Literature DB >> 36258912

Molecular Dynamic Simulations and Molecular Docking as a Potential Way for Designed New Inhibitor Drug without Resistance.

Jafar Aghajani1, Poopak Farnia2, Parissa Farnia1, Jalaledin Ghanavi1, Ali Akbar Velayati1.   

Abstract

Mycobacterium tuberculosis is the cause of tuberculosis in humans and is responsible for more than 2 million deaths per year. Despite the development of anti-tuberculosis drugs (Isoniazid, Rifampicin, Ethambutol, pyrazinamide, streptomycin, etc.) and the TB vaccine, this disease has claimed the lives of many people around the world. Drug resistance in this disease is increasing day by day. Conventional methods for discovering and developing drugs are usually time-consuming and expensive. Therefore, a better method is needed to identify, design, and manufacture TB drugs without drug resistance. Bioinformatics applications in obtaining new drugs at the structural level include studies of the mechanism of drug resistance, detection of drug interactions, and prediction of mutant protein structure. In the present study, computer-based approaches including molecular dynamics simulation and molecular docking as a novel and efficient method for the identification and investigation of new cases as well as the investigation of mutated proteins and compounds will be examined . Copyright
© 2022 National Research Institute of Tuberculosis and Lung Disease.

Entities:  

Keywords:  Drug design; Drug resistance; Molecular docking; Molecular dynamic simulation; Mycobacterium tuberculosis

Year:  2022        PMID: 36258912      PMCID: PMC9571241     

Source DB:  PubMed          Journal:  Tanaffos        ISSN: 1735-0344


  95 in total

1.  OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.

Authors:  Edward Harder; Wolfgang Damm; Jon Maple; Chuanjie Wu; Mark Reboul; Jin Yu Xiang; Lingle Wang; Dmitry Lupyan; Markus K Dahlgren; Jennifer L Knight; Joseph W Kaus; David S Cerutti; Goran Krilov; William L Jorgensen; Robert Abel; Richard A Friesner
Journal:  J Chem Theory Comput       Date:  2015-12-01       Impact factor: 6.006

2.  Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.

Authors:  Jason B Cross; David C Thompson; Brajesh K Rai; J Christian Baber; Kristi Yi Fan; Yongbo Hu; Christine Humblet
Journal:  J Chem Inf Model       Date:  2009-06       Impact factor: 4.956

3.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.

Authors:  Y Duan; P A Kollman
Journal:  Science       Date:  1998-10-23       Impact factor: 47.728

4.  CHARMM36m: an improved force field for folded and intrinsically disordered proteins.

Authors:  Jing Huang; Sarah Rauscher; Grzegorz Nawrocki; Ting Ran; Michael Feig; Bert L de Groot; Helmut Grubmüller; Alexander D MacKerell
Journal:  Nat Methods       Date:  2016-11-07       Impact factor: 28.547

Review 5.  Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review.

Authors:  Zhifeng Liu; Yujie Liu; Guangming Zeng; Binbin Shao; Ming Chen; Zhigang Li; Yilin Jiang; Yang Liu; Yu Zhang; Hua Zhong
Journal:  Chemosphere       Date:  2018-03-27       Impact factor: 7.086

6.  Systematic validation of protein force fields against experimental data.

Authors:  Kresten Lindorff-Larsen; Paul Maragakis; Stefano Piana; Michael P Eastwood; Ron O Dror; David E Shaw
Journal:  PLoS One       Date:  2012-02-22       Impact factor: 3.240

7.  Investigation of the anti-TB potential of selected propolis constituents using a molecular docking approach.

Authors:  Mohammad Tuhin Ali; Natalia Blicharska; Jamil A Shilpi; Veronique Seidel
Journal:  Sci Rep       Date:  2018-08-16       Impact factor: 4.379

8.  Developing a molecular dynamics force field for both folded and disordered protein states.

Authors:  Paul Robustelli; Stefano Piana; David E Shaw
Journal:  Proc Natl Acad Sci U S A       Date:  2018-05-07       Impact factor: 11.205

9.  Integrating protein structural dynamics and evolutionary analysis with Bio3D.

Authors:  Lars Skjærven; Xin-Qiu Yao; Guido Scarabelli; Barry J Grant
Journal:  BMC Bioinformatics       Date:  2014-12-10       Impact factor: 3.169

10.  PubChem Substance and Compound databases.

Authors:  Sunghwan Kim; Paul A Thiessen; Evan E Bolton; Jie Chen; Gang Fu; Asta Gindulyte; Lianyi Han; Jane He; Siqian He; Benjamin A Shoemaker; Jiyao Wang; Bo Yu; Jian Zhang; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2015-09-22       Impact factor: 16.971

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