View source for 22dr


==Crystal structure of SARS-CoV-2 3CL protease in complex with compound 7c==
<StructureSection load='22dr' size='340' side='right'caption='[[22dr]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[22dr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=22DR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=22DR FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1MDL:7-[(3~{R})-3-fluoranylpyrrolidin-1-yl]-5-methoxy-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[3,4,5-tris(fluoranyl)phenyl]methyl]pyrido[4,3-d]pyrimidine-2,4-dione'>A1MDL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=22dr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=22dr OCA], [https://pdbe.org/22dr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=22dr RCSB], [https://www.ebi.ac.uk/pdbsum/22dr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=22dr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/R1A_SARS2 R1A_SARS2] Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.[UniProtKB:P0C6X7]  Inhibits host translation by interacting with the 40S ribosomal subunit. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response.[UniProtKB:P0C6X7]  May play a role in the modulation of host cell survival signaling pathway by interacting with host PHB and PHB2. Indeed, these two proteins play a role in maintaining the functional integrity of the mitochondria and protecting cells from various stresses.[UniProtKB:P0C6X7]  Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B signaling.[UniProtKB:P0C6X7]  Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.[UniProtKB:P0C6X7]  Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Also able to bind an ADP-ribose-1''-phosphate (ADRP).[UniProtKB:P0C6X7]  Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic. Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes.[UniProtKB:P0C6X7]  Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7]  Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7]  May participate in viral replication by acting as a ssRNA-binding protein.[UniProtKB:P0C6X7]  Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease and nsp16 2'-O-methyltransferase activities. Therefore plays an essential role in viral mRNAs cap methylation.[UniProtKB:P0C6X7]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
COVID-19, an infectious disease caused by SARS-CoV-2, first identified in Wuhan, China, in 2019 and rapidly spread around the world. In response to this worldwide crisis, the research and development of antiviral drugs advanced together with vaccines, and several medications are currently being used for treatment. This study aimed to explore the structure-activity relationships (SAR) of non-covalent inhibitors of the SARS-CoV-2 3CL protease (3CL(pro)) and to develop more potent inhibitors starting from ensitrelvir, a potent non-peptide small-molecule 3CL(pro) inhibitor discovered by Shionogi &amp; Co., Ltd. Although a previously reported dihydrofuran-ring-fused tricyclic compound 1 exhibited high antiviral activity, there were issues with its metabolic stability and solubility. Therefore, we focused on compound 2, which has a pyridopyrimidinedione scaffold, and tried to optimize its structure. Here we report compounds that have improved antiviral activity while maintaining enzyme inhibitory activity and enhanced solubility. In particular, compound 18f demonstrated a balance of potent activity, high solubility, and excellent metabolic stability. Its favorable pharmacokinetics were also confirmed in rat PK tests, suggesting that this compound offers promise as a new therapeutic agent.

Optimization of pyridopyrimidinedione derivatives as non-covalent SARS-CoV-2 3CL protease inhibitors.,Taoda Y, Hirai K, Sugiyama S, Tanaka S, Tomida Y, Akiyama T, Nakahara K, Unoh Y, Tachibana Y, Uehara S, Sako Y, Yamamoto S, Kawashima S, Nobori H, Kato T Bioorg Med Chem Lett. 2026 Mar 10;136:130619. doi: 10.1016/j.bmcl.2026.130619. PMID:41819156<ref>PMID:41819156</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 22dr" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Severe acute respiratory syndrome coronavirus 2]]
[[Category: Akiyama T]]
[[Category: Hirai K]]
[[Category: Kato T]]
[[Category: Kawashima S]]
[[Category: Nakahara K]]
[[Category: Nobori H]]
[[Category: Sako Y]]
[[Category: Sugiyama S]]
[[Category: Tachibana Y]]
[[Category: Tanaka S]]
[[Category: Taoda Y]]
[[Category: Tomida Y]]
[[Category: Uehara S]]
[[Category: Unoh Y]]
[[Category: Yamamoto S]]