An ECD and NMR/DP4+ Computational Pipeline for Structure Revision and Elucidation of Diphenazine-Based Natural Products

• Published in: Journal of natural products (Washington, D.C.) Vol. 86; no. 7; pp. 1801 - 1814
• Main Authors: Zhuang, Yihao, Yang, Fei, Menon, Arya, Song, James M., Espinoza, Rosa V., Schultz, Pamela J., Garner, Amanda L., Tripathi, Ashootosh
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society and American Society of Pharmacognosy 28-07-2023
• Subjects: Biological Products - chemistry; Magnetic Resonance Spectroscopy; Molecular Structure; Phenazines - chemistry; Phenol
• ISSN: 0163-3864; 1520-6025; 1520-6025
• DOI: 10.1021/acs.jnatprod.3c00306

Discovery and structure elucidation of natural products available in infinitesimally small quantities are recognized challenge. This challenge is epitomized by the diphenazine class of molecules that contain three bridged stereocenters, several conformations, ring fusions, and multiple spatially isolated phenols. Because empirical NMR and spatial analyses using ROESY/NOESY were unsuccessful in tackling these challenges, we developed a computational pipeline to determine the relative and absolute configurations and phenol positions of diphenazines as inhibitors of eukaryotic translation initiation factor 4E (eIF4E) protein–protein interactions. In this pipeline, we incorporated ECD and GIAO NMR calculations coupled with a DP4+ probability measure, enabling the structure revision of phenazinolin D (4), izumiphenazine A (5), and baraphenazine G (7) and the structure characterization of two new diphenazines, baraphenazine H (3) and izumiphenazine E (6). Importantly, through these efforts, we demonstrate the feasibility of NMR/DP4+ analysis for the determination of phenol positions in phenazine-based molecules, further expanding the limits of computational methods for the structure elucidation of complex natural products.