In silico Prediction of New Drug Candidates Against the Multidrug-Resistant and Potentially Zoonotic Fish Pathogen Serotype III Streptococcus agalactiae

Abstract

Streptococcus agalactiae is an invasive multi-host pathogen that causes invasive diseases mainly in newborns, elderly, and individuals with underlying health complications. In fish, S. agalactiae causes streptococcosis, which is characterized by septicemia and neurological signs, and leads to great economic losses to the fish farming industry worldwide. These bacteria can be classified into different serotypes based on capsular antigens, and into different sequence types (ST) based on multilocus sequence typing (MLST). In 2015, serotype III ST283 was identified to be associated with a foodborne invasive disease in non-pregnant immunocompetent humans in Singapore, and the infection was related to raw fish consumption. In addition, a serotype III strain isolated from tilapia in Brazil has been reported to be resistant to five antibiotic classes. This specific serotype can serve as a reservoir of resistance genes and pose a serious threat to public health. Thus, new approaches for the control and treatment of S. agalactiae infections are needed. In the present study, 24 S. agalactiae serotype III complete genomes, isolated from human and fish hosts, were compared. The core genome was identified, and, using bioinformatics tools and subtractive criteria, five proteins were identified as potential drug targets. Furthermore, 5,008 drug-like natural compounds were virtually screened against the identified targets. The ligands with the best binding properties are suggested for further in vitro and in vivo analysis.

Keywords: bioinformatics; core genome; drug discovery; fish disease; molecular docking; streptococcosis; subtractive genomics.

FIGURE 1

Phylogenetic tree based on whole genomes of Streptococcus agalactiae serotype III isolates from human and fish hosts constructed using neighbor-joining method. The scale bar represents a difference of 1% in average BLASTN score similarity. Different colors indicate different clusters. Purple: ST23 cluster; blue: ST12 cluster; green: ST283 subcluster; yellow: ST283 subcluster; orange: ST17 cluster; red: CC19 cluster.

FIGURE 2

Circular alignment of genomes of representative Streptococcus agalactiae serotype III strains. The intensity of the ring color indicates the identity between that genome and the S73 strain, which was used as reference for the alignment. Rings of the same color indicate genomes of strains from the same cluster in the phylogenetic tree. Arranged from the center to the edge: GC content and GC skew of strain S73; strain SG-M4; strain CUGBS591; strain SGEHI2015-25; strain CU_GBS_98; strain SG-M29; strain SGEHI2015-95; strain 32790-3A; strain Sag158; strain H002; strain HU-GS582; predicted genomic islands in strain S73; and essential non-host homologous proteins of strain S73.

FIGURE 3

Three-dimensional representation of the interaction between drug-like natural compounds and Streptococcus agalactiae serotype III drug target proteins. The blue areas indicate the druggable pocket of the protein. Hydrogen bonds are represented in dark yellow and the amino acid residues involved are identified. (A) and (B) represent interaction between WP_000077187 (phosphopentomutase) and ZINC05410520; (C) and (D) represent interaction between WP_001068667 (ribosomal protein L19) and ZINC03838587; (E) and (F) represent interaction between WP_001090621 (RegM/CcpA) and ZINC04236030; (G) and (H) represent interaction between WP_001067088 (FMN-binding oxidoreductase) and ZINC03839958; and (I) and (J) represent interaction between WP_000282567 (flavoprotein-related protein) and ZINC04222225.