Background
SARS-CoV-2 is a single-stranded RNA virus. The virus has four major structural proteins, including spike protein (S), membrane protein (M), envelope protein (E), and nucleocapsid protein (N), where the N protein helps to properly form the capsid and overall viral structure, and the S helps the virus attach to a host cell. SARS-CoV-2 is closely related to SARS-CoV, sharing approximately 79% of their genome, and both receptors are angiotensin-converting enzyme 2 (ACE2), making the pathogenesis of these two viral infections similar.
Figure 1. The structure and combination of COVID-19 virus and ACE2
(Source: Zhou H, et al. 2021)
SARS-CoV-2 is transmitted by respiratory droplets and aerosols. The incubation period after human infection is usually 4-5 days, and some infected people have no obvious symptoms, but most patients show mild to moderate respiratory illness with cough, fever, headache, myalgia and diarrhea. In severe cases, hypoxemia-induced dyspnea develops and some patients progress to progressive respiratory failure. COVID-19 patients with acute respiratory distress syndrome (ARDS) develop systemic hyperinflammation with elevated levels of proinflammatory cytokines and markers of inflammation such as interleukins, TNF, D-dimer and C-reactive protein (CRP). Therefore, close monitoring of serum levels of IL-6, IL-8 and TNF in hospitalized patients predicts disease progression and prognosis. In addition, patients with severe COVID-19 may have extrapulmonary disease manifested by gastrointestinal symptoms, acute cardiac, renal and hepatic injury, rhabdomyolysis, coagulopathy and shock.
There are no effective drugs for SARS-CoV-2, and drug repurposing is generally done by selecting effective drugs from existing drugs, which reduces the time and cost of drug discovery. Several antiviral drugs are available for the treatment of COVID-19, such as camostat, uminovir and ritonavir, a class of drugs that work primarily by preventing viral replication, thereby shortening the course of the disease and reducing the index of infection. Anti-inflammatory drugs are used to prevent tissue damage from cytokine storms. Anticoagulants are used to prevent thrombosis in a rational manner, depending on the patient's disease progression. Based on the fact that SARS-CoV2 enters host cells through ACE2 receptors, angiotensin-converting enzyme inhibitors (ACEIs) have been tried in the clinical treatment of COVID-19 and have been shown to reduce epithelial cell apoptosis, mesenchymal fibrosis, and collagen deposition, thereby reducing the incidence of lung injury. The use of ACEIs also reduces lung, kidney and heart damage caused by RAS overactivation. However, the drug requires attention to safety concerns.
References
- 1. Ghareeb DA, et al. Potential therapeutic and pharmacological strategies for SARS-CoV2. J Pharm Investig. 2021;51(3):281-296.
- 2. Zhou H, et al. A Review of SARS-CoV2: Compared With SARS-CoV and MERS-CoV. Front Med (Lausanne). 2021 Dec 7;8:628370.
References
Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir
Nature
Authors: Duan Y, Zhou H, Liu X, Iketani S, Lin M, Zhang X, Bian Q, Wang H, Sun H, Hong SJ, Culbertson B, Mohri H, Luck MI, Zhu Y, Liu X, Lu Y, Yang X, Yang K, Sabo Y, Chavez A, Goff SP, Rao Z, Ho DD, Yang H.
Abstract
Nirmatrelvir is a specific antiviral drug that targets the main protease (Mpro) of SARS-CoV-2 and has been approved to treat COVID-191,2. As an RNA virus characterized by high mutation rates, whether SARS-CoV-2 will develop resistance to nirmatrelvir is a question of concern. Our previous studies have shown that several mutational pathways confer resistance to nirmatrelvir, but some result in a loss of viral replicative fitness, which is then compensated for by additional alterations3. The molecular mechanisms for this observed resistance are unknown. Here we combined biochemical and structural methods to demonstrate that alterations at the substrate-binding pocket of Mpro can allow SARS-CoV-2 to develop resistance to nirmatrelvir in two distinct ways. Comprehensive studies of the structures of 14 Mpro mutants in complex with drugs or substrate revealed that alterations at the S1 and S4 subsites substantially decreased the level of inhibitor binding, whereas alterations at the S2 and S4' subsites unexpectedly increased protease activity. Both mechanisms contributed to nirmatrelvir resistance, with the latter compensating for the loss in enzymatic activity of the former, which in turn accounted for the restoration of viral replicative fitness, as observed previously3. Such a profile was also observed for ensitrelvir, another clinically relevant Mpro inhibitor. These results shed light on the mechanisms by which SARS-CoV-2 evolves to develop resistance to the current generation of protease inhibitors and provide the basis for the design of next-generation Mpro inhibitors.
Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane
Nature
Authors: Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B.
Abstract
The entry of SARS-CoV-2 into host cells depends on the refolding of the virus-encoded spike protein from a prefusion conformation, which is metastable after cleavage, to a lower-energy stable postfusion conformation1,2. This transition overcomes kinetic barriers for fusion of viral and target cell membranes3,4. Here we report a cryogenic electron microscopy (cryo-EM) structure of the intact postfusion spike in a lipid bilayer that represents the single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membrane-interacting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.