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The Chemical Educator

ISSN: 1430-4171 (electronic version)

Table of Contents

Abstract Volume 22 (2017) pp 146-150

Neurotransmitter Flexible Alignment and Pharmacophore Development with MOE Software

Trent N. Ford and Donna H. Perygin*,†

Physical and Earth Sciences, Jacksonville State University, 700 Pelham Road North, Jacksonville, AL 36265,; Chemistry Department, University of Alabama, Tuscaloosa, AL
Received May 24, 2017. Accepted August 7, 2017.

Published: 27 September 2017

Abstract. This computational exercise introduces first-year Organic students to pharmaceutical chemistry, by guiding them through the identification of novel neurotransmitters. The process includes building in-silico models of known neurotransmitters, creating a flexible alignment of the molecules in MOE, generating a pharmacophore model from that alignment, and finally performing an online database search through the Pharmit portal. Students then analyze the results to identify the molecules most likely to have similar pharmacophore features, and therefore are the most likely to be suitable novel neurotransmitters. In our study, students submitted their data for further refinement. While gaining experience with the MOE software suite, this process gives students first-hand experience with high throughput screening via in-silico simulations and pharmacophore searching.

Key Words: Computers in Chemistry; organic chemistry; computational chemistry; pharmaceutical chemistry

(*) Corresponding author. (E-mail:

Article in PDF format (167 KB) HTML format

Supporting Materials:

A supporting file of the Molecular Modeling Laboratory handout is available. (429 KB)

The Chemical Educator 1996-2017