Coarse-grained molecular dynamics of ligands binding into protein

The case of HIV-1 protease inhibitors

Dechang Li, Ming S. Liu, Baohua Ji*, Kehchih Hwang, Yonggang Huang

*Corresponding author for this work

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Binding dynamics and pathways of ligands or inhibitors to target proteins are challenging both experimental and theoretical biologists. A dynamics understanding of inhibitors interacting with protein is essential for the design of novel potent drugs. In this work we applied a coarse-grained molecular dynamics method for simulating inhibitors entering the binding cavity of human immunodeficiency virus type 1 protease (PR). It shows that the coarse-grained dynamics, consistent with the experimental results, can capture the essential molecular dynamics of various inhibitors binding into PR. The primary driving force for the binding processes is the nonbond interaction between inhibitors and PR. The size and topology of inhibitors and the interacting strength between inhibitors and PR have great influence on the binding mode and processes. The interaction strength between the PR and various inhibitors is also analyzed by atomistic molecular mechanics and Poisson-Boltzmann solvation area method.

Original languageEnglish (US)
Article number215102
JournalJournal of Chemical Physics
Volume130
Issue number21
DOIs
StatePublished - Jun 22 2009

Fingerprint

protease
human immunodeficiency virus
Protease Inhibitors
inhibitors
Molecular dynamics
molecular dynamics
Ligands
proteins
ligands
Peptide Hydrolases
Molecular mechanics
Solvation
Viruses
Proteins
Topology
Pharmaceutical Preparations
Human immunodeficiency virus 1 p16 protease
Carrier Proteins
solvation
drugs

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

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title = "Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors",
abstract = "Binding dynamics and pathways of ligands or inhibitors to target proteins are challenging both experimental and theoretical biologists. A dynamics understanding of inhibitors interacting with protein is essential for the design of novel potent drugs. In this work we applied a coarse-grained molecular dynamics method for simulating inhibitors entering the binding cavity of human immunodeficiency virus type 1 protease (PR). It shows that the coarse-grained dynamics, consistent with the experimental results, can capture the essential molecular dynamics of various inhibitors binding into PR. The primary driving force for the binding processes is the nonbond interaction between inhibitors and PR. The size and topology of inhibitors and the interacting strength between inhibitors and PR have great influence on the binding mode and processes. The interaction strength between the PR and various inhibitors is also analyzed by atomistic molecular mechanics and Poisson-Boltzmann solvation area method.",
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Coarse-grained molecular dynamics of ligands binding into protein : The case of HIV-1 protease inhibitors. / Li, Dechang; Liu, Ming S.; Ji, Baohua; Hwang, Kehchih; Huang, Yonggang.

In: Journal of Chemical Physics, Vol. 130, No. 21, 215102, 22.06.2009.

Research output: Contribution to journalArticle

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AU - Li, Dechang

AU - Liu, Ming S.

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AU - Hwang, Kehchih

AU - Huang, Yonggang

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AB - Binding dynamics and pathways of ligands or inhibitors to target proteins are challenging both experimental and theoretical biologists. A dynamics understanding of inhibitors interacting with protein is essential for the design of novel potent drugs. In this work we applied a coarse-grained molecular dynamics method for simulating inhibitors entering the binding cavity of human immunodeficiency virus type 1 protease (PR). It shows that the coarse-grained dynamics, consistent with the experimental results, can capture the essential molecular dynamics of various inhibitors binding into PR. The primary driving force for the binding processes is the nonbond interaction between inhibitors and PR. The size and topology of inhibitors and the interacting strength between inhibitors and PR have great influence on the binding mode and processes. The interaction strength between the PR and various inhibitors is also analyzed by atomistic molecular mechanics and Poisson-Boltzmann solvation area method.

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