A modular approach to structurally diverse bidentate chelate ligands for transition metal catalysis

A modular approach to a new class of structurally diverse bidentate P/N, P/P, P/S, and P/Se chelate ligands has been developed. Starting from hydroquinone, various ligands were synthesized in a divergent manner via orthogonally bis-protected bromohydroquinones as the central building block. The first donor functionality (L1) is introduced to the aromatic (hydroquinone) ligand backbone either by Pd-catalyzed cross-coupling (Suzuki coupling) with hetero-aryl bromides, by Pd-catalyzed amination, or by lithiation and subsequent treatment with electrophiles (e.g., chlorophosphanes, disulfides, diselenides, or carbamoyl chlorides). After selective deprotection, the second ligand tooth (L2) is attached by reaction of the phenolic OH functionality with a chlorophosphane, a chlorophosphite, or a related reagent. Some of the resulting chelate ligands were converted into the respective PdX2 complexes (X = Cl, I), two of which were characterized by X-ray crystallography. The methodology developed opens an access to a broad variety of new chiral and achiral transition metal complexes and is generally suited for the solid-phase synthesis of combinatorial libraries, as will be reported separately.     

Synthesis of structurally diverse biflavonoids

Synthetic biflavonoids are associated with interesting biological activities, yet they remain poorly explored within drug discovery. Recent years have witnessed a growing interest in synthetic approaches that can provide access to structurally novel biflavonoids so that the biological usefulness of this compound class can be more fully investigated. Herein, we report upon the exploration of strategies based around Suzuki-Miyaura cross-coupling and alcohol methylenation for the synthesis of two classes of biflavonoids: (i) rare ‘hybrid’ derivatives containing flavonoid monomers belonging to different subclasses, and (ii) homodimeric compounds in which the two flavonoid monomers are linked by a methylenedioxy group. Application of these strategies enabled the preparation of a structurally diverse collection of novel biflavonoids from readily-available starting materials, thereby facilitating the probing of uncharted regions of biologically interesting chemical space.     

Retention of structurally diverse drugs in human serum albumin chromatography and its potential to simulate plasma protein binding

The retention behavior of 39 structurally diverse neutral, basic and acidic drugs was investigated on an HSA stationary phase using PBS buffer (pH 7.0) and acetonitrile or 2-propanol as organic modifiers. Extrapolated or directly measured log k_w values as well as isocratic retention factors were correlated with plasma protein binding data taken from the literature. Retention factors determined in the presence of 10% acetonitrile led to high quality 1:1 correlation with apparent log K_HSA values. The derived reference equation was successfully validated using a secondary set of 24 drugs. Further analysis of HSA retention into more fundamental properties revealed the involvement of anionic species in solute-stationary phase interactions, expressed by the negatively charged fraction, besides the partitioning mechanism which was reflected by lipophilicity. Protonation of basic drugs, although less important, may also influence retention, leading to reduced partitioning into the HSA surface as a net effect, while it seems to have no effect on HSA binding. The above results were further confirmed by linear solvation energy relationships (LSER).     

Scavenger receptors: diverse activities and promiscuous binding of polyanionic ligands

Scavenger receptors are a diverse family of proteins that share a common property - the binding of modified lipoprotein - but they have recently been shown to recognise a diverse range of ligands. Understanding the molecular interaction of receptor-ligand binding should provide insight into how scavenger receptors contribute to important biological processes.     

Convergent assembly of structurally diverse quinazolines

A convergent and versatile Vilsmeier-Haack-based carbo-annulation strategy that exhibits an unusually elevated bond-forming efficiency has been developed. By virtue of its innovative approach, structure economy and simple execution conditions the methodology reported here constitutes a very attractive protocol that enables the rapid assembly of structurally diverse quinazoline chemotypes.     

Synthesis of structurally diverse bis-peptide oligomers

We have developed second-generation monomers 1 and 2 and improved conditions for rapidly and simultaneously closing multiple diketopiperazines on solid support. These new conditions involve either the microwave heating of a suspension of solid-supported amino-tetrafluoropropyl esters in acetic acid/triethylamine catalyst solution or continuous flow of catalyst solution through the resin, heated in a flow cell apparatus. We demonstrate that the new monomers 1 and 2 can be combined with the new conditions easily to synthesize previously inaccessible hetero and homo spiro ladder oligomers 3 and 4 and others.     

Diamidodipyrrins: versatile bipyrrolic ligands with multiple metal binding modes

A straightforward, facile synthesis of diamidodipyrromethenes (diamidodipyrrins, DADP (R,R')) is presented. These tetradentate ligands readily form complexes with metal ions such as Ni (2+) and Cu (2+) and can adopt different binding modes with these metals. One version of the ligand (DADP (Ph, iPr )) has been structurally characterized in its "free base" form, as a HBr salt, and as the Ni (2+) and Cu (2+) complexes. A symmetric NNOO donor set is found for the Cu (2+) complex in the solid state, involving two carbonyl oxygen atoms and two dipyrrin nitrogen atoms, and this coordination mode has been confirmed in solution by electron paramagnetic resonance. An asymmetric NNNO binding mode found for the Ni (2+) complex in the solid state persists in solution as revealed by (1)H NMR. The HBr salt form of the ligand shows an intriguing hydrogen-bonded head-to-head dimer arrangement. Experiments show that Cu (2+), but not Ni (2+), can mediate the rapid oxidation of the diamidodipyrromethane precursors to the diamidodipyrromethene ligands in the presence of dioxygen. The work here shows that diamidodipyrrins are a versatile new class of ligands in the area of nonporphyrinic pyrrole-based compounds that merit further investigation.     

Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase

Pathogenic protozoa such as Trypanosome and Leishmania species cause tremendous suffering worldwide. Because of their dependence on glycolysis for energy, the glycolytic enzymes of these organisms, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. Using the adenine part of NAD as a lead compound, several 2,6-disubstituted purines were synthesized as inhibitors of Leishmania mexicana GPDH (LmGPDH). The electron densities for the inhibitor 2-bromo-6-chloro-purine bound to LmGPDH using a "conventional" wavelength around 1 A displayed a quasisymmetric shape. The anomalous signals from data collected at 1.77 A clearly indicated the positions of the halogen atoms and revealed the multiple binding modes of this inhibitor. Intriguing differences in the observed binding modes of the inhibitor between very similarly prepared crystals illustrate the possibility of crystal-to-crystal variations in protein-ligand complex structures.     

Exploration of 3D activity cliffs on the basis of compound binding modes and comparison of 2D and 3D cliffs

Activity cliffs are formed by pairs or groups of structurally similar compounds having large differences in potency and are focal points of structure-activity relationship (SAR) analysis. The choice of molecular representations is a critically important aspect of activity cliffs analysis. Thus far, activity cliffs have predominantly been defined on the basis of molecular graph or fingerprint representations. Herein we introduce 3D activity cliffs derived from comparisons of experimentally determined compound binding modes. The analysis of 3D activity cliffs is generally applicable to target proteins for which structures of multiple ligand complexes are available. For two popular targets, β-secretase 1 (BACE1) and factor Xa (FXa), public domain X-ray structures with bound inhibitors were collected. Crystallographic binding modes of inhibitors were systematically compared using a 3D similarity method taking conformational, positional, and atomic property differences into account. In addition, standard 2D similarity relationships were also determined. SAR information associated with individual compounds substantially changed when either bioactive conformations or 2D molecular graphs were used for similarity evaluation. 3D activity cliffs were identified for BACE1 and FXa inhibitor sets and systematically compared to 2D cliffs. It was found that less than 40% of 3D activity cliffs were conserved when 2D similarity was applied. The limited conservation of 3D and 2D cliffs provides further evidence for the strong molecule representation dependence of activity cliffs. Moreover, 3D cliffs represent a new class of activity cliffs that convey SAR information in ways that differ from graph-based similarity measures. In cases where sufficient structural information is available, the comparison of 3D and 2D cliffs is expected to aid in SAR analysis and mapping of critical binding determinants.     

Combinatorial liquid-phase synthesis of structurally diverse benzimidazole libraries

An expedient liquid-phase synthesis for construction of the diverse benzimidazole libraries is described. Nucleophilic aryl substitution of poly(ethylene glycol)-supported 4-fluoro-3-nitrobenzoic acid 3 with several primary amines under basic conditions, followed by Zn/NH(4)Cl mediated nitro group reduction, gave the PEG bound diamines 5. Subsequent cyclization of immobilized o-phenylenediamine 5 using thiocarbonyldiimidazole (TCD) or thiophosgene in dichloromethane furnished benzimidazole-2-thiones 6. Treatment of 6 with alkyl halides and benzylic halides in the presence of triethylamine provided 1-substituted-2-alkylthio-5-carbamoylbenzimidazoles on the support. The desired products 8 were severed from the PEG under mild conditions in high yield and high purity.     

Novel routes for the generation of structurally diverse labdane diterpenes from andrographolide

Andrographolide 1, the major constituent of the Indian medicinal plant Andrographis paniculata (Acanthaceae) was converted into the key intermediate 4 by selective oxidative degradation of the C-12,13 olefin bond. The aldehyde functional group present in 4 has been utilized for synthesizing a number of structurally diverse labdane diterpenes. Synthesis and in vitro cytotoxic activity results of the compounds prepared are discussed.     

Structure-activity relationships for a collection of structurally diverse inhibitors of purine nucleoside phosphorylase

Values of inhibition constants, Ki, and concentrations required for 50% inhibition, IC50, for a collection of structurally diverse competitive inhibitors of calf spleen purine nucleoside phosphorylase have been determined employing inosine as substrate. These values have been employed to create predictive quantitative structure-activity relationships (QSAR) which link structure to values of Ki and IC50. These QSAR models have substantial power to predict values and the associated uncertainties for Ki and IC50 for unknown, structurally diverse inhibitors of purine nucleoside phosphorylase.     

Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes

Despite its central role in structure based drug design the determination of the binding mode (position, orientation and conformation in addition to protonation and tautomeric states) of small heteromolecular ligands in protein:ligand complexes based on medium resolution X-ray diffraction data is highly challenging. In this perspective we demonstrate how a combination of molecular dynamics simulations and free energy (FE) calculations can be used to correct and identify thermodynamically stable binding modes of ligands in X-ray crystal complexes. The consequences of inappropriate ligand structure, force field and the absence of electrostatics during X-ray refinement are highlighted. The implications of such uncertainties and errors for the validation of virtual screening and fragment-based drug design based on high throughput X-ray crystallography are discussed with possible solutions and guidelines.