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A Modular Approach to the Discovery and Affinity Maturation of Sequence-Selective RNA-Binding Compounds

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RNA Therapeutics

Part of the book series: Topics in Medicinal Chemistry ((TMC,volume 27))

Abstract

This chapter describes a strategy developed at the University of Rochester that relies on a two-step process for the generation of high-affinity, sequence-selective RNA-binding compounds with target-relevant biological activity. First, a natural product-inspired dynamic combinatorial library (DCL) is employed to rapidly produce “hit” compounds able to bind the target RNA. Second, a process of analog synthesis is employed to enhance affinity, bioavailability, and sequence selectivity. This strategy has been used to successfully produce compounds able to bind target RNAs with high (nanomolar) affinity, and target-relevant activity in cellular assays and in vivo. In particular, approaches to RNA targets of critical importance in Myotonic Dystrophy (a triplet repeat RNA-mediated disease) and in the life cycle of HIV will be discussed.

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References

  1. Dervan PB, Burli RW (1999) Sequence-specific DNA recognition by polyamides. Curr Opin Chem Biol 3:688–693

    Article  CAS  Google Scholar 

  2. Thomas JR, Hergenrother PJ (2008) Targeting RNA with small molecules. Chem Rev 108:1171–1224

    Article  CAS  Google Scholar 

  3. Georgianna WE, Young DD (2011) Development and utilization of non-coding RNA-small molecule interactions. Org Biomol Chem 9:7969–7978

    Article  CAS  Google Scholar 

  4. Guan L, Disney MD (2012) Recent advances in developing small molecules targeting RNA. ACS Chem Biol 7:73–86

    Article  CAS  Google Scholar 

  5. Corbett PT, Leclaire J, Vial L, West KR, Wietor JL, Sanders JKM, Otto S (2006) Dynamic combinatorial chemistry. Chem Rev 106:3652–3711

    Article  CAS  Google Scholar 

  6. Ramström O, Bunyapaiboonsri T, Lohmann S, Lehn JM (2002) Chemical biology of dynamic combinatorial libraries. Biochim Biophys Acta 1572:178–186

    Article  Google Scholar 

  7. Miller BL (ed) (2009) Dynamic combinatorial chemistry. Wiley, New York, NY

    Google Scholar 

  8. Rideout D (1986) Self-assembling cytotoxins. Science 233:561–563

    Article  CAS  Google Scholar 

  9. Feldman KS, Bobo JS, Ensel SM, Lee YB, Weinreb PH (1990) Template-controlled oligomerization support studies. Template synthesis and functionalization. J Org Chem 55:474–481

    Article  CAS  Google Scholar 

  10. Miller BL, Bonner WA (1995) Enantioselective autocatalysis. III. Configurational and conformational studies on a 1,4-benzodiazepinooxazole derivative. Orig Life Evol Biosph 25:539–547

    Article  CAS  Google Scholar 

  11. Krämer R, Lehn JM, Marquis-Rigault A (1993) Self-recognition in helicate self-assembly: spontaneous formation of helical metal complexes from mixtures of ligands and metal ions. Proc Natl Acad Sci U S A 90:5394–5398

    Article  Google Scholar 

  12. Brady PA, Sanders JKM (1997) Thermodynamically-controlled cyclisation and interconversion of oligocholates: metal ion templated “living” macrolactonisation. J Chem Soc Perkin Trans 1 1997:3237–3253

    Article  Google Scholar 

  13. Hioki H, Still WC (1998) Chemical evolution: a model system that selects and amplifies a receptor for the tripeptide (D)Pro(L)Val(D)Val. J Org Chem 63:904–905

    Article  CAS  Google Scholar 

  14. Huc I, Lehn JM (1997) Virtual combinatorial libraries: dynamic generation of molecular and supramolecular diversity by self-assembly. Proc Natl Acad Sci U S A 94:2106–2110

    Article  CAS  Google Scholar 

  15. Klug A (2010) The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu Rev Biochem 79:213–231

    Article  CAS  Google Scholar 

  16. Schepartz A, McDevitt JP (1989) Self-assembling ionophores. J Am Chem Soc 111:5976–5977

    Article  CAS  Google Scholar 

  17. Klekota B, Hammond MH, Miller BL (1997) Generation of novel DNA-binding compounds by selection and amplification from self-assembled combinatorial libraries. Tetrahedron Lett 38:8639–8643

    Article  CAS  Google Scholar 

  18. Klekota B, Miller BL (1999) Selection of DNA_binding compounds via multistage molecular evolution. Tetrahedron 55:11687–11697

    Article  CAS  Google Scholar 

  19. Karan C, Miller BL (2001) RNA-selective coordination complexes identified via dynamic combinatorial chemistry. J Am Chem Soc 123:7455–7456

    Article  CAS  Google Scholar 

  20. Ludlow RF, Otto S (2008) Two-vial, LC-MS identification of ephedrine receptors from a solution-phase dynamic combinatorial library of over 9000 components. J Am Chem Soc 130:12218–12219

    Article  CAS  Google Scholar 

  21. Bugaut A, Jantos K, Wietor JL, Rodriguez R, Sanders JKM, Balasubramanian S (2008) Exploring the differential recognition of DNA G-quadruplex targets by small molecules using dynamic combinatorial chemistry. Angew Chem Int Ed Engl 47:2677–2680

    Article  CAS  Google Scholar 

  22. Buhler E, Sreenivasachary N, Candau SJ, Lehn JM (2007) Modulation of the supramolecular structure of G-quartet assemblies by dynamic covalent decoration. J Am Chem Soc 129:10058–10059

    Article  CAS  Google Scholar 

  23. Harrington CA, Rosenow C, Retief J (2000) Monitoring gene expression using DNA microarrays. Curr Opin Microbiol 3:285–291

    Article  CAS  Google Scholar 

  24. Tan DS, Burbaum JJ (2000) Ligand discovery using encoded combinatorial libraries. Curr Opin Drug Discov Devel 3:439–453

    CAS  Google Scholar 

  25. Hattori K, Koike K, Okuda K, Hirayama T, Ebihara M, Takenaka M, Nagasawa H (2016) Solution-phase synthesis and biological evaluation of triostin A and its analogues. Org Biomol Chem 14:2090–2111

    Article  CAS  Google Scholar 

  26. Szajewski RP, Whitesides GM (1980) Rate constants and equilibrium-constants for thiol-disulfide interchange reactions involving oxidized glutathione. J Am Chem Soc 102:2011–2026

    Article  CAS  Google Scholar 

  27. McNaughton BR, Miller BL (2006) Resin-bound dynamic combinatorial chemistry. Org Lett 8:1803–1806

    Article  CAS  Google Scholar 

  28. Addess KJ, Sinsheimer JS, Feigon J (1993) Solution structure of a complex between [N-MeCys3, N-MeCys7]TANDEM and [d(GATATC)]2. Biochemistry 32:2498–2508

    Article  CAS  Google Scholar 

  29. Addess KJ, Feigon J (1994) Sequence specificity of quinoxaline antibiotics. 2. NMR studies of the binding f [N-MeCys3, N-MCys7]TANDEM and triostin A to DNA containing a CpI step. Biochemistry 33:12397–12404

    Article  CAS  Google Scholar 

  30. Mankodi A, Teng-Umnuay P, Krym M, Henderson D, Swanson M, Thornton CA (2003) Ribonuclear inclusions in skeletal muscle in myotonic dystrophy types 1 and 2. Ann Neurol 54:760–768

    Article  CAS  Google Scholar 

  31. Ashizawa T, Dubel JR, Harati Y (1993) Somatic instability of CTG repeat in myotonic dystrophy. Neurology 43:2674–2678

    Article  CAS  Google Scholar 

  32. Thornton CA, Johnson K, Moxley RT (1994) Myotonic dystrophy patients have larger CTG expansions in skeletal muscle than in leukocytes. Ann Neurol 35:104–107

    Article  CAS  Google Scholar 

  33. Pushechnikov A, Lee MM, Childs-Disney JL, Sobczak K, French JM, Thornton CA, Disney MD (2009) Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3. J Am Chem Soc 131:9767–9779

    Article  CAS  Google Scholar 

  34. Arambula JF, Ramisetty SR, Baranger AM, Zimmerman SC (2009) A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding. Proc Natl Acad Sci U S A 106:16068–16073

    Article  CAS  Google Scholar 

  35. Warf MB, Nakamori M, Matthys CM, Thornton CA, Berglund JA (2009) Pentamidine reverses the splicing defects associated with myotonic dystrophy. Proc Natl Acad Sci U S A 106:18551–118556

    Article  CAS  Google Scholar 

  36. Liquori CL, Ricker K, Moseley ML, Jacobsen JF, Kress W, Naylor SL, Day JW, Ranum LPW (2001) Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science 293:864–867

    Article  CAS  Google Scholar 

  37. Tian B, White RJ, Xia T, Welle S, Turner DH, Mathews MB, Thornton CA (2000) Expanded CUG repeat RNAs form hairpins that activate the double-stranded RNA-dependent protein kinase PKR. RNA 6:79–87

    Article  CAS  Google Scholar 

  38. Belew AT, Dinman JD (2015) Cell cycle control (and more) by programmed -1 ribosomal frameshifting: implications for disease and therapeutics. Cell Cycle 14:172–178

    Article  CAS  Google Scholar 

  39. Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV (2016) Ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use. Nucleic Acids Res 44:7007–7078

    Google Scholar 

  40. Biswas P, Jiang X, Pacchia AL, Dougherty JP, Peltz SW (2004) The human immunodeficiency virus type 1 ribosomal frameshifting site is an invariant sequence determinant and an important target for antiviral therapy. J Virol 78:2082–2087

    Article  CAS  Google Scholar 

  41. Staple DW, Butcher SE (2005) Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element. J Mol Biol 349:1011–1023

    Article  CAS  Google Scholar 

  42. Low JT, Garcia-Miranda P, Mouzakis KD, Gorelick RJ, Butcher SE, Weeks KM (2014) Structure and dynamics of the HIV-1 frameshift element RNA. Biochemistry 53:4282–4291

    Article  CAS  Google Scholar 

  43. Shehu-Xhilaga M, Crowe SM, Mak J (2001) Maintenance of the Gag/Gag-Pol ratio is important for human immunodeficiency virus type 1 RNA dimerization and viral infectivity. J Virol 75:1834–1841

    Article  CAS  Google Scholar 

  44. Dulude D, Berchiche YA, Gendron K, Brakier-Gingras L, Heveker N (2006) Decreasing the frameshift efficiency translates into an equivalent reduction of the replication of the human immunodeficiency virus type 1. Vaccine 345:127–136

    CAS  Google Scholar 

  45. Hung M, Patel P, Davis S, Green SR (1998) Importance of ribosomal frameshifting for human immunodeficiency virus type 1 particle assembly and replication. J Virol 72:4819–4824

    CAS  Google Scholar 

  46. Marcheschi RJ, Tonelli M, Kumar A, Butcher SE (2011) Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication. ACS Chem Biol 6:857–864

    Article  CAS  Google Scholar 

  47. Tan DS, Foley MA, Stockwell BR, Shair MD, Schreiber SL (1999) Synthesis and preliminary evaluation of a library of polycyclic small molecules for use in chemical genetic assays. J Am Chem Soc 121:9073–9087

    Article  CAS  Google Scholar 

  48. McNaughton BR, Gareiss PC, Miller BL (2007) Identification of a selective small-molecule frameshift-inducing stem-loop RNA from an 11,325 member resin bound dynamic combinatorial library. J Am Chem Soc 129:11306–11307

    Article  CAS  Google Scholar 

  49. Gareiss PC, Sobczak K, McNaughton BR, Palde PB, Thornton CA, Miller BL (2008) Dynamic combinatorial selection of molecules capable of inhibiting the (CUG) repeat RNA-MBNL1 interaction in vitro: discovery of lead compounds targeting myotonic dystrophy (DM1). J Am Chem Soc 130:16254–16261

    Article  CAS  Google Scholar 

  50. Olson KR, Eglen RM (2007) Beta galactosidase complementation: a cell-based luminescent assay platform for drug discovery. Assay Drug Dev Technol 5:137–144

    Article  CAS  Google Scholar 

  51. McGovern SL, Helfand BT, Feng B, Shoichet BK (2003) A specific mechanism of nonspecific inhibition. J Med Chem 46:4265–4272

    Article  CAS  Google Scholar 

  52. Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK (2008) Small-molecule aggregates inhibit amyloid polymerization. Nat Chem Biol 4:197–199

    Article  CAS  Google Scholar 

  53. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus TL, Dupuis M, Montgomery JA (1993) General atomic and molecular electronic structure system. J Comput Chem 14:1347–1363

    Article  CAS  Google Scholar 

  54. Fotouhi N, Joshi P, Tilley JW, Rowan K, Schwinge V, Wolitzky B (2000) Cyclic thioether peptide mimetics as VCAM-VLA-4 antagonists. Bioorg Med Chem Lett 10:1167–1169

    Article  CAS  Google Scholar 

  55. Stymiest JL, Mitchell BF, Wong S, Vederas JC (2003) Synthesis of biologically active dicarba analogues of the peptide hormone oxytocin using ring-closing metathesis. Org Lett 5:47–49

    Article  CAS  Google Scholar 

  56. Berezowska I, Chung NN, Lemieux C, Wilkes BC, Schiller PW (2007) Dicarba analogues of the cyclic enkephalin peptides H-Tyr-c[D-Cys-Gly-Phe-D(or L)-Cys]NH(2) retain high opioid activity. J Med Chem 50:1414–1417

    Article  CAS  Google Scholar 

  57. Mollica A, Guardiani G, Davis P, Ma S, Porreca F, Lai J, Mannina L, Sobolev AP, Hruby VJ (2007) Synthesis of stable and potent delta/mu opioid peptides: analogues of H-Tyr-c[D-Cys-Gly-Phe-D-Cys]-OH by ring-closing metathesis. J Med Chem 50:3138–3142

    Article  CAS  Google Scholar 

  58. Nicolaou KC, Hughes R, Cho SY, Winssinger N, Smethurst C, Labischinski H, Endermann R (2000) Target-accelerated combinatorial synthesis and discovery of highly potent antibiotics effective against vancomycin-resistant bacteria. Angew Chem Int Ed Engl 39:3823–3828

    Article  CAS  Google Scholar 

  59. Neto BAD, Lapis AAM (2009) Recent developments in the chemistry of deoxyribonucleic acid (DNA) intercalators: principles, design, synthesis, applications and trends. Molecules 14:1725–1746

    Article  CAS  Google Scholar 

  60. Chatterjee J, Gilon C, Hoffman A, Kessler H (2008) N-methylation of peptides: a new perspective in medicinal chemistry. Acc Chem Res 41:1331–1342

    Article  CAS  Google Scholar 

  61. Luedtke N, Tor Y (2000) A novel solid-phase assembly for identifying potent and selective RNA ligands. Angew Chem Int Ed Engl 39:1788–1790

    Article  CAS  Google Scholar 

  62. Ofori LO, Hilimire TA, Bennett RP, Brown NW, Smith HC, Miller BL (2014) High-affinity recognition of HIV-1 frameshift-stimulating RNA alters frameshifting in vitro and interferes with HIV-1 infectivity. J Med Chem 57:723–732

    Article  CAS  Google Scholar 

  63. Buttke TMT, McCubrey JAJ, Owen TCT (1993) Use of an aqueous soluble tetrazolium/formazan assay to measure viability and proliferation of lymphokine-dependent cell lines. J Immunol Methods 157:233–240

    Article  CAS  Google Scholar 

  64. Grentzmann G, Ingram JA, Kelly PJ, Gesteland RF, Atkins JF (1998) A dual-luciferase reporter system for studying recoding signals. RNA 4:479–486

    Article  CAS  Google Scholar 

  65. Miller JH, Presnyak V, Smith HC (2007) The dimerization domain of HIV-1 viral infectivity factor Vif is required to block virion incorporation of APOBEC3G. Retrovirology 4:81

    Article  Google Scholar 

  66. Finnegan CM, Rawat SS, Puri A, Wang JM, Ruscetti FW, Blumenthal R (2004) Ceramide, a target for antiretroviral therapy. Proc Natl Acad Sci U S A 101:15452–15457

    Article  CAS  Google Scholar 

  67. Hilimire TA, Bennett RP, Stewart RA, Garcia-Miranda P, Blume A, Becker J, Sherer N, Helms ED, Butcher SE, Smith HC, Miller BL (2016) N-methylation as a strategy for enhancing the affinity and selectivity of RNA-binding peptides: application to the HIV-1 frameshift-stimulating RNA. ACS Chem Biol 11:88–94

    Article  CAS  Google Scholar 

  68. Miller SC, Scanlan TS (1997) Site-selective N-methylation of peptides on solid support. J Am Chem Soc 119:2301–2302

    Article  CAS  Google Scholar 

  69. Ofori LO, Hoskins J, Nakamori M, Thornton CA, Miller BL (2012) From dynamic combinatorial “hit” to lead: in vitro and in vivo activity of compounds targeting the pathogenic RNAs that cause myotonic dystrophy. Nucleic Acids Res 40:6380–6390

    Article  CAS  Google Scholar 

  70. Crothers DM (1968) Calculation of binding isotherms for heterogeneous polymers. Biopolymers 6:575–584

    Article  CAS  Google Scholar 

  71. Mankodi A, Logigian E, Callahan L, McClain C, White R, Henderson D, Krym M, Thornton CA (2000) Myotonic dystrophy in transgenic mice expressing an expanded CUG repeat. Science 298:1769–1773

    Article  Google Scholar 

  72. Rodriguez-Docampo Z, Otto S (2008) Orthogonal or simultaneous use of disulfide and hydrazone exchange in dynamic covalent chemistry in aqueous solution. Chem Commun 2008:5301–5303

    Article  Google Scholar 

  73. Escalante AM, Orrillo AG, Furlan RLE (2010) Simultaneous and orthogonal covalent exchange processes in dynamic combinatorial libraries. J Comb Chem 12:410–413

    Article  CAS  Google Scholar 

  74. Gromova AV, Ciszewski JM, Miller BL (2012) Ternary resin-bound dynamic combinatorial chemistry. Chem Commun 2012:2131–2133

    Article  Google Scholar 

  75. Dirksen A, Dirksen S, Hackeng TM, Dawson PE (2006) Nucleophilic catalysis of hydrazone formation and transimination: implications for dynamic covalent chemistry. J Am Chem Soc 128:15602–15603

    Article  CAS  Google Scholar 

  76. Bhat VT, Caniard AM, Luksch T, Brenk R, Campopiano DJ, Greaney MF (2010) Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry. Nat Chem 2:490–497

    Article  CAS  Google Scholar 

  77. Larsen D, Pittelkow M, Karmakar S, Kool ET (2015) New organocatalyst scaffolds with high activity in promoting hydrazone and oxime formation at neutral pH. Org Lett 17:274–277

    Article  CAS  Google Scholar 

  78. McAnany JD, Reichert JP, Miller BL (2016) Probing the geometric constraints of RNA binding via dynamic covalent chemistry. Bioorg Med Chem 24:3940–3946

    Article  CAS  Google Scholar 

  79. Corbett PT, Tong LH, Sanders JKM, Otto S (2005) Diastereoselective amplification of an induced-fit receptor from a dynamic combinatorial library. J Am Chem Soc 127:8902–8903

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Dermatology, University of Rochester Medical Center, Rochester, NY, 14642, USA

    Benjamin L. Miller

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  1. Benjamin L. Miller
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Correspondence to Benjamin L. Miller .

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  1. Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA

    Amanda L. Garner

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Miller, B.L. (2017). A Modular Approach to the Discovery and Affinity Maturation of Sequence-Selective RNA-Binding Compounds. In: Garner, A. (eds) RNA Therapeutics. Topics in Medicinal Chemistry, vol 27. Springer, Cham. https://doi.org/10.1007/7355_2016_23

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