Towards the discovery of molecules with anti-COVID-19 activity: Relationships between screening and docking results DOI Creative Commons
Dmytro Anokhin, Sergiy M. Kovalenko, Pavlo V. Trostianko

et al.

Kharkov University Bulletin Chemical Series, Journal Year: 2024, Volume and Issue: 42, P. 6 - 14

Published: June 21, 2024

The study presents the results of a combined approach to theoretical description potential antiviral activity against COVID-19. We found that pharmacophore screening based on limited experimental data "protein-ligand" binding complexes might have low predictive ability. Therefore, in this study, we build model statistical QSAR for obtained from docking which serves as basis adequate prediction ligand activity. use logistic regression construct main protease Mpro inhibitors.

Language: Английский

Nanoparticles of Natural Product-derived Medicines: Beyond the Pandemic DOI Creative Commons
Yedi Herdiana

Heliyon, Journal Year: 2025, Volume and Issue: 11(4), P. e42739 - e42739

Published: Feb. 1, 2025

This review explores the synergistic potential of natural products and nanotechnology for viral infections, highlighting key antiviral, immunomodulatory, antioxidant properties to combat pandemics caused by highly infectious viruses. These often result in severe public health crises, particularly affecting vulnerable populations due respiratory complications increased mortality rates. A cytokine storm is initiated when an overload pro-inflammatory cytokines chemokines released, leading a systemic inflammatory response. Viral mutations limited availability effective drugs, vaccines, therapies contribute continuous transmission virus. The coronavirus disease-19 (COVID-19) pandemic has sparked renewed interest product-derived antivirals. efficacy traditional medicines against infections examined. Their anti-inflammatory, are highlighted. discusses how enhances herbal combating infections.

Language: Английский

Citations

1
Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme DOI Creative Commons
Hamlet Khachatryan, Mher Matevosyan,

Vardan Harutyunyan

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: June 20, 2024

Abstract The coronavirus disease 19 pandemic, caused by severe acute respiratory syndrome 2 (SARS-CoV-2), has led to a global health crisis with millions of confirmed cases and related deaths. main protease (Mpro) SARS-CoV-2 is crucial for viral replication presents an attractive target drug development. Despite the approval some drugs, search effective treatments continues. In this study, we systematically evaluated 342 holo-crystal structures Mpro identify optimal conformations structure-based virtual screening (SBVS). Our analysis revealed limited structural flexibility among structures. Three docking programs, AutoDock Vina, rDock, Glide were employed assess efficiency screening, revealing diverse performances across selected We found that 5RHE, 7DDC, 7DPU (PDB Ids) consistently displayed lowest EF, AUC, BEDROCK scores. Furthermore, these demonstrated worst pose prediction results in all programs. Two differences contribute variations performance: absence S1 subsite 7DDC 7DPU, presence subpocket S2 5RHE. These findings underscore importance selecting appropriate SBVS, providing valuable insights advancing discovery efforts.

Language: Английский

Citations

6
Rerouting therapeutic peptides and unlocking their potential against SARS-CoV2 DOI

Namrata Prashar,

Sameer Khairullah MOHAMMED,

Raja Natesan Sella

et al.

3 Biotech, Journal Year: 2025, Volume and Issue: 15(5)

Published: April 4, 2025

Language: Английский

Citations

0
Thiophene-fused γ-lactams inhibit the SARS-CoV-2 main protease via reversible covalent acylation DOI Creative Commons

Gayatri Tehlan,

Lennart Brewitz, Lewis T. Ibbotson

et al.

Chemical Science, Journal Year: 2024, Volume and Issue: 15(20), P. 7667 - 7678

Published: Jan. 1, 2024

Thiophene-fused γ-lactams are reversible covalent inhibitors of the SARS-CoV-2 main protease, a nucleophilic cysteine enzyme. γ-Lactams can inhibit enzymes by S -acylation as well serine O -acylation.

Language: Английский

Citations

3
Critical assessment of popular biomolecular force fields for molecular dynamics simulations of folding and enzymatic activity of main protease of coronavirus SARS-CoV-2 DOI
Kateryna Lohachova, Alexander Kyrychenko, Oleg N. Kalugin

et al.

Biophysical Chemistry, Journal Year: 2024, Volume and Issue: 311, P. 107258 - 107258

Published: May 16, 2024

Language: Английский

Citations

2
Support Enzyme Loading Influences the Effect of Aldehyde Dextran Modification on the Specificity of Immobilized Ficin for Large Proteins DOI Creative Commons

El Hocine Siar,

Pedro Abellanas‐Perez, Javier Rocha‐Martín

et al.

Molecules, Journal Year: 2024, Volume and Issue: 29(15), P. 3674 - 3674

Published: Aug. 2, 2024

It has been reported that the modification of immobilized glyoxyl-ficin with aldehyde dextran can promote steric hindrances greatly reduce activity protease against hemoglobin, while still maintained a reasonable level casein. In this paper, we studied if effect may be different depending on amount ficin loaded support. For purpose, both moderately and overloaded biocatalysts were prepared modified dextran. While biocatalyst had significantly reduced activity, mainly was almost maintained. This suggests able to modify areas enzyme not available when overloaded. promoted significant increase in stability for biocatalysts, but higher (perhaps due combination inter- intramolecular crosslinking).

Language: Английский

Citations

1
Molecular evolutionary analysis of the SARS-CoV-2 through the mutation analysis of Spike, Envelope and RdRp proteins DOI Creative Commons
Dženita Omerkić Dautović,

Amra Džuho,

Adna Ašić

et al.

Genetics & Applications, Journal Year: 2024, Volume and Issue: 8(1)

Published: June 18, 2024

COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), was declared in 2020 World Health Organization. New mutations have been identified, leading to various variants of this virus, including Alpha, Beta, Gamma, Delta, and Omicron, which are classified as concern (VOCs) raised considerable concerns for global public health. Such constant spread changes genome virus require continuous monitoring. This research focuses on evolution SARS-CoV-2 through a detailed presentation viral genome, protein structure interpretation, with phylogenetic characteristics patterns. We obtained sequence data from European region focusing S, E, RdRp proteins publicly available NCBI database. next used MEGA11 package generate multiple alignments create trees. The SWISS-MODEL server connected Protein Data Bank tertiary images all presented paper. Stability studies were performed via MUpro online tool. results indicate substantial impact Omicron variant relative others, particularly concerning alterations observed spike (S) protein, is crucial infection process.

Language: Английский

Citations

0
Inhibition of SARS-CoV-2 3CLpro by chemically modified tyrosinase from Agaricus bisporus DOI Creative Commons

David Aguilera-Rodriguez,

David Ortega-Alarcón, Ángela Vázquez-Calvo

et al.

RSC Medicinal Chemistry, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

A novel antiviral and non-cytotoxic bioconjugate of tyrosinase from Agaricus bisporus (AbTyr)-dextran-aspartic acid (6 kDa) polymer is developed.

Language: Английский

Citations

0
Towards the computational design of organic molecules with specified properties DOI
Anton B. Zakharov, Mariia Kyrpa, Alexander Kyrychenko

et al.

Structural Chemistry, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 26, 2024

Language: Английский

Citations

0
Towards the discovery of molecules with anti-COVID-19 activity: Relationships between screening and docking results DOI Creative Commons
Dmytro Anokhin, Sergiy M. Kovalenko, Pavlo V. Trostianko

et al.

Kharkov University Bulletin Chemical Series, Journal Year: 2024, Volume and Issue: 42, P. 6 - 14

Published: June 21, 2024

The study presents the results of a combined approach to theoretical description potential antiviral activity against COVID-19. We found that pharmacophore screening based on limited experimental data "protein-ligand" binding complexes might have low predictive ability. Therefore, in this study, we build model statistical QSAR for obtained from docking which serves as basis adequate prediction ligand activity. use logistic regression construct main protease Mpro inhibitors.

Language: Английский

Citations

0