G-rich VEGF aptamer as a potential inhibitor of chitin trafficking signal in emerging opportunistic yeast infection

Vahed, Mohammad; Ahmadian, Gholamreza; Niyoosha, Ameri; Vahed, Majid

doi:10.1016/j.compbiolchem.2019.03.007

Cited by 8 publications

(7 citation statements)

References 33 publications

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“…Once the host’s defenses are decreased, Saccharomyces cerevisiae ( S. cerevisiae ) becomes an opportunist fungal pathogen and causes severe health problems. One aptamer with antifungal properties is the GVEGF aptamer [144]. This aptamer was applied to S. cerevisiae to inhibit the chitin synthesis pathway, an essential process for fungi cell growth.…”

Section: Other Applicationsmentioning

confidence: 99%

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G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

2019

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G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.

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Section: Other Applicationsmentioning

confidence: 99%

“…The binding of the GVEGF aptamer to the CHS6 protein disrupts the CHS5-CHS6 complex formation and affects the CHS3 protein transportation to the lipid membrane and consequently disorders chitin localization. The GVEGF aptamer was shown to be a promising antifungal agent for drug development [144].…”

Section: Other Applicationsmentioning

confidence: 99%

G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

2019

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“…Two residues of docking are considered in contact if a pair of (any) atoms belonging to two residues are closer than a defined cut-off distance. The advantages of using contact map representations for protein–protein interfaces have also been shown in a previous study [ 36 ].…”

Section: Methodsmentioning

confidence: 54%

Structural Analysis of the Novel Variants of SARS-CoV-2 and Forecasting in North America

Quinonez

Vahed

Shahraki

et al. 2021

Viruses

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Background: little is known about the forecasting of new variants of SARS-COV-2 in North America and the interaction of variants with vaccine-derived neutralizing antibodies. Methods: the affinity scores of the spike receptor-binding domain (S-RBD) of B.1.1.7, B. 1.351, B.1.617, and P.1 variants in interaction with the neutralizing antibody (CV30 isolated from a patient), and human angiotensin-converting enzyme 2 (hACE2) receptor were predicted using the template-based computational modeling. From the Nextstrain global database, we identified prevalent mutations of S-RBD of SARS-CoV-2 from December 2019 to April 2021. Pre- and post-vaccination time series forecasting models were developed based on the prediction of neutralizing antibody affinity scores for S-RBD of the variants. Results: the proportion of the B.1.1.7 variant in North America is growing rapidly, but the rate will reduce due to high affinity (~90%) to the neutralizing antibody once herd immunity is reached. Currently, the rates of isolation of B. 1.351, B.1.617, and P.1 variants are slowly increasing in North America. Herd immunity is able to relatively control these variants due to their low affinity (~70%) to the neutralizing antibody. The S-RBD of B.1.617 has a 110% increased affinity score to the human angiotensin-converting enzyme 2 (hACE2) in comparison to the wild-type structure, making it highly infectious. Conclusion: The newly emerged B.1.351, B.1.617, and P.1 variants escape from vaccine-induced neutralizing immunity and continue circulating in North America in post- herd immunity era. Our study strongly suggests that a third dose of vaccine is urgently needed to cover novel variants with affinity scores (equal or less than 70%) to eliminate developing viral mutations and reduce transmission rates.

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“…All of the structures were visualized using PYMOL Chimera software Version 1.7.4 (30). The calculation procedure was almost the same as that in our previous works (31-34).…”

Section: Methodsmentioning

confidence: 99%

Impacts of 203/204: RG>KR mutation in the N protein of SARS-CoV-2

Vahed¹,

Calcagno

Quinonez

et al. 2021

Preprint

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We present a structure-based model of phosphorylation-dependent binding and sequestration of SARS-CoV-2 nucleocapsid protein and the impact of two consecutive amino acid changes R203K and G204R. Additionally, we studied how mutant strains affect HLA-specific antigen presentation and correlated these findings with HLA allelic population frequencies. We discovered RG>KR mutated SARS-CoV-2 expands the ability for differential expression of the N protein epitope on Major Histocompatibility Complexes (MHC) of varying Human Leukocyte Antigen (HLA) origin. The N protein LKR region K203, R204 of wild type (SARS-CoVs) and (SARS-CoV-2) observed HLA-A*30:01 and HLA-A*30:21, but mutant SARS-CoV-2 observed HLA-A*31:01 and HLA-A*68:01. Expression of HLA-A genotypes associated with the mutant strain occurred more frequently in all populations studied.ImportanceThe novel coronavirus known as SARS-CoV-2 causes a disease renowned as 2019-nCoV (or COVID-19). HLA allele frequencies worldwide could positively correlate with the severity of coronavirus cases and a high number of deaths.

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G-rich VEGF aptamer as a potential inhibitor of chitin trafficking signal in emerging opportunistic yeast infection

Cited by 8 publications

References 33 publications

G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

Structural Analysis of the Novel Variants of SARS-CoV-2 and Forecasting in North America

Impacts of 203/204: RG>KR mutation in the N protein of SARS-CoV-2

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