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Albani M, Fassi EMA, Moretti RM, Garofalo M, Montagnani Marelli M, Roda G, Sgrignani J, Cavalli A, Grazioso G. Computational Design of Novel Cyclic Peptides Endowed with Autophagy-Inhibiting Activity on Cancer Cell Lines. Int J Mol Sci 2024; 25:4622. [PMID: 38731842 PMCID: PMC11083565 DOI: 10.3390/ijms25094622] [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: 03/26/2024] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
(1) Autophagy plays a significant role in development and cell proliferation. This process is mainly accomplished by the LC3 protein, which, after maturation, builds the nascent autophagosomes. The inhibition of LC3 maturation results in the interference of autophagy activation. (2) In this study, starting from the structure of a known LC3B binder (LIR2-RavZ peptide), we identified new LC3B ligands by applying an in silico drug design strategy. The most promising peptides were synthesized, biophysically assayed, and biologically evaluated to ascertain their potential antiproliferative activity on five humans cell lines. (3) A cyclic peptide (named Pep6), endowed with high conformational stability (due to the presence of a disulfide bridge), displayed a Kd value on LC3B in the nanomolar range. Assays accomplished on PC3, MCF-7, and A549 cancer cell lines proved that Pep6 exhibited cytotoxic effects comparable to those of the peptide LIR2-RavZ, a reference LC3B ligand. Furthermore, it was ineffective on both normal prostatic epithelium PNT2 and autophagy-defective prostate cancer DU145 cells. (4) Pep6 can be considered a new autophagy inhibitor that can be employed as a pharmacological tool or even as a template for the rational design of new small molecules endowed with autophagy inhibitory activity.
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Affiliation(s)
- Marco Albani
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.A.); (G.R.)
| | - Enrico Mario Alessandro Fassi
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.A.); (G.R.)
| | - Roberta Manuela Moretti
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy; (R.M.M.); (M.M.M.)
| | - Mariangela Garofalo
- Department of Pharmaceutical and Pharmacological Sciences, Università di Padova, Via F. Marzolo 5, 35131 Padova, Italy;
| | - Marina Montagnani Marelli
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy; (R.M.M.); (M.M.M.)
| | - Gabriella Roda
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.A.); (G.R.)
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Via Chiesa 5, 6500 Bellinzona, Switzerland; (J.S.); (A.C.)
| | - Andrea Cavalli
- Institute for Research in Biomedicine (IRB), Via Chiesa 5, 6500 Bellinzona, Switzerland; (J.S.); (A.C.)
- Swiss Institute of Bioinformatics (SIB), University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipôle, 1015 Lausanne, Switzerland
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.A.); (G.R.)
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2
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Fassi EMA, Citarella A, Albani M, Milano EG, Legnani L, Lammi C, Silvani A, Grazioso G. PCSK9 inhibitors: a patent review 2018-2023. Expert Opin Ther Pat 2024:1-17. [PMID: 38588538 DOI: 10.1080/13543776.2024.2340569] [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: 11/30/2023] [Accepted: 03/28/2024] [Indexed: 04/10/2024]
Abstract
INTRODUCTION Proprotein convertase subtilisin/kexin 9 (PCSK9) plays a crucial role in breaking down the hepatic low-density lipoprotein receptor (LDLR), thereby influencing the levels of circulating low-density lipoprotein cholesterol (LDL-C). Consequently, inhibiting PCSK9 through suitable ligands has been established as a validated therapeutic strategy for combating hypercholesterolemia and cardiovascular diseases. AREA COVERED Patent literature claiming novel compounds inhibiting PCSK9 disclosed from 2018 to June 2023 available in the espacenet database, which contains more than 150 million patent documents from over 100 patent-granting authorities worldwide. EXPERT OPINION The undisputable beneficial influence of PCSK9 as a pharmacological target has prompted numerous private and public institutions to patent chemical frameworks as inhibitors of PCSK9. While several compounds have advanced to clinical trials for treating hypercholesterolemia, they have not completed these trials yet. These compounds must contend in a complex market where new, costly, and advanced drugs, such as monoclonal antibodies and siRNA, are prescribed instead of inexpensive and less potent statins.
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Affiliation(s)
| | - Andrea Citarella
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
| | - Marco Albani
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy
| | - Erica Ginevra Milano
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy
| | - Laura Legnani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy
| | - Alessandra Silvani
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy
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3
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Ratti A, Fassi EMA, Forlani F, Zangrossi M, Mori M, Cappitelli F, Roda G, Villa S, Villa F, Grazioso G. Unlocking the Antibiofilm Potential of Natural Compounds by Targeting the NADH:quinone Oxidoreductase WrbA. Antioxidants (Basel) 2023; 12:1612. [PMID: 37627607 PMCID: PMC10451263 DOI: 10.3390/antiox12081612] [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: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Biofilm-dwelling cells endure adverse conditions, including oxidative imbalances. The NADH:quinone oxidoreductase enzyme WrbA has a crucial role in the mechanism of action of antibiofilm molecules such as ellagic and salicylic acids. This study aimed to exploit the potential of the WrbA scaffold as a valuable target for identifying antibiofilm compounds at non-lethal concentrations. A three-dimensional computational model, based on the published WrbA structure, was used to screen natural compounds from a virtual library of 800,000 compounds. Fisetin, morin, purpurogallin, NZ028, and NZ034, along with the reference compound ellagic acid, were selected. The antibiofilm effect of the molecules was tested at non-lethal concentrations evaluating the cell-adhesion of wild-type and WrbA-deprived Escherichia coli strains through fluorochrome-based microplate assays. It was shown that, except for NZ028, all of the selected molecules exhibited notable antibiofilm effects. Purpurogallin and NZ034 showed excellent antibiofilm performances at the lowest concentration of 0.5 μM, in line with ellagic acid. The observed loss of activity and the level of reactive oxygen species in the mutant strain, along with the correlation with terms contributing to the ligand-binding free energy on WrbA, strongly indicates the WrbA-dependency of purpurogallin and NZ034. Overall, the molecular target WrbA was successfully employed to identify active compounds at non-lethal concentrations, thus revealing, for the first time, the antibiofilm efficacy of purpurogallin and NZ034.
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Affiliation(s)
- Alessandro Ratti
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Enrico M A Fassi
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Fabio Forlani
- Department of Food Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Maurizio Zangrossi
- Department of Food Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Francesca Cappitelli
- Department of Food Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Gabriella Roda
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Federica Villa
- Department of Food Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
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4
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Ratti A, Fassi EMA, Forlani F, Mori M, Villa F, Cappitelli F, Sgrignani J, Roda G, Cavalli A, Villa S, Grazioso G. Mechanistic Insights into the Antibiofilm Mode of Action of Ellagic Acid. Pharmaceutics 2023; 15:1757. [PMID: 37376205 DOI: 10.3390/pharmaceutics15061757] [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: 05/11/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Bacterial biofilm is a major contributor to the persistence of infection and the limited efficacy of antibiotics. Antibiofilm molecules that interfere with the biofilm lifestyle offer a valuable tool in fighting bacterial pathogens. Ellagic acid (EA) is a natural polyphenol that has shown attractive antibiofilm properties. However, its precise antibiofilm mode of action remains unknown. Experimental evidence links the NADH:quinone oxidoreductase enzyme WrbA to biofilm formation, stress response, and pathogen virulence. Moreover, WrbA has demonstrated interactions with antibiofilm molecules, suggesting its role in redox and biofilm modulation. This work aims to provide mechanistic insights into the antibiofilm mode of action of EA utilizing computational studies, biophysical measurements, enzyme inhibition studies on WrbA, and biofilm and reactive oxygen species assays exploiting a WrbA-deprived mutant strain of Escherichia coli. Our research efforts led us to propose that the antibiofilm mode of action of EA stems from its ability to perturb the bacterial redox homeostasis driven by WrbA. These findings shed new light on the antibiofilm properties of EA and could lead to the development of more effective treatments for biofilm-related infections.
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Affiliation(s)
- Alessandro Ratti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Enrico M A Fassi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Fabio Forlani
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Via G. Celoria 2, 20133 Milano, Italy
| | - Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Federica Villa
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Via G. Celoria 2, 20133 Milano, Italy
| | - Francesca Cappitelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Via G. Celoria 2, 20133 Milano, Italy
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Via Chiesa 5, 6500 Bellinzona, Switzerland
| | - Gabriella Roda
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Andrea Cavalli
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Via Chiesa 5, 6500 Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
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5
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Lammi C, Fassi EMA, Manenti M, Brambilla M, Conti M, Li J, Roda G, Camera M, Silvani A, Grazioso G. Computational Design, Synthesis, and Biological Evaluation of Diimidazole Analogues Endowed with Dual PCSK9/HMG-CoAR-Inhibiting Activity. J Med Chem 2023. [PMID: 37261954 DOI: 10.1021/acs.jmedchem.3c00279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Proprotein convertase subtilisin/kexin 9 (PCSK9) is responsible for the degradation of the hepatic low-density lipoprotein receptor (LDLR), which regulates circulating cholesterol levels. Consequently, the PCSK9 inhibition is a valuable therapeutic approach for the treatment of hypercholesterolemia and cardiovascular diseases. In our studies, we discovered Rim13, a polyimidazole derivative reducing the protein-protein interaction between PCSK9 and LDLR with an IC50 of 1.6 μM. The computational design led to the optimization of the shape of the PCSK9/ligand complementarity, enabling the discovery of potent diimidazole derivatives. In fact, carrying out biological assays to fully characterize the cholesterol-lowering activity of the new analogues and using both biochemical and cellular techniques, compound Dim16 displayed improved PCSK9 inhibitory activity (IC50 0.9 nM). Interestingly, similar to other lupin-derived peptides and their synthetic analogues, some compounds in this series showed dual hypocholesterolemic activity since some of them complementarily inhibited the 3-hydroxy-3-methylglutaryl coenzyme A reductase.
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Affiliation(s)
- Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Enrico M A Fassi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Marco Manenti
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 10, 20133 Milan, Italy
| | - Marta Brambilla
- Centro Cardiologico Monzino IRCCS, via Parea 4, 20138 Milan, Italy
| | - Maria Conti
- Centro Cardiologico Monzino IRCCS, via Parea 4, 20138 Milan, Italy
| | - Jianqiang Li
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Gabriella Roda
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Marina Camera
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
- Centro Cardiologico Monzino IRCCS, via Parea 4, 20138 Milan, Italy
| | - Alessandra Silvani
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 10, 20133 Milan, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
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6
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Ciceri S, Colombo D, Fassi EMA, Ferraboschi P, Grazioso G, Grisenti P, Iannone M, Castellano C, Meneghetti F. Elagolix Sodium Salt and Its Synthetic Intermediates: A Spectroscopic, Crystallographic, and Conformational Study. Molecules 2023; 28:molecules28093861. [PMID: 37175271 PMCID: PMC10180344 DOI: 10.3390/molecules28093861] [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: 04/03/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Elagolix sodium salt is the first marketed orally active non-peptide gonadotropin-releasing hormone receptor antagonist (GnRHR-ant) for the management of hormone dependent diseases, such as endometriosis and uterine fibroids. Despite its presence on the market since 2018, a thorough NMR analysis of this drug, together with its synthetic intermediates, is still lacking. Hence, with the aim of filling this literature gap, we here performed a detailed NMR investigation, which allowed the complete assignment of the 1H, 13C, and 15N NMR signals. These data allowed, with the support of the conformational analysis, the determination of the stereochemical profile of the two atropisomers, detectable in solution. Moreover, these latter were also detected by means of cellulose-based chiral HPLC, starting from a sample prepared through an implemented synthetic procedure with respect to the reported ones. Overall, these results contribute to further understanding of the topic of atropisomerism in drug discovery and could be applied in the design of safe and stable analogs, endowed with improved target selectivity.
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Affiliation(s)
- Samuele Ciceri
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via C. Saldini 50, 20133 Milano, Italy
| | - Diego Colombo
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via C. Saldini 50, 20133 Milano, Italy
| | - Enrico M A Fassi
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Patrizia Ferraboschi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via C. Saldini 50, 20133 Milano, Italy
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Paride Grisenti
- Chemical-Pharmaceutical Consulting and IP Management, Viale G. da Cermenate 58, 20141 Milano, Italy
| | - Marco Iannone
- Tecnomed Foundation, University of Milano-Bicocca, Via Pergolesi 33, 20900 Monza, Italy
| | - Carlo Castellano
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy
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7
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Chiacchio MA, Legnani L, Fassi EMA, Roda G, Grazioso G. Development of AMBER Parameters for Molecular Simulations of Selected Boron-Based Covalent Ligands. Molecules 2023; 28:molecules28062866. [PMID: 36985837 PMCID: PMC10057150 DOI: 10.3390/molecules28062866] [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: 03/06/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Boron containing compounds (BCCs) aroused increasing interest in the scientific community due to their wide application as drugs in various fields. In order to design new compounds hopefully endowed with pharmacological activity and also investigate their conformational behavior, the support of computational studies is crucial. Nevertheless, the suitable molecular mechanics parameterization and the force fields needed to perform these simulations are not completely available for this class of molecules. In this paper, Amber force field parameters for phenyl-, benzyl-, benzylamino-, and methylamino-boronates, a group of boron-containing compounds involved in different branches of the medicinal chemistry, were created. The robustness of the obtained data was confirmed through molecular dynamics simulations on ligand/β-lactamases covalent complexes. The ligand torsional angles, populated over the trajectory frames, were confirmed by values found in the ligand geometries, located through optimizations at the DFT/B3LYP/6-31g(d) level, using water as a solvent. In summary, this study successfully provided a library of parameters, opening the possibility to perform molecular dynamics simulations of this class of boron-containing compounds.
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Affiliation(s)
- Maria Assunta Chiacchio
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Laura Legnani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | | | - Gabriella Roda
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
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8
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Sgrignani J, Cecchinato V, Fassi EMA, D'Agostino G, Garofalo M, Danelon G, Pedotti M, Simonelli L, Varani L, Grazioso G, Uguccioni M, Cavalli A. Systematic Development of Peptide Inhibitors Targeting the CXCL12/HMGB1 Interaction. J Med Chem 2021; 64:13439-13450. [PMID: 34510899 DOI: 10.1021/acs.jmedchem.1c00852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During inflammatory reactions, the production and release of chemotactic factors guide the recruitment of selective leukocyte subpopulations. The alarmin HMGB1 and the chemokine CXCL12, both released in the microenvironment, can form a heterocomplex, which exclusively acts on the chemokine receptor CXCR4, enhancing cell migration, and in some pathological conditions such as rheumatoid arthritis exacerbates the immune response. An excessive cell influx at the inflammatory site can be diminished by disrupting the heterocomplex. Here, we report the computationally driven identification of the first peptide (HBP08) binding HMGB1 and selectively inhibiting the activity of the CXCL12/HMGB1 heterocomplex. Furthermore, HBP08 binds HMGB1 with the highest affinity reported so far (Kd of 0.8 ± 0.4 μM). The identification of this peptide represents an important step toward the development of innovative pharmacological tools for the treatment of severe chronic inflammatory conditions characterized by an uncontrolled immune response.
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Affiliation(s)
- Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Valentina Cecchinato
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Enrico M A Fassi
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland.,Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milan, Italy
| | - Gianluca D'Agostino
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Maura Garofalo
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Gabriela Danelon
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milan, Italy
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, 20090 Milan, Italy
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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9
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Tombling BJ, Lammi C, Lawrence N, Gilding EK, Grazioso G, Craik DJ, Wang CK. Bioactive Cyclization Optimizes the Affinity of a Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) Peptide Inhibitor. J Med Chem 2020; 64:2523-2533. [PMID: 33356222 DOI: 10.1021/acs.jmedchem.0c01766] [Citation(s) in RCA: 10] [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: 12/19/2022]
Abstract
Peptides are regarded as promising next-generation therapeutics. However, an analysis of over 1000 bioactive peptide candidates suggests that many have underdeveloped affinities and could benefit from cyclization using a bridging linker sequence. Until now, the primary focus has been on the use of inert peptide linkers. Here, we show that affinity can be significantly improved by enriching the linker with functional amino acids. We engineered a peptide inhibitor of PCSK9, a target for clinical management of hypercholesterolemia, to demonstrate this concept. Cyclization linker optimization from library screening produced a cyclic peptide with ∼100-fold improved activity over the parent peptide and efficiently restored low-density lipoprotein (LDL) receptor levels and cleared extracellular LDL. The linker forms favorable interactions with PCSK9 as evidenced by thermodynamics, structure-activity relationship (SAR), NMR, and molecular dynamics (MD) studies. This PCSK9 inhibitor is one of many peptides that could benefit from bioactive cyclization, a strategy that is amenable to broad application in pharmaceutical design.
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Affiliation(s)
- Benjamin J Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Nicole Lawrence
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld 4072, Australia
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10
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Sgrignani J, Fassi EMA, Lammi C, Roda G, Grazioso G. Exploring Proprotein Convertase Subtilisin/Kexin 9 (PCSK9) Autoproteolysis Process by Molecular Simulations: Hints for Drug Design. ChemMedChem 2020; 15:1601-1607. [PMID: 32558225 DOI: 10.1002/cmdc.202000431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 06/15/2020] [Indexed: 12/28/2022]
Abstract
Proprotein convertase subtilisin/kexin 9 (PCSK9) is a notable target for the treatment of hypercholesterolemia because it regulates the population of the low-density lipoprotein receptor (LDLR) on liver cells. The PCSK9 zymogen is a serine protease that spontaneously undergoes a double self-cleavage step. Available X-ray structures depict the PCSK9 mature state, but the atomic details of the zymogen state of the enzyme are still unknown. Additionally, why the protease activity of PCSK9 is blocked after the second autoprocessing step remains unclear, as this deviates from other members of the PCSK family. By performing constant-pH molecular dynamics (MD) simulations, we investigated the protonation state of the catalytic triad of PCSK9 and found that it strongly influences the catalytic properties of the enzyme. Moreover, we determined the final step of the maturation process by classical and steered MD simulations. This study could facilitate the identification of ligands capable of interfering with the PCSK9 maturation process.
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Affiliation(s)
- Jacopo Sgrignani
- Istituto di Ricerca in Biomedicina (IRB), Università della Svizzera Italiana (USI), Via V. Vela 6, 6500, Bellinzona, Switzerland
| | - Enrico M A Fassi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Gabriella Roda
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
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11
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Bassini E, Gazzotti S, Sannio F, Lo Presti L, Sgrignani J, Docquier JD, Grazioso G, Silvani A. Isonitrile-Based Multicomponent Synthesis of β-Amino Boronic Acids as β-Lactamase Inhibitors. Antibiotics (Basel) 2020; 9:E249. [PMID: 32408714 PMCID: PMC7277116 DOI: 10.3390/antibiotics9050249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 04/10/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/28/2022] Open
Abstract
The application of various isonitrile-based multicomponent reactions to protected (2-oxoethyl)boronic acid (as the carbonyl component) is described. The Ugi reaction, both in the four components and in the four centers-three components versions, and the van Leusen reaction, proved effective at providing small libraries of MIDA-protected β-aminoboronic acids. The corresponding free β-aminoboronic acids, quantitatively recovered through basic mild deprotection, were found to be quite stable and were fully characterized, including by 11B-NMR spectroscopy. Single-crystal X-ray diffraction analysis, applied both to a MIDA-protected and a free β-aminoboronic acid derivative, provided evidence for different conformations in the solid-state. Finally, the antimicrobial activities of selected compounds were evaluated by measuring their minimal inhibitory concentration (MIC) values, and the binding mode of the most promising derivative on OXA-23 class D β-lactamase was predicted by a molecular modeling study.
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Affiliation(s)
- Emanuele Bassini
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy; (E.B.); (S.G.); (L.L.P.)
| | - Stefano Gazzotti
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy; (E.B.); (S.G.); (L.L.P.)
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, 53100 Siena, Italy; (F.S.); (J.-D.D.)
| | - Leonardo Lo Presti
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy; (E.B.); (S.G.); (L.L.P.)
| | - Jacopo Sgrignani
- Istituto di Ricerca in Biomedicina (IRB), Università della Svizzera Italiana (USI), Via V. Vela 6, CH-6500 Bellinzona, Switzerland;
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, 53100 Siena, Italy; (F.S.); (J.-D.D.)
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy;
| | - Alessandra Silvani
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy; (E.B.); (S.G.); (L.L.P.)
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12
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Garofalo M, Grazioso G, Cavalli A, Sgrignani J. How Computational Chemistry and Drug Delivery Techniques Can Support the Development of New Anticancer Drugs. Molecules 2020; 25:E1756. [PMID: 32290224 PMCID: PMC7180704 DOI: 10.3390/molecules25071756] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/17/2023] Open
Abstract
The early and late development of new anticancer drugs, small molecules or peptides can be slowed down by some issues such as poor selectivity for the target or poor ADME properties. Computer-aided drug design (CADD) and target drug delivery (TDD) techniques, although apparently far from each other, are two research fields that can give a significant contribution to overcome these problems. Their combination may provide mechanistic understanding resulting in a synergy that makes possible the rational design of novel anticancer based therapies. Herein, we aim to discuss selected applications, some also from our research experience, in the fields of anticancer small organic drugs and peptides.
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Affiliation(s)
- Mariangela Garofalo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, University of Milano, 20133 Milan, Italy
| | - Andrea Cavalli
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), 6500 Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), 6500 Bellinzona, Switzerland
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13
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Fassi EMA, Sgrignani J, D'Agostino G, Cecchinato V, Garofalo M, Grazioso G, Uguccioni M, Cavalli A. Oxidation State Dependent Conformational Changes of HMGB1 Regulate the Formation of the CXCL12/HMGB1 Heterocomplex. Comput Struct Biotechnol J 2019; 17:886-894. [PMID: 31333815 PMCID: PMC6617219 DOI: 10.1016/j.csbj.2019.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 03/08/2019] [Revised: 05/28/2019] [Accepted: 06/18/2019] [Indexed: 12/15/2022] Open
Abstract
High-mobility Group Box 1 (HMGB1) is an abundant protein present in all mammalian cells and involved in several processes. During inflammation or tissue damage, HMGB1 is released in the extracellular space and, depending on its redox state, can form a heterocomplex with CXCL12. The heterocomplex acts exclusively via the chemokine receptor CXCR4 enhancing leukocyte recruitment. Here, we used multi-microsecond molecular dynamics (MD) simulations to elucidate the effect of the disulfide bond on the structure and dynamics of HMGB1. The results of the MD simulations show that the presence or lack of the disulfide bond between Cys23 and Cys45 modulates the conformational space explored by HMGB1, making the reduced protein more suitable to form a complex with CXCL12.
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Key Words
- CXCL12
- CXCL12, C-X-C motif chemokine 12
- CXCR4, C-X-C chemokine receptor type 4
- Conformational ensemble
- HMGB1
- HMGB1, High-mobility Group Box 1
- MD, Molecular dynamics
- Molecular dynamics
- Protein-protein docking
- RMSD, Root mean square deviation
- RoG, Radius of gyration
- SASA, Solvent accessible surface area
- TLR2 or TLR4, Toll-like Receptor 2 or 4
- ds-HMGB1, Disulfide High-mobility Group Box 1
- fr-HMGB1, Full reduced High-mobility Group Box 1
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Affiliation(s)
- Enrico M A Fassi
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland
| | - Gianluca D'Agostino
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland
| | - Valentina Cecchinato
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland
| | - Maura Garofalo
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland.,University of Lausanne (UNIL), CH-1015, Lausanne, Switzerland
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland.,Humanitas University, Department of Biomedical Sciences, 20090, Pieve Emanuele, Milan, Italy
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Lammi C, Sgrignani J, Arnoldi A, Lesma G, Spatti C, Silvani A, Grazioso G. Computationally Driven Structure Optimization, Synthesis, and Biological Evaluation of Imidazole-Based Proprotein Convertase Subtilisin/Kexin 9 (PCSK9) Inhibitors. J Med Chem 2019; 62:6163-6174. [DOI: 10.1021/acs.jmedchem.9b00402] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Universitá degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Jacopo Sgrignani
- Istituto di Ricerca in Biomedicina (IRB), Universitá della Svizzera Italiana (USI), Via V. Vela 6, CH-6500 Bellinzona, Switzerland
| | - Anna Arnoldi
- Dipartimento di Scienze Farmaceutiche, Universitá degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Giordano Lesma
- Dipartimento di Chimica, Universitá degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Claudia Spatti
- Dipartimento di Chimica, Universitá degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Alessandra Silvani
- Dipartimento di Chimica, Universitá degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Universitá degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
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15
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Lammi C, Sgrignani J, Roda G, Arnoldi A, Grazioso G. Inhibition of PCSK9 D374Y/LDLR Protein-Protein Interaction by Computationally Designed T9 Lupin Peptide. ACS Med Chem Lett 2019; 10:425-430. [PMID: 30996774 DOI: 10.1021/acsmedchemlett.8b00464] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/03/2018] [Indexed: 12/23/2022] Open
Abstract
The inhibition of the PCSK9/LDLR protein-protein interaction is a promising strategy for developing new hypocholesterolemic agents. Familial hypercholesterolemia is linked to specific PCSK9 mutations: the D374Y is the most potent gain-of-function (GOF) PCSK9 mutation among clinically relevant ones. Recently, a lupin peptide (T9) showed inhibitory effects on this mutant PCSK9 form, being also capable to increase liver uptake of low density lipoprotein cholesterol. In this Letter, aiming to improve the potency of this peptide, the T9 residues mainly responsible for the interaction with PCSK9D374Y (hot spots) were computationally predicted. Then, the "non-hot" residues were suitably substituted by new amino acids capable to theoretically increase the structural complementarity between T9 and PCSK9D374Y. The outcomes of this study were confirmed by in vitro biochemical assays and cellular investigations, showing that a new T9 analog is able to increase the LDLR expression on the liver cell surface by 84% at the concentration of 10 μM.
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Affiliation(s)
- Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Jacopo Sgrignani
- Istituto di Ricerca in Biomedicina (IRB), Università della Svizzera Italiana (USI), Via V. Vela 6, CH-6500 Bellinzona, Switzerland
| | - Gabriella Roda
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Anna Arnoldi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
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16
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Spinello A, Martini S, Berti F, Pennati M, Pavlin M, Sgrignani J, Grazioso G, Colombo G, Zaffaroni N, Magistrato A. Rational design of allosteric modulators of the aromatase enzyme: An unprecedented therapeutic strategy to fight breast cancer. Eur J Med Chem 2019; 168:253-262. [DOI: 10.1016/j.ejmech.2019.02.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/29/2022]
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17
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Grazioso G, Bollati C, Sgrignani J, Arnoldi A, Lammi C. First Food-Derived Peptide Inhibitor of the Protein-Protein Interaction between Gain-of-Function PCSK9 D374Y and the Low-Density Lipoprotein Receptor. J Agric Food Chem 2018; 66:10552-10557. [PMID: 30226051 DOI: 10.1021/acs.jafc.8b03233] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) is involved in cholesterol homeostasis, because it induces the low-density lipoprotein receptor (LDLR) degradation. This protein may carry some positive or negative mutations: PCSK9D374Y is one of the most dangerous gain-of-function mutations. This paper reports the identification of the first food-derived peptide able to inhibit the protein-protein interaction (PPI) between PCSK9D374Y and LDLR. In fact, T9 (GQEQSHQDEGVIVR), an absorbable peptide deriving from lupin β-conglutin, is able to impair the PPI between PCSK9D374Y and the LDLR, with an IC50 value equal to 285.6 ± 2.46 μM. The consequence of this inhibition is an increase of the protein level of the LDLR located on hepatic cell membranes up to 74.3 ± 4.4% and the restoration of the functional capability of HepG2 cells to uptake extracellular low-density lipoprotein up to 83.1 ± 1.6%. Finally, the putative binding mode of T9 to the LDLR binding site located on PCSK9D374Y was postulated by in silico tools.
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Affiliation(s)
- Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche , Università degli Studi di Milano , Via Luigi Mangiagalli 25 , 20133 Milan , Italy
| | - Carlotta Bollati
- Dipartimento di Scienze Farmaceutiche , Università degli Studi di Milano , Via Luigi Mangiagalli 25 , 20133 Milan , Italy
| | - Jacopo Sgrignani
- Istituto di Ricerca in Biomedicina (IRB) , Università della Svizzera Italiana (USI) , Via Vincenzo Vela 6 , CH-6500 Bellinzona , Switzerland
| | - Anna Arnoldi
- Dipartimento di Scienze Farmaceutiche , Università degli Studi di Milano , Via Luigi Mangiagalli 25 , 20133 Milan , Italy
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche , Università degli Studi di Milano , Via Luigi Mangiagalli 25 , 20133 Milan , Italy
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18
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Cattò C, Grazioso G, Dell'Orto S, Gelain A, Villa S, Marzano V, Vitali A, Villa F, Cappitelli F, Forlani F. The response of Escherichia coli biofilm to salicylic acid. Biofouling 2017; 33:235-251. [PMID: 28270055 DOI: 10.1080/08927014.2017.1286649] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
In this research, salicylic acid is proposed as an alternative biocide-free agent suitable for a preventive or integrative anti-biofilm approach. Salicylic acid has been proved to: (1) reduce bacterial adhesion up to 68.1 ± 5.6%; (2) affect biofilm structural development, reducing viable biomass by 97.0 ± 0.7% and extracellular proteins and polysaccharides by 83.9 ± 2.5% and 49.5 ± 5.5% respectively; and (3) promote biofilm detachment 3.4 ± 0.6-fold. Moreover, salicylic acid treated biofilm showed an increased amount of intracellular (2.3 ± 0.2-fold) and extracellular (2.1 ± 0.3-fold) reactive oxygen species, and resulted in increased production of the quorum sensing signal indole (7.6 ± 1.4-fold). For the first time, experiments revealed that salicylic acid interacts with proteins that play a role in quorum sensing, reactive oxygen species accumulation, motility, extracellular polymeric matrix components, transport and metabolism.
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Affiliation(s)
- Cristina Cattò
- a Department of Food Environmental and Nutritional Sciences , Università degli Studi di Milano , Milan , Italy
| | - Giovanni Grazioso
- b Department of Pharmaceutical Sciences , Università degli Studi di Milano , Milan , Italy
| | - Silvia Dell'Orto
- b Department of Pharmaceutical Sciences , Università degli Studi di Milano , Milan , Italy
| | - Arianna Gelain
- b Department of Pharmaceutical Sciences , Università degli Studi di Milano , Milan , Italy
| | - Stefania Villa
- b Department of Pharmaceutical Sciences , Università degli Studi di Milano , Milan , Italy
| | - Valeria Marzano
- c Institute of Biochemistry and Clinical Biochemistry , Catholic University , Rome , Italy
| | - Alberto Vitali
- d Institute of Chemistry of Molecular Recognition-UOS Roma , CNR , Rome , Italy
| | - Federica Villa
- a Department of Food Environmental and Nutritional Sciences , Università degli Studi di Milano , Milan , Italy
| | - Francesca Cappitelli
- a Department of Food Environmental and Nutritional Sciences , Università degli Studi di Milano , Milan , Italy
| | - Fabio Forlani
- a Department of Food Environmental and Nutritional Sciences , Università degli Studi di Milano , Milan , Italy
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19
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Legnani L, Colombo D, Venuti A, Pastori C, Lopalco L, Toma L, Mori M, Grazioso G, Villa S. Diazabicyclo analogues of maraviroc: synthesis, modeling, NMR studies and antiviral activity. Medchemcomm 2017; 8:422-433. [PMID: 30108760 PMCID: PMC6071814 DOI: 10.1039/c6md00575f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/12/2016] [Indexed: 01/07/2023]
Abstract
Two diazabicyclo analogues of maraviroc, in which the azabicyclooctane moiety is replaced by diazabicyclooctane or diazabicyclononane, were synthesized and tested, through a viral neutralization assay, on a panel of six pseudoviruses. The diazabicyclooctane derivative maintained a significant infectivity reduction power, whereas the diazabicyclononane was less effective. Biological data were rationalized through a computational study that allowed the conformational preferences of the compounds to be determined and a correlation between the inhibitory activity, the bridge length of the bicycle, and the rotational barrier around dihedral angle τ7 to be hypothesized. A high-field NMR analysis supported the modeling results.
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Affiliation(s)
- L Legnani
- Dipartimento di Chimica , Università di Pavia , Via Taramelli 12 , 27100 Pavia , Italy
- Dipartimento di Scienze del Farmaco , Università di Catania , V.le A. Doria 6 , 95125 Catania , Italy
| | - D Colombo
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , Via Saldini 50 , 20133 Milano , Italy
| | - A Venuti
- Division of Immunology, Transplantation and Infectious Diseases , San Raffaele Scientific Institute , Milan , Italy
| | - C Pastori
- Division of Immunology, Transplantation and Infectious Diseases , San Raffaele Scientific Institute , Milan , Italy
| | - L Lopalco
- Division of Immunology, Transplantation and Infectious Diseases , San Raffaele Scientific Institute , Milan , Italy
| | - L Toma
- Dipartimento di Chimica , Università di Pavia , Via Taramelli 12 , 27100 Pavia , Italy
| | - M Mori
- Dipartimento di Scienze Farmaceutiche , Università di Milano , Via L. Mangiagalli 25 , 20133 Milano , Italy . ; ; Tel: +39 02 503 19368
| | - G Grazioso
- Dipartimento di Scienze Farmaceutiche , Università di Milano , Via L. Mangiagalli 25 , 20133 Milano , Italy . ; ; Tel: +39 02 503 19368
| | - S Villa
- Dipartimento di Scienze Farmaceutiche , Università di Milano , Via L. Mangiagalli 25 , 20133 Milano , Italy . ; ; Tel: +39 02 503 19368
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20
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Sgrignani J, Grazioso G, De Amici M. Insight into the Mechanism of Hydrolysis of Meropenem by OXA-23 Serine-β-lactamase Gained by Quantum Mechanics/Molecular Mechanics Calculations. Biochemistry 2016; 55:5191-200. [PMID: 27534275 DOI: 10.1021/acs.biochem.6b00461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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
The fast and constant development of drug resistant bacteria represents a serious medical emergency. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this work, we investigated, at the atomistic level, the mechanisms of hydrolysis of Meropenem by OXA-23, a class D β-lactamase, combining unbiased classical molecular dynamics and umbrella sampling simulations with classical force field-based and quantum mechanics/molecular mechanics potentials. Our calculations provide a detailed structural and dynamic picture of the molecular steps leading to the formation of the Meropenem-OXA-23 covalent adduct, the subsequent hydrolysis, and the final release of the inactive antibiotic. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements, validating the expected reaction path.
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Affiliation(s)
- Jacopo Sgrignani
- Istituto di Chimica del Riconoscimento Molecolare, CNR , Via Mario Bianco 9, 20131 Milan, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Marco De Amici
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
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21
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Lammi C, Zanoni C, Aiello G, Arnoldi A, Grazioso G. Lupin Peptides Modulate the Protein-Protein Interaction of PCSK9 with the Low Density Lipoprotein Receptor in HepG2 Cells. Sci Rep 2016; 6:29931. [PMID: 27424515 PMCID: PMC4947907 DOI: 10.1038/srep29931] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [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: 04/01/2016] [Accepted: 06/23/2016] [Indexed: 12/20/2022] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) has been recently identified as a new useful target for hypercholesterolemia treatment. This work demonstrates that natural peptides, deriving from the hydrolysis of lupin protein and absorbable at intestinal level, are able to inhibit the protein-protein interaction between PCSK9 and the low density lipoprotein receptor (LDLR). In order to sort out the best potential inhibitors among these peptides, a refined in silico model of the PCSK9/LDLR interaction was developed. Docking, molecular dynamics (MD) simulations and peptide binding energy estimations, by MM-GBSA approach, permitted to select the two best candidates among tested peptides that were synthesized and evaluated for their inhibitory activity. The most active was P5 that induced a concentration dependent inhibition of the PCSK9-LDLR binding, with an IC50 value equal to 1.6 ± 0.33 μM. Tested at a 10 μM concentration, this peptide increased by 66 ± 21.4% the ability of HepG2 cells to take up LDL from the extracellular environment.
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Affiliation(s)
- Carmen Lammi
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Chiara Zanoni
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Gilda Aiello
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Anna Arnoldi
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
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22
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Stucchi M, Grazioso G, Lammi C, Manara S, Zanoni C, Arnoldi A, Lesma G, Silvani A. Disrupting the PCSK9/LDLR protein–protein interaction by an imidazole-based minimalist peptidomimetic. Org Biomol Chem 2016; 14:9736-9740. [DOI: 10.1039/c6ob01642a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a tetraimidazole-based β-strand minimalist peptidomimetic as a novel inhibitor of LDLR–PCSK9 protein–protein interaction, a promising target for hypercholesterolemia.
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Affiliation(s)
- Mattia Stucchi
- Dipartimento di Chimica
- Università degli Studi di Milano
- 20133 Milano
- Italy
- Dipartimento di Scienze della Vita
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Silvia Manara
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Chiara Zanoni
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Anna Arnoldi
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Giordano Lesma
- Dipartimento di Chimica
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Alessandra Silvani
- Dipartimento di Chimica
- Università degli Studi di Milano
- 20133 Milano
- Italy
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Stucchi M, Cairati S, Cetin-Atalay R, Christodoulou MS, Grazioso G, Pescitelli G, Silvani A, Yildirim DC, Lesma G. Application of the Ugi reaction with multiple amino acid-derived components: synthesis and conformational evaluation of piperazine-based minimalist peptidomimetics. Org Biomol Chem 2015; 13:4993-5005. [PMID: 25821154 DOI: 10.1039/c5ob00218d] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The concurrent employment of α-amino acid-derived chiral components such as aldehydes and α-isocyanoacetates, in a sequential Ugi reaction/cyclization two-step strategy, opens the door to the synthesis of three structurally distinct piperazine-based scaffolds, characterized by the presence of L-Ala and/or L-Phe-derived side chains and bearing appropriate functionalities to be easily applied in peptide chemistry. By means of computational studies, these scaffolds have been demonstrated to act as minimalist peptidomimetics, able to mimic a well defined range of peptide secondary structures and therefore potentially useful for the synthesis of small-molecule PPI modulators. Preliminary biological evaluation of two different resistant hepatocellular carcinoma cellular lines, for which differentiation versus resistance ability seem to be strongly correlated with well defined types of PPIs, has revealed a promising antiproliferative activity for selected compounds.
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Affiliation(s)
- Mattia Stucchi
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy.
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Grazioso G, Sgrignani J, Capelli R, Matera C, Dallanoce C, De Amici M, Cavalli A. Allosteric Modulation of Alpha7 Nicotinic Receptors: Mechanistic Insight through Metadynamics and Essential Dynamics. J Chem Inf Model 2015; 55:2528-39. [PMID: 26569022 DOI: 10.1021/acs.jcim.5b00459] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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
Increasing attention has recently been devoted to allosteric modulators, as they can provide inherent advantages over classic receptor agonists. In the field of nicotinic receptors (nAChRs), the main advantage is that allosteric modulators can trigger pharmacological responses, limiting receptor desensitization. Most of the known allosteric ligands are "positive allosteric modulators" (PAMs), which increase both sensitivity to receptor agonists and current amplitude. Intriguingly, some allosteric modulators are also able to activate the α7 receptor (α7-nAChR) even in the absence of orthosteric agonists. These compounds have been named "ago-allosteric modulators" and GAT107 has been studied in depth because of its unique mechanism of action. We here investigate by molecular dynamics simulations, metadynamics, and essential dynamics the activation mechanism of α7-nAChR, in the presence of different nicotinic modulators. We determine the free energy profiles associated with the closed-to-open motion of the loop C, and we highlight mechanistic differences observed in the presence of different modulators. In particular, we demonstrate that GAT107 triggers conformational motions and cross-talk similar to those observed when the α7-nACh receptor is in complex with both an agonist and an allosteric modulator.
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Affiliation(s)
- Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Jacopo Sgrignani
- Institute of Research in Biomedicine (IRB) , Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Romina Capelli
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Carlo Matera
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Clelia Dallanoce
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Marco De Amici
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Andrea Cavalli
- Drug Discovery and Development-Computation, Istituto Italiano di Tecnologia , Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotecnology, University of Bologna , Via Belmeloro 6, 40126 Bologna, Italy
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Sgrignani J, Novati B, Colombo G, Grazioso G. Covalent docking of selected boron-based serine beta-lactamase inhibitors. J Comput Aided Mol Des 2015; 29:441-50. [DOI: 10.1007/s10822-015-9834-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
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Sgrignani J, Grazioso G, De Amici M, Colombo G. Inactivation of TEM-1 by Avibactam (NXL-104): Insights from Quantum Mechanics/Molecular Mechanics Metadynamics Simulations. Biochemistry 2014; 53:5174-85. [DOI: 10.1021/bi500589x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jacopo Sgrignani
- Istituto di Chimica
del Riconscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milan, Italy
| | - Giovanni Grazioso
- Dipartimento
di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica “Pietro
Pratesi”, Università degli Studi di Milano, Via
Mangiagalli 25, 20133, Milan, Italy
| | - Marco De Amici
- Dipartimento
di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica “Pietro
Pratesi”, Università degli Studi di Milano, Via
Mangiagalli 25, 20133, Milan, Italy
| | - Giorgio Colombo
- Istituto di Chimica
del Riconscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milan, Italy
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Ettari R, Micale N, Grazioso G, Bova F, Schirmeister T, Grasso S, Zappalà M. Synthesis and Molecular Modeling Studies of Derivatives of a Highly Potent Peptidomimetic Vinyl Ester as Falcipain-2 Inhibitors. ChemMedChem 2012; 7:1594-600. [DOI: 10.1002/cmdc.201200274] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Indexed: 11/10/2022]
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Savion M, Memeo MG, Bovio B, Grazioso G, Legnani L, Quadrelli P. Synthesis and molecular modeling of novel dihydroxycyclopentane-carbonitrile nor-nucleosides by bromonitrile oxide 1,3-dipolar cycloaddition. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.12.086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Grazioso G, Limongelli V, Branduardi D, Novellino E, De Micheli C, Cavalli A, Parrinello M. Investigating the Mechanism of Substrate Uptake and Release in the Glutamate Transporter Homologue GltPh through Metadynamics Simulations. J Am Chem Soc 2011; 134:453-63. [DOI: 10.1021/ja208485w] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche “Pietro Pratesi”, Università degli Studi di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Vittorio Limongelli
- Department of Chemistry and Applied Biosciences, Eidgenössiche Technische Hochschule (ETH), Zurich, Switzerland
- Institute of Computational Science (ICS), Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Davide Branduardi
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genoa, Italy
| | - Ettore Novellino
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Carlo De Micheli
- Dipartimento di Scienze Farmaceutiche “Pietro Pratesi”, Università degli Studi di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Andrea Cavalli
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genoa, Italy
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, Eidgenössiche Technische Hochschule (ETH), Zurich, Switzerland
- Institute of Computational Science (ICS), Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
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30
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Pucci L, Grazioso G, Dallanoce C, Rizzi L, De Micheli C, Clementi F, Bertrand S, Bertrand D, Longhi R, De Amici M, Gotti C. Engineering of α-conotoxin MII-derived peptides with increased selectivity for native α6β2* nicotinic acetylcholine receptors. FASEB J 2011; 25:3775-89. [PMID: 21778325 DOI: 10.1096/fj.10-179853] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
α6β2* Nicotinic acetylcholine receptors are expressed in selected central nervous system areas, where they are involved in striatal dopamine (DA) release and its behavioral consequences, and other still uncharacterized brain activities. α6β2* receptors are selectively blocked by the α-conotoxins MII and PIA, which bear a characteristic N-terminal amino acid tail [arginine (R), aspartic acid (D), and proline (P)]. We synthesized a group of PIA-related peptides in which R1 was mutated or the RDP motif gradually removed. Binding and striatal DA release assays of native rat α6β2* receptors showed that the RDP sequence, and particularly residue R1, is essential for the activity of PIA. On the basis of molecular modeling analyses, we synthesized a hybrid peptide (RDP-MII) that had increased potency (7-fold) and affinity (13-fold) for α6β2* receptors but not for the very similar α3β2* subtype. As docking studies also suggested that E11 of MII might be a key residue engendering α6β2* vs. α3β2* selectivity, we prepared MII[E11R] and RDP-MII[E11R] peptides. Their affinity and potency for native α6β2* receptors were similar to those of their parent analogues, whereas, for the oocyte expressed rat α3β2* subtype, they showed a 31- and 14-fold lower affinity and 21- and 3.5-fold lower potency. Thus, MII[E11R] and RDP-MII[E11R] are potent antagonists showing a degree of α6β2* vs. α3β2* selectivity in vivo.
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Affiliation(s)
- Luca Pucci
- Consiglio Nazionale delle Ricerche, Istituto di Neuroscienze, Farmacologia Cellulare e Molecolare e Dipartimento di Farmacologia, Chemioterapia e Tossicologia Medica, Milan, Italy
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31
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Legnani L, Compostella F, Grazioso G, Albini FM, Toma L. Molecular dynamics simulations of the Salmonella typhi Vi antigenic polysaccharide and effects of the introduction of a zwitterionic motif. Org Biomol Chem 2011; 9:5554-9. [PMID: 21701726 DOI: 10.1039/c1ob05617d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of hexasaccharides corresponding to the Vi capsular polysaccharide, a polymer of α-(1→4)-galacturonic acid, and analogs containing a zwitterionic motif with various degrees of acetylation at positions 3 have been modeled. When submitted to molecular dynamics simulations in a water box, all the structures visited only two quite restricted regions of the φ/ψ conformational space both corresponding to extended geometries without any tendency towards supercoiling. The most stable conformation showed a clockwise helix arrangement of substituents on the molecular surface whereas the opposite arrangement was observed for the other conformation. The flexibility of the system and the hydrophobic character of the molecular surface are modulated by the 3-O-acetyl groups that confer rigidity to the system. In the zwitterionic analogs, the introduction of positive charges in the place of the acetamido groups alters the hydrophobicity that can be regained by methylation of the amino groups. The needed molecular flexibility can be obtained by the complete deacetylation at positions 3.
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Affiliation(s)
- Laura Legnani
- Dipartimento di Chimica, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
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32
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Dallanoce C, Magrone P, Matera C, Frigerio F, Grazioso G, De Amici M, Fucile S, Piccari V, Frydenvang K, Pucci L, Gotti C, Clementi F, De Micheli C. Design, synthesis, and pharmacological characterization of novel spirocyclic quinuclidinyl-Δ2-isoxazoline derivatives as potent and selective agonists of α7 nicotinic acetylcholine receptors. ChemMedChem 2011; 6:889-903. [PMID: 21365765 DOI: 10.1002/cmdc.201000514] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 01/13/2011] [Indexed: 11/08/2022]
Abstract
A set of racemic spirocyclic quinuclidinyl-Δ(2)-isoxazoline derivatives was synthesized using a 1,3-dipolar cycloaddition-based approach. Target compounds were assayed for binding affinity toward rat neuronal homomeric (α7) and heteromeric (α4β2) nicotinic acetylcholine receptors. Δ(2) -Isoxazolines 3 a (3-Br), 6 a (3-OMe), 5 a (3-Ph), 8 a (3-OnPr), and 4 a (3-Me) were the ligands with the highest affinity for the α7 subtype (K(i) values equal to 13.5, 14.2, 25.0, 71.6, and 96.2 nM, respectively), and showed excellent α7 versus α4β2 subtype selectivity. These compounds, tested in electrophysiological experiments against human α7 and α4β2 receptors stably expressed in cell lines, behaved as partial α7 agonists with varying levels of potency. The two enantiomers of (±)-3-methoxy-1-oxa-2,7-diaza-7,10-ethanospiro[4.5]dec-2-ene sesquifumarate 6 a were prepared using (+)-dibenzoyl-L- or (-)-dibenzoyl-D-tartaric acid as resolving agents. Enantiomer (R)-(-)-6 a was found to be the eutomer, with K(i) values of 4.6 and 48.7 nM against rat and human α7 receptors, respectively.
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Affiliation(s)
- Clelia Dallanoce
- Dipartimento di Scienze Farmaceutiche Pietro Pratesi, Università degli Studi di Milano, Milan, Italy
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Dallanoce C, Frigerio F, Martelli G, Grazioso G, Matera C, Pomè DY, Pucci L, Clementi F, Gotti C, Amici MD. Novel tricyclic Δ2-isoxazoline and 3-oxo-2-methyl-isoxazolidine derivatives: Synthesis and binding affinity at neuronal nicotinic acetylcholine receptor subtypes. Bioorg Med Chem 2010; 18:4498-508. [DOI: 10.1016/j.bmc.2010.04.065] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 04/20/2010] [Accepted: 04/21/2010] [Indexed: 10/19/2022]
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Sgrignani J, Bonaccini C, Grazioso G, Chioccioli M, Cavalli A, Gratteri P. Insights into docking and scoring neuronal alpha4beta2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations. J Comput Chem 2009; 30:2443-54. [PMID: 19360794 DOI: 10.1002/jcc.21251] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A combined quantum mechanical (QM)-polarized docking and molecular dynamics approach to study the binding mode and to predict the binding affinity of ligands acting at the alpha4beta2-nAChR is presented. The results obtained in this study indicate that the quantum mechanical/molecular mechanics docking protocol well describes the charge-driven interactions occurring in the binding of nicotinic agonists, and it is able to represent the polarization effects on the ligand exerted by the surrounding atoms of the receptor at the binding site. This makes it possible to properly score agonists of alpha4beta2-nAChR and to reproduce the experimental binding affinity data with good accuracy, within a mean error of 2.2 kcal/mol. Moreover, applying the QM-polarized docking to an ensemble of nAChR conformations obtained from MD simulations enabled us to accurately capture nAChR-ligand induced-fit effects.
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Affiliation(s)
- Jacopo Sgrignani
- Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy
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Dallanoce C, Magrone P, Bazza P, Grazioso G, Rizzi L, Riganti L, Gotti C, Clementi F, Frydenvang K, De Amici M. New Analogues of Epiboxidine Incorporating the 4,5-Dihydroisoxazole Nucleus: Synthesis, Binding Affinity at Neuronal Nicotinic Acetylcholine Receptors, and Molecular Modeling Investigations. Chem Biodivers 2009; 6:244-59. [DOI: 10.1002/cbdv.200800077] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Calabrò ML, Raneri D, Ficarra P, Mennini T, Colleoni S, Grazioso G, Micale N, Zappalà M, Grasso S. Synthesis, chiral resolution and pharmacological evaluation of a 2,3-benzodiazepine-derived noncompetitive AMPA receptor antagonist. ChemMedChem 2009; 4:415-20. [PMID: 19137515 DOI: 10.1002/cmdc.200800341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The resolution of 1-(4-aminophenyl)-3,5-dihydro-3-N-ethylcarbamoyl-5-methyl-7,8-methylenedioxy-4H-2,3-benzodiazepin-4-one (R,S)-(+/-)-5 by chiral HPLC and assignment of the absolute configuration of the two enantiomers was carried out. Compound (R,S)-(+/-)-5 and its enantiomers were tested in a binding assay to evaluate their affinity for AMPA receptors. Enantiomer (S)-(-)-5 appears to be more potent than its optical antipode (R)-(+)-5. In a primary culture of rat cerebellar granule cells, which express AMPA receptors, (R,S)-(+/-)-5 and (S)-(-)-5 inhibited kainate- induced [Ca(2+)](i) increase, thus confirming the antagonism at the AMPA receptor.
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Affiliation(s)
- Maria Luisa Calabrò
- Dipartimento Farmaco Chimico, University of Messina, Via le Annunziata, 98168, Messina, Italy
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Grazioso G, Cavalli A, De Amici M, Recanatini M, De Micheli C. Alpha7 nicotinic acetylcholine receptor agonists: prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach. J Comput Chem 2008; 29:2593-602. [PMID: 18478580 DOI: 10.1002/jcc.21019] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A group of agonists for the alpha7 neuronal nicotinic acetylcholine receptors (nAChRs) was investigated, and their free energies of binding DeltaG(bind) were calculated by applying the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach. This method, based on molecular dynamics simulations of fully solvated protein-ligand complexes, allowed us to estimate the contribution of both polar and nonpolar terms as well as the entropy to the overall free energy of binding. The calculated results were in a good agreement with the experimentally determined DeltaG(bind) values, thereby pointing to the MM-PBSA protocol as a valuable computational tool for the rational design of specific agents targeting the neuronal alpha7 nAChR subtypes.
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Affiliation(s)
- Giovanni Grazioso
- Istituto di Chimica Farmaceutica e Tossicologica "Pietro Pratesi", Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
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Conti P, Pinto A, Tamborini L, Grazioso G, De Sarro G, Bräuner-Osborne H, Szabo G, Gábor Hársing L, De Micheli C. Synthesis of conformationally constrained glutamic acid homologues and investigation of their pharmacological profiles. ChemMedChem 2008; 2:1639-47. [PMID: 17849399 DOI: 10.1002/cmdc.200700118] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [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: 11/06/2022]
Abstract
Homologation of the glutamic acid chain together with conformational constraint is a commonly used strategy to achieve selectivity towards different types of glutamate receptors. We investigated the effects of a further increase in the distance between the amino acid moiety and the distal carboxylate group of model compounds (+/-)-1 and (+/-)-2 on their activity/selectivity profiles. We therefore synthesized new derivatives (+/-)-3-(+/-)-6, which are homologues of glutamic acid containing three additional carbon units. Moreover, because the potency of NMDA antagonists can be markedly increased by replacing the distal carboxylate with the bioisosteric phosphonate group, we also prepared the corresponding phosphonate derivatives (+/-)-7-(+/-)-10. All new compounds were submitted to binding assays with iGluRs, and derivatives (+/-)-3-(+/-)-6 were also tested in second messenger assays at representative mGluR subtypes. All the applied structural modifications were detrimental to the interaction with NMDA receptors. Conversely, structural variation of the nonselective mGluR ligand (+/-)-2 led to derivative (+/-)-5, which behaved as a selective group I metabotropic receptor antagonist. Notably, upon i.c.v. administration in DBA/2 mice, amino acid (+/-)-5 produced a significant protection against audiogenic seizures, whereas it was inactive after i.p. administration.
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Affiliation(s)
- Paola Conti
- Istituto di Chimica Farmaceutica e Tossicologica Pietro Pratesi, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy.
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Conti P, Grazioso G, di Ventimiglia SJ, Pinto A, Roda G, Madsen U, Bräuner-Osborne H, Nielsen B, Costagli C, Galli A. Synthesis of novel N1-substituted bicyclic pyrazole amino acids and evaluation of their interaction with glutamate receptors. Chem Biodivers 2006; 2:748-57. [PMID: 17192018 DOI: 10.1002/cbdv.200590052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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: 11/07/2022]
Abstract
N1-substituted bicyclic pyrazole amino acids (S)-9a-9c and (R)-9a-9c, which are conformationally constrained analogues of glutamic acid, were prepared via a strategy based on a 1,3-dipolar cycloaddition. The new amino acids were tested for activity at ionotropic and metabotropic glutamate receptors. Some of them turned out to be selective for the NMDA receptors, where they behaved as weak antagonists. The biological activity is mainly due to the interaction with the glutamate binding site, and not with the glycine co-agonist site.
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Affiliation(s)
- Paola Conti
- Istituto di Chimica Farmaceutica e Tossicologica, Università degli Studi di Milano, Viale Abruzzi 42, I-20131 Milano.
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Conti P, De Amici M, Pinto A, Tamborini L, Grazioso G, Frølund B, Nielsen B, Thomsen C, Ebert B, De Micheli C. Synthesis of 3-Hydroxy- and 3-Carboxy-Δ2-isoxazoline Amino Acids and Evaluation of Their Interaction with GABA Receptors and Transporters. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600628] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Dallanoce C, Bazza P, Grazioso G, De Amici M, Gotti C, Riganti L, Clementi F, De Micheli C. Synthesis of Epibatidine-Related Δ2-Isoxazoline Derivatives and Evaluation of Their Binding Affinity at Neuronal Nicotinic Acetylcholine Receptors. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600231] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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42
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Dallanoce C, Bazza P, Grazioso G, Amici MD, Micheli CD. Synthesis of novel epibatidine-related derivatives through 1,3-dipolar cycloaddition of pyridinenitrile oxides. ARKIVOC 2006. [DOI: 10.3998/ark.5550190.0007.803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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43
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Zappalà M, Postorino G, Micale N, Caccamese S, Parrinello N, Grazioso G, Roda G, Menniti FS, De Sarro G, Grasso S. Synthesis, Chiral Resolution, and Enantiopharmacology of a Potent 2,3-Benzodiazepine Derivative as Noncompetitive AMPA Receptor Antagonist. J Med Chem 2005; 49:575-81. [PMID: 16420043 DOI: 10.1021/jm050552y] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [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: 11/28/2022]
Abstract
This paper describes the synthesis of racemic 3,5-dihydro-5-methyl-7,8-methylenedioxy-4H-2,3-benzodiazepin-4-one (+/-)-5, attempted stereoselective synthesis of its enantiomers, chiral HPLC resolution of the racemate, and assignment of the absolute configuration. Enantiomer (5S)-(-)-5 is provided with an in vivo anticonvulsant activity 8 times higher than its enantiomer (5R)-(+)-5. This result is confirmed in the in vitro test by the ability to inhibit the kainate-induced increase of the [Ca(2+)](i) in a primary culture of rat cerebellar granule cells which express alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors. Binding affinity of compound (+/-)-5 at the AMPA and N-methyl-d-aspartic acid (NMDA) receptors was also evaluated.
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Affiliation(s)
- Maria Zappalà
- Dipartimento Farmaco-Chimico, Università di Messina, 98168 Messina, Italy
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Conti P, De Amici M, Grazioso G, Roda G, Pinto A, Hansen KB, Nielsen B, Madsen U, Bräuner-Osborne H, Egebjerg J, Vestri V, Pellegrini-Giampietro DE, Sibille P, Acher FC, De Micheli C. Synthesis, binding affinity at glutamic acid receptors, neuroprotective effects, and molecular modeling investigation of novel dihydroisoxazole amino acids. J Med Chem 2005; 48:6315-25. [PMID: 16190758 DOI: 10.1021/jm0504499] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [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: 11/29/2022]
Abstract
The four stereoisomers of 5-(2-amino-2-carboxyethyl)-4,5-dihydroisoxazole-3-carboxylic acid(+)-4, (-)-4, (+)-5, and (-)-5 were prepared by stereoselective synthesis of two pairs of enantiomers, which were subsequently resolved by enzymatic procedures. These four stereoisomers and the four stereoisomers of the bicyclic analogue 5-amino-4,5,6,6a-tetrahydro-3aH-cyclopenta[d]isoxazole-3,5-dicarboxylic acid (+)-2, (-)-2, (+)-3, and (-)-3 were tested at ionotropic and metabotropic glutamate receptor subtypes. The most potent NMDA receptor antagonists [(+)-2, (-)-4, and (+)-5] showed a significant neuroprotective effect when tested in an oxygen glucose deprivation (OGD) cell culture test. The same compounds were preliminarily assayed using Xenopus oocytes expressing cloned rat NMDA receptors containing the NR1 subunit in combination with either NR2A, NR2B, NR2C, or NR2D subunit. In this assay, all three derivatives showed high antagonist potency with preference for the NR2A and NR2B subtypes, with derivative (-)-4 behaving as the most potent antagonist. The biological data are discussed on the basis of homology models reported in the literature for NMDA receptors and mGluRs.
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MESH Headings
- Amino Acids/chemical synthesis
- Amino Acids/chemistry
- Amino Acids/pharmacology
- Animals
- Binding Sites
- CHO Cells
- Cells, Cultured
- Cerebral Cortex/cytology
- Cerebral Cortex/metabolism
- Cricetinae
- Cricetulus
- Female
- In Vitro Techniques
- Isoxazoles/chemical synthesis
- Isoxazoles/chemistry
- Isoxazoles/pharmacology
- Mice
- Models, Molecular
- Neuroprotective Agents/chemical synthesis
- Neuroprotective Agents/chemistry
- Neuroprotective Agents/pharmacology
- Oocytes/drug effects
- Oocytes/physiology
- Patch-Clamp Techniques
- Protein Subunits/chemistry
- Protein Subunits/genetics
- Protein Subunits/metabolism
- Radioligand Assay
- Rats
- Receptors, Glutamate/drug effects
- Receptors, Glutamate/genetics
- Receptors, Glutamate/metabolism
- Receptors, Metabotropic Glutamate/agonists
- Receptors, Metabotropic Glutamate/chemistry
- Receptors, Metabotropic Glutamate/genetics
- Receptors, N-Methyl-D-Aspartate/antagonists & inhibitors
- Receptors, N-Methyl-D-Aspartate/chemistry
- Receptors, N-Methyl-D-Aspartate/genetics
- Second Messenger Systems/drug effects
- Stereoisomerism
- Structure-Activity Relationship
- Xenopus laevis
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Affiliation(s)
- Paola Conti
- Istituto di Chimica Farmaceutica e Tossicologica, Università degli Studi di Milano, Viale Abruzzi 42, 20131 Milano, Italy
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Grazioso G, Moretti L, Scapozza L, De Amici M, De Micheli C. Development of a three-dimensional model for the N-methyl-D-aspartate NR2A subunit. J Med Chem 2005; 48:5489-94. [PMID: 16107147 DOI: 10.1021/jm050174x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [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: 11/29/2022]
Abstract
NR2 subunits of N-methyl-d-aspartic acid (NMDA) receptors are known to bind the neurotransmitter glutamate, competitive agonists, and antagonists. Since crystallographic data of these proteins are not available, we built a homology model of the ligand binding domain of the NR2A subunit. A consensus binding mode of selected AP5-like NMDA antagonists has been ascertained using molecular docking. The present 3D model gives insights for the design of new NMDA subtype selective compounds.
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Affiliation(s)
- Giovanni Grazioso
- Istituto di Chimica Farmaceutica e Tossicologica, Università degli Studi di Milano, Viale Abruzzi 42, 20131 Milano, Italy
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46
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Conti P, De Amici M, Grazioso G, Roda G, Barberis Negra FF, Nielsen B, Stensbøl TB, Madsen U, Bräuner-Osborne H, Frydenvang K, De Sarro G, Toma L, De Micheli C. Design, Synthesis, and Pharmacological Characterization of Novel, Potent NMDA Receptor Antagonists. J Med Chem 2004; 47:6740-8. [PMID: 15615523 DOI: 10.1021/jm049409f] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [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: 11/30/2022]
Abstract
The two diastereomeric pairs of acidic amino acids 5-(2-amino-2-carboxyethyl)-4,5-dihydroisoxazole-3-carboxylic acid (8A/8B) and 4-(2-amino-2-carboxyethyl)-5,5-dimethyl-4,5-dihydroisoxazole-3-carboxylic acid (10A/10B) were prepared via a strategy based on a 1,3-dipolar cycloaddition. The four amino acids were tested at ionotropic and metabotropic glutamate receptors. None of the compounds was active, neither as agonists nor as antagonists, at 1 mM on metabotropic receptors (mGluR1, -2, -4, and -5 expressed in CHO cell lines). Conversely, the pair of stereoisomers 8A/8B showed a remarkable affinity, antagonist potency, and selectivity for NMDA receptors, when tested on ionotropic glutamate receptors. The affinity of 8A proved to be 5 times higher than that of diastereomer 8B (K(i) values 0.21 and 0.96 microM, respectively). Furthermore, compounds 8A and 8B exhibited a noteworthy anticonvulsant activity in in vivo tests on DBA/2 mice. Derivative 10A was inactive at all ionotropic glutamate receptors, whereas its stereoisomer 10B displayed a seizable binding to both NMDA and AMPA receptors.
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Affiliation(s)
- Paola Conti
- Istituto di Chimica Farmaceutica e Tossicologica, Università degli Studi di Milano, Viale Abruzzi 42, 20131 Milano, Italy
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Conti P, De Amici M, Grazioso G, Roda G, Stensbøl T, Bräuner-Osborne H, Madsen U, Toma L, De Micheli C. Design of Cyclopentaisoxazoline Amino Acids as Conformationally Constrained Agonists at Glutamate Receptors. European J Org Chem 2003. [DOI: 10.1002/ejoc.200300424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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