Comparative molecular dynamics simulations of mitogen-activated protein kinase-activated protein kinase 5

Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis

Ostrinia furnacalis is a species of moth in the Crambidae family that is harmful to maize and other corn crops in Southeast Asia and the Western Pacific regions. Ostrinia furnacalis causes devastating losses to economically important corn fields. The β-N-acetyl-D-hexosaminidase is an essential enzyme in O. furnacalis and its substrate binding +1 active site is different from that of the plants and humans β-N-acetyl-D-hexosaminidases. To develop environment-friendly insecticides against OfHex1, we conducted structure-guided computational insecticide discovery to identify potential inhibitors that can bind the active site and inhibit the substrate binding and activity of the enzyme. We adopted a three-pronged strategy to conduct virtual screening using Glide and virtual screening workflow (VSW) in Schrödinger Suite-2022-3, against crystal structures of OfHex1 (PDB Id:3NSN), its homologue in humans (PDB Id: 1NP0) and Alphafold model of β-N-acetyl-D-hexosaminidase from Trichogramma pretiosum, an egg parasitoid that protects the crops from O. furnacalis. A library of 20,313 commercially available and "insecticide-like" compounds was extracted from published literature. LigPrep enabled 44,943 ready-to-dock conformers generation. Glide docking revealed 18 OfHex1-specific hits that were absent in human and T. pretiosum screens. Reference docking was conducted using inhibitors/natural ligands in the crystal structures and hits with better docking scores than the reference were selected for MD simulations using Desmond to understand the stability of hit-target interactions. We noted five compounds that bound to OfHex1 TMX active-site based on their docking scores, consistent binding as noted by MD simulations and their insecticide/pesticide likeliness as noted by the Comprehensive Pesticide Likeness Analysis.Communicated by Ramaswamy H. Sarma.

The functional regulatory details of ERK2 in complex with RSK1: an in silico insight

Protein kinases play a significant role in cellular activation procedures by exhibiting a vivid selection in the target, as well as recognizing and phosphorylating them. Extracellular signal-regulated kinase 2 (ERK2) is one of the main kinases in the mitogen-activated protein kinase (MAPK) signaling cascade and engages in dynamically regulating the activities of signaling proteins and physiological processes, including cell proliferation, differentiation, adhesion, migration, and survival. Predicting collective dynamic and structural motions in biological macromolecules is pivotal to obtain a better understanding of the majority of biological processes. Here, through molecular dynamic simulation and normal mode analysis, we investigated ERK2 conformations, in the forms of active (phosphorylated), inactive (unphosphorylated), and in a complex with its substrate, ribosomal protein S6 kinase alpha-1 (RSK1), to determine functional characteristics. Our finding demonstrated that ERK2 plays a switch role in the regulation of pathways. In the case that this protein kinase is in the active form, all critical regions shift to be prepared to accept the substrate and catalytic action. Meanwhile, inactive ERK2 shows contrasting results in which all motions tend to close the catalytic site and cease the phosphorylation action in the MAPK cascade. These findings are in line with those from other similar studies and provide us with novel molecular target regions and recent details on how this mechanism works.

DFG, αC-helix orientation regarding the active site position and distance between K54 and Glu71 in the active and inactive states of ERK2.

MK5: A novel regulator of cardiac fibroblast function?

MAP kinase-activated protein kinases (MKs), protein serine/threonine kinases downstream of the MAPKs, regulate a number of biological functions. MK5 was initially identified as a substrate for p38 MAPK but subsequent studies revealed that MK5 activity is regulated by atypical MAPKs ERK3 and ERK4. However, the roles of these MAPKs in activating MK5 remain controversial. The interactome and physiological function of MK5 are just beginning to be understood. Here, we provide an overview of the structure-function of MK5 including recent progress in determining its role in cardiac structure and function. The cardiac phenotype of MK5 haplodeficient mice, and the effect of reduced MK5 expression on cardiac remodeling, is also discussed. © 2017 IUBMB Life, 69(10):785-794, 2017.

Gatekeeper tyrosine phosphorylation is autoinhibitory for Symbiosis Receptor Kinase

Plant receptor-like kinases (RLKs) are distinguished by having a tyrosine in the 'gatekeeper' position. Previously we reported Symbiosis Receptor Kinase from Arachis hypogaea (AhSYMRK) to autophosphorylate on the gatekeeper tyrosine (Y670), though this phosphorylation was not necessary for the kinase activity. Here we report that recombinant catalytic domain of AhSYMRK with a phosphomimic substitution in the gatekeeper position (Y670E) is catalytically almost inactive and is conformationally quite distinct from the corresponding native enzyme. Additionally, we show that gatekeeper-phosphorylated AhSYMRK polypeptides are inactive and depletion of this inactive form leads to activation of intramolecular autophosphorylation of AhSYMRK. Together, our results suggest gatekeeper tyrosine autophosphorylation to be autoinhibitory for AhSYMRK.