Molecular modeling study of DNA abasic sites

We use molecular modeling calculations to study the structure and the flexibility of abasic (AP sites) and for the design of anticancer drugs targeted against AP sites. For either adenine or cytosine on the opposing strand within the same sequence context, the results are in line with experimental data which show that the two unpaired bases lead to intrahelical forms, but with differences in induced curvature. Results on flexibility, indicate that the two duplexes have the same bending rigidity for cytosine. In previous work a series of polyfunctional molecules, such as ATAc, were designed to selectively recognize and cleave abasic sites in DNA. The nitrobenzamide group which was added to the ATAc molecule to obtain a new molecule, termed ATAc4, can induce a second lesion under irradiation in close proximity to the abasic site. The different conformations of ATAc4 interacting with a DNA oligomer containing a stable analog of the abasic site were compared to the photoinduced cleavage pattern observed experimentally. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 12 May 2000     

Synthesis and conformational analysis of Substance P antagonist analogues based on a 1,7-naphthyridine scaffold

Two analogues of formerly described piperidine-based Substance P antagonists have been synthesised using an intramolecular Diels-Alder reaction of 1-(4-pentenyl)-3-phenyl-2(1H)-pyrazinones, followed by acidic methanolysis of the strained adducts to form the 8-oxo-6-phenyldecahydro [1,7]-naphthyridine-6-carboxylate esters and further conversion to the corresponding O-benzyl substituted 6-(hydroxymethyl) target compounds. Conformational analyses of intermediates and the final products are presented, based on ¹H NMR and modelling data.     

Molecular modeling of 8-methoxy quinolone analogues by using quantitative structure activity relationship

Quantitative structure activity relationship (QSAR) studies on a series of 8-methoxy quinolone are found to correlate well with steric parameters and electronic parameter. The results are critically discussed on the basis of regression data, Pogliani factor Q and cross validation technique. The results are found to be useful in discussing the mechanism of drug – receptor interaction. Steric parameter ‘Mr’ and electronic parameter ‘Pz’ gives the best model.     

Dependence of DNA sequence selectivity and cell cytotoxicity on azinomycin A and B epoxyamide stereochemistry

Evaluation of the importance of C18/C19 stereochemistry of azinomycin A/B epoxyamide partial structures with respect to DNA alkylation sequence selectivity is reported using a unique assay with a DNA oligomer containing imbedded normal (5'-GGC-3'/3'-CCG-5') and inverted (5'-CGG-3'/3'-GCC-5') azinomycin consensus cross-linking sequences. Both species were found to have unique selectivity profiles and alkylate DNA in a manner distinct from azinomycin B. Computational docking experiments support altered binding modes for the enantiomers.     

Organogelators based on the norbornane scaffold

Using the rigid norbornane scaffold, a series of low-molecular-weight organogelators has been synthesised and evaluated. Three separate compounds (16, 19 and 20) were identified as organogelators in three aromatic organic solvents (PhMe, anisole and o-xylene). The formation of fibrillar assemblies at nanometre level was confirmed using atomic force microscopy and transmission electron microscopy.     

UV cross-linking of unmodified DNA on glass surfaces

The performance of DNA microarrays strongly depends on their surface properties. Furthermore, the immobilization method of the capture molecules is of importance for the efficiency of the microarray in terms of sensitivity and specificity. This work describes the immobilization of single-stranded capture oligonucleotides by UV cross-linking on silanated (amino and epoxy) glass surfaces. Thereby we used amino (NH₂) and poly thymine/poly cytosine modifications of the capture sequences as well as unmodified capture molecules. The results were compared to UV cross-linking of the same DNA oligonucleotides on unmodified glass surfaces. Immobilization and hybridization efficiency was demonstrated by fluorescence and enzyme-induced deposition of silver nanoparticles. We found out that single-stranded DNA molecules do not require a special modification to immobilize them by UV cross-linking on epoxy- or amino-modified glass surfaces. However, higher binding rates can be achieved when using amino-modified oligonucleotides on an epoxy surface. The limit of detection for the used settings was 5 pM.     

Discovery of potential M2 channel inhibitors based on the amantadine scaffold via virtual screening and pharmacophore modeling

The M2 channel protein on the influenza A virus membrane has become the main target of the anti-flu drugs amantadine and rimantadine. The structure of the M2 channel proteins of the H3N2 (PDB code 2RLF) and 2009-H1N1 (Genbank accession number GQ385383) viruses may help researchers to solve the drug-resistant problem of these two adamantane-based drugs and develop more powerful new drugs against influenza A virus. In the present study, we searched for new M2 channel inhibitors through a combination of different computational methodologies, including virtual screening with docking and pharmacophore modeling. Virtual screening was performed to calculate the free energies of binding between receptor M2 channel proteins and 200 new designed ligands. After that, pharmacophore analysis was used to identify the important M2 protein-inhibitor interactions and common features of top binding compounds with M2 channel proteins. Finally, the two most potential compounds were determined as novel leads to inhibit M2 channel proteins in both H3N2 and 2009-H1N1 influenza A virus.     

Molecular modeling on garuganin-I

Summary The conformation of garuganin-I was analyzed in terms of the mobility of the cyclic structure. Molecular mechanics calculations were applied to show that the interconversion of the optical isomers is not possible at room temperature due to steric interactions. Different possibilities of the distortion of the molecular conformations were calculated and compared with molecular dynamics simulations.

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Molekulares Modelling von Garuganin-I

Zusammenfassung Die Konformation von Garuganin-I wurde bezüglich der Mobilität der cyclischen Struktur analysiert. Es wurden molekularmechanische Berechnungen herangezogen, die zeigten, daß die Interkonversion der optischen Isomeren bei Raumtemperatur wegen sterischer Wechselwirkungen nicht möglich ist. Es wurden verschiedene Möglichkeiten von Konformationsänderungen berechnet und mit einer Simulation der Molekulardynamik verglichen.

     

Total synthesis of cryptophycin analogues via a scaffold approach

[reaction: see text] Allylation of in situ generated beta,gamma-unsaturated aldehydes affords rapid access to vinyl halide analogues of fragment A of the cryptophycins. Three scaffolds are prepared in gram quantities by a ring-closing metathesis approach. Derivatization via a variety of cross-coupling protocols is possible, which affords novel analogues of these potent antimitotic agents.     

Role of the azinomycin naphthoate and central amide in sequence-dependent DNA alkylation and cytotoxicity of epoxide-bearing substructures

Studies report a strong correlation between duplex DNA alkylation and in vitro cytotoxicity for a series of azinomycin partial structures 2-6 bearing the biologically relevant epoxide. Compounds lacking the naphthoate ester (e.g., 5 and 6) were poorly reactive toward DNA and were biologically inactive, as were compounds bearing the naphthoate but lacking the terminal carboxamide (e.g., 2). Compounds were evaluated for cytotoxicity against two breast cancer cell lines. [structure: see text]     

Molecular solution to the optimal linear arrangement problem based on DNA computation

Due to massive parallelism, enormous memory storage and very low energy consumption, biomolecular operations have been suggested to solve various NP-hard problems that are beyond the capability of the fastest known digital computer. The optimal linear arrangement (OLA) problem is a well-known NP-hard combinatorial optimization problem. Based on a DNA computational model, this paper describes a novel algorithm for the OLA problem, which is executed in O(n ³log₂ n) DNA operations on tubes of (nK + n + m + L + 1)-bits DNA strands, where and . With the advance in molecular biology techniques, this algorithm may be of practical utility.     

Triplex-directed covalent cross-linking of a DNA nanostructure

The triplex approach to DNA recognition is exploited to direct covalent inter-strand cross-links to unique locations within a pre-assembled DNA nanostructure. This approach can be used to improve the stability of DNA nanostructures and demonstrates the feasibility of directing other reactive groups to unique locations within these complexes.     

In vitro biosynthesis of the antitumor agent azinomycin B

[reaction: see text] Azinomycins have potential therapeutic value as antitumor agents; however, their biosynthesis is poorly understood. Here, we provide the first demonstration of a protein cell-free system capable of supporting complete in vitro biosynthesis of the antitumor agent azinomycin B. The cell-free system is utilized to probe the cofactor dependence and substrate requirements of the pathway en route to azinomycin.     

Ifenprodil-like NMDA receptor modulator based on the biphenyl scaffold

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DNA as supramolecular scaffold for porphyrin arrays on the nanometer scale

Tetraphenyl porphyrin substituted deoxyuridine was used as a building block to create discrete multiporphyrin arrays via site specific incorporation into DNA. The successful covalent attachment of up to 11 tetraphenyl porphyrins in a row onto DNA shows that there is virtually no limitation in the amount of substituents, and the porphyrin arrays thus obtained reach the nanometer scale (approximately 10 nm). The porphyrin substituents are located in the major groove of the dsDNA and destabilize the duplex by deltaT(m) 5-7 degrees C per porphyrin modification. Force-field structure minimization shows that the porphyrins are either in-line with the groove in isolated modifications or aligned parallel to the nucleobases in adjacent modifications. The CD signals of the porphyrins are dominated by a negative peak arising from the intrinsic properties of the building block. In the single strands, the porphyrins induce stabilization of a secondary helical structure which is confined to the porphyrin modified part. This arrangement can be reproduced by force-field minimization and reveals an elongated helical arrangement compared to the double helix of the porphyrin-DNA. This secondary structure is disrupted above approximately 55 degrees C (T(p)) which is shown by various melting experiments. Both absorption and emission spectroscopy disclose electronic interactions between the porphyrin units upon stacking along the outer rim of the DNA leading to a broadening of the absorbance and a quenching of the emission. The single-stranded and double-stranded form show different spectroscopic properties due to the different arrangement of the porphyrins. Above T(p) the electronic properties (absorption and emission) of the porphyrins change compared to room temperature measurements due to the disruption of the porphyrin stacking at high temperature. The covalent attachment of porphyrins to DNA is therefore a suitable way of creating helical stacks of porphyrins on the nanometer scale.     

Synthesis of somatostatin mimetics based on the 1-deoxymannojirimycin scaffold

A novel synthesis of somatostatin mimetics based on the 1-deoxymannojirimycin (DMJ) scaffold has been developed. This involved development of a route suitable for the strategic grafting of pharmacophoric tryptophan and lysine side chains to the nitrogen atom of the piperidine ring and to the primary hydroxyl group of DMJ, respectively. The novel peptidomimetics were found to bind with higher affinity to sst4 receptors than to sst5 receptors.     

Synthesis of fluorescent probes based on the pyochelin siderophore scaffold

Pyochelin is a siderophore common to several pathogenic bacterial strains. Two conjugates, 1 and 2, between the NBD (4-nitro-benzo[1,2,5]oxadiazole) fluorophore and an N3'-functionalized pyochelin were synthesized. These fluorescent probes unexpectedly increased their fluorescence in an aqueous medium in the presence of iron(III) and were transported into bacterial cells.     

AZT binding to DNA and RNA: Molecular modeling and biological significance

In this review we report the application of molecular modeling based on different analytical methods to locate the binding sites of anti-AIDS drug azidothymidine (AZT) in the major and minor grooves of DNA and RNA duplexes. The effects of drug complexation on nucleic acids secondary structures and the biological implication are discussed.     

Molecular scaffold for the construction of three-armed and cage-like receptors

An efficient procedure was developed for the synthesis of the C3-symmetric molecular scaffold 2. The latter can easily be converted by a single step into either the three-armed receptors 11-16 or the cage-like receptor 17. X-ray structures were obtained for 2, 11, and 16, which are discussed in regard to their aptitude as receptor platforms. The interaction of the three-armed receptors 12-16 and the cage-like receptor 17 with phloroglucinol was investigated. In accordance with the conclusions obtained from molecular modeling and X-ray crystallographic studies on the host-guest complexes, the three-armed bipyridine receptor 16 exhibits, due to its induced fit, a larger association constant toward phloroglucinol than the cage 17. This new receptor system shows all of the positive features characteristic of 2,4,6-trialkylbenzene receptor systems, such as conformational control by steric gearing, ready availability, and versatility in derivatization. These attributes, combined with the advantageous size of the components, allows this system to be readily tailored to provide receptors for larger, biologically important molecules.