Molecular Mechanism of the Non-Covalent Orally Targeted SARS-CoV-2 Mpro Inhibitor S-217622 and Computational Assessment of Its Effectiveness against Mainstream Variants.

Convenient and efficient therapeutic agents are urgently needed to block the continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, the mechanism for the novel orally targeted SARS-CoV-2 main protease (Mpro) inhibitor S-217622 is revealed through a molecular dynamics simulation. The difference in the movement modes of the S-217622-Mpro complex and apo-Mpro suggested S-217622 could inhibit the motility intensity of Mpro, thus maintaining their stable binding. Subsequent energy calculations showed that the P2 pharmacophore possessed the highest energy contribution among the three pharmacophores of S-217622. Additionally, hot-spot residues H41, M165, C145, E166, and H163 have strong interactions with S-217622. To further investigate the resistance of S-217622 to six mainstream variants, the binding modes of S-217622 with these variants were elucidated. The subtle differences in energy compared to that of the wild type implied that the binding patterns of these systems were similar, and S-217622 still inhibited these variants. We hope this work will provide theoretical insights for optimizing novel targeted Mpro drugs.

The correlation study on chest CT features and kidney injury in severe COVID-19 pneumonia from a multicenter cohort study.

Background: Among confirmed severe COVID-19 patients, although the serum creatinine level is normal, they also have developed kidney injury. Early detection of kidney injury can guide doctors to choose drugs reasonably. Study found that COVID-19 have some special chest CT features. The study aimed to explore which chest CT features are more likely appear in severe COVID-19 and the relationship between related (special) chest CT features and kidney injury or clinical prognosis. Methods: In this retrospective study, 162 patients of severe COVID-19 from 13 medical centers in China were enrolled and divided into three groups according to the estimated glomerular filtration rate (eGFR) level: Group A (eGFR < 60 ml/min/1.73 m2), Group B (60 ml/min/1.73 m2 ≤ eGFR < 90 ml/min/1.73 m2), and Group C (eGFR ≥ 90 ml/min/1.73 m2). The demographics, clinical features, auxiliary examination, and clinical prognosis were collected and compared. The chest CT features and eGFR were assessed using univariate and multivariate Cox regression. The influence of chest CT features on eGFR and clinical prognosis were calculated using the Cox proportional hazards regression model. Results: Demographic and clinical features showed significant differences in age, hypertension, and fatigue among the Group A, Group B, and Group C (all P < 0.05). Auxiliary examination results revealed that leukocyte count, platelet count, C-reactive protein, aspartate aminotransferase, creatine kinase, respiratory rate ≥ 30 breaths/min, and CT images rapid progression (>50%) within 24-48 h among the three groups were significantly different (all P < 0.05). Compared to Group C (all P < 0.017), Groups A and B were more likely to show crazy-paving pattern. Logistic regression analysis indicated that eGFR was an independent risk factor of the appearance of crazy-paving pattern. The eGFR and crazy-paving pattern have a mutually reinforcing relationship, and eGFR (HR = 0.549, 95% CI = 0.331-0.909, P = 0.020) and crazy-paving pattern (HR = 2.996, 95% CI = 1.010-8.714, P = 0.048) were independent risk factors of mortality. The mortality of severe COVID-19 with the appearance of crazy-paving pattern on chest CT was significantly higher than that of the patients without its appearance (all P < 0.05). Conclusions: The crazy-paving pattern is more likely to appear in the chest CT of patients with severe COVID-19. In severe COVID-19, the appearance of the crazy-paving pattern on chest CT indicates the occurrence of kidney injury and proneness to death. The crazy-paving pattern can be used by doctors as an early warning indicator and a guidance of reasonable drug selection.

Immune Escape Mechanisms of SARS-CoV-2 Delta and Omicron Variants against Two Monoclonal Antibodies That Received Emergency Use Authorization.

Multiple-site mutated SARS-CoV-2 Delta and Omicron variants may trigger immune escape against existing monoclonal antibodies. Here, molecular dynamics simulations combined with the interaction entropy method reveal the escape mechanism of Delta/Omicron variants to Bamlanivimab/Etesevimab. The result shows the significantly reduced binding affinity of the Omicron variant for both antibodies, due to the introduction of positively charged residues that greatly weaken their electrostatic interactions. Meanwhile, significant structural deflection induces fewer atomic contacts and an unstable binding mode. As for the Delta variant, the reduced binding affinity for Bamlanivimab is owing to the alienation of the receptor-binding domain to the main part of this antibody, and the binding mode of the Delta variant to Etesevimab is similar to that of the wild type, suggesting that Etesevimab could still be effective against the Delta variant. We hope this work will provide timely theoretical insights into developing antibodies to prevalent and possible future variants of SARS-CoV-2.

The correlation study on chest CT features and kidney injury in severe COVID-19 pneumonia from a multicenter cohort study

Background Among confirmed severe COVID-19 patients, although the serum creatinine level is normal, they also have developed kidney injury. Early detection of kidney injury can guide doctors to choose drugs reasonably. Study found that COVID-19 have some special chest CT features. The study aimed to explore which chest CT features are more likely appear in severe COVID-19 and the relationship between related (special) chest CT features and kidney injury or clinical prognosis. Methods In this retrospective study, 162 patients of severe COVID-19 from 13 medical centers in China were enrolled and divided into three groups according to the estimated glomerular filtration rate (eGFR) level: Group A (eGFR < 60 ml/min/1.73 m2), Group B (60 ml/min/1.73 m2 ≤ eGFR < 90 ml/min/1.73 m2), and Group C (eGFR ≥ 90 ml/min/1.73 m2). The demographics, clinical features, auxiliary examination, and clinical prognosis were collected and compared. The chest CT features and eGFR were assessed using univariate and multivariate Cox regression. The influence of chest CT features on eGFR and clinical prognosis were calculated using the Cox proportional hazards regression model. Results Demographic and clinical features showed significant differences in age, hypertension, and fatigue among the Group A, Group B, and Group C (all P < 0.05). Auxiliary examination results revealed that leukocyte count, platelet count, C-reactive protein, aspartate aminotransferase, creatine kinase, respiratory rate ≥ 30 breaths/min, and CT images rapid progression (>50%) within 24–48 h among the three groups were significantly different (all P < 0.05). Compared to Group C (all P < 0.017), Groups A and B were more likely to show crazy-paving pattern. Logistic regression analysis indicated that eGFR was an independent risk factor of the appearance of crazy-paving pattern. The eGFR and crazy-paving pattern have a mutually reinforcing relationship, and eGFR (HR = 0.549, 95% CI = 0.331–0.909, P = 0.020) and crazy-paving pattern (HR = 2.996, 95% CI = 1.010–8.714, P = 0.048) were independent risk factors of mortality. The mortality of severe COVID-19 with the appearance of crazy-paving pattern on chest CT was significantly higher than that of the patients without its appearance (all P < 0.05). Conclusions The crazy-paving pattern is more likely to appear in the chest CT of patients with severe COVID-19. In severe COVID-19, the appearance of the crazy-paving pattern on chest CT indicates the occurrence of kidney injury and proneness to death. The crazy-paving pattern can be used by doctors as an early warning indicator and a guidance of reasonable drug selection.

Insights from computational analysis: how does the SARS-CoV-2 Delta (B.1.617.2) variant hijack ACE2 more effectively?

The SARS-CoV-2 Delta (B.1.617.2) variant was identified in India in October 2020, and it has quickly become the mainstream strain with strong toxicity and spread, posing great challenges to epidemic control. However, the molecular mechanism of its powerful infectivity remains unclear. It is meaningful to investigate the process of Delta variant's receptor-binding domain (RBD) binding to angiotensin-converting enzyme 2 (ACE2). Here, we performed three repeated molecular dynamics simulations for each system to avoid accidents, and the alanine scanning combined with the interaction entropy (ASIE) method was utilized to evaluate the binding free energy. Through the detailed energy and conformational analysis, the binding mechanism of the Delta variant was illustrated. The results showed that the existence of L452R and T478K mutations can trigger the effective hijacking of ACE2 by the Delta variant through the following three ways: (i) these two mutations can significantly enhance the electrostatic energy of the system by the introduction of two positively charged amino acids (Arg and Lys), thereby increasing the binding affinity of RBD and ACE2, (ii) the Loops 1, 3, and 4 in the receptor-binding motif (RBM) of RBD form a tighter conformation under the dominance of the T478K mutation, allowing ACE2 to be captured more effectively than the wild-type system, and (iii) these conformational changes lead to a more stable hydrogen bond in the Delta variant, which further ensures the stability of the binding. In addition, to explore the effect of mutations on the antibody, the key residues contributing to the changes in the binding ability of RBD in the Delta variant with the existing 42 neutralizing monoclonal antibodies (mAbs) have been preliminarily evaluated. The present study reveals the molecular mechanism for the increased infectivity of SARS-CoV-2 caused by mutations, and the key sites that cause antigenic changes were screened. It provides important theoretical insights for the development of novel targeted RBD drugs and antibodies.

Origin of the tight binding mode to ACE2 triggered by multi-point mutations in the omicron variant: a dynamic insight.

The continuous spread of the newly emerged SARS-CoV-2 Omicron variant (B.1.1.529) has become an important reason for the surge in COVID-19 infections. Its numerous mutated residues containing key sites on the receptor-binding domain (RBD) undoubtedly pose new challenges for epidemic control. Although the preventive measures are becoming more sophisticated, the effects of mutations on the binding of the virus to the receptor protein remain to be elucidated. Here, we used molecular dynamics (MD) simulations to investigate the differences in the binding mode between the Omicron variant and the angiotensin-converting enzyme 2 (ACE2) compared to the wild-type strain (WT). Multi-point mutations in the Omicron variant RBD could cause the conformation shift in the large Loop (where T478K and E484A are located), which makes it easier to wrap the N-terminal helix of ACE2 and form tighter contacts. The stronger electrostatic interaction was the main reason for its enhanced binding affinity as compared to WT. This was due to the large number of positively charged patches (N440K, T478K, Q493R, Q498R, and Y505H) formed by the substitution of neutral amino acids at multiple sites. The appearance of these highly polar hydrophilic amino acids may cause local perturbations and affect the electrostatic complementarity of RBD with the ACE2, and further mediate conformational changes. Thus, a more extensive interaction network was found in the mutation system and the complex interaction cluster was formed near E37@ACE2, which was essential for the stable binding of the two. In addition, we speculated that these mutations may affect the electrostatic complementarity with the four potential antibodies to reduce the sensitivity of the virus to antibodies. This study reveals the key details of the Omicron variant binding to ACE2 and provides important theoretical views for the enhanced infectivity of this variant. We hope that these observations can provide timely molecular insights for responding to the Omicron variant pandemic.

Targeting mechanism for SARS-CoV-2 in silico: interaction and key groups of TMPRSS2 toward four potential drugs.

The global dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seriously endangered human health. The number of confirmed cases is still increasing; however, treatment options are limited. Transmembrane protease serine 2 (TMPRSS2), as a key protease that primes the binding of SARS-CoV-2 spike protein and angiotensin-converting enzyme 2 (ACE2), has become an attractive target and received widespread attention. Thus, four potential drugs (bromhexine, camostat, gabexate, and nafamostat) were used to explore the mechanism of binding with TMPRSS2 in this work. A 65 ns molecular dynamics simulation was performed three times for each drug-TMPRSS2 system for reliable energy calculation and conformational analysis, of which the simulations of nafamostat-TMPRSS2 systems were further extended to 150 ns three times due to the discovery of two binding modes. Through the results of calculating binding free energy by nine methods, the binding affinity of camostat, gabexate, and nafamostat to TMPRSS2 showed great advantages compared with bromhexine, where the nafamostat was surprisingly found to present two reasonable binding conformations (forward and reverse directions). Two negatively charged amino acids (Asp435 and Glu299) can clamp the two positively charged groups (guanidinium group and amidinium group) in either forward or reverse fashion, and the forward one is more stable than the reverse. In addition, compared with gabexate, the dimethylamino group in camostat forms more van der Waals interactions with surrounding hot-spots His296 and Val280, resulting in a stronger affinity to TMPRSS2. For bromhexine, multiple binding sites are displayed in the binding pocket due to its small molecular structure, and van der Waals interactions play the dominant role in the binding process. In particular, six typical hot-spots were identified in the last three serine protease inhibitor systems, i.e., Asp435, Ser436, Gln438, Trp461, Ser463, and Gly464. The guanidinium groups of the drugs have powerful interactions with adjacent residues due to the formation of more hydrogen bonds, suggesting that this may be the critical site for drug design against TMPRSS2. This work provides valuable molecular insight into these four drug-TMPRSS2 binding mechanisms and is helpful for designing and screening drugs targeting TMPRSS2.

Coronary artery calcification and risk of mortality and adverse outcomes in patients with COVID-19: a Chinese multicenter retrospective cohort study.

Background: Coronary artery calcification (CAC) is an independent risk factor of major adverse cardiovascular events; however, the impact of CAC on in-hospital death and adverse clinical outcomes in patients with coronavirus disease 2019 (COVID-19) remains unclear. Objective: To explore the association between CAC and in-hospital mortality and adverse events in patients with COVID-19. Methods: This multicenter retrospective cohort study enrolled 2067 laboratory-confirmed COVID-19 patients with definitive clinical outcomes (death or discharge) admitted from 22 tertiary hospitals in China between January 3, 2020 and April 2, 2020. Demographic, clinical, laboratory results, chest CT findings, and CAC on admission were collected. The primary outcome was in-hospital death and the secondary outcome was composed of in-hospital death, admission to intensive care unit (ICU), and requiring mechanical ventilation. Multivariable Cox regression analysis and Kaplan-Meier plots were used to explore the association between CAC and in-hospital death and adverse clinical outcomes. Results: The mean age was 50 years (SD,16) and 1097 (53.1%) were male. A total of 177 patients showed high CAC level, and compared with patients with low CAC, these patients were older (mean age: 49 vs. 69 years, P < 0.001) and more likely to be male (52.0% vs. 65.0%, P = 0.001). Comorbidities, including cardiovascular disease (CVD) ([33.3%, 59/177] vs. [4.7%, 89/1890], P < 0.001), presented more often among patients with high CAC, compared with patients with low CAC. As for laboratory results, patients with high CAC had higher rates of increased D-dimer, LDH, as well as CK-MB (all P < 0.05). The mean CT severity score in high CAC group was also higher than low CAC group (12.6 vs. 11.1, P = 0.005). In multivariable Cox regression model, patients with high CAC were at a higher risk of in-hospital death (hazard ratio [HR], 1.731; 95% CI 1.010-2.971, P = 0.046) and adverse clinical outcomes (HR, 1.611; 95% CL 1.087-2.387, P = 0.018). Conclusion: High CAC is a risk factor associated with in-hospital death and adverse clinical outcomes in patients with confirmed COVID-19, which highlights the importance of calcium load testing for hospitalized COVID-19 patients and calls for attention to patients with high CAC. Supplementary Information: The online version contains supplementary material available at 10.1007/s42058-021-00072-4.

Inhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 Mpro by large-scale molecular dynamic simulations combined with accurate binding free energy calculations.

Coronavirus disease 2019 (COVID-19), which is caused by a new coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is spreading around the world. However, a universally effective treatment regimen has not been developed to date. The main protease (Mpro), a key enzyme of SARS-CoV-2, plays a crucial role in the replication and transcription of this virus in cells and has become the ideal target for rational antiviral drug design. In this study, we performed molecular dynamics simulations three times for these complexes of Mpro (monomeric and dimeric) and nine potential drugs that have a certain effect on the treatment of COVID-19 to explore their binding mechanism. In addition, a total of 12 methods for calculating binding free energy were employed to determine the optimal drug. Ritonavir, Arbidol, and Chloroquine consistently showed an outstanding binding ability to monomeric Mpro under various methods. Ritonavir, Arbidol, and Saquinavir presented the best performance when binding to a dimer, which was independent of the protonated state of Hie41 (protonated at Nε) and Hid41 (protonated at Nδ), and these findings suggest that Chloroquine may not effectively inhibit the activity of dimeric Mproin vivo. Furthermore, three common hot-spot residues of Met165, Hie41, and Gln189 of monomeric Mpro systems dominated the binding of Ritonavir, Arbidol, and Chloroquine. In dimeric Mpro, Gln189, Met165, and Met49 contributed significantly to binding with Ritonavir, Arbidol, and Saquinavir; therefore, Gln189 and Met165 might serve as the focus in the discovery and development of anti-COVID-19 drugs. In addition, the van der Waals interaction played a significant role in the binding process, and the benzene ring of the drugs showed an apparent inhibitory effect on the normal function of Mpro. The binding cavity had great flexibility to accommodate these different drugs. The results would be notably helpful for enabling a detailed understanding of the binding mechanisms for these important drug-Mpro interactions and provide valuable guidance for the design of potent inhibitors.

[Preventing Infection Measures of COVID-19 Patients during Mechanical Ventilation].

OBJECTIVE: To explore the preventing infection measures of new coronavirus disease 2019(COVID-19) patients during mechanical ventilation, and to provide reference for the safe application of mechanical ventilation. METHODS: Retrieved from PubMed, Ovid and other databases, and combined with the application experience of mechanical ventilation were collected to explore the preventing infection measures of COVID-19 patients during mechanical ventilation. RESULTS: This paper put forward the preventing infection measures of external circuit, internal circuit, outer surface, filter and special parts in ventilator. The preventing infection measures of sputum suction and nebulization were summarized. CONCLUSIONS: The preventing infection measures of COVID-19 patients during mechanical ventilation are successfully completed, which can provide suggestions for the application and maintenance of mechanical ventilation.

Risk factors for adverse clinical outcomes with COVID-19 in China: a multicenter, retrospective, observational study.

Background: The risk factors for adverse events of Coronavirus Disease-19 (COVID-19) have not been well described. We aimed to explore the predictive value of clinical, laboratory and CT imaging characteristics on admission for short-term outcomes of COVID-19 patients. Methods: This multicenter, retrospective, observation study enrolled 703 laboratory-confirmed COVID-19 patients admitted to 16 tertiary hospitals from 8 provinces in China between January 10, 2020 and March 13, 2020. Demographic, clinical, laboratory data, CT imaging findings on admission and clinical outcomes were collected and compared. The primary endpoint was in-hospital death, the secondary endpoints were composite clinical adverse outcomes including in-hospital death, admission to intensive care unit (ICU) and requiring invasive mechanical ventilation support (IMV). Multivariable Cox regression, Kaplan-Meier plots and log-rank test were used to explore risk factors related to in-hospital death and in-hospital adverse outcomes. Results: Of 703 patients, 55 (8%) developed adverse outcomes (including 33 deceased), 648 (92%) discharged without any adverse outcome. Multivariable regression analysis showed risk factors associated with in-hospital death included ≥ 2 comorbidities (hazard ratio [HR], 6.734; 95% CI; 3.239-14.003, p < 0.001), leukocytosis (HR, 9.639; 95% CI, 4.572-20.321, p < 0.001), lymphopenia (HR, 4.579; 95% CI, 1.334-15.715, p = 0.016) and CT severity score > 14 (HR, 2.915; 95% CI, 1.376-6.177, p = 0.005) on admission, while older age (HR, 2.231; 95% CI, 1.124-4.427, p = 0.022), ≥ 2 comorbidities (HR, 4.778; 95% CI; 2.451-9.315, p < 0.001), leukocytosis (HR, 6.349; 95% CI; 3.330-12.108, p < 0.001), lymphopenia (HR, 3.014; 95% CI; 1.356-6.697, p = 0.007) and CT severity score > 14 (HR, 1.946; 95% CI; 1.095-3.459, p = 0.023) were associated with increased odds of composite adverse outcomes. Conclusion: The risk factors of older age, multiple comorbidities, leukocytosis, lymphopenia and higher CT severity score could help clinicians identify patients with potential adverse events.

[Clinical observation of 6 severe COVID-19 patients treated with plasma exchange or tocilizumab]

OBJECTIVE: To observe the clinical effect of plasma exchange and tocilizumab in treatment of patients with severe coronavirus disease 2019 (COVID-19). METHODS: Six patients with severe COVID-19 admitted in First Affiliated Hospital of Bengbu Medical College from January 25 to February 25, 2020. Three patients were treated with plasma exchange and three patients were treated with tocilizumab. The effect on excessive inflammatory reaction of plasma exchange and tocilizumab was observed. RESULTS: The C-reactive protein (CRP) and IL-6 levels were significantly decreased and the lymphocyte and prothrombin time were improved in 3 patients after treatment with plasma exchange;while inflammation level was not significantly decreased, and lymphocyte and prothrombin time did not improve in 3 patients treated with tocilizumab. CONCLUSIONS: For severe COVID-19 patients with strong inflammatory reaction, plasma exchange may be preferred.