Corrigendum: Targeting the N-terminus domain of the coronavirus nucleocapsid protein induces abnormal oligomerization via allosteric modulation.

[This corrects the article DOI: 10.3389/fmolb.2022.871499.].

Severe Acute Respiratory Syndrome Coronavirus 2 Epitope Mapping for Antibodies.

Epitope mapping of the interactions between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Abs is challenging because of complexity in protein three-dimensional structures. Protein structure fingerprint technology was applied for epitope mapping of 44 SARS-CoV-2 Abs with three-dimensional structure complexes. The results defined how the epitopes were distributed on SARS-CoV-2 and how the patterns of six CDRs from Abs participated in neutralization. Also, the residue-residue recognition revealed that certain residues had higher frequencies on the interfaces between SARS-CoV-2 and Abs, and the activity correlated with the physicochemical properties of the residues at the interface. Thus, epitope mapping provides significant lead information for development of epitope-based designs for Abs, vaccines, and diagnostic reagents. This is a bioinformatics project of structural data analysis; no animals or cells were used.

Targeting the N-Terminus Domain of the Coronavirus Nucleocapsid Protein Induces Abnormal Oligomerization via Allosteric Modulation.

Epidemics caused by coronaviruses (CoVs), namely the severe acute respiratory syndrome (SARS) (2003), Middle East respiratory syndrome (MERS) (2012), and coronavirus disease 2019 (COVID-19) (2019), have triggered a global public health emergency. Drug development against CoVs is inherently arduous. The nucleocapsid (N) protein forms an oligomer and facilitates binding with the viral RNA genome, which is critical in the life cycle of the virus. In the current study, we found a potential allosteric site (Site 1) using PARS, an online allosteric site predictor, in the CoV N-N-terminal RNA-binding domain (NTD) to modulate the N protein conformation. We identified 5-hydroxyindole as the lead via molecular docking to target Site 1. We designed and synthesized four 5-hydroxyindole derivatives, named P4-1 to P4-4, based on the pose of 5-hydroxyindole in the docking model complex. Small-angle X-ray scattering (SAXS) data indicate that two 5-hydroxyindole compounds with higher hydrophobic R-groups mediate the binding between N-NTD and N-C-terminal dimerization domain (CTD) and elicit high-order oligomerization of the whole N protein. Furthermore, the crystal structures suggested that these two compounds act on this novel cavity and create a flat surface with higher hydrophobicity, which may mediate the interaction between N-NTD and N-CTD. Taken together, we discovered an allosteric binding pocket targeting small molecules that induces abnormal aggregation of the CoV N protein. These novel concepts will facilitate protein-protein interaction (PPI)-based drug design against various CoVs.

Diabetes patients with comorbidities had unfavorable outcomes following COVID-19: A retrospective study.

BACKGROUND: Previous studies have shown that diabetes mellitus is a common comorbidity of coronavirus disease 2019 (COVID-19), but the effects of diabetes or anti-diabetic medication on the mortality of COVID-19 have not been well described. AIM: To investigate the outcome of different statuses (with or without comorbidity) and anti-diabetic medication use before admission of diabetic after COVID-19. METHODS: In this multicenter and retrospective study, we enrolled 1422 consecutive hospitalized patients from January 21, 2020, to March 25, 2020, at six hospitals in Hubei Province, China. The primary endpoint was in-hospital mortality. Epidemiological material, demographic information, clinical data, laboratory parameters, radiographic characteristics, treatment and outcome were extracted from electronic medical records using a standardized data collection form. Most of the laboratory data except fasting plasma glucose (FPG) were obtained in first hospitalization, and FPG was collected in the next day morning. Major clinical symptoms, vital signs at admission and comorbidities were collected. The treatment data included not only COVID-19 but also diabetes mellitus. The duration from the onset of symptoms to admission, illness severity, intensive care unit (ICU) admission, and length of hospital stay were also recorded. All data were checked by a team of sophisticated physicians. RESULTS: Patients with diabetes were 10 years older than non-diabetic patients [(39 - 64) vs (56 - 70), P < 0.001] and had a higher prevalence of comorbidities such as hypertension (55.5% vs 21.4%, P < 0.001), coronary heart disease (CHD) (9.9% vs 3.5%, P < 0.001), cerebrovascular disease (CVD) (3% vs 2.2%, P < 0.001), and chronic kidney disease (CKD) (4.7% vs 1.5%, P = 0.007). Mortality (13.6% vs 7.2%, P = 0.003) was more prevalent among the diabetes group. Further analysis revealed that patients with diabetes who took acarbose had a lower mortality rate (2.2% vs 26.1, P < 0.01). Multivariable Cox regression showed that male sex [hazard ratio (HR) 2.59 (1.68 - 3.99), P < 0.001], hypertension [HR 1.75 (1.18 - 2.60), P = 0.006), CKD [HR 4.55 (2.52-8.20), P < 0.001], CVD [HR 2.35 (1.27 - 4.33), P = 0.006], and age were risk factors for the COVID-19 mortality. Higher HRs were noted in those aged ≥ 65 (HR 11.8 [4.6 - 30.2], P < 0.001) vs 50-64 years (HR 5.86 [2.27 - 15.12], P < 0.001). The survival curve revealed that, compared with the diabetes only group, the mortality was increased in the diabetes with comorbidities group (P = 0.009) but was not significantly different from the non-comorbidity group (P = 0.59). CONCLUSION: Patients with diabetes had worse outcomes when suffering from COVID-19; however, the outcome was not associated with diabetes itself but with comorbidities. Furthermore, acarbose could reduce the mortality in diabetic.