Predicting and Virtually Screening the Selective Inhibitors of MMP-13 over MMP-1 by Molecular Descriptors and Machine Learning Methods

Matrix metalloproteinase-13(MMP-13) is an interesting target for the prevention and therapy of osteoarthritis(OA). Interruption of MMP-13 activity with an inhibitor has the potential to affect OA. However, a broad-spectrum inhibitor, which restrains the other members of the MMP family, especially MMP-1, can cause musculoskeletal syndrome. So, the design and discovery of potential and highly selective inhibitors for MMP-13 over MMP-1 are necessary and of great significance for the development of novel therapeutic agents against OA. Two machine-learning(ML) methods, support vector machine and random forest(RF), were explored in this work to develop classification models for predicting selective inhibitors of MMP-13 over MMP-1 from diverse compounds. These ML models achieved promising prediction accuracies. Among the two ML models, RF gave the better performance, i.e., 97.58% for MMP-13 selective inhibitors and 100% for non-inhibitors. We also used different feature selection methods to extract the molecular features most relevant to selective inhibition of MMP-13 over MMP-1 from the two models. In addition, the better-performing RF model was used to perform virtual screening of MMP-13 selective inhibitors against the "fragment-like"subset of the ZINC database to enrich the potential active agents, thereby obtaining a series of the most potent candidates. Our study suggests that ML methods, particularly RF, are potentially useful for facilitating the discovery of MMP-13 inhibitors and for identifying the molecular descriptors associated with MMP-13 selective inhibitors.