1
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Cinti S, Tomassi S, Ciardiello C, Migliorino R, Pirozzi M, Leone A, Di Gennaro E, Campani V, De Rosa G, D'Amore VM, Di Maro S, Donati G, Singh S, Raucci A, Di Leva FS, Kessler H, Budillon A, Marinelli L. Paper-based electrochemical device for early detection of integrin αvβ6 expressing tumors. Commun Chem 2024; 7:60. [PMID: 38514757 PMCID: PMC10957923 DOI: 10.1038/s42004-024-01144-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
Despite progress in the prevention and diagnosis of cancer, current technologies for tumor detection present several limitations including invasiveness, toxicity, inaccuracy, lengthy testing duration and high cost. Therefore, innovative diagnostic techniques that integrate knowledge from biology, oncology, medicinal and analytical chemistry are now quickly emerging in the attempt to address these issues. Following this approach, here we developed a paper-based electrochemical device for detecting cancer-derived Small Extracellular Vesicles (S-EVs) in fluids. S-EVs were obtained from cancer cell lines known to express, at a different level, the αvβ6 integrin receptor, a well-established hallmark of numerous epithelial cancer types. The resulting biosensor turned out to recognize αvβ6-containing S-EVs down to a limit of 0.7*103 S-EVs/mL with a linear range up to 105 S-EVs /mL, and a relative standard deviation of 11%, thus it may represent a novel opportunity for αvβ6 expressing cancers detection.
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Affiliation(s)
- Stefano Cinti
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy.
| | - Stefano Tomassi
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Chiara Ciardiello
- Experimental Pharmacology Unit, Istituto Nazionale Tumori-IRCCS- Fondazione G. Pascale, Via Mariano Semmola, 53, 80131, Naples, Italy
| | - Rossella Migliorino
- Experimental Pharmacology Unit, Istituto Nazionale Tumori-IRCCS- Fondazione G. Pascale, Via Mariano Semmola, 53, 80131, Naples, Italy
| | - Marinella Pirozzi
- Second Unit, Institute of Experimenal Endocrinology and Oncology "G. Salvatore" (IEOS), National Research Council (CNR), Naples, Italy
| | - Alessandra Leone
- Experimental Pharmacology Unit, Istituto Nazionale Tumori-IRCCS- Fondazione G. Pascale, Via Mariano Semmola, 53, 80131, Naples, Italy
| | - Elena Di Gennaro
- Experimental Pharmacology Unit, Istituto Nazionale Tumori-IRCCS- Fondazione G. Pascale, Via Mariano Semmola, 53, 80131, Naples, Italy
| | - Virginia Campani
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Giuseppe De Rosa
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Vincenzo Maria D'Amore
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Salvatore Di Maro
- Department DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100, Caserta, Italy
| | - Greta Donati
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Sima Singh
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Ada Raucci
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Francesco Saverio Di Leva
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Alfredo Budillon
- Istituto Nazionale Tumori -IRCCS- Fondazione G. Pascale, Via Mariano Semmola, 53, 80131, Naples, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy.
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2
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Donati G, Viviano M, D'Amore VM, Cipriano A, Diakogiannaki I, Amato J, Tomassi S, Brancaccio D, Russomanno P, Di Leva FS, Arosio D, Seneci P, Taliani S, Magiera-Mularz K, Musielak B, Skalniak L, Holak TA, Castellano S, La Pietra V, Marinelli L. A combined approach of structure-based virtual screening and NMR to interrupt the PD-1/PD-L1 axis: Biphenyl-benzimidazole containing compounds as novel PD-L1 inhibitors. Arch Pharm (Weinheim) 2024; 357:e2300583. [PMID: 38110703 DOI: 10.1002/ardp.202300583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]
Abstract
Immunotherapy has emerged as a game-changing approach for cancer treatment. Although monoclonal antibodies (mAbs) targeting the programmed cell death protein 1/programmed cell death protein 1 ligand 1 (PD-1/PD-L1) axis have entered the market revolutionizing the treatment landscape of many cancer types, small molecules, although presenting several advantages including the possibility of oral administration and/or reduced costs, struggled to enter in clinical trials, suffering of water insolubility and/or inadequate potency compared with mAbs. Thus, the search for novel scaffolds for both the design of effective small molecules and possible synergistic strategies is an ongoing field of interest. In an attempt to find novel chemotypes, a virtual screening approach was employed, resulting in the identification of new chemical entities with a certain binding capability, the most versatile of which was the benzimidazole-containing compound 10. Through rational design, a small library of its derivatives was synthesized and evaluated. The homogeneous time-resolved fluorescence (HTRF) assay revealed that compound 17 shows the most potent inhibitory activity (IC50 ) in the submicromolar range and notably, differently from the major part of PD-L1 inhibitors, exhibits satisfactory water solubility properties. These findings highlight the potential of benzimidazole-based compounds as novel promising candidates for PD-L1 inhibition.
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Affiliation(s)
- Greta Donati
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Monica Viviano
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | | | | | | | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | | | - Daniela Arosio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | | | | | | | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Cracow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Cracow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Cracow, Poland
| | | | - Valeria La Pietra
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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3
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Russo C, Russomanno P, D'Amore VM, Alfano AI, Santoro F, Guzelj S, Gobec M, Amato J, Pagano B, Marinelli L, Carotenuto A, Tron GC, Di Leva FS, Jakopin Ž, Brancaccio D, Giustiniano M. Discovery of 2,3-Diaminoindole Derivatives as a Novel Class of NOD Antagonists. J Med Chem 2024; 67:3004-3017. [PMID: 38301029 DOI: 10.1021/acs.jmedchem.3c02094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
NOD1 and NOD2 are members of the pattern recognition receptors involved in the innate immune response. Overactivation of NOD1 is implicated in inflammatory disorders, multiple sclerosis, and cancer cell metastases. NOD1 antagonists would represent valuable pharmacological tools to gain further insight into protein roles, potentially leading to new therapeutic strategies. We herein report the expansion of the chemical space of NOD1 antagonists via a multicomponent synthetic approach affording a novel chemotype, namely, 2,3-diaminoindoles. These efforts resulted in compound 37, endowed with low micromolar affinity toward NOD1. Importantly, a proof-of-evidence of direct binding to NOD1 of Noditinib-1 and derivative 37 is provided here for the first time. Additionally, the combination of computational studies and NMR-based displacement assays enabled the characterization of the binding modality of 37 to NOD1, thus providing key unprecedented knowledge for the design of potent and selective NOD1 antagonists.
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Affiliation(s)
- Camilla Russo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Pasquale Russomanno
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Antonella Ilenia Alfano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Federica Santoro
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Samo Guzelj
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Jussara Amato
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Gian Cesare Tron
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, Novara 28100, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Žiga Jakopin
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Mariateresa Giustiniano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
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4
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Merlino F, Pecoraro A, Longobardi G, Donati G, Di Leva FS, Brignola C, Piccarducci R, Daniele S, Martini C, Marinelli L, Russo G, Quaglia F, Conte C, Russo A, La Pietra V. Development and Nanoparticle-Mediated Delivery of Novel MDM2/MDM4 Heterodimer Peptide Inhibitors to Enhance 5-Fluorouracil Nucleolar Stress in Colorectal Cancer Cells. J Med Chem 2024; 67:1812-1824. [PMID: 38285632 DOI: 10.1021/acs.jmedchem.3c01312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Colorectal cancer (CRC) often involves wild-type p53 inactivation by MDM2 and MDM4 overexpression, promoting tumor progression and resistance to 5-fluoruracil (5-FU). Disrupting the MDM2/4 heterodimer can proficiently reactivate p53, sensitizing cancer cells to 5-FU. Herein, we developed 16 peptides based on Pep3 (1), the only known peptide acting through this mechanism. The new peptides, notably 3 and 9, showed lower IC50 values than 1. When incorporated into tumor-targeted biodegradable nanoparticles, these exhibited cytotoxicity against three different CRC cell lines. Notably, NPs/9 caused a significant increase in p53 levels associated with a strong increment of its main downstream target p21 inducing apoptosis. Also, the combined treatment of 9 with 5-FU caused the activation of nucleolar stress and a synergic apoptotic effect. Hence, the co-delivery of MDM2/4 heterodimer disruptors with 5-FU through nanoparticles might be a promising strategy to overcome drug resistance in CRC.
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Affiliation(s)
- Francesco Merlino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Annalisa Pecoraro
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Giuseppe Longobardi
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Greta Donati
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
| | | | - Chiara Brignola
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Rebecca Piccarducci
- Department of Pharmacy, University of Pisa, via Bonanno, 6, 56126 Pisa, PI, Italy
| | - Simona Daniele
- Department of Pharmacy, University of Pisa, via Bonanno, 6, 56126 Pisa, PI, Italy
| | - Claudia Martini
- Department of Pharmacy, University of Pisa, via Bonanno, 6, 56126 Pisa, PI, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Giulia Russo
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Fabiana Quaglia
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Claudia Conte
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Annapina Russo
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Valeria La Pietra
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, NA, Italy
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5
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Gambacorta N, Gasperi V, Guzzo T, Di Leva FS, Ciriaco F, Sánchez C, Tullio V, Rozzi D, Marinelli L, Topai A, Nicolotti O, Maccarrone M. Exploring the 1,3-benzoxazine chemotype for cannabinoid receptor 2 as a promising anti-cancer therapeutic. Eur J Med Chem 2023; 259:115647. [PMID: 37478557 DOI: 10.1016/j.ejmech.2023.115647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
The discovery of selective agonists of cannabinoid receptor 2 (CB2) is strongly pursued to successfully tuning endocannabinoid signaling for therapeutic purposes. However, the design of selective CB2 agonists is still challenging because of the high homology with the cannabinoid receptor 1 (CB1) and for the yet unclear molecular basis of the agonist/antagonist switch. Here, the 1,3-benzoxazine scaffold is presented as a versatile chemotype for the design of CB2 agonists from which 25 derivatives were synthesized. Among these, compound 7b5 (CB2 EC50 = 110 nM, CB1 EC50 > 10 μM) demonstrated to impair proliferation of triple negative breast cancer BT549 cells and to attenuate the release of pro-inflammatory cytokines in a CB2-dependent manner. Furthermore, 7b5 abrogated the activation of extracellular signal-regulated kinase (ERK) 1/2, a key pro-inflammatory and oncogenic enzyme. Finally, molecular dynamics studies suggested a new rationale for the in vitro measured selectivity and for the observed agonist behavior.
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Affiliation(s)
- Nicola Gambacorta
- Department of Pharmacy-Pharmaceutical Sciences, University of the Studies of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Valeria Gasperi
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Tatiana Guzzo
- C4T S.r.l Colosseum Combinatorial Chemistry Centre for Technology, Via Della Ricerca Scientifica Snc, 00133, Rome, Italy
| | | | - Fulvio Ciriaco
- Department of Chemistry, University of the Studies of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Cristina Sánchez
- Department of Biochemistry and Molecular Biology, School of Biology, Complutense University, C/ José Antonio Nováis, 12, 28040, Madrid, Spain
| | - Valentina Tullio
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Diego Rozzi
- C4T S.r.l Colosseum Combinatorial Chemistry Centre for Technology, Via Della Ricerca Scientifica Snc, 00133, Rome, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | - Alessandra Topai
- C4T S.r.l Colosseum Combinatorial Chemistry Centre for Technology, Via Della Ricerca Scientifica Snc, 00133, Rome, Italy.
| | - Orazio Nicolotti
- Department of Pharmacy-Pharmaceutical Sciences, University of the Studies of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy.
| | - Mauro Maccarrone
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100, Coppito, L'Aquila, Italy; European Center for Brain Research/Santa Lucia Foundation IRCCS, Via Del Fosso di Fiorano 64, 00143, Rome, Italy.
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6
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D’Amore V, Donati G, Lenci E, Ludwig BS, Kossatz S, Baiula M, Trabocchi A, Kessler H, Di Leva FS, Marinelli L. Molecular View on the iRGD Peptide Binding Mechanism: Implications for Integrin Activity and Selectivity Profiles. J Chem Inf Model 2023; 63:6302-6315. [PMID: 37788340 PMCID: PMC10598797 DOI: 10.1021/acs.jcim.3c01071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Indexed: 10/05/2023]
Abstract
Receptor-selective peptides are widely used as smart carriers for specific tumor-targeted delivery. A remarkable example is the cyclic nonapeptide iRGD (CRGDKPGDC, 1) that couples intrinsic cytotoxic effects with striking tumor-homing properties. These peculiar features are based on a rather complex multistep mechanism of action, where the primary event is the recognition of RGD integrins. Despite the high number of preclinical studies and the recent success of a phase I trial for the treatment of pancreatic ductal adenocarcinoma (PDAC), there is little information available about the iRGD three-dimensional (3D) structure and integrin binding properties. Here, we re-evaluate the peptide's affinity for cancer-related integrins including not only the previously known targets αvβ3 and αvβ5 but also the αvβ6 isoform, which is known to drive cell growth, migration, and invasion in many malignancies including PDAC. Furthermore, we use parallel tempering in the well-tempered ensemble (PT-WTE) metadynamics simulations to characterize the in-solution conformation of iRGD and extensive molecular dynamics calculations to fully investigate its binding mechanism to integrin partners. Finally, we provide clues for fine-tuning the peptide's potency and selectivity profile, which, in turn, may further improve its tumor-homing properties.
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Affiliation(s)
- Vincenzo
Maria D’Amore
- Department
of Pharmacy, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Greta Donati
- Department
of Pharmacy, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Elena Lenci
- Department
of Chemistry “Ugo Schiff″, University of Florence, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Florence, Italy
| | - Beatrice Stefanie Ludwig
- Department
of Nuclear Medicine, University Hospital Klinikum Rechts der Isar
and Central Institute for Translational Cancer Research (TranslaTUM), Technical University Munich, Munich 81675, Germany
| | - Susanne Kossatz
- Department
of Nuclear Medicine, University Hospital Klinikum Rechts der Isar
and Central Institute for Translational Cancer Research (TranslaTUM), Technical University Munich, Munich 81675, Germany
- Department
of Chemistry, Institute for Advanced Study, Technical University Munich, Garching 85748, Germany
| | - Monica Baiula
- Department
of Pharmacy and Biotechnology, University
of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Andrea Trabocchi
- Department
of Chemistry “Ugo Schiff″, University of Florence, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Florence, Italy
| | - Horst Kessler
- Department
of Chemistry, Institute for Advanced Study, Technical University Munich, Garching 85748, Germany
| | - Francesco Saverio Di Leva
- Department
of Pharmacy, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Luciana Marinelli
- Department
of Pharmacy, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
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7
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Donati G, D’Amore VM, Russomanno P, Cerofolini L, Amato J, Marzano S, Salobehaj M, Rizzo D, Assoni G, Carotenuto A, La Pietra V, Arosio D, Seneci P, Fragai M, Brancaccio D, Di Leva FS, Marinelli L. Theoretical and experimental studies on the interaction of biphenyl ligands with human and murine PD-L1: Up-to-date clues for drug design. Comput Struct Biotechnol J 2023; 21:3355-3368. [PMID: 37384351 PMCID: PMC10293680 DOI: 10.1016/j.csbj.2023.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023] Open
Abstract
Today it is widely recognized that the PD-1/PD-L1 axis plays a fundamental role in escaping the immune system in cancers, so that anti-PD-1/PD-L1 antibodies have been evaluated for their antitumor properties in more than 1000 clinical trials. As a result, some of them have entered the market revolutionizing the treatment landscape of specific cancer types. Nonetheless, a new era based on the development of small molecules as anti PD-L1 drugs has begun. There are, however, some limitations to advancing these compounds into clinical stages including the possible difficulty in counteracting the PD-1/PD-L1 interaction in vivo, the discrepancy between the in vitro IC50 (HTFR assay) and cellular EC50 (immune checkpoint blockade co-culture assay), and the differences in ligands' affinity between human and murine PD-L1, which can affect their preclinical evaluation. Here, an extensive theoretical study, assisted by MicroScale Thermophoresis binding assays and NMR experiments, was performed to provide an atomistic picture of the binding event of three representative biphenyl-based compounds in both human and murine PD-L1. Structural determinants of the species' specificity were unraveled, providing unprecedented details useful for the design of next generation anti-PD-L1 molecules.
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Affiliation(s)
- Greta Donati
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Vincenzo Maria D’Amore
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Pasquale Russomanno
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center and Department of Chemistry, University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Maria Salobehaj
- Magnetic Resonance Center and Department of Chemistry, University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Domenico Rizzo
- Magnetic Resonance Center and Department of Chemistry, University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Giulia Assoni
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, Povo I-38123, Trento, Italy
- Department of Chemistry, University of Milan, Via C. Golgi 19, 20133 Milan, Italy
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Valeria La Pietra
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Daniela Arosio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Consiglio Nazionale delle Ricerche (CNR), Via C. Golgi 19, Milan 20133, Italy
| | - Pierfausto Seneci
- Department of Chemistry, University of Milan, Via C. Golgi 19, 20133 Milan, Italy
| | - Marco Fragai
- Magnetic Resonance Center and Department of Chemistry, University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | | | - Luciana Marinelli
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
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8
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Finamore C, Festa C, Fiorillo B, Leva FSD, Roselli R, Marchianò S, Biagioli M, Spinelli L, Fiorucci S, Limongelli V, Zampella A, De Marino S. Expanding the Library of 1,2,4-Oxadiazole Derivatives: Discovery of New Farnesoid X Receptor (FXR) Antagonists/Pregnane X Receptor (PXR) Agonists. Molecules 2023; 28:molecules28062840. [PMID: 36985811 PMCID: PMC10057480 DOI: 10.3390/molecules28062840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Compounds featuring a 1,2,4-oxadiazole core have been recently identified as a new chemotype of farnesoid X receptor (FXR) antagonists. With the aim to expand this class of compounds and to understand the building blocks necessary to maintain the antagonistic activity, we describe herein the synthesis, the pharmacological evaluation, and the in vitro pharmacokinetic properties of a novel series of 1,2,4-oxadiazole derivatives decorated on the nitrogen of the piperidine ring with different N-alkyl and N-aryl side chains. In vitro pharmacological evaluation showed compounds 5 and 11 as the first examples of nonsteroidal dual FXR/Pregnane X receptor (PXR) modulators. In HepG2 cells, these compounds modulated PXR- and FXR-regulated genes, resulting in interesting leads in the treatment of inflammatory disorders. Moreover, molecular docking studies supported the experimental results, disclosing the ligand binding mode and allowing rationalization of the activities of compounds 5 and 11.
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Affiliation(s)
- Claudia Finamore
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Carmen Festa
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Bianca Fiorillo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1468 Madison Ave, New York, NY 10029, USA
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Rosalinda Roselli
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi, 1-06132 Perugia, Italy
| | - Silvia Marchianò
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi, 1-06132 Perugia, Italy
| | - Michele Biagioli
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi, 1-06132 Perugia, Italy
| | - Lucio Spinelli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Stefano Fiorucci
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi, 1-06132 Perugia, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Angela Zampella
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Simona De Marino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
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9
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Stefanelli I, Corona A, Cerchia C, Cassese E, Improta S, Costanzi E, Pelliccia S, Morasso S, Esposito F, Paulis A, Scognamiglio S, Di Leva FS, Storici P, Brindisi M, Tramontano E, Cannalire R, Summa V. Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination. Eur J Med Chem 2023; 253:115311. [PMID: 37043904 PMCID: PMC10068823 DOI: 10.1016/j.ejmech.2023.115311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Despite the approval of vaccines, monoclonal antibodies and restrictions during the pandemic, the demand for new efficacious and safe antivirals is compelling to boost the therapeutic arsenal against the COVID-19. The viral 3-chymotrypsin-like protease (3CLpro) is an essential enzyme for replication with high homology in the active site across CoVs and variants showing an almost unique specificity for Leu-Gln as P2-P1 residues, allowing the development of broad-spectrum inhibitors. The design, synthesis, biological activity, and cocrystal structural information of newly conceived peptidomimetic covalent reversible inhibitors are herein described. The inhibitors display an aldehyde warhead, a Gln mimetic at P1 and modified P2-P3 residues. Particularly, functionalized proline residues were inserted at P2 to stabilize the β-turn like bioactive conformation, modulating the affinity. The most potent compounds displayed low/sub-nM potency against the 3CLpro of SARS-CoV-2 and MERS-CoV and inhibited viral replication of three human CoVs, i.e. SARS-CoV-2, MERS-CoV, and HCoV 229 in different cell lines. Particularly, derivative 12 exhibited nM-low μM antiviral activity depending on the virus, and the highest selectivity index. Some compounds were co-crystallized with SARS-CoV-2 3CLpro validating our design. Altogether, these results foster future work toward broad-spectrum 3CLpro inhibitors to challenge CoVs related pandemics.
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10
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Cannalire R, Cerchia C, Beccari AR, Di Leva FS, Summa V. Targeting SARS-CoV-2 Proteases and Polymerase for COVID-19 Treatment: State of the Art and Future Opportunities. J Med Chem 2022; 65:2716-2746. [PMID: 33186044 PMCID: PMC7688049 DOI: 10.1021/acs.jmedchem.0c01140] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Indexed: 02/07/2023]
Abstract
The newly emerged coronavirus, called SARS-CoV-2, is the causing pathogen of pandemic COVID-19. The identification of drugs to treat COVID-19 and other coronavirus diseases is an urgent global need, thus different strategies targeting either virus or host cell are still under investigation. Direct-acting agents, targeting protease and polymerase functionalities, represent a milestone in antiviral therapy. The 3C-like (or Main) protease (3CLpro) and the nsp12 RNA-dependent RNA-polymerase (RdRp) are the best characterized SARS-CoV-2 targets and show the highest degree of conservation across coronaviruses fostering the identification of broad-spectrum inhibitors. Coronaviruses also possess a papain-like protease, another essential enzyme, still poorly characterized and not equally conserved, limiting the identification of broad-spectrum agents. Herein, we provide an exhaustive comparative analysis of SARS-CoV-2 proteases and RdRp with respect to other coronavirus homologues. Moreover, we highlight the most promising inhibitors of these proteins reported so far, including the possible strategies for their further development.
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Affiliation(s)
- Rolando Cannalire
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Carmen Cerchia
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | | | - Francesco Saverio Di Leva
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Summa
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
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11
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Abstract
The newly emerged coronavirus, called SARS-CoV-2, is the causing pathogen of pandemic COVID-19. The identification of drugs to treat COVID-19 and other coronavirus diseases is an urgent global need, thus different strategies targeting either virus or host cell are still under investigation. Direct-acting agents, targeting protease and polymerase functionalities, represent a milestone in antiviral therapy. The 3C-like (or Main) protease (3CLpro) and the nsp12 RNA-dependent RNA-polymerase (RdRp) are the best characterized SARS-CoV-2 targets and show the highest degree of conservation across coronaviruses fostering the identification of broad-spectrum inhibitors. Coronaviruses also possess a papain-like protease, another essential enzyme, still poorly characterized and not equally conserved, limiting the identification of broad-spectrum agents. Herein, we provide an exhaustive comparative analysis of SARS-CoV-2 proteases and RdRp with respect to other coronavirus homologues. Moreover, we highlight the most promising inhibitors of these proteins reported so far, including the possible strategies for their further development.
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Affiliation(s)
- Rolando Cannalire
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Carmen Cerchia
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Andrea R Beccari
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Summa
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
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12
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Tomassi S, D’Amore VM, Di Leva FS, Vannini A, Quilici G, Weinmüller M, Reichart F, Amato J, Romano B, Izzo AA, Di Maro S, Novellino E, Musco G, Gianni T, Kessler H, Marinelli L. Halting the Spread of Herpes Simplex Virus-1: The Discovery of an Effective Dual αvβ6/αvβ8 Integrin Ligand. J Med Chem 2021; 64:6972-6984. [PMID: 33961417 PMCID: PMC8279406 DOI: 10.1021/acs.jmedchem.1c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Indexed: 02/08/2023]
Abstract
Over recent years, αvβ6 and αvβ8 Arg-Gly-Asp (RGD) integrins have risen to prominence as interchangeable co-receptors for the cellular entry of herpes simplex virus-1 (HSV-1). In fact, the employment of subtype-specific integrin-neutralizing antibodies or gene-silencing siRNAs has emerged as a valuable strategy for impairing HSV infectivity. Here, we shift the focus to a more affordable pharmaceutical approach based on small RGD-containing cyclic pentapeptides. Starting from our recently developed αvβ6-preferential peptide [RGD-Chg-E]-CONH2 (1), a small library of N-methylated derivatives (2-6) was indeed synthesized in the attempt to increase its affinity toward αvβ8. Among the novel compounds, [RGD-Chg-(NMe)E]-CONH2 (6) turned out to be a potent αvβ6/αvβ8 binder and a promising inhibitor of HSV entry through an integrin-dependent mechanism. Furthermore, the renewed selectivity profile of 6 was fully rationalized by a NMR/molecular modeling combined approach, providing novel valuable hints for the design of RGD integrin ligands with the desired specificity profile.
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Affiliation(s)
- Stefano Tomassi
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Vincenzo Maria D’Amore
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Francesco Saverio Di Leva
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Andrea Vannini
- Department
of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
| | - Giacomo Quilici
- Biomolecular
NMR Unit c/o IRCCS S. Raffaele, Via Olgettina 58, 20132 Milano, Italy
| | - Michael Weinmüller
- Institute
for Advanced Study, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Florian Reichart
- Institute
for Advanced Study, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Jussara Amato
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Barbara Romano
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Angelo Antonio Izzo
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Salvatore Di Maro
- DiSTABiF, University of Campania
“Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
- Facoltà
di Medicina e Chirurgia, Università
Cattolica del Sacro Cuore, Largo Francesco Vito, 1, 00168 Roma, Italy
| | - Giovanna Musco
- Biomolecular
NMR Unit c/o IRCCS S. Raffaele, Via Olgettina 58, 20132 Milano, Italy
| | - Tatiana Gianni
- Department
of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
| | - Horst Kessler
- Institute
for Advanced Study, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Luciana Marinelli
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
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13
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Ludwig BS, Tomassi S, Di Maro S, Di Leva FS, Benge A, Reichart F, Nieberler M, Kühn FE, Kessler H, Marinelli L, Reuning U, Kossatz S. The organometallic ferrocene exhibits amplified anti-tumor activity by targeted delivery via highly selective ligands to αvβ3, αvβ6, or α5β1 integrins. Biomaterials 2021; 271:120754. [PMID: 33756215 DOI: 10.1016/j.biomaterials.2021.120754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/17/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
High levels of reactive oxygen species (ROS) in tumors have been shown to exert anti-tumor activity, leading to the concept of ROS induction as therapeutic strategy. The organometallic compound ferrocene (Fc) generates ROS through a reversible one-electron oxidation. Incorporation of Fc into a tumor-targeting, bioactive molecule can enhance its therapeutic activity and enable tumor specific delivery. Therefore, we conjugated Fc to five synthetic, Arg-Gly-Asp (RGD)-based integrin binding ligands to enable targeting of the cell adhesion and signaling receptor integrin subtypes αvβ3, α5β1, or αvβ6, which are overexpressed in various, distinct tumors. We designed and synthesized a library of integrin-ligand-ferrocene (ILF) derivatives and showed that ILF conjugates maintained the high integrin affinity and selectivity of their parent ligands. A thorough biological characterization allowed us to identify the two most promising ligands, an αvβ3 (L2b) and an αvβ6 (L3b) targeting ILF, which displayed selective integrin-dependent cell uptake and pronounced ferrocene-mediated anti-tumor effects in vitro, along with increased ROS production and DNA damage. Hence, ILFs are promising candidates for the selective, tumor-targeted delivery of ferrocene to maximize its anti-cancer efficacy and minimize systemic toxicity, thereby improving the therapeutic window of ferrocene compared to currently used non-selective anti-cancer drugs.
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Affiliation(s)
- Beatrice Stefanie Ludwig
- Department of Nuclear Medicine, University Hospital Klinikum rechts der Isar, Technical University Munich, Munich, Germany; Central Institute for Translational Cancer Research (TranslaTUM), Technical University of Munich, Munich, Germany
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Salvatore Di Maro
- Università degli Studi della Campania "Luigi Vanvitelli", Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Caserta, Italy
| | | | - Anke Benge
- Department of Obstetrics and Gynecology, Clinical Research Unit, University Hospital Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Florian Reichart
- Institute for Advanced Study, Department of Chemistry, Technical University Munich, Garching, Germany
| | - Markus Nieberler
- Department of Oral and Maxillofacial Surgery, University Hospital Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Fritz E Kühn
- Molecular Catalysis, Catalysis Research Center, Technical University Munich, Munich, Germany; Department of Chemistry, Technical University Munich, Munich, Germany
| | - Horst Kessler
- Institute for Advanced Study, Department of Chemistry, Technical University Munich, Garching, Germany
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Ute Reuning
- Department of Obstetrics and Gynecology, Clinical Research Unit, University Hospital Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Susanne Kossatz
- Department of Nuclear Medicine, University Hospital Klinikum rechts der Isar, Technical University Munich, Munich, Germany; Central Institute for Translational Cancer Research (TranslaTUM), Technical University of Munich, Munich, Germany; Department of Chemistry, Technical University Munich, Munich, Germany.
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14
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Tomassi S, Trotta AM, Ieranò C, Merlino F, Messere A, Rea G, Santoro F, Brancaccio D, Carotenuto A, D'Amore VM, Di Leva FS, Novellino E, Cosconati S, Marinelli L, Scala S, Di Maro S. Disulfide Bond Replacement with 1,4‐ and 1,5‐Disubstituted [1,2,3]‐Triazole on C‐X‐C Chemokine Receptor Type 4 (CXCR4) Peptide Ligands: Small Changes that Make Big Differences. Chemistry 2020; 26:10113-10125. [DOI: 10.1002/chem.202002468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/29/2020] [Indexed: 01/10/2023]
Affiliation(s)
- Stefano Tomassi
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Anna Maria Trotta
- U.O.C. “Bersagli molecolari del microambiente” Istituto Nazionale Tumori—IRCCS—Fondazione “G. Pascale” Via M. Semmola 80131 Naples Italy
| | - Caterina Ieranò
- U.O.C. “Bersagli molecolari del microambiente” Istituto Nazionale Tumori—IRCCS—Fondazione “G. Pascale” Via M. Semmola 80131 Naples Italy
| | - Francesco Merlino
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Anna Messere
- DiSTABiF University of Campania “Luigi Vanvitelli” Via Vivaldi 43 81100 Caserta Italy
| | - Giuseppina Rea
- U.O.C. “Bersagli molecolari del microambiente” Istituto Nazionale Tumori—IRCCS—Fondazione “G. Pascale” Via M. Semmola 80131 Naples Italy
| | - Federica Santoro
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Diego Brancaccio
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Alfonso Carotenuto
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Ettore Novellino
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Sandro Cosconati
- DiSTABiF University of Campania “Luigi Vanvitelli” Via Vivaldi 43 81100 Caserta Italy
| | - Luciana Marinelli
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Stefania Scala
- U.O.C. “Bersagli molecolari del microambiente” Istituto Nazionale Tumori—IRCCS—Fondazione “G. Pascale” Via M. Semmola 80131 Naples Italy
| | - Salvatore Di Maro
- DiSTABiF University of Campania “Luigi Vanvitelli” Via Vivaldi 43 81100 Caserta Italy
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15
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Marino SD, Finamore C, Biagioli M, Carino A, Marchianò S, Roselli R, Giorgio CD, Bordoni M, Di Leva FS, Novellino E, Cassiano C, Limongelli V, Zampella A, Festa C, Fiorucci S. GPBAR1 Activation by C6-Substituted Hyodeoxycholane Analogues Protect against Colitis. ACS Med Chem Lett 2020; 11:818-824. [PMID: 32435390 DOI: 10.1021/acsmedchemlett.9b00636] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/02/2020] [Indexed: 12/14/2022] Open
Abstract
GPBAR1 agonists have been identified as potential leads for the treatment of diseases related to colon inflammation such as Crohn's and ulcerative colitis. In this paper, we report the discovery of a small library of hyodeoxycholane analogues, decorated at C-6 with different substituents, as potent and selective GPBAR1 agonists. In vitro pharmacological assays showed that compound 6 selectively activates GPBAR1 (EC50 = 0.3 μM) and reduces the production of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α) in THP1 cells. The binding mode of compound 6 in GPBAR1 was elucidated by docking calculations. Moreover, compound 6 protects against TNBS-induced colitis in Gpbar1+/+ rodent model, representing an intriguing lead for the treatment of these inflammatory disorders.
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Affiliation(s)
- Simona De Marino
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Claudia Finamore
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Michele Biagioli
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia CH-6900, Italy
| | - Adriana Carino
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia CH-6900, Italy
| | - Silvia Marchianò
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia CH-6900, Italy
| | - Rosalinda Roselli
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Cristina Di Giorgio
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia CH-6900, Italy
| | - Martina Bordoni
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia CH-6900, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Chiara Cassiano
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
- Faculty of Biomedical Sciences, Institute of Computational Science, Center for Computational Medicine in Cardiology, Università della Svizzera italiana (USI), Via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Angela Zampella
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Carmen Festa
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Stefano Fiorucci
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia CH-6900, Italy
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16
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D’Annessa I, Di Leva FS, La Teana A, Novellino E, Limongelli V, Di Marino D. Bioinformatics and Biosimulations as Toolbox for Peptides and Peptidomimetics Design: Where Are We? Front Mol Biosci 2020; 7:66. [PMID: 32432124 PMCID: PMC7214840 DOI: 10.3389/fmolb.2020.00066] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Peptides and peptidomimetics are strongly re-emerging as amenable candidates in the development of therapeutic strategies against a plethora of pathologies. In particular, these molecules are extremely suitable to treat diseases in which a major role is played by protein-protein interactions (PPIs). Unlike small organic compounds, peptides display both a high degree of specificity avoiding secondary off-targets effects and a relatively low degree of toxicity. Further advantages are provided by the possibility to easily conjugate peptides to functionalized nanoparticles, so improving their delivery and cellular uptake. In many cases, such molecules need to assume a specific three-dimensional conformation that resembles the bioactive one of the endogenous ligand. To this end, chemical modifications are introduced in the polypeptide chain to constrain it in a well-defined conformation, and to improve the drug-like properties. In this context, a successful strategy for peptide/peptidomimetics design and optimization is to combine different computational approaches ranging from structural bioinformatics to atomistic simulations. Here, we review the computational tools for peptide design, highlighting their main features and differences, and discuss selected protocols, among the large number of methods available, used to assess and improve the stability of the functional folding of the peptides. Finally, we introduce the simulation techniques employed to predict the binding affinity of the designed peptides for their targets.
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Affiliation(s)
- Ilda D’Annessa
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milan, Italy
| | | | - Anna La Teana
- Department of Life and Environmental Sciences, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
- Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
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17
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D'Aria F, D'Amore VM, Di Leva FS, Amato J, Caterino M, Russomanno P, Salerno S, Barresi E, De Leo M, Marini AM, Taliani S, Da Settimo F, Salgado GF, Pompili L, Zizza P, Shirasawa S, Novellino E, Biroccio A, Marinelli L, Giancola C. Targeting the KRAS oncogene: Synthesis, physicochemical and biological evaluation of novel G-Quadruplex DNA binders. Eur J Pharm Sci 2020; 149:105337. [PMID: 32311457 DOI: 10.1016/j.ejps.2020.105337] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
The oncogene KRAS is involved in the pathogenesis of many tumors such as pancreatic, lung and colorectal cancers, thereby representing a relevant target for the treatment of these diseases. The KRAS P1 promoter contains a nuclease hypersensitive, guanine-rich sequence able to fold into a G-quadruplex motif (G4). The stabilization of this G4 structure by small molecules is emerging as a feasible approach to downregulate KRAS expression. Here, a set of novel stabilizing molecules was identified through a virtual screening campaign on the NMR structure of the 22-mer KRAS G4. The most promising hits were then submitted to structure-activity relationships studies which allowed improving their binding affinity and selectivity over double helix DNA and different G4 topologies. The best derivative (19) underwent fluorescence titration experiments and further computational studies to disclose its binding mechanism to KRAS G4. Finally, biological assays showed that this compound is capable to reduce the viability of colorectal cancer cells in which mutated KRAS acts as a driver oncogene. Thus, 19 might represent the prototype of a new class of drugs for the treatment of tumors that, expressing mutated forms of KRAS, are refractory to current therapeutic regimens.
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Affiliation(s)
- Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | | | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Marco Caterino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Pasquale Russomanno
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Silvia Salerno
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Elisabetta Barresi
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Marinella De Leo
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Anna Maria Marini
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Sabrina Taliani
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Federico Da Settimo
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Gilmar F Salgado
- ARNA Laboratory, IECB, University of Bordeaux, Inserm U1212, CNRS UMR 5320, F-33600 Pessac, France
| | - Luca Pompili
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Senji Shirasawa
- Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy.
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18
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Esposito F, Sechi M, Pala N, Sanna A, Koneru PC, Kvaratskhelia M, Naesens L, Corona A, Grandi N, di Santo R, D'Amore VM, Di Leva FS, Novellino E, Cosconati S, Tramontano E. Discovery of dihydroxyindole-2-carboxylic acid derivatives as dual allosteric HIV-1 Integrase and Reverse Transcriptase associated Ribonuclease H inhibitors. Antiviral Res 2019; 174:104671. [PMID: 31812637 DOI: 10.1016/j.antiviral.2019.104671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 10/25/2022]
Abstract
The management of Human Immunodeficiency Virus type 1 (HIV-1) infection requires life-long treatment that is associated with chronic toxicity and possible selection of drug-resistant strains. A new opportunity for drug intervention is offered by antivirals that act as allosteric inhibitors targeting two viral functions (dual inhibitors). In this work, we investigated the effects of 5,6-dihydroxyindole-2-carboxylic acid (DHICA) derivatives on both HIV-1 Integrase (IN) and Reverse Transcriptase associated Ribonuclease H (RNase H) activities. Among the tested compounds, the dihydroxyindole-carboxamide 5 was able to inhibit in the low micromolar range (1-18 μM) multiple functions of IN, including functional IN-IN interactions, IN-LEDGF/p75 binding and IN catalytic activity. Docking and site-directed mutagenesis studies have suggested that compound 5 binds to a previously described HIV-1 IN allosteric pocket. These observations indicate that 5 is structurally and mechanistically distinct from the published allosteric HIV-1 IN inhibitors. Moreover, compound 5 also inhibited HIV-1 RNase H function, classifying this molecule as a dual HIV-1 IN and RNase H inhibitor able to impair the HIV-1 virus replication in cell culture. Overall, we identified a new scaffold as a suitable platform for the development of novel dual HIV-1 inhibitors.
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Affiliation(s)
- Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy.
| | - Mario Sechi
- Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Nicolino Pala
- Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Adele Sanna
- Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Pratibha Chowdary Koneru
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, B-3000, Leuven, Belgium
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy
| | - Roberto di Santo
- Department of Drug Chemistry and Technologies, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Roma, Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | | | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi Vanvitelli, Via Vivaldi, 43, 81100, Caserta, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy
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19
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Festa C, Finamore C, Marchianò S, Di Leva FS, Carino A, Monti MC, del Gaudio F, Ceccacci S, Limongelli V, Zampella A, Fiorucci S, De Marino S. Investigation around the Oxadiazole Core in the Discovery of a New Chemotype of Potent and Selective FXR Antagonists. ACS Med Chem Lett 2019; 10:504-510. [PMID: 30996787 DOI: 10.1021/acsmedchemlett.8b00534] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/08/2019] [Indexed: 01/07/2023] Open
Abstract
Recent findings have shown that Farnesoid X Receptor (FXR) antagonists might be useful in the treatment of cholestasis and related metabolic disorders. In this paper, we report the discovery of a new chemotype of FXR antagonists featured by a 3,5-disubstituted oxadiazole core. In total, 35 new derivatives were designed and synthesized, and notably, compounds 3f and 13, containing a piperidine ring, displayed the best antagonistic activity against FXR with promising cellular potency (IC50 = 0.58 ± 0.27 and 0.127 ± 0.02 μM, respectively). The excellent pharmacokinetic properties make compound 3f the most promising lead identified in this study.
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Affiliation(s)
- Carmen Festa
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, Naples 80131, Italy
| | - Claudia Finamore
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, Naples 80131, Italy
| | - Silvia Marchianò
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia 06132, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, Naples 80131, Italy
| | - Adriana Carino
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia 06132, Italy
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, Fisciano, Salerno 84084, Italy
| | - Federica del Gaudio
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, Fisciano, Salerno 84084, Italy
| | - Sara Ceccacci
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, Fisciano, Salerno 84084, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, Naples 80131, Italy
- Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology, Università della Svizzera italiana (USI), Via G. Buffi 13, Lugano CH-6900, Switzerland
| | - Angela Zampella
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, Naples 80131, Italy
| | - Stefano Fiorucci
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia 06132, Italy
| | - Simona De Marino
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, Naples 80131, Italy
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20
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Sepe V, Marchianò S, Finamore C, Baronissi G, Di Leva FS, Carino A, Biagioli M, Fiorucci C, Cassiano C, Monti MC, del Gaudio F, Novellino E, Limongelli V, Fiorucci S, Zampella A. Novel Isoxazole Derivatives with Potent FXR Agonistic Activity Prevent Acetaminophen-Induced Liver Injury. ACS Med Chem Lett 2019; 10:407-412. [PMID: 30996771 DOI: 10.1021/acsmedchemlett.8b00423] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/06/2018] [Indexed: 12/24/2022] Open
Abstract
Acetaminophen misuse is a leading cause of acute liver failure and liver transplantation for which therapy is poorly effective. FXR ligands have shown effective in reducing liver injury in several experimental and clinical settings. In this Letter, we have elaborated on the structure of GW4064, the first nonsteroidal agonist for FXR, to identify novel isoxazoles endowed with FXR agonistic activity and improved ADME properties. The pharmacological characterization and molecular docking studies for the structure-activity rationalization allowed the identification of several FXR agonists with nanomolar potency in transactivation and SRC-1 recruitment assays. This characterization resulted in the identification of a potent FXR agonist, compound 20 that was orally active, and rescued mice from acute liver failure caused by acetaminophen overdose in a FXR-dependent manner.
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Affiliation(s)
- Valentina Sepe
- Department of Pharmacy, University of Naples “Federico II”, via D. Montesano 49, 80131 Naples, Italy
| | - Silvia Marchianò
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia, Italy
| | - Claudia Finamore
- Department of Pharmacy, University of Naples “Federico II”, via D. Montesano 49, 80131 Naples, Italy
| | - Giuliana Baronissi
- Department of Pharmacy, University of Naples “Federico II”, via D. Montesano 49, 80131 Naples, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples “Federico II”, via D. Montesano 49, 80131 Naples, Italy
| | - Adriana Carino
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia, Italy
| | - Michele Biagioli
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia, Italy
| | - Chiara Fiorucci
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia, Italy
| | - Chiara Cassiano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Federica del Gaudio
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples “Federico II”, via D. Montesano 49, 80131 Naples, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples “Federico II”, via D. Montesano 49, 80131 Naples, Italy
- Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology, Via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Stefano Fiorucci
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Perugia, Italy
| | - Angela Zampella
- Department of Pharmacy, University of Naples “Federico II”, via D. Montesano 49, 80131 Naples, Italy
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21
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Finamore C, Baronissi G, Marchianò S, Di Leva FS, Carino A, Monti MC, Limongelli V, Zampella A, Fiorucci S, Sepe V. Introduction of Nonacidic Side Chains on 6-Ethylcholane Scaffolds in the Identification of Potent Bile Acid Receptor Agonists with Improved Pharmacokinetic Properties. Molecules 2019; 24:E1043. [PMID: 30884797 PMCID: PMC6470523 DOI: 10.3390/molecules24061043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 01/09/2023] Open
Abstract
As a cellular bile acid sensor, farnesoid X receptor (FXR) and the membrane G-coupled receptor (GPBAR1) participate in maintaining bile acid, lipid, and glucose homeostasis. To date, several selective and dual agonists have been developed as promising pharmacological approach to metabolic disorders, with most of them possessing an acidic conjugable function that might compromise their pharmacokinetic distribution. Here, guided by docking calculations, nonacidic 6-ethyl cholane derivatives have been prepared. In vitro pharmacological characterization resulted in the identification of bile acid receptor modulators with improved pharmacokinetic properties.
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Affiliation(s)
- Claudia Finamore
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Naples, Italy.
| | - Giuliana Baronissi
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Naples, Italy.
| | - Silvia Marchianò
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Piazza Lucio Severi, 1 - 06132 Perugia, Italy.
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Naples, Italy.
| | - Adriana Carino
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Piazza Lucio Severi, 1 - 06132 Perugia, Italy.
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy.
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Naples, Italy.
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology, Via G. Buffi 13, CH-6900 Lugano, Switzerland.
| | - Angela Zampella
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Naples, Italy.
| | - Stefano Fiorucci
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, Piazza Lucio Severi, 1 - 06132 Perugia, Italy.
| | - Valentina Sepe
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Naples, Italy.
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22
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Reichart F, Maltsev OV, Kapp TG, Räder AFB, Weinmüller M, Marelli UK, Notni J, Wurzer A, Beck R, Wester HJ, Steiger K, Di Maro S, Di Leva FS, Marinelli L, Nieberler M, Reuning U, Schwaiger M, Kessler H. Selective Targeting of Integrin αvβ8 by a Highly Active Cyclic Peptide. J Med Chem 2019; 62:2024-2037. [DOI: 10.1021/acs.jmedchem.8b01588] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Florian Reichart
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Oleg V. Maltsev
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Tobias G. Kapp
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Andreas F. B. Räder
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Michael Weinmüller
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Udaya Kiran Marelli
- Central NMR Facility and Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
| | - Johannes Notni
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Alexander Wurzer
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Roswitha Beck
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Hans-Jürgen Wester
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Katja Steiger
- Department of Pathology, Technische Universität München, Trogerstraße 18, 81675 München, Germany
| | - Salvatore Di Maro
- DiSTABiF, Università degli Studi della Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Francesco Saverio Di Leva
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Markus Nieberler
- Department of Oral and Maxillofacial Surgery, University Hospital Rechts der Isar, Technische Universität München, Ismaninger Straße 22, 81679 München, Germany
| | | | | | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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23
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Abstract
In this chapter we provide an exhaustive overview of the binding modes of bile acid (BA) and non-BA ligands to the nuclear farnesoid X receptor (FXR) and the G-protein bile acid receptor 1 (GPBAR1). These two receptors play a key role in many diseases related to lipid and glucose disorders, thus representing promising pharmacological targets. We pay particular attention to the chemical and structural features of the ligand-receptor interaction, providing guidelines to achieve ligands endowed with selective or dual activity towards the receptor and paving the way to future drug design studies.
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Affiliation(s)
| | - Daniele Di Marino
- Faculty of Biomedical Sciences, Institute of Computational Science, Center for Computational Medicine in Cardiology, Università della Svizzera italiana (USI), Lugano, Switzerland.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy. .,Faculty of Biomedical Sciences, Institute of Computational Science, Center for Computational Medicine in Cardiology, Università della Svizzera italiana (USI), Lugano, Switzerland.
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24
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Merlino F, Daniele S, La Pietra V, Di Maro S, Di Leva FS, Brancaccio D, Tomassi S, Giuntini S, Cerofolini L, Fragai M, Luchinat C, Reichart F, Cavallini C, Costa B, Piccarducci R, Taliani S, Da Settimo F, Martini C, Kessler H, Novellino E, Marinelli L. Simultaneous Targeting of RGD-Integrins and Dual Murine Double Minute Proteins in Glioblastoma Multiforme. J Med Chem 2018; 61:4791-4809. [PMID: 29775303 DOI: 10.1021/acs.jmedchem.8b00004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In the fight against Glioblastoma Multiforme, recent literature data have highlighted that integrin α5β1 and p53 are part of convergent pathways in the control of glioma apoptosis. This observation prompted us to seek a molecule able to simultaneously modulate both target families. Analyzing the results of a previous virtual screening against murine double minute 2 protein (MDM2), we envisaged that Arg-Gly-Asp (RGD)-mimetic molecules could be inhibitors of MDM2/4. Herein, we present the discovery of compound 7, which inhibits both MDM2/4 and α5β1/αvβ3 integrins. A lead optimization campaign was carried out on 7 with the aim to preserve the activities on integrins while improving those on MDM proteins. Compound 9 turned out to be a potent MDM2/4 and α5β1/αvβ3 blocker. In p53-wild type glioma cells, 9 arrested cell cycle and proliferation and strongly reduced cell invasiveness, emerging as the first molecule of a novel class of integrin/MDM inhibitors, which might be especially useful in subpopulations of patients with glioblastoma expressing a functional p53 concomitantly with a high level of α5β1 integrin.
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Affiliation(s)
- Francesco Merlino
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , via D. Montesano 49 , 80131 Napoli , Italy
| | - Simona Daniele
- Dipartimento di Farmacia , Università di Pisa , via Bonanno 6 , 56126 Pisa , Italy
| | - Valeria La Pietra
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , via D. Montesano 49 , 80131 Napoli , Italy
| | - Salvatore Di Maro
- DiSTABiF , Università degli Studi della Campania "Luigi Vanvitelli" , via Vivaldi 43 , 81100 Caserta , Italy
| | - Francesco Saverio Di Leva
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , via D. Montesano 49 , 80131 Napoli , Italy
| | - Diego Brancaccio
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , via D. Montesano 49 , 80131 Napoli , Italy
| | - Stefano Tomassi
- DiSTABiF , Università degli Studi della Campania "Luigi Vanvitelli" , via Vivaldi 43 , 81100 Caserta , Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM) University of Florence , via L. Sacconi 6 , 50019 Sesto Fiorentino ( FI ), Italy.,Department of Chemistry "Ugo Schiff" , University of Florence , via della Lastruccia 3-13 , 50019 Sesto Fiorentino ( FI ), Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM) University of Florence , via L. Sacconi 6 , 50019 Sesto Fiorentino ( FI ), Italy.,Department of Chemistry "Ugo Schiff" , University of Florence , via della Lastruccia 3-13 , 50019 Sesto Fiorentino ( FI ), Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) University of Florence , via L. Sacconi 6 , 50019 Sesto Fiorentino ( FI ), Italy.,Department of Chemistry "Ugo Schiff" , University of Florence , via della Lastruccia 3-13 , 50019 Sesto Fiorentino ( FI ), Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) University of Florence , via L. Sacconi 6 , 50019 Sesto Fiorentino ( FI ), Italy.,Department of Chemistry "Ugo Schiff" , University of Florence , via della Lastruccia 3-13 , 50019 Sesto Fiorentino ( FI ), Italy
| | - Florian Reichart
- Institute for Advanced Study and Center for Integrated Protein Science, Department of Chemistry , Technische Universität München , Lichtenbergstr. 4 , 85747 Garching , Germany
| | - Chiara Cavallini
- Dipartimento di Farmacia , Università di Pisa , via Bonanno 6 , 56126 Pisa , Italy
| | - Barbara Costa
- Dipartimento di Farmacia , Università di Pisa , via Bonanno 6 , 56126 Pisa , Italy
| | - Rebecca Piccarducci
- Dipartimento di Farmacia , Università di Pisa , via Bonanno 6 , 56126 Pisa , Italy
| | - Sabrina Taliani
- Dipartimento di Farmacia , Università di Pisa , via Bonanno 6 , 56126 Pisa , Italy
| | - Federico Da Settimo
- Dipartimento di Farmacia , Università di Pisa , via Bonanno 6 , 56126 Pisa , Italy
| | - Claudia Martini
- Dipartimento di Farmacia , Università di Pisa , via Bonanno 6 , 56126 Pisa , Italy
| | - Horst Kessler
- Institute for Advanced Study and Center for Integrated Protein Science, Department of Chemistry , Technische Universität München , Lichtenbergstr. 4 , 85747 Garching , Germany
| | - Ettore Novellino
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , via D. Montesano 49 , 80131 Napoli , Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , via D. Montesano 49 , 80131 Napoli , Italy
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25
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Brancaccio D, Diana D, Di Maro S, Di Leva FS, Tomassi S, Fattorusso R, Russo L, Scala S, Trotta AM, Portella L, Novellino E, Marinelli L, Carotenuto A. Ligand-Based NMR Study of C-X-C Chemokine Receptor Type 4 (CXCR4)–Ligand Interactions on Living Cancer Cells. J Med Chem 2018. [DOI: 10.1021/acs.jmedchem.7b01830] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Diego Brancaccio
- Dipartimento di Farmacia, Università di Napoli Federico II, 80131 Naples, Italy
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, C.N.R., 80134 Naples, Italy
| | - Salvatore Di Maro
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | | | - Stefano Tomassi
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Stefania Scala
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy
| | - Anna Maria Trotta
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy
| | - Luigi Portella
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli Federico II, 80131 Naples, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università di Napoli Federico II, 80131 Naples, Italy
| | - Alfonso Carotenuto
- Dipartimento di Farmacia, Università di Napoli Federico II, 80131 Naples, Italy
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26
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Kapp TG, Di Leva FS, Notni J, Räder AFB, Fottner M, Reichart F, Reich D, Wurzer A, Steiger K, Novellino E, Marelli UK, Wester HJ, Marinelli L, Kessler H. N-Methylation of isoDGR Peptides: Discovery of a Selective α5β1-Integrin Ligand as a Potent Tumor Imaging Agent. J Med Chem 2018; 61:2490-2499. [DOI: 10.1021/acs.jmedchem.7b01752] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Tobias G. Kapp
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Francesco Saverio Di Leva
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Johannes Notni
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Andreas F. B. Räder
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Maximilian Fottner
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Florian Reichart
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Dominik Reich
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Alexander Wurzer
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Katja Steiger
- Department of Pathology, Technische Universität München, Trogerstraße 18, 81675 München, Germany
| | - Ettore Novellino
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Udaya Kiran Marelli
- Central NMR Facility and Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
| | - Hans-Jürgen Wester
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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27
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Weinmüller M, Rechenmacher F, Kiran Marelli U, Reichart F, Kapp TG, Räder AFB, Di Leva FS, Marinelli L, Novellino E, Muñoz-Félix JM, Hodivala-Dilke K, Schumacher A, Fanous J, Gilon C, Hoffman A, Kessler H. Overcoming the Lack of Oral Availability of Cyclic Hexapeptides: Design of a Selective and Orally Available Ligand for the Integrin αvβ3. Angew Chem Int Ed Engl 2017; 56:16405-16409. [PMID: 29072809 DOI: 10.1002/anie.201709709] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/24/2017] [Indexed: 11/12/2022]
Abstract
A highly systematic approach for the development of both orally bioavailable and bioactive cyclic N-methylated hexapeptides as high affinity ligands for the integrin αvβ3 is based on two concepts: a) screening of systematically designed libraries with spatial diversity and b) masking of the peptide charge with a lipophilic protecting group. The key steps of the method are 1) initial design of a combinatorial library of N-methylated analogues of the stem peptide cyclo(d-Ala-Ala5 ); 2) selection of cyclic peptides with the highest intestinal permeability; 3) design of sublibraries with the bioactive RGD sequence in all possible positions; 4) selection of the best ligands for RGD-recognizing integrin subtypes; 5) fine-tuning of the affinity and selectivity by additional Ala to Xaa substitutions; 6) protection of the charged functional groups according to the prodrug concept to regain intestinal and oral permeability; 7) proof of biological effects in mice after oral administration.
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Affiliation(s)
- Michael Weinmüller
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Florian Rechenmacher
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Udaya Kiran Marelli
- Central NMR Facility and Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India
| | - Florian Reichart
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Tobias G Kapp
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Andreas F B Räder
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | | | - Luciana Marinelli
- Dipartimento di Farmacia, Università di Napoli Federico II, Napoli, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli Federico II, Napoli, Italy
| | - José M Muñoz-Félix
- Centre for Tumour Biology, Barts Cancer Institute, -, Queen Mary University of London, John Vane Science Centre, Londonn, UK
| | - Kairbaan Hodivala-Dilke
- Centre for Tumour Biology, Barts Cancer Institute, -, Queen Mary University of London, John Vane Science Centre, Londonn, UK
| | - Adi Schumacher
- Institutes of Chemistry and Drug Research, The Hebrew University of Jerusalem, Israel
| | - Joseph Fanous
- Institutes of Chemistry and Drug Research, The Hebrew University of Jerusalem, Israel
| | - Chaim Gilon
- Institutes of Chemistry and Drug Research, The Hebrew University of Jerusalem, Israel
| | - Amnon Hoffman
- Institutes of Chemistry and Drug Research, The Hebrew University of Jerusalem, Israel
| | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
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28
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Di Maro S, Di Leva FS, Trotta AM, Brancaccio D, Portella L, Aurilio M, Tomassi S, Messere A, Sementa D, Lastoria S, Carotenuto A, Novellino E, Scala S, Marinelli L. Structure–Activity Relationships and Biological Characterization of a Novel, Potent, and Serum Stable C-X-C Chemokine Receptor Type 4 (CXCR4) Antagonist. J Med Chem 2017; 60:9641-9652. [DOI: 10.1021/acs.jmedchem.7b01062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Salvatore Di Maro
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Caserta 81100, Italy
| | - Francesco Saverio Di Leva
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Anna Maria Trotta
- Functional
Genomics Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori “Fondazione Giovanni Pascale”, IRCCS, Via M. Semmola 52, 80131 Naples, Italy
| | - Diego Brancaccio
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Luigi Portella
- Functional
Genomics Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori “Fondazione Giovanni Pascale”, IRCCS, Via M. Semmola 52, 80131 Naples, Italy
| | - Michela Aurilio
- Nuclear
Medicine Unit, Department of Diagnostic Imaging, Radiant and Metabolic
Therapy, Istituto Nazionale per lo Studio e la Cura dei Tumori “Fondazione Giovanni Pascale”, IRCCS, Via M. Semmola
52, 80131 Naples, Italy
| | - Stefano Tomassi
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Caserta 81100, Italy
| | - Anna Messere
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Caserta 81100, Italy
| | - Deborah Sementa
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Secondo Lastoria
- Nuclear
Medicine Unit, Department of Diagnostic Imaging, Radiant and Metabolic
Therapy, Istituto Nazionale per lo Studio e la Cura dei Tumori “Fondazione Giovanni Pascale”, IRCCS, Via M. Semmola
52, 80131 Naples, Italy
| | - Alfonso Carotenuto
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Ettore Novellino
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Stefania Scala
- Functional
Genomics Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori “Fondazione Giovanni Pascale”, IRCCS, Via M. Semmola 52, 80131 Naples, Italy
| | - Luciana Marinelli
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
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29
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Salvati E, Botta L, Amato J, Di Leva FS, Zizza P, Gioiello A, Pagano B, Graziani G, Tarsounas M, Randazzo A, Novellino E, Biroccio A, Cosconati S. Lead Discovery of Dual G-Quadruplex Stabilizers and Poly(ADP-ribose) Polymerases (PARPs) Inhibitors: A New Avenue in Anticancer Treatment. J Med Chem 2017; 60:3626-3635. [PMID: 28445046 DOI: 10.1021/acs.jmedchem.6b01563] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
G-quadruplex stabilizers are an established opportunity in anticancer chemotherapy. To circumvent the antiproliferative effects of G4 ligands, cancer cells recruit PARP enzymes at telomeres. Herein, starting from the structural similarity of a potent G4 ligand previously discovered by our group and a congeneric PARP inhibitor, a library of derivatives was synthesized to discover the first dual G4/PARP ligand. We demonstrate that a properly decorated thieno[3,2-c]quinolin-4(5H)-one stabilizes the G4 fold in vitro and in cells, induces a DNA damage response localized to telomeres, inhibits PARylation in cells, and has an antiproliferative effect in BRCA2 deficient tumor cells.
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Affiliation(s)
- Erica Salvati
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute , 00158 Rome, Italy
| | - Lorenzo Botta
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | | | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute , 00158 Rome, Italy
| | - Antimo Gioiello
- Department of Pharmaceutical Science, University of Perugia , I-06123 Perugia, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Grazia Graziani
- Department of Systems Medicine, University of "Tor Vergata" , 00173 Rome, Italy
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford , Old Road Campus Research Building, Oxford OX3 7DQ, U.K
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute , 00158 Rome, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi Vanvitelli , 81100 Caserta, Italy
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30
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De Marino S, Carino A, Masullo D, Finamore C, Sepe V, Marchianò S, Di Leva FS, Limongelli V, Fiorucci S, Zampella A. Epoxide functionalization on cholane side chains in the identification of G-protein coupled bile acid receptor (GPBAR1) selective agonists. RSC Adv 2017. [DOI: 10.1039/c7ra04922f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Decoration of the bile acid side chain with an epoxide ring afforded potent and selective GPBAR1 agonists.
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Affiliation(s)
- Simona De Marino
- Department of Pharmacy
- University of Naples “Federico II”
- Naples
- Italy
| | - Adriana Carino
- Department of Surgery and Biomedical Sciences
- Nuova Facoltà di Medicina
- Perugia
- Italy
| | - Dario Masullo
- Department of Pharmacy
- University of Naples “Federico II”
- Naples
- Italy
| | - Claudia Finamore
- Department of Pharmacy
- University of Naples “Federico II”
- Naples
- Italy
| | - Valentina Sepe
- Department of Pharmacy
- University of Naples “Federico II”
- Naples
- Italy
| | - Silvia Marchianò
- Department of Surgery and Biomedical Sciences
- Nuova Facoltà di Medicina
- Perugia
- Italy
| | | | - Vittorio Limongelli
- Department of Pharmacy
- University of Naples “Federico II”
- Naples
- Italy
- Università della Svizzera Italiana (USI)
| | - Stefano Fiorucci
- Department of Surgery and Biomedical Sciences
- Nuova Facoltà di Medicina
- Perugia
- Italy
| | - Angela Zampella
- Department of Pharmacy
- University of Naples “Federico II”
- Naples
- Italy
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31
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Di Maro S, Trotta AM, Brancaccio D, Di Leva FS, La Pietra V, Ieranò C, Napolitano M, Portella L, D'Alterio C, Siciliano RA, Sementa D, Tomassi S, Carotenuto A, Novellino E, Scala S, Marinelli L. Exploring the N-Terminal Region of C-X-C Motif Chemokine 12 (CXCL12): Identification of Plasma-Stable Cyclic Peptides As Novel, Potent C-X-C Chemokine Receptor Type 4 (CXCR4) Antagonists. J Med Chem 2016; 59:8369-80. [PMID: 27571038 DOI: 10.1021/acs.jmedchem.6b00695] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We previously reported the discovery of a CXCL12-mimetic cyclic peptide (2) as a selective CXCR4 antagonist showing promising in vitro and in vivo anticancer activity. However, further development of this peptide was hampered by its degradation in biological fluids as well as by its low micromolar affinity for the receptor. Herein, extensive chemical modifications led to the development of a new analogue (10) with enhanced potency, specificity, and plasma stability. A combined approach of Ala-amino acid scan, NMR, and molecular modeling unraveled the reasons behind the improved binding properties of 10 vs 2. Biological investigations on leukemia (CEM) and colon (HT29 and HCT116) cancer cell lines showed that 10 is able to impair CXCL12-mediated cell migration, ERK-phosphorylation, and CXCR4 internalization. These outcomes might pave the way for the future preclinical development of 10 in CXCR4 overexpressing leukemia and colon cancer.
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Affiliation(s)
- Salvatore Di Maro
- DiSTABiF, Second University of Naples , Via Vivaldi 43, 81100 Caserta, Italy
| | - Anna Maria Trotta
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione "Giovanni Pascale", IRCCS-ITALY , Via M. Semmola, 80131 Naples, Italy
| | - Diego Brancaccio
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , via D. Montesano 49, 80131 Naples, Italy.,Laboratory of Food Chemistry, Dipartimento di Agraria (QuaSic.A.Tec.), Università Mediterranea di Reggio Calabria , Reggio Calabria, loc. Feo di Vito, 89122 Reggio Calabria, Italy
| | - Francesco Saverio Di Leva
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , via D. Montesano 49, 80131 Naples, Italy
| | - Valeria La Pietra
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , via D. Montesano 49, 80131 Naples, Italy
| | - Caterina Ieranò
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione "Giovanni Pascale", IRCCS-ITALY , Via M. Semmola, 80131 Naples, Italy
| | - Maria Napolitano
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione "Giovanni Pascale", IRCCS-ITALY , Via M. Semmola, 80131 Naples, Italy
| | - Luigi Portella
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione "Giovanni Pascale", IRCCS-ITALY , Via M. Semmola, 80131 Naples, Italy
| | - Crescenzo D'Alterio
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione "Giovanni Pascale", IRCCS-ITALY , Via M. Semmola, 80131 Naples, Italy
| | - Rosa Anna Siciliano
- Istituto di Scienze dell'Alimentazione, CNR , Via Roma 64, 83100 Avellino, Italy
| | - Deborah Sementa
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , via D. Montesano 49, 80131 Naples, Italy
| | - Stefano Tomassi
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , via D. Montesano 49, 80131 Naples, Italy
| | - Alfonso Carotenuto
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , via D. Montesano 49, 80131 Naples, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , via D. Montesano 49, 80131 Naples, Italy
| | - Stefania Scala
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione "Giovanni Pascale", IRCCS-ITALY , Via M. Semmola, 80131 Naples, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , via D. Montesano 49, 80131 Naples, Italy
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32
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Vullo D, Durante M, Di Leva FS, Cosconati S, Masini E, Scozzafava A, Novellino E, Supuran CT, Carta F. Monothiocarbamates Strongly Inhibit Carbonic Anhydrases in Vitro and Possess Intraocular Pressure Lowering Activity in an Animal Model of Glaucoma. J Med Chem 2016; 59:5857-67. [PMID: 27253845 DOI: 10.1021/acs.jmedchem.6b00462] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A series of monothiocarbamates (MTCs) were prepared from primary/secondary amines and COS as potential carbonic anhydrase (CA, EC 4.2.1.1) inhibitors, using the dithiocarbamates, the xanthates, and the trithiocarbonates as lead compounds. The MTCs effectively inhibited the pharmacologically relevant human (h) hCAs isoforms I, II, IX, and XII in vitro and showed KIs spanning between the low and medium nanomolar range. By means of a computational study, the MTC moiety binding mode on the CAs was explained. Furthermore, a selection of MTCs were evaluated in a normotensive glaucoma rabbit model for their intraocular pressure (IOP) lowering effects and showed interesting activity.
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Affiliation(s)
- Daniela Vullo
- Polo Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze , Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Mariaconcetta Durante
- Dipartimento NEUROFARBA, Sezione di Farmacologia, Università degli Studi di Firenze , Viale Pieraccini 6, 50139 Florence, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II" , Via D. Montesano 49, 80131 Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, Seconda Università di Napoli , Via Vivaldi 43, 81100 Caserta, Italy
| | - Emanuela Masini
- Dipartimento NEUROFARBA, Sezione di Farmacologia, Università degli Studi di Firenze , Viale Pieraccini 6, 50139 Florence, Italy
| | - Andrea Scozzafava
- Polo Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze , Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II" , Via D. Montesano 49, 80131 Naples, Italy
| | - Claudiu T Supuran
- Polo Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze , Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.,Dipartimento NEUROFARBA, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze , Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Fabrizio Carta
- Polo Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze , Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
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33
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Hegemann JD, Fage CD, Zhu S, Harms K, Di Leva FS, Novellino E, Marinelli L, Marahiel MA. The ring residue proline 8 is crucial for the thermal stability of the lasso peptide caulosegnin II. Mol BioSyst 2016; 12:1106-9. [DOI: 10.1039/c6mb00081a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lasso peptides are fascinating natural products with a unique structural fold that can exhibit tremendous thermal stability.
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Affiliation(s)
- Julian D. Hegemann
- Department of Chemistry/Biochemistry
- LOEWE Center for Synthetic Microbiology
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Christopher D. Fage
- Department of Chemistry/Biochemistry
- LOEWE Center for Synthetic Microbiology
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Shaozhou Zhu
- Department of Chemistry/Biochemistry
- LOEWE Center for Synthetic Microbiology
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Klaus Harms
- Department of Chemistry/Biochemistry
- LOEWE Center for Synthetic Microbiology
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | | | - Ettore Novellino
- Department of Pharmacy
- Università di Napoli “Federico II”
- 80131 Napoli
- Italy
| | - Luciana Marinelli
- Department of Pharmacy
- Università di Napoli “Federico II”
- 80131 Napoli
- Italy
| | - Mohamed A. Marahiel
- Department of Chemistry/Biochemistry
- LOEWE Center for Synthetic Microbiology
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
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34
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Maltsev OV, Marelli UK, Kapp TG, Di Leva FS, Di Maro S, Nieberler M, Reuning U, Schwaiger M, Novellino E, Marinelli L, Kessler H. Stable Peptides Instead of Stapled Peptides: Highly Potent αvβ6-Selective Integrin Ligands. Angew Chem Int Ed Engl 2015; 55:1535-9. [PMID: 26663660 DOI: 10.1002/anie.201508709] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/26/2015] [Indexed: 12/15/2022]
Abstract
The αvβ6 integrin binds the RGD-containing peptide of the foot and mouth disease virus with high selectivity. In this study, the long binding helix of this ligand was downsized to an enzymatically stable cyclic peptide endowed with sub-nanomolar binding affinity toward the αvβ6 receptor and remarkable selectivity against other integrins. Computational studies were performed to disclose the molecular bases underlying the high binding affinity and receptor subtype selectivity of this peptide. Finally, the utility of the ligand for use in biomedical studies was also demonstrated here.
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Affiliation(s)
- Oleg V Maltsev
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Udaya Kiran Marelli
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Tobias G Kapp
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Francesco Saverio Di Leva
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Salvatore Di Maro
- DiSTABiF, Secondo Università di Napoli, Via Vivaldi 43, 81100, Caserta, Italy
| | - Markus Nieberler
- Department of Oral and Maxillofacial Surgery, University Hospital rechts der Isar, Technische Universität München, Ismaninger Strasse 22, 81675, München, Germany
| | - Ute Reuning
- Klinische Forschergruppe der Frauenklinik, University Hospital rechts der Isar, Technische Universität München, Ismaninger Strasse 22, 81675, München, Germany
| | - Markus Schwaiger
- Department of Nuclear Medicine, University Hospital rechts der Isar, Technische Universität München, Ismaninger Strasse 22, 81675, München, Germany
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Horst Kessler
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany.
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35
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Di Leva FS, Festa C, Renga B, Sepe V, Novellino E, Fiorucci S, Zampella A, Limongelli V. Structure-based drug design targeting the cell membrane receptor GPBAR1: exploiting the bile acid scaffold towards selective agonism. Sci Rep 2015; 5:16605. [PMID: 26567894 PMCID: PMC4645117 DOI: 10.1038/srep16605] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/16/2015] [Indexed: 12/21/2022] Open
Abstract
Bile acids can regulate nutrient metabolism through the activation of the cell membrane receptor GPBAR1 and the nuclear receptor FXR. Developing an exogenous control over these receptors represents an attractive strategy for the treatment of enterohepatic and metabolic disorders. A number of dual GPBAR1/FXR agonists are known, however their therapeutic use is limited by multiple unwanted effects due to activation of the diverse downstream signals controlled by the two receptors. On the other hand, designing selective GPBAR1 and FXR agonists is challenging since the two proteins share similar structural requisites for ligand binding. Here, taking advantage of our knowledge of the two targets, we have identified through a rational drug design study a series of amine lithocholic acid derivatives as selective GPBAR1 agonists. The presence of the 3α-NH2 group on the steroidal scaffold is responsible for the selectivity over FXR unveiling unprecedented structural insights into bile acid receptors activity modulation.
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Affiliation(s)
- Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Carmen Festa
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Barbara Renga
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, P.zza L. Severi, I-06132 Perugia, Italy
| | - Valentina Sepe
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Stefano Fiorucci
- Department of Surgery and Biomedical Sciences, Nuova Facoltà di Medicina, P.zza L. Severi, I-06132 Perugia, Italy
| | - Angela Zampella
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy.,Università della Svizzera Italiana (USI), Faculty of Informatics, Institute of Computational Science, via G. Buffi 13, CH-6900 Lugano, Switzerland
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36
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Cuzzucoli Crucitti G, Pescatori L, Messore A, Madia VN, Pupo G, Saccoliti F, Scipione L, Tortorella S, Di Leva FS, Cosconati S, Novellino E, Debyser Z, Christ F, Costi R, Di Santo R. Discovery of N-aryl-naphthylamines as in vitro inhibitors of the interaction between HIV integrase and the cofactor LEDGF/p75. Eur J Med Chem 2015; 101:288-94. [PMID: 26150289 DOI: 10.1016/j.ejmech.2015.06.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 11/26/2022]
Abstract
A series of N-aryl-naphthylamines, exemplified by the structures 11-16, were chosen for an in-house library screening to assay their ability to disrupt the interaction between the LEDGF cofactor and the HIV integrase. Structure modification led also to design and synthesize new compounds 17a-f. Compounds 11e,h,k,n, 13b, and 14 showed good activity in AlphaScreen assay. The most active compound 11e (IC50 = 2.5 μM) was selected for molecular modeling studies and showed a binding mode similar to the one of the known LEDGIN 8.
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Affiliation(s)
- Giuliana Cuzzucoli Crucitti
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, 00185 Roma, Italy
| | - Luca Pescatori
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, 00185 Roma, Italy
| | - Antonella Messore
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, 00185 Roma, Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, 00185 Roma, Italy
| | - Giovanni Pupo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, 00185 Roma, Italy
| | - Francesco Saccoliti
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, 00185 Roma, Italy
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, 00185 Roma, Italy
| | - Silvano Tortorella
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, 00185 Roma, Italy
| | - Francesco Saverio Di Leva
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Sandro Cosconati
- DiSTABiF, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Zeger Debyser
- Molecular Virology and Gene Therapy, Molecular Medicine Katholieke Universiteit Leuven, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Frauke Christ
- Molecular Virology and Gene Therapy, Molecular Medicine Katholieke Universiteit Leuven, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, 00185 Roma, Italy.
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, 00185 Roma, Italy
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37
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Pescatori L, Métifiot M, Chung S, Masoaka T, Cuzzucoli Crucitti G, Messore A, Pupo G, Madia VN, Saccoliti F, Scipione L, Tortorella S, Di Leva FS, Cosconati S, Marinelli L, Novellino E, Le Grice SFJ, Pommier Y, Marchand C, Costi R, Di Santo R. N-Substituted Quinolinonyl Diketo Acid Derivatives as HIV Integrase Strand Transfer Inhibitors and Their Activity against RNase H Function of Reverse Transcriptase. J Med Chem 2015; 58:4610-23. [PMID: 25961960 DOI: 10.1021/acs.jmedchem.5b00159] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bifunctional quinolinonyl DKA derivatives were first described as nonselective inhibitors of 3'-processing (3'-P) and strand transfer (ST) functions of HIV-1 integrase (IN), while 7-aminosubstituted quinolinonyl derivatives were proven IN strand transfer inhibitors (INSTIs) that also displayed activity against ribonuclease H (RNase H). In this study, we describe the design, synthesis, and biological evaluation of new quinolinonyl diketo acid (DKA) derivatives characterized by variously substituted alkylating groups on the nitrogen atom of the quinolinone ring. Removal of the second DKA branch of bifunctional DKAs, and the amino group in position 7 of quinolinone ring combined with a fine-tuning of the substituents on the benzyl group in position 1 of the quinolinone, increased selectivity for IN ST activity. In vitro, the most potent compound was 11j (IC50 = 10 nM), while the most active compounds against HIV infected cells were ester derivatives 10j and 10l. In general, the activity against RNase H was negligible, with only a few compounds active at concentrations higher than 10 μM. The binding mode of the most potent IN inhibitor 11j within the IN catalytic core domain (CCD) is described as well as its binding mode within the RNase H catalytic site to rationalize its selectivity.
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Affiliation(s)
- Luca Pescatori
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Mathieu Métifiot
- ‡Laboratory of Molecular Pharmacology and Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, Maryland 20892-4255, United States
| | - Suhman Chung
- §Resistance Mechanisms Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Takashi Masoaka
- §Resistance Mechanisms Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Giuliana Cuzzucoli Crucitti
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Antonella Messore
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Giovanni Pupo
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Valentina Noemi Madia
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Francesco Saccoliti
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Luigi Scipione
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Silvano Tortorella
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Francesco Saverio Di Leva
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Sandro Cosconati
- ⊥DiSTABiF, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luciana Marinelli
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Stuart F J Le Grice
- §Resistance Mechanisms Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Yves Pommier
- ‡Laboratory of Molecular Pharmacology and Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, Maryland 20892-4255, United States
| | - Christophe Marchand
- ‡Laboratory of Molecular Pharmacology and Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, Maryland 20892-4255, United States
| | - Roberta Costi
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Roberto Di Santo
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
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38
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Sepe V, Renga B, Festa C, D'Amore C, Masullo D, Cipriani S, Di Leva FS, Monti MC, Novellino E, Limongelli V, Zampella A, Fiorucci S. Modification on ursodeoxycholic acid (UDCA) scaffold. discovery of bile acid derivatives as selective agonists of cell-surface G-protein coupled bile acid receptor 1 (GP-BAR1). J Med Chem 2014; 57:7687-701. [PMID: 25162837 DOI: 10.1021/jm500889f] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bile acids are signaling molecules interacting with the nuclear receptor FXR and the G-protein coupled receptor 1 (GP-BAR1/TGR5). GP-BAR1 is a promising pharmacological target for the treatment of steatohepatitis, type 2 diabetes, and obesity. Endogenous bile acids and currently available semisynthetic bile acids are poorly selective toward GP-BAR1 and FXR. Thus, in the present study we have investigated around the structure of UDCA, a clinically used bile acid devoid of FXR agonist activity, to develop a large family of side chain modified 3α,7β-dihydroxyl cholanoids that selectively activate GP-BAR1. In vivo and in vitro pharmacological evaluation demonstrated that administration of compound 16 selectively increases the expression of pro-glucagon 1, a GP-BAR1 target, in the small intestine, while it had no effect on FXR target genes in the liver. Further, compound 16 results in a significant reshaping of bile acid pool in a rodent model of cholestasis. These data demonstrate that UDCA is a useful scaffold to generate novel and selective steroidal ligands for GP-BAR1.
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Affiliation(s)
- Valentina Sepe
- Department of Pharmacy, University of Naples "Federico II" , Via D. Montesano, 49, 80131 Napoli, Italy
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39
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Hegemann JD, De Simone M, Zimmermann M, Knappe TA, Xie X, Di Leva FS, Marinelli L, Novellino E, Zahler S, Kessler H, Marahiel MA. Rational Improvement of the Affinity and Selectivity of Integrin Binding of Grafted Lasso Peptides. J Med Chem 2014; 57:5829-34. [DOI: 10.1021/jm5004478] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julian D. Hegemann
- Department
of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Mariarosaria De Simone
- Department
of Chemistry, Institute for Advanced Study, Center of Integrated Protein
Science (CIPSM), Technische Universität München, Lichtenbergstrasse
4, 85747 Garching, Germany
- Department
of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Marcel Zimmermann
- Department
of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Thomas A. Knappe
- Department
of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Xiulan Xie
- Department
of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Francesco Saverio Di Leva
- Department
of Pharmacy, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Luciana Marinelli
- Department
of Pharmacy, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- Department
of Pharmacy, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Stefan Zahler
- Department
of Pharmacy, Ludwig Maximilian University, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Horst Kessler
- Department
of Chemistry, Institute for Advanced Study, Center of Integrated Protein
Science (CIPSM), Technische Universität München, Lichtenbergstrasse
4, 85747 Garching, Germany
- Department
of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Mohamed A. Marahiel
- Department
of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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40
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Di Leva FS, Novellino E, Cavalli A, Parrinello M, Limongelli V. Mechanistic insight into ligand binding to G-quadruplex DNA. Nucleic Acids Res 2014; 42:5447-55. [PMID: 24753420 PMCID: PMC4027208 DOI: 10.1093/nar/gku247] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Revised: 03/10/2014] [Accepted: 03/13/2014] [Indexed: 12/12/2022] Open
Abstract
Specific guanine-rich regions in human genome can form higher-order DNA structures called G-quadruplexes, which regulate many relevant biological processes. For instance, the formation of G-quadruplex at telomeres can alter cellular functions, inducing apoptosis. Thus, developing small molecules that are able to bind and stabilize the telomeric G-quadruplexes represents an attractive strategy for antitumor therapy. An example is 3-(benzo[d]thiazol-2-yl)-7-hydroxy-8-((4-(2-hydroxyethyl)piperazin-1-yl)methyl)-2H-chromen-2-one (compound 1: ), recently identified as potent ligand of the G-quadruplex [d(TGGGGT)]4 with promising in vitro antitumor activity. The experimental observations are suggestive of a complex binding mechanism that, despite efforts, has defied full characterization. Here, we provide through metadynamics simulations a comprehensive understanding of the binding mechanism of 1: to the G-quadruplex [d(TGGGGT)]4. In our calculations, the ligand explores all the available binding sites on the DNA structure and the free-energy landscape of the whole binding process is computed. We have thus disclosed a peculiar hopping binding mechanism whereas 1: is able to bind both to the groove and to the 3' end of the G-quadruplex. Our results fully explain the available experimental data, rendering our approach of great value for further ligand/DNA studies.
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Affiliation(s)
- Francesco Saverio Di Leva
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, I-16163 Genoa, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano, 49, I-80131 Naples, Italy
| | - Andrea Cavalli
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, I-16163 Genoa, Italy Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, via Belmeloro, 6, I-40126 Bologna, Italy
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, via G. Buffi, 13, CH-6900 Lugano, Switzerland
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano, 49, I-80131 Naples, Italy
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41
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Costi R, Métifiot M, Chung S, Cuzzucoli Crucitti G, Maddali K, Pescatori L, Messore A, Madia VN, Pupo G, Scipione L, Tortorella S, Di Leva FS, Cosconati S, Marinelli L, Novellino E, Le Grice SFJ, Corona A, Pommier Y, Marchand C, Di Santo R. Basic quinolinonyl diketo acid derivatives as inhibitors of HIV integrase and their activity against RNase H function of reverse transcriptase. J Med Chem 2014; 57:3223-34. [PMID: 24684270 PMCID: PMC4203401 DOI: 10.1021/jm5001503] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
A series
of antiviral basic quinolinonyl diketo acid derivatives
were developed as inhibitors of HIV-1 IN. Compounds 12d,f,i inhibited HIV-1 IN with IC50 values below 100 nM for strand transfer and showed a 2 order of
magnitude selectivity over 3′-processing. These strand transfer
selective inhibitors also inhibited HIV-1 RNase H with low micromolar
potencies. Molecular modeling studies based on both the HIV-1 IN and
RNase H catalytic core domains provided new structural insights for
the future development of these compounds as dual HIV-1 IN and RNase
H inhibitors.
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Affiliation(s)
- Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma , P.le Aldo Moro 5, I-00185 Roma, Italy
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42
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Neubauer S, Rechenmacher F, Brimioulle R, Di Leva FS, Bochen A, Sobahi TR, Schottelius M, Novellino E, Mas-Moruno C, Marinelli L, Kessler H. Pharmacophoric modifications lead to superpotent αvβ3 integrin ligands with suppressed α5β1 activity. J Med Chem 2014; 57:3410-7. [PMID: 24654918 DOI: 10.1021/jm500092w] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The selective targeting of the αvβ3 integrin subtype without affecting the structurally closely related receptor α5β1 is crucial for understanding the details of their biological and pathological functions and thus of great relevance for diagnostic and therapeutic approaches in cancer treatment. Here, we present the synthesis of highly active RGD peptidomimetics for the αvβ3 integrin with remarkable selectivity against α5β1. Incorporation of a methoxypyridine building block into a ligand scaffold and variation of different functional moieties led to αvβ3-antagonistic activities in the low nanomolar or even subnanomolar range. Furthermore, docking studies were performed to give insights into the binding modes of the novel compounds. The presented library comprises powerful ligands for specific addressing and blocking of the αvβ3 integrin subtype, thereby representing privileged tools for integrin-based personalized medicine.
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Affiliation(s)
- Stefanie Neubauer
- Department Chemie, Institute for Advanced Study (IAS) and Center of Integrated Protein Science (CIPSM), Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany
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43
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D’Amore C, Di Leva FS, Sepe V, Renga B, Del Gaudio C, D’Auria MV, Zampella A, Fiorucci S, Limongelli V. Design, Synthesis, and Biological Evaluation of Potent Dual Agonists of Nuclear and Membrane Bile Acid Receptors. J Med Chem 2014; 57:937-54. [DOI: 10.1021/jm401873d] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Claudio D’Amore
- Dipartimento
di Medicina Clinica e Sperimentale, Nuova Facoltà di Medicina, Università degli Studi di Perugia, Via Gambuli, 1-06132 Perugia, Italy
| | | | - Valentina Sepe
- Dipartimento
di Farmacia, Università di Napoli “Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Barbara Renga
- Dipartimento
di Medicina Clinica e Sperimentale, Nuova Facoltà di Medicina, Università degli Studi di Perugia, Via Gambuli, 1-06132 Perugia, Italy
| | - Chiara Del Gaudio
- Dipartimento
di Farmacia, Università di Napoli “Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Maria Valeria D’Auria
- Dipartimento
di Farmacia, Università di Napoli “Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Angela Zampella
- Dipartimento
di Farmacia, Università di Napoli “Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Stefano Fiorucci
- Dipartimento
di Medicina Clinica e Sperimentale, Nuova Facoltà di Medicina, Università degli Studi di Perugia, Via Gambuli, 1-06132 Perugia, Italy
| | - Vittorio Limongelli
- Dipartimento
di Farmacia, Università di Napoli “Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
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44
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Di Leva FS, Zizza P, Cingolani C, D'Angelo C, Pagano B, Amato J, Salvati E, Sissi C, Pinato O, Marinelli L, Cavalli A, Cosconati S, Novellino E, Randazzo A, Biroccio A. Exploring the chemical space of G-quadruplex binders: discovery of a novel chemotype targeting the human telomeric sequence. J Med Chem 2013; 56:9646-54. [PMID: 24256368 DOI: 10.1021/jm401185b] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent findings have unambiguously demonstrated that DNA G-rich sequences can adopt a G-quadruplex folding in living cells, thus further validating them as crucial targets for anticancer therapy. Herein, to identify new potent G4 binders as antitumor drug candidates, we have targeted a 24-nt G4-forming telomeric sequence employing a receptor-based virtual screening approach. Among the best candidates, in vitro binding experiments allowed identification of three novel G4 ligands. Among them, the best compound features an unprecedented binding selectivity for the human telomeric DNA G-quadruplex with no detectable binding for other G4-forming sequences present at different genomic sites. This behavior correlates with the detected ability to generate DNA damage response in tumor cells at the telomeric level and efficient antiproliferative effect on different tumor cell lines at low micromolar concentrations.
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Affiliation(s)
- Francesco Saverio Di Leva
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , via Morego 30, 16163 Genova, Italy
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45
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Taliani S, Pugliesi I, Barresi E, Salerno S, Marchand C, Agama K, Simorini F, La Motta C, Marini AM, Di Leva FS, Marinelli L, Cosconati S, Novellino E, Pommier Y, Di Santo R, Da Settimo F. Phenylpyrazolo[1,5-a]quinazolin-5(4H)-one: a suitable scaffold for the development of noncamptothecin topoisomerase I (Top1) inhibitors. J Med Chem 2013; 56:7458-62. [PMID: 23987476 DOI: 10.1021/jm400932c] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In search for a novel chemotype to develop topoisomerase I (Top1) inhibitors, the pyrazolo[1,5-a]quinazoline nucleus, structurally related to the indenoisoquinoline system precursor of well-known Top1 poisons, was variously decorated (i.e., a substituted phenyl ring at 2- or 3-position, a protonable side chain at 4- or 5-position), affording a number of Top1 inhibitors with cleavage patterns common to CPT and MJ-III-65. SARs data were rationalized by means of an advanced docking protocol.
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Affiliation(s)
- Sabrina Taliani
- Department of Pharmacy, University of Pisa , via Bonanno 6, 56126 Pisa, Italy
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46
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Di Leva FS, Festa C, D'Amore C, De Marino S, Renga B, D'Auria MV, Novellino E, Limongelli V, Zampella A, Fiorucci S. Binding mechanism of the farnesoid X receptor marine antagonist suvanine reveals a strategy to forestall drug modulation on nuclear receptors. Design, synthesis, and biological evaluation of novel ligands. J Med Chem 2013; 56:4701-17. [PMID: 23656455 DOI: 10.1021/jm400419e] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here, we report suvanine, a marine sponge sesterterpene, as an antagonist of the mammalian bile acid sensor farnesoid-X-receptor (FXR). Using suvanine as a template, we shed light on the molecular bases of FXR antagonism, identifying the essential conformational changes responsible for the transition from the agonist to the antagonist form. Molecular characterization of the nuclear corepressor NCoR and coactivator Src-1 revealed that receptor conformational changes are associated with a specific dynamic of recruitment of these cofactors to the promoter of OSTα, a FXR regulated gene. Using suvanine as a novel hit, a library of semisynthetic derivatives has been designed and prepared, leading to pharmacological profiles ranging from agonism to antagonism toward FXR. Deep pharmacological evaluation demonstrated that derivative 19 represents a new chemotype of FXR modulator, whereas alcohol 6, with a simplified molecular scaffold, exhibits excellent antagonistic activity.
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Affiliation(s)
- Francesco Saverio Di Leva
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
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47
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Bochen A, Marelli UK, Otto E, Pallarola D, Mas-Moruno C, Di Leva FS, Boehm H, Spatz JP, Novellino E, Kessler H, Marinelli L. Biselectivity of isoDGR peptides for fibronectin binding integrin subtypes α5β1 and αvβ6: conformational control through flanking amino acids. J Med Chem 2013; 56:1509-19. [PMID: 23362923 DOI: 10.1021/jm301221x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrins are the major class of cell adhesion proteins. Their interaction with different ligands of the extracellular matrix is diverse. To get more insight into these interactions, artificial ligands endowed with a well-defined activity/selectivity profile are necessary. Herein, we present a library of cyclic pentapeptides, based on our previously reported peptide motif c(-phg-isoDGR-X-), in which high activity toward fibronectin binding integrins α5β1 and αvβ6 and not on vitronectin binding integrins αvβ3 and αvβ5 has been achieved by changing the flanking amino acids. The structure of the most promising candidates has been determined using a combined approach of NMR, distance geometry, and molecular dynamics simulations, and docking studies have been further used to elucidate the peptide-integrin interactions at the molecular level. The peptides' binding affinity has been characterized by enzyme linked immunosorbent assay experiments, and the results have been verified by cell adhesion experiments on specifically functionalized surfaces.
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Affiliation(s)
- Alexander Bochen
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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48
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Cosconati S, Marinelli L, Di Leva FS, La Pietra V, De Simone A, Mancini F, Andrisano V, Novellino E, Goodsell DS, Olson AJ. Protein flexibility in virtual screening: the BACE-1 case study. J Chem Inf Model 2012; 52:2697-704. [PMID: 23005250 DOI: 10.1021/ci300390h] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simulating protein flexibility is a major issue in the docking-based drug-design process for which a single methodological solution does not exist. In our search of new anti-Alzheimer ligands, we were faced with the challenge of including receptor plasticity in a virtual screening campaign aimed at finding new β-secretase inhibitors. To this aim, we incorporated protein flexibility in our simulations by using an ensemble of static X-ray enzyme structures to screen the National Cancer Institute database. A unified description of the protein motion was also generated by computing and combining a set of grid maps using an energy weighting scheme. Such a description was used in an energy-weighted virtual screening experiment on the same molecular database. Assessment of the enrichment factors from these two virtual screening approaches demonstrated comparable predictive powers, with the energy-weighted method being faster than the ensemble method. The in vitro evaluation demonstrated that out of the 32 tested ligands, 17 featured the predicted enzyme inhibiting property. Such an impressive success rate (53.1%) demonstrates the enhanced power of the two methodologies and suggests that energy-weighted virtual screening is a more than valid alternative to ensemble virtual screening given its reduced computational demands and comparable performance.
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Affiliation(s)
- Sandro Cosconati
- Dipartimento Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
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La Pietra V, Marinelli L, Cosconati S, Di Leva FS, Nuti E, Santamaria S, Pugliesi I, Morelli M, Casalini F, Rossello A, La Motta C, Taliani S, Visse R, Nagase H, da Settimo F, Novellino E. Identification of novel molecular scaffolds for the design of MMP-13 inhibitors: a first round of lead optimization. Eur J Med Chem 2011; 47:143-52. [PMID: 22088955 DOI: 10.1016/j.ejmech.2011.10.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 09/29/2011] [Accepted: 10/18/2011] [Indexed: 10/15/2022]
Abstract
Osteoarthritis (OA) is the leading cause of joint pain and disability in middle-aged and elderly patients, and is characterized by progressive loss of articular cartilage. Among the various matrix metalloproteinases (MMPs), MMP-13 is specifically expressed in the cartilage of human OA patients and is not present in normal adult cartilage. Thus, MMP-13-selective inhibitors are promising candidates in osteoarthritis therapy. Recently, we designed an N-isopropoxy-arylsulfonamide-based hydroxamate inhibitor, which showed low nanomolar activity and high selectivity for MMP-13. In parallel to further studies aiming to assess the in vivo activity of our compound, we screened the Life Chemicals database through computational docking to seek for novel scaffolds as zinc-chelating non-hydroxamate inhibitors. Experimental evaluation of 20 selected candidate compounds verified five novel leads with IC(50) in the low μM range. These newly discovered inhibitors are structurally unrelated to the ones known so far and provide useful scaffolds to develop compounds with more desirable properties. Finally, a first round of structure-based optimization on lead 1 was accomplished and led to an increase in potency of more than 5 fold.
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Affiliation(s)
- Valeria La Pietra
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli Federico II Via D. Montesano 49, 80131 Napoli, Italy
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