To Bind or Not to Bind? A Comprehensive Characterization of TIR1 and Auxins Using Consensus In Silico Approaches

Author:

Prieto-Martínez Fernando D.1ORCID,Mendoza-Cañas Jennifer2ORCID,Martínez-Mayorga Karina13

Affiliation:

1. Instituto de Química Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz, Km. 4.5, Ucú 97357, Mexico

2. Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico

3. Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Mérida, Universidad Nacional Autónoma de México, Sierra Papacal, Mérida 97302, Mexico

Abstract

Auxins are chemical compounds of wide interest, mostly due to their role in plant metabolism and development. Synthetic auxins have been used as herbicides for more than 75 years and low toxicity in humans is one of their most advantageous features. Extensive studies of natural and synthetic auxins have been made in an effort to understand their role in plant growth. However, molecular details of the binding and recognition process are still an open question. Herein, we present a comprehensive in silico pipeline for the assessment of TIR1 ligands using several structure-based methods. Our results suggest that subtle dynamics within the binding pocket arise from water–ligand interactions. We also show that this trait distinguishes effective binders. Finally, we construct a database of putative ligands and decoy compounds, which can aid further studies focusing on synthetic auxin design. To the best of our knowledge, this study is the first of its kind focusing on TIR1.

Funder

CONAHCyT

Publisher

MDPI AG

Reference83 articles.

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