Molecular Dynamics Simulation in Drug Discovery: Opportunities and Challenges

[1]  Matthew H Todd,et al.  Computer-aided organic synthesis. , 2005, Chemical Society reviews.

[2]  Modesto Orozco,et al.  Exploration of conformational transition pathways from coarse-grained simulations , 2013, Bioinform..

[3]  Bruno L. Victor,et al.  Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model. , 2013, Journal of chemical theory and computation.

[4]  E. Tajkhorshid,et al.  Exploring transmembrane diffusion pathways with molecular dynamics. , 2010, Physiology.

[5]  Luís C. Lamb,et al.  Three-dimensional protein structure prediction: Methods and computational strategies , 2014, Comput. Biol. Chem..

[6]  Y. Sugita,et al.  Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments , 2018, Journal of physics. Conference series.

[7]  Nenad Trinajstic,et al.  QSAR of Flavylium Salts as Inhibitors of Xanthine Oxidase , 1998, J. Chem. Inf. Comput. Sci..

[8]  M. Orozco,et al.  Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations. , 2012, Journal of chemical theory and computation.

[9]  A. Laio,et al.  Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science , 2008 .

[10]  Philippe Derreumaux,et al.  High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields. , 2017, The journal of physical chemistry. B.

[11]  Jürgen Schlitter,et al.  Targeted Molecular Dynamics Simulation of Conformational Change-Application to the T ↔ R Transition in Insulin , 1993 .

[12]  I. Bahar,et al.  Coarse-grained normal mode analysis in structural biology. , 2005, Current opinion in structural biology.

[13]  Santosh A. Khedkar,et al.  Successful applications of computer aided drug discovery: moving drugs from concept to the clinic. , 2010, Current topics in medicinal chemistry.

[14]  Anthony Nicholls,et al.  Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures , 2012, J. Chem. Inf. Model..

[15]  Csaba Böde,et al.  Network analysis of protein dynamics , 2007, FEBS letters.

[16]  R. Dror,et al.  How Fast-Folding Proteins Fold , 2011, Science.

[17]  Ville R. I. Kaila,et al.  Conformational processing of oncogenic v-Src kinase by the molecular chaperone Hsp90 , 2015, Proceedings of the National Academy of Sciences.

[18]  T. Tripathi,et al.  Structural basis of urea‐induced unfolding of Fasciola gigantica glutathione S‐transferase , 2018, Journal of cellular physiology.

[19]  Charlotte M. Deane,et al.  Exploring the potential of template-based modelling , 2010, Bioinform..

[20]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.

[21]  Richard Bonneau,et al.  Ab initio protein structure prediction: progress and prospects. , 2001, Annual review of biophysics and biomolecular structure.

[22]  John Moult,et al.  A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. , 2005, Current opinion in structural biology.

[23]  Ron O. Dror,et al.  Molecular Dynamics Simulation for All , 2018, Neuron.

[24]  G. Parisi,et al.  Simulated tempering: a new Monte Carlo scheme , 1992, hep-lat/9205018.

[25]  B. Talin,et al.  Classical molecular dynamics simulations of hydrogen plasmas and development of an analytical statistical model for computational validity assessment , 2018, Physical Review E.

[26]  Daniel R. Roe,et al.  Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations , 2016, J. Chem. Inf. Model..

[27]  Stefano Piana,et al.  Refinement of protein structure homology models via long, all‐atom molecular dynamics simulations , 2012, Proteins.

[28]  Ryan Day,et al.  All-atom simulations of protein folding and unfolding. , 2003, Advances in protein chemistry.

[29]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[30]  Michelle L Coote,et al.  Molecular dynamics-driven drug discovery: leaping forward with confidence. , 2017, Drug discovery today.

[31]  Yang Zhang,et al.  I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.

[32]  Diwakar Shukla,et al.  To milliseconds and beyond: challenges in the simulation of protein folding. , 2013, Current opinion in structural biology.

[33]  Y. Sugita,et al.  Replica-exchange molecular dynamics method for protein folding , 1999 .

[34]  M. Mckee,et al.  Estimated Research and Development Investment Needed to Bring a New Medicine to Market, 2009-2018. , 2020, JAMA.

[35]  Sonya M. Hanson,et al.  Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation , 2015, Biophysical journal.

[36]  T. Tripathi,et al.  Structure-function studies of the asparaginyl-tRNA synthetase from Fasciola gigantica: understanding the role of catalytic and non-catalytic domains. , 2018, The Biochemical journal.

[37]  G. Hummer,et al.  Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations. , 2018, The journal of physical chemistry letters.

[38]  T. Tripathi,et al.  Unfolding of Acinetobacter baumannii MurA proceeds through a metastable intermediate: A combined spectroscopic and computational investigation. , 2019, International journal of biological macromolecules.

[39]  T. Šolmajer,et al.  Targeted molecular dynamics simulation studies of binding and conformational changes in E. coli MurD , 2007, Proteins.

[40]  Keehyoung Joo,et al.  High accuracy template based modeling by global optimization , 2007, Proteins.

[41]  Anton Arkhipov,et al.  Architecture and Membrane Interactions of the EGF Receptor , 2013, Cell.

[42]  Victor Guallar,et al.  PELE:  Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique. , 2005, Journal of chemical theory and computation.

[43]  Modesto Orozco,et al.  MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. , 2010, Structure.

[44]  Vincent A. Voelz,et al.  Computational Screening and Selection of Cyclic Peptide Hairpin Mimetics by Molecular Simulation and Kinetic Network Models , 2014, J. Chem. Inf. Model..

[45]  T Darden,et al.  New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. , 1999, Structure.

[46]  Hongtao Yu,et al.  Toward accurately modeling N-methylated cyclic peptides. , 2017, Physical chemistry chemical physics : PCCP.

[47]  D. Koshland Application of a Theory of Enzyme Specificity to Protein Synthesis. , 1958, Proceedings of the National Academy of Sciences of the United States of America.

[48]  R. Glen,et al.  Molecular similarity: a key technique in molecular informatics. , 2004, Organic & biomolecular chemistry.

[49]  J. Trylska,et al.  Molecular dynamics simulations suggest why the A2058G mutation in 23S RNA results in bacterial resistance against clindamycin , 2018, Journal of Molecular Modeling.

[50]  Corwin Hansch,et al.  Camptothecins: a SAR/QSAR study. , 2009, Chemical reviews.

[51]  T. Tripathi,et al.  Activity loss by H46A mutation in Mycobacterium tuberculosis isocitrate lyase is due to decrease in structural plasticity and collective motions of the active site. , 2018, Tuberculosis.

[52]  R. Kumari,et al.  Mycobacterium tuberculosis nucleoside diphosphate kinase shows interaction with putative ATP binding cassette (ABC) transporter, Rv1273c , 2020, Journal of biomolecular structure & dynamics.

[53]  M. Karplus,et al.  Dynamics of folded proteins , 1977, Nature.

[54]  P. Derreumaux,et al.  Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction. , 2014, Journal of chemical theory and computation.

[55]  Julio C. Facelli,et al.  iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment , 2013, J. Chem. Inf. Model..

[56]  Taehoon Kim,et al.  CHARMM‐GUI: A web‐based graphical user interface for CHARMM , 2008, J. Comput. Chem..

[57]  D. LeMaster,et al.  Statistical allosteric coupling to the active site indole ring flip equilibria in the FK506-binding domain. , 2014, Biophysical chemistry.

[58]  T. Tripathi,et al.  Structural insights into natural compounds as inhibitors of Fasciola gigantica thioredoxin glutathione reductase , 2018, Journal of cellular biochemistry.

[59]  D. P. Vercauteren,et al.  Reduced Point Charge Models of Proteins: Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems. , 2017, The journal of physical chemistry. B.

[60]  J. Kästner Umbrella sampling , 2011 .

[61]  Nenad Trinajstic,et al.  The Use of the Ordered Orthogonalized Multivariate Linear Regression in a Structure-Activity Study of Coumarin and Flavonoid Derivatives as Inhibitors of Aldose Reductase , 1997, J. Chem. Inf. Comput. Sci..

[62]  V. Mordvinov,et al.  Identification of novel natural inhibitors of Opisthorchis felineus cytochrome P450 using structure-based screening and molecular dynamic simulation , 2018, Journal of biomolecular structure & dynamics.

[63]  Alexander D. MacKerell,et al.  Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. , 2011, Current computer-aided drug design.

[64]  D. Koshland,et al.  Comparison of experimental binding data and theoretical models in proteins containing subunits. , 1966, Biochemistry.

[65]  S. Genheden,et al.  The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities , 2015, Expert opinion on drug discovery.

[66]  J. Changeux,et al.  ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL. , 1965, Journal of molecular biology.

[67]  Rohit Shukla,et al.  Structure-based screening and molecular dynamics simulations offer novel natural compounds as potential inhibitors of Mycobacterium tuberculosis isocitrate lyase , 2018, Journal of biomolecular structure & dynamics.

[68]  K. Misura,et al.  PROTEINS: Structure, Function, and Bioinformatics 59:15–29 (2005) Progress and Challenges in High-Resolution Refinement of Protein Structure Models , 2022 .

[69]  Hongtao Yu,et al.  Mapping the sequence-structure relationships of simple cyclic hexapeptides. , 2017, Physical chemistry chemical physics : PCCP.

[70]  Mateusz Z. Brela,et al.  Born-Oppenheimer Molecular Dynamics Study on Proton Dynamics of Strong Hydrogen Bonds in Aspirin Crystals, with Emphasis on Differences between Two Crystal Forms. , 2016, The journal of physical chemistry. B.

[71]  Rohit Shukla,et al.  Alterations in conformational topology and interaction dynamics caused by L418A mutation leads to activity loss of Mycobacterium tuberculosis isocitrate lyase. , 2017, Biochemical and biophysical research communications.

[72]  Yang Zhang Protein structure prediction: when is it useful? , 2009, Current opinion in structural biology.

[73]  J Andrew McCammon,et al.  Discovery of a novel binding trench in HIV integrase. , 2004, Journal of medicinal chemistry.

[74]  Dev Bukhsh Singh,et al.  Identification of potential inhibitors of Fasciola gigantica thioredoxin1: computational screening, molecular dynamics simulation, and binding free energy studies , 2018, Journal of biomolecular structure & dynamics.

[75]  Modesto Orozco,et al.  Approaching Elastic Network Models to Molecular Dynamics Flexibility. , 2010, Journal of chemical theory and computation.

[76]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[77]  P. Declerck,et al.  Extending the capabilities of targeted molecular dynamics: Simulation of a large conformational transition in plasminogen activator inhibitor 1 , 2001, Protein science : a publication of the Protein Society.

[78]  T. Tripathi,et al.  A combined biochemical and computational studies of the rho-class glutathione s-transferase sll1545 of Synechocystis PCC 6803. , 2017, International journal of biological macromolecules.

[79]  Philip M. Kim,et al.  Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights , 2006, Science.

[80]  J. Changeux,et al.  Allosteric proteins and cellular control systems. , 1963, Journal of molecular biology.

[81]  H. Villar,et al.  Strategies for Indirect Computer-Aided Drug Design , 1993, Pharmaceutical Research.

[82]  R. Dror,et al.  Long-timescale molecular dynamics simulations of protein structure and function. , 2009, Current opinion in structural biology.

[83]  K. Lindorff-Larsen,et al.  Atomic-level description of ubiquitin folding , 2013, Proceedings of the National Academy of Sciences.

[84]  Sheng-Yong Yang,et al.  Pharmacophore modeling and applications in drug discovery: challenges and recent advances. , 2010, Drug discovery today.

[85]  Arne Elofsson,et al.  3D-Jury: A Simple Approach to Improve Protein Structure Predictions , 2003, Bioinform..

[86]  V. Daggett,et al.  Long timescale simulations. , 2000, Current opinion in structural biology.

[87]  Yuko Okamoto,et al.  Communication: Simulated tempering with fast on-the-fly weight determination. , 2013, The Journal of chemical physics.

[88]  Yuguang Mu,et al.  Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. , 2015, The journal of physical chemistry. B.

[89]  T. Tripathi,et al.  Molecular Dynamics Simulation of Protein and Protein–Ligand Complexes , 2020 .

[90]  Bertrand Caron,et al.  Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane. , 2018, Journal of chemical theory and computation.

[91]  Yuni Xia,et al.  DCMS: A data analytics and management system for molecular simulation , 2014, Journal of Big Data.

[92]  Comprehensive analysis of the catalytic and structural properties of a mu-class glutathione s-transferase from Fasciola gigantica , 2017, Scientific Reports.

[93]  Yoshinobu Ishikawa,et al.  A Script for Automated 3-Dimentional Structure Generation and Conformer Search from 2- Dimentional Chemical Drawing , 2013, Bioinformation.

[94]  Klaus Schulten,et al.  Challenges in protein-folding simulations , 2010 .

[95]  C. Zhang,et al.  Comparison of sampling efficiency between simulated tempering and replica exchange. , 2008, The Journal of chemical physics.

[96]  T. Tripathi,et al.  Identification and characterization of glyceraldehyde 3-phosphate dehydrogenase from Fasciola gigantica , 2019, Parasitology Research.

[97]  A. Good,et al.  3-D pharmacophores in drug discovery. , 2001, Current pharmaceutical design.

[98]  Jacob D. Durrant,et al.  Molecular dynamics simulations and drug discovery , 2011, BMC Biology.

[99]  Yang Hong,et al.  A comprehensive review on the molecular dynamics simulation of the novel thermal properties of graphene , 2015 .

[100]  Rohit Shukla,et al.  Distant Phe345 mutation compromises the stability and activity of Mycobacterium tuberculosis isocitrate lyase by modulating its structural flexibility , 2017, Scientific Reports.

[101]  Denis Noble,et al.  Will genomics revolutionise pharmaceutical R&D? , 2003, Trends in Biotechnology.

[102]  Mai Suan Li,et al.  Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ(16-22) dimer and trimer. , 2011, Physical chemistry chemical physics : PCCP.

[103]  S. Moro,et al.  Understanding allosteric interactions in G protein-coupled receptors using Supervised Molecular Dynamics: A prototype study analysing the human A3 adenosine receptor positive allosteric modulator LUF6000. , 2015, Bioorganic & medicinal chemistry.

[104]  Kresten Lindorff-Larsen,et al.  Protein folding kinetics and thermodynamics from atomistic simulation , 2012, Proceedings of the National Academy of Sciences.

[105]  D. M. F. Aalten,et al.  PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules , 1996, J. Comput. Aided Mol. Des..

[106]  Mark A. Wilson,et al.  Intrinsic motions along an enzymatic reaction trajectory , 2007, Nature.

[107]  A. Laio,et al.  Flexible docking in solution using metadynamics. , 2005, Journal of the American Chemical Society.

[108]  Markus Wagener,et al.  A flexible approach to induced fit docking. , 2007, Journal of medicinal chemistry.

[109]  Jitender Verma,et al.  3D-QSAR in drug design--a review. , 2010, Current topics in medicinal chemistry.

[110]  Kresten Lindorff-Larsen,et al.  Comparing Molecular Dynamics Force Fields in the Essential Subspace , 2015, PloS one.

[111]  G. Chirikjian,et al.  Efficient generation of feasible pathways for protein conformational transitions. , 2002, Biophysical journal.