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    Scope of Natural Plant Extract to Deactivate COVID-19 MESHD

    Authors: Md Abdus Shahid; Mohammad Asaduzzaman Chowdhury; Mohammod Abul Kashem

    doi:10.21203/rs.3.rs-19240/v1 Date: 2020-03-24 Source: ResearchSquare

    The outbreak of coronavirus disease 2019 MESHD ( COVID-19 MESHD) has emerged as a severe threat for public health and economy throughout the world. The structure of corona virus is composed of RNA based proteins that contains amino (-NH2) and carboxyl (-COOH) groups.  It includes nucleocapsid protein (N PROTEIN- protein), spike PROTEIN protein (S PROTEIN S-protein HGNC protein), envelope PROTEIN and hemagglutinin-esterase dimer (HE). These proteins affect adversely on human gastrointestinal system, heart, kidney, liver, and central nervous system leading to several organ damages. This investigation reveals that the extracted components of natural plants, especially hydroxyl (-OH) groups react chemically to deactivate the active components of the virus by esterification   process. As a case study, using one of the natural resources, as for example, licorice (Glycyrrhiza glabra) which has the components of glycyrrhizin, glycyrrhetic acid, liquiritin and isoliquiritin that can be used to neutralize the activeness of COVID-19 MESHD and it can be used as an antiviral drug. The extracted licorice is further processed with PVA solution to form antiviral nano-membrane for potential application as wound dressing materials, musk, gloves and against skin infection MESHD by electrospinning.  The morphology of the membrane is characterized using scanning electron microscope (SEM). The research suggests that the other plants having deactivate components against virus can be applicable to resolve the human health crisis of the globe. 

    Repurposing Therapeutics for COVID-19 MESHD: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein PROTEIN and Viral Spike Protein PROTEIN-Human ACE2 HGNC Interface

    Authors: Micholas Smith; Jeremy C. Smith

    doi:10.26434/chemrxiv.11871402.v4 Date: 2020-03-11 Source: ChemRxiv

    The novel Wuhan coronavirus (SARS-CoV-2) has been sequenced, and the virus shares substantial similarity with SARS-CoV MESHD. Here, using a computational model of the spike protein (S PROTEIN S-protein HGNC) of SARS-CoV-2 interacting with the human ACE2 HGNC receptor, we make use of the world's most powerful supercomputer, SUMMIT, to enact an ensemble docking virtual high-throughput screening campaign and identify small-molecules which bind to either the isolated Viral S-protein HGNC S-protein PROTEIN at its host receptor region or to the S protein PROTEIN-human ACE2 HGNC interface. We hypothesize the identified small-molecules may be repurposed to limit viral recognition of host cells and/or disrupt host-virus interactions. A ranked list of compounds is given that can be tested experimentally.

    Predictions for the binding domain and potential new drug targets of 2019-nCoV

    Authors: Zehua Zeng; Luo Zhi; Hongwu Du

    doi:10.1101/2020.02.26.961938 Date: 2020-03-02 Source: bioRxiv

    An outbreak of new SARS-like viral in Wuhan, China has been named 2019-nCoV. The current state of the epidemic is increasingly serious, and there has been the urgent necessity to develop an effective new drug. In previous studies, it was found that the conformation change in CTD1 was the region where SARS-CoV MESHD bound to human ACE2 HGNC. Although there are mutations of the 2019-nCoV, the binding energy of ACE2 HGNC remains high. The surface glycoprotein of 2019-nCoV was coincident with the CTD1 region of the S-protein HGNC S-protein PROTEIN by comparing the I-TASSER prediction model with the actual SARS model, which suggests that 2019-nCoV may bind to the ACE2 HGNC receptor through conformational changes. Furthermore, site prediction on the surface glycoprotein of 2019-nCoV suggests some core amino acid area may be a novel drug target against 2019-nCoV.

    A Multiscale and Comparative Model for Receptor Binding of 2019 Novel Coronavirus and the Implication of its Life Cycle in Host Cells

    Authors: Zhaoqian Su; Yinghao Wu

    doi:10.1101/2020.02.20.958272 Date: 2020-02-21 Source: bioRxiv

    The respiratory syndrome MESHD caused by a new type of coronavirus has been emerging from China and caused more than 1000 death globally since December 2019. This new virus, called 2019 novel coronavirus (2019-nCoV) uses the same receptor called Angiotensinconverting enzyme 2 ( ACE2 HGNC) to attack humans as the coronavirus that caused the severe acute respiratory syndrome MESHD (SARS) seventeen years ago. Both viruses recognize ACE2 HGNC through the spike proteins (S PROTEIN S-protein HGNC) on their surfaces. It was found that the S-protein PROTEIN S-protein HGNC from the SARS coronavirus ( SARS-CoV MESHD) bind stronger to ACE2 HGNC than 2019-nCoV. However, function of a bio-system is often under kinetic, rather than thermodynamic, control. To address this issue, we constructed a structural model for complex formed between ACE2 HGNC and the S-protein PROTEIN S-protein HGNC from 2019-nCoV, so that the rate of their association can be estimated and compared with the binding of S-protein HGNC S-protein PROTEIN from SARS-CoV MESHD by a multiscale simulation method. Our simulation results suggest that the association of new virus to the receptor is slower than SARS, which is consistent with the experimental data obtained very recently. We further integrated this difference of association rate between virus and receptor into a mathematical model which describes the life cycle of virus in host cells and its interplay with the innate immune system. Interestingly, we found that the slower association between virus and receptor can result in longer incubation period, while still maintaining a relatively higher level of viral concentration in human body. Our computational study therefore provides, from the molecular level, one possible explanation that the new disease by far spread much faster than SARS.

    Structural basis for the recognition of the 2019-nCoV by human ACE2

    Authors: Renhong Yan; Yuanyuan Zhang; Yingying Guo; Lu Xia; Qiang Zhou

    doi:10.1101/2020.02.19.956946 Date: 2020-02-20 Source: bioRxiv

    Angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC) has been suggested to be the cellular receptor for the new coronavirus (2019-nCoV) that is causing the coronavirus disease 2019 MESHD ( COVID-19 MESHD). Like other coronaviruses such as the SARS-CoV, the 2019-nCoV uses the receptor binding domain (RBD) of the surface spike glycoprotein PROTEIN ( S protein PROTEIN S protein HGNC) to engage ACE2 HGNC. We most recently determined the structure of the full-length human ACE2 HGNC in complex with a neutral amino acid transporter B0AT1 HGNC. Here we report the cryo-EM structure of the full-length human ACE2 HGNC bound to the RBD of the 2019-nCoV at an overall resolution of 2.9 [A] in the presence of B0AT1 HGNC. The local resolution at the ACE2 HGNC-RBD interface is 3.5 [A], allowing analysis of the detailed interactions between the RBD and the receptor. Similar to that for the SARS-CoV MESHD, the RBD of the 2019-nCoV is recognized by the extracellular peptidase domain (PD) of ACE2 HGNC mainly through polar residues. Pairwise comparison reveals a number of variations that may determine the different affinities between ACE2 HGNC and the RBDs from these two related viruses.

    Fast assessment of human receptor-binding capability of 2019 novel coronavirus (2019-nCoV)

    Authors: Qiang Huang; Andreas Herrmann

    doi:10.1101/2020.02.01.930537 Date: 2020-02-03 Source: bioRxiv

    The outbreaks of 2002/2003 SARS, 2012/2015 MERS and 2019/2020 Wuhan respiratory syndrome MESHD clearly indicate that genome evolution of an animal coronavirus (CoV) may enable it to acquire human transmission ability, and thereby to cause serious threats to global public health. It is widely accepted that CoV human transmission is driven by the interactions of its spike protein (S PROTEIN S-protein HGNC) with human receptor on host cell surface; so, quantitative evaluation of these interactions may be used to assess the human transmission capability of CoVs. However, quantitative methods directly using viral genome data are still lacking. Here, we perform large-scale protein-protein docking to quantify the interactions of 2019-nCoV S-protein HGNC S-protein PROTEIN receptor-binding domain (S-RBD) with human receptor ACE2 HGNC, based on experimental SARS-CoV S-RBD MESHD- ACE2 HGNC complex structure. By sampling a large number of thermodynamically probable binding conformations with Monte Carlo algorithm, this approach successfully identified the experimental complex structure as the lowest-energy receptor-binding conformations, and hence established an experiment-based strength reference for evaluating the receptor-binding affinity of 2019-nCoV via comparison with SARS-CoV MESHD. Our results show that this binding affinity is about 73% of that of SARS-CoV MESHD, supporting that 2019-nCoV may cause human transmission similar to that of SARS-CoV MESHD. Thus, this study presents a method for rapidly assessing the human transmission capability of a newly emerged CoV and its mutant strains, and demonstrates that post-genome analysis of protein-protein interactions may provide early scientific guidance for viral prevention and control.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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