Rational Drug Design Via Molecular Dynamics Simulations of HIV-1 Protease Inhibitor Complexes

1991 ◽  
Author(s):  
W. Guba ◽  
H. Kessler ◽  
G. Muller
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Protease Inhibitor ◽  
Molecular Dynamics Simulations ◽  
Rational Drug Design ◽  
Rational Drug ◽  
Dynamics Simulations ◽  
Hiv 1

Molecular Dynamics Simulations on the Bioactive Molecule of hIAPP22–29 (NFGAILSS) and Rational Drug Design

2018 ◽  
pp. 1-16
Author(s):  
Panagiotis Lagarias ◽  
Youness Elkhou ◽  
Jayson Vedad ◽  
Athina Konstantinidi ◽  
Adam A. Profit ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Molecular Dynamics Simulations ◽  
Rational Drug Design ◽  
Rational Drug ◽  
Bioactive Molecule ◽  
Dynamics Simulations

Restrained molecular dynamics simulations of HIV-1 protease: The first step in validating a new target for drug design

Biopolymers ◽  
2006 ◽  
Vol 82 (3) ◽  
pp. 272-284 ◽  
Author(s):  
Alexander L. Perryman ◽  
Jung-Hsin Lin ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Hiv 1 ◽  
Restrained Molecular Dynamics

scholarly journals Molecular Dynamics Simulations of the First Steps of the Reaction Catalyzed by HIV-1 Protease

2002 ◽  
Vol 83 (2) ◽  
pp. 794-807 ◽  
Author(s):  
Joanna Trylska ◽  
Piotr Bała ◽  
Maciej Geller ◽  
Paweł Grochowski
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Hiv 1

scholarly journals Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations

2018 ◽  
Vol 115 (45) ◽  
pp. 11519-11524 ◽  
Author(s):  
Caitlin M. Quinn ◽  
Mingzhang Wang ◽  
Matthew P. Fritz ◽  
Brent Runge ◽  
Jinwoo Ahn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Building Blocks ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Capsid Assembly ◽  
Dynamic Regulation ◽  
Angle Spinning ◽  
Dynamics Simulations ◽  
Hiv 1

The host factor protein TRIM5α plays an important role in restricting the host range of HIV-1, interfering with the integrity of the HIV-1 capsid. TRIM5 triggers an antiviral innate immune response by functioning as a capsid pattern recognition receptor, although the precise mechanism by which the restriction is imposed is not completely understood. Here we used an integrated magic-angle spinning nuclear magnetic resonance and molecular dynamics simulations approach to characterize, at atomic resolution, the dynamics of the capsid’s hexameric and pentameric building blocks, and the interactions with TRIM5α in the assembled capsid. Our data indicate that assemblies in the presence of the pentameric subunits are more rigid on the microsecond to millisecond timescales than tubes containing only hexamers. This feature may be of key importance for controlling the capsid’s morphology and stability. In addition, we found that TRIM5α binding to capsid induces global rigidification and perturbs key intermolecular interfaces essential for higher-order capsid assembly, with structural and dynamic changes occurring throughout the entire CA polypeptide chain in the assembly, rather than being limited to a specific protein-protein interface. Taken together, our results suggest that TRIM5α uses several mechanisms to destabilize the capsid lattice, ultimately inducing its disassembly. Our findings add to a growing body of work indicating that dynamic allostery plays a pivotal role in capsid assembly and HIV-1 infectivity.

scholarly journals Pressure induced structural changes and dimer destabilization of HIV-1 protease studied by molecular dynamics simulations

2014 ◽  
Vol 16 (47) ◽  
pp. 25906-25915 ◽  
Author(s):  
Eva Kutálková ◽  
Josef Hrnčiřík ◽  
Marek Ingr
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Changes ◽  
Dynamics Simulations ◽  
Hiv 1

scholarly journals Hybrid Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of HIV-1 Integrase/Inhibitor Complexes

2007 ◽  
Vol 93 (10) ◽  
pp. 3613-3626 ◽  
Author(s):  
Nadtanet Nunthaboot ◽  
Somsak Pianwanit ◽  
Vudhichai Parasuk ◽  
Jerry O. Ebalunode ◽  
James M. Briggs ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Integrase Inhibitor ◽  
Quantum Mechanical ◽  
Dynamics Simulations ◽  
Hiv 1
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