Coarse-grained molecular dynamics of inhibitors binding into HIV-1 protease

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

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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 (HIV-1 PR). It shows that the coarse-grained dynamics, in consistent with the experimental results, can capture the essential binding dynamics of inhibitors into protease. The primary driving force for the binding processes is the non-bond interaction between inhibitors and PR. Meanwhile, the interacting strength between inhibitors and protease, have great influence on the binding processes. This study also provides important guidelines for design of novel inhibitors with optimized binding pathway and fast binding kinetics.

Original languageEnglish (US)
Title of host publicationWorld Congress on Medical Physics and Biomedical Engineering
Subtitle of host publicationImage Processing, Biosignal Processing, Modelling and Simulation, Biomechanics
Pages623-625
Number of pages3
Edition4
DOIs
StatePublished - Dec 1 2009
EventWorld Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics - Munich, Germany
Duration: Sep 7 2009Sep 12 2009

Publication series

NameIFMBE Proceedings
Number4
Volume25
ISSN (Print)1680-0737

Other

OtherWorld Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics
CountryGermany
CityMunich
Period9/7/099/12/09

Fingerprint

Molecular dynamics
Peptide Hydrolases
Protease Inhibitors
Viruses
Kinetics
Human immunodeficiency virus 1 p16 protease

Keywords

  • Binding free energy
  • Coarse-grained dynamics
  • HIV-1 protease
  • Inhibition
  • Ligands binding

ASJC Scopus subject areas

  • Bioengineering
  • Biomedical Engineering

Cite this

Li, D., Ji, B., Liu, M. S., Hwang, K. C., & Huang, Y. (2009). Coarse-grained molecular dynamics of inhibitors binding into HIV-1 protease. In World Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics (4 ed., pp. 623-625). (IFMBE Proceedings; Vol. 25, No. 4). https://doi.org/10.1007/978-3-642-03882-2-165
Li, Dechang ; Ji, Baohua ; Liu, Ming S. ; Hwang, K. C. ; Huang, Yonggang. / Coarse-grained molecular dynamics of inhibitors binding into HIV-1 protease. World Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics. 4. ed. 2009. pp. 623-625 (IFMBE Proceedings; 4).
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keywords = "Binding free energy, Coarse-grained dynamics, HIV-1 protease, Inhibition, Ligands binding",
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Li, D, Ji, B, Liu, MS, Hwang, KC & Huang, Y 2009, Coarse-grained molecular dynamics of inhibitors binding into HIV-1 protease. in World Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics. 4 edn, IFMBE Proceedings, no. 4, vol. 25, pp. 623-625, World Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics, Munich, Germany, 9/7/09. https://doi.org/10.1007/978-3-642-03882-2-165

Coarse-grained molecular dynamics of inhibitors binding into HIV-1 protease. / Li, Dechang; Ji, Baohua; Liu, Ming S.; Hwang, K. C.; Huang, Yonggang.

World Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics. 4. ed. 2009. p. 623-625 (IFMBE Proceedings; Vol. 25, No. 4).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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AB - 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 (HIV-1 PR). It shows that the coarse-grained dynamics, in consistent with the experimental results, can capture the essential binding dynamics of inhibitors into protease. The primary driving force for the binding processes is the non-bond interaction between inhibitors and PR. Meanwhile, the interacting strength between inhibitors and protease, have great influence on the binding processes. This study also provides important guidelines for design of novel inhibitors with optimized binding pathway and fast binding kinetics.

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Li D, Ji B, Liu MS, Hwang KC, Huang Y. Coarse-grained molecular dynamics of inhibitors binding into HIV-1 protease. In World Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics. 4 ed. 2009. p. 623-625. (IFMBE Proceedings; 4). https://doi.org/10.1007/978-3-642-03882-2-165