In silico screening, molecular dynamic simulations, and in vitro activity of selected natural compounds as an inhibitor of Leishmania donovani 3-mercaptopyruvate sulfurtransferase

Abstract

In Leishmania sp., the enzymes of de novo cysteine biosynthesis pathway require sulfide. Other organisms utilize sulfide through the sulfide reduction pathway, but Leishmania lacks the gene that encodes these enzymes. Hence, the major source of sulfide for Leishmania is believed to be from the action of 3-mercaptopyruvate sulfurtransferase (3MST) on 3-mercapto-pyruvate (3MP). There has been no effort reported in the past to screen inhibitors against L. donovani 3MST (Ld3MST). As a result, this study examines natural compounds that are potent against Ld3MST and validates it by in vitro activity and cytotoxicity tests. Initially, a library of ~ 5000 natural compounds was subjected to molecular docking approach for screening, and the best hit was validated using a long-term molecular dynamic simulation (MD). Among the docking results, quercetine-3-rutinoside (Rutin) was deemed the best hit. The results of the MD indicated that Rutin was highly capable of interacting with the varied active site segments, possibly blocking substrate access. Additionally, promastigotes and amastigotes were tested for Rutin activity and the IC50 was found to be 40.95 and 90.09 μM, respectively. Similarly, the cytotoxicity assay revealed that Rutin was not toxic even at a concentration of 819.00 μM to THP-1 cell lines. Additionally, the Ld3MST was cloned, purified, and evaluated for enzyme activity in the presence of Rutin. Reduction in the enzyme activity (~ 85%) was observed in the presence of ~ 40 μM Rutin. Thus, this study suggests that Rutin may act as a potent inhibitor of Ld3MST. With further in vivo investigations, Rutin could be a small molecule of choice for combating leishmaniasis. Supplementary Information The online version contains supplementary material available at 10.1007/s00436-022-07532-5.

Inhibiting Leishmania donovani Sterol Methyltransferase to Identify Lead Compounds Using Molecular Modelling

“…The probability distribution function (PDF) analysis revealed that all of the complexes, including the unbound protein, had only one peak, meaning the complexes and the unbound protein were stable with fewer deviations. This corroborates SARS-CoV-2 main protease (M pro ) studies using malaria box compounds as hits [ 102 ] and the screening of inhibitors against Leishmania donovani 3-mercapto pyruvate sulfurtransferase [ 103 ]. The unbound protein, 22,26-azasterol, STOCK6S-84928, and STOCK6S-65920 complexes reached equilibrium with an average RMSD of 0.25 nm ( Supplementary Figure S2a,b ).…”

“…To determine the effect of loose packing on solvent accessibility, the SASA of the entire protein was computed to provide information on the protein–solvent interactions [ 103 , 105 ]. Generally, high SASA values imply an increase in structural enlargement for the protein–ligand complexes under the influence of solvent surface charges, resulting in a more flexible and unstable conformation [ 105 ].…”

“…Generally, high SASA values imply an increase in structural enlargement for the protein–ligand complexes under the influence of solvent surface charges, resulting in a more flexible and unstable conformation [ 105 ]. A complex of L. donovani 3-mercapto pyruvate sulfurtransferase and rutin complex had an average SASA value of 44 nm 2 , which was more compact than the unbound protein with an average SASA of 48 nm 2 [ 103 ]. In the current study, no differences were observed ( Supplementary Figure S5a ) for the unbound protein, the three hits, and 22,26-azasterol complexes.…”

Docking and Molecular Dynamics Identify Leads against 5 Alpha Reductase 2 for Benign Prostate Hyperplasia Treatment

“…Next, solvent accessible surface area (SASA) was evaluated to determine the efects of the solvent behavior on the stability of the protein-ligand complexes [119,120]. From the SASA graph, it was observed that all the protein-ligand complexes showed similar trajectories with an average SASA value of 115 nm 2 (Figure 8(a)).…”