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

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

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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 / Revised: 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 support vector machine; SVM; classification; topoisomerase; anticancer; benzo[c]phenanthridine; drug design; pharmacoinformatics
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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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.

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