Preclinical evaluation of stereopure antisense oligonucleotides for allele-selective lowering of mutant .

Huntington's disease (HD) is an autosomal dominant disease caused by the expansion of cytosine-adenine-guanine (CAG) repeats in one copy of the gene (mutant HTT, mHTT). The unaffected gene encodes wild-type HTT (wtHTT) protein, which supports processes important for the health and function of the central nervous system. Selective lowering of mHTT for the treatment of HD may provide a benefit over nonselective HTT-lowering approaches, as it aims to preserve the beneficial activities of wtHTT.

Endogenous ADAR-mediated RNA editing in non-human primates using stereopure chemically modified oligonucleotides.

Technologies that recruit and direct the activity of endogenous RNA-editing enzymes to specific cellular RNAs have therapeutic potential, but translating them from cell culture into animal models has been challenging. Here we describe short, chemically modified oligonucleotides called AIMers that direct efficient and specific A-to-I editing of endogenous transcripts by endogenous adenosine deaminases acting on RNA (ADAR) enzymes, including the ubiquitously and constitutively expressed ADAR1 p110 isoform. We show that fully chemically modified AIMers with chimeric backbones containing stereopure phosphorothioate and nitrogen-containing linkages based on phosphoryl guanidine enhanced potency and editing efficiency 100-fold compared with those with uniformly phosphorothioate-modified backbones in vitro.

Impact of guanidine-containing backbone linkages on stereopure antisense oligonucleotides in the CNS.

Attaining sufficient tissue exposure at the site of action to achieve the desired pharmacodynamic effect on a target is an important determinant for any drug discovery program, and this can be particularly challenging for oligonucleotides in deep tissues of the CNS. Herein, we report the synthesis and impact of stereopure phosphoryl guanidine-containing backbone linkages (PN linkages) to oligonucleotides acting through an RNase H-mediated mechanism, using Malat1 and C9orf72 as benchmarks. We found that the incorporation of various types of PN linkages to a stereopure oligonucleotide backbone can increase potency of silencing in cultured neurons under free-uptake conditions 10-fold compared with similarly modified stereopure phosphorothioate (PS) and phosphodiester (PO)-based molecules.

Control of backbone chemistry and chirality boost oligonucleotide splice switching activity.

Although recent regulatory approval of splice-switching oligonucleotides (SSOs) for the treatment of neuromuscular disease such as Duchenne muscular dystrophy has been an advance for the splice-switching field, current SSO chemistries have shown limited clinical benefit due to poor pharmacology. To overcome limitations of existing technologies, we engineered chimeric stereopure oligonucleotides with phosphorothioate (PS) and phosphoryl guanidine-containing (PN) backbones. We demonstrate that these chimeric stereopure oligonucleotides have markedly improved pharmacology and efficacy compared with PS-modified oligonucleotides, preventing premature death and improving median survival from 49 days to at least 280 days in a dystrophic mouse model with an aggressive phenotype.

Quantitative Measurement of Cytosolic and Nuclear Penetration of Oligonucleotide Therapeutics.

A major obstacle in the development of effective oligonucleotide therapeutics is a lack of understanding about their cytosolic and nuclear penetration. To address this problem, we have applied the chloroalkane penetration assay (CAPA) to oligonucleotide therapeutics. CAPA was used to quantitate cytosolic delivery of antisense oligonucleotides (ASOs) and siRNAs and to explore the effects of a wide variety of commonly used chemical modifications and their patterning.

A Potential of an Anti-HTLV-I gp46 Neutralizing Monoclonal Antibody (LAT-27) for Passive Immunization against Both Horizontal and Mother-to-Child Vertical Infection with Human T Cell Leukemia Virus Type-I.

Although the number of human T-cell leukemia virus type-I (HTLV-I)-infected individuals in the world has been estimated at over 10 million, no prophylaxis vaccines against HTLV-I infection are available. In this study, we took a new approach for establishing the basis of protective vaccines against HTLV-I. We show here the potential of a passively administered HTLV-I neutralizing monoclonal antibody of rat origin (LAT-27) that recognizes epitopes consisting of the HTLV-I gp46 amino acids 191-196.

ELISA system for human endothelial lipase.

Background: Endothelial lipase (EL) regulates the metabolism of HDL cholesterol (HDL-C). However, the role of EL in regulating plasma HDL-C concentrations and EL's potential involvement in atherosclerosis in humans has not been fully investigated due to the lack of reliable assays for EL mass. We developed an ELISA system for serum EL mass.

Theoretical simulation of Kelvin probe force microscopy for Si surfaces by taking account of chemical forces.

A new method of theoretical simulation for Kelvin probe force microscopy (KPFM) imaging on semiconductor or metal samples is proposed. The method is based on a partitioned real space (PR) density functional based tight binding (DFTB) calculation of the electronic states to determine the multi-pole electro-static force, which is augmented with the chemical force obtained by a perturbation treatment of the orbital hybridization. With the PR-DFTB method, the change of the total energy is calculated together with the induced charge distribution in the tip and the sample by their approach under an applied bias voltage, and the KPFM images, namely the patterns of local contact potential difference (LCPD) distribution, are obtained with the minimum condition of the interaction force.

Solid-phase synthesis of oligodeoxyribonucleotides without base protection utilizing O-selective reaction of oxazaphospholidine derivatives.

A study on the development of a novel method to synthesize oligodeoxyribonucleotides without base protection is described. We found that nucleoside 3'-O-oxazaphospholidine derivatives exclusively react with the hydroxy group of nucleosides in the presence of unprotected nucleobase amino groups. Since the O-chemoselectivity of the oxazaphospholidine derivatives is likely due to their ring structure, which allows the regeneration of the oxazaphospholidine derivatives from the corresponding base phosphitylation adducts via an intramolecular recyclization, the method is expected to be compatible with any kinds of acidic activators.

Solid-phase synthesis of backbone-modified DNA analogs by the boranophosphotriester method using new protecting groups for nucleobases.

Backbone-modified DNA analogs were synthesized in good yields by the boranophosphotriester method on a solid support. The oligodeoxyribonucleoside boranophosphates, protected with 2-(azidomethyl)benzoyl groups for nucleobases, were converted into DNA and its backbone-modified analogs via the corresponding H-phosphonate intermediates. A new protecting group for the O6 position of 2'-deoxyguanosine, 4-azidobenzyl (ABn) group, was also developed.

Convenient method for the preparation of carbamates, carbonates, and thiocarbonates.

A convenient, rapid, and efficient method for the preparation of carbamates from amines with 1-alkoxycarbonyl-3-nitro-1,2,4-triazole transfer reagents is reported. Reactions of newly synthesized stable crystalline reagents with alkyl amines were completed in a few minutes without any additional base, and highly pure carbamates were obtained without chromatographic purification. These highly active reagents are also useful for the selective protection of nucleobases and preparation of carbonates and thiocarbonates.

DNase X is a glycosylphosphatidylinositol-anchored membrane enzyme that provides a barrier to endocytosis-mediated transfer of a foreign gene.

DNase X is the first mammalian DNase to be isolated that is homologous to DNase I. In this study, we have examined its function using a novel monoclonal antibody and showed it to be expressed on the cell surface as a glycosylphosphatidylinositolanchored membrane protein. High level expression was observed in human muscular tissues and in myotubes obtained in vitro from RD rhabdomyosarcoma cells.

Stereocontrolled synthesis of dinucleoside boranophosphates by an oxazaphospholidine method.

Stereodefined dinucleoside boranophosphates were synthesized from diastereopure nucleoside 3'-oxazaphospholidine derivatives. The new method is based on the stereospecific formation of dinucleoside phosphite intermediates catalyzed by a non-nucleophilic acidic activator, N-(cyanomethyl)pyrrolidinium triflate, and the boronation of the intermediates.

A novel method for the synthesis of DNA and its analogs by the use of BH3 as a protecting group for phosphonic acid.

Recently, we have developed a novel reaction for the transformation of boranophosphate diesters to the corresponding H-phosphonate diesters in the presence of trityl cation under acidic conditions. In this study, DNA and backbone-modified DNA analogs were synthesized in good yields upon applying this reaction. We report the transformation of boranophosphate DNAs, fully protected with 2-azidomethylbenzoyl groups, to various backbone-modified DNA analogs via the H-phosphonate intermediates in solution and on a solid support.

Solid-phase synthesis of oligodeoxyribonucleoside boranophosphates by the boranophosphotriester method.

Oligodeoxyribonucleoside boranophosphates (BH3-ODNs), containing four kinds of nucleobases, were synthesized by the solid-phase boranophosphotriester method. The 2'-deoxyribonucleoside 3'-boranophosphate monomers having 2-cyanoethyl (CE) groups as the phosphorus protecting groups were synthesized in good yields. A new condensing reagent, 1,3-dimethyl-2-(3-nitro-1,2,4-triazol-1-yl)-2-pyrrolidin-1-yl-1,3,2-diazaphospholidinium hexafluorophosphate, was found to be highly effective for the condensation reaction on the solid support.

Stereoselective synthesis of dinucleoside boranophosphates by an oxazaphospholidine method.

A stereoselective synthesis of dinucleoside boranophosphates by using nucleoside 3'-oxazaphospholidine derivatives is described. The diastereoselectivity of the internucleotidic bond formation reactions varied with the nucleobase used. (Rp)- and (Sp)-dithymidine boranophosphates were synthesized with excellent diastereoselectivity both in solution and on a solid-support, whereas a loss of diastereopurity was observed for the 2'-deoxycytidine derivative having an unprotected nucleobase amino group.

A novel method for the synthesis of dinucleoside boranophosphates by a boranophosphotriester method.

2'-Deoxyribonucleoside-3'-boranophosphates (nucleotide monomers), including four kinds of nucleobases, were synthesized in good yields by the use of new boranophosphorylating reagents. We have explored various kinds of condensing reagents as well as nucleophilic catalysts for the boranophosphorylation reaction with nucleosides. In the synthesis of dinucleoside boranophosphates, undesirable side reactions occurred at the O-4 of thymine and the O-6 of N2-phenylacetylguanine bases.

Synthesis of dinucleoside boranophosphates by a boranophosphotriester approach.

Dinucleoside boranophosphates including four kinds of nucleobases were synthesized by a boranophosphotriester method in good yields. In the present boranophosphotriester method, side-reactions at the nucleobases, which caused by a borane reagent, were completely avoided.