Tiziano Tuccinardi

Matrix metalloproteinase inhibitors: new challenges in the era of post broad-spectrum inhibitors.

More than two decades have been spent to develop many families of synthetic matrix metalloproteinases inhibitors (MMPI) as therapeutical agents for serious pathologies. Unfortunately, clinical trials conducted on broad-spectrum inhibitors have yielded disappointing results, especially in the cancer pathology area. Despite these outcomes, some small synthetic MMPI are in advanced trials or launched in clinical ones for cancer, arthritis, periodontal diseases. Today many groups are developing intensive efforts to find new classes of inhibitors characterized by improved potency and, above all, high selectivity against the specific MMP involved in each targeted pathology. The new challenges include the development of new MMPI bearing more effective ZBGs and the development of new allosteric non-zinc binding inhibitors, devoid of ZBGs. An analysis of more recent results in this field reported on journals and patents will be developed, to consider some of the more interesting new highly selective synthetic MMPI, their SARs, the new theoretical approaches used for modelling and the results of their biological evaluations.

CDK Inhibitors: From the Bench to Clinical Trials

Cell cycle deregulation is one of the first steps that transform normal cells into tumor cells. CDKs are a family of proteins devoted to controlling cell cycle entry, progression and exit. Studies from animal models show a tissue-specific essentiality of the single CDKs. In cancer cells, mis-regulation of CDK function is a common event. For this reason the pioneer compound Flavopiridol was developed and many new drugs are currently under development. ATP and the last generation of non-ATP competitive inhibitors are now emerging as one of the most potentially powerful target therapies. Many clinical trials are ongoing, as either a single agent or in combination with the classical cytotoxic agents. In this review, we discuss new strategies and methods to design more potent, selective and specific CDK inhibitors, starting from evidence emerging from animal and cancer cell models.

Docking-based virtual screening: recent developments.

Virtual (database) screening (VS) of molecules promises to accelerate the discovery of new drugs and reduce costs by identifying molecules with high probabilities of binding to a target receptor. The large amount of available protein X-ray crystal structures, together with the development of more effective homology modelling techniques, has led recently to a steep increase in docking-based VS studies. This approach needs computational fitting of molecules into a receptor active site using advanced algorithms, followed by the scoring and ranking of these molecules to identify potential leads. In this review, the main published docking-based VS studies developed over the last eight years are investigated, and details are provided about the software used, the results achieved and the novel methods employed.

Protein Kinases: Docking and Homology Modeling Reliability

A database of about 700 high-resolution kinase structures was used to test the reliability of 17 docking procedures (using six docking software packages) by means of self- and cross-docking studies. The analysis of about 80 000 docking calculations suggests that the docking of an unknown ligand into a kinase has a probability of only 30-37% to be a correct ligand pose. However, based on the hypothesis that docking calculations are more reliable if the ligand to be docked is similar to the ligand present in the complex from which the target docking protein has been extracted, we propose an automated procedure that is able to improve the docking accuracy, suggest the best protein for docking studies, and assess the statistical reliability of docking calculations. The results were also transferred to the homology modeling field and led us to propose an alternative strategy based on ligand similarity for the development of kinase models whose experimental structure was not known. Our results suggest that in many cases this approach can give better results than the classical homology modeling procedure based exclusively on the sequence homology.

Targeting Toxic RNAs that Cause Myotonic Dystrophy Type 1 (DM1) with a Bisamidinium Inhibitor.

A working hypothesis for the pathogenesis of myotonic dystrophy type 1 (DM1) involves the aberrant sequestration of an alternative splicing regulator, MBNL1, by expanded CUG repeats, r(CUG)exp. It has been suggested that a reversal of the myotonia and potentially other symptoms of the DM1 disease can be achieved by inhibiting the toxic MBNL1-r(CUG)exp interaction. Using rational design, we discovered an RNA-groove binding inhibitor (ligand 3) that contains two triaminotriazine units connected by a bisamidinium linker. Ligand 3 binds r(CUG)12 with a low micromolar affinity (Kd = 8 ± 2 μM) and disrupts the MBNL1-r(CUG)12 interaction in vitro (Ki = 8 ± 2 μM). In addition, ligand 3 is cell and nucleus permeable, exhibits negligible toxicity to mammalian cells, dissolves MBNL1-r(CUG)exp ribonuclear foci, and restores misregulated splicing of IR and cTNT in a DM1 cell culture model. Importantly, suppression of r(CUG)exp RNA-induced toxicity in a DM1 Drosophila model was observed after treatment with ligand 3. These results suggest ligand 3 as a lead for the treatment of DM1.

N-O-isopropyl sulfonamido-based hydroxamates: design, synthesis and biological evaluation of selective matrix metalloproteinase-13 inhibitors as potential therapeutic agents for osteoarthritis.

Matrix metalloproteinase-13 (MMP-13) is a key enzyme implicated in the degradation of the extracellular matrix in osteoarthritis (OA). For this reason, MMP-13 synthetic inhibitors are being sought as potential therapeutic agents to prevent cartilage degradation and to halt the progression of OA. Herein, we report the synthesis and in vitro evaluation of a new series of selective MMP-13 inhibitors possessing an arylsulfonamidic scaffold. Among these potential inhibitors, a very promising compound was discovered exhibiting nanomolar activity for MMP-13 and was highly selective for this enzyme compared to MMP-1, -14, and TACE. This compound acted as a slow-binding inhibitor of MMP-13 and was demonstrated to be effective in an in vitro collagen assay and in a model of cartilage degradation. Furthermore, a docking study was conducted for this compound in order to investigate its binding interactions with MMP-13 and the reasons for its selectivity toward MMP-13 versus other MMPs.

Indoles and Related Compounds as Cannabinoid Ligands

The discovery of the endocannabinoid system has lead to great strides in research development. At present, two cannabinoid receptors, CB1R and CB2R, are known. They belong to Class A rhodopsin-like GPCRs, and possess a different tissue distribution. Many synthetic compounds have been synthesized and tested for their cannabinoid activity. A particular class among them, the aminoalkylindole derivatives (typified by WIN55212-2) are hypothesized to interact in a binding site different from the main cannabinoid agonists. In this review we report the main aminoalkylindole derivatives, and other compounds which are hypothesized to interact in the same binding site. Furthermore we analyze the pharmacological profiles, the mutagenesis data and the computational models that describe their interaction in the cannabinoid receptors, evaluating the most important aspects for their activity and selectivity.

Dual inhibitors of matrix metalloproteinases and carbonic anhydrases: iminodiacetyl-based hydroxamate-benzenesulfonamide conjugates.

Matrix metalloproteinases (MMPs) and carbonic anhydrases (CAs) are two classes of zinc enzymes with different roles and catalytic targets, such as the degradation of most of the extracellular matrix (ECM) proteins and the regulation of the CO(2)/HCO(3)(-) equilibrium in the cells, respectively. Both families have isoforms which were proved to be involved in several stages of carcinogenic processes, and so the selective inhibition of these enzymes might be of interest in cancer therapy. We report herein the design, synthesis, and in vitro evaluation of a series of compounds possessing the iminodiacetic acid as the main backbone and two functional groups attached, namely, the hydroxamic acid and the arylsulfonamide (ArSO(2)NH(2)) moieties, to enable the inhibition of MMPs and CAs, respectively. These compounds were demonstrated to strongly inhibit both MMPs and CAs, some of them from the nanomolar to subnanomolar range. Furthermore, a docking study for MMPs was reported for the most promising compound in order to investigate its binding interactions with the different MMPs.

Computational studies of epidermal growth factor receptor: docking reliability, three-dimensional quantitative structure-activity relationship analysis, and virtual screening studies.

An aberrant activity of the epidermal growth factor receptor (EGFR) has been shown to be related to many human cancers, such as breast and liver cancers, thus making EGFR an attractive target for antitumor drug discovery. In this study we evaluated the reliability of various kinds of docking software and procedures to predict the binding disposition of EGFR inhibitors. By application of the best procedure and use of more than 200 compounds, a receptor-based 3D-QSAR model for EGFR inhibition was developed. On the basis of the results obtained, the possibility of developing virtual screening studies was also evaluated. The VS procedure that proved to be the most reliable from a computational point of view was then used to filter the Maybridge database in order to identify new EGFR inhibitors. Enzymatic assays revealed that among the eight top-scoring compounds, seven proved to inhibit EGFR activity at a concentration of 100 microM, two of them exhibiting IC(50) values in the low micromolar range and one in the nanomolar range. These results demonstrate the validity of the methodologies followed. Furthermore, the two low micromolar compounds may be considered as very interesting leads for the development of new EGFR inhibitors.

Extensive consensus docking evaluation for ligand pose prediction and virtual screening studies.

Molecular docking strategies are one of the most widely used techniques for predicting the binding mode of a ligand and for obtaining new hits in virtual screening studies. In order to improve the accuracy of this approach, we tested the reliability of applying a consensus docking protocol by combining ten different docking procedures. The analysis was carried out in terms of consensus cross-docking and by using an enriched database. The results highlight that from a qualitative point of view consensus docking is able to predict the ligand binding pose better than the single docking programs and is also able to give hints concerning the reliability of the docking pose. With regard to the virtual screening studies, consensus docking was evaluated for three different targets of the Directory of Useful Decoys (DUD), and the obtained results suggest that this approach performs as well as the best available methods found in the literature, therefore supporting the idea that this procedure can be profitably applied for the identification of new hits.