skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

Journal Article · · Journal of Physical Chemistry Letters
 [1];  [1];  [1];  [1];  [1]
  1. Beckman Institute, and ‡Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Univ. of Illinois at Urbana-Champaign, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1250973
Alternate ID(s):
OSTI ID: 1344922
Journal Information:
Journal of Physical Chemistry Letters, Journal Name: Journal of Physical Chemistry Letters Vol. 7 Journal Issue: 10; ISSN 1948-7185
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 63 works
Citation information provided by
Web of Science

References (77)

Visualization of a missing link in retrovirus capsid assembly journal February 2009
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K a Values journal June 2011
Twenty-five years of nucleic acid simulations journal June 2013
Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field journal September 2014
Virus assembly, allostery and antivirals journal January 2011
Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors journal February 2016
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility journal December 2009
Physical Principles in the Construction of Regular Viruses journal January 1962
Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model journal September 2014
Hepatitis B virus and Homo sapiens proteomewide analysis: A profusion of viral peptide overlaps in neuron-specific human proteins journal April 2010
Compensatory Substitutions in the HIV-1 Capsid Reduce the Fitness Cost Associated with Resistance to a Capsid-Targeting Small-Molecule Inhibitor journal October 2014
Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data journal November 2012
Contributions of Charged Residues in Structurally Dynamic Capsid Surface Loops to Rous Sarcoma Virus Assembly journal April 2016
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics journal May 2013
The SAMPL4 host–guest blind prediction challenge: an overview journal March 2014
A heteroaryldihydropyrimidine activates and can misdirect hepatitis B virus capsid assembly journal May 2005
The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning journal January 2015
Structural basis of HIV-1 capsid recognition by PF74 and CPSF6 journal December 2014
HIV-1 uncoating: connection to nuclear entry and regulation by host proteins journal April 2014
Using Situs for the integration of multi-resolution structures journal January 2010
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing journal November 2012
Computation-Guided Discovery of Influenza Endonuclease Inhibitors journal November 2013
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields journal January 2009
Molecular Architecture of the Retroviral Capsid journal May 2016
MATCH: An atom-typing toolset for molecular mechanics force fields journal November 2011
Classical Electrostatics for Biomolecular Simulations journal August 2013
Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method journal July 2015
X-Ray Structures of the Hexameric Building Block of the HIV Capsid journal June 2009
Rapid parameterization of small molecules using the force field toolkit journal September 2013
Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome journal May 2014
Development and testing of a general amber force field journal January 2004
Small-Molecule Effectors of Hepatitis B Virus Capsid Assembly Give Insight into Virus Life Cycle journal August 2008
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges journal November 2012
HIV-1 assembly, release and maturation journal June 2015
Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion journal February 2015
UCSF Chimera?A visualization system for exploratory research and analysis journal January 2004
Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics journal May 2008
Structural Convergence between Cryo-EM and NMR Reveals Intersubunit Interactions Critical for HIV-1 Capsid Function journal November 2009
Atomic-level modelling of the HIV capsid journal January 2011
Molecular dynamics simulations and drug discovery journal October 2011
Two Pathways Mediate Interdomain Allosteric Regulation in Pin1 journal January 2015
Characterization of Poliovirus Variants Selected for Resistance to the Antiviral Compound V-073 journal August 2012
HIV-1 capsid: the multifaceted key player in HIV-1 infection journal July 2015
The future of molecular dynamics simulations in drug discovery journal December 2011
Neuraminidase Inhibitors for Influenza journal September 2005
Comparative Protein Structure Modeling Using Modeller journal September 2006
Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly journal October 2014
The Future of HIV-1 Therapeutics: Resistance Is Futile? book January 2015
All-atom polarizable force field for DNA based on the classical drude oscillator model journal April 2014
Defining Hsp70 Subnetworks in Dengue Virus Replication Reveals Key Vulnerability in Flavivirus Infection journal November 2015
Global Structural Changes in Hepatitis B Virus Capsids Induced by the Assembly Effector HAP1 journal August 2006
HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention journal December 2010
X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability journal June 2015
Dynamic allostery governs cyclophilin A–HIV capsid interplay journal November 2015
Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins journal August 2013
Macromolecular Modeling with Rosetta journal June 2008
Magic Angle Spinning NMR Reveals Sequence-Dependent Structural Plasticity, Dynamics, and the Spacer Peptide 1 Conformation in HIV-1 Capsid Protein Assemblies journal November 2013
Capsid proteins of enveloped viruses as antiviral drug targets journal April 2014
pH-REMD Simulations Indicate That the Catalytic Aspartates of HIV-1 Protease Exist Primarily in a Monoprotonated State journal October 2014
Molecular dynamics simulations of large macromolecular complexes journal April 2015
Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site journal March 2016
A model for cofactor use during HIV-1 reverse transcription and nuclear entry journal February 2014
Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics journal July 2015
ViennaRNA Package 2.0 journal November 2011
VIPERdb2: an enhanced and web API enabled relational database for structural virology journal January 2009
Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism: Explicit Solvent CPHMD of Proteins journal January 2014
Dynamical networks in tRNA:protein complexes journal April 2009
NetworkView: 3D display and analysis of protein{middle dot}RNA interaction networks journal September 2012
Computational approaches to mapping allosteric pathways journal April 2014
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations journal May 2012
Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis journal August 2015
Rational Prediction with Molecular Dynamics for Hit Identification journal September 2012
Small-Molecule Inhibition of Human Immunodeficiency Virus Type 1 Infection by Virus Capsid Destabilization journal October 2010
Cyclophilin A: a key player for human disease journal October 2013
Systematic Improvement of a Classical Molecular Model of Water journal August 2013
VMD: Visual molecular dynamics journal February 1996
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation journal February 2014