Molecular dynamics simulations and drug discovery

被引:802
|
作者
Durrant, Jacob D. [1 ]
McCammon, J. Andrew [1 ,2 ,3 ]
机构
[1] Univ Calif San Diego, Dept Chem & Biochem, NSF Ctr Theoret Biol Phys, La Jolla, CA 92093 USA
[2] Univ Calif San Diego, Dept Pharmacol, La Jolla, CA 92093 USA
[3] Univ Calif San Diego, Howard Hughes Med Inst, La Jolla, CA 92093 USA
来源
BMC BIOLOGY | 2011年 / 9卷
关键词
molecular dynamics simulations; computer-aided; drug discovery; cryptic binding sites; allosteric binding sites; virtual screening; free-energy prediction; FREE-ENERGY CALCULATIONS; ACCOMMODATING RECEPTOR FLEXIBILITY; GRAPHICS PROCESSING UNITS; RELAXED COMPLEX SCHEME; BINDING FREE-ENERGIES; RNA-EDITING LIGASE; TRYPANOSOMA-BRUCEI; FOLDING FUNNELS; FORCE-FIELD; BIOMOLECULAR SIMULATION;
D O I
10.1186/1741-7007-9-71
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
This review discusses the many roles atomistic computer simulations of macromolecular (for example, protein) receptors and their associated small-molecule ligands can play in drug discovery, including the identification of cryptic or allosteric binding sites, the enhancement of traditional virtual-screening methodologies, and the direct prediction of small-molecule binding energies. The limitations of current simulation methodologies, including the high computational costs and approximations of molecular forces required, are also discussed. With constant improvements in both computer power and algorithm design, the future of computer-aided drug design is promising; molecular dynamics simulations are likely to play an increasingly important role.
引用
收藏
页数:9
相关论文
共 50 条
  • [1] Molecular dynamics simulations and drug discovery
    Jacob D Durrant
    J Andrew McCammon
    [J]. BMC Biology, 9
  • [2] Molecular Dynamics Simulations in Drug Discovery
    Nascimento, Igor Jose dos Santos
    de Moura, Ricardo Olimpio
    [J]. MINI-REVIEWS IN MEDICINAL CHEMISTRY, 2024, 24 (11) : 1061 - 1062
  • [3] Molecular dynamics simulations and novel drug discovery
    Liu, Xuewei
    Shi, Danfeng
    Zhou, Shuangyan
    Liu, Hongli
    Liu, Huanxiang
    Yao, Xiaojun
    [J]. EXPERT OPINION ON DRUG DISCOVERY, 2018, 13 (01) : 23 - 37
  • [4] The future of molecular dynamics simulations in drug discovery
    David W. Borhani
    David E. Shaw
    [J]. Journal of Computer-Aided Molecular Design, 2012, 26 : 15 - 26
  • [5] The future of molecular dynamics simulations in drug discovery
    Borhani, David W.
    Shaw, David E.
    [J]. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2012, 26 (01) : 15 - 26
  • [6] Molecular dynamics simulations of protein dynamics and their relevance to drug discovery
    Salsbury, Freddie R., Jr.
    [J]. CURRENT OPINION IN PHARMACOLOGY, 2010, 10 (06) : 738 - 744
  • [7] The Multifaceted Roles of Molecular Dynamics Simulations in Drug Discovery
    Fox, Stephen John
    Li, Jianguo
    Tan, Yaw Sing
    Nguyen, Minh N.
    Pal, Arumay
    Ouaray, Zohra
    Yadahalli, Shilpa
    Kannan, Srinivasaraghavan
    [J]. CURRENT PHARMACEUTICAL DESIGN, 2016, 22 (23) : 3585 - 3600
  • [8] Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
    Salo-Ahen, Outi M. H.
    Alanko, Ida
    Bhadane, Rajendra
    Bonvin, Alexandre M. J. J.
    Honorato, Rodrigo Vargas
    Hossain, Shakhawath
    Juffer, Andre H.
    Kabedev, Aleksei
    Lahtela-Kakkonen, Maija
    Larsen, Anders Stottrup
    Lescrinier, Eveline
    Marimuthu, Parthiban
    Mirza, Muhammad Usman
    Mustafa, Ghulam
    Nunes-Alves, Ariane
    Pantsar, Tatu
    Saadabadi, Atefeh
    Singaravelu, Kalaimathy
    Vanmeert, Michiel
    [J]. PROCESSES, 2021, 9 (01) : 1 - 63
  • [9] Use of molecular dynamics simulations in structure based drug discovery
    Friesner, Richard
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2017, 253
  • [10] Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery
    Bera, Indrani
    Payghan, Pavan, V
    [J]. CURRENT PHARMACEUTICAL DESIGN, 2019, 25 (31) : 3339 - 3349