Phytochemicals of Swertia chirayita Roxb. ex Fleming against malarial dihydroorotate dehydrogenase: an in silico study

Abstract

The global economic burden of malaria is rising and lack of effective drugs against it have imposed an insurmountable challenge in designing it that is both affordable and resistanceless. The plants with ethnobotanical values are relatively safer and its use is a viable option as therapeutics for various demographic locations. In this regard, the chemical components of a plant, Swertia chirayita Roxb. ex Fleming (traditionally used as an antimalarial agent) were explored by multiple computational tools against dihydroorotate dehydrogenase (DHODH) protein of Plasmodium falciparum (PDB ID: 6GJG), a causative agent of the disease. The docking scores were calculated to be − 10.220, − 10.131, − 10.071, − 10.024, and − 9.905 kcal/mol for the top five molecules (decussatin, swerchirin, 1-hydroxy-3,5,8-trimethoxyxanthen-9-one, swertinin, and chiratol), respectively with the native ligand possessing a higher value of − 9.873 kcal/mol. The adducts were geometrically and thermodynamically stable as revealed by several parameters extracted from 200 ns molecular dynamics simulations (MDS) and verified by a single run of 600 ns. The smooth RMSD profiles from a cumulative MDS of 2.0 μs, pointed towards a sturdy nature of the receptor geometry with limited translational or rotational motion of the ligands. The involvement of LEU11, CYS14, LEU15, CYS23, PHE27, ILE102, ARG104, TYR337, LEU340, and VAL341 amino acid residues with mainly hydrophobic interactions at the orthosteric site were observed for most of the adducts. The binding free energy changes (up to − 30.18 ± 4.38 kcal/mol) hinted at the feasibility and sustained thermodynamical spontaneity of the forward reaction of the complex formation. The hit molecules could possibly disrupt or inhibit the normal functioning of the DHODH receptor leading to the likely prevention and cure of the disease and are recommended for experimental trials.