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The design and optimization of a novel trans-1,4-dioxycyclohexane GPR119 agonist series is described. A lead compound 21 was found to be a potent and efficacious GPR119 agonist across species, and possessed overall favorable pharmaceutical properties. Compound 21 demonstrated robust acute and chronic regulatory effects on glycemic parameters in the diabetic or non-diabetic rodent models.

S1P1 is a validated target for treatment of autoimmune disease, and functional antagonists with superior safety and pharmacokinetic properties are being sought as second generation therapeutics. We describe the discovery and optimization of (7-benzyloxy-2,3-dihydro-1H-pyrrolo[1,2-a]indol-1-yl)acetic acids as potent, centrally available, direct acting S1P1 functional antagonists, with favorable pharmacokinetic and safety properties.

APD334 was discovered as part of our internal effort to identify potent, centrally available, functional antagonists of the S1P1 receptor for use as next generation therapeutics for treating multiple sclerosis (MS) and other autoimmune diseases. APD334 is a potent functional antagonist of S1P1 and has a favorable PK/PD profile, producing robust lymphocyte lowering at relatively low plasma concentrations in several preclinical species. This new agent was efficacious in a mouse experimental autoimmune encephalomyelitis (EAE) model of MS and a rat collagen induced arthritis (CIA) model and was found to have appreciable central exposure.

Two series of fused tricyclic indoles were identified as potent and selective S1P(1) agonists. In vivo these agonists produced a significant reduction in circulating lymphocytes which translated into robust efficacy in several rodent models of autoimmune disease. Importantly, these agonists were devoid of any activity at the S1P(3) receptor in vitro, and correspondingly did not produce S1P(3) mediated bradycardia in telemeterized rat.

S1P1 receptor driven lymphopenia has proven utility in the treatment of an array of autoimmune disease states. As a part of our efforts to develop potent and selective S1P1 receptor agonists, we have identified a novel chemical series of 4-oxo-4-(5-(5-phenyl-1,2,4-oxadiazol-3-yl)indolin-1-yl)butanoic acid S1P1 receptor agonists.

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.

Modulators of S1P1 have proven utility for the treatment of autoimmune disease and efforts to identify new agents with improved safety and pharmacokinetic parameters are ongoing. Several new S1P1 chemotypes were designed and optimized for potency and oral bioavailability. These new agents are characterized by a ‘tricyclic fused indole array’ and are highly potent agonists of the S1P1 receptor.

A series of 5-fluoro-4,6-dialkoxypyrimidine GPR119 modulators were discovered and optimized for in vitro agonist activity. A lead molecule was identified that has improved agonist efficacy relative to our clinical compound (APD597) and possesses reduced CYP2C9 inhibitory potential. This optimized lead was found to be efficacious in rodent models of glucose control both alone and in combination with a Dipeptidyl peptidase-4 (DPP-4) inhibitor.

Antisense oligonucleotides with 2'-O-(2-[N,N-dimethyl)aminooxy]ethyl) or (2'-O-DMAOE) modification were synthesized and evaluated for nuclease resistance and pharmacology both in vitro and in vivo. This modification exhibits very high nuclease resistance and efficacy in various biological (ICAM-1, C-raf and PKC-alpha) targets.

A novel 2′-modification, 2′-O-[3-(N,N-dimethylamino)propyl] or 2′-O-DMAP, has been incorporated into oligonucleotides and compared to the known 2′-O-(3-aminopropyl) or 2′-O-AP modification for antisense properties. The 2′-O-DMAP modified oligonucleotides exhibit very high nuclease resistance like the 2′-O-AP modification due to the ‘charge effect’ and maintain high binding affinity to target RNA relative to known modifications when a few 2′-O-DMAP residues are dispersed throughout the oligonucleotide.

The alkylation of N -3-benzyloxymethyl-5-methyluridine with 1,3,2-dioxathiolane 2,2-dioxide or 1,3,2-dioxathiane 2,2-dioxide resulted in a 2′- O versus 3′- O selectivity of 3:1, respectively. The resulting product has a built-in sulfate leaving group at the terminal end of an ethyl or propyl carbon chain, which can be displaced with sulfur and nitrogen nucleophiles to produce modifications at the 2′- O or 3′- O positions.

Chemical modifications to improve the efficacy of an antisense oligonucleotide are designed to increase the binding affinity to target RNA, to enhance the nuclease resistance, and to improve cellular delivery. Among the different sites available for chemical modification in a nucleoside building block, the 2′-position of the carbohydrate moiety1 has proven to be the most valuable for various reasons: (1) 2′-modification can confer an RNA-like 3′-endo conformation to the antisense oligonucleotide. Such a preorganization for an RNA like conformation2,3,4,5 greatly improves the binding affinity to the target RNA; (2) 2′-modification provides nuclease resistance to oligonucleotides; (3) 2′-modification provides chemical stability against potential depurination conditions pharmacology evaluations and correlation with pharmacokinetic changes are emerging from these novel chemical modifications. Analytical chemistry of modified oligonucleotides before and after biological administration of antisense oli...

The novel RNA mimic 2′-O-AOE has been incorporated into antisense oligonucleotides. This 2′-O-modification significantly enhances hybridization against target RNA, and furthermore, exhibits specificity for RNA over DNA. The nuclease resistance (SVPD) of 2′-O-AOE modified phosphodiester oligonucleotides is significantly higher than the unmodified DNA and comparable to the 2′-O-MOE oligonucleotides.

Use of solution phase combinatorial library synthesis led to the discovery of several oxyamine-containing antibacterial compounds. Solution-phase simultaneous addition of meta-substituted benzyl bromides and “fix-last” combinatorial strategies were used to prepare libraries. Additional structure−activity relationship studies were conducted by reductive cleavage of the oxyamine moiety and led to loss of antibacterial activity. Several single compounds were designed and synthesized on the basis of library screening results and were shown to have antibacterial activity.

We have synthesized the novel 2′-O-AOE- and MIOE-5-methyluridine and -adenosine nucleosides and successfully incorporated them into oligonucleotides. The 2′-O-modifications significantly enhance hybridization against RNA (1.2 deg C/substitution) and furthermore, exhibits specificity for RNA vs. DNA. The nuclease resistance (SVPD) of 2′-O-AOE and MIOE modified oligonucleotides is comparable to that of 2′-O-MOE.

The alkylation of N -3-benzyloxymethyl-5-methyluridine with 1,3,2-dioxathiolane 2,2-dioxide or 1,3,2-dioxathiane 2,2-dioxide resulted in a 2′- O versus 3′- O selectivity of 3:1, respectively. The resulting product has a built-in sulfate leaving group at the terminal end of an ethyl or propyl carbon chain, which can be displaced with sulfur and nitrogen nucleophiles to produce modifications at the 2′- O or 3′- O positions.

The tricyclic nucleoside 8-amino-4-methylthio-6-methyl-2-(β-D-ribofuranosyl)-1,2,3,5,6,7-hexaazaacenaphthylene (3) was synthesized from 3-cyano-4,6-bis(methylthio)-1-(β-D-ribofuranosyl)pyrazolo[3,4-d]pyrimidine (1). Attempts to synthesize 8-amino-6-methyl-2-(β-D-ribofuranosyl)-1H-2,6-dihydro-1,2,3,5,6,7-hexaazaacenaphthylene (5) ([an aza analog of 6-amino-4-methyl-8-(β-D-ribofuranosyl)-1,3,4,5,8-pentaazaacenaphthylene (TCN)], which is a potent antitumor agent), by the treatment of 3 with Raney nickel did not afford the desired aza analog of TCN. Instead, it was established that a reductive cleavage of the pyridazine moiety of 3 had occurred to give 4-methylamino-6-methylthio-1-(β-D-ribofuranosyl)-1H-pyrazolo[3,4-d]pyrimidine-3-carboxamidine (6). Assuming that solubility was a problem in the reductive step, the isopropylidene derivative of 3, 8-amino-6-methyl-4-methylthio-2-(2,3-O-isopropylidene-β-D-ribofuranosyl)-2,6-dihydro-1,2,3,5,6,7-hexaazaacenaphthylene (8), was treated with Raney nickel, only to observe that a similar reductive ring cleavage of 8 had occurred to afford 4-methylamino-6-methylthio-1-(2,3-O-isopropylidene-β-D-ribofuranosyl)-1H-pyrazolo[3,4-d]pyrimidine-3-carboxamidine (10) and 4-methylamino-1-(2,3-O-isopropylidene-β-D-ribofuranosyl)-1H-pyrazolo[3,4-d]pyrimidine-3-carboxamidine (11). Structural assignments for all products were established by physico-chemical procedures.

We have recently described a method to prepare combinatorial chemistry libraries by solution phase simultaneous addition of functionalities (SPSAF).1–2 SPSAF has been used to create libraries based on the purine heterocycle. The nucleophilic sites (secondary nitrogens) in the planer heteroaromatic purine scaffold were built in via linkers. Thus, to continue the use of electophilic functionalities, as in previous libraries, a bifunctional nucleophilic linker was required. Piperazines readily served this purpose. Nucleophilic displacement of the chloro groups on 2,6-dichloropurine with piperazines provides reactive, constrained secondary amines for combinatorialization (Figure 1, 1). An additional piperazine was placed in the 9-position by alkylation of 2,6-dipiperazinylpurine. In this manner, the functionality that differentiates each pool (sublibrary) could be placed last in the synthetic scheme (fix last concept).1

A number of 2'- O-modified antisense oligonucleotides have been reported for their potential use in oligonucleotide-based therapeutics. To date, most of the in vivo data has been generated for 2'-O-MOE (2'-O-methoxyethyl)- and 2'-O-Me (2'-O-methyl)-modified ASOs (antisense oligonucleotides). We now report the synthesis and biological activity of another 2'-O-modification, namely 2'-O-[2-(methylamino)-2-oxoethyl] (2'-O-NMA). This modification resulted in an increase in the affinity of antisense oligonucleotides to complementary RNA similar to 2'-O-MOE-modified ASOs as compared to first-generation antisense oligodeoxynucleotides. The ASO modified with 2'-O-NMA reduced expression of PTEN mRNA in vitro and in vivo in a dose-dependent manner similar to 2'-O-MOE modified ASO. Importantly, toxicity parameters such as AST, ALT, organ weights, and body weights were found to be normal similar to 2'-O-MOE ASO-treated animal models. The data generated in these experiments suggest that 2'-O-NMA is a useful modification for potential application in both antisense and other oligonucleotide-based drug discovery efforts.

The tricyclic nucleoside 8-amino-6-N-methyl-2-beta-D-ribofuranosyl-1,2,3,5,6, 7-hexaazaacenaphthylene was synthesized from 8-amino-6-N-methyl-4-(methylthio)-2-beta-D-ribofuranosyl-1,2,3,5,6, 7-hexaazaacenaphthylene. The 2'-deoxy analogue of 5, 8-amino-6-N-methyl-2-(2-deoxy-beta-D-ribofuranosyl)-1,2,3,5,6, 7-hexaazaacenaphthylene (11), and the arabino analogue of (5), 8-amino-6-N-methyl-2-beta-D-arabinofuranosyl-1,2,3,5,6, 7-hexaazaacenaphthylene (14) were synthesized from 5. Nucleosides 2,3,4,5,11, and 14 were evaluated for potential anticancer activity by measuring their ability to inhibit the growth of L1210 and H. Ep. 2 tumor cells in vitro.

[structure: see text] Oligonucleotides with novel modifications, 2'-O-[2-(amino)-2-oxoethyl] (2'-O-NAc), 2'-O-[2-(methylamino)-2-oxoethyl] (2'-O-NMAc), 2'-O-[2-(dimethylamino)-2-oxoethyl] (2'-O-DMAc), and 2'-O-[2-[[2-(dimethylamino)ethyl]amino]-2-oxoethyl] (2'-O-DMAEAc), have been synthesized. These modified oligonucleotides exhibit high binding affinity to complementary RNA (and not to DNA) and considerably enhance the nuclease stability of oligonucleotides with t(1/2)24 h.

A versatile synthetic route has been developed for the synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] (abbreviated as 2'-O-DMAOE) modified purine and pyrimidine nucleosides and their corresponding nucleoside phosphoramidites and solid supports. To synthesize 2'-O-DMAOE purine nucleosides, the key intermediate B (Scheme 1) was obtained from the 2'-O-allyl purine nucleosides (13a and 15) via oxidative cleavage of the carbon-carbon bond to the corresponding aldehydes followed by reduction. To synthesize pyrimidine nucleosides, opening the 2,2'-anhydro-5-methyluridine 5 with the borate ester of ethylene glycol gave the key intermediate B. The 2'-O-(2-hydroxyethyl) nucleosides were converted, in excellent yield, by a regioselective Mitsunobu reaction, to the corresponding 2'-O-[2-[(1,3-dihydro-1,3-dioxo-2H-isoindol-2-yl)oxy]ethyl] nucleosides (18, 19, and 20). These compounds were subsequently deprotected and converted into the 2'-O-[2-[(methyleneamino)oxy]ethyl] derivatives (22, 23, and 24). Reduction and a second reductive amination with formaldehyde yielded the corresponding 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] nucleosides (25, 26, and 27). These nucleosides were converted to their 3'-O-phosphoramidites and controlled-pore glass solid supports in excellent overall yield. Using these monomers, modified oligonucleotides containing pyrimidine and purine bases were synthesized with phosphodiester, phosphorothioate, and both linkages (phosphorothioate and phosphodiester) present in the same oligonucleotide as a chimera in high yields. The oligonucleotides were characterized by HPLC, capillary gel electrophoresis, and ESMS. The effect of this modification on the affinity of the oligonucleotides for complementary RNA and on nuclease stability was evaluated. The 2'-O-DMAOE modification enhanced the binding affinity of the oligonucleotides for the complementary RNA (and not for DNA). The modified oligonucleotides that possessed the phosphodiester backbone demonstrated excellent resistance to nuclease with t(1/2) > 24 h.

[structure] Oligonucleotides with two novel modifications, 2'-O-¿2-[N, N-(dimethyl)aminooxy]ethyl¿ (2'-O-DMAOE) and 2'-O-¿2-[N, N-(diethyl)aminooxy]ethyl¿ (2'-O-DEAOE), have been synthesized. These modifications exhibit high binding affinity to target RNA (and not to DNA) and enhance the nuclease stability of oligonucleotides considerably with t(1/2)24 h as a phosphodiester.

A novel 2′-modification, 2′-O-[3-(N,N-dimethylamino)propyl] or 2′-O-DMAP, has been incorporated into oligonucleotides and compared to the known 2′-O-(3-aminopropyl) or 2′-O-AP modification for antisense properties. The 2′-O-DMAP modified oligonucleotides exhibit very high nuclease resistance like the 2′-O-AP modification due to the ‘charge effect’ and maintain high binding affinity to target RNA relative to known modifications when a few 2′-O-DMAP residues are dispersed throughout the oligonucleotide.

"Uniformly" modified phosphodiester or phosphorothioate oligonucleotides incorporating 2'-deoxy-2'-fluoroadenosine, -guanosine, -uridine, and -cytidine, reported herein for the first time, when hybridized with RNA afforded consistent additive enhancement of duplex stability without compromising base-pair specificity. CD spectra of the 2'-deoxy-2'-fluoro-modified oligonucleotides hybridized with RNA indicated that the duplex adopts a fully A-form conformation. The 2'-deoxy-2'-fluoro-modified oligonucleotides in phosphodiester form were not resistant to nucleases; however, the modified phosphorothioate oligonucleotides were highly nuclease resistant and retained exceptional binding affinity to the RNA targets. The stabilizing effects of the 2'-deoxy-2'-fluoro modifications on RNA-DNA duplexes were shown to be superior to those of the 2'-O-methylribo substitutions. RNA hybrid duplexes with uniformly 2'-deoxy-2'-fluoro-modified oligonucleotides did not support HeLa RNase H activity; however, incorporation of the modifications into "chimeric" oligonucleotides has been shown to activate mammalian RNase H. "Uniformly" modified 2'-deoxy-2'-fluoro phosphorothioate oligonucleotides afforded antisense molecules with (1) high binding affinity and selectivity for the RNA target and (2) stability toward nucleases.

Oligonucleotides with modifications at the carbohydrate 2′-position offer potential second-generation drug candidates1. ISIS 13312, a chimeric compound targeting CMV retinitis, has 2′-O-methoxyethyl2 (2′-MOE) modifications at the ends to offer enhanced binding affinity and nuclease resistance is an example of this trend. 2′-MOE modification offers high binding affinity and nuclease resistance presumably due to conformational constraints placed on the linkage by the oxygen-oxygen gauche effect3. On the other hand, 2′-O-aminopropyl modification (2′-AP) exhibits the highest nuclease resistance4, due to the presence of a cationic charge at the physiological pH. However, it lacks the binding affinity advantage of MOE due to the lack of oxygen-oxygen gauche effect. To optimize the antisense properties of both 2′-MOE and 2′-AP modifications, we have designed and constructed 2′-O-(aminooxyethyl) modification (2′-AOE)5 and 2′-O-(dimethylaminooxy ethyl) modification (2′-DMAOE) and synthesized oligomers hav...

We have synthesized the novel 2′-O-AOE- and MIOE-5-methyluridine and -adenosine nucleosides and successfully incorporated them into oligonucleotides. The 2′-O-modifications significantly enhance hybridization against RNA (1.2 deg C/substitution) and furthermore, exhibits specificity for RNA vs. DNA. The nuclease resistance (SVPD) of 2′-O-AOE and MIOE modified oligonucleotides is comparable to that of 2′-O-MOE.

We have effectively used the SPSAF method with purine and pyrimidine based scaffolds to rapidly generate diverse libraries with antibacterial activity. Deconvolution via HPLC fractionation resulted in libraries with reduced complexity (2–10 compounds), a number of which retained good antibacterial activity.

The protected tricyclic heterocycle 8-amino-6-N-methyl-2-(tetrahydropyran-2-yl)-1,2,3,5,6,7-hexaazaacenaphthylene (11) was prepared from 3-cyano-4,6-bis-methylthiopyrazolo[3,4-d]pyrimidine in a six-step reaction sequence. Treatement of 11 with hydrogen chloride gas under anhydrous conditions has afforded 8-amino-6-N-methyl-1,2,3,5,6,7-hexaazaacenaphthylene in a moderate yield.

Studies on an unexpected reaction involving a reductive cleavage of the pyridazine moiety of a tricyclic heterocycle are described. Structure assignments for the products obtained from the reductive cleavage were made using physicochemical methods.

A total synthesis of 2-amino-7-(O-D-ribofuranosyl)pyrrolo(2,3-dlpyrimidin-4-one- properties. We now wish to report a total synthesis of the nucleoside 2-amino-7-(B-D-ribo- furanosyl)pyrrolo(2,3-dlpyrimidin-4-one-5-carboxylic acid (2, cadeguomycin). We initiated two separate routes for the total synthesis of cadeguomycin, with each route being designed to ultimately afford the desired antibiotic. In the first route investigated, we envisaged the use of 2-amino-7-(O-D-ribofuranosyl)pyrrolo(2,3-dl-pyrimidin-4-one-5- - carboxamide (4) as the immediate precursor of cadeguomycin. The synthesis of this precursor (4-j was accomplished from the nucleoside antibiotic toyocamycin via a seven step sequence. - However, the low yield (14%) from the last step, treatment of 2-amino-5-cyano-7-(&D- ribofuranosyl)pyrrolo(2,3-dl-pyrimidin-l-one 8