Kazim, M. | bioRxiv Science

bioRxiv2025

Granzyme-targeting quenched activity-based probes for assessing tumor response to immunotherapy

Molecular imaging of immune activation holds tremendous potential for the development of novel immunotherapy. In particular, chemical probes capable of detecting immune responses before changes in tumor size occur can guide early therapeutic strategies. Here, we present quenched activity-based probes targeting granzymes as a biomarker of antitumor immunity. Through optimization of peptide recognition element and functional chemical warhead, we have developed an optical imaging probe Cy5-IEPCyaPhP-QSY21, which rapidly reacts with GzmB at substoichiometric concentrations and enables efficient, selective labeling of the active enzyme in a complex proteome. With high specificity and minimal background signal, this probe produces GzmB-induced near-infrared fluorescence signals in the tumors of living mice shortly after injection. Both in vivo and ex vivo fluorescence signals correlate with GzmB expression and activity, and the population of CD8+ cells in tumor tissues. Moreover, it demonstrates the potential to track tumor response to immunotherapy. Thus, this study offers a chemical tool for assessing immune-mediated anticancer activity using noninvasive optical imaging. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/643086v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1bff748org.highwire.dtl.DTLVardef@3c80dorg.highwire.dtl.DTLVardef@4301ceorg.highwire.dtl.DTLVardef@12b7c8a_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Bioinformatics techniques for efficient structure prediction of SARS-CoV-2 protein ORF7a via structure prediction approaches

Protein is the building block for all organisms. Protein structure prediction is always a complicated task in the field of proteomics. DNA and protein databases can find the primary sequence of the peptide chain and even similar sequences in different proteins. Mainly, there are two methodologies based on the presence or absence of a template for Protein structure prediction. Template-based structure prediction (threading and homology modeling) and Template-free structure prediction (ab initio). Numerous web-based servers that either use templates or do not can help us forecast the structure of proteins. In this current study, ORF7a, a transmembrane protein of the SARS-coronavirus, is predicted using Phyre2, IntFOLD, and Robetta. The protein sequence is straightforwardly entered into the sequence bar on all three web servers. Their findings provided information on the domain, the region with the disorder, the global and local quality score, the predicted structure, and the estimated error plot. Our study presents the structural details of the SARS-CoV protein ORF7a. This immunomodulatory component binds to immune cells and induces severe inflammatory reactions.

microbiology↗