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Majhi J, Matsuo B, Oh H, Kim S, Sharique M, Molander GA. Photochemical Deoxygenative Hydroalkylation of Unactivated Alkenes Promoted by a Nucleophilic Organocatalyst. Angew Chem Int Ed Engl 2024; 63:e202317190. [PMID: 38109703 DOI: 10.1002/anie.202317190] [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: 11/28/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/20/2023]
Abstract
The direct utilization of simple and abundant feedstocks in carbon-carbon bond-forming reactions to embellish sp3 -enriched chemical space is highly desirable. Herein, we report a novel photochemical deoxygenative hydroalkylation of unactivated alkenes with readily available carboxylic acid derivatives. The reaction displays broad functional group tolerance, accommodating carboxylic acid-, alcohol-, ester-, ketone-, amide-, silane-, and boronic ester groups, as well as nitrile-containing substrates. The reaction is operationally simple, mild, and water-tolerant, and can be carried out on multigram-scale, which highlights the utility of the method to prepare value-added compounds in a practical and scalable manner. The synthetic application of the developed method is further exemplified through the synthesis of suberanilic acid, a precursor of vorinostat, a drug used for the treatment of cutaneous T-cell lymphoma. A novel mechanistic approach was identified using thiol as a nucleophilic catalyst, which forms a key intermediate for this transformation. Furthermore, electrochemical studies, quantum yield, and mechanistic experiments were conducted to support a proposed catalytic cycle for the transformation.
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Affiliation(s)
- Jadab Majhi
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, 19104-6323, Philadelphia, PA, USA
| | - Bianca Matsuo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, 19104-6323, Philadelphia, PA, USA
| | - Hyunjung Oh
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, 19104-6323, Philadelphia, PA, USA
| | - Saegun Kim
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, 19104-6323, Philadelphia, PA, USA
| | - Mohammed Sharique
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, 19104-6323, Philadelphia, PA, USA
| | - Gary A Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, 19104-6323, Philadelphia, PA, USA
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Jin Y, Wang S, Xu S, Zhao S, Xu X, Poongavanam V, Menéndez-Arias L, Zhan P, Liu X. Targeting hepatitis B virus cccDNA levels: recent progress in seeking small molecule drug candidates. Drug Discov Today 2023; 28:103617. [PMID: 37196762 DOI: 10.1016/j.drudis.2023.103617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Hepatitis B virus (HBV) infection is a major global health problem that puts people at high risk of death from cirrhosis and liver cancer. The presence of covalently closed circular DNA (cccDNA) in infected cells is considered to be the main obstacle to curing chronic hepatitis B. At present, the cccDNA cannot be completely eliminated by standard treatments. There is an urgent need to develop drugs or therapies that can reduce HBV cccDNA levels in infected cells. We summarize the discovery and optimization of small molecules that target cccDNA synthesis and degradation. These compounds are cccDNA synthesis inhibitors, cccDNA reducers, core protein allosteric modulators, ribonuclease H inhibitors, cccDNA transcriptional modulators, HBx inhibitors and other small molecules that reduce cccDNA levels. Teaser: HBV covalently closed circular DNA (cccDNA) can be stably maintained in infected cells for a prolonged period, and this is the fundamental reason why hepatitis B cannot be completely cured. Here, we review recent progress in the development of small molecules that can reduce cccDNA levels in infected cells.
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Affiliation(s)
- Yu Jin
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shuo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shujie Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xiangrui Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Luis Menéndez-Arias
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), 28049 Madrid, Spain.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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Williams OP, Chmiel AF, Mikhael M, Bates DM, Yeung CS, Wickens ZK. Practical and General Alcohol Deoxygenation Protocol. Angew Chem Int Ed Engl 2023; 62:e202300178. [PMID: 36840940 PMCID: PMC10121858 DOI: 10.1002/anie.202300178] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 02/26/2023]
Abstract
Herein, we describe a practical protocol for the removal of alcohol functional groups through reductive cleavage of their benzoate ester analogs. This transformation requires a strong single electron transfer (SET) reductant and a means to accelerate slow fragmentation following substrate reduction. To accomplish this, we developed a photocatalytic system that generates a potent reductant from formate salts alongside Brønsted or Lewis acids that promote fragmentation of the reduced intermediate. This deoxygenation procedure is effective across structurally and electronically diverse alcohols and enables a variety of difficult net transformations. This protocol requires no precautions to exclude air or moisture and remains efficient on multigram scale. Finally, the system can be adapted to a one-pot benzoylation-deoxygenation sequence to enable direct alcohol deletion. Mechanistic studies validate that the role of acidic additives is to promote the key C(sp3 )-O bond fragmentation step.
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Affiliation(s)
- Oliver P. Williams
- Department of Chemistry, University of Wisconsin-Madison; Madison, Wisconsin, 53706, United States
| | - Alyah F. Chmiel
- Department of Chemistry, University of Wisconsin-Madison; Madison, Wisconsin, 53706, United States
| | - Myriam Mikhael
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, United States
| | - Desiree M. Bates
- Department of Chemistry, University of Wisconsin-Madison; Madison, Wisconsin, 53706, United States
| | - Charles S. Yeung
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, United States
| | - Zachary K. Wickens
- Department of Chemistry, University of Wisconsin-Madison; Madison, Wisconsin, 53706, United States
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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.
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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.
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Hajjar M, Chim N, Liu C, Herdewijn P, Chaput J. Crystallographic analysis of engineered polymerases synthesizing phosphonomethylthreosyl nucleic acid. Nucleic Acids Res 2022; 50:9663-9674. [PMID: 36124684 PMCID: PMC9508818 DOI: 10.1093/nar/gkac792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Xeno-nucleic acids (XNAs) are synthetic genetic polymers with backbone structures composed of non-ribose or non-deoxyribose sugars. Phosphonomethylthreosyl nucleic acid (pTNA), a type of XNA that does not base pair with DNA or RNA, has been suggested as a possible genetic material for storing synthetic biology information in cells. A critical step in this process is the synthesis of XNA episomes using laboratory-evolved polymerases to copy DNA information into XNA. Here, we investigate the polymerase recognition of pTNA nucleotides using X-ray crystallography to capture the post-catalytic complex of engineered polymerases following the sequential addition of two pTNA nucleotides onto the 3'-end of a DNA primer. High-resolution crystal structures reveal that the polymerase mediates Watson-Crick base pairing between the extended pTNA adducts and the DNA template. Comparative analysis studies demonstrate that the sugar conformation and backbone position of pTNA are structurally more similar to threose nucleic acid than DNA even though pTNA and DNA share the same six-atom backbone repeat length. Collectively, these findings provide new insight into the structural determinants that guide the enzymatic synthesis of an orthogonal genetic polymer, and may lead to the discovery of new variants that function with enhanced activity.
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Affiliation(s)
- Mohammad Hajjar
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Nicholas Chim
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Chao Liu
- 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
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
- Department of Chemistry, University of California, Irvine, CA 92697-3958, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3958, USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697-3958, USA
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Design and synthesis of novel quinazolinone derivatives as anti-HBV agents with TLR8 agonist effect. Eur J Med Chem 2022; 231:114159. [DOI: 10.1016/j.ejmech.2022.114159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 01/04/2023]
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