A potential strain, Paenibacillus sp. JNUCC32, was isolated and subjected to whole-genome sequencing. Genome functional annotation revealed its active metabolic capabilities. This study aimed to investigate the pivotal secondary metabolites in the biological system. Fermentation and extraction were performed, resulting in the isolation of seven known compounds: tryptophol (1), 3-(4-hydroxyphenyl)propionic acid (2), ferulic acid (3), maculosin (4), brevianamide F (5), indole-3-acetic acid (6), and butyric acid (7). Tryptophol exhibited favorable pharmacokinetic properties and demonstrated certain tyrosinase inhibitory activity (IC₅₀ = 999 μM). For further analysis of its inhibition mechanism through molecular docking and molecular dynamics (MD) simulation, tryptophol formed three hydrogen bonds and a pro-Michaelis complex with tyrosinase (binding energy = −5.3 kcal/mol). The MD simulation indicated favorable stability for the tryptophol–mushroom tyrosinase complex, primarily governed by hydrogen bond interactions. The crucial residues VAL-283 and HIS-263 in the docking were also validated. This study suggests tryptophol as a potential candidate for antibrowning agents and dermatological research.

Tyrosinase, a key enzyme in melanin synthesis, represents a crucial therapeutic target for hyperpigmentation disorders due to excessive melanin production. This study aimed to design and evaluate a series of indole–thiourea derivatives by conjugating thiosemicarbazones with strong tyrosinase inhibitory activity to indole. Among these derivatives, compound 4b demonstrated tyrosinase inhibitory activity with an IC₅₀ of 5.9 ± 2.47 μM, outperforming kojic acid (IC₅₀ = 16.4 ± 3.53 μM). Kinetic studies using Lineweaver–Burk plots confirmed competitive inhibition by compound 4b. Its favorable ADMET and drug-likeness properties make compound 4b a promising therapeutic candidate with a reduced risk of toxicity. Molecular docking revealed that the compounds bind strongly to mushroom tyrosinase (mTYR) and human tyrosinase-related protein 1 (TYRP1), with compound 4b showing superior binding energies of −7.0 kcal/mol (mTYR) and −6.5 kcal/mol (TYRP1), surpassing both kojic acid and tropolone. Molecular dynamics simulations demonstrated the stability of the mTYR−4b complex with low RMSD and RMSF and consistent Rg and SASA values. Persistent strong hydrogen bonds with mTYR, along with favorable Gibbs free energy and MM/PBSA calculations (−19.37 kcal/mol), further support stable protein–ligand interactions. Overall, compound 4b demonstrated strong tyrosinase inhibition and favorable pharmacokinetics, highlighting its potential for treating pigmentary disorders.

The investigation of melanogenesis and tyrosinase inhibitors is essential for developing safe and effective natural compounds to treat pigmentation disorders. This study aimed to evaluate the effects of maculosin, a cyclic dipeptide composed of tyrosine and proline, on melanin production and tyrosinase activity using the B16F10 melanoma cell model, while elucidating its mechanism of action through molecular docking and molecular dynamics (MD) simulations. Experimental results demonstrated that maculosin inhibited intracellular melanin content and tyrosinase activity in a concentration-dependent manner in B16F10 melanoma cells. Molecular docking analyses revealed that maculosin exhibited high binding affinities with mushroom tyrosinase (mTYR), tyrosinase-related protein 1 (TYRP1), and Bacillus megaterium tyrosinase (BmTYR) with binding energies of −7.7, −6.8, and −7.5 kcal/mol, respectively. Furthermore, MD simulations confirmed the structural stability and dynamic flexibility of maculosin–protein complexes, as indicated by RMSD, RMSF, Rg, SASA, hydrogen bond interactions, PCA, and DCCM analyses. Binding free energy calculations using the MM/PBSA method showed that maculosin exhibited binding energies of −28.76 kcal/mol with mTYR and −22.23 kcal/mol with TYRP1, outperforming standard co-crystal inhibitors such as tropolone (−12.47 kcal/mol) and kojic acid (−12.73 kcal/mol). Critical residues, including VAL-283 and HIS-263 in mTYR and HIS-381, GLY-389, and THR-391 in TYRP1, were identified as key contributors to maculosin binding, corroborating molecular docking findings and displaying strong correlations in DCCM analyses. Collectively, these results suggest that maculosin is a highly promising candidate for the treatment of pigmentation disorders, offering significant inhibitory effects on melanogenesis and tyrosinase activity.

The formation of atroposelective biaryl compounds in plants and fungi is well understood; however, polyketide aglycone synthesis and dimerization in bacteria remain unclear. Thus, the biosynthetic gene cluster (BGC) responsible for antibacterial setomimycin production from Streptomyces nojiriensis JCM3382 was examined in comparison with the BGCs of spectomycin, julichromes, lincolnenins, and huanglongmycin. The setomimycin BGC includes post-polyketide synthase (PKS) assembly/cycling enzymes StmD (C-9 ketoreductase), StmE (aromatase), and StmF (thioesterase) as key components. The heterodimeric TcmI-like cyclases StmH and StmK are proposed to aid in forming the setomimycin monomer. In addition, StmI (P-450) is predicted to catalyze the biaryl coupling of two monomeric setomimycin units, with StmM (ferredoxin) specific to the setomimycin BGC. The roles of StmL and StmN, part of the nuclear transport factor 2 (NTF-2)-like protein family and unique to setomimycin BGCs, could particularly interest biochemists and combinatorial biologists. α-Glucosidase, a key enzyme in type 2 diabetes, hydrolyzes carbohydrates into glucose, thereby elevating blood glucose levels. This study aimed to assess the α-glucosidase inhibitory activity of EtOAc extracts of JCM 3382 and setomimycin. The JCM 3382 EtOAc extract and setomimycin exhibited greater potency than the standard inhibitor, acarbose, with IC₅₀ values of 285.14 ± 2.04 μg/mL and 231.26 ± 0.41 μM, respectively. Molecular docking demonstrated two hydrogen bonds with maltase-glucoamylase chain A residues Thr205 and Lys480 (binding energy = −6.8 kcal·mol⁻¹), two π–π interactions with Trp406 and Phe450, and one π–cation interaction with Asp542. Residue-energy analysis highlighted Trp406 and Phe450 as key in setomimycin’s binding to maltase-glucoamylase. These findings suggest that setomimycin is a promising candidate for further enzymological research and potential antidiabetic therapy.

The formation of atroposelective biaryl compounds in plants and fungi is well understood; however, the polyketide aglycone synthesis and dimerization in bacteria remain unclear. Thus, the biosynthetic gene cluster (BGC) responsible for antibacterial setomimycin production from Streptomyces nojiriensis JCM3382 was examined in comparison with the BGCs of spectomycin, julichromes, lincolnenins, and huanglongmycin. Setomimycin BGC includes post-PKS assembly/cycling enzymes StmD (C-9 ketoreductase), StmE (aromatase), and StmF (thioesterase) as key components. The heterodimeric TcmI-like cyclases StmH and StmK are proposed to aid in forming the setomimycin monomer. In addition, StmI (P-450) is predicted to catalyze biaryl coupling of two monomeric setomimycin units, with StmM (ferredoxin) specific to setomimycin BGC. The roles of StmL and StmN, part of the nuclear transport factor 2 (NTF-2)-like protein family and unique to setomimycin BGCs, could particularly interest biochemists and combinatorial biologists. α-Glucosidase, a key enzyme in type 2 diabetes, hydrolyzes carbohydrates into glucose, thereby elevating blood glucose levels. This study aimed to assess the α-glucosidase inhibitory activity of EtOAc extracts of JCM 3382 and setomimycin. The JCM 3382 EtOAc extract and setomimycin exhibited greater potency than the standard inhibitor, acarbose, with IC50 values of 285.14 ± 2.04 μg/mL and 231.26 ± 0.41 μM, respectively. Kinetic analysis revealed that setomimycin acts as a competitive inhibitor of α-glucosidase. Molecular docking demonstrated two hydrogen bonds with maltase-glucoamylase chain A residues Thr205 and Lys480 (binding energy = −6.8 kcal·mol⁻¹), two π-π interactions with Trp406 and Phe450, and one π-cation interaction with Asp542. Residue-energy analysis highlighted Trp406 and Phe450 as key in setomimycin's binding to maltase-glucoamylase. These findings suggest that setomimycin is a promising candidate for further enzymological research and potential antidiabetic therapy.

Hyperpigmentation disorders, characterized by aberrant melanin accumulation, pose a significant clinical challenge, driving the search for novel therapeutic agents. Rifampicin, a clinically approved antibiotic, has recently emerged as a potential candidate for regulating melanogenesis, with preliminary evidence indicating it may target key proteins involved in melanin synthesis and signaling pathways—specifically tyrosinase-related protein 1 (TYRP1), phosphoinositide 3-kinase (PI3K), protein kinase A (PKA), p38 mitogen-activated protein kinase (p38 MAPK), and glycogen synthase kinase-3β (GSK-3β).​ To elucidate the underlying molecular mechanism, this study employed molecular docking and molecular dynamics (MD) simulations. Molecular docking analyses revealed strong binding of rifampicin to TYRP1 (−6.6 kcal/mol), p38 MAPK (−9.6 kcal/mol), PKA (−9.2 kcal/mol), and GSK-3β (−8.5 kcal/mol), with affinities comparable to or exceeding those of their native ligands. In contrast, its affinity for PI3K was lower (−7.8 kcal/mol), suggesting limited involvement in the PI3K/AKT pathway.​ MD simulations confirmed the stability of rifampicin-protein complexes, as evidenced by consistent root-mean-square deviation (RMSD), radius of gyration, and solvent-accessible surface area (SASA) values, alongside minimal residue fluctuations and stable hydrogen bonds. Gibbs free energy landscape analysis further validated the compact, stable nature of these complexes. MM/GBSA calculations yielded favorable binding free energies (ΔG_total: –50.07 to –30.8 kcal/mol), with van der Waals interactions identified as the primary driver of binding. Key interacting residues included Leu382 (TYRP1), Tyr35 (p38 MAPK), Lys896 (PKA), Ile62 (GSK-3β), and Phe439 (PI3K).​ These findings support a multitarget mechanism for rifampicin in melanogenesis regulation and underscore its potential for repurposing as a therapeutic agent for hyperpigmentation.​