View source for 3C-like protease

{{Short description|Class of enzymes}}
{{see also|COVID-19 drug development}}
{{Infobox enzyme
| Name       = SARS coronavirus main proteinase
| EC_number  = 3.4.22.69
| CAS_number =
| GO_code    = 
| image      = File:DOI.10.1126.science.abb4489.S2.png
| width      = 258
| caption    = [[SARS-CoV-2]] main proteinase [[Protein dimer|dimer]] with the [[catalytic triad#Cys-His-Asp|catalytic dyad]] ([[histidine|H41]]; [[Cystine|C145]]) in complex with a [[covalent]] [[peptidomimetic]] protease inhibitor ("11a", magenta). From {{PDB|6LZE}}.<ref name="pmid32321856" />
| name       =  
}}
{{Pfam box
|Name=Peptidase C30, Coronavirus endopeptidase
|InterPro=IPR008740
|Pfam=PF05409
|PROSITE=PS51442
|Symbol=Peptidase_C30
|MEROPS=C30
|SCOP=d1q2wb1
}}
The '''3C-like protease''' ('''3CL<sup>pro</sup>''') or '''main protease''' ('''M<sup>pro</sup>'''), formally known as '''C30 endopeptidase''' or '''3-chymotrypsin-like protease''',<ref>{{cite journal|vauthors=Ahmad B, Batool M, Ain QU, Kim MS, Choi S|date=August 2021|title=Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations|journal=International Journal of Molecular Sciences|volume=22|issue=17|page=9124|doi=10.3390/ijms22179124|pmc=8430524|pmid=34502033|doi-access=free}}</ref> is the main [[protease]] found in [[coronavirus]]es. 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 [[Catalytic triad#Cys-His-Asp|cysteine-histidine catalytic dyad]] at its [[active site]] and cleaves a [[Glutamine|Gln]]–([[Serine|Ser]]/[[Alanine|Ala]]/[[Glycine|Gly]]) [[peptide bond]].

The [[Enzyme Commission number|Enzyme Commission]] refers to this family as '''SARS coronavirus main proteinase''' ('''M<sup>pro</sup>'''; {{EC number|3.4.22.69}}). The 3CL protease corresponds to coronavirus '''[[nonstructural protein]] 5''' (nsp5). The "3C" in the common name refers to the [[Picornain 3C|3C protease]] (3C<sup>pro</sup>) which is a [[Sequence homology|homologous]] protease found in [[picornavirus]]es.

== Function ==

The 3C-like protease is able to [[Proteolysis|catalytically cleave]] a peptide bond between a [[glutamine]] at position P1 and a small [[amino acid]] ([[serine]], [[alanine]], or [[glycine]]) at position P1'. The [[Severe acute respiratory syndrome coronavirus|SARS coronavirus]] 3CLpro can for instance self-cleave the following [[peptide]]s:<ref>{{cite journal | vauthors = Goetz DH, Choe Y, Hansell E, Chen YT, McDowell M, Jonsson CB, Roush WR, McKerrow J, Craik CS | title = Substrate specificity profiling and identification of a new class of inhibitor for the major protease of the SARS coronavirus | journal = Biochemistry | volume = 46 | issue = 30 | pages = 8744–52 | date = July 2007 | pmid = 17605471 | doi = 10.1021/bi0621415 }}</ref><ref name=":0">{{cite journal | vauthors = Fan K, Wei P, Feng Q, Chen S, Huang C, Ma L, Lai B, Pei J, Liu Y, Chen J, Lai L | title = Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase | journal = The Journal of Biological Chemistry | volume = 279 | issue = 3 | pages = 1637–42 | date = January 2004 | pmid = 14561748 | doi = 10.1074/jbc.m310875200 | pmc = 7980035 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Akaji K, Konno H, Onozuka M, Makino A, Saito H, Nosaka K | title = Evaluation of peptide-aldehyde inhibitors using R188I mutant of SARS 3CL protease as a proteolysis-resistant mutant | journal = Bioorganic & Medicinal Chemistry | volume = 16 | issue = 21 | pages = 9400–8 | date = November 2008 | pmid = 18845442 | doi = 10.1016/j.bmc.2008.09.057 | pmc = 7126698 }}</ref>

{{blockquote|TSAVL[[Glutamine|Q]]-[[Serine|S]]GFRK-NH2 and SGVTF[[Glutamine|Q]]-[[Glycine|G]]KFKK are the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase|author=|title=|source=}}

The protease is important in the processing of the coronavirus [[replicase]] polyprotein ({{UniProt|P0C6U8}}). It is the main protease in coronaviruses and corresponds to nonstructural protein 5 (nsp5).<ref name="Fehr_2015">{{cite book|title=Coronaviruses|vauthors=Fehr AR, Perlman S|date=2015|publisher=Springer|isbn=978-1-4939-2438-7|veditors=Maier HJ, Bickerton E, Britton P|series=Methods in Molecular Biology|volume=1282|pages=1–23|chapter=Coronaviruses: an overview of their replication and pathogenesis|doi=10.1007/978-1-4939-2438-7_1|pmc=4369385|pmid=25720466|quote=See section: Virion Structure.}}</ref> It cleaves the coronavirus polyprotein at 11 conserved sites. The 3CL protease has a [[Catalytic triad#Cys-His-Asp|cysteine-histidine catalytic dyad]] at its active site.<ref name=":0" /> The [[Thiol|sulfur]] of the [[cysteine]] acts as a [[nucleophile]] and the [[Imidazole|imidazole ring]] of the [[histidine]] as a [[Base (chemistry)|general base]].<ref name="pmid20167482">{{cite journal | vauthors = Ryu YB, Park SJ, Kim YM, Lee JY, Seo WD, Chang JS, Park KH, Rho MC, Lee WS |display-authors = 6| title = SARS-CoV 3CLpro inhibitory effects of quinone-methide triterpenes from Tripterygium regelii | journal = Bioorganic & Medicinal Chemistry Letters | volume = 20 | issue = 6 | pages = 1873–6 | date = March 2010 | pmid = 20167482 | pmc = 7127101 | doi = 10.1016/j.bmcl.2010.01.152 | issn=0960-894X }}</ref>
{| class="wikitable"
|+ Substrate preferences for 3CL proteases (from table 2)<ref name="pmid22073294">{{cite journal | vauthors = Chuck CP, Chow HF, Wan DC, Wong KB | title = Profiling of substrate specificities of 3C-like proteases from group 1, 2a, 2b, and 3 coronaviruses | journal = PLOS ONE | volume = 6 | issue = 11 | pages = e27228 | date = 2011 | pmid = 22073294 | pmc = 3206940 | doi = 10.1371/journal.pone.0027228 | bibcode = 2011PLoSO...627228C | doi-access = free }}</ref>
|-
! Position !! Substrate preference
|-
| P5 || No strong preference
|-
| P4 || Small [[hydrophobic]] residues
|-
| P3 || Positively charged residue
|-
| P2 || High hydrophobicity and absence of [[Branched-chain amino acid|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 ==
[[Image:Nirtalmatrelvir on 3CL.png|thumb|left|[[Nirmatrelvir]] bound to 3CL {{PDB|7RFW}}]]
[[Image:PF-07321332.svg|thumb|left|[[Nirmatrelvir]], a 3CLpro inhibitor developed by [[Pfizer]] in [[Phases of clinical research|phase II/III clinical trial]]s as a [[combination drug]] with [[ritonavir]].<ref name="pmid34029993">{{cite journal | vauthors = Vandyck K, Deval J | title = Considerations for the discovery and development of 3-chymotrypsin-like cysteine protease inhibitors targeting SARS-CoV-2 infection | journal = Curr Opin Virol | volume = 49 | issue = | pages = 36–40 | date = August 2021 | pmid = 34029993 | pmc = 8075814 | doi = 10.1016/j.coviro.2021.04.006 }}</ref><ref name=arena>{{cite web | url = https://www.clinicaltrialsarena.com/news/pfizer-antiviral-covid-trial/ | title = Pfizer begins dosing in Phase II/III trial of antiviral drug for Covid-19. | work = Clinical Trials Arena | date = 2 September 2021 }}</ref>]]
A number of [[Protease inhibitor (pharmacology)|protease inhibitors]] are being developed targeting 3CLpro and homologous [[Picornain 3C|3Cpro]], including [[3CLpro-1|CLpro-1]], [[GC376]], [[rupintrivir]], [[lufotrelvir]], [[PF-07321332]], and [[AG7404]].<ref name="Tian_2021">{{cite journal | vauthors = Tian D, Liu Y, Liang C, Xin L, Xie X, Zhang D, Wan M, Li H, Fu X, Liu H, Cao W | title = An update review of emerging small-molecule therapeutic options for COVID-19 | journal = Biomedicine & Pharmacotherapy | volume = 137 | issue = | pages = 111313 | date = May 2021 | pmid = 33556871 | pmc = 7857046 | doi = 10.1016/j.biopha.2021.111313 }}</ref><ref>{{cite journal | vauthors = Morse JS, Lalonde T, Xu S, Liu WR | title = Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV | journal = ChemBioChem | volume = 21 | issue = 5 | pages = 730–738 | date = March 2020 | pmid = 32022370 | pmc = 7162020 | doi = 10.1002/cbic.202000047 }}</ref><ref>{{cite journal | vauthors = Liu C, Zhou Q, Li Y, Garner LV, Watkins SP, Carter LJ, Smoot J, Gregg AC, Daniels AD, Jervey S, Albaiu D | display-authors = 6 | title = Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases | journal = ACS Central Science | volume = 6 | issue = 3 | pages = 315–331 | date = March 2020 | pmid = 32226821 | doi = 10.1021/acscentsci.0c00272 | pmc = 7094090 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Ramajayam R, Tan KP, Liang PH | title = Recent development of 3C and 3CL protease inhibitors for anti-coronavirus and anti-picornavirus drug discovery | journal = Biochemical Society Transactions | volume = 39 | issue = 5 | pages = 1371–5 | date = October 2011 | pmid = 21936817 | doi = 10.1042/BST0391371 | doi-access =  }}</ref><ref name="pmid32321856">{{cite journal | vauthors = Dai W, Zhang B, Jiang XM, Su H, Li J, Zhao Y, Xie X, Jin Z, Peng J, Liu F, Li C, Li Y, Bai F, Wang H, Cheng X, Cen X, Hu S, Yang X, Wang J, Liu X, Xiao G, Jiang H, Rao Z, Zhang LK, Xu Y, Yang H, Liu H | display-authors = 6|title = Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease | journal = Science | volume = 368 | issue = 6497 | pages = 1331–1335 | date = June 2020 | pmid = 32321856 | pmc = 7179937 | doi = 10.1126/science.abb4489 |bibcode=2020Sci...368.1331D|doi-access = free}}</ref> The [[Intravenous therapy|intravenous]] administered [[prodrug]] [[PF-07304814]] (lufotrelvir) entered [[clinical trial]]s in September 2020.<ref>{{cite journal |url=https://clinicaltrials.gov/ct2/show/NCT04535167 |title=First-In-Human Study To Evaluate Safety, Tolerability, And Pharmacokinetics Following Single Ascending And Multiple Ascending Doses of PF-07304814 In Hospitalized Participants With COVID-19. |author=<!--Not stated--> |date=24 June 2021 |website=Clinical Trials |access-date=3 July 2021}}</ref>

After clinical trials, in December 2021, the oral medication [[nirmatrelvir]] (formerly PF-07321332) became commercially available under [[emergency use authorization]]s (EUA), as part of the [[nirmatrelvir/ritonavir]] combination therapy (brand name Paxlovid).<ref name="fda-factsheet">{{cite tech report |title=Fact sheet for healthcare providers: Emergency Use Authorization for Paxlovid |number=LAB-1492-0.8 |publisher=[[Pfizer]] |date=22 December 2021 |url=https://www.fda.gov/media/155050/download |format=PDF |archive-url=https://web.archive.org/web/20211223210430/https://www.fda.gov/media/155050/download |archive-date=23 December 2021 |url-status=live}}</ref><ref name="Pfizer PR 20211222">{{cite press release | title=Pfizer Receives U.S. FDA Emergency Use Authorization for Novel COVID-19 Oral Antiviral Treatment | publisher=[[Pfizer]] | date=22 December 2021 | url=https://www.businesswire.com/news/home/20211221005795/en/Pfizer-Receives-U.S.-FDA-Emergency-Use-Authorization-for-Novel-COVID-19-Oral-Antiviral-Treatment | access-date=22 December 2021 | via=Business Wire | archive-date=22 December 2021 | archive-url=https://web.archive.org/web/20211222175027/https://www.businesswire.com/news/home/20211221005795/en/Pfizer-Receives-U.S.-FDA-Emergency-Use-Authorization-for-Novel-COVID-19-Oral-Antiviral-Treatment | url-status=live }}</ref> In May 2023, the medication got full FDA approval for high-risk adults, while children 12–18 were still covered under the EUA.<ref name="FDA PR 20230525">{{cite press release | title=FDA Approves First Oral Antiviral for Treatment of COVID-19 in Adults | website=U.S. [[Food and Drug Administration]] (FDA) | date=26 May 2023 | url=https://www.fda.gov/news-events/press-announcements/fda-approves-first-oral-antiviral-treatment-covid-19-adults | access-date=26 May 2023}} {{PD-notice}}</ref>

The 3C-like protease inhibitor [[ensitrelvir]] received authorization to treat COVID-19 in Japan in 2022.<ref name="Shionogi PR 20221122">{{cite press release | title=Xocova (Ensitrelvir Fumaric Acid) Tablets 125mg Approved in Japan for the Treatment of SARS-CoV-2 Infection, under the Emergency Regulatory Approval System | website=[[Shionogi]] | date=22 November 2022 | url=https://www.shionogi.com/us/en/news/2022/11/xocova-ensitrelvir-fumaric-acid-tablets-125mg-approved-in-japan-for-the-treatment-of-sars-cov-2-infection,-under-the-emergency-regulatory-approval-system.html | access-date=28 November 2022}}</ref><ref name="Lenharo 2023">{{cite web |last=Lenharo |first=Mariana |title=New Pill Helps COVID Smell and Taste Loss Fade Quickly |website=[[Scientific American]] |date=18 October 2023 |url=https://www.scientificamerican.com/article/new-pill-helps-covid-smell-and-taste-loss-fade-quickly/ |access-date=28 October 2023}}</ref>

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.<ref name="pmid35142215">{{cite journal | vauthors = Luttens A, Gullberg H, Abdurakhmanov E, Vo DD, Akaberi D, Talibov VO, Nekhotiaeva N, Vangeel L, De Jonghe S, Jochmans D, Krambrich J, Tas A, Lundgren B, Gravenfors Y, Craig AJ, Atilaw Y, Sandström A, Moodie LK, Lundkvist Å, van Hemert MJ, Neyts J, Lennerstrand J, Kihlberg J, Sandberg K, Danielson UH, Carlsson J |display-authors = 6| title = Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses | journal = J Am Chem Soc | volume = 144 | issue = 7 | pages = 2905–2920 | date = February 2022 | pmid = 35142215 | pmc = 8848513 | doi = 10.1021/jacs.1c08402 | issn = 0002-7863}}</ref>

[[File:Doi.10.1126.science.abb4489.F3.large.C.jpg|thumb|right|A ligand-binding diagram showing the [[amino acid residue]]s in contact with a [[covalent]]ly bound [[peptidomimetic]] [[Protease inhibitor (biology)|protease inhibitor]]. The small red spheres are [[water molecule]]s.<ref name="pmid32321856" />]]

== 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 [[Catalytic triad|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:<ref>{{cite journal | vauthors = Kim Y, Lovell S, Tiew KC, Mandadapu SR, Alliston KR, Battaile KP, Groutas WC, Chang KO | display-authors = 6 | title = Broad-spectrum antivirals against 3C or 3C-like proteases of picornaviruses, noroviruses, and coronaviruses | journal = Journal of Virology | volume = 86 | issue = 21 | pages = 11754–62 | date = November 2012 | pmid = 22915796 | pmc = 3486288 | doi = 10.1128/JVI.01348-12 }}</ref>
* This entry is the coronavirus 3CL<sup>pro</sup>.
* ''[[Picornavirus|Picornaviridae]]'' have a picornavirus [[Picornain 3C|3C<sup>pro</sup>]] ({{EC number|3.4.22.28}}; {{InterPro|IPR000199}}; MEROPS C03). This is the earliest-studied family.  Examples include the ones found in [[poliovirus]] and in [[rhinovirus]] (both are members of genus ''[[Enterovirus]]'').
* ''[[Caliciviridae]]'' have a 3CL<sup>pro</sup> ({{InterPro|IPR001665}}; MEROPS C37). Examples include the one found in [[Norwalk virus]].

Additional members are known from ''[[Potyviridae]]'' and non-''Coronaviridae'' ''[[Nidovirales]]''.<ref>{{cite journal | vauthors = Ziebuhr J, Bayer S, Cowley JA, Gorbalenya AE | title = The 3C-like proteinase of an invertebrate nidovirus links coronavirus and potyvirus homologs | journal = Journal of Virology | volume = 77 | issue = 2 | pages = 1415–26 | date = January 2003 | pmid = 12502857 | doi = 10.1128/jvi.77.2.1415-1426.2003 | pmc = 140795 | doi-access = free }}</ref>

{{clear}}

== See also ==
* [[3CLpro-1]]
* [[Carmofur]]
* [[COVID Moonshot]]
* [[Ebselen]]
* [[EDP-235]]
* [[Eganelisib]]
* [[GC376]]
* [[GRL-0617]]
* [[MK-7845]]
* [[Nirmatrelvir]]
* [[Olgotrelvir]]
* [[RAY1216]]
* [[Rupintrivir]]
* [[SIM0417]]
* [[Theaflavin digallate]]
* [[Tollovir]]
* [[Y180]]
* [[Tetrahydrocannabutol]]

== References ==
{{reflist}}

== Further reading ==
{{refbegin}}
* {{cite journal | vauthors = Chuck CP, Chow HF, Wan DC, Wong KB | title = Profiling of substrate specificities of 3C-like proteases from group 1, 2a, 2b, and 3 coronaviruses | journal = PLOS ONE | volume = 6 | issue = 11 | pages = e27228 | date = 2 November 2011 | pmid = 22073294 | pmc = 3206940 | doi = 10.1371/journal.pone.0027228 | doi-access = free | bibcode = 2011PLoSO...627228C }}
{{refend}}

== External links ==
* {{MeshName|SARS+coronavirus+main+proteinase}}
* Peptidase C30/C16 in coronavirus, {{InterPro|IPR013016}}. The MEROPS C16 one is the "papain-like" PL-PRO.

{{Coronavirus genomes}}
{{Cysteine proteases}}
{{Viral proteins}}
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[[Category:EC 3.4.22]]
[[Category:Coronavirus proteins]]
[[Category:Viral nonstructural proteins]]