Modares Journal of Biotechnology

Abstract The countries’ social and economic conditions have been threatened by corona epidemic and a large number of people’s death in the world. SARS-CoV-2 virus, a form of corona virus family, is responsible for corona disease and its spread in the present century. The study of the receptor binding region (RBD) in the spike protein is very important for scientists because the new corona virus uses its surface spike protein for binding to the ACE2 surface protein and entering its genetic material to the host cells. By this protein and its receptor binding region inhibition, the prevention of virus entrance to the cell is possible. The virus’s genes can be multiplied by cloning and its protein can be purified. The usage of antiviral peptides as the most practical methods and binding inhibitory peptides of RBD to the ACE2 receptor for SARS-CoV-2 treatment, are of great interest to scientists. In the present research, RBD cloning in PET28a expression vector, RBD protein expression and GFP/RBD fusion protein were performed in prokaryotic host. Due to this protein’s insolubility in the prokaryotic host, column refolding was performed with urea gradient with a nickel-agarose column and the synthesized protein was confirmed through western blot technique. Three nominated peptides from articles used to compare their binding to RBD using bioinformatics and their tendency to bind to each other was investigated by molecular docking. The mentioned peptides can be used in this virus infection treatment due to their binding potential to RBD, if their interaction is proven.

Abstract In the last month of 2019, an unknown virus appeared in Wuhan, China. Sequencing studies have shown that the virus is a new member of the coronavirus family, which mostly causes a respiratory disease with pneumonia-like symptoms. The new coronavirus consists of 25 proteins, including 4 important structural proteins and 15 non-structural proteins. Spike protein is one of the most important structural proteins on the surface of the virus; It is highly glycosylated and plays a key role in the virus binding to the host cells. The binding of glycans to proteins affects their structure and function in two ways; They lead to proper protein folding, and can play an important role in protein interactions, and also, by covering the surface of the protein, it causes the virus to escape from the immune system. So it is obvious that the study of glycan structures becomes more important when either a vaccine is going to be designed or glycan structures have important roles in the folding, activity, and interaction of a protein. Therefore, since the spike protein is a non-functional structural protein, the study of glycan structures is important for two goals of vaccine design and investigating the role of glycans in protein interactions. In this article, we are going to review the most important findings on spike protein glycosylation and compare the amount of glycosylation in different viruses, indicating the importance of glycan structures in designing an effective vaccine.

Abstract The COVID-19 pandemic has created a global health crisis, and developing effective treatments is essential to prevent the spread of the disease and save millions of lives. One of the key proteins involved in the replication cycle of SARS-CoV-2, the virus that causes COVID-19, is the main protease enzyme, 3CL^pro. Due to its high importance, this enzyme is the subject of molecular, structural, and clinical investigations, and efforts have been made to develop drugs that can inhibit its activity. One such drug is the chemical compound N3, which has been found to have a high inhibitory effect against 3CL^pro. However, traditional medicine perspectives on this issue have been less explored. In this research, molecular docking interaction simulation and all-atom molecular dynamics (MD) simulation were conducted to study the potential inhibitory capability of generally available 21 plant-extracted compounds against the 3CL^pro enzyme. Three compounds with the highest inhibition probability were selected from the molecular docking results and subjected to 100 ns of MD simulation to investigate their stability and structural-dynamic-energetic features. Beside the complexes stability, the results from the simulation demonstrated that, all our selected three compounds induce N3 comparable structural-dynamics characteristics to 3CL^pro and, therefore, are expected to have a similar inhibitory ability against this enzyme. Compound number 5 was found to have the most favorable binding energy and was proposed as the best plant substitute for N3. The results from this research can be directly used to design experimental research for 3CLpro enzyme inhibition, saving the time-financial cost.