Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design

2012 ◽  
Vol 8 (7) ◽  
pp. 2204-2214 ◽  
Author(s):  
Rima Chaudhuri ◽  
Oliver Carrillo ◽  
Charles Anthony Laughton ◽  
Modesto Orozco
Keyword(s):  
Molecular Dynamics ◽  
Virtual Screening ◽  
Drug Design ◽  
Rational Drug Design ◽  
Essential Dynamics ◽  
Rational Drug

scholarly journals Discovery of novel aminopiperidinyl amide CXCR4 modulators through virtual screening and rational drug design

2020 ◽  
Vol 201 ◽  
pp. 112479 ◽  
Author(s):  
Yoon Hyeun Oum ◽  
Steven A. Kell ◽  
Younghyoun Yoon ◽  
Zhongxing Liang ◽  
Pieter Burger ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Drug Design ◽  
Rational Drug Design ◽  
Rational Drug

scholarly journals A Novel Approach for Computer-Aided “Rational” Drug Design: Theoretical and Experimental Assessment of a Promising Method for Virtual Screening and in silico Design of New Antimalarial Compounds

2005 ◽  
Author(s):  
Yovani Marrero-Ponce ◽  
Alina Montero-Torres ◽  
Maité Iyarreta-Veitía ◽  
Carlos Romero-Zaldivar ◽  
Carlos Brandt ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Drug Design ◽  
In Silico ◽  
Rational Drug Design ◽  
Promising Method ◽  
Experimental Assessment ◽  
In Silico Design ◽  
Novel Approach ◽  
Rational Drug ◽  
Computer Aided

scholarly journals Rational Drug Design of Antineoplastic Agents Using 3D-QSAR, Cheminformatic, and Virtual Screening Approaches

2019 ◽  
Vol 26 (21) ◽  
pp. 3874-3889 ◽  
Author(s):  
Jelica Vucicevic ◽  
Katarina Nikolic ◽  
John B.O. Mitchell
Keyword(s):  
Virtual Screening ◽  
Drug Design ◽  
Antineoplastic Agents ◽  
Drug Targets ◽  
3D Qsar ◽  
Pharmacophore Modeling ◽  
Rational Drug Design ◽  
Bioactive Molecules ◽  
Computational Approaches ◽  
Rational Drug

Background: Computer-Aided Drug Design has strongly accelerated the development of novel antineoplastic agents by helping in the hit identification, optimization, and evaluation. Results: Computational approaches such as cheminformatic search, virtual screening, pharmacophore modeling, molecular docking and dynamics have been developed and applied to explain the activity of bioactive molecules, design novel agents, increase the success rate of drug research, and decrease the total costs of drug discovery. Similarity, searches and virtual screening are used to identify molecules with an increased probability to interact with drug targets of interest, while the other computational approaches are applied for the design and evaluation of molecules with enhanced activity and improved safety profile. Conclusion: In this review are described the main in silico techniques used in rational drug design of antineoplastic agents and presented optimal combinations of computational methods for design of more efficient antineoplastic drugs.

scholarly journals Virtual screening following rational drug design based approach for introducing new anti amyloid beta aggregation agent

2017 ◽  
Vol 13 (02) ◽  
pp. 42-45 ◽  
Author(s):  
Garshasb Rigi ◽  
◽  
Mohammad Vala Ashdar Nakhaei ◽  
Hoda Eidipour ◽  
Arshia Najimi ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Drug Design ◽  
Amyloid Beta ◽  
Rational Drug Design ◽  
Rational Drug

Molecular Dynamics Simulations on the Bioactive Molecule of hIAPP22–29 (NFGAILSS) and Rational Drug Design

2018 ◽  
pp. 1-16
Author(s):  
Panagiotis Lagarias ◽  
Youness Elkhou ◽  
Jayson Vedad ◽  
Athina Konstantinidi ◽  
Adam A. Profit ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Molecular Dynamics Simulations ◽  
Rational Drug Design ◽  
Rational Drug ◽  
Bioactive Molecule ◽  
Dynamics Simulations

Characterization of the Trypanosoma brucei Pteridine Reductase Active- Site using Computational Docking and Virtual Screening Techniques

2020 ◽  
Vol 16 (5) ◽  
pp. 583-598 ◽  
Author(s):  
Hina Shamshad ◽  
Abdul Hafiz ◽  
Ismail I. Althagafi ◽  
Maria Saeed ◽  
Agha Zeeshan Mirza
Keyword(s):  
Virtual Screening ◽  
Drug Design ◽  
Trypanosoma Brucei ◽  
Active Site ◽  
Critical Role ◽  
Rational Drug Design ◽  
Small Scale ◽  
Chain Flexibility ◽  
Rational Drug

Background: Human African trypanosomiasis is a fatal disease prevalent in approximately 36 sub-Saharan countries. Emerging reports of drug resistance in Trypanosoma brucei are a serious cause of concern as only limited drugs are available for the treatment of the disease. Pteridine reductase is an enzyme of Trypanosoma brucei. Methods: It plays a critical role in the pterin metabolic pathway that is absolutely essential for its survival in the human host. The success of finding a potent inhibitor in structure-based drug design lies within the ability of computational tools to efficiently and accurately dock a ligand into the binding cavity of the target protein. Here we report the computational characterization of Trypanosoma brucei pteridine reductase (Tb-PR) active-site using twenty-four high-resolution co-crystal structures with various drugs. Structurally, the Tb-PR active site can be grouped in two clusters; one with high Root Mean Square Deviation (RMSD) of atomic positions and another with low RMSD of atomic positions. These clusters provide fresh insight for rational drug design against Tb-PR. Henceforth, the effect of several factors on docking accuracy, including ligand and protein flexibility were analyzed using Fred. Results: The online server was used to analyze the side chain flexibility and four proteins were selected on the basis of results. The proteins were subjected to small-scale virtual screening using 85 compounds, and statistics were calculated using Bedroc and roc curves. The enrichment factor was also calculated for the proteins and scoring functions. The best scoring function was used to understand the ligand protein interactions with top common compounds of four proteins. In addition, we made a 3D structural comparison between the active site of Tb-PR and Leishmania major pteridine reductase (Lm- PR). We described key structural differences between Tb-PR and Lm-PR that can be exploited for rational drug design against these two human parasites. Conclusion: The results indicated that relying just on re-docking and cross-docking experiments for virtual screening of libraries isn’t enough and results might be misleading. Hence it has been suggested that small scale virtual screening should be performed prior to large scale screening.

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