Homology modeling, binding site identification, molecular docking and molecular dynamics simulation study of emerging and promising drug target of Wnt signaling – Human Porcupine enzyme

Abstract

Wnt signaling is a critical pathway involved in cell proliferation, differentiation and cellular homeostasis. To address treatment need of diseases associated with the dysregulated Wnt signaling like cancer, Alzheimer’s disease, Osteoporosis, Myocardial infarction etc.; small molecules that target the very first and unique component of the Wnt pathway, Porcupine enzyme, have been proven to be effective. Till date, none of the Porcupine inhibitor has reached to market. To design the novel Porcupine inhibitors, there was a need of crystal structure of Porcupine but in 2019, it was not resolved and deposited in the protein data bank. So, with an aim to predict its 3D structure, homology modeling study was performed using two distinct platforms; I-TASSER and Molsoft ICMPro so that we could use the best validated model for the designing of NCEs. Both the generated homology models were compared through Ramachandran plot, Protein health tool of Molsoft ICM and other tools available on metaserver, SAVES v6.0. Molsoft model was found better with 84.6 % residues in most favored region and only 0.3 % residues in disallowed region in Ramachandran plot in comparison to 75.9 % and 1.7 % residues respectively in I-TASSER model. The ICM model was further refined for 50 ns under MD simulation where it got stabilized after 36 ns. Quantification of protein was done by Radius of Gyration (ROG) where model showed larger ROG value of 23.25°A which indicated closely packed structure. Binding site in the predicted structure of Porcupine was identified using ICM binding pocket identifier and used for molecular docking of known Porcupine inhibitors like IWP-2, IWP-3, IWP-L6, and LKG974. Key binding site residues; Arg124, Phe257, Leu261, Val302, Trp305, Asn306, Ser310, Leu313, His341, Phen345, Ala349, Val350 etc. involved in the interaction were identified after MD simulation which can be useful in designing of novel porcupine inhibitors in future.