key: cord-0771404-7hwb0q5u
authors: Mengist, Hylemariam Mihiretie; Fan, Xiaojiao; Jin, Tengchuan
title: Designing of improved drugs for COVID-19: Crystal structure of SARS-CoV-2 main protease M(pro)
date: 2020-05-09
journal: Signal Transduct Target Ther
DOI: 10.1038/s41392-020-0178-y
sha: 3057c5eea1c8006681601d8afdbf8156f4b3f2c0
doc_id: 771404
cord_uid: 7hwb0q5u

nan

enzymes. SARS-CoV-2 M pro forms a tight dimer and has a contact interface mainly between domain II of molecule A and the NH 2terminal residues of molecule B where this dimerization is important for catalytic activity. Unlike SARS-CoV-2, SARS-CoV M pro dimer has a polar interaction between the two domains III involving a 2.60 Å hydrogen bond between the side chain hydroxyl groups of Thr 285 of each protomer which is also supported by a hydrophobic interaction between the side chain of Ile 286 and Thr 285 . In SARS-CoV-2 M pro , threonine is replaced with alanine and isoleucine with leucine. As suggested by authors, Alanine replacements change the enzyme dynamics and increase its catalytic activity by allowing the two domains III to be in a close contact; although, the catalytic activity of SARS-CoV-2 M pro was only slightly higher with similar K d of dimer dissociation (~2.5 μM).

The authors named the modified α-ketoamide inhibitor 13a. Compared to 11r, 13a has a 3 fold increase in plasma half-life in mice, highly soluble in plasma with a 19 fold increase in solubility in-vitro and a 13 fold increase in thermodynamic solubility. Further the binding of 13a with plasma proteins was reported to decrease to 97% as compared to 11r which showed 99% binding activity with plasma proteins. Provided these improvements, the structural modification resulted in loss of some inhibitory activities against the main protease of SARS-CoV-2 and 3C proteases of enteroviruses as evidenced by increased IC 50 value.

The authors increase the antiviral activity of 13b against beta coronaviruses of clade b by sacrificing the broad-spectrum nature of 13a through replacing the P2 cyclohexyl moiety in 13a with a small cyclopropyl in 13b. The authors determined the X-ray structure of α-ketoamide 13b and SARS-CoV-2 M pro complex at 1.95 and 2.20 Å resolution. In one of the structures, the authors found that the key residue, Glu 166 , forms inactive conformation in protomer B while the 13b compound is bound in the same fashion as in molecule A. Authors also found that the inhibitor binds to the shallow substrate-binding site at the surface of protomers between domains I and II in the inhibited SARS-CoV-2 M pro .

The Boc group was removed in compound 14b resulting in inactive form which means the Boc group is necessary to cross the cellular membrane and even more hydrophobic moiety may be advantageous provided that it may result in increased plasma protein binding. Hilgenfeld's group assessed the pharmacokinetics of 13a and 13b and found that the absorption-distributionmetabolism-excretion of both compounds was similar with a 90% binding to human plasma proteins. The 13b showed less Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons. After entering into the host cell, SARS-CoV-2 releases its genomic RNA. The process of translation yields polyproteins pp1a and pp1ab, which are cleaved to the main protease M pro and nonstructural proteins (nsps). M pro is involved in the producing of nsps. Nsps is essential for assembling the viral replication transcription complex (RTC) to engage in RNA synthesis. Once inhibitors, such as 11r, 13a, and 13b, act in the cell, they bind to M pro and inhibit the activity of this enzyme, resulting in failure of virion assembly. Ultimately, host cell fails to release the new intact virions. Colored box highlight the modifications from 11r to 14b. Due to lacking Boc group, 14b could not cross the cellular membrane to inhibit viral replication

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