Multi-objective Genetic Algorithm for De Novo Drug Design (MoGADdrug)

被引：8

作者：

Devi, R. Vasundhara ^{[1
]}

Sathya, S. Siva ^{[1
]}

Coumar, Mohane S. ^{[2
]}

机构：

[1] Pondicherry Univ, Dept Comp Sci, Pondicherry, India

[2] Pondicherry Univ, Ctr Bioinformat, Pondicherry, India

来源：

CURRENT COMPUTER-AIDED DRUG DESIGN | 2021年 / 17卷 / 03期

关键词：

De novo drug design; drug-likeness; genetic algorithm; multi-objective optimization; oral bio-availability; tanimoto similarity; DEVELOPMENT KIT CDK; SOURCE [!text type='JAVA']JAVA[!/text] LIBRARY; LIGAND DESIGN; EVOLUTIONARY ALGORITHMS; MOLECULES; DISCOVERY; PROGRAM; KINASE; AURORA;

D O I：

10.2174/1573409916666200620194143

中图分类号：

R914 [药物化学];

学科分类号：

100701 ;

摘要：

Background: A multi-objective genetic algorithm for De novo drug design (MoGADdrug) has been proposed in this paper for the design of novel drug-like molecules similar to some reference molecules. The algorithm developed accepts a set of fragments extracted from approved drugs and available in fragment libraries and combines them according to specified rules to discover new drugs through the in-silico method. Methods: For this process, a genetic algorithm has been used, which encodes the fragments as genes of variable length chromosomes and applies various genetic operators throughout the generations. A weighted sum approach is used to simultaneously optimize the structural similarity of the new drug to a reference molecule as well as its drug-likeness property. Results: Five reference molecules namely Lidocaine, Furano-pyrimidine derivative, Imatinib, Atorvastatin and Glipizide have been chosen for the performance evaluation of the algorithm. Conclusion: Also, the newly designed molecules were analyzed using ZINC, PubChem databases and docking investigations.

引用

页码：445 / 457

页数：13

共 44 条

[1] FragmentStore-a comprehensive database of fragments linking metabolites, toxic molecules and drugs [J].

Ahmed, Jessica ;

Worth, Catherine L. ;

Thaben, Paul ;

Matzig, Christian ;

Blasse, Corinna ;

Dunkel, Mathias ;

Preissner, Robert .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D1049-D1054

[2]

[Anonymous], 2012, GLIDE

[3] A Structure-Based Drug Discovery Paradigm [J].

Batool, Maria ;

Ahmad, Bilal ;

Choi, Sangdun .

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2019, 20 (11)

[4] Chemoinformatics-An Introduction for Computer Scientists [J].

Brown, Nathan .

ACM COMPUTING SURVEYS, 2009, 41 (02) :1-38

[5] Structure-based ligand design by a build-up approach and genetic algorithm search in conformational space [J].

Budin, N ;

Majeux, N ;

Tenette-Souaille, C ;

Caflisch, A .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2001, 22 (16) :1956-1970

[6] What has computer-aided molecular design ever done for drug discovery? [J].

Clark, David E. .

EXPERT OPINION ON DRUG DISCOVERY, 2006, 1 (02) :103-110

[7] Fast-Forwarding Hit to Lead: Aurora and Epidermal Growth Factor Receptor Kinase Inhibitor Lead Identification [J].

Coumar, Mohane Selvaraj ;

Chu, Chang-Ying ;

Lin, Cheng-Wei ;

Shiao, Hui-Yi ;

Ho, Yun-Lung ;

Reddy, Randheer ;

Lin, Wen-Hsing ;

Chen, Chun-Hwa ;

Peng, Yi-Hui ;

Leou, Jiun-Shyang ;

Lien, Tzu-Wen ;

Huang, Chin-Ting ;

Fang, Ming-Yu ;

Wu, Szu-Huei ;

Wu, Jian-Sung ;

Chittimalla, Santhosh Kumar ;

Song, Jen-Shin ;

Hsu, John T. -A. ;

Wu, Su-Ying ;

Liao, Chun-Chen ;

Chao, Yu-Sheng ;

Hsieh, Hsing-Pang .

JOURNAL OF MEDICINAL CHEMISTRY, 2010, 53 (13) :4980-4988

[8]

Deb K., 2001, MULTIOBJECTIVE OPTIM

[9]

Devi R. V., 2014, Int. J. Soft Comput. Eng. (IJSCE), V4, P92

[10] Evolutionary algorithms for de novo drug design - A survey [J].

Devi, R. Vasundhara ;

Sathya, S. Siva ;

Coumar, Mohane Selvaraj .

APPLIED SOFT COMPUTING, 2015, 27 :543-552

← 1 2 3 4 5 →