Cui, S. Y. | Search bioRxiv

bioRxiv2026

The fossil record of siliceous sponge spicules can be taken at face value

Modern sponges (Porifera) diverged by the Cryogenian, but their silicious skeletons do not appear in the fossil record until one hundred million years later, a time-span termed the "spicule gap" and thought to be a taphonomic artifact even though sponges convergently evolved siliceous spicules. Due to sponges position in animal phylogeny and important role in regulating ocean chemistry, the timing of their biomineralization has major implications for the changing tempo and mode of Earth systems as animals radiate. In a comprehensive dataset of Ediacaran and Cambrian sponges, we find that spicules are readily preserved in Cambrian environments more extreme than those of the Ediacaran. Given the convergent evolution of siliceous spicules, we find that the fossil record accurately represents when spicules first evolved in the different sponge lineages.

paleontology↗

bioRxiv2024

An SH3-binding allosteric modulator stabilizes the global conformation of the AML-associated Src-family kinase, Hck

While ATP-site inhibitors for protein-tyrosine kinases are often effective drugs, their clinical utility can be limited by off-target activity and acquired resistance mutations due to the conserved nature of the ATP-binding site. However, combining ATP-site and allosteric kinase inhibitors can overcome these shortcomings in a double-drugging framework. Here we explored the allosteric effects of two pyrimidine diamines, PDA1 and PDA2, on the conformational dynamics and activity of the Src-family tyrosine kinase Hck, a promising drug target for acute myeloid leukemia. Using 1H-15N HSQC NMR, we mapped the binding site for both analogs to the SH3 domain. Despite the shared binding site, PDA1 and PDA2 had opposing effects on near-full-length Hck dynamics by hydrogen-deuterium exchange mass spectrometry, with PDA1 stabilizing and PDA2 disrupting the overall kinase conformation. Kinase activity assays were consistent with these observations, with PDA2 enhancing kinase activity while PDA1 was without effect. Molecular dynamics simulations predicted selective bridging of the kinase domain N-lobe and SH3 domain by PDA1, a mechanism of allosteric stabilization supported by site-directed mutagenesis of N-lobe contact sites. Cellular thermal shift assays confirmed SH3 domaindependent interaction of PDA1 with wild-type Hck in myeloid leukemia cells and with a kinase domain gatekeeper mutant (T338M). These results identify PDA1 as a starting point for Src-family kinase allosteric inhibitor development that may work in concert with ATP-site inhibitors to suppress the evolution of resistance.

pharmacology and toxicology↗