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semen armeniacae amarum

Background: Coronavirus disease 2019 (COVID-19) outbreak is progressing rapidly, and poses significant threats to public health A number of clinical practice results showed that traditional Chinese medicine (TCM) plays a significant role for COVID-19 treatment Objective: To explore the active components and molecular mechanism of semen armeniacae amarum treating COVID-19 by network pharmacology and molecular docking technology Methods: The active components and potential targets of semen armeniacae amarum were retrieved from traditional Chinese medicine systems pharmacology (TCMSP) database Coronavirus disease 2019-associated targets were collected in the GeneCards, TTD, OMIM and PubChem database Compound target, compound-target pathway and medicine-ingredient-target disease networks were constructed by Cytoscape 3 8 0 Protein-protein interaction (PPI) networks were drawn using the STRING database and Cytoscape 3 8 0 software David database was used for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis The main active components were verified by AutoDock Vina 1 1 2 software A lipopolysaccharide (LPS)-induced lung inflammation model in Institute of Cancer Research (ICR) mice was constructed and treated with amygdalin to confirm effects of amygdalin on lung inflammation and its underlying mechanisms by western blot analyses and immunofluorescence Results: The network analysis revealed that nine key, active components regulated eight targets (Protooncogene tyrosine-protein kinase SRC (SRC), interleukin 6 (IL6), mitogen-activated protein kinase 1 (MAPK1), mitogen-activated protein kinase 3 (MAPK3), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), HRAS proto-oncogene (HRAS), caspase-3 (CASP3)) Gene ontology and KEGG enrichment analysis suggested that semen armeniacae amarum plays a role in COVID-19 by modulating 94 biological processes, 13 molecular functions, 15 cellular components and 80 potential pathways Molecular docking indicated that amygdalin had better binding activity to key targets such as IL6, SRC, MAPK3, SARS coronavirus-2 3C-like protease (SARS-CoV-2 3CLpro) and SARS-CoV-2 angiotensin converting enzyme II (ACE2) Experimental validation revealed that the lung pathological injury and inflammatory injury were significantly increased in the model group and were improved in the amygdalin group Conclusion: Amygdalin is a candidate compound for COVID-19 treatment by regulating IL6, SRC, MAPK1 EGFR and VEGFA to involve in PI3K-Akt signalling pathway, VEGF signalling pathway and MAPK signalling pathway Meanwhile, amygdalin has a strong affinity for SARS-CoV-2 3CLpro and SARS-CoV-2 ACE2 and therefore prevents the virus transcription and dissemination.

The mechanism and active compounds of semen armeniacae amarum treating coronavirus disease 2019 based on network pharmacology and molecular docking

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10.1021/acs.jmedchem.1c01214

Compound 1 exhibited a SARS-CoV-2 3CLpro inhibitory IC50 value of 250 nM and an antiviral EC50 value of 2.

Indole Chloropyridinyl Ester-Derived SARS-CoV-2 3CLpro Inhibitors: Enzyme Inhibition, Antiviral Efficacy, Structure–Activity Relationship, and X-ray Structural Studies

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10.1080/14756366.2021.1873977

baicalensis and its major component, baicalein, inhibit SARS-CoV-2 3CLpro activity in vitro with IC50’s of 8.

Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro

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10.1080/07391102.2021.1918256

Our study gives an explanation of the structure activity relationship required for targeting SARS-CoV-2 3CLpro and Spike proteins and also facilitates the future design and synthesis of new potential drugs exhibiting better affinity and specificity.

In a search for potential drug candidates for combating COVID-19: computational study revealed salvianolic acid B as a potential therapeutic targeting 3CLpro and spike proteins.

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10.1101/2021.07.28.454072

The biosensors were constructed by linking a green fluorescent protein (GFP2) to the N-terminus and a Renilla luciferase (RLuc8) to the C-terminus of SARS-CoV-2 3CLpro, with the linkers derived from the cleavage sequences of 3CLpro.

BRET-based self-cleaving biosensors for SARS-CoV-2 3CLpro Inhibitor Discovery

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10.26434/CHEMRXIV.14781690.V1

A series of non-deuterated and deuterated dipeptidyl aldehyde and masked aldehyde inhibitors that incorporate in their structure a conformationally-constrained cyclohexane moiety was synthesized and found to potently inhibit SARS-CoV-2 3CL protease in biochemical and cell-based assays.

Structure-Guided Design of Conformationally-Constrained Cyclohexane Inhibitors of SARS-CoV-2 3CL Protease

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10.1038/s41467-021-23751-3

Here we describe the discovery of myricetin, a flavonoid found in many food sources, as a non-peptidomimetic and covalent inhibitor of the SARS-CoV-2 3CLpro.

Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease

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10.3390/molecules26175230

Further characterization on the single isolated compound by NMR showed that 6 was identified and possessed 75% inhibitory activity on SARS-CoV-2 3CL protease enzyme that was slightly different with the positive control GC376 (77%).

GC-MS, LC-MS/MS, Docking and Molecular Dynamics Approaches to Identify Potential SARS-CoV-2 3-Chymotrypsin-Like Protease Inhibitors from Zingiber officinale Roscoe

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10.1016/j.cjac.2021.09.006

We explore the interaction between the newly designed molecule and SARS-CoV-2 3CLpro by molecular docking.

Molecular design, molecular docking and ADMET study of cyclic sulfonamide derivatives as SARS-CoV-2 inhibitors

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10.26355/eurrev_202105_25958

Coronaviruses require the SARS-CoV-2 3CL-Protease (3CL-protease) for cleavage of its polyprotein to yield a single useful protein and assume a basic role in the disease progression.

Punicalagin and zinc (II) ions inhibit the activity of SARS-CoV-2 3CL-protease in vitro.

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10.1016/j.cyto.2021.155697

In this investigation, 293T cells were transfected with SARS-CoV-2 3CL and then infected with Sendai virus (SeV) to induce the RIG-I like receptor (RLR)-based immune pathway.

SARS-CoV-2 3C-like protease antagonizes interferon-beta production by facilitating the degradation of IRF3

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10.1186/s13020-021-00427-0

The molecular docking results showed that the main active ingredients of AE have good affinity with SARS-COV-2 3CLpro and ACE2, which are consistent with the above analysis.

The important herbal pair for the treatment of COVID-19 and its possible mechanisms

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10.1101/2021.02.14.431129

ALG-097111 potently inhibited SARS-CoV-2 3CLpro (IC50 = 7 nM) without affecting the activity of human cathepsin L (IC50 > 10 μM).

ALG-097111, a potent and selective SARS-CoV-2 3-chymotrypsin-like cysteine protease inhibitor exhibits in vivo efficacy in a Syrian Hamster model

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10.1038/s41467-021-22362-2

We report the identification of three structurally diverse compounds – compound 4, GC376, and MAC-5576 – as inhibitors of the SARS-CoV-2 3CL protease.

Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors

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10.33774/CHEMRXIV-2021-TNDBS

We present a detailed analysis of the binding mode and reactivity of the novel oral inhibitor PF-07321332 developed against SARS-CoV-2 3CL protease.

Binding and Reactivity of a Nitrile Oral Inhibitor of SARS-CoV-2 Main Protease Revealed by Computational Simulations

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10.1021/acs.jmedchem.1c00665

We report peptidomimetic compounds with a unique benzothiazolyl ketone as a warhead group, which display potent activity against SARS-CoV-2 3CLpro.

3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.

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10.3390/molecules26040797

Taken together, the performed simulations allowed the rational development of highly performing virtual screening workflows, which could be further optimized by considering different 3CL-Pro structures and, more importantly, by including true SARS-CoV-2 3CL-Pro inhibitors (as learning set) when available.

Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease

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10.1177/24725552211023211

The ligands identified by SAMDI-ASMS were further validated using differential scanning fluorimetry (DSF) and in functional protease assays against HRV3C and the related SARS-CoV-2 3CLpro enzyme.

High-Throughput Affinity Selection Mass Spectrometry Using SAMDI-MS to Identify Small-Molecule Binders of the Human Rhinovirus 3C Protease

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10.1002/cmdc.202100576

The SARS-CoV-2 3CL protease (3CLpro) is deemed an attractive drug target as it plays an essential role in viral polyprotein processing and pathogenesis, although no inhibitors have been approved.

A patent review on SARS coronavirus main protease (3CLpro) inhibitors.

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10.3389/fphar.2021.619373

Kaempferol 6) exhibited the highest fitting towards β-lactamase, SARS-CoV-2PLpro, and SARS-CoV-2 3CLpro active sites.

Phytoconstituents, In Vitro Anti-Infective Activity of Buddleja indica Lam., and In Silico Evaluation of its SARS-CoV-2 Inhibitory Potential

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10.21203/RS.3.RS-314304/V2

Moreover, kaempferol-3-o-gentiobioside, vicenin-2 and isoschaftoside were first reported to have SARS-CoV-2 3CLpro inhibitory activity.

An Integrated Method For Optimized Identification of Effective Natural Inhibitors Against SARS-CoV-2 3CLpro

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10.1016/j.molstruc.2021.130506

The results confirmed that Marchantin E could inhibit SARS-CoV-2 3CLpro and RBD of SGP as well as reveals excellent pharmacokinetic properties.

Screening of cryptogamic secondary metabolites as putative inhibitors of SARS-CoV-2 main protease and ribosomal binding domain of spike glycoprotein by molecular docking and molecular dynamics approaches

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10.1016/j.compbiomed.2021.104671

Among these, six compounds (neoandrographolide, vernolide, isorhamnetin, chicoric acid, luteolin, and myricetin) exhibited the highest binding tendencies to the equilibrated conformers of SARS-CoV-2 3CLpro in an in-depth docking analysis to 5 different representative conformations from the cluster analysis of the molecular dynamics simulation (MDS) trajectories of the protein.

Structure-based virtual screening suggests inhibitors of 3-Chymotrypsin-Like Protease of SARS-CoV-2 from Vernonia amygdalina and Occinum gratissimum

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10.1007/978-3-030-75275-0_99

Our results point out that scopoletin has a potential to bind to and inhibit the SARS-CoV-2 3Clpro main protease similarly to hydroxychloroquine that have been proven as antiviral in previous preclinical and clinical studies.

In Silico Analysis of Scopoletin Interaction with Potential SARS-CoV-2 Target

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10.1021/acsomega.1c01797

The inhibitory effect of dalcetrapib on the SARS-CoV-2 3CL protease and viral replication warrants its clinical evaluation for the treatment of COVID-19.

Inhibition of the 3CL Protease and SARS-CoV-2 Replication by Dalcetrapib

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10.19193/0393-6384_2021_4_307

Molecular docking was performed based on the hub compounds and hub target genes and the SARS-CoV-2 3CL hydrolase (SARS-CoV-2 3CLpro) and angiotensin converting enzyme II (ACE2), respectively.

Study on mechanism of fangyi qingfei decoction against Covid-19 associated lung and kidney injury based on network pharmacology and molecular docking

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10.1016/j.molliq.2020.114999

In this work, the structural and dynamic behaviors as well as binding efficiency of the four peptidomimetic inhibitors (N3, 11a, 13b, and 14b) recently co-crystalized with SARS-CoV-2 3CLpro were studied and compared using all-atom molecular dynamics (MD) simulations and solvated interaction energy-based binding free energy calculations.

Computational study on peptidomimetic inhibitors against SARS-CoV-2 main protease

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10.7717/peerj.11261

This study employed a comprehensive computational approach to screen inhibitors for SARS-CoV-2 3CL-PRO (also known as the main protease), a prime molecular target to treat coronavirus diseases.

Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation

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10.29219/FNR.V65.5623

Background: Coronavirus disease 2019 (COVID-19) outbreak is progressing rapidly, and poses significant threats to public health A number of clinical practice results showed that traditional Chinese medicine (TCM) plays a significant role for COVID-19 treatment Objective: To explore the active components and molecular mechanism of semen armeniacae amarum treating COVID-19 by network pharmacology and molecular docking technology Methods: The active components and potential targets of semen armeniacae amarum were retrieved from traditional Chinese medicine systems pharmacology (TCMSP) database Coronavirus disease 2019-associated targets were collected in the GeneCards, TTD, OMIM and PubChem database Compound target, compound-target pathway and medicine-ingredient-target disease networks were constructed by Cytoscape 3 8 0 Protein-protein interaction (PPI) networks were drawn using the STRING database and Cytoscape 3 8 0 software David database was used for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis The main active components were verified by AutoDock Vina 1 1 2 software A lipopolysaccharide (LPS)-induced lung inflammation model in Institute of Cancer Research (ICR) mice was constructed and treated with amygdalin to confirm effects of amygdalin on lung inflammation and its underlying mechanisms by western blot analyses and immunofluorescence Results: The network analysis revealed that nine key, active components regulated eight targets (Protooncogene tyrosine-protein kinase SRC (SRC), interleukin 6 (IL6), mitogen-activated protein kinase 1 (MAPK1), mitogen-activated protein kinase 3 (MAPK3), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), HRAS proto-oncogene (HRAS), caspase-3 (CASP3)) Gene ontology and KEGG enrichment analysis suggested that semen armeniacae amarum plays a role in COVID-19 by modulating 94 biological processes, 13 molecular functions, 15 cellular components and 80 potential pathways Molecular docking indicated that amygdalin had better binding activity to key targets such as IL6, SRC, MAPK3, SARS coronavirus-2 3C-like protease (SARS-CoV-2 3CLpro) and SARS-CoV-2 angiotensin converting enzyme II (ACE2) Experimental validation revealed that the lung pathological injury and inflammatory injury were significantly increased in the model group and were improved in the amygdalin group Conclusion: Amygdalin is a candidate compound for COVID-19 treatment by regulating IL6, SRC, MAPK1 EGFR and VEGFA to involve in PI3K-Akt signalling pathway, VEGF signalling pathway and MAPK signalling pathway Meanwhile, amygdalin has a strong affinity for SARS-CoV-2 3CLpro and SARS-CoV-2 ACE2 and therefore prevents the virus transcription and dissemination.

The mechanism and active compounds of semen armeniacae amarum treating coronavirus disease 2019 based on network pharmacology and molecular docking

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10.26434/CHEMRXIV.14781567.V1

We describe herein the results of our studies related to the application of X-ray crystallography, the Thorpe-Ingold effect, deuteration, and stereochemistry in the design of highly potent and non-toxic inhibitors of SARS-CoV-2 3CLpro to combat SARS-CoV-2 and emerging variants.

Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.

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10.1016/j.ijbiomac.2021.04.129

SARS-CoV-2 3CLpro is essential for processing the viral polyproteins into mature non-structural proteins, making it an attractive target for developing antiviral agents.

Identification of Vitamin K3 and its analogues as covalent inhibitors of SARS-CoV-2 3CLpro

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10.4314/tjpr.v20i6.21

With the aid of Discovery Studio 2016 software, bio-active components were selected to dock with SARS-COV-2 3CL and ACE2.

Identification of the anti-COVID-19 mechanism of action of Han-Shi Blocking Lung using network pharmacology-integrated molecular docking

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10.1016/j.bbadva.2021.100016

Furthermore, the structural differences between the predecessor SARS-CoV 3CLpro and SARS-CoV-2 3CLpro have not been fully understood.

Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water

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10.1016/j.compbiomed.2021.104538

Among these, some limonoids, namely deacetylnomilin, ichangin and nomilin, and the terpenoid β-amyrin provided good interaction energies with SARS-CoV-2 3CL hydrolase (Mpro) in molecular dynamic simulation.

Interaction of selected terpenoids with two SARS-CoV-2 key therapeutic targets: An in silico study through molecular docking and dynamics simulations

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10.1021/acs.jmedchem.1c00616

Compounds with potent SARS-CoV-2 3CL protease and in vitro viral replication inhibition were identified with low cytotoxicity and good plasma and glutathione stability.

Peptidomimetic α-Acyloxymethylketone Warheads with Six-Membered Lactam P1 Glutamine Mimic: SARS-CoV-2 3CL Protease Inhibition, Coronavirus Antiviral Activity, and in Vitro Biological Stability

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10.1039/d1cc03953a

We present a detailed computational analysis of the binding mode and reactivity of the novel oral inhibitor PF-07321332 developed against the SARS-CoV-2 3CL protease.

Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease.

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10.26434/chemrxiv.13087742.v2

Previously reported SARS-CoV 3CLpro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CLpro.

Design, Synthesis and Biological Evaluation of Novel SARS-CoV-2 3CLpro Covalent Inhibitors

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10.1038/s41392-021-00628-x

Recently, several SARS-CoV-2 3CL inhibitors were discovered by structural-based drug design and high-throughput screening.

Bardoxolone and bardoxolone methyl, two Nrf2 activators in clinical trials, inhibit SARS-CoV-2 replication and its 3C-like protease

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10.1107/S2052252521001159

Over 100 models of SARS-CoV-2 3CLpro, a major drug-design target for COVID-19, have been carefully validated and assembled in a dedicated database.

Crystallographic models of SARS-CoV-2 3CLpro: in-depth assessment of structure quality and validation

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10.1016/j.ijbiomac.2021.02.012

Multiple strategies were performed to screen potent inhibitors of SARS-CoV-2 3CLpro from the active ingredients of TCMs, including network pharmacology, molecular docking, surface plasmon resonance (SPR) binding assay and fluorescence resonance energy transfer (FRET)-based inhibition assay.

Epigallocatechin-3-gallate, an active ingredient of Traditional Chinese Medicines, inhibits the 3CLpro activity of SARS-CoV-2

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10.1007/s11030-021-10330-3

In the present work, 9101 drugs obtained from the drug bank database were screened against SARS-CoV-2 3CLpro prosing deep learning, molecular docking, and molecular dynamics simulation techniques.

Computational investigation of drug bank compounds against 3C-like protease (3CLpro) of SARS-CoV-2 using deep learning and molecular dynamics simulation

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10.2174/0929867328666210726094955

It also presents in silico studies performed on these selected natural products using SARS-CoV-2 3CLpro and PLpro as targets to propose a list of hit compounds.

Natural Products with tandem Anti-inflammatory, Immunomodulatory and Anti-SARS-CoV/2 effects: A Drug Discovery Perspective against SARS-CoV-2.

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10.1016/j.virol.2021.01.010

Here we describe a luminescence-based biosensor assay for evaluating small molecule inhibitors of SARS-CoV-2 3CLpro/main protease.

Detecting SARS-CoV-2 3CLpro expression and activity using a polyclonal antiserum and a luciferase-based biosensor

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10.1016/j.bbrc.2021.02.016

Recently, EGCG, a green tea polyphenol, was reported to inhibit SARS-CoV-2 3CL-protease, however the effect of EGCG on coronavirus replication is unknown.

EGCG, a green tea polyphenol, inhibits human coronavirus replication in vitro

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10.3390/foods10071503

Using a targeted approach, we identified 17 plant products that are included in current and traditional cuisines as promising inhibitors of SARS-CoV-2 3CLPro activity.

Potential In Vitro Inhibition of Selected Plant Extracts against SARS-CoV-2 Chymotripsin-Like Protease (3CLPro) Activity

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10.1021/acs.jmedchem.1c00598

X-ray structures of SARS-CoV-1 and SARS-CoV-2 3CLpro enzymes in complex with multiple ML300-based inhibitors, including the original probe ML300, were obtained and proved instrumental in guiding chemistry toward probe compound 41 (CCF0058981).

Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CLpro)

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10.1016/j.coviro.2021.04.006

Here we review first-generation SARS-CoV-2 3CLpro inhibitors PF-07304814, GC-376, and CDI-45205 that are being delivered either by injection or inhalation due to their low intrinsic oral bioavailability.

Considerations for the discovery and development of 3-chymotrypsin-like cysteine protease inhibitors targeting SARS-CoV-2 infection

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10.1080/07391102.2021.1927845

The SARS-CoV-2 3CL protease (3CLpro) shows a high similarity with 3CL proteases of other beta-coronaviruses, such as SARS and MERS.

Proposition of a new allosteric binding site for potential SARS-CoV-2 3CL protease inhibitors by utilizing molecular dynamics simulations and ensemble docking

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10.1101/2021.08.29.458083

The T285A mutation from SARS-CoV 3CLpro to SARS-CoV-2 3CLpro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CLpro seems to have increased activity relative to that of SARS-CoV 3CLpro.

Allosteric regulation of 3CL protease of SARS-CoV-2 and SARS-CoV observed in the crystal structure ensemble

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10.1080/07391102.2021.1871863

MD simulation of morin with SARS-CoV-2 3CLPro and PLPro displayed strong stability at 300 K.

Flavonol morin targets host ACE2, IMP-α, PARP-1 and viral proteins of SARS-CoV-2, SARS-CoV and MERS-CoV critical for infection and survival: a computational analysis

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10.3390/v13081669

Herein, we developed high throughput screening for SARS-CoV-2 3CLpro inhibitor based on AlphaScreen.

All-Trans Retinoic Acid Exhibits Antiviral Effect against SARS-CoV-2 by Inhibiting 3CLpro Activity

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10.3389/fmolb.2021.661424

In this work, a computational docking approach was developed to identify potential small-molecule inhibitors for SARS-CoV-2 3CLpro.

An Integrated Computational and Experimental Approach to Identifying Inhibitors for SARS-CoV-2 3CL Protease

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10.2174/1573406417666210806154129

The interactions of some compounds with SARS-CoV-2 3CLprotease or RNA-dependent RNA polymerase were described using 2D protein-ligand interaction diagrams based on known crystal structures.

Structural bioinformatics used to predict the protein targets of remdesivir and flavones in SARS-CoV-2 infection.

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10.3390/ijms221910693

The hit compounds were subsequently docked into the active site and molecular docking analyses revealed that both drugs can bind the active site of SARS-CoV-2 3CLpro, PLpro, NSP15, COX-2 and PLA2 targets with a number of important binding interactions.

Tomatidine and Patchouli Alcohol as Inhibitors of SARS-CoV-2 Enzymes (3CLpro, PLpro and NSP15) by Molecular Docking and Molecular Dynamics Simulations

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10.3390/v13020173

To address these limitations, we have developed a novel cell-based luciferase complementation reporter assay to identify inhibitors of SARS-CoV-2 3CLpro in a BSL-2 setting.

Development of a Cell-Based Luciferase Complementation Assay for Identification of SARS-CoV-2 3CLpro Inhibitors

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10.1016/j.bmcl.2021.128263

The SARS-CoV-2 3CL protease (3CLpro) is deemed an attractive drug target due to its essential role in viral polyprotein processing and pathogenesis.

A head-to-head comparison of the inhibitory activities of 15 peptidomimetic SARS-CoV-2 3CLpro inhibitors

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10.1016/j.jbi.2021.103821

The purpose of this study was to explore various ML approaches for molecular property prediction and illustrate their utility for identifying potential SARS-CoV-2 3CLpro inhibitors.

Machine learning enabled identification of potential SARS-CoV-2 3CLpro inhibitors based on fixed molecular fingerprints and Graph-CNN neural representations☆

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10.1016/j.bbrc.2021.03.096

ALG-097111 potently inhibited SARS-CoV-2 3CLpro (IC50 = 7 nM) without affecting the activity of human cathepsin L (IC50 > 10 μM).

ALG-097111, a potent and selective SARS-CoV-2 3-chymotrypsin-like cysteine protease inhibitor exhibits in vivo efficacy in a Syrian Hamster model

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10.3389/fphar.2021.720018

Importantly, UJ has a distinct inhibitory activity against SARS-CoV-2 3CLpro, compared to luteolin, kaempferol, and isokaempferide.

Ugonin J Acts as a SARS-CoV-2 3C-like Protease Inhibitor and Exhibits Anti-inflammatory Properties

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10.1016/j.antiviral.2021.105020

We previously reported the evaluation of SARS-CoV-2 3CLpro inhibitors in a novel self-assembled monolayer desorption ionization mass spectrometry (SAMDI-MS) enzymatic assay (Gurard-Levin, Liu et al.

Dual inhibition of SARS-CoV-2 and human rhinovirus with protease inhibitors in clinical development

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10.3390/molecules26195782

We report the design and synthesis of a series of new 5-chloropyridinyl esters of salicylic acid, ibuprofen, indomethacin, and related aromatic carboxylic acids for evaluation against SARS-CoV-2 3CL protease enzyme.

Chloropyridinyl Esters of Nonsteroidal Anti-Inflammatory Agents and Related Derivatives as Potent SARS-CoV-2 3CL Protease Inhibitors

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10.3390/biomedicines9040375

The overall results have implications in the drug-design of quercetin analogs, and possibly other antivirals, to target the catalytic site of the SARS-CoV-2 3CLpro.

Rutin Is a Low Micromolar Inhibitor of SARS-CoV-2 Main Protease 3CLpro: Implications for Drug Design of Quercetin Analogs

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10.1021/acs.jcim.1c00994

Thus, the results demonstrate a synergistic mechanism between the two compounds that enhances the inhibition activity against SARS-CoV-2 3CL protease.

Synergistic Effects of Natural Compounds Toward Inhibition of SARS-CoV-2 3CL Protease.

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10.2174/1389201022666210604150041

OBJECTIVE In the present study, a chemical library was screened for molecules against three coronavirus 3CL-like protease enzymes (SARS-CoV-2 3CLpro, SARS-CoV 3CLpro and MERS-CoV 3CLpro), which are a key player in the viral replication cycle.

Identification of novel drug candidates for the inhibition of catalytic cleavage activity of coronavirus 3CL-like protease enzyme.

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10.3390/pr9061004

The SARS-CoV-2 3CL main protease (Mpro) is one of the most attractive targets in the virus life cycle, which is responsible for the processing of the viral polyprotein and is a key for the ribosomal translation of the SARS-CoV-2 genome.

Toward the Identification of Potential α-Ketoamide Covalent Inhibitors for SARS-CoV-2 Main Protease: Fragment-Based Drug Design and MM-PBSA Calculations

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10.1101/2021.03.19.435806

Here, we used high-throughput docking to screen 6000 compounds within the DrugBank library for their potential to bind and inhibit the SARS-CoV-2 3CL main protease, a chymotrypsin-like enzyme that is essential for viral replication.

Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir

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10.1016/j.fitote.2021.104909

This study aims to discover the naturally occurring SARS-CoV-2 3CLpro inhibitors from herbal constituents, as well as to investigate the inhibitory mechanism of the newly identified efficacious SARS-CoV-2 3CLpro inhibitors.

Discovery of naturally occurring inhibitors against SARS-CoV-2 3CLpro from Ginkgo biloba leaves via large-scale screening

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10.1016/j.ijbiomac.2021.07.167

Among all isolated flavonoids, dihydromyricetin, isodihydromyricetin and myricetin strongly inhibited SARS-CoV-2 3CLpro in a time-dependent manner.

Flavonoids in Ampelopsis grossedentata as covalent inhibitors of SARS-CoV-2 3CLpro: Inhibition potentials, covalent binding sites and inhibitory mechanisms

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10.1016/j.chemolab.2021.104421

Surprisingly, the two compounds 4b and 4c showed the highest binding scores against SARS-CoV-2 3CLpro (-8.

Anti-COVID-19 activity of some benzofused 1,2,3-triazolesulfonamide hybrids using in silico and in vitro analyses

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10.2217/fca-2020-0201

However, this was not the only mechanism involved in the pathogenesis of the novel coronavirus, as further investigations suggested the potential role of SARS-CoV-2 3CLpro in the instigation of COVID-19 [5].

Targeting the SARS-CoV-2 3CLpro and NO/cGMP/PDE5 pathway in COVID-19: a commentary on PDE5 inhibitors

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10.4155/fmc-2020-0248

Background: The SARS-CoV-2 3CLpro is one of the primary targets for designing new and repurposing known drugs.

Can natural products stop the SARS-CoV-2 virus? A docking and molecular dynamics study of a natural product database

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10.1021/acscatal.0c05522

We here investigate the mechanism of SARS-CoV-2 3CL protease inhibition by one of the most promising families of inhibitors, those containing an aldehyde group as a warhead.

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism

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10.1080/14756366.2020.1850710

Given the well-studied properties of FDA-approved drugs, identification of SARS-CoV-2 3CLpro inhibitors in an FDA-approved drug library would be of great therapeutic value.

Repurposing existing drugs: identification of SARS-CoV-2 3C-like protease inhibitors

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10.21203/RS.3.RS-383586/V1

Based on this information and due to the high sequence identity between SARS-CoV and SARS-CoV-2 3CLpro, these three compounds could be candidate inhibitors of SARS-CoV-2 3CLpro.

Elucidation of the inhibitory activity of plant-derived SARS-CoV inhibitors and their potential as SARS-CoV-2 inhibitors

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10.1080/07391102.2021.1938234

Based on this information and due to the high sequence identity between SARS-CoV and SARS-CoV-2 3CLpro, these three compounds could be candidate inhibitors of SARS-CoV-2 3CLpro.

Elucidation of the inhibitory activity of plant-derived SARS-CoV inhibitors and their potential as SARS-CoV-2 inhibitors.

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10.1016/j.jmb.2021.167324

The T285A mutation from SARS-CoV 3CLpro to SARS-CoV-2 3CLpro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CLpro seems to have increased activity relative to that of SARS-CoV 3CLpro.

Allosteric regulation of 3CL protease of SARS-CoV-2 and SARS-CoV observed in the crystal structure ensemble

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10.1080/1062936X.2021.1914721

In this article, 70 diverse chemicals having experimental SARS-CoV-2 3CLproinhibitory activity were accounted for robust classification-based QSAR analysis statistically validated with 4 different methodologies to recognize the crucial structural features responsible for imparting the activity.

Robust classification-based molecular modelling of diverse chemical entities as potential SARS-CoV-2 3CLpro inhibitors: theoretical justification in light of experimental evidences

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10.1016/j.bbrc.2020.12.106

Therefore, developing an effective SARS-CoV-2 3CLpro inhibitor to treat COVID-19 is imperative.

The inhibitory effects of PGG and EGCG against the SARS-CoV-2 3C-like protease

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10.3390/v13050873

Surface plasmon resonance (SPR) experiments demonstrated that quinacrine and suramin alone possessed a moderate or weak affinity with SARS-CoV-2 3CLpro but suramin binding increased quinacrine interaction by around a factor of eight.

The Repurposed Drugs Suramin and Quinacrine Cooperatively Inhibit SARS-CoV-2 3CLpro In Vitro

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10.1021/acsptsci.0c00216

A subset of eight inhibitors showed anticytopathic effect in a Vero-E6 cell line, and the compounds thioguanosine and MG-132 were analyzed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro.

Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen

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10.1111/jfbc.13707

The molecular docking binding energies of the six index components of SARS-CoV-2 3Clpro were all less than -5.

Study on the mechanism of active components of Liupao tea on 3CLpro based on HPLC-DAD fingerprint and molecular docking technique.

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10.1002/anie.202110027

We present the results of classical and QM/MM simulations for the inhibition of SARS-CoV-2 3CL protease by a hydroxymethylketone inhibitor, PF-00835231.

Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations. Insights for Improved Designs.

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Sars Cov 2 3cl - Compound 1 exhibited a SARS-CoV-2 3CLpro inhibitory IC50 value of 250 nM and an antiviral EC50 value of 2. [1] baicalensis and its major component, baicalein, inhibit SARS-CoV-2 3CLpro activity in vitro with IC50’s of 8. [2] Our study gives an explanation of the structure activity relationship required for targeting SARS-CoV-2 3CLpro and Spike proteins and also facilitates the future design and synthesis of new potential drugs exhibiting better affinity and specificity. [3] The biosensors were constructed by linking a green fluorescent protein (GFP2) to the N-terminus and a Renilla luciferase (RLuc8) to the C-terminus of SARS-CoV-2 3CLpro, with the linkers derived from the cleavage sequences of 3CLpro. [4] A series of non-deuterated and deuterated dipeptidyl aldehyde and masked aldehyde inhibitors that incorporate in their structure a conformationally-constrained cyclohexane moiety was synthesized and found to potently inhibit SARS-CoV-2 3CL protease in biochemical and cell-based assays. [5] Here we describe the discovery of myricetin, a flavonoid found in many food sources, as a non-peptidomimetic and covalent inhibitor of the SARS-CoV-2 3CLpro. [6] Further characterization on the single isolated compound by NMR showed that 6 was identified and possessed 75% inhibitory activity on SARS-CoV-2 3CL protease enzyme that was slightly different with the positive control GC376 (77%). [7] We explore the interaction between the newly designed molecule and SARS-CoV-2 3CLpro by molecular docking. [8] Coronaviruses require the SARS-CoV-2 3CL-Protease (3CL-protease) for cleavage of its polyprotein to yield a single useful protein and assume a basic role in the disease progression. [9] In this investigation, 293T cells were transfected with SARS-CoV-2 3CL and then infected with Sendai virus (SeV) to induce the RIG-I like receptor (RLR)-based immune pathway. [10] The molecular docking results showed that the main active ingredients of AE have good affinity with SARS-COV-2 3CLpro and ACE2, which are consistent with the above analysis. [11] ALG-097111 potently inhibited SARS-CoV-2 3CLpro (IC50 = 7 nM) without affecting the activity of human cathepsin L (IC50 > 10 μM). [12] We report the identification of three structurally diverse compounds – compound 4, GC376, and MAC-5576 – as inhibitors of the SARS-CoV-2 3CL protease. [13] We present a detailed analysis of the binding mode and reactivity of the novel oral inhibitor PF-07321332 developed against SARS-CoV-2 3CL protease. [14] We report peptidomimetic compounds with a unique benzothiazolyl ketone as a warhead group, which display potent activity against SARS-CoV-2 3CLpro. [15] Taken together, the performed simulations allowed the rational development of highly performing virtual screening workflows, which could be further optimized by considering different 3CL-Pro structures and, more importantly, by including true SARS-CoV-2 3CL-Pro inhibitors (as learning set) when available. [16] The ligands identified by SAMDI-ASMS were further validated using differential scanning fluorimetry (DSF) and in functional protease assays against HRV3C and the related SARS-CoV-2 3CLpro enzyme. [17] The SARS-CoV-2 3CL protease (3CLpro) is deemed an attractive drug target as it plays an essential role in viral polyprotein processing and pathogenesis, although no inhibitors have been approved. [18] Kaempferol 6) exhibited the highest fitting towards β-lactamase, SARS-CoV-2PLpro, and SARS-CoV-2 3CLpro active sites. [19] Moreover, kaempferol-3-o-gentiobioside, vicenin-2 and isoschaftoside were first reported to have SARS-CoV-2 3CLpro inhibitory activity. [20] The results confirmed that Marchantin E could inhibit SARS-CoV-2 3CLpro and RBD of SGP as well as reveals excellent pharmacokinetic properties. [21] Among these, six compounds (neoandrographolide, vernolide, isorhamnetin, chicoric acid, luteolin, and myricetin) exhibited the highest binding tendencies to the equilibrated conformers of SARS-CoV-2 3CLpro in an in-depth docking analysis to 5 different representative conformations from the cluster analysis of the molecular dynamics simulation (MDS) trajectories of the protein. [22] Our results point out that scopoletin has a potential to bind to and inhibit the SARS-CoV-2 3Clpro main protease similarly to hydroxychloroquine that have been proven as antiviral in previous preclinical and clinical studies. [23] The inhibitory effect of dalcetrapib on the SARS-CoV-2 3CL protease and viral replication warrants its clinical evaluation for the treatment of COVID-19. [24] Molecular docking was performed based on the hub compounds and hub target genes and the SARS-CoV-2 3CL hydrolase (SARS-CoV-2 3CLpro) and angiotensin converting enzyme II (ACE2), respectively. [25] In this work, the structural and dynamic behaviors as well as binding efficiency of the four peptidomimetic inhibitors (N3, 11a, 13b, and 14b) recently co-crystalized with SARS-CoV-2 3CLpro were studied and compared using all-atom molecular dynamics (MD) simulations and solvated interaction energy-based binding free energy calculations. [26] This study employed a comprehensive computational approach to screen inhibitors for SARS-CoV-2 3CL-PRO (also known as the main protease), a prime molecular target to treat coronavirus diseases. [27] Background: Coronavirus disease 2019 (COVID-19) outbreak is progressing rapidly, and poses significant threats to public health A number of clinical practice results showed that traditional Chinese medicine (TCM) plays a significant role for COVID-19 treatment Objective: To explore the active components and molecular mechanism of semen armeniacae amarum treating COVID-19 by network pharmacology and molecular docking technology Methods: The active components and potential targets of semen armeniacae amarum were retrieved from traditional Chinese medicine systems pharmacology (TCMSP) database Coronavirus disease 2019-associated targets were collected in the GeneCards, TTD, OMIM and PubChem database Compound target, compound-target pathway and medicine-ingredient-target disease networks were constructed by Cytoscape 3 8 0 Protein-protein interaction (PPI) networks were drawn using the STRING database and Cytoscape 3 8 0 software David database was used for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis The main active components were verified by AutoDock Vina 1 1 2 software A lipopolysaccharide (LPS)-induced lung inflammation model in Institute of Cancer Research (ICR) mice was constructed and treated with amygdalin to confirm effects of amygdalin on lung inflammation and its underlying mechanisms by western blot analyses and immunofluorescence Results: The network analysis revealed that nine key, active components regulated eight targets (Protooncogene tyrosine-protein kinase SRC (SRC), interleukin 6 (IL6), mitogen-activated protein kinase 1 (MAPK1), mitogen-activated protein kinase 3 (MAPK3), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), HRAS proto-oncogene (HRAS), caspase-3 (CASP3)) Gene ontology and KEGG enrichment analysis suggested that semen armeniacae amarum plays a role in COVID-19 by modulating 94 biological processes, 13 molecular functions, 15 cellular components and 80 potential pathways Molecular docking indicated that amygdalin had better binding activity to key targets such as IL6, SRC, MAPK3, SARS coronavirus-2 3C-like protease (SARS-CoV-2 3CLpro) and SARS-CoV-2 angiotensin converting enzyme II (ACE2) Experimental validation revealed that the lung pathological injury and inflammatory injury were significantly increased in the model group and were improved in the amygdalin group Conclusion: Amygdalin is a candidate compound for COVID-19 treatment by regulating IL6, SRC, MAPK1 EGFR and VEGFA to involve in PI3K-Akt signalling pathway, VEGF signalling pathway and MAPK signalling pathway Meanwhile, amygdalin has a strong affinity for SARS-CoV-2 3CLpro and SARS-CoV-2 ACE2 and therefore prevents the virus transcription and dissemination. [28] We describe herein the results of our studies related to the application of X-ray crystallography, the Thorpe-Ingold effect, deuteration, and stereochemistry in the design of highly potent and non-toxic inhibitors of SARS-CoV-2 3CLpro to combat SARS-CoV-2 and emerging variants. [29] SARS-CoV-2 3CLpro is essential for processing the viral polyproteins into mature non-structural proteins, making it an attractive target for developing antiviral agents. [30] With the aid of Discovery Studio 2016 software, bio-active components were selected to dock with SARS-COV-2 3CL and ACE2. [31] Furthermore, the structural differences between the predecessor SARS-CoV 3CLpro and SARS-CoV-2 3CLpro have not been fully understood. [32] Among these, some limonoids, namely deacetylnomilin, ichangin and nomilin, and the terpenoid β-amyrin provided good interaction energies with SARS-CoV-2 3CL hydrolase (Mpro) in molecular dynamic simulation. [33] Compounds with potent SARS-CoV-2 3CL protease and in vitro viral replication inhibition were identified with low cytotoxicity and good plasma and glutathione stability. [34] We present a detailed computational analysis of the binding mode and reactivity of the novel oral inhibitor PF-07321332 developed against the SARS-CoV-2 3CL protease. [35] Previously reported SARS-CoV 3CLpro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CLpro. [36] Recently, several SARS-CoV-2 3CL inhibitors were discovered by structural-based drug design and high-throughput screening. [37] Over 100 models of SARS-CoV-2 3CLpro, a major drug-design target for COVID-19, have been carefully validated and assembled in a dedicated database. [38] Multiple strategies were performed to screen potent inhibitors of SARS-CoV-2 3CLpro from the active ingredients of TCMs, including network pharmacology, molecular docking, surface plasmon resonance (SPR) binding assay and fluorescence resonance energy transfer (FRET)-based inhibition assay. [39] In the present work, 9101 drugs obtained from the drug bank database were screened against SARS-CoV-2 3CLpro prosing deep learning, molecular docking, and molecular dynamics simulation techniques. [40] It also presents in silico studies performed on these selected natural products using SARS-CoV-2 3CLpro and PLpro as targets to propose a list of hit compounds. [41] Here we describe a luminescence-based biosensor assay for evaluating small molecule inhibitors of SARS-CoV-2 3CLpro/main protease. [42] Recently, EGCG, a green tea polyphenol, was reported to inhibit SARS-CoV-2 3CL-protease, however the effect of EGCG on coronavirus replication is unknown. [43] Using a targeted approach, we identified 17 plant products that are included in current and traditional cuisines as promising inhibitors of SARS-CoV-2 3CLPro activity. [44] X-ray structures of SARS-CoV-1 and SARS-CoV-2 3CLpro enzymes in complex with multiple ML300-based inhibitors, including the original probe ML300, were obtained and proved instrumental in guiding chemistry toward probe compound 41 (CCF0058981). [45] Here we review first-generation SARS-CoV-2 3CLpro inhibitors PF-07304814, GC-376, and CDI-45205 that are being delivered either by injection or inhalation due to their low intrinsic oral bioavailability. [46] The SARS-CoV-2 3CL protease (3CLpro) shows a high similarity with 3CL proteases of other beta-coronaviruses, such as SARS and MERS. [47] The T285A mutation from SARS-CoV 3CLpro to SARS-CoV-2 3CLpro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CLpro seems to have increased activity relative to that of SARS-CoV 3CLpro. [48] MD simulation of morin with SARS-CoV-2 3CLPro and PLPro displayed strong stability at 300 K. [49] Herein, we developed high throughput screening for SARS-CoV-2 3CLpro inhibitor based on AlphaScreen. [50]

semen armeniacae amarum

Background: Coronavirus disease 2019 (COVID-19) outbreak is progressing rapidly, and poses significant threats to public health A number of clinical practice results showed that traditional Chinese medicine (TCM) plays a significant role for COVID-19 treatment Objective: To explore the active components and molecular mechanism of semen armeniacae amarum treating COVID-19 by network pharmacology and molecular docking technology Methods: The active components and potential targets of semen armeniacae amarum were retrieved from traditional Chinese medicine systems pharmacology (TCMSP) database Coronavirus disease 2019-associated targets were collected in the GeneCards, TTD, OMIM and PubChem database Compound target, compound-target pathway and medicine-ingredient-target disease networks were constructed by Cytoscape 3 8 0 Protein-protein interaction (PPI) networks were drawn using the STRING database and Cytoscape 3 8 0 software David database was used for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis The main active components were verified by AutoDock Vina 1 1 2 software A lipopolysaccharide (LPS)-induced lung inflammation model in Institute of Cancer Research (ICR) mice was constructed and treated with amygdalin to confirm effects of amygdalin on lung inflammation and its underlying mechanisms by western blot analyses and immunofluorescence Results: The network analysis revealed that nine key, active components regulated eight targets (Protooncogene tyrosine-protein kinase SRC (SRC), interleukin 6 (IL6), mitogen-activated protein kinase 1 (MAPK1), mitogen-activated protein kinase 3 (MAPK3), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), HRAS proto-oncogene (HRAS), caspase-3 (CASP3)) Gene ontology and KEGG enrichment analysis suggested that semen armeniacae amarum plays a role in COVID-19 by modulating 94 biological processes, 13 molecular functions, 15 cellular components and 80 potential pathways Molecular docking indicated that amygdalin had better binding activity to key targets such as IL6, SRC, MAPK3, SARS coronavirus-2 3C-like protease (SARS-CoV-2 3CLpro) and SARS-CoV-2 angiotensin converting enzyme II (ACE2) Experimental validation revealed that the lung pathological injury and inflammatory injury were significantly increased in the model group and were improved in the amygdalin group Conclusion: Amygdalin is a candidate compound for COVID-19 treatment by regulating IL6, SRC, MAPK1 EGFR and VEGFA to involve in PI3K-Akt signalling pathway, VEGF signalling pathway and MAPK signalling pathway Meanwhile, amygdalin has a strong affinity for SARS-CoV-2 3CLpro and SARS-CoV-2 ACE2 and therefore prevents the virus transcription and dissemination. [1]