Rational selection of structurally diverse natural product scaffolds with favorable ADME properties for drug discovery

Natural product analogs are significant sources for therapeutic agents. To capitalize efficiently on the effective features of naturally occurring substances, a natural product-based library production platform has been devised at Aurigene for drug lead discovery. This approach combines the attractive biological and physicochemical properties of natural product scaffolds, provided by eons of natural selection, with the chemical diversity available from parallel synthetic methods. Virtual property analysis, using computational methods described here, guides the selection of a set of natural product scaffolds that are both structurally diverse and likely to have favorable pharmacokinetic properties. The experimental characterization of several in vitro ADME properties of twenty of these scaffolds, and of a small set of designed congeners based upon one scaffold, is also described. These data confirm that most of the scaffolds and the designed library members have properties favorable to their utilization for creating libraries of lead-like molecules.These authors have contributed equally to this work.     

Chemical construction and structural permutation of neurotoxic natural product,antillatoxin: importance of the three-dimensional structure of the bulky side chain

Antillatoxin 1 is a unique natural product that displays potent neurotoxic and neuritogenic activities through activation of voltage-gated sodium channels. The peptidic macrocycle of 1 was attached to a side chain with an exceptionally high degree of methylation. In this review, we discuss the total synthesis and biological evaluation of 1 and its analogues. First we describe an efficient synthetic route to 1. This strategy enabled the unified preparation of nine side chain analogues. Structure-activity relationship studies of these analogues revealed that subtle side chain modification leads to dramatic changes in activity, and detailed structural analyses indicated the importance of the overall size and three dimensional shape of the side chain. Based on these data, we designed and synthesized a photoresponsive analogue, proving that the activity of 1 was modulated via a photochemical reaction. The knowledge accumulated through these studies will be useful for the rational design of new tailor-made molecules to control the function and behavior of ion channels.     

Computational study of the proton affinity and basicity of structurally diverse α1‐adrenoceptor ligands

The α₁‐adrenoceptor is a target for the treatment of several conditions from hypertension to benign prostatic hyperplasia. In this paper, we describe a new analysis approach to explore the conformational space of several ligands of the α₁‐adrenoceptor and we also present the calculation of their proton affinity and basicity. For each compound a conformational search followed by a semi‐empirical optimisation was performed and a selection of conformations for each ligand was subjected to further optimisation using density functional theory methods. Different positions were explored to determine the favoured site of protonation, and then, the proton affinity (in the gas phase) and basicity (using the polarisable continuum model for the aqueous solution) were calculated for each of them. In addition, an alternative method using one explicit water molecule in combination with the polarisable continuum model for aqueous solvent was explored. Moreover, the acid dissociation constant (pK_a) in water of these 26 compounds was calculated because this is an important parameter for a ligand when binding to its receptor. The experimental pK_a values of six of these ligands and those of two compounds with a very low and a very large pK_a were used to validate the theoretical methodology. Copyright © 2011 John Wiley & Sons, Ltd.     

Stimulated Raman scattering in natural crystals of fluorapatite,Ca5(PO4)3F

Hexagonal Ca₅(PO₄)₃F, known as natural crystal fluorapatite and oldest host‐crystal for Ln³⁺‐lasant ions, is presented as a Raman‐active material. High‐order Raman‐induced χ⁽³⁾‐nonlinear processes are discovered in natural crystals of fluorapatite under picosecond pumping at 1.064 μm and 0.532 μm wavelength. A multitude of Stokes and anti‐Stokes components is generated in the ultraviolet, visible and near‐infrared spectral region by stimulated Raman scattering (SRS) and Raman four‐wave mixing (FWHM), resulting in a frequency comb with a width of 520 THz. The spectral lines are identified and attributed to the ν₁(A_g) vibration mode of the tetrahedral [PO₄] units which is related to a Raman shift of ω_SRS ≈ 965 cm⁻¹. The first Stokes steady‐state Raman gain coefficient in the near‐infrared spectral range is estimated to be >0.38 cm·GW⁻¹. Finally, a short review of SRS‐promoting vibration modes and observed χ⁽³⁾‐ nonlinear interactions in all known SRS‐active natural crystals (minerals) is given.