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Mesaros EF, Dugan BJ, Gao M, Sheraz M, McGovern-Gooch K, Xu F, Fan KY, Nguyen D, Kultgen SG, Lindstrom A, Stever K, Tercero B, Binder RJ, Liu F, Micolochick Steuer HM, Mani N, Harasym TO, Thi EP, Cuconati A, Dorsey BD, Cole AG, Lam AM, Sofia MJ. Discovery of C-Linked Nucleoside Analogues with Antiviral Activity against SARS-CoV-2. ACS Infect Dis 2024; 10:1780-1792. [PMID: 38651692 DOI: 10.1021/acsinfecdis.4c00122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The recent COVID-19 pandemic underscored the limitations of currently available direct-acting antiviral treatments against acute respiratory RNA-viral infections and stimulated major research initiatives targeting anticoronavirus agents. Two novel nsp5 protease (MPro) inhibitors have been approved, nirmatrelvir and ensitrelvir, along with two existing nucleos(t)ide analogues repurposed as nsp12 polymerase inhibitors, remdesivir and molnupiravir, but a need still exists for therapies with improved potency and systemic exposure with oral dosing, better metabolic stability, and reduced resistance and toxicity risks. Herein, we summarize our research toward identifying nsp12 inhibitors that led to nucleoside analogues 10e and 10n, which showed favorable pan-coronavirus activity in cell-infection screens, were metabolized to active triphosphate nucleotides in cell-incubation studies, and demonstrated target (nsp12) engagement in biochemical assays.
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Affiliation(s)
- Eugen F Mesaros
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Benjamin J Dugan
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Min Gao
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Muhammad Sheraz
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | | | - Fran Xu
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Kristi Yi Fan
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Duyan Nguyen
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Steven G Kultgen
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Aaron Lindstrom
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Kim Stever
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Breanna Tercero
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Randall J Binder
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Fei Liu
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | | | - Nagraj Mani
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Troy O Harasym
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Emily P Thi
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Andrea Cuconati
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Bruce D Dorsey
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Andrew G Cole
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Angela M Lam
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Michael J Sofia
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
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Liu ZQ. Is it still worth renewing nucleoside anticancer drugs nowadays? Eur J Med Chem 2024; 264:115987. [PMID: 38056297 DOI: 10.1016/j.ejmech.2023.115987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/11/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023]
Abstract
Nucleoside has situated the convergence point in the discovery of novel drugs for decades, and a large number of nucleoside derivatives have been constructed for screening novel pharmacological properties at various experimental platforms. Notably, nearly 20 nucleosides are approved to be used in the clinic treatment of various cancers. Nevertheless, the blossom of synthetic nucleoside analogs in comparison with the scarcity of nucleoside anticancer drugs leads to a question: Is it still worth insisting on the screening of novel anticancer drugs from nucleoside derivatives? Hence, this review attempts to emphasize the importance of nucleoside analogs in the discovery of novel anticancer drugs. Firstly, we introduce the metabolic procedures of nucleoside anticancer drug (such as 5-fluorouracil) and summarize the designing of novel nucleoside anticancer candidates based on clinically used nucleoside anticancer drugs (such as gemcitabine). Furthermore, we collect anticancer properties of some recently synthesized nucleoside analogs, aiming at emphasizing the availability of nucleoside analogs in the discovery of anticancer drugs. Finally, a variety of synthetic strategies including the linkage of sugar moiety with nucleobase scaffold, modifications on the sugar moiety, and variations on the nucleobase structure are collected to exhibit the abundant protocols in the achievement of nucleoside analogs. Taken the above discussions collectively, nucleoside still advantages for the finding of novel anticancer drugs because of the clearly metabolic procedures, successfully clinic applications, and abundantly synthetic routines.
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Affiliation(s)
- Zai-Qun Liu
- Department of Organic Chemistry, College of Chemistry, Jilin University, Changchun, 130021, People's Republic of China.
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Cardoza S, Shrivash MK, Riva L, Chatterjee AK, Mandal A, Tandon V. Multistep Synthesis of Analogues of Remdesivir: Incorporating Heterocycles at the C-1' Position. J Org Chem 2023; 88:9105-9122. [PMID: 37276453 DOI: 10.1021/acs.joc.3c00754] [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: 06/07/2023]
Abstract
Studies suggest that the 1'β-CN moiety in remdesivir sterically clashes with the Ser861 residue of the RNA-dependent-RNA polymerase (RdRp), causing a delayed chain termination in the RNA replication process. Replacing C1'β-CN with 5-membered heterocycles such as tetrazoles, oxadiazoles, and triazoles can augment the inhibitory activity and pharmacokinetic profile of C-nucleotides. Synthesis of tetrazole-, triazole-, and oxadiazole-integrated C1' analogues of remdesivir was attempted using general synthetic routes. The final compounds 26, 28, and 29 did not inhibit viral replication; however, the synthetic intermediates, i.e., 27 and 50, exhibited an IC90 = 14.1 μM each. The trifluoromethyl-substituted 1,2,4-oxadiazole 59 showed an IC90 of 33.5 μM. This work adds to the growing evidence of the beneficial medicinal impact of C1,1'-disubstituted C-nucleotides.
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Affiliation(s)
- Savio Cardoza
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Kumar Shrivash
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211012, Uttar Pradesh, India
| | - Laura Riva
- Calibr, Scripps Research, La Jolla, 11119 North Torrey Pines Road Suite 100, California 92037, United States
| | - Arnab K Chatterjee
- Calibr, Scripps Research, La Jolla, 11119 North Torrey Pines Road Suite 100, California 92037, United States
| | - Ajay Mandal
- Symbol Discovery Ltd, ASPIRE-TBI, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
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Li W, Girt GC, Radadiya A, Stewart JJP, Richards NGJ, Naismith JH. Experimental and computational snapshots of C-C bond formation in a C-nucleoside synthase. Open Biol 2023; 13:220287. [PMID: 36629016 PMCID: PMC9832568 DOI: 10.1098/rsob.220287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The biosynthetic enzyme, ForT, catalyses the formation of a C-C bond between 4-amino-1H-pyrazoledicarboxylic acid and MgPRPP to produce a C-nucleoside precursor of formycin A. The transformation catalysed by ForT is of chemical interest because it is one of only a few examples in which C-C bond formation takes place via an electrophilic substitution of a small, aromatic heterocycle. In addition, ForT is capable of discriminating between the aminopyrazoledicarboxylic acid and an analogue in which the amine is replaced by a hydroxyl group; a remarkable feat given the steric and electronic similarities of the two molecules. Here we report biophysical measurements, structural biology and quantum chemical calculations that provide a detailed molecular picture of ForT-catalysed C-C bond formation and the conformational changes that are coupled to catalysis. Our findings set the scene for employing engineered ForT variants in the biocatalytic production of novel, anti-viral C-nucleoside and C-nucleotide analogues.
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Affiliation(s)
- Wenbo Li
- Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK,Division of Structural Biology, Nuffield Department of Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Georgina C. Girt
- Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK
| | - Ashish Radadiya
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | | | - Nigel G. J. Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK,Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - James H. Naismith
- Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK,Division of Structural Biology, Nuffield Department of Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
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Poudel TN, Panda S, Orimoloye M, Hegde P, Aldrich CC. 1'-Cyano Intermediate Enables Rapid and Stereoretentive Access to 1'-Modified Remdesivir Nucleosides. J Org Chem 2022; 87:14452-14462. [PMID: 36223099 DOI: 10.1021/acs.joc.2c01897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
While biochemical, structural, and computational studies have shown the importance of remdesivir's C1'-substituent in its perturbation of SARS-CoV-2 RdRp action, we recognized the paucity of methods to stereoselectively install substituents at this position as an obstacle to rigorous explorations of SAR and mechanism. We report the utilization of an anomerically pure 1'-cyano intermediate as an entry point to a chemically diverse set of substitutions, allowing for 1'diversification while obviating the need for the tedious separation of anomeric mixtures.
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Affiliation(s)
- Tej Narayan Poudel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Subhankar Panda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Moyosore Orimoloye
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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