Pieter Hendrickx

Synthesis and Biological Evaluation of Bicyclic Nucleosides as Inhibitors of M. tuberculosis Thymidylate Kinase

Herein we describe the synthesis and conformational analysis of a series of bicyclic thymidine derivatives and their evaluation as inhibitors of thymidine monophosphate kinase from Mycobacterium tuberculosis (TMPKmt), based on previously discovered bicyclic sugar nucleosides. With a Ki value of 2.3 μm, 1‐[3‐aminomethyl‐3,5‐dideoxy‐2‐O,6‐N‐(thiocarbonyl)‐β‐D‐ribofuranosyl]thymine emerged as the most potent TMPK inhibitor of this series. Moreover, this promising compound displays inhibitory potency against Mycobacteria cultures with an IC99 value of 100 μg mL−1, thus promoting TMPKmt for the first time as a validated target for further inhibitory design. Attempts to rationalise the observed structure–activity relationship (SAR) involving molecular modelling and conformational analysis are described.

The Solution Structure and Self‐Association Properties of the Cyclic Lipodepsipeptide Pseudodesmin A Support Its Pore‐Forming Potential

Pseudodesmin A is a cyclic lipodepsipeptide (CLP) of the viscosin group with a moderate in vitro biological activity. For several CLPs, including members of this group, this activity has been related to the ability to form ion pores in cellular membranes. As their size does not allow individual CLPs to span the membrane bilayer, individual monomers must somehow assemble into a larger structure. NMR spectroscopy has been used to demonstrate that in chloroform and other apolar organic solvents, pseudodesmin A monomers assemble into a supramolecular structure. These self-assembled structures can become sufficiently large to span the membrane bilayer as demonstrated with translational diffusion NMR spectroscopic measurements. With the aim to obtain more insight into the structural nature of this assembly, the solution conformation of pseudodesmin A was first determined by using ROESY (rOe) restraints measured in acetonitrile, in which no self-association occurs. The structure, which is found to be mostly similar to the previously described crystal structure, is shown to be retained within the supramolecular complex. Intermolecular rOe contacts obtained in chloroform together with chemical shift perturbation data provides structural insight into the organization of the self-associated complex. Based upon this analysis, a model for the organization of pseudodesmin A monomers in the supramolecular assembly is proposed, which is in agreement with the formation of bilayer spanning hydrophilic pores and provides the basis for a structure-function relationship for this type of CLPs. Finally, it is demonstrated that the differences previously reported between the crystal and solution conformation of the white line inducing principle (WLIP), a close analogue of pseudodesmin A, are the result of the use of dimethyl sulfoxide as solvent, whose strong hydrogen-bonding capacity induces conformational exchange.

Sn12O8(OH)4(OEt)28(HOEt)4 : an Additional Member in the Family of Dodecameric Oxo Clusters

A tin(IV) oxoalkoxo cluster with unprecedented architecture has been prepared and characterized by single-crystal X-ray diffraction. The cluster obeys the formula Sn 12O 8(OH) 4(OEt) 28(HOEt) 4 (1) and is based on an elongated centrosymmetric assembly of 12 six-coordinate tin centers, 28 peripheral ethoxy groups (terminal and bridging), 8 oxo bridges (mu2 and mu3), 4 hydroxy bridges (mu2), and 4 ethanol molecules that are all bound to tin atoms and interact strongly, through hydrogen bonds, with an ethoxy group located on a vicinal tin atom. This compound has also been fully characterized in solution by multinuclear 1D and 2D NMR, with all of its (119)Sn, (1)H, and (13)C NMR resonances assigned with respect to the structure. Altogether, the data allowed unambiguous location of the hydroxy groups. Information on the exchange of the ethoxy groups is also presented.

Quantification of hydrolytic charge loss of DMAEA-Q-based polyelectrolytes by proton NMR spectroscopy and implications for colloid titration

Copolymers of acrylamide and quaternised dimethylaminoethyl acrylate (DMAEA-Q) constitute an economically important range of cationic polyelectrolytes used in sludge conditioning. The latter treatment involves charge neutralisation and bridging induced by these polymers. Since both of these phenomena rely on charge-driven sorption onto the negatively charged colloidal particles, the accurate assessment of their charge density is of primary importance in polyelectrolyte characterisation. The experimental determination of this characteristic generally relies on colloidal charge titration, in which the cationic polymer is titrated against an anionic polymer. Hereby, one of the requirements to have a stoichiometric reaction between the oppositely charged polymers is a sufficiently low polymer concentration. In this study, it is shown that such a low polymer concentration may entail a pronounced hydrolysis effect for DMAEA-Q-based polymers, which leads to a release of the cationic side groups and hence causes considerable errors on the charge titration results. Proton nuclear magnetic resonance spectroscopy was applied to investigate the fast hydrolysis kinetics of DMAEA-Q polymers together with time-dependent charge titration measurements. Diffusion NMR spectroscopy was used to assist in establishing the nature of the hydrolysis compounds. The results from both techniques indicate that a high degree of hydrolysis is reached within minutes after dilution of a concentrated polymer stock solution into aqueous solutions of slightly acidic to neutral pH values. Therefore, a modification to the classic colloid titration procedure is proposed, using a buffered dilution liquid to avoid polymer hydrolysis. It is shown that a buffer pH value of 4.5 avoids not only polymer hydrolysis effects but also possible protonation of the anionic titrant, thereby avoiding overestimation of the charge density. By means of this procedure, reproducible and time-independent charge titration results are obtained.

Asymmetric Synthesis and Conformational Analysis by NMR Spectroscopy and MD of Aba- and α-MeAba-Containing Dermorphin Analogues

Dermorphin analogues, containing a (S)‐ and (R)‐4‐amino‐1,2,4,5‐tetrahydro‐2‐benzazepin‐3‐one scaffold (Aba) and the α‐methylated analogues as conformationally constrained phenylalanines, were prepared. Asymmetric phase‐transfer catalysis was unable to provide the (S)‐α‐Me‐o‐cyanophenylalanine precursor for (S)‐α‐MeAba in acceptable enantiomeric purity. However, by using a Schöllkopf chiral auxiliary, this intermediate was obtained in 88 % ee. [(S)‐Aba 3‐Gly 4]dermorphin retained μ‐opioid affinity but displayed an increased δ‐affinity. The corresponding R epimer was considerably less potent. In contrast, the [(R)‐α‐MeAba 3‐Gly 4]dermorphin isomer was more potent than its S epimer. Tar‐MD simulations of both non‐methylated [Aba 3‐Gly 4]dermorphin analogues showed a degree of folding at the C‐terminal residues toward the N terminus of the peptide, without however, adopting a stabilized β‐turn conformation. The α‐methylated analogues, on the other hand, exhibited a type I/I′ β‐turn conformation over the α‐MeAba 3 and Gly 4 residues, which was stabilized by a hydrogen bond involving Tyr 5‐HN and D‐Ala 2‐CO.

Assignment and conformational investigation of asymmetric phenylindenylidene ruthenium complexes bearing N,O-bidentate ligands.

The NMR conformational study of three asymmetric phenylindenylidene ruthenium complexes 4.1–4.3, is presented. Complete 1H and 13C assignments could be obtained for 4.1–4.3 in benzene solution from multiple 2D homonuclear and heteronuclear NMR techniques. Our NMR analysis shows that each complex exists as a 55:45 mixture of two rotational isomers in slow exchange on the NMR chemical shift timescale. They are shown to be related by a 180° flip of the indenylidene ligand along the RuCR bond. Both rotational isomers can be discriminated by means of NOEs contacts between the various ligands coordinating to the Ru. By matching these stereospecific assignments to the chemical shift, a chemical shift based fingerprint of the isomers that may allow straightforward assignment of future asymmetric phenylindenylidene ruthenium complexes is proposed. Copyright

Ruthenium–Indenylidene Complexes Bearing Saturated N-Heterocyclic Carbenes: Synthesis and Application in Ring-Closing Metathesis Reactions

The synthesis of complexes of the general formula Cl2Ru(SIMes)(L)(3-phenylinden-1-ylidene), 3a (L = PCy3), 3b (L = PPh3), 3c (L = py) and Cl2Ru(SIMe)(L)(3-phenylinden-1-ylidene), 4c (L = PCy3), 4b (L = PPh3), 4c (L = py) from commercially available Cl2Ru(PR3)2(3-phenylinden-1-ylidene), 2a (R = Cy), 2b (R = Ph), is reported, and the summed complexes proved to be useful catalysts for various ring-closing metathesis reactions. The catalytic data reported furthermore demonstrate that the substitution pattern of the N-aryl group has a definite influence on the activity of the second generation indenylidene catalysts for a given metathesis reaction, i.e. catalysts containing the SIMe-ligand showed improved initiation compared to the more robust SIMes substituted catalysts. A strong temperature effect was observed on all of the reactions tested. It is shown that complexes containing the SIMe-ligand display higher initiation efficiency then their corresponding SIMes analogues.