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 catalyzes (increases reaction rate or "speeds up") proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the ...

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 com ...

es. It cleaves the coronavirus polyprotein 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 Chund ...

and a member of the

PA clan of proteases The PA clan ( Proteases of mixed nucleophile, superfamily A) is the largest group of proteases with common ancestry as identified by structural homology. Members have a chymotrypsin-like fold and similar proteolysis mechanisms but can have identit ...

. 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 (binding site) a ...

and cleaves a Gln–(

Ser Ser or SER may refer to: Places * Ser, a village in Bogdand Commune, Satu Mare County, Romania * Serpens (Ser), an astronomical constellation of the northern hemisphere * Serres, known as Ser in Serbian, a city in Macedonia, Greece Organization ...

Ala Ala, ALA, Alaa or Alae may refer to: Places * Ala, Hiiu County, Estonia, a village * Ala, Valga County, Estonia, a village * Ala, Alappuzha, Kerala, India, a village * Ala, Iran, a village in Semnan Province * Ala, Gotland, Sweden * Alad, Seydu ...

Gly 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 (carbamic acid is unstable), with the chemical formula NH2‐ CH2‐ COOH. Glycine is one of the proteinogeni ...

)

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 The International Union of Biochemistry and Molecular Biology (IUBMB) is an international non-governmental organisation concerned with biochemistry and molecular biology. Formed in 1955 as the International Union of Biochemistry (IUB), the union ...

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 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 Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...

(

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 − form un ...

, alanine, or glycine) at position P1'. The

SARS coronavirus Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1; or Severe acute respiratory syndrome coronavirus, SARS-CoV) is a strain of coronavirus that causes severe acute respiratory syndrome (SARS), the respiratory illness responsible for th ...

3CLpro can for instance self-cleave the following

peptide Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A ...

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 (or sulphur in British English) is a chemical element with the symbol S and atomic number 16. It is abundant, multivalent and nonmetallic. Under normal conditions, sulfur atoms form cyclic octatomic molecules with a chemical formula ...

of the

cysteine Cysteine (symbol Cys or C; ) is a semiessential proteinogenic amino acid with the formula . The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile. When present as a deprotonated catalytic residue, sometime ...

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 Imidazole (ImH) is an organic compound with the formula C3N2H4. It is a white or colourless solid that is soluble in water, producing a mildly alkaline solution. In chemistry, it is an aromatic heterocycle, classified as a diazole, and has non-a ...

of the

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

as a

general base Thomas Kukula (born 1965 in Düsseldorf) is a German DJ, Eurodance musician and music producer, that released music under monikers such as General Base, Candy Beat, T.H.K. and Red 5. Life and career Kukula started working as a DJ in 1986 in his ...

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

The protease 3CLpro is a potential drug target for coronavirus infections due to its essential role in processing the polyproteins that are translated from the

viral RNA An RNA virus is a virusother than a retrovirusthat has ribonucleic acid (RNA) as its genetic material. The nucleic acid is usually single-stranded RNA (ssRNA) but it may be double-stranded (dsRNA). Notable human diseases caused by RNA viruses ...

. 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 for a treatment of

SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19 (coronavirus disease 2019), the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus previously had a ...

infection. A number of protease inhibitors 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 clinic ...

PF-07321332 Nirmatrelvir is an antiviral medication developed by Pfizer which acts as an orally active 3C-like protease inhibitor. It is part of a nirmatrelvir/ritonavir combination used to treat COVID-19 and sold under the brand name Paxlovid. Dev ...

, 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 nutrie ...

administered

prodrug A prodrug is a 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 used to improve how the drug ...

PF-07304814 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 ...

(lufotrelvir) entered

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

s in September 2020. The orally-active follow-up drug

is in phase II/III clinical trials as a combination drug with ritonavir, and in November 2021, results were announced including 89% reduction in hospitalizations when given within three days after

COVID-19 Coronavirus disease 2019 (COVID-19) is a contagious disease caused by a virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The first known case was COVID-19 pandemic in Hubei, identified in Wuhan, China, in December ...

symptom onset. 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. On 25 May 2022,

Insilico Medicine Insilico Medicine is a biotechnology company based in Pak Shek Kok, Hong Kong in Hong Kong Science Park near the Chinese University of Hong Kong and in New York, at The Cure by Deerfield. The company combines genomics, big data analysis, and dee ...

explored use of 3CL protease inhibitor for COVID-19 treatment. The preclinical candidate has a specialized structure designed by

Artificial Intelligence Artificial intelligence (AI) is intelligence—perceiving, synthesizing, and inferring information—demonstrated by machines, as opposed to intelligence displayed by animals and humans. Example tasks in which this is done include speech re ...

to target 3C-like proteases. It acts as an inhibitor and binds to 3C-like proteases of SARS-COV-2 and MERS viruses, disabling them and inhibiting viral replication. The preclinical candidate is used for treating people who are already infected by preventing the coronavirus from replicating. Doi

Other 3C(-like) proteases

3C-like proteases (3C(L)pro) are widely found in

(+)ssRNA Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a dis ...

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 Businesses and organisations * Triad (American fraternities), certain historic groupings of seminal college fraternities in North America * Triad (organized crime), a Chinese transnational orga ...

. 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: * 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 i ...

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

poliovirus A 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: types 1, 2, and 3. Poliovirus is composed of an ...

and in

rhinovirus The rhinovirus (from the grc, ῥίς, rhis "nose", , romanized: "of the nose", and the la, vīrus) is the most common viral infectious agent in humans and is the predominant cause of the common cold. Rhinovirus infection proliferates in tem ...

(both are members of genus '' Enterovirus''). * ''

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 p ...

'' have a 3CL^pro (; MEROPS C37). Examples include the one found in Norwalk virus. Additional members are known from '' Potyviridae'' and non-''Coronaviridae'' ''

Nidovirales ''Nidovirales'' is an order of enveloped, positive-strand RNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, molluscs, and helminths. The order includes the fami ...

''.

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