Molecular insights into the inhibition mechanism of harringtonine against essential proteins associated with SARS-CoV-2 entry.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently posed a serious threat to global public health. Harringtonine (HT), as a small-molecule antagonist, has antiviral activity against a variety of viruses. There is evidence that HT can inhibit the SARS-CoV-2 entry into host cells by blocking the Spike protein and transmembrane protease serine 2 (TMPRSS2). However, the molecular mechanism underlying the inhibition effect of HT is largely elusive. Here, docking and all-atom molecular dynamics simulations were used to investigate the mechanism of HT against the receptor binding domain (RBD) of Spike, TMPRSS2, as well as the complex of RBD and angiotensin-converting enzyme 2 complex (RBD-ACE2). The results reveal that HT binds to all proteins primarily through hydrogen bond and hydrophobic interactions. Binding with HT influences the structural stability and dynamic motility processes of each protein. The interactions of HT with residues N33, H34 and K353 of ACE2, and residue K417 and Y453 of RBD contribute to disrupting the binding affinity between RBD and ACE2, which may hinder the virus entry into host cells. Our research provides molecular insights into the inhibition mechanism of HT against SARS-CoV-2 associated proteins, which will help for the novel antiviral drugs development.

Identification of Potential Lead Compounds Targeting Novel Druggable Cavity of SARS-CoV-2 Spike Trimer by Molecular Dynamics Simulations.

The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become an urgent public health problem. Spike (S) protein mediates the fusion between the virus and the host cell membranes, consequently emerging as an important target of drug design. The lack of comparisons of in situ full-length S homotrimer structures in different states hinders understanding the structures and revealing the function, thereby limiting the discovery and development of therapeutic agents. Here, the steady-state structures of the in situ full-length S trimer in closed and open states (Sclosed and Sopen) were modeled with the constraints of density maps, associated with the analysis of the dynamic structural differences. Subsequently, we identified various regions with structure and property differences as potential binding pockets for ligands that promote the formation of inactive trimeric protein complexes. By using virtual screening strategy and a newly defined druggable cavity, five ligands were screened with potential bioactivities. Then molecular dynamic (MD) simulations were performed on apo protein structures and ligand bound complexes to reveal the conformational changes upon ligand binding. Our simulation results revealed that sulforaphane (SFN), which has the best binding affinity, could inhibit the conformational changes of S homotrimer that would occur during the viral membrane fusion. Our results could aid in the understanding of the regulation mechanism of S trimer aggregation and the structure-activity relationship, facilitating the development of potential antiviral agents.

High-Throughput Screening for the Potential Inhibitors of SARS-CoV-2 with Essential Dynamic Behavior.

Global health security has been challenged by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. Due to the lengthy process of generating vaccinations, it is vital to reposition currently available drugs in order to relieve anti-epidemic tensions and accelerate the development of therapies for Coronavirus Disease 2019 (COVID-19), the public threat caused by SARS-CoV-2. High throughput screening techniques have established their roles in the evaluation of already available medications and the search for novel potential agents with desirable chemical space and more cost-effectiveness. Here, we present the architectural aspects of highthroughput screening for SARS-CoV-2 inhibitors, especially three generations of virtual screening methodologies with structural dynamics: ligand-based screening, receptor-based screening, and machine learning (ML)-based scoring functions (SFs). By outlining the benefits and drawbacks, we hope that researchers will be motivated to adopt these methods in the development of novel anti- SARS-CoV-2 agents.

MIL-101(CuFe) Nanozymes with Excellent Peroxidase-like Activity for Simple, Accurate, and Visual Naked-Eye Detection of SARS-CoV-2.

The COVID-19 pandemic has spread to every corner of the world and seriously affected our health and daily activities in the past three years; thereby, it is still urgent to develop various simple, quick, and accurate methods for early detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Nanozymes, a kind of nanomaterial with intrinsic enzyme-mimicking activity, have emerged as a suitable alternative for both therapy and diagnosis of SARS-CoV-2. Here, ultrasensitive and ultrafast MIL-101(CuFe)-CD147 biosensors are established for the detection of SARS-CoV-2 by a simple colorimetric method. A MIL-101(CuFe) metal-organic framework has excellent peroxidase-like activity due to the synergistic effect of Fe and Cu atoms. In addition, the MIL-101(CuFe)-CD147 biosensor shows great potential to detect the various variants of SARS-CoV-2 due to the universal receptor of CD147. The enzyme-based biosensor for the detection of SARS-CoV-2 achieves a very low limit of detection (about 3 PFU/mL) within 30 min. Therefore, the present method provides a new generation of an alternative approach for highly sensitive and visual diagnosis of COVID-19.

Estimates of Power Shortages and Affected Populations during the Initial Period of the Ukrainian-Russian Conflict

Since the outbreak of the Ukrainian-Russian conflict on 24 February 2022, Ukraine’s economy, society, and cities have been devastated and struck on multiple fronts, with large numbers of refugees fleeing to neighboring countries. The lighting systems in Ukrainian cities have been severely restricted due to Russian missile bombing and curfew policies. The power shortages adversely affected the livelihoods of the Ukrainian residents dramatically. For a timely assessment of the power shortages’ extent and the affected population in Ukraine, this study tracked the dynamics of nighttime light emissions in Ukraine based on the newly developed daily Black Marble product (VNP46A2) from NASA. The results show that the average light radiance in Ukrainian urban areas has decreased by about 37% since the eruption of the war, with Kiev city being the most dramatic region, having a post-conflict decrease of about 51%. In addition, by introducing near-real-time population data, we have implemented a survey of the affected population in Ukraine suffering from war-induced power shortages. Estimates show that about 17.3 million Ukrainian residents were affected by power shortages. In more detail, the number of children under 10 years old was about 2.35 million (about 5.24% of the total population), while the number of elderly people over 60 years old was about 3.53 million (about 7.86% of the total population). Generally, the results of this study could contribute positively to the timely assessment of the impact of the conflict and the implementation of humanitarian relief.

SEIARN: Intelligent Early Warning Model of Epidemic Spread Based on LSTM Trajectory Prediction

A SEIARN compartment model with the asymptomatic infection and secondary infection is proposed to predict the trend of COVID-19 more accurately. The model is extended according to the propagation characteristics of the novel coronavirus, the concepts of the asymptomatic infected compartment and secondary infection are introduced, and the contact rate parameters of the improved model are updated in real time by using the LSTM trajectory, in order to make accurate predictions. This SEIARN model first builds on the traditional SEIR compartment model, taking into account the asymptomatic infection compartment and secondary infection. Secondly, it considers the disorder of the trajectory and uses the improved LSTM model to predict the future trajectory of the current patients and cross-track with the susceptible patients to obtain the contact rate. Then, we conduct real-time updating of exposure rates in the SEIARN model and simulation of epidemic trends in Tianjin, Xi'an, and Shijiazhuang. Finally, the comparison experiments show that the SEIARN model performs better in prediction accuracy, MSE, and RMSE.

Recognition between CD147 and cyclophilin A deciphered by accelerated molecular dynamics simulations.

CD147 functions as the receptor of extracellular cyclophilin A (CypA) in various diseases, and CD147-CypA binding ulteriorly underlies the pathological process of various viral infections including HIV-1, SARS, and SARS-CoV-2. Although CyPA has been identified as a key intermediate pro-inflammatory factor, the mechanism by which CD147 cooperates with CypA in the development of the cytokine storm remains largely unknown, and the binding profile of CD147 with CypA remains to be elucidated as well. Here, we prepared three binding models of the CD147-CypA complex, including the active site of CypA severally binding to the groove bound by the Ig1 and Ig2 domains (model-0), P180-G181 (model-1), and P211 (model-2) of CD147, as well as introducing mutations P180A-G181A and P211A individually in each model. All systems were studied using accelerated molecular dynamics simulations and the molecular mechanics generalized Born surface area (MM/GBSA) method. For model-0, CypA bound to the ectodomain of CD147 with the highest binding affinity. Moreover, mutations P180A-G181A of CD147 in model-0 decreased the binding affinity and weakened the dynamic correlation between CD147 and CypA, which resulted in CypA shifting from the initial binding location. Other residue mutations of CD147 did not significantly affect the CD147-CypA binding, as reflected by the energy and structural analyses. Compared with surface plasmon resonance results and nuclear magnetic resonance shift signals, CypA should tend to reciprocally bind to the groove of CD147, and the binding process might be modulated by P180-G181 rather than P211. Besides, residue R201 of CD147 is critical for CD147-CypA binding and needs further experimental verification. These findings further our understanding of the recruitment between CD147 and CypA and its potential role in the development of inflammation and viral infection.

The Effects of ATIR Blocker on the Severity of COVID-19 in Hypertensive Inpatients and Virulence of SARS-CoV-2 in Hypertensive hACE2 Transgenic Mice.

Angiotensin-converting enzyme 2 (ACE2) is required for the cellular entry of the severe acute respiratory syndrome coronavirus 2. ACE2, via the Ang-(1-7)-Mas-R axis, is part of the antihypertensive and cardioprotective effects of the renin-angiotensin system. We studied hospitalized COVID-19 patients with hypertension and hypertensive human(h) ACE2 transgenic mice to determine the outcome of COVID-19 with or without AT1 receptor (AT1R) blocker treatment. The severity of the illness and the levels of serum cardiac biomarkers (CK, CK-BM, cTnI), as well as the inflammation markers (IL-1, IL-6, CRP), were lesser in hypertensive COVID-19 patients treated with AT1R blockers than those treated with other antihypertensive drugs. Hypertensive hACE2 transgenic mice, pretreated with AT1R blocker, had increased ACE2 expression and SARS-CoV-2 in the kidney and heart, 1 day post-infection. We conclude that those hypertensive patients treated with AT1R blocker may be at higher risk for SARS-CoV-2 infection. However, AT1R blockers had no effect on the severity of the illness but instead may have protected COVID-19 patients from heart injury, via the ACE2-angiotensin1-7-Mas receptor axis.

Computational Simulation of HIV Protease Inhibitors to the Main Protease (Mpro) of SARS-CoV-2: Implications for COVID-19 Drugs Design.

SARS-CoV-2 is highly homologous to SARS-CoV. To date, the main protease (Mpro) of SARS-CoV-2 is regarded as an important drug target for the treatment of Coronavirus Disease 2019 (COVID-19). Some experiments confirmed that several HIV protease inhibitors present the inhibitory effects on the replication of SARS-CoV-2 by inhibiting Mpro. However, the mechanism of action has still not been studied very clearly. In this work, the interaction mechanism of four HIV protease inhibitors Darunavir (DRV), Lopinavir (LPV), Nelfinavir (NFV), and Ritonavire (RTV) targeting SARS-CoV-2 Mpro was explored by applying docking, molecular dynamics (MD) simulations, and MM-GBSA methods using the broad-spectrum antiviral drug Ribavirin (RBV) as the negative and nonspecific control. Our results revealed that LPV, RTV, and NFV have higher binding affinities with Mpro, and they all interact with catalytic residues His41 and the other two key amino acids Met49 and Met165. Pharmacophore model analysis further revealed that the aromatic ring, hydrogen bond donor, and hydrophobic group are the essential infrastructure of Mpro inhibitors. Overall, this study applied computational simulation methods to study the interaction mechanism of HIV-1 protease inhibitors with SARS-CoV-2 Mpro, and the findings provide useful insights for the development of novel anti-SARS-CoV-2 agents for the treatment of COVID-19.

Molecular insights into the binding variance of the SARS-CoV-2 spike with human, cat and dog ACE2 proteins.

SARS-CoV-2 has recently caused an epidemic in humans and poses a huge threat to global public health. As a primary receptor of SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2) exists in different hosts that are in close contact with humans, especially cats and dogs. However, the underlying mechanism of how the spike receptor binding domain (RBD) of SARS-CoV-2 cooperates with human ACE2 (hACE2), cat ACE2 (cACE2) and dog ACE2 (dACE2) and the variation in binding remains largely unsolved. Therefore, we explored the binding behavior of the spike RBD with cACE2, dACE2 and hACE2 via all-atom molecular dynamics simulations. In accordance with the binding free energies and residue interactions, the spike RBD has respective binding specificities with cACE2, dACE2 and hACE2, and the binding affinities decrease in the order of hACE2, cACE2, dACE2, mainly due to changes in the amino acids Q24L, H34Y, and M82T in cACE2 or dACE2. Furthermore, alanine scanning analysis results validated some key residues of the spike RBD interact with ACE2 and provided clues to the variation of amino acid that could influence the transmissibility or immune responses of SARS-CoV-2. Decreasing dynamic correlations strengths of ACE2 with the RBD were found in all hACE2-RBD, cACE2-RBD and dACE2-RBD systems. The ACE2 protein shows variable motion modes across the zinc metallopeptidase domain, which induces different interactions between ACE2 and the RBD. Our studies reveal that the motion pattern of the zinc metallopeptidase domain is critical to the binding behavior of RBD with ACE2. These findings could aid our understanding of selective recognition involving various ACE2 with the SARS-CoV-2 spike and shed further light on the binding mechanisms.

Clinical Characteristics, Serological and Radiological Longitudinal Changes of Patients with COVID-19.

BACKGROUND: Since December 2019, an outbreak of coronavirus disease 2019 (COVID-19) began in Wuhan and rapidly spread globally. The speed and scope of the spread of COVID-19 makes it urgent to define clinical characteristics, serological and radiological changes of the affected patients. METHODS: Seven patients with laboratory-confirmed COVID-19 who were admitted to the Third Affiliated Hospital of Sun Yat-Sen University Yuedong Hospital from January 2020 to March 2020 were retrospectively enrolled and their clinical features, serological and radiological longitudinal changes were analyzed. RESULTS: Among the 7 patients, all (100%) had a clear epidemiological history. The most common symptoms were respiratory symptoms 6 (85.7%), and only 2 (28.6%) of the patients had fever at their first visit. The cohort included 4 (57.1%) common types and 3 (42.9%) severe types. Two (28.6%) common type patients developed to severe type in a short time. All of the 7 patients (100%) had abnormal liver function, normal renal function, and normal procalcitonin. The detection time of specific antibody in 7 patients was 5 - 13 days after symptoms. Before the specific antibody could be detected, the absolute value of lymphocytes decreased in 2 (28.6%) common type cases transferred to severe type cases accompanied with obvious progress in pulmonary imaging. The phenomenon of decreased albumin and elevated globulin occurred in 6 patients (85.7%). The predominant pattern of lung lesions observed was bilateral (71.4%) and mainly near the pleura at the first diagnosis. Bilateral pulmonary involvement occurred in 6 cases (85.7%) during the course of disease. In 4 cases (57.1%) with obvious pulmonary lesions, the absolute value of lymphocytes decreased, albumin decreased, and globulin increased during the course of the disease. CONCLUSIONS: Serum specific antibodies can be detected within 2 weeks of onset. Close observation of the dynamic changes of absolute value of blood lymphocytes, serum albumin, and globulin which were related to pulmonary imaging changes in patients will contribute to assessment of COVID-19.

A Convalescent of COVID-19 with RT-PCR Test Continues Positive in Stool.

BACKGROUND: Coronavirus disease (COVID-19) has affected more than 100 countries worldwide and the discharge criteria of patients with COVID-19 vary across different countries. In China, patients with two negative respiratory viral RNA tests taken at least one day apart can be discharged with no further quarantine required. Currently, PCR testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in fecal sample is not routinely performed. METHODS: We present a patient with COVID-19, whose respiratory swabs became negative but fecal sample remained positive for SARS-CoV-2 RNA. RESULTS: Stool sample collected on 27th of February was still positive for SARS-CoV-2 RNA, 24 days after the first negative respiratory swab. CONCLUSIONS: Based on the experience from the 2003 SARS epidemic, we recommend that fecal RNA testing of SARS-CoV-2 should be incorporated into the discharge criteria to minimize the risk of transmission from the gastrointestinal tract.

CD147-spike protein is a novel route for SARS-CoV-2 infection to host cells.

In face of the everlasting battle toward COVID-19 and the rapid evolution of SARS-CoV-2, no specific and effective drugs for treating this disease have been reported until today. Angiotensin-converting enzyme 2 (ACE2), a receptor of SARS-CoV-2, mediates the virus infection by binding to spike protein. Although ACE2 is expressed in the lung, kidney, and intestine, its expressing levels are rather low, especially in the lung. Considering the great infectivity of COVID-19, we speculate that SARS-CoV-2 may depend on other routes to facilitate its infection. Here, we first discover an interaction between host cell receptor CD147 and SARS-CoV-2 spike protein. The loss of CD147 or blocking CD147 in Vero E6 and BEAS-2B cell lines by anti-CD147 antibody, Meplazumab, inhibits SARS-CoV-2 amplification. Expression of human CD147 allows virus entry into non-susceptible BHK-21 cells, which can be neutralized by CD147 extracellular fragment. Viral loads are detectable in the lungs of human CD147 (hCD147) mice infected with SARS-CoV-2, but not in those of virus-infected wild type mice. Interestingly, virions are observed in lymphocytes of lung tissue from a COVID-19 patient. Human T cells with a property of ACE2 natural deficiency can be infected with SARS-CoV-2 pseudovirus in a dose-dependent manner, which is specifically inhibited by Meplazumab. Furthermore, CD147 mediates virus entering host cells by endocytosis. Together, our study reveals a novel virus entry route, CD147-spike protein, which provides an important target for developing specific and effective drug against COVID-19.

Rapid Structure-Based Screening Informs Potential Agents for Coronavirus Disease (COVID-19) Outbreak

Coronavirus Disease 2019 (COVID-19), caused by the novel coronavirus, has spread rapidly across China. Consequently, there is an urgent need to sort and develop novel agents for the prevention and treatment of viral infections. A rapid structure-based virtual screening is used for the evaluation of current commercial drugs, with structures of human angiotensin converting enzyme II (ACE2), and viral main protease, spike, envelope, membrane and nucleocapsid proteins. Our results reveal that the reported drugs Arbidol, Chloroquine and Remdesivir may hinder the entry and release of virions through the bindings with ACE2, spike and envelope proteins. Due to the similar binding patterns, NHC (β-d-N4-hydroxycytidine) and Triazavirin are also in prospects for clinical use. Main protease (3CLpro) is likely to be a feasible target of drug design. The screening results to target 3CL-pro reveal that Mitoguazone, Metformin, Biguanide Hydrochloride, Gallic acid, Caffeic acid, Sulfaguanidine and Acetylcysteine seem be possible inhibitors and have potential application in the clinical therapy of COVID-19.