Discovery of New Antioxidant Molecules Enhancing the Nrf2-Mediated Pathway: Docking Studies and Biological Evaluation Simona De Vita, Elena González-Burgos, Stefania Terracciano, Maria Giovanna Chini, María Pilar Gómez-Serranillos, Giuseppe Bifulco International Journal of Molecular Sciences, 2026 Oxidative stress has been reported to be implicated in the pathogenesis of many neurodegenerative diseases, such as Alzheimer’s and Parkinson’s diseases. Enhancing antioxidant response, through the activation of the transcription factor Nrf2, may represent a potential strategy, based on in vitro models. To identify scaffolds potentially able to modulate the Nrf2-Keap1 interaction, docking experiments were carried out using a library of commercially available and in-house synthesized molecules. Compounds 1–4 were selected, and their direct and indirect antioxidant activity was evaluated in an acute oxidative stress model induced by Fenton’s reaction in the human neuroblastoma SH-SY5Y cell line. Results showed that these compounds exerted the most pronounced protective effect under the tested conditions at the following concentrations: 10 μM for 1, 25 μM for 2, 10 μM for 3, and 5 μM for 4. Moreover, these molecules notably decreased intracellular ROS production and lipid peroxidation by-products and increased the GSH/GSSG ratio. Furthermore, these molecules promoted the protein expression of antioxidant enzymes downstream of the Nrf2 transcriptional pathway. Interestingly, compound 3 resulted in being the most active among the four.
Untargeted Diversity-Oriented Synthesis for the Discovery of New Antitumor Agents: An Integrated Approach of Inverse Virtual Screening, Bioinformatics, and Omics for Target Deconvolution Tania Ciaglia, Valeria Napolitano, Maria Rosaria Miranda, Danila La Gioia, Simona Musella, Aniello Schiano Moriello, Fabrizio Merciai, Veronica Di Sarno, Simona De Vita, Ester Colarusso, Gerardina Smaldone, Francesca Di Matteo, Eduardo Maria Sommella, Poulami Kumar, Marco Allarà, Alessia Ligresti, Isabel M. Gomez-Monterrey, Giuseppe Bifulco, Gianluigi Lauro, Pietro Campiglia, Carmine Ostacolo, Vincenzo Vestuto, Alessia Bertamino Journal of Medicinal Chemistry, 2025 Molecular diversity is one of the most pursued objectives in drug discovery, and diversity-oriented synthesis (DOS) perfectly responds to the achievement of this goal. In this paper, we describe a DOS approach applied to the antitumor field with the aim of identifying new anticancer structures and their associated targets. To accomplish this ambitious project, after an initial stage of phenotypic evaluation, we set up an integrated platform of inverse virtual screening (IVS), bioinformatics, and omics to predict the biological targets of the most promising compounds 31 and 63. Several proteins emerged from this study, and the most interesting ones were assessed by biophysical and in cellulo experiments, leading to the validation of six targets involved in calcium regulation, endoplasmic reticulum stress, and apoptosis. This work allowed us to identify two hit compounds with an interesting antitumor mechanism, but principally, to validate our platform as a fruitful tool for untargeted DOS campaigns.
Exploring the Potential of Phytocannabinoids Against Multidrug-Resistant Bacteria Carmina Sirignano, Simona De Vita, Ernesto Gargiulo, Massimiliano Lucidi, Daniela Visaggio, Maria Giovanna Chini, Gianluigi Lauro, Giuseppina Chianese, Paolo Visca, Giuseppe Bifulco, Orazio Taglialatela-Scafati Plants, 2025 The rapid emergence of multidrug-resistant (MDR) bacterial pathogens poses a critical threat to global health, creating an urgent need for novel antimicrobial agents. In this study, we evaluated a small library of natural and semisynthetic phytocannabinoids against a broad panel of MDR Gram-positive bacterial strains, evidencing very good activity in the low µM range. We provide evidence of the antibacterial activity of the two separated enantiomers of cannabidiol, offering novel insights into the stereochemical aspects of their bioactivity. To investigate the possible molecular targets and clarify the mechanism of action, we employed Inverse Virtual Screening (IVS), a computational approach optimized for predicting potential protein–ligand interactions, on three selected MDR bacterial species. Interestingly, key targets belonging to important bacterial metabolic pathways and defense mechanisms were retrieved, and the results were used to rationalize the observed biological activities. To the best of our knowledge, this study marks the first application of IVS to microorganisms, offering a novel strategy for identifying bacterial protein targets. The results pave the way for future experimental validation, structure-based drug design, and the development of novel antibacterial agents.
Corylus avellana cultivar “Tonda di Giffoni”, source of antioxidant diarylheptanoids: Biological evaluation and molecular docking analysis Antonietta Cerulli, Simona De Vita, Milena Masullo, Carmen Bove, Paloma Bermejo Bescós, Giuseppe Bifulco, Sonia Piacente Journal of Functional Foods, 2024 • Giffonins E, H, J and carpinontriol B were isolated from Corylus avellana . • The diarylheptanoids showed protection against H 2 O 2 -induced cytotoxic damage. • The compounds were able to decrease ROS production and lipid peroxidation. • Molecular docking experiments and Western blot analysis were performed. • The compounds resulted disruptors of the Nrf2/keap1 complex. Hazelnut “Tonda di Giffoni” ( Corylus avellana L.) is a PGI (Protected Geographical Indication) product of the Campania region, Southern Italy, marked for its processing quality which guarantees origin, typical features, high physicochemical quality, and organoleptic properties. Previous investigations on hazelnut and its byproducts revealed the presence of diarylheptanoid derivatives, natural compounds with antioxidant properties. With the aim of exploring the nutraceutical properties of hazelnut diarylheptanoids, the antioxidant properties of giffonins E ( 1 ), H ( 2 ), and J ( 3 ), three cyclic diaryletherheptanoids, and carpinontriol B ( 4 ), a cyclic diarylheptanoid, were investigated. Tested compounds showed significant protection against hydrogen peroxide (H 2 O 2 )-induced cytotoxic damage in human neuroblastoma and embryonic kidney cell lines. Compounds 1 – 4 were also able to prevent oxidative stress by decreasing reactive oxygen species (ROS) production and levels of lipid peroxidation, and attenuating cell apoptosis (caspase-3 activity). Moreover, considering that the nuclear factor erythroid 2-related factor 2 (Nrf2) is responsible for regulating an extensive panel of antioxidant enzymes, the capability of these natural products to disrupt the interaction between Kelch-like ECH-associated protein 1 (Keap1), thereby activating the Nrf2-mediated pathway, was evaluated by molecular docking experiments and in vitro tests. The Western blot analysis revealed that giffonin H and carpinontriol B had an indirect antioxidant action, as evidenced by a significant rise in the translocated protein following their administration.
PharmaCore: The Automatic Generation of 3D Structure-Based Pharmacophore Models from Protein/Ligand Complexes Simona De Vita, Ester Colarusso, Maria Giovanna Chini, Giuseppe Bifulco, Gianluigi Lauro Journal of Chemical Information and Modeling, 2024 In this work, we present PharmaCore: a new, completely automatic workflow aimed at generating three-dimensional (3D) structure-based pharmacophore models toward any target of interest. The proposed approach relies on using cocrystallized ligands to create the input files for generating the pharmacophore hypotheses, integrating not only the three-dimensional structural information on the ligand but also data concerning the binding mode of these molecules put in the protein cavity. We developed a Python library that, starting from the specific UniProt ID of the protein under investigation as the only element that requires user intervention, subsequently collects and aligns the corresponding structures bearing a known ligand in a fully automated fashion, bringing them all into the same coordinate system. The protocol includes a final phase in which the aligned small molecules are used to produce the pharmacophore hypotheses directly onto the protein structure using a specific software, e.g., Phase (Schrödinger LLC). To validate the entire procedure and highlight the possible applications in the field of drug discovery and repositioning, we first generated pharmacophores for soluble epoxide hydrolase (sEH) and compared with already-published ones. Then, we reproduced the binding profile of a reported selective binder of ATAD2 bromodomain (AM879), testing it against a panel of 1741 pharmacophores related to 16 epigenetic proteins and automatically generated with PharmaCore, finally disclosing putative unprecedented off-targets. The computational predictions were successfully validated with AlphaScreen assays, highlighting the applicability of the proposed workflow in drug discovery and repositioning. Finally, the process was also validated on tankyrase 2 and SARS-CoV-2 MPro, confirming the robustness of PharmaCore.
Demethylcalabaxanthone from Garcinia mangostana Exerts Antioxidant Effects through the Activation of the Nrf2 Pathway as Assessed via Molecular Docking and Biological Evaluation Simona De Vita, Milena Masullo, Sabrina Grambone, Paloma Bermejo Bescós, Sonia Piacente, Giuseppe Bifulco Antioxidants, 2023 Nuclear factor erythroid 2-related factor 2 (Nrf2) pathway activation promotes the expression of antioxidant enzymes in response to rising oxidative stress, resulting in reactive oxygen species (ROS) detoxification and playing a central role in the maintenance of intracellular redox homeostasis and regulation of inflammation. Moreover, the biological effects of Nrf2 pathway activation contribute to reducing apoptosis and enhancing cell survival. The activity of Nrf2 is negatively regulated by Kelch-like ECH-associated protein 1 (Keap1). Prompted by the recent results reporting the impact of xanthone metabolites on oxidative stress, cancer, and inflammation, the antioxidant properties of xanthones isolated from Garcinia mangostana (γ-mangostin, α-mangostin, 8-deoxygartanin, demethylcalabaxanthone, garcinone D) were assessed. In particular, the capability of these natural products to disrupt the interaction between Kelch-like ECH-associated protein 1 (Keap1) and nuclear factor erythroid 2-related factor 2 (Nrf2), triggering the activation of the Nrf2-mediated pathway, was evaluated using molecular docking experiments and in vitro tests. The modulation of some key Nrf2-related mediators like glutathione (GSH) and lactate dehydrogenase (LDH) to highlight a possible direct antioxidant effect was investigated. Among the tested compounds, demethylcalabaxanthone showed an indirect antioxidant effect, as corroborated by a Western blot assay, displaying a significant increase in the translocated protein upon its administration.
2-Substituted 1,5-benzothiazepine-based HDAC inhibitors exert anticancer activities on human solid and acute myeloid leukemia cell lines Simona De Vita, Sara Meninno, Lucia Capasso, Ester Colarusso, Maria Giovanna Chini, Gianluigi Lauro, Romolo Rinaldi, Annalisa De Cicco, Veronica Sian, Stefania Terracciano, Angela Nebbioso, Alessandra Lattanzi, Giuseppe Bifulco Bioorganic and Medicinal Chemistry, 2023 Herein, we report the development of a new series of histone deacetylase inhibitors (HDACi) containing a 2-substituted 1,5-benzothiazepine scaffold. First, a virtual combinatorial library (∼1.6×103 items) was built according to a convenient synthetic route, and then it was submitted to molecular docking experiments on seven HDACs isoforms belonging to classes I and II. A series of integrated computational filters were used to select the most promising ones and then synthesized through an optimized approach, also amenable to generating both racemic and enantioenriched benzothiazepine-based derivatives. The obtained compounds showed potent HDAC inhibitory activity, especially those containing the sulphone moiety, endowed with IC50 in the nanomolar range. In addition, in vitro outcomes of our synthesized compounds demonstrated a cytotoxic effect on U937 and HCT116 cell lines and an arrest in the G2/M phase (13 ≤ IC50 ≤ 18 µM). Finally, Western blot analyses outlined the modulation of the histone acetyl markers such as H3K9/14, acetyl-tubulin, and the apoptotic indicator p21 in both cancer cell lines, disclosing a good HDAC inhibitor activity exerted by the designed items. Given the key role of HDACs in many cellular pathways, which makes these enzymes appealing and “hot” drug targets, our findings highlighted the importance of these 2-substituted 1,5-benzothiazepine scaffolds (both in the reduced and oxidized version) for the development of novel epidrugs.
Target identification by structure-based computational approaches: Recent advances and perspectives Simona De Vita, Maria Giovanna Chini, Giuseppe Bifulco, Gianluigi Lauro Bioorganic and Medicinal Chemistry Letters, 2023 The use of computational techniques in the early stages of drug discovery has recently experienced a boost, especially in the target identification step. Finding the biological partner(s) for new or existing synthetic and/or natural compounds by "wet" approaches may be challenging; therefore, preliminary in silico screening is even more recommended. After a brief overview of some of the most known target identification techniques, recent advances in structure-based computational approaches for target identification are reported in this digest, focusing on Inverse Virtual Screening and its recent applications. Moreover, future perspectives concerning the use of such methodologies, coupled or not with other approaches, are analyzed.
Phytochemical Analysis of the Methanolic Extract and Essential Oil from Leaves of Industrial Hemp Futura 75 Cultivar: Isolation of a New Cannabinoid Derivative and Biological Profile Using Computational Approaches Simona De Vita, Claudia Finamore, Maria Giovanna Chini, Gabriella Saviano, Vincenzo De Felice, Simona De Marino, Gianluigi Lauro, Agostino Casapullo, Francesca Fantasma, Federico Trombetta, Giuseppe Bifulco, Maria Iorizzi Plants, 2022 Cannabis sativa L. is a plant belonging to the Cannabaceae family, cultivated for its psychoactive cannabinoid (Δ9-THC) concentration or for its fiber and nutrient content in industrial use. Industrial hemp shows a low Δ9-THC level and is a valuable source of phytochemicals, mainly represented by cannabinoids, flavones, terpenes, and alkaloids, with health-promoting effects. In the present study, we investigated the phytochemical composition of leaves of the industrial hemp cultivar Futura 75, a monoecious cultivar commercially used for food preparations or cosmetic purposes. Leaves are generally discarded, and represent waste products. We analyzed the methanol extract of Futura 75 leaves by HPLC and NMR spectroscopy and the essential oil by GC-MS. In addition, in order to compare the chemical constituents, we prepared the water infusion. One new cannabinoid derivative (1) and seven known components, namely, cannabidiol (2), cannabidiolic acid (3), β-cannabispirol (4), β-cannabispirol (5), canniprene (6), cannabiripsol (7), and cannflavin B (8) were identified. The content of CBD was highest in all preparations. In addition, we present the outcomes of a computational study focused on elucidating the role of 2α-hydroxy-Δ3,7-cannabitriol (1), CBD (2), and CBDA (3) in inflammation and thrombogenesis.
Phytochemical Characterization and Pharmacological Properties of Lichen Extracts from Cetrarioid Clade by Multivariate Analysis and Molecular Docking Isabel Ureña-Vacas, Elena González-Burgos, Simona De Vita, Padreep K. Divakar, Giuseppe Bifulco, M. Pilar Gómez-Serranillos Evidence Based Complementary and Alternative Medicine, 2022 Introduction. Lichens, due to the presence of own secondary metabolites such as depsidones and depsides, became a promising source of health-promoting organisms with pharmacological activities. However, lichens and their active compounds have been much less studied. Therefore, the present study aims to evaluate for the first time the antioxidant capacity and enzyme inhibitory activities of 14 lichen extracts belonging to cetrarioid clade in order to identify new natural products with potential pharmacological activity. Materials and Methods. In this study, an integrated strategy was applied combining multivariate statistical analysis (principal component analysis and hierarchical cluster analysis), phytochemical identification, activity evaluation (in vitro battery of antioxidant assays FRAP, DPPH, and ORAC), and enzyme inhibitory activity against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) and molecular profiling with in silico docking studies of the most promising secondary metabolites. Results. Among fourteen lichen samples, Dactylina arctica stands out for its higher antioxidant capacities, followed by Nephromopsis stracheyi, Tuckermannopsis americana, Vulpicida pinastri, and Asahinea scholanderi. Moreover, Asahinea scholanderi and Cetraria cucullata extracts were the best inhibitors of AChE and BuChE. The major secondary metabolites identified by HPLC were alectoronic acid and α-collatolic acid for Asahinea scholanderi and usnic acid and protolichesterinic acid for Cetraria cucullata. Molecular docking studies revealed that alectoronic acid exhibited the strongest binding affinity with both AChE and BuChE with and without water molecules. Conclusions. Our results concluded that these species could be effective in the treatment of neurodegenerative diseases, being mandatory further investigation in cell culture and in vivo models.
