Discovery of a Broad-Spectrum Fluorogenic Agonist for Strigolactone Receptors through a Computational Approach

Abstract

Strigolactones (SLs) are plant hormones that play various roles in plant physiology, including provoking the germination of parasitic weeds Orobanche and Striga. A family of α/β-hydrolases have been proposed to be the SL receptor proteins. Effective assays for measuring the activity of SL receptors could promote the development of SL-related biology and chemistry. In this study, we developed a new approach called pharmacophore-linked probe virtual screening (PPVS). Its application yielded an effective "off−on" probe named Xilatone Red (XLR). This probe showed a broad spectrum and excellent sensitivity toward SL receptors, including ShD14 (Striga D14), for which the detection limit was determined to be in the micromolar range, outperforming that of the commercial fluorogenic agonist Yoshimulactone Green (YLG). Upon hydrolysis by SL receptors, XLR provided fluorogenic and colorimetric signaling responses. Furthermore, XLR could induce germination of Phelipanche aegyptiaca seeds and prevent Arabidopsis max4-1 branching defects at micromolar concentrations. Our molecular simulations revealed the essential factors in the molecular perception of XLR. We anticipate that this study can prompt the discovery of high-performance SL agonists/antagonists to combat parasitic weeds.

Expansion of the Strigolactone Profluorescent Probes Repertory: The Right Probe for the Right Application

“…These molecules could be valuable tools to study the effect of substitutions on the coumarin moiety, especially to evaluate the influence of the molecule reactivity (p K a of the leaving group) and hydrophobicity (log P ) on both biological and biochemical activity toward the various SL receptors, in order to perform SAR studies ( Figure 2 ). A resorufin moiety was also targeted [(±)-GC93 = XLR (Wang et al, 2021 ), (±)-GC247 ( Figure 2 )], which has optical properties compatible for in planta imaging, contrary to coumarins. The excitation and emission maxima of resorufin (568 and 581 nm) and fluorescein (475 and 520 nm) made it suitable for use in plant tissue imaging compared to the other fluorophores (coumarin and DiFMU, 350–360 and 450–460 nm; Figure 3 , Supplementary Figure 1 ).…”

“…Thanks to the structure–activity relationship (SAR) studies, fluorescent-labeled SLs have been designed by replacing the editable SL cargo group with a fluorophore, which becomes fluorescent only after perception and cleavage of the D-ring ( Figure 1B ). These so-called profluorescent probes allow the dynamic/temporal monitoring of the enzymatic activity of SL receptors in vitro (Tsuchiya et al, 2015 ; de Saint Germain et al, 2016 ; Wang et al, 2021 ) and in planta (Tsuchiya et al, 2015 , 2018 ; Wang et al, 2021 ).…”

“…The YLG is commercially available and has been used thereafter to identify SL receptor antagonists as tolfenamic acid (Hamiaux et al, 2018 ), KK094, and DL1b (Nakamura et al, 2019 ; Yoshimura et al, 2020 ) toward DAD2 and AtD14 proteins, respectively, highlighting the usefulness of this probe. Very recently, a novel resorufin-based SL profluorescent probe, Xilatone Red (XLR) based on a resorufin moiety has been developed (Wang et al, 2021 ).…”

In Silico Structure-Guided Optimization and Molecular Simulation Studies of 3-Phenoxy-4-(3-trifluoromethylphenyl)pyridazines as Potent Phytoene Desaturase Inhibitors

“…To understand the binding details of the synthesized inhibitors to Synechococcus PDS, we carried out molecular dynamic (MD) simulation studies for the representative compound 2a with Synechococcus PDS. First, we docked 2a to the active site of Synechococcus PDS using Autodock 4 software, and the best binding mode of 2a to the protein was selected, based on the binding score [19]. Next, we performed a 30 ns MD simulation of the 2a-Synechococcus PDS complex using the Amber14 program (Figure 4A).…”

“…The structure of Synechococcus PDS was built based on chain A of the structure of OsPDS (PDB id: 5MOG) by MODELER 9v19 [14,15], then optimized using Amber 14 [27,28]. The docking of 1 and 2a to the catalytic site of Synechococcus PDS was performed using Autodock 4 [16], and the best binding mode of each molecule was selected based on the docking score [19,29]. The parameters for the molecular dynamic (MD) simulations were prepared using the tleap program, the optimization of the 2a-Synechococcus PDS complex was performed using Sander, and the production of MD was performed using the pmemd module.…”