Antibiotic-Receptor Molecular Interactions

Juan H Pacheco Sánchez

doi:10.34297/ajbsr.2019.01.000544

Abstract

The antibiotic (penicillin G) and receptor Escherichia Coli (e-coli) have been gotten from Protein Data Bank (pdb). Molecular interactions between these molecules are achieved through calculations of potential energy surface (PES) and molecular dynamics. These calculations are related to the structure of the molecules. Single point calculations of penicillin G interacting with e-coli molecules are carried out to obtain potential wells, for knowing whether there is attraction or repulsion between them. When calculating and graphing the minimum energies, we can realize that there is physisorption between these molecules. Furthermore, molecular dynamics of one system of 8 molecules of penicillin G with 1 molecule of e-coli, and another of 8 molecules of e-coli with 1 of penicillin G are accomplished. A histogram is made with the distances obtained from centroids of each molecule, and the radial distribution is calculated to obtain dispersion of the molecules according to the distance. The graphs of radial distribution g(r) in both cases have similar variation according to the distance. Universal Forcefield with Forcite of BIOVIA Materials Studio has been used for either energy calculations or molecular dynamics. We infer that e-coli microorganism is pulled out by means of physisorption with antibiotic penicillin G.

Highlights

The distribution of molecules is determinant in their macroscopic properties
Diverse researchers have been interested in investigating molecular interactions with molecular dynamics method to simulate variables according to Newton’s formulas, and know antibiotics behavior against microorganisms at a given time, so much in proteins, as base pairs, among others
We investigate the molecular interactions of e-coli and penicillin G molecules found on Protein Data Bank using Forcite from BIOVIA Materials Studio with Universal Forcefield

Summary

Introduction

The distribution of molecules is determinant in their macroscopic properties. The structure of the molecules is based on the chemical bonds that are the forces that hold the atoms together [1]. The internal core components of the LPS include certain unique sugars that are characteristic such as 3-deoxy-D-mannoktonosonic (Kdo) and L-glycero-D-mannoheptose, at least one Kdo residue, or a derivative is present in all known lipopolysaccharides, whereby this sugar indicates an essential role in the survival and growth of bacteria [8] It has been found great interest in bacterial resistance to antibiotics by focusing on simulating molecular dynamics, which is one of the most serious public health problems. The calculation of minimum energy and distance corresponds to the equilibrium points This is to know the behavior when interacting these two molecules, followed by the calculation of molecular dynamics using Forcite again, and the g(r) (radial distribution function) graphs, to know how they are distributed according to its density [17,18]

Methodology

Results

Conclusions