Class of enzymes
The 3C-like protease (3CLpro ) or main protease (Mpro ), formally known as C30 endopeptidase or 3-chymotrypsin-like protease ,
[2] is the main
protease found in
coronaviruses . It cleaves the coronavirus
polyprotein at eleven conserved sites. It is a
cysteine protease and a member of the
PA clan of proteases . It has a
cysteine-histidine catalytic dyad at its
active site and cleaves a
Gln –(
Ser /
Ala /
Gly )
peptide bond .
The
Enzyme Commission refers to this family as SARS coronavirus main proteinase (Mpro ;
EC
3.4.22.69 ). The 3CL protease corresponds to coronavirus
nonstructural protein 5 (nsp5). The "3C" in the common name refers to the
3C protease (3Cpro ) which is a
homologous protease found in
picornaviruses .
Function
The 3C-like protease is able to
catalytically cleave a peptide bond between a
glutamine at position P1 and a small
amino acid (
serine ,
alanine , or
glycine ) at position P1'. The
SARS coronavirus 3CLpro can for instance self-cleave the following
peptides :
[3]
[4]
[5]
TSAVL
Q -
S GFRK-NH2 and SGVTF
Q -
G KFKK are the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase
The protease is important in the processing of the coronavirus
replicase polyprotein (
P0C6U8 ). It is the main protease in coronaviruses and corresponds to nonstructural protein 5 (nsp5).
[6] It cleaves the coronavirus polyprotein at 11 conserved sites. The 3CL protease has a
cysteine-histidine catalytic dyad at its active site.
[4] The
sulfur of the
cysteine acts as a
nucleophile and the
imidazole ring of the
histidine as a
general base .
[7]
Substrate preferences for 3CL proteases (from table 2)
[8]
Position
Substrate preference
P5
No strong preference
P4
Small
hydrophobic residues
P3
Positively charged residue
P2
High hydrophobicity and absence of
beta-branch
P1
Glutamine
P1'
Small residues
P2'
Small residues
P3'
No strong preference
Nomenclature
Alternative names provided by the EC include 3CLpro , 3C-like protease , coronavirus 3C-like protease , Mpro , SARS 3C-like protease , SARS coronavirus 3CL protease , SARS coronavirus main peptidase , SARS coronavirus main protease , SARS-CoV 3CLpro enzyme , SARS-CoV main protease , SARS-CoV Mpro and severe acute respiratory syndrome coronavirus main protease .
As a treatment target
Nirmatrelvir bound to 3CL
PDB :
7RFW
Nirmatrelvir , a 3CLpro inhibitor developed by
Pfizer in
phase II/III clinical trials as a
combination drug with
ritonavir .
[9]
[10]
The protease 3CLpro is used as a
drug target for coronavirus infections due to its essential role in processing the polyproteins that are translated from the
viral RNA .
[11]
[12] The
X-ray structures of the unliganded SARS-CoV-2 protease 3CLpro and its complex with an α-ketoamide inhibitor provides a basis for design of α-ketoamide inhibitors
[13] for a treatment of
SARS-CoV-2 infection.
[14]
[15]
[16]
[17]
[18]
A number of
protease inhibitors are being developed targeting 3CLpro and homologous
3Cpro , including
CLpro-1 ,
GC376 ,
rupintrivir ,
lufotrelvir ,
PF-07321332 , and
AG7404 .
[19]
[20]
[21]
[22]
[1] The
intravenous administered
prodrug
PF-07304814 (lufotrelvir) entered
clinical trials in September 2020.
[23]
After clinical trials, in December 2021, the oral medication
nirmatrelvir (formerly PF-07321332) became commercially available under
emergency use authorizations (EUA), as part of the
nirmatrelvir/ritonavir combination therapy (brand name Paxlovid).
[24]
[25] In May 2023, the medication got full FDA approval for high-risk adults, while children 12–18 were still covered under the EUA.
[26]
The 3C-like protease inhibitor
ensitrelvir received authorization to treat COVID-19 in Japan in 2022.
[27]
[28]
In 2022, an ultralarge virtual screening campaign of 235 million molecules was able to identify a novel broad-spectrum inhibitor targeting the main protease of several coronaviruses. It is unusually not a peptidomimetic.
[29]
A ligand-binding diagram showing the
amino acid residues in contact with a
covalently bound
peptidomimetic
protease inhibitor . The small red spheres are
water molecules .
[1]
Other 3C(-like) proteases
3C-like proteases (3C(L)pro) are widely found in
(+)ssRNA viruses. All of them are cysteine proteases with a
chymotrypsin -like fold (PA clan), using a catalytic dyad or
triad . They share some general similarities on
substrate specificity and inhibitor effectiveness. They are divided into subfamilies by sequence similarity, corresponding to the family of viruses they are found in:
[30]
Additional members are known from
Potyviridae and non-Coronaviridae
Nidovirales .
[31]
See also
References
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Further reading
External links