Molecular Modeling of Macrolide Antibiotic Conformational Sampling and Interactions in the 50S Ribosomal Subunit for the Development of Novel Antibiotics

Abstract

Overcoming microbial resistance is a major challenge in the development of antibiotics. Bacteria limit the effectiveness of antibiotics using three major mechanisms: extrusion of the drug via efflux pumps, metabolism to an inactive metabolite, or inhibition of binding by modification of the drug target. The macrolides are an important class of antibiotics that target the ribosome and recent generation macrolides have largely addressed resistance stemming from the first two mechanisms. However, they remain susceptible to resistance due to modification of the ribosome, mainly modification of base A2058 (E. coli numbering throughout) that resides within the heart of the macrolide binding pocket. While crystal structures are available for bacterial 70S ribosomes with macrolides bound, there are none available for A2058-modified ribosomes. Thus, the molecular details underlying A2058 modification-based resistance are unclear. The motivation underlying the present work is to address the need for novel antibiotics, including those addressing A2058 modification-based resistance. To accomplish this, a three-pronged approach has been employed that incorporates both ligand- and structure-based drug design. First, utilizing a ligand-based strategy, the effects of macrolide desmethylation are investigated using molecular dynamics and a pharmacophore-based method known as Conformationally Sampled Pharmacophore (CSP). This will be the subject of Chapter 2. In Chapter 3, the focus shifts to the structure. Molecular dynamics simulations of the 50S subunit are used to understand the impact of A2058 modification on the binding of third generation macrolide antibiotic telithromycin. And, to complete the three-pronged approach, a fragment-based computer- aided drug design method known as Site-Identification by Ligand Competitive Saturation (SILCS) is applied to the ribosome leading to macrolide antibiotics with novel functionality and the potential for enhanced activity against A2058-modified ribosomes. This is the subject of Chapter 4. The methodology underlying all of this work is the use of empirical force field- based simulations, which will be the focus of Chapter 1. As an extension of force fields, Chapter 5 will deal with the optimization of small molecule aldehydes and ketones as Chapter 5 will deal with the optimization of small molecule aldehydes and ketones as well as acyclic sugars toward the development of a comprehensive CHARMM polarizable biomolecular force field based on the classical Drude oscillator.