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Auto Summaries - Structure
Last updated: 2021 Sep 7
Total hit(s): 629
S.No.
1
34404957
Molecular docking and dynamic simulations of Cefixime, Etoposide and Nebrodenside A against the pathogenic proteins of SARS-CoV-2
Millions of people were infected and several hundred thousand died of the COVID-19 pandemic across the world. There is no clear targeted drug therapy available for the treatment of the patients. An instantly qualifying approach is needed to utilize the current drugs and isolated compounds. Promising results were obtained via complimentary analysis of molecular dynamics (MD) simulations performed for the complexes of three proteins with etoposide drug.
J Mol Struct
2022 Jan 5
2.19
1
2
34248201
Novel piperazine based compounds as potential inhibitors for SARS-CoV-2 Protease Enzyme: Synthesis and molecular docking study
Piperazine-based compounds hybrid with thiadiazole, isatin or with sulfur/nitrogen functionalities were synthesized. The structures of the new compounds were established based on their spectral data and elemental analysis. The present in silico study provided some guidance to facilitate drug design targeting the SARS-CoV-2 main protease.
J Mol Struct
2021 Dec 5
2.19
1
3
34305174
Seq12, Seq12m, and Seq13m, peptide analogues of the spike glycoprotein shows antiviral properties against SARS-CoV-2: An in silico study through molecular docking, molecular dynamics simulation, and MM-PB/GBSA calculations
SARS-CoV-2, the causative agent of COVID-19 acquiring mutations and circulating as new variants. Antiviral peptides can block the receptor-binding domain (RBD) which is necessary for communicating with the angiotensin-converting enzyme 2 (ACE2) These AVPs sustain their antiviral properties, even after the insertion of 25 mutations in the RBD (Rosetta and FoldX based)
J Mol Struct
2021 Dec 15
2.19
1
4
34305175
Targeting SARS-CoV-2 main protease by teicoplanin: A mechanistic insight by docking, MM/GBSA and molecular dynamics simulation
The main protease (M(Pro) is considered as an attractive drug target for rational drug design against SARS-CoV-2. Teicoplanin is a glycopeptide class of antibiotic which is regularly used for treating Gram-positive bacterial infections, has shown potential therapeutic efficacy against the disease in vitro.
J Mol Struct
2021 Dec 15
2.19
1
5
34077310
Identifying the molecular targets and mechanisms of xuebijing injection for the treatment of COVID-19 via network parmacology and molecular docking
Identify the potential molecular targets of the Xuebijing injection.Determine the therapeutic targets of the Xuebijing injection.Understand the role of AKT1 in the Xuebijing injection.
Bioengineered
2021 Dec
1
6
33685335
In silico identification of novel SARS-COV-2 2'-O-methyltransferase (nsp16) inhibitors: structure-based virtual screening, molecular dynamics simulation and MM-PBSA approaches
Learn about the potential nsp16 inhibitor.Understand that there are no vaccines or drugs available for COVID-19.
J Enzyme Inhib Med Chem
2021 Dec
1
7
33517789
Study on mechanism of matrine in treatment of COVID-19 combined with liver injury by network pharmacology and molecular docking technology
Analyze the pharmacological mechanism of matrine.Determine the therapeutic mechanism of matrine on COVID-19 combined with liver injury.
Drug Deliv
2021 Dec
1
8
34121768
Comparative analysis of non structural protein 1 of SARS-CoV2 with SARS-CoV1 and MERS-CoV: An in silico study
Understand that SARS-CoV2 nsp1 is found in all beta coronavirus.Understand that SARS-CoV2 nsp1 is found in all B-cell and T-cell epitopes.
J Mol Struct
2021 Nov 5
2.19
1
9
34031619
Chemical reactivities and molecular docking studies of parthenolide with the main protease of HEP-G2 and SARS-CoV-2
Use bioinformatics to identify drugs for COVID-19.Determine the epoxidation of Parthenolide 1 using peracids.Determine the chemoselectivity of the double bond C(3)[bond, double bond]C(4).
J Mol Struct
2021 Nov 5
2.19
1
10
34098482
Computational details of molecular structure, spectroscopic properties, topological studies and SARS-Cov-2 enzyme molecular docking simulation of substituted triazolo pyrimidine thione heterocycles
Analyze the molecular structure of the heterocyclic ligands.Determine the reactive nucleophilic and electrophilic sites.Use molecular docking simulation.
Spectrochim Acta A Mol Biomol Spectrosc
2021 Nov 15
2.99
1
11
34421325
Repurposing the inhibitors of COVID-19 key proteins through molecular docking approach
Trandolapril, Benazepril, and Moexipril were evaluated as the best non-carcinogenic and non-toxic potential inhibitors of spike glycoprotein, Mpro, and RdRp. The drugs showed significant binding affinities against the active sites of respective SARS_CoV-2 target proteins.
Process Biochem
2021 Nov
1
12
33989977
Tuning the Computational Evaluation of Spectroscopic, ELF, LOL, NCI analysis and Molecular Docking of Novel Anti COVID-19 Molecule 4-Dimethylamino Pyridinium 3, 5-Dichlorosalicylate
Analyze UV-vis, FT-IR, FT-Raman, 5-dichlorosalicylate and NMR spectra.Attribute vibrational spectra.Attribute the energy gap.Determine the bioactivity of the molecule.
Spectrochim Acta A Mol Biomol Spectrosc
2021 Oct 5
2.99
1
13
34287986
Identification of novel inhibitors of SARS-CoV-2 main protease (M(pro) ) from Withania sp. by molecular docking and molecular dynamics simulation
To date, no medicine is available for the responsible virus SARS-CoV-2. The study includes investigation, screening, and identification of potent leads from (Withania sps.), against SARS CoV 2. Seventy-three natural compounds from this important medicinal plant were screened. Compounds 27-hydroxywithanolide F (W32, -11.5 kcal/mol), withanolide A (W56) and withacoagulin H showed highest binding energy. Study also compared the bonding energy of already reported repurposed and newly synthesized drugs. Further, absorption, distribution, metabolism, and excretion predictions were made to found a good balance of potency.
J Comput Chem
2021 Oct 5
3.28
1
14
34421159
Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models
COVID-19 pandemic has accelerated the study of the potential of multi-target drugs (MTDs) The mixture of homologues called ivermectin has been shown to be a MTD with potential antiviral activity against SARS-CoV-2 in vitro.
J Mol Liq
2021 Oct 15
4.85
1
15
34312571
Identification of Food Compounds as inhibitors of SARS-CoV-2 main protease using molecular docking and molecular dynamics simulations
M(pro) (Main Protease) enzyme has been identified as essential proteins for the survival of SARS-CoV-2. At present, there is no drug available for this deadly disease. Lipinski's rules and molecular docking have been performed to identify plausible inhibitors using food compounds.
Chemometr Intell Lab Syst
2021 Oct 15
3.01
1
16
34054142
DFT, molecular docking and molecular dynamics simulation studies on some newly introduced natural products for their potential use against SARS-CoV-2
Learn about natural compounds.Learn about the role of SARS-CoV-2 main protease in COVID-19.Learn about DFT calculations.Learn about molecular dynamics simulations.Learn about ADME predictions and drug-likeness analyses.
J Mol Struct
2021 Oct 15
2.19
1
17
34276059
Multistep rational molecular design and combined docking for discovery of novel classes of inhibitors of SARS-CoV-2 main protease 3CLpro
The main protease (3CLpro) of SARS-CoV is a promising target for discovery of novel antiviral agents. New possible inhibitors of 3CLpro with high predicted binding affinity were detected through computer-aided molecular design and bioisosteric replacements.
Chem Phys Lett
2021 Oct
1.92
1
18
33903778
In search of RdRp and Mpro inhibitors against SARS CoV-2: Molecular docking, molecular dynamic simulations and ADMET analysis
Understand the risk factors of SARS CoV-2.Understand that SARS CoV-2 is a global pandemic.
J Mol Struct
2021 Sep 5
2.19
1
19
33903779
Synthesis, X-ray crystal structure, IR and Raman spectroscopic analysis, quantum chemical computational and molecular docking studies on hydrazone-pyridine compound: As an insight into the inhibitor capacity of main protease of SARS-CoV2
Analyze the CCPEHP structure in chloroform solvent.Determine the optimal geometry of CCPEHP.
J Mol Struct
2021 Sep 5
2.19
1
20
33967344
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
Identify the cryptogamic secondary metabolites as potent inhibitors of SARS-CoV-2.Determine the role of Marchantin E and Zeorin to inhibit SARS-CoV-2 3CL(pro) and RBD of SGP (PDB ID:6W41).Determine whether Marchantin E and Zeorin could inhibit SARS-CoV-2 3CL(pro) and RBD of SGP.
J Mol Struct
2021 Sep 15
2.19
1
21
34099985
In silico molecular docking analysis for repurposing approved antiviral drugs against SARS-CoV-2 main protease
Screen approved antiviral drugs against COVID-19.Use molecular docking analysis to determine the binding of Remdesivir and Mycophenolic acid acyl glucuronide with the protein drug target.
Biochem Biophys Rep
2021 Sep
1.65
1
22
34369638
Online bioinformatics teaching practice: Comparison of popular docking programs using SARS-CoV-2 spike RBD-ACE2 complex as a benchmark
Many bioinformatics textbooks at present mainly focus on theories, which hinders the vigorous development of scientific research. Five students used the RBD-ACE2 complex as a benchmark to conduct a systematic comparison of several open-source online molecular docking programs. Through docking and comparing predicted structures to the crystal structure, students gained the opportunity to practice different bioinformics tools independently and conduct research collaboratively.
Biochem Mol Biol Educ
2021 Aug 9
1.13
1
23
34384783
Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein
The T cell response directed towards SARS-CoV-2 spike protein-derived S(269-277) peptide presented by the HLA-A*02:01 allomorph is, to date, the most immunodominant epitope found in individuals bearing this allele. We show via surface plasmon resonance and tetramer studies that the TRAV12(+) T cell repertoire cross-reacts poorly with these analogous epitopes.
J Biol Chem
2021 Aug 9
3.96
1
24
34370631
Quantitative structure-activity relationships, molecular docking and molecular dynamics simulations reveal drug repurposing candidates as potent SARS-CoV-2 main protease inhibitors
The current outbreak of COVID-19 is leading an unprecedented scientific effort focusing on targeting SARS-CoV-2 proteins critical for its viral replication. Herein, we performed high-throughput virtual screening of more than eleven thousand FDA-approved drugs using backpropagation-based artificial neural networks. We simulated stability of Acarbose-derived hexasaccharide, Naratriptan, Peramivir, Dihydrostreptomycin, Enviomycin and Viomycin.
J Biomol Struct Dyn
2021 Aug 9
3.22
1
25
34365955
Structural bioinformatics used to predict the protein targets of remdesivir and flavones in SARS-CoV-2 infection
Researchers predict interactions between SARS-CoV-2 proteins and protein targets from the human body for some flavone molecules (kaempferol, morin, pectolinarin, myricitrin, and herbacetin) in comparison to synthetic compounds (hydroxychloroquine, remdesivir, ribavirin, ritonavir, AMD-070, favipiravir) Findings were based on various structural and functional features of compounds such as their amphiphilic field, flexibility, and steric features.
Med Chem
2021 Aug 6
1