Computationally assisted assignment of kahalalide Y configuration using an NMR-constrained conformational search.

ABSTRACT: Assignment of the absolute configuration of cyclic peptides frequently yields challenges, leaving one or more stereogenic centers unassigned due to small quantities of sample and the limited utility of Marfey's or other methods for assigning amino or hydroxy acids. Here, we report isolation of kahalalide Y (1) from Bryopsis pennata for the first time; in addition, the application of a combination of molecular modeling and NOE distance constraint calculations was utilized to determine the conformation of 1 and the absolute configuration of the final stereogenic center of 1. Using the Schrödinger suite, the structure of 1 was sketched in Maestro and minimized using the OPLS2005 force field in Macromodel. A conformational search was performed separately for structures having an R or S configu

SUBMITTER: Albadry MA 

PROVIDER: S-EPMC3583380 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature