Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA

Journal of the American Chemical Society

Volumn 139, Issue 25, 2017, Pages 8537-8546

  Schlegel, Mark K ^a   Foster, Donald J ^a   Kel'In, Alexander V ^a   Zlatev, Ivan ^a   Bisbe, Anna ^a   Jayaraman, Muthusamy ^a   Lackey, Jeremy G ^a   Rajeev, Kallanthottathil G ^a   Charissé, Klaus ^a   Harp, Joel ^b   Pallan, Pradeep S ^b   Maier, Martin A ^a   Egli, Martin ^b   Manoharan, Muthiah ^a  

^a ALNYLAM PHARMACEUTICALS   (United States)

^b VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; GLYCOLS; HYDROGEN BONDS; MAMMALS; NUCLEIC ACIDS;

ACID MODIFICATION; DUPLEX STRUCTURES; NUCLEIC ACID ANALOGUES; PHOSPHATE BACKBONE; SNAKE VENOM PHOSPHODIESTERASE; STRUCTURAL IMPACT; WATSON-CRICK BASE PAIRING; WATSON-CRICK BASE PAIRS;

NUCLEOTIDES;

DINUCLEOTIDE; GLYCOL; GLYCOL NUCLEIC ACID; HYDROGEN; MESSENGER RNA; NUCLEIC ACID; PHOSPHODIESTERASE; SMALL INTERFERING RNA; SPLEEN EXONUCLEASE; UNCLASSIFIED DRUG; ALBUMIN RECEPTOR; HETERODUPLEX; TRANSTHYRETIN RECEPTOR;

ARTICLE; CHIRALITY; CONFORMATION; CRYSTAL STRUCTURE; ENZYME DEGRADATION; GENE SILENCING; MELTING POINT; RNA STRUCTURE; THERMOSTABILITY; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; DRUG EFFECT; IC50; MOUSE; TEMPERATURE; X RAY CRYSTALLOGRAPHY;

ANIMALS; CRYSTALLOGRAPHY, X-RAY; GENE SILENCING; GLYCOLS; INHIBITORY CONCENTRATION 50; MICE; MODELS, BIOLOGICAL; NUCLEIC ACID HETERODUPLEXES; NUCLEIC ACIDS; RECEPTORS, ALBUMIN; RNA, SMALL INTERFERING; TEMPERATURE;

EID: 85021626270     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/jacs.7b02694     Document Type: Article

References (50)

1. Elbashir, S. M.; Harborth, J.; Lendeckel, W.; Yalcin, A.; Weber, K.; Tuschl, T. Nature 2001, 411, 494 10.1038/35078107
2. Wang, H.-W.; Noland, C.; Siridechadilok, B.; Taylor, D. W.; Ma, E.; Felderer, K.; Doudna, J. A.; Nogales, E. Nat. Struct. Mol. Biol. 2009, 16, 1148 10.1038/nsmb.1673
3. Meister, G.; Landthaler, M.; Patkaniowska, A.; Dorsett, Y.; Teng, G.; Tuschl, T. Mol. Cell 2004, 15, 185 10.1016/j.molcel.2004.07.007
4. Liu, J.; Carmell, M. A.; Rivas, F. V.; Marsden, C. G.; Thomson, J. M.; Song, J.-J.; Hammond, S. M.; Joshua-Tor, L.; Hannon, G. J. Science 2004, 305, 1437 10.1126/science.1102513
5. Martinez, J.; Patkaniowska, A.; Urlaub, H.; Lührmann, R.; Tuschl, T. Cell 2002, 110, 563 10.1016/S0092-8674(02)00908-X
6. Deleavey, G. F.; Watts, J. K.; Damha, M. J. Current Protocols in Nucleic Acid Chemistry; Wiley: New York, 2009; Chapter 16, Unit 16.3.
7. Nair, J. K.; Willoughby, J. L. S.; Chan, A.; Charisse, K.; Alam, M. R.; Wang, Q.; Hoekstra, M.; Kandasamy, P.; Kel'in, A. V.; Milstein, S.; Taneja, N.; O'Shea, J.; Shaikh, S.; Zhang, L.; van der Sluis, R. J.; Jung, M. E.; Akinc, A.; Hutabarat, R.; Kuchimanchi, S.; Fitzgerald, K.; Zimmermann, T.; van Berkel, T. J. C.; Maier, M. A.; Rajeev, K. G.; Manoharan, M. J. Am. Chem. Soc. 2014, 136, 16958 10.1021/ja505986a
8. Chan, A.; Liebow, A.; Yasuda, M.; Gan, L.; Racie, T.; Maier, M.; Kuchimanchi, S.; Foster, D.; Milstein, S.; Charisse, K.; Sehgal, A.; Manoharan, M.; Meyers, R.; Fitzgerald, K.; Simon, A.; Desnick, R. J.; Querbes, W. Mol. Ther. - Nucleic Acids 2015, 4, e263 10.1038/mtna.2015.36
9. Liebow, A.; Li, X.; Racie, T.; Hettinger, J.; Bettencourt, B. R.; Najafian, N.; Haslett, P.; Fitzgerald, K.; Holmes, R. P.; Erbe, D.; Querbes, W.; Knight, J. J. Am. Soc. Nephrol. 2017, 28, 494 10.1681/ASN.2016030338
10. Fitzgerald, K.; White, S.; Borodovsky, A.; Bettencourt, B. R.; Strahs, A.; Clausen, V.; Wijngaard, P.; Horton, J. D.; Taubel, J.; Brooks, A.; Fernando, C.; Kauffman, R. S.; Kallend, D.; Vaishnaw, A.; Simon, A. N. Engl. J. Med. 2017, 376, 41 10.1056/NEJMoa1609243
11. Laursen, M. B.; Pakula, M. M.; Gao, S.; Fluiter, K.; Mook, O. R.; Baas, F.; Langklaer, N.; Wengel, S. L.; Wengel, J.; Kjems, J.; Bramsen, J. B. Mol. BioSyst. 2010, 6, 862 10.1039/b918869j
12. Kenski, D. M.; Cooper, A. J.; Li, J. J.; Willingham, A. T.; Haringsma, H. J.; Young, T. A.; Kuklin, N. A.; Jones, J. J.; Cancilla, M. T.; McMasters, D. R.; Mathur, M.; Sachs, A. B.; Flanagan, W. M. Nucleic Acids Res. 2010, 38, 660 10.1093/nar/gkp913
13. Kamiya, Y.; Takai, J.; Ito, H.; Murayama, K.; Kashida, H.; Asanuma, H. ChemBioChem 2014, 15, 2549 10.1002/cbic.201402369
14. Alagia, A.; Terrazas, M.; Eritja, R. Molecules 2015, 20, 7602 10.3390/molecules20057602
15. Khvorova, A.; Reynolds, A.; Jayasena, S. D. Cell 2003, 115, 209 10.1016/S0092-8674(03)00801-8
16. Sano, M.; Sierant, M.; Miyagishi, M.; Nakanishi, M.; Takagi, Y.; Sutou, S. Nucleic Acids Res. 2008, 36, 5812 10.1093/nar/gkn584
17. Bramsen, J. B.; Laursen, M. B.; Nielsen, A. F.; Hansen, T. B.; Bus, C.; Langkjær, N.; Babu, B. R.; Højland, T.; Abramov, M.; Van Aerschot, A.; Odadzic, D.; Smicius, R.; Haas, J.; Andree, C.; Barman, J.; Wenska, M.; Srivastava, P.; Zhou, C.; Honcharenko, D.; Hess, S.; Müller, E.; Bobkov, G. V.; Mikhailov, S. N.; Fava, E.; Meyer, T. F.; Chattopadhyaya, J.; Zerial, M.; Engels, J. W.; Herdewijn, P.; Wengel, J.; Kjems, J. Nucleic Acids Res. 2009, 37, 2867 10.1093/nar/gkp106
18. Addepalli, H.; Meena; Peng, C. G.; Wang, G.; Fan, Y.; Charisse, K.; Jayaprakash, K. N.; Rajeev, K. G.; Pandey, R. K.; Lavine, G.; Zhang, L.; Jahn-Hofmann, K.; Hadwiger, P.; Manoharan, M.; Maier, M. A. Nucleic Acids Res. 2010, 38, 7320 10.1093/nar/gkq568
19. Zhang, L.; Peritz, A.; Meggers, E. J. Am. Chem. Soc. 2005, 127, 4174 10.1021/ja042564z
20. Schlegel, M. K.; Peritz, A. E.; Kittigowittana, K.; Zhang, L.; Meggers, E. ChemBioChem 2007, 8, 927 10.1002/cbic.200600435
21. Schlegel, M. K.; Essen, L.-O.; Meggers, E. J. Am. Chem. Soc. 2008, 130, 8158 10.1021/ja802788g
22. Schlegel, M. K.; Essen, L.-O.; Meggers, E. Chem. Commun. 2010, 46, 1094 10.1039/B916851F
23. Johnson, A. T.; Schlegel, M. K.; Meggers, E.; Essen, L.-O.; Wiest, O. J. Org. Chem. 2011, 76, 7964 10.1021/jo201469b
24. Elkayam, E.; Kuhn, C.-D.; Tocilj, A.; Haase, A. D.; Greene, E. M.; Hannon, G. J.; Joshua-Tor, L. Cell 2012, 150, 100 10.1016/j.cell.2012.05.017
25. Roberts, C.; Bandaru, R.; Switzer, C. J. Am. Chem. Soc. 1997, 119, 4640 10.1021/ja970123s
26. Chen, X.; Kierzek, R.; Turner, D. H. J. Am. Chem. Soc. 2001, 123, 1267 10.1021/ja002623i
27. Allerson, C. R.; Sioufi, N.; Jarres, R.; Prakash, T. P.; Naik, N.; Berdeja, A.; Wanders, L.; Griffey, R. H.; Swayze, E. E.; Bhat, B. J. Med. Chem. 2005, 48, 901 10.1021/jm049167j
28. Deleavey, G. F.; Damha; Masad, J. Chem. Biol. 2012, 19, 937 10.1016/j.chembiol.2012.07.011
29. Kenski, D. M.; Butora, G.; Willingham, A. T.; Cooper, A. J.; Fu, W.; Qi, N.; Soriano, F.; Davies, I. W.; Flanagan, W. M. Mol. Ther. - Nucleic Acids 2012, 1, e5 10.1038/mtna.2011.4
30. Schirle, N. T.; MacRae, I. J. Science 2012, 336, 1037 10.1126/science.1221551
31. Schirle, N. T.; Sheu-Gruttadauria, J.; MacRae, I. J. Science 2014, 346, 608 10.1126/science.1258040
32. Manoharan, M.; Akinc, A.; Pandey, R. K.; Qin, J.; Hadwiger, P.; John, M.; Mills, K.; Charisse, K.; Maier, M. A.; Nechev, L.; Greene, E. M.; Pallan, P. S.; Rozners, E.; Rajeev, K. G.; Egli, M. Angew. Chem., Int. Ed. 2011, 50, 2284 10.1002/anie.201006519
33. Nakanishi, K. Wiley Interdiscip. Rev.: RNA 2016, 7, 637 10.1002/wrna.1356
34. Ueda, N.; Kawabata, T.; Takemoto, K. J. Heterocycl. Chem. 1971, 8, 827 10.1002/jhet.5570080527
35. Seita, T.; Yamauchi, K.; Kinoshita, M.; Imoto, M. Makromol. Chem. 1972, 154, 255 10.1002/macp.1972.021540123
36. Holý, A.; Ivanova, G. S. Nucleic Acids Res. 1974, 1, 19 10.1093/nar/1.1.19
37. Cook, P. D.; Acevedo, O. L.; Davis, P. W.; Ecker, D. J.; Hebert, N. Monomeric Diols and Phosphate Linked Oligomers Formed Therefrom. PCT Int. Appl. WO 9518820, 1995.
38. Cook, P. D.; Acevedo, O. L.; Davis, P. W.; Ecker, D. J.; Hebert, N. Phospate Linked Oligomers. U.S. Patent 5,886,177, 1999.
39. Nielsen, P.; Dreiøe, L. H.; Wengel, J. Bioorg. Med. Chem. 1995, 3, 19 10.1016/0968-0896(94)00143-Q
40. Zhang, L.; Peritz, A. E.; Carroll, P. J.; Meggers, E. Synthesis 2006, 2006, 645 10.1055/s-2006-926313
41. Schlegel, M. K.; Meggers, E. J. Org. Chem. 2009, 74, 4615 10.1021/jo900365a
42. Jancarik, J.; Kim, S.-H. J. Appl. Crystallogr. 1991, 24, 409 10.1107/S0021889891004430
43. Otwinowski, Z.; Minor, W. Methods Enzymol. 1997, 276, 307 10.1016/S0076-6879(97)76066-X
44. Schneider, T. R.; Sheldrick, G. M. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2002, 58, 1772 10.1107/S0907444902011678
45. Pape, T.; Schneider, T. R. J. Appl. Crystallogr. 2004, 37, 843 10.1107/S0021889804018047
46. Emsley, P.; Cowtan, K. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 2126 10.1107/S0907444904019158
47. Brunger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J.-S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Acta Crystallogr., Sect. D: Biol. Crystallogr. 1998, 54, 905 10.1107/S0907444998003254
48. Adams, P. D.; Afonine, P. V.; Bunkoczi, G.; Chen, V. B.; Davis, I. W.; Echols, N.; Headd, J. J.; Hung, L.-W.; Kapral, G. J.; Grosse-Kunstleve, R. W.; McCoy, A. J.; Moriarty, N. W.; Oeffner, R.; Read, R. J.; Richardson, D. C.; Richardson, J. S.; Terwilliger, T. C.; Zwart, P. H. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 213 10.1107/S0907444909052925
49. Afonine, P. V.; Grosse-Kunstleve, R. W.; Echols, N.; Headd, J. J.; Moriarty, N. W.; Mustyakimov, M.; Terwilliger, T. C.; Urzhumtsev, A.; Zwart, P. H.; Adams, P. D. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2012, 68, 352 10.1107/S0907444912001308
50. Schuttelkopf, A. W.; van Aalten, D. M. F. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 1355 10.1107/S0907444904011679