Author: Andrey Alekseenko

Dr. Kozakov and Dr. Padhorny in collaboration with researchers from Boston University and Boston National Emerging Infectious Diseases Laboratories (NEIDL), have analyzed the difference in phosphorylation patterns between SARS-COV2 virus-infected and healthy alveolar lung cell (AT2). This survey revealed 4,688 differential phosphosites mapping to 1,166 unique proteins, which were clustered into distinct clusters based on temporal enrichment, associated with protein domains and cellular processes linked to infection, such as viral messenger RNA synthesis and export of viral ribonucleoproteins, as an immediate response to SARS- CoV-2 entry. Our group has performed in silico structural modeling of experimentally observed viral-host protein-protein interactions, using award-winning computational tools developed in our lab. That enabled us to structurally characterize the interactions that were detected in MS experiments and independently corroborate experimental observations. Our modeling identified several key types of proteins that dominated these interactions, including the kinases of GSK3, MAPK, and CK1 families, and a number of other targets. We hypothesized that modulating those targets might have antiviral effect. We have identified and modeled interactions of several clinically safe compounds from BROAD database targeting those families using our award wining LigTBM molecular modeling approach. Six of the selected compounds have efficiently inhibited viral replication by more than 90% in the AT2 lung cells. The paper has appeared in Molecular Cell.

During the current crisis, it is everyone’s responsibility to make their best efforts. Our group is now targeting the research towards the search of new compounds targeting SARS-CoV-2 proteins. We tightly collaborate with experimental and computational groups on these projects. Besides doing our part in helping with the current epidemic, we hope that the methods and tools developed will allow faster response to future viral threats. More information is available on a dedicated page: https://abcgroup.cluspro.org/research/covid-19/

On April 28th, the results of the IACS Seed Grant competition were announced. The joint project of our group and Dr. Rezaul Chowdhury, “Speeding up flexible peptide-protein docking using convolutional neural networks,” was chosen as one of the two winners. We’re grateful for this support and are happy that the grant committee shares our belief in the idea of applying state-of-the-art deep learning methodology to the notorious for its complexity important scientific and medical problem of structure prediction of protein-peptide complexes.