Absolute configuration and protein tyrosine phosphatase 1B inhibitory activity of xanthoepocin, a dimeric naphtopyrone from Penicillium sp. IQ-429

• Published in: Bioorganic chemistry 2021-10, Vol.115, p.105166-105166, Article 105166
• Main Authors: Martínez-Aldino, Ingrid Y., Villaseca-Murillo, Martha, Morales-Jiménez, Jesús, Rivera-Chávez, José
• Format: Article
• Language: English
• Subjects: Allosteric modulators/inhibitors; Allosteric Regulation - drug effects; Binding Sites; Catalytic Domain; Computational chemistry; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - metabolism; Enzyme Inhibitors - pharmacology; Epoxy Compounds - chemistry; Epoxy Compounds - metabolism; Epoxy Compounds - pharmacology; Half-Life; hPTP1B1-400; Humans; Kinetics; Molecular Docking Simulation; Molecular Dynamics Simulation; Penicillium - chemistry; Penicillium - metabolism; Penicillium sp; Protein Isoforms - antagonists & inhibitors; Protein Isoforms - metabolism; Protein Tyrosine Phosphatase, Non-Receptor Type 1 - antagonists & inhibitors; Protein Tyrosine Phosphatase, Non-Receptor Type 1 - metabolism; Pyrones - chemistry; Pyrones - metabolism; Pyrones - pharmacology; Thermodynamics; Xanthoepocin
• ISSN: 0045-2068; 1090-2120
• DOI: 10.1016/j.bioorg.2021.105166

[Display omitted] •The absolute configuration of xanthoepocin was determined to be 7R8S9R7′R8′S9′R.•Xanthoepocin inhibits hPTP1B1-400 in a concentration-dependent manner via a mixed mechanism.•Xanthoepocin binds to hPTP1B1-400, inducing large-scale conformational changes and disrupting the WPD loop dynamics.•Xanthoepocin inhibits hPTP1B1-400 by a different allosteric modulation mechanism that targets the C-terminal domain. Protein tyrosine phosphatase 1B (PTP1B) is an active target for developing drugs to treat type II diabetes, obesity, and cancer. However, in the past, research programs targeting this enzyme focused on discovering inhibitors of truncated models (hPTP1B1-282, hPTP1B1-298, or hPTP1B1-321), losing valuable information about the ligands' mechanism of inhibition and selectivity. Nevertheless, finding an allosteric site in hPTP1B1-321, and the full-length (hPTP1B1-400) protein expression, have shifted the strategies to discover new PTP1B inhibitors. Accordingly, as part of a research program directed at finding non-competitive inhibitors of hPTP1B1-400 from Pezizomycotina, the extract of Penicillium sp. (IQ-429) was chemically investigated. This study led to xanthoepocin (1) isolation, which was elucidated by means of spectroscopic and spectrometric data. The absolute configuration of 1 was determined to be 7R8S9R7′R8′S9′R by comparing the theoretical and experimental ECD spectra and by GIAO-NMR DP4 + statistical analysis. Xanthoepocin (1) inhibited the phosphatase activity of hPTP1B1-400 (IC50 value of 8.8 ± 1.0 µM) in a mixed type fashion, with ki and αki values of 5.5  and 6.6 μM, respectively. Docking xanthoepocin (1) with a homologated model of hPTP1B1-400 indicated that it binds in a pocket different from the catalytic triad at the interface of the N and C-terminal domains. Molecular dynamics (MD) simulations showed that 1 locks the WPD loop of hPTP1B1-400 in a closed conformation, avoiding substrate binding, products release, and catalysis, suggesting an allosteric modulation triggered by large-scale conformational and dynamics changes. Intrinsic quenching fluorescence experiments indicated that 1 behaves like a static quencher of hPTP1B1-400 (KSV = 1.1 × 105 M−1), and corroborated that it binds to the enzyme with an affinity constant (ka) of 3.7 × 105 M−1. Finally, the drug-likeness and medicinal chemistry friendliness of 1 were predicted with SwissADME.