Integrated Multi-omics, Virtual Screening and Molecular Docking Analysis of Methicillin-Resistant Staphylococcus aureus USA300 for the Identification of Potential Therapeutic Targets: An In-Silico Approach

Abstract

Staphylococcus aureus infection is a leading cause of mortality and morbidity in community, hospital and live-stock sectors, especially with the widespread emergence of methicillin-resistant S. aureus (MRSA) strains. To identify new drug molecules to treat MRSA patients, we have undertaken to search essential proteins that are indispensable for their survival but nonhomologous to human host proteins. The current study utilizes a subtractive genome and proteome approach to screen the possible therapeutic targets against S. aureus USA300. Bacterial essential genes are obtained from the DEG database and are compared to avoid cross-reactivity with human host genes. In silico analysis shows 198 proteins that may be considered as therapeutic candidates. Depending on their sub-cellular localization, proteins are grouped as either vaccine or drug targets or both. Extracellular proteins such as cell division proteins (Q2FZ91, Q2FZ95), penicillin-binding proteins (Q2FZ94, Q2FYI0) of the bacterial cell wall, phosphoglucomutase (Q2FE11) and lipoteichoic acid synthase (Q2FIS2) are considered as vaccine targets, and their epitopes have been mapped. Altogether, 53 drug targets are identified, which have shown similarity with the drug targets available in the DrugBank database. Predicted drug targets belong to the common metabolic pathways of MRSA, such as fatty acid biosynthesis, folate biosynthesis, peptidoglycan biosynthesis, ribosome, etc. Protein-protein interaction analysis emphasizing peptidoglycan biosynthesis reveals the connection between penicillin-binding proteins, mur-family proteins and FemXAB proteins. In this study, staphylococcal FemA protein (P0A0A5) is subjected to structure-based virtual screening for the drug repurposing approach. There are 20 residues missing in the crystal structure of FemA, and 12 of these residues are located at the catalytic site. The missing residues are modelled, and stereochemistry is checked. FDA approved drugs available in the DrugBank database have been used in virtual screening with FemA in search of potential repurposed molecules. This approach provides us with 10 drugs that may be used in the treatment of methicillin-resistant staphylococcal mediated diseases. AutoDock 4.2 is used for in silico screening and shows a comparable inhibition constant (Ki) for all 10 FDA-approved drugs towards FemA. Most of these drugs are used in the treatment of various cancers, migraines and leukaemia. Protein-drug interaction analysis shows that the drugs mostly interact with hydrophobic residues of FemA. Moreover, Tyr328 and Lys383 contribute largely to hydrogen bondings during interactions. All interacting amino acids that bind to the drugs are part of the active site cavity of FemA.

Identification of Putative Vaccine and Drug Targets against the Methicillin-Resistant Staphylococcus aureus by Reverse Vaccinology and Subtractive Genomics Approaches

“…Earlier studies reported that PBP1 and PBP2 are considered potential therapeutic targets for their cellular importance. These proteins were found interacting with the staphylococcal femXAB family protein, mur-family proteins, Ddl, and MraY and play a curial role in the peptidoglycan biosynthesis pathway [ 57 , 58 ]. Also, these proteins have immunogenic properties and could be vaccine candidates in N. meningitidis [ 59 ].…”

“…The target enzyme MurE ligase is a complex molecule that initiates the peptidoglycan biosynthesis [ 83 ] by adding meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate during the synthesis of murein in the cytoplasm [ 84 ]. As this enzyme is vital to the survivability of S. aureus strains, it can be used as a potential antibacterial drug target [ 57 , 58 , 83 ]. Based on the interaction between the crystallographic structure of the MurE template (4C12 from S. aureus ) and the crystallographic ligand uridine 5′ diphospho N-acetyl muramoyl-L-Alanyl-D-Glutamyl-L-Lysine (UML), it was found that the active site residues involved in H-bond interactions were Ser456, Glu460, Asp406, Thr152, Ser179, Arg187, Arg383, His205, Asn151, Thr153, Thr45, Thr46, Val47, Thr28, Ser30, and Val47.…”

Targeting Staphylococcal Cell–Wall Biosynthesis Protein FemX Through Steered Molecular Dynamics and Drug-Repurposing Approach

“…Additionally, several other auxillary (aux) genes have also been identified that play a crucial role in methicillin resistance, namely, factors essential for methicillin-resistance (fem) family genes . Three of these genes, femX , femA, and femB , play a vital role in the latter stage of the peptidoglycan (PG) biosynthesis process of Staphylococci and can be served as potential targets for developing new antimicrobial therapeutics. , Staphylococcal PG-repeat unit consists of a disaccharide, a pentapeptide stem, and a penta-glycine bridge structure. The PG disaccharide unit (DU) is composed of N -acetyl-glucosamine (NAG) and N -acetyl-muramic acid (NAM) and is conserved among all eubacteria, whereas the pentapeptide stem and bridge structure vary between species .…”