1,721,131 research outputs found
Modellistica computazionale di peptidomimetici modulatori di interazioni proteina-proteina
No full textLe interazioni proteina-proteina (PPI) giocano un ruolo chiave nella maggior parte dei processi cellulari e quindi costituiscono un’ampia e promettente classe di bersagli per la scoperta di nuovi farmaci. Lo sviluppo di piccole molecole capaci di modulare con selettività e potenza queste interazioni è un obiettivo di elevato potenziale terapeutico ma di difficile realizzazione, a causa di una serie di fattori. I più importanti sono in genere la mancanza di strutture di partenza, la natura estesa dell’interfaccia proteica e la sua flessibilità. Tuttavia, sfruttando l’esistenza di hot spots di energia libera di interazione e strategie innovative di ricerca, recenti studi hanno riportato esempi di successo di modulazione di PPI con piccole molecole, specie in campo oncologico.1
Uno degli approcci più utilizzati consiste nel trasferire l’epitopo di legame di una delle proteine su piccoli peptidi o peptidomimetici. Tale approccio ha fornito risultati di rilievo specie per brevi sequenze continue di riconoscimento, quali ad esempio il tripeptide RGD (che media l’interazione tra proteine di matrice e integrine nell’angiogenesi tumorale) o il tetrapeptide AVPI (che media l’interazione tra la proteina pro-apoptotica Smac e la proteina inibitrice dell’apoptosi XIAP).1
Nella presentazione verrà discusso il contributo di diverse tecniche computazionali allo sviluppo di peptidomimetici a base RGD o AVPI in grado di modulare le interazioni mediate da integrine o da XIAP attraverso la riproduzione degli elementi di struttura secondaria della loro interfaccia di binding.2,3 In particolare, verrà illustrato l’uso integrato di calcoli di meccanica, dinamica e docking molecolare con dati sperimentali (x-ray, NMR) per definire la conformazione di peptidomimetici lineari o ciclici contenenti scaffold rigidi e il loro modo di interazione con il target proteico a livello molecolare.
1. A. Loregian, G. Palù J. Cell. Physiol. 2005, 204, 750-762.
2. A.S.M. da Ressurreição, A. Vidu, M. Civera, L. Belvisi et al. Chem. Eur. J. 2009, 15, 12184-12188.
3. P. Seneci, A. Bianchi, C. Battaglia, L. Belvisi et al. Bioorg. & Med. Chem. 2009, 17, 5834-5856
Design of Cyclopeptidic Drugs
No full textCyclic peptides and peptidomimetics are emerging as promising therapeutics for the modulation of protein-protein interactions because of their favorable properties, in terms of pharmacokinetic, bioavailability, metabolic stability and target specificity[1]. For instance, cyclization, possibly combined with other conformational constraints, can significantly decrease the entropic penalty to obtain an active conformation, enhancing the binding affinity to a specific receptor.
However, the computational study of cyclic systems is hampered by the critical problem to calculate their three-dimensional structures, both in the unbound and the bound state. Indeed, due to the constrained nature of cyclic peptides, most docking algorithms are unable to accomplish the concerted motions required for rigorous macrocycle conformation sampling. As a result, the use of poorly representative input structures strongly affects the predictability of molecular docking results. Thus, the exhaustive and reliable study of cyclopeptide conformations is increasingly regarded as an essential step prior to docking calculations and the use of multiple conformers has become the standard for the docking of cyclic systems[2].
Nevertheless, the comprehensive conformational sampling of cyclic peptides and peptidomimetics is not trivial: in these molecules, the investigation of equilibrium conformations is limited by the difficulties to cross high free-energy barriers and to perform the concerted rotation of several dihedrals required for the transition from one conformation to another. Moreover, the force fields implemented in molecular modeling softwares could be not appropriate for the structure determination of highly constrained cyclic peptides containing non-standard amino acids or peptidomimetic scaffolds.
In this workshop, the challenging issues affecting the computational study of cyclic peptides and peptidomimetics and some approaches for their solution will be discussed in the context of integrin ligands, where several cyclic peptides reached advanced phases of clinical investigation[3].
The presentation will also include an introduction to some tools from Schrodinger[4] that have been successfully used in the study of cyclic peptidomimetic integrin ligands[5].
REFERENCES:
[1] L. Nevola, E. Giralt, Chem. Commun. 2015, 51, 3302-3315. [2] S. E. Allen, N. V. Dokholyan, A. A. Bowers, ACS Chem. Biol. 2016, 11, 10−24. [3] C. Mas-Moruno, R. Fraioli, F. Rechenmacher, S. Neubauer, T. G. Kapp, H. Kessler, Angew. Chem. Int. Ed. 2016, 55, 7048 – 7068, and references therein. [4]https://www.schrodinger.com [5] M. Marchini, M. Mingozzi, R. Colombo, I. Guzzetti, L. Belvisi, F. Vasile, D. Potenza, U. Piarulli, D. Arosio, C. Gennari, Chem. Eur. J. 2012, 18, 6195−6207; M. Mingozzi, A. Dal Corso, M. Marchini, I. Guzzetti, M. Civera, U. Piarulli, D. Arosio, L. Belvisi, D. Potenza, L. Pignataro, C. Gennari, Chem. Eur. J. 2013, 19, 3563−3567
SALICYLALDEHYDE-TAGGED PEPTIDES FOR THE REVERSIBLE-COVALENT ENGAGEMENT OF PROTEIN LYSINE RESIDUES
Full text linkInserting electrophilic species into small molecule ligands or peptides is a well-established method for enhancing binding affinity to target proteins. The amino acid Lysine (Lys) is highly abundant in the proteome and one of the most frequent residues on the outer structural layers of proteins. For these reasons, the derivatization of synthetic ligands with aldehyde tags capable of imine bond formation with Lys ɛ-amino groups may represent a general strategy for the discovery of potent small-molecule inhibitors.
Ortho-hydroxy aldehydes such as pyridoxal or salicylaldehyde (SA) derivatives have been used to form imines in aqueous media, stabilized by an intramolecular H-bond between the imine N atom and the ortho-phenolic proton. By virtue of this reactivity, SA derivatives are being installed into various classes of protein ligands, aimed at the reversible-covalent engagement of protein Lys residues.1,2
This talk will describe our recent contribution to this field, with focus on the installation of the Lys-engaging SA module into peptide ligands.3,4
Figure 1. Left: Binding mechanism of a reversible-covalent ligand equipped with a salicylaldehyde (SA) tag. Ideally, SA forms a remarkably stable imine bond with a Lys(ε-NH2) residue proximal to the ligand binding site. This covalent ligand-protein connection is stabilized by a H bond between the OH phenolic proton and the imine N atom. As a result, the final ligand-protein complex is stabilized by a combination of non-covalent and covalent interactions. Right: Current options for the SA tag installation at different peptide positions, recently developed by our group.
References
1. A. Dal Corso, M. Catalano, A. Schmid, J. Scheuermann, D. Neri, Angew. Chem. Int. Ed. 2018, 57, 17178.
2. M. Mason, L. Belvisi, L. Pignataro, A. Dal Corso, ChemBioChem 2023, e202300743.
3. G. Sacco, D. Arosio, M. Paolillo, A. Gloger, J. Scheuermann, L. Pignataro, L. Belvisi, A. Dal Corso, C. Gennari, Chem. Eur. J. 2023, e202203768.
4. M. Mason, B. Nava, L. Belvisi, L. Pignataro, A. Dal Corso, Eur. J. Org. Chem. 2024, 27, 202400229
Tumor targeting integrin ligands: from computational design to biomedical applications
No full textThe integrin family of adhesion molecules regulates diverse cell functions crucial to the initiation, progression and metastasis of tumors. aVb3, aVb5 and a5b1 integrins appear to be particularly important in angiogenesis and cancer, where preclinical studies have provided rationale for the development of small-molecule integrin antagonists related to the common recognition motif Arg-Gly-Asp, as both anti-tumor and anti-angiogenic agents [1].
In addition to their appeal as targets for cancer therapy, integrins have recently proved valuable targets for tumor directed delivery of diagnostics and/or therapeutics. Integrin-targeted molecular systems containing imaging biomarkers or anticancer drugs have great potential to improve the efficacy of diagnostic tools and decrease the toxic side effects of conventional chemotherapy [1].
In this context, we have recently developed an interdisciplinary approach, based on the interplay between synthetic organic, computational, structural chemistry and biology, to target integrins involved in tumor angiogenesis and overexpressed in tumor cells.
We have investigated the synthesis and the biological properties of a new class of cyclic peptidomimetics containing a bifunctional diketopiperazine (DKP) scaffold and the tripeptide sequence Arg-Gly-Asp (RGD) [2] or isoAsp-Gly-Arg (isoDGR) [3] as potent integrin ligands. The conformation of the cyclic peptidomimetics and their interactions with integrin receptors were studied by computational techniques and NMR experiments with intact cancer cells. The different stereochemistry and the different substitution of the scaffold, as well as the RGD or RGD-like recognition sequence, strongly influence the conformations adopted in the free-state and the binding mode of these ligands in the active site of aVb3 and a5b1 integrins [4].
A small library of integrin ligand – Paclitaxel conjugates was synthesized with the aim of using the tumor-homing cyclo[DKP-RGD] peptidomimetics for site-directed delivery of the cytotoxic drug. These Paclitaxel-RGD constructs showed in vitro cytotoxic activity similar to that of Paclitaxel, and a superior in vivo activity despite the lower (ca. half) molar dosage used [5]
Approcci computazionali per la progettazione di piccole molecole che interferiscono con processi di riconoscimento proteina-proteina
No full textInvestigating the interaction of peptidomimetic ligands with e-cadherin using NMR and computational studies
Full text linkClassical cadherins are versatile calcium-dependent cell–cell adhesion proteins, differentially and specifically expressed in different tissues. Cadherins form homophilic cell–cell interactions by forming dimers between the N-terminal extracellular domains of two cadherins on adjacent cells. Cadherins are known to play a key role in important physiological processes, such as tissue morphogenesis and stability, as well as in the immune system regulation [1]. Over the past 20 years,the expression and/or the dysregulation of several cadherins have been shown to correlate with tumor progression [2]. Thus, cadherins are becoming valuable diagnostic indicators as well as potential therapeutic targets.Recently, our group set up a docking protocol to rationally design small peptidomimetic ligands mimicking the N- and E-cadherin adhesive homodimer interface. Accordingly, the first mimics based on the tetrapeptide sequence Asp1-Trp2-Val3-Ile4 (DWVI) of the N-terminal EC1 domain were achieved (by replacing the central dipeptide Trp2-Val3 with several scaffolds developed in our laboratories) and proved to inhibit adhesion of epithelial ovarian cancer cells with millimolar potency [3]. Molecular Dynamics (MD) simulations were performed starting form the most representative docking poses to discriminate between the stable and unstable docked poses and to equilibrate the system to achieve a stable conformation. MD trajectories have been analyzed according to the experimental information on ligand-cadherin interaction obtained by STD (Saturation Transfer Difference) NMR experiments in the presence of EC1-EC2 construct of the epithelial E-cadherin. NMR data and MD simulations suggest a highly dynamic behavior of both the ligand and the protein and prompt towards an integrated computational and experimental approach to design new small peptidomimetic molecules able to interfere efficiently with cadherin-mediated cell-cell adhesion.
Acknowledgements: we gratefully acknowledge Ministero dell’Università e della Ricerca for financial support (FIRB project RBFR088ITV).
References
1) D. Leckband, S. Sivasankar, Curr. Opin. Cell Biol. 2012, 24, 620.
2) G. Berx, F. van Roy, Cold Spring Harbor Perspectives in Biology 2009, 1, a003129.
3) F. Doro, C. Colombo, C. Alberti, D. Arosio, L. Belvisi, C. Casagrande, R. Fanelli, L. Manzoni, E. Parisini, U. Piarulli, E. Luison, M. Figini, A. Tomassetti, M. Civera, Org. Biomol. Chem. 2015, 13, 2570
Transferred-NOE NMR Experiments on Intact Human Platelets: Receptor-Bound Conformation of RGD-Peptide Mimics.
No full textThe aim of this work is to show that transferred-NOE provides useful and detailed information on membrane-bound receptor-ligand interactions in living cells. Here, we study the interaction between intact human platelets and some ligands containing the RGD sequence. Conformational properties of the free and bound pentapeptides are reported. This journal i
A fragment-based virtual screening approach to identify e-cadherin lingands
Full text linkCadherins are calcium-dependent cell-cell adhesion proteins which are overexpressed in several solid tumors [1]. They contain an extracellular region consisting of five immunoglobulin-like domains that extend from the cell surface. Recent crystal structures have shown that classical cadherins dimerize through a ‘strand-swap’ trans-adhesive interface involving the N-terminal EC1 domains of two cadherins on adjacent cells [2, 3].
Despite a growing interest in the field, the rational design of small ligands targeting cadherins is still in a very early stage. Recently, our group set up a docking protocol (Glide v 5.7) to rationally design peptidomimetic ligands mimicking the N- and E-cadherin adhesive homodimer interface. Accordingly, the first mimics based on the tetrapeptide sequence Asp1-Trp2-Val3-Ile4 (DWVI) of the N-terminal adhesion arm were achieved and proved to inhibit the adhesion of epithelial ovarian cancer cells with millimolar potency [4]. Herein, a fragment-based virtual screening approach was applied to identify novel chemical entries targeting the DWVI binding site. Commercially available Maybridge and Life chemicals collections were used. The most promising fragments identified by the docking calculations were purchased and their binding to E-cadherin was evaluated by means of STD (Saturation Transfer Difference) NMR experiments.
Acknowledgements: We thank MIUR (PRIN 2015 project 20157WW5EH) for financial support.
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[1] G. Berx, F. van Roy, Cold Spring Harbor Perspectives in Biology 2009, 1, a003129.
[2] D. Leckband, S. Sivasankar, Curr. Opin. Cell Biol. 2012, 24, 620-627.
[3] J. Vendome, K. Felsovalyi, H. Song, Z. Yang, X. Jin, J. Brasch, O. J. Harrison, G. Ahlsen, F. Bahna, A. Kaczynska, P. S. Katsamba, D. Edmond, W. L. Hubbell, L. Shapiro, B. Honig, PNAS 2014, 111, E4175-E4184.
[4] F. Doro, C. Colombo, C. Alberti, D. Arosio, L. Belvisi, C. Casagrande, R. Fanelli, L. Manzoni, E. Parisini, U. Piarulli, E. Luison, M. Figini, A. Tomassetti, M. Civera, Org. Biomol. Chem. 2015, 13, 2570-2573
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