Exploring the inhibitory potential of South African natural compounds against Mycobacterium tuberculosis fatty acyl- AMP ligase.

Abstract

Background: Tuberculosis is one of the leading infectious diseases causing mortality worldwide. Factors such as the increasing prevalence of drug-resistant strains and toxicity profiles of current drugs have made it nearly impossible to eradicate TB. This calls for urgent discovery and development of potent and safe tuberculosis drug candidates with a novel mechanism of action. Usage of natural compounds and their derivatives is being prioritized for drug development owing to their accessibility, potency, and safety profiles. Aim: To identify natural inhibitors of M. tuberculosis FadD23 and characterize their potential mechanism of inhibition. Methodology: A crystal structure of FaD23 (PDB ID 8hdf) with a resolution of 2.2 Å was obtained from RCSB Protein Data Bank. Virtual screening of seven antitubercular compounds from the South African Natural Compounds Database (SANCDB), namely SANC00937, SANC00520, SANC00522, SANC00519, SANC00834, SANC01098, and SANC01097, was performed using molecular docking principles to identify potential inhibitors of FadD23. FadD23-docked compounds underwent 130 ns molecular dynamics (MD) simulation using Amber18 software package. MD trajectories from simulations were used to calculate MM/GBSA binding free energy to determine binding affinities of compounds to FadD23. Various metrics, including root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), hydrogen bonding, and secondary structure elements, were used to characterise conformational dynamics between FadD23-ligand complexes under simulated physiological conditions. The safety profile of the simulated compounds was also evaluated using the SwissADME and ProTox 3.0 servers. Results: The docking results identified compound SANC00937, a flavonoid, as a top candidate that effectively binds at the ATP-binding site of FadD23 with the highest docking score of -8.4 kcal/mol, stabilized by hydrophobic and hydrogen-bond interactions. To achieve accuracy of docking results, all docked compounds were subjected to 130 ns MD simulations to further characterize their interaction with the protein. MM/GBSA calculations revealed SANC01098 to have the highest binding affinity of -28.86 kcal/mol to the protein with reference to ANP. However, SANC01098 resided adjacent to the ATP binding site. SANC00937 showed a second highest binding affinity of -27.83 kcal/mol with reference to ANP, and interacted with key ATP-binding site residues Ala328, Asp222, Gly330, and Ser300 which significantly contributed to a stronger binding affinity and a more stable interaction with FadD23. All complexes exhibited RMSd values below 2 Å highlighting stable association of ligands with the protein. However, the average Rg and RMSd values indicated that SANC01098 forms a more stable association with FadD23 than ANP, suggesting a possibility of competitive binding between SANC00937 and ATP. The secondary structure analysis revealed that SANC00937 deforms the Pi structural component of FadD23, optimizing its binding affinity within the binding site. This was alsosu pported by large hydrophobic interactions and few hydrogen bonds that stabilized FadD23- SANC00937 complex. Pharmacokinetic evaluation showed that SANC01097 exhibits optimal oral drug-like properties, characterized by a high bioavailability score, minimal interference with major Cytochrome P-450 enzymes. Conclusion: This study has identified SANC00937 as a potential ligand to interfere with FadD23 function by competing and displacing ATP in the active site. This opens an interest in experimental evaluation of this natural compound for drug-like properties against FadD23. A positive outcome of such evaluation could potentially lead to the development of novel, alternative and naturally safe TB therapeutics that are accessible in abundance to Africans. In absence of an approved FadD23 inhibitors, these results provide a lead baseline for further laboratory-based experiments to confirm the biological relevance of both SANC00937 and SANC01098 compounds as potential inhibitors of FadD23.