Subtractive proteomics approach to Unravel the druggable proteins of the emerging pathogen Waddlia chondrophila and drug repositioning on its MurB protein

Abstract

Waddlia chondrophila is an emerging pathogen that has been implicated in numerous unpropitious pregnancy events in humans and ruminants. Taking into account its association with abortigenic events, possible modes of transmission, and future risk, immediate clinical measures are required to prevent widespread damage caused by this organism and hence this study. Here, a subtractive proteomics approach was employed to identify druggable proteins of W. chondrophila. Considering the essential genes, antibiotic resistance proteins, and virulence factors, 676 unique important proteins were initially identified for this bacterium. Afterward, NCBI BLASTp performed against human proteome identified 223 proteins that were further pushed into KEGG Automatic Annotation Server (KAAS) for automatic annotation. Using the information from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database 14 Waddlia specific metabolic pathways were identified with respect to humans. Analyzing the data from KAAS and KEGG databases, forty-eight metabolic pathway-dependent, and seventy metabolic pathway independent proteins were identified. Standalone BLAST search against DrugBank FDA approved drug targets revealed eight proteins that are finally considered druggable proteins. Prediction of three-dimensional structures was done for the eight proteins through homology modeling and the Ramachandran plot model showed six models as a valid prediction. Finally, virtual screening against MurB protein was performed using FDA approved drugs to employ the drug repositioning strategy. Three drugs showed promising docking results that can be used for therapeutic purposes against W. chondrophila following the clinical validation of the study.

Keywords: DrugBank; KEGG; Modelling; Molecular docking; Subtractive proteomics; Waddlia chondrophila.

Figure 1

Illustration of the workflow of the entire research project.

Figure 2

3D structure (SWISS-MODEL) and corresponding Ramachandran plot (PROCHEK) for A. Putative multidrug resistance protein MdtC (D6YSV9), B. Putative D-alanyl-D-alanine carboxypeptidase (D6YS23), C. Putative cytochrome d ubiquinol oxidase subunit 2 (D6YVJ2), D. DNA topoisomerase III (D6YVX0), E. UDP-N-acetylenol pyruvoyl glucosamine reductase (D6YVJ9), F. Glycerol-3-phosphate dehydrogenase [NAD(P)+] (D6YST7), G. Chorismate synthase (D6YWA2), and H. Riboflavin synthase, alpha subunit (D6YVD7).

Figure 3

Image of UDP-N-acetylenol pyruvoyl glucosamine reductase docked with flavin-adenine dinucleotide (Red) and A. Bupivacaine hydrochloride (Blue), B. Nilotinib hydrochloride monohydrate (Blue), and C. Regorafenib (Blue).

Figure 4

2D interaction plots for UDP-N-acetylenol pyruvoyl glucosamine reductase docked with A. Flavin-adenine dinucleotide, B. Bupivacaine hydrochloride, C. Nilotinib hydrochloride monohydrate, and D. Regorafenib.