Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure‐Based Design of Inhibitors for Trypsin‐Like Serine Proteases

In the absence of X‐ray data, the exploration of compound binding modes continues to be a challenging task. For structure‐based design, specific features of active sites in different targets play a major role in rationalizing ligand binding characteristics. For example, dibasic compounds have been reported as potent inhibitors of various trypsin‐like serine proteases, the active sites of which contain several binding pockets that can be targeted by cationic moieties. This results in several possible orientations within the active site, complicating the binding mode prediction of such compounds by docking tools. Therefore, we introduced symmetry in bi‐ and tribasic compounds to reduce conformational space in docking calculations and to simplify binding mode selection by limiting the number of possible pocket occupations. Asymmetric bisbenzamidines were used as starting points for a multistage and structure‐guided optimization. A series of 24 final compounds with either two or three benzamidine substructures was ultimately synthesized and evaluated as inhibitors of five serine proteases, leading to potent symmetric inhibitors for the pharmaceutical drug targets matriptase, matriptase‐2, thrombin and factor Xa. This study underlines the relevance of ligand symmetry for chemical biology.     

Benzamidines in cyclocondensation with hexafluoroacetone and methyl trifluoropyruvate acyl- and ethoxycarbonylimines

The reactions of hexafluoroacetone and methyl trifluoropyruvate acyl- and ethoxycarbonylimines with benzamidines afford fluoro containing heterocycles of four structural types: dihydrotriazines, dihydrotriazinones, imidazoles, and imidazooxazoles.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 462–465, February, 2005     

One‐Pot Synthesis of Highly Substituted Polyheteroaromatic Compounds by Rhodium(III)‐Catalyzed Multiple CH Activation and Annulation

A new method for the synthesis of highly substituted naphthyridine‐based polyheteroaromatic compounds in high yields proceeds through rhodium(III)‐catalyzed multiple C? H bond cleavage and C? C and C? N bond formation in a one‐pot process. Such highly substituted polyheteroaromatic compounds have attracted much attention because of their unique π‐conjugation, which make them suitable materials for organic semiconductors and luminescent materials. Furthermore, a possible mechanism, which involves multiple chelation‐assisted ortho C? H activation, alkyne insertion, and reductive elimination, is proposed for this transformation.     

Odd-even chain length-dependent order in pH-switchable self-assembled layers

The reversible self-assembly of a series of bipolar amphiphiles, alpha,omega-bis(3- or 4-amidinophenoxy)alkanes (chain length n = 5-12), on mercaptoalkanoic acid-functionalized gold surfaces (chain length n = 10, 11, 14, 15) has been studied by in-situ ellipsometry, IR reflection absorption spectroscopy (IRAS), and atomic force microscopy (AFM). The layer order, amphiphile orientation, and tendency to form bilayers depends on the position of the amidine substituent, the alkyl chain length of both the amidine amphiphile and the underlying acid self-assembled monolayer (SAM), and whether the amidine alkyl chain contained an even or odd number of methylene groups. Thus, para-substituted bisbenzamidines containing more than six methylene groups (n>6) and with an odd number (n = 7, 9, 11) tended to form bilayered structures, whereas those containing an even number formed monolayers when adsorbed on SAMs of the long-chain acids (n = 14, 15). This behavior also correlated with the average tilt angle of the benzene moieties of the amphiphiles, as estimated by IRAS. The odd-numbered chains gave lower tilt angles than the even-numbered ones, and a possible model that accounts for these results is proposed. IRAS also revealed a higher order of the odd-numbered chains and an increasing hydrogen-bonding contribution with increasing chain length. Additional evidence for the proposed bilayered assemblies and their reversibility was obtained by AFM. Images obtained from the assembly of decamidine on a SAM of mercaptohexadecanoic acid in a pH 9 borate buffer revealed domains of similar size to that of the underlying acid SAM (20-30 nm), but less densely packed. By acidifying the solution, the second layer was destabilized and a very smooth layer with few defects appeared. Further acidification to pH 3 also destabilized the first layer.