2'-O-aminopropyl ribonucleotides: a zwitterionic modification that enhances the exonuclease resistance and biological activity of antisense oligonucleotides.

Oligonucleotides containing 2'-O-aminopropyl-substituted RNA have been synthesized. The 2'-O-(aminopropyl)adenosine (APA), 2'-O-(aminopropyl)cytidine (APC), 2'-O-(aminopropyl)-guanosine (APG), and 2'-O-(aminopropyl)uridine (APU) have been prepared in high yield from the ribonucleoside, protected, and incorporated into an oligonucleotide using conventional phosphoramidite chemistry. Molecular dynamics studies of a dinucleotide in water demonstrates that a short alkylamine located off the 2'-oxygen of ribonucleotides alters the sugar pucker of the nucleoside but does not form a tight ion pair with the proximate phosphate. A 5-mer with the sequence ACTUC has been characterized using NMR. As predicted from the modeling results, the sugar pucker of the APU moiety is shifted toward a C3'-endo geometry. In addition, the primary amine rotates freely and is not bound electrostatically to any phosphate group, as evidenced by the different sign of the NOE between sugar proton resonances and the signals from the propylamine chain. Incorporation of aminopropyl nucleoside residues into point-substituted and fully modified oligomers does not decrease the affinity for complementary RNA compared to 2'-O-alkyl substituents of the same length. However, two APU residues placed at the 3'-terminus of an oligomer gives a 100-fold increase in resistance to exonuclease degradation, which is greater than observed for phosphorothioate oligomers. These structural and biophysical characteristics make the 2'-O-aminopropyl group a leading choice for incorporation into antisense therapeutics. A 20-mer phosphorothioate oligonucleotide capped with two phosphodiester aminopropyl nucleotides targeted against C-raf mRNA has been transfected into cells via electroporation. This oligonucleotide has 5-10-fold greater activity than the control phosphorothioate for reducing the abundance of C-raf mRNA and protein.

Detection of oligonucleotide-ligand complexes by ESI-MS (DOLCE-MS) as a component of high throughput screening.

With the advent of combinatorial chemistry and high throughput screening, a major bottleneck in the pharmaceutical industry has changed from quickly finding active compounds to limiting them to a manageable number for proper follow-up. With hundreds to thousands of active compounds identified by a multitude of biological screens, there need to be rapid and unambiguous methods for eliminating false positive, toxic, or otherwise difficult compounds from further scrutiny. We have used electrospray ionization mass spectrometry as a rapid screening method to identify compounds from viral screens that yield a positive assay response by interaction with DNA rather than inhibiting the target enzyme. Both the sample preparation and data acquisition have been automated, allowing the screening of all hits from relevant biological screens (up to 1,000/week). The assay was validated using several known DNA intercalators and minor groove binders. These "standards" and many but not all of our "active compounds" were shown to form noncovalent complexes with a variety of different DNA:DNA and DNA:RNA duplexes.

Characterization of oligonucleotide metabolism in vivo via liquid chromatography/electrospray tandem mass spectrometry with a quadrupole ion trap mass spectrometer.

The pattern of nuclease degradation observed for an antisense phosphorothioate oligonucleotide in pig kidney was determined using liquid chromatography/electrospray mass spectrometry (LC/ESI-MS) and LC/ESI-MS/MS with a quadrupole ion trap mass spectrometer. Metabolites were separated by length using reversed-phase high-performance liquid chromatography with aqueous hexafluoropropan-2-ol-triethylamine and a methanol gradient. The individual masses of metabolites in each LC peak were determined via deconvolution and converted into potential nucleotide compositions. The nucleotide composition was used to locate metabolites within the known oligomer sequence. The identity of metabolites was confirmed using on-line LC/MS/MS to generate fragment ions suitable for sequence verification. A limited number of shorter oligonucleotide fragments were observed, suggesting that metabolism in vivo may be sequence dependent.

Negative ionization micro electrospray mass spectrometry of oligonucleotides and their complexes.

The utility of negative ionization micro electrospray (microspray) mass spectrometry is demonstrated for detection of oligonucleotides and their non-covalent complexes. A simple microspray ionization source is fabricated from an outer stainless-steel needle and an inner fused-silica capillary. Under these conditions, the liquid flow rate can be reduced 15-fold from 7.5 microL/min to 0.5 microL/min. Studies of a 14-mer DNA oligonucleotide show no change in the charge-state distribution and quantity of adducted salt ions during the microspray process compared to pneumatically assisted electrospray mass spectrometry. The microspray ion source is less sensitive to the presence of solution buffers, and an 11-fold increase in integrated ion abundance from oligonucleotide analyte is observed with a 10 mM concentration of ammonium acetate, compared to pneumatically assisted nebulization (PAN). A > 100-fold increase in the duplex:single strand ratio for a 14-mer oligodeoxynucleotide and its complementary strand is observed using the microspray ion source relative to experiments performed with PAN. Studies of duplexes between DNA and a peptide nucleic acid suggest that this effect may be related to the degree of adduction of counterions to the DNA during ionization.

Hydrogen/deuterium exchange of nucleotides in the gas phase.

Gas-phase hydrogen/deuterium exchange reactions have been performed on the 5'- and 3'-nucleotide monophosphates and on the 3'5'-cyclic nucleotides. Following negative mode electrospray ionization and transport to a Fourier transform ion cyclotron resonance cell, each nucleotide was reacted with gaseous D2O for up to 600 s. Extensive deuterium exchange was observed for the 3'- and 5'-nucleotides in negative ion mass spectra with relative rates of exchange following the trend 5'dCMP > 5'-dAMP > 5'dTMP >> 5'-dGMP and 3'-dGMP > 3'-dAMP approximately equal to 3'-dCMP approximately equal to 3'-dTMP. At least two classes of exchanging protons are observed. The more facile class is assigned to the amino protons of the bases, with a slower class attributed to the phosphate and/or hydroxyl proton. Overall, the 3'-nucleotides exchange more quickly than the 5'-oligonucleotides. The cyclic nucleotides did not undergo deuterium exchange, suggesting that a charged phosphate group proximate to the base is required to catalyze the exchange reaction. Exchange through tautomerization of the bases is no observed, although molecular modeling suggests an energy barrier of < 30 kcal.

Packed column supercritical fluid chromatography/mass spectrometry for high-throughput analysis.

A supercritical fluid chromatograph was interfaced to a mass spectrometer, and the system was evaluated for applications requiring high sample throughput. Experiments presented demonstrate the high-speed separation capability of supercritical fluid chromatography (SFC) and the effectiveness of supercritical fluid chromatography/mass spectrometry (SFC/MS) for fast, accurate determinations of multicomponent mixtures. A high-throughput liquid chromatography/mass spectrometry (LC/MS) analysis cycle time is reduced 3-fold using our general SFC/MS high-throughput method, resulting in substantial time saving for large numbers of samples. Unknown mixture characterization is improved due to the increased selectivity of SFC/MS compared to LC/MS. This was demonstrated with sample mixtures from a 96-well combinatorial library plate. In this paper, we report a negative mode atmospheric pressure chemical ionization (APCI) method for SFC/MS suitable for most of the components in library production mixtures. Flow injection analysis (FIA) also benefits from this SFC/MS system. A broader range of solvents is amenable to the SFC mobile phase compared with standard LC/MS solvents, and solutes elute more rapidly from the SFC/MS system, reducing sample carryover and cycle time. Finally, our instrumental setup allows for facile conversion between LC/MS and SFC/MS modes of operation.

Packed column supercritical fluid chromatography/mass spectrometry for high-throughput analysis. Part 2.

A supercritical fluid chromatograph was previously interfaced to a mass spectrometer (SFC/MS) and the system evaluated for applications requiring high sample throughput using negative-mode atmospheric-pressure chemical ionization (APCI) (Ventura et al. Anal. Chem. 1999, 71, 2410-2416). This report extends the previous work demonstrating the effectiveness of SFC/MS, using positive ion APCI for the analysis of compounds with a wide range of polarities. Substituting SFC/MS for LC/MS results in substantial time saving, increased chromatographic efficiency, and more precise quantitation of sample mixtures. Flow injection analysis (FIA) also benefits from our SFC/MS system. A broader range of solvents is compatible with the SFC mobile phase compared with LC/MS, and solutes elute more rapidly from the SFC/MS system, reducing sample carryover and cycle time. Our instrumental setup also allows for facile conversion between LC/MS and SFC/MS modes of operation.

Pharmacokinetic properties of several novel oligonucleotide analogs in mice.

Biophysical and pharmacokinetic properties of five analogs of ISIS 3082, a 20-mer phosphorothioate oligodeoxynucleotide that inhibits the expression of mouse intercellular adhesion molecule 1, were evaluated. Compared to the parent compound, ISIS 3082, the 2'-propoxy modified phosphodiester, ISIS 9044 and the 2'-propoxy phosphorothioate, ISIS 9045, had greater affinity for complementary RNA and were more lipophilic. A chimeric oligonucleotide comprised of 2'-propoxy diester wings and a phosphorothioate deoxy center (ISIS 9046) had equal affinity. It was also more lipophilic than ISIS 3082, but less so than the other 2'-propoxy modified analogs. The two analogs with 5'-lipophilic conjugates, ISIS 9047 (5'-octadecylamine) and ISIS 8005 (5'-(2'-O-hexylamino-carbonyl-oxycholesterol) were more lipophilic than ISIS 3082 (3- and 7-fold, respectively) but had similar affinity for complementary RNA. Binding of ISIS 3082 to bovine serum albumin was salt-dependent and, at physiological concentration (320 mOsmol), the dissociation constant (Kd) was 140 microM. Similarly, the 2'-propoxy phosphodiester, ISIS 9044, displayed salt-dependent bovine serum albumin binding, but not binding was measurable at physiological salt conditions. In contrast, the more lipophilic phosphorothioate analogs displayed much higher affinity to bovine serum albumin at 320 mOsmol than ISIS 3082. After bolus injection to mice, the initial volumes of distribution of the more lipophilic phosphorothioate analogs, ISIS 9045, ISIS 9047 and ISIS 8005, were less and the initial clearance from plasma was slower than ISIS 3082. The pharmacokinetics of the other analogs was similar to ISIS 3082. Distribution of ISIS 3082 into peripheral tissues was similar to that reported for other phosphorothioates with liver and kidney accumulating the highest fraction of the dose. The only modification to markedly influence distribution was the very lipophilic cholesterol conjugate (ISIS 8005), which increased substantially the fraction of the dose accumulated by the liver. Little intact drug was found in urine or feces for any analog, and the patterns of metabolites suggested that for all analogs the principal metabolic pathway was due to 3'-exonuclease activity. The metabolism of ISIS 3082 was similar to that reported for other phosphorothioates. After 2 hr, most of the radioactivity in plasma represented metabolites but, in tissues, intact ISIS 3082 was present for much longer periods of time and metabolites accumulated more slowly. The 24-hr exposure to ISIS 3082 of liver and kidney was 20.7 and 67.9 microM/hr, respectively. The rates of metabolism in plasma, liver and kidney of the two 5'-conjugates, ISIS 9047 and ISIS 8005, were similar to ISIS 3082, as was the pattern of metabolism. The rate of metabolism of ISIS 9044 (2'-propoxy phosphodiester oligonucleotide) was much more rapid in liver and plasma, but surprisingly much slower in the kidney. ISIS 9045 (full 2-propoxy phosphorothioate) was much more stable than ISIS in all tissues, the enhanced stability of ISIS 9045 resulted in increased exposure of liver and kidney to the drug, whereas the exposure of the liver to the two more lipophilic analogs, ISIS 9047 and ISIS 8005, was greater because a higher fraction of the dose was distributed to the liver. The exposure of the kidney to ISIS 9044 was also greater than that to ISIS 3082 due to the surprising stability of the drug in the kidney.