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Casagrande FV, Amadeo A, Cartelli D, Calogero AM, Modena D, Costa I, Cantele F, Onelli E, Moscatelli A, Ascagni M, Pezzoli G, Cappelletti G. The imbalance between dynamic and stable microtubules underlies neurodegeneration induced by 2,5-hexanedione. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165581. [DOI: 10.1016/j.bbadis.2019.165581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/17/2019] [Accepted: 10/12/2019] [Indexed: 01/10/2023]
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2
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Pecnikaj I, Foschi F, Bucci R, Gelmi ML, Castellano C, Meneghetti F, Penso M. Stereoselective Synthesis of α,α′-Dihydroxy-β,β′-diaryl-β-amino Acids by Mannich-Like Condensation of Hydroarylamides. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ilir Pecnikaj
- Department of Chemistry; University of Milan; Via Golgi 19 20133 Milano Italy
| | - Francesca Foschi
- Department of Chemistry; University of Milan; Via Golgi 19 20133 Milano Italy
| | - Raffaella Bucci
- Department of Pharmaceutical Sciences (DISFARM); University of Milan; Via Venezian 21 20133 Milano Italy
| | - Maria Luisa Gelmi
- Department of Pharmaceutical Sciences (DISFARM); University of Milan; Via Venezian 21 20133 Milano Italy
| | - Carlo Castellano
- Department of Chemistry; University of Milan; Via Golgi 19 20133 Milano Italy
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences (DISFARM); University of Milan; Via Venezian 21 20133 Milano Italy
| | - Michele Penso
- CNR-Institute of Molecular Science and Technologies (ISTM); Via Golgi 19 20133 Milano Italy
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3
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Contini A, Ferri N, Bucci R, Lupo MG, Erba E, Gelmi ML, Pellegrino S. Peptide modulators of Rac1/Tiam1 protein-protein interaction: An alternative approach for cardiovascular diseases. Biopolymers 2017; 110. [PMID: 29178143 DOI: 10.1002/bip.23089] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/25/2017] [Accepted: 10/30/2017] [Indexed: 01/01/2023]
Abstract
Rac1 GTPase interaction with guanine nucleotide exchange factor Tiam1 is involved in several cancer types and cardiovascular diseases. Although small molecules interfering with their protein-protein interaction (PPI) were identified and studied, the ability of small peptides and peptide mimics acting as Rac1/Tiam1 PPI inhibitors has not been yet explored. Using computational alanine scanning (CAS), the "hot" interfacial residues have been determined allowing the design of a small library of putative PPI inhibitors. In particular, the insertion of an unnatural alpha, alpha disubstituted amino acid, that is norbornane amino acid, and the side chain stapling have been evaluated regarding both conformational stability and biological activity. REMD calculations and CD studies have indicated that one single norbornane amino acid at the N-terminus is not sufficient to stabilize the helix structure, while the side-chain stapling is a more efficient strategy. Furthermore, both engineered peptides have been found able to reduce Rac1-GTP levels in cultured human smooth muscle cells, while wild type sequence is not active.
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Affiliation(s)
- Alessandro Contini
- Department of Pharmaceutical Sciences, University of Milano, Milano, Italy
| | - Nicola Ferri
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Raffaella Bucci
- Department of Pharmaceutical Sciences, University of Milano, Milano, Italy
| | - Maria Giovanna Lupo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Emanuela Erba
- Department of Pharmaceutical Sciences, University of Milano, Milano, Italy
| | - Maria Luisa Gelmi
- Department of Pharmaceutical Sciences, University of Milano, Milano, Italy
| | - Sara Pellegrino
- Department of Pharmaceutical Sciences, University of Milano, Milano, Italy
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Abstract
α-Synuclein is a presynaptic protein associated to Parkinson’s disease, which is unstructured when free in the cytoplasm and adopts α helical conformation when bound to vesicles. After decades of intense studies, α-Synuclein physiology is still difficult to clear up due to its interaction with multiple partners and its involvement in a pletora of neuronal functions. Here, we looked at the remarkably neglected interplay between α-Synuclein and microtubules, which potentially impacts on synaptic functionality. In order to identify the mechanisms underlying these actions, we investigated the interaction between purified α-Synuclein and tubulin. We demonstrated that α-Synuclein binds to microtubules and tubulin α2β2 tetramer; the latter interaction inducing the formation of helical segment(s) in the α-Synuclein polypeptide. This structural change seems to enable α-Synuclein to promote microtubule nucleation and to enhance microtubule growth rate and catastrophe frequency, both in vitro and in cell. We also showed that Parkinson’s disease-linked α-Synuclein variants do not undergo tubulin-induced folding and cause tubulin aggregation rather than polymerization. Our data enable us to propose α-Synuclein as a novel, foldable, microtubule-dynamase, which influences microtubule organisation through its binding to tubulin and its regulating effects on microtubule nucleation and dynamics.
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Maffucci I, Contini A. Improved Computation of Protein–Protein Relative Binding Energies with the Nwat-MMGBSA Method. J Chem Inf Model 2016; 56:1692-704. [DOI: 10.1021/acs.jcim.6b00196] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche
− Sezione di Chimica Generale e Organica “Alessandro
Marchesini”, Università degli Studi di Milano, Via
Venezian, 21, 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche
− Sezione di Chimica Generale e Organica “Alessandro
Marchesini”, Università degli Studi di Milano, Via
Venezian, 21, 20133 Milano, Italy
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Verma K, Ramanathan K. Investigation of Paclitaxel Resistant R306C Mutation in β-Tubulin—A Computational Approach. J Cell Biochem 2016; 116:1318-24. [PMID: 25735511 DOI: 10.1002/jcb.25087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/16/2015] [Indexed: 11/12/2022]
Abstract
Paclitaxel is the most effective chemotherapeutic agent used for the treatment of a broad spectrum of solid tumors. However, observed paclitaxel resistance in clinical trials presents one of the major obstacles for cancer chemotherapy. Most importantly, resistance due to β-tubulin mutations (R306C) has been intensely debated in recent years. Despite all efforts, mechanism of resistance is still not well understood. In this study, computational techniques were employed to uncover the effect of R306C mutation in the β-tubulin structure and its function. The tools such as I-Mutant, CUPSAT and Fold-X were employed to address the consequence of R306C mutation in the structural stability of β-tubulin. Further, molecular docking and molecular dynamics study was employed to understand the functional impact of β-tubulin mutation. Our results suggest that the R306C mutation causes a significant reduction in the binding affinity between β-tubulin and paclitaxel. Further, docked complex analysis indicates that destruction of conservative hydrogen bond maintained by the residues Arg282 and Gly360 should be responsible for the large conformation changes of the binding pocket in R306C mutant. Finally, molecular dynamics simulations study confirms the stable binding of paclitaxel with native type β-tubulin structure rather than mutant (R306C) type. We certainly believe that this study will provide useful guidance for the development of novel inhibitors that are less susceptible to drug resistance.
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Affiliation(s)
- Kanika Verma
- Industrial Biotechnology Division, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - K Ramanathan
- Industrial Biotechnology Division, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
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7
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Exploring the impact of F270V mutation in the β-tubulin (Bos Taurus) structure and its function: a computational perspective. Biotechnol Lett 2015; 37:1003-11. [DOI: 10.1007/s10529-015-1765-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/06/2015] [Indexed: 10/24/2022]
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8
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Pellegrino S, Ronda L, Annoni C, Contini A, Erba E, Gelmi ML, Piano R, Paredi G, Mozzarelli A, Bettati S. Molecular insights into dimerization inhibition of c-Maf transcription factor. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2108-15. [PMID: 25220806 DOI: 10.1016/j.bbapap.2014.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/01/2014] [Accepted: 09/02/2014] [Indexed: 01/01/2023]
Abstract
The Maf protein family belongs to the activator protein 1 (AP-1) superfamily of transcription factors that bind specific DNA target sequences through a basic region and exploit a leucine zipper (LZ) motif for protein-protein interactions leading to homo- or hetero-dimerization. Mafs unique DNA-binding domain contains a highly conserved extended homology region (EHR) that allows to recognize longer DNA sequences than other basic leucine zipper (bZIP) transcription factors. Inspired by the fact that overexpression of Mafs is observed in about 50% of cases of multiple myeloma, a hematological malignant disorder, we undertook a peptide inhibitor approach. The LZ domain of c-Maf, one of large Mafs, was produced by solid phase peptide synthesis. We characterized its secondary structure and dimerization properties, and found that dimerization and folding events are strictly coupled. Moreover, potential peptidic c-Maf dimerization inhibitors were computationally designed and synthesized. These compounds were demonstrated by circular dichroism (CD) spectroscopy and MALDI-TOF mass spectrometry to bind to c-Maf LZ monomers, to drive folding of their partially disordered structure and to efficiently compete with dimerization, suggesting a way for interfering with the function of c-Maf and, more generally, of intrinsically disordered proteins, till now considered undruggable targets.
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Affiliation(s)
- Sara Pellegrino
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Luca Ronda
- Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Chiara Annoni
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Alessandro Contini
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Emanuela Erba
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Maria Luisa Gelmi
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Riccardo Piano
- Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Gianluca Paredi
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; SITEIA.PARMA Interdepartmental Center, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; National Institute of Biostructures and Biosystems, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Stefano Bettati
- Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; National Institute of Biostructures and Biosystems, Viale Medaglie d'Oro 305, 00136 Rome, Italy.
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9
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Ruffoni A, Ferri N, Bernini SK, Ricci C, Corsini A, Maffucci I, Clerici F, Contini A. 2-Amino-3-(phenylsulfanyl)norbornane-2-carboxylate: An Appealing Scaffold for the Design of Rac1–Tiam1 Protein–Protein Interaction Inhibitors. J Med Chem 2014; 57:2953-62. [DOI: 10.1021/jm401924s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alessandro Ruffoni
- Dipartimento
di Scienze Farmaceutiche—Sezione di Chimica Generale e Organica
“Alessandro Marchesini”, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Nicola Ferri
- Dipartimento
di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
- Multimedica IRCCS, Milan, Italy
| | - Sergio K. Bernini
- Dipartimento
di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Chiara Ricci
- Dipartimento
di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Alberto Corsini
- Dipartimento
di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Irene Maffucci
- Dipartimento
di Scienze Farmaceutiche—Sezione di Chimica Generale e Organica
“Alessandro Marchesini”, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Francesca Clerici
- Dipartimento
di Scienze Farmaceutiche—Sezione di Chimica Generale e Organica
“Alessandro Marchesini”, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento
di Scienze Farmaceutiche—Sezione di Chimica Generale e Organica
“Alessandro Marchesini”, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
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Maffucci I, Contini A. Explicit Ligand Hydration Shells Improve the Correlation between MM-PB/GBSA Binding Energies and Experimental Activities. J Chem Theory Comput 2013; 9:2706-17. [PMID: 26583864 DOI: 10.1021/ct400045d] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) and Molecular Mechanics Generalized Born Surface Area (MM-GBSA) methods are widely used for drug design/discovery purposes. However, it is not clear if the correlation between predicted and experimental binding affinities can be improved by explicitly considering selected water molecules in the calculation of binding energies, since different and sometimes diverging opinions are found in the literature. In this work, we evaluated how variably populated hydration shells explicitly considered around the ligands may affect the correlation between MM-PB/GBSA computed binding energy and biological activities (IC50 and ΔGbind, depending on the available experimental data). Four different systems-namely, the DNA-topoisomerase complex, α-thrombin, penicillopepsin, and avidin-were considered and ligand hydration shells populated by 10-70 water molecules were systematically evaluated. We found that the consideration of a hydration shell populated by a number of water residues (Nwat) between 30 and 70 provided, in all of the considered examples, a positive effect on correlation between MM-PB/GBSA calculated binding affinities and experimental activities, with a negligible increment of computational cost.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche-Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche-Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy
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11
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Casoni A, Clerici F, Contini A. Molecular dynamic simulation of mGluR5 amino terminal domain: essential dynamics analysis captures the agonist or antagonist behaviour of ligands. J Mol Graph Model 2013; 41:72-8. [DOI: 10.1016/j.jmgm.2013.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 01/09/2013] [Accepted: 02/04/2013] [Indexed: 11/24/2022]
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