Rational and efficient geometric definition of pharmacophores is essential for the patent process.

The geometric description of pharmacophores suffers from approximations. No consensus has been clearly established, despite the increasing interest in using pharmacophores in drug design and in patent applications. We therefore propose an original definition of a pharmacophore using spherical coordinates. These coordinates give a precise description of each point using three parameters: distance to a geometric origin and two angles. If necessary, these parameters can be easily and rapidly converted to cartesian coordinates. Our method can guarantee, to the patent applicant, the safe protection of his intellectual property by both improving markedly the readability of a pharmacophore definition and bringing, to the person who is skilled in the art, enough information to understand easily the essence of the invention.

Cation-π Interactions in Serotonin: Conformational, Electronic Distribution, and Energy Decomposition Analysis.

An adiabatic conformational analysis of serotonin (5-hydroxytryptamine, 5-HT) using quantum chemistry led to six stable conformers that can be either +gauche (Gp), -gauche (Gm), and anti (At) depending upon the value taken by ethylamine side chain and 5-hydroxyl group dihedral angles φ1, φ2, and φ4, respectively. Further vibrational frequency analysis of the GmGp, GmGm, and GmAt conformers with the 5-hydroxyl group in the anti position revealed an additional red-shifted N-H stretch mode band in GmGp and GmGm that is absent in GmAt. This band corresponds to the 5-HT side-chain N-H bond involved in an intramolecular nonbonded interaction with the 5-hydroxy indole ring. The influence of this nonbonded interaction on the electronic distribution was assessed by analysis of the spin-spin coupling constants of GmGp and GmGm that show a marked increase for C2-C3 and C8-C9 bonds in GmGm and GmGp, respectively, with a decrease of their double bond character and an increase of their length. The Atoms in Molecules (AIM), Natural Bond Orbital (NBO), and fluorescence and CD spectra (TDDFT method) analyses confirmed the existence in GmGp and GmGm of a through-space charge-transfer between the HOMO and the HOMO-1 π-orbital of the indole ring and the LUMO σ* N-H antibonding orbital of the ammonium group. The strength of the cation-π interaction was determined by calculating binding energies of the NH4(+)/5-hydroxyindole complexes extracted from stable conformers. The energy decomposition analysis indicated that cationic-π interactions in the GmGp and GmGm conformers are governed by the electrostatic term with significant contributions from polarization and charge transfer. The lower stability of the GmGm over the GmGp comes from a higher exchange repulsion and a weaker polarization contributions. Our results provide insight into the nature of intramolecular forces that influence the conformational properties of 5-HT.