C-Type LECTIN receptor-like kinase 1 and ACTIN DEPOLYMERIZING FACTOR 3 are key components of plasmodesmata callose modulation.

Plasmodesmata (PDs) are intercellular organelles carrying multiple membranous nanochannels that allow the trafficking of cellular signalling molecules. The channel regulation of PDs occurs dynamically and is required in various developmental and physiological processes. It is well known that callose is a critical component in regulating PD permeability or symplasmic connectivity, but the understanding of the signalling pathways and mechanisms of its regulation is limited. Here, we used the reverse genetic approach to investigate the role of C-type lectin receptor-like kinase 1 (CLRLK1) in the aspect of PD callose-modulated symplasmic continuity. Here, we found that loss-of-function mutations in CLRLK1 resulted in excessive PD callose deposits and reduced symplasmic continuity, resulting in an accelerated gravitropic response. The protein interactome study also found that CLRLK1 interacted with actin depolymerizing factor 3 (ADF3) in vitro and in plants. Moreover, mutations in ADF3 result in elevated PD callose deposits and faster gravitropic response. Our results indicate that CLRLK1 and ADF3 negatively regulate PD callose accumulation, contributing to fine-tuning symplasmic opening apertures. Overall, our studies identified two key components involved in the deposits of PD callose and provided new insights into how symplasmic connectivity is maintained by the control of PD callose homoeostasis.

Computational studies of novel chymase inhibitors against cardiovascular and allergic diseases: mechanism and inhibition.

To provide a new idea for drug design, a computational investigation is performed on chymase and its novel 1,4-diazepane-2,5-diones inhibitors that explores the crucial molecular features contributing to binding specificity. Molecular docking studies of inhibitors within the active site of chymase were carried out to rationalize the inhibitory properties of these compounds and understand their inhibition mechanism. The density functional theory method was used to optimize molecular structures with the subsequent analysis of highest occupied molecular orbital, lowest unoccupied molecular orbital, and molecular electrostatic potential maps, which revealed that negative potentials near 1,4-diazepane-2,5-diones ring are essential for effective binding of inhibitors at active site of enzyme. The Bayesian model with receiver operating curve statistic of 0.82 also identified arylsulfonyl and aminocarbonyl as the molecular features favoring and not favoring inhibition of chymase, respectively. Moreover, genetic function approximation was applied to construct 3D quantitative structure-activity relationships models. Two models (genetic function approximation model 1 r(2) = 0.812 and genetic function approximation model 2 r(2) = 0.783) performed better in terms of correlation coefficients and cross-validation analysis. In general, this study is used as example to illustrate how combinational use of 2D/3D quantitative structure-activity relationships modeling techniques, molecular docking, frontier molecular orbital density fields (highest occupied molecular orbital and lowest unoccupied molecular orbital), and molecular electrostatic potential analysis may be useful to gain an insight into the binding mechanism between enzyme and its inhibitors.

Molecular docking and dynamics simulation, receptor-based hypothesis: application to identify novel sirtuin 2 inhibitors.

Sirtuin, NAD(+)-dependent histone deacetylase enzyme, emerged as a potential therapeutic target, and modulations by small molecules could be effective drugs for various diseases. Owing to the absence of complex structure of sirtuin 2 (SIRT2), sirtinol was docked in the NAD(+) binding site and subjected to 5-nseconds molecular dynamics (MD) simulation. LigandScout was used to develop hypotheses based on 3-representative SIRT2 complex structures from MD. Three structure-based hypotheses are generated and merged to form dynamics hypothesis. The dynamics hypothesis was validated using test and decoy sets. The results showed that dynamic hypothesis represents the complementary features of SIRT2 active site. Dynamic hypothesis was used to screen ChemDiv database, and hits were filtered through ADMET, rule of five, and two different molecular docking studies. Finally, 21 molecules were selected as potent leads based on consensus score from LigandFit, Gold fitness score, binding affinity from VINA as well as based on the important interactions with critical residues in SIRT2 active site. Hence, we suggest that the dynamic hypothesis will be reliable in the identification of SIRT2 new lead as well as to reduce time and cost in the drug discovery process.