Analyses of Structure and Functional Dynamics of Penicillin-binding Proteins in Staphylococci

Abstract

Addressing the challenge posed by multi-resistant bacterial infections, particularly those caused by Staphylococcus epidermidis and Staphylococcus aureus, is paramount in modern medical research. This dissertation delves into the study of Penicillin-binding Proteins (PBPs), with a specific focus on SePBP3, as essential targets for novel antibacterial drug development. Central to this study is the structure-analysis of SePBP3 in complex with the antibiotics cefotaxime and vaborbactam. Cefotaxime, a widely utilized third-generation cephalosporin, known for its efficacy against a broad spectrum of Gram-positive and Gram-negative bacteria. It is often employed in treating severe infections, typically in conjunction with beta-lactamase inhibitors like vaborbactam to augment its antibacterial range and potency. The observed high-affinity interaction between SePBP3 and these antibiotics suggests the potential role of SePBP3 as a decoy receptor, offering a novel strategy to counteract bacterial resistance. Additionally, in terms of my research activities, I performed an in-depth analysis of the dynamic structural states of SePBP3, employing Small Angle X-ray Scattering (SAXS) measurements and molecular dynamics (MD) simulations to identify its open and closed conformations, pivotal for interactions with yet-unknown molecular entities. Investigating SePBP3’S interaction with cefotaxime and vaborbactam substantially contributes to the understanding of bacterial resistance mechanisms, thus providing data to develop innovative antibacterial therapy approaches.

Further, this thesis expands the knowledge of PBP2a from Staphylococcus aureus and Staphylococcus epidermidis. The study encompasses extensive in silico analysis of PBP2a, integrating molecular docking and MD simulations with natural compounds sourced from the Karachi library. These analyses uncover complex interactions, notably demonstrating the binding efficacy of specific quercetin derivatives and introducing a new class of compounds for PBP2a, triterpenes. The triterpenes' binding at the allosteric site of PBP2a induces a significant conformational change, opening the active site cavity. This transformation is characterized by a displacement of the protein's lid, which facilitates a shift in the helix structure, making the active serine site accessible for antibiotic interaction. The analysis of triterpene binding at the allosteric site through both docking and MD simulations not only enhances our understanding of PBP2a's molecular dynamics but also opens up new avenues for developing therapeutic agents against antibiotic-resistant Staphylococcus aureus. Additionally, in terms of this study, a novel expression and purification protocol for PBP2a was developed. This advanced protocol facilitates the efficient production of soluble protein suitable for crystallization studies. A significant advantage of this method is the reduction in process time for PBP2a harvesting. Contrary to the established protocol, the occurrence of inclusion bodies is notably absent, thereby eliminating the need for time-consuming protein unfolding and refolding steps.

This dissertation thus presents a comprehensive exploration of PBPs in the context of antibiotic resistance, offering novel insights and potential strategies for developing effective treatments against resistant strains of Staphylococcus.