جستجوی مقالات مرتبط با کلیدواژه « sars-cov-2 » در نشریات گروه « زیست شناسی »

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, 3CLpro. 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 3CLpro. 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 3CLpro 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 3CLpro 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.

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.

It has been more than two years since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China. The SARS-CoV-2 has created an unprecedented pandemic (COVID-19) in the modern era and challenged all the scientific, economic, and social structures of the world. Extensive worldwide research has been conducted to study the structure and function of the SARS-CoV-2 spike protein since the beginning of the pandemic. The role and importance of spike protein in the introduction of SARS-CoV-2 into human cells has been proven. Among the important and effective factors in controlling the Covid-19 pandemic is understanding the structural changes of spike protein in different variants of the virus and the effectiveness of drugs and vaccines against new SARS-CoV-2 variants. Due to the great importance of spike protein SARS-CoV-2, it was tried to study its structure and interaction with cellular receptors using bioinformatics tools in this study. Furthermore, the effects of different SARS-CoV-2 variants on existing drugs and vaccines were reviewed.

The bioinformatics methods and molecular docking was used to study the binding function of spike protein to its various cellular receptors in the human body. HDOCK web server was used to perform the molecular docking process and in the next step, the PDBsum web server was used for post-docking checks and to ensure the accuracy of the obtained data. PyMOL software was also used to study and visualize replacement and deletion mutations in the spike protein.

Extensive mutations in the spike protein in the omicron variant indicate a redesign in the spike protein. These massive mutations cause extensive changes in the structure and function of the spike protein. The data obtained from molecular docking and comparing the energy level (docking score) of spike protein binding of different variants of the virus with different cellular receptors indicate a high tendency of the spike protein to bind, with lower energy levels and more stable, to KREMEN1 receptor than the main ACE2 receptor.  The level of spike protein binding energy levels of different virus variants was almost similar to other receptors (except the KREMEN1 receptor) or slightly different from the spike protein binding energy levels with the main ACE2 receptor.

There is not much difference in the tendency of spike protein binding of emerging and important variants of the virus (main, alpha, delta, and omicron) to ACE2 receptor, but the tendency to bind to KREMEN1 receptor is increasing and has reached its peak in the delta variant. The energy level of the spike protein binding to the KREMEN1 receptor is significantly negative compared to other receptors, indicating greater binding and stability. Also, considering the level of energy received from the HDOCK web server, it can be concluded that although the ACE2 receptor is the main receptor for the spike protein, other receptors can still bind to the spike protein with good stability. Based on the available information, so far there have been no reports of docking between spike protein and other non-main spike protein receptors (AXL, ASGR1, KREMEN1). Therefore, more comprehensive research is needed to confirm or refute these findings.

 Covid-19 disease with acute respiratory symptoms appeared in 2019. The disease was associated with fever, cough, and severe respiratory distress. The causative agent of the disease belonged to the beta-coronavirus family and was named SARS-CoV-2. The outbreak of Covid-19 and the creating of a global epidemic led to many attempts to understand the structure and function of the virus. The spike protein is a relatively heavy glycosylated protein consisting of three identical subunits that appear as a homo-trimmer on the virus's surface. After binding to the surface cell receptor (angiotensin-converting enzyme), the protein conformational changes and eventually causes the virus to enter the host cell. This process is necessary for viruses to enter human cells and infect them. Therefore, investigating the structural details of the spike protein through molecular dynamics simulation can play an influential role in understanding how the subunits connect and identifying the hotspot amino acids.

 First, the tertiary structure of spike proteins related to SARS-CoV-2, bat-SL-CoVZC21 (Bat Coronavirus), and PCoV_GX-P4L (Pangolin coronavirus) was constructed through modeling homology. After evaluation and validation, these structures were simulated using NAMD software. The structural properties of spike proteins were evaluated in the level of 3D structure, measurement of the interface area between monomers, thermodynamic parameters, trimmer structures' stability, and hotspot amino acids' identification in making connections between subunits.

 Evaluation of the trimeric structure of spike protein showed that this protein in SARS-CoV-2 has the highest ΔGdiss value (113.2 kcal/mol), which indicates the stability of the oligomeric protein structure among other spike proteins. The lowest ΔGdiss (100.6 kcal/mol) was obtained for the spike protein of PCoV_GX-P4L. The interface area between the subunits was almost the same in all spike proteins. Y369, D405, Y707 in subunit A, Y369, D574, Y707, Y837, D985 in subunit B, and Y707 in subunit C were identified as red hotspot amino acids for SARS-CoV-2 spike protein.

 The study of the structure of virus surface proteins at the atomic scale, and the recognition of hotspot residues that play an essential role in establishing monomeric connections, has created a window to further recognition and function of the virus. Thus, it can provide new information about neutralizing the virus.

Since an effective drug against Covid-19 was not approved, researchers worldwide are trying to develop an effective vaccine against the disease to prevent related morbidity and mortality. According to the latest report of the World Health Organization, August 5, 2022, there are about 170 vaccine candidates for SARS-coronavirus-2 in the clinical and 198 vaccine candidates in the pre-clinical stage. In this review article, emphasis is placed on only 7 vaccines that have passed clinical phase IV. The mechanism of action of most of the proposed vaccines is the induction of a neutralizing antibody against the spike protein (glycoprotein S). These antibodies prevent the virus from entering the host cell by blocking the virus from attaching to its cell receptor (ACE-2). In this review, the role of SARS-coronavirus-2 proteins in the viral replication cycle and its pathogenic mechanism, and also the variants of SARS-coronavirus-2 are discussed to have an overview of the goals of designed vaccines. Then, the technology of producing various types of vaccines and the effectiveness of these vaccines against the virus variants are discussed.

Numerous and increasing human progress in the field of various sciences, apart from the positive aspects that it can have for the welfare, comfort, and excellence of human beings, has another dimension, called bioterrorism, which is the abuse of various sciences such as biology and microbiology by various countries or organizations aimed to hit an enemy or rival groups. The purpose of writing this article is to review bioterrorism and its history, as well as to study the various dimensions of the emergence and spread of the emerging coronavirus (SARS-CoV-2) and its negative effects on various issues of human life (health, economic, social, and psychological areas). In this article, we try to review the various related evidence to find out the possibility of an association between the emerging coronavirus, and bioterrorism, and then point out the negative consequences of the Covid-19 pandemic on the economy and order of the world community.

Coronaviruses cause diseases such as the Middle East respiratory syndrome and acute respiratory syndrome. SARS-CoV-2, which causes COVID-19 and ongoing pandemic, was first identified in Wuhan, China. SARS-CoV-2 mainly infects the respiratory tract leading to infect other organs. Gastrointestinal symptom, for instance, have been widely reported in patients with COVID-19. In fact, numerous investigations have shown that SARS-CoV-2 can be detected in feces and this may be associated with the risk of viral transmission. The presence of SARS-CoV-2 in human feces and transmission in the sewage system is a public health concern. Therefore, wastewater-based epidemiology can play a critical role in the early detection of COVID-19 outbreaks in rural and urban areas. Compared to conventional viral detection methods, it has been suggested that SARS-CoV-2 can be rapidly detected in sewage even one week before observing the symptom in a population. In this study, we first focus on the importance of sewage system monitoring and screening to control the COVID-19 pandemic and the required protocols and factors to remove and to disinfect wastewater from the virus to provide safe water recycling and environmental health protection.

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is one of the common factors of mortality worldwide in the 21st century. A lot of research is being done in the world with the aim of introducing new and effective SARS-COV-2 antiviral compounds, especially herbal compounds. The purpose of this study to screening main protease (Mpro) inhibitors and spike glycoprotein from among plant phenolic and terpenoid compounds using bioinformatics tools.Three dimension and chemical structures of virus proteins and plant phenolic and terpenoid compounds were retrieval from Protein Data Bank and Pubchem database respectively. Finally, plant compounds on the main protease (Mpro) and virus S virus, molecular docking was investigated using iGemdock 2.1 software and then,In the next step, physicochemical properties of the candidate plant compounds for permeability, solubility and gastrointestinal absorption were predicted using SwissADME software.4 terpenoid compounds, glycyrrhizic acid, Saikosaponin B2, Polyphyllin I and Withaferin A and 7 phenolic compounds, EGCG ، Rosmarinic acid ، Silibinin ، Chlorogenic acid ، Proanthocyanidin ، Procyanidin B2 , Anthocyanin with Strong binding energy compared to reference medicinal compounds such as Azithramycine and Remdesivir are good candidate for inhibiting spike Glycoprotein and the main protease of the virus (Mpro).According to results both phenolic and terpenoid compounds compared to standard chemical drugs had good inhibitory effects for Mpro proteinase and Spike glycoprotein virus and can be good candidates for in vitro and in vivo studies.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus responsible for an ongoing human pandemic (COVID-19). There is a massive international effort underway to develop diagnostic reagents, vaccines, and antiviral drugs in a bid to slow down the spread of the disease and save lives. One part of that international effort involves the research community working with plants, bringing researchers from all over the world together with commercial enterprises to achieve the rapid supply of protein antigens and antibodies for diagnostic kits, and scalable production systems for the emergency manufacturing of vaccines and antiviral drugs. Here, we look at some of the ways in which plants can and are being used in the fight against COVID-19.