Comprehensive computational investigation for ligand recognition and binding dynamics of SdiA: a degenerate LuxR -type receptor in Klebsiella pneumoniae.

SdiA is a LuxR-type receptor that controls the virulence of Klebsiella pneumoniae, a Gram-negative bacterium that causes various infections in humans. SdiA senses exogenous acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2), two types of quorum sensing signals produced by other bacterial species. However, the molecular details of how SdiA recognizes and binds to different ligands and how this affects its function and regulation in K. pneumoniae still need to be better understood. This study uses computational methods to explore the protein-ligand binding dynamics of SdiA with 11 AHLs and 2 AI-2 ligands. The 3D structure of SdiA was predicted through homology modeling, followed by molecular docking with AHLs and AI-2 ligands. Binding affinities were quantified using MM-GBSA, and complex stability was assessed via Molecular Dynamics (MD) simulations. Results demonstrated that SdiA in Klebsiella pneumoniae exhibits a degenerate binding nature, capable of interacting with multiple AHLs and AI-2. Specific ligands, namely C10-HSL, C8-HSL, 3-oxo-C8-HSL, and 3-oxo-C10-HSL, were found to have high binding affinities and formed critical hydrogen bonds with key amino acid residues of SdiA. This finding aligns with the observed preference of SdiA for AHLs having 8 to 10 carbon-length acyl chains and lacking hydroxyl groups. In contrast, THMF and HMF demonstrated poor binding properties. Furthermore, AI-2 exhibited a low affinity, corroborating the inference that SdiA is not the primary receptor for AI-2 in K. pneumoniae. These findings provide insights into the protein-ligand binding dynamics of SdiA and its role in quorum sensing and virulence of K. pneumoniae.

Potential dual inhibition of SE and CYP51 by eugenol conferring inhibition of Candida albicans: Computationally curated study with experimental validation.

Ergosterol is the key sterol component in the cell membrane of fungi including moulds and yeasts. Any decrease in the levels of ergosterol in the cell membrane of fungi render them venerable to cell membrane damage and even its death. Majority of antifungal drug targets the key enzymes involved in ergosterol biosynthesis pathway. The biochemical pathway for the synthesis of Ergosterol is a complex one, though the reactions carried by Squalene Epoxidase (SE) and 14α-demethylase (CYP51- a member of Cytochrome P450 family) serves to the key rate limiting reactions that can impact the overall production of Ergosterol. Allylamines class of antifungal drug target SE while Azoles target the CYP51. Currently advancement in the drug development is focused to introduce newer drugs that can simultaneously inhibit both this rate limiting enzymes. However, natural compounds established to possess antifungal activity but the major loophole about their understanding lies in the fact that their mode of action are severely unstudied. One such well-established antifungal natural phytochemical is Eugenol, and in current manuscript we investigated its efficacy to interact with both, SE and CYP51 of Candida albicans using molecular Docking, Free energy change calculations and Molecular Dynamics (MD) simulation, showing promising outcomes. For experimental studies, terbinafine, clotrimazole and eugenol showed 4 µg/ml, 2 µg/ml, and 512 µg/ml MIC90 values, respectively against C. albicans and also showed reduction in Ergosterol production at sub-MIC levels. The obtained result indicates the involvement of eugenol in the inhibition of enzymes require in the ergosterol biosynthesis pathway.