Biophysical and In-Silico Studies of Phytochemicals Targeting Chorismate Synthase from Drug-Resistant Moraxella Catarrha
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Biophysical and In‑Silico Studies of Phytochemicals Targeting Chorismate Synthase from Drug‑Resistant Moraxella Catarrhalis Neetu Neetu1 · Monica Sharma1 · Jai Krishna Mahto1 · Pravindra Kumar1 Accepted: 30 September 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Chorismate serves as a crucial precursor for the synthesis of many aromatic compounds essential for the survival and virulence in various bacteria and protozoans. Chorismate synthase, a vital enzyme in the shikimate pathway, is responsible for the formation of chorismate from enolpyruvylshikimate-3-phosphate (EPSP). Moraxella catarrhalis is reported to be resistant to many beta-lactam antibiotics and causes chronic ailments such as otitis media, sinusitis, laryngitis, and bronchopulmonary infections. Here, we have cloned the aroC gene from Moraxella catarrhalis in pET28c and heterologously produced the chorismate synthase (~ 43 kDa) in Escherichia coli BL21(DE3) cells. We have predicted the three-dimensional structure of this enzyme and used the refined model for ligand-based virtual screening against Supernatural Database using PyRx tool that led to the identification of the top three molecules (caffeic acid, gallic acid, and o-coumaric acid). The resultant protein–ligand complex structures were subjected to 50 ns molecular dynamics (MD) simulation using GROMACS. Further, the binding energy was calculated by MM/PBSA approach using the trajectory obtained from MD simulation. The binding affinities of these compounds were validated with ITC experiments, which suggest that gallic acid has the highest binding affinity amongst these three phytochemicals. Together, these results pave the way for the use of these phytochemicals as potential anti-bacterial compounds. Keywords Moraxella catarrhalis · Chorismate synthase · Homology modeling · Isothermal calorimetry · Virtual screening · Molecular dynamics simulation
1 Introduction Moraxella catarrhalis is a gram-negative aerobic diplococcus, formerly known as Neisseria catarrhalis or Micrococcus catarrhalis, often found to commensurate within the upper and lower respiratory tract [1, 2]. It has been identified Neetu Neetu and Monica Sharma have contributed equally to this work. * Pravindra Kumar [email protected] Neetu Neetu [email protected] Monica Sharma [email protected] Jai Krishna Mahto [email protected] 1
Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
as one of the most common respiratory tract bacterial pathogens. This strain has attracted a lot of attention because of its ability to produce two class-A β-lactamases, BRO-1, and BRO-2; therefore, it can hydrolyze penicillin, methicillin, ampicillin, and cefaclor [3]. This bacteria colonizes the human nasopharynx’s mucous surface and is a significant reason for the acute otitis medium [4]. It shows seasonal variations, and it increases during winter [5]. Moraxella catarrhalis is a prevalent cause of many infections, such as pneumonia, endocarditis, sep
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