A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the aetiological agent responsible for the 2019–2020 viral pneumonia outbreak of coronavirus disease 2019 (COVID-19)1–4. Currently, there are no targeted therapeutic agents for the treatment of this disease, and effective treatment options remain very limited. Here we describe the results of a programme that aimed to rapidly discover lead compounds for clinical use, by combining structure-assisted drug design, virtual drug screening and high-throughput screening. This programme focused on identifying drug leads that target main protease (Mpro) of SARS-CoV-2: Mpro is a key enzyme of coronaviruses and has a pivotal role in mediating viral replication and transcription, making it an attractive drug target for SARS-CoV-25,6. We identified a mechanism-based inhibitor (N3) by computer-aided drug design, and then determined the crystal structure of Mpro of SARS-CoV-2 in complex with this compound. Through a combination of structure-based virtual and high-throughput screening, we assayed more than 10,000 compounds—including approved drugs, drug candidates in clinical trials and other pharmacologically active compounds—as inhibitors of Mpro. Six of these compounds inhibited Mpro, showing half-maximal inhibitory concentration values that ranged from 0.67 to 21.4 μM. One of these compounds (ebselen) also exhibited promising antiviral activity in cell-based assays. Our results demonstrate the efficacy of our screening strategy, which can lead to the rapid discovery of drug leads with clinical potential in response to new infectious diseases for which no specific drugs or vaccines are available. A programme of structure-assisted drug design and high-throughput screening identifies six compounds that inhibit the main protease of SARS-CoV-2, demonstrating the ability of this strategy to isolate drug leads with clinical potential.

/pdf/structure-of-mpro-from-sars-cov-2-and-discovery-of-its-2hyiph66s6.pdf

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

The recent emergence of a novel coronavirus (2019-nCoV), which is causing an outbreak of unusual viral pneumonia in patients in Wuhan, a central city in China, is another warning of the risk of CoVs posed to public health. In this minireview, we provide a brief introduction of the general features of CoVs and describe diseases caused by different CoVs in humans and animals. This review will help understand the biology and potential risk of CoVs that exist in richness in wildlife such as bats.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/jmv.25681

Emerging coronaviruses: Genome structure, replication, and pathogenesis.

Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), which are caused by coronaviruses, have attracted substantial attention owing to their high mortality rates and potential to cause epidemics. Yuen and colleagues discuss progress with treatment options for these syndromes, including virus- and host-targeted drugs, and the challenges that need to be overcome in their further development. In humans, infections with the human coronavirus (HCoV) strains HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1 usually result in mild, self-limiting upper respiratory tract infections, such as the common cold. By contrast, the CoVs responsible for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), which were discovered in Hong Kong, China, in 2003, and in Saudi Arabia in 2012, respectively, have received global attention over the past 12 years owing to their ability to cause community and health-care-associated outbreaks of severe infections in human populations. These two viruses pose major challenges to clinical management because there are no specific antiviral drugs available. In this Review, we summarize the epidemiology, virology, clinical features and current treatment strategies of SARS and MERS, and discuss the discovery and development of new virus-based and host-based therapeutic options for CoV infections.

/pdf/coronaviruses-drug-discovery-and-therapeutic-options-1rkhv204qf.pdf

Coronaviruses - drug discovery and therapeutic options.

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the etiological agent responsible for the global COVID-19 (coronavirus disease 2019) outbreak. The main protease of SARS-CoV-2, Mpro, is a key enzyme that plays a pivotal role in mediating viral replication and transcription. We designed and synthesized two lead compounds (11a and 11b) targeting Mpro Both exhibited excellent inhibitory activity and potent anti-SARS-CoV-2 infection activity. The x-ray crystal structures of SARS-CoV-2 Mpro in complex with 11a or 11b, both determined at a resolution of 1.5 angstroms, showed that the aldehyde groups of 11a and 11b are covalently bound to cysteine 145 of Mpro Both compounds showed good pharmacokinetic properties in vivo, and 11a also exhibited low toxicity, which suggests that these compounds are promising drug candidates.

Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

/pdf/rcsb-protein-data-bank-powerful-new-tools-for-exploring-3d-2ttwqgo63f.pdf

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.

To date, an effective therapeutic treatment that confers strong attenuation toward coronaviruses (CoVs) remains elusive. Of all the potential drug targets, the helicase of CoVs is considered to be one of the most important. Here, we first present the structure of the full-length Nsp13 helicase of SARS-CoV (SARS-Nsp13) and investigate the structural coordination of its five domains and how these contribute to its translocation and unwinding activity. A translocation model is proposed for the Upf1-like helicase members according to three different structural conditions in solution characterized through H/D exchange assay, including substrate state (SARS-Nsp13-dsDNA bound with AMPPNP), transition state (bound with ADP-AlF4-) and product state (bound with ADP). We observed that the β19-β20 loop on the 1A domain is involved in unwinding process directly. Furthermore, we have shown that the RNA dependent RNA polymerase (RdRp), SARS-Nsp12, can enhance the helicase activity of SARS-Nsp13 through interacting with it directly. The interacting regions were identified and can be considered common across CoVs, which provides new insights into the Replication and Transcription Complex (RTC) of CoVs.

/pdf/delicate-structural-coordination-of-the-severe-acute-2g3lvldx75.pdf

Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis.

Emerging Infection Disease Program, High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin 300457, China Correspondence: raozh@xtal.tsinghua.edu.cnFrom the global outbreak of SARS-CoV caused infection disease in 2003, coronaviruses (CoVs) are known to be a great threat to the human health. Recently, a new SARS-like coronavirus, human betacoronavirus 2c EMC/2012 (HCoV-EMC), has been identified and the appearance of this new CoV raises concerns that a new spread of CoV may occurs in the future. By solving the crystal structure of HCoV-EMC main protease with a wide-spectrum anti-CoV inhibitor N3, we conﬁ rmed that that N3 blocks the function of HCoV-EMC main protease through a similar mechanism to other CoVs. Together with the good pharmaceutical features, N3 is conceiv-able to be effective to HCoV-EMC and other CoVs appearing in the future. These ﬁ ndings make it convincing that CoVs will not be a threat to human health.In the year of 2012, a new respira-tory illness similar to severe acute res-piratory syndrome (SARS) that spread globally in 2003 and infected over 8,000 people with more than 800 fatalities (Li et al., 2010), was identiﬁ ed in Europe, the Middle East and Hong Kong. The infection was reported to manifest clini-cally with fever, cough and breathing dif-ﬁ culties. Some patients also developed acute renal failure. Sequence analysis suggested that the causative agent of this newly emerged SARS-like illness is a new coronavirus (CoV) which has been named as the human betacorona-virus 2c EMC/2012 (HCoV-EMC). No clinically approved treatment is available for CoV infection since the outbreak of SARS in 2003, the appearance of this new CoV raises concerns that a new epidemic of CoV infection may occur in future.CoVs are positive-sense, single-stranded RNA viruses and are featured by the largest viral RNA genomes known to date (Yang et al., 2003). Rep-lication of coronavirus requires correct proteolytic processing of the replicase polyprotein by viral proteases, in particu-lar a chymotrypsin-like protease (3CL

/pdf/the-newly-emerged-sars-like-coronavirus-hcov-emc-also-has-an-21cphmvpbs.pdf

The newly emerged SARS-Like coronavirus HCoV-EMC also has an 'Achilles' heel': current effective inhibitor targeting a 3C-like protease

Avian infectious bronchitis virus (IBV) is a member of the group III coronaviruses, which differ from the other groups of coronaviruses in that they do not encode the essential pathogenic factor nonstructural protein 1 (nsp1) and instead start with nsp2. IBV nsp2 is one of the first replicase proteins to be translated and processed in the viral life cycle; however, it has an entirely unknown function. In order to better understand the structural details and functional mechanism of IBV nsp2, the recombinant protein was cloned, overexpressed in Escherichia coli, purified and crystallized. The crystals diffracted to 2.8 A resolution and belonged to space group P21, with unit-cell parameters a = 57.0, b = 192.3, c = 105.7 A, β = 90.8°. Two molecules were found in the asymmetric unit; the Matthews coefficient was 3.9 A3 Da−1, corresponding to a solvent content of 68.2%.

Purification, crystallization and preliminary X-ray analysis of nonstructural protein 2 (nsp2) from avian infectious bronchitis virus

SARS coronavirus (SARS-CoV) is the aetiological agent of the highly infectious severe acute respiratory syndrome (SARS). To gain a better understanding of SARS-CoV replication and transcription proteins, a preliminary X-ray crystallo­graphic study of the C-terminal domain of SARS-CoV nonstructural protein 2 (nsp2) is reported here. The C-­terminal domain of SARS-CoV nsp2 was cloned, overexpressed, purified and crystallized using polyethylene glycol 5000 monomethyl ether as the precipitant; the crystals diffracted to 2.5 A resolution. The crystals belonged to space group P65, with unit-cell parameters a = b = 112.8, c = 91.1 A, α = β = 90, γ = 120°. One molecule is assumed to be present per asymmetric unit, which gives a Matthews coefficient of 2.89 A3 Da−1 and a solvent content of 56.2%.

/pdf/expression-crystallization-and-preliminary-crystallographic-uub0khijv6.pdf

Zhilin Ren

Papers

Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis.

The newly emerged SARS-Like coronavirus HCoV-EMC also has an 'Achilles' heel': current effective inhibitor targeting a 3C-like protease

Purification, crystallization and preliminary X-ray analysis of nonstructural protein 2 (nsp2) from avian infectious bronchitis virus

Expression, crystallization and preliminary crystallographic study of the C-terminal half of nsp2 from SARS coronavirus.