Pharmacophore-similarity-based QSAR (PS-QSAR) for group-specific biological activity predictions

Journal of Biomolecular Structure and Dynamics

Volumn 33, Issue 1, 2015, Pages 56-69

  Prasanth Kumar, Sivakumar ^a   Jasrai, Yogesh T ^a   Pandya, Himanshu A ^a   Rawal, Rakesh M ^b  

^a GUJARAT UNIVERSITY   (India)

^b GUJARAT CANCER AND RESEARCH INSTITUTE   (India)

Author keywords

2D QSAR; Antimalarials; group based QSAR; Pharmacophore similarity based QSAR (PS QSAR); Topological pharmacophore descriptors

Indexed keywords

3 HYDROXYPYRIDINONE DERIVATIVE; ANTIMALARIAL AGENT; UNCLASSIFIED DRUG; 3-HYDROXY-4-PYRIDONE; IRON CHELATING AGENT; PYRIDONE DERIVATIVE;

ANTIMALARIAL ACTIVITY; ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOLOGICAL ACTIVITY; CONTROLLED STUDY; INTERMETHOD COMPARISON; MOLECULAR MODEL; PHARMACOPHORE; PHARMACOPHORE SIMILARITY BASED QUANTITATIVE STRUCTURE ACTIVITY RELATION; PHYSICAL CHEMISTRY; PREDICTION; PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; ALGORITHM; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; DRUG EFFECTS; GROWTH, DEVELOPMENT AND AGING; MEDICINAL CHEMISTRY; PLASMODIUM FALCIPARUM; PROCEDURES;

ALGORITHMS; ANTIMALARIALS; CHEMISTRY, PHARMACEUTICAL; DRUG DESIGN; IRON CHELATING AGENTS; MODELS, CHEMICAL; MOLECULAR STRUCTURE; PLASMODIUM FALCIPARUM; PYRIDONES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84908564243     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2013.849618     Document Type: Article

References (31)

1. Ajmani, S., Jadhav, K., & Kulkarni, S. A. (2009). Group-based QSAR (G-QSAR): Mitigating interpretation challenges in QSAR. QSAR & Combinatorial Science, 28, 36-51.
2. ChemAxon LLC. (2012). Marvin Sketch 5.11.4. www.chemaxon.com.
3. Cohen, L., & Holliday, M. (1996). Practical statistics for students: An introductory text. New Delhi: Sage.
4. da Cunha, E. F. F., Mancini, D. T., & Ramalho, T. C. (2012). Molecular modeling of the Toxoplasma gondii adenosine kinase inhibitors. Medicinal Chemistry Research, 21, 590-600.
5. Devinyak, O., Zimenkovsky, B., & Lesyk, R. (2012). Biologically active 4-thiazolidinones: a review of QSAR studies and QSAR modeling of antitumor activity. Current Topics in Medicinal Chemistry, 12, 2763-2784.
6. Dehkordi, L. S., Liu, Z. D., & Hider, R. C. (2008). Basic 3-hydroxypyridin- 4-ones: Potential antimalarial agents. European Journal of Medicinal Chemistry, 43, 1035-1047.
7. Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., ... Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24, 1999-2012.
8. Gasteiger, J., & Engel, T. (2003). Chemoinformatics: A Textbook. Weinheim: Wiley-VCH.
9. Güner, O. F. (2000). Pharmacophore - Perception, development, and use in drug design. La Jolla, CA: International University Line.
10. Hansch, C., Kurup, A., Garg, R., & Gao, H. (2001). Chembioinformatics and QSAR: A review of QSAR lacking positive hydrophobic terms. Chemical Reviews, 101, 619-672.
11. Hershko, C., Theanacho, E. N., Spira, D. T., Peter, H. H., Dobbin, P., & Hider, R. C. (1991). The effect of N-alkyl modification on the antimalarial activity of 3-hydroxypyridin- 4-one oral iron chelators. Blood, 77, 637-643.
12. JustNN (4.0). Neural Planner Software. Cheshire: Neural Planner Software Ltd.
13. Kennard, R. W., & Stone, L. A. (1969). Computer aided design of experiments. Technometrics, 11, 137-149.
14. Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A., & Vriend, G. (2004). Making optimal use of empirical energy functions: Force-field parameterization in crystal space. Proteins Structure Function and Bioinformatics, 57, 678-683.
15. Kubinyi, H. (1993). QSAR: Hansch analysis and related approaches. Weinheim: Wiley-VCH.
16. Kumar, S. P., Jasrai, Y. T., Pandya, H. A., George, L. B., & Patel, S. K. (2013). Structural insights into the theoretical model of Plasmodium falciparum NADH dehydrogenase and its interaction with artemisinin and derivatives: Towards global health therapeutics. OMICS: A Journal of Integrative Biology, 17, 231-241.
17. Kumar, S. P., Patel, S. K., Kapopara, R. G., Jasrai, Y. T., & Pandya, H. A. (2012). Evolutionary and molecular aspects of Indian tomato leaf curl virus coat protein. International Journal of Plant Genomics, 417935, doi:10.1155/2012/417935
18. Langer, T., & Hoffmann, R. D. (2006). Pharmacophores and pharmacophore searches. Weinheim: Wiley-VCH.
19. McGregor, M. J., & Muskal, S. M. (1999). Pharmacophore fingerprinting. 1. Application to QSAR and focused library design. Journal of Chemical Information and Modeling, 39, 569-574.
20. Modh, R. P., Kumar, S. P., Jasrai, Y. T., & Chikhalia, K. H. (2013). Design, synthesis, biological evaluation and molecular modeling of coumarin-piperazine derivatives as acetylcholinesterase inhibitors. Archiv der Pharmazie, 346, doi:10.1002/ardp.201300242
21. Myint, K. Z., Ma, C., Wang, L., & Xie, X. Q. (2011). Fragment- similarity-based QSAR (FS-QSAR) algorithm for ligand biological activity predictions. SAR and QSAR in Environmental Research, 22, 385-410.
22. Ojha, P. K., Mitra, I., Das, R., & Roy, K. (2011). Further exploring rm2 metrics for validation of QSPR models. Chemometrics and Intelligent Laboratory Systems, 107, 194-205.
23. Pattanapanyasat, K., Kotipun, K., Yongvanitchit, K., Hider, R. C., Kyle, D. E., Heppner, D. G., & Walsh, D. S. (2001). Effects of hydroxypyridinone iron chelators in combination with antimalarial drugs on the in vitro growth of Plasmodium falciparum. The Southeast Asian Journal of Tropical Medicine and Public Health, 32, 64-69.
24. Pearson, K. (1901). On lines and planes of closest fit to systems of points in space. Philosophical Magazine, 2, 559-572.
25. Saghaie, L., Sakhi, H., Sabzyan, H., Shahlaei, M., & Shamshirian, D. (2013). Stepwise MLR and PCR QSAR study of the pharmaceutical activities of antimalarial 3-hydroxypyridinone agents using B3LYP/6-311++G∗∗ descriptors. Medicinal Chemistry Research, 22, 1679-1688.
26. Santos, M. A., Marques, S. M., & Chaves, S. (2012). Hydroxypyridinones as "privileged" chelating structures for the design of medicinal drugs. Coordination Chemistry Reviews, 256, 240-259.
27. Shahlaei, M., Fassihi, A., & Nezami, A. (2009). QSAR Study of some 5-methyl/trifluoromethoxy-1H-indole-2,3-dione-3- thiosemicarbazone derivatives as anti-tubercular agents. Research in Pharmaceutical Sciences, 4, 123-131.
28. Shaw, P. J. A. (2003). Multivariate statistics for the environmental sciences. Chichester: Wiley-VCH.
29. SPSS Inc. (2007). SPSS for Windows (16.0). Chicago: IBM Corporation.
30. Sud, M. (March, 2012). MayaChemTools: An open source package for computational discovery, 243rd ACS National Meeting & Exposition. San Diego, CA.
31. VLifeMDS: Molecular Design Suite. (2010). Pune: VLife Sciences Technologies Pvt. Ltd. www.vlifesciences.com .