scholarly journals Omicron and Delta Variant of SARS-CoV-2: A Comparative Computational Study of Spike protein

2021 ◽  
Author(s):  
Suresh Kumar ◽  
Thiviya S. Thambiraja ◽  
Kalimuthu Karuppanan ◽  
Gunasekaran Subramaniam
Keyword(s):  
Amino Acids ◽  
Computational Study ◽  
Alpha Helix ◽  
Docking Studies ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Diagnostic Equipment ◽  
Hydrophobic Amino Acids ◽  
Second Wave ◽  
High Binding Affinity

AbstractEmerging SARS-CoV-2 variants, especially those of concern, may have an impact on the virus’s transmissibility and pathogenicity, as well as diagnostic equipment performance and vaccine effectiveness. Even though the SARS-CoV-2 Delta variant (B.1.617.2) emerged during India’s second wave of infections, Delta variants have grown dominant internationally and are still evolving. On November 26, 2021, WHO identified the variant B.1.1.529 as a variant of concern, naming it Omicron, based on evidence that Omicron contains numerous mutations that may influence its behaviour. However, the mode of transmission and severity of the Omicron variant remains unknown. We used computational studies to examine the Delta and Omicron variants in this work and found that the Omicron variant had a higher affinity for human ACE2 than the Delta variant due to a significant number of mutations in the SARS-CoV-2 receptor binding domain, indicating a higher potential for transmission. Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2. In comparison to the Delta variant, both the entire spike protein and the RBD in Omicron include a high proportion of hydrophobic amino acids such as leucine and phenylalanine. These amino acids are located within the protein’s core and are required for structural stability. Omicron has a higher percentage of alpha-helix structure than the Delta variant in both whole spike protein and RBD, indicating that it has a more stable structure. We observed a disorder-order transition in the Omicron variant between spike protein RBD regions 468-473, and it may be significant in the influence of disordered residues/regions on spike protein stability and binding to ACE2. A future study might investigate the epidemiological and biological consequences of the Omicron variant.

scholarly journals Human Coronavirus 229E: Receptor Binding Domain and Neutralization by Soluble Receptor at 37°C

2003 ◽  
Vol 77 (7) ◽  
pp. 4435-4438 ◽  
Author(s):  
Jamie J. Breslin ◽  
Irene Mørk ◽  
M. K. Smith ◽  
Lotte K. Vogel ◽  
Erin M. Hemmila ◽  
...  
Keyword(s):  
Amino Acids ◽  
Receptor Binding ◽  
Conformational Changes ◽  
Virus Entry ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Soluble Receptor ◽  
Human Coronavirus ◽  
Virus Receptor ◽  
Human Coronavirus 229E

ABSTRACT Truncated human coronavirus HCoV-229E spike glycoproteins containing amino acids 407 to 547 bound to purified, soluble virus receptor, human aminopeptidase N (hAPN). Soluble hAPN neutralized the infectivity of HCoV-229E virions at 37°C, but not 4°C. Binding of hAPN may therefore trigger conformational changes in the viral spike protein at 37°C that facilitate virus entry.

scholarly journals Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein

RSC Advances ◽  
2020 ◽  
Vol 10 (65) ◽  
pp. 39831-39841
Author(s):  
Puja Adhikari ◽  
Wai-Yim Ching
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Receptor Binding ◽  
Nearest Neighbor ◽  
Binding Domain ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Non Local

Gly504 interacting with two nearest neighbor and one non-local amino acids.

scholarly journals In silico studies on milk derived peptides as potential inhibitors against SARS CoV-2 spike protein receptor binding domain

2021 ◽  
Author(s):  
Sutanu Mukhopadhyay ◽  
Anasua Sarkar
Keyword(s):  
Receptor Binding ◽  
Computational Study ◽  
Protein Docking ◽  
Binding Domain ◽  
Spike Protein ◽  
Receptor Protein ◽  
Extensive Literature ◽  
Receptor Binding Domain ◽  
Peptide Docking ◽  
In Silico Studies

Abstract COVID-19 (Corona Virus Infected Diseases-19) is caused by a strain of coronavirus called SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2). There’s no permanent diagnosis available till date to combat the disease. The viral infection in humans is initiated by binding of RBD (receptor binding domain) of spike protein to human angiotensin-converting enzyme 2 (hACE2) receptor protein. In this computational study, milk-derived peptides are screened against Receptor Binding Domain (RBD) of spike protein of the virus. Milk is considered as one of the most nutrient-rich liquid foods having several antibacterial and antiviral activities. Milk derived peptides including Casein and Whey derived peptides are known to have profound anti-viral and immunomodulatory activities. After extensive literature search, some peptides having anti-viral activities against different viruses, are shortlisted for this study and their three-dimensional structures are modelled for protein-peptide docking against SARS-CoV-2 spike protein RBD. After performing protein-peptide docking and protein-protein docking using different servers such as HPEPDOCK, FIREDOCK, HADDOCK, HDOCK, it has been observed that in presence of the peptides, the interaction between spike RBD and hACE2 has been reasonably decreased, which implies that milk-derived peptides can be potential peptide-inhibitors against the RBD of the virus along with other medications. Further studies on milk-derived peptides should be performed to develop peptide drugs based on milk-derived peptides.

scholarly journals Self and Nonself Short Constituent Sequences of Amino Acids in the SARS-CoV-2 Proteome for Vaccine Development

COVID ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 555-574
Author(s):  
Joji M. Otaki ◽  
Wataru Nakasone ◽  
Morikazu Nakamura
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
Human Proteome ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Amino Acid Residues

Current SARS-CoV-2 vaccines take advantage of the viral spike protein required for infection in humans. Considering that spike proteins may contain both “self” and “nonself” sequences (sequences that exist in the human proteome and those that do not, respectively), nonself sequences are likely to be better candidate epitopes than self sequences for vaccines to efficiently eliminate pathogenic proteins and to reduce the potential long-term risks of autoimmune diseases. This viewpoint is likely important when one considers that various autoantibodies are produced in COVID-19 patients. Here, we comprehensively identified self and nonself short constituent sequences (SCSs) of 5 amino acid residues in the proteome of SARS-CoV-2. Self and nonself SCSs comprised 91.2% and 8.8% of the SARS-CoV-2 proteome, respectively. We identified potentially important nonself SCS clusters in the receptor-binding domain of the spike protein that overlap with previously identified epitopes of neutralizing antibodies. These nonself SCS clusters may serve as functional epitopes for effective, safe, and long-term vaccines against SARS-CoV-2 infection. Additionally, analyses of self/nonself status changes in mutants revealed that the SARS-CoV-2 proteome may be evolving to mimic the human proteome. Further SCS-based proteome analyses may provide useful information to predict epidemiological dynamics of the current COVID-19 pandemic.

scholarly journals Self and Nonself Short Constituent Sequences of Amino Acids in The SARS-CoV-2 Proteome for Vaccine Development

2021 ◽  
Author(s):  
Joji Otaki ◽  
Wataru Nakasone ◽  
Morikazu Nakamura
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Autoimmune Diseases ◽  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Amino Acid Residues

Abstract Current SARS-CoV-2 vaccines take advantage of the viral spike protein required for infection in humans. However, spike proteins may contain both “self” and “nonself” sequences (sequences that exist in the human proteome and those that do not, respectively). Nonself sequences are likely to be better candidate epitopes than self sequences for vaccines to efficiently eliminate pathogenic proteins and to reduce the potential long-term risks of autoimmune diseases. Here, we comprehensively identified self and nonself short constituent sequences (SCSs) of 5 amino acid residues in the proteome of SARS-CoV-2. Self and nonself SCSs comprised 91.2% and 8.8% of the SARS-CoV-2 proteome, respectively. We identified potentially important nonself SCS clusters in the receptor binding domain of the spike protein that overlap with previously identified epitopes of neutralizing antibodies. These nonself SCS clusters may serve as functional epitopes for effective, safe, and long-term vaccines against SARS-CoV-2 infection to resolve the current COVID-19 pandemic.

scholarly journals Catechin and curcumin interact with S protein of SARS-CoV2 and ACE2 of human cell membrane: insights from computational studies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Atala B. Jena ◽  
Namrata Kanungo ◽  
Vinayak Nayak ◽  
G. B. N. Chainy ◽  
Jagneshwar Dandapat
Keyword(s):  
Amino Acid ◽  
Binding Affinity ◽  
Receptor Binding ◽  
Computational Study ◽  
Cell Receptor ◽  
Binding Domain ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Amino Acid Residues ◽  
S Protein

AbstractThe recent outbreak of the coronavirus (SARS-CoV2) is an unprecedented threat to human health and society across the globe. In this context, development of suitable interventions is the need of the hour. The viral spike protein (S Protein) and the cognate host cell receptor ACE2 can be considered as effective and appropriate targets for interventions. It is evident from the present computational study, that catechin and curcumin, not only exhibit strong binding affinity to viral S Protein and host receptor ACE2 but also to their complex (receptor-binding domain (RBD) of the spike protein of SARS-CoV2 and ACE2; RBD/ACE2-complex). The binding affinity values of catechin and curcumin for the S protein, ACE2 and RBD/ACE2-complex are − 10.5 and − 7.9 kcal/mol; − 8.9 and − 7.8 kcal/mol; and − 9.1 and − 7.6 kcal/mol, respectively. Curcumin directly binds to the receptor binding domain (RBD) of viral S Protein. Molecular simulation study over a period of 100 ns further substantiates that such interaction within RBD site of S Protein occurs during 40–100 ns out of 100 ns simulation trajectory. Contrary to this, catechin binds with amino acid residues present near the RBD site of S Protein and causes fluctuation in the amino acid residues of the RBD and its near proximity. Both catechin and curcumin bind the interface of ‘RBD/ACE2-complex’ and intervene in causing fluctuation of the alpha helices and beta-strands of the protein complex. Protein–protein interaction studies in presence of curcumin or catechin also corroborate the above findings suggesting the efficacy of these two polyphenols in hindering the formation of S Protein-ACE2 complex. In conclusion, this computational study for the first time predicts the possibility of above two polyphenols for therapeutic strategy against SARS-CoV2.

scholarly journals Neutralization of SARS-CoV-2 VOC 501Y.V2 by human antisera elicited by both inactivated BBIBP-CorV and recombinant dimeric RBD ZF2001 vaccines

2021 ◽  
Author(s):  
Baoying Huang ◽  
Lianpan Dai ◽  
Hui Wang ◽  
Zhongyu Hu ◽  
Xiaoming Yang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Receptor Binding ◽  
Vaccine Efficacy ◽  
Host Immunity ◽  
Binding Domain ◽  
The Other ◽  
Spike Protein ◽  
Inactivated Vaccine ◽  
Receptor Binding Domain

AbstractRecently, the emerged and rapidly spreading SARS-CoV-2 variant of concern (VOC) 501Y.V2 with 10 amino acids in spike protein were found to escape host immunity induced by infection or vaccination. Global concerns have been raised for its potential to affect vaccine efficacy. Here, we evaluated the neutralization activities of two vaccines developed in China against 501Y.V2. One is licensed inactivated vaccine BBIBP-CorV and the other one is recombinant dimeric receptor-binding domain (RBD) vaccine ZF2001. Encouragingly, both vaccines largely preserved neutralizing titres, with slightly reduction, against 501Y.V2 authentic virus compare to their titres against both original SARS-CoV-2 and the currently circulating D614G virus. These data indicated that 501Y.V2 variant will not escape the immunity induced by vaccines targeting whole virus or RBD.

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