Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (99)

NSP5 (7)

ProteinN (4)

ComplexRdRp (4)

ProteinE (2)


SARS-CoV-2 Proteins
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    Accurate Evaluation on the Interactions of SARS-CoV-2 with Its Receptor ACE2 HGNC and Antibodies CR3022/CB6

    Authors: Hong-ming Ding; Yue-wen Yin; Song-di Ni; Yan-jing Sheng; Yu-qiang Ma

    id:2102.03305v1 Date: 2021-01-17 Source: arXiv

    The spread of the coronavirus disease 2019 MESHD ( COVID-19 MESHD) caused by severe acute respiratory syndrome coronavirus-2 MESHD (SARS-CoV-2) has become a global health crisis. The binding affinity of SARS-CoV-2 (in particular the receptor binding domain, RBD) to its receptor angiotensin converting enzyme 2 HGNC ( ACE2 HGNC) and the antibodies is of great importance in understanding the infectivity of COVID-19 MESHD and evaluating the candidate therapeutic for COVID-19 MESHD. In this work, we propose a new method based on molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) to accurately calculate the free energy of SARS-CoV-2 RBD MESHD binding to ACE2 HGNC and antibodies. The calculated binding free energy of SARS-CoV-2 RBD MESHD to ACE2 HGNC is -13.3 kcal/mol, and that of SARS-CoV RBD MESHD to ACE2 HGNC is -11.4 kcal/mol, which agrees well with experimental result (-11.3 kcal/mol and -10.1 kcal/mol, respectively). Moreover, we take two recently reported antibodies as the example, and calculate the free energy of antibodies binding to SARS-CoV-2 RBD MESHD, which is also consistent with the experimental findings. Further, within the framework of the modified MM/PBSA, we determine the key residues and the main driving forces for the SARS-CoV-2 RBD/CB6 interaction by the computational alanine scanning method. The present study offers a computationally efficient and numerically reliable method to evaluate the free energy of SARS-CoV-2 binding to other proteins, which may stimulate the development of the therapeutics against the COVID-19 MESHD disease in real applications.

    Snake venom phospholipases A2 possess a strong virucidal activity against SARS-CoV-2 in vitro and block the cell fusion mediated by spike glycoprotein PROTEIN interaction with the ACE2 HGNC receptor

    Authors: Andrei E Siniavin; Maria A Nikiforova; Svetlana D Grinkina; Vladimir A Gushchin; Vladislav G Starkov; Alexey V Osipov; Victor I Tsetlin; Yuri N Utkin; Dimiter S Dimitrov; Katharine Tuttle; Steven Zhou; Sagar Chittori; Sriram Subramaniam; Alyson Ann Ann Kelvin; Mohamed G. Al Kuwari; Hamad Eid Al Romaihi; Mohamed H. Al-Thani; Roberto Bertollini; Abdullatif Al Khal; Laith J Abu-Raddad; Menno D. de Jong; Marije K Bomers

    doi:10.1101/2021.01.12.426042 Date: 2021-01-12 Source: bioRxiv

    A new coronavirus was recently discovered and named severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2). In the absence of specific therapeutic and prophylactic agents, the virus has infected almost hundred million people, of whom nearly two million have died from the viral disease COVID-19 MESHD. The ongoing COVID-19 pandemic MESHD is a global threat requiring new therapeutic strategies. Among them, antiviral studies based on natural molecules are a promising approach. The superfamily of phospholipases A2 ( PLA2s HGNC) consists of a large number of members that catalyze the hydrolysis of phospholipids at a specific position. Here we show that secreted PLA2s HGNC from the venom of various snakes protect to varying degrees the Vero E6 cells widely used for the replication of viruses with evident cytopathic action, from SARS-CoV-2 infection MESHD PLA2s HGNC showed low cytotoxicity MESHD to Vero E6 cells and the high antiviral activity against SARS-CoV-2 with IC50 values ranged from 0.06 to 7.71 ug/ml. Dimeric PLA2 HDP-2 from the viper Vipera nikolskii, as well as its catalytic and inhibitory subunits, had potent virucidal (neutralizing) activity against SARS-CoV-2. Inactivation of the enzymatic activity of the catalytic subunit of dimeric PLA2 led to a significant decrease in antiviral activity. In addition, dimeric PLA2 inhibited cell-cell fusion mediated by SARS-CoV-2 spike PROTEIN glycoprotein. These results suggest that snake PLA2s HGNC, in particular dimeric ones, are promising candidates for the development of antiviral drugs that target lipid bilayers of the viral envelope and may be good tools to study the interaction of viruses with host cell membranes.

    Virtual Screening of Potential AEC2 Inhibitors for COVID-19 MESHD from Traditional Chinese Medicine

    Authors: Xiang He; JUNYI WANG; Lei Zhang; Qin Ran; Anying Xiong; Shengbin Liu; Dehong Wu; Bin Niu; Ying Xiong; Guoping Li

    doi:10.21203/ Date: 2021-01-11 Source: ResearchSquare

    Background: Angiotensin-converting enzyme 2 ( ACE2 HGNC), a negative regulator of the renin-angiotensin system and the severe acute respiratory syndrome-coronavirus MESHD ( SARS-CoV MESHD) and SARS-CoV-2 receptor, plays an important role in viral genome replication and immune response. ACE2 HGNC has been proposed as a potential therapeutic target. Traditional Chinese medicine (TCM) could be considered as a promising complementary therapeutic option in the management of COVID-19 MESHD. However, the active components and action mechanisms that account for its therapeutic effects remain controversial. Methods: ACE2 HGNC was employed as a target related to COVID-19 MESHD to explore the active ingredients from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database. And the PharmMapper database and TCMSP database were used to predict the targets of the compounds. Moreover, the potential therapeutic targets of COVID-19 MESHD were acquired by intersection among genes differentially expressed in COVID-19 MESHD patients, genes screened from five public databases and genes targeted by active compounds. Finally, molecular docking verification and function analysis were performed.Results: In this study, puerarin, the common active compound for targeting ACE2 HGNC across the five TCMs (Radix Cyathulae, Flos Puerariac, Radix Bupleuri, Radix Puerariac and Radix Hemerocallis), was found. Due to the comprehensive analysis, we revealed that puerarin might prevent the entrance of SARS-CoV-2 entry into cells by blocking ACE2 HGNC, chiefly modulated the T cell immunity and regulate pro-inflammatory cytokine response by affecting TNF, STAT1 HGNC and RNASE3 HGNC. Conclusion: Taken together, the present study found that puerarin might have a therapeutic effect on COVID-19 MESHD through regulation of the immune system, inhibition of inflammation MESHD and prevention of virus entry into cells.

    Immunogenicity and efficacy of the COVID-19 MESHD candidate vector vaccine MVA SARS 2 S in preclinical vaccination

    Authors: Alina Tscherne; Jan Hendrik Schwarz; Cornelius Rohde; Alexandra Kupke; Georgia Kalodimou; Leonard Limpinsel; Nisreen M.A. Okba; Berislav Bosnjak; Inga Sandrock; Sandro Halwe; Lucie Sauerhering; Katrin Printz; Liangliang Nan; Elke Duell; Sylvia Jany; Astrid Freudenstein; Joerg Schmidt; Anke Werner; Michelle Gellhorn; Michael Kluever; Wolfgang Guggemos; Michael Seilmaier; Clemens Wendtner; Reinhold Foerster; Bart Haagmans; Stephan Becker; Gerd Sutter; Asisa Volz

    doi:10.1101/2021.01.09.426032 Date: 2021-01-11 Source: bioRxiv

    The severe acute respiratory syndrome MESHD (SARS) coronavirus 2 (SARS-CoV-2) has emerged as the infectious agent causing the pandemic coronavirus disease MESHD coronavirus disease 2019 MESHD ( COVID-19 MESHD) with dramatic consequences for global human health and economics. Previously, we reached clinical evaluation with our vector vaccine based on vaccinia virus MVA against the Middle East respiratory syndrome coronavirus (MERS-CoV) MESHD, which causes an infection in humans similar to SARS and COVID-19 MESHD. Here, we describe the construction and preclinical characterization of a recombinant MVA expressing full-length SARS-CoV-2 spike PROTEIN ( S) protein PROTEIN (MVA-SARS-2-S). Genetic stability and growth characteristics of MVA-SARS-2-S, plus its robust synthesis of S antigen, make it a suitable candidate vaccine for industrial scale production. Vaccinated mice produced S antigen-specific CD8+ T cells and serum antibodies binding to S glycoprotein PROTEIN that neutralized SARS-CoV 2. Prime-boost vaccination with MVA-SARS-2-S MESHD protected mice sensitized with a human ACE2 HGNC-expressing adenovirus from SARS-CoV-2 infection MESHD. MVA-SARS-2-S is currently being investigated in a phase I clinical trial as aspirant for developing a safe and efficacious vaccine against COVID-19 MESHD.

    Evaluation of vertical transmission of SARS-CoV-2 in utero: nine pregnant women and their newborns

    Authors: Liang Dong; Shiyao Pei; Qin Ren; Shuxiang Fu; Liang Yu; Hui Chen; Xiang Chen; Mingzhu Yin

    doi:10.1101/2020.12.28.20248874 Date: 2021-01-08 Source: medRxiv

    BackgroundSevere acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2), mainly transmitted by droplets and close contact, has caused a pandemic worldwide as of November 2020. According to the current case reports and cohort studies, the symptoms of pregnant women infected with SARS-CoV-2 were similar to normal adults and may cause a series of adverse consequences of pregnancy (placental abruption, fetal distress, epilepsy MESHD during pregnancy, etc.). However, whether SARS-CoV-2 can be transmitted to the fetus through the placental barrier is still a focus of debate. MethodsIn this study, in order to find out whether SARS-CoV-2 infect MESHD fetus through placental barrier, we performed qualitative detection of virus structural protein (spike PROTEIN protein and nucleoprotein PROTEIN) and targeted receptor protein ( ACE2 HGNC, CD147 HGNC and GRP78 HGNC) expression on the placental tissue of seven pregnant women diagnosed with COVID-19 MESHD through immunohistochemistry. Amniotic fluid, neonatal throat, anal swab and breastmilk samples were collected immediately in the operating room for verification after delivery, which were all tested for SARS-CoV-2 by reverse transcriptionpolymerase chain reaction (RT-PCR). Results: The result showed that CD147 HGNC was expressed on the basal side of the chorionic trophoblast cell membrane and ACE2 HGNC was expressed on the maternal side, while GRP78 HGNC was strongly expressed in the cell membrane and cytoplasm. The RT-PCR results of Amniotic fluid, neonatal throat, anal swab and breastmilk samples were all negative. Conclusions: We believed that despite the detection of viral structural proteins in the placenta, SARS-CoV-2 cannot be transmitted to infants due to the presence of the placental barrier.

    Circulating ACE2 HGNC-expressing Exosomes Block SARS-CoV-2 Infection MESHD as an Innate Antiviral Mechanism

    Authors: Lamiaa El-Shennawy; Andrew Hoffmann; Nurmaa Dashzeveg; Paul Mehl; Zihao Yu; Valerie Tokars; Vlad Nicolaescu; Carolina Ostiguin; Yuzhi Jia; Lin Li; Kevin Furlong; Chengsheng Mao; Jan Wysocki; Daniel Batlle; Thomas Hope; Yang Shen; Yuan Luo; Young Chae; Hui Zhang; Suchitra Swaminathan; Glenn Randall; Alexis Demonbreun; Michael Ison; Deyu Fang; Huiping Liu

    doi:10.21203/ Date: 2021-01-06 Source: ResearchSquare

    The severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) causes the coronavirus disease 2019 MESHD ( COVID-19 MESHD) with innate and adaptive immune response triggered in such patients by viral antigens. Both convalescent plasma and engineered high affinity human monoclonal antibodies have shown therapeutic potential to treat COVID-19 MESHD. Whether additional antiviral soluble factors exist in peripheral blood remain understudied. Herein, we detected circulating exosomes that express the SARS-CoV-2 viral entry receptor angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC) in plasma of both healthy donors and convalescent COVID-19 MESHD patients. We demonstrated that exosomal ACE2 HGNC competes with cellular ACE2 HGNC for neutralization of SARS-CoV-2 infection MESHD. ACE2 HGNC-expressing ( ACE2 HGNC+) exosomes, but not the ACE2 HGNC-negative controls, blocked the binding of the viral spike (S) protein PROTEIN RBD to ACE2 HGNC+ cells in a dose dependent manner, which was 400- to 700-fold more potent than that of vesicle-free recombinant human ACE2 HGNC extracellular domain protein (rhACE2). As a consequence, exosomal ACE2 HGNC prevented SARS-CoV-2 pseudotype virus tethering and infection of human host cells at a 50–150 fold higher efficacy than rhACE2. A similar antiviral activity of exosomal ACE2 HGNC was further demonstrated to block wild-type live SARS-CoV-2 infection MESHD. Of note, depletion of ACE2 HGNC+ exosomes from COVID-19 MESHD patient plasma impaired the ability to block SARS-CoV-2 RBD MESHD binding to host cells. Furthermore, a dramatic increase in plasma ACE2 HGNC+ exosome levels were detected in patients with severe COVID-19 MESHD pathogenesis. Our data demonstrate that ACE2 HGNC+ exosomes can serve as a decoy therapeutic and a possible innate antiviral mechanism to block SARS-CoV-2 infection MESHD.

    Free Energy Landscapes for RBD Opening in SARS-CoV-2 Spike PROTEIN SARS-CoV-2 Spike MESHD Glycoprotein Simulations Suggest Key Interactions and a Potentially Druggable Allosteric Pocket

    Authors: Lucy Fallon; Kellon Belfon; Lauren Raguette; Yuzhang Wang; Christopher Corbo; Darya Stepanenko; Abbigayle Cuomo; Jose Guerra; Stephanie Budhan; Sarah Varghese; Robert Rizzo; Carlos Simmerling

    doi:10.26434/chemrxiv.13502646.v1 Date: 2020-12-31 Source: ChemRxiv

    The severe acute respiratory syndrome coronavirus-2 MESHD (SARS-CoV-2) an enveloped, positive-sense single-stranded RNA virus that is responsible for the COVID-19 MESHD pandemic. The viral spike is a class I viral fusion glycoprotein that extends from the viral surface and is responsible for viral entry into the host cell, and is the primary target of neutralizing antibodies. However, antibody recognition often involves variable surface epitopes on the spike, and the receptor binding domain (RBD) of the spike hides from immune recognition underneath a glycan shield aside from brief dynamic excursions to search for the host-cell surface receptor ACE2 HGNC. Using an atomistic model of the glycosylated wild-type spike in the closed and 1-up RBD conformations, we identified specific interactions that stabilize the closed RBD, and mapped the free energy landscape for RBD opening. We characterized a transient pocket associated with a hinge motion during opening of the RBD, suggesting the possibility of allosteric control of the RBD via this region. Substitution of a conserved alanine to bulkier leucine in the pocket shifted the RBD equilibrium to favor the open, exposed state, as did removal of a conserved lysine that forms a critical salt-bridge in the closed, hidden state. Results from our virtual screening, MD simulations and free energy landscape calculations for wild-type spike suggest that small molecules can spontaneously bind to the highly conserved hinge pocket, and that such binding can shift the RBD equilibrium to favor the open state. Stabilizing the open state may facilitate antibody recognition by forcing the spike to expose critical RBD epitopes, and also could increase the likelihood of premature triggering of the spike fusion machinery via S1 shedding, neutralizing the infectious ability of the virus.

    An Ultrasensitive Biosensor for Quantifying the Interaction of SARS-CoV-2 and Its Receptor ACE2 HGNC in Cells and in vitro

    Authors: Lidong Liu; Yee Wah So; Yutian Wang; Zeynep Sena Karahan; Gozde Turkoz; Merkaya Aras; Canan Eren; Uluhan Sili; Huseyin Bilginer; Ilke Suder; Baris Can Mandaci; Baran Dingiloglu; Ozge Tatli; Gizem Dinler Doganay; Safa Baris; Nesrin Ozoren; Tolga Sutlu; Linxiang Yu; Jin Yan; Fanping Meng; Changqing Bai; Xiaoshan Wang; Xiaopan Liu; Kai Gao; Liang Wu; Longqi F. Liu; Ying Gu; Yuhai J. Bi; Yi Shi; Shaogeng Zhang; Chen Zhu; Xun Xu; Guizhen Wu; George Gao; Naibo Yang; William Liu; Penghui Yang

    doi:10.1101/2020.12.29.424698 Date: 2020-12-29 Source: bioRxiv

    The severe acute respiratory syndrome coronavirus-2 MESHD (SARS-CoV-2) is currently spreading and mutating with increasing speed worldwide. Therefore, there is an urgent need for a simple, sensitive, and high-throughput (HTP) assay to quantify virus-host interaction in order to quickly evaluate infectious ability of mutant virus and develop or validate virus-inhibiting drugs. Here we have developed an ultrasensitive bioluminescent biosensor to evaluate virus-cell interaction by quantifying the interaction between SARS-CoV-2 receptor binding domain (RBD) and its cellular receptor angiotensin-converting enzyme 2 ( ACE2 HGNC) both in living cells and in vitro. We have successfully used this novel biosensor to analyze SARS-CoV-2 RBD mutants, and evaluated candidate small molecules (SMs), antibodies, and peptides that may block RBD: ACE2 HGNC interaction. This simple, rapid and HTP biosensor tool will significantly expedite detection of viral mutants and anti- COVID-19 MESHD drug discovery processes.

    Enzalutamide, a prostate cancer MESHD therapeutic, downregulates TMPRSS2 HGNC in lung and reduces cellular entry of SARS-CoV-2

    Authors: D. A. Leach; A. Mohr; E. S. Giotis; A. M. Isac; L. L. Yates; W. S. Barclay; R. M. Zwacka; C. L. Bevan; G. N. Brooke

    doi:10.21203/ Date: 2020-12-29 Source: ResearchSquare

    The COVID-19 pandemic MESHD, caused by the novel human coronavirus SARS-CoV-2 coronavirus MESHD, attacks various organs but most destructively the lung. It has been shown that SARS-CoV-2 entry into lung cells requires two host cell surface proteins: ACE2 HGNC and TMPRSS2 HGNC. Downregulation of one or both of these is thus a potential therapeutic approach for COVID-19 MESHD TMPRSS2 HGNC is a known target of the androgen receptor HGNC, a ligand-activated transcription factor; activation of the androgen receptor HGNC increases TMPRSS2 HGNC levels in various tissues, most notably the prostate. We show here that treatment with the antiandrogen enzalutamide – a well-tolerated drug widely used in advanced prostate cancer MESHD – reduces TMPRSS2 HGNC levels in human lung cells. Further, enzalutamide treatment of mice dramatically decreased Tmprss2 levels in the lung. To determine therapeutic potential, we assessed uptake of SARS-CoV-2 Spike MESHD SARS-CoV-2 Spike PROTEIN protein pseudotyped lentivirus and live SARS-CoV-2 into human lung cells and saw a significant reduction in viral entry and infection upon treatment with the antiandrogens enzalutamide and bicalutamide. In support of this new experimental data, analysis of existing datasets shows striking co-expression of AR and TMPRSS2 HGNC, including in specific lung cell types that are targeted by SARS-CoV-2. Together, the data presented provides strong evidence to support clinical trials to assess the efficacy of antiandrogens as a treatment option for COVID-19 MESHD.

    Evaluation of the Effect of D614G, N501Y and S477N Mutation in SARS-CoV-2 through Computational Approach

    Authors: Sarmilah Mathavan; Suresh Kumar

    id:10.20944/preprints202012.0710.v1 Date: 2020-12-28 Source:

    Severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) causes an outbreak of COVID-19 MESHD disease in humans with the aid of spike protein PROTEIN. It consists of a receptor-binding domain (RBD) that recognizes and binds to the host receptor angiotensin-converting enzyme 2 ( ACE2 HGNC). The aim of this study was to examine the mutational effect of spike protein PROTEIN on the sequence through an interaction study of the mutant spike protein PROTEIN and the human ACE2 HGNC protein at the structural level. A total of 17,227 spike proteins PROTEIN from Asia, Africa, Europe, Oceania, South America, and North America were compared to the Wuhan spike protein PROTEIN reference sequence (Wuhan-Hu-1). The structural and stability implications of D614G, N501Y, and S477N mutations were evaluated. The binding affinity between mutated RBD and human ACE2 HGNC protein was also studied. The D614G mutation may have originated in Germany, Europe based on the date of the first sample collection report. It is now widely circulated all over the world with most occurrences in North America. The mutations N501Y and S477N may have originated from Oceania based on the date of the first sample collection report and also have the highest occurrences in Oceania. Based on the computational analysis of mutational effects, the D614G, N501Y, and S477N mutations decreased stability and were tolerated. For disease propensity prediction, N501Y was more prone to disease compared to D614G, while S477N was not prone to disease. The mutation of D to G at position 614 and S to N at position 477 for secondary structure prediction shows no changes in secondary structure while remaining in the coil region, whereas the mutation of N to Y at position 501 changes from coil structure to extended strand. N501Y mutation has a higher affinity to human ACE2 HGNC protein compared to D614G and S477N based on a docking study. D614G spike mutation was identified to exist between the two hosts based on a comparison of SARS-CoV-2 derived between the mink and human. Further research is needed on the link between the mink mutation N501T and the mutation N501Y in humans, which has evolved as a separate variant.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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