Anticoagulant Oligonucleotide–Peptide Conjugates: Identification of Thrombin Aptamer Conjugates with Improved Characteristics
Oligonucleotide–peptide conjugates (OPCs) are a promising class of biologically active compounds with proven potential for improving nucleic acid therapeutics. OPCs are commonly recognized as an efficient instrument to enhance the cellular delivery of therapeutic nucleic acids. In addition to this a...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-03-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/7/3820 |
| _version_ | 1797439007757434880 |
|---|---|
| author | Vladimir B. Tsvetkov Irina V. Varizhuk Nikolay N. Kurochkin Sergei A. Surzhikov Igor P. Smirnov Andrey A. Stomakhin Natalia A. Kolganova Edward N. Timofeev |
| author_facet | Vladimir B. Tsvetkov Irina V. Varizhuk Nikolay N. Kurochkin Sergei A. Surzhikov Igor P. Smirnov Andrey A. Stomakhin Natalia A. Kolganova Edward N. Timofeev |
| author_sort | Vladimir B. Tsvetkov |
| collection | DOAJ |
| description | Oligonucleotide–peptide conjugates (OPCs) are a promising class of biologically active compounds with proven potential for improving nucleic acid therapeutics. OPCs are commonly recognized as an efficient instrument to enhance the cellular delivery of therapeutic nucleic acids. In addition to this application field, OPCs have an as yet unexplored potential for the post-SELEX optimization of DNA aptamers. In this paper, we report the preparation of designer thrombin aptamer OPCs with peptide side chains anchored to a particular thymidine residue of the aptamer. The current conjugation strategy utilizes unmodified short peptides and support-bound protected oligonucleotides with activated carboxyl functionality at the T3 thymine nucleobase. The respective modification of the oligonucleotide strand was implemented using N3-derivatized thymidine phosphoramidite. Aptamer OPCs retained the G-quadruplex architecture of the parent DNA structure and showed minor to moderate stabilization. In a series of five OPCs, conjugates bearing T3–Ser–Phe–Asn (SFN) or T3–Tyr–Trp–Asn (YWN) side chains exhibited considerably improved anticoagulant characteristics. Molecular dynamics studies of the aptamer OPC complexes with thrombin revealed the roles of the amino acid nature and sequence in the peptide subunit in modulating the anticoagulant activity. |
| first_indexed | 2024-03-09T11:45:35Z |
| format | Article |
| id | doaj.art-8a6f2607147a4ee49c452c3fc4d206ae |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T11:45:35Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-8a6f2607147a4ee49c452c3fc4d206ae2023-11-30T23:22:37ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-03-01237382010.3390/ijms23073820Anticoagulant Oligonucleotide–Peptide Conjugates: Identification of Thrombin Aptamer Conjugates with Improved CharacteristicsVladimir B. Tsvetkov0Irina V. Varizhuk1Nikolay N. Kurochkin2Sergei A. Surzhikov3Igor P. Smirnov4Andrey A. Stomakhin5Natalia A. Kolganova6Edward N. Timofeev7Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, RussiaFederal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, RussiaOligonucleotide–peptide conjugates (OPCs) are a promising class of biologically active compounds with proven potential for improving nucleic acid therapeutics. OPCs are commonly recognized as an efficient instrument to enhance the cellular delivery of therapeutic nucleic acids. In addition to this application field, OPCs have an as yet unexplored potential for the post-SELEX optimization of DNA aptamers. In this paper, we report the preparation of designer thrombin aptamer OPCs with peptide side chains anchored to a particular thymidine residue of the aptamer. The current conjugation strategy utilizes unmodified short peptides and support-bound protected oligonucleotides with activated carboxyl functionality at the T3 thymine nucleobase. The respective modification of the oligonucleotide strand was implemented using N3-derivatized thymidine phosphoramidite. Aptamer OPCs retained the G-quadruplex architecture of the parent DNA structure and showed minor to moderate stabilization. In a series of five OPCs, conjugates bearing T3–Ser–Phe–Asn (SFN) or T3–Tyr–Trp–Asn (YWN) side chains exhibited considerably improved anticoagulant characteristics. Molecular dynamics studies of the aptamer OPC complexes with thrombin revealed the roles of the amino acid nature and sequence in the peptide subunit in modulating the anticoagulant activity.https://www.mdpi.com/1422-0067/23/7/3820thrombin binding aptamerG-quadruplexoligonucleotide–peptide conjugatecircular dichroismanticoagulant activitymolecular dynamics |
| spellingShingle | Vladimir B. Tsvetkov Irina V. Varizhuk Nikolay N. Kurochkin Sergei A. Surzhikov Igor P. Smirnov Andrey A. Stomakhin Natalia A. Kolganova Edward N. Timofeev Anticoagulant Oligonucleotide–Peptide Conjugates: Identification of Thrombin Aptamer Conjugates with Improved Characteristics International Journal of Molecular Sciences thrombin binding aptamer G-quadruplex oligonucleotide–peptide conjugate circular dichroism anticoagulant activity molecular dynamics |
| title | Anticoagulant Oligonucleotide–Peptide Conjugates: Identification of Thrombin Aptamer Conjugates with Improved Characteristics |
| title_full | Anticoagulant Oligonucleotide–Peptide Conjugates: Identification of Thrombin Aptamer Conjugates with Improved Characteristics |
| title_fullStr | Anticoagulant Oligonucleotide–Peptide Conjugates: Identification of Thrombin Aptamer Conjugates with Improved Characteristics |
| title_full_unstemmed | Anticoagulant Oligonucleotide–Peptide Conjugates: Identification of Thrombin Aptamer Conjugates with Improved Characteristics |
| title_short | Anticoagulant Oligonucleotide–Peptide Conjugates: Identification of Thrombin Aptamer Conjugates with Improved Characteristics |
| title_sort | anticoagulant oligonucleotide peptide conjugates identification of thrombin aptamer conjugates with improved characteristics |
| topic | thrombin binding aptamer G-quadruplex oligonucleotide–peptide conjugate circular dichroism anticoagulant activity molecular dynamics |
| url | https://www.mdpi.com/1422-0067/23/7/3820 |
| work_keys_str_mv | AT vladimirbtsvetkov anticoagulantoligonucleotidepeptideconjugatesidentificationofthrombinaptamerconjugateswithimprovedcharacteristics AT irinavvarizhuk anticoagulantoligonucleotidepeptideconjugatesidentificationofthrombinaptamerconjugateswithimprovedcharacteristics AT nikolaynkurochkin anticoagulantoligonucleotidepeptideconjugatesidentificationofthrombinaptamerconjugateswithimprovedcharacteristics AT sergeiasurzhikov anticoagulantoligonucleotidepeptideconjugatesidentificationofthrombinaptamerconjugateswithimprovedcharacteristics AT igorpsmirnov anticoagulantoligonucleotidepeptideconjugatesidentificationofthrombinaptamerconjugateswithimprovedcharacteristics AT andreyastomakhin anticoagulantoligonucleotidepeptideconjugatesidentificationofthrombinaptamerconjugateswithimprovedcharacteristics AT nataliaakolganova anticoagulantoligonucleotidepeptideconjugatesidentificationofthrombinaptamerconjugateswithimprovedcharacteristics AT edwardntimofeev anticoagulantoligonucleotidepeptideconjugatesidentificationofthrombinaptamerconjugateswithimprovedcharacteristics |