Romain M. Wolf

Development and testing of a general amber force field.

We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root‐mean‐square displacement of 0.26 Å, which is comparable to that of the Tripos 5.2 force field (0.25 Å) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 Å, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6‐31G* results. The RMS of displacements and relative energies were 0.25 Å and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 Å and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.

Proton-sensing G-protein-coupled receptors

Blood pH is maintained in a narrow range around pH 7.4 mainly through regulation of respiration and renal acid extrusion. The molecular mechanisms involved in pH homeostasis are not completely understood. Here we show that ovarian cancer G-protein-coupled receptor 1 (OGR1), previously described as a receptor for sphingosylphosphorylcholine, acts as a proton-sensing receptor stimulating inositol phosphate formation. The receptor is inactive at pH 7.8, and fully activated at pH 6.8—site-directed mutagenesis shows that histidines at the extracellular surface are involved in pH sensing. We find that GPR4, a close relative of OGR1, also responds to pH changes, but elicits cyclic AMP formation. It is known that the skeleton participates in pH homeostasis as a buffering organ, and that osteoblasts respond to pH changes in the physiological range, but the pH-sensing mechanism operating in these cells was hitherto not known. We detect expression of OGR1 in osteosarcoma cells and primary human osteoblast precursors, and show that these cells exhibit strong pH-dependent inositol phosphate formation. Immunohistochemistry on rat tissue sections confirms the presence of OGR1 in osteoblasts and osteocytes. We propose that OGR1 and GPR4 are proton-sensing receptors involved in pH homeostasis.

Receptors for Protons or Lipid Messengers or Both

The subfamily of G protein-coupled receptors comprising GPR4, OGR1, TDAG8, and G2A was originally characterized as a group of proteins mediating biological responses to the lipid messengers sphingosylphosphorylcholine (SPC), lysophosphatidylcholine (LPC), and psychosine. We challenged this view by reporting that OGR1 and GPR4 sense acidic pH and that this process is not affected by concentrations of SPC or LPC previously reported as agonistic. The original publications describing GPR4, OGR1, and G2A as receptors for LPC or SPC have now been retracted, and the first studies exploring receptors of this family as pH sensors in physiology have appeared. Here we review the status of this field and we confirm that GPR4, OGR1, and TDAG8 should be considered as proton-sensing receptors. Negative regulation of these receptors by high micromolar concentrations of lipids appears not specific in our experiments.

Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, "Development and testing of a general amber force field"Journal of Computational Chemistry(2004) 25(9) 1157–1174

The original article to which this Erratum refers was published in Journal of Computational Chemistry (2004) 25(9) 1157–1174

Chromatographic resolution of racemates on chiral stationary phases : I. Influence of the supramolecular structure of cellullose triacetate

Abstract The influence of the supramolecular structure of cellulose triacetate (CTA) on the chromatographic resolution of several racemates has been investigated in detail. The best optical resolution power was displayed by the crystallographic form CTA I, obtained by the heterogeneous acetylation of microcrystalline cellulose. Enhancing the crystallinity of CTA I (by annealing) was found to have a negative influence on its separation power. The other crystallographic modification of cellulose triacetate, CTA II, in general yielded poor optical resolutions. Models for different possible interaction mechanisms between the racemates and the optically active polymer are discussed on the basis of experimental results. The inclusion of low-molecular-weight chiral molecules into a specific spatial arrangement of the glucose units of the polysaccharide chains is proposed as a pre-requisite for the chiral discrimination process.

Chromatographic resolution on methylbenzoylcellulose beads : modulation of the chiral recognition by variation of the position of the methyl group on the aromatic ring

Abstract The preparation of cellulose-based chiral stationary phases (CSPs) in the pure polymer from (i.e., without an achiral support such as silica gel), according to a process already reported for benzoyl cellulose, was extended to substituted benzoylcellulose derivatives. The chiral recognition abilities of benzoylcellulose and o-, m- and p-methylbenzoylcellulose were compared. The four CSPs are shown to exhibit different selectivites and in numerous instances an inversion of the elution order was observed on the different methylbenzoylcellulose CSPs, indicating that the CSPs undergo different interactions with the same racemic solute. The broad variety of racemic structures that can be resolved on the four CSPs indicate the great application potential of the new cellulose-based sorbents. This should be the case especially for preparative separations, as the materials are not deposited on an achiral supporting matrix and thus have a higher loading capacity than coated CSPs.

SAR of 2,6-Diamino-3,5-difluoropyridinyl Substituted Heterocycles as Novel p38MAP Kinase Inhibitors

2,6-Diamino-3,5-difluoropyridinyl substituted pyridinylimidazoles, -pyrroles, -oxazoles, -thiazoles and -triazoles have been identified as novel p38alpha inhibitors. Pyridinylimidazole 11 potently inhibited LPS-induced TNFalpha in mice, showed good efficacy in the established rat adjuvant (ED(50): 10 mg/kg po b.i.d.) and collagen induced arthritis (ED(50): 5 mg/kg po b.i.d.) with disease modifying properties based on histological analysis of the joints.

Comparison of two amides as backbone replacement of the phosphodiester linkage in oligodeoxynucleotides

Abstract The two isomeric amide modifications 1 and 2 show similar effects on the melting temperature of RNA/DNA duplexes, when they replace the natural phosphodiester linkage in the DNA strand. The synthesis of the amide dimer 1 is presented.

Replacement of the phosphodiester linkage in oligonucleotides : comparison of two structural amide isomers

Abstract The two structural amide isomers 2 and 3 as backbone replacement in oligonucleotides lead to very similar results for the binding affinities (Tm) of the duplexes formed with their complementary RNA strands.

1-Alkyl-4-phenyl-6-alkoxy-1H-quinazolin-2-ones: a novel series of potent calcium-sensing receptor antagonists.

Parathyroid hormone (PTH) is an effective bone anabolic agent. However, only when administered by daily sc injections exposure of short duration is achieved, a prerequisite for an anabolic response. Instead of applying exogenous PTH, mobilization of endogenous stores of the hormone can be envisaged. The secretion of PTH stored in the parathyroid glands is mediated by a calcium sensing receptor (CaSR) a GPCR localized at the cell surface. Antagonists of CaSR (calcilytics) mimic a state of hypocalcaemia and stimulate PTH release to the bloodstream. Screening of the internal compound collection for inhibition of CaSR signaling function afforded 2a. In vitro potency could be improved >1000 fold by optimization of its chemical structure. The binding mode of our compounds was predicted based on molecular modeling and confirmed by testing with mutated receptors. While the compounds readily induced PTH release after iv application a special formulation was needed for oral activity. The required profile was achieved by using microemulsions. Excellent PK/PD correlation was found in rats and dogs. High levels of PTH were reached in plasma within minutes which reverted to baseline in about 1-2 h in both species.