1
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Siani P, Frigerio G, Donadoni E, Di Valentin C. Molecular dynamics simulations of cRGD-conjugated PEGylated TiO 2 nanoparticles for targeted photodynamic therapy. J Colloid Interface Sci 2022; 627:126-141. [PMID: 35842963 DOI: 10.1016/j.jcis.2022.07.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 12/20/2022]
Abstract
The conjugation of high-affinity cRGD-containing peptides is a promising approach in nanomedicine to efficiently reduce off-targeting effects and enhance the cellular uptake by integrin-overexpressing tumor cells. Herein we utilize atomistic molecular dynamics simulations to evaluate key structural-functional parameters of these targeting ligands for an effective binding activity towards αVβ3 integrins. An increasing number of cRGD ligands is conjugated to PEG chains grafted to highly curved TiO2 nanoparticles to unveil the impact of cRGD density on the ligand's presentation, stability, and conformation in an explicit aqueous environment. We find that a low density leads to an optimal spatial presentation of cRGD ligands out of the "stealth" PEGylated layer around the nanosystem, favoring a straight upward orientation and spaced distribution of the targeting ligands in the bulk-water phase. On the contrary, high densities favor over-clustering of cRGD ligands, driven by a concerted mechanism of enhanced ligand-ligand interactions and reduced water accessibility over the ligand's molecular surface. These findings strongly suggest that the ligand density modulation is a key factor in the design of cRGD-targeting nanodevices to maximize their binding efficiency into over-expressed αVβ3 integrin receptors.
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Affiliation(s)
- Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Giulia Frigerio
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Edoardo Donadoni
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy; BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, Italy.
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2
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Thakare P, Vasile F, Vallaro M, Visentin S, Caron G, Licandro E, Cauteruccio S. Acid-base and lipophilic properties of peptide nucleic acid derivatives. J Pharm Anal 2021; 11:638-645. [PMID: 34765277 PMCID: PMC8572665 DOI: 10.1016/j.jpha.2020.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/26/2022] Open
Abstract
The first combined experimental and theoretical study on the ionization and lipophilic properties of peptide nucleic acid (PNA) derivatives, including eleven PNA monomers and two PNA decamers, is described. The acidity constants (pKa) of individual acidic and basic centers of PNA monomers were measured by automated potentiometric pH titrations in water/methanol solution, and these values were found to be in agreement with those obtained by MoKa software. These results indicate that single nucleobases do not change their pKa values when included in PNA monomers and oligomers. In addition, immobilized artificial membrane chromatography was employed to evaluate the lipophilic properties of PNA monomers and oligomers, which showed the PNA derivatives had poor affinity towards membrane phospholipids, and confirmed their scarce cell penetrating ability. Overall, our study not only is of potential relevance to evaluate the pharmacokinetic properties of PNA, but also constitutes a reliable basis to properly modify PNA to obtain mimics with enhanced cell penetration properties. The first study on acid-base and lipophilic properties of peptide nucleic acids (PNA). pKa of acid-base centers of PNA evaluated by potentiometric method and MoKa prediction. NMR experiments provide additional information on the protonation of PNA monomers. Lipophilicity of PNA monomers and oligomers is investigated by IAM chromatography. This study can lay the basis of evaluating the pharmacokinetic properties of PNA.
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Affiliation(s)
- Pramod Thakare
- Department of Chemistry, University of Milan, 20133, Milan, Italy
| | - Francesca Vasile
- Department of Chemistry, University of Milan, 20133, Milan, Italy
| | - Maura Vallaro
- Molecular Biotechnology & Health Sciences Department, University of Turin, 10135, Turin, Italy
| | - Sonja Visentin
- Molecular Biotechnology & Health Sciences Department, University of Turin, 10135, Turin, Italy
| | - Giulia Caron
- Molecular Biotechnology & Health Sciences Department, University of Turin, 10135, Turin, Italy
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3
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Ermondi G, Lavore F, Vallaro M, Tiana G, Vasile F, Caron G. Managing Experimental 3D Structures in the Beyond-Rule-of-5 Chemical Space: The Case of Rifampicin. Chemistry 2021; 27:10394-10404. [PMID: 34114271 PMCID: PMC8361677 DOI: 10.1002/chem.202100961] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Indexed: 12/29/2022]
Abstract
The beyond-Rule-of-5 (bRo5) chemical space is a source of new oral drugs and includes large and flexible compounds. Because of their size and conformational variability, bRo5 molecules assume different privileged conformations in the compartments of human body, i. e., they can exhibit chameleonic properties. The elucidation of the ensemble of 3D structures explored by such molecules under different conditions is therefore critical to check the role played by chameleonicity to modulate cell permeability. Here we characterized the conformational ensembles of rifampicin, a bRo5 drug, in polar and nonpolar solvents and in the solid state. We performed NMR experiments, analyzed their results with a novel algorithm and set-up a pool of ad hoc in silico strategies to investigate crystallographic structures retrieved from the CSD. Moreover, a polarity descriptor often related to permeability (SA-3D-PSA) was calculated for all the conformers and its variation with the environment analyzed. Results showed that the conformational behavior of rifampicin in solution and in the solid state is not superposable. The identification of dynamic intramolecular hydrogen bonds can be assessed by NMR spectroscopy but not by X-ray structures. Moreover, SA-3D-PSA revealed that dynamic IMHBs do not provide rifampicin with chameleonic properties. Overall, this study highlights that the peculiarity of rifampicin, which is cell permeable probably because of the presence of static IMHBs but is devoid of any chameleonic behavior, can be assessed by a proper analysis of experimental 3D structures.
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Affiliation(s)
- Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept.Università degli Studi di Torinovia Quarello 1510135TorinoItaly
| | - Francesca Lavore
- Department of ChemistryUniversità degli Studi di Milanovia Golgi 1920133MilanoItaly
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept.Università degli Studi di Torinovia Quarello 1510135TorinoItaly
| | - Guido Tiana
- Department of Physics and Center for Complexity and BiosystemsUniversità degli Studi di Milano and INFNvia Celoria 1620133MilanoItaly
| | - Francesca Vasile
- Department of ChemistryUniversità degli Studi di Milanovia Golgi 1920133MilanoItaly
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Dept.Università degli Studi di Torinovia Quarello 1510135TorinoItaly
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4
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Ambrosio FA, Coricello A, Costa G, Lupia A, Micaelli M, Marchesi N, Sala F, Pascale A, Rossi D, Vasile F, Alcaro S, Collina S. Identification of Compounds Targeting HuD. Another Brick in the Wall of Neurodegenerative Disease Treatment. J Med Chem 2021; 64:9989-10000. [PMID: 34219450 DOI: 10.1021/acs.jmedchem.1c00191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
ELAV-like (ELAVL) RNA-binding proteins play a pivotal role in post-transcriptional processes, and their dysregulation is involved in several pathologies. This work was focused on HuD (ELAVL4), which is specifically expressed in nervous tissues, and involved in differentiation and synaptic plasticity mechanisms. HuD represents a new, albeit unexplored, candidate target for the treatment of several relevant neurodegenerative diseases. The aim of this pioneering work was the identification of new molecules able to recognize and bind HuD, thus interfering with its activity. We combined virtual screening, molecular dynamics (MD), and STD-NMR techniques. Starting from around 51 000 compounds, four promising hits eventually provided experimental evidence of their ability to bind HuD. Among the selected best hits, folic acid was found to be the most interesting one, being able to well recognize the HuD binding site. Our results provide a basis for the identification of new HuD interfering compounds which may be useful against neurodegenerative syndromes.
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Affiliation(s)
- Francesca Alessandra Ambrosio
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Campus "S. Venuta", 88100 Catanzaro, Italy
| | - Adriana Coricello
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Campus "S. Venuta", 88100 Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Campus "S. Venuta", 88100 Catanzaro, Italy.,Net4Science Academic Spin-Off, Università "Magna Græcia" di Catanzaro, Campus "S. Venuta", 88100 Catanzaro, Italy.,Associazione CRISEA-Centro di Ricerca e Servizi Avanzati per l'Innovazione Rurale, Località Condoleo, Belcastro, Catanzaro, Italy
| | - Antonio Lupia
- Net4Science Academic Spin-Off, Università "Magna Græcia" di Catanzaro, Campus "S. Venuta", 88100 Catanzaro, Italy.,Associazione CRISEA-Centro di Ricerca e Servizi Avanzati per l'Innovazione Rurale, Località Condoleo, Belcastro, Catanzaro, Italy
| | - Mariachiara Micaelli
- CIBIO-Department of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, Povo, 38123 Trento, Italy
| | - Nicoletta Marchesi
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Federico Sala
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy.,Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy
| | - Alessia Pascale
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Francesca Vasile
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Campus "S. Venuta", 88100 Catanzaro, Italy.,Net4Science Academic Spin-Off, Università "Magna Græcia" di Catanzaro, Campus "S. Venuta", 88100 Catanzaro, Italy.,Associazione CRISEA-Centro di Ricerca e Servizi Avanzati per l'Innovazione Rurale, Località Condoleo, Belcastro, Catanzaro, Italy
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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5
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Panzeri S, Arosio D, Gazzola S, Belvisi L, Civera M, Potenza D, Vasile F, Kemker I, Ertl T, Sewald N, Reiser O, Piarulli U. Cyclic RGD and isoDGR Integrin Ligands Containing cis-2-amino-1-cyclopentanecarboxylic ( cis-β-ACPC) Scaffolds. Molecules 2020; 25:molecules25245966. [PMID: 33339382 PMCID: PMC7766232 DOI: 10.3390/molecules25245966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023] Open
Abstract
Integrin ligands containing the tripeptide sequences Arg-Gly-Asp (RGD) and iso-Asp-Gly- Arg (isoDGR) were actively investigated as inhibitors of tumor angiogenesis and directing unit in tumor-targeting drug conjugates. Reported herein is the synthesis, of two RGD and one isoDGR cyclic peptidomimetics containing (1S,2R) and (1R,2S) cis-2-amino-1-cyclopentanecarboxylic acid (cis-β-ACPC), using a mixed solid phase/solution phase synthetic protocol. The three ligands were examined in vitro in competitive binding assays to the purified αvβ3 and α5β1 receptors using biotinylated vitronectin (αvβ3) and fibronectin (α5β1) as natural displaced ligands. The IC50 values of the ligands ranged from nanomolar (the two RGD ligands) to micromolar (the isoDGR ligand) with a pronounced selectivity for αvβ3 over α5β1. In vitro cell adhesion assays were also performed using the human skin melanoma cell line WM115 (rich in integrin αvβ3). The two RGD ligands showed IC50 values in the same micromolar range as the reference compound (cyclo[RGDfV]), while for the isoDGR derivative an IC50 value could not be measured for the cell adhesion assay. A conformational analysis of the free RGD and isoDGR ligands by NMR (VT-NMR and NOESY experiments) and computational studies (MC/EM and MD), followed by docking simulations performed in the αVβ3 integrin active site, provided a rationale for the behavior of these ligands toward the receptor.
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Affiliation(s)
- Silvia Panzeri
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy; (S.P.); (S.G.)
- Institute of Organic Chemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany; (T.E.); (O.R.)
| | - Daniela Arosio
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Scienze e Tecnologie Chimiche (SCITEC), Giulio Natta, Via C. Golgi 19, 20133 Milan, Italy;
| | - Silvia Gazzola
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy; (S.P.); (S.G.)
| | - Laura Belvisi
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milan, Italy; (L.B.); (M.C.); (D.P.); (F.V.)
| | - Monica Civera
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milan, Italy; (L.B.); (M.C.); (D.P.); (F.V.)
| | - Donatella Potenza
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milan, Italy; (L.B.); (M.C.); (D.P.); (F.V.)
| | - Francesca Vasile
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milan, Italy; (L.B.); (M.C.); (D.P.); (F.V.)
| | - Isabell Kemker
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany; (I.K.); (N.S.)
| | - Thomas Ertl
- Institute of Organic Chemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany; (T.E.); (O.R.)
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany; (I.K.); (N.S.)
| | - Oliver Reiser
- Institute of Organic Chemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany; (T.E.); (O.R.)
| | - Umberto Piarulli
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy; (S.P.); (S.G.)
- Correspondence:
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6
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Lazzari F, Manfredi A, Alongi J, Ganazzoli F, Vasile F, Raffaini G, Ferruti P, Ranucci E. Hydrogen Bonding in a l-Glutamine-Based Polyamidoamino Acid and its pH-Dependent Self-Ordered Coil Conformation. Polymers (Basel) 2020; 12:E881. [PMID: 32290338 PMCID: PMC7240574 DOI: 10.3390/polym12040881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/29/2022] Open
Abstract
This paper reports on synthesis, acid-base properties, and self-structuring in water of a chiral polyamidoamino acid, M-l-Gln, obtained from the polyaddition of N,N'-methylenebisacrylamide with l-glutamine, with the potential of establishing hydrogen bonds through its prim-amide pendants. The M-l-Gln showed pH-responsive circular dichroism spectra, revealing ordered conformations. Structuring was nearly insensitive to ionic strength but sensitive to denaturing agents. The NMR diffusion studies were consistent with a population of unimolecular nanoparticles thus excluding aggregation. The M-l-Gln had the highest molecular weight and hydrodynamic radius among all polyamidoamino acids described. Possibly, transient hydrogen bonds between l-glutamine molecules and M-l-Gln growing chains facilitated the polyaddition reaction. Theoretical modeling showed that M-l-Gln assumed pH-dependent self-ordered coil conformations with main chain transoid arrangements reminiscent of the protein hairpin motif owing to intramolecular dipole moments and hydrogen bonds. The latter were most numerous at the isoelectric point (pH 4.5), where they mainly involved even topologically distant main chain amide N-H and side chain amide C=O brought to proximity by structuring. Hydrogen bonds at pH 4.5 were also suggested by variable temperature NMR. The 2D NOESY experiments at pH 4.5 confirmed the formation of compact structures through the analysis of the main chain/side chain hydrogen contacts, in line with MD simulations.
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Affiliation(s)
- Federica Lazzari
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy; (F.L.); (A.M.); (J.A.); (F.V.)
| | - Amedea Manfredi
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy; (F.L.); (A.M.); (J.A.); (F.V.)
| | - Jenny Alongi
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy; (F.L.); (A.M.); (J.A.); (F.V.)
| | - Fabio Ganazzoli
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica “G. Natta” Politecnico di Milano, Piazza Leonardo da Vinci 32, 20131 Milano, Italy;
| | - Francesca Vasile
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy; (F.L.); (A.M.); (J.A.); (F.V.)
| | - Giuseppina Raffaini
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica “G. Natta” Politecnico di Milano, Piazza Leonardo da Vinci 32, 20131 Milano, Italy;
| | - Paolo Ferruti
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy; (F.L.); (A.M.); (J.A.); (F.V.)
| | - Elisabetta Ranucci
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy; (F.L.); (A.M.); (J.A.); (F.V.)
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7
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Cavalloro V, Russo K, Vasile F, Pignataro L, Torretta A, Donini S, Semrau MS, Storici P, Rossi D, Rapetti F, Brullo C, Parisini E, Bruno O, Collina S. Insight into GEBR-32a: Chiral Resolution, Absolute Configuration and Enantiopreference in PDE4D Inhibition. Molecules 2020; 25:E935. [PMID: 32093112 PMCID: PMC7070305 DOI: 10.3390/molecules25040935] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/12/2020] [Accepted: 02/16/2020] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease is the most common type of dementia, affecting millions of people worldwide. One of its main consequences is memory loss, which is related to downstream effectors of cyclic adenosine monophosphate (cAMP). A well-established strategy to avoid cAMP degradation is the inhibition of phosphodiesterase (PDE). In recent years, GEBR-32a has been shown to possess selective inhibitory properties against PDE type 4 family members, resulting in an improvement in spatial memory processes without the typical side effects that are usually correlated with this mechanism of action. In this work, we performed the HPLC chiral resolution and absolute configuration assignment of GEBR-32a. We developed an efficient analytical and semipreparative chromatographic method exploiting an amylose-based stationary phase, we studied the chiroptical properties of both enantiomers and we assigned their absolute configuration by 1H-NMR (nuclear magnetic resonance). Lastly, we measured the IC50 values of both enantiomers against both the PDE4D catalytic domain and the long PDE4D3 isoform. Results strongly support the notion that GEBR-32a inhibits the PDE4D enzyme by interacting with both the catalytic pocket and the regulatory domains.
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Affiliation(s)
- Valeria Cavalloro
- Department of Drug Sciences, University of Pavia, 27100 Pavia, Italy
- Department of Earth and Environmental Sciences, University of Pavia, 27100 Pavia, Italy
| | - Katia Russo
- Department of Drug Sciences, University of Pavia, 27100 Pavia, Italy
| | - Francesca Vasile
- Università degli Studi di Milano, Dipartimento di Chimica, via C. Golgi 19, 20133 Milano, Italy
| | - Luca Pignataro
- Università degli Studi di Milano, Dipartimento di Chimica, via C. Golgi 19, 20133 Milano, Italy
| | - Archimede Torretta
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
| | - Stefano Donini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
| | - Marta S Semrau
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14-km 163.5 in AREA Science Park, 34149 Trieste, Italy
| | - Paola Storici
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14-km 163.5 in AREA Science Park, 34149 Trieste, Italy
| | - Daniela Rossi
- Department of Drug Sciences, University of Pavia, 27100 Pavia, Italy
| | - Federica Rapetti
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, 16132 Genoa, Italy
| | - Chiara Brullo
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, 16132 Genoa, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Olga Bruno
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, 16132 Genoa, Italy
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, 27100 Pavia, Italy
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8
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Vasile F, Tiana G. Determination of Structural Ensembles of Flexible Molecules in Solution from NMR Data Undergoing Spin Diffusion. J Chem Inf Model 2019; 59:2973-2979. [PMID: 31117510 DOI: 10.1021/acs.jcim.9b00259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Spin diffusion is a formidable problem when interpreting NMR data of chemical compounds. We developed a method to reconstruct the conformational ensemble of flexible molecules displaying spin diffusion, which minimizes the subjective bias in the interpretation of experimental data and which can be used routinely to obtain sets of structures with the correct thermodynamic weights. We showed in the case of a flexible molecule that the correct conformational ensemble is quite different from that obtained with standard methods.
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Affiliation(s)
- Francesca Vasile
- Department of Chemistry , Università degli Studi di Milano , I-20133 Milano , Italy
| | - Guido Tiana
- Department of Physics and Center for Complexity and Biosystems , Università degli Studi di Milano and INFN , I-20133 Milano , Italy
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9
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Civera M, Vasile F, Potenza D, Colombo C, Parente S, Vettraino C, Prosdocimi T, Parisini E, Belvisi L. Exploring E-cadherin-peptidomimetics interaction using NMR and computational studies. PLoS Comput Biol 2019; 15:e1007041. [PMID: 31158220 PMCID: PMC6564044 DOI: 10.1371/journal.pcbi.1007041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 06/13/2019] [Accepted: 04/22/2019] [Indexed: 02/02/2023] Open
Abstract
Cadherins are homophilic cell-cell adhesion molecules whose aberrant expression has often been shown to correlate with different stages of tumor progression. In this work, we investigate the interaction of two peptidomimetic ligands with the extracellular portion of human E-cadherin using a combination of NMR and computational techniques. Both ligands have been previously developed as mimics of the tetrapeptide sequence Asp1-Trp2-Val3-Ile4 of the cadherin adhesion arm, and have been shown to inhibit E-cadherin-mediated adhesion in epithelial ovarian cancer cells with millimolar potency. To sample a set of possible interactions of these ligands with the E-cadherin extracellular portion, STD-NMR experiments in the presence of two slightly different constructs, the wild type E-cadherin-EC1-EC2 fragment and the truncated E-cadherin-(Val3)-EC1-EC2 fragment, were carried out at three temperatures. Depending on the protein construct, a different binding epitope of the ligand and also a different temperature effect on STD signals were observed, both suggesting an involvement of the Asp1-Trp2 protein sequence among all the possible binding events. To interpret the experimental results at the atomic level and to probe the role of the cadherin adhesion arm in the dynamic interaction with the peptidomimetic ligand, a computational protocol based on docking calculations and molecular dynamics simulations was applied. In agreement with NMR data, the simulations at different temperatures unveil high variability/dynamism in ligand-cadherin binding, thus explaining the differences in ligand binding epitopes. In particular, the modulation of the signals seems to be dependent on the protein flexibility, especially at the level of the adhesive arm, which appears to participate in the interaction with the ligand. Overall, these results will help the design of novel cadherin inhibitors that might prevent the swap dimer formation by targeting both the Trp2 binding pocket and the adhesive arm residues. Classical cadherins are the main adhesive proteins at the intercellular junctions and play an essential role in tissue morphogenesis and homeostasis. A large number of studies have shown that cadherin aberrant expression and/or dysregulation often correlate with pathological processes, such as tumor development and progression. Notwithstanding the emerging role played by cadherins in a number of solid tumors, the rational design of small inhibitors targeting these proteins is still in its infancy, likely due to the challenges posed by the development of small drug-like molecules that modulate protein-protein interactions and to the structural complexity of the various cadherin dimerization interfaces that constantly form and disappear as the protein moves along its highly dynamic and reversible homo-dimerization trajectory. In this work, we study the interaction of two small molecules with the extracellular portion of human E-cadherin using a combination of spectroscopic and computational techniques. The availability of molecules interfering in the cadherin homophilic interactions could provide a useful tool for the investigation of cadherin function in tumors, and potentially pave the way to the development of novel alternative diagnostic and therapeutic interventions in cadherin-expressing solid tumors.
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Affiliation(s)
- Monica Civera
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), Consiglio Nazionale delle Ricerche, Milan, Italy
- * E-mail: (MC); (FV)
| | - Francesca Vasile
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), Consiglio Nazionale delle Ricerche, Milan, Italy
- * E-mail: (MC); (FV)
| | - Donatella Potenza
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
| | - Cinzia Colombo
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
| | - Sara Parente
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Como, Italy
| | - Chiara Vettraino
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Milan, Italy
| | - Tommaso Prosdocimi
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Milan, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Milan, Italy
| | - Laura Belvisi
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), Consiglio Nazionale delle Ricerche, Milan, Italy
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10
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Guskova O, Savchenko V, König U, Uhlmann P, Sommer JU. How do immobilised cell-adhesive Arg–Gly–Asp-containing peptides behave at the PAA brush surface? MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1502429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Olga Guskova
- Leibniz Institut für Polymerforschung Dresden e.V., Dresden, Germany
- Dresden Center for Computational Materials Science, Technische Universität Dresden, Dresden, Germany
| | - Vladyslav Savchenko
- Fakultät Umweltwissenschaften, Technische Universität Dresden, Dresden, Germany
| | - Ulla König
- Leibniz Institut für Polymerforschung Dresden e.V., Dresden, Germany
| | - Petra Uhlmann
- Leibniz Institut für Polymerforschung Dresden e.V., Dresden, Germany
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jens-Uwe Sommer
- Leibniz Institut für Polymerforschung Dresden e.V., Dresden, Germany
- Dresden Center for Computational Materials Science, Technische Universität Dresden, Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, Dresden, Germany
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11
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Vasile F, Panigada M, Siccardi A, Potenza D, Tiana G. A Combined NMR-Computational Study of the Interaction between Influenza Virus Hemagglutinin and Sialic Derivatives from Human and Avian Receptors on the Surface of Transfected Cells. Int J Mol Sci 2018; 19:E1267. [PMID: 29695047 PMCID: PMC5983646 DOI: 10.3390/ijms19051267] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 12/31/2022] Open
Abstract
The development of small-molecule inhibitors of influenza virus Hemagglutinin could be relevant to the opposition of the diffusion of new pandemic viruses. In this work, we made use of Nuclear Magnetic Resonance (NMR) spectroscopy to study the interaction between two derivatives of sialic acid, Neu5Ac-α-(2,6)-Gal-β-(1⁻4)-GlcNAc and Neu5Ac-α-(2,3)-Gal-β-(1⁻4)-GlcNAc, and hemagglutinin directly expressed on the surface of recombinant human cells. We analyzed the interaction of these trisaccharides with 293T cells transfected with the H5 and H1 variants of hemagglutinin, which thus retain their native trimeric conformation in such a realistic environment. By exploiting the magnetization transfer between the protein and the ligand, we obtained evidence of the binding event, and identified the epitope. We analyzed the conformational features of the glycans with an approach combining NMR spectroscopy and data-driven molecular dynamics simulations, thus obtaining useful information for an efficient drug design.
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Affiliation(s)
- Francesca Vasile
- Department of Chemistry, University of Milano, Via Golgi 19, 20133 Milano, Italy.
| | - Maddalena Panigada
- Molecular Immunology Unit, San Raffaele Research Institute, via Olgettina 58, 20132 Milano, Italy.
| | - Antonio Siccardi
- Molecular Immunology Unit, San Raffaele Research Institute, via Olgettina 58, 20132 Milano, Italy.
| | - Donatella Potenza
- Department of Chemistry, University of Milano, Via Golgi 19, 20133 Milano, Italy.
| | - Guido Tiana
- Center for Complexity and Biosystems and Department of Physics, University of Milano and INFN, Via Celoria 16, 20133 Milano, Italy.
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12
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Vasile F, Gubinelli F, Panigada M, Soprana E, Siccardi A, Potenza D. NMR interaction studies of Neu5Ac-α-(2,6)-Gal-β-(1-4)-GlcNAc with influenza-virus hemagglutinin expressed in transfected human cells. Glycobiology 2017; 28:42-49. [DOI: 10.1093/glycob/cwx092] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/20/2017] [Indexed: 12/20/2022] Open
Affiliation(s)
- Francesca Vasile
- Department of Chemistry, University of Milano, Via Golgi 19, 20133 Milano, Italy
| | - Francesco Gubinelli
- Molecular Immunology Unit, San Raffaele Research Istitute, via Olgettina 58, 20132 Milano, Italy
| | - Maddalena Panigada
- Molecular Immunology Unit, San Raffaele Research Istitute, via Olgettina 58, 20132 Milano, Italy
| | - Elisa Soprana
- Molecular Immunology Unit, San Raffaele Research Istitute, via Olgettina 58, 20132 Milano, Italy
| | - Antonio Siccardi
- Molecular Immunology Unit, San Raffaele Research Istitute, via Olgettina 58, 20132 Milano, Italy
| | - Donatella Potenza
- Department of Chemistry, University of Milano, Via Golgi 19, 20133 Milano, Italy
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13
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Investigating the Interaction of Cyclic RGD Peptidomimetics with α Vβ₆ Integrin by Biochemical and Molecular Docking Studies. Cancers (Basel) 2017; 9:cancers9100128. [PMID: 28934103 PMCID: PMC5664067 DOI: 10.3390/cancers9100128] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 01/15/2023] Open
Abstract
The interaction of a small library of cyclic RGD (Arg-Gly-Asp) peptidomimetics with αVβ6 integrin has been investigated by means of competitive solid phase binding assays to the isolated receptor and docking calculations in the crystal structure of the αVβ6 binding site. To this aim, a rigid receptor-flexible ligand docking protocol has been set up and then applied to predict the binding mode of the cyclic RGD peptidomimetics to αVβ6 integrin. Although the RGD interaction with αVβ6 recapitulates the RGD binding mode observed in αVβ3, differences between the integrin binding pockets can strongly affect the ligand binding ability. In general, the peptidomimetics exhibited IC50 values for integrin αVβ6 (i.e., the concentration of compound required for 50% inhibition of biotinylated fibronectin binding to isolated αVβ6 integrin) in the nanomolar range (77–345 nM), about 10–100 times higher than those for the related αVβ3 receptor, with a single notable ligand displaying a low nanomolar IC50 value (2.3 nM). Insights from the properties of the binding pocket combined with the analysis of the docking poses provided a rationale for ligand recognition and selectivity.
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14
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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15
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Bonomi M, Heller GT, Camilloni C, Vendruscolo M. Principles of protein structural ensemble determination. Curr Opin Struct Biol 2017; 42:106-116. [PMID: 28063280 DOI: 10.1016/j.sbi.2016.12.004] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/18/2016] [Accepted: 12/06/2016] [Indexed: 01/19/2023]
Abstract
The biological functions of protein molecules are intimately dependent on their conformational dynamics. This aspect is particularly evident for disordered proteins, which constitute perhaps one-third of the human proteome. Therefore, structural ensembles often offer more useful representations of proteins than individual conformations. Here, we describe how the well-established principles of protein structure determination should be extended to the case of protein structural ensembles determination. These principles concern primarily how to deal with conformationally heterogeneous states, and with experimental measurements that are averaged over such states and affected by a variety of errors. We first review the growing literature of recent methods that combine experimental and computational information to model structural ensembles, highlighting their similarities and differences. We then address some conceptual problems in the determination of structural ensembles and define future goals towards the establishment of objective criteria for the comparison, validation, visualization and dissemination of such ensembles.
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Affiliation(s)
| | | | - Carlo Camilloni
- Department of Chemistry and Institute for Advanced Study, Technische Universität München, D-85747 Garching, Germany
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