Biology subjects

Montelione, G. T.

Publications and source records attributed to Montelione, G. T..

3 recordsLinked to original sources

bioRxiv2020

Hepatitis C Virus Drugs Simeprevir and Grazoprevir Synergize with Remdesivir to Suppress SARS-CoV-2 Replication in Cell Culture

Effective control of COVID-19 requires antivirals directed against SARS-CoV-2 virus. Here we assess ten available HCV protease inhibitor drugs as potential SARS-CoV-2 antivirals. There is a striking structural similarity of the substrate binding clefts of SARS- CoV-2 Mpro and HCV NS3/4A proteases, and virtual docking experiments show that all ten HCV drugs can potentially bind into the Mpro binding cleft. Seven of these HCV drugs inhibit SARS-CoV-2 Mpro protease activity, while four dock well into the PLpro substrate binding cleft and inhibit PLpro protease activity. These same seven HCV drugs inhibit SARS-CoV-2 virus replication in Vero and/or human cells, demonstrating that HCV drugs that inhibit Mpro, or both Mpro and PLpro, suppress virus replication. Two HCV drugs, simeprevir and grazoprevir synergize with the viral polymerase inhibitor remdesivir to inhibit virus replication, thereby increasing remdesivir inhibitory activity as much as 10-fold. HighlightsO_LISeveral HCV protease inhibitors are predicted to inhibit SARS-CoV-2 Mpro and PLpro. C_LIO_LISeven HCV drugs inhibit Mpro enzyme activity, four HCV drugs inhibit PLpro. C_LIO_LISeven HCV drugs inhibit SARS-CoV-2 replication in Vero and/or human cells. C_LIO_LIHCV drugs simeprevir and grazoprevir synergize with remdesivir to inhibit SARS- CoV-2. C_LI eTOC blurbBafna, White and colleagues report that several available hepatitis C virus drugs inhibit the SARS-CoV-2 Mpro and/or PLpro proteases and SARS-CoV-2 replication in cell culture. Two drugs, simeprevir and grazoprevir, synergize with the viral polymerase inhibitor remdesivir to inhibit virus replication, increasing remdesivir antiviral activity as much as 10-fold. O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/422511v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1c12181org.highwire.dtl.DTLVardef@7ed993org.highwire.dtl.DTLVardef@1fe56aaorg.highwire.dtl.DTLVardef@ebc34e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins

The extra-terminal (ET) domain of BRD3 is conserved among BET proteins (BRD2, BRD3, BRD4), interacting with multiple host and viral protein-protein networks. Solution NMR structures of complexes formed between BRD3-ET domain with either the 79-residue murine leukemia virus integrase (IN) C-terminal domain (IN329-408), or its 22-residue IN tail peptide (TP) (IN386-407) alone, reveal similar intermolecular three-stranded {beta}-sheet formation. 15N relaxation studies reveal a 10-residue linker region (IN379-388) tethering the SH3 domain (IN329-378) to the ET-binding motif (IN389-405)-ET complex. This linker has restricted flexibility, impacting its potential range of orientations in the IN - nucleosome complex. The complex of the ET-binding peptide of host NSD3 protein (NSD3148-184) and BRD3-ET domain includes a similar three-stranded {beta}-sheet interaction, but the orientation of the {beta}-hairpin is flipped compared to the two IN : ET complexes. These studies expand our understanding of molecular recognition polymorphism in complexes of ET-binding motifs with viral and host proteins. HighlightsO_LIThe BRD3 ET domain binds to key peptide motifs of diverse host and viral proteins. C_LIO_LIThese complexes reveal conformational plasticity in molecular recognition. C_LIO_LINMR studies demonstrate restricted interdomain motion in the IN CTD / ET complex. C_LIO_LIA cost-effective approach is described for producing isotopically-labeled peptides. C_LI Etoc BlurbWe address structurally how the MLV Integrase (IN) usurps the host function of the BET protein through comparative studies of the IN : Brd3 ET complex with that of the host NSD3. MLV integration and thus its pathogenesis is driven through protein interactions of the IN : BET family.

microbiology↗

bioRxiv2020

REDCRAFT: A Computational Platform Using Residual Dipolar Coupling NMR Data for Determining Structures of Perdeuterated Proteins Without NOEs

Nuclear Magnetic Resonance (NMR) spectroscopy is one of the two primary experimental means of characterizing macromolecular structures, including protein structures. Structure determination by NMR spectroscopy has traditionally relied heavily on distance restraints derived from nuclear Overhauser effect (NOE) measurements. While structure determination of proteins from NOE-based restraints is well understood and broadly used, structure determination by NOEs imposes increasing quantity of data for analysis, increased cost of structure determination and is less available in the study of perdeuterated proteins. In the recent decade, Residual Dipolar Couplings (RDCs) have been investigated as an alternative source of data for structural elucidation of proteins by NMR. Several methods have been reported that utilize RDCs in addition to NOEs, and a few utilize RDC data alone. While these methods have individually demonstrated some successes, none of these methods have exposed the full potential of protein structure determination from RDCs. To date, structure determination of proteins from RDCs is limited to small proteins (less than 8.5 kDa) using RDC data from many alignment media (>3) that cannot be collected from larger proteins. Here we present the latest version of the REDCRAFT software package designed for structure determination of proteins from RDC data alone. We have demonstrated the success of REDCRAFT in structure determination of proteins ranging in size from 50 to 145 residues using experimentally collected data and large proteins (145 to 573 residues) using simulated RDC data that can be collected from perdeuterated proteins. Finally, we demonstrate the accuracy of structure determination of REDCRAFT from RDCs alone in application to the structurally novel PF.2048 protein. The RDC-based structure of PF.2048 exhibited 1.0 [A] of BB-RMSD with respect to the NOE-based structure by only using a small amount of backbone RDCs ([~]3 restraints per residue) compared to what is required by other approaches. Author SummaryResidual Dipolar Couplings have the potential to reduce the cost and the time needed to characterize protein structures. In addition, RDC data have been demonstrated to concurrently elucidate structure of proteins, perform assignment of resonances, and be used in characterization of the internal dynamics of proteins. Given all the advantages associated with the study of proteins from RDC data, based on the statistics provided by the Protein Databank (PDB), surprisingly the only 124 proteins (out of nearly 150,000 proteins) have utilized RDCs as part of their structure determination. Even a smaller subset of these proteins (approximately 7) have utilized RDCs as the primary source of data for structure determination. The impeding factor in the use of RDCs is the challenging computational and analytical aspects of this source of data. In this report, we demonstrate the success of the REDCRAFT software package in structure determination of proteins using RDC data that can be collected from small and large proteins in a routine fashion. REDCRAFT accomplishes the challenging task of structure determination from RDCs by introducing a unique search and optimization technique that is both robust and computationally tractable. Structure determination from routinely collectable RDC data using REDCRAFT can lead to faster and cheaper study of larger and more complex proteins by NMR spectroscopy in solution state.

bioinformatics↗