PyPLIF-ASSISTED REDOCKING INDOMETHACIN-(R)-ALPHA-ETHYL-ETHANOLAMIDE INTO CYCLOOXYGENASE-1

https://doi.org/10.22146/ijc.21289

Muhammad Radifar(1*), Nunung Yuniarti(2), Enade Perdana Istyastono(3)

(1) Molecular Modeling Center “MOLMOD.ORG” Yogyakarta
(2) Laboratory of Pharmacology and Toxicology, Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Gadjah Mada, Sekip Utara, Yogyakarta, 55281
(3) Pharmaceutical Technology Laboratory, Sanata Dharma University, Paingan, Maguwoharjo, Depok, Sleman, Yogyakarta 55281
(*) Corresponding Author

Abstract


Identification of Protein-Ligand Interaction Fingerprints (PLIF) has been performed as the rescoring strategy to identify the best pose for the docked poses of indomethacin-(R)-α-ethyl-etanolamide (IMM) in the binding site of cyclooxygenase-1 (COX-1) from simulations using PLANTS molecular docking software version 1.2 (PLANTS1.2). Instead of using the scoring functions included in the docking software, the strategy presented in this article used external software called PyPLIF that could identify the interactions of the ligand to the amino acid residues in the binding pocket and presents them as binary bitstrings, which subsequently were compared to the interaction bitstrings of the co-crystal ligand pose. The results show that PyPLIF-assisted redocking strategy could select the correct pose much better compared to the pose selection without rescoring. Out of 1000 iterative attempts, PyPLIF-assisted redocking simulations could identify 971 correct poses (more than 95%), while the redocking simulations without PyPLIF could only identify 500 correct poses (50%).These works have also provided us with the initial step of the construction of a valid Structure-Based Virtual Screening (SBVS) protocol to identify COX-1 inhibitors.

Keywords


PyPLIF; rescoring; Structure-Based Virtual Screening (SBVS); molecular docking

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DOI: https://doi.org/10.22146/ijc.21289

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