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LUCA PINZI

Ricercatore Legge 240/10 - t.det.
Dipartimento Scienze della Vita sede ex Scienze Farmaceutiche Via Campi 103

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Pubblicazioni

2023 - Design, synthesis, biological evaluation and crystal structure determination of dual modulators of carbonic anhydrases and estrogen receptors [Articolo su rivista]
Tinivella, Annachiara; Nwachukwu, J. C.; Angeli, A.; Foschi, F.; Benatti, Annalaura; Pinzi, Luca; Izard, T.; Ferraroni, M.; Erumbi, R.; Christodoulou, M. S.; Passarella, D.; Supuran, C.; Nettles, K. W.; Rastelli, Giulio
abstract

2023 - Discovery of potent pyrrolo-pyrimidine and purine HDAC inhibitors for the treatment of advanced prostate cancer [Articolo su rivista]
Moi, Davide; Bonanni, Davide; Belluti, Silvia; Linciano, Pasquale; Citarella, Andrea; Franchini, Silvia; Sorbi, Claudia; Imbriano, Carol; Pinzi, Luca; Rastelli, Giulio
abstract

2023 - Identification of Promising Drug Candidates against Prostate Cancer through Computationally-Driven Drug Repurposing [Articolo su rivista]
Bernal, Leonardo; Pinzi, Luca; Rastelli, Giulio
abstract

2023 - Insights into the Structural Conformations of the Tau Protein in Different Aggregation Status [Articolo su rivista]
Pinzi, L.; Bisi, N.; Sorbi, C.; Franchini, S.; Tonali, N.; Rastelli, G.
abstract

Tau is a protein characterized by large structural portions displaying extended conformational changes. Unfortunately, the accumulation of this protein into toxic aggregates in neuronal cells leads to a number of severe pathologies, collectively named tauopathies. In the last decade, significant research advancements were achieved, including a better understanding of Tau structures and their implication in different tauopathies. Interestingly, Tau is characterized by a high structural variability depending on the type of disease, the crystallization conditions, and the formation of pathologic aggregates obtained from in vitro versus ex vivo samples. In this review, we reported an up-to-date and comprehensive overview of Tau structures reported in the Protein Data Bank, with a special focus on discussing the connections between structural features, different tauopathies, different crystallization conditions, and the use of in vitro or ex vivo samples. The information reported in this article highlights very interesting links between all these aspects, which we believe may be of particular relevance for a more informed structure-based design of compounds able to modulate Tau aggregation.

2023 - Structure-activity exploration of a small-molecule allosteric inhibitor of T790M/L858R double mutant EGFR [Articolo su rivista]
Foschi, FRANCESCA MADDALENA; Tinivella, Annachiara; Crippa, Valeria; Pinzi, Luca; Mologni, Luca; Passarella, Daniele; Rastelli, Giulio
abstract

2022 - Development of machine learning classifers to predict compound activity on prostate cancer cell lines. [Articolo su rivista]
Bonanni, Davide; Pinzi, Luca; Rastelli, Giulio
abstract

2022 - Dual Targeting Strategies On Histone Deacetylase 6 (HDAC6) And Heat Shock Protein 90 (Hsp90) [Articolo su rivista]
Bonanni, Davide; Citarella, Andrea; Moi, Davide; Pinzi, Luca; Bergamini, Elisa; Rastelli, Giulio
abstract

The design of multi-target drugs acting simultaneously on multiple signaling pathways is a growing field in medicinal chemistry, especially for the treatment of complex diseases, such as cancer. Histone deacetylase 6 (HDAC6) is an established anticancer drug target involved in tumor cells transformation. Being an epigenetic enzyme at the interplay of many biological processes, HDAC6 has become an attractive target for polypharmacology studies aimed at improving the therapeutic efficacy of anticancer drugs. For example, the molecular chaperone Heat shock protein 90 (Hsp90) is a substrate of HDAC6 deacetylation, and several lines of evidence demonstrate that simultaneous inhibition of HDAC6 and Hsp90 promotes synergistic antitumor effects on different cancer cell lines, highlighting the potential benefits of developing a single molecule endowed with multi-target activity. This review will summarize the complex interplay between HDAC6 and Hsp90, providing also useful hints for multi-target drug design and discovery approaches in this field. To this end, crystallographic structures of HDAC6 and Hsp90 complexes will be extensively reviewed in light of discussing binding pockets features and pharmacophore requirements and providing useful guidelines for the design of dual inhibitors. The few examples of multi-target inhibitors obtained so far, mostly based on chimeric approaches, will be summarized and put into context. Finally, the main features of HDAC6 and Hsp90 inhibitors will be compared, and ligand- and structure-based strategies potentially useful for the development of small molecular weight dual inhibitors will be proposed and discussed.

2022 - Identification of potential biological targets of oxindole scaffolds via in silico repositioning strategies [Articolo su rivista]
Tinivella, Annachiara; Pinzi, Luca; Gambacorta, Guido; Baxendale, Ian; Rastelli, Giulio
abstract

2022 - On the development of B-Raf inhibitors acting through innovative mechanisms [Articolo su rivista]
Pinzi, L.
abstract

B-Raf is a protein kinase participating to the regulation of many biological processes in cells. Several studies have demonstrated that this protein is frequently upregulated in human cancers, especially when it bears activating mutations. In the last years, few ATP-competitive inhibitors of B-Raf have been marketed for the treatment of melanoma and are currently under clinical evaluation on a variety of other types of cancer. Although the introduction of drugs targeting B-Raf has provided significant advances in cancer treatment, responses to ATP-competitive inhibitors remain limited, mainly due to selectivity issues, side effects, narrow therapeutic windows, and the insurgence of drug resistance. Impressive research efforts have been made so far towards the identification of novel ATP-competitive modulators with improved efficacy against cancers driven by mutant Raf monomers and dimers, some of them showing good promises. However, several limitations could still be envisioned for these compounds, according to literature data. Besides, increased attentions have arisen around approaches based on the design of allosteric modulators, polypharmacology, proteolysis targeting chimeras (PROTACs) and drug repurposing for the targeting of B-Raf proteins. The design of compounds acting through such innovative mechanisms is rather challenging. However, valuable therapeutic opportunities can be envisioned on these drugs, as they act through innovative mechanisms in which limitations typically observed for approved ATP-competitive B-Raf inhibitors are less prone to emerge. In this article, current approaches adopted for the design of non-ATP competitive inhibitors targeting B-Raf are described, discussing also on the possibilities, ligands acting through such innovative mechanisms could provide for the obtainment of more effective therapies.

2022 - Synthesis of potent and selective HDAC6 inhibitors led to unexpected opening of a quinazoline ring [Articolo su rivista]
Moi, D.; Citarella, A.; Bonanni, D.; Pinzi, L.; Passarella, D.; Silvani, A.; Giannini, C.; Rastelli, G.
abstract

Histone deacetylase (HDAC) inhibitors are highly involved in the regulation of many pharmacological responses, which results in anti-inflammatory and anti-cancer effects. In the present work, chemoinformatic analyses were performed to obtain two potent and selective aminotriazoloquinazoline-based HDAC6 inhibitors. We unexpectedly obtained an aminotriazole from a water-driven ring opening of the triazoloquinazoline scaffold. Both compounds were evaluated as HDAC6 inhibitors, resulting in subnanomolar inhibitory activity and high selectivity with respect to class I HDAC1 and HDAC8. Importantly, the compounds were about 3- and 15-fold more potent compared to the reference compound trichostatin A. Additionally, the predicted binding modes were investigated with docking. Considering that the aminotriazole scaffold has never been embedded into the chemical structure of HDAC6 inhibitors, the present study suggests that both the aminotriazoloquinazoline and aminotriazole classes of compounds could be excellent starting points for further optimization of potential anticancer compounds, introducing such novel groups into a relevant and new area of investigation.

2021 - Antifungal Activity and DNA Topoisomerase Inhibition of Hydrolysable Tannins from Punica granatum L. [Articolo su rivista]
Brighenti, V.; Iseppi, R.; Pinzi, L.; Mincuzzi, A.; Ippolito, A.; Messi, P.; Sanzani, S. M.; Rastelli, G.; Pellati, F.
abstract

Punica granatum L. (pomegranate) fruit is known to be an important source of bioactive phenolic compounds belonging to hydrolysable tannins. Pomegranate extracts have shown antifungal activity, but the compounds responsible for this activity and their mechanism/s of action have not been completely elucidated up to now. The aim of the present study was the investigation of the inhibition ability of a selection of pomegranate phenolic compounds (i.e., punicalagin, punicalin, ellagic acid, gallic acid) on both plant and human fungal pathogens. In addition, the biological target of punicalagin was identified here for the first time. The antifungal activity of pomegranate phenolics was evaluated by means of Agar Disk Diffusion Assay and minimum inhibitory concentration (MIC) evaluation. A chemoinformatic analysis predicted for the first time topoisomerases I and II as potential biological targets of punicalagin, and this prediction was confirmed by in vitro inhibition assays. Concerning phytopathogens, all the tested compounds were effective, often similarly to the fungicide imazalil at the label dose. Particularly, punicalagin showed the lowest MIC for Alternaria alternata and Botrytis cinerea, whereas punicalin was the most active compound in terms of growth control extent. As for human pathogens, punicalagin was the most active compound among the tested ones against Candida albicans reference strains, as well as against the clinically isolates. UHPLC coupled with HRMS indicated that C. albicans, similarly to the phytopathogen Coniella granati, is able to hydrolyze both punicalagin and punicalin as a response to the fungal attack. Punicalagin showed a strong inhibitory activity, with IC50 values of 9.0 and 4.6 µM against C. albicans topoisomerases I and II, respectively. Altogether, the results provide evidence that punicalagin is a valuable candidate to be further exploited as an antifungal agent in particular against human fungal infections.

2021 - Chemoinformatics Analyses of Tau Ligands Reveal Key Molecular Requirements for the Identification of Potential Drug Candidates against Tauopathies [Articolo su rivista]
Pinzi, Luca; Tinivella, Annachiara; Rastelli, Giulio
abstract

Tau is a highly soluble protein mainly localized at a cytoplasmic level in the neuronal cells, which plays a crucial role in the regulation of microtubule dynamic stability. Recent studies have demonstrated that several factors, such as hyperphosphorylation or alterations of Tau metabolism, may contribute to the pathological accumulation of protein aggregates, which can result in neuronal death and the onset of a number of neurological disorders called Tauopathies. At present, there are no available therapeutic remedies able to reduce Tau aggregation, nor are there any structural clues or guidelines for the rational identification of compounds preventing the accumulation of protein aggregates. To help identify the structural properties required for anti-Tau aggregation activity, we performed extensive chemoinformatics analyses on a dataset of Tau ligands reported in ChEMBL. The performed analyses allowed us to identify a set of molecular properties that are in common between known active ligands. Moreover, extensive analyses of the fragment composition of reported ligands led to the identification of chemical moieties and fragment combinations prevalent in the more active compounds. Interestingly, many of these fragments were arranged in recurring frameworks, some of which were clearly present in compounds currently under clinical investigation. This work represents the first in-depth chemoinformatics study of the molecular properties, constituting fragments and similarity profiles, of known Tau aggregation inhibitors. The datasets of compounds employed for the analyses, the identified molecular fragments and their combinations are made publicly available as supplementary material.

2021 - Design and Synthesis of Hsp90 Inhibitors with B-Raf and PDHK1 Multi-Target Activity [Articolo su rivista]
Pinzi, L.; Foschi, F.; Christodoulou, M. S.; Passarella, D.; Rastelli, G.
abstract

The design of multi-target ligands has become an innovative approach for the identification of effective therapeutic treatments against complex diseases, such as cancer. Recent studies have demonstrated that the combined inhibition of Hsp90 and B-Raf provides synergistic effects against several types of cancers. Moreover, it has been reported that PDHK1, which presents an ATP-binding pocket similar to that of Hsp90, plays an important role in tumor initiation, maintenance and progression, participating also to the senescence process induced by B-Raf oncogenic proteins. Based on these premises, the simultaneous inhibition of these targets may provide several benefits for the treatment of cancer. In this work, we set up a design strategy including the assembly and integration of molecular fragments known to be important for binding to the Hsp90, PDHK1 and B-Raf targets, aided by molecular docking for the selection of a set of compounds potentially able to exert Hsp90-B-Raf-PDHK1 multi-target activities. The designed compounds were synthesized and experimentally validated in vitro. According to the in vitro assays, compounds 4 a, 4 d and 4 e potently inhibited Hsp90 and moderately inhibited the PDHK1 kinase. Finally, molecular dynamics simulations were performed to provide further insights into the structural basis of their multi-target activity.

2021 - Development and application of LigAdvisor, a user-friendly web-platform for polypharmacology and drug repurposing [Abstract in Atti di Convegno]
Pinzi, Luca; Tinivella, Annachiara; Rastelli, Giulio
abstract

2021 - Drug Repurposing and Polypharmacology to Fight SARS-CoV-2 Through Inhibition of the Main Protease [Articolo su rivista]
Pinzi, Luca; Tinivella, Annachiara; Caporuscio, Fabiana; Rastelli, Giulio
abstract

The outbreak of a new coronavirus (SARS-CoV-2), which is responsible for the COVID-19 disease and is spreading rapidly around the world, urgently requires effective therapeutic treatments. In this context, drug repurposing represents a valuable strategy, as it enables accelerating the identification of drug candidates with already known safety profiles, possibly aiding in the late stages of clinical evaluation. Moreover, therapeutic treatments based on drugs with beneficial multi-target activities (polypharmacology) may show an increased antiviral activity or help to counteract severe complications concurrently affecting COVID-19 patients. In this study, we present the results of a computational drug repurposing campaign that aimed at identifying potential inhibitors of the main protease (Mpro) of the SARS-CoV-2. The performed in silico screening allowed the identification of 22 candidates with putative SARS-CoV-2 Mpro inhibitory activity. Interestingly, some of the identified compounds have recently entered clinical trials for COVID-19 treatment, albeit not being assayed for their SARS-CoV-2 antiviral activity. Some candidates present a polypharmacology profile that may be beneficial for COVID-19 treatment and, to the best of our knowledge, have never been considered in clinical trials. For each repurposed compound, its therapeutic relevance and potential beneficial polypharmacological effects that may arise due to its original therapeutic indication are thoroughly discussed.

2021 - Hydroxamic Acid Derivatives: From Synthetic Strategies to Medicinal Chemistry Applications [Articolo su rivista]
Citarella, A.; Moi, D.; Pinzi, L.; Bonanni, D.; Rastelli, G.
abstract

Since the approval of three hydroxamic acid-based HDAC inhibitors as anticancer drugs, such functional groups acquired even more notoriety in synthetic medicinal chemistry. The ability of hydroxamic acids (HAs) to chelate metal ions makes this moiety an attractive metal binding group - in particular, Fe(III) and Zn(II) - so that HA derivatives find wide applications as metalloenzymes inhibitors. In this minireview, we will discuss the most relevant features concerning hydroxamic acid derivatives. In a first instance, the physicochemical characteristics of HAs will be summarized; then, an exhaustive description of the most relevant methods for the introduction of such moiety into organic substrates and an overview of their uses in medicinal chemistry will be presented.

2021 - Inhibitors of histone deacetylase 6 based on a novel 3-hydroxy-isoxazole zinc binding group [Articolo su rivista]
Linciano, P.; Pinzi, L.; Belluti, S.; Chianese, U.; Benedetti, R.; Moi, D.; Altucci, L.; Franchini, S.; Imbriano, C.; Sorbi, C.; Rastelli, G.
abstract

Histone deacetylase 6 (HDAC6) is an established drug target for cancer treatment. Inhibitors of HDAC6 based on a hydroxamic acid zinc binding group (ZBG) are often associated with undesirable side effects. Herein, we describe the identification of HDAC6 inhibitors based on a completely new 3-hydroxy-isoxazole ZBG. A series of derivatives decorated with different aromatic or heteroaromatic linkers, and various cap groups were synthesised and biologically tested. In vitro tests demonstrated that some compounds are able to inhibit HDAC6 with good potency, the best candidate reaching an IC50 of 700 nM. Such good potency obtained with a completely new ZBG make these compounds particularly attractive. The effect of the most active inhibitors on the acetylation levels of histone H3 and α- tubulin and their anti-proliferative activity of DU145 cells were also investigated. Docking studies were performed to evaluate the binding mode of these new derivatives and discuss structure-activity relationships.

2021 - Investigation of the effect of different linker chemotypes on the inhibition of histone deacetylases (HDACs) [Articolo su rivista]
Linciano, P.; Benedetti, R.; Pinzi, L.; Russo, F.; Chianese, U.; Sorbi, C.; Altucci, L.; Rastelli, G.; Brasili, L.; Franchini, S.
abstract

Histone Deacetylases (HDACs) are among the most attractive and interesting targets in anticancer drug discovery. The clinical relevance of HDAC inhibitors (HDACIs) is testified by four FDA-approved drugs for cancer treatment. However, one of the main drawbacks of these drugs resides in the lack of selectivity against the different HDAC isoforms, resulting in severe side effects. Thus, the identification of selective HDACIs represents an exciting challenge for medicinal chemists. HDACIs are composed of a cap group, a linker region, and a metal-binding group interacting with the catalytic zinc ion. While the cap group has been extensively investigated, less information is available about the effect of the linker on isoform selectivity. To this aim, in this work, we explored novel linker chemotypes to direct isoform selectivity. A small library of 25 hydroxamic acids with hitherto unexplored linker chemotypes was prepared. In vitro tests demonstrated that, depending on the linker type, some candidates selectively inhibit HDAC1 over HDAC6 isoform or vice versa. Docking calculations were performed to rationalize the effect of the novel linker chemotypes on biologic activity. Moreover, four compounds were able to increase the levels of acetylation of histone H3 or tubulin. These compounds were also assayed in breast cancer MCF7 cells to test their antiproliferative effect. Three compounds showed a significant reduction of cancer proliferation, representing valuable starting points for further optimization.

2021 - LigAdvisor: A versatile and user-friendly web-platform for drug design [Articolo su rivista]
Pinzi, L.; Tinivella, A.; Gagliardelli, L.; Beneventano, D.; Rastelli, G.
abstract

Although several tools facilitating in silico drug design are available, their results are usually difficult to integrate with publicly available information or require further processing to be fully exploited. The rational design of multi-target ligands (polypharmacology) and the repositioning of known drugs towards unmet therapeutic needs (drug repurposing) have raised increasing attention in drug discovery, although they usually require careful planning of tailored drug design strategies. Computational tools and data-driven approaches can help to reveal novel valuable opportunities in these contexts, as they enable to efficiently mine publicly available chemical, biological, clinical, and disease-related data. Based on these premises, we developed LigAdvisor, a data-driven webserver which integrates information reported in DrugBank, Protein Data Bank, UniProt, Clinical Trials and Therapeutic Target Database into an intuitive platform, to facilitate drug discovery tasks as drug repurposing, polypharmacology, target fishing and profiling. As designed, LigAdvisor enables easy integration of similarity estimation results with clinical data, thereby allowing a more efficient exploitation of information in different drug discovery contexts. Users can also develop customizable drug design tasks on their own molecules, by means of ligand- and target-based search modes, and download their results. LigAdvisor is publicly available at https://ligadvisor.unimore.it/.

2021 - LigAdvisor: a web platform designed for charting novel polypharmacology and drug repurposing routes from crystallographic ligands and known drugs [Poster]
Pinzi, Luca; Tinivella, Annachiara; Rastelli, Giulio
abstract

2021 - LigAdvisor: a web server to perform in silico explorations on crystallographic ligands and known drugs for polypharmacology and drug repurposing. [Abstract in Atti di Convegno]
Pinzi, Luca; Tinivella, Annachiara; Rastelli, Giulio
abstract

2021 - Prediction of activity and selectivity profiles of human Carbonic Anhydrase inhibitors using machine learning classification models [Articolo su rivista]
Tinivella, Annachiara; Pinzi, Luca; Rastelli, Giulio
abstract

The development of selective inhibitors of the clinically relevant human Carbonic Anhydrase (hCA) isoforms IX and XII has become a major topic in drug research, due to their deregulation in several types of cancer. Indeed, the selective inhibition of these two isoforms, especially with respect to the homeostatic isoform II, holds great promise to develop anticancer drugs with limited side effects. Therefore, the development of in silico models able to predict the activity and selectivity against the desired isoform(s) is of central interest. In this work, we have developed a series of machine learning classification models, trained on high confidence data extracted from ChEMBL, able to predict the activity and selectivity profiles of ligands for human Carbonic Anhydrase isoforms II, IX and XII. The training datasets were built with a procedure that made use of flexible bioactivity thresholds to obtain well-balanced active and inactive classes. We used multiple algorithms and sampling sizes to finally select activity models able to classify active or inactive molecules with excellent performances. Remarkably, the results herein reported turned out to be better than those obtained by models built with the classic approach of selecting an a priori activity threshold. The sequential application of such validated models enables virtual screening to be performed in a fast and more reliable way to predict the activity and selectivity profiles against the investigated isoforms.

2021 - Promising Non-cytotoxic Monosubstituted Chalcones to Target Monoamine Oxidase-B [Articolo su rivista]
Iacovino, L. G.; Pinzi, L.; Facchetti, G.; Bortolini, B.; Christodoulou, M. S.; Binda, C.; Rastelli, G.; Rimoldi, I.; Passarella, D.; Di Paolo, M. L.; Dalla Via, L.
abstract

A library of monosubstituted chalcones (1-17) bearing electron-donating and electron-withdrawing groups on both aromatic rings were selected. The cell viability on human tumor cell lines was evaluated first. The compounds unable to induce detectable cytotoxicity (1, 13, and 14) were tested using the monoamine oxidase (MAO) activity assay. Interestingly, they inhibit MAO-B, acting as competitive inhibitors, with 13 and 14 showing the best profiles. In particular, 13 exhibited a potency higher than that of safinamide, taken as a reference. Docking studies and crystallographic analysis showed that in human MAO-B 13 binds with the halogen-substituted aromatic ring in the entrance cavity, similar to safinamide, whereas 14 is accommodated in the opposite way. The main conclusion of this cell biology, biochemistry, and structural study is to highlights 13 as a chalcone derivative that is worth consideration for the development of novel MAO-B-selective inhibitors for the treatment of neurodegenerative diseases.

2021 - Tackling polypharmacology and drug repurposing with the LigAdvisor webserver. [Poster]
Pinzi, Luca; Tinivella, Annachiara; Rastelli, Giulio
abstract

2021 - Targeting the allosteric sites of the B-Raf protein kinase through an in silico approach [Poster]
Pinzi, Luca; Rastelli, Giulio
abstract

2020 - Design of dual inhibitors of histone deacetylase 6 and heat shock protein 90 [Articolo su rivista]
Pinzi, L.; Benedetti, R.; Altucci, L.; Rastelli, G.
abstract

Histone deacetylase 6 (HDAC6) and heat shock protein 90 (Hsp90) are widely investigated anticancer drug targets. Importantly, several lines of evidence indicate that their regulation and activity are intimately linked, and that their combined inhibition may lead to impressive therapeutic benefits. In this study, we developed and applied an integrated computational strategy to design dual inhibitors of HDAC6 and Hsp90. Although the two targets share very little homology, an integrated ligand-based and structure-based virtual screening approach indicated a subset of compounds possessing the key structural requirements for binding at both targets. In vitro tests demonstrated that some of the selected candidates are able to selectively inhibit HDAC6 over HDAC1, to increase the acetylation levels of tubulin on cell assays and to reduce cell proliferation. The discovered compounds represent valuable starting points for further hit optimization.

2020 - Identification of Target Associations for Polypharmacology from Analysis of Crystallographic Ligands of the Protein Data Bank [Articolo su rivista]
Pinzi, L.; Rastelli, G.
abstract

The design of a chemical entity that potently and selectively binds to a biological target of therapeutic relevance has dominated the scene of drug discovery so far. However, recent findings suggest that multitarget ligands may be endowed with superior efficacy and be less prone to drug resistance. The Protein Data Bank (PDB) provides experimentally validated structural information about targets and bound ligands. Therefore, it represents a valuable source of information to help identifying active sites, understanding pharmacophore requirements, designing novel ligands, and inferring structure-activity relationships. In this study, we performed a large-scale analysis of the PDB by integrating different ligand-based and structure-based approaches, with the aim of identifying promising target associations for polypharmacology based on reported crystal structure information. First, the 2D and 3D similarity profiles of the crystallographic ligands were evaluated using different ligand-based methods. Then, activity data of pairs of similar ligands binding to different targets were inspected by comparing structural information with bioactivity annotations reported in the ChEMBL, BindingDB, BindingMOAD, and PDBbind databases. Afterward, extensive docking screenings of ligands in the identified cross-targets were made in order to validate and refine the ligand-based results. Finally, the therapeutic relevance of the identified target combinations for polypharmacology was evaluated from comparison with information on therapeutic targets reported in the Therapeutic Target Database (TTD). The results led to the identification of several target associations with high therapeutic potential for polypharmacology.

2020 - Repositioning natural products in drug discovery [Articolo su rivista]
Rastelli, G.; Pellati, F.; Pinzi, L.; Gamberini, M. C.
abstract

No abstract available

2019 - 2-Phenyloxazole-4-carboxamide as a Scaffold for Selective Inhibition of Human Monoamine Oxidase B [Articolo su rivista]
Di Paolo, M. L.; Christodoulou, M. S.; Calogero, A. M.; Pinzi, L.; Rastelli, G.; Passarella, D.; Cappelletti, G.; Dalla Via, L.
abstract

A series of 2-phenyloxazoles bearing an amide group at position 4 were designed and synthesized for evaluation as potential inhibitors of human recombinant monoamine oxidases (hrMAOs). Results of kinetics experiments demonstrated that all compounds behave as competitive MAO inhibitors, with good selectivity toward the MAO-B isoform. The most potent and selective derivatives are characterized by inhibition constant (Ki) values in the sub-micromolar range and a good selectivity index (Ki MAO-A/Ki MAO-B>50). Some derivatives were also found to be able to inhibit MAO activity in nerve growth factor (NGF)-differentiated PC12 cells, taken as a model of neuronal cells. In particular, 2-(2-hydroxyphenyl)-N-phenyloxazole-4-carboxamide (compound 4 a) may be a promising new scaffold, exerting the highest selectivity and inhibitory effect toward MAOs in NGF-differentiated PC12 cell lysates, without compromising cell viability. Molecular docking analysis allowed a rationalization of the experimentally observed binding affinity and selectivity.

2019 - Evaluation of Amides, Carbamates, Sulfonamides, and Ureas of 4-Prop-2-ynylidenecycloalkylamine as Potent, Selective, and Bioavailable Negative Allosteric Modulators of Metabotropic Glutamate Receptor 5 [Articolo su rivista]
Graziani, Davide; Caligari, Silvia; Callegari, Elisa; De Toma, Carlo; Longhi, Matteo; Frigerio, Fabio; Dilernia, Roberto; Menegon, Sergio; Pinzi, Luca; Pirona, Lorenza; Tazzari, Valerio; Valsecchi, Anna Elisa; Vistoli, Giulio; Rastelli, Giulio; Ruga Riva, Carlo
abstract

Negative allosteric modulators (NAMs) of the metabotropic glutamate receptor 5 (mGlu 5 ) hold great promise for the treatment of a variety of central nervous system disorders. We have recently reported that prop-2-ynylidenecycloalkylamine derivatives are potent and selective NAMs of the mGlu 5 receptor. In this work, we explored the amide, carbamate, sulfonamide, and urea derivatives of prop-2-ynylidenecycloalkylamine compounds with the aim of improving solubility and metabolic stability. In silico and experimental analyses were performed on the synthesized series of compounds to investigate structure-activity relationships. Compounds 12, 32, and 49 of the carbamate, urea, and amide classes, respectively, showed the most suitable cytochrome inhibition and metabolic stability profiles. Among them, compound 12 showed excellent selectivity, solubility, and stability profiles as well as suitable in vitro and in vivo pharmacokinetic properties. It was highly absorbed in rats and dogs and was active in anxiety, neuropathic pain, and lower urinary tract models.

2019 - In silico repositioning of cannabigerol as a novel inhibitor of the enoyl acyl carrier protein (ACP) reductase (INHA) [Articolo su rivista]
Pinzi, L.; Lherbet, C.; Baltas, M.; Pellati, F.; Rastelli, G.
abstract

Cannabigerol (CBG) and cannabichromene (CBC) are non-psychoactive cannabinoids that have raised increasing interest in recent years. These compounds exhibit good tolerability and low toxicity, representing promising candidates for drug repositioning. To identify novel potential therapeutic targets for CBG and CBC, an integrated ligand-based and structure-based study was performed. The results of the analysis led to the identification of CBG as a low micromolar inhibitor of the Enoyl acyl carrier protein (ACP) reductase (InhA) enzyme.

2019 - Molecular docking: Shifting paradigms in drug discovery [Articolo su rivista]
Pinzi, L.; Rastelli, G.
abstract

Molecular docking is an established in silico structure-based method widely used in drug discovery. Docking enables the identification of novel compounds of therapeutic interest, predicting ligand-target interactions at a molecular level, or delineating structure-activity relationships (SAR), without knowing a priori the chemical structure of other target modulators. Although it was originally developed to help understanding the mechanisms of molecular recognition between small and large molecules, uses and applications of docking in drug discovery have heavily changed over the last years. In this review, we describe how molecular docking was firstly applied to assist in drug discovery tasks. Then, we illustrate newer and emergent uses and applications of docking, including prediction of adverse effects, polypharmacology, drug repurposing, and target fishing and profiling, discussing also future applications and further potential of this technique when combined with emergent techniques, such as artificial intelligence.

2019 - Refinement and rescoring of virtual screening results [Articolo su rivista]
Rastelli, G.; Pinzi, L.
abstract

High-throughput docking is an established computational screening approach in drug design. This methodology enables a rapid identification of biologically active hit compounds, providing an efficient and cost-effective complement or alternative to experimental high-throughput screenings. However, limitations inherent to the methodology make docking results inevitably approximate. Two major Achille’s heels include the use of approximated scoring functions and the limited sampling of the ligand-target complexes. Therefore, docking results require careful evaluation and further post-docking analyses. In this article, we will overview our approach to post-docking analysis in virtual screenings. BEAR (Binding Estimation After Refinement) was developed as a post-docking processing tool that refines docking poses by means of molecular dynamics (MD) and then rescores the ligands based on more accurate scoring functions (MM-PB(GB)SA). The tool has been validated and used prospectively in drug discovery applications. Future directions regarding refinement and rescoring in virtual screening are discussed.

2019 - Unveiling target associations for polypharmacology from analysis of crystallographic ligands in the Protein Data Bank [Abstract in Atti di Convegno]
Pinzi, Luca; Rastelli, Giulio
abstract

2019 - Virtual screening for dual Hsp90/B-Raf inhibitors [Capitolo/Saggio]
Anighoro, A.; Pinzi, L.; Rastelli, G.; Bajorath, J.
abstract

In this chapter, we describe a computational strategy leading to the identification of the first dual inhibitors of Heat Shock Protein 90 (Hsp90) and protein kinase B-Raf. Both proteins are validated targets for anti-cancer drug discovery. There is strong evidence that the simultaneous inhibition of Hsp90 and B-Raf provides therapeutic benefits compared to exclusive engagement of one or the other target. Hence, we have been interested in searching for dual Hsp90/B-Raf inhibitors. Virtual compound screening led to the identification of two compounds with micromolar activity against both targets. The computational approach faced a number of challenges that needed to be overcome, as described herein.

2018 - Identification of 4-aryl-1H-pyrrole[2,3-b]pyridine derivatives for the development of new B-Raf inhibitors [Articolo su rivista]
Pinzi, Luca; Anighoro, Andrew; Bajorath, Jürgen; Rastelli, Giulio
abstract

During the last years, a significant interest in the identification of new classes of B-Raf inhibitors has emerged. In this study, which was conceived within an effort that culminated in the recent report of the first dual inhibitors of B-Raf and Hsp90, we describe the identification of four compounds based on 4-aryl-1H-pyrrole[2,3-b]pyridine scaffold as interesting starting points for the development of new B-Raf inhibitors. Structure-activity relationships and predicted binding modes are discussed. Moreover, the novelty of the newly identified structures with respect to currently known B-Raf inhibitors was assessed through a ligand-based dissimilarity assessment. Finally, structural modifications with the potential ability to improve the activity toward B-Raf are put forward. This article is protected by copyright. All rights reserved.

2018 - Identification of small-molecule EGFR allosteric inhibitors by high-Throughput docking [Articolo su rivista]
Caporuscio, Fabiana; Tinivella, Annachiara; Restelli, Valentina; Semrau, Marta S; Pinzi, Luca; Storici, Paola; Broggini, Massimo; Rastelli, Giulio
abstract

Aim: The EGFR inhibitors represent the first-line treatment of non-small-cell lung cancer. However, the emergence of resistance urgently requires the development of new inhibitors targeting drug-resistant mutants. Methodology: A recently released structure of an EGFR kinase domain in complex with an allosteric inhibitor and a mutant protein model derived from it were used to set up a low-cost high-Throughput docking protocol for the fast identification of EGFR allosteric inhibitors. Conclusion: The virtual screening of commercially available compounds led to the identification of interesting new hit compounds. The most promising hit was confirmed to be a new allosteric inhibitor of wild-Type and T790M/L858R double mutant EGFR which was able to inhibit the growth of non-small-cell lung cancer cell lines.

2018 - Selection of protein conformations for structure-based polypharmacology studies [Articolo su rivista]
Pinzi, Luca; Caporuscio, Fabiana; Rastelli, Giulio
abstract

Several drugs exert their therapeutic effect through the modulation of multiple targets. Structure-based approaches hold great promise for identifying compounds with the desired polypharmacological profiles. These methods use knowledge of the protein binding sites to identify stereoelectronically complementary ligands. The selection of the most suitable protein conformations to be used in the design process is vital, especially for multitarget drug design in which the same ligand has to be accommodated in multiple binding pockets. Herein, we focus on currently available techniques for the selection of the most suitable protein conformations for multitarget drug design, compare the potential advantages and limitations of each method, and comment on how their combination could help in polypharmacology drug design.

2018 - Structure–Activity Relationships of Hexahydrocyclopenta[c]quinoline Derivatives as Allosteric Inhibitors of CDK2 and EGFR [Articolo su rivista]
Carlino, Luca; Christodoulou, Michael S.; Restelli, Valentina; Caporuscio, Fabiana; Foschi, FRANCESCA MADDALENA; Semrau, MARTA STEFANIA; Costanzi, Elisa; Tinivella, Annachiara; Pinzi, Luca; Lo Presti, Leonardo; Battistutta, Roberto; Storici, Paola; Broggini, Massimo; Passarella, Daniele; Rastelli, Giulio
abstract

Following the discovery of a type III allosteric modulator of cyclin-dependent kinase 2 (CDK2) characterized by a hexahydrocyclopenta[c]quinolone scaffold, three different series of its derivatives were synthesized and biologically evaluated. Docking of the synthesized compounds into the allosteric pocket of CDK2 allowed the elucidation of structure–activity relationships (SARs). Moreover, the compounds were tested on the wild-type epidermal growth factor receptor (EGFR) kinase domain (KD) and its clinically relevant T790M/L858R mutant form. Herein we describe the first SAR investigation of allosteric ligands that bind to the type III inhibitor pocket of CDK2 and EGFR-KD. Although the activity of the synthesized inhibitors needs to be improved, the obtained results provide clear-cut indications about pharmacophore requirements and selectivity determinants. Remarkably, this study led to the identification of a selective T790M/L858R EGFR allosteric inhibitor that is inactive toward both wild-type EGFR and CDK2. Finally, docking into the T790M/L858R EGFR-KD led us to hypothesize that the compounds bind to the double-mutant EGFR-KD by adopting a binding mode different from that in CDK2, thus rationalizing the observed selectivity profile.

2017 - Heat shock protein 90 and serine/threonine kinase B-Raf inhibitors have overlapping chemical space [Articolo su rivista]
Anighoro, A.; Pinzi, Luca; Marverti, Gaetano; Bajorath, J; Rastelli, Giulio
abstract

Heat shock protein 90 (Hsp90) and B-Raf are validated targets for anticancer drug discovery. Although there is strong evidence that concomitant inhibition of Hsp90 and B-Raf may provide significant therapeutic benefits, molecules endowed with dual activity against the two targets have not been reported. For the first time, we show that Hsp90 and B-Raf inhibitors have overlapping chemical space and we disclose the first-in-class dual inhibitors. The compounds were identified through a computational strategy especially devised for detecting ligands with dual-target activity. Although the two targets had only remote binding site similarity, we were able to identify dual inhibitors with well-balanced in vitro potencies and relatively low molecular weight. Remarkably, they also inhibited the V600E mutant form of B-Raf with similar potency. This study provides the first direct proof that designing dual ligands of Hsp90 and a kinase is possible, thus opening the way to new interesting possibilities in drug discovery.

2017 - On the integration of in silico drug design methods for drug repurposing [Articolo su rivista]
MARCH VILA, Eric; Pinzi, Luca; Sturm, Noã; Tinivella, Annachiara; Engkvist, Ola; Chen, Hongming; Rastelli, Giulio
abstract

Drug repurposing has become an important branch of drug discovery. Several computational approaches that help to uncover new repurposing opportunities and aid the discovery process have been put forward, or adapted from previous applications. A number of successful examples are now available. Overall, future developments will greatly benefit from integration of different methods, approaches and disciplines. Steps forward in this direction are expected to help to clarify, and therefore to rationally predict, new drug-target, target-disease, and ultimately drug-disease associations.

2016 - An unexpected reversal in the pharmacological stereoselectivity of benzothiadiazine AMPA positive allosteric modulators [Articolo su rivista]
Battisti, UMBERTO MARIA; Citti, Cinzia; Rastelli, Giulio; Pinzi, Luca; Puja, Giulia; Ravazzini, Federica; Ciccarella, Giuseppe; Braghiroli, Daniela; Cannazza, Giuseppe
abstract

Benzothiadiazine type compounds (BTDs) have gained great attention for their potential therapeutic activity as nootropic and neuroprotective agents. BTDs, acting as AMPA positive allosteric modulators, potentiate the glutamatergic neurotransmission without the side effects typically associated with direct agonists. Studies regarding the binding mode of racemic BTDs into the receptor binding pocket demonstrated that one enantiomer establishes a more favourable interaction and possesses a higher biological activity with respect to the other one. The S enantiomer was proved to be the eutomer for both IDRA21 and S18986, two of the most studied BTD AMPA positive allosteric modulators. However, recent data highlighted an opposite stereoselectivity for some substituted BTDs (7-chloro-9-(furan-3-yl)-2,3,3a,4-tetrahydro-1H-benzo[e]pyrrolo[2,1-c][1,2,4]thiadiazine 5,5-dioxide and 7-chloro-2,3,4-trimethyl-3,4-dihydro-2H-benzo[e][1,2,4]thiadiazine 1,1-dioxide) showing unexpected structure-activity relationships. In this work, the synthesis and configuration assignment of the stereoisomers of 7-chloro-5-(3-furanyl)-3-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide, one of the most active BTDs, are reported. Electrophysiological tests demonstrated that the R form is the eutomer. Docking and molecular dynamics simulations on the AMPA GluA2 binding site revealed new insights into the stereodiscrimination process. Lastly, metabolic studies disclosed a stereoselective hepatic metabolization of this chiral BTD.

2016 - Polypharmacology predictions in the Protein Data Bank [Poster]
Pinzi, Luca; Rastelli, Giulio
abstract

2016 - Predicting drug polypharmacology using structural databases [Abstract in Atti di Convegno]
Pinzi, Luca; Rastelli, Giulio
abstract

2015 - Computational polypharmacology comes of age [Articolo su rivista]
Rastelli, Giulio; Pinzi, Luca
abstract

No abstract

2015 - Rational design of dual inhibitors of Hsp90 and B-Raf as a novel pharmacological approach against melanomas [Poster]
Pinzi, Luca; Rastelli, Giulio
abstract

2015 - Rational design of dual inhibitors of Hsp90 and Braf as a novel pharmacological approach against melanomas [Abstract in Atti di Convegno]
Pinzi, Luca; Rastelli, Giulio
abstract