In vivo uptake of antisense oligonucleotide drugs predicted by ab initio quantum mechanical calculations.

Liver and kidney uptake and antisense activity is studied for a series of Locked Nucleic Acid (LNA) oligonucleotides with fully stereo-defined, internucleoside linkages. These stereo-specific phosphorothioates are made with a newly developed synthesis method and are being analyzed both theoretically and experimentally. Their structures are obtained theoretically by using many-body Schrödinger equations applied to a group of 11 stereo-defined LNA antisense oligonucleotides selected for biological experiments. The fully converged electronic structures were obtained from ab initio quantum calculations providing the specific electronic structures. One important result was the observation that the calculated electronic structure, represented by the iso-surface area of the electron density in Å2, correlated linearly with LNA oligonucleotide uptake in the liver and kidney. This study also shows that more complex biological phenomena, such as drug activity, will require more molecular and cellular identifiers than used here before a correlation can be found. Establishing biological correlations between quantum mechanical (QM) calculated structures and antisense oligonucleotides is novel, and this method may constitute new tools in drug discovery.

Electronic Structures of LNA Phosphorothioate Oligonucleotides.

Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces are essential in this study and have been calculated from the wave functions derived from the QM calculations that provide binding information and other properties of these molecules. The QM calculations give details of the electronic structures in terms of e.g., energy and bonding, which make them distinguish or differentiate between the individual PS diastereoisomers determined by the position of sulfur atoms. Rules are derived from the electronic calculations of these molecules and include the effects of the phosphorothioate chirality and formation of electrostatic potential surfaces. Physical and electrochemical descriptors of the PS oligonucleotides are compared to the experiments in which chiral states on these molecules can be distinguished. The calculations demonstrate that electronic structure, electrostatic potential, and topology are highly sensitive to single PS configuration changes and can give a lead to understanding the activity of the molecules.

Ab Initio Assessment of the Bonding in Disulfonates Containing Divalent Nitrogen and Phosphorus Atoms.

The iminodisulfonate, [N(SO3)2]3-, and phosphinodisulfonate, [P(SO3)2]3-, ions have been investigated by performing ab initio MP2/6-311+G** calculations. The nitrogen and phosphorus atoms as part of the ions are shown to be divalent with a negative charge and two lone pairs on the nitrogen and phosphorus atoms. The experimentally known calcium sodium iminodisulfonate trihydrate and the analogous unknown compound calcium sodium phosphinodisulfonate trihydrate have also been investigated using the MP2/6-311+G** calculations. For the nitrogen compound, only minor changes occur in the iminodisulfonate ion when it becomes part of the calcium sodium iminodisulfonate trihydrate. For the phosphorus compound, the geometry of the phosphinodisulfonate ion changes significantly as part of calcium sodium phosphinodisulfonate trihydrate. Furthermore, the charges associated with the atoms in calcium sodium phosphinodisulfonate trihydrate are quite different from those of the phosphinodisulfonate ion. For calcium sodium iminodisulfonate trihydrate, the Raman spectrum has been measured, and it compares well with the spectrum derived using HF/6-311+G** calculations.

Quantum mechanical studies of DNA and LNA.

Quantum mechanical (QM) methodology has been employed to study the structure activity relations of DNA and locked nucleic acid (LNA). The QM calculations provide the basis for construction of molecular structure and electrostatic surface potentials from molecular orbitals. The topologies of the electrostatic potentials were compared among model oligonucleotides, and it was observed that small structural modifications induce global changes in the molecular structure and surface potentials. Since ligand structure and electrostatic potential complementarity with a receptor is a determinant for the bonding pattern between molecules, minor chemical modifications may have profound changes in the interaction profiles of oligonucleotides, possibly leading to changes in pharmacological properties. The QM modeling data can be used to understand earlier observations of antisense oligonucleotide properties, that is, the observation that small structural changes in oligonucleotide composition may lead to dramatic shifts in phenotypes. These observations should be taken into account in future oligonucleotide drug discovery, and by focusing more on non RNA target interactions it should be possible to utilize the exhibited property diversity of oligonucleotides to produce improved antisense drugs.

Structure-activity relationship study of selective excitatory amino acid transporter subtype 1 (EAAT1) inhibitor 2-amino-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile (UCPH-101) and absolute configurational assignment using infrared and vibrational circular dichroism spectroscopy in combination with ab initio Hartree-Fock calculations.

The excitatory amino acid transporters (EAATs) play essential roles in regulating the synaptic concentration of the neurotransmitter glutamate in the mammalian central nervous system. To date, five subtypes have been identified, named EAAT1-5 in humans, and GLAST, GLT-1, EAAC1, EAAT4, and EAAT5 in rodents, respectively. In this paper, we present the design, synthesis, and pharmacological evaluation of seven 7-N-substituted analogues of UCPH-101/102. Analogue 9 inhibited EAAT1 in the micromolar range (IC(50) value 20 µM), whereas analogues 8 and 10 were inactive (IC(50) values >100 µM). The diastereomeric pairs 11a/11b and 12a/12b were separated by HPLC and the absolute configuration assigned by VCD technique in combination with ab initio Hartree-Fock calculations. Analogues 11a (RS-isomer) and 12b (RR-isomer) inhibited EAAT1 (IC(50) values 5.5 and 3.8 µM, respectively), whereas analogues 11b (SS-isomer) and 12a (SR-isomer) failed to inhibit EAAT1 uptake (IC(50) values >300 µM).

Structures of strontium diformate and strontium fumarate. A synchrotron powder diffraction study.

The crystal structures of strontium diformate in space groups P2(1)2(1)2(1) (alpha form, 295 K), P4(1)2(1)2 (beta form, 334 and 540 K) and I4(1)/amd (delta form, 605 K), and strontium fumarate in space groups Fddd (beta form, 105 K) and I4(1)/amd (alpha form, 293 K) have been determined from synchrotron X-ray powder diffraction data. Except for the alpha-strontium diformate, all the structures are based on a diamond-like Sr-ion arrangement, as in strontium acetylene dicarboxylate. The formate ions are disordered in the delta phase owing to steric hindrance. The fumarate ions are disordered over four (alpha) or two (beta) symmetry-equivalent orientations. alpha-Strontium fumarate crystallizes with a unique 90 degree carboxylate dihedral angle, and is stable up to 773 K.

Raman and ab initio studies of simple and binary 1-alkyl-3-methylimidazolium ionic liquids.

Raman spectra of the ionic liquids, 1-butyl-3-methylimidazolium hexafluorophosphate ([C4mim][PF6]), 1-hexyl-3-methylimidazolium chloride ([C6mim]Cl), and 1-hexyl-3-methylimidazolium hexafluorophosphate ([C6mim][PF6]), and binary mixtures thereof, have been assigned using ab initio MP2 calculations. The previously reported anti and gauche forms of the [C4mim]+ cation have been observed, and this study reveals this to be a general feature of the long-chain 1-alkyl derivatives. Analysis of mixtures of [C6mim]Cl and [C6mim][PF6] has provided information on the nature of the hydrogen bonding between the imidazolium headgroup and the anions, and the invariance of the essentially 50:50 mixture of the predominant conformers informs on the nature of glass formation in these systems.