SBIR-STTR Award

The use of modified deoxyoligonucleotides for the inhibition of HIV replication via the binding to specific sequences of mRNA or DNA shows great promise. Most previous synthetic work in this area has focused on chiral analogs of the phosphate backbone. Neutral analogs are of special interest because of their possible ability to penetrate into cells by passive diffusion. This research has two aspects. The first aspect is the development of synthetic methods for the facile synthesis of deoxyoligonucleotide analogs bearing a new neutral, achiral and stable internucleotide analog linkage-namely, formacetal. Synthetic methods will be used for the improved synthesis of formacetals. Promising chemistries will be adapted to polymer bound synthesis. The second aspect focuses on the in vitro hybridization of these modified analogs toward complementary RNA and their triplex formation ability with duplex DNA. The RNA interaction will be studied by classical thermal denaturation experiments and a new kinetic assay described in the preliminary data. The triplex interaction will be studied by foot-printing assays on a novel DNA target reported in the preliminary data. The combined goal is the facile synthesis of neutral formacetal containing deoxyoligonucleotides which have enhanced sequence specific binding to HIV RNA and duplex DNA.Awardee's statement of the potential commercial applications of the research:Currently, AIDS is a serious disease with no adequate therapy and offers a large commercial pharmaceutical potential. The deoxyoligonucleotide analogs described have the promise of arresting the course of the disease via targeting the viral MRNA and curing the disease by attacking latent integrated virus via triple strand formation.National Institute of Allergy and Infectious Diseases (NIAID)

Two modifications of oligonucleotides have been identified that may enhance oligonucleotide affinity for complementary RNA. The 5' position of pyrimidines has been modified with a propenyl group that results in higher specific binding affinity in vitro and in enhanced antisense potency. The enhancement is about 100 fold, based on a well controlled cellular assay. Independently, the phosphate internucleotide linkage has been replaced with an achiral neutral isostere, the 3' thioformacetal. This modification results in higher m vitro binding affinity toward a complementary RNA. Our aims will focus on efforts to combine the two modifications into one molecule, namely, to synthesize fullv-substituted 3' thioformacetal oligonucleotides containing 5- (1)- propenyl)-pyrimidines and purines.This approach will be directed at HIV by synthesis of oligonucleotide analogs targeted to HIV sites that are conserved throughout all known strains. Antisense and antiviral activities will be evaluated. The ultimate goal is the identification of an analog sequence that warrants study in primate models and human trials.Awardee's statement of the potential commercial applications of the research:Current chemotherapy for HIV infection is inadequate. Drug resistance has emerged as a significant problem for effective antiviral therapy. Antisense oligonucleotides which have been optimized for potency and which are targeted toward absolutely conserved regions of the viral messenger RNA offer the possibility of an effective treatment for HIV infection.National Institute of Allergy and Infectious Diseases (NIAID)