3D similarities between the binding sites of monoaminergic target proteins

PloS One
Gabriel Núñez-VivancoMiguel Reyes-Parada

Abstract

The study of binding site similarities can be relevant to understand the interaction of different drugs at several molecular targets. The increasing availability of protein crystal structures and the development of novel algorithms designed to evaluate three-dimensional similarities, represent a great opportunity to explore the existence of electronic and shape features shared by clinically relevant proteins, which could assist drug design and discovery. Proteins involved in the recognition of monoaminergic neurotransmitters, such as monoamine transporters or monoamine oxidases (MAO) have been related to several psychiatric and neurological disorders such as depression or Parkinson's disease. In this work, we evaluated the possible existence of similarities among the binding sites of the serotonin transporter (SERT), the dopamine transporter (DAT), MAO-A and MAO-B. This study was carried out using molecular simulation methodologies linked to the statistical algorithm PocketMatch, which was modified in order to obtain similarities profiles. Our results show that DAT and SERT exhibit a high degree of 3-D similarities all along the pathway that is presumably involved in the substrate transport process. Distinct differences, on the...Continue Reading

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Citations

Jul 3, 2019·International Journal of Molecular Sciences·Alejandro Valdés-JiménezMiguel Reyes-Parada
Feb 11, 2020·Frontiers in Pharmacology·Miguel Reyes-ParadaBruce K Cassels
Nov 19, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Fabrizzio G GuajardoRamón Sotomayor-Zárate

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Methods Mentioned

BETA
X-ray

Software Mentioned

BLAST
MAO
SERT
MultiBind
NAMD
Procheck
VMD
NAMD2
PROSAII

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