In silico investigation of the anti-leishmanial role of algae and corals active substances using molecular dynamic simulation and Molecular docking methods

Materials and Methods From the PubChem database, three-dimensional structures of Leishmania major proteins zinc leishmanolysin Glycoprotein 63 (GP63), Farnesyl diphosphate synthase (FPPS), and N-myristoyltransferase (NMT), as well as repressors and 389 coral compounds and 624 algal compounds, were obtained. Using PyRx and AutoDock vina software, molecular docking analysis was performed for each of the three Leishmania proteins using individual protein combinations and blockers. The activity, daily carcinogenicity and properties of ADMET are derived from the Swiss drug ADME, Lazar and Way 2. Using the GROMACS program, the coral and algal compounds with the highest binding scores for each protein were selected for molecular dynamics simulations. Results According to the results of molecular docking experiments, Alga-utd-01 and Coral-utd-01 have strong affinity for GP63 protein. Additionally, Alga-utd-05 and Coral-utd-02 showed the highest binding affinity to FPPS, while the top compounds for NMT were Alga-utd-14 and Coral-utd-03. In addition, Alga-utd-05, Alga-utd-22 and Alga-utd-16 are common algal compounds among the three proteins, and Coral-utd-01, Coral-utd-02, Coral-utd-03, Coral -utd-06 and Coral-utd-12 are common compounds of corals. The MD results confirm relatively stable interactions between the proposed compounds and three important Leishmania proteins. Also, according to the mentioned important medicinal sites, the mentioned compounds have the least interference and the most anti-parasitic properties. Conclusion According to information collected from pharmaceutical databases, the substances in question may have anti-inflammatory and therapeutic properties in addition to protein blocking. Therefore, experimental examination of these algae, corals and compounds may provide valuable clues for the control and treatment of leishmaniasis.