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Parisi G, Piacentini R, Incocciati A, Bonamore A, Macone A, Rupert J, Zacco E, Miotto M, Milanetti E, Tartaglia GG, Ruocco G, Boffi A, Di Rienzo L. Design of protein-binding peptides with controlled binding affinity: the case of SARS-CoV-2 receptor binding domain and angiotensin-converting enzyme 2 derived peptides. Front Mol Biosci 2024; 10:1332359. [PMID: 38250735 PMCID: PMC10797010 DOI: 10.3389/fmolb.2023.1332359] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024] Open
Abstract
The development of methods able to modulate the binding affinity between proteins and peptides is of paramount biotechnological interest in view of a vast range of applications that imply designed polypeptides capable to impair or favour Protein-Protein Interactions. Here, we applied a peptide design algorithm based on shape complementarity optimization and electrostatic compatibility and provided the first experimental in vitro proof of the efficacy of the design algorithm. Focusing on the interaction between the SARS-CoV-2 Spike Receptor-Binding Domain (RBD) and the human angiotensin-converting enzyme 2 (ACE2) receptor, we extracted a 23-residues long peptide that structurally mimics the major interacting portion of the ACE2 receptor and designed in silico five mutants of such a peptide with a modulated affinity. Remarkably, experimental KD measurements, conducted using biolayer interferometry, matched the in silico predictions. Moreover, we investigated the molecular determinants that govern the variation in binding affinity through molecular dynamics simulation, by identifying the mechanisms driving the different values of binding affinity at a single residue level. Finally, the peptide sequence with the highest affinity, in comparison with the wild type peptide, was expressed as a fusion protein with human H ferritin (HFt) 24-mer. Solution measurements performed on the latter constructs confirmed that peptides still exhibited the expected trend, thereby enhancing their efficacy in RBD binding. Altogether, these results indicate the high potentiality of this general method in developing potent high-affinity vectors for hindering/enhancing protein-protein associations.
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Affiliation(s)
- Giacomo Parisi
- Department of Basic and Applied Sciences for Engineering (SBAI), Università“Sapienza”, Roma, Italy
| | - Roberta Piacentini
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Università“Sapienza”, Roma, Italy
| | - Alessio Incocciati
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Università“Sapienza”, Roma, Italy
| | - Alessandra Bonamore
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Università“Sapienza”, Roma, Italy
| | - Alberto Macone
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Università“Sapienza”, Roma, Italy
| | - Jakob Rupert
- Department of Biology and Biotechnologies “Charles Darwin”, Università“Sapienza”, Roma, Italy
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Elsa Zacco
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Mattia Miotto
- Center for Life Nano and Neuro Science, Istituto Italiano di Tecnologia (IIT), Roma, Italy
| | - Edoardo Milanetti
- Center for Life Nano and Neuro Science, Istituto Italiano di Tecnologia (IIT), Roma, Italy
- Department of Physics, Università“Sapienza”, Roma, Italy
| | - Gian Gaetano Tartaglia
- Department of Biology and Biotechnologies “Charles Darwin”, Università“Sapienza”, Roma, Italy
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Giancarlo Ruocco
- Center for Life Nano and Neuro Science, Istituto Italiano di Tecnologia (IIT), Roma, Italy
- Department of Physics, Università“Sapienza”, Roma, Italy
| | - Alberto Boffi
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Università“Sapienza”, Roma, Italy
| | - Lorenzo Di Rienzo
- Center for Life Nano and Neuro Science, Istituto Italiano di Tecnologia (IIT), Roma, Italy
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2
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Incocciati A, Kubeš J, Piacentini R, Cappelletti C, Botta S, Bertuccini L, Šimůnek T, Boffi A, Macone A, Bonamore A. Hydrophobicity-enhanced ferritin nanoparticles for efficient encapsulation and targeted delivery of hydrophobic drugs to tumor cells. Protein Sci 2023; 32:e4819. [PMID: 37883077 PMCID: PMC10661074 DOI: 10.1002/pro.4819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/02/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023]
Abstract
Ferritin, a naturally occurring iron storage protein, has gained significant attention as a drug delivery platform due to its inherent biocompatibility and capacity to encapsulate therapeutic agents. In this study, we successfully genetically engineered human H ferritin by incorporating 4 or 6 tryptophan residues per subunit, strategically oriented towards the inner cavity of the nanoparticle. This modification aimed to enhance the encapsulation of hydrophobic drugs into the ferritin cage. Comprehensive characterization of the mutants revealed that only the variant carrying four tryptophan substitutions per subunit retained the ability to disassemble and reassemble properly. As a proof of concept, we evaluated the loading capacity of this mutant with ellipticine, a natural hydrophobic indole alkaloid with multimodal anticancer activity. Our data demonstrated that this specific mutant exhibited significantly higher efficiency in loading ellipticine compared to human H ferritin. Furthermore, to evaluate the versatility of this hydrophobicity-enhanced ferritin nanoparticle as a drug carrier, we conducted a comparative study by also encapsulating doxorubicin, a commonly used anticancer drug. Subsequently, we tested both ellipticine and doxorubicin-loaded nanoparticles on a promyelocytic leukemia cell line, demonstrating efficient uptake by these cells and resulting in the expected cytotoxic effect.
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Affiliation(s)
- Alessio Incocciati
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
| | - Jan Kubeš
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec KrálovéCharles UniversityHradec KrálovéCzech Republic
| | - Roberta Piacentini
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
- Center of Life Nano‐ and Neuro‐ScienceItalian Institute of TechnologyRomeItaly
| | - Chiara Cappelletti
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
| | - Sofia Botta
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
| | | | - Tomáš Šimůnek
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec KrálovéCharles UniversityHradec KrálovéCzech Republic
| | - Alberto Boffi
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
| | - Alberto Macone
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
| | - Alessandra Bonamore
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
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3
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Piacentini R, Centi L, Miotto M, Milanetti E, Di Rienzo L, Pitea M, Piazza P, Ruocco G, Boffi A, Parisi G. Lactoferrin Inhibition of the Complex Formation between ACE2 Receptor and SARS CoV-2 Recognition Binding Domain. Int J Mol Sci 2022; 23:ijms23105436. [PMID: 35628247 PMCID: PMC9141661 DOI: 10.3390/ijms23105436] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 04/20/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 02/07/2023] Open
Abstract
The present investigation focuses on the analysis of the interactions among human lactoferrin (LF), SARS-CoV-2 receptor-binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2) receptor in order to assess possible mutual interactions that could provide a molecular basis of the reported preventative effect of lactoferrin against CoV-2 infection. In particular, kinetic and thermodynamic parameters for the pairwise interactions among the three proteins were measured via two independent techniques, biolayer interferometry and latex nanoparticle-enhanced turbidimetry. The results obtained clearly indicate that LF is able to bind the ACE2 receptor ectodomain with significantly high affinity, whereas no binding to the RBD was observed up to the maximum “physiological” lactoferrin concentration range. Lactoferrin, above 1 µM concentration, thus appears to directly interfere with RBD–ACE2 binding, bringing about a measurable, up to 300-fold increase of the KD value relative to RBD–ACE2 complex formation.
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Affiliation(s)
- Roberta Piacentini
- Department of Biochemistry, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy; (R.P.); (L.C.); (A.B.)
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
| | - Laura Centi
- Department of Biochemistry, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy; (R.P.); (L.C.); (A.B.)
| | - Mattia Miotto
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Edoardo Milanetti
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo Di Rienzo
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
| | - Martina Pitea
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
- D-Tails s.r.l., Via di Torre Rossa 66, 00165 Rome, Italy
| | - Paolo Piazza
- EDIF Instruments s.r.l., Via Ardeatina 132, 00147 Rome, Italy;
| | - Giancarlo Ruocco
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alberto Boffi
- Department of Biochemistry, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy; (R.P.); (L.C.); (A.B.)
| | - Giacomo Parisi
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
- Correspondence:
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Soloperto A, Quaglio D, Baiocco P, Romeo I, Mori M, Ardini M, Presutti C, Sannino I, Ghirga S, Iazzetti A, Ippoliti R, Ruocco G, Botta B, Ghirga F, Di Angelantonio S, Boffi A. Rational design and synthesis of a novel BODIPY-based probe for selective imaging of tau tangles in human iPSC-derived cortical neurons. Sci Rep 2022; 12:5257. [PMID: 35347170 PMCID: PMC8960764 DOI: 10.1038/s41598-022-09016-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 11/26/2021] [Accepted: 03/15/2022] [Indexed: 12/26/2022] Open
Abstract
Numerous studies have shown a strong correlation between the number of neurofibrillary tangles of the tau protein and Alzheimer's disease progression, making the quantitative detection of tau very promising from a clinical point of view. However, the lack of highly reliable fluorescent probes for selective imaging of tau neurofibrillary tangles is a major challenge due to sharing similar β–sheet motifs with homologous Amyloid-β fibrils. In the current work, we describe the rational design and the in silico evaluation of a small-size focused library of fluorescent probes, consisting of a BODIPY core (electron acceptor) featuring highly conjugated systems (electron donor) with a length in the range 13–19 Å at C3. Among the most promising probes in terms of binding mode, theoretical affinity and polarity, BT1 has been synthesized and tested in vitro onto human induced pluripotent stem cells derived neuronal cell cultures. The probe showed excellent photophysical properties and high selectivity allowing in vitro imaging of hyperphosphorylated tau protein filaments with minimal background noise. Our findings offer new insight into the structure-activity relationship of this class of tau selective fluorophores, paving the way for boosting tau tangle detection in patients possibly through retinal spectral scans.
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Affiliation(s)
- Alessandro Soloperto
- Center for Life Nano- & Neuro-Science, Istituto Italiano Di Tecnologia, 00161, Rome, Italy
| | - Deborah Quaglio
- Department of Chemistry and Technology of Drugs, Department of Excellence 2018-2022, Sapienza University of Rome, 00185, Rome, Italy
| | - Paola Baiocco
- Center for Life Nano- & Neuro-Science, Istituto Italiano Di Tecnologia, 00161, Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185, Rome, Italy
| | - Isabella Romeo
- Center for Life Nano- & Neuro-Science, Istituto Italiano Di Tecnologia, 00161, Rome, Italy.,Department of Chemistry and Technology of Drugs, Department of Excellence 2018-2022, Sapienza University of Rome, 00185, Rome, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, 53100, Siena, Italy
| | - Matteo Ardini
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Caterina Presutti
- Center for Life Nano- & Neuro-Science, Istituto Italiano Di Tecnologia, 00161, Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185, Rome, Italy
| | - Ida Sannino
- Center for Life Nano- & Neuro-Science, Istituto Italiano Di Tecnologia, 00161, Rome, Italy
| | - Silvia Ghirga
- Center for Life Nano- & Neuro-Science, Istituto Italiano Di Tecnologia, 00161, Rome, Italy
| | - Antonia Iazzetti
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, 00168, Rome, Italy
| | - Rodolfo Ippoliti
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Giancarlo Ruocco
- Center for Life Nano- & Neuro-Science, Istituto Italiano Di Tecnologia, 00161, Rome, Italy
| | - Bruno Botta
- Department of Chemistry and Technology of Drugs, Department of Excellence 2018-2022, Sapienza University of Rome, 00185, Rome, Italy
| | - Francesca Ghirga
- Department of Chemistry and Technology of Drugs, Department of Excellence 2018-2022, Sapienza University of Rome, 00185, Rome, Italy.
| | - Silvia Di Angelantonio
- Center for Life Nano- & Neuro-Science, Istituto Italiano Di Tecnologia, 00161, Rome, Italy. .,Department of Physiology and Pharmacology, Sapienza University of Rome, 00185, Rome, Italy.
| | - Alberto Boffi
- Center for Life Nano- & Neuro-Science, Istituto Italiano Di Tecnologia, 00161, Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185, Rome, Italy
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5
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Miotto M, Di Rienzo L, Gosti G, Bo' L, Parisi G, Piacentini R, Boffi A, Ruocco G, Milanetti E. Inferring the stabilization effects of SARS-CoV-2 variants on the binding with ACE2 receptor. Commun Biol 2022; 5:20221. [PMID: 34992214 PMCID: PMC8738749 DOI: 10.1038/s42003-021-02946-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 04/27/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022] Open
Abstract
As the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic continues to spread, several variants of the virus, with mutations distributed all over the viral genome, are emerging. While most of the variants present mutations having little to no effects at the phenotypic level, some of these variants are spreading at a rate that suggests they may present a selective advantage. In particular, these rapidly spreading variants present specific mutations on the spike protein. These observations call for an urgent need to characterize the effects of these variants’ mutations on phenotype features like contagiousness and antigenicity. With this aim, we performed molecular dynamics simulations on a selected set of possible spike variants in order to assess the stabilizing effect of particular amino acid substitutions on the molecular complex. We specifically focused on the mutations that are both characteristic of the top three most worrying variants at the moment, i.e the English, South African, and Amazonian ones, and that occur at the molecular interface between SARS-CoV-2 spike protein and its human ACE2 receptor. We characterize these variants’ effect in terms of (i) residue mobility, (ii) compactness, studying the network of interactions at the interface, and (iii) variation of shape complementarity via expanding the molecular surfaces in the Zernike basis. Overall, our analyses highlighted greater stability of the three variant complexes with respect to both the wild type and two negative control systems, especially for the English and Amazonian variants. In addition, in the three variants, we investigate the effects a not-yet observed mutation in position 501 could provoke on complex stability. We found that a phenylalanine mutation behaves similarly to the English variant and may cooperate in further increasing the stability of the South African one, hinting at the need for careful surveillance for the emergence of these mutations in the population. Ultimately, we show that the proposed observables describe key features for the stability of the ACE2-spike complex and can help to monitor further possible spike variants. Miotto et al. perform molecular dynamics simulations on a selected set of possible SARS-CoV-2 spike variants in order to assess the stabilizing effect of particular amino acid substitutions on the molecular complex. Their analysis can help to monitor further possible spike variants.
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Affiliation(s)
- Mattia Miotto
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Lorenzo Di Rienzo
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Giorgio Gosti
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Leonardo Bo'
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Giacomo Parisi
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Roberta Piacentini
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy.,Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.Le A. Moro 5, 00185, Rome, Italy
| | - Alberto Boffi
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy.,Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.Le A. Moro 5, 00185, Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy.,Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Edoardo Milanetti
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy. .,Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy.
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6
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Kiraga Ł, Kucharzewska P, Paisey S, Cheda Ł, Domańska A, Rogulski Z, Rygiel TP, Boffi A, Król M. Nuclear imaging for immune cell tracking in vivo – Comparison of various cell labeling methods and their application. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214008] [Citation(s) in RCA: 1] [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: 01/01/2023]
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7
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Pediconi N, Ghirga F, Del Plato C, Peruzzi G, Athanassopoulos CM, Mori M, Crestoni ME, Corinti D, Ugozzoli F, Massera C, Arcovito A, Botta B, Boffi A, Quaglio D, Baiocco P. Design and Synthesis of Piperazine-Based Compounds Conjugated to Humanized Ferritin as Delivery System of siRNA in Cancer Cells. Bioconjug Chem 2021; 32:1105-1116. [PMID: 33978420 PMCID: PMC8253483 DOI: 10.1021/acs.bioconjchem.1c00137] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/27/2021] [Indexed: 01/23/2023]
Abstract
Gene expression regulation by small interfering RNA (siRNA) holds promise in treating a wide range of diseases through selective gene silencing. However, successful clinical application of nucleic acid-based therapy requires novel delivery options. Herein, to achieve efficient delivery of negatively charged siRNA duplexes, the internal cavity of "humanized" chimeric Archaeal ferritin (HumAfFt) was specifically decorated with novel cationic piperazine-based compounds (PAs). By coupling these rigid-rod-like amines with thiol-reactive reagents, chemoselective conjugation was efficiently afforded on topologically selected cysteine residues properly located inside HumAfFt. The capability of PAs-HumAfFt to host and deliver siRNA molecules through human transferrin receptor (TfR1), overexpressed in many cancer cells, was explored. These systems allowed siRNA delivery into HeLa, HepG2, and MCF-7 cancer cells with improved silencing effect on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene expression with respect to traditional transfection methodologies and provided a promising TfR1-targeting system for multifunctional siRNA delivery to therapeutic applications.
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Affiliation(s)
- Natalia Pediconi
- Center
for Life Nano- & Neuro-Science, Fondazione
Istituto Italiano di Tecnologia (IIT), V.le Regina Elena 291, 00161 Rome, Italy
| | - Francesca Ghirga
- Department
of Chemistry and Technology of Drugs, “Department of Excellence
2018−2022”, Sapienza University
of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Cristina Del Plato
- Center
for Life Nano- & Neuro-Science, Fondazione
Istituto Italiano di Tecnologia (IIT), V.le Regina Elena 291, 00161 Rome, Italy
- Department
of Chemistry and Technology of Drugs, “Department of Excellence
2018−2022”, Sapienza University
of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Giovanna Peruzzi
- Center
for Life Nano- & Neuro-Science, Fondazione
Istituto Italiano di Tecnologia (IIT), V.le Regina Elena 291, 00161 Rome, Italy
| | - Constantinos M. Athanassopoulos
- Department
of Chemistry, University of Patras, GR-26504 Rio-Patras, Greece
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Mattia Mori
- Department
of Biotechnology, Chemistry and Pharmacy, “Department of Excellence
2018−2022”, University of
Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Maria Elisa Crestoni
- Department
of Chemistry and Technology of Drugs, “Department of Excellence
2018−2022”, Sapienza University
of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Davide Corinti
- Department
of Chemistry and Technology of Drugs, “Department of Excellence
2018−2022”, Sapienza University
of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Franco Ugozzoli
- Department
of Engineering and Architecture, University
of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Chiara Massera
- Department
of Chemical Sciences, Life and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Alessandro Arcovito
- Dipartimento
di Scienze Biotecnologiche di base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Roma, Italy
| | - Bruno Botta
- Department
of Chemistry and Technology of Drugs, “Department of Excellence
2018−2022”, Sapienza University
of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Alberto Boffi
- Center
for Life Nano- & Neuro-Science, Fondazione
Istituto Italiano di Tecnologia (IIT), V.le Regina Elena 291, 00161 Rome, Italy
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
- Institute
of Molecular Biology and Pathology, National
Research Council, P.le
A. Moro 7, 00185 Rome, Italy
| | - Deborah Quaglio
- Department
of Chemistry and Technology of Drugs, “Department of Excellence
2018−2022”, Sapienza University
of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Paola Baiocco
- Center
for Life Nano- & Neuro-Science, Fondazione
Istituto Italiano di Tecnologia (IIT), V.le Regina Elena 291, 00161 Rome, Italy
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
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8
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Marcelli A, Patrizi B, Bonamore A, Boffi A, Becucci M, Foggi P. Exciplex Formation in Lipid-bound Escherichia coli Flavohemoglobin. Chemphyschem 2021; 22:1134-1140. [PMID: 33794073 DOI: 10.1002/cphc.202100019] [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: 01/14/2021] [Revised: 03/30/2021] [Indexed: 11/10/2022]
Abstract
Flavohemoglobins have the particular capability of binding unsaturated and cyclopropanated fatty acids as free acids or phospholipids. Fatty acid binding to the ferric heme results in a weak but direct bonding interaction. Ferrous and ferric protein, in presence or absence of a bound lipid molecule, have been characterized by transient absorption spectroscopy. Measurements have been also carried out both on the ferrous deoxygenated and on the CO bound protein to investigate possible long-range interaction between the lipid acyl chain moiety and the ferrous heme. After excitation of the deoxygenated derivatives the relaxation process reveals a slow dynamics (350 ps) in lipid-bound protein but is not observed in the lipid-free protein. The latter feature and the presence of an extra contribution in the absorption spectrum, indicates that the interaction of iron heme with the acyl chain moiety occurs only in the excited electronic state and not in the ground electronic state. Data analysis highlights the formation of a charge-transfer complex in which the iron ion of the lipid-bound protein in the expanded electronic excited state, possibly represented by a high spin Fe III intermediate, is able to bind to the sixth coordination ligand placed at a distance of at 3.5 Å from the iron. A very small nanosecond geminate rebinding is observed for CO adduct in lipid-free but not in the lipid-bound protein. The presence of the lipid thus appears to inhibit the mobility of CO in the heme pocket.
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Affiliation(s)
- Agnese Marcelli
- European Laboratory for Non-Linear Spectroscopy (LENS), Via Nello Carrara, 1, 50019 Sesto Fiorentino, Florence), Italy
| | - Barbara Patrizi
- European Laboratory for Non-Linear Spectroscopy (LENS), Via Nello Carrara, 1, 50019 Sesto Fiorentino, Florence), Italy.,National Institute of Optics-National Research Council (INO-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino (Florence), Italy
| | - Alessandra Bonamore
- Istituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche, Università "Sapienza" di Roma, P. Aldo Moro 5, 00185, Rome, Italy
| | - Alberto Boffi
- Istituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche, Università "Sapienza" di Roma, P. Aldo Moro 5, 00185, Rome, Italy
| | - Maurizio Becucci
- European Laboratory for Non-Linear Spectroscopy (LENS), Via Nello Carrara, 1, 50019 Sesto Fiorentino, Florence), Italy.,Department of Chemistry Ugo Schiff, University of Florence, Via Della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence), Italy
| | - Paolo Foggi
- European Laboratory for Non-Linear Spectroscopy (LENS), Via Nello Carrara, 1, 50019 Sesto Fiorentino, Florence), Italy.,National Institute of Optics-National Research Council (INO-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino (Florence), Italy.,Department of Chemistry, University of Perugia, Via Elce di sotto 8, 06100, Perugia, Italy
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9
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Di Rienzo L, Monti M, Milanetti E, Miotto M, Boffi A, Tartaglia GG, Ruocco G. Computational optimization of angiotensin-converting enzyme 2 for SARS-CoV-2 Spike molecular recognition. Comput Struct Biotechnol J 2021; 19:3006-3014. [PMID: 34002118 PMCID: PMC8116125 DOI: 10.1016/j.csbj.2021.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/08/2021] [Accepted: 05/09/2021] [Indexed: 12/13/2022] Open
Abstract
Since the beginning of the Covid19 pandemic, many efforts have been devoted to identifying approaches to neutralize SARS-CoV-2 replication within the host cell. A promising strategy to block the infection consists of using a mutant of the human receptor angiotensin-converting enzyme 2 (ACE2) as a decoy to compete with endogenous ACE2 for the binding to the SARS-CoV-2 Spike protein, which decreases the ability of the virus to enter the host cell. Here, using a computational framework based on the 2D Zernike formalism we investigate details of the molecular binding and evaluate the changes in ACE2-Spike binding compatibility upon mutations occurring in the ACE2 side of the molecular interface. We demonstrate the efficacy of our method by comparing our results with experimental binding affinities changes upon ACE2 mutations, separating ones that increase or decrease binding affinity with an Area Under the ROC curve ranging from 0.66 to 0.93, depending on the magnitude of the effects analyzed. Importantly, the iteration of our approach leads to the identification of a set of ACE2 mutants characterized by an increased shape complementarity with Spike. We investigated the physico-chemical properties of these ACE2 mutants and propose them as bona fide candidates for Spike recognition.
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Affiliation(s)
- Lorenzo Di Rienzo
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Michele Monti
- RNA System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Edoardo Milanetti
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Mattia Miotto
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alberto Boffi
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Gian Gaetano Tartaglia
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- RNA System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
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10
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Miotto M, Di Rienzo L, Bò L, Boffi A, Ruocco G, Milanetti E. Molecular Mechanisms Behind Anti SARS-CoV-2 Action of Lactoferrin. Front Mol Biosci 2021; 8:607443. [PMID: 33659275 PMCID: PMC7917183 DOI: 10.3389/fmolb.2021.607443] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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: 09/17/2020] [Accepted: 01/11/2021] [Indexed: 12/15/2022] Open
Abstract
Despite the huge effort to contain the infection, the novel SARS-CoV-2 coronavirus has rapidly become pandemic, mainly due to its extremely high human-to-human transmission capability, and a surprisingly high viral charge of symptom-less people. While the seek for a vaccine is still ongoing, promising results have been obtained with antiviral compounds. In particular, lactoferrin is regarded to have beneficial effects both in preventing and soothing the infection. Here, we explore the possible molecular mechanisms with which lactoferrin interferes with SARS-CoV-2 cell invasion, preventing attachment and/or entry of the virus. To this aim, we search for possible interactions lactoferrin may have with virus structural proteins and host receptors. Representing the molecular iso-electron surface of proteins in terms of 2D-Zernike descriptors, we 1) identified putative regions on the lactoferrin surface able to bind sialic acid present on the host cell membrane, sheltering the cell from the virus attachment; 2) showed that no significant shape complementarity is present between lactoferrin and the ACE2 receptor, while 3) two high complementarity regions are found on the N- and C-terminal domains of the SARS-CoV-2 spike protein, hinting at a possible competition between lactoferrin and ACE2 for the binding to the spike protein.
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Affiliation(s)
- Mattia Miotto
- Department of Physics, University of Rome `La Sapienza', Rome, Italy
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
| | - Lorenzo Di Rienzo
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
| | - Leonardo Bò
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
| | - Alberto Boffi
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
- Department of Biochemical Sciences “A. Rossi Fanelli” Sapienza University, Rome, Italy
| | - Giancarlo Ruocco
- Department of Physics, University of Rome `La Sapienza', Rome, Italy
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
| | - Edoardo Milanetti
- Department of Physics, University of Rome `La Sapienza', Rome, Italy
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
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11
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Di Fabio E, Incocciati A, Palombarini F, Boffi A, Bonamore A, Macone A. Ethylchloroformate Derivatization for GC-MS Analysis of Resveratrol Isomers in Red Wine. Molecules 2020; 25:molecules25204603. [PMID: 33050326 PMCID: PMC7587181 DOI: 10.3390/molecules25204603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/31/2022] Open
Abstract
Resveratrol (3,5,4′-trihydroxystilbene) is a natural compound that can be found in high concentrations in red wine and in many typical foods found in human diet. Over the past decades, resveratrol has been widely investigated for its potential beneficial effects on human health. At the same time, numerous analytical methods have been developed for the quantitative determination of resveratrol isomers in oenological and food matrices. In the present work, we developed a very fast and sensitive GC–MS method for the determination of resveratrol in red wine based on ethylchloroformate derivatization. Since this reaction occurs directly in the water phase during the extraction process itself, it has the advantage of significantly reducing the overall processing time for the sample. This method presents low limits of quantification (LOQ) (25 ng/mL and 50 ng/mL for cis- and trans-resveratrol, respectively) and excellent accuracy and precision. Ethylchloroformate derivatization was successfully applied to the analysis of resveratrol isomers in a selection of 15 commercial Italian red wines, providing concentration values comparable to those reported in other studies. As this method can be easily extended to other classes of molecules present in red wine, it allows further development of new GC–MS methods for the molecular profiling of oenological matrices.
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12
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Di Rienzo L, Milanetti E, Testi C, Montemiglio LC, Baiocco P, Boffi A, Ruocco G. A novel strategy for molecular interfaces optimization: The case of Ferritin-Transferrin receptor interaction. Comput Struct Biotechnol J 2020; 18:2678-2686. [PMID: 33101606 PMCID: PMC7548301 DOI: 10.1016/j.csbj.2020.09.020] [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: 06/16/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/24/2022] Open
Abstract
Protein-protein interactions regulate almost all cellular functions and rely on a fine tune of surface amino acids properties involved on both molecular partners. The disruption of a molecular association can be caused even by a single residue mutation, often leading to a pathological modification of a biochemical pathway. Therefore the evaluation of the effects of amino acid substitutions on binding, and the ad hoc design of protein-protein interfaces, is one of the biggest challenges in computational biology. Here, we present a novel strategy for computational mutation and optimization of protein-protein interfaces. Modeling the interaction surface properties using the Zernike polynomials, we describe the shape and electrostatics of binding sites with an ordered set of descriptors, making possible the evaluation of complementarity between interacting surfaces. With a Monte Carlo approach, we obtain protein mutants with controlled molecular complementarities. Applying this strategy to the relevant case of the interaction between Ferritin and Transferrin Receptor, we obtain a set of Ferritin mutants with increased or decreased complementarity. The extensive molecular dynamics validation of the method results confirms its efficacy, showing that this strategy represents a very promising approach in designing correct molecular interfaces.
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Affiliation(s)
- Lorenzo Di Rienzo
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Edoardo Milanetti
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Claudia Testi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | | | - Paola Baiocco
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Biochemical Sciences ‘A. Rossi Fanelli’ Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alberto Boffi
- Department of Biochemical Sciences ‘A. Rossi Fanelli’ Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
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13
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Francioso A, Federico R, Maggiore A, Fontana M, Boffi A, D’Erme M, Mosca L. Green Route for the Isolation and Purification of Hyrdoxytyrosol, Tyrosol, Oleacein and Oleocanthal from Extra Virgin Olive Oil. Molecules 2020; 25:molecules25163654. [PMID: 32796621 PMCID: PMC7464626 DOI: 10.3390/molecules25163654] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 07/06/2020] [Revised: 07/29/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022] Open
Abstract
Extra virgin olive oil (EVOO) phenols represent a significant part of the intake of antioxidants and bioactive compounds in the Mediterranean diet. In particular, hydroxytyrosol (HTyr), tyrosol (Tyr), and the secoiridoids oleacein and oleocanthal play central roles as anti-inflammatory, neuro-protective and anti-cancer agents. These compounds cannot be easily obtained via chemical synthesis, and their isolation and purification from EVOO is cumbersome. Indeed, both processes involve the use of large volumes of organic solvents, hazardous reagents and several chromatographic steps. In this work we propose a novel optimized procedure for the green extraction, isolation and purification of HTyr, Tyr, oleacein and oleocanthal directly from EVOO, by using a Natural Deep Eutectic Solvent (NaDES) as an extracting phase, coupled with preparative high-performance liquid chromatography. This purification method allows the total recovery of the four components as single pure compounds directly from EVOO, in a rapid, economic and ecologically sustainable way, which utilizes biocompatible reagents and strongly limits the use or generation of hazardous substances.
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Affiliation(s)
- Antonio Francioso
- Department of Biochemical Sciences, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (M.F.); (A.B.); (M.D.); (L.M.)
- Correspondence: ; Tel.: +39-06-4991-0987
| | - Rodolfo Federico
- MOLIROM s.r.l, via Carlo Bartolomeo Piazza 8, 00161 Rome, Italy;
| | - Anna Maggiore
- Department of Biochemical Sciences, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (M.F.); (A.B.); (M.D.); (L.M.)
| | - Mario Fontana
- Department of Biochemical Sciences, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (M.F.); (A.B.); (M.D.); (L.M.)
| | - Alberto Boffi
- Department of Biochemical Sciences, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (M.F.); (A.B.); (M.D.); (L.M.)
- MOLIROM s.r.l, via Carlo Bartolomeo Piazza 8, 00161 Rome, Italy;
| | - Maria D’Erme
- Department of Biochemical Sciences, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (M.F.); (A.B.); (M.D.); (L.M.)
| | - Luciana Mosca
- Department of Biochemical Sciences, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (M.F.); (A.B.); (M.D.); (L.M.)
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14
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Ascenzi P, Bettinelli M, Boffi A, Botta M, De Simone G, Luchinat C, Marengo E, Mei H, Aime S. Rare earth elements (REE) in biology and medicine. Rend Fis Acc Lincei 2020. [DOI: 10.1007/s12210-020-00930-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThis survey reports on topics that were presented at the workshop on “Challenges with Rare Earth Elements. The Periodic Table at work for new Science & Technology” hold at the Academia dei Lincei in November 2019. The herein reported materials refer to presentations dealing with studies and applications of rare earth elements (REE) in several areas of Biology and Medicine. All together they show the tremendous impact REE have in relevant fields of living systems and highlight, on one hand, the still existing knowledge gap for an in-depth understanding of their function in natural systems as well as the very important role they already have in providing innovative scientific and technological solutions in a number of bio-medical areas and in fields related to the assessment of the origin of food and on their manufacturing processes. On the basis of the to-date achievements one expects that new initiatives will bring, in a not too far future, to a dramatic increase of our understanding of the REE involvement in living organisms as well as a ramp-up in the exploitation of the peculiar properties of REE for the design of novel applications in diagnostic procedures and in the set-up of powerful medical devices. This scenario calls the governmental authorities for new responsibilities to guarantee a continuous availability of REE to industry and research labs together with providing support to activities devoted to their recovery/recycling.
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15
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Kiraga Ł, Cerutti G, Braniewska A, Strzemecki D, Sas Z, Boffi A, Savino C, Montemiglio LC, Turnham D, Seaton G, Bonamore A, Clarkson R, Dabkowski AM, Paisey SJ, Taciak B, Kucharzewska P, Rygiel TP, Król M. Biodistribution PET/CT Study of Hemoglobin-DFO- 89Zr Complex in Healthy and Lung Tumor-Bearing Mice. Int J Mol Sci 2020; 21:ijms21144991. [PMID: 32679799 PMCID: PMC7404105 DOI: 10.3390/ijms21144991] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 07/11/2020] [Indexed: 01/26/2023] Open
Abstract
Proteins, as a major component of organisms, are considered the preferred biomaterials for drug delivery vehicles. Hemoglobin (Hb) has been recently rediscovered as a potential drug carrier, but its use for biomedical applications still lacks extensive investigation. To further explore the possibility of utilizing Hb as a potential tumor targeting drug carrier, we examined and compared the biodistribution of Hb in healthy and lung tumor-bearing mice, using for the first time 89Zr labelled Hb in a positron emission tomography (PET) measurement. Hb displays a very high conjugation yield in its fast and selective reaction with the maleimide-deferoxamine (DFO) bifunctional chelator. The high-resolution X-ray structure of the Hb-DFO complex demonstrated that cysteine β93 is the sole attachment moiety to the αβ-protomer of Hb. The Hb-DFO complex shows quantitative uptake of 89Zr in solution as determined by radiochromatography. Injection of 0.03 mg of Hb-DFO-89Zr complex in healthy mice indicates very high radioactivity in liver, followed by spleen and lungs, whereas a threefold increased dosage results in intensification of PET signal in kidneys and decreased signal in liver and spleen. No difference in biodistribution pattern is observed between naïve and tumor-bearing mice. Interestingly, the liver Hb uptake did not decrease upon clodronate-mediated macrophage depletion, indicating that other immune cells contribute to Hb clearance. This finding is of particular interest for rapidly developing clinical immunology and projects aiming to target, label or specifically deliver agents to immune cells.
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Affiliation(s)
- Łukasz Kiraga
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (L.K.); (B.T.); (P.K.)
| | - Gabriele Cerutti
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, 00-185 Rome, Italy; (G.C.); (A.B.); (A.B.)
| | - Agata Braniewska
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (A.B.); (D.S.); (Z.S.); (T.P.R.)
| | - Damian Strzemecki
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (A.B.); (D.S.); (Z.S.); (T.P.R.)
| | - Zuzanna Sas
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (A.B.); (D.S.); (Z.S.); (T.P.R.)
| | - Alberto Boffi
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, 00-185 Rome, Italy; (G.C.); (A.B.); (A.B.)
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, 00-185 Rome, Italy; (C.S.); (L.C.M.)
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, 00-185 Rome, Italy; (C.S.); (L.C.M.)
| | - Daniel Turnham
- European Cancer Stem Cell Research Institute (ECSCRI), School of Biosciences, Haydn Ellis Building, Cardiff University, Cardiff CF24 4HQ, Wales, UK; (D.T.); (G.S.); (R.C.)
| | - Gillian Seaton
- European Cancer Stem Cell Research Institute (ECSCRI), School of Biosciences, Haydn Ellis Building, Cardiff University, Cardiff CF24 4HQ, Wales, UK; (D.T.); (G.S.); (R.C.)
| | - Alessandra Bonamore
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, 00-185 Rome, Italy; (G.C.); (A.B.); (A.B.)
| | - Richard Clarkson
- European Cancer Stem Cell Research Institute (ECSCRI), School of Biosciences, Haydn Ellis Building, Cardiff University, Cardiff CF24 4HQ, Wales, UK; (D.T.); (G.S.); (R.C.)
| | - Adam M. Dabkowski
- Wales Research & Diagnostic PET Imaging Centre (PETIC), School of Medicine, Heath Park, Cardiff University, Cardiff CF14 4XN, Wales, UK; (A.M.D.); (S.J.P.)
| | - Stephen J. Paisey
- Wales Research & Diagnostic PET Imaging Centre (PETIC), School of Medicine, Heath Park, Cardiff University, Cardiff CF14 4XN, Wales, UK; (A.M.D.); (S.J.P.)
| | - Bartłomiej Taciak
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (L.K.); (B.T.); (P.K.)
| | - Paulina Kucharzewska
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (L.K.); (B.T.); (P.K.)
| | - Tomasz P. Rygiel
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (A.B.); (D.S.); (Z.S.); (T.P.R.)
| | - Magdalena Król
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (L.K.); (B.T.); (P.K.)
- Correspondence: ; Tel.: +48-22-59-362-59
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16
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Palombarini F, Di Fabio E, Boffi A, Macone A, Bonamore A. Ferritin Nanocages for Protein Delivery to Tumor Cells. Molecules 2020; 25:E825. [PMID: 32070033 PMCID: PMC7070480 DOI: 10.3390/molecules25040825] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
The delivery of therapeutic proteins is one of the greatest challenges in the treatment of human diseases. In this frame, ferritins occupy a very special place. Thanks to their hollow spherical structure, they are used as modular nanocages for the delivery of anticancer drugs. More recently, the possibility of encapsulating even small proteins with enzymatic or cytotoxic activity is emerging. Among all ferritins, particular interest is paid to the Archaeoglobus fulgidus one, due to its peculiar ability to associate/dissociate in physiological conditions. This protein has also been engineered to allow recognition of human receptors and used in vitro for the delivery of cytotoxic proteins with extremely promising results.
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Affiliation(s)
| | | | | | - Alberto Macone
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (F.P.); (E.D.F.); (A.B.)
| | - Alessandra Bonamore
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (F.P.); (E.D.F.); (A.B.)
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17
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Francioso A, Laštovičková L, Mosca L, Boffi A, Bonamore A, Macone A. Gas Chromatographic-Mass Spectrometric Method for the Simultaneous Determination of Resveratrol Isomers and 2,4,6-Trihydroxyphenanthrene in Red Wines Exposed to UV-Light. J Agric Food Chem 2019; 67:11752-11757. [PMID: 31554403 DOI: 10.1021/acs.jafc.9b05992] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 06/10/2023]
Abstract
Resveratrol (3,5,4'-trihydroxystilbene) is one of the most abundant polyphenols in red grapes, and red wine represents one of the most important dietary sources of this compound. Although its beneficial properties on human health have been widely investigated over the last 30 years, very little is known about its derivatives. Resveratrol can indeed undergo glycosylation, oligomerization and, upon UV-light exposure, it can isomerize from the trans-to the cis-isomer, which can further cyclize to 2,4,6-trihydroxyphenanthrene (THP). Although the effects of THP on human health are not yet known, being a polycyclic aromatic hydrocarbon, it can be potentially harmful. Because no data about THP occurrence in plant food and beverages are available, a simple procedure based on liquid-liquid extraction and gas chromatography-mass spectrometry has been developed and validated for the simultaneous qualitative and quantitative analysis of trans-resveratrol, cis-resveratrol, and THP in red wine, before and after UV-light exposure.
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Affiliation(s)
- Antonio Francioso
- Department of Biochemical Sciences , "Sapienza" University of Rome , p.le A.Moro 5 , 00185 Rome , Italy
| | - Lenka Laštovičková
- Department of Biological and Biochemical Sciences , University of Pardubice , Studentská 573 , 530 10 Pardubice 2 , Czech Republic
| | - Luciana Mosca
- Department of Biochemical Sciences , "Sapienza" University of Rome , p.le A.Moro 5 , 00185 Rome , Italy
| | - Alberto Boffi
- Department of Biochemical Sciences , "Sapienza" University of Rome , p.le A.Moro 5 , 00185 Rome , Italy
| | - Alessandra Bonamore
- Department of Biochemical Sciences , "Sapienza" University of Rome , p.le A.Moro 5 , 00185 Rome , Italy
| | - Alberto Macone
- Department of Biochemical Sciences , "Sapienza" University of Rome , p.le A.Moro 5 , 00185 Rome , Italy
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18
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Macone A, Masciarelli S, Palombarini F, Quaglio D, Boffi A, Trabuco MC, Baiocco P, Fazi F, Bonamore A. Ferritin nanovehicle for targeted delivery of cytochrome C to cancer cells. Sci Rep 2019; 9:11749. [PMID: 31409839 PMCID: PMC6692331 DOI: 10.1038/s41598-019-48037-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023] Open
Abstract
In this work, we have exploited the unique properties of a chimeric archaeal-human ferritin to encapsulate, deliver and release cytochrome c and induce apoptosis in a myeloid leukemia cell line. The chimeric protein combines the versatility in 24-meric assembly and cargo incorporation capability of Archaeglobus fulgidus ferritin with specific binding of human H ferritin to CD71, the "heavy duty" carrier responsible for transferrin-iron uptake. Delivery of ferritin-encapsulated cytochrome C to the Acute Promyelocytic Leukemia (APL) NB4 cell line, highly resistant to transfection by conventional methods, was successfully achieved in vitro. The effective liberation of cytochrome C within the cytosolic environment, demonstrated by double fluorescent labelling, induced apoptosis in the cancer cells.
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Affiliation(s)
- Alberto Macone
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Pizzale Aldo Moro 5, 00185, Rome, Italy.
| | - Silvia Masciarelli
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology and Medical Embryology, Sapienza University of Rome, laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Federica Palombarini
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Pizzale Aldo Moro 5, 00185, Rome, Italy
| | - Deborah Quaglio
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Pizzale Aldo Moro 5, 00185, Rome, Italy
| | - Alberto Boffi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Pizzale Aldo Moro 5, 00185, Rome, Italy
| | - Matilde Cardoso Trabuco
- Center for Life Nano Science @ Sapienza, Italian Institute of Technology, Viale Regina Elena 291, Rome, 00161, Italy
| | - Paola Baiocco
- Center for Life Nano Science @ Sapienza, Italian Institute of Technology, Viale Regina Elena 291, Rome, 00161, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology and Medical Embryology, Sapienza University of Rome, laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Alessandra Bonamore
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Pizzale Aldo Moro 5, 00185, Rome, Italy.
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Palombarini F, Ghirga F, Boffi A, Macone A, Bonamore A. Application of crossflow ultrafiltration for scaling up the purification of a recombinant ferritin. Protein Expr Purif 2019; 163:105451. [PMID: 31301427 DOI: 10.1016/j.pep.2019.105451] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 05/28/2019] [Revised: 06/21/2019] [Accepted: 07/08/2019] [Indexed: 01/07/2023]
Abstract
Ferritin proteins are taking center stage as smart nanocarriers for drug delivery due to their hollow cage-like structures and their unique 24-meric assembly. Among all ferritins, the chimeric Archaeoglobus ferritin (HumFt) is able assemble/disassemble varying the ionic strength of the medium while recognizing human TfR1 receptor overexpressed in cancer cells. In this paper we present a highly efficient, large scale purification protocol mainly based on crossflow ultrafiltration, starting from fermented bacterial paste. This procedure allows one to obtain about 2 g of purified protein starting from 100 g of fermented bacterial paste. The current procedure can easily remove contaminant proteins as well as DNA molecules in the absence of expensive and time consuming chromatographic steps.
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Affiliation(s)
- Federica Palombarini
- Department of Biochemical Sciences, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Francesca Ghirga
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Alberto Boffi
- Department of Biochemical Sciences, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Alberto Macone
- Department of Biochemical Sciences, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy.
| | - Alessandra Bonamore
- Department of Biochemical Sciences, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy.
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20
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Montemiglio LC, Testi C, Ceci P, Falvo E, Pitea M, Savino C, Arcovito A, Peruzzi G, Baiocco P, Mancia F, Boffi A, des Georges A, Vallone B. Cryo-EM structure of the human ferritin-transferrin receptor 1 complex. Nat Commun 2019; 10:1121. [PMID: 30850661 PMCID: PMC6408514 DOI: 10.1038/s41467-019-09098-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/13/2019] [Indexed: 12/31/2022] Open
Abstract
Human transferrin receptor 1 (CD71) guarantees iron supply by endocytosis upon binding of iron-loaded transferrin and ferritin. Arenaviruses and the malaria parasite exploit CD71 for cell invasion and epitopes on CD71 for interaction with transferrin and pathogenic hosts were identified. Here, we provide the molecular basis of the CD71 ectodomain-human ferritin interaction by determining the 3.9 Å resolution single-particle cryo-electron microscopy structure of their complex and by validating our structural findings in a cellular context. The contact surfaces between the heavy-chain ferritin and CD71 largely overlap with arenaviruses and Plasmodium vivax binding regions in the apical part of the receptor ectodomain. Our data account for transferrin-independent binding of ferritin to CD71 and suggest that select pathogens may have adapted to enter cells by mimicking the ferritin access gate. The human transferrin receptor 1 (CD71) is a transmembrane protein responsible for iron uptake. Here the authors present the 3.9 Å resolution cryo-EM structure of the CD71 ectodomain-human ferritin (H-Ft) complex and find that H-Ft binds a CD71 region different from the transferrin one that overlaps with the surface recognized by select pathogens.
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Affiliation(s)
- Linda Celeste Montemiglio
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Claudia Testi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy.,Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161, Rome, Italy
| | - Pierpaolo Ceci
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Elisabetta Falvo
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Martina Pitea
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Largo F. Vito 1, 00168, Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161, Rome, Italy
| | - Paola Baiocco
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161, Rome, Italy
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Russ Berrie Pavilion, Columbia University Medical Center, 1150 St Nicholas Ave, New York, NY, 10032, USA
| | - Alberto Boffi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Amédée des Georges
- Advanced Science Research Center at The Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY, 10031, USA. .,Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA. .,Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Beatrice Vallone
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy. .,Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
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21
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Calisti L, Trabuco MC, Boffi A, Testi C, Montemiglio LC, des Georges A, Benni I, Ilari A, Taciak B, Białasek M, Rygiel T, Król M, Baiocco P, Bonamore A. Engineered ferritin for lanthanide binding. PLoS One 2018; 13:e0201859. [PMID: 30102720 PMCID: PMC6089422 DOI: 10.1371/journal.pone.0201859] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/23/2018] [Indexed: 11/18/2022] Open
Abstract
Ferritin H-homopolymers have been extensively used as nanocarriers for diverse applications in the targeted delivery of drugs and imaging agents, due to their unique ability to bind the transferrin receptor (CD71), highly overexpressed in most tumor cells. In order to incorporate novel fluorescence imaging properties, we have fused a lanthanide binding tag (LBT) to the C-terminal end of mouse H-chain ferritin, HFt. The HFt-LBT possesses one high affinity Terbium binding site per each of the 24 subunits provided by six coordinating aminoacid side chains and a tryptophan residue in its close proximity and is thus endowed with strong FRET sensitization properties. Accordingly, the characteristic Terbium emission band at 544 nm for the HFt-LBT Tb(III) complex was detectable upon excitation of the tag enclosed at two order of magnitude higher intensity with respect to the wtHFt protein. X-ray data at 2.9 Å and cryo-EM at 7 Å resolution demonstrated that HFt-LBT is correctly assembled as a 24-mer both in crystal and in solution. On the basis of the intrinsic Tb(III) binding properties of the wt protein, 32 additional Tb(III) binding sites, located within the natural iron binding sites of the protein, were identified besides the 24 Tb(III) ions coordinated to the LBTs. HFt-LBT Tb(III) was demonstrated to be actively uptaken by selected tumor cell lines by confocal microscopy and FACS analysis of their FITC derivatives, although direct fluorescence from Terbium emission could not be singled out with conventional, 295-375 nm, fluorescence excitation.
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Affiliation(s)
- Lorenzo Calisti
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | | | - Alberto Boffi
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Claudia Testi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Amédée des Georges
- The City University of New York Advanced Science Research Center, New York, NY
| | - Irene Benni
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Bartłomiej Taciak
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
- Cellis Ltd., Warsaw, Poland
| | - Maciej Białasek
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
| | - Tomasz Rygiel
- Cellis Ltd., Warsaw, Poland
- Department of Immunology, Center for Biostructure Research, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Król
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
- Cellis Ltd., Warsaw, Poland
| | - Paola Baiocco
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- * E-mail:
| | - Alessandra Bonamore
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
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22
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Benni I, Trabuco MC, Di Stasio E, Arcovito A, Boffi A, Malatesta F, Bonamore A, De Panfilis S, de Turris V, Baiocco P. Excimer based fluorescent pyrene-ferritin conjugate for protein oligomerization studies and imaging in living cells. RSC Adv 2018; 8:12815-12822. [PMID: 35541244 PMCID: PMC9079363 DOI: 10.1039/c8ra00210j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 01/08/2018] [Accepted: 03/23/2018] [Indexed: 11/21/2022] Open
Abstract
Ferritin self-assembly has been widely exploited for the synthesis of a variety of nanoparticles for drug-delivery and diagnostic applications. However, despite the crucial role of ferritin self-assembly mechanism for probes encapsulation, little is known about the principles behind the oligomerization mechanism. In the present work, the novel "humanized" chimeric Archaeal ferritin HumAfFt, displaying the transferrin receptor-1 (TfR1) recognition motif typical of human H homopolymer and the unique salt-triggered oligomerization properties of Archaeoglobus fulgidus ferritin (AfFt), was site-selectively labeled with N-(1-pyrenyl)maleimide on a topologically selected cysteine residue inside the protein cavity, next to the dimer interface. Pyrene characteristic fluorescence features were exploited to investigate the transition from a dimeric to a cage-like 24-meric state and to visualize the protein in vitro by two photon fluorescence microscopy. Indeed, pyrene fluorescence changes upon ferritin self-assembly allowed to establish, for the first time, the kinetic and thermodynamic details of the archaeal ferritins oligomerization mechanism. In particular, the magnesium induced oligomerization proved to be faster than the monovalent cation-triggered process, highly cooperative, complete at low MgCl2 concentrations, and reversed by treatment with EDTA. Moreover, pyrene intense excimer fluorescence was successfully visualized in vitro by two photon fluorescence microscopy as pyrene-labeled HumAfFt was actively uptaken into HeLa cells by human transferrin receptor TfR1 recognition, thus representing a unique nano-device building block for two photon fluorescence cell imaging.
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Affiliation(s)
- Irene Benni
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome P.le A. Moro 5 00185 Rome Italy
| | - Matilde Cardoso Trabuco
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome P.le A. Moro 5 00185 Rome Italy
- Molirom srl via Ravenna 8 00161 Rome Italy
| | - Enrico Di Stasio
- Institute of Biochemistry and Clinical Biochemistry, Catholic University Largo Francesco Vito, 1 00168 Rome Italy
| | - Alessandro Arcovito
- Institute of Biochemistry and Clinical Biochemistry, Catholic University Largo Francesco Vito, 1 00168 Rome Italy
| | - Alberto Boffi
- Institute of Molecular Biology and Pathology, National Research Council P.le A. Moro 7 00185 Rome Italy
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia V.le Regina Elena 291 00161 Rome Italy
| | - Francesco Malatesta
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome P.le A. Moro 5 00185 Rome Italy
| | - Alessandra Bonamore
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome P.le A. Moro 5 00185 Rome Italy
| | - Simone De Panfilis
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia V.le Regina Elena 291 00161 Rome Italy
| | - Valeria de Turris
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia V.le Regina Elena 291 00161 Rome Italy
| | - Paola Baiocco
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia V.le Regina Elena 291 00161 Rome Italy
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Francioso A, Dinarelli S, Girasole M, Cervoni L, d’Erme M, Mura F, Boffi A, Montanari E, Mosca L. Behind Resveratrol Stabilization by Carboxymethylated (1,3/1,6)-β-d-Glucan: Does the Polyphenol Play a Role in Polymer Structural Organization? Int J Mol Sci 2017; 18:ijms18092006. [PMID: 32961650 PMCID: PMC5618655 DOI: 10.3390/ijms18092006] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 02/02/2023] Open
Abstract
Resveratrol stability in solution can be improved by combining the polyphenol with carboxymethylated (1,3/1,6)-β-d-glucan (CM-glucan), a carbohydrate polymer widely used in the food and pharmaceutical industries. The present work was undertaken to elucidate the mechanism behind this stabilizing effect. The supramolecular structural, physico-chemical and morphological features of the CM-glucan/resveratrol complex have been studied under different physical and chemical stimuli by means of spectroscopic techniques, microscopy and physical methods such as UV-Visible spectroscopy (UV-Vis), spectrofluorimetry, Circular Dichroism (CD), Infrared spectroscopy (FT-IR), Differential Scanning Calorimetry (DSC), Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM). Our experimental data indicate that CM-glucan conformational organized architecture in aqueous solution is enhanced in the presence of resveratrol, suggesting that the polyphenol is able to confer a high degree of order to the polymer by a probable cooperative structural organization that results in a long term stabilization for the polyphenol.
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Affiliation(s)
- Antonio Francioso
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Rome, Italy; (L.C.); (M.d’E.); (A.B.); (L.M.)
- Correspondence: ; Tel.: +39-06-4991-0923; Fax: +39-06-4440-062
| | - Simone Dinarelli
- ISM Institute of Material Structure, CNR National Research Council-Rome, 00185 Rome, Italy; (S.D.); (M.G.)
| | - Marco Girasole
- ISM Institute of Material Structure, CNR National Research Council-Rome, 00185 Rome, Italy; (S.D.); (M.G.)
| | - Laura Cervoni
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Rome, Italy; (L.C.); (M.d’E.); (A.B.); (L.M.)
| | - Maria d’Erme
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Rome, Italy; (L.C.); (M.d’E.); (A.B.); (L.M.)
| | - Francesco Mura
- CNIS Research center for Nanotechnology Applications-Rome, 00185 Rome, Italy;
| | - Alberto Boffi
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Rome, Italy; (L.C.); (M.d’E.); (A.B.); (L.M.)
| | - Elita Montanari
- Department of Drug Chemistry and Technology, Sapienza University of Rome, 00185 Rome, Italy;
| | - Luciana Mosca
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Rome, Italy; (L.C.); (M.d’E.); (A.B.); (L.M.)
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de Turris V, Cardoso Trabuco M, Peruzzi G, Boffi A, Testi C, Vallone B, Celeste Montemiglio L, Georges AD, Calisti L, Benni I, Bonamore A, Baiocco P. Humanized archaeal ferritin as a tool for cell targeted delivery. Nanoscale 2017; 9:647-655. [PMID: 27942679 DOI: 10.1039/c6nr07129e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Human ferritins have been extensively studied to be used as nanocarriers for diverse applications and could represent a convenient alternative for targeted delivery of anticancer drugs and imaging agents. However, the most relevant limitation to their applications is the need for highly acidic experimental conditions during the initial steps of particle/cargo assembly, a process that could affect both drug stability and the complete reassembly of the ferritin cage. To overcome this issue the unique assembly of Archaeoglobus fulgidus ferritin was genetically engineered by changing a surface exposed loop of 12 amino acids connecting B and C helices to mimic the sequence of the analogous human H-chain ferritin loop. This new chimeric protein was shown to maintain the unique, cation linked, association-dissociation properties of Archaeoglobus fulgidus ferritin occurring at neutral pH values, while exhibiting the typical human H-homopolymer recognition by the transferrin receptor TfR1. The chimeric protein was confirmed to be actively and specifically internalized by HeLa cells, thus representing a unique nanotechnological tool for cell-targeted delivery of possible payloads for diagnostic or therapeutic purposes. Moreover, it was demonstrated that the 12 amino acids' loop is necessary and sufficient for binding to the transferrin receptor. The three-dimensional structure of the humanized Archaeoglobus ferritin has been obtained both as crystals by X-ray diffraction and in solution by cryo-EM.
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Affiliation(s)
- Valeria de Turris
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome 00161, Italy.
| | | | - Giovanna Peruzzi
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome 00161, Italy.
| | - Alberto Boffi
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome 00161, Italy. and Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro, 7, 00185, Rome, Italy
| | - Claudia Testi
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome 00161, Italy.
| | - Beatrice Vallone
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro, 7, 00185, Rome, Italy
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy
| | - Amédée Des Georges
- The City University of New York Advanced Science Research Center 85 St. Nicholas Terrace, New York, NY 10031, USA
| | - Lorenzo Calisti
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy
| | - Irene Benni
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy
| | - Alessandra Bonamore
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy
| | - Paola Baiocco
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome 00161, Italy.
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25
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Calisti L, Benni I, Cardoso Trabuco M, Baiocco P, Ruzicka B, Boffi A, Falvo E, Malatesta F, Bonamore A. Probing bulky ligand entry in engineered archaeal ferritins. Biochim Biophys Acta Gen Subj 2016; 1861:450-456. [PMID: 27755975 DOI: 10.1016/j.bbagen.2016.10.007] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/01/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND A set of engineered ferritin mutants from Archaeoglobus fulgidus (Af-Ft) and Pyrococcus furiosus (Pf-Ft) bearing cysteine thiols in selected topological positions inside or outside the ferritin shell have been obtained. The two apo-proteins were taken as model systems for ferritin internal cavity accessibility in that Af-Ft is characterized by the presence of a 45Å wide aperture on the protein surface whereas Pf-Ft displays canonical (threefold) channels. METHODS Thiol reactivity has been probed in kinetic experiments in order to assess the protein matrix permeation properties towards the bulky thiol reactive DTNB (5,5'-dithiobis-2-nitrobenzoic acid) molecule. RESULTS Reaction of DTNB with thiols was observed in all ferritin mutants, including those bearing free cysteine thiols inside the ferritin cavity. As expected, a ferritin mutant from Pf-Ft, in which the cysteine thiol is on the outer surface displays the fastest binding kinetics. In turn, also the Pf-Ft mutant in which the cysteine thiol is placed within the internal cavity, is still capable of full stoichiometric DTNB binding albeit with an almost 200-fold slower rate. The behaviour of Af-Ft bearing a cysteine thiol in a topologically equivalent position in the internal cavity was intermediate among the two Pf-Ft mutants. CONCLUSIONS AND GENERAL SIGNIFICANCE The data thus obtained indicate clearly that the protein matrix in archaea ferritins does not provide a significant barrier against bulky, negatively charged ligands such as DTNB, a finding of relevance in view of the multiple biotechnological applications of these ferritins that envisage ligand encapsulation within the internal cavity.
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Affiliation(s)
- Lorenzo Calisti
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, I-00185 Rome, Italy
| | - Irene Benni
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, I-00185 Rome, Italy
| | - Matilde Cardoso Trabuco
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, I-00185 Rome, Italy
| | - Paola Baiocco
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome I-00185, Italy
| | - Barbara Ruzicka
- Istituto dei Sistemi Complessi del Consiglio Nazionale delle Ricerche (ISC-CNR) Sede Sapienza and Dipartimento di Fisica, Sapienza University of Rome, P.le Aldo Moro 5, I-00185 Rome, Italy
| | - Alberto Boffi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, I-00185 Rome, Italy; Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche (IBPM-CNR) Sede Sapienza University of Rome, P.le Aldo Moro 5, I-00185 Rome, Italy
| | - Elisabetta Falvo
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche (IBPM-CNR) Sede Sapienza University of Rome, P.le Aldo Moro 5, I-00185 Rome, Italy
| | - Francesco Malatesta
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, I-00185 Rome, Italy
| | - Alessandra Bonamore
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le Aldo Moro 5, I-00185 Rome, Italy.
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Shipovskov S, Bonamore A, Boffi A, Ferapontova EE. Electrocatalytic interconversion of NADH and NAD(+) by Escherichia coli flavohemoglobin. Chem Commun (Camb) 2016; 51:16096-8. [PMID: 26389555 DOI: 10.1039/c5cc06317e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
E. coli flavohemoglobin, oriented at electrodes via amphiphilic polymyxin B, electrocatalytically interconverts NADH and NAD(+) at its heme potentials operating as an electron transfer relay between the electrode and the protein FAD, where NADH/NAD(+) is transformed. The results are crucial for the development of NAD(+)-dependent bioelectrodes for biosynthesis, biosensors and biofuel cells.
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Affiliation(s)
- S Shipovskov
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
| | - A Bonamore
- Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University "La Sapienza", 00185 Rome, Italy
| | - A Boffi
- Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University "La Sapienza", 00185 Rome, Italy
| | - E E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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27
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Bonamore A, Calisti L, Calcaterra A, Ismail OH, Gargano M, D'Acquarica I, Botta B, Boffi A, Macone A. A Novel Enzymatic Strategy for the Synthesis of Substituted Tetrahydroisoquinolines. ChemistrySelect 2016. [DOI: 10.1002/slct.201600134] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Alessandra Bonamore
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari (IBPM), CNR; Sapienza Università di Roma; Piazzale Aldo Moro 5 Roma 00185 Italy
- MOLIROM s.r.l; Via Carlo Bartolomeo Piazza 8 Roma 00161 Italy
| | - Lorenzo Calisti
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari (IBPM), CNR; Sapienza Università di Roma; Piazzale Aldo Moro 5 Roma 00185 Italy
| | - Andrea Calcaterra
- Dipartimento di Chimica e Tecnologia del Farmaco; Sapienza Università di Roma; Piazzale Aldo Moro 5 Roma 00185 Italy
| | - Omar H. Ismail
- Dipartimento di Chimica e Tecnologia del Farmaco; Sapienza Università di Roma; Piazzale Aldo Moro 5 Roma 00185 Italy
| | - Maurizio Gargano
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari (IBPM), CNR; Sapienza Università di Roma; Piazzale Aldo Moro 5 Roma 00185 Italy
| | - Ilaria D'Acquarica
- Dipartimento di Chimica e Tecnologia del Farmaco; Sapienza Università di Roma; Piazzale Aldo Moro 5 Roma 00185 Italy
| | - Bruno Botta
- Dipartimento di Chimica e Tecnologia del Farmaco; Sapienza Università di Roma; Piazzale Aldo Moro 5 Roma 00185 Italy
- MOLIROM s.r.l; Via Carlo Bartolomeo Piazza 8 Roma 00161 Italy
| | - Alberto Boffi
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari (IBPM), CNR; Sapienza Università di Roma; Piazzale Aldo Moro 5 Roma 00185 Italy
- MOLIROM s.r.l; Via Carlo Bartolomeo Piazza 8 Roma 00161 Italy
| | - Alberto Macone
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari (IBPM), CNR; Sapienza Università di Roma; Piazzale Aldo Moro 5 Roma 00185 Italy
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28
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Falvo E, Tremante E, Arcovito A, Papi M, Elad N, Boffi A, Morea V, Conti G, Toffoli G, Fracasso G, Giacomini P, Ceci P. Improved Doxorubicin Encapsulation and Pharmacokinetics of Ferritin-Fusion Protein Nanocarriers Bearing Proline, Serine, and Alanine Elements. Biomacromolecules 2015; 17:514-22. [PMID: 26686226 DOI: 10.1021/acs.biomac.5b01446] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A novel human ferritin-based nanocarrier, composed of 24 modified monomers able to auto-assemble into a modified protein cage, was produced and used as selective carrier of anti-tumor payloads. Each modified monomer derives from the genetic fusion of two distinct modules, namely the heavy chain of human ferritin (HFt) and a stabilizing/protective PAS polypeptide sequence rich in proline (P), serine (S), and alanine (A) residues. Two genetically fused protein constructs containing PAS polymers with 40- and 75-residue lengths, respectively, were compared. They were produced and purified as recombinant proteins in Escherichia coli at high yields. Both preparations were highly soluble and stable in vitro as well as in mouse plasma. Size-exclusion chromatography, dynamic light scattering, and transmission electron microscopy results indicated that PASylated ferritins are fully assembled and highly monodispersed. In addition, yields and stability of encapsulated doxorubicin were significantly better for both HFt-PAS proteins than for wild-type HFt. Importantly, PAS sequences considerably prolonged the half-life of HFt in the mouse bloodstream. Finally, our doxorubicin-loaded nanocages preserved the pharmacological activity of the drug. Taken together, these results indicate that both of the developed HFt-PAS fusion proteins are promising nanocarriers for future applications in cancer therapy.
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Affiliation(s)
- Elisabetta Falvo
- Institute of Molecular Biology and Pathology CNR, National Research Council of Italy , 00185 Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", University "Sapienza" , 00185 Rome, Italy
| | - Elisa Tremante
- Regina Elena National Cancer Institute , 00144 Rome, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore , Largo F. Vito 1, 00168 Rome, Italy
| | - Massimiliano Papi
- Istituto di Fisica, Università Cattolica del Sacro Cuore , Largo F. Vito 1, 00168, Rome, Italy
| | - Nadav Elad
- Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Alberto Boffi
- Institute of Molecular Biology and Pathology CNR, National Research Council of Italy , 00185 Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", University "Sapienza" , 00185 Rome, Italy.,Center for Life Nano Science at Sapienza, Istituto Italiano di Tecnologia (IIT) , 00161 Rome, Italy
| | - Veronica Morea
- Institute of Molecular Biology and Pathology CNR, National Research Council of Italy , 00185 Rome, Italy
| | - Giamaica Conti
- Department of Neurological, Biomedical and Movement Sciences, University of Verona , 37134 Verona, Italy
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, CRO Aviano National Cancer Institute , 33081Aviano (Pordenone), Italy
| | - Giulio Fracasso
- Department of Medicine, University of Verona , 37134 Verona, Italy
| | | | - Pierpaolo Ceci
- Institute of Molecular Biology and Pathology CNR, National Research Council of Italy , 00185 Rome, Italy
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Bonamore A, Gargano M, Calisti L, Francioso A, Mosca L, Boffi A, Federico R. A Novel Direct Method for Determination of Riboflavin in Alcoholic Fermented Beverages. FOOD ANAL METHOD 2015. [DOI: 10.1007/s12161-015-0259-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Boffi A, Favero G, Federico R, Macone A, Antiochia R, Tortolini C, Sanzó G, Mazzei F. Amine oxidase-based biosensors for spermine and spermidine determination. Anal Bioanal Chem 2015; 407:1131-7. [PMID: 25407429 DOI: 10.1007/s00216-014-8324-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 10/30/2014] [Accepted: 11/05/2014] [Indexed: 12/23/2022]
Abstract
The present work describes the development and optimization of electrochemical biosensors for specific determination of the biogenic polyamine spermine (Spm) and spermidine (Spmd) whose assessment represents a novel important analytical tool in food analysis and human diagnostics. These biosensors have been prepared using novel engineered enzymes: polyamine oxidase (PAO) endowed with selectivity towards Spm and Spmd and spermine oxidase (SMO) characterized by strict specificity towards Spm. The current design entails biosensors in which the enzymes were entrapped in poly(vinyl alcohol) bearing styrylpyridinium groups (PVA-SbQ), a photocrosslinkable gel, onto an electrode surface. Screen-printed electrodes (SPEs) were used as electrochemical transducers for enzymatically produced hydrogen peroxide, operating at different potential vs Ag/AgCl according to the material of the working electrode (WE): +700 mV for graphite (GP) or -100 mV for Prussian blue (PB)-modified SPE, respectively. Biosensor performances were evaluated by means of flow injection amperometric (FIA) measurements. The modified electrodes showed good sensitivity, long-term stability and reproducibility. Under optimal conditions, the PAO biosensor showed a linear range 0.003-0.3 mM for Spm and 0.01-0.4 mM for Spmd, while with the SMO biosensor, a linear range of 0.004-0.5 mM for Spm has been obtained. The main kinetic parameters apparent Michaelis constant (K M), turnover number (K cat) and steady-state current (I max) were determined. The proposed device was then applied to the determination of biogenic amines in blood samples. The results obtained were in good agreement with those obtained with the GC-MS reference method.
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Affiliation(s)
- Alberto Boffi
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
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31
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Howes BD, Boechi L, Boffi A, Estrin DE, Smulevich G. Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins: Insights from Thermobifida fusca HbO. Adv Microb Physiol 2015; 67:85-126. [PMID: 26616516 DOI: 10.1016/bs.ampbs.2015.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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] [Indexed: 12/12/2022]
Abstract
In this chapter, we will discuss the paradigmatic case of Thermobifida fusca (Tf-trHb) HbO in its ferrous and ferric states and its behaviour towards a battery of possible ligands. This choice was dictated by the fact that it has been one of the most extensively studied truncated haemoglobins, both in terms of spectroscopic and molecular dynamics studies. Tf-trHb typifies the structural properties of group II trHbs, as the active site is characterized by a highly polar distal environment in which TrpG8, TyrCD1, and TyrB10 provide three potential H-bond donors in the distal cavity capable of stabilizing the incoming ligands. The role of these residues in key topological positions, and their interplay with the iron-bound ligands, has been addressed in studies carried out on the CO, F(-), OH(-), CN(-), and HS(-) adducts formed with the wild-type protein and a combinatorial set of mutants, in which the distal polar residues, TrpG8, TyrCD1, and TyrB10, have been singly, doubly, or triply replaced by a Phe residue. In this context, such a complete analysis provides an excellent benchmark for the investigation of the relationship between protein structure and function, allowing one to translate physicochemical properties of the active site into the observed functional behaviour. Tf-trHb will be compared with other members of the group II trHbs and, more generally, with members of the other trHb subgroups.
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Affiliation(s)
- Barry D Howes
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Alberto Boffi
- Dipartimento di Scienze Biochimiche, Università "Sapienza", Rome, Italy
| | - Dario E Estrin
- Departamento de Química Inorgánica, Analítica y Química Física and Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy.
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32
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Vannucci L, Falvo E, Failla CM, Carbo M, Fornara M, Canese R, Cecchetti S, Rajsiglova L, Stakheev D, Krizan J, Boffi A, Carpinelli G, Morea V, Ceci P. In Vivo Targeting of Cutaneous Melanoma Using an Melanoma Stimulating Hormone-Engineered Human Protein Cage with Fluorophore and Magnetic Resonance Imaging Tracers. J Biomed Nanotechnol 2015; 11:81-92. [DOI: 10.1166/jbn.2015.1946] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Nicoletti FP, Bustamante JP, Droghetti E, Howes BD, Fittipaldi M, Bonamore A, Baiocco P, Feis A, Boffi A, Estrin DA, Smulevich G. Interplay of the H-Bond Donor–Acceptor Role of the Distal Residues in Hydroxyl Ligand Stabilization of Thermobifida fusca Truncated Hemoglobin. Biochemistry 2014; 53:8021-30. [DOI: 10.1021/bi501132a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco P. Nicoletti
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | | | - Enrica Droghetti
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Barry D. Howes
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Maria Fittipaldi
- INSTM
and Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, via Sansone 1, I-50019 Sesto Fiorentino, Italy
| | - Alessandra Bonamore
- Institute
Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences
and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Paola Baiocco
- Center of
Life Nano Sciences, Italian Institute of Technology, Viale Regina
Elena 291, I-00161 Rome, Italy
| | - Alessandro Feis
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Alberto Boffi
- Institute
Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences
and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | | | - Giulietta Smulevich
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
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Francioso A, Boffi A, Villani C, Manzi L, D’Erme M, Macone A, Mosca L. Isolation and Identification of 2,4,6-Trihydroxyphenanthrene as a Byproduct of trans-Resveratrol Photochemical Isomerization and Electrocyclization. J Org Chem 2014; 79:9381-4. [DOI: 10.1021/jo501405m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antonio Francioso
- Department of Biochemical Sciences and ‡Department of
Chemistry and Pharmaceutical
Technology, Sapienza University, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Alberto Boffi
- Department of Biochemical Sciences and ‡Department of
Chemistry and Pharmaceutical
Technology, Sapienza University, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Claudio Villani
- Department of Biochemical Sciences and ‡Department of
Chemistry and Pharmaceutical
Technology, Sapienza University, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Lucio Manzi
- Department of Biochemical Sciences and ‡Department of
Chemistry and Pharmaceutical
Technology, Sapienza University, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Maria D’Erme
- Department of Biochemical Sciences and ‡Department of
Chemistry and Pharmaceutical
Technology, Sapienza University, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Alberto Macone
- Department of Biochemical Sciences and ‡Department of
Chemistry and Pharmaceutical
Technology, Sapienza University, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Luciana Mosca
- Department of Biochemical Sciences and ‡Department of
Chemistry and Pharmaceutical
Technology, Sapienza University, p.le Aldo Moro 5, 00185 Rome, Italy
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35
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Patrizi B, Lapini A, Di Donato M, Marcelli A, Lima M, Righini R, Foggi P, Baiocco P, Bonamore A, Boffi A. Role of local structure and dynamics of small ligand migration in proteins: a study of a mutated truncated hemoprotein from Thermobifida fusca by time resolved MIR spectroscopy. J Phys Chem B 2014; 118:9209-17. [PMID: 25019316 DOI: 10.1021/jp504499b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Carbon monoxide recombination dynamics in a mutant of the truncated hemoglobin from Thermobida fusca (3F-Tf-trHb) has been analyzed by means of ultrafast Visible-pump/MidIR-probe spectroscopy and compared with that of the wild-type protein. In 3F-Tf-trHb, three topologically relevant amino acids, responsible for the ligand stabilization through the formation of a H-bond network (TyrB10 TyrCD1 and TrpG8), have been replaced by Phe residues. X-ray diffraction data show that Phe residues in positions B10 and G8 maintain the same rotameric arrangements as Tyr and Trp in the wild-type protein, while Phe in position CD1 displays significant rotameric heterogeneity. Photodissociation of the ligand has been induced by exciting the sample with 550 nm pump pulses and the CO rebinding has been monitored in two mid-IR regions respectively corresponding to the ν(CO) stretching vibration of the iron-bound CO (1880-1980 cm(-1)) and of the dissociated free CO (2050-2200 cm(-1)). In both the mutant and wild-type protein, a significant amount of geminate CO rebinding is observed on a subnanosecond time scale. Despite the absence of the distal pocket hydrogen-bonding network, the kinetics of geminate rebinding in 3F-Tf-trHb is very similar to the wild-type, showing how the reactivity of dissociated CO toward the heme is primarily regulated by the effective volume and flexibility of the distal pocket and by caging effects exerted on the free CO on the analyzed time scale.
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Affiliation(s)
- Barbara Patrizi
- LENS (European Laboratory for Nonlinear Spectroscopy) Via N. Carrara 1, Sesto Fiorentino, Florence 50019, Italy
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36
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Vannucci L, Falvo E, Failla CM, Carbo M, Fornara M, Canese R, Cecchetti S, Rajsiglova L, Stakheev D, Krizan J, Boffi A, Carpinelli G, Morea V, Ceci P. In vivo targeting of cutaneous melanoma using an MSH-engineered human protein cage bearing fluorophore and MRI tracers. Lab Invest 2014. [PMCID: PMC4108896 DOI: 10.1186/1479-5876-12-s1-p6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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37
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Francioso A, Mastromarino P, Restignoli R, Boffi A, d'Erme M, Mosca L. Improved stability of trans-resveratrol in aqueous solutions by carboxymethylated (1,3/1,6)-β-D-glucan. J Agric Food Chem 2014; 62:1520-1525. [PMID: 24467639 DOI: 10.1021/jf404155e] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Resveratrol is a polyphenolic compound endowed with multiple health benefits. However, its limited bioavailability and poor stability in solution hamper its use in pharmaceutical applications. Due to its low solubility in water, solvents such as ethanol and dimethyl sulfoxide are often used to dissolve resveratrol. However, these solvents have adverse effects on cultured cells or in vivo. The purpose of this study was to develop an aqueous liquid formulation of resveratrol in combination with a modified glucan, the carboxymethylated (1,3/1,6)-β-D-glucan (CM-glucan). The proposed liquid formulation conferred stability to resveratrol without affecting its antioxidant capability. Shelf-life measurements revealed that resveratrol in aqueous solution is degraded within a few weeks, due to spontaneous oxidation. In contrast, the combination with CM-glucan matrix exerted a strong stabilizing effect in aqueous medium and increased resveratrol stability up to 12 months at 25 °C. These data provide evidence of a stable resveratrol formulation in liquid suspensions and support the possible development of pharmaceutical applications of this association in biopharmaceutics and drug delivery.
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Affiliation(s)
- Antonio Francioso
- Department of Biochemical Sciences and ‡Department of Public Health and Infectious Diseases, Section of Microbiology, Sapienza University , p.le Aldo Moro 5, 00185 Roma, Italy
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38
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Bustamante JP, Abbruzzetti S, Marcelli A, Gauto D, Boechi L, Bonamore A, Boffi A, Bruno S, Feis A, Foggi P, Estrin DA, Viappiani C. Ligand uptake modulation by internal water molecules and hydrophobic cavities in hemoglobins. J Phys Chem B 2014; 118:1234-45. [PMID: 24410478 DOI: 10.1021/jp410724z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Internal water molecules play an active role in ligand uptake regulation, since displacement of retained water molecules from protein surfaces or cavities by incoming ligands can promote favorable or disfavorable effects over the global binding process. Detection of these water molecules by X-ray crystallography is difficult given their positional disorder and low occupancy. In this work, we employ a combination of molecular dynamics simulations and ligand rebinding over a broad time range to shed light into the role of water molecules in ligand migration and binding. Computational studies on the unliganded structure of the thermostable truncated hemoglobin from Thermobifida fusca (Tf-trHbO) show that a water molecule is in the vicinity of the iron heme, stabilized by WG8 with the assistance of YCD1, exerting a steric hindrance for binding of an exogenous ligand. Mutation of WG8 to F results in a significantly lower stabilization of this water molecule and in subtle dynamical structural changes that favor ligand binding, as observed experimentally. Water is absent from the fully hydrophobic distal cavity of the triple mutant YB10F-YCD1F-WG8F (3F), due to the lack of residues capable of stabilizing it nearby the heme. In agreement with these effects on the barriers for ligand rebinding, over 97% of the photodissociated ligands are rebound within a few nanoseconds in the 3F mutant case. Our results demonstrate the specific involvement of water molecules in shaping the energetic barriers for ligand migration and binding.
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Affiliation(s)
- Juan P Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires, Argentina
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Falvo E, Tremante E, Fraioli R, Leonetti C, Zamparelli C, Boffi A, Morea V, Ceci P, Giacomini P. Antibody-drug conjugates: targeting melanoma with cisplatin encapsulated in protein-cage nanoparticles based on human ferritin. Nanoscale 2013; 5:12278-12285. [PMID: 24150593 DOI: 10.1039/c3nr04268e] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A novel antibody-drug conjugate (ADC) was synthesized incorporating ferritin-based nanoparticles. An average of three molecules of monoclonal antibody (mAb) Ep1 to the human melanoma-specific antigen CSPG4 were conjugated to a single ferritin cage encapsulating about 50 cisplatin molecules (HFt-Pt-Ep1). The HFt-Pt-Ep1 nanoparticle had an estimated molecular size of about 900 kD and 33 nm, and flow cytometry demonstrated specific binding to a CSPG4(+) melanoma cell line, but not to a CSPG4(-) breast carcinoma cell line. As compared to the cisplatin-containing ferritin nanoparticle alone (HFt-Pt), which inhibited thymidine incorporation more efficiently in breast carcinoma than melanoma cells, the mAb-derivatized HFt-Pt-Ep1 nanoparticle had a 25-fold preference for the latter. A similar preference for melanoma was observed upon systemic intravenous administration of HFt-Pt-Ep1 to nude mice xenotransplanted with pre-established, palpable melanoma and breast carcinoma tumors. Thus, we have been able to determine precise combinations and stoichiometric relationships between mAbs and nanoparticle protein cages, whereby the latter lose their tropism for ubiquitously distributed cellular receptors, and acquire instead remarkably lineage-selective binding. HFt-Pt-Ep1 is therefore an interesting model to improve the therapeutic index of antiblastic therapy in a tumor such as melanoma, which at its advanced stages is totally refractory to mono- and combination-chemotherapy.
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Affiliation(s)
- Elisabetta Falvo
- CNR - National Research Council of Italy, Institute of Molecular Biology and Pathology, Rome, Italy.
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Nicoletti FP, Droghetti E, Howes BD, Bustamante JP, Bonamore A, Sciamanna N, Estrin DA, Feis A, Boffi A, Smulevich G. H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin. Biochim Biophys Acta 2013; 1834:1901-9. [PMID: 23467007 DOI: 10.1016/j.bbapap.2013.02.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/19/2013] [Accepted: 02/22/2013] [Indexed: 10/27/2022]
Abstract
The ferric form of truncated hemoglobin II from Thermobifida fusca (Tf-trHb) and its triple mutant WG8F-YB10F-YCD1F at neutral and alkaline pH, and in the presence of CN(-) have been characterized by resonance Raman spectroscopy, electron paramagnetic resonance spectroscopy, and molecular dynamics simulations. Tf-trHb contains three polar residues in the distal site, namely TrpG8, TyrCD1 and TyrB10. Whereas TrpG8 can act as a potential hydrogen-bond donor, the tyrosines can act as donors or acceptors. Ligand binding in heme-containing proteins is determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. Since both the RR Fe-OH(-) and Fe-CN(-) frequencies are very sensitive to the distal environment, detailed information on structural variations has been obtained. The hydroxyl ligand binds only the WT protein giving rise to two different conformers. In form 1 the anion is stabilized by H-bonds with TrpG8, TyrCD1 and a water molecule, in turn H-bonded to TyrB10. In form 2, H-bonding with TyrCD1 is mediated by a water molecule. Unlike the OH(-) ligand, CN(-) binds both WT and the triple mutant giving rise to two forms with similar spectroscopic characteristics. The overall results clearly indicate that H-bonding interactions both with distal residues and water molecules are important structural determinants in the active site of Tf-trHb. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Colotti G, Ilari A, Boffi A, Morea V. Metals and metal derivatives in medicine. Mini Rev Med Chem 2013; 13:211-221. [PMID: 23438056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 02/21/2012] [Accepted: 02/28/2012] [Indexed: 06/01/2023]
Abstract
Several chemical elements are required by living organisms in addition to the four elements carbon, hydrogen, nitrogen and oxygen usually present in common organic molecules. Many metals (e.g. sodium, potassium, magnesium, calcium, iron, zinc, copper, manganese, chromium, molybdenum and selenium) are known to be required for normal biological functions in humans. Disorders of metal homeostasis and of metal bioavailability, or toxicity caused by metal excess, are responsible for a large number of human diseases. Metals are also extensively used in medicine as therapeutic and/or diagnostic agents. In the past 5000 years, metals such as arsenic, gold and iron have been used to treat a variety of human diseases. Nowadays, an ever-increasing number of metal-based drugs is available. These contain a broad spectrum of metals, many of which are not among those essential for humans, able to target proteins and/or DNA. This mini-review describes metal-containing compounds targeting DNA or proteins currently in use, or designed to be used, as therapeutics against cancer, arthritis, parasitic and other diseases, with a special focus on the available information, often provided by X-ray studies, about their mechanism of action at a molecular level. In addition, an overview of metal complexes used for diagnosing diseases is presented.
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Affiliation(s)
- Gianni Colotti
- CNR-National Research Council of Italy, Institute of Molecular Biology and Pathology, 00185 Rome, Italy.
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Sosna M, Bonamore A, Gorton L, Boffi A, Ferapontova EE. Direct electrochemistry and Os-polymer-mediated bioelectrocatalysis of NADH oxidation by Escherichia coli flavohemoglobin at graphite electrodes. Biosens Bioelectron 2012. [PMID: 23208089 DOI: 10.1016/j.bios.2012.10.094] [Citation(s) in RCA: 23] [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: 10/27/2022]
Abstract
Escherichia coli flavohemoglobin (HMP), which contains one heme and one FAD as prosthetic groups and is capable of reducing O₂ by its heme at the expense of NADH oxidized at its FAD site, was electrochemically studied at graphite (Gr) electrodes. Two signals were observed in voltammograms of HMP adsorbed on Gr, at -477 and -171 mV vs. Ag|AgCl, at pH 7.4, correlating with electrochemical responses from the FAD and heme domains, respectively. The electron transfer rate constant for ET reaction between FAD of HMP and the electrode was estimated to be 83 s⁻¹. Direct bioelectrocatalytic oxidation of NADH by HMP was not observed, presumably due to impeded substrate access to HMP orientated on Gr through the FAD-domain and/or partial denaturation of HMP. Bioelectrocatalysis was achieved when HMP was wired to Gr by the Os redox polymers, with the onset of NADH oxidation at the formal potential of the particular Os complex (+140 mV or -195 mV). Apparent Michaelis constants K(M)(app) and j(max) were determined, showing bioelectrocatalytic efficiency of NADH oxidation by HMP exceeding the one earlier shown with diaphorase, which makes HMP very attractive as a component of bioanalytical and bioenergetic devices.
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Affiliation(s)
- Maciej Sosna
- Interdisciplinary Nanoscience Center-iNANO, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
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Fiorillo A, Colotti G, Boffi A, Baiocco P, Ilari A. The crystal structures of the tryparedoxin-tryparedoxin peroxidase couple unveil the structural determinants of Leishmania detoxification pathway. PLoS Negl Trop Dis 2012; 6:e1781. [PMID: 22928053 PMCID: PMC3424247 DOI: 10.1371/journal.pntd.0001781] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 07/03/2012] [Indexed: 12/20/2022] Open
Abstract
Leishmaniasis is a neglected disease caused by Leishmania, an intracellular protozoan parasite which possesses a unique thiol metabolism based on trypanothione. Trypanothione is used as a source of electrons by the tryparedoxin/tryparedoxin peroxidase system (TXN/TXNPx) to reduce the hydroperoxides produced by macrophages during infection. This detoxification pathway is not only unique to the parasite but is also essential for its survival; therefore, it constitutes a most attractive drug target. Several forms of TXNPx, with very high sequence identity to one another, have been found in Leishmania strains, one of which has been used as a component of a potential anti-leishmanial polyprotein vaccine. The structures of cytosolic TXN and TXNPx from L. major (LmTXN and LmTXNPx) offer a unique opportunity to study peroxide reduction in Leishmania parasites at a molecular level, and may provide new tools for multienzyme inhibition-based drug discovery. Structural analyses bring out key structural features to elucidate LmTXN and LmTXNPx function. LmTXN displays an unusual N-terminal α-helix which allows the formation of a stable domain-swapped dimer. In LmTXNPx, crystallized in reducing condition, both the locally unfolded (LU) and fully folded (FF) conformations, typical of the oxidized and reduced protein respectively, are populated. The structural analysis presented here points to a high flexibility of the loop that includes the peroxidatic cysteine which facilitates Cys52 to form an inter-chain disulfide bond with the resolving cysteine (Cys173), thereby preventing over-oxidation which would inactivate the enzyme. Analysis of the electrostatic surface potentials of both LmTXN and LmTXNPx unveils the structural elements at the basis of functionally relevant interaction between the two proteins. Finally, the structural analysis of TXNPx allows us to identify the position of the epitopes that make the protein antigenic and therefore potentially suitable to be used in an anti-leishmanial polyprotein vaccine. Leishmania spp. are protozoa responsible for Leishmaniases, neglected diseases killing up to 60,000 people every year. Current therapies rely mainly on antimonial drugs that are inadequate due to poor drug efficacy and safety, combined with increasing drug resistance. To overcome these problems, there is an urgent need to find new and more affordable drugs. Leishmania reduces the hydrogen peroxide produced by macrophages during the infection by means of the tryparedoxin/tryparedoxin peroxidase couple. The two enzymes are potentially suitable drug targets since they are both necessary for parasite survival and absent in the human host. To understand the molecular basis of peroxide reduction in the Leishmania parasites, we have solved the X-ray crystal structures of both enzymes. Structural analyses highlight oligomerization of the two proteins and allow the regions responsible for their interaction to be identified. Moreover, based on the X-ray structures and on electronic microscopy data present in literature for the homologous proteins from Trypanosoma brucei, we have generated a model of interaction between tryparedoxin and tryparedoxin peroxidase from L. major. From the X-ray structure and from this model, we have identified the epitopes of tryparedoxin peroxidase, which is part of a potential threecomponent vaccine that is presently being studied in animal models and in human.
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Affiliation(s)
- Annarita Fiorillo
- Dipartimento di Scienze Biochimiche, University Sapienza, Rome, Italy
| | - Gianni Colotti
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
- * E-mail: (AI), (GC)
| | - Alberto Boffi
- Dipartimento di Scienze Biochimiche, University Sapienza, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche, Università di Roma “Sapienza”, Rome, Italy
| | - Paola Baiocco
- Dipartimento di Scienze Biochimiche, University Sapienza, Rome, Italy
| | - Andrea Ilari
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
- * E-mail: (AI), (GC)
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Lapini A, Di Donato M, Patrizi B, Marcelli A, Lima M, Righini R, Foggi P, Sciamanna N, Boffi A. Carbon monoxide recombination dynamics in truncated hemoglobins studied with visible-pump midIR-probe spectroscopy. J Phys Chem B 2012; 116:8753-61. [PMID: 22759230 DOI: 10.1021/jp3019149] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [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
Carbon monoxide recombination dynamics upon photodissociation with visible light has been characterized by means of ultrafast visible-pump/MidIR probe spectroscopy for the truncated hemoglobins from Thermobifida fusca and Bacillus subtilis. Photodissociation has been induced by exciting the sample at two different wavelengths: 400 nm, corresponding to the heme absorption in the B-band, and 550 nm, in the Q-bands. The bleached iron-CO coordination band located at 1850-1950 cm(-1) and the free CO absorption band in the region 2050-2200 cm(-1) have been observed by probe pulses tuned in the appropriate infrared region. The kinetic traces measured at 1850-1950 cm(-1) reveal multiexponential subnanosecond dynamics that have been interpreted as arising from fast geminate recombination of the photolyzed CO. A compared analysis of the crystal structure of the two proteins reveals a similar structure of their distal heme pocket, which contains conserved polar and aromatic amino acid residues closely interacting with the iron ligand. Although fast geminate recombination is observed in both proteins, several kinetic differences can be evidenced, which can be interpreted in terms of a different structural flexibility of the corresponding heme distal pockets. The analysis of the free CO band-shape and of its dynamic evolution brings out novel features about the nature of the docking site inside the protein cavity.
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Affiliation(s)
- Andrea Lapini
- LENS (European Laboratory for Nonlinear Spectroscopy), via N. Carrara 1, 50019 Sesto Fiorentino (FI), Italy
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Marcelli A, Abbruzzetti S, Bustamante JP, Feis A, Bonamore A, Boffi A, Gellini C, Salvi PR, Estrin DA, Bruno S, Viappiani C, Foggi P. Following ligand migration pathways from picoseconds to milliseconds in type II truncated hemoglobin from Thermobifida fusca. PLoS One 2012; 7:e39884. [PMID: 22792194 PMCID: PMC3391200 DOI: 10.1371/journal.pone.0039884] [Citation(s) in RCA: 22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 05/28/2012] [Indexed: 11/18/2022] Open
Abstract
CO recombination kinetics has been investigated in the type II truncated hemoglobin from Thermobifida fusca (Tf-trHb) over more than 10 time decades (from 1 ps to ∼100 ms) by combining femtosecond transient absorption, nanosecond laser flash photolysis and optoacoustic spectroscopy. Photolysis is followed by a rapid geminate recombination with a time constant of ∼2 ns representing almost 60% of the overall reaction. An additional, small amplitude geminate recombination was identified at ∼100 ns. Finally, CO pressure dependent measurements brought out the presence of two transient species in the second order rebinding phase, with time constants ranging from ∼3 to ∼100 ms. The available experimental evidence suggests that the two transients are due to the presence of two conformations which do not interconvert within the time frame of the experiment. Computational studies revealed that the plasticity of protein structure is able to define a branched pathway connecting the ligand binding site and the solvent. This allowed to build a kinetic model capable of describing the complete time course of the CO rebinding kinetics to Tf-trHb.
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Affiliation(s)
- Agnese Marcelli
- LENS, European Laboratory for Non-linear Spectroscopy, Florence, Italy.
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Colotti G, Ilari A, Boffi A, Morea V. Metals and Metal derivatives in Medicine. Mini Rev Med Chem 2012:MRMC-EPUB-20120413-009. [PMID: 22512556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 02/21/2012] [Accepted: 02/23/2012] [Indexed: 05/31/2023]
Abstract
Several chemical elements are required by living organisms in addition to the four elements carbon, hydrogen, nitrogen and oxygen usually present in common organic molecules. Many metals (e.g. sodium, potassium, magnesium, calcium, iron, zinc, copper, manganese, chromium, molybdenum and selenium) are known to be required for normal biological functions in humans. Disorders of metal homeostasis and of metal bioavailability, or toxicity caused by metal excess, are responsible for a large number of human diseases. Metals are also extensively used in medicine as therapeutic and/or diagnostic agents. In the past 5000 years, metals such as arsenic, gold and iron have been used to treat a variety of human diseases. Nowadays, an ever-increasing number of metal-based drugs is available. These contain a broad spectrum of metals, many of which are not among those essential for humans, able to target proteins and/or DNA. This mini-review describes metal-containing compounds targeting DNA or proteins currently in use, or designed to be used, as therapeutics against cancer, arthritis, parasitic and other diseases, with a special focus on the available information, often provided by X-ray studies, about their mechanism of action at a molecular level. In addition, an overview of metal complexes used for diagnosing diseases is presented.
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Affiliation(s)
- Gianni Colotti
- Gianni Colotti. CNR - National Research Council of Italy, Institute of Molecular Biology and Pathology c/o Dept. of Biochemical Sciences "A. Rossi Fanelli", University "Sapienza" P.le A.Moro 5, 00185, Rome, Italy.
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Vannucci L, Falvo E, Fornara M, Di Micco P, Benada O, Krizan J, Svoboda J, Hulikova-Capkova K, Morea V, Boffi A, Ceci P. Selective targeting of melanoma by PEG-masked protein-based multifunctional nanoparticles. Int J Nanomedicine 2012; 7:1489-509. [PMID: 22619508 PMCID: PMC3356193 DOI: 10.2147/ijn.s28242] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [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] [Indexed: 11/23/2022] Open
Abstract
Background Nanoparticle-based systems are promising for the development of imaging and therapeutic agents. The main advantage of nanoparticles over traditional systems lies in the possibility of loading multiple functionalities onto a single molecule, which are useful for therapeutic and/or diagnostic purposes. These functionalities include targeting moieties which are able to recognize receptors overexpressed by specific cells and tissues. However, targeted delivery of nanoparticles requires an accurate system design. We present here a rationally designed, genetically engineered, and chemically modified protein-based nanoplatform for cell/tissue-specific targeting. Methods Our nanoparticle constructs were based on the heavy chain of the human protein ferritin (HFt), a highly symmetrical assembly of 24 subunits enclosing a hollow cavity. HFt-based nanoparticles were produced using both genetic engineering and chemical functionalization methods to impart several functionalities, ie, the α-melanocyte-stimulating hormone peptide as a melanoma-targeting moiety, stabilizing and HFt-masking polyethylene glycol molecules, rhodamine fluorophores, and magnetic resonance imaging agents. The constructs produced were extensively characterized by a number of physicochemical techniques, and assayed for selective melanoma-targeting in vitro and in vivo. Results Our HFt-based nanoparticle constructs functionalized with the α-melanocyte-stimulating hormone peptide moiety and polyethylene glycol molecules were specifically taken up by melanoma cells but not by other cancer cell types in vitro. Moreover, experiments in melanoma-bearing mice indicate that these constructs have an excellent tumor-targeting profile and a long circulation time in vivo. Conclusion By masking human HFt with polyethylene glycol and targeting it with an α-melanocyte-stimulating hormone peptide, we developed an HFt-based melanoma-targeting nanoplatform for application in melanoma diagnosis and treatment. These results could be of general interest, because the same strategy can be exploited to develop ad hoc nanoplatforms for specific delivery towards any cell/tissue type for which a suitable targeting moiety is available.
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Affiliation(s)
- Luca Vannucci
- Institute of Microbiology, Academy of Sciences of the Czech Republic, VVI, Prague, Czech Republic
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Nicoletti FP, Droghetti E, Boechi L, Bonamore A, Sciamanna N, Estrin DA, Feis A, Boffi A, Smulevich G. Fluoride as a Probe for H-Bonding Interactions in the Active Site of Heme Proteins: The Case of Thermobifida fusca Hemoglobin. J Am Chem Soc 2011; 133:20970-80. [DOI: 10.1021/ja209312k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Francesco P. Nicoletti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Enrica Droghetti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alessandra Bonamore
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Natascia Sciamanna
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alessandro Feis
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Alberto Boffi
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
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