title: Design of siRNA Therapeutics from the Molecular Scale.
abstract: While protein-based therapeutics is well-established in the market, development of nucleic acid therapeutics has lagged. Short interfering RNAs (siRNAs) represent an exciting new direction for the pharmaceutical industry. These small, chemically synthesized RNAs can knock down the expression of target genes through the use of a native eukaryotic pathway called RNA interference (RNAi). Though siRNAs are routinely used in research studies of eukaryotic biological processes, transitioning the technology to the clinic has proven challenging. Early efforts to design an siRNA therapeutic have demonstrated the difficulties in generating a highly-active siRNA with good specificity and a delivery vehicle that can protect the siRNA as it is transported to a specific tissue. In this review article, we discuss design considerations for siRNA therapeutics, identifying criteria for choosing therapeutic targets, producing highly-active siRNA sequences, and designing an optimized delivery vehicle. Taken together, these design considerations provide logical guidelines for generating novel siRNA therapeutics.
authors: Department of Chemical Engineering and Materials Science, Michigan State University, 428 S. Shaw Lane, Room 2527, East Lansing, MI 48824, USA; angartph@msu.edu (P.A.); vocelled@msu.edu (D.V.); krischan@egr.msu.edu (C.C.).
authors: Phillip
authors: P
authors: Angart
authors: Daniel
authors: D
authors: Vocelle
authors: Christina
authors: C
authors: Chan
authors: S Patrick
authors: SP
authors: Walton
keywords: RNAi; delivery vehicle design; liver cancer; siRNA design; siRNA therapeutic
references: Trends Pharmacol Sci. 2009 Nov;30(11):592-9
references: 19837467
references: Science. 2003 Sep 26;301(5641):1921-5
references: 14512631
references: Pharm Res. 2009 Jan;26(1):235-43
references: 18712584
references: Leukemia. 1990 Nov;4(11):745-50
references: 2232885
references: Biomaterials. 2010 May;31(13):3657-66
references: 20138662
references: N Engl J Med. 2008 Jul 24;359(4):378-90
references: 18650514
references: J Control Release. 2000 Mar 1;65(1-2):271-84
references: 10699287
references: J Mol Biol. 2005 May 13;348(4):883-93
references: 15843020
references: Cell Mol Life Sci. 2012 Feb;69(3):389-404
references: 22015612
references: Adv Drug Deliv Rev. 2003 Feb 24;55(3):329-47
references: 12628320
references: Cold Spring Harb Symp Quant Biol. 2006;71:523-30
references: 17381335
references: Nat Rev Mol Cell Biol. 2007 Aug;8(8):603-12
references: 17609668
references: Cell. 2009 Feb 20;136(4):642-55
references: 19239886
references: Chem Soc Rev. 2011 Mar;40(3):1647-71
references: 21082078
references: Mol Ther Nucleic Acids. 2012 Jan 24;1:e5
references: 23344622
references: Chem Soc Rev. 2012 Jun 7;41(11):4306-34
references: 22481569
references: Mol Ther. 2007 Sep;15(9):1663-9
references: 17579574
references: Genes Dev. 2001 Jan 15;15(2):188-200
references: 11157775
references: BMC Bioinformatics. 2006 Nov 27;7:516
references: 17129386
references: Nature. 2000 Mar 16;404(6775):293-6
references: 10749213
references: Nature. 2001 Jan 18;409(6818):363-6
references: 11201747
references: Biochem Pharmacol. 2006 Feb 28;71(5):702-10
references: 16376306
references: Biochemistry. 2003 Jul 8;42(26):7967-75
references: 12834349
references: RNA. 2007 Mar;13(3):385-95
references: 17237357
references: RNA. 2008 May;14(5):853-61
references: 18367722
references: Adv Drug Deliv Rev. 2010 Apr 30;62(6):633-49
references: 20338203
references: FEBS Lett. 2005 Oct 31;579(26):5850-7
references: 16199039
references: Mol Syst Biol. 2010 Nov 16;6:433
references: 21081925
references: Biotechnol J. 2011 Sep;6(9):1130-46
references: 21744502
references: Int J Nanomedicine. 2012;7:5577-91
references: 23144561
references: Nat Struct Mol Biol. 2005 May;12(5):469-70
references: 15852021
references: RNA. 2008 Sep;14(9):1714-9
references: 18658119
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W135-41
references: 15215366
references: Nat Methods. 2012 Feb 19;9(4):363-6
references: 22343343
references: Mol Ther. 2009 Apr;17(4):725-32
references: 19156133
references: Nat Rev Drug Discov. 2010 Jan;9(1):57-67
references: 20043028
references: Nucleic Acids Res. 2009 May;37(9):2867-81
references: 19282453
references: Proc Natl Acad Sci U S A. 2011 May 31;108(22):9208-13
references: 21576459
references: Mol Pharm. 2009 May-Jun;6(3):659-68
references: 19267452
references: Nat Biotechnol. 2004 Mar;22(3):326-30
references: 14758366
references: Cancer Res. 2012 Nov 15;72(22):5663-8
references: 23139207
references: Nucleic Acids Res. 2007;35(4):e27
references: 17259216
references: Front Genet. 2012 Aug 20;3:154
references: 22934103
references: RNA. 2011 Oct;17(10):1858-69
references: 21878547
references: Mol Biosyst. 2007 Jan;3(1):43-50
references: 17216055
references: Nat Biotechnol. 2005 Apr;23(4):457-62
references: 15778705
references: Nature. 2008 Apr 3;452(7187):591-7
references: 18368052
references: ACS Chem Biol. 2012 Jul 20;7(7):1214-20
references: 22512638
references: Nat Methods. 2007 Apr;4(4):337-44
references: 17351622
references: Science. 2004 Nov 19;306(5700):1377-80
references: 15550672
references: Nucleic Acids Res. 2013 Feb 1;41(3):1383-94
references: 23241392
references: Mol Pharm. 2011 Oct 3;8(5):1662-8
references: 21740056
references: Cell. 2012 Aug 31;150(5):883-94
references: 22939618
references: Glycoconj J. 2007 Apr;24(2-3):107-23
references: 17268860
references: Annu Rev Immunol. 2003;21:335-76
references: 12524386
references: J Mol Biol. 2005 May 20;348(5):1079-90
references: 15854645
references: Nat Mater. 2011 Dec 04;11(1):82-90
references: 22138789
references: Front Genet. 2012 Jun 11;3:102
references: 22701467
references: J Exp Med. 2008 Jul 7;205(7):1601-10
references: 18591409
references: Nat Cell Biol. 2005 Jul;7(7):719-23
references: 15937477
references: Annu Rev Biochem. 2009;78:857-902
references: 19317650
references: Cell. 2005 Nov 18;123(4):621-9
references: 16271385
references: Int Immunol. 2009 May;21(5):607-19
references: 19332442
references: J Biol Chem. 1987 Jun 5;262(16):7932-7
references: 3034910
references: RNA. 2012 Jan;18(1):24-30
references: 22106413
references: Adv Drug Deliv Rev. 2002 Sep 13;54(5):631-51
references: 12204596
references: Genes Dev. 2003 Feb 15;17(4):438-42
references: 12600936
references: Nat Struct Mol Biol. 2004 Jul;11(7):599-606
references: 15170178
references: Science. 2004 Mar 5;303(5663):1526-9
references: 14976262
references: J Polym Sci B Polym Phys. 2011 Jun 15;49(12):832-864
references: 21769165
references: BMC Bioinformatics. 2006 Nov 30;7:520
references: 17137497
references: Cytokine Growth Factor Rev. 2007 Oct-Dec;18(5-6):363-71
references: 17698400
references: Nucleic Acids Res. 2004 Feb 03;32(2):691-9
references: 14762201
references: Nat Biotechnol. 2006 May;24(5):559-65
references: 16648842
references: Annu Rev Pharmacol Toxicol. 2012;52:481-503
references: 22035254
references: Antisense Nucleic Acid Drug Dev. 1998 Aug;8(4):281-93
references: 9743466
references: Biochem J. 2010 Feb 24;426(3):293-306
references: 20001965
references: Nature. 2004 Feb 12;427(6975):645-9
references: 14961122
references: Jpn J Cancer Res. 1998 Mar;89(3):307-14
references: 9600125
references: Pharm Res. 2012 Feb;29(2):362-74
references: 21842305
references: Nucleic Acids Res. 2005 Aug 19;33(15):4704-10
references: 16113241
references: Biotechnol Bioeng. 2008 Jul 1;100(4):744-55
references: 18306428
references: Nat Methods. 2006 Mar;3(3):199-204
references: 16489337
references: Nucleic Acids Res. 2008 Feb;36(2):640-7
references: 18073195
references: Traffic. 2009 Apr;10(4):364-71
references: 19192253
references: Chem Soc Rev. 2012 Apr 7;41(7):2545-61
references: 22334259
references: ACS Nano. 2011 May 24;5(5):3599-606
references: 21517083
references: Nat Biotechnol. 2003 Jun;21(6):635-7
references: 12754523
references: Nucleic Acids Res. 2007;35(17):5886-97
references: 17726057
references: Wiley Interdiscip Rev RNA. 2010 Jul-Aug;1(1):117-31
references: 21956909
references: Mol Cell Biol. 1992 Nov;12(11):5238-48
references: 1357546
references: Science. 2007 Nov 30;318(5855):1455-8
references: 18048689
references: BMC Immunol. 2009 Jul 24;10:40
references: 19630977
references: Biochem Biophys Res Commun. 2004 Jun 18;319(1):256-63
references: 15158470
references: Hepatology. 2008 Oct;48(4):1312-27
references: 18821591
references: Nat Nanotechnol. 2011 Apr 24;6(6):385-91
references: 21516092
references: RNA. 2012 Mar;18(3):557-68
references: 22294662
references: EMBO J. 2001 Dec 3;20(23):6877-88
references: 11726523
references: J Mol Biol. 2005 May 13;348(4):871-81
references: 15843019
references: Nat Genet. 2002 Apr;30(4):363-4
references: 11896390
references: Oligonucleotides. 2009 Jun;19(2):191-202
references: 19344210
references: Biomaterials. 2006 Aug;27(24):4356-73
references: 16650890
references: Genes Dev. 2004 Mar 1;18(5):504-11
references: 15014042
references: RNA. 2007 Oct;13(10):1631-40
references: 17684233
references: Nature. 2001 Oct 18;413(6857):732-8
references: 11607032
references: Mol Ther. 2004 Aug;10(2):373-85
references: 15294184
references: J Biol Chem. 2003 May 2;278(18):15991-7
references: 12604614
references: J Biol Chem. 2003 Nov 7;278(45):44312-9
references: 12952966
references: Curr Opin Struct Biol. 2010 Feb;20(1):90-7
references: 20053548
references: Biochem Biophys Res Commun. 2004 Apr 16;316(4):1050-8
references: 15044091
references: Adv Drug Deliv Rev. 2012 Dec;64(15):1730-7
references: 22732527
references: Nucleic Acid Ther. 2012 Jun;22(3):139-46
references: 22703279
references: Cell. 2007 Jul 13;130(1):101-12
references: 17632058
references: Adv Drug Deliv Rev. 2012 Feb;64(2):179-89
references: 21983079
references: Proc Natl Acad Sci U S A. 2003 May 27;100(11):6347-52
references: 12746500
references: FEBS J. 2010 Dec;277(23):4828-36
references: 21078117
references: Cell. 2002 Sep 6;110(5):563-74
references: 12230974
references: Prog Lipid Res. 2008 Sep;47(5):340-7
references: 18424270
references: RNA. 2004 Jan;10(1):12-8
references: 14681580
references: Comput Biol Chem. 2009 Oct;33(5):368-72
references: 19682951
references: RNA. 2006 Jun;12(6):988-93
references: 16611941
references: J Mol Biol. 1999 May 21;288(5):911-40
references: 10329189
references: Nat Struct Mol Biol. 2006 Sep;13(9):849-51
references: 16921378
references: RNA. 2006 Jul;12(7):1188-96
references: 16682561
references: Cell. 2001 Nov 2;107(3):309-21
references: 11701122
references: Immunology. 2012 May;136(1):64-77
references: 22260507
references: Nat Biotechnol. 2005 Aug;23(8):995-1001
references: 16025102
references: Pharmacol Rev. 2006 Mar;58(1):32-45
references: 16507881
references: FEBS Lett. 2004 Jan 16;557(1-3):193-8
references: 14741366
references: Nat Biotechnol. 2010 Feb;28(2):172-6
references: 20081866
references: Science. 2004 Mar 19;303(5665):1818-22
references: 15031496
references: Genome Res. 2003 Aug;13(8):1863-72
references: 12902380
references: Adv Drug Deliv Rev. 2008 Dec 14;60(15):1615-26
references: 18840489
references: Cell. 2004 Mar 19;116(6):831-41
references: 15035985
references: Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1892-7
references: 14769924
references: Eur J Pharm Biopharm. 2004 Sep;58(2):327-41
references: 15296959
references: Mol Ther. 2011 Sep;19(9):1688-94
references: 21750531
references: RNA Biol. 2006 Apr;3(2):82-9
references: 17114944
references: Nucleic Acids Res. 2004 Feb 09;32(3):936-48
references: 14769950
references: Biochemistry. 2010 Apr 13;49(14):3148-55
references: 20184375
references: RNA. 2005 Jun;11(6):864-72
references: 15923373
references: Gastroenterology. 2011 May;140(5):1410-26
references: 21406195
references: Int J Clin Pharmacol Ther. 2012 Jan;50(1):76-8
references: 22192654
references: Nucleic Acids Res. 2007;35(2):433-40
references: 17169992
references: PLoS One. 2011;6(10):e26466
references: 22039495
references: Nucleic Acid Ther. 2011 Jun;21(3):201-14
references: 21749297
references: Nucleic Acids Res. 2003 Jan 15;31(2):589-95
references: 12527766
references: Mol Ther. 2005 Sep;12(3):468-74
references: 15963763
references: Nat Biotechnol. 2008 May;26(5):578-83
references: 18438400
references: Nat Med. 2005 Mar;11(3):263-70
references: 15723075
references: Nature. 2004 May 20;429(6989):318-322
references: 15152257
references: Cell. 2000 Mar 31;101(1):25-33
references: 10778853
references: Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4930-4
references: 16549762
references: RNA. 2006 Jul;12(7):1179-87
references: 16682560
references: Mol Cell. 2009 Jan 30;33(2):204-14
references: 19187762
references: Mol Cell. 2011 Jul 8;43(1):110-21
references: 21726814
references: Chem Biol. 2012 Jan 27;19(1):60-71
references: 22284355
references: Oligonucleotides. 2008 Jun;18(2):187-200
references: 18637735
references: Nat Rev Drug Discov. 2010 Aug;9(8):615-27
references: 20616808
references: Cell. 2009 Jan 23;136(2):215-33
references: 19167326
references: Nucleic Acids Res. 2009 Dec;37(22):7560-9
references: 19815667
references: Mol Pharm. 2008 Jul-Aug;5(4):487-95
references: 18510338
references: Angew Chem Int Ed Engl. 2011 Mar 1;50(10):2284-8
references: 21351337
references: Nat Struct Mol Biol. 2004 Jun;11(6):576-7
references: 15156196
references: EMBO Rep. 2010 Jul;11(7):522-7
references: 20539312
references: Proc Natl Acad Sci U S A. 2007 Aug 7;104(32):12982-7
references: 17652171
references: Am J Physiol Renal Physiol. 2005 Apr;288(4):F605-13
references: 15753324
references: Exp Cell Res. 2004 Oct 15;300(1):248-56
references: 15383331
references: Cell. 2003 Oct 17;115(2):209-16
references: 14567918
references: Nanomedicine. 2012 Feb;8(2):147-66
references: 21703993
references: Nucleic Acids Res. 2003 May 1;31(9):2401-7
references: 12711685
references: Nature. 2005 Aug 4;436(7051):740-4
references: 15973356
references: Cell. 2003 Dec 26;115(7):787-98
references: 14697198
references: Nucleic Acids Res. 2006 Jan 12;34(1):322-33
references: 16410612
references: Nat Struct Mol Biol. 2005 Apr;12(4):340-9
references: 15800637
references: Nucleic Acids Res. 2011 Mar;39(4):1510-25
references: 20972213
references: Silence. 2011 Jun 07;2:4
references: 21649885
references: Nat Biotechnol. 2008 Dec;26(12):1379-82
references: 19029911
references: Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):12996-3001
references: 21784981
references: Eur J Pharm Sci. 2010 Jun 14;40(3):159-70
references: 20359532
references: FEBS J. 2010 Dec;277(23):4806-13
references: 21078115
references: Nano Lett. 2010 May 12;10(5):1664-70
references: 20377197
references: Nat Protoc. 2006;1(2):508-17
references: 17406276
references: Nat Biotechnol. 2005 Nov;23(11):1440-4
references: 16258545
references: Silence. 2011 Mar 14;2:3
references: 21401928
references: Mol Ther. 2011 Sep;19(9):1676-87
references: 21673662
references: BMC Genomics. 2010 Mar 15;11:175
references: 20230625
references: Science. 2004 Mar 5;303(5663):1529-31
references: 14976261
references: Nucleic Acids Res. 2012 May;40(9):4125-36
references: 22253019
references: Chem Res Toxicol. 2012 Nov 19;25(11):2265-84
references: 22823891
references: Cell. 2005 Nov 18;123(4):607-20
references: 16271386
references: EMBO J. 2011 Aug 31;30(17):3481-500
references: 21878991
references: J Mol Biol. 2007 Jan 5;365(1):90-108
references: 17054988
references: Small. 2011 Jul 18;7(14):1919-31
references: 21695781
references: RNA. 2006 Jul;12(7):1197-205
references: 16682562
references: Mol Ther Nucleic Acids. 2012 Feb 07;1:e8
references: 23344723
references: J Immunol. 2004 Jun 1;172(11):6545-9
references: 15153468
references: BMC Bioinformatics. 2006 Feb 12;7:65
references: 16472402
references: Proteome Sci. 2003 Jun 10;1(1):3
references: 12831399
references: Science. 1999 Oct 29;286(5441):950-2
references: 10542148
references: Nat Struct Mol Biol. 2010 Jan;17(1):17-23
references: 19966796
references: RNA. 2005 Apr;11(4):371-82
references: 15703442
references: PLoS One. 2010 Apr 06;5(4):e10051
references: 20386614
references: Nucleic Acid Ther. 2012 Jun;22(3):205-10
references: 22519815
references: Radiol Oncol. 2011 Mar;45(1):1-16
references: 22933928
references: Mol Cancer Ther. 2008 Mar;7(3):579-89
references: 18347144
references: Science. 2004 Sep 3;305(5689):1437-41
references: 15284456
references: Eur J Immunol. 2006 Dec;36(12):3256-67
references: 17111347
references: Cell. 2003 Oct 17;115(2):199-208
references: 14567917
references: J Immunol. 2008 Mar 15;180(6):3729-38
references: 18322178
references: RNA. 2006 Sep;12(9):1620-5
references: 16870995
references: Biochemistry. 1996 Aug 6;35(31):9983-94
references: 8756460
references: FASEB J. 2010 Dec;24(12):4844-55
references: 20732955
references: PLoS Genet. 2006 Sep 8;2(9):e140
references: 16965178
references: Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):512-7
references: 18178619
references: Nat Cell Biol. 2003 Sep;5(9):834-9
references: 12942087
references: Biochemistry. 1988 May 3;27(9):3119-23
references: 3291943
references: Nat Protoc. 2006;1(4):1832-9
references: 17487166
references: Mol Pharm. 2012 May 7;9(5):1031-40
references: 22280459
references: BMC Genomics. 2011 May 20;12:250
references: 21599879
references: Hum Gene Ther. 2008 Feb;19(2):125-32
references: 18257677
references: J Biol Chem. 2009 Jan 23;284(4):2535-48
references: 19017633
references: RNA. 2003 Sep;9(9):1034-48
references: 12923253
references: PLoS One. 2011;6(7):e21503
references: 21750714
references: Nature. 2010 Jun 10;465(7299):818-22
references: 20505670
references: Mol Pharmacol. 2011 Jun;79(6):953-63
references: 21427169
references: Nat Rev Clin Oncol. 2011 May;8(5):292-301
references: 21386818
references: Nucleic Acids Res. 2011 Jun;39(11):4827-35
references: 21335607
references: Biopolymers. 2000-2001;56(3):209-27
references: 11745112
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7
references: 21037258
references: RNA. 2005 May;11(5):674-82
references: 15811921
references: Small. 2009 Jan;5(1):126-34
references: 19051182
references: Nucleic Acids Res. 2005 Aug 09;33(14):4527-35
references: 16091630
references: Adv Drug Deliv Rev. 2012 Oct;64(13):1508-21
references: 22975009
references: J Biol Chem. 2003 Feb 28;278(9):7108-18
references: 12500975
references: Pharm Res. 2011 Feb;28(2):187-99
references: 20549313
references: EMBO Rep. 2006 Mar;7(3):314-20
references: 16439995
references: Nature. 2006 May 25;441(7092):537-41
references: 16724069
references: Toxicol In Vitro. 2011 Oct;25(7):1343-52
references: 21575712
references: J Proteome Res. 2009 Feb;8(2):787-97
references: 19105742
references: Oligonucleotides. 2010 Feb;20(1):27-32
references: 19943801
references: J Med Chem. 2005 Feb 24;48(4):901-4
references: 15715458
references: ACS Nano. 2012 Feb 28;6(2):1230-8
references: 22208867
references: Biochem Biophys Res Commun. 2009 Oct 16;388(2):317-22
references: 19665006
references: Cell Cycle. 2004 Jun;3(6):790-5
references: 15118413
references: Silence. 2010 Jul 08;1(1):14
references: 20615220