Mario Ippolito

IKK-β inhibitors: An analysis of drug–receptor interaction by using Molecular Docking and Pharmacophore 3D-QSAR approaches

The IKK kinases family represents a thrilling area of research because of its importance in regulating the activity of NF-kB transcription factors. The discovery of the central role played by IKK-beta in the activation of transcription in response to apoptotic or inflammatory stimuli allowed to considerate its modulation as a promising tool for the treatment of chronic inflammation and cancer. To date, several IKK-beta inhibitors have been discovered and tested. In this work, an analysis of the interactions between different classes of inhibitors and their biological target was performed, through the application of Molecular Docking and Pharmacophore/3D-QSAR approaches to a set of 141 inhibitors included in the Binding Database. In order to overcome the difficulty due to the lack of crystallographic data for IKK-beta, a homology model of this protein has been built and validated. The results allowed to study in depth the structural bases for the interaction of each family of inhibitors and provided clues for further modifications, with the aim of improving the activity and selectivity of designed drugs targeting this enzyme.

Molecular Modeling Approaches in the Discovery of New Drugs for Anti-Cancer Therapy: The Investigation of p53-MDM2 Interaction and its Inhibition by Small Molecules

The mdm2 oncogene product, MDM2, is an ubiquitin protein ligase that inhibits the transcriptional activity of the tumor suppressor p53 and promotes its degradation. About 50% of all human cancers present mutations or deletions in the TP53 gene. In the remaining half of all human neoplasias that express the wild-type protein, aberrations of p53 regulators, such as MDM2, account for p53 inhibition. For this reason, designing small-molecule inhibitors of the p53-MDM2 protein-protein interaction is a promising strategy for the treatment of cancers retaining wild-type p53. The development of inhibitors has been challenging. Although many small-molecule MDM2 inhibitors have shown potent in vitro activity, only a limited number of compounds have demonstrated to possess acceptable pharmacokinetic properties for in vivo evaluation. To date, the most studied chemotypes have been cis-imidazolines (such as nutlins), benzodiazepines, and spiro-oxindoles. The cis-imidazolines were the first discovered potent and selective small-molecule inhibitors of the p53-MDM2 interaction and they continue to show therapeutic potential. This review will focus on recent molecular modeling approaches (molecular dynamics, pharmacophore-based, molecular docking, structure-based design) used with the aim to better understand the behavior of these proteins and to discover new small-molecule inhibitors of the p53-MDM2 protein-protein interaction for the treatment of cancer.

Inside the Hsp90 inhibitors binding mode through induced fit docking.

During the last few decades, the development of new anticancer strategies had to face the instability of many tumors, occurring when the genetic plasticity of cells produces new drug-resistant cancers. It has been shown that a chaperone protein, heat shock protein 90 (Hsp90), is one of the fundamental factors involved in the cell response to stresses, and its role in many biochemical pathways has been demonstrated. Thus, the inhibition of Hsp90 represents a new target of antitumor therapy, since it may influence many specific signaling pathways. The natural antibiotic Geldanamycin is the first Hsp90 inhibitor that has been identified. Nevertheless, more potent and water-soluble small molecules are currently in development, and many X-ray crystallographic structures of Hsp90-inhibitor complexes are available for drug discovery purposes. Here we used the complexes of Hsp90 with eight different ligands, belonging to several chemical classes, to perform molecular docking experiments, using a novel technique called induced fit. Through this approach, it was possible to take into account the flexibility of the residues in the active site and to maintain a high level of precision in docking algorithms. The results allowed to identify several conserved residues involved in the interaction between Hsp90 and its inhibitor. Moreover, the exposition of the active site to solvent allows many water molecules to insert within the complex, providing additional hydrogen and polar interactions. Our models also provided template structures for further experiments and reproduces with a good degree of reliability, the conformations of the inhibitors as observed in experimental structures.

Brief communication: Principal component analysis on molecular descriptors as an alternative point of view in the search of new Hsp90 inhibitors

Inhibiting a protein that regulates multiple signal transduction pathways in cancer cells is an attractive goal for cancer therapy. Heat shock protein 90 (Hsp90) is one of the most promising molecular targets for such an approach. In fact, Hsp90 is a ubiquitous molecular chaperone protein that is involved in folding, activating and assembling of many key mediators of signal transduction, cellular growth, differentiation, stress-response and apoptothic pathways. With the aim to analyze which molecular descriptors have the higher importance in the binding interactions of these classes, we first performed molecular docking experiments on the 187 Hsp90 inhibitors included in the BindingDB, a public database of measured binding affinities. Further, for each frozen conformation obtained from the docking, a set of 250 molecular descriptors was calculated, and the resulting Structure/Descriptors matrix was submitted to Principal Component Analysis. From the factor scores it emerged a good clusterization among similar compounds both in terms of structural class and activity spectrum, while examination of the loadings of the first two factors also allowed to study the classes of descriptors which mainly contribute to each one.

Molecular Modelling and QSAR in the Discovery of HIV-1 Integrase Inhibitors

The treatment regimens for the HIV-1 have mainly included reverse transcriptase or protease inhibitors but their long-term clinical utility is limited by severe side effects and viral drug resistance. A new attractive target for chemotherapeutic intervention can be the Integrase enzyme, that mediates the integration of HIV-1 DNA into a host chromosome, for which there is no known counterparts in the host cell. A number of derivatives have been found to inhibit IN in in vitro assays, but no successful drug based on them has emerged so far, although many compounds have been proposed. Moreover most of the inhibitors do not belong to a very precise structural class: this fact makes these compounds a suitable target to be approached by all QSAR methods (classical and 3D) which therefore have been used to study the IN inhibitors. This review focuses on the molecular basis and rationale for developing integrase inhibitors and assesses the literature results of the chemometric study on classes of these inhibitors. Rational drug design by mean of the pharmacophore approach, rigid and flexible docking methods, and de novo design contributed to the identification of the most promising class of inhibitors, the DKAs. Moreover molecular dynamics studies were included since they can contribute to give further insight into the inhibitors binding modes already explored by means of the docking simulations.