Biology subjects

Napolitano, V.

Publications and source records attributed to Napolitano, V..

3 recordsLinked to original sources

bioRxiv2025

The essential co-chaperone Sgt1 regulates client dwell time in the Hsp90 chaperone cycle

The Hsp90 machinery is the most complex chaperone system in the eukaryotic cell. It is characterized by numerous co-chaperones that modulate the function of Hsp90. In S. cerevisiae, most of these cofactors can be deleted without affecting viability. Of the three essential ones, only the function of Sgt1 remained enigmatic. Our in vivo and in vitro experiments define key structural elements and determine the essential function of Sgt1 in the chaperoning of client proteins. We show that yeast Sgt1 exhibits a unique binding mode to Hsp90. The simultaneous interaction of Sgt1 with Hsp90 and client proteins enhances client maturation efficiency. Specifically, Sgt1 stabilizes Hsp90-client complexes and prevents their dissociation by the co-chaperone Aha1. Together, our findings reveal a distinct regulatory mechanism of the Hsp90 function, highlighting Sgt1 as a critical modulator of chaperone cycle progression.

biochemistry↗

bioRxiv2024

Quantum Chemistry in a Pocket: A Multifaceted Tool to Link Structure and Activity

We introduce In-Pocket Analysis, a simple and efficient protein-ligand complex structure optimization algorithm. It provides structural biology and structure-based drug discovery with a much-needed tool for data curation and quantification analysis. In-pocket analysis removes unphysical tension from experimental structures, yielding high-quality atomic models. This includes deformed bonds, structural clashes, proton refinement, and solvent envelope. The algorithm is compatible with quantum methods or force fields, delivering precise calculations of binding energies and QSAR. Its applications include refinement of experimental structures, calculation of inter- and intramolecular energetics, scoring of docked poses, scaffold decoration/hopping, or building of explainable QSAR. For validation and benchmarking we used high-resolution crystal structures of the N-terminal domain of PEX14 with small-molecule inhibitors. PEX14 is a target candidate against Trypanosomiasis and Leishmaniasis. The application of our algorithm allowed for an explanation of unexpected binding poses, rationalization of binding energies, and affinities as well as precise quantification of solvent-mediated interactions. TABLE OF CONTENTS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/590615v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@11f4173org.highwire.dtl.DTLVardef@1020358org.highwire.dtl.DTLVardef@12986ecorg.highwire.dtl.DTLVardef@1590617_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2021

Acriflavine, a clinically aproved drug, inhibits SARS-CoV-2 and other betacoronaviruses

SO_SCPLOWUMMARYC_SCPLOWThe COVID-19 pandemic caused by SARS-CoV-2 has been socially and economically devastating. Despite an unprecedented research effort, effective therapeutics are still missing to limit severe disease and mortality. Using high-throughput screening, we identified acriflavine as a potent papain-like protease (PLpro) inhibitor. NMR titrations and a co-crystal structure confirm that acriflavine blocks the PLpro catalytic pocket in an unexpected binding mode. We show that the drug inhibits viral replication at nanomolar concentration in cellular models, in vivo in mice and ex vivo in human airway epithelia, with broad range activity against SARS-CoV-2 and other betacoronaviruses. Considering that acriflavine is an inexpensive drug approved in some countries, it may be immediately tested in clinical trials and play an important role during the current pandemic and future outbreaks.

microbiology↗