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

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

doi:10.1007/978-3-642-03882-2_165

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

Civil and Environmental Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Scopus citations

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 language	English (US)
Title of host publication	World Congress on Medical Physics and Biomedical Engineering
Subtitle of host publication	Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics
Publisher	Springer Verlag
Pages	623-625
Number of pages	3
Edition	4
ISBN (Print)	9783642038815
DOIs	https://doi.org/10.1007/978-3-642-03882-2_165
State	Published - 2009
Event	World Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics - Munich, Germany Duration: Sep 7 2009 → Sep 12 2009

Publication series

Name	IFMBE Proceedings
Number	4
Volume	25
ISSN (Print)	1680-0737

Other

Other	World Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics
Country/Territory	Germany
City	Munich
Period	9/7/09 → 9/12/09

Keywords

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

ASJC Scopus subject areas

Bioengineering
Biomedical Engineering

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1007/978-3-642-03882-2_165

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). Springer Verlag. https://doi.org/10.1007/978-3-642-03882-2_165

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title = "Coarse-grained molecular dynamics of inhibitors binding into HIV-1 protease",

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.",

keywords = "Binding free energy, Coarse-grained dynamics, HIV-1 protease, Inhibition, Ligands binding",

author = "Dechang Li and Baohua Ji and Liu, {Ming S.} and Hwang, {K. C.} and Yonggang Huang",

note = "Copyright: Copyright 2021 Elsevier B.V., All rights reserved.; World Congress on Medical Physics and Biomedical Engineering: Image Processing, Biosignal Processing, Modelling and Simulation, Biomechanics ; Conference date: 07-09-2009 Through 12-09-2009",

year = "2009",

doi = "10.1007/978-3-642-03882-2_165",

language = "English (US)",

isbn = "9783642038815",

series = "IFMBE Proceedings",

publisher = "Springer Verlag",

number = "4",

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booktitle = "World Congress on Medical Physics and Biomedical Engineering",

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

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - Coarse-grained molecular dynamics of inhibitors binding into HIV-1 protease

AU - Li, Dechang

AU - Ji, Baohua

AU - Liu, Ming S.

AU - Hwang, K. C.

AU - Huang, Yonggang

PY - 2009

Y1 - 2009

N2 - 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.

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.

KW - Binding free energy

KW - Coarse-grained dynamics

KW - HIV-1 protease

KW - Inhibition

KW - Ligands binding

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Y2 - 7 September 2009 through 12 September 2009

ER -

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

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Keywords

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UN SDGs

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