Structural evolution of Delta lineage of SARS-CoV-2

Gomari, Mohammad Mahmoudi; Tarighi, Parastoo; Choupani, Edris; Abkhiz, Shadi; Mohamadzadeh, Masoud; Rostami, Neda; Sadroddiny, Esmaeil; Baammi, Soukayna; Uversky, Vladimir N.; Dokholyan, Nikolay V.

doi:10.1016/j.ijbiomac.2022.11.227

Cited by 7 publications

(9 citation statements)

References 122 publications

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“…Examining the energy levels of the residues in the CD44-peptides complex also disclosed that the mutated regions in the IK1 peptide, which include K1R (À102.1 kJ/mol) and S4F (À20.2 kJ/mol), had more optimal binding energy level compared to A6 (K1 À38.6 kJ/mol , S4 À1.4 kJ/mol ) and IK2 (K1D À44.3 kJ/mol , S4T À7.1 kJ/ mol ). In addition, the examination of parameters such as FEL, RMSF, H-bond, and minimum distance which are widely used in the analysis of biomolecules, 59,110 showed that the designed peptides (especially IK1) compared to the peptide A6 have more stability and binding affinity to interact with CD44. So, it is expected that compared to A6 which has a short half-life and low ability to prevent the recurrence of cancer in people with ovarian cancer, the designed peptides have better performance.…”

Section: Discussionmentioning

confidence: 99%

“…During the simulation, parameters such as the root mean square deviation (RMSD), 52 root mean square fluctuation (RMSF), 53 the radius of gyration (RG), 54 solvent‐accessible surface area (SASA), 55 free energy landscape (FEL), 56 and principal component analysis (PCA), 57 were employed for checking structure attributes of complexes. In addition, the number of H‐bonds, 58 minimum distance, 59 and the number of contacts 60 were examined for analysis of CD44 interaction with designed peptides. MD simulation was accomplished by the GROMACS ( v2021.2 ) software package 61 .…”

Section: Methodsmentioning

confidence: 99%

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Rational peptide design for targeting cancer cell invasion

Gomari,

Arab,

Balalaie

et al. 2023

Proteins

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Cell invasion is an important process in cancer progression and recurrence. Invasion and implantation of cancer cells from their original place to other tissues, by disabling vital organs, challenges the treatment of cancer patients. Given the importance of the matter, many molecular treatments have been developed to inhibit cancer cell invasion. Because of their low production cost and ease of production, peptides are valuable therapeutic molecules for inhibiting cancer cell invasion. In recent years, advances in the field of computational biology have facilitated the design of anti‐cancer peptides. In our investigation, using computational biology approaches such as evolutionary analysis, residue scanning, protein–peptide interaction analysis, molecular dynamics, and free energy analysis, our team designed a peptide library with about 100 000 candidates based on A6 (acetyl‐KPSSPPEE‐amino) sequence which is an anti‐invasion peptide. During computational studies, two of the designed peptides that give the highest scores and showed the greatest sequence similarity to A6 were entered into the experimental analysis workflow for further analysis. In experimental analysis steps, the anti‐metastatic potency and other therapeutic effects of designed peptides were evaluated using MTT assay, RT‐qPCR, zymography analysis, and invasion assay. Our study disclosed that the IK1 (acetyl‐RPSFPPEE‐amino) peptide, like A6, has great potency to inhibit the invasion of cancer cells.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Rational peptide design for targeting cancer cell invasion

Gomari,

Arab,

Balalaie

et al. 2023

Proteins

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“…Studies on the SARS-CoV-2 genome have shown mutations that could change a virus’s virulence and transmissibility. Mutations in the genome occur due to errors during RNA replication, resulting in many SARS-CoV-2 variants [ 4 ]. The high genetic recombination and mutation rates of SARS-CoV-2 contribute to its ecological diversity [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

“…The Alpha variant, first detected in the United Kingdom in September 2020, possesses a wide range of mutations, some of which have greatly affected the function of the S protein [ 4 , 11 ]. In addition, a 50–100% higher reproduction number compared to other non-VOC lineages was observed [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…According to the epidemiological data, the percentage of Beta variant-associated infections increased to ∼50% of the total daily infections within approximately three months since its outbreak [ 13 ]. Beta variants contain nine S mutations, of which the most significant substitutions of the amino acids are located in the RBD region [ 4 ]. Because mutations in the Beta variant cause escape from NT antibodies, the possibility for reinfection is relatively high [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

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Neutralizing Activity of SARS-CoV-2 Antibodies in Patients with COVID-19 and Vaccinated Individuals

Vilibic-Cavlek,

Stevanovic,

Kovac

et al. 2023

Antibodies

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Background: Serological diagnosis of COVID-19 is complex due to the emergence of different SARS-CoV-2 variants. Methods: 164 serum samples from (I) patients who recovered from COVID-19 (n = 62) as well as (II) vaccinated individuals (n = 52) and (III) vaccinated individuals who were infected with different SARS-CoV-2 variants after vaccination (n = 50) were included. All samples were tested using EIA (binding antibodies) and a virus neutralization test (VNT) using the Wuhan strain (NT antibodies). Group III was further tested with a VNT using the Alpha/Delta/Omicron strains. Results: The highest antibody index (AI) was observed in vaccinated individuals infected with COVID-19 (median AI = 50, IQR = 27–71) and the lowest in vaccinated individuals (median AI = 19, IQR = 8–48). Similarly, NT antibody titer was highest in vaccinated individuals infected with COVID-19 (median 128; IQR = 32–256) compared to vaccinated individuals (median 32, IQR = 4–128) and patients with COVID-19 (median 32, IQR = 8–64). The correlation between AI and NT titer was strongly positive in vaccinated individuals and moderately positive in patients with COVID-19. No significant correlation was observed in vaccinated individuals infected with COVID-19. In patients infected with Alpha and Delta, the lowest VNT positivity rate was for the Omicron variant (85.0%/83.3%). Patients infected with the Alpha variant showed the lowest NT titer for the Omicron variant (median titer 32) compared to the Wuhan/Delta variants (64/128). Patients infected with the Delta variant had the lowest NT titer to the Omicron variant (median 32), compared to the Wuhan/Alpha variants (64/128). Patients infected with the Omicron variant showed similar titers to the Delta/Wuhan variants (128) and higher to the Alpha variant (256). Conclusions: The cross-immunity to SARS-CoV-2 is lowest for the Omicron variant compared to the Alpha/Delta variants.

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