scholarly journals molecular dynamics in drug design

2008 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Drug Design

Molecular dynamics in drug design

2015 ◽  
Vol 91 ◽  
pp. 4-14 ◽  
Author(s):  
Hongtao Zhao ◽  
Amedeo Caflisch
Keyword(s):  
Molecular Dynamics ◽  
Drug Design

A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling, docking, de novo drug design and molecular dynamics analysis

2009 ◽  
Vol 14 (2) ◽  
pp. 257-276 ◽  
Author(s):  
Serdar Durdagi ◽  
Manthos G. Papadopoulos ◽  
Panagiotis G. Zoumpoulakis ◽  
Catherine Koukoulitsa ◽  
Thomas Mavromoustakos
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Homology Modeling ◽  
Cannabinoid Receptors ◽  
De Novo ◽  
Computational Study ◽  
Dynamics Analysis ◽  
De Novo Drug Design

scholarly journals Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

2021 ◽  
Vol 14 (10) ◽  
pp. 1062
Author(s):  
Tomasz Róg ◽  
Mykhailo Girych ◽  
Alex Bunker
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Active Site ◽  
Lipid Membranes ◽  
Md Simulation ◽  
Lipid Membrane ◽  
Pharmaceutical Research ◽  
Specific Protein ◽  
Design Tool ◽  
Drug Molecules

We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard “lock and key” paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

scholarly journals Molecular insights into the improved clinical performance of PEGylated interferon therapeutics: a molecular dynamics perspective

RSC Advances ◽  
2018 ◽  
Vol 8 (5) ◽  
pp. 2315-2322 ◽  
Author(s):  
Dong Xu ◽  
Nikolai Smolin ◽  
Rance K. Shaw ◽  
Samuel R. Battey ◽  
Aoxiang Tao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Therapeutic Efficacy ◽  
Clinical Performance ◽  
Pegylated Interferon ◽  
Computational Approach ◽  
Molecular Evidence ◽  
Protein Drug ◽  
Pegylated Protein

We discovered molecular evidence that links PEGylation to improved clinical performance, yet at the expense of decreased bioactivity. Our computational approach will facilitate PEGylated protein drug design and optimize its overall therapeutic efficacy.

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