/22/2013] [Indexed: 10/26/2022]
Abstract
The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes.
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Affiliation(s)
- Subha Kalyaanamoorthy
- Department of Computer Science and Computer Engineering, Faculty of Science, Technology and Engineering, La Trobe University, Melbourne, VIC 3086, Australia
| | - Yi-Ping Phoebe Chen
- Department of Computer Science and Computer Engineering, Faculty of Science, Technology and Engineering, La Trobe University, Melbourne, VIC 3086, Australia.
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26
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Abstract
This minireview focuses on recent developments in the application of molecular dynamics to drug design. Recent applications of endpoint free-energy computational methods such as molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and generalized Born surface area (MM-GBSA) and linear response methods are described. Recent progress in steered molecular dynamics applied to drug design is reviewed.
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27
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Zhang YB, Chen LY. In silico study of Aquaporin V: Effects and affinity of the central pore-occluding lipid. Biophys Chem 2012. [PMID: 23176748 DOI: 10.1016/j.bpc.2012.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Because of its roles in human physiology, Aquaporin V (AQP5), a major intrinsic protein, has been a subject of many in vitro studies. In particular, a 2008 experiment produced its crystal structure at 2.0Å resolution, which is in a tetrameric conformation consisting of four protomers. Each protomer forms an amphipathic pore that is fit for water permeation. The tetramer has a pore along its quasi-symmetry axis formed by quadruplets of hydrophobic residues (every protomer contributes equally to the quadruplets). A lipid, phosphatidylserine (PS6), is bound to AQP5 in the central pore, totally occluding it. A 2009 experiment showed that AQP5 facilitates not only permeation of water but also permeation of hydrophobic gas molecules across the cell membrane. In this article, we present an in silico study of AQP5 to elucidate the effects of PS6's binding to and dissociating from AQP5's central pore. Computing the lipid's chemical-potential along its dissociation path, we find that PS6 inhibits the function of the central pore with an IC(50) in the micromolar range. Examining the central pore and the interstices between two adjacent protomers, we propose that nonpolar gas molecules (O(2)) permeate through AQP5's hydrophobic central pore when un-occluded.
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Affiliation(s)
- Y B Zhang
- Department of Physics, University of Texas at San Antonio, San Antonio, TX 78249, United States
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28
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Sgrignani J, Magistrato A. Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study. J Chem Inf Model 2012; 52:1595-606. [DOI: 10.1021/ci300151h] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Jacopo Sgrignani
- CNR-IOM-Democritos National Simulation Center c/o International Studies for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste
(TS), Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o International Studies for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste
(TS), Italy
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29
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Valente M, Sousa SF, Magalhães AL, Freire C. Decomplexation and complexation of alkali metal cations by a crown-ether-type podand in dichloromethane: a steered molecular dynamics study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1171-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Valente M, Sousa SF, Magalhães AL, Freire C. Transfer of the K+ cation across a water/dichloromethane interface: a steered molecular dynamics study with implications in cation extraction. J Phys Chem B 2012; 116:1843-9. [PMID: 22260719 DOI: 10.1021/jp210786j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper we report the characterization of the dichloromethane (DCM)/water interface in terms of density profile, width, and surface structure. The use of steered molecular dynamics (SMD) to study the transfer of the K(+) cation from the organic layer to the water layer is also described. The corresponding free energy is in semiquantitative agreement with published experimental and theoretical results. The transference of the K(+) cation from the water layer toward the DCM layer occurs with concomitant water transport as a water microdroplet that detaches itself from the water layer after ca. 16 Å of penetration into the organic layer by breaking the thin water thread that unites both. Complexation of the water microdroplet by a polyethylene-glycol type podand induces the loss of water molecules from the water microdroplet to bulk DCM and, eventually, to the water layer.
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Affiliation(s)
- Mário Valente
- REQUIMTE-Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
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31
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González A, Perez-Acle T, Pardo L, Deupi X. Molecular basis of ligand dissociation in β-adrenergic receptors. PLoS One 2011; 6:e23815. [PMID: 21915263 PMCID: PMC3168429 DOI: 10.1371/journal.pone.0023815] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 07/25/2011] [Indexed: 01/25/2023] Open
Abstract
The important and diverse biological functions of β-adrenergic receptors (βARs) have promoted the search for compounds to stimulate or inhibit their activity. In this regard, unraveling the molecular basis of ligand binding/unbinding events is essential to understand the pharmacological properties of these G protein-coupled receptors. In this study, we use the steered molecular dynamics simulation method to describe, in atomic detail, the unbinding process of two inverse agonists, which have been recently co-crystallized with β1 and β2ARs subtypes, along four different channels. Our results indicate that this type of compounds likely accesses the orthosteric binding site of βARs from the extracellular water environment. Importantly, reconstruction of forces and energies from the simulations of the dissociation process suggests, for the first time, the presence of secondary binding sites located in the extracellular loops 2 and 3 and transmembrane helix 7, where ligands are transiently retained by electrostatic and Van der Waals interactions. Comparison of the residues that form these new transient allosteric binding sites in both βARs subtypes reveals the importance of non-conserved electrostatic interactions as well as conserved aromatic contacts in the early steps of the binding process.
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Affiliation(s)
- Angel González
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, Spain
- Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Tomas Perez-Acle
- Computational Biology Lab, Center for Mathematical Modeling, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
- Centro Interdisciplinario de Neurociencias de Valparaíso, Playa Ancha, Valparaíso, Chile
- Fundación Ciencia para la Vida, Ñuñoa, Santiago, Chile
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, Spain
| | - Xavier Deupi
- Condensed Matter Theory Group and Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzerland
- * E-mail:
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32
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Aci-Sèche S, Genest M, Garnier N. Ligand entry pathways in the ligand binding domain of PPARγ receptor. FEBS Lett 2011; 585:2599-603. [DOI: 10.1016/j.febslet.2011.07.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/29/2011] [Accepted: 07/11/2011] [Indexed: 11/16/2022]
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33
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Chen LY. Exploring the free-energy landscapes of biological systems with steered molecular dynamics. Phys Chem Chem Phys 2011; 13:6176-83. [PMID: 21359274 PMCID: PMC3111135 DOI: 10.1039/c0cp02799e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We perform steered molecular dynamics (SMD) simulations and use the Brownian dynamics fluctuation-dissipation-theorem (BD-FDT) to accurately compute the free-energy profiles for several biophysical processes of fundamental importance: hydration of methane and cations, binding of benzene to T4-lysozyme L99A mutant, and permeation of water through aquaglyceroporin. For each system, the center-of-mass of the small molecule (methane, ion, benzene, and water, respectively) is steered (pulled) at a given speed over a period of time, during which the system transitions from one macroscopic state/conformation (State A) to another one (State B). The mechanical work of pulling the system is measured during the process, sampling a forward pulling path. Then the reverse pulling is conducted to sample a reverse path from B back to A. Sampling a small number of forward and reverse paths, we are able to accurately compute the free-energy profiles for all the afore-listed systems that represent various important aspects of biological physics. The numerical results are in excellent agreement with the experimental data and/or other computational studies available in the literature.
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Affiliation(s)
- L Y Chen
- Department of Physics, University of Texas at San Antonio, San Antonio, Texas 78249, USA.
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Hu G, Chen LY. In silico experiments of single-chain antibody fragment against drugs of abuse. Biophys Chem 2010; 153:97-103. [PMID: 21056529 DOI: 10.1016/j.bpc.2010.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/10/2010] [Accepted: 10/12/2010] [Indexed: 11/29/2022]
Abstract
Three sets of in silico experiments have been conducted to elucidate the binding mechanics of two drugs, (+)-methamphetamine (METH) and amphetamine (AMP) to the single-chain variable fragment (scFv) recently engineered from anti-METH monoclonal antibody mAb6H4 (IgG, κlight chain, K(d)=11nM). The first set of in silico experiments are long time equilibration runs of scFv:drug complexes and of drug-free scFv both in the solution. They demonstrate how the solution structures of scFv deviate from its crystallographic form with or without drug molecules bound to it. They lead to the prediction that the Arrhenius activation barrier is nearly zero for transitions from the dissociated state to the bound state. The second set of in silico experiments are nonequilibrium dynamics of pulling the drug molecules out of the binding pocket of scFv and the equilibration runs for drugs to fall back into the binding pocket. They demonstrate that extra water molecules (in addition to the two crystallographic waters) exist inside the binding pocket, underneath the drug molecules. These extra waters must have been evaporated from the binding pockets during the crystallization process of the in vitro experiments of structural determination. The third set of in silico experiments are nonequilibrium steered molecular dynamics simulations to determine the absolute binding free energies of METH and AMP to scFv. The center of mass of a drug molecule (METH or AMP) is steered (pulled) towards (forward) and away from (reverse) the binding site, sampling forward and reverse pulling paths. Mechanic work is measured along the pulling paths. The work measurements are averaged through the Brownian dynamics fluctuation dissipation theorem to produce the free-energy profiles of the scFv:drug complexes as a function of the drug-scFv separation. These experiments lead to the theoretical prediction of absolute binding energies of METH and AMP that are in agreement with the in vitro experimental results.
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Affiliation(s)
- Guodong Hu
- Department of Physics, University of Texas at San Antonio, 78249, USA
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Le L, Lee EH, Hardy DJ, Truong TN, Schulten K. Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases. PLoS Comput Biol 2010; 6. [PMID: 20885781 PMCID: PMC2944783 DOI: 10.1371/journal.pcbi.1000939] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 08/23/2010] [Indexed: 11/19/2022] Open
Abstract
Oseltamivir (Tamiflu) is currently the frontline antiviral drug employed to fight the flu virus in infected individuals by inhibiting neuraminidase, a flu protein responsible for the release of newly synthesized virions. However, oseltamivir resistance has become a critical problem due to rapid mutation of the flu virus. Unfortunately, how mutations actually confer drug resistance is not well understood. In this study, we employ molecular dynamics (MD) and steered molecular dynamics (SMD) simulations, as well as graphics processing unit (GPU)-accelerated electrostatic mapping, to uncover the mechanism behind point mutation induced oseltamivir-resistance in both H5N1 “avian” and H1N1pdm “swine” flu N1-subtype neuraminidases. The simulations reveal an electrostatic binding funnel that plays a key role in directing oseltamivir into and out of its binding site on N1 neuraminidase. The binding pathway for oseltamivir suggests how mutations disrupt drug binding and how new drugs may circumvent the resistance mechanisms. Oseltamivir (Tamiflu) is the main antiviral drug used to fight viral influenza outbreaks such as the recent swine flu (H1N1pdm) global pandemic and avian (H5N1) outbreak in Asia. Oseltamivir inhibits a protein on the surface of flu viruses called neuraminidase, which is responsible for releasing newly formed viruses. The rapid emergence of drug resistance in H5N1 avian flu (and recently the H1N1pdm strain) has already motivated numerous studies to understand how mutations render oseltamivir ineffective, but no focused investigation has yet elucidated the specific mechanism behind mutation-induced drug resistance. Here, large scale computer simulations are employed to study both H5N1 and H1N1pdm neuraminidase to answer the questions: how does N1-subtype neuraminidase bind oseltamivir, and how would mutations alter this process? The key finding revealed in our simulations is the discovery of oseltamivir binding to neuraminidase by a charged pathway on the protein surface. We suggest that point mutations may disrupt drug binding by interfering with this pathway. Our results explain the fundamental mechanism behind oseltamivir resistance and pave the way for the design of drugs that circumvent viral drug resistance.
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Affiliation(s)
- Ly Le
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemistry, University of Utah, Salt Lake City, Utah, United States of America
- School of Biotechnology, Ho Chi Minh International University and Saigon Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Eric H. Lee
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - David J. Hardy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Thanh N. Truong
- Department of Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Klaus Schulten
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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