Molecular mechanism study of the structural regulation of the N-terminal domain binding antibody on the receptor binding domain of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the global spread of the coronavirus disease (COVID-19), which has caused great loss of life and property worldwide. We investigated the regulatory mechanism with the antibody targeting the N-terminal domain (NTD) of the S protein by molecular dynamic simulation. It was found that the structure of the S1-4A8 complex experienced the largest change when the receptor binding domain (RBD) of S1 was in the Up state. By calculating the angle between domains of S1 in the Down and Up states, we found that the RBD angle changed more in the Up state. We further performed binding free energy calculations for S1-4A8 complexes in both Up and Down states, and the results showed that 4A8 has a stronger affinity with NTD in the Up state. These results indicate that 4A8 plays a stronger regulatory role in the RBD Up state. The N3 and N5 loops on the NTD are the main antigen-antibody binding sites, and residues on the antibody complementarity determining region 3 (CDR3) in the Up state can penetrate deeper into the hydrophobic pocket at the bottom of the N5 loop to form a tighter binding. Through the tICA method, we found that except the residues at the binding interface, distant residues including A609, V610, G652, and A653 at the linker region of subdomain 2, and residues S359 and N360 near the bottom of RBD are able to influence the regulatory effect in the long-range. This work provides new insights into the neutralization mechanism of targeting NTD antibodies in SARS-CoV-2.

A triple-target reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid and accurate detection of SARS-CoV-2 virus.

The spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across the world has impacted people's health and lives worldwide in recent years. Rapid and accurate diagnosis is crucial for curbing the pandemic of coronavirus disease 2019 (COVID-19). Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has great potential for SARS-CoV-2 detection but fails to completely replace conventional PCR due to the high false-positive rate (FPR). We proposed a triple-target RT-LAMP method for dual-signal, sensitive, and simultaneous detection of conserved genes of SARS-CoV-2. Multiple LAMP primer sets were designed for N, E, and M genes and their amplification efficacy were screened. Then, using artificial plasmids and RNA, the optimal primer set for each gene was examined on specificity, sensitivity, and detection range. The RT-LAMP initiated by these primer sets exhibited better specificity and sensitivity than that of RT-qPCR, and the triple-target RT-LAMP could determine different variants of SARS-CoV-2. By testing 78 artificial RNA samples, the total FPR of triple-target RT-LAMP was eliminated compared with that of mono-target RT-LAMP. The triple-target RT-LAMP method precisely identified throat swab specimens through colorimetry and fluorescent signals within 60 min, and the limit of detection (LOD) was as low as 187 copies/reaction. In the future, the triple-target RT-LAMP can be applied to in-field and on-site diagnosis of symptomatic and asymptomatic virus carriers.

High-Affinity Antibodies Designing of SARS-CoV-2 Based on Molecular Dynamics Simulations.

SARS-CoV-2 has led to a global pandemic of new crown pneumonia, which has had a tremendous impact on human society. Antibody drug therapy is one of the most effective way of combating SARS-CoV-2. In order to design potential antibody drugs with high affinity, we used antibody S309 from patients with SARS-CoV as the target antibody and RBD of S protein as the target antigen. Systems with RBD glycosylated and non-glycosylated were constructed to study the influence of glycosylation. From the results of molecular dynamics simulations, the steric effects of glycans on the surface of RBD plays a role of "wedge", which makes the L335-E340 region of RBD close to the CDR3 region of the heavy chain of antibody and increases the contact area between antigen and antibody. By mutating the key residues of antibody at the interaction interface, we found that the binding affinities of antibody mutants G103A, P28W and Y100W were all stronger than that of the wild-type, especially for the G103A mutant. G103A significantly reduces the distance between the binding region of L335-K356 in the antigen and P28-Y32 of heavy chain in the antibody through structural transition. Taken together, the antibody design method described in this work can provide theoretical guidance and a time-saving method for antibody drug design.

Antiviral Effects of ABMA and DABMA against Influenza Virus In Vitro and In Vivo via Regulating the Endolysosomal Pathway and Autophagy

Influenza virus is an acute and highly contagious respiratory pathogen that causes great concern to public health and for which there is a need for extensive drug discovery. The small chemical compound ABMA and its analog DABMA, containing an adamantane or a dimethyl-adamantane group, respectively, have been demonstrated to inhibit multiple toxins (diphtheria toxin, Clostridium difficile toxin B, Clostridium sordellii lethal toxin) and viruses (Ebola, rabies virus, HSV-2) by acting on the host’s vesicle trafficking. Here, we showed that ABMA and DABMA have antiviral effects against both amantadine-sensitive influenza virus subtypes (H1N1 and H3N2), amantadine-resistant subtypes (H3N2), and influenza B virus with EC50 values ranging from 2.83 to 7.36 µM (ABMA) and 1.82 to 6.73 µM (DABMA), respectively. ABMA and DABMA inhibited the replication of influenza virus genomic RNA and protein synthesis by interfering with the entry stage of the virus. Molecular docking evaluation together with activity against amantadine-resistant influenza virus strains suggested that ABMA and DABMA were not acting as M2 ion channel blockers. Subsequently, we found that early internalized H1N1 virions were retained in accumulated late endosome compartments after ABMA treatment. Additionally, ABMA disrupted the early stages of the H1N1 life cycle or viral RNA synthesis by interfering with autophagy. ABMA and DABMA protected mice from an intranasal H1N1 challenge with an improved survival rate of 67%. The present study suggests that ABMA and DABMA are potential antiviral leads for the development of a host-directed treatment against influenza virus infection.

Manifestations and mechanisms of central nervous system damage caused by SARS-CoV-2.

The global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its threat to humans have drawn worldwide attention. The acute and long-term effects of SARS-CoV-2 on the nervous system pose major public health challenges. Patients with SARS-CoV-2 present diverse symptoms of the central nervous system. Exploring the mechanism of coronavirus damage to the nervous system is essential for reducing the long-term neurological complications of COVID-19. Despite rapid progress in characterizing SARS-CoV-2, the long-term effects of COVID-19 on the brain remain unclear. The possible mechanisms of SARS-CoV-2 injury to the central nervous system include: 1) direct injury of nerve cells, 2) activation of the immune system and inflammatory cytokines caused by systemic infection, 3) a high affinity of the SARS-CoV-2 spike glycoprotein for the angiotensin-converting enzyme ACE2, 4) cerebrovascular disease caused by hypoxia and coagulation dysfunction, and 5) a systemic inflammatory response that promotes cognitive impairment and neurodegenerative diseases. Although we do not fully understand the mechanism by which SARS-CoV-2 causes nerve injury, we hope to provide a framework by reviewing the clinical manifestations, complications, and possible mechanisms of neurological damage caused by SARS-CoV-2. With hope, this will facilitate the early identification, diagnosis, and treatment of possible neurological sequelae, which could contribute toward improving patient prognosis and preventing transmission.

Novel coronavirus (SARS-CoV-2) infection in a renal transplant recipient: Case report.

An ongoing outbreak of pneumonia associated with the severe acute respiratory coronavirus 2 (SARS-CoV-2) started in Wuhan, China, with cases now confirmed in multiple countries. The clinical course of patients remains to be fully characterized, clinical presentation ranges from asymptomatic infection to acute respiratory distress syndrome and acute renal failure, and no pharmacological therapies of proven efficacy yet exist. We report a case of SARS-CoV-2 infection in a renal transplant recipient with excellent outcome. This case states the importance of close monitoring of the concentration of cyclosporine in patients treated with lopinavir/ritonavir; the routine treatment of corticosteroid can be continued. This is a rare report of SARS-CoV-2 infection in a renal transplant recipient. Further data are needed to achieve better understanding of the impact of immunosuppressive therapy on the clinical presentation, severity, and outcome of SARS-CoV-2 infections in solid organ transplant recipients.