Exploration of Streptococcus core genome to reveal druggable targets and novel therapeutics against S. pneumoniae

Abstract

Streptococcus pneumoniae (S. pneumoniae), the major etiological agent of community-acquired pneumonia (CAP) contributes significantly to the global burden of infectious diseases which is getting resistant day by day. Nearly 30% of the S. pneumoniae genomes encode hypothetical proteins (HPs), and better understandings of these HPs in virulence and pathogenicity plausibly decipher new treatments. Some of the HPs are present across many Streptococcus species, systematic assessment of these unexplored HPs will disclose prospective drug targets. In this study, through a stringent bioinformatics analysis of the core genome and proteome of S. pneumoniae PCS8235, we identified and analyzed 28 HPs that are common in many Streptococcus species and might have a potential role in the virulence or pathogenesis of the bacteria. Functional annotations of the proteins were conducted based on the physicochemical properties, subcellular localization, virulence prediction, protein-protein interactions, and identification of essential genes, to find potentially druggable proteins among 28 HPs. The majority of the HPs are involved in bacterial transcription and translation. Besides, some of them were homologs of enzymes, binding proteins, transporters, and regulators. Protein-protein interactions revealed HP PCS8235_RS05845 made the highest interactions with other HPs and also has TRP structural motif along with virulent and pathogenic properties indicating it has critical cellular functions and might go under unconventional protein secretions. The second highest interacting protein HP PCS8235_RS02595 interacts with the Regulator of chromosomal segregation (RocS) which participates in chromosome segregation and nucleoid protection in S. pneumoniae. In this interacting network, 54% of protein members have virulent properties and 40% contain pathogenic properties. Among them, most of these proteins circulate in the cytoplasmic area and have hydrophilic properties. Finally, molecular docking and dynamics simulation demonstrated that the antimalarial drug Artenimol can act as a drug repurposing candidate against HP PCS8235_RS 04650 of S. pneumoniae. Hence, the present study could aid in drugs against S. pneumoniae.

Fig 1. A schematic representation of the workflow involved to identify potential anti-streptococci drug targets.

Fig 2. Circular representation of the S. pneumoniae genome and related species.

The brown bar of the circular plot represents the core genes.

Fig 3. Categories of annotated S. pneumoniae hypothetical proteins classified according to their biological, molecular, and cellular functions.

Proteins involved in molecular functions were relatively higher compared to others.

Fig 4. Venn diagram representing the number of hypothetical proteins with virulence factor pathogenicity.

Fig 5. String results of PPI revealed several HPs that interact with pneumococcal vaccine antigen A and Ribosomal silencing factor; PCS8235_RS05845 and PCS8235_RS02595 have the highest nodes.

Fig 6

Interaction between the best drug for the HPs in S. pneumoniae and the active site amino acid residues of each of the HPs (a) PCS8235_RS04650- Artenimol (b) PCS8235_RS04650- Aspartate beryllium trifluoride (c) PCS8235_RS02820-2-(N-morpholino) ethanesulfonic acid.

Fig 7

RMSD analysis of (A) PCS8235_RS02820 (green) and PCS8235_RS02820-2-(N-morpholino) ethanesulfonic acid complex (purple) (B) PCS8235_RS04650 (red) and PCS8235_RS04650 –Artenimol (purple) and PCS8235_RS04650-Aspartate beryllium trifluoride (gray) at 100ns.

Fig 8

RMSF analysis of (A) PCS8235_RS02820 (brown) and PCS8235_RS02820-2-(N-morpholino) ethanesulfonic acid complex (blue) (B) PCS8235_RS04650 (blue) and PCS8235_RS04650 –Artenimol (golden) and PCS8235_RS04650-Aspartate beryllium trifluoride (green) at 100 ns.

Fig 9

SASA calculation of (A) PCS8235_RS02820 (golden) and PCS8235_RS02820-2-(N-morpholino) ethanesulfonic acid complex (green) (B) PCS8235_RS04650 (blue) and PCS8235_RS04650 –Artenimol (green) and PCS8235_RS04650-Aspartate beryllium trifluoride (red) at 100ns.

Fig 10

Rg measurement of (A) PCS8235_RS02820 (green) and PCS8235_RS02820-2-(N-morpholino) ethanesulfonic acid complex (red) (B) PCS8235_RS04650 (green) and PCS8235_RS04650 –Artenimol (red) and PCS8235_RS04650-Aspartate beryllium trifluoride (yellow) at 100 ns.