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WO 2016/180784 Al 17 November 2016 (17.11.2016) P O P C T

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WO 2016/180784 Al 17 November 2016 (17.11.2016) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/180784 Al 17 November 2016 (17.11.2016) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every A61K 31/60 (2006.01) A61P 43/00 (2006.01) kind of national protection available): AE, AG, AL, AM, A61K 31/7125 (2006.01) A61P 7/02 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, A61K 45/06 (2006.01) G01N 33/86 (2006.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (21) International Application Number: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, PCT/EP20 16/060344 KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, (22) International Filing Date: MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, May 2016 (09.05.2016) PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, (25) Filing Language: English TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (26) Publication Language: English (84) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of regional protection available): ARIPO (BW, GH, 1507926.2 8 May 2015 (08.05.2015) GB GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, (71) Applicant: PROQR THERAPEUTICS II B.V. [NL/NL]; TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, Darwinweg 24, 2333 CR Leiden (NL). DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, (72) Inventor: KLEIN, Bart; c/o ProQR Therapeutics II B.V., SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Darwinweg 24, 2333 CR Leiden (NL). GW, KM, ML, MR, NE, SN, TD, TG). (74) Agents: MARSHALL, Cameron, John et al; Carpmaels Published: & Ransford LLP, One Southampton Row, London WC1B 5HA (GB). — with international search report (Art. 21(3)) 00 o 00 o (54) Title: IMPROVED TREATMENTS USING OLIGONUCLEOTIDES (57) Abstract: Potential side effects of unintentional activation of platelets by phosphorothioated oligonucleotides are minimised in various ways, including a combination therapy, wherein PS-ONs are combined, in one composition, a kit-of-parts, and/or in a com bination therapy regime, with either or both specific platelet activation pathway inhibitors, and/or the common platelet aggregation pathway. IMPROVED TREATMENTS USING OLIGONUCLEOTIDES FIELD OF THE INVENTION The present invention relates to the field of medicine, more in particular of combination therapy involving oligonucleotides. BACKGROUND OF THE INVENTION The use of oligonucleotides in medicine has rapidly evolved over the last two decades. Oligonucleotides are being used, for example, to interfere with gene expression, by up-regulating or down-regulating genes involved in the disease pathway on the level of transcription, pre- mRNA splicing or translation. In addition, oligonucleotides are being used to reverse genetic mutations at the DNA or RNA level, by oligonucleotide-guided repair. It is now possible to alter the symptoms or the severity of a host of genetic diseases by directly interfering with the genetic cause of disease, be it at the DNA or at the RNA level. The recent successes of oligonucleotide- based therapies is in part attributable to chemical modifications that increase the affinity of the ON for its target and/or that protect the ONs against degradation by nucleases. One chemical modification that has particularly contributed to the widespread use of ONs in today's medicine is the modification of the backbone of the ON, normally consisting of phosphodiester internucleosidic linkages, by exchanging one, or two, non-linking oxygens in backbone of the ON. Nowadays, mono-thio (PS-) and di-thio (PS2) modified oligodeoxyribonucleotides and oligoribonucleotides are routinely used for medicinal use in humans. Relatively recently, it has been reported that a fully phosphorothioated oligodeoxynucleotide (ODN) administered intravenously was capable of activating blood platelets through platelet-specific receptor glycoprotein VI (GPVI), thereby mediating platelet aggregation and thrombus formation in vitro, in an in vivo mouse model (a murine carotid artery ferric chloride model, described on page 133, left col. ultimate paragraph, in Flierl et al., supra), as well as in mice (Flierl et al. J. Exp. Med. 2015 Vol. 212 No. 2, 129-137). The activation of platelets was reported to be sequence independent and to require PS-modification. Several tests pointed to glycoprotein VI (GPVI) as the receptor for the PS-modified oligodeoxyribonucleotide ODN2395. A function blocking anti-GPVI antibody prevented ODN2395-induced platelet aggregation. The authors postulate a potential mechanism of interference between the PS- modified ODN and GPVI, by explaining that the poly-anionic PS-backbone is electrostatically attracted to a sequence of positively charged amino acids in a groove of the collagen binding domain of GPVI. The authors advise that appropriate hematological tests should be developed to monitor these platelet-activating effects during clinical trials. Moreover, the authors conclude that their findings support the development of alternative chemical modifications to provide nuclease resistance for nucleotide-based therapeutics. SUMMARY OF THE INVENTION The present inventors, being aware of the potential side effects of unintentional activation of platelets by phosphorothioated oligonucleotides, propose an alternative solution to deal with these potential side effects. Accordingly, solutions are provided, including a combination therapy, wherein PS-ONs are combined, in one composition, a kit-of-parts, and/or in a combination therapy regime, with either or both specific platelet activation pathway inhibitors, and/or the common platelet aggregation pathway. The solutions offered are not limited to PS-ONs. ONs of different chemistry but with similar characteristics as PS-ONs in terms of platelet activation, aggregation and/or initiation or stimulation of thrombus formation may benefit from some of the proposed solutions just the same. Thus the invention provides a method for the treatment of an individual in need thereof with an oligonucleotide (ON) to treat or prevent a disease, wherein the ON is capable of causing platelet activation, platelet aggregation and/or thrombus formation at a ON blood plasma concentration of between about 0.01 and 10 µΜ , characterized in that a countermeasure is taken to reduce such platelet activation, aggregation and/or thrombus formation, and/or any side effects thereof. Such countermeasures are discussed below in more detail. The invention also provides a pharmaceutical composition or a kit of parts comprising: (A) an ON capable of causing platelet activation, platelet aggregation and/or thrombus formation in an individual to be treated, at a ON blood plasma concentration of between about 0.01 and 10 µΜ , and (B) an inhibitor of platelet activation, aggregation or thrombus formation selected from the group consisting of: (i) an inhibitor of collagen (platelet-specific) collagen-receptor interaction, such as an antibody (e.g. anti-GPVI antibody JAQ1) (ii) a COX 1-inhibitor (e.g. acetylsalicylic acid or a pharmaceutically acceptable salt thereof, or a carbasalate salt); (iii) an inhibitor of the ADP - P2Y12 interaction (iv) an inhibitor of the fibrinogen-GPIIb/IIIa interaction; (v) a NOX- inhibitor, such as NOX1-inhibitor ML171, apocynin, or 2 acetylphenothiazine; (vi) an antioxidant, such as vitamin C or diferuloylmethane, or a combination of one or more of (i) to (vi) above. The invention also provides a method for modifying a first therapeutic oligonucleotide to give a second therapeutic oligonucleotide, wherein (a) the first therapeutic oligonucleotide binds to a target nucleic acid, includes one or more phosphorothioate linkages, and causes platelet activation, platelet aggregation and/or thrombus formation; and (b) the second therapeutic oligonucleotide binds to the target nucleic acid, includes one or more phosphorothioate linkages, and causes less platelet activation, platelet aggregation and/or thrombus formation than the first therapeutic oligonucleotide, wherein the method comprises one or more of the following: (i) where the first therapeutic oligonucleotide is 18 or more nucleotides long, reducing its length to give a second therapeutic oligonucleotide which is less than 18 nucleotides long; (ii) reducing the total number of phosphorothioate linkages, such that the second therapeutic oligonucleotide has fewer phosphorothioate linkages than the first therapeutic oligonucleotide; and/or (iii) reducing the number of consecutive phosphorothioate linkages, such that the second therapeutic oligonucleotide has fewer consecutive phosphorothioate linkages than the first therapeutic oligonucleotide. The invention also provides a method for producing an oligonucleotide specific for a target nucleic acid, comprising steps of: (a) preparing a first therapeutic oligonucleotide which binds to a target nucleic acid, includes one or more phosphorothioate linkages; (b) determining the first therapeutic oligonucleotide's ability to cause platelet activation, platelet aggregation and/or thrombus formation; (c) preparing a second therapeutic oligonucleotide which also binds to the target nucleic acid and includes one or more phosphorothioate linkages; (d) determining the second therapeutic oligonucleotide's ability to cause platelet activation, platelet aggregation and/or thrombus formation; and (e) if the second therapeutic oligonucleotide has a lower ability to cause platelet activation, platelet aggregation and/or thrombus formation than the first therapeutic oligonucleotide, synthesizing and purifying the second therapeutic oligonucleotide for use as a pharmaceutical. Step (b) and (d) will generally be assessed by the same criteria, and suitable assays are known e.g. a reduction of O D 5 over time, upon incubation of platelet rich plasma in the presence of said oligonucleotides in an in vitro assay.
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