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Zharkov TD, Mironova EM, Markov OV, Zhukov SA, Khodyreva SN, Kupryushkin MS. Fork- and Comb-like Lipophilic Structures: Different Chemical Approaches to the Synthesis of Oligonucleotides with Multiple Dodecyl Residues. Int J Mol Sci 2023; 24:14637. [PMID: 37834092 PMCID: PMC10572690 DOI: 10.3390/ijms241914637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Lipophilic oligonucleotide conjugates represent a powerful tool for nucleic acid cellular delivery, and many methods for their synthesis have been developed over the past few decades. In the present study, a number of chemical approaches for the synthesis of different fork- and comb-like dodecyl-containing oligonucleotide structures were performed, including use of non-nucleotide units and different types of phosphate modifications such as alkyl phosphoramidate, phosphoryl guanidine, and triazinyl phosphoramidate. The influence of the number of introduced lipophilic residues, their mutual arrangement, and the type of formed modification backbone on cell penetration was evaluated. The results obtained indicate great potential in the developed chemical approaches, not only for the synthesis of complex oligonucleotide structures but also for the fine-tuning of their properties.
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Affiliation(s)
| | | | | | | | | | - Maxim S. Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (T.D.Z.); (E.M.M.); (O.V.M.); (S.A.Z.); (S.N.K.)
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Kupryushkin MS, Filatov AV, Mironova NL, Patutina OA, Chernikov IV, Chernolovskaya EL, Zenkova MA, Pyshnyi DV, Stetsenko DA, Altman S, Vlassov VV. Antisense oligonucleotide gapmers containing phosphoryl guanidine groups reverse MDR1-mediated multiple drug resistance of tumor cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:211-226. [PMID: 34976439 PMCID: PMC8693280 DOI: 10.1016/j.omtn.2021.11.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/28/2021] [Indexed: 10/26/2022]
Abstract
Antisense gapmer oligonucleotides containing phosphoryl guanidine (PG) groups, e.g., 1,3-dimethylimidazolidin-2-imine, at three to five internucleotidic positions adjacent to the 3' and 5' ends were prepared via the Staudinger chemistry, which is compatible with conditions of standard automated solid-phase phosphoramidite synthesis for phosphodiester and, notably, phosphorothioate linkages, and allows one to design a variety of gapmeric structures with alternating linkages, and deoxyribose or 2'-O-methylribose backbone. PG modifications increased nuclease resistance in serum-containing medium for more than 21 days. Replacing two internucleotidic phosphates by PG groups in phosphorothioate-modified oligonucleotides did not decrease their cellular uptake in the absence of lipid carriers. Increasing the number of PG groups from two to seven per oligonucleotide reduced their ability to enter the cells in the carrier-free mode. Cationic liposomes provided similar delivery efficiency of both partially PG-modified and unmodified oligonucleotides. PG-gapmers were designed containing three to four PG groups at both wings and a central "window" of seven deoxynucleotides with either phosphodiester or phosphorothioate linkages targeted to MDR1 mRNA providing multiple drug resistance of tumor cells. Gapmers efficiently silenced MDR1 mRNA and restored the sensitivity of tumor cells to chemotherapeutics. Thus, PG-gapmers can be considered as novel, promising types of antisense oligonucleotides for targeting biologically relevant RNAs.
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Affiliation(s)
- Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Anton V Filatov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Nadezhda L Mironova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Olga A Patutina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Ivan V Chernikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Elena L Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Dmitry A Stetsenko
- Department of Physics, Novosibirsk State University, Pirogov Str. 2, Novosibirsk 630090, Russia.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 10, Novosibirsk 630090, Russia
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.,Life Sciences, Arizona State University, Tempe, AZ 85281, USA.,Montreal Clinical Research Institute, Montreal QC H2W 1R7, Canada
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
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Kanarskaya MA, Golyshev VM, Pyshnyi DV, Lomzov AA. Structure and hybridization properties of phosphoryl guanidine oligonucleotides under crowding conditions. Biochem Biophys Res Commun 2021; 577:110-115. [PMID: 34509722 DOI: 10.1016/j.bbrc.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
Phosphoryl guanidine oligonucleotides (PGOs) are promising uncharged analogs of nucleic acids and are used in a variety of applications. The importance of hydration is frequently ignored during the design of modified nucleic acid probes. Such hydrophobic modifications (phosphoryl guanidine) are expected to have a significant impact on the structure and thermal stability of the affected oligo with complementary nucleic acids. Here we aimed to investigate (by the osmotic stress method) hydration changes upon the formation of a duplex of a PGO with complementary DNA. According to our results, the presence of phosphoryl guanidines in one or both strands of a duplex only minimally affects hydration alterations under crowding conditions. The secondary structure of native and modified duplexes did not change significantly in the presence of ethanol, ethylene glycol, polyethylene glycol 200, or polyethylene glycol 1000. After the addition of a cosolvent, the thermodynamic stability of the PGO complexes changed in the same manner as that seen in a corresponding DNA duplex. The findings reported here and our previous studies form the basis for efficient use of PGOs in basic research and a variety of applications.
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Affiliation(s)
- Maria A Kanarskaya
- Laboratory of Biomedical Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Victor M Golyshev
- Laboratory of Biomedical Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Dmitrii V Pyshnyi
- Laboratory of Biomedical Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Alexander A Lomzov
- Laboratory of Biomedical Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
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Zhou J, Krishnan N, Jiang Y, Fang RH, Zhang L. Nanotechnology for virus treatment. NANO TODAY 2021; 36:101031. [PMID: 33519948 PMCID: PMC7836394 DOI: 10.1016/j.nantod.2020.101031] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 04/14/2023]
Abstract
The continued emergence of novel viruses poses a significant threat to global health. Uncontrolled outbreaks can result in pandemics that have the potential to overburden our healthcare and economic systems. While vaccination is a conventional modality that can be employed to promote herd immunity, antiviral vaccines can only be applied prophylactically and do little to help patients who have already contracted viral infections. During the early stages of a disease outbreak when vaccines are unavailable, therapeutic antiviral drugs can be used as a stopgap solution. However, these treatments do not always work against emerging viral strains and can be accompanied by adverse effects that sometimes outweigh the benefits. Nanotechnology has the potential to overcome many of the challenges facing current antiviral therapies. For example, nanodelivery vehicles can be employed to drastically improve the pharmacokinetic profile of antiviral drugs while reducing their systemic toxicity. Other unique nanomaterials can be leveraged for their virucidal or virus-neutralizing properties. In this review, we discuss recent developments in antiviral nanotherapeutics and provide a perspective on the application of nanotechnology to the SARS-CoV-2 outbreak and future virus pandemics.
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Affiliation(s)
- Jiarong Zhou
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nishta Krishnan
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yao Jiang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ronnie H Fang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Liangfang Zhang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
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