Potential Therapeutic Candidates against Chlamydia pneumonia Discovered and Developed In Silico Using Core Proteomics and Molecular Docking and Simulation-Based Approaches

Roqayah H. Kadi, Khadijah A. Altammar, Mohamed M. Hassan, Abdullah F. Shater, Fayez M. Saleh, Hattan Gattan, Bassam M. Al-ahmadi, Qwait AlGabbani and Zuhair M. Mohammedsaleh
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Roqayah H. Kadi: Department of Biology, College of Science, University of Jeddah, Jeddah 21959, Saudi Arabia
Khadijah A. Altammar: Department of Biology, College of Science, University of Hafr Al Batin, P.O. Box 1803, Hafr Al Batin 31991, Saudi Arabia
Mohamed M. Hassan: Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
Abdullah F. Shater: Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
Fayez M. Saleh: Department of Medical Microbiology, Faculty of Medicine, University of Tabuk, Tabuk 71491, Saudi Arabia
Hattan Gattan: Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 22254, Saudi Arabia
Bassam M. Al-ahmadi: Department of Biology, Faculty of Science, Taibah University, Medina 42353, Saudi Arabia
Qwait AlGabbani: Department of Biology, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj 16278, Saudi Arabia
Zuhair M. Mohammedsaleh: Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia

IJERPH, 2022, vol. 19, issue 12, 1-18

Abstract: Chlamydia pneumonia, a species of the family Chlamydiacea, is a leading cause of pneumonia. Failure to eradicate C. pneumoniae can lead to chronic infection, which is why it is also considered responsible for chronic inflammatory disorders such as asthma, arthritis, etc. There is an urgent need to tackle the major concerns arising due to persistent infections caused by C. pneumoniae as no FDA-approved drug is available against this chronic infection. In the present study, an approach named subtractive proteomics was employed to the core proteomes of five strains of C. pneumonia using various bioinformatic tools, servers, and software. However, 958 non-redundant proteins were predicted from the 4754 core proteins of the core proteome. BLASTp was used to analyze the non-redundant genes against the proteome of humans, and the number of potential genes was reduced to 681. Furthermore, based on subcellular localization prediction, 313 proteins with cytoplasmic localization were selected for metabolic pathway analysis. Upon subsequent analysis, only three cytoplasmic proteins, namely 30S ribosomal protein S4, 4-hydroxybenzoate decarboxylase subunit C, and oligopeptide binding protein, were identified, which have the potential to be novel drug target candidates. The Swiss Model server was used to predict the target proteins’ three-dimensional (3D) structure. The molecular docking technique was employed using MOE software for the virtual screening of a library of 15,000 phytochemicals against the interacting residues of the target proteins. Molecular docking experiments were also evaluated using molecular dynamics simulations and the widely used MM-GBSA and MM-PBSA binding free energy techniques. The findings revealed a promising candidate as a novel target against C. pneumonia infections.

Keywords: phytochemicals; molecular docking; drug candidates; molecular dynamic simulation (search for similar items in EconPapers)
JEL-codes: I I1 I3 Q Q5 (search for similar items in EconPapers)
Date: 2022
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