Conformation-activity relationship of apoptosis-inducing phosphodiester oligonucleotides
AssigneeBionicrie Life Sciences, Inc.
InventorsNigel C. Phillips, Mario C. Filion, Zdenek Richard Holan
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Abstract
The present invention facilitates in silico evaluation of molecules for biological activity by providing a computer-based method to predict whether oligonucleotides may possess biological activity and the efficacy of the biological activity based on the three-dimensional structure and charge characteristics of the oligonucleotides. Biological activities include, but are not limited to, cellular proliferation, induction of cell cycle arrest and apoptosis.
Claims9
A computer-based method of predicting biological activity of an oligonucleotide sequence comprising analysis of the oligonucleotide sequence to determine if the oligonucleotide sequence contains at least one centrum.
A computer-based method of predicting biological activity of an oligonucleotide sequence comprising:
- drawing the sequence using chemical drawing software;
- checking the drawn sequence for errors;
- creating a three dimensional model of the drawn sequence;
- minimizing energy of the three dimensional model;
- calculating molecular dynamics using chemical analytical software;
- displaying a solvent accessible surface of the three dimensional model on a display means;
- identifying globular and linear domains in the three dimensional model;
- identifying intramolecular hydrogen bonds;
- identifying phosphate groups capable of forming an electronegative centrum;
- evaluating spatial orientation of bases in the three dimensional model for electropositive framing with respect to the phosphate groups in the electronegative centrum;
- measuring interatomic distances of amino/amido groups, and 3′ and 5′ hydroxyls from phosphate groups;
- and, predicting whether the sequence possesses the biological activity.
Dependencies are inferred from the claim text.