Corpus overview


Overview

MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

NSP5 (33)

ComplexRdRp (13)

ProteinS (10)

NSP3 (6)

ProteinS1 (2)


Filter

Genes
Diseases
SARS-CoV-2 Proteins
    displaying 1 - 10 records in total 33
    records per page




    SARS-CoV-2 Nsp5 HGNC Protein Causes Acute Lung Inflammation MESHD: A Dynamical Mathematical Model

    Authors: José Díaz; Elena R. Álvarez-Buylla; Antonio Bensussen

    id:10.20944/preprints202012.0749.v2 Date: 2021-03-15 Source: Preprints.org

    In the present work we propose a dynamical mathematical model of the lung cells inflammation process MESHD in response to SARS-CoV-2 infection MESHD. In this scenario the main protease PROTEIN Nsp5 HGNC enhances the inflammatory process, increasing the levels of NF kB, IL-6 HGNC, Cox2 HGNC, and PGE2 with respect to a reference state without the virus. In presence of the virus the translation rates of NF kB and IkB arise to a high constant value, and when the translation rate of IL-6 HGNC also increases above the threshold value of 7 pg mL-1 s-1 the model predicts a persistent over stimulated immune state with high levels of the cytokine IL-6 HGNC. Our model shows how such over stimulated immune state becomes autonomous of the signals from other immune cells such as macrophages and lymphocytes, and does not shut down by itself. We also show that in the context of the dynamical model presented here, Dexamethasone or Nimesulide have little effect on such inflammation MESHD state of the infected lung cell, and the only form to suppress it is with the inhibition of the activity of the viral protein Nsp5 HGNC.To that end, our model suggest that drugs like Saquinavir may be useful. In this form, our model suggests that Nsp5 HGNC is effectively a central node underlying the severe acute lung inflammation MESHD during SARS-CoV-2 infection MESHD. The persistent production of IL-6 HGNC by lung cells can be one of the causes of the cytokine storm observed in critical patients with COVID19 MESHD. Nsp5 HGNC seems to be the switch to start inflammation MESHD, the consequent overproduction of the ACE2 HGNC receptor, and an important underlying cause of the most severe cases of COVID19 MESHD.

    Active constituents and Molecular Analysis of Psidium guajava Against Multiple Protein of SARS-CoV-2

    Authors: Fadilah Fadilah; Linda Erlina; Rafika Indah Paramita; Khaerunissa Anbar Istiadi; Raden Rara Diah Handayani

    doi:10.21203/rs.3.rs-271919/v1 Date: 2021-02-23 Source: ResearchSquare

    Background The severe acute respiratory syndrome MESHD COVID-19 MESHD declared as a global pandemic by the World Health Organization has become the present wellbeing worry to the whole world. The latest development of COVID-19 MESHD spread in Indonesia has reached 1.024.298 cases, with 28.855 patients died, updated on January 28, 2021. Unfortunately, these numbers continue to overgrow, and no drug has yet been approved for effective treatment. There is an emergent need to search for possible medications and explore the potential of Indonesian herbal compounds. Ministry of Health Indonesia stated that Psidium guajava can be use as daily nutritional supplement during COVID-19 pandemic MESHD. This study aims to determine the potential active constituents in Psidium guajava as an inhibitor for multiple SARS-CoV-2 proteins using molecular analysis.Methods Molecular docking was performed by using Autodocktools 1.5.6. We performed a structure-based virtual screening of fourteen 3D structure of Psidium guajava compounds, three antivirals (lopinavir, remdesivir, and ritonavir) against multiple SARS-CoV-2 proteins. We download the main protease PROTEIN (3CLPro), Papain Like Protease PROTEIN (PL Pro), MPro, Spike and ACE2 HGNC as protein target from human against from Protein Data Bank (PDB). We used PyMOL to analyse the interactions between the SARS-CoV-2 proteins and 14 compounds from Psidium guajava and three antiviral (lopinavir, remdesivir and ritonavir) used as positive control.Results Based on the molecular docking analysis, it was found there are two potential compounds that showed higher binding affinity score namely gamma sitosterol and peri-xanthenoxanthene-4,10-dione,2,8-bis (1-methylethyl).Conclusions Gamma sitosterol and peri-xanthenoxanthene-4,10-dione,2,8-bis (1-methylethyl) from Psidium guajava have potential as antiviral candidates for SARS-CoV-2 multiple proteins such as main protease PROTEIN (3CLPro), Papain Like Protease PROTEIN (PL Pro), MPro, Spike and ACE2 HGNC.

    Post-infection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection MESHD

    Authors: Chamandi Dampalla; Jian Zheng; Krishani Perera; Lok Yin Roy Wong; David Meyerholz; Harry Nguyen; Maithri Kashipathy; Kevin Battaile; Scott Lovell; Yunjeong Kim; Stanley Perlman; William Groutas; Kyeong-Ok Chang

    doi:10.1101/2021.02.05.429937 Date: 2021-02-05 Source: bioRxiv

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to be a serious global public health threat. The 3C-like protease ( 3CLpro PROTEIN) is a virus protease encoded by SARS-CoV-2, which is essential for virus replication. We have previously reported a series of small molecule 3CLpro PROTEIN inhibitors effective for inhibiting replication of human coronaviruses including SARS-CoV-2 in cell culture and in animal models. Here we generated a series of deuterated variants of a 3CLpro PROTEIN inhibitor, GC376, and evaluated the antiviral effect against SARS-CoV-2. The deuterated GC376 displayed potent inhibitory activity against SARS-CoV-2 in the enzyme and the cell-based assays. The K18- hACE2 HGNC mice develop mild to lethal infection commensurate with SARS-CoV-2 challenge doses and was proposed as a model for efficacy testing of antiviral agents. We treated lethally infected mice with a deuterated derivative of GC376. Treatment of K18- hACE2 HGNC mice at 24 hr post infection with a derivative (compound 2) resulted in increased survival of mice compared to vehicle-treated mice. Lung virus titers were decreased, and histopathological changes were ameliorated in compound 2-treated mice compared to vehicle-treated mice. Structural investigation using high-resolution crystallography illuminated binding interactions of 3CLpro PROTEIN of SARS-CoV-2 and SARS-CoV MESHD with deuterated variants of GC376. Taken together, deuterated GC376 variants have excellent potential as antiviral agents against SARS-CoV-2.

    Efficacy of GC-376 against SARS-CoV-2 virus infection MESHD in the K18 hACE2 HGNC transgenic mouse model

    Authors: C. Joaquin Caceres; Stivalis Cardenas-Garcia; Silvia Carnaccini; Brittany Seibert; Daniela S Rajao; Jun Wang; Daniel R Perez; Amanda J. Martinot; Cesar Piedra-Mora; Sidney Beecy; Sarah Ducat; Ronnie Chamanza; Sietske Rosendahl Huber; Leslie van der Fits; Erica N. Borducchi; Michelle Lifton; Jinyan Liu; Felix Nampanya; Shivani Patel; Lauren Peter; Lisa H. Tostanoski; Laurent Pessaint; Alex Van Ry; Brad Finneyfrock; Jason Velasco; Elyse Teow; Renita Brown; Anthony Cook; Hanne Andersen; Mark G. Lewis; Hanneke Schuitemaker; Dan H. Barouch; Christian Lavallee; Pierre-Olivier Hetu; Jean-Sebastien Paquette; Sylvie Levesque; Marieve Cossette; Anna Nozza; Malorie Chabot-Blanchet; Marie-Pierre Dube; Marie-Claude Guertin; Guy Boivin

    doi:10.1101/2021.01.27.428428 Date: 2021-01-27 Source: bioRxiv

    The COVID-19 pandemic MESHD caused by the Severe Acute Respiratory Syndrome Coronavirus-2 MESHD (SARS-CoV-2) is the defining global health emergency of this century. GC-376 is a Mpro PROTEIN inhibitor with antiviral activity against SARS-CoV-2 in vitro. Using the K18- hACE2 HGNC mouse model, the in vivo antiviral efficacy of GC-376 against SARS-CoV-2 was evaluated. GC-376 treatment was not toxic in K18- hACE2 HGNC mice and produced milder tissue lesions, reduced viral loads, fewer presence of viral antigen, and reduced inflammation MESHD in comparison to vehicle-treated controls, most notably in the brain in mice challenged with a low virus dose. Although GC-376 was not sufficient to improve neither clinical symptoms nor survival, it did show a positive effect against SARS-CoV-2 in vivo. This study supports the notion that the K18- hACE2 HGNC mouse model is suitable to study antiviral therapies against SARS-CoV-2, and GC-376 represents a promising lead candidate for further development to treat SARS-CoV-2 infection MESHD.

    The neutralization effect of Montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies

    Authors: Serdar Durdagi; Timucin Avsar; Muge Didem Orhan; Muge Serhatli; Bertan Koray Balcioglu; Hasan Umit Ozturk; Alisan Kayabolen; Yuksel Cetin; Seyma Aydinlik; Tugba Bagci-Onder; Saban Tekin; Hasan Demirci; Mustafa Guzel; Atilla Akdemir; Seyma Calis; Lalehan Oktay; Ilayda Tolu; Yasar Enes Butun; Ece Erdemoglu; Alpsu Olkan; Nurettin Tokay; Seyma Isik; Aysenur Ozcan; Elif Acar; Sehriban Buyukkilic; Yesim Yumak

    doi:10.1101/2020.12.26.424423 Date: 2020-12-27 Source: bioRxiv

    Small molecule inhibitors have previously been investigated in different studies as possible therapeutics in the treatment of SARS-CoV-2. In the current drug repurposing study, we identified the leukotriene (D4) receptor antagonist Montelukast as a novel agent that simultaneously targets two important drug targets of SARS-CoV-2. We initially demonstrated the dual inhibition profile of Montelukast through multiscale molecular modeling studies. Next, we characterized its effect on both targets by different in vitro experiments including the Fluorescent Resonance Energy Transfer (FRET)-based main protease PROTEIN enzyme inhibition assay, surface plasmon resonance ( SPR HGNC) spectroscopy, pseudovirus neutralization on HEK293T / hACE2 HGNC, and virus neutralization assay using xCELLigence MP real time cell analyzer. Our integrated in silico and in vitro results confirmed the dual potential effect of the Montelukast both on virus entry into the host cell (Spike/ ACE2 HGNC) and on the main protease PROTEIN enzyme inhibition. The virus neutralization assay results showed that while no cytotoxicity of the Montelukast was observed at 12 M concentration, the cell index time 50 (CIT50) value was delayed for 12 hours. Moreover, it was also shown that Favipiravir, a well-known antiviral used in COVID-19 MESHD therapy, should be used by 16-fold higher concentrations than Montelukast in order to have the same effect of Montelukast. The rapid use of new small molecules in the pandemic is very important today. Montelukast, whose pharmacokinetic and pharmacodynamic properties are very well characterized and has been widely used in the treatment of asthma MESHD since 1998, should urgently be completed in clinical phase studies and if its effect is proven in clinical phase studies, it should be used against COVID-19 MESHD.

    Tea flavonoids blocking multiple SARS-CoV-2 protein targets judged from molecular docking

    Authors: Lufei Wang; Siyao Sang; Mingjie Su; Simin Wang; Hui Li

    doi:10.21203/rs.3.rs-122589/v1 Date: 2020-12-05 Source: ResearchSquare

    Severe Acute Respiratory Syndrome Coronavirus 2 MESHD (SARS-CoV-2) has caused Severe Acute Respiratory Syndrome Coronavirus 2 MESHD (SARS-CoV-2) pandemic. Flavonoids derived Chinese patent medicines has outstanding curative effects for the improvement and treatment of COVID-19 MESHD. There are numerous studies suggesting that flavonoids-rich tea have antiviral effects. However, bioactive compounds from tea flavonoids with anti- COVID-19 MESHD effect, and the potential molecular mechanisms are unclear. In this study, we performed a molecular docking of 468 tea flavonoids and its derivatives with main protease PROTEIN ( Mpro PROTEIN), angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC), RNA dependent RNA polymerase PROTEIN ( RdRp PROTEIN), compared with the positive control drugs of each target. The results suggested that ACE2 HGNC and RdRp PROTEIN are the main targets inhibited by tea flavonoids.Q3G Isovitexin, and TF would be considered as the potential candidate compounds of RdRp PROTEIN and ACE2 HGNC. Our study provides a theoretical basis for further drug design of anti- COVID-19 MESHD.

    A pomegranate peel extract as inhibitor of SARS-CoV-2 Spike PROTEIN binding to human ACE2 HGNC (in vitro): a promising source of novel antiviral drugs

    Authors: Annalisa Tito; Antonio Colantuono; Luciano Pirone; Emilia Maria Pedone; Daniela Intartaglia; Giuliana Giamundo; Ivan Conte; Paola Vitaglione; Fabio Apone; Daniel A. Hofmanner; Pedro D. Wendel Garcia; Matthias P. Hilty; Philipp Karl Buehler; Reto A. Schuepbach; Silvio D Brugger; Annelies S. Zinkernagel; Philippe Menu; Marion Brayer; Lars M Steinmetz; Ali Si-Mohammed; Josiane Chuisseu; Richard Stevens; Pantelis Constantoulakis; Michela Sali; Gilbert Greub; Carsten Tiemann; Vicent Pelechano; Adrian Willig; Zhenyu Xu

    doi:10.1101/2020.12.01.406116 Date: 2020-12-01 Source: bioRxiv

    Plant extracts are rich in bioactive compounds, such as polyphenols, sesquiterpenes and triterpenes, with potential antiviral activities. As the dramatic outbreak of the pandemic COVID-19 MESHD, caused by the SARS-CoV-2 virus, thousands of scientists are working tirelessly trying to understand the biology of this new virus and the disease pathophysiology, with the main goal to discover effective preventive treatments and therapeutic agents. Plant-derived secondary metabolites may play key roles in preventing and counteracting the rapid spread of SARS-CoV-2 infections MESHD by inhibiting the activity of several viral proteins, in particular those involved in the virus entry into the host cells and its replication. In this study, by using different in vitro approaches, we uncovered the role of a pomegranate peel extract in attenuating the interaction between the SARS-CoV-2 Spike PROTEIN glycoprotein and the human Angiotensin-Converting Enzyme 2 HGNC ( ACE2 HGNC) receptor, and in inhibiting the activity of the virus 3CL protease PROTEIN. Although further studies will be determinant to assess the efficacy of this extract in vivo, our results open up new promising opportunities to employ natural extracts for the development of effective and innovative therapies in the fight against SARS-CoV-2.

    In Vitro: Natural Compounds (Thymol, Carvacrol, Hesperidine, And Thymoquinone) Against Sars-Cov2 Strain Isolated From Egyptian Patients

    Authors: Mohamed G Seadawy; Ahmed F. Gad; Mohamed Shamel; Bassem Elharty; Mostfa F. Mohamed; Abdo A. Elfiky; Aya Ahmed; Abdel Rahman N. Zekri

    doi:10.21203/rs.3.rs-119568/v1 Date: 2020-12-01 Source: ResearchSquare

    Background: The current pandemic of the coronavirus disease-2019 ( COVID-19 MESHD) has badly affected our life during the year 2020. SARS-CoV-2 is the primary causative agent of the newly emerged pandemic. Natural flavonoids, Terpenoid and Thymoquinone are tested against different viral and host-cell protein targets. These natural compounds have a good history in treating Hepatitis C Virus MESHD ( HCV MESHD) and Human Immunodeficiency Virus (HIV) MESHD. Methods: Molecular docking combined with cytotoxicity MESHD and plaque reduction assay is used to test the natural compounds against different viral (Spike, RdRp PROTEIN, and Mpro PROTEIN) and host-cell (TMPRSS II, keap 1 HGNC, and ACE2 HGNC) targets. Results: The results demonstrate the binding possibility of the natural compounds (Thymol, Carvacrol, Hesperidine, and Thymoquinone) to the viral main protease PROTEIN ( Mpro PROTEIN). Some of these natural compounds were approved to start clinical trail from Egypt Center for Research and Regenerative Medicine ECRRM IRB (Certificate No.IRB00012517)Conclusion: Development of an effective anti-viral for SARS-CoV-2  could help to limit the viral load. Benchmarking testing of those natural compounds against other potential antivirals for SARS-CoV-2 with alternative mechanisms of action would thus be important as soon as practicable.

    Approach Towards Drugs Repurposing: Docking Studies with Multiple Target Proteins Associated with SARS-CoV-2

    Authors: Shiwani Rana; Meghali Panwar; Kalyan Sundar Ghosh

    doi:10.26434/chemrxiv.12469172.v2 Date: 2020-11-09 Source: ChemRxiv

    The current pandemic outbreak of COVID-19 MESHD due to viral infections MESHD by SARS-CoV-2 is now become associated with severe commotion on global healthcare and economy. In this extreme situation when vaccine or drugs against COVID-19 MESHD are not available, the only quick and feasible therapeutic alternative would be the drug repurposing approach. In the present work, in silico screening of some antiviral and antiprotozoal drugs using Autodock docking tool was performed. Two known antiviral drugs sorivudine and noricumazole B are predicted to bind to the active site of the viral proteases namely cysteine like protease PROTEIN or 3CL protease PROTEIN ( 3CLpro PROTEIN) and papain like protease PROTEIN ( PLpro PROTEIN) respectively with a highly favorable free energy of binding. Further, the promising molecules were subjected for checking their activity on other molecular targets like spike protein S1 PROTEIN, RNA dependent RNA polymerase PROTEIN ( RdRp PROTEIN) and angiotensin converting enzyme 2 HGNC ( ACE2 HGNC) receptor. But the compounds were found not effective on rest other molecular targets.

    Kuwanons, Promising inhibitors against the ACE-2 HGNC, main protease PROTEIN of SARS-CoV-2 and falcipan-2 using molecular docking

    Authors: Kamlesh Kumari; Durgseh Kumar; Ramappa Venkatesh Kumar; Prashant Singh

    doi:10.21203/rs.3.rs-104699/v1 Date: 2020-11-08 Source: ResearchSquare

    In the present scenario, the COVID-19 MESHD has affected the nations throughout the world. Till date, neither a vaccine nor a potential medicine is available for the cure from SARS-CoV-2 infection MESHD. Main protease PROTEIN of SARS-CoV-2 is responsible for the replication and transcription. Further, this virus binds to the angiotensin converting enzyme-2 HGNC ( ACE-2 HGNC) so there is need to find molecule, to avoid the binding of novel virus to ACE-2 HGNC. It is reported that the molecules binds to falcipan-2 can help in the reduction of infection MESHD due to SARS-CoV-2. Therefore, there is a need to find promising candidate against the receptors, spread COVID-19 MESHD. In the present work, kuwanons are proposed to be promising candidates against the main protease PROTEIN of SARS-CoV-2, ACE-2 HGNC and falcipan-2. The interaction between the different kuwanons with different receptors has been studied using the binding energy. Kuwanon M was found to best inhibitor against the main protease PROTEIN of SARS-CoV-2 and ACE-2 HGNC. Further, the drug-likeness properties of all the 16 kuwanons were studied. Kuwanon-M found to be best inhibitor against the ACE-2 HGNC and main protease PROTEIN of SARS-CoV-2 with binding energy of -165.349 and -149.952 kcal/mol respectively while kuwanon-G found out to promising against the falcipan-2 with a binding energy of -149.573 kcal/mol.

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from Preprints.org and is updated on a daily basis (7am CET/CEST).
The web page can also be accessed via API.

Sources


Annotations

All
None
MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


Export subcorpus as...

This service is developed in the project nfdi4health task force covid-19 which is a part of nfdi4health.

nfdi4health is one of the funded consortia of the National Research Data Infrastructure programme of the DFG.