Tag Archives: SARS-COV-2
Cathepsin inhibitors as potent inhibitors against SARS-CoV-2 main protease. In silico molecular screening and toxicity prediction
O. Sekiou1*, W. Kherfane2, M. Boumendjel3,
H. Cheniti4, A. Benselhoub1*, S. Bellucci5
1Environmental Research Center, Annaba, Algeria;
2Laboratory of Geodynamics and Natural Resources, Department of Hydraulics,
Badji Mokhtar Annaba University, Annaba, Algeria;
3Laboratory of Biochemistry and Environmental Toxicology,
Badji Mokhtar Annaba University, Algeria;
4National High School of Technology and Engineering (ESTI), Annaba, Algeria;
5INFN Frascati National Laboratories, Rome, Italy;
*e-mail: aissabenselhoub@cre.dz; sekiouomar@yahoo.fr
Received: 05 March 2023; Revised: 28 March 2023;
Accepted: 13 April 2023; Available on-line: 27 April 2023
Since the emergence of the newly identified Coronavirus SARS-CoV-2, no targeted therapeutic agents for COVID-19 treatment are available, and effective treatment options remain very limited. Successful crystallization of the SARS-CoV-2 main protease (Mpro, PDB-ID 6LU7) made possible the research on finding its potential inhibitors for the prevention of virus replication. To conduct molecular docking, we selected ten representatives of the Cathepsin inhibitors family as possible ligands with a high potential of binding the active site of SARS-CoV-2 main protease as a potential target. The results of molecular docking studies revealed that Ligand1 and Ligand2, with vina scores -8.8 and -8.7 kcal/mol for Mpro, respectively, were the most effective in binding. In silico prediction of physicochemical and toxicological behavior of assessed ligands approved the possibility of their use in clinical essays against SARS-COVID-19.
CRISPR as a novel technique for COVID-19 diagnosis: a review
A. A. Saleem1*, A. F. Annooz2, I. M. A. Hadi3, A. H. H. Kabla4
1Medical Laboratory Techniques, Al-Hakim General Hospital, Najaf, Iraq;
2Faculty of Medicine, University of Kufa, Najaf, Iraq;
3Medical Laboratory Techniques, Al-Sadr Medical city, Najaf, Iraq;
4National Advanced IPv6 Centre, Universiti Sains Malaysia, Penang, Malaysia;
*e-mail: aliadil41994@gmail.com
Received: 30 November 2022; Revised: 21 February 2023;
Accepted: 13 April 2023; Available on-line: 27 April 2023
To this moment, the human coronavirus disease COVID-19 that occurs as a result of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is still a critical case that provokes concern around the world. In January 2022, there were over 300 million infections and over 5 million fatalities from COVID-19. As a countermeasure against this rapid spread, there is a vital need for effective and low-cost diagnosis methods in order to control the danger of this pandemic. CRISPR technology has proved its efficiency in detecting COVID-19 due to its simplicity, specificity and high sensitivity. This paper reviews the state-of-the-art of developing the CRISPR platforms for the purpose of COVID-19 diagnosis and treatment. Limitations and challenges of CRISPR in terms of nucleic acid analytical methods for viral infection diagnosis are discussed.
Computational investigation of honeybee venom proteins as potential Omicron SARS-CoV-2 inhibitors
H. A. Al-Madhagi1*, M. G. Saleh2
1Biochemical Technology Program, Faculty of Applied Sciences, Dhamar University, Yemen;
2Division of Microbiology, Biology Department, Faculty of Applied Sciences, Dhamar University, Yemen;
*e-mail: bio.haitham@gmail.com
Received: 01 October 2022; Revised: 07 November 2022;
Accepted: 17 February 2023; Available on-line: 27 February 2023
Because of the catastrophic consequences of COVID-19 on the world population, there should be novel interventions to handle ongoing infections and daily death cases. The aim of the current study is to examine the effectiveness of HBV (Honeybee venom) proteins on spike protein RBD by in silico tools. The sequences of 5 HBV proteins were used for homology modeling by Phyre 2. The generated protein models were employed for protein-protein docking against Omicron Spike glycoprotein receptor binding domain (RBD) (PDB ID# 7T9L) through HDock and ClusPro platforms followed by prediction of binding affinity using PRODIGY web portal and PDBsum for revealing interaction details. It was found that all of the examined HBV proteins exhibited strong docking scores and binding affinity profiles toward RBD. The findings of the present study indicate the possible HBV as preventive as well as treatment options against Omicron SARS-CoV-2.
Structural proteins in the mechanisms of betacoronavirus virion assembly
I. Zaloilo1*, О. Zaloilo2, Y. Rud3, L. Buchatskyi3
1National University of Life and Environmental Sciences of Ukraine, Kyiv;
2Institute of Fisheries of the National Academy of Agrarian Sciences of Ukraine, Kyiv;
3ESC Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Ukraine;
*e-mail: zaloilo76@gmail.com, iridolpb@gmail.com
Received: 08 August 2022; Revised: 31 August 2022;
Accepted: 04 November 2022; Available on-line: 14 November 2022
The emergence of SARS-CoV-2 caused an urgent need to investigate the molecular mechanisms of its reproduction. However, the detailed step-by-step mechanism of SARS-CoV-2 virion assembly has not been described yet. In the presented review the data on the role of structural proteins in the efficient assembly of betacoronavirus particles are analyzed.
Decamethoxin virucidal activity: in vitro and in silico studies
I. V. Semenyuta1*, O. P. Trokhimenko2, I. V. Dziublyk2, S. O. Soloviov2,3,
V. V. Trokhymchuk2, O. L. Bororova4, D. M. Hodyna1,
M. P. Smetiukh3, O. K. Yakovenko5, L. О. Metelytsia1
1V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, Kyiv;
2Shupyk National Healthcare University of Ukraine, Kyiv;
3National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute”, Kyiv;
4F. G. Yanovsky Institute of Tuberculosis and Pulmonology, National Academy of Medical Sciences of Ukraine, Kyiv;
5Volyn Regional Clinical Hospital, Lutsk, Ukraine;
*e-mail: ivan@bpci.kiev.ua
Received: 09 June 2021; Revised: 11 September 2022;
Accepted: 29 September 2022; Available on-line: 06 October 2022
The data on the representative of decamethoxin short-term action on infectious bronchitis virus (IBV) strain H120 used as a human-safe model of SARS-CoV-2 virus are presented. The viral activity was estimated with the use of inverted microscope PrimoVert (Germany) by destructive effect on BHK21 fibroblastic cell line. In vitro results demonstrated that decamethoxin (100 μg/ml) completely inactivated IBV coronavirus strain at exposure of 30 sec and more. At the lowest decamethoxin exposure of 10 sec the antiseptic virucidal activity was 33% and 36% of control at 24 and 48 h of cultivation respectively. Molecular docking analysis indicated the significant similarity of IBV and SARS-CoV-2 main protease (Mpro) structure. Docking studies of decamethoxin interaction with IBV Mpro and SARS-CoV-2 Mpro active centers demonstrated the ligand-protein complexes formation with the estimated binding energy of -8.6, -8.4 kcal/mol and key amino acid residues ASN26, GLY141, GLU187, GLU164, THR24, THR25, ASN142, GLY143, CYS145, HIS164 and GLU166.
Production of recombinant SARS-COV-2 proteins and diphtheria toxoid CRM197-based fusion
O. I. Krynina1, S. I. Romaniuk1, O. B. Gorbatiuk1,2,
O. H. Korchynskyi1,3,4, А. V. Rebriiev1, Ya. S. Kulyk1,
Ye. O. Kozadaieva1, A. A. Siromolot1,5, M. M. Guzyk1,
D. V. Kolybo1*, S. V. Komisarenko1
1Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
2State Institute of Genetic and Regenerative Medicine, National Academy of Medical Sciences of Ukraine, Kyiv;
3Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland;
4S. Gzhytskyi National University of Veterinary Medicine and Biotechnologies, Lviv, Ukraine;
5ESC “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, Ukraine;
*e-mail: kolibo@biochem.kiev.ua
Received: 10 October 2021; Accepted: 12 November 2021
The quickly emerged global COVID-19 pandemic raised a desperate need in the development of protecting vaccines targeting this disease. Therefore, a generation of effective producers of recombinant SARS-CoV-2 proteins became an urgent task. Its resolving contributes to the study of functional SARS-CoV-2 properties, as well as will allow developing the domestic COVID-19 vaccine in Ukraine, thus playing an important strategic role in tackling the pandemics. The aim of the study was to generate prokaryotic and eukaryotic producers of recombinant SARS-CoV-2 proteins and to isolate nucleocapsid (N) protein, receptor-binding domain (RBD) of spike (S) protein, as well as RBD fused to the carrier – diphtheria toxoid CRM197. For this purpose, appropriate genetic constructs, in particular, replication deficient recombinant AdvC5-based adenoviral vectors expressing the SARS-CoV-2 proteins and CRM197-fused conjugate were created through methods of molecular biology and genetic engineering. Restriction analysis and/or DNA sequencing confirmed that we created the correct constructs. Immobilized metal affinity chromatography was used to purify the recombinant proteins. Compliance of their properties was confirmed by the results from polyacrylamide gel electrophoresis, Western blotting, immunoenzymatic assay and MALDI-TOF mass spectrometry. As a result, we generated E. coli Rosetta (DE3) bacterial strain and HEK293 cell line producing recombinant SARS-CoV-2 proteins and CRM197-based fusion. In addition, pure N protein, RBD of S protein and RBD-CRM197 fusion protein were isolated. The obtained recombinant SARS-CoV-2 proteins can be used to study immunogenic and antigenic properties of the SARS-CoV-2 proteins. Cells producing recombinant SARS-CoV-2 proteins and RBD-CRM197 fusion protein are able to provide cheap and safe synthesis of the antigenic substances for domestic development and production of immunodiagnostics for COVID-19 and COVID-19 vaccines in Ukraine.
Determination the binding ability of N-acetyl cysteine and its derivatives with SARS-COV-2 main protease using molecular docking and molecular dynamics studies
A. H. Shntaif*, N. A. Alrazzak, A. Bader, A. M. Almarzoqi
University of Babylon, College of Science for Women, Iraq;
*e-mail: ahmed1979sh@gmail.com
Received: 25 May 2021; Accepted: 22 September 2021
N-acetyl cysteine (NAC) drug has been used as an antioxidant and anti-inflammatory agent in clinical practice and more recently in the treatment of COVID-19 patients. Using docking analysis and molecular dynamics studies we compare the interaction between of N-acetyl cysteine and its derivatives with SARS-COV-2 main protease (Mpro) which is essential for processing the proteins translated from the viral RNA. The results obtained from this study showed that NAC benzyl ester (NACBn), NAC ethyl ester (NACEt) and NAC amide (NACA) could bind with SARS-COV-2 protease better than NAC drug.