Inhibiting a dynamic viral protease by targeting a non-catalytic cysteine

. Author manuscript; available in PMC: 2023 May 19.

Published in final edited form as: Cell Chem Biol. 2022 Mar 31;29(5):785–798.e19. doi: 10.1016/j.chembiol.2022.03.007

Key resources table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit monoclonal anti-DYKDDDDK tag	Cell Signaling Technology	D6W5B
Bacterial and virus strains
XL-10 Ultracompetent cells	Agilent Technologies	200315
Rosettat^™ 2(DE3) Singles^™ Competent cells	MilliporeSigma	71400
BL21(DE3)pLysS Singles™ Competent Cells	MilliporeSigma	70236
Human herpesvirus 5	American Type Culture Collection	VR-2356
Biological samples
Chemicals, peptides, and recombinant proteins
NH₂-Lys(MCA)-Tbg-Tbg-Asn-Ala-Ser-Ser-Arg-Leu-Lys(Dnp)-Arg-OH	GenScript USA Inc.	N/A
NH2-Lys(MCA)-His-Thr-Tyr-Lys-Gln-Ala-Ser-Glu-Lys-Phe-Lys-Lys(Dnp)-OH	This paper	N/A
Human Cytomegalovirus Protease	This paper	N/A
Human Cytomegalovirus Protease Δ221	This paper	N/A
Human Cytomegalovirus Protease L222D	This paper	N/A
Human Cytomegalovirus Protease C161A	This paper	N/A
Human Cytomegalovirus Protease C84A, C87A, C138A, C202A	This paper	N/A
Human Cytomegalovirus Protease C84A, C87A, C138A, C161A, C202A	This paper	N/A
Human Cytomegalovirus Protease C84A, C87A, C138A, C202A, L222D	This paper	N/A
Human Cytomegalovirus Protease C84A, C87A, C138A, C202A, S225M	This paper	N/A
Epstein-Barr virus protease	This paper	N/A
Herpes simplex virus 1 protease	This paper	N/A
1-Chloro-3-(4-phenyl-1H-1,2,3-triazol-1-yl)propan-2-one	This paper	N/A
1-(Oxiran-2-ylmethyl)-4-phenyl-1H-1,2,3-triazole	This paper	N/A
1-(4-Phenyl-1H-1,2,3-triazol-1-yl)-3-(2,3,5,6-tetrafluorophenoxy)propan-2-one	This paper	N/A
1-Chloro-3-(4-(4-nitrophenyl)-1H-1,2,3-triazol-1-yl)propan-2-one	This paper	N/A
4-(1-(3-Chloro-2-oxopropyl)-1H-1,2,3-triazol-4-yl)benzonitrile	This paper	N/A
1-(4-(4-Bromophenyl)-1H-1,2,3-triazol-1-yl)-3-chloropropan-2-one	This paper	N/A
1-Chloro-3-(4-(4-chlorophenyl)-1H-1,2,3-triazol-1-yl)propan-2-one	This paper	N/A
1-Chloro-3-(4-(3-chlorophenyl)-1H-1,2,3-triazol-1-yl)propan-2-one	This paper	N/A
N-(3-(1-(3-Chloro-2-oxopropyl)-1H-1,2,3-triazol-4-yl)phenyl)acetamide	This paper	N/A
3-((1-(3-Chloro-2-oxopropyl)-1H-1,2,3-triazol-4-yl)methyl)-1H-indene-1,2(3H)-dione	This paper	N/A
(1-(3-Chloro-2-oxopropyl)-4-phenyl-1H-1,2,3-triazol-5-yl)methyl methylcarbamate	This paper	N/A
(1-(3-Chloro-2-oxopropyl)-4-phenyl-1H-1,2,3-triazol-5-yl)methyl dimethylcarbamate	This paper	N/A
(1-(3-Chloro-2-oxopropyl)-4-phenyl-1H-1,2,3-triazol-5-yl)methyl benzylcarbamate	This paper	N/A
(1-(3-Chloro-2-oxopropyl)-4-phenyl-1H-1,2,3-triazol-5-yl)methyl (2-methoxyethyl)carbamate	This paper	N/A
(1-(3-Chloro-2-oxopropyl)-4-phenyl-1H-1,2,3-triazol-5-yl)methyl morpholine-4-carboxylate	This paper	N/A
(1-(3-Chloro-2-oxopropyl)-4-phenyl-1H-1,2,3-triazol-5-yl)methyl (2-morpholinoethyl)carbamate	This paper	N/A
(1-(3-Chloro-2-oxopropyl)-4-phenyl-1H-1,2,3-triazol-5-yl)methyl (3-(2-oxopyrrolidin-1-yl)propyl)carbamate	This paper	N/A
1-(3-chloro-2-oxopropyl)-4-phenyl-1H-1,2,3-triazol-5-yl)methyl prop-2-yn-1ylcarbamate	This paper	N/A
Critical commercial assays
QuikChange Lightning Site Directed Mutagenesis Kit	Agilent Technologies	210518
The PEGs suite, condition #7	Qiagen	134307
CellTiter-Glo® Luminescent Cell Viability Assay	Promega	G7570
β-Galactosidase Enzyme Assay System with Reporter Lysis Buffer kit	Promega	E2000
Beta-Glo® Assay System kit	Promega	E4720
TransIT®−293 Transfection Reagent	Mirus Bio	MIR 2700
Deposited data
Human Cytomegalovirus protease Δ221 ¹H-¹³C and ¹H-¹⁵N assignments	Biological Magnetic Resonance Bank	Accession number 51211
Human Cytomegalovirus Protease C84A, C87A, C138A, C202A co-crystal structure with inhibitor 43	Protein Data Bank	PDB ID: 7TCZ
Complex structure of Human Cytomegalovirus Protease and a peptidomimetic inhibitor	Khayat et al., 2003	PDB ID: 1NJU
Experimental models: Cell lines
Human: MRC-5 cells	American Type Culture Collection	CCL-171
Human: HFF-1 cells	American Type Culture Collection	SCRC-1041
Human: Huh7 cells	Chan Zuckerberg Biohub, Andreas Puschnik	N/A
Human: HeLa cells	Chan Zuckerberg Biohub, Andreas Puschnik	N/A
Human: HEK293T cells	American Type Culture Collection	CRL-3216
Experimental models: Organisms/strains
Oligonucleotides
Recombinant DNA
Plasmid: 6xHis Human Cytomegalovirus Protease	Lee et al., 2011	N/A
Plasmid: 6xHis Human Cytomegalovirus Protease Δ221	Lee et al., 2011	N/A
Plasmid: 6xHis Human Cytomegalovirus Protease L222D	Lee et al., 2011	N/A
Plasmid: 6xHis Human Cytomegalovirus Protease C161A	This paper	N/A
Plasmid: 6xHis Human Cytomegalovirus Protease C84A, C87A, C138A, C202A	This paper	N/A
Plasmid: 6xHis Human Cytomegalovirus Protease C84A, C87A, C138A, C161A, C202A	This paper	N/A
Plasmid: 6xHis Human Cytomegalovirus Protease C84A, C87A, C138A, C202A, L222D	This paper	N/A
Plasmid: 6xHis Human Cytomegalovirus Protease C84A, C87A, C138A, C202A, S225M	This paper	N/A
Plasmid: FLAG Human Cytomegalovirus Protease	GenScript USA Inc.	N/A
Plasmid: 6xHis Epstein-Barr virus protease	Gable et al., 2014	N/A
Plasmid: 6xHis Herpes simplex virus protease	GenScript USA Inc.	N/A
Software and algorithms
MassLynx 4.1	Waters	https://www.waters.com/waters/en_US/MassLynx-Mass-Spectrometry-Software-/nav.htm?cid=513164&locale=en_US
HiTS	UCSF Small Molecule Discovery Center	hits.ucsf.edu
BioTek Gen5 2.03	Agilent	https://www.biotek.com/products/software-robotics-software/gen5-microplate-reader-and-imager-software/
Prism 8	GraphPad	https://www.graphpad.com
REDiii	Bohn and Schiffer, 2015	DOI:10.1107/S139900471500303X
xia2	Diamond Light Source	https://xia2.github.io
Phenix.Refine 1.11.1–2575	Phenix	https://phenix-online.org
Coot 0.9.5 EL	MRC Laboratory of Molecular Biology	https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
TopSpin 2 and 4	Bruker	https://www.bruker.com/en/products-and-solutions/mr/nmr-software/topspin.html
NMRpipe and NMRdraw 8.2	NIST IBBR	https://www.ibbr.umd.edu/nmrpipe
Sparky 1.414	NMRFAM	https://nmrfam.wisc.edu/nmrfam-sparky-distribution
Gaussian 16	Frisch et al. 2016	https://gaussian.com
Amber 16	D.A. Case et al., 2016	https://ambermd.org
ModLoop	ModBase	https://modbase.compbio.ucsf.edu/modloop/
Unicorn 6.3	Cytvia	https://www.cytivalifesciences.com/en/us/shop/unicorn-6-3-p-01118
Image Lab 5.0	BioRad	https://www.biorad.com/en-us/product/image-lab-software?ID=KRE6P5E8Z
ImageJ 1.53a	Schneider et al., 2012	https://imagej.nih.gov/ij/
ChemDraw 18.2	PerkinElmer	https://perkinelmerinformatics.com/products/research/chemdraw/
Other
Acquity LC/Xevo G2-XS QTof MS	Waters	https://www.waters.com/waters/en_US/Xevo-G2-XS-QTof-Quadrupole-Time-of-Flight-Mass-Spectrometer/nav.htm?cid=134798222&locale=en_US
Bruker Avance DRX 500 MHz	UCSF Nuclear Magnetic Resonance Laboratory	https://pharm.ucsf.edu/nmr/instruments/bruker-500
Bruker Avance AV 800 MHz	UCSF Nuclear Magnetic Resonance Laboratory	https://pharm.ucsf.edu/nmr/instruments/bruker-800
ÄKTA™ pure	Cytvia	https://www.cytivalifesciences.com/en/us/shop/chromatography/chromatography-systems/akta-pure-p-05844
ChemiDoc Imaging System	BioRad	https://www.biorad.com/en-us/product/chemidoc-imaging-system?ID=OI91XQ15