Conformational templates for rational drug design: Flexibility of cyclo(D-Pro1Ala2-Ala3-Ala4-Ala 5) in DMSO solution

Xiaoming Zhang, Gregory V. Nikiforovich, Garland R. Marshall

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

Long MD simulations (100 ns) for the important model cyclopentapeptide cyclo(D-Pro1-Ala2-Ala3-Ala4-Ala 5) were performed in explicit DMSO solution using both OPLS-AA and AMBER03 force fields. Simulations revealed conformational transitions between two main conformers, a predominant one (population 93-99%) and a minor conformer (population 0.4-6.7%). These results are in excellent agreement with 20 experimental proton-proton distances estimated for this cyclopentapeptide. The previously discussed γ-turn-like conformation for Ala4 was present only in a minor conformer.

Original languageEnglish
Pages (from-to)2921-2925
Number of pages5
JournalJournal of Medicinal Chemistry
Volume50
Issue number12
DOIs
StatePublished - Jun 14 2007

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