Ballim, T. | bioRxiv Science

bioRxiv2025

Computational Repurposing and Phytochemical Screening of Inhibitors Against ClpK from Klebsiella pneumoniae.

Over the years, the increase in antibiotic resistant Klebsiella pneumoniae has highlighted the urgent need for the identification of novel therapeutic compounds and targets. ClpK is a caseinolytic ATPase that plays an important role in protein quality control and thermotolerance, making it a promising drug target. This study used in silico methods including ADMET screening, molecular docking and molecular dynamics simulations to evaluate binding efficiency and dynamic stability of selected natural and synthetic compounds with ClpK under varying ionic conditions. ADMET screening of synthetic and natural compounds excluded compounds violating Lipinskis rule of 5 or showing predicted toxicity. Sclerotiamide P was identified as the top binder (-10.9 kcal/mol), while compound D3 had the weakest binding (-4.5 kcal/mol). The top ten compounds with the most favourable binding scores were then further investigated using molecular dynamics simulations in the presence of NaCl and MgCl2. Trajectory and MM-GBSA binding analyses confirmed that ClpK-ligand complexes remained stable in both ionic environments, with negative binding free energy values indicative of favourable interactions. Overall, the study highlighted ADEP3 and sclerotiamide derivatives as promising ClpK inhibitors and provides a foundation for further experimental validation.

biochemistry↗

bioRxiv2025

ClpK as a Chaperone Hub: Computational Exploration of its Protein Interaction Landscape.

Protein-protein interaction networks provide a foundation for understanding the molecular mechanisms within cells and are increasingly recognized as promising targets for therapeutic intervention. However, the experimental elucidation of these interactions is complicated by the complexity and dynamic nature of protein interaction networks. In silico methods have become invaluable allowing researchers to identify potential interactions and focus on those that may be biologically significant to guide experimental validation and drug discovery. This study employed computational modelling, visualization, and network analysis to investigate the interactions of ClpK, a Clp ATPase integral to protein homeostasis and thermotolerance of Klebsiella pneumoniae. Potential interacting partners of ClpK were predicted using the STRING database with ClpB used as a structural proxy for ClpK. The proteins with edge confidence scores greater than 0.8 were selected for molecular docking and molecular dynamics simulations to assess interaction stability and binding affinities. Molecular docking using the ClusPro server confirmed stable interactions between ClpK and its predicted partners, which were further characterised using PDBsum and Hawkdock to visualise binding interfaces and estimate binding free energies MM-GBSA calculation. Among the predicted complexes, KPN_01323 had the highest interaction score, highlighting it as the most promising candidate for further investigation. Molecular dynamics simulations further confirmed the stabilisation of putative partners upon interaction with ClpK supporting the robustness of this interaction. Collectively, these findings provide insight into the ClpK interaction network and establish a framework for future in vitro and in vivo studies contributing to elucidate the biological role and therapeutic potential of ClpK.

biochemistry↗