PDBsum entry 6fv1

Hydrolase

PDB id: 6fv1

Contents

Protein chains

300 a.a.

Ligands

E8E ×3

GOL ×5

DMS ×2

SO4

Waters ×474

PDB id:

6fv1

Name:

Hydrolase

Title:

Structure of human coronavirus nl63 main protease in complex with the alpha-ketoamide (s)-n-((s)-4-(benzylamino)-3,4-dioxo-1-((s)-2- oxopyrrolidin-3-yl)butan-2-yl)-2-cinnamamido-4-methylpentanamide (cinnamoyl-leucine-glnlactam-co-co-nh-benzyl)

Structure:

3c-like proteinase. Chain: a, b, c. Synonym: 3cl-pro,3clp,m-pro,nsp5,p34. Engineered: yes

Source:

Human coronavirus nl63. Hcov-nl63. Organism_taxid: 277944. Gene: rep, 1a-1b. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.30Å R-factor: 0.197 R-free: 0.231

Authors:

L.Zhang,R.Hilgenfeld

Key ref:

L.Zhang et al. (2020). α-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment. J Med Chem, 63, 4562-4578. PubMed id: 32045235 DOI: 10.1021/acs.jmedchem.9b01828

Date:

28-Feb-18 Release date: 20-Mar-19

Protein chains

P0C6X5  (R1AB_CVHNL) -  Replicase polyprotein 1ab from Human coronavirus NL63

Seq: 6729 a.a.

Struc: 300 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.1.1.57 - methyltransferase cap1.
• Reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺
• Enzyme class 3: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 4: E.C.2.7.7.50 - mRNA guanylyltransferase.
• Reaction: a 5'-end diphospho-ribonucleoside in mRNA + GTP + H⁺ = a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate
• Enzyme class 5: E.C.3.1.13.- - ?????
• Enzyme class 6: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
• Enzyme class 7: E.C.3.4.22.- - ?????
• Enzyme class 8: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 9: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 10: E.C.4.6.1.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/acs.jmedchem.9b01828

J Med Chem 63:4562-4578 (2020)

PubMed id: 32045235

α-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment.

L.Zhang, D.Lin, Y.Kusov, Y.Nian, Q.Ma, J.Wang, A.von Brunn, P.Leyssen, K.Lanko, J.Neyts, A.de Wilde, E.J.Snijder, H.Liu, R.Hilgenfeld.

ABSTRACT

The main protease of coronaviruses and the 3C protease of enteroviruses share a similar active-site architecture and a unique requirement for glutamine in the P1 position of the substrate. Because of their unique specificity and essential role in viral polyprotein processing, these proteases are suitable targets for the development of antiviral drugs. In order to obtain near-equipotent, broad-spectrum antivirals against alphacoronaviruses, betacoronaviruses, and enteroviruses, we pursued a structure-based design of peptidomimetic α-ketoamides as inhibitors of main and 3C proteases. Six crystal structures of protease-inhibitor complexes were determined as part of this study. Compounds synthesized were tested against the recombinant proteases as well as in viral replicons and virus-infected cell cultures; most of them were not cell-toxic. Optimization of the P2 substituent of the α-ketoamides proved crucial for achieving near-equipotency against the three virus genera. The best near-equipotent inhibitors, 11u (P2 = cyclopentylmethyl) and 11r (P2 = cyclohexylmethyl), display low-micromolar EC₅₀ values against enteroviruses, alphacoronaviruses, and betacoronaviruses in cell cultures. In Huh7 cells, 11r exhibits three-digit picomolar activity against the Middle East Respiratory Syndrome coronavirus.