1
|
Li X, Groaz E, Herdewijn P, Lescrinier E. Impact of Single Acyclic Phosphonate Nucleotide (ZNA) Modifications on DNA Duplex Stability. Chemistry 2024:e202401254. [PMID: 38687344 DOI: 10.1002/chem.202401254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
An acyclic phosphonate-linked nucleic acid backbone (ZNA) demonstrated the capability to support duplex formation and propagate genetic information in vivo, unveiling its potential for evolution into a synthetic genetic system (XNA). To determine the structural impact of such modification, modified Dickerson Drew DNA dodecamers (DDDs) were prepared by solid phase synthesis, each containing either an (R) or (S) isomeric form of a cytosine ZNA nucleotide. While the DDD is known to adopt a stable duplex, both duplex and hairpin forms were simultaneously observed for both modified oligonucleotides by NMR spectroscopy over a broad temperature range (5-65 °C). Diffusion-ordered spectroscopy (DOSY) experiments allowed to separate duplex and hairpin signals based on the different diffusion constants of both conformational states. For the oligomer containing (R)-ZNA, only the duplex form occurred at 5 °C, while it was not possible to determine by NMR a single hairpin conformation at higher temperatures. In the case of the (S)-ZNA nucleoside modified oligomer, both hairpin and duplex forms were observable at 0 °C, while a single hairpin conformation was detected at 37 °C, suggesting a higher destabilizing effect on dsDNA.
Collapse
Affiliation(s)
- Xinlu Li
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, Leuven, B-3000, Belgium
| | - Elisabetta Groaz
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, Leuven, B-3000, Belgium
| | - Piet Herdewijn
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, Leuven, B-3000, Belgium
| | - Eveline Lescrinier
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, Leuven, B-3000, Belgium
| |
Collapse
|
2
|
Xu Y, Groaz E, Rihon J, Herdewijn P, Lescrinier E. Synthesis, antiviral activity, and computational study of β-d-xylofuranosyl nucleoside phosphonates. Eur J Med Chem 2023; 255:115379. [PMID: 37120998 DOI: 10.1016/j.ejmech.2023.115379] [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: 01/31/2023] [Revised: 03/14/2023] [Accepted: 04/12/2023] [Indexed: 05/02/2023]
Abstract
Molecular dynamics (MD) simulations provided insights into the favorable interactions between xylose nucleosides bearing a phosphonate moiety at their 3'-position and specific residues at the active site of the archetypal RNA-dependent RNA-polymerase (RdRp) of Enterovirus 71. Therefore, a series of xylosyl nucleoside phosphonates with adenine, uracil, cytosine, guanosine, and hypoxanthine as nucleobases were synthesized through multistep sequences starting from a single common precursor. Following antiviral activity evaluation, the adenine containing analogue was found to possess good antiviral activity against RNA viruses displaying an EC50 of 12 and 16 μM against measles virus (MeV) and enterovirus-68 (EV-68), respectively, whereas lacking cytotoxicity.
Collapse
Affiliation(s)
- Yuqing Xu
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Elisabetta Groaz
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium; Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Jérôme Rihon
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| |
Collapse
|
3
|
Tan S, Groaz E, Kalkeri R, Ptak R, Korba BE, Herdewijn P. Reshaping an Acyclic Nucleoside Phosphonate into a Selective Anti-hepatitis B Virus Compound. J Med Chem 2022; 65:9396-9417. [PMID: 35754374 DOI: 10.1021/acs.jmedchem.2c00667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Minor structural modifications of acyclic nucleoside phosphonates can dramatically affect their antiviral properties. This work discloses a shift in the selectivity spectrum of 3-hydroxy-2-(phosphonomethoxy)propyl (HPMP) nucleotides from herpesviruses toward hepatitis B virus (HBV) induced by their acyclic chain 2-substitution with a nonpolar group. Two series of racemic (R,S)-2-methyl-3-hydroxy-2-(phosphonomethoxy)propyl (MHPMP) and (R,S)-2-ethynyl-3-hydroxy-2-(phosphonomethoxy)propyl (EHPMP) nucleotides were initially synthesized. Among these, guanine-containing derivatives exhibited significant anti-HBV activities in the submicromolar range. Enantioenriched MHPMPG and EHPMPG analogues were subsequently obtained by Sharpless asymmetric epoxidation. The (S)-enantiomers possessed an 8- to 26-fold higher potency than the relative (R)-forms. A further comparison of the EC90 values indicated that (S)-EHPMPG inhibited HBV replication more effectively than its 2-methyl analogue. A phosphonodiamidate prodrug of (S)-EHPMPG was thus prepared and found to exert a remarkably high anti-HBV activity (EC50 = 9.27 nM) with excellent selectivity (SI50 > 10,787), proving to be a promising candidate for anti-HBV drug development.
Collapse
Affiliation(s)
- Shuai Tan
- Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000 Leuven, Belgium.,Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Raj Kalkeri
- Department of Infectious Disease Research, Drug Development, Southern Research Institute, 431 Aviation Way, Frederick, Maryland 21701, United States
| | - Roger Ptak
- Department of Infectious Disease Research, Drug Development, Southern Research Institute, 431 Aviation Way, Frederick, Maryland 21701, United States
| | - Brent E Korba
- Department of Microbiology and Immunology, Georgetown University Medical Center, 20057 Washington, D.C., United States
| | - Piet Herdewijn
- Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000 Leuven, Belgium
| |
Collapse
|
4
|
Klejch T, Keough DT, King G, Doleželová E, Česnek M, Buděšínský M, Zíková A, Janeba Z, Guddat LW, Hocková D. Stereo-Defined Acyclic Nucleoside Phosphonates are Selective and Potent Inhibitors of Parasite 6-Oxopurine Phosphoribosyltransferases. J Med Chem 2022; 65:4030-4057. [PMID: 35175749 DOI: 10.1021/acs.jmedchem.1c01881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pathogens such as Plasmodium and Trypanosoma spp. are unable to synthesize purine nucleobases. They rely on the salvage of these purines and their nucleosides from the host cell to synthesize the purine nucleotides required for DNA/RNA production. The key enzymes in this pathway are purine phosphoribosyltransferases (PRTs). Here, we synthesized 16 novel acyclic nucleoside phosphonates, 12 with a chiral center at C-2', and eight bearing a second chiral center at C-6'. Of these, bisphosphonate (S,S)-48 is the most potent inhibitor of the Plasmodium falciparum and P. vivax 6-oxopurine PRTs and the most potent inhibitor of two Trypanosoma brucei (Tbr) 6-oxopurine PRTs yet discovered, with Ki values as low as 2 nM. Crystal structures of (S,S)-48 in complex with human and Tbr 6-oxopurine PRTs show that the inhibitor binds to the enzymes in different conformations, providing an explanation for its potency and selectivity (i.e., 35-fold in favor of the parasite enzymes).
Collapse
Affiliation(s)
- Tomáš Klejch
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic
| | - Dianne T Keough
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Gordon King
- The Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane 4072, Australia
| | - Eva Doleželová
- Institute of Parasitology, Biology Centre ASCR, České Budějovice 37005, Czech Republic
| | - Michal Česnek
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic
| | - Miloš Buděšínský
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre ASCR, České Budějovice 37005, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice 37005, Czech Republic
| | - Zlatko Janeba
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Dana Hocková
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic
| |
Collapse
|
5
|
Marino C, Bordoni AV. Deoxy sugars. General methods for carbohydrate deoxygenation and glycosidation. Org Biomol Chem 2022; 20:934-962. [PMID: 35014646 DOI: 10.1039/d1ob02001c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Deoxy sugars represent an important class of carbohydrates, present in a large number of biomolecules involved in multiple biological processes. In various antibiotics, antimicrobials, and therapeutic agents the presence of deoxygenated units has been recognized as responsible for biological roles, such as adhesion or great affinity to receptors, or improved efficacy. The characterization of glycosidases and glycosyltranferases requires substrates, inhibitors and analogous compounds. Deoxygenated sugars are useful for carrying out specific studies for these enzymes. Deoxy sugars, analogs of natural substrates, may behave as substrates or inhibitors, or may not interact with the enzyme. They are also important for glycodiversification studies of bioactive natural products and glycobiological processes, which could contribute to discovering new therapeutic agents with greater efficacy by modification or replacement of sugar units. Deoxygenation of carbohydrates is, thus, of great interest and numerous efforts have been dedicated to the development of methods for the reduction of sugar hydroxyl groups. Given that carbohydrates are the most important renewable chemicals and are more oxidized than fossil raw materials, it is also important to have methods to selectively remove oxygen from certain atoms of these renewable raw materials. The different methods for removal of OH groups of carbohydrates and representative or recent applications of them are presented in this chapter. Glycosidic bonds in general, and 2-deoxy glycosidic linkages, are included. It is not the scope of this survey to cover all reports for each specific technique.
Collapse
Affiliation(s)
- Carla Marino
- CIHIDECAR, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Ciudad Universitaria, 1428 Buenos Aires, Argentina.
| | - Andrea V Bordoni
- Gerencia Química & Instituto de Nanociencia y Nanotecnología - Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, CONICET, Av. Gral. Paz 1499, B1650KNA San Martín, Buenos Aires, Argentina
| |
Collapse
|
6
|
Liu FW, Ji S, Gao Y, Meng Y, Xu W, Wang H, Yang J, Huang H, Herdewijn P, Wang C. Synthesis and in vitro antitumour activity of 4(R)-methyl-3-O-phosphonomethyl-α-l-threose nucleosides. Eur J Med Chem 2021; 221:113513. [PMID: 34000485 DOI: 10.1016/j.ejmech.2021.113513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 04/16/2021] [Accepted: 04/27/2021] [Indexed: 11/26/2022]
Abstract
A series of novel α-l-threose nucleoside phosphonate analogs, 4(R)-methyl-3-O-phosphonomethyl-α-l-threose nucleosides, were synthesized in multistep sequences starting from d-xylose. The synthetic sequence consisted of the following key stages: (i) the multistep synthesis of 1,2-O-isopropylidenyl-4(R)-methyl-3-O-phosphonomethyl-l-threose, (ii) the transformation of 1,2-O-isopropylidenyl sugar into suitable 1,2-di-O-acyl l-threose precursor, and (iii) the construction of target α-l-threose nucleoside phosphonate analogs by Vorbrüggen glycosidation reaction, deprotection of acyl group, and hydrolysis of diethyl group on phosphonate. The target nucleoside phosphonates were evaluated for their antitumour activities in cell culture-based assays. Compound 8g, 2-fluroadenosine phosphonate, showed remarkable activity against human breast cancer cell lines (MCF-7 and MDA-MB-231) with IC50 values of 0.476 and 0.391 μM, corresponding to 41- and 47-fold higher potency than the reference compound 5-FU, respectively. Subsequent investigations found that the compound 8g can inhibit the proliferation of breast cancer cells and cell cloning. The mechanistic studies indicated that compound 8g could cause DNA damage to breast cancer cells through the ATM-Chk1/Chk2-cdc25c pathway, leading to blockage of the G2/M phase cycle of breast cancer cells, which ultimately led to apoptosis. Moreover, 8g could inhibit the PI3K/AKT signaling pathway and induce apoptosis. These results indicate that compound 8g holds promising potential as an antitumour agent.
Collapse
Affiliation(s)
- Feng-Wu Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Shujie Ji
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yingying Gao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yao Meng
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Wenke Xu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Haixia Wang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Jing Yang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Hao Huang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Cong Wang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China.
| |
Collapse
|
7
|
Groaz E, De Jonghe S. Overview of Biologically Active Nucleoside Phosphonates. Front Chem 2021; 8:616863. [PMID: 33490040 PMCID: PMC7821050 DOI: 10.3389/fchem.2020.616863] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/30/2020] [Indexed: 12/25/2022] Open
Abstract
The use of the phosphonate motif featuring a carbon-phosphorous bond as bioisosteric replacement of the labile P–O bond is widely recognized as an attractive structural concept in different areas of medicinal chemistry, since it addresses the very fundamental principles of enzymatic stability and minimized metabolic activation. This review discusses the most influential successes in drug design with special emphasis on nucleoside phosphonates and their prodrugs as antiviral and cancer treatment agents. A description of structurally related analogs able to interfere with the transmission of other infectious diseases caused by pathogens like bacteria and parasites will then follow. Finally, molecules acting as agonists/antagonists of P2X and P2Y receptors along with nucleotidase inhibitors will also be covered. This review aims to guide readers through the fundamentals of nucleoside phosphonate therapeutics in order to inspire the future design of molecules to target infections that are refractory to currently available therapeutic options.
Collapse
Affiliation(s)
- Elisabetta Groaz
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| |
Collapse
|
8
|
Luo M, Wu S, Kalkeri R, Ptak RG, Zhou T, Van Mellaert L, Wang C, Dumbre SG, Block T, Groaz E, De Jonghe S, Li Y, Herdewijn P. Scalable Synthesis, In Vitro cccDNA Reduction, and In Vivo Antihepatitis B Virus Activity of a Phosphonomethoxydeoxythreosyl Adenine Prodrug. J Med Chem 2020; 63:13851-13860. [PMID: 33191744 DOI: 10.1021/acs.jmedchem.0c01381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Standard literature procedures for the chemical synthesis of l-threose nucleosides generally employ l-ascorbic acid as starting material. Herein, we have explored two alternative routes that start from either l-arabitol or l-diethyl tartrate, both affording 2-O-methyl-l-threofuranose as a key building block for nucleobase incorporation. The access to multigram quantities of this glycosyl donor in a reproducible fashion allows for the preparation of 2'-deoxy-α-l-threofuranosyl phosphonate nucleosides on a large scale. This methodology was applied to the gram scale synthesis of an aryloxy amidate prodrug of phosphonomethoxydeoxythreosyl adenine. This prodrug exerted potent activity against an entecavir-resistant hepatitis B virus (HBV) strain, while leading to a significant reduction in the levels of HBV covalently closed circular DNA in a cellular assay. Furthermore, its remarkable anti-HBV efficacy was also confirmed in vivo using a hydrodynamic injection-based HBV mouse model, without relevant toxicity and systemic exposure occurring.
Collapse
Affiliation(s)
- Min Luo
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49-box 1041, 3000 Leuven, Belgium
| | - Shuo Wu
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1, Tiantan Xili, 100050 Beijing, China
| | - Raj Kalkeri
- Department of Infectious Disease Research, Southern Research Institute, 431 Aviation Way, Frederick, Maryland 21701, United States
| | - Roger G Ptak
- Department of Infectious Disease Research, Southern Research Institute, 431 Aviation Way, Frederick, Maryland 21701, United States
| | - Tianlun Zhou
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania 18902, United States
| | - Lieve Van Mellaert
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Bacteriology, KU Leuven, Rega Institute for Medical Research, Herestraat 49-box 1037, 3000 Leuven, Belgium
| | - Chuanmin Wang
- Department of Infectious Diseases, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Shrinivas G Dumbre
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49-box 1041, 3000 Leuven, Belgium
| | - Timothy Block
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania 18902, United States
| | - Elisabetta Groaz
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49-box 1041, 3000 Leuven, Belgium
| | - Steven De Jonghe
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, KU Leuven, Rega Institute for Medical Research, Herestraat 49-box 1043, 3000 Leuven, Belgium
| | - Yuhuan Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1, Tiantan Xili, 100050 Beijing, China
| | - Piet Herdewijn
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49-box 1041, 3000 Leuven, Belgium
| |
Collapse
|
9
|
Chen X, Luo W, Wang Y, Li Z, Ma X, Peng AY. Efficient Synthesis of Phosphonamidates through One-Pot Sequential Reactions of Phosphonites with Iodine and Amines. Chemistry 2020; 26:14474-14480. [PMID: 32776399 DOI: 10.1002/chem.202002934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 11/10/2022]
Abstract
A one-pot sequential strategy to construct phosphonamidates has been developed by generating phosphonites in situ from arylmagnesium bromides and triethyl phosphite followed by treatment with iodine and amines. A variety of phosphonamidates were obtained with good to excellent yields at room temperature from easily available materials.
Collapse
Affiliation(s)
- Xunwei Chen
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| | - Wenjun Luo
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| | - Yanlin Wang
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| | - Zikang Li
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| | - Xiaorui Ma
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| | - Ai-Yun Peng
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| |
Collapse
|
10
|
Luo M, Groaz E, Snoeck R, Andrei G, Herdewijn P. Amidate Prodrugs of O-2-Alkylated Pyrimidine Acyclic Nucleosides Display Potent Anti-Herpesvirus Activity. ACS Med Chem Lett 2020; 11:1410-1415. [PMID: 32676147 DOI: 10.1021/acsmedchemlett.0c00090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/19/2020] [Indexed: 12/14/2022] Open
Abstract
Three series of amidate prodrugs of O-2-alkylated acyclic nucleosides of the 3-fluoro-2-(phosphonomethoxy)propyl (FPMP), cyclic 3-hydroxy-2-(phosphonomethoxypropyl) (cHPMP), and 2-(phosphonomethoxypropyl) (PMP)-type featuring cytosine and 5-fluorocytosine as nucleobases were readily synthesized. Both the aspartic acid ester and valine ester prodrugs of (R)-O-2-alkylated FPMPC exhibited potent anti-HCMV and VZV activity in the micromolar range. In addition, the valine ester prodrugs of 5-fluorocytosine (R)-O-2-alkylated FPMP and (R)-O-2-alkylated cHPMPC showed inhibitory activity at molar concentrations against these viruses.
Collapse
Affiliation(s)
- Min Luo
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49 box 1043, 3000 Leuven, Belgium
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49 box 1043, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 box 1041, 3000 Leuven, Belgium
| |
Collapse
|
11
|
Abstract
Phosphonates, often used as isosteric replacements for phosphates, can provide important interactions with an enzyme. Due to their high charge at physiological pH, however, permeation into cells can be a challenge. Protecting phosphonates as prodrugs has shown promise in drug delivery. Thus, a variety of structures and cleavage/activation mechanisms exist, enabling release of the active compound. This review describes the structural diversity of these pro-moieties, relevant cleavage mechanisms and recent advances in the design of phosphonate prodrugs.
Collapse
|
12
|
Imoto S, Onitsuka K, Yamaguchi K, Tokuda R, Higashi-Kuwata N, Kuwahara S, Kumamoto H, Maeda K, Haraguchi K, Mitsuya H. Design and Synthesis of 4'-Cyano Dideoxy Isonucleosides and Their Activity against HIV-1 and HBV. HETEROCYCLES 2020. [DOI: 10.3987/com-20-14312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
13
|
Synthesis of a Threosyl-C-nucleoside Phosphonate. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
14
|
Onitsuka K, Tokuda R, Kuwata-Higashi N, Kumamoto H, Aoki M, Amano M, Kohgo S, Das D, Haraguchi K, Mitsuya H, Imoto S. Synthesis and evaluation of the anti-hepatitis B virus activity of 4'-Azido-thymidine analogs and 4'-Azido-2'-deoxy-5-methylcytidine analogs: structural insights for the development of a novel anti-HBV agent. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:518-529. [PMID: 31514570 DOI: 10.1080/15257770.2019.1664749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) infection is a major worldwide health problem that requires the development of improved antiviral therapies. Here, a series of 4'-Azido-thymidine/4'-Azido-2'-deoxy-5-methylcytidine derivatives (6, 10-15) were synthesized, and their anti-HBV activities evaluated. Compounds 10-15 were synthesized via an SNAr reaction of 18, in which the 4-position of the thymine moiety was activated as the 2,4,6-triisopropylbenzenesulfonate. Compounds 11-15 showed no antiviral activity. However, 4'-Azido thymidine (6) and 4'-Azido-2'-deoxy-5-methylcytidine (10) displayed significant anti-HBV activity (EC50 = 0.63 and 5.99 µM, respectively) with no detectable cytotoxicity against MT-2 cells up to 100 µM.
Collapse
Affiliation(s)
- Kengo Onitsuka
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Ryoh Tokuda
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Nobuyo Kuwata-Higashi
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Hiroki Kumamoto
- Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, Saitama, Japan
| | - Manabu Aoki
- Experimental Retrovirology Section, HIV & AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Masayuki Amano
- Departments of Infectious Diseases and Hematology, Kumamoto University School of Medicine, Kumamoto, Japan
| | - Satoru Kohgo
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Debananda Das
- Experimental Retrovirology Section, HIV & AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kazuhiro Haraguchi
- Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, Saitama, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.,Experimental Retrovirology Section, HIV & AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Departments of Infectious Diseases and Hematology, Kumamoto University School of Medicine, Kumamoto, Japan
| | - Shuhei Imoto
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| |
Collapse
|
15
|
Hermi M, Kaminsky W, Ben Nasr C, Touil S. An Operationally Simple One-Step Chemo- and Diastereoselective Synthesis of cis-5-Hydroxy-2-phosphono-2,5-dihydrofurans. ORG PREP PROCED INT 2018. [DOI: 10.1080/00304948.2018.1468986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Marwa Hermi
- Laboratory of Heteroatom Organic Chemistry, Faculty of Sciences of Bizerte, University of Carthage, 7021-Jarzouna, Tunisia
| | - Werner Kaminsky
- Department of Chemistry, University of Washington, BOX 351700, Seattle, WA 98195, USA
| | - Cherif Ben Nasr
- Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, Université de Carthage, 7021-Jarzouna, Tunisie
| | - Soufiane Touil
- Laboratory of Heteroatom Organic Chemistry, Faculty of Sciences of Bizerte, University of Carthage, 7021-Jarzouna, Tunisia
| |
Collapse
|
16
|
Liu C, Cozens C, Jaziri F, Rozenski J, Maréchal A, Dumbre S, Pezo V, Marlière P, Pinheiro VB, Groaz E, Herdewijn P. Phosphonomethyl Oligonucleotides as Backbone-Modified Artificial Genetic Polymers. J Am Chem Soc 2018; 140:6690-6699. [DOI: 10.1021/jacs.8b03447] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chao Liu
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | | | - Faten Jaziri
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | | | - Shrinivas Dumbre
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Valérie Pezo
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Philippe Marlière
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Vitor B. Pinheiro
- University College London, Gower Street, London WC1E 6BT, U.K
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, U.K
| | - Elisabetta Groaz
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| |
Collapse
|
17
|
Luo M, Groaz E, De Jonghe S, Snoeck R, Andrei G, Herdewijn P. Amidate Prodrugs of Cyclic 9-( S)-[3-Hydroxy-2-(phosphonomethoxy)propyl]adenine with Potent Anti-Herpesvirus Activity. ACS Med Chem Lett 2018; 9:381-385. [PMID: 29670705 DOI: 10.1021/acsmedchemlett.8b00079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/09/2018] [Indexed: 12/24/2022] Open
Abstract
A series of amidate prodrugs of cyclic 9-[3-hydroxy-2-(phosphonomethoxy)propyl]adenine (cHPMPA) featuring different amino acid motifs were synthesized. All phosphonamidates derived from (S)-cHPMPA displayed a broad spectrum activity against herpesviruses with EC50 values in the low nanomolar range. A phosphonobisamidate prodrug of (S)-HPMPA also exhibited a remarkably potent antiviral activity. In addition, the leucine ester prodrug of (S)-cHPMPA and phosphonobisamidate valine ester prodrug of (S)-HPMPA proved stable in human plasma. These data warrant further development of cHPMPA prodrugs, especially against human cytomegalovirus (HCMV), for which there is a high need for treatment in transplant recipients.
Collapse
Affiliation(s)
- Min Luo
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49 bus 1043, 3000 Leuven, Belgium
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49 bus 1043, 3000 Leuven, Belgium
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49 bus 1043, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| |
Collapse
|
18
|
Liu C, Dumbre SG, Pannecouque C, Korba B, De Jonghe S, Herdewijn P. Synthesis and antiviral evaluation of base-modified deoxythreosyl nucleoside phosphonates. Org Biomol Chem 2018. [PMID: 28628181 DOI: 10.1039/c7ob01265a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
l-α-2'-Deoxythreosyl nucleoside phosphonates and their phosphonodiamidate prodrugs with a hypoxanthine, 2,6-diaminopurine, 2-amino-6-cyclopropylaminopurine, 7-deazaadenine, 5-fluorouracil and 5-methylcytosine heterocycle as a nucleobase were synthesized and evaluated for their inhibitory activity against HIV and HBV. The 2,6-diaminopurine modified analogue 23a displayed the most potent activity against HIV, with an EC50 value of 11.17 μM against HIV-1 (IIIB) and an EC50 value of 8.15 μM against HIV-2 (ROD). The application of the prodrug strategy on nucleoside phosphonate 23a led to a 200-fold boost in anti-HIV potency. None of the compounds showed any activity against HBV at the highest concentration tested.
Collapse
Affiliation(s)
- Chao Liu
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, 3000 Leuven, Belgium.
| | | | | | | | | | | |
Collapse
|
19
|
Wang M, Srivastava P, Liu C, Snoeck R, Andrei G, De Jonghe S, Herdewijn P. Synthesis and antiviral evaluation of cyclopentyl nucleoside phosphonates. Eur J Med Chem 2018; 150:616-625. [PMID: 29550734 DOI: 10.1016/j.ejmech.2018.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 12/15/2022]
Abstract
The synthesis of both 2'-hydroxy-3'-deoxy and 2'-deoxy-3'-hydroxy cyclopentyl nucleoside phosphonates with the natural nucleobases adenine, thymine, cytosine and guanine from a single precursor has been performed. The guanine containing analogues showed antiviral activity. Especially the 3'-deoxy congener 23 was active, displaying an EC50 of 5.35 μM against TK+ VZV strain and an EC50 of 8.83 μM against TK- VZV strain, besides lacking cytotoxicity. However, the application of phosphonodiamidate prodrug strategy did not lead to a boost in antiviral activity.
Collapse
Affiliation(s)
- Mengmeng Wang
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Puneet Srivastava
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Chao Liu
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| |
Collapse
|
20
|
Sengmany S, Ollivier A, Le Gall E, Léonel E. A mild electroassisted synthesis of (hetero)arylphosphonates. Org Biomol Chem 2018; 16:4495-4500. [DOI: 10.1039/c8ob00500a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The first example of a nickel-catalyzed electrochemical coupling between dimethyl phosphite and (hetero)aryl halides to furnish (hetero)arylphosphonates is described.
Collapse
Affiliation(s)
- Stéphane Sengmany
- Électrochimie et Synthèse Organique
- Université Paris Est
- ICMPE (UMR 7182)
- CNRS
- UPEC
| | - Anthony Ollivier
- Électrochimie et Synthèse Organique
- Université Paris Est
- ICMPE (UMR 7182)
- CNRS
- UPEC
| | - Erwan Le Gall
- Électrochimie et Synthèse Organique
- Université Paris Est
- ICMPE (UMR 7182)
- CNRS
- UPEC
| | - Eric Léonel
- Électrochimie et Synthèse Organique
- Université Paris Est
- ICMPE (UMR 7182)
- CNRS
- UPEC
| |
Collapse
|
21
|
Luo M, Groaz E, Andrei G, Snoeck R, Kalkeri R, Ptak RG, Hartman T, Buckheit RW, Schols D, De Jonghe S, Herdewijn P. Expanding the Antiviral Spectrum of 3-Fluoro-2-(phosphonomethoxy)propyl Acyclic Nucleoside Phosphonates: Diamyl Aspartate Amidate Prodrugs. J Med Chem 2017; 60:6220-6238. [PMID: 28682067 DOI: 10.1021/acs.jmedchem.7b00416] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Acyclic nucleosides containing a 3-fluoro-2-(phosphonomethoxy)propyl (FPMP) side chain are known to be moderately potent antihuman immunodeficiency virus (HIV) agents, while being completely devoid of antiviral activity against a wide range of DNA viruses. The derivatization of the phosphonic acid functionality of FPMPs with a diamyl aspartate phenoxyamidate group led to a novel generation of compounds that not only demonstrate drastically improved antiretroviral potency but also are characterized by an expanded spectrum of activity that also covers hepatitis B and herpes viruses. The best compound, the (S)-FPMPA amidate prodrug, exerts anti-HIV-1 activity in TZM-bl and peripheral blood mononuclear cells at low nanomolar concentrations and displays excellent potency against hepatitis B virus (HBV) and varicella-zoster virus (VZV). This prodrug is stable in acid and human plasma media, but it is efficiently processed in human liver microsomes with a half-life of 2 min. The (R) isomeric guanine derivative emerged as a selectively active anti-HIV and anti-HBV inhibitor, while being nontoxic to human hepatoblastoma cells. Notably, the pyrimidine containing prodrug (S)-Asp-FPMPC is the only congener within this series to demonstrate micromolar antihuman cytomegalovirus (HCMV) potency.
Collapse
Affiliation(s)
- Min Luo
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven , Herestraat 49, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven , Herestraat 49, 3000 Leuven, Belgium
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven , Herestraat 49 bus 1043, 3000 Leuven, Belgium
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven , Herestraat 49 bus 1043, 3000 Leuven, Belgium
| | - Raj Kalkeri
- Department of Infectious Disease Research, Southern Research Institute , 431 Aviation Way, Frederick, Maryland 21701, United States
| | - Roger G Ptak
- Department of Infectious Disease Research, Southern Research Institute , 431 Aviation Way, Frederick, Maryland 21701, United States
| | - Tracy Hartman
- Anti-Infective Research, ImQuest BioSciences , Frederick, Maryland 21704, United States
| | - Robert W Buckheit
- Anti-Infective Research, ImQuest BioSciences , Frederick, Maryland 21704, United States
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven , Herestraat 49 bus 1043, 3000 Leuven, Belgium
| | - Steven De Jonghe
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven , Herestraat 49, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven , Herestraat 49, 3000 Leuven, Belgium
| |
Collapse
|
22
|
Yoshimura Y. Development of a Glycosylation Reaction: A Key to Accessing Structurally Unique Nucleosides. HETEROCYCLES 2017. [DOI: 10.3987/rev-17-865] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|