Considering epitopes conservity in targeting SARS-CoV-2 mutations in variants: a novel immunoinformatics approach to vaccine design DOI Creative Commons
Mohammad Aref Bagherzadeh, Mohammad Izadi, Kazem Baesi

et al.

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Aug. 18, 2022

Abstract Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has gained mutations at an alarming rate in the past years. Developing can increase virus's pathogenicity and virulence; reduce efficacy of vaccines, antibodies neutralization, even challenge adaptive immunity. So, it is essential to identify conserved epitopes (with fewer mutations) different variants with appropriate antigenicity target by vaccine design. Yet as, 3369 SARS-CoV-2 genomes were collected from global initiative on sharing avian flu data. Then, immunodominant regions (IDRs), immune epitope database (IEDB) epitopes, also predicted calculated. In following, conservity score against total number events (mutations) mutated sites each was weighted Shannon entropy then calculated Technique for Order Preference Similarity Ideal Solution (TOPSIS). Based TOPSIS score, plotted. The result demonstrates that almost all IDRs various lengths have numbers dissimilar sites. Herein, our two-step calculation recommends only 8 IDRs, 14 IEDB 10 among epitopes. selected ones higher immunogenicity. This method open-source multi-criteria decision-making platform, which provides a scientific approach selecting immunogenicity; ever-changing viruses.

Language: Английский

Single nucleotide polymorphisms located in TNFA, IL1RN, IL6R, and IL6 genes are associated with COVID‐19 risk and severity in an Iranian population DOI Open Access
Mohsen Rokni, Mohammad Sarhadi, Milad Heidari Nia

et al.

Cell Biology International, Journal Year: 2022, Volume and Issue: 46(7), P. 1109 - 1127

Published: May 6, 2022

Abstract Cytokines play pivotal functions in coronavirus disease 2019 (COVID‐19) pathogenesis. However, little is known about the rationale and importance of genetic variations associated with immune system responses, so‐called “immunogenetic profiling.” We studied whether polymorphisms IL6, IL6R, TNFA , IL1RN affect disorder severity outcome patients infected COVID19. recruited 317 hospitalized laboratory‐confirmed COVID‐19 from Bu‐Ali hospital high‐risk participants who had high exposure to but a negative real‐time‐polymerase chain reaction (PCR) test. Multiple regression analyses were applied. indicated that carrying A allele ‐rs361525, G>A ( p < .004), C IL1RN‐ rs419598 T>C IL6R ‐rs2228145, A>C = .047) are more susceptible develop COVID‐19. In contrast, those carry G IL6 ‐rs2069827, G>T .01), protected Also, we compared various genotypes regarding poor prognosis; found AA genotype related aggressive illness bad prognostic contrast other inflammatory cytokines' genotypes. addition, level indications, such as neutrophil‐to‐lymphocyte ratio systemic immune‐inflammation index, was observed deceased survived subjects .0001). advised considering cytokines main item realize therapeutic response against acute respiratory distress syndrome induced by SARS‐CoV‐2 virus.

Language: Английский

Citations

29
Comparative docking studies of drugs and phytocompounds for emerging variants of SARS-CoV-2 DOI Open Access
Ananya Chugh,

Ishita Sehgal,

Nimisha Khurana

et al.

3 Biotech, Journal Year: 2023, Volume and Issue: 13(1)

Published: Jan. 1, 2023

Language: Английский

Citations

17
Theaflavin 3-gallate inhibits the main protease (Mpro) of SARS-CoV-2 and reduces its count in vitro DOI Creative Commons

Mahima Chauhan,

Vijay Kumar Bhardwaj, Asheesh Kumar

et al.

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: July 30, 2022

Abstract The main protease (M pro ) of SARS-CoV-2 has been recognized as an attractive drug target because its central role in viral replication. Our previous preliminary molecular docking studies showed that theaflavin 3-gallate (a natural bioactive molecule derived from and found high abundance black tea) exhibited better scores than repurposed drugs (Atazanavir, Darunavir, Lopinavir). In this study, conventional steered MD-simulations analyses revealed stronger interactions with the active site residues M a standard GC373 known inhibitor novel broad-spectrum anti-viral agent). Theaflavin inhibited protein IC 50 value 18.48 ± 1.29 μM. Treatment (Indian/a3i clade/2020 isolate) 200 μM vitro using Vero cells quantifying transcripts demonstrated reduction count by 75% (viral particles reduced Log10 6.7 to 6.1 ). Overall, our findings suggest effectively targets thus limiting replication virus vitro.

Language: Английский

Citations

28
Potential anti-hyperglycemic activity of black tea theaflavins through inhibiting α-amylase DOI Creative Commons
Maiquan Li, Yunxia Dong,

Mangjun Kang

et al.

Food Chemistry X, Journal Year: 2024, Volume and Issue: 22, P. 101296 - 101296

Published: March 16, 2024

Hyperglycemia can cause early damage to cells of vasculature and target organs develop into diabates that will severely threaten human healthy. The effectively clinical treatment hyperglycemiais is by inhibiting the activity α-amylase. Black tea has been reported show inhibitory effect on α-amylase be used for hyperglycemia treatment. However, mechanism underlying unclear. In this study, in vivo experiment showed black theaflavins extract (BTE) alleviated hyperglycemia. vitro effects may caused interation between TF1 TF3 were mixed type inhibitors α-amylase, while TF2A TF2B competitive Molecular docking analysis monomers interacted with hydrophobic region Further study verified monomer-α-amylase complex was spontaneously formed depending interactions. Taken together, potential anti-hyperglycemia via activity. Our results suggested might utilized as a new inhibitor prevent cure

Language: Английский

Citations

5
In silico analysis of SARS-CoV-2 proteins as targets for clinically available drugs DOI Creative Commons
Wallace Chan, Keith M. Olson, Jesse W. Wotring

et al.

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: March 29, 2022

Abstract The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires treatments with rapid clinical translatability. Here we develop a multi-target and multi-ligand virtual screening method to identify FDA-approved drugs potential activity against SARS-CoV-2 at traditional understudied viral targets. 1,268 small molecule were docked 47 putative binding sites across 23 proteins. We compared between filtered out compounds that had no reported in an vitro screen infection of human liver (Huh-7) cells. This identified 17 “high-confidence”, 97 “medium-confidence” drug-site pairs. “high-confidence” group was subjected molecular dynamics simulations yield six stable poses their optimal target Three drugs—amprenavir, levomefolic acid, calcipotriol—were predicted bind 3 different on the spike protein, domperidone Mac1 domain non-structural protein (Nsp) 3, avanafil Nsp15, nintedanib nucleocapsid involved packaging RNA. Our “two-way” docking also provides framework prioritize for testing future emergencies requiring rapidly available and/or treating diseases where moderate number targets are known.

Language: Английский

Citations

22
Natural and Semi-Synthetic Flavonoid Anti-SARS-CoV-2 Agents for the Treatment of Long COVID-19 Disease and Neurodegenerative Disorders of Cognitive Decline DOI Creative Commons
James Melrose, Margaret M. Smith

Frontiers in Bioscience-Elite, Journal Year: 2022, Volume and Issue: 14(4), P. 27 - 27

Published: Oct. 9, 2022

The aim of this review is to highlight the beneficial attributes flavonoids, a diverse family widely-distributed polyphenolic phytochemicals that have cell and tissue protective properties. Phytochemicals are widely distributed in plants, herbs shrubs used traditional complimentary medical formulations for centuries. bioactive components convey medicinal effects these complex herbal preparations now being identified using network pharmacology molecular docking procedures identify their targets. Flavonoids anti-oxidant, anti-inflammatory, antiviral, antibacterial anti-cancer properties inspired development potent multifunctional derivatised flavonoids improved efficacy. antiviral emergence severe acute respiratory syndrome (SARS-CoV-2) pandemic has resulted resurgence interest search efficacious compounds can prevent viral infection or replication, with many promising plant identified. Promising semi-synthetic flavonoid derivatives also been developed inhibit multiple pathological neurodegenerative processes; offer considerable promise treatment diseases cognitive decline. Clinical trials currently undertaken evaluate efficacy dietary supplements rich virally-mediated diseases. Such expected be harnessed biomedical applications may serve as supportive adjunctive conventional anti-viral drug therapies against such COVID-19.

Language: Английский

Citations

19
Discovery of Camellia sinensis catechins as SARS-CoV-2 3CL protease inhibitors through molecular docking, intra and extra cellular assays DOI Open Access
Shiyu Liu, Wei Wang,

Jia-Ping Ke

et al.

Phytomedicine, Journal Year: 2021, Volume and Issue: 96, P. 153853 - 153853

Published: Nov. 8, 2021

Language: Английский

Citations

26
GC-MS profiling of Bauhinia variegata major phytoconstituents with computational identification of potential lead inhibitors of SARS-CoV-2 Mpro DOI
Pallavi More-Adate, Kiran Bharat Lokhande, K. Venkateswara Swamy

et al.

Computers in Biology and Medicine, Journal Year: 2022, Volume and Issue: 147, P. 105679 - 105679

Published: June 1, 2022

Language: Английский

Citations

17
6-Octadecenoic and Oleic Acid in Liquid Smoke Rice Husk Showed COVID-19 Inhibitor Properties DOI Creative Commons
Ira Arundina, Neni Frimayanti, Meircurius Dwi Condro Surboyo

et al.

Advances in Pharmacological and Pharmaceutical Sciences, Journal Year: 2024, Volume and Issue: 2024, P. 1 - 9

Published: April 25, 2024

In recent years, liquid smoke rice husk (LSRH) has shown its therapeutic potency to diabetes, wound healing, stomatitis, and periodontitis. The phenol, 6-octadecenoic acid, oleic 9-octadecanoic acid were responsible for their effect. LSRH also demonstrated potential infectious diseases such as coronavirus disease (COVID-19). Therefore, the molecular dynamics (MDs) simulation pharmacophore analysis was performed analyse binding stability of acid. Based on MD simulation, acids seemed retain interactions with Ser144 Thr24, respectively, hydrogen bond distance less than 2.9 Å. This interaction stable during hydrophobic bonds/acceptors. confirmed have great inhibitors COVID-19. These compounds showed that existence bonds/acceptors could increase biological activity.

Language: Английский

Citations

3
SARS‐CoV‐2 and influenza viruses: Strategies to cope with coinfection and bioinformatics perspective DOI
Habib Ghaznavi, Milad Shirvaliloo, Saman Sargazi

et al.

Cell Biology International, Journal Year: 2022, Volume and Issue: 46(7), P. 1009 - 1020

Published: March 24, 2022

Abstract Almost a century after the devastating pandemic of Spanish flu, humankind is facing relatively comparable global outbreak COVID‐19. COVID‐19 an infectious disease caused by SARS‐CoV‐2 with unprecedented transmission pattern. In face recent repercussions COVID‐19, many have argued that clinical experience influenza through last may tremendous implications in containment this newly emerged viral disease. During 2 years, from emergence advances been made diagnosing and treating coinfections. Several approved vaccines are available now for primary prevention specific treatments exist to alleviate symptoms. The present review article aims discuss pathophysiology, diagnosis, treatment A virus coinfection while delivering bioinformatics‐based insight into subject matter.

Language: Английский

Citations

16