A Novel Generalized 3D-QSAR Model of Camptothecin Analogs.

In the present paper, we are interested to explore if the application of docking-driven conformational analysis could increase the goodness of 3D-QSAR statistical models, as alternative approach to a conventional ligand-based conformer generation. In particular, we have selected as peculiar key-study an ensemble of Camptothecin (CPT) analogs classified as human DNA Topoisomerase I (Top1) selective inhibitors. The CPT analogs dataset has been recently analyzed by Hansch and Verma using a classical 2D-QSAR study.

Structure-activity relationship study of 16 a-thiocamptothecins: an integrated in vitro and in silico approach.

The instability of the hydroxylactone E ring represents a critical drawback of camptothecins, because the lactone ring is recognized to be essential for stabilization of topoisomerase I-mediated DNA cleavage. In an attempt to investigate the effect of the thiopyridone pharmacophofore on the molecular and pharmacological features of the drug, we prepared a series of novel 16 a-thiocamptothecin analogues. Due to the sulfur atom, a destabilization of the hydrogen bond between the hydroxy group in position 17 of the opened E ring and the carbonyl of the pyridone moiety is predicted, thus shifting the equilibrium toward the closed lactone form and increasing the lipophilic properties of the compounds.

Rational design, synthesis, and DNA binding properties of novel sequence-selective peptidyl congeners of ametantrone.

Natural and synthetic compounds characterized by an anthraquinone nucleus represent an important class of anti-neoplastic agents, the mechanism of action of which is related to intercalation into DNA. Ametantrone (AM) is a synthetic 9,10-anthracenedione bearing two (hydroxyethylamino)ethylamino residues at positions 1 and 4; along with other anthraquinones and anthracyclines, it shares a polycyclic intercalating moiety and charged side chains that stabilize DNA binding. All these drugs elicit adverse side effects, which represent a challenge for antitumor chemotherapy.

Semisynthesis, biological activity, and molecular modeling studies of C-ring-modified camptothecins.

The synthesis, biological activity, and molecular modeling studies of C-ring-modified camptothecins are reported. A general synthetic protocol, based on "C-5 camptothecin (C-5-CPT) enolate chemistry", allows one to obtain various C5-substituted analogues. All new compounds, obtained as 1:1 epimeric mixtures, were tested for their antiproliferative activity.

Novel camptothecin derivatives as topoisomerase I inhibitors.

Background: Camptothecin (CPT), a pentacyclic alkaloid isolated by Wall et al. in 1958 from the Chinese tree Camptotheca acuminata, was reported to possess an interesting antitumor activity. Late in 1985, it was reported by Liu et al.

Relationship between the structure and the DNA binding properties of diazoniapolycyclic duplex- and triplex-DNA binders: efficiency, selectivity, and binding mode.

The association of dicationic polycyclic ligands, namely, four diazoniapentaphene derivatives, three diazoniaanthra[1,2-a]anthracenes, diazoniahexaphene, and a partly saturated hydroxy-substituted diazoniapentaphene with double-stranded and triple-helical DNA, was investigated by spectrophotometric and viscosimetric titrations, CD and LD spectroscopy, DNA melting experiments, and molecular modeling studies. All experimental and theoretical data reveal an intercalative DNA-binding mode of the diazoniapentaphenes and diazoniaanthra[1,2-a]anthracenes; the latter have approximately 10-fold higher affinity for the DNA duplex. CD spectroscopic investigations and molecular modeling studies show that only one azonianaphthalene part of the ligand is intercalated between the DNA base pairs, whereas the remaining part of the ligand points outside the intercalation pocket.

Accuracy of binding mode prediction with a cascadic stochastic tunneling method.

We investigate the accuracy of the binding modes predicted for 83 complexes of the high-resolution subset of the ASTEX/CCDC receptor-ligand database using the atomistic FlexScreen approach with a simple forcefield-based scoring function. The median RMS deviation between experimental and predicted binding mode was just 0.83 A.