Oligonucleotide promoted peptide bond formation using a tRNA mimicking approach.

TransferRNA's role in protein translation is the prime example of an Informational Leaving Group (ILG). A simplified model produced oligophenylalanine with a modified uracil as an ILG in the presence of specific oligonucleotides. Our preliminary studies contribute to the importance of hybrid species in bridging the gap between peptides and nucleic acids.

The 5-chlorouracil:7-deazaadenine base pair as an alternative to the dT:dA base pair.

5-Chloro-2'-deoxyuridine as a possible component of a chemically modified genome has been discussed in terms of its influence on duplex stability and DNA polymerase incorporation properties. The search for its counterpart among different deoxyadenosine analogs (7-deaza-, 8-aza- and 8-aza-7-deaza-2'-deoxyadenosines) showed that the stable duplex formation as well as the synthesis of long constructs, more than 2 kb, were successful with the 5-chloro-2'-deoxyuridine and 7-deaza-2'-deoxyadenosine combination and with Taq DNA polymerase.

NMR study on the interaction of the conserved CREX 'stem-loop' in the Hepatitis E virus genome with a naphthyridine-based ligand.

A 2-amino-1,8-naphthyridine derivative that is described to bind single guanine bulges in RNA-DNA and RNA-RNA duplexes was synthesized and its interaction with the single G bulge in the conserved CREX of the Hepatitis E Virus (HEV) genome was explored by NMR and molecular modeling. Results indicate that the ligand intercalates in the internal loop, though none of the expected hydrogen bonds with the single G in the bulge could be demonstrated.

Achiral, acyclic nucleic acids: synthesis and biophysical studies of a possible prebiotic polymer.

The search for prebiotic, nucleic acid precursors is, at its best, a speculative undertaking. Given the complex structure of RNA, it is not very likely that RNA was the first information system in the universe and thus finding possible precursor/s i.e. pre-RNA remains an open challenge. We, in this paper, have tried to construct nucleic acid polymers with a simple acyclic, achiral backbone. Such a linear, achiral backbone may have been formed from simple monomers that may have existed in the "prebiotic soup". We have shown that such polymers are capable of identifying the complementary "other self" and thus forming a potential system for information storage and transmission. This study thus involves investigation of nucleic acid analogues with a modified backbone that are likely to have formed in the prebiotic setting.

Contribution of dihydrouridine in folding of the D-arm in tRNA.

Posttranscriptional modifications of transfer RNAs (tRNAs) are proven to be critical for all core aspects of tRNA function. While the majority of tRNA modifications were discovered in the 1970s, their contribution in tRNA folding, stability, and decoding often remains elusive. In this work an NMR study was performed to obtain more insight in the role of the dihydrouridine (D) modification in the D-arm of tRNAi(Met) from S. pombe. While the unmodified oligonucleotide adopted several undefined conformations that interconvert in solution, the presence of a D nucleoside triggered folding into a hairpin with a stable stem and flexible loop region. Apparently the D modification is required in the studied sequence to fold into a stable hairpin. Therefore we conclude that D contributes to the correct folding and stability of D-arm in tRNA. In contrast to what is generally assumed for nucleic acids, the sharp 'imino' signal for the D nucleobase at 10 ppm in 90% H2O is not indicative for the presence of a stable hydrogen bond. The strong increase in pKa upon loss of the aromatic character in the modified nucleobase slows down the exchange of its 'imino' proton significantly, allowing its observation even in an isolated D nucleoside in 90% H2O in acidic to neutral conditions.

Sulfonate derived phosphoramidates as active intermediates in the enzymatic primer-extension of DNA.

Novel unnatural 5'-phosphoramidate nucleosides, capable of being processed as substrates by DNA polymerases for multiple nucleotide incorporations, have been designed. The mimics feature metabolites such as taurine and a broad range of aliphatic sulfonates coupled through a P-N bond to the 5'-phosphate position of deoxynucleotides, to allow binding interactions in the enzyme active site. The utility of all of the analogues as pyrophosphate mimics was demonstrated for the chain elongation of DNA, using both thermophilic and mesophilic microbial polymerases.

Redesigning the leaving group in nucleic acid polymerization.

Artificial nucleic acids have the potential to propagate genetic information in vivo purposefully insulated from the canonical replication and transcription processes of cells. Natural nucleic acids are synthesized using nucleoside triphosphates as building blocks and polymerases as catalysts, pyrophosphate functioning as the universal leaving group for DNA and RNA biosynthesis. In order to avoid entanglement between the propagation of artificial nucleic acids in vivo and the cellular information processes, we promote the biosynthesis of natural and xenobiotic nucleic acids (XNA) dependent on the involvement of leaving groups distinct from pyrophosphate. The feasibility of such radically novel biochemical systems relies on the systematic exploration of the chemical diversity of nucleic acid leaving groups that can undergo the catalytic mechanism of phosphotransfer in nucleic acid polymerization. Initial forays in this research area demonstrate the wide acceptance of polymerases and augur well for in vivo implementation and integration with canonical metabolism.

Ajuga remota Benth.: from ethnopharmacology to phytomedical perspective in the treatment of malaria.

Treatment and control of malaria have become more difficult with the spread of drug-resistant parasites and insecticide-resistant mosquito vectors. In the search for new antimalarial drugs, ethnopharmacological sources should merit more attention. Establishing the safety of traditional herbal medicines, along with identifying their active principles, are essential steps in the production of a properly standardized and accessible herbal medicine. Phytochemical characterization could also serve as a base for the development of new chemical compounds. The genus of Ajuga belongs to the family Lamiaceae and contains at least 301 species. Many of these plants have been used in traditional medicine. Ajuga remota in particular is traditionally used as a herbal remedy for fever and infections, and is prescribed for malaria by 66% of the Kenyan herbalists. A large number of compounds have already been isolated from A. remota, including ergosterol-5,8-endoperoxide (6), ajugarin-I (1), 8-O-acetylharpagide (5) and several phytoecdysteroids. In vitro pharmacological studies have been conducted on constituents of A. remota of which some of them displayed a concentration-dependent inhibition of chloroquine-sensitive and -resistant Plasmodium falciparum and Mycobacterium tuberculosis. Inhibition of parasitaemia was demonstrated in mouse models with P. berghei, supporting the traditional use of the plant against malaria. In this state-of-the-art review, A. remota as a possible therapeutic tool for malaria is discussed.

Antibacterial 5'-O-(N-dipeptidyl)-sulfamoyladenosines.

The aminoacyl-tRNA synthetase (aaRS) class of enzymes is a validated target for antimicrobial development. Aminoacyl analogues of 5'-O-(N-L-aminoacyl)-sulfamoyladenosines are known to be potent inhibitors of aaRS, but whole cell antibacterial activity of these compounds is very limited, and poor penetration into bacteria has been proposed as the main reason for this. Aiming to find derivatives that better penetrate bacteria, we developed a simple and short method to prepare dipeptidyl-derivatives of 5'-O-(N-L-aminoacyl)-sulfamoyladenosines, and used this method to prepare 18 5'-O-(N-dipeptidyl)-sulfamoyladenosines. The antibacterial activity of these derivatives and a number of reference compounds against S. aureus, E. faecalis and E. coli was determined. Several of the new derivatives showed improved antibacterial activity and an altered spectrum of antibacterial activity.

Imidazo[4,5-c]pyridines inhibit the in vitro replication of the classical swine fever virus and target the viral polymerase.

Selective inhibitors of the replication of the classical swine fever virus (CSFV) may have the potential to control the spread of the infection in an epidemic situation. We here report that 5-[(4-bromophenyl)methyl]-2-phenyl-5H-imidazo[4,5-c]pyridine (BPIP) is a highly potent inhibitor of the in vitro replication of CSFV. The compound resulted in a dose-dependent antiviral effect in PK(15) cells with a 50% effective concentration (EC(50)) for the inhibition of CSFV Alfort(187) (subgroup 1.1) of 1.6+/-0.4 microM and for CSFV Wingene (subgroup 2.3) 0.8+/-0.2 microM. Drug-resistant virus was selected by serial passage of the virus in increasing drug-concentration. The BPIP-resistant virus (EC(50): 24+/-4.0 microM) proved cross-resistant with VP32947 [3-[((2-dipropylamino)ethyl)thio]-5H-1,2,4-triazino[5,6-b]indole], an unrelated earlier reported selective inhibitor of pestivirus replication. BPIP-resistant CSFV carried a T259S mutation in NS5B, encoding the RNA-dependent RNA-polymerase (RdRp). This mutation is located near F224, a residue known to play a crucial role in the antiviral activity of BPIP against bovine viral diarrhoea virus (BVDV). The T259S mutation was introduced in a computational model of the BVDV RdRp. Molecular docking of BPIP in the BVDV polymerase suggests that T259S may have a negative impact on the stacking interaction between the imidazo[4,5-c]pyridine ring system of BPIP and F224.

Polymerase-catalyzed synthesis of DNA from phosphoramidate conjugates of deoxynucleotides and amino acids.

Some selected amino acids, in particular L-aspartic acid (L-Asp) and L-histidine (L-His), can function as leaving group during polymerase-catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. Although L-Asp-dAMP and L-His-dAMP bind, most probably, in a different way in the active site of the enzyme, aspartic acid and histidine can be considered as mimics of the pyrophosphate moiety of deoxyadenosine triphosphate. L-Aspartic acid is more efficient than D-aspartic acid as leaving group. Such P-N conjugates of amino acids and deoxynucleotides provide a novel experimental ground for diversifying nucleic acid metabolism in the field of synthetic biology.

Molecular dipstick test for diagnosis of sleeping sickness.

Human African trypanosomiasis (HAT) or sleeping sickness is a neglected disease that affects poor rural populations across sub-Saharan Africa. Confirmation of diagnosis is based on detection of parasites in either blood or lymph by microscopy. Here we present the development and the first-phase evaluation of a simple and rapid test (HAT-PCR-OC [human African trypanosomiasis-PCR-oligochromatography]) for detection of amplified Trypanosoma brucei DNA. PCR products are visualized on a dipstick through hybridization with a gold-conjugated probe (oligochromatography). Visualization is straightforward and takes only 5 min. Controls both for the PCR and for DNA migration are incorporated into the assay. The lower detection limit of the test is 5 fg of pure T. brucei DNA. One parasite in 180 microl of blood is still detectable. Sensitivity and specificity for T. brucei were calculated at 100% when tested on blood samples from 26 confirmed sleeping sickness patients, 18 negative controls (nonendemic region), and 50 negative control blood samples from an endemic region. HAT-PCR-OC is a promising new tool for diagnosis of sleeping sickness in laboratory settings, and the diagnostic format described here may have wider application for other infectious diseases.

Interaction of HIV-1 reverse transcriptase with modified oligonucleotide primers containing 2'-O-beta-D-ribofuranosyladenosine.

Modified synthetic oligodeoxyribonucleotides containing 2'-O-beta-D-ribofuranosyladenosine were used as primers in the RNA-dependent DNA synthesis catalyzed by HIV-1 reverse transcriptase. The degree of elongation of the primers depends on the position of the additional ribose unit, its presence in the specific position of the primer (-4) (and only in it) completely preventing elongation. Computer-modeled binding of the modified primers to the active site of reverse transcriptase demonstrated that steric hindrances arising from the interaction of the additional ribose residue with the reverse transcriptase region 262-270 interacting with the minor groove of the DNA substrate prevents elongation in the above mentioned case.

Synthesis and antiviral evaluation of ribavirin congeners containing a hexitol moiety.

Several ribavirin congeners containing a hexitol moiety were prepared via ring opening of two different epoxides with the methylcarboxylate ester of triazole and further elaboration. Unfortunately, none of the newly synthesized compounds displayed appreciable antiviral activity.

Chemical incorporation of 1-methyladenosine, minor tRNA component, into oligonucleotides.

The synthesis of suitably protected 1-methyladenosine derivatives has been developed and its successful chemical incorporation into oligonucleotides was achieved.

Oligonucleotides containing disaccharide nucleosides: synthesis, physicochemical, and substrate properties.

The efficient synthesis of oligonucleotides containing 2'-O-beta-D-ribofuranosyl (and beta-D-ribopyranosyl)nucleosides, 2'-O-alpha-D-arabinofuranosyl (and alpha-L-arabinofuranosyl)nucleosides. 2'-O-beta-D-erythrofuranosylnucleosides, and 2'-O-(5'-amino-5-deoxy-beta-D-ribofuranosyl)nucleosides have been developed.

Methylated hexitol nucleic acids, towards congeners with improved antisense potential.

In an effort to further improve the hybridisation potential of anhydro-hexitol nucleoside analogues, the 1'-methoxyl and 3'-methoxyl substituents were introduced and evaluated for their antisense potential. In view of the selectivity of pairing with RNA, especially the introduction of a 3'-O-alkyl moiety deserves further study.

RNA as a target for drug design, the example of Tat-TAR interaction.

One of the new targets in the battle against HIV-1 infection is the interaction between the viral transactivator and the transactivation response (TAR) element, which is necessary for HIV-1 replication. After an overview of the most recent structural studies of the Tat-TAR system, new TAR-targeted inhibitors are presented in several classes: antisense oligonucleotides, cationic peptides, intercalators and a large class of small RNA binding molecules. The method of library screening of RNA binding ligands in the search for new inhibitors is explained in detail. Inhibition of Tat-TAR interaction is considered as a realistic approach to develop new anti-HIV compounds. The RNA binding molecules in this review also demonstrate that the development of drugs that target RNA will become a feasible goal and that such compounds will be added in the future to the therapeutic arsenal to combat several diseases.

[Modified oligonucleotides containing 1-beta-D-galactopyranosylthymine: synthesis and substrate properties]. / Modifitsirovannye oligonukleotidy, soderzhashchie 1-beta-D-galaktopiranoziltimin: sintez i substraktnye svoistva.

A convenient method of regioselective introduction of 1-beta-D-galactopyranosylthymine into oligonucleotides was developed and the substrate properties of the modified oligonucleotides were investigated in the enzymic reaction of formation and hydrolysis of internucleotide bonds. The English version of the paper.

An additional 2'-ribofuranose residue at a specific position of the DNA primer prevents Its elongation by HIV-1 reverse transcriptase.

Oligodeoxynucleotides containing 2'-O-beta-D-ribofuranosyladenosine were prepared and used as modified primers in RNA-templated DNA synthesis catalyzed by HIV reverse transcriptase. It was shown that the additional 2'-ribofuranose residue in specific position of primer prevents its elongation.