New insights into the neuroprotective and beta-secretase1 inhibitor profiles of tirandamycin B isolated from a newly found Streptomyces composti sp. nov

Abstract

Tirandamycin (TAM B) is a tetramic acid antibiotic discovered to be active on a screen designed to find compounds with neuroprotective activity. The producing strain, SBST2-5^T, is an actinobacterium that was isolated from wastewater treatment bio-sludge compost collected from Suphanburi province, Thailand. Taxonomic characterization based on a polyphasic approach indicates that strain SBST2-5^T is a member of the genus Streptomyces and shows low average nucleotide identity (ANI) (81.7%), average amino-acid identity (AAI) (78.5%), and digital DNA-DNA hybridization (dDDH) (25.9%) values to its closest relative, Streptomyces thermoviolaceus NBRC 13905^T, values that are significantly below the suggested cut-off values for the species delineation, indicating that strain SBST2-5^T could be considered to represent a novel species of the genus Streptomyces. The analysis of secondary metabolites biosynthetic gene clusters (smBGCs) in its genome and chemical investigation led to the isolation of TAM B. Interestingly, TAM B at 20 µg/mL displayed a suppressive effect on beta-secretase 1 (BACE1) with 68.69 ± 8.84% inhibition. Molecular docking simulation reveals the interaction mechanism between TAM B and BACE1 that TAM B was buried in the pocket of BACE-1 by interacting with amino acids Thr231, Asp 228, Gln73, Lys 107 via hydrogen bond and Leu30, Tyr71, Phe108, Ile118 via hydrophobic interaction, indicating that TAM B represents a potential active BACE1 inhibitor. Moreover, TAM B can protect the neuron cells significantly (% neuron viability = 83.10 ± 9.83% and 112.72 ± 6.83%) from oxidative stress induced by serum deprivation and Aβ_1-42 administration models at 1 ng/mL, respectively, without neurotoxicity on murine P19-derived neuron cells nor cytotoxicity against Vero cells. This study was reportedly the first study to show the neuroprotective and BACE1 inhibitory activities of TAM B.

Figure 1

Scanning electron micrograph of strain SBST2-5^T grown on ISP 2 agar for 14 days at 30 °C. Bar, 2 μm.

Figure 2

Phylogenomic analysis of strain SBST2-5^T and type strains affiliated to the genus Streptomyces based on 120 bacterial conserved single copied gene sets of the members. The bootstrap values on the nodes are displayed by > 50. Bar, 0.05 represents the nucleotide substitution per position.

Figure 3

3D structure of compound 1 with the selected NOESY correlations.

Figure 4

Chemical structures of compound 1 isolated from Streptomyces sp. SBST2-5^T.

Figure 5

The three-dimensional structure of human BACE1 representing the search space size of 15 × 15 × 15 Å covering the binding site area for docking protocol (A). The amino acid residues lining in the binding site were depicted, including key residues (Asp32, Tyr71, Asp228, Gly230 and Ala335) for binding of atabecestat (B).

Figure 6

The reliability of docking protocol represented by the re-docked pose of atabecestat into the binding site of human BACE1. The structures of atabecestat were represented in stick by superposition of docking pose (green-carbon) and co-crystallized structure (cyan-carbon).

Figure 7

The binding mode of TAM B in the binding site of human BACE1. The binding residues within a radius of 4 Å from the bound TAM were illustrated in 3D graphic (A) and 2D diagram (B), indicating the types of binding interactions and interacting amino acids in the active site of human BACE1.