1
|
Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. Selective enhancement of (6-4) photoproduct formation in dithymine dinucleotides driven by specific sugar puckering. Org Biomol Chem 2024; 22:3025-3034. [PMID: 38530278 DOI: 10.1039/d4ob00279b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Four dinucleotide analogs of thymidylyl(3'-5')thymidine (TpT) have been designed and synthesized with a view to increase the selectivity, with respect to CPD, of efficient UV-induced (6-4) photoproduct formation. The deoxyribose residues of these analogs have been modified to increase north and south conformer populations at 5'- and 3'-ends, respectively. Dinucleotides whose 5'-end north population exceeds ca. 60% and whose 3'-end population is almost completely south display a three-fold selective enhancement in (6-4) adduct production when exposed to UV radiation, compared to TpT. These experimental results undoubtedly provide robust foundations for studying the singular ground-state proreactive species involved in the (6-4) photoproduct formation mechanism.
Collapse
Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Clément Denhez
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR des Sciences Exactes et Naturelles, Reims, France
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, F-38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| |
Collapse
|
2
|
i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds. Commun Chem 2023; 6:31. [PMID: 36797370 PMCID: PMC9935537 DOI: 10.1038/s42004-023-00831-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
G-quadruplex and i-motif nucleic acid structures are believed to fold through kinetic partitioning mechanisms. Such mechanisms explain the structural heterogeneity of G-quadruplex metastable intermediates which have been extensively reported. On the other hand, i-motif folding is regarded as predictable, and research on alternative i-motif folds is limited. While TC5 normally folds into a stable tetrameric i-motif in solution, we report that 2'-deoxy-2'-fluoroarabinocytidine (araF-C) substitutions can prompt TC5 to form an off-pathway and kinetically-trapped dimeric i-motif, thereby expanding the scope of i-motif folding landscapes. This i-motif is formed by two strands, associated head-to-head, and featuring zero-nucleotide loops which have not been previously observed. Through spectroscopic and computational analyses, we also establish that the dimeric i-motif is stabilized by fluorine and non-fluorine hydrogen bonds, thereby explaining the superlative stability of araF-C modified i-motifs. Comparative experimental findings suggest that the strength of these interactions depends on the flexible sugar pucker adopted by the araF-C residue. Overall, the findings reported here provide a new role for i-motifs in nanotechnology and also pose the question of whether unprecedented i-motif folds may exist in vivo.
Collapse
|
3
|
Pal S, Chandra G, Patel S, Singh S. Fluorinated Nucleosides: Synthesis, Modulation in Conformation and Therapeutic Application. CHEM REC 2022; 22:e202100335. [PMID: 35253973 DOI: 10.1002/tcr.202100335] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/22/2022] [Indexed: 12/17/2022]
Abstract
Over the last twenty years, fluorination on nucleoside has established itself as the most promising tool to use to get biologically active compounds that could sustain the clinical trial by affecting the pharmacodynamics and pharmacokinetic properties. Due to fluorine's inherent unique properties and its judicious introduction into the molecule, makes the corresponding nucleoside metabolically very stable, lipophilic, and opens a new site of intermolecular binding. Fluorination on various nucleosides has been extensively studied as a result, a series of fluorinated nucleosides come up for different therapeutic uses which are either approved by the FDA or under the advanced stage of the clinical trial. Here in this review, we are summarizing the latest development in the chemistry of fluorination on nucleoside that led to varieties of new analogs like carbocyclic, acyclic, and conformationally biased nucleoside and their biological properties, the influence of fluorine on conformation, oligonucleotide stability, and their use in therapeutics.
Collapse
Affiliation(s)
- Shantanu Pal
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
| | - Girish Chandra
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Samridhi Patel
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Sakshi Singh
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
| |
Collapse
|
4
|
Jana SK, Harikrishna S, Sudhakar S, El-Khoury R, Pradeepkumar PI, Damha MJ. Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA-RNA Hybrids. J Org Chem 2022; 87:2367-2379. [PMID: 35133166 DOI: 10.1021/acs.joc.1c02254] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we describe results on the pairing properties of synthetic DNA and RNA oligonucleotides that contain nucleotide analogues with a 7-membered sugar ring (oxepane nucleotides). Specifically, we describe the stereoselective synthesis of a set of three oxepane thymine nucleosides (OxT), their conversion to phosphoramidite derivatives, and their use in solid-phase synthesis to yield chimeric OxT-DNA and OxT-RNA strands. The different regioisomeric OxT phosphoramidites allowed for positional variations of the phosphate bridge and assessment of duplex stability when the oxepane nucleotides were incorporated in dsDNA, dsRNA, and DNA-RNA hybrids. Little to no destabilization was observed when two of the three regioisomeric OxT units were incorporated in the DNA strand of DNA-RNA hybrids, a remarkable result considering the dramatically different structure of oxepanes in comparison to 2'-deoxynucleosides. Extensive molecular modeling and dynamics studies further revealed the various structural features responsible for the tolerance of both OxT modifications in DNA-RNA duplexes, such as base-base stacking and sugar-phosphate H-bond interactions. These studies suggest that oxepane nucleotide analogues may find applications in synthetic biology, where synthetic oligonucleotides can be used to create new tools for biotechnology and medicine.
Collapse
Affiliation(s)
- Sunit Kumar Jana
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - S Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Roberto El-Khoury
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| |
Collapse
|
5
|
Zafrani Y, Parvari G, Amir D, Ghindes-Azaria L, Elias S, Pevzner A, Fridkin G, Berliner A, Gershonov E, Eichen Y, Saphier S, Katalan S. Modulation of the H-Bond Basicity of Functional Groups by α-Fluorine-Containing Functions and its Implications for Lipophilicity and Bioisosterism. J Med Chem 2021; 64:4516-4531. [PMID: 33844540 DOI: 10.1021/acs.jmedchem.0c01868] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Modulation of the H-bond basicity (pKHB) of various functional groups (FGs) by attaching fluorine functions and its impact on lipophilicity and bioisosterism considerations are described. In general, H/F replacement at the α-position to H-bond acceptors leads to a decrease of the pKHB value, resulting, in many cases, in a dramatic increase in the compounds' lipophilicity (log Po/w). In the case of α-CF2H, we found that these properties may also be affected by intramolecular H-bonds between CF2H and the FG. A computational study of ketone and sulfone series revealed that α-fluorination can significantly affect overall polarity, charge distribution, and conformational preference. The unique case of α-di- and trifluoromethyl ketones, which exist in octanol/water phases as ketone, hemiketal, and gem-diol forms, in equilibrium, prevents direct log Po/w determination by conventional methods, and therefore, the specific log Po/w values of these species were determined directly, for the first time, using Linclau's 19F NMR-based method.
Collapse
Affiliation(s)
- Yossi Zafrani
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Galit Parvari
- Schulich Faculty of Chemistry Technion, Israel Institute of Technology, Technion City, Haifa 3200008, Israel
| | - Dafna Amir
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Lee Ghindes-Azaria
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Shlomi Elias
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Alexander Pevzner
- Department of Physical Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Gil Fridkin
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Anat Berliner
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Eytan Gershonov
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Yoav Eichen
- Schulich Faculty of Chemistry Technion, Israel Institute of Technology, Technion City, Haifa 3200008, Israel
| | - Sigal Saphier
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Shahaf Katalan
- Department of Pharmacology, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| |
Collapse
|
6
|
Liu Y, Jiang S, Yan W, Qin J, He M, Qin S, Yu J. Enhanced mechanical and thermal properties of polyamide 6/p (N-(4-F-phenylmaleimide)–alt-styrene) composites based on interfacial complexation inducing crystal transformation. POLYMER 2021. [DOI: 10.1016/j.polymer.2020.123237] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
7
|
Zhang W, Feng Z, Yang Y, Sun W, Pooley S, Cao J, Gao Z. Bi-functional hydrogen and coordination bonding surfactant: A novel and promising collector for improving the separation of calcium minerals. J Colloid Interface Sci 2020; 585:787-799. [PMID: 33131784 DOI: 10.1016/j.jcis.2020.10.059] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 10/23/2022]
Abstract
Mono-functional chelating collectors exhibit limited selectivity in the flotation of minerals. In particular, the selective separation of calcium minerals presents a significant challenge because mono-functional chelating collectors, such as fatty acid, indistinguishably adsorb onto mineral surfaces by coordinating with the same metal cation (Ca2+). Thus, there is an urgent need to develop new-mode-functional collectors to separate calcium minerals and a need to understand the underlying chemoselectivity. Given the difference of the hydrogen bonding ability of anions with fluorite, calcite and scheelite surfaces, the introduction of additional hydrogen bonding functional groups into collector molecules is a novel strategy to improve selectivity. In this study, a hydrogen and coordination bonding (bi-functional) collector, 2-cyano-N-ethylcarbamoyl acetamide (CEA) was developed, which could form coordination bonds with the Ca2+ ions (by carbonyl groups) and hydrogen bonds with the anions (by amino groups) on calcium mineral surfaces. The results of flotation tests showed that CEA can selectively separate fluorite and calcite from scheelite at pH 7. The promising selectivity of CEA lies in both the electrical properties and the anions' hydrogen bonding ability with the three calcium minerals. The negatively charged scheelite surfaces are not conducive to coordination bonding with CEA while the positively charged fluorite and calcite surfaces are. Besides, the hydrogen bonding ability of fluorite (F-) and calcite (CO32-) with carbamido in CEA is higher than that of scheelite (WO42-), and this also plays an essential role. This coordination and hydrogen bonding based surfactant design protocol has a great potential in the development of tail-made collectors/depressants for the separation of other oxidized minerals.
Collapse
Affiliation(s)
- Wanjia Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Hunan Province for Clean and Efficient Utilization of Strategic Calcium-containing Mineral Resources, Central South University, Changsha, China
| | - Zhitao Feng
- Department of Chemistry, University of California-Davis, Davis, United States
| | - Yuhang Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; School of Materials Science and Engineering, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Wei Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Hunan Province for Clean and Efficient Utilization of Strategic Calcium-containing Mineral Resources, Central South University, Changsha, China
| | - Stephen Pooley
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Hunan Province for Clean and Efficient Utilization of Strategic Calcium-containing Mineral Resources, Central South University, Changsha, China
| | - Jian Cao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Hunan Province for Clean and Efficient Utilization of Strategic Calcium-containing Mineral Resources, Central South University, Changsha, China.
| | - Zhiyong Gao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Hunan Province for Clean and Efficient Utilization of Strategic Calcium-containing Mineral Resources, Central South University, Changsha, China.
| |
Collapse
|
8
|
Labbé MO, Li F, Chau I, Xiong ZJ, Santhakumar V, Dostie S, Guindon Y. Identification of a C2′ -fluorinated SAH analogue. CAN J CHEM 2020. [DOI: 10.1139/cjc-2020-0029] [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 progress towards the development of a nucleoside analogue with inhibitory properties against SETDB1, a histone methyltransferase (HMT), is described. Based on the structure of the natural cofactor S-adenosyl-L-methionine (SAM), novel fluorinated nucleoside analogues were synthesized. Two of these compounds bearing a C2′-F and C5′-primary amine moiety showed moderate inhibition of SETDB1, a lysine HMT for which there is only one reported inhibitor.
Collapse
Affiliation(s)
- Marc-Olivier Labbé
- Bio-organic Chemistry Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
- Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Zi-Jian Xiong
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | | | - Starr Dostie
- Bio-organic Chemistry Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Yvan Guindon
- Bio-organic Chemistry Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
- Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| |
Collapse
|
9
|
|
10
|
Zafrani Y, Sod-Moriah G, Yeffet D, Berliner A, Amir D, Marciano D, Elias S, Katalan S, Ashkenazi N, Madmon M, Gershonov E, Saphier S. CF 2H, a Functional Group-Dependent Hydrogen-Bond Donor: Is It a More or Less Lipophilic Bioisostere of OH, SH, and CH 3? J Med Chem 2019; 62:5628-5637. [PMID: 31091098 DOI: 10.1021/acs.jmedchem.9b00604] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of the CF2H moiety on H-bond (HB) acidity and lipophilicity of various compounds, when attached directly to an aromatic ring or to other functions like alkyls, ethers/thioethers, or electron-withdrawing groups, are discussed. It was found that the CF2H group acts as a HB donor with a strong dependence on the attached functional group ( A = 0.035-0.165). Regarding lipophilicity, the CF2H group may act as a more lipophilic bioisostere of OH but as a similar or less lipophilic bioisostere of SH and CH3, respectively, when attached to Ar or alkyl. In addition, the lipophilicity of ethers, sulfoxides, and sulfones is dramatically increased upon CH3/CF2H exchange at the α position. Interestingly, this exchange significantly affects not only the polarity and the volume of the solutes but also their HB-accepting ability, the main factors influencing log Poct. Accordingly, this study may be helpful in the rational design of drugs containing this moiety.
Collapse
Affiliation(s)
- Yossi Zafrani
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Gali Sod-Moriah
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Dina Yeffet
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Anat Berliner
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Dafna Amir
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Daniele Marciano
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Shlomi Elias
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Shahaf Katalan
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Nissan Ashkenazi
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Moran Madmon
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Eytan Gershonov
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| | - Sigal Saphier
- The Department of Organic Chemistry , Israel Institute for Biological Research , Ness-Ziona 74100 , Israel
| |
Collapse
|