1,721,056 research outputs found
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
A library approach to the development of chiral supramolecular ligands for asymmetric hydrogenation
No full textThe creation of chiral ligands of simple structure and truly easy preparation is the condition for supramolecular catalysis to become of practical industrial use. To this end, we developed a library of chiral monodentate phosphites, named BenzaPhos,[1] which can be prepared in only two simple steps from readily available compounds. The new ligands, containing a benzoic acid primary amide group capable of hydrogen bonding interactions, showed excellent activity and stereocontrol in the enantioselective hydrogenation of both benchmark substrates and ‘challenging’ olefins.
A series of experiments and computational studies strongly suggest that ligand-substrate H-bonding crucially affects these outstanding catalytic properties.
[1] L. Pignataro, C. Bovio, M. Civera, U. Piarulli, C. Gennari, Chem. Eur. J. 2012, 18, DOI: 10.1002/chem.201201032
Investigating 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
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
Structure based design of RSH inhibitors
No full textOne of the reasons why infections become chronic, is that some bacterial cells become dormant and survive antibiotic treatment. These cells are a bacterial phenotype called persisters. One of the hypothesis for their formation is based on the so-called stringent response, a signalling cascade leading to metabolic slowdown. The first step of the stringent response cascade is the accumulation of guanosine pentaphosphate (pppGpp) or tetraphosphate (ppGpp), collectively called (p)ppGpp. The synthesis of this molecule is catalyzed by the RelA/SpoT homolog (RSH) enzyme superfamily.
In order to synthetize new potential inhibitors against these enzymes to stop or to reduce the synthesis of (p)ppGpp, we performed virtual screening of several commercially available fragment libraries using a validated docking protocol within the SCHRÖDINGER® suite (Glide v. 10, Maestro). The highest scoring fragments were analysed and the four main chemotypes expanded based on structural similarity using Pubchem. Useful structural information was gathered for the design of the first generation of RSH inhibitors. The preliminary results of this work will be presented
Computer-aided design of peptidomimetic molecules targeting cadherin-mediated protein-protein interactions
No full textCadherins are cell-cell adhesion proteins which are overexpressed in several solid tumors. They contain an extracellular region consisting of five immunoglobulin-like domains (EC1–EC5) that extend from the cell surface. In 1995, structural data of the N-cadherin suggested an homodimeric interface involving the peptide chains HAVDI and INPI contained in the middle EC1 sequence. Based on these studies, mimics of His-Ala-Val sequence have been patented. More recently, the crystal structures of the complete (EC1-EC5) ectodomains of N- and E-cadherins have been solved highlighting that cadherins dimerize through a ‘strand-swap’ trans-adhesive interface involving the N-terminal EC1 domains.
In this framework, a thorough study of the adhesion dimer structures was attempted with the aim of characterizing cadherin binding interfaces and developing computational tools for the design of small peptidomimetics that target the homophilic interactions of the extracellular cadherin domains. Possible approaches included mapping the hotspot interactions into pharmacophores for database screening and mapping the epitope of one of the proteins onto a small peptidomimetic.
The communication will discuss the first results obtained in the computer-aided design, focusing on the most promising peptidomimetics found by virtual screening of database and rational design of small libraries of tetrapeptide mimics (Figure 1). The synthesis of few candidates has already been completed and their biological evaluation started
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Binding of RGD-peptide mimics to intact human platelets : an NMR study
No full textThe interactions of small peptides with biological membranes is central to a number of biological
processes. In contrast to soluble proteins there is comparatively little information available about ligandreceptor
interactions that occur at membrane surfaces. The biophysical environment of a membrane is
considerably different from the isotropic extracellular medium. It is therefore desirable to investigate
membrane proteins and their binding specificity directly in living cells. The integrin aIIbb3 is the most
abundant platelet cell surface glycoprotein and plays a key role in adhesion of platelet to protein-coated
surfaces and platelet/platelet aggregation. Therefore, aIIbb3 receptor is an excellent target for drug design
and delivery. The ligands are cyclic pentapeptide mimics incorporating stereoisomeric 5,6- and 5,7-fused
bicyclic lactams and the tripeptide sequence Arg-Gly-Asp (RGD)[1], a common amino acid motif found in
a number of adhesive proteins.
In order to study these binding processes at molecular level, we used trNOE experiments directly on
whole human platelets.[2] Conformational properties of the free and bound mimics are investigated by
computational and NMR studies.
Utilizing structural information by NMR tr-NOE experiments and docking studies, we have discovered a
new higher affinity aIIbb3 ligand, which is able to inhibit the adhesion of platelets
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