Characterization of Streptomyces Species and Validation of Antimicrobial Activity of Their Metabolites through Molecular Docking

Abstract

Finding new antibacterial agents from natural products is urgently necessary to address the growing cases of antibiotic-resistant pathogens. Actinomycetes are regarded as an excellent source of therapeutically important secondary metabolites including antibiotics. However, they have not yet been characterized and explored in great detail for their utility in developing countries such as Nepal. In silico molecular docking in addition to antimicrobial assays have been used to examine the efficacy of chemical scaffolds biosynthesized by actinomycetes. This paper depicts the characterization of actinomycetes based on their morphology, biochemical tests, and partial molecular sequencing. Furthermore, antimicrobial assays and mass spectrometry-based metabolic profiling of isolates were studied. Seventeen actinomycete-like colonies were isolated from ten soil samples, of which three isolates showed significant antimicrobial activities. Those isolates were subsequently identified to be Streptomyces species by partial 16S rRNA gene sequencing. The most potent Streptomyces species_SB10 has exhibited an MIC and MBC of 1.22 μg/mL and 2.44 μg/mL, respectively, against each Staphylococcus aureus and Shigella sonnei. The extract of S. species_SB10 showed the presence of important metabolites such as albumycin. Ten annotated bioactive metabolites (essramycin, maculosin, brevianamide F, cyclo (L-Phe-L-Ala), cyclo (L-Val-L-Phe), cyclo (L-Leu-L-Pro), cyclo (D-Ala-L-Pro), N6, N6-dimethyladenosine, albumycin, and cyclo (L-Tyr-L-Leu)) were molecularly docked against seven antimicrobial target proteins. Studies on binding energy, docking viability, and protein-ligand molecular interactions showed that those metabolites are responsible for conferring antimicrobial properties. These findings indicate that continuous research on the isolation of the Streptomyces species from Nepal could lead to the discovery of novel and therapeutically relevant antimicrobial agents in the future.

Screening and Characterization of Streptomyces spp. Isolated from Soil Producing a Potential Inhibitors of the Proteus mirabilis

“…in a phylogenetic tree based on the neighborhood-joining method (Figure 1). The Streptomyces S11 isolate demonstrated distinct genetic variance from other species, indicating the likelihood of representing a new Streptomyces species [27,28]. Moreover, MALDI-TOF MS was applied to evaluate the proteome profiles of intact bacterial cells, generating spectra revealing several characteristic peaks, including a discernible one at m/z 5381 in Streptomyces triticirhizae, demonstrating the analysis's credibility up to the genus level with an 8.0 score.…”

“…Furthermore, 9,12-octadecadienoic acid (Z, Z) exhibits anti-inflammatory, anti-cancer, and anti-arthritic characteristics. This indicates the potential of the metabolite extract in pharmaceutical applications as an antibiotic product [28][29][30][31][32][33][34]. The HR-LCMS system was employed to analyze the metabolite extract of the Streptomyces S11 isolate, identifying a total of 28 components through negative ionization and 29 components through positive ionization.…”

Determination of potential combination of non‐β‐lactam, β‐lactam, and β‐lactamase inhibitors/β‐lactam enhancer against class D oxacillinases producing Acinetobacter baumannii: Evidence from in‐vitro, molecular docking and dynamics simulation

“…The structures were saved in PDBQT format following Kollman charges optimization and polar hydrogen addition using AutoDock software. The antibiotics were downloaded from PubChem in.sdf format, then PyMOL converted them to.pdb format 30 . A 3D affinity grid box near the protein binding sites with a size of 60 × 60 × 60 Å .…”

“…The antibiotics were downloaded from PubChem in.sdf format, then PyMOL converted them to.pdb format. 30 A 3D affinity grid box near the protein binding sites with a size of 60 × 60 × 60 Å. It concentrated on the crucial residues in all target proteins where important ligands would bind.…”

Characterization and Antibacterial Activity of Soil Actinomycetes from Diverse Land Use Systems in Meru South, Eastern Kenya

“…It also poduces Hygromycin A (HA) that has antibacterial properties due to its capacity to inhibit protein synthesis via a methylenedioxy bridged-aminocyclitol structure. A study report by Bhandari et al [59] identified Streptomyces species, namely S. species_SB1, S. species_SB3, and S. species_SB10, that showed potential antibacterial characteristics in their study on the characterization of antibioticproducing Streptomyces species from untouched habitats in Nepal.…”