Discovery of a Novel Small-Molecule Modulator for Full-length YB-1 Protein via Integrated Computational and in vitro Biophysical Approaches.

The human Y-box binding protein (YB-1) is a multifaceted protein that plays a crucial role in the progression of diseases such as HIV, cancer, and therapy resistance. The absence of a resolved three-dimensional structure of YB-1 has hindered efforts to design potential allosteric modulators targeting full protein. Our study unveils the first comprehensive structural model of YB-1 protein. We validated this structure via 300 ns molecular dynamics (MD) simulations and mapped the YB-1 interaction protein (PPIs) network to better understand its role in disease progression. Then, we designed four 1,4-naphthoquinone analogues as potential YB-1 small molecule modulators and evaluated their drug-like properties. Among them, AIGM-2024–4 showed favorable binding affinity with YB-1, and its interaction stability assessed through 300 ns MD. We synthesized this modulator utilizing chemo-selective functionalization and confirmed its interactions with recombinant full-length YB-1 protein validated through Microscale Thermophoresis (MST). The biophysical interaction validation confirms our in silico investigations, with AIGM-2024–4 demonstrating a ̴15.8% higher binding affinity with YB-1 compared to a control molecule, fisetin. Thus, AIGM-2024–4 shows promise for developing a new class of YB-1 inhibitors for the treatment of diseases associated with YB-1.