8W1T | pdb_00008w1t

SARS-CoV-2 Main protease bound to a non-covalent non-peptidic HTS hit

• PDB DOI: https://doi.org/10.2210/pdb8W1T/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-18 Released: 2024-11-20 
• Deposition Author(s): Bian, X., Tang, S., Sacchettini, J.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

An oral non-covalent non-peptidic inhibitor of SARS-CoV-2 Mpro ameliorates viral replication and pathogenesis in vivo.

Zhou, N.E., Tang, S., Bian, X., Parai, M.K., Krieger, I.V., Flores, A., Jaiswal, P.K., Bam, R., Wood, J.L., Shi, Z., Stevens, L.J., Scobey, T., Diefenbacher, M.V., Moreira, F.R., Baric, T.J., Acharya, A., Shin, J., Rathi, M.M., Wolff, K.C., Riva, L., Bakowski, M.A., McNamara, C.W., Catanzaro, N.J., Graham, R.L., Schultz, D.C., Cherry, S., Kawaoka, Y., Halfmann, P.J., Baric, R.S., Denison, M.R., Sheahan, T.P., Sacchettini, J.C.

(2024) Cell Rep 43: 114929-114929

• PubMed: 39504242 
• DOI: https://doi.org/10.1016/j.celrep.2024.114929
• Primary Citation Related Structures: 
  8W1T, 8W1U


• PubMed Abstract: 
  

  Safe, effective, and low-cost oral antiviral therapies are needed to treat those at high risk for developing severe COVID-19. To that end, we performed a high-throughput screen to identify non-peptidic, non-covalent inhibitors of the SARS-CoV-2 main protease (Mpro), an essential enzyme in viral replication. NZ-804 was developed from a screening hit through iterative rounds of structure-guided medicinal chemistry. NZ-804 potently inhibits SARS-CoV-2 Mpro (0.009 μM IC ₅₀ ) as well as SARS-CoV-2 replication in human lung cell lines (0.008 μM EC ₅₀ ) and primary human airway epithelial cell cultures. Antiviral activity is maintained against distantly related sarbecoviruses and endemic human CoV OC43. In SARS-CoV-2 mouse and hamster disease models, NZ-804 therapy given once or twice daily significantly diminished SARS-CoV-2 replication and pathogenesis. NZ-804 synthesis is low cost and uncomplicated, simplifying global production and access. These data support the exploration of NZ-804 as a therapy for COVID-19 and future emerging sarbecovirus infections.

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Organizational Affiliation: 
• Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77840, USA.
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Calibr-Skaggs Institute for Innovative Medicine, La Jolla, CA 92037, USA.
Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA.
Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. Electronic address: [e-mail].
Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77840, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.22 kDa 
• Atom Count: 5,381 
• Modeled Residue Count: 611 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AFD (Subject of Investigation/LOI)	I [auth A], N [auth B]	(5-bromopyridin-3-yl){4-[(S)-(4-chlorophenyl)(phenyl)methyl]piperazin-1-yl}methanone C23 H21 Br Cl N3 O HUHIPWIDNVSBFL-QFIPXVFZSA-N
A1A21 (Subject of Investigation/LOI)	H [auth A], O [auth B]	(5-bromopyridin-3-yl){4-[(R)-(4-chlorophenyl)(phenyl)methyl]piperazin-1-yl}methanone C23 H21 Br Cl N3 O HUHIPWIDNVSBFL-JOCHJYFZSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A], J [auth B], K [auth B], L [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.146	α = 79.6
b = 54.223	β = 70.18
c = 59.906	γ = 88.46

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Bian, X., Tang, S., Sacchettini, J.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release