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Knouse KW, Flood DT, Vantourout JC, Schmidt MA, Mcdonald IM, Eastgate MD, Baran PS. Nature Chose Phosphates and Chemists Should Too: How Emerging P(V) Methods Can Augment Existing Strategies. ACS CENTRAL SCIENCE 2021; 7:1473-1485. [PMID: 34584948 PMCID: PMC8461637 DOI: 10.1021/acscentsci.1c00487] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Indexed: 05/27/2023]
Abstract
Phosphate linkages govern life as we know it. Their unique properties provide the foundation for many natural systems from cell biology and biosynthesis to the backbone of nucleic acids. Phosphates are ideal natural moieties; existing as ionized species in a stable P(V)-oxidation state, they are endowed with high stability but exhibit enzymatically unlockable potential. Despite intense interest in phosphorus catalysis and condensation chemistry, organic chemistry has not fully embraced the potential of P(V) reagents. To be sure, within the world of chemical oligonucleotide synthesis, modern approaches utilize P(III) reagent systems to create phosphate linkages and their analogs. In this Outlook, we present recent studies from our laboratories suggesting that numerous exciting opportunities for P(V) chemistry exist at the nexus of organic synthesis and biochemistry. Applications to the synthesis of stereopure antisense oligonucleotides, cyclic dinucleotides, methylphosphonates, and phosphines are reviewed as well as chemoselective modification to peptides, proteins, and nucleic acids. Finally, an outlook into what may be possible in the future with P(V) chemistry is previewed, suggesting these examples represent just the tip of the iceberg.
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Affiliation(s)
- Kyle W. Knouse
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Julien C. Vantourout
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael A. Schmidt
- Chemical
and Synthetic Development, Bristol Myers
Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Ivar M. Mcdonald
- Small
Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Martin D. Eastgate
- Chemical
and Synthetic Development, Bristol Myers
Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Phil S. Baran
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Huang Y, Knouse KW, Qiu S, Hao W, Padial NM, Vantourout JC, Zheng B, Mercer SE, Lopez-Ogalla J, Narayan R, Olson RE, Blackmond DG, Eastgate MD, Schmidt MA, McDonald IM, Baran PS. A P(V) platform for oligonucleotide synthesis. Science 2021; 373:1265-1270. [PMID: 34516793 PMCID: PMC8579956 DOI: 10.1126/science.abi9727] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The promise of gene-based therapies is being realized at an accelerated pace, with more than 155 active clinical trials and multiple U.S. Food and Drug Administration approvals for therapeutic oligonucleotides, by far most of which contain modified phosphate linkages. These unnatural linkages have desirable biological and physical properties but are often accessed with difficulty using phosphoramidite chemistry. We report a flexible and efficient [P(V)]–based platform that can install a wide variety of phosphate linkages at will into oligonucleotides. This approach uses readily accessible reagents and can install not only stereodefined or racemic thiophosphates but any combination of (S, R or rac)–PS with native phosphodiester (PO2) and phosphorodithioate (PS2) linkages into DNA and other modified nucleotide polymers. This platform easily accesses this diversity under a standardized coupling protocol with sustainably prepared, stable P(V) reagents.
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Affiliation(s)
- Yazhong Huang
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Kyle W. Knouse
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Elsie Biotechnologies, 4955 Directors Pl, San Diego, CA 92121
| | - Shenjie Qiu
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Wei Hao
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Natalia M. Padial
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Julien C. Vantourout
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Bin Zheng
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Stephen E. Mercer
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Javier Lopez-Ogalla
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Rohan Narayan
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Richard E. Olson
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Donna G. Blackmond
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Martin D. Eastgate
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Michael A. Schmidt
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Ivar M. McDonald
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Phil S. Baran
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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Radzikowska E, Kaczmarek R, Korczyński D, Krakowiak A, Mikołajczyk B, Baraniak J, Guga P, Wheeler KA, Pawlak T, Nawrot B. P-stereocontrolled synthesis of oligo(nucleoside N3'→O5' phosphoramidothioate)s - opportunities and limitations. RSC Adv 2020; 10:35185-35197. [PMID: 35515667 PMCID: PMC9056831 DOI: 10.1039/d0ra04987e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/15/2020] [Indexed: 12/29/2022] Open
Abstract
3'-N-(2-Thio-1,3,2-oxathiaphospholane) derivatives of 5'-O-DMT-3'-amino-2',3'-dideoxy-ribonucleosides (NOTP-N), that bear a 4,4-unsubstituted, 4,4-dimethyl, or 4,4-pentamethylene substituted oxathiaphospholane ring, were synthesized. Within these three series, NOTP-N differed by canonical nucleobases (i.e., AdeBz, CytBz, GuaiBu, or Thy). The monomers were chromatographically separated into P-diastereomers, which were further used to prepare NNPSN' dinucleotides (3), as well as short P-stereodefined oligo(deoxyribonucleoside N3'→O5' phosphoramidothioate)s (NPS-) and chimeric NPS/PO- and NPS/PS-oligomers. The condensation reaction for NOTP-N monomers was found to be 5-6 times slower than the analogous OTP derivatives. When the 5'-end nucleoside of a growing oligomer adopts a C3'-endo conformation, a conformational 'clash' with the incoming NOTP-N monomer takes place, which is a main factor decreasing the repetitive yield of chain elongation. Although both isomers of NNPSN' were digested by the HINT1 phosphoramidase enzyme, the isomers hydrolyzed at a faster rate were tentatively assigned the R P absolute configuration. This assignment is supported by X-ray analysis of the protected dinucleotide DMTdGiBu NPSMeTOAc, which is P-stereoequivalent to the hydrolyzed faster P-diastereomer of dGNPST.
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Affiliation(s)
- Ewa Radzikowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Dariusz Korczyński
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Agnieszka Krakowiak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Barbara Mikołajczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Janina Baraniak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Kraig A Wheeler
- Whitworth University, Department of Chemistry 300 W. Hawthorne Rd. Spokane WA 99251 USA
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
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Simulescu V, Ilia G. Solid-phase Synthesis of Phosphorus Derivatives. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190213112019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The solid-phase synthesis (SPS) of phosphorus-containing compounds is based mainly on the fact that the chemical process is conducted in a two-phase system. One of the components is connected via covalent bonds to a solid support, which is in general an insoluble polymer, representing the solid phase of the process. The other components involved into the process are solubilized in a solution. The method is suitable to be applied to almost any organic compounds. A common example of using solid-phase synthesis is for obtaining products nucleotide containing, similar to nucleic acids. During the whole process, the nucleotide is always on the solid phase, after the condensation reaction, except for the last step, when the synthesis is already finished. Then, the product is released and separated very easily by filtration. The obtained polymer-oligonucleotide product can participate further in condensation reactions as well. Other important biomolecules synthesized by solid-phase approach during the last decades are nucleoside di- and triphosphates, nucleoside diphosphate sugars and dinucleoside polyphosphates. Those products are precursors of deoxysugars, aminodeoxysugars, uronic acids or glycoconjugates, and are also necessary for DNA and RNA synthesis. The use of the solid-phase method in the context of immobilized oligomers is of great interest nowadays. The solid-phase synthesis offers many advantages in comparison with the conventional solution-phase method, because it takes much less time, it is highly stereoselective, the products are separated and purified usually by a simple filtration or decantation, solvents with high boiling points could be used, the whole process is based on solid polymer support and the obtained compounds should not be isolated.
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Affiliation(s)
- Vasile Simulescu
- Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul Bvd., 300223 Timisoara, Romania
| | - Gheorghe Ilia
- Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul Bvd., 300223 Timisoara, Romania
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Honcharenko M, Honcharenko D, Strömberg R. Efficient Conjugation to Phosphorothioate Oligonucleotides by Cu-Catalyzed Huisgen 1,3-Dipolar Cycloaddition. Bioconjug Chem 2019; 30:1622-1628. [PMID: 31067031 DOI: 10.1021/acs.bioconjchem.9b00217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Improving oligonucleotide delivery is critical for the further development of oligonucleotide-based therapeutics. Covalent attachment of reporter molecules is one of the most promising approaches toward efficient oligonucleotide-based therapies. An efficient methods for the attachment of a variety of reporter groups is Cu(I)-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition. However, the majority of potential oligonucleotide (ON) therapeutics in clinical trials are carrying phosphorothioate (PS) linkages, and this robust conjugation method is not yet established for these ONs due to a general concern of Cu-S interaction. Here, we developed a method allowing for efficient conjugation of peptides to PS oligonucleotides. The method utilizes solid supported oligonucleotides that can be readily transformed into "clickable ONs" by simple linker conjugation and further reacted with an azido containing moiety (e.g., a peptide) using the CuBr × Me2S complex as a superior catalyst in that reaction. This study opens the way for further development of PS oligonucleotide-conjugates by means of efficient Cu(I)-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition.
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Affiliation(s)
- Malgorzata Honcharenko
- Department of Biosciences and Nutrition , Karolinska Institute , SE-14183 Huddinge , Sweden
| | - Dmytro Honcharenko
- Department of Biosciences and Nutrition , Karolinska Institute , SE-14183 Huddinge , Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition , Karolinska Institute , SE-14183 Huddinge , Sweden
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Krawczyk T, Zalewski M, Szołtysik R, Korytkowska-Wałach A. Determination of silyl peroxides by ultra-performance liquid chromatography/electrospray ionisation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:2040-2046. [PMID: 30221410 DOI: 10.1002/rcm.8282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/10/2018] [Accepted: 09/10/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Residual initiators in polymers are a concern in the case of products that come directly into contact with the human body or food. Due to low concentrations and difficulties in the sample preparation, highly sensitive and selective methods are required. METHODS A series of bis-silyl- and alkyl-silyl peroxides were analysed by electrospray ionisation mass spectrometry (ESI-MS) on an ultra-performance liquid chromatography/time-of-flight (UPLC/TOF) instrument. Li, Na, K, and NH4 acetates were used to promote the formation of [M + Me]+ ions. The sample preparation involved only dissolution of the polymer sample in 0.1 mL of acetonitrile, followed by precipitation with 1 mL of water. A portion of 0.1-1 μL of the solution was then analysed without further treatment by UPLC/ESI-MS. RESULTS Limits of detection (LODs) were in the range of 0.06-9 pmol, depending on the peroxide structure. On average, the signal intensity increased with the number of phenyl groups in a peroxide and decreased in the order Na > Li > K > NH4 . Peroxides that did not contain phenyl groups could not be detected. Collision-induced dissociation experiments can be used for structural investigations of alkyl-silyl peroxides. It was possible to detect 2 × 10-4 % (LOD = 7 × 10-5 %) of unreacted Ph3 SiOOt-Bu in the poly(methyl methacrylate) sample. CONCLUSIONS The method is suitable for the analysis of trace peroxide initiators in polymers and for other purposes where LODs in the pmol range are required.
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Affiliation(s)
- Tomasz Krawczyk
- Department of Chemical Organic Technology and Petrochemistry, Faculty of Chemistry, Silesian University of Technology, ul. Krzywoustego 4, 44-100, Gliwice, Poland
| | - Mariusz Zalewski
- Department of Chemical Organic Technology and Petrochemistry, Faculty of Chemistry, Silesian University of Technology, ul. Krzywoustego 4, 44-100, Gliwice, Poland
| | - Rafał Szołtysik
- Department of Chemical Organic Technology and Petrochemistry, Faculty of Chemistry, Silesian University of Technology, ul. Krzywoustego 4, 44-100, Gliwice, Poland
| | - Anna Korytkowska-Wałach
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Faculty of Chemistry, Silesian University of Technology, ul. Krzywoustego 4, 44-100, Gliwice, Poland
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7
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Kulik K, Kaczmarek R, Baraniak J, Ślepokura K, Gryaznov S. Novel method for the synthesis of dinucleoside-(N3′ →P5′)-phosphoramidothioates. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.04.094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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8
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Nukaga Y, Oka N, Wada T. Stereocontrolled Solid-Phase Synthesis of Phosphate/Phosphorothioate (PO/PS) Chimeric Oligodeoxyribonucleotides on an Automated Synthesizer Using an Oxazaphospholidine–Phosphoramidite Method. J Org Chem 2016; 81:2753-62. [DOI: 10.1021/acs.joc.5b02793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Yohei Nukaga
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Natsuhisa Oka
- Department
of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Takeshi Wada
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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