PyPLIF HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors |
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Authors: | Enade P. Istyastono Nunung Yuniarti Vivitri D. Prasasty Sudi Mungkasi |
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Affiliation: | 1.Faculty of Pharmacy, Sanata Dharma University, Yogyakarta 55282, Indonesia;2.Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia;3.Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta 12930, Indonesia;4.Department of Mathematics, Faculty of Science and Technology, Sanata Dharma University, Yogyakarta 55282, Indonesia; |
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Abstract: | Identification of molecular determinants of receptor-ligand binding could significantly increase the quality of structure-based virtual screening protocols. In turn, drug design process, especially the fragment-based approaches, could benefit from the knowledge. Retrospective virtual screening campaigns by employing AutoDock Vina followed by protein-ligand interaction fingerprinting (PLIF) identification by using recently published PyPLIF HIPPOS were the main techniques used here. The ligands and decoys datasets from the enhanced version of the database of useful decoys (DUDE) targeting human G protein-coupled receptors (GPCRs) were employed in this research since the mutation data are available and could be used to retrospectively verify the prediction. The results show that the method presented in this article could pinpoint some retrospectively verified molecular determinants. The method is therefore suggested to be employed as a routine in drug design and discovery. |
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Keywords: | PyPLIF HIPPOS AutoDock Vina drug discovery fragment-based molecular determinant G protein-coupled receptor |
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