Identification of genetic targets for modulation by oligonucleotides and generation of oligonucleotides for gene modulation

Abstract

Interative, preferably computer based iterative processes for generating synthetic compounds with desired physical, chemical and / or bioactive properties, i.e., active compounds, are provided. During iterations of the processes, a target nucleic acid sequence is provided or selected, and a library of candidate nucleobase sequences is generated in silico according to defined criteria. A “virtual” oligonucleotide chemistry is chosen and a library of virtual oligonucleotide compounds having the selected nucleobase sequences is generated. These virtual compounds are reviewed and compounds predicted to have particular properties are selected. The selected compounds are robotically synthesized and are preferably robotically assayed for a desired physical, chemical or biological activity. Active compounds are thus generated and, at the same time, preferred sequences and regions of the target nucleic acid that are amenable to oligonucleotide or sequence-based modulation are identified.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application is a continuation of U.S. Ser. No. 09 / 067,638 filed Apr. 28, 1998, which claims priority to U.S. provisional application Ser. No. 60 / 081,483 filed Apr. 13, 1998, each which is incorporated herein by reference in its entirety.FIELD OF THE INVENTION [0002] The present invention relates generally to the generation of synthetic compounds having defined physical, chemical or bioactive properties. More particularly, the present invention relates to the automated generation of oligonucleotide compounds targeted to a given nucleic acid sequence via computer-based, iterative robotic synthesis of synthetic oligonucleotide compounds and robotic or robot-assisted analysis of the activities of such compounds. Information gathered from assays of such compounds is used to identify nucleic acid sequences that are tractable to a variety of nucleotide sequence-based technologies, for example, antisense drug discovery and target validatio...

AI Technical Summary

Problems solved by technology

Although “SAR” and its handmaiden, rational drug design, has been utilized with some degree of success, there are a number of limitations to these approaches to lead compound generation, particularly as it pertains to the discovery of bioactive oligonucleotide compounds.

Heretofore, the search for lead antisense compounds has been limited to the manual synthesis and analysis of such compounds.

Consequently, a fundamental limitation of the conventional approach is its dependence upon the availability, number and cost of antisense compounds produced by manual, or at best semi-automated, means.

Moreover, the assaying of such compounds has traditionally been performed by tedious manual techniques.

Thus, the traditional approach to generating active antisense compounds is limited by the relatively high cost and long time required to synthesize and screen a relatively small number of candidate antisense compounds.

Although some approaches to this problem have been suggested, no solution has yet emerged.

Another approach, looking at the proteins encoded by genes, is developing but “this approach is more complex and big obstacles remain” (Kahn, Science, 1995, 270, 369).

Furthermore, neither of these approaches allows one to directly utilize nucleotide sequence information to perform gene function analysis.

Although the practicality and value of this empirical approach to developing active antisense compounds has been acknowledged in the art, it has also been stated that this approach “is beyond the means of most laboratories and is not feasible when a new gene sequence is identified, but whose function and therapeutic potential are unknown” (Szoka, Nature Biotechnology, 1997, 15, 509).

The challenge represented by this plethora of information is how to use such nucleotide sequences to identify and rank valid targets for drug discovery.

Antisense technology provides one means by which this might be accomplished; however, the many manual, labor-intensive and costly steps involved in traditional methods of developing active antisense compounds has limited their use in target validation (Szoka, Nature Biotechnology, 1997, 15, 509).

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