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Knizhnik E, Chumakov S, Svetlova J, Pavlova I, Khodarovich Y, Brylev V, Severov V, Alieva R, Kozlovskaya L, Andreev D, Aralov A, Varizhuk A. Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication. Biomolecules 2023; 13:1660. [PMID: 38002341 PMCID: PMC10668963 DOI: 10.3390/biom13111660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Ribosomal frameshifting (RFS) at the slippery site of SARS-CoV-2 RNA is essential for the biosynthesis of the viral replication machinery. It requires the formation of a pseudoknot (PK) structure near the slippery site and can be inhibited by PK-disrupting oligonucleotide-based antivirals. We obtained and compared three types of such antiviral candidates, namely locked nucleic acids (LNA), LNA-DNA gapmers, and G-clamp-containing phosphorothioates (CPSs) complementary to PK stems. Using optical and electrophoretic methods, we showed that stem 2-targeting oligonucleotide analogs induced PK unfolding at nanomolar concentrations, and this effect was particularly pronounced in the case of LNA. For the leading PK-unfolding LNA and CPS oligonucleotide analogs, we also demonstrated dose-dependent RSF inhibition in dual luciferase assays (DLAs). Finally, we showed that the leading oligonucleotide analogs reduced SARS-CoV-2 replication at subtoxic concentrations in the nanomolar range in two human cell lines. Our findings highlight the promise of PK targeting, illustrate the advantages and limitations of various types of DNA modifications and may promote the future development of oligonucleotide-based antivirals.
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Affiliation(s)
- Ekaterina Knizhnik
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Stepan Chumakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.C.); (Y.K.); (V.B.); (D.A.)
| | - Julia Svetlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
| | - Iulia Pavlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Yuri Khodarovich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.C.); (Y.K.); (V.B.); (D.A.)
- Research and Educational Resource Center for Cellular Technologies of The Peoples’ Friendship University of Russia, 117198 Moscow, Russia
| | - Vladimir Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.C.); (Y.K.); (V.B.); (D.A.)
| | - Vjacheslav Severov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
| | - Rugiya Alieva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia;
- Raman Spectroscopy Laboratory, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Liubov Kozlovskaya
- Chumakov Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences (Institute of Poliomyelitis), 108819 Moscow, Russia;
| | - Dmitry Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.C.); (Y.K.); (V.B.); (D.A.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Andrey Aralov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.C.); (Y.K.); (V.B.); (D.A.)
| | - Anna Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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Traykovska M, Penchovsky R. Targeting SAM-I Riboswitch Using Antisense Oligonucleotide Technology for Inhibiting the Growth of Staphylococcus aureus and Listeria monocytogenes. Antibiotics (Basel) 2022; 11:1662. [PMID: 36421306 PMCID: PMC9686682 DOI: 10.3390/antibiotics11111662] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 08/05/2023] Open
Abstract
With the discovery of antibiotics, a productive period of antibacterial drug innovation and application in healthcare systems and agriculture resulted in saving millions of lives. Unfortunately, the misusage of antibiotics led to the emergence of many resistant pathogenic strains. Some riboswitches have risen as promising targets for developing antibacterial drugs. Here, we describe the design and applications of the chimeric antisense oligonucleotide (ASO) as a novel antibacterial agent. The pVEC-ASO-1 consists of a cell-penetrating oligopeptide known as pVEC attached to an oligonucleotide part with modifications of the first and the second generations. This combination of modifications enables specific mRNA degradation under multiple turnover conditions via RNase H. The pVEC-ASO targets the S-adenosyl methionine (SAM)-I riboswitch found in the genome of many Gram-positive bacteria. The SAM-I riboswitch controls not only the biosynthesis but also the transport of SAM. We have established an antibiotic dosage of 700 nM (4.5 µg/mL) of pVEC-ASO that inhibits 80% of the growth of Staphylococcus aureus and Listeria monocytogenes. The pVEC-ASO-1 does not show any toxicity in the human cell line at MIC80's concentration. We have proven that the SAM-I riboswitch is a suitable target for antibacterial drug development based on ASO. The approach is rational and easily adapted to other bacterial RNA targets.
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Traykovska M, Otcheva LA, Penchovsky R. Targeting TPP Riboswitches Using Chimeric Antisense Oligonucleotide Technology for Antibacterial Drug Development. ACS APPLIED BIO MATERIALS 2022; 5:4896-4902. [PMID: 36170638 DOI: 10.1021/acsabm.2c00628] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nowadays, the emergence and the transmission of multidrug-resistant pathogenic bacteria are a severe menace mounting a lot of pressure on the healthcare systems worldwide. Many severe outbreaks of bacterial infections have been reported worldwide in recent years. Thus, there is an immediate demand to develop antibiotics. Some riboswitches are potential targets for overcoming bacterial resistance. This paper demonstrates the bacteriostatic effect of an antisense oligonucleotide (ASO) engineered to suppress the growth of pathogenic bacteria such as Listeria monocytogenes by targeting the Thiamine Pyrophosphate (TPP) riboswitch. It does not inhibit the growth of the conditional pathogenic bacteria Escherichia coli, as it lacks the TPP riboswitch, showing the specificity of action of our ASO. It is covalently bonded with the cell-penetrating protein pVEC. We did bioinformatics analyses of the thiamine pyrophosphate riboswitch regarding its role in synthesizing the metabolite thiamine pyrophosphate, which is essential for bacteria. L. monocytogenes is intrinsically resistant to cephalosporins and usually is treated with ampicillin. A dosage of ASO has been established that inhibits 80% of bacterial growth at 700 nM (4.5 μg/mL). Thus, the TPP riboswitch is a valuable antibacterial target.
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Affiliation(s)
- Martina Traykovska
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia 1164, Bulgaria
| | - Lozena A Otcheva
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia 1164, Bulgaria
| | - Robert Penchovsky
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia 1164, Bulgaria
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Pavlova N, Penchovsky R. Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets. Antibiotics (Basel) 2022; 11:antibiotics11091177. [PMID: 36139956 PMCID: PMC9495176 DOI: 10.3390/antibiotics11091177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
Antibiotic resistance (AR) is an acute problem that results in prolonged and debilitating illnesses. AR mortality worldwide is growing and causes a pressing need to research novel mechanisms of action and untested target molecules. This article presents in silico analyses of eight bacterial riboswitches for their suitability for antibacterial drug targets. Most bacterial riboswitches are located in the 5′-untranslated region of messenger RNAs, act as allosteric cis-acting gene control elements, and have not been found in humans before. Sensing metabolites, the riboswitches regulate the synthesis of vital cellular metabolites in various pathogenic bacteria. The analyses performed in this article represent a complete and informative genome-wide bioinformatics analysis of the adequacy of eight riboswitches as antibacterial drug targets in different pathogenic bacteria based on four criteria. Due to the ability of the riboswitch to control biosynthetic pathways and transport proteins of essential metabolites and the presence/absence of alternative biosynthetic pathways, we classified them into four groups based on their suitability for use as antibacterial drug targets guided by our in silico analyses. We concluded that some of them are promising targets for antibacterial drug discovery, such as the PreQ1, MoCo RNA, cyclic-di-GMP I, and cyclic-di-GMP II riboswitches.
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Versatile tools of synthetic biology applied to drug discovery and production. Future Med Chem 2022; 14:1325-1340. [PMID: 35975897 DOI: 10.4155/fmc-2022-0063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although synthetic biology is an emerging research field, which has come to prominence within the last decade, it already has many practical applications. Its applications cover the areas of pharmaceutical biotechnology and drug discovery, bringing essential novel methods and strategies such as metabolic engineering, reprogramming the cell fate, drug production in genetically modified organisms, molecular glues, functional nucleic acids and genome editing. This review discusses the main avenues for synthetic biology application in pharmaceutical biotechnology. The authors believe that synthetic biology will reshape drug development and drug production to a similar extent as the advances in organic chemical synthesis in the 20th century. Therefore, synthetic biology already plays an essential role in pharmaceutical, biotechnology, which is the main focus of this review.
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Penchovsky R, Pavlova N, Kaloudas D. RSwitch: A Novel Bioinformatics Database on Riboswitches as Antibacterial Drug Targets. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:804-808. [PMID: 32248122 DOI: 10.1109/tcbb.2020.2983922] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The RSwitch is a MySQL database implemented on a PHP-based server, which also provides various useful tools for analyses of DNA, RNA, and protein sequences applying a user-friendly interface. The RSwitch database currently contains information and annotations of 215 bacterial riboswitches from 16 different types found in 50 human pathogenic bacteria. The riboswitch classes include those sensing FMN, glmS, Cobalamin, Lysine, SAH, SAM, Purine, TPP, c-di-GMPI, c-di-GMPII, Moco, PreQ1, Fluoride, Glycine, Mg2+, and Mn2+ type of bacterial riboswitches. The database provides information about the riboswitch aptamer sequences, the thermodynamic ensemble of the RNA structures on partition function and on free minimum energy function. Additionally, the database presents the centroid structure and the positional entropy for each position of the aptamer sequences. The database also provides the biochemical pathways in which the riboswitches are involved in, as well as multiple sequence alignments, multi-drug resistance bacterial strains and consensus motifs for each type of the switches. The RSwitch database is permanently available online without any restrictions. This bioinformatics database provides for the first time all information needed for assessing the suitability of the presented riboswitches as antibacterial drug targets.
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Pavlova N, Penchovsky R. Genome-wide bioinformatics analysis of FMN, SAM-I, glmS, TPP, lysine, purine, cobalamin, and SAH riboswitches for their applications as allosteric antibacterial drug targets in human pathogenic bacteria. Expert Opin Ther Targets 2019; 23:631-643. [DOI: 10.1080/14728222.2019.1618274] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nikolet Pavlova
- Department of Genetics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Robert Penchovsky
- Department of Genetics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
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