Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (52)

ComplexRdRp (52)

NSP5 (18)

NSP3 (15)

ORF3a (8)


SARS-CoV-2 Proteins
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    Ayurveda botanicals in COVID-19 MESHD management: An in silico- multitarget approach

    Authors: Swapnil Borse; Manali Joshi; Akash Saggam; Vedika Bhat; Safal Walia; Sneha Sagar; Preeti Chavan-Gautam; Girish Tillu

    doi:10.21203/ Date: 2020-05-19 Source: ResearchSquare

    The Coronavirus disease MESHD ( COVID-19 MESHD) caused by the virus SARS-CoV-2 has become a global pandemic in a very short time span. Currently, there is no specific treatment or vaccine to counter this highly contagiousdisease. Presently, existing anti-virals and disease-modifying agents are being repurposed to manage COVID-19 MESHD. There is an urgent need to find a specific cure for the disease and global efforts are directed at developing SARS-CoV-2 specific anti-viralsand immunomodulators.The objective of this study is to explore the immunomodulatory and anti-SARS-CoV-2 potential of key phytoconstituents from Ayurveda based Rasayana drugs, Withania somnifera (Ashwagandha), Tinospora cordifolia (Guduchi) and Asparagus racemosus (Shatavari) using in silico approaches like network pharmacology, and molecular docking. The SWISS-ADME tool was used to predict the pharmacokinetic and pharmacodynamic (PK-PD) interactions and drug likeliness potential. Using these approaches we propose a library of phytomolecules with potential to be developed as phytopharmaceuticals for COVID 19 management.The plant extracts were prepared as per Ayurvedic procedures and a total of 31 phytoconstituents were identified using HPLC and MS studies. The network pharmacology model shows that these phytoconstituents possess the potential to modulate several immune pathways. Amongst the three botanicalsWithania somnifera was found to be the most potent immunomodulator through its potential to modulate T cell differentiation, NK cell cytotoxicity MESHD as well as T cell, B cell and NOD-like receptor signalling pathways.Molecular docking studies showed thatseveral phytoconstituents possess good affinity for the Spike protein PROTEIN, Main Protease PROTEIN and RNA dependent RNA polymerase PROTEIN of SARS-CoV-2 suggesting their application for the termination of viral life cycle. Further, predictive tools indicate that there would beneficial herb-drug pharmacokinetic-pharmacodynamic interactions with concomitantly administered drug therapy. We thus make a compelling case to evaluate the potential of these Rasayana botanicals in the management of COVID-19 MESHD following rigorous experimental validation.

    Non-synonymous Mutations of SARS-Cov-2 Leads Epitope Loss and Segregates its Varaints

    Authors: Aayatti Mallick Gupta; Sukhendu Mandal

    doi:10.21203/ Date: 2020-05-18 Source: ResearchSquare

    The non-synonymous mutations of SARS-Cov-2 isolated from across the world have been identified during the last few months. The surface glycoprotein spike PROTEIN of SARS-Cov-2 forms the most important hotspot for amino acid alterations followed by the ORF1a PROTEIN/ ORF1ab PROTEIN poly-proteins. It is evident that the D614G mutation in spike glycoprotein PROTEIN and P4715L in RdRp PROTEIN is the important determinant of SARS-Cov-2 evolution since its emergence. P4715L in RdRp PROTEIN, G251V in ORF3a PROTEIN and S1498F of Nsp3 HGNC is associated with the epitope loss that may influence pathogenesis caused by antibody escape variants. Phylogenomics distinguished the ancestral viral samples from China and most part of Asia, isolated between Dec, 2019 to Feb, 2020 and the evolved variants isolated from Europe and Americas from Mar, 2020 to April, 2020. The evolved variants have been found to predominant globally with the loss of epitopes from its proteins. These have implications for SARS-Cov-2 transmission, pathogenesis and immune interventions. 

    In silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19 MESHD

    Authors: Seshu Vardhan; Suban K Sahoo

    id:2005.07955v2 Date: 2020-05-16 Source: arXiv

    Virtual screening of phytochemicals was performed through molecular docking, simulation, in silico ADMET and drug-likeness prediction to identify the potential hits that can inhibit the effects of SARS-CoV-2. Considering the published literature on medicinal importance, total 154 phytochemicals with analogous structure from limonoids and triterpenoids were selected to search potential inhibitors for the five therapeutic protein targets of SARS-CoV-2, i.e., 3CLpro PROTEIN ( main protease PROTEIN), PLpro PROTEIN ( papain-like protease PROTEIN), SGp-RBD ( spike glycoprotein PROTEIN-receptor binding domain), RdRp PROTEIN ( RNA dependent RNA polymerase PROTEIN) and ACE2 (angiotensin-converting enzyme 2). The in silico computational results revealed that the phytochemicals such as glycyrrhizic acid, limonin, 7-deacetyl-7-benzoylgedunin, maslinic acid, corosolic acid, obacunone and ursolic acid were found to be effective against the target proteins of SARS-CoV-2. The protein-ligand interaction study revealed that these phytochemicals bind with the amino acid residues at the active site of the target proteins. Therefore, the core structure of these potential hits can be used for further lead optimization to design drugs for SARS-CoV-2. Also, the medicinal plants containing these phytochemicals like licorice, neem, tulsi, citrus and olives can be used to formulate suitable therapeutic approaches in traditional medicines.

    Nsp7 and Spike Glycoprotein PROTEIN of SARS-CoV-2 Are Envisaged as Potential Targets of Vitamin D and Ivermectin

    Authors: Jhimli Dasgupta; Udayaditya Sen; Abhisek Bakshi; Abhijit Dasgupta; Krishnendu Manna; Chinmay Saha; Rajat K. De; Satinath Mukhopadhyay; Nitai P. Bhattacharyya

    id:10.20944/preprints202005.0084.v1 Date: 2020-05-05 Source:

    COVID-19 MESHD has emerged as deadly pandemic worldwide with no vaccine or suitable antiviral drugs to prevent or cure the disease. Because of the time-consuming process to develop new vaccines or antiviral agents, there has been a growing interest in repurposing some existing drugs to combat SARS-CoV-2. Vitamin D is known to be protective against acute respiratory distress syndrome (ARDS), pneumonia and cytokine storm. Recently it has been used as a repurposed drug for the treatment of H5N1 virus-induced lung injury. Circumstantial evidences indicate that people with low level of vitamin D are more susceptible to SARS-CoV-2. Although, vitamin D was suggested to interfere with viral replication, its interaction with any SARS-CoV-2 protein is unexplored yet. Beside this, ivermectin, a well-known anti-parasitic agent, exhibits potent anti-viral activities in vitro against viruses such as HIV-1 and dengue. Very recently, ivermectin has been found to reduce viral load of SARS-CoV-2 in vitro. We have analyzed available structures of SARS-CoV-2 proteins to identify probable binding partner(s) of vitamin D and ivermectin through knowledge-based docking studies and figured out possible implication of their binding in SARS-CoV-2 infection MESHD. Our observations suggest that the non-structural protein nsp7 possesses a potential site to house 25-hydroxyvitamin D3 (VDY) or the active form of Vitamin D, calcitrol. Binding of vitamin D with nsp7 likely to hamper the formation of nsp7-nsp8 complex which is required to bind with RNA dependent RNA polymerase PROTEIN ( RdRP PROTEIN), nsp12 for optimal function. On the other hand, potential binding site of ivermectin has been identified in the S2 subunit of trimeric spike( S) glycoprotein PROTEIN of SARS-CoV-2. We propose that deeply inserted mode of ivermectin binding at three inter-subunit junctions may restrict large scale conformational changes of S2 helices which is necessary for efficient fusion of viral and host membrane. Our study, therefore, opens up avenues for further investigations to consider vitamin D and ivermectin as potential drugs against SARS-CoV-2.

    Molecular docking of natural compounds from tulsi (Ocimum sanctum) and neem (Azadirachta indica) against SARS-CoV-2 protein targets

    Authors: Arun Kumar

    doi:10.21203/ Date: 2020-05-05 Source: ResearchSquare

    Background: Antiviral activity of tulsi and neem extracts are widely reported. Selected natural compounds from tulsi and neem were hence screened for their efficacy against SARS-CoV-2 targets. Materials and Methods: Using molecular docking tools, the binding efficacy of natural compounds from tulsi and neem were tested against three key SARS-CoV-2 targets i.e., 1) surface glycoprotein (6VSB) responsible for viral attachment, 2) RNA dependent RNA polymerase PROTEIN (6M71) responsible for viral replication and 3) main protease PROTEIN (6Y84) responsible for viral replication. Results: Methyl eugenol, oleanolic acid and ursolic acid had high binding efficacy against surface spike glycoprotein PROTEIN and RNA polymerase of SARS-CoV-2. Epoxyazadiradione, Gedunin, Methyl eugenol, Oleanolic acid and Ursolic acid showed high binding efficacy against the main protease PROTEIN of SARS-CoV-2. Binding efficacy of natural compounds from tulsi and neem was superior to that of the standard drugs Lopinavir/Ritonavir and Remdesivir. Conclusion: Natural compounds from tulsi and neem have high binding efficacy against SARS-CoV-2 targets involved in viral attachment and replication, hence will be useful in the management of infection caused by SARS-CoV-2.

    Development and validation of direct RT-LAMP for SARS-CoV-2

    Authors: Abu Naser Mohon; Jana Hundt; Guido van Marle; Kanti Pabbaraju; Byron Berenger; Thomas Griener; Luiz Lisboa; Deirdre Church; Markus Czub; Alexander Greninger; Keith Jerome; Cody Doolan; Dylan R Pillai

    doi:10.1101/2020.04.29.20075747 Date: 2020-05-04 Source: medRxiv

    We have developed a reverse-transcriptase loop mediated amplification (RT-LAMP) method targeting genes encoding the Spike (S) protein PROTEIN and RNA-dependent RNA polymerase PROTEIN ( RdRP PROTEIN) of SARS-CoV-2. The LAMP assay achieves comparable limit of detection as commonly used RT-PCR protocols based on artificial targets, recombinant Sindbis virus, and clinical samples. Clinical validation of single-target (S gene) LAMP (N=120) showed a positive percent agreement (PPA) of 41/42 (97.62%) and negative percent agreement (NPA) of 77/78 (98.72%) compared to reference RT-PCR. Dual-target RT-LAMP (S and RdRP PROTEIN gene) achieved a PPA of 44/48 (91.97%) and NPA 72/72 (100%) when including discrepant samples. The assay can be performed without a formal extraction procedure, with lyophilized reagents which do need cold chain, and is amenable to point-of-care application with visual detection.

    Evaluation of Yashtimadhu (Glycyrrhiza glabra) active Phytochemicals Against Novel Coronavirus (SARS-CoV-2)

    Authors: Dharmendra Kumar Maurya

    doi:10.21203/ Date: 2020-05-02 Source: ResearchSquare

    Corona Virus Disease 2019 ( COVID-19 MESHD) caused by a novel coronavirus emerged from Wuhan, China in December 2019. It has spread to more than 205 countries and become pandemic now. Currently, there are no FDA approved drugs or vaccines available and hence several studies are going on in search of suitable drug that can target viral proteins or host receptor for the prevention and management of COVID-19 MESHD. The search for plant-based anti-viral agents against the SARS-CoV-2 is promising because several of plants have been shown to possess anti-viral activities against different viruses. Here, we used molecular docking approach to explore the use of Indian Ayurvedic herbs, Yashtimadhu in prevention and management of COVID-19 MESHD. In the present study we have evaluated the effectiveness of phytochemicals found in Yashtimadhu against Main Protease PROTEIN ( Mpro PROTEIN), Spike (S) protein PROTEIN and RNA-dependent RNA polymerase PROTEIN ( RdRp PROTEIN) of SARS-CoV-2 as well as human angiotensin converting enzyme 2 HGNC ( ACE2 HGNC) receptor and furin protease. Apart from this, we have also performed in-silico drug-likeness and predicted pharmacokinetics of the selected phytochemicals found in the Yashtimadhu. Our study shows that several phytochemicals found in this plant have potential to bind with important proteins of SARS-CoV-2 which are essential for viral infection MESHD and replication. Overall our study provides scientific basis in terms of binding of active ingredients present in Yashtimadhu with SARS-CoV-2 target proteins. Our docking studies reveal that Yashtimadhu may inhibit the viral severity by interfering with viral entry as well as its multiplication in the infected persons. Thus Yashtimadhu may be helpful in the prevention and management of the COVID-19 MESHD.

    Not One, But Five: Virtual Screening-Driven Drug Discovery of SARS-CoV2 Enzyme Inhibitors Targeting Viral Attachment, Replication and Post-Translational Infection Mechanisms

    Authors: Mark Tristan J. Quimque; Kin Israel Notarte; Rey Arturo T. Fernandez; Mark Andrew O. Mendoza; Rhenz Alfred D. Liman; Justin Allen K. Lim; Luis Agustin E. Pilapil; Jehiel Karsten H. Ong; Adriel M. Pastrana; Allan Patrick Macabeo

    doi:10.26434/chemrxiv.12170424.v2 Date: 2020-04-28 Source: ChemRxiv

    The novel coronavirus SARS-CoV2, the causative agent of the worldwide pandemic disease COVID-19 MESHD, emerged in December 2019 forcing lockdown of communities in many countries. The absence of specific drugs and vaccines, the rapid transmission of the virus, and the increasing number of deaths MESHD worldwide have necessitated the need to discover substances that can be tapped for drug development. With the aid of bioinformatics and computational modelling, ninety seven secondary metabolites from fungi previously reported to exhibit antiviral properties were docked onto SARS-CoV2 enzymes involved in viral attachment, replication and post-translational mechanisms followed by in silico ADMET prediction (absorption, distribution, metabolism, excretion and toxicity MESHD) of the hit compounds. Thus, two fumiquinazoline alkaloids quinadoline B (19), scedapin C (15), and the polyketide isochaetochromin D1 (8) exhibited high binding affinities depending on the target protein. The compounds were active against the cysteine proteases, papain-like PROTEIN protease ( PLpro PROTEIN) and chymotrypsin-like protease ( 3CLpro PROTEIN) which are involved in post-translational modifications, RNA-directed RNA polymerase ( RdRp PROTEIN) which is essential in viral replication, non-structural protein 15 PROTEIN (nsp15) which is involved in evasion of host immunity, and the spike protein PROTEIN which is responsible for binding to GRP78 HGNC. Quinadoline B (19) was predicted to confer favorable ADMET values, high gastrointestinal absorptive probability and poor blood-brain barrier crossing capacities.

    Searching inhibitors for three important proteins of COVID-19 MESHD through molecular docking studies

    Authors: Seshu Vardhan; Suban K Sahoo

    id:2004.08095v3 Date: 2020-04-17 Source: arXiv

    The lack of recommended drugs or vaccines to deal with the COVID-19 MESHD is the main concern of this pandemic. The approved drugs for similar health problems, drugs under clinical trials, and molecules from medicinal plants extracts are investigated randomly to deal with the COVID-19 MESHD infection. Molecular docking, one of the best approach to search therapeutically potent drugs/molecules in real time with possible hope to apply on COVID-19 MESHD. In this communication, molecular docking studies of 18 ligands were carried out with the three therapeutic target proteins of SARS-CoV-2, i.e., RNA-dependent RNA polymerase PROTEIN ( RdRp PROTEIN), angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC) and spike glycoprotein PROTEIN (SGp). The obtained results revealed that the phytochemicals showed better dock score in compared to the drugs paracetmol and hydroxychloroquine. Combining the dock score and medicinal properties, we believe the terpenoids based phytochemicals limonin and scopadulcic acid B can be further explored for potential use against COVID-19 MESHD.

    In silico studies reveal potential antiviral activity of phytochemicals from medicinal plants for the treatment of COVID-19 MESHD infection

    Authors: Mansi Pandit; N. Latha

    doi:10.21203/ Date: 2020-04-13 Source: ResearchSquare

    The spread of COVID-19 MESHD across continents has led to a global health emergency. COVID-19 MESHD disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected nearly all the continents with around 1.52 million confirmed cases worldwide. Currently only a few regimes have been suggested to fight the infection and no specific antiviral agent or vaccine is available. Repurposing of the existing drugs or use of natural products are the fastest options available for the treatment. The present study is aimed at employing computational approaches to screen phytochemicals from the medicinal  plants targeting the proteins of SARS-CoV2 MESHD  for identification of antiviral therapeutics. The study focuses on three target proteins important in the life cycle of SARS-CoV-2 namely Spike ( S) glycoprotein PROTEIN, main protease PROTEIN ( Mpro PROTEIN) and RNA-dependent RNA-polymerase PROTEIN ( RdRp PROTEIN). Molecular docking was performed to screen phytochemicals in medicinal plants to determine their feasibility as potential inhibitors of these target viral proteins. Of the 30 plant phytochemicals screened, Silybin, an active constituent found in Silybum marianum exhibited higher binding affinity with targets in SARS-CoV-2 in comparison to currently used repurposed drugs against SARS-CoV-2. Withaferin A from Withania somnifera also showed significant binding to the targets proteins. In addition, phytochemicals from Tinospora cordiofolia and Aloe barbadensis displayed good binding energetics with the target proteins in SARS-CoV-2. These results provide a basis for the use of traditional medicinal plants as alternative lines of treatment for COVID-19 MESHD infection.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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