Arthur Van Aerschot

A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity

The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3′-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.

Anti-Hiv-1 Activity of 2′,3′-Dideoxinucleoside Analogues : Structure-Activity Relationship

Abstract Among the purine and pyrimidine 2′,3′-dideoxynucleosides, 2′,3′-didehydro-2′,3′-dideoxynucleosides, 3′-azido-2′,3′-dideoxynucleosides and 3′-fluoro-2′,3′-dideoxynucleosides, several congeners have been identified which achieve a potent and selective inhibition of HIV-1 replication in vitro.

Aminoacyl-tRNA synthetase inhibitors as potential antibiotics

Increasing resistance to antibiotics is a major problem worldwide and provides the stimulus for development of new bacterial inhibitors with preferably different modes of action. In search for new leads, several new bacterial targets are being exploited beside the use of traditional screening methods. Hereto, inhibition of bacterial protein synthesis is a long-standing validated target. Aminoacyl-tRNA synthetases (aaRSs) play an indispensable role in protein synthesis and their structures proved quite conserved in prokaryotes and eukaryotes. However, some divergence has occurred allowing the development of selective aaRS inhibitors. Following an outline on the action mechanism of aaRSs, an overview will be given of already existing aaRS inhibitors, which are largely based on mimics of the aminoacyl-adenylates, the natural reaction intermediates. This is followed by a discussion on more recent developments in the field and the bioavailability problem.

Inhibition of MDR1 expression with altritol-modified siRNAs

Altritol-modified nucleic acids (ANAs) support RNA-like A-form structures when included in oligonucleotide duplexes. Thus altritol residues seem suitable as candidates for the chemical modification of siRNAs. Here we report that ANA-modified siRNAs targeting the MDR1 gene can exhibit improved efficacy as compared to unmodified controls. This was particularly true of ANA modifications at or near the 3′ end of the sense or antisense strands, while modification at the 5′ end of the antisense strand resulted in complete loss of activity. Multiple ANA modifications within the sense strand were also well tolerated. Duplexes with ANA modifications at appropriate positions in both strands were generally more effective than duplexes with one modified and one unmodified strand. Initial evidence suggests that the loss of activity associated with ANA modification of the 5′-antisense strand may be due to reduced phosphorylation at this site by cellular kinases. Treatment of drug resistant cells with MDR1-targeted siRNAs resulted in reduction of P-glycoprotein (Pgp) expression, parallel reduction in MDR1 message levels, increased accumulation of the Pgp substrate rhodamine 123, and reduced resistance to anti-tumor drugs. Interestingly, the duration of action of some of the ANA-modified siRNAs was substantially greater than that of unmodified controls. These observations suggest that altritol modifications may be helpful in developing siRNAs with enhanced pharmacological effectiveness.

Impact of spacers on the hybridization efficiency of mixed self-assembled DNA/alkanethiol films

The immobilization of DNA strands is an essential step in the development of any DNA biosensor. Self-assembled mixed DNA/alkanethiol films are often used for coupling DNA probes covalently to the sensor surface. Although this strategy is well accepted, the effect of introducing a spacer molecule to increase the distance between the specific DNA sequence and the surface has rarely been assessed. The major goal of this work was to evaluate a number of such spacers and to assess their impact on for example the sensitivity and the reproducibility. Besides the commonly used mercaptohexyl (C(6)) spacer, a longer mercapto-undecyl (C(11)) spacer was selected. The combination of both spacers with tri(ethylene)glycol (TEG) and hexa(ethylene)glycol (HEG) was studied as well. The effect of the different spacers on the immobilization degree as well as on the consecutive hybridization was studied using surface plasmon resonance (SPR). When using the longer C(11) spacer the mixed DNA/alkanethiol films were found to be more densely packed. Further hybridization studies have indicated that C(11) modified probes improve the sensitivity, the corresponding detection limit as well as the reproducibility. In addition two different immobilization pathways, i.e. flow vs. diffusion controlled, were compared with respect to the hybridization efficiency. These data suggest that a flow-assisted approach is beneficial for DNA immobilization and hybridization events. In conclusion, this work demonstrates the considerable impact of spacers on the biosensor performance but also shows the importance of a flow-assisted immobilization approach.

Antimicrobial resistance in bacteria

The development of antimicrobial resistance by bacteria is inevitable and is considered as a major problem in the treatment of bacterial infections in the hospital and in the community. Despite efforts to develop new therapeutics that interact with new targets, resistance has been reported even to these agents. In this review, an overview is given of the many therapeutic possibilities that exist for treatment of bacterial infections and how bacteria become resistant to these therapeutics.

Acyclic oligonucleotides: possibilities and limitations

Abstract Oligonucleotides containing acyclic nucleosides with a 3( S ),5-dihydroxypentyl ( 1a–e ) or 4( R )-methoxy-3( S ),5-dihydroxypentyl ( 2a ) side chain were prepared and their hybridization properties as well as their stability towards degradation with snake venom posphodiesterase were studied. Attachment of an acyclic nucleoside at the 3′-end of an oligonucleotide makes it extremely resistant against enzymatic breakdown. Whereas oligonucleotides consisting completely of acyclic 2′-deoxyadenosine analogues ( 1a or 2a ) can still hybridize with an unmodified oligothymidylate, completely modified oligothymidylates or hetero-oligomers do not hybridize with their unmodified complementary oligonucleotide. This can be explained by the favourable enthalpy change on hybridization for the oligomers with adenine bases because of their higher degree of stacking and the ability to form T- A * .T triplets. In base-pairing with the natural DNA-nucleosides (dA,dC,dG,T), the acyclic nucleoside analogues ( 1a–e ) discriminate less compared to the natural 2′-deoxynucleosides. 9-(3( S ),5-Dihydroxypentyl)hypoxanthine shows the least spreading in melting temperature on hybridization with the four natural 2′-deoxynucleosides. Because of their conformational flexibility, acyclic nucleosides can be considered as universal nucleoside for the design of probes with ambiguous positions.

Synthetic Microcin C Analogs Targeting Different Aminoacyl-tRNA Synthetases

Microcin C (McC) is a potent antibacterial agent produced by some strains of Escherichia coli. McC consists of a ribosomally synthesized heptapeptide with a modified AMP attached through a phosphoramidate linkage to the alpha-carboxyl group of the terminal aspartate. McC is a Trojan horse inhibitor: it is actively taken inside sensitive cells and processed there, and the product of processing, a nonhydrolyzable aspartyl-adenylate, inhibits translation by preventing aminoacylation of tRNA(Asp) by aspartyl-tRNA synthetase (AspRS). Changing the last residue of the McC peptide should result in antibacterial compounds with targets other than AspRS. However, mutations that introduce amino acid substitutions in the last position of the McC peptide abolish McC production. Here, we report total chemical synthesis of three McC-like compounds containing a terminal aspartate, glutamate, or leucine attached to adenosine through a nonhydrolyzable sulfamoyl bond. We show that all three compounds function in a manner similar to that of McC, but the first compound inhibits bacterial growth by targeting AspRS while the latter two inhibit, respectively, GluRS and LeuRS. Our approach opens a way for creation of new antibacterial Trojan horse agents that target any 1 of the 20 tRNA synthetases in the cell.

SYNTHESIS AND PAIRING PROPERTIES OF OLIGONUCLEOTIDES CONTAINING 3-HYDROXY-4-HYDROXYMETHYL-1-CYCLOHEXANYL NUCLEOSIDES

Cyclohexanyl nucleic acid (CNA) represents a novel enantioselective Watson–Crick base-pairing system. Homochiral oligomers of equivalent chirality show antiparallel Watson–Crick pairing, while those of opposite sense do not. D-CNA hybridizes with natural nucleic acids, preferentially with RNA. A conformational change involving chair inversion is expected to occur upon duplex formation (A→B).

Maturation of the Translation Inhibitor Microcin C

Microcin C (McC), an inhibitor of the growth of enteric bacteria, consists of a heptapeptide with a modified AMP residue attached to the backbone of the C-terminal aspartate through an N-acyl phosphamidate bond. Here we identify maturation intermediates produced by cells lacking individual mcc McC biosynthesis genes. We show that the products of the mccD and mccE genes are required for attachment of a 3-aminopropyl group to the phosphate of McC and that this group increases the potency of inhibition of the McC target, aspartyl-tRNA synthetase.