Spike glycoprotein

This study aims to protocolize the utilization of the center-of-mass (CoM) distance method in GROMACS MD simulation software as a useful method for evaluating the binding affinity change in heterodimeric protein due to induced changes in one of the units. The hypothesis underlines the basic principles in biophysics, that an increase of the binding affinity is expected to reduce the relative CoM distance between monomers, while the opposite is expected to increase the relative CoM distance. However, it has been found that the CoM distance analysis must be strictly preformed during the convergent phase of systems' dynamics, once the monomers enter mutually stable conformation-a limitation which has usually been overlooked. The method was used to study the impact of K417Y severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface glycoprotein (S-protein) mutation. It has been found that the K417Y mutation favors reduced binding affinity between SARS-CoV-2 S-protein and human angiotensin-converting enzyme 2 (hACE2) receptor, which is due to the loss of the permanent K417-D30 salt bridge in favor of a temporary Y417-D30 hydrogen bond. The destabilizing impact of K417Y mutation on S-protein-hACE2 complex was confirmed by radius of gyration analysis.

The ongoing global threat posed by SARS-CoV-2 necessitates the rapid development of effective vaccines. This study employed a computational pipeline to design a multiepitope vaccine targeting the spike (S) glycoprotein of SARS-CoV-2. Cytotoxic T lymphocyte (CTL) epitopes were predicted using immunoinformatics tools and were screened based on their non-toxicity, immunogenicity, and antigenicity. High-affinity epitopes were sequentially linked via AAY linkers to construct a rationally designed vaccine candidate. The tertiary structure of the construct was modeled and evaluated for structural stability and desirable physicochemical properties. To assess immunogenic potential, molecular docking was performed with key immune receptors, including Toll-like receptor 3 (TLR3) and major histocompatibility complex class I (MHC-I), demonstrating strong and specific binding interactions. Furthermore, the vaccine gene was codon-optimized and in silico cloned into the pET-28b(+) expression vector, yielding a construct of 5476 base pairs. The collective in silico findings support the designed multi-epitope vaccine as a promising candidate capable of inducing robust and long-lasting cell-mediated immunity against SARS-CoV-2. Experimental validation is warranted to confirm these computational predictions.

The search for effective therapeutics against COVID-19 remains
imperative, and natural compounds have emerged as promising candidates.
Our study explores the potential of bioactive phytochemicals from the
traditional Siddha formulation MilagaiKudineer as inhibitors against
key target proteins of the SARS-CoV-2 virus. Through in-silico docking
analyses, the interactions of phytochemicals from Cuminum cyminum,
Curcuma longa, and Capsicum annuum with the receptor-binding domain
of the SARS-CoV-2 spike glycoprotein (PDB ID: 6VSB), the SARSCoV2 RNA-dependent RNA polymerase (PDB ID: 6NUR), and the main
protease, 3CL pro (PDB ID: 6LU7) were examined. Notable compounds
such as Curcumin, Quercetin, Capsaicin, and Ascorbic acid demonstrated
significant binding affinities towards these viral targets, suggesting
mechanisms by which these phytochemicals may disrupt viral entry and
replication. Our findings also highlight the potential of compounds like
Carvacrol, Cuminaldehyde, Linalool, and Dihydrocapsaicin in mediating
antiviral effects by interfacing with key amino acid residues of the
spike glycoprotein. These interactions are indicative of their capacity
to hinder the virus-host cellbinding process. Moreover, the interaction
of select phytochemicals with the SARS-CoV2 RNA-dependent RNA
polymerase and the 3CLpro enzyme suggests a possible inhibitory effect
on viral replication. Given the promising interactions observed, these
phytochemicals warrant further investigation through in vitro and in
vivo studies to validate their antiviral efficacy against COVID-19. This
research underscores the importance of exploring traditional medicinal
formulations for potential therapeutic agents in the fight against emerging
infectious diseases.

Fusion peptides (FPs) in spike proteins are key players mediating early events in cell-to-cell fusion, vital for intercellular viral spread. A proline residue located at the central FP region has often been suggested to have a distinctive role in this fusion event. The spike glycoprotein from strain RSA59 (PP) of mouse hepatitis virus (MHV) contains two central, consecutive prolines in the FP. Here, we report that deletion of one of these proline residues, resulting in RSA59 (P), significantly affected neural cell syncytia formation and viral titers postinfection in vitro. Transcranial inoculation of C57Bl/6 mice with RSA59 (PP) or RSA59 (P) yielded similar degrees of necrotizing hepatitis and meningitis, but only RSA59 (PP) produced widespread encephalitis that extended deeply into the brain parenchyma. By day 6 postinfection, both virus variants were mostly cleared from the brain. Interestingly, inoculation with the RSA59 (P)–carrying MHV significantly reduced demyelination at the...

Se formulan recomendaciones de un grupo de consenso de expertos sobre los criterios para evaluar el desempeño diagnóstico (tamaño y selección de muestras para sensibilidad y especificidad analíticas, criterios para establecer límites de detección, criterios para establecer el estándar de oro para las serologías) que deberían ser tenidos en cuenta al evaluar y validar las pruebas diagnósticas para SARS CoV-2. Con el propósito de asegurar la calidad de las pruebas serológicas a utilizar en el país, se recomienda la participación en un programa de control de calidad externo, que garantice la idoneidad y desempeño en la realización de las pruebas diagnósticas serológicas y moleculares durante esta pandemia, ya que su uso tiene profundas implicaciones para las medidas de intervención clínicas individuales y de seguimiento y control en salud pública.

Se validó y evaluó un método de RT-PCR en tiempo real usando cebadores y sondas específicas para los genes RdRP de SARS-CoV-2 y GAPDH de humanos; este último fue usado como control endógeno. Se evaluó la especificidad y sensibilidad; además, se evaluó otros parámetros como la robustez, la repetibilidad, reproducibilidad, comparabilidad y el límite de detección. La sensibilidad, especificidad, los valores predictivos positivo y negativo, la robustez, comparabilidad y la repetibilidad-reproducibilidad de la prueba de RT-PCR en tiempo real dúplex fue de 100%, con un límite de detección de 100 copias/μL, de acuerdo con los criterios de aceptación establecidos para validación del protocolo. Esta prueba estandarizada es una buena alternativa para el diagnóstico de COVID-19; además, la prueba fue aplicada de manera exitosa en personas sospechosas de la enfermedad permitiendo controlar el número de falsos negativos.

The spike glycoprotein of the SARS-CoV-2 virus, which causes COVID-19, has attracted attention for its vaccine potential and binding capacity to host cell surface receptors. Much of this research focus has centered on the ectodomain of the spike protein. The ectodomain is anchored to a transmembrane region, followed by a cytoplasmic tail. Here we report a distant sequence similarity between the cysteine-rich cytoplasmic tail of the coronavirus spike protein and the hepcidin protein that is found in humans and other vertebrates. Hepcidin is thought to be the key regulator of iron metabolism in humans through its inhibition of the iron-exporting protein ferroportin. An implication of this preliminary observation is to suggest a potential route of investigation in the coronavirus research field making use of an already-established literature on the interplay of local and systemic iron regulation, cytokine-mediated inflammatory processes, respiratory infections and the hepcidin protein. The question of possible homology and an evolutionary connection between the viral spike protein and hepcidin is not assessed in this report, but some scenarios for its study are discussed.

The spike glycoprotein of the SARS-CoV-2 virus, which causes COVID-19, has attracted attention for its vaccine potential and binding capacity to host cell surface receptors. Much of this research focus has centered on the ectodomain of the spike protein. The ectodomain is anchored to a transmembrane region, followed by a cytoplasmic tail. Here we report a distant sequence similarity between the cysteine-rich cytoplasmic tail of the coronavirus spike protein and the hepcidin protein that is found in humans and other vertebrates. Hepcidin is thought to be the key regulator of iron metabolism in humans through its inhibition of the iron-exporting protein ferroportin. An implication of this preliminary observation is to suggest a potential route of investigation in the coronavirus research field making use of an already-established literature on the interplay of local and systemic iron regulation, cytokine-mediated inflammatory processes, respiratory infections and the hepcidin protein. The question of possible homology and an evolutionary connection between the viral spike protein and hepcidin is not assessed in this report, but some scenarios for its study are discussed.

The spike glycoprotein of the SARS-CoV-2 virus, which causes COVID-19, has attracted attention for its vaccine potential and binding capacity to host cell surface receptors. Much of this research focus has centered on the ectodomain of the spike protein. The ectodomain is anchored to a transmembrane region, followed by a cytoplasmic tail. Here we report a distant sequence similarity between the cysteine-rich cytoplasmic tail of the coronavirus spike protein and the hepcidin protein that is found in humans and other vertebrates. Hepcidin is thought to be the key regulator of iron metabolism in humans through its inhibition of the iron-exporting protein ferroportin. An implication of this preliminary observation is to suggest a potential route of investigation in the coronavirus research field making use of an already-established literature on the interplay of local and systemic iron regulation, cytokine-mediated inflammatory processes, respiratory infections and the hepcidin protein....

Coagulopathy and syncytial formation are relevant effects of the SARS-CoV-2 infection, but the underlying molecular mechanisms triggering these processes are not fully elucidated. Here, we identified a potential consensus pattern in the Spike S glycoprotein present within the cytoplasmic domain; this consensus pattern was detected in only 79 out of 561,000 proteins (UniProt bank). Interestingly, the pattern was present in both human and bat the coronaviruses S proteins, in many proteins involved in coagulation process, cell–cell interaction, protein aggregation and regulation of cell fate, such as von Willebrand factor, coagulation factor X, fibronectin and Notch, characterized by the presence of the cysteine-rich EGF-like domain. This finding may suggest functional similarities between the matched proteins and the CoV-2 S protein, implying a new possible involvement of the S protein in the molecular mechanism that leads to the coagulopathy and cell fusion in COVID-19 disease.

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

An outbreak of 2019 novel coronavirus disease (COVID-19/ 2019-nCoV) has quickly spread nationwide in Wuhan, China. It has been classified as a zoonotic coronavirus similar to coronavirus SARS and coronavirus MERS. Aim: To identify a potential drug and determine the specific binding region in the human coronavirus protein via insilico docking method. Materials and Methods: There is a herb called Acorus Calamus which contains various compounds in it. Hence, one of the most widely known ligand is galangin which is used as a therapeutic target for the treatment of cancer, neurodegeneration, diabetes, cardiovascular effects and also bronchitis diseases. Thus, the ligand was taken from the PubChem database and downloaded in the SDF form. Then, the liability of the ligand was tested through the PreADMET database. On the other hand, human coronavirus protein was downloaded from NCBI VIRUS in FASTA format. Next, by using RPBS WEB PORTAL online server proper docking was done with the chosen receptor and ligand. Results and Discussions: Galangin was recognized as one of the main ligand which can able to bind to a specific region in human coronavirus protein. Conclusion: From this study, galangin was identified as one of the useful ligand to cure COVID-19. This result suggests the potential role of galangin and this ligand to serve as a useful drug in the medical field.

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

Allergy is the reaction of the immune system against the active substance entering the body. Drug allergy is caused by the entry of drug allergens into the body. Drug allergies are examined in two groups, Type A and Type B. Type A describes expected drug reactions and Type B describes unexpected drug reactions. Therefore, drug allergies are in the Type B category. Age, gender, past drug reactions, and genetic polymorphisms are important risk factors for drug allergy. Active drug substances are also particularly important for drug reactions, and drugs containing certain active substances are more prone to allergic reactions. Penicillin, cephalosporin, and fluoroquinolone active ingredients are especially important in beta-lactam antibiotics. At the same time, it is the examination of the use of different drugs belonging to the same group, without experiencing an allergic reaction, with only mild side effects. Especially if we think about the treatment method, CRISPR has been used successfully in various fields in recent years. According to a review study, there was a reduction in the rate of disease progression as a result of cloning research on mice with Type 1 diabetes using CRISPR technology and the disease-specific peptide. This technology may become available in the future by identifying the appropriate peptide group specific to the pharmacological groups for allergic reactions. In terms of diagnostic procedures, provocation tests and immunotherapy are still being studied clinically. As a future aspect of this review, targeted cell or drug content modification using CRISPR may become available for overcoming the allergy.

Following the spread of the different Viral Variants of COVID-19 [1-5] which seems unstoppable, perhaps a strategy could be implemented for the production of a DEFINITIVE vaccine capable of neutralizing the Virus despite the presence of variants. A few days ago I appreciated the good news that researchers published about the vaccine with the covid N protein in mice [6]. This confirms that multiple targets such as antigens allow to overcome the appearance of variants.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Reports of new variants that potentially increase virulence and viral transmission, as well as reduce the efficacy of available vaccines, have recently emerged. In this study, we computationally analyzed the N439K, S477 N, and T478K variants for their ability to bind Angiotensin-converting enzyme 2 (ACE2). We used the protein-protein docking approach to explore whether the three variants displayed a higher binding affinity to the ACE2 receptor than the wild type. We found that these variants alter the hydrogen bonding network and the cluster of interactions. Additional salt bridges, hydrogen bonds, and a high number of non-bonded contacts (i.e., non-bonded interactions between atoms in the same molecule and those in other molecules) were observed only in the mutant complexes, allowing efficient binding to the ACE2 receptor. Furthermore, we used a 2.0-μs allatoms simulation approach to detect differences in the structural dynamic features of the resulting protein complexes. Our findings revealed that the mutant complexes possessed stable dynamics, consistent with the global trend of mutations yielding variants with improved stability and enhanced affinity. Binding energy calculations based on molecular mechanics/generalized Born surface area (MM/GBSA) further revealed that electrostatic interactions principally increased net binding energies. The stability and binding energies of N439K, S477 N, and T478K variants were enhanced compared to the wild-type-ACE2 complex. The net binding energy of the systems was − 31.86 kcal/mol for the wild-type-ACE2 complex, − 67.85 kcal/mol for N439K, − 69.82 kcal/ mol for S477 N, and − 69.64 kcal/mol for T478K. The current study provides a basis for exploring the enhanced binding abilities and structural features of SARS-CoV-2 variants to design novel therapeutics against the virus.

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) emerged in China exponentially and is recognized as a multisystem disease that gradually elevates markers associated with iron metabolism as the infection becomes more intense, becoming a critical factor in the investigation of prognosis. We review the latest scientific findings on the behavior of iron and ferritin in pathophysiology and as laboratory markers in COVID-19 (Coronavirus Disease 2019). The findings showed that iron and ferritin play a key role in the pathogenesis of COVID-19, contributing to the worsening of the disease. Therefore, iron dysmetabolism, marked by hyperferritinemia, is associated with inflammatory states in SARS-CoV-2 infection, and ferritin measurement has been shown to be a useful laboratory marker with a clinical and discriminatory potential to define the severity and mortality during COVID-19. RESUMO O SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) surgiu na China, de maneira exponencial e foi reconhecida como uma doença multissistêmica que eleva gradativamente marcadores associados ao metabolismo do ferro à medida que a infecção se torna mais intensa, sendo fator chave na investigação de prognóstico. Analisamos as últimas descobertas científicas sobre o comportamento do ferro e da ferritina na fisiopatologia e como marcador laboratorial na COVID-19 (Coronavirus Disease 2019). As descobertas evidenciaram que o ferro e a ferritina tem papel chave na patogênese da COVID-19 contribuindo para o agravamento da doença. Portanto, o dismetabolismo do ferro, marcado pela hiperferritinemia, está associado a estados inflamatórios na infecção por SARS-CoV-2 e a dosagem de ferritina mostrou ser um marcador laboratorial útil, com um potencial clínico e discriminatório para definir a gravidade e mortalidade durante o curso do COVID-19.

The highly infectious disease COVID-19 is induced by SARS-coronavirus 2 (SARS-CoV-2), which has spread rapidly around the globe and was announced as a pandemic by the World Health Organization (WHO) in March 2020. SARS-CoV-2 binds to the host cell's angiotensin converting enzyme 2 (ACE2) receptor through the viral surface spike glycoprotein (S-protein). ACE2 is expressed in the oral mucosa and can therefore constitute an essential route for entry of SARS-CoV-2 into hosts through the tongue and lung epithelial cells. At present, no effective treatments for SARS-CoV-2 are yet in place. Blocking entry of the virus by inhibiting ACE2 is more advantageous than inhibiting the subsequent stages of the SARS-CoV-2 life cycle. Based on current published evidence, we have summarized the different in silico based studies and repurposing of anti-viral drugs to target ACE2, SARS-CoV-2 S-Protein: ACE2 and SARS-CoV-2 S-RBD: ACE2. This review will be useful to researchers looking to effectively recognize and deal with SARS-CoV-2, and in the development of repurposed ACE2 inhibitors against COVID-19. Keywords Coronavirus • SARS-CoV-2 • Repurposed • Angiotensin Converting Enzyme-2 (ACE2) • COVID-19 Abbreviations CoV Coronavirus + ssRNA Single-stranded RNA ICTV International Committee on Taxonomy of Viruses SARS severe acute respiratory syndrome SARS-CoV 1 Severe acute respiratory syndrome coronavirus 1 This article is part of the Topical Collection ''Antiviral Drug Research''; edited by Guangxin Liang, Zheng Yin.

Coronavirus disease 2019 (COVID-19) has spread out as a pandemic threat affecting over 2 million people. The infectious process initiates via binding of SARS-CoV-2 Spike (S) glycoprotein to host angiotensin-converting enzyme 2 (ACE2). The interaction is mediated by the receptor-binding domain (RBD) of S glycoprotein, promoting host receptor recognition and binding to ACE2 peptidase domain (PD), thus representing a promising target for therapeutic intervention. Herein, we present a computational study aimed at identifying small molecules potentially able to target RBD. Although targeting PPI remains a challenge in drug discovery, our investigation highlights that interaction between SARS-CoV-2 RBD and ACE2 PD might be prone to small molecule modulation, due to the hydrophilic nature of the bi-molecular recognition process and the presence of druggable hot spots. The fundamental objective is to identify, and provide to the international scientific community, hit molecules potentially suitable to enter the drug discovery process, preclinical validation and development.

Anaphylactic reactions were observed after Singapore’s national coronavirus disease 2019 (COVID-19) vaccination programme started in December 2020. We report the clinical and laboratory features of three patients in our institution who developed anaphylactic reactions after receiving the Pifzer BNT162b2 vaccine. IgM and IgG antibodies, but not IgE antibodies to the Pfizer BNT162b2 vaccine, were detected in all subjects. Similarly, mild to high elevated levels of anti-polyethylene glycol (PEG) IgG (1035–19709 U/mL, vs. vaccine-naive < 265 U/mL, vaccine-tolerant < 785 U/mL) and IgM (1682–5310 U/mL, vs. vaccine-naive < 1011 U/mL, vaccine-tolerant < 1007 U/mL) were detected in two out of three patients via commercial ELISA. High levels of serum anaphylatoxin C3a (79.0 ± 6.3 μg/mL, mean ± SD, vs. normal < 10 μg/mL) were observed in all three patients during the acute phase of the reaction, while tryptase levels, a marker of mast cell activation, were not elevated. Finally,...

El 31 de diciembre de 2019 la comisión municipal de salud de Wuhan (provincia de Hubei, China) informa sobre un inusitado brote de casos de neumonía en la ciudad. Posteriormente se determina que se trata de un nuevo coronavirus designado inicialmente como 2019-nCoV y posteriormente, SARS-CoV-2. El SARS-CoV-2 infecta y se replica en los neumocitos y macrófagos del sistema respiratorio específicamente en el parénquima pulmonar en donde reside el receptor celular ACE-2. Esta revisión describe aspectos relacionados con la transmisión, prevención, generalidades bioquímicas del SARS-CoV-2 y métodos diagnósticos del COVID-19. Inicialmente se describe la forma de transmisión del virus y algunas recomendaciones generales para su prevención. Posteriormente, se hace una descripción detallada de los aspectos bioquímicos del SARS-CoV-2, su ciclo infeccioso y la estructura de la proteína S, la cual está involucrada con el proceso de ingreso del virus a la célula. Finalmente, se describen los méto...

Objective: Coronaviruses are a group of similar viruses which cause fatal infection and responsible for affecting the upper respiratory tract in many organisms. Throughout the time these viruses have been found to affect human life by causing major pandemics like SARS, MERS and COVID-19 due to their high rate of mutation and zoonotic transmission. Repurposing of a drug could be a solution for this challenge, as many previously available drugs hold great potential to act as a drug molecule. Interfering this interaction could be a potent mechanism to stop the viral infection and propagation. Methods: In the current study we have predicted the evolutionary relationship of nCoV using three viral proteins Nucleocapsid phosphoprotein, membrane glycoprotein and Envelop protein with accession number YP_009724397, YP_009724393 and YP_009724392 respectively. Phylogenetic tree was constructed and evaluated using the bootstrap method. Homology modeling and docking studies has been done to ident...

The Food and Drug Administration (FDA) has recently authorized the two messenger RNA (mRNA) vaccines BNT162b2 and mRNA-1273 for emergency use against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the COVID-19 coronavirus disease. BNT162b2 and mRNA-1273 vaccines were developed by Pfizer-BioNTech and Moderna, respectively, in 2020. The United Kingdom,

Background SARS-CoV-2 developed global-pandemic with millions of infections/deaths. As it is urgently necessary it is assumed that some blockers/inhibitors of ACE2 could be helpful to resist the binding of viral-spike Receptor-Binding-Domain (RBD). Methods Here, conserved RBD from 186-countries were compared with WUHAN-Hu-1 wild-type (CLUSTAL-X2/Pymol). The RBD of ACE2-bound nCOV2 crystal-structure 6VW1 was analyzed by Haddock-PatchDock. Extensive structural study/trial to introduce point/double/triple mutations in the different locations of CUT4 (most-effective from total 4 proposed fragments; CUTs) were tested with Swiss-Model-Expacy. Results Blind-docking of mutated-CUTs in ACE2 completely rejected the nCOV2 binding to ACE2. Further, competitive-docking/binding-analyses (by PRODIGY) demonstrated few more bonding (LYS31-PHE490 and GLN42-GLN498) of CUT4 (than wild) and hindered TYR41-THR500 interaction with ACE2. Moreover, mutated-CUT4 even showed higher blocking effect against spi...

SARS-CoV-2 developed global-pandemic with millions of infections/deaths. Blocker/inhibitor of ACE2 and viral-spikes Receptor-Binding-Domain RBD-blockers are helpful. Here, conserved RBD (CUTs) from 186-countries were compared with WUHAN-Hu-1 wild-type by CLUSTAL-X2 and Structural-alignment using Pymol. The RBD of ACE2-bound nCOV2 crystal-structure (2.68Å) 6VW1 was analyzed by Haddock-PatchDock. Extensive structural study/trial to introduce point/double/triple mutations in the following locations (Y489S/Y453S/T500S/T500Y)/(Y489S,Y453S/Y489S,T500S/Y489S,T500Y/Y453S,T500S/Y453S, T500Y)/ (Y489S,Y453S,T500S/Y489S,Y453S,T500Y) of CUT4 (most-effective) were tested with Swiss-Model-Expacy. Blind-docking of mutated-CUTs to ACE2 (6VW1) by Haddock-Hawkdock was performed and optimally complete-rejection of nCOV2 to ACE2 was noticed. Further, competitive-docking/binding-analyses were done by PRODIGY. Present results suggest that compared to the wild-spike, CUT4 showed extra LYS31-PHE490/GLN42-GL...

A large population in the world has been infected by COVID-19. Understanding the mechanisms of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is important for the management and treatment of COVID-19. When it comes to the infection process, one of the most important proteins in SARS-CoV-2 is the spike (S) protein, which is able to bind to human Angiotensin-Converting Enzyme 2 (ACE2) and initializes the entry of the host cell. In this study, we implemented multiscale computational approaches to study the electrostatic features of the interfaces of the SARS-CoV-2 S protein receptor binding domain and ACE2. The simulations and analyses were performed on highperformance computing resources in the Texas Advanced Computing Center. Our study identified key residues on SARS-CoV-2, which can be used as targets for future drug design. The results shed light on future drug design and therapeutic targets for COVID-19. & THE NUMBER OF confirmed cases of Coronavirus Disease 2019 (COVID-19) is increasing dramatically 1 due to the fast spread of SARS-CoV-2. The large coronavirus family includes hundreds of viruses that usually do not pose a threat to human health. SARS-CoV-2 is the seventh member of those coronaviruses that infect the human body. Of these, four (HCoV-229E, HCoV-OC43, HCoV-NL63, HKU1) 2 cause mild to moderate symptoms, while the other three can cause serious, even fatal diseases. SARS coronavirus (SARS-CoV) broke out in 2002 and caused Severe Acute Respiratory Syndrome (SARS). MERS coronavirus (MERS-CoV)

Objective: Coronaviruses are a group of similar viruses which cause fatal infection and responsible for affecting the upper respiratory tract in many organisms. Throughout the time these viruses have been found to affect human life by causing major pandemics like SARS, MERS and COVID-19 due to their high rate of mutation and zoonotic transmission. Repurposing of a drug could be a solution for this challenge, as many previously available drugs hold great potential to act as a drug molecule. Interfering this interaction could be a potent mechanism to stop the viral infection and propagation. Methods: In the current study we have predicted the evolutionary relationship of nCoV using three viral proteins Nucleocapsid phosphoprotein, membrane glycoprotein and Envelop protein with accession number YP_009724397, YP_009724393 and YP_009724392 respectively. Phylogenetic tree was constructed and evaluated using the bootstrap method. Homology modeling and docking studies has been done to identify the interaction and binding affinity of SARS drugs. Results: Phylogenetic tree shows that Nucleocapsid phosphoprotein is originated from Hypsugo Bat Coronavirus, Membrane glycoprotein is originated from MERS Corona Virus and Envelop proteins have originated from Ferret coronavirus. From the docking result we concluded that Precose (glide score-8.372) shows that it has stable and strong interaction with Spike glycoprotein. Conclusion: Precose which is commonly known as Acarbose can act as a potential inhibitor for the spike glycoprotein. This paper described and highlighted the importance of repurposing of the previously available drug to act as a potent inhibitor in the newly discovered or novel diseases.

The novel coronavirus SARS-CoV-2, the infective agent causing COVID-19, is having a global impact both in terms of human disease as well as socially and economically. Its heavily glycosylated spike glycoprotein is fundamental for the infection process, via its receptor-binding domains interaction with the glycoprotein angiotensin-converting enzyme 2 on human cell surfaces. We therefore utilized an integrated glycomic and glycoproteomic analytical strategy to characterize both N- and O- glycan site-specific glycosylation within the receptor-binding domain. We demonstrate the presence of complex-type N-glycans with unusual fucosylated LacdiNAc at both sites N331 and N343 and a single site of O-glycosylation on T323.

The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI’s data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.

COVID-19 produces cytokine-mediated persistent inflammation and is associated with elevated iron stores and low circulating iron. It is believed that central to the pathophysiological mechanism is interleukin 6 and hepcidin. A state of iron overload, termed hyperferritinemia, and inflammatory anemia take place. Both conditions are linked to a worse result in critically ill patients. Blocking the interleukin 6—hepcidin pathway with Tocilizumab could present favorable outcomes. The aim of this study was to evaluate if Tocilizumab influences survival, the occurrence of sepsis, anemia and transfusions in critically ill patients suffering from COVID-19. This prospective observational study focused on levels of interleukin 6, hepcidin and blood iron parameters in patients treated with Tocilizumab. Data were compared before and after therapy as well as between treated and control groups. Results indicate that there is no difference in terms of survival nor in the rate of anemia or sepsis o...

The Food and Drug Administration (FDA) has recently authorized the two messenger RNA (mRNA) vaccines BNT162b2 and mRNA-1273 for emergency use against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the COVID-19 coronavirus disease. BNT162b2 and mRNA-1273 vaccines were developed by Pfizer-BioNTech and Moderna, respectively, in 2020. The United Kingdom,

Coronavirus disease 2019 (COVID-19) has spread out as a pandemic threat affecting over 2 million people. The infectious process initiates via binding of SARS-CoV-2 Spike (S) glycoprotein to host angiotensin-converting enzyme 2 (ACE2). The interaction is mediated by the receptor-binding domain (RBD) of S glycoprotein, promoting host receptor recognition and binding to ACE2 peptidase domain (PD), thus representing a promising target for therapeutic intervention. Herein, we present a computational study aimed at identifying small molecules potentially able to target RBD. Although targeting PPI remains a challenge in drug discovery, our investigation highlights that interaction between SARS-CoV-2 RBD and ACE2 PD might be prone to small molecule modulation, due to the hydrophilic nature of the bi-molecular recognition process and the presence of druggable hot spots. The fundamental objective is to identify, and provide to the international scientific community, hit molecules potentially suitable to enter the drug discovery process, preclinical validation and development.

In this investigation, we sought to answer the following questions: 'Is It Possible to Genetically Engineer The Next SuperHuman Coronavirus? What are the steps? What's the rationale behind doing so? What would be the essential ingredient for the vaccine? We began our investigation by examining the Human Coronavirus strains that were present up to January 2021. Those strains are HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, MERS-CoV, SARS-CoV, and SARS-CoV2 (Al Mansoori et al.). The strains that showed the highest fatality and pandemic infectiousness were MERS-Cov (Al Mansoori et al.) and SARS-Cov2 (Abdelrahman et al.), respectively. Since the Spike Glycoprotein "is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells" (InterPro), we decided to analyze the functions of the domains found on the Spike Glycoprotein sequences of MERS-Cov and SARS-Cov2. First, we obtained the Spike glycoprotein sequences for MERS-Cov and SARS-Cov2 using the National Library of Medicine, National Center for Biotechnology Information (NCBI) database. Next, to identify the domains that are unique to MERS-Cov and SARS-Cov2's spike glycoproteins and their functions, we used the online protein classification database called InterPro. We discovered that the domain sequences unique to MERS-Cov Spike Glycoprotein were cd21626, cd21486, and G3DSA:2.20.210.30. The domain sequences unique to SARS-Cov2 Spike Glycoprotein were cd21480, G3DSA:1.20.5.79, and cd21624. We learned that the following four unique domains contributed to a high affinity Virus-cell attachment mediation: cd21626, cd21486, cd21480, and cd21624. As for the functions and descriptions of the remaining domains, G3DSA:1.20.5.79 and G3DSA:2.20.210.30, no data was available. That means, we do not know what role these domains play in enhancing virus fatality and pandemic infectiousness, if any. Using the SARS-Cov2 Spike Glycoprotein sequence as our host, we

Significance During the ongoing COVID-19 pandemic, protein engineering offers a rapid and powerful approach for building therapeutics to treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We use computational design, affinity maturation, and fusion to dimerization domains to engineer “receptor traps” based on wild-type angiotensin-converting enzyme II (ACE2), the target for viral spike-mediated SARS-CoV-2 entry into cells. The optimized ACE2 receptor traps neutralize authentic SARS-CoV-2 infections as effectively as high-affinity antibodies isolated from convalescent patients and also bind viral spike proteins from other coronaviruses known to cause respiratory diseases. ACE2 receptor traps have large binding interfaces and block the entire receptor binding interface, limiting the potential impact of viral escape mutations.

Anaphylactic reactions were observed after Singapore’s national coronavirus disease 2019 (COVID-19) vaccination programme started in December 2020. We report the clinical and laboratory features of three patients in our institution who developed anaphylactic reactions after receiving the Pifzer BNT162b2 vaccine. IgM and IgG antibodies, but not IgE antibodies to the Pfizer BNT162b2 vaccine, were detected in all subjects. Similarly, mild to high elevated levels of anti-polyethylene glycol (PEG) IgG (1035–19709 U/mL, vs. vaccine-naive < 265 U/mL, vaccine-tolerant < 785 U/mL) and IgM (1682–5310 U/mL, vs. vaccine-naive < 1011 U/mL, vaccine-tolerant < 1007 U/mL) were detected in two out of three patients via commercial ELISA. High levels of serum anaphylatoxin C3a (79.0 ± 6.3 μg/mL, mean ± SD, vs. normal < 10 μg/mL) were observed in all three patients during the acute phase of the reaction, while tryptase levels, a marker of mast cell activation, were not elevated. Finally,...

Four coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E) are endemic in human populations. All these viruses are seasonal and generate short-term immunity. Like the highly pathogenic coronaviruses, the endemic coronaviruses have zoonotic origins. Thus, understanding the evolutionary dynamics of these human viruses might provide insight into the future trajectories of SARS-CoV-2 evolution. Because the zoonotic sources of HCoV-OC43 and HCoV-229E are known, we applied a population genetics–phylogenetic approach to investigate which selective events accompanied the divergence of these viruses from the animal ones. Results indicated that positive selection drove the evolution of some accessory proteins, as well as of the membrane proteins. However, the spike proteins of both viruses and the hemagglutinin-esterase (HE) of HCoV-OC43 represented the major selection targets. Specifically, for both viruses, most positively selected sites map to the receptor-binding domains (RBDs) a...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Reports of new variants that potentially increase virulence and viral transmission, as well as reduce the efficacy of available vaccines, have recently emerged. In this study, we computationally analyzed the N439K, S477 N, and T478K variants for their ability to bind Angiotensin-converting enzyme 2 (ACE2). We used the protein-protein docking approach to explore whether the three variants displayed a higher binding affinity to the ACE2 receptor than the wild type. We found that these variants alter the hydrogen bonding network and the cluster of interactions. Additional salt bridges, hydrogen bonds, and a high number of non-bonded contacts (i.e., non-bonded interactions between atoms in the same molecule and those in other molecules) were observed only in the mutant complexes, allowing efficient binding to the ACE2 receptor. Furthermore, we used a 2.0-μs allatoms simulation approach to detect differences in the structural dynamic features of the resulting protein complexes. Our findings revealed that the mutant complexes possessed stable dynamics, consistent with the global trend of mutations yielding variants with improved stability and enhanced affinity. Binding energy calculations based on molecular mechanics/generalized Born surface area (MM/GBSA) further revealed that electrostatic interactions principally increased net binding energies. The stability and binding energies of N439K, S477 N, and T478K variants were enhanced compared to the wild-type-ACE2 complex. The net binding energy of the systems was − 31.86 kcal/mol for the wild-type-ACE2 complex, − 67.85 kcal/mol for N439K, − 69.82 kcal/ mol for S477 N, and − 69.64 kcal/mol for T478K. The current study provides a basis for exploring the enhanced binding abilities and structural features of SARS-CoV-2 variants to design novel therapeutics against the virus.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Reports of new variants that potentially increase virulence and viral transmission, as well as reduce the efficacy of available vaccines, have recently emerged. In this study, we computationally analyzed the N439K, S477 N, and T478K variants for their ability to bind Angiotensin-converting enzyme 2 (ACE2). We used the protein-protein docking approach to explore whether the three variants displayed a higher binding affinity to the ACE2 receptor than the wild type. We found that these variants alter the hydrogen bonding network and the cluster of interactions. Additional salt bridges, hydrogen bonds, and a high number of non-bonded contacts (i.e., non-bonded interactions between atoms in the same molecule and those in other molecules) were observed only in the mutant complexes, allowing efficient binding to the ACE2 receptor. Furthermore, we used a 2.0-μs allatoms simulation approach to detect differences in the structural dynamic features of the resulting protein complexes. Our findings revealed that the mutant complexes possessed stable dynamics, consistent with the global trend of mutations yielding variants with improved stability and enhanced affinity. Binding energy calculations based on molecular mechanics/generalized Born surface area (MM/GBSA) further revealed that electrostatic interactions principally increased net binding energies. The stability and binding energies of N439K, S477 N, and T478K variants were enhanced compared to the wild-type-ACE2 complex. The net binding energy of the systems was − 31.86 kcal/mol for the wild-type-ACE2 complex, − 67.85 kcal/mol for N439K, − 69.82 kcal/ mol for S477 N, and − 69.64 kcal/mol for T478K. The current study provides a basis for exploring the enhanced binding abilities and structural features of SARS-CoV-2 variants to design novel therapeutics against the virus.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Reports of new variants that potentially increase virulence and viral transmission, as well as reduce the efficacy of available vaccines, have recently emerged. In this study, we computationally analyzed the N439K, S477 N, and T478K variants for their ability to bind Angiotensin-converting enzyme 2 (ACE2). We used the protein-protein docking approach to explore whether the three variants displayed a higher binding affinity to the ACE2 receptor than the wild type. We found that these variants alter the hydrogen bonding network and the cluster of interactions. Additional salt bridges, hydrogen bonds, and a high number of non-bonded contacts (i.e., non-bonded interactions between atoms in the same molecule and those in other molecules) were observed only in the mutant complexes, allowing efficient binding to the ACE2 receptor. Furthermore, we used a 2.0-μs allatoms simulation approach to detect differences in the structural dynamic features of the resulting protein complexes. Our findings revealed that the mutant complexes possessed stable dynamics, consistent with the global trend of mutations yielding variants with improved stability and enhanced affinity. Binding energy calculations based on molecular mechanics/generalized Born surface area (MM/GBSA) further revealed that electrostatic interactions principally increased net binding energies. The stability and binding energies of N439K, S477 N, and T478K variants were enhanced compared to the wild-type-ACE2 complex. The net binding energy of the systems was − 31.86 kcal/mol for the wild-type-ACE2 complex, − 67.85 kcal/mol for N439K, − 69.82 kcal/ mol for S477 N, and − 69.64 kcal/mol for T478K. The current study provides a basis for exploring the enhanced binding abilities and structural features of SARS-CoV-2 variants to design novel therapeutics against the virus.

Background The sarbecovirus subgenus of betacoronaviruses is widely distributed throughout bats and other mammals globally and includes human pathogens, SARS-CoV and SARS-CoV-2. The most studied sarbecoviruses use the host protein, ACE2, to infect cells. Curiously, the majority of sarbecoviruses identified to date do not use ACE2 and cannot readily acquire ACE2 binding through point mutations. We previously screened a broad panel of sarbecovirus spikes for cell entry and observed bat-derived viruses that could infect human cells, independent of ACE2. Here we further investigate the sequence determinants of cell entry for ACE2-independent bat sarbecoviruses. Methods We employed a network science-based approach to visualize sequence and entry phenotype similarities across the diversity of sarbecovirus spike protein sequences. We then verified these computational results and mapped determinants of viral entry into human cells using recombinant chimeric spike proteins within an established viral pseudotype assay. Findings We show ACE2-independent viruses that can infect human and bat cells in culture have a similar putative receptor binding motif, which can impart human cell entry into other bat sarbecovirus spikes that cannot otherwise infect human cells. These sequence determinants of human cell entry map to a surface-exposed protrusion from the predicted bat sarbecovirus spike receptor binding domain structure. Interpretation Our findings provide further evidence of a group of bat-derived sarbecoviruses with zoonotic potential and demonstrate the utility in applying network science to phenotypic mapping and prediction.

A possible role for GRP78 in cross vaccination against COVID-19 Dear Editor, We previously reported in this Journal 1 that cell-surface Glucose Regulated Protein 78 (CS-GRP78), also termed heat shock protein A5 (HSPA5), could be a possible route for SARS-CoV-2 internalization. We predicted the binding site on the spike protein of SARS-CoV-2 that can recognize CS-GRP78. A recent communication by Braun and colleagues reported that the spike glycoprotein of the

Cutaneous leishmaniasis (CL) is caused by the protozoan parasite L. maxicana is one of the major parasitic diseases throughout the world. Due to the lack of approved vaccines against CL, chemotherapy is the only modern treatment. These treatments have some major consequences including prolonged treatment, parenteral administration, tolerability, teratogenicity, etc. Presently, none of the current CL drugs have high levels of efficacy. Thus, the development of new and safer drugs possessing cost-effective, efficacious, oral and short course drugs is urgently needed. Drug repurposing is another method that can be used for the development of new therapeutic activities.When a new therapeutic activity would have been identified, the entities could be rapidly advanced into clinical trials. Phosphomannomutase (PMM) has become highlighted as potential drug targets due to its important role in the biosynthesis of glycoconjugates.These glycoconjugates are essential for parasite virulence.To i...

SARS-CoV2 main protease is important for viral replication and one of the most potential targets for drug development in this current pandemic. Drug repurposing is a promising field to provide potential short-term acceptable therapy for management of coronavirus till a specific anti-viral for coronavirus is developed. In-silico drug repurposing screening is the current fastest way to repurpose drugs by targeting active sites in fraction of seconds. In this study, SARS-CoV2 main protease is being targeted by 1050 FDA-approved drugs to inhibit its activity thereby interfering with viral replication. Chemotherapeutic drugs and anti-retroviral drugs have shown potential binding as inhibitor. In-vitro and clinical trials required to establish final fact.

Identification of potential drug-target interaction for approved drugs serves as the basis of repurposing drugs. Studies have shown polypharmacology as common phenomenon. In-silico approaches help in screening large compound libraries at once which could take years in a laboratory. We screened a library of 1050 FDA-approved drugs against spike glycoprotein of SARS-CoV2 in-silico. Anti-cancer drugs have shown good binding affinity which is much better than hydroxychloroquine and arbidol. We have also introduced a hypothesis named “Bump” hypothesis which and be developed further in field of computational biology.