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Flex-Nucleosides – A Strategic Approach to Antiviral Therapeutics

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Handbook of Chemical Biology of Nucleic Acids

Abstract

One of the most common classes of drugs is nucleoside analogues, which have long served as a cornerstone for antiviral, antiparasitic, and anticancer treatments. This is due to their close resemblance to the naturally occurring nucleosides found in many biological processes. In terms of antiviral drug design, typically viral proteins or cellular proteins are targeted. Each has its pros and cons; however, both carry the risk of the development of drug resistance, making it imperative that novel and more effective antivirals are developed. This chapter will focus on a specific class of shaped-modified nucleoside analogues called fleximers. These flexible nucleoside analogues possess a split purine ring system, which endows flexibility to the nucleobase scaffold. This flexibility has been shown to be beneficial for increased antiviral activity but also results in broad-spectrum antiviral activity as well as the potential to overcome point mutations related to viral drug resistance. For over two decades now, the fleximer technology has been applied to numerous nucleoside analogues and has led to potent, broad-spectrum activity against a wide array of viruses including flaviviruses, filoviruses, and coronaviruses, among others. Their history and development, the various synthetic routes to realize them, and some of the biological data obtained to date for the fleximers will be discussed within this chapter.

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References

  • Andersson J, Sköldenberg B, Ernberg I, Britton S, Henle W, Andersson U (1985) Acyclovir treatment in primary Epstein-Barr virus infection. A double-blind placebo-controlled study. Scand J Infect Dis Suppl 47:107–115

    CAS  PubMed  Google Scholar 

  • Barkholt L, Lewensohn-Fuchs I, Ericzon BG, Tydén G, Andersson J (1999) High-dose acyclovir prophylaxis reduces cytomegalovirus disease in liver transplant patients. Transpl Infect Dis 1(2):89–97

    Article  CAS  PubMed  Google Scholar 

  • Chiang PK (1998) Biological effects of inhibitors of S-adenosylhomocysteine hydrolase. Pharmacol Ther 77(2):115–134

    Article  CAS  PubMed  Google Scholar 

  • Chudinov MV (2020) Nucleoside Analogs with Fleximer nucleobase. Chem Heterocycl Compd (NY, US) 56(6):636–643

    Article  CAS  Google Scholar 

  • Clercq ED, Holý A (2005) Acyclic nucleoside phosphonates: a key class of antiviral drugs. Nat Rev Drug Discov 4(11):928–940

    Article  PubMed  Google Scholar 

  • De Clercq E (1994) Antiviral activity Spectrum and target of action of different classes of nucleoside analogues. Nucleosides Nucleotides 13(6–7):1271–1295

    Article  Google Scholar 

  • De Clercq E (2002) Strategies in the design of antiviral drugs. Natl Rev Drug Discov 1(1):13–25

    Article  Google Scholar 

  • De Clercq E (2005a) Antiviral drug discovery and development: where chemistry meets with biomedicine. Antivir Res 67(2):56–75

    Article  PubMed  Google Scholar 

  • De Clercq E (2005b) Recent highlights in the development of new antiviral drugs. Curr Opin Microbiol 8(5):552–560

    Article  PubMed  PubMed Central  Google Scholar 

  • De Clercq E, Neyts J (2009) Antiviral agents acting as DNA or RNA chain terminators. Handb Exp Pharmacol 189:53–84

    Article  Google Scholar 

  • De Winter H, Herdewijn P (1996) Understanding the binding of 5-substituted 2′-deoxyuridine substrates to thymidine kinase of herpes simplex virus type-1. J Med Chem 22(39(24)):4727–4737

    Article  Google Scholar 

  • Deval J (2009) Antimicrobial strategies: inhibition of viral polymerases by 3′-hydroxyl nucleosides. Drugs 69(2):151–166

    Article  CAS  PubMed  Google Scholar 

  • Deval J, Powdrill MH, D'Abramo CM, Cellai L, Götte M (2007) Pyrophosphorolytic excision of nonobligate chain terminators by hepatitis C virus NS5B polymerase. Antimicrob Agents Chemother 51(8):2920–2928

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Docea A, Tsatsakis A, Albulescu D, Cristea O, Zlatian O, Vinceti M, Moschos S, Tsoukalas D, Goumenou M, Drakoulis N, Dumanov J, Tutelyan V, Onischenko G, Aschner M, Spandidos D, Calina D (2020) A new threat from an old enemy: re-emergence of coronavirus (review). Int J Mol Med 45

    Google Scholar 

  • Fischer E (1894) Einfluss der Configuration auf die Wirkung der Enzyme. Ber Dtsch Chem Ges 27(3):2985–2993

    Article  CAS  Google Scholar 

  • Greco NJ, Tor Y (2005) Simple fluorescent pyrimidine analogues detect the presence of DNA Abasic sites. J Am Chem Soc 127(31):10784–10785

    Article  CAS  PubMed  Google Scholar 

  • Khandazhinskaya A, Eletskaya B, Fateev I, Kharitonova M, Konstantinova I, Barai V, Azhayev A, Hyvonen MT, Keinanen TA, Kochetkov S, Seley-Radtke K, Khomutov A, Matyugina E (2021) Novel fleximer pyrazole-containing adenosine analogues: chemical, enzymatic and highly efficient biotechnological synthesis. Org Biomol Chem 19

    Google Scholar 

  • Koshland DE (1958) Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci U S A 44(2):98–104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ku T, Lopresti N, Shirley M, Mori M, Marchant J, Heng X, Botta M, Summers MF, Seley-Radtke KL (2019) Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1. Bioorg Med Chem 27(13):2883–2892

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leonard NJ, Hiremath SP (1986) Dimensional probes of binding and activity. Tetrahedron 42(7):1917–1961

    Article  CAS  Google Scholar 

  • Leonard NJ, Morrice AG, Sprecker MA (1975) Linear benzoadenine. Stretched-out analog of adenine. J Org Chem 40(3):356–363

    Article  CAS  PubMed  Google Scholar 

  • Mattelaer H-P, Van Hool A-S, de Jong F, Van der Auweraer M, Van Meervelt L, Dehaen W, Herdewijn P (2020) New metal-free route towards imidazole substituted uridine. Eur J Org Chem 2020

    Google Scholar 

  • Matyugina ES, Khandazhinskaya AL, Kochetkov SN, Seley-Radtke KL (2020) Synthesis of 3-hetarylpyrroles by Suzuki-Miyaura cross-coupling. Mendeleev Commun 30(2):231–232

    Article  CAS  Google Scholar 

  • McGuigan C, Cahard D, Sheeka HM, De Clercq E, Balzarini J (1996) Aryl phosphoramidate derivatives of d4T have improved anti-HIV efficacy in tissue culture and may act by the generation of a novel intracellular metabolite. J Med Chem 39(8):1748–1753

    Article  CAS  PubMed  Google Scholar 

  • McGuigan C, Hassan-Abdallah A, Srinivasan S, Wang Y, Siddiqui A, Daluge SM, Gudmundsson KS, Zhou H, McLean EW, Peckham JP, Burnette TC, Marr H, Hazen R, Condreay LD, Johnson L, Balzarini J (2006) Application of phosphoramidate ProTide technology significantly improves antiviral potency of carbocyclic adenosine derivatives. J Med Chem 49(24):7215–7226

    Article  CAS  PubMed  Google Scholar 

  • Mcguigan C, Madela K, Aljarah M, Gilles A, Brancale A, Zonta N, Chamberlain S, Vernachio J, Hutchins J, Hall A, Ames B, Gorovits E, Ganguly B, Kolykhalov A, Wang J, Muhammad J, Patti JM, Henson G (2010) Design, synthesis and evaluation of a novel double pro-drug: INX-08189. A new clinical candidate for hepatitis C virus. Bioorg Med Chem Lett 20(16):4850–4854

    Article  CAS  PubMed  Google Scholar 

  • Mehellou Y, Rattan HS, Balzarini J (2018) The ProTide prodrug technology: from the concept to the clinic. J Med Chem 61(6):2211–2226

    Article  CAS  PubMed  Google Scholar 

  • Mori M, Dietrich U, Manetti F, Botta M (2010) Molecular dynamics and DFT study on HIV-1 Nucleocapsid Protein-7 in complex with viral genome. J Chem Inf Model 50(4):638–650

    Article  CAS  PubMed  Google Scholar 

  • Mori M, Manetti F, Botta M (2011) Predicting the binding mode of known NCp7 inhibitors to facilitate the Design of Novel Modulators. J Chem Inf Model 51(2):446–454

    Article  CAS  PubMed  Google Scholar 

  • Morrice AG, Sprecker MA, Leonard NJ (1975) The angular benzoadenines. 9-Aminoimidazo[4,5-f]quinazoline and 6-aminoimidazo [4,5-h]quinazoline. J Org Chem 40(3):363–366

    Article  CAS  PubMed  Google Scholar 

  • Najjar A, Karaman R (2019) The prodrug approach in the era of drug design. Expert Opin Drug Deliv 16(1):1–5

    Article  PubMed  Google Scholar 

  • Nguyen Van T, Hospital A, Lionne C, Jordheim LP, Dumontet C, Périgaud C, Chaloin L, Peyrottes S (2016) Beta-hydroxyphosphonate ribonucleoside analogues derived from 4-substituted-1,2,3-triazoles as IMP/GMP mimics: synthesis and biological evaluation. Beilstein J Organ Chem 12:1476–1486

    Article  Google Scholar 

  • OʼBrien JJ, Campoli-Richards DM (1989) Acyclovir. Drugs 37(3):233–309

    Article  PubMed  Google Scholar 

  • Ouellette R, Rawn JD (2018) Nucleosides, nucleotides, and nucleic acid. Organic chemistry: Structure, mechanism, synthesis. Academic Press, London, pp 973–1000

    Google Scholar 

  • Périgaud C, Gosselin G, Imbach JL (1992) Nucleoside analogues as chemotherapeutic agents: a review. Nucleosides Nucleotides 11(2–4):903–945

    Article  Google Scholar 

  • Peters, H. L. (2015). The design, synthesis, and biological evaluation of a series of acyclic Fleximer nucleoside antivirals. Ph.D, University of Maryland, Baltimore County

    Google Scholar 

  • Peters HL, Jochmans D, de Wilde AH, Posthuma CC, Snijder EJ, Neyts J, Seley-Radtke KL (2015) Design, synthesis and evaluation of a series of acyclic fleximer nucleoside analogues with anti-coronavirus activity. Bioorg Med Chem Lett 25(15):2923–2926

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pierson TC, Diamond MS (2020) The continued threat of emerging flaviviruses. Nat Microbiol 5(6):796–812

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Polak M, Seley KL, Plavec J (2004) Conformational properties of shape modified nucleosides - Fleximers. J Am Chem Soc 126(26):8159–8166

    Article  CAS  PubMed  Google Scholar 

  • Quirk S, Seley KL (2005) Identification of catalytic amino acids in the human GTP fucose pyrophosphorylase active site. Biochemistry 44(39):13172–13178

    Article  CAS  PubMed  Google Scholar 

  • Ross BS, Ganapati Reddy P, Zhang H-R, Rachakonda S, Sofia MJ (2011) Synthesis of Diastereomerically pure nucleotide Phosphoramidates. J Org Chem 76(20):8311–8319

    Article  CAS  PubMed  Google Scholar 

  • Sadler JM, Ojewoye O, Seley-Radtke KL (2008) "reverse fleximers": introduction of a series of 5-substituted carbocyclic uridine analogues. Nucleic Acids Symp Ser (Oxf) (52):571–572

    Article  Google Scholar 

  • Seley KL, Zhang L, Hagos A (2001) "Fleximers". Design and synthesis of two novel Split nucleosides. Org Lett 3(20):3209–3210

    Article  CAS  PubMed  Google Scholar 

  • Seley KL, Zhang L, Hagos A, Quirk S (2002) "Fleximers". Design and synthesis of a new class of novel shape-modified nucleosides. J Org Chem 67(10):3365–3373

    Article  CAS  PubMed  Google Scholar 

  • Seley KL, Quirk S, Salim S, Zhang L, Hagos A (2003) Unexpected inhibition of S-adenosyl-L-homocysteine hydrolase by a guanosine nucleoside. Bioorg Med Chem Lett 13(12):1985–1988

    Article  CAS  PubMed  Google Scholar 

  • Seley KL, Salim S, Zhang L (2005) "molecular chameleons". Design and synthesis of C-4-substituted imidazole Fleximers. Org Lett 7(1):63–66

    Article  CAS  PubMed  Google Scholar 

  • Seley-Radtke K (2018) Flexibility-not just for yoga anymore! Antivir Chem Chemother 26:2040206618756788

    Article  PubMed  PubMed Central  Google Scholar 

  • Seley-Radtke KL, Sunkara NK (2009) Carbocyclic thymidine analogues for use as potential therapeutic agents. Nucleosides Nucleotides Nucleic Acids 28(5–7):633–641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Seley-Radtke KL, Yates MK (2018) The evolution of nucleoside analogue antivirals: a review for chemists and non-chemists. Part 1: early structural modifications to the nucleoside scaffold. Antivir Res 154:66–86

    Article  CAS  PubMed  Google Scholar 

  • Slusarczyk M, Serpi M, Pertusati F (2018) Phosphoramidates and phosphonamidates (ProTides) with antiviral activity. Antivir Chem Chemother 26:204020661877524

    Article  Google Scholar 

  • St. Amant AH, Bean LA, Guthrie JP, Hudson RHE (2012) Click fleximers: a modular approach to purine base-expanded ribonucleoside analogs. Org Biomol Chem 10(32):6521–6525

    Article  CAS  PubMed  Google Scholar 

  • Tan ELC, Ooi EE, Lin C-Y, Tan HC, Ling AE, Lim B, Stanton LW (2004) Inhibition of SARS coronavirus infection in vitro with clinically approved antiviral drugs. Emerg Infect Dis 10(4):581–586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thames JE, Waters CD, Valle C, Bassetto M, Aouadi W, Martin B, Selisko B, Falat A, Coutard B, Brancale A, Canard B, Decroly E, Seley-Radtke KL (2020) Synthesis and biological evaluation of novel flexible nucleoside analogues that inhibit flavivirus replication in vitro. Bioorg Med Chem 28(22):115713

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tripathi A, Bankaitis V (2017) Molecular docking: from lock and key to combination lock. J Mol Med Clin Appl 2(1)

    Google Scholar 

  • Vichier-Guerre S, Dugué L, Pochet S (2014) A convenient synthesis of 4(5)-(hetero)aryl-1H-imidazoles via microwave-assisted Suzuki–Miyaura cross-coupling reaction. 55(46):6347–6350

    Google Scholar 

  • Vichier-Guerre S, Ku TC, Pochet S, Seley-Radtke KL (2020) An expedient synthesis of flexible nucleosides through enzymatic glycosylation of proximal and distal Fleximer bases. Chembiochem 21(10):1412–1417

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wauchope OR, Velasquez M, Seley-Radtke K (2012) Synthetic routes to a series of proximal and distal 2′-deoxy fleximers. Synthesis 44(22):3496–3504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wigerinck P, Pannecouque C, Snoeck R, Claes P, De Clercq E, Herdewijn P (1991) 5-(5-Bromothien-2-yl)-2′-deoxyuridine and 5-(5-chlorothien-2-yl)-2′-deoxyuridine are equipotent to (E)-5-(2-bromovinyl)-2′-deoxyuridine in the inhibition of herpes simplex virus type I replication. J Med Chem 34(8):2383–2389

    Article  CAS  PubMed  Google Scholar 

  • Yates MK, Seley-Radtke KL (2019) The evolution of antiviral nucleoside analogues: a review for chemists and non-chemists. Part II: complex modifications to the nucleoside scaffold. Antivir Res 162:5–21

    Article  CAS  PubMed  Google Scholar 

  • Yates MK, Raje MR, Chatterjee P, Spiropoulou CF, Bavari S, Flint M, Soloveva V, Seley-Radtke KL (2017) Flex-nucleoside analogues - novel therapeutics against filoviruses. Bioorg Med Chem Lett 27(12):2800–2802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yates MK, Chatterjee P, Flint M, Arefeayne Y, Makuc D, Plavec J, Spiropoulou CF, Seley-Radtke KL (2019) Probing the effects of pyrimidine functional group switches on acyclic fleximer analogues for antiviral activity. Molecules 24(17):3184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yin D, Yang X, Hu Y, Kuczera K, Schowen RL, Borchardt RT, Squier TC (2000) Substrate binding stabilizes S-adenosylhomocysteine hydrolase in a closed conformation. Biochemistry 39(32):9811–9818

    Article  CAS  PubMed  Google Scholar 

  • Zimmermann SC, Sadler JM, Andrei G, Snoeck R, Balzarini J, Seley-Radtke KL (2011) Carbocyclic 5′-nor "reverse" fleximers. Design, synthesis, and preliminary biological activity. Medchemcomm 2(7)

    Google Scholar 

  • Zimmermann SC, Sadler JM, O'Daniel PI, Kim NT, Seley-Radtke KL (2013) “Reverse” carbocyclic Fleximers: synthesis of a new class of adenosine deaminase inhibitors. Nucleosides Nucleotides Nucleic Acids 32(3):137–154

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zimmermann SC, O'Neill E, Ebiloma GU, Wallace LJM, De Koning HP, Seley-Radtke KL (2014) Design and synthesis of a series of truncated neplanocin fleximers. Molecules 19(12):21200–21214. 21215 pp

    Article  PubMed  PubMed Central  Google Scholar 

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Correspondence to Katherine L. Seley-Radtke .

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Seley-Radtke, K.L., Kutz, C.H.M., Thames, J.E. (2022). Flex-Nucleosides – A Strategic Approach to Antiviral Therapeutics. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids. Springer, Singapore. https://doi.org/10.1007/978-981-16-1313-5_67-1

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