The 3C-like protease (3CL^pro) or main protease (M^pro), formally known as C30 endopeptidase or 3-chymotrypsin-like protease, is the main

protease A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalysis, catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products ...

found in

coronavirus Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In humans and birds, they cause respiratory tract infections that can range from mild to lethal. Mild illnesses in humans include some cases of the comm ...

es. It cleaves the coronavirus

polyprotein Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Protein degradation is a major regulatory mechanism of gene expression and contributes substantially to shaping mammalian proteomes. Uncatalysed, the hydrolysis o ...

at eleven conserved sites. It is a

cysteine protease Cysteine proteases, also known as thiol proteases, are hydrolase enzymes that degrade proteins. These proteases share a common catalytic mechanism that involves a nucleophilic cysteine thiol in a catalytic triad or dyad. Discovered by Gopal Chu ...

and a member of the PA clan of proteases. It has a cysteine-histidine catalytic dyad at its

active site In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the ''binding s ...

and cleaves a Gln–( Ser/ Ala/ Gly)

peptide bond In organic chemistry, a peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide or protein cha ...

. The

Enzyme Commission An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as produc ...

refers to this family as SARS coronavirus main proteinase (M^pro; ). The 3CL protease corresponds to coronavirus

nonstructural protein In virology, a nonstructural protein is a protein encoded by a virus but that is not part of the viral particle. They typically include the various enzymes and transcription factors the virus uses to replicate itself, such as a viral protease ( 3CL ...

5 (nsp5). The "3C" in the common name refers to the 3C protease (3C^pro) which is a homologous protease found in

picornavirus Picornaviruses are a group of related Viral envelope, nonenveloped RNA viruses which infect vertebrates including fish, mammals, and birds. They are viruses that represent a large family of small, Positive-sense single-stranded RNA virus, positi ...

es.

Function

The 3C-like protease is able to catalytically cleave a peptide bond between a

glutamine Glutamine (symbol Gln or Q) is an α-amino acid that is used in the biosynthesis of proteins. Its side chain is similar to that of glutamic acid, except the carboxylic acid group is replaced by an amide. It is classified as a charge-neutral ...

at position P1 and a small

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

(

serine Serine (symbol Ser or S) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α- amino group (which is in the protonated − form under biological conditions), a carboxyl group (which is in the deprotonated − ...

alanine Alanine (symbol Ala or A), or α-alanine, is an α-amino acid that is used in the biosynthesis of proteins. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group sid ...

, or

glycine Glycine (symbol Gly or G; ) is an amino acid that has a single hydrogen atom as its side chain. It is the simplest stable amino acid. Glycine is one of the proteinogenic amino acids. It is encoded by all the codons starting with GG (G ...

) at position P1'. The

SARS coronavirus Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), previously known as severe acute respiratory syndrome coronavirus (SARS-CoV), is a strain of coronavirus that causes severe acute respiratory syndrome (SARS), the respiratory illn ...

3CLpro can for instance self-cleave the following

peptide Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty am ...

s: The protease is important in the processing of the coronavirus

replicase RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to ...

polyprotein (). It is the main protease in coronaviruses and corresponds to nonstructural protein 5 (nsp5). It cleaves the coronavirus polyprotein at 11 conserved sites. The 3CL protease has a cysteine-histidine catalytic dyad at its active site. The

sulfur Sulfur ( American spelling and the preferred IUPAC name) or sulphur ( Commonwealth spelling) is a chemical element; it has symbol S and atomic number 16. It is abundant, multivalent and nonmetallic. Under normal conditions, sulfur atoms ...

of the

cysteine Cysteine (; symbol Cys or C) is a semiessential proteinogenic amino acid with the chemical formula, formula . The thiol side chain in cysteine enables the formation of Disulfide, disulfide bonds, and often participates in enzymatic reactions as ...

acts as a

nucleophile In chemistry, a nucleophile is a chemical species that forms bonds by donating an electron pair. All molecules and ions with a free pair of electrons or at least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they are ...

and the imidazole ring of the

histidine Histidine (symbol His or H) is an essential amino acid that is used in the biosynthesis of proteins. It contains an Amine, α-amino group (which is in the protonated –NH3+ form under Physiological condition, biological conditions), a carboxylic ...

as a general base.

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

A number of

protease inhibitors Protease inhibitors (PIs) are medications that act by interfering with protease, enzymes that cleave proteins. Some of the most well known are antiviral drugs widely used to treat HIV/AIDS, hepatitis C and COVID-19. These protease inhibitors pre ...

are being developed targeting 3CLpro and homologous 3Cpro, including CLpro-1, GC376,

rupintrivir Rupintrivir (AG-7088, Rupinavir) is a peptidomimetic antiviral drug which acts as a 3C and 3CL protease inhibitor. It was developed for the treatment of rhinoviruses, and has subsequently been investigated for the treatment of other viral dise ...

lufotrelvir Lufotrelvir (PF-07304814) is an antiviral drug developed by Pfizer which acts as a 3CL protease inhibitor. It is a prodrug with the phosphate group being cleaved ''in vivo'' to yield the active agent PF-00835231. Lufotrelvir is in human clinica ...

PF-07321332 Nirmatrelvir is an antiviral medication developed by Pfizer which acts as an orally active 3C-like protease, 3C-like Protease inhibitor (pharmacology), protease inhibitor. It is part of a nirmatrelvir/ritonavir combination used to treat COVI ...

, and AG7404. The

intravenous Intravenous therapy (abbreviated as IV therapy) is a medical technique that administers fluids, medications and nutrients directly into a person's vein. The intravenous route of administration is commonly used for rehydration or to provide nutr ...

administered

prodrug A prodrug is a pharmacologically inactive medication or compound that, after intake, is metabolized (i.e., converted within the body) into a pharmacologically active drug. Instead of administering a drug directly, a corresponding prodrug can be ...

PF-07304814 (lufotrelvir) entered

clinical trial Clinical trials are prospective biomedical or behavioral research studies on human subject research, human participants designed to answer specific questions about biomedical or behavioral interventions, including new treatments (such as novel v ...

s in September 2020. 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 Nirmatrelvir/ritonavir, sold under the brand name Paxlovid, is a co-packaged medication used as a treatment for COVID19. It contains the antiviral medications nirmatrelvir and ritonavir and was developed by Pfizer. Nirmatrelvir inhibits ...

combination therapy (brand name Paxlovid). In May 2023, the medication got full FDA approval for high-risk adults, while children 12–18 were still covered under the EUA. The 3C-like protease inhibitor ensitrelvir received authorization to treat COVID-19 in Japan in 2022. 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. Doi

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 Chymotrypsin (, chymotrypsins A and B, alpha-chymar ophth, avazyme, chymar, chymotest, enzeon, quimar, quimotrase, alpha-chymar, alpha-chymotrypsin A, alpha-chymotrypsin) is a digestive enzyme component of pancreatic juice acting in the duodenu ...

-like fold (PA clan), using a catalytic dyad or

triad Triad or triade may refer to: * a group of three Humanities * Trichotomy (philosophy), often called triads * Triad (sociology), a group of three people as a unit of study * Triad (relationship), or ''ménage à trois'' Music * Triad (music ...

. They share some general similarities on

substrate specificity Chemical specificity is the ability of binding site of a macromolecule (such as a protein) to bind specific ligands. The fewer ligands a protein can bind, the greater its specificity. Specificity describes the strength of binding between a given ...

and inhibitor effectiveness. They are divided into subfamilies by sequence similarity, corresponding to the family of viruses they are found in: * This entry is the coronavirus 3CL^pro. * ''

Picornaviridae Picornaviruses are a group of related nonenveloped RNA viruses which infect vertebrates including fish, mammals, and birds. They are viruses that represent a large family of small, positive-sense, single-stranded RNA viruses with a 30 nm ...

'' have a picornavirus 3C^pro (; ; MEROPS C03). This is the earliest-studied family. Examples include the ones found in

poliovirus Poliovirus, the causative agent of polio (also known as poliomyelitis), is a serotype of the species '' Enterovirus C'', in the family of '' Picornaviridae''. There are three poliovirus serotypes, numbered 1, 2, and 3. Poliovirus is composed ...

and in

rhinovirus The rhinovirus (from the "nose", , romanized: "of the nose", and the ) is a Positive-sense single stranded RNA virus, positive-sense, single-stranded RNA virus belonging to the genus ''Enterovirus'' in the family ''Picornaviridae''. Rhinoviru ...

(both are members of genus ''

Enterovirus ''Enterovirus'' is a genus of positive-sense single-stranded RNA viruses associated with several human and mammalian diseases. Enteroviruses are named by their transmission-route through the intestine ('enteric' meaning intestinal). Serologic ...

''). * ''

Caliciviridae The ''Caliciviridae'' are a family of "small round structured" viruses, members of Class IV of the Baltimore scheme. Caliciviridae bear resemblance to enlarged picornavirus and was formerly a separate genus within the picornaviridae. They are ...

'' have a 3CL^pro (; MEROPS C37). Examples include the one found in

Norwalk virus Norovirus, also known as Norwalk virus and sometimes referred to as the winter vomiting disease, is the most common cause of gastroenteritis. Infection is characterized by non-bloody diarrhea, vomiting, and stomach pain. Fever or headaches may ...

. Additional members are known from ''

Potyviridae ''Potyviridae'' is a family of positive-strand RNA viruses that encompasses more than 30% of known plant viruses, many of which are of great agricultural significance. The family contains 13 genera that contain 259 species. Structure Potyviri ...

'' and non-''Coronaviridae'' ''

Nidovirales ''Nidovirales'' is an order of Viral envelope, enveloped, positive-strand RNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, Mollusca, molluscs, and helminths. Th ...

''.

References

External links

* * Peptidase C30/C16 in coronavirus, . The MEROPS C16 one is the "papain-like" PL-PRO. {{Portal bar, Biology, border=no EC 3.4.22 Coronavirus proteins Viral nonstructural proteins