In SilicoStructure Prediction of Human Fatty Acid Synthase–Dehydratase: A Plausible Model for Understanding Active Site Interactions

Abstract

Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. X-ray crystallographic structures of some of its domains, such as β-ketoacyl synthase, acetyl transacylase, malonyl transacylase, enoyl reductase, β-ketoacyl reductase, and thioesterase, (TE) are already reported. Here, we have attempted an in silico elucidation of the uncrystallized dehydratase (DH) catalytic domain of human FASN. This theoretical model for DH domain was predicted using comparative modeling methods. Different stand-alone tools and servers were used to validate and check the reliability of the predicted models, which suggested it to be a highly plausible model. The stereochemical analysis showed 92.0% residues in favorable region of Ramachandran plot. The initial physiological substrate β-hydroxybutyryl group was docked into active site of DH domain using Glide. The molecular dynamics simulations carried out for 20 ns in apo and holo states indicated the stability and accuracy of the predicted structure in solvated condition. The predicted model provided useful biochemical insights into the substrate–active site binding mechanisms. This model was then used for identifying potential FASN inhibitors using high-throughput virtual screening of the National Cancer Institute database of chemical ligands. The inhibitory efficacy of the top hit ligands was validated by performing molecular dynamics simulation for 20 ns, where in the ligand NSC71039 exhibited good enzyme inhibition characteristics and exhibited dose-dependent anticancer cytotoxicity in retinoblastoma cancer cells in vitro.

Exploring the Potential of Natural Products as FoxO1 Inhibitors: an In Silico Approach

“…This optimization employed Epik 2.0 and considered a pH range of 7.0 ± 2.0 to generate various ionization states, tautomers, and ring conformations for each input ligand. A single, energy-minimized, low-energy conformer for each molecule was generated using the OPLS 2005 force field ( John et al ., 2016 ; Sahu et al ., 2020 ).…”

Review on target domains and natural compound‐based inhibitors of fatty acid synthase for anticancer drug discovery

“…Glutamine cannot be replaced with alanine/threonine but can tolerate replacement with His due to similar codons and the imidazole side chain can form hydrogen bonding with carbonyl of active site aspartate (Pasta et al, 2007). John et al, studied the binding affinity and amino acid interactions of β‐hydroxy‐butyryl group, with the DH domain using porcine FASN protein for DH mapping (John et al, 2016). Oxygen atom showed strong H‐bond with Gln1035 (directly aids in OH quenching), it also formed H‐bonds with Ala888 and Asp1032 which help in the abstraction of OH during DNL.…”

“…This indicated the interactions of the substrate with two catalytic residues with proper orientation at the binding site. High throughput screening of NCI database compounds to DH had yielded NSC71039 as a hit aligned in the helix funnel active site forming a strong H‐bonding with catalytic diad and few other hydrophobic interactions (John et al, 2016).…”