A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers (2022)
Mironov, V., Shchugoreva, I. A., Artyushenko, P. V., Morozov, D., Borbone, N., Oliviero, G., Zamay, T. N., Moryachkov, R. V., Kolovskaya, O. S., Lukyanenko, K. A., Song, Y., Merkuleva, I. A., Zabluda, V. N., Peters, G., Koroleva, L. S., Veprintsev, D. V., Glazyrin, Y. E., Volosnikova, E. A., Belenkaya, S. V., . . . Kichkailo, A. S. (2022). Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers. Chemistry : A European Journal, 28(12), Article e202104481. https://doi.org/10.1002/chem.202104481
JYU-tekijät tai -toimittajat
Julkaisun tiedot
Julkaisun kaikki tekijät tai toimittajat: Mironov, Vladimir; Shchugoreva, Irina A.; Artyushenko, Polina V.; Morozov, Dmitry; Borbone, Nicola; Oliviero, Giorgia; Zamay, Tatiana N.; Moryachkov, Roman V.; Kolovskaya, Olga S.; Lukyanenko, Kirill A.; et al.
Lehti tai sarja: Chemistry : A European Journal
ISSN: 0947-6539
eISSN: 1521-3765
Julkaisuvuosi: 2022
Ilmestymispäivä: 13.01.2022
Volyymi: 28
Lehden numero: 12
Artikkelinumero: e202104481
Kustantaja: Wiley-VCH Verlag
Julkaisumaa: Saksa
Julkaisun kieli: englanti
DOI: https://doi.org/10.1002/chem.202104481
Julkaisun avoin saatavuus: Muulla tavalla avoin
Julkaisukanavan avoin saatavuus:
Julkaisu on rinnakkaistallennettu (JYX): https://jyx.jyu.fi/handle/123456789/79486
Tiivistelmä
Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity using small-angle X-ray scattering, cytometry, and fluorescence polarization. Using a new iterative design procedure, Interaction Based Drug Design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.
YSO-asiasanat: SARS-CoV-2-virus; lääkesuunnittelu; oligonukleotidit; proteiinit; laskennallinen kemia; molekyylidynamiikka
Vapaat asiasanat: aptamers; fragment molecular orbitals method; molecular dynamics; SARS-CoV-2; SAXS
Liittyvät organisaatiot
OKM-raportointi: Kyllä
Raportointivuosi: 2022
JUFO-taso: 2
