Design of novel PhMTNA inhibitors, targeting neurological disorder through homology modeling, molecular docking, and dynamics approaches

Abstract

Vanishing white matter (VWM) is a hereditary human disease, mostly prevalent in childhood caused by the defects in the eukaryotic initiation factor beta subunits. It is the first disease involved in the translation initiation factor, eIF2B. There is no specific treatment for VWM which mainly affect the brain and ovaries. The gray matter remains normal in all characteristics while the white matter changes texture, coming to the pathophysiology, many initiation factors are involved in the initiation of translation of mRNAs into polypeptides. In this study, the three-dimensional structure of PhMTNA protein was modeled and the stability ascertained through Molecular dynamic simulation (MDS) for 100 ns. The active site residues are conserved with the reported BsMTNA structure which is also confirmed through sitemap prediction. Through virtual screening and induced fit docking, top five leads against PhMTNA protein was identified based on their binding mode and affinity. ADME properties and DFT (Density Functional Theory) studies of these compounds were studied. In addition to that, computational mutagenesis studies were performed to identify the hotspot residues involved in the protein-ligand interactions. Overall analysis showed that the compound NCI_941 has a highest binding energy of −46.256 kcal mol⁻¹ in the Arg57Ala mutant. Thus, the results suggest that NCI_941 would act as a potent inhibitor against PhMTNA protein.

Keywords:

• Bs-Bacillus subtilis
• density functional theory
• homology modeling
• molecular dynamics
• MTNA
• Ph-Pyrococcus horikoshii OT3
• virtual screening

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The authors acknowledge the financial grant supported by Department of Biotechnology (DBT) [Project No: BT/302/NE/TBP/2012], University Grants Commission, New Delhi, India [Grant number: F(0).14–13/2013 (Inno/ASIST) dated 30.03.2013], DST [F.No. EMR/2016/000498], DST-FIST [SR/FST/LSI-667/2016(C)], DST-PURSE [SR/PURSE Phase 2/38 (G)] and MHRD-RUSA 2.0 [F.24/51/2014-U, Policy (TNMulti-Gen), Department of Education, Government of India] and UGC Research award [RA-2016–18-OB-TAM-7124] to carry out this work.