Design considerations and computer modeling related to the development of molecular scaffolds and peptide mimetics for combinatorial chemistry

Summary A critical issue in drug discovery utilizing combinatorial chemistry as part of the discovery process is the choice of scaffolds to be used for a proper presentation, in a three-dimensional space, of the critical elements of structure necessary for molecular recognition (binding) and information transfer (agonist/ antagonist). In the case of polypeptide ligands, considerations related to the properties of various backbone structures (-helix, -sheets, etc.; , space) and those related to three-dimensional presentation of side-chain moieties (topography; (chi) space) must be addressed, although they often present quite different elements in the molecular recognition puzzle. We have addressed aspects of this problem by examining the three-dimensional structures of chemically different scaffolds at various distances from the scaffold to evaluate their putative diversity. We find that chemically diverse scaffolds can readily become topographically similar. We suggest a topographical approach involving design in chi space to deal with these problems.     

A Product Formed from Glycylglycine in the Presence of Vanadate and Hydrogen Peroxide: The (Glycylde-N-hydroglycinato-kappa(3)N(2),N(N)(),O(1))oxoperoxovanadate(V) Anion

A crystalline glycylglycine complex of monoperoxovanadate has been obtained and its X-ray structure determined. The coordination is pentagonal bipyramidal with the peroxo group and a tridentate glycylglycine occupying the equatorial positions. The axial positions of the anion are occupied by the oxo ligand and by one oxygen of the peroxo group of the adjacent anion. The latter interaction establishes the seventh bond and produces a dimeric structure in the crystalline material. NMR studies of its dissolution in water combined with previously reported results from equilibrium measurements show that the dimer dissociates in water to the monomeric precursor. It is proposed that this monomer corresponds to the complex responsible for the inhibition of the vanadium-catalyzed decomposition of hydrogen peroxide by glycylglycine. Crystal structure of [NEt(4)][VO(O(2))(GlyGly)].1.58H(2)O: monoclinic, space group P2(1); Z = 4; a = 10.618(2) ?; b = 14.803(2) ?; c = 11.809(2) ?; beta = 101.37(2) degrees; V = 1819.7 ?(3); T = 198 K; R(F)() = 0.029 for 2664 data (I(o) >/= 2.5sigma(I(o))) and 431 variables.     

β-lithiations of carboxamides. Synthesis of β-substituted-α,β-unsaturated amides

N-Methyl-2-methyl-3-(benzotriazol-l-yl)propanamide, on treatment with butyllithium forms a dianion which on treatment with alkyl and benzyl halides, aldehydes and ketones affords monosubstituted products; with ethyl p-toluate, a lactam is formed. The alkylated derivatives eliminate benzotriazole in the presence of base to afford trisubstituted α,β-unsaturated amides.     

Solid-phase synthesis of pyrazolines and isoxazolines with sodium benzenesulfinate as a traceless linker

[reaction: see text] The preparation of pyrazoline and isoxazoline derivatives with traceless solid-phase sulfone linker strategy is described. Key steps involved in the solid-phase synthetic procedure include (i) sulfinate S-alkylation, (ii) sulfone anion alkylation, (iii) gamma-hydroxy sulfone --> gamma-ketosulfone oxidation, and (iv) traceless product release via elimination-cyclization. A library of 12 pyrazolines and isoxazolines was synthesized.     

Mononuclear nitrogen/sulfur-ligated zinc methoxide and hydroxide complexes: investigating ligand effects on the hydrolytic stability of zinc alkoxide species

The synthesis and properties of mononuclear zinc methoxide ([(ebnpa)Zn-OCH3]ClO4) (1) and hydroxide ([(ebnpa)Zn-OH]ClO4) (2) complexes of a new mixed nitrogen/sulfur ligand (ebnpa = N-2-(ethylthio)ethyl-N,N-bis(6-neopentylamino-2-pyridylmethyl)amine) are reported. The structures of 1 and 2 were determined by X-ray diffraction. Each possesses a single zinc-coordinated anion (methoxide or hydroxide) and exhibits an overall trigonal bipyramidal geometry. Structural and spectroscopic studies indicate the presence of two hydrogen-bonding interactions involving the oxygen atom of the zinc-bound anion in each complex. Treatment of [(ebnpa)Zn-OH]ClO4 with CH3OH results in the formation of an equilibrium mixture of 1 and 2. 1H NMR spectroscopic methods were used to examine the equilibrium as a function of temperature, yielding KMe (304 K) = 0.30(8), DeltaHMe = -0.9(1) kcal/mol, and DeltaSMe = -5(1) eu. The negative enthalpy indicates that spontaneous zinc alkoxide formation from a hydroxide precursor occurs in this system at low temperature. Using the experimentally determined DeltaHMe value, we found the homolytic Zn-O bond dissociation energy (BDE) in the Zn-OCH3 unit to be approximately -14 kcal/mol relative to the Zn-O BDE in the Zn-OH unit.