Coronavirus MPro proteaseThe content of this page was edited by matteoferla on the 2020-06-22 14:19:14.728645.
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Since the release of the genome of the new coronavirus (2019-nCoV), there has been a flurry of open activity both on the vaccine front and on the drug design front, including several clinical trials to repurpose several existing drugs. In terms of structural biology, the structure of the 3C-like protease was released on the 5th February and was quickly followed by several other structures.
The most studied of the coronavirus enzymes is most definitely the protease 3CL (also known as MPro).with (protease from PDB:6Y2E and peptide TSAVLQSGFRK from SARS protease PDB:2Q6G).
To save genetic space, many RNA viruses employ a strategy wherein different protein acting at the same stage of the infection cycle are produced as a single long peptide that gets cut up by a protease at given recognition sequences. In the case modelled here,.
(figure from Kiemer et al. 2004)
A protease works thanks to a catalytic triad: an acid hydrogen bonds to a base, which in turns deprotonates a nucleophile making it more active. In the case of viral protease the acid is part of the ligand, so it's a dyad. With 2019-nCoV (and SARS)is the base and is the nucleophile.
The. The is highly unstable and the N-terminal half of the peptide leaves. The thioester between the enzyme and the intermediate is more stable but undergoes a substition reaction with water (hydrolysis) freeing the enzyme for another round of catalysis and releasing the second half of the substrate.
Given the following:
- it is a very essential protein, so inhibiting it will stop the infection
- its substrate is large, which means it has an exposed active site to accommodate its substrate, so drug design is easier
- its substrate is a long peptide, so it is easy to make peptidomimetic drugs.
It is clear why viral protease made good candidates. In fact, the crystallisation of the HIV protease was a big deal —appearing the Voet and Voet textbook and featuring in the book The Billion-Dollar Molecule and there are many HIV protease inhibitors on the market (NB. HIV protease has a diffent structure but works on the same principle).
The Yang et al., 2005) —the 2019-nCoV protease is 96% identical to SARS protease (also a coronavirus). How it works is that the reaction starts, but gets stuck because the substrate is not quite the same. First, the , but, instead of attacking a ketone of a peptide bond like a normal hydrolysis, it goes for the more electrophilic double bond next to it, which therefore acts as a Michael acceptor, forming a very stable, so goes nowehere and the enzyme is broken!was released with found by the same authors in a SARS protease drug screen (
In terms of the structure of the peptide N3, reading it from the N-terminus (biochemistry way, as opposed to chemistry way): N-terminal cap - alanine - valine - leucine - Lipinski's rule of five).- C-terminal cap. The AVL part is the same as the consensus sequence, but then instead of a glutamate there is an amino acid of similar length that has a closed ring at the end. However, this large peptide has micromolar affinity for the protease of SARS and is very large, making it not ideal as drug (cf.
The, contains what the depositors call . This consists of: N-terminal cap - an aromatic ringed backbone amino acid - cyclopropylalanine - the same oxidanylidenepyrrolidine side chain amino acid as N3 - C-terminal cap. That is cyclopropylalanine is taking the place of leucine and the more rigid cyclic amino acid is taking the place of valine. The reason for the latter is that peptides are very flexible, which makes them less drug like.
Recently Diamond have done a fragment screen against the protease. Fragment screens are great as starting data for virtual screens as the protein side chains or mobile loops may adopt different conformations potentially resulting in stronger affinity.
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There are other enzymes in 2019-nCoV that are not crystallised, most notably the RNA polymerase (nsp12), which is potently inhibited by the drug remdesivir.
the I-Tasser authors have released the predicted protein structures of all of the proteins in the viral genome.