A Support Vector Machine Classification Model for Benzo[c]phenathridine Analogues with Topoisomerase-I Inhibitory Activity

doi:10.3390/molecules17044560

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Molecules 2012, 17(4), 4560-4582; doi:10.3390/molecules17044560

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A Support Vector Machine Classification Model for Benzo[c]phenathridine Analogues with Topoisomerase-I Inhibitory Activity

Khac-Minh Thai * , Thuy-Quyen Nguyen, Trieu-Du Ngo, Thanh-Dao Tran and Thi-Ngoc-Phuong Huynh

Department of Medicinal Chemistry, School of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, 41 Dinh Tien Hoang St., District 1, Ho Chi Minh City, Vietnam

* Author to whom correspondence should be addressed.

Received: 13 March 2012; in revised form: 8 April 2012 / Accepted: 10 April 2012 / Published: 17 April 2012

(This article belongs to the Section Medicinal Chemistry)

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Abstract: Benzo[c]phenanthridine (BCP) derivatives were identified as topoisomerase I (TOP-I) targeting agents with pronounced antitumor activity. In this study, a support vector machine model was performed on a series of 73 analogues to classify BCP derivatives according to TOP-I inhibitory activity. The best SVM model with total accuracy of 93% for training set was achieved using a set of 7 descriptors identified from a large set via a random forest algorithm. Overall accuracy of up to 87% and a Matthews coefficient correlation (MCC) of 0.71 were obtained after this SVM classifier was validated internally by a test set of 15 compounds. For two external test sets, 89% and 80% BCP compounds, respectively, were correctly predicted. The results indicated that our SVM model could be used as the filter for designing new BCP compounds with higher TOP-I inhibitory activity.

Keywords: support vector machine; SVM; classification; topoisomerase; anticancer; benzo[c]phenanthridine; drug design; pharmacoinformatics

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MDPI and ACS Style

Thai, K.-M.; Nguyen, T.-Q.; Ngo, T.-D.; Tran, T.-D.; Huynh, T.-N.-P. A Support Vector Machine Classification Model for Benzo[c]phenathridine Analogues with Topoisomerase-I Inhibitory Activity. Molecules 2012, 17, 4560-4582.

AMA Style

Thai K-M, Nguyen T-Q, Ngo T-D, Tran T-D, Huynh T-N-P. A Support Vector Machine Classification Model for Benzo[c]phenathridine Analogues with Topoisomerase-I Inhibitory Activity. Molecules. 2012; 17(4):4560-4582.

Chicago/Turabian Style

Thai, Khac-Minh; Nguyen, Thuy-Quyen; Ngo, Trieu-Du; Tran, Thanh-Dao; Huynh, Thi-Ngoc-Phuong. 2012. "A Support Vector Machine Classification Model for Benzo[c]phenathridine Analogues with Topoisomerase-I Inhibitory Activity." Molecules 17, no. 4: 4560-4582.

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