Molecular docking analysis of long-chain alkanes with the β-lactamase BEL-1 from P. aeruginosa.

ISSN 0973-2063 (online) 0973-8894 (print) ©Biomedical Informatics (2022) Bioinformation 18(5): 460-463 (2022) www.bioinformation.net Volume 18(5) Research Article Received April 6, 2022; Revised May 31, 2022; Accepted May 31, 2022, Published May 31, 2022 DOI: 10.6026/97320630018460 Declaration on Publication Ethics: The author’s state that they adhere with COPE guidelines on publishing ethics as described elsewhere at https://publicationethics.org/. The authors also undertake that they are not associated with any other third party (governmental or non-governmental agencies) linking with any form of unethical issues connecting to this publication. The authors also declare that they are not withholding any information that is misleading to the publisher in regard to this article. Declaration on official E-mail: The corresponding author declares that lifetime official e-mail from their institution is not available for all authors License statement: This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License Comments from readers: Articles published in BIOINFORMATION are open for relevant post publication comments and criticisms, which will be published immediately linking to the original article without open access charges. Comments should be concise, coherent and critical in less than 1000 words. Edited by P Kangueane Citation: Gayathri et al. Bioinformation 18(5): 460-463 (2022) Molecular docking analysis of long-chain alkanes with the β-lactamase BEL-1 from P. aeruginosa VR Gayathri1, B Prakash1,2*, JV Yashika1, Subash Vetri Selvi3 & D. Jegadeesh Kumar4 1Department of Biotechnology, Vivekanandha College of Arts & Science for Women (Autonomous) Trichengode, Tamilnadu, India; 2Department of Biotechnology, Vels Institute of Science Technology & Advanced Studies, Chennai, Tamil Nadu, India; 3Electroanalysis and Bioelectrochemistry Lab, Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei 106, Taiwan, ROC; 4Chromopark Research Centre, Namakkal, Tamilnadu, India; *Corresponding Author Author contacts: Prakash B – E-mail: Abstract: Pseudomonas aeruginosa is a gram-negative opportunistic bacterium that is a concern worldwide due to its innate antibiotic resistance properties. This warrants the development of non-antibiotic compounds that can potentially address the growing concern. Therefore, it is of interest to document the molecular docking analysis data of three long-chain alkanes, namely, eicosane, triacontane, and nonadecane with β-lactamase BEL-1. Data shows that nonadecane have good binding features and drug-likeness when compared to triacontane and nonadecane. It is well known that nonadecane is a compound that is abundantly available from natural resources for further consideration. 460 ISSN 0973-2063 (online) 0973-8894 (print) ©Biomedical Informatics (2022) Bioinformation 18(5): 460-463 (2022) Keywords: β-lactamase BEL-1, P. aeruginosa, nonadecane, long-chain alkanes Background: Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that can be seen along with nosocomial infections [1]. The genome sequence of P. aeruginosa is relatively large (5.5-7 Mbp) [2]. They are resistant to external stress, colonise easily, and rapidly develop a matrix of biofilm. P. aeruginosa consists of resistance-nodulation division efflux pumps which protect against antibiotics [3, 4]. The biofilm formed also provides resistance to antibiotics. P. aeruginosa strains have multiple drug-resistant [5]. A clinical strain of P. aeruginosa consisting of clavulanic acid-inhibited ambler class A extended-spectrum β-lactamase (BEL-1) was reported [6, 7]. BEL-1 is chromosomally encoded in class 1 integrons and has an association with cephalosporinase and penicillinase and it shows resistance against β-lactam antibiotics, including carbapenems [6, 8]. The development of BEL-1 strain containing P. aeruginosa is a concern amidst the growing multi drug resistance bacterial species. Besides, the BEL-1 strain containing P. aeruginosa have low MIC and is sparsely detectable with conventional methods [9]. The World Health Organisation listed carbapenem resistant P. aeruginosa as a bacterial species that requires the development of a novel class of antibiotics for treatment [10]. New class of antibiotics will become vulnerable to the antibiotic resistance properties of the bacterium [11]. Non-antibiotic compounds with features such as inhibition of quorum sensing and bacterial lectins, phage therapy, vaccines, nanoparticles, etc are known [12, 13]. There are several research groups working on developing novel therapies from naturally available resources such as fungi, plants, etc [14-17]. Therefore, it is of interest to document the molecular docking analysis data of plant derived three long-chain alkanes, namely, eicosane, triacontane, and nonadecane with β-lactamase BEL-1. Materials and Methods: Protein preparation: Molecular structure reported at the Protein Data Bank (PDB) was retrieved for extended-spectrum β-lactamase BEL-1 (PDB ID: 5EUA). The structure was energy minimised and converted to PDBQT format. Ligand preparation: The compounds eicosane, triacontane, and nonadecane were selected as ligands for docking and their 3D structures were taken from PubChem. It was then minimized by applying Gasteiger and Kollman's charge. The root of the structure was detected, torsion was applied, and the structures were saved in PDBQT and Mol2 format. Molecular Docking and binding profile: Molecular docking analyses were carried out using PyRx – Python Prescription 0.8. The compounds were targeted to the protein with a grid-box docking model to determine the binding energies. Furthermore, the interaction between the amino acids and compounds was identified using Cresset Flare 4.0.1. Besides, clogP, PSA, TSA, TPSA, drug-likeness, etc., were determined using Osiris Data warrior 5.5.0. Table 1: Molecular drug docking chemical properties of compounds using Osiris Datawarrior 5.5.0.andPyRx 0.8 Parameters Nonadecane Eicosane Binding Affinity -5.9 -5 MW 256.4 273.5 #Atoms 19 20 SlogP 5.6 6.4 TPSA 0 0 Flexibility 11.8 13.8 #RB 12 14 cLogP 8.1976 9.1564 cLogS -5.118 -5.844 H-Acceptors 0 0 H-Donors 0 0 Total Surface Area 269.9 285.7 Relative PSA 0 0 Polar Surface Area 0 0 Druglikeness -23.454 -20.398 LE from Binding Affinity LLE from Binding Affinity LELP from Binding Affinity Mutagenic none none Tumorigenic none none Results and Discussion: Phytoactive compounds such as eicosane, triacontane, and nonadecane that are identified in M. acumanata acetone extract were used in the docking analysis to understand the binding activity, binding energy and inhibitory activity against β-lactamase BEL-1 of P. aeruginosa. Figures 1 shows the docking of proteins and ligands create (...truncated)