Mechanism of the Temperature-Dependent Self-Assembly and Polymorphism of Chitin

Chitin is the second most abundant natural biopolymer. Its crystalline structures have been extensively studied. However, the mechanism of chitin’s self-assembly is unknown. Here, we applied all-atom molecular dynamics to study chitin’s self-assembly process at different temperatures. Strikingly, at 278 K, an amorphous aggregate was formed, whereas at 300 K single-sheet and at 323 K both single-sheet and multisheet nanofibril regions were formed. The nanofibrils contain antiparallel, parallel, or mixed orientation chains, with antiparallel being slightly preferred, recapitulating chitin’s polymorphism observed in nature. The inverse temperature dependence is consistent with a recent experiment conducted in the aqueous KOH/urea solution. The analysis suggested that the multisheet nanofibrils are assembled by stacking the single nanofibril sheets, which are formed through two types of pathways in which hydrophobic collapse either precedes or is concomitant with the increasing number of interchain hydrogen bonds and solvent expulsion. Furthermore, the antiparallel and parallel chains are mediated by different interchain hydrogen bonds. The analysis also suggested that the inverse temperature dependence may be attributed to the hydrophobic effect reminiscent of the low critical solution temperature phase behavior. The present study provides a rich, atomic-level view of chitin’s polymorphic self-assembly process, paving the way for the rational design of chitin-derived novel materials

Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases

The ERK pathway is one of the most important signaling cascades involved in tumorigenesis. So far, eight noncovalent inhibitors of RAF and MEK kinases in the ERK pathway have been approved by the FDA for the treatment of cancers; however, their efficacies are limited due to various resistance mechanisms. There is an urgent need to develop novel targeted covalent inhibitors. Here we report a systematic study of the covalent ligandabilities of the ERK pathway kinases (ARAF, BRAF, CRAF, KSR1, KSR2, MEK1, MEK2, ERK1, and ERK2) using constant pH molecular dynamics titration and pocket analysis. Our data revealed that the hinge GK (gate keeper)+3 cysteine in RAF family kinases (ARAF, BRAF, CRAF, KSR1, and KSR2) and the back loop cysteine in MEK1 and MEK2 are reactive and ligandable. Structure analysis suggests that the type II inhibitors belvarafenib and GW5074 may be used as scaffolds for designing pan-RAF or CRAF-selective covalent inhibitors directed at the GK+3 cysteine, while the type III inhibitor cobimetinib may be modified to label the back loop cysteine in MEK1/2. The reactivities and ligandabilities of the remote cysteine in MEK1/2 and the DFG-1 cysteine in MEK1/2 and ERK1/2 are also discussed. Our work provides a starting point for medicinal chemists to design novel covalent inhibitors of the ERK pathway kinases. The computational protocol is general and can be applied to the systematic evaluation of covalent ligandabilities of the human cysteinome