Probing Anti-Leukemic Metabolites from Marine-Derived Streptomyces sp. LY1209

Molecular docking, molecular dynamics simulations and binding free energy studies of interactions between Mycobacterium tuberculosis Pks13, PknG and bioactive constituents of extremophilic bacteria

Mycobacterial pathogens present a significant challenge to disease control efforts globally due to their inherent resistance to multiple antibiotics. The rise of drug-resistant strains of Mycobacterium tuberculosis has prompted an urgent need for innovative therapeutic solutions. One promising way to discover new tuberculosis drugs is by utilizing natural products from the vast biochemical space. Multidisciplinary methods can used to harness the bioactivity of these natural products. This study aimed to evaluate the antimycobacterial efficacy of functional crude extracts from bacteria isolated from gold mine tailings in South Africa. Bacterial strains were identified using 16S rRNA sequencing. The crude extracts obtained from the bacteria were tested against Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. Untargeted HPLC-qTOF and molecular networking were used to identify the functional constituents present in extracts that exhibited inhibitory activity. A virtual screening workflow (VSW) was used to filter compounds that were strong binders to Mycobacterium tuberculosis Pks13 and PknG. The ligands returned from the VSW were subjected to optimization using density functional theory (DFT) at M06-2X/6-311++ (d,p) level of theory and basis set implemented in Gaussian16 Rev.C01. The optimized ligands were re-docked against Mycobacterium tuberculosis Pks13 and PknG. Molecular dynamics simulation and molecular mechanics generalized born surface area were used to evaluate the stability of the protein-ligand complexes formed by the identified hits. The hit that showed promising binding characteristics was virtually modified through multiple synthetic routes using reaction-driven enumeration. Three bacterial isolates showed significant activity against the two strains of Mycobacterium, while only two, Bacillus subtilis and Bacillus licheniformis, exhibited activity against both Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. The tentatively identified compounds from the bacterial crude extracts belonged to various classes of natural compounds associated with antimicrobial activity. Two compounds, cyclo-(L-Pro-4-OH-L-Leu) and vazabitide A, showed strong binding against PknG and Pks13, with pre-MD MM-GBSA values of - 42.8 kcal/mol and - 47.6 kcal/mol, respectively. The DFT-optimized compounds exhibited the same docking scores as the ligands optimized using the OPSL-4 force field. After modifying vazabitide A, its affinity to the Pks13 binding site increased to - 85.8 kcal/mol, as revealed by the post-MD MM-GBSA analysis. This study highlights the potential of bacteria isolates from gold mine tailings as a source of new scaffolds for designing and optimizing anti-Mycobacterium agents. These agents synthesized in-silico can be further tested in-vitro to evaluate their efficacy.

Marine natural products

Covering: January to the end of December 2022This review covers the literature published in 2022 for marine natural products (MNPs), with 645 citations (633 for the period January to December 2022) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, the submerged parts of mangroves and other intertidal plants. The emphasis is on new compounds (1417 in 384 papers for 2022), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of NP structure class diversity in relation to biota source and biome is discussed.

Capnellenes from Capnella imbricata: Deciphering Their Anti-Inflammatory-Associated Chemical Features

Through our ongoing research on investigating new anti-inflammatory terpenoids derived from soft corals, seven capnellenes sourced from Capnella imbricata were discovered. Among these, three were previously unknown compounds named Δ⁹⁽¹²⁾-capnellene-6α,8β-diol (1), Δ⁹⁽¹²⁾-capnellene-6α,8β,10α-triol (2), and Δ⁹⁽¹²⁾-capnellene-2β,8β,10α-triol (3). The structures of all compounds were determined by spectroscopic analysis (IR, MS, 1D-, and 2D-NMR) and a comparison with the existing literature data. The compounds 1 and 2 were found to be the first-ever identified 6-hydroxy capnellenes. In the inflammation inhibitory assessments, compounds 1-7 were tested for their in vitro activities against inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) protein expressions in LPS-induced RAW264.7 cells. Capnellenes 2 and 5 demonstrated significant reductions in iNOS levels (27.73% and 47.61%) at a concentration of 10 μM. Additionally, capnellenes 1, 5, and 7 (at 10 μM) exhibited statistically significant inhibitions (ranging from 7.64% to 12.57%) against COX-2 protein expressions. Our findings indicated that the oxygen-bearing functionalities at C-8 and C-10 play critical roles in inhibiting iNOS protein induction, which can promote inflammation in LPS-induced RAW264.7 cells. Furthermore, a principal component analysis tool, the chemical global positioning system for natural products (ChemGPS-NP), was applied to confirm these capnellane-based sesquiterpenes as promising candidates for future anti-inflammatory agents targeting iNOS-related targets.