1
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Alemany-Chavarria M, Rodríguez-Guerra J, Maréchal JD. TALAIA: a 3D visual dictionary for protein structures. Bioinformatics 2023; 39:btad476. [PMID: 37549048 PMCID: PMC10423020 DOI: 10.1093/bioinformatics/btad476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/30/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023] Open
Abstract
MOTIVATION Graphical analysis of the molecular structure of proteins can be very complex. Full-atom representations retain most geometric information but are generally crowded, and key structural patterns can be challenging to identify. Non-full-atom representations could be more instructive on physicochemical aspects but be insufficiently detailed regarding shapes (e.g. entity beans-like models in coarse grain approaches) or simple properties of amino acids (e.g. representation of superficial electrostatic properties). In this work, we present TALAIA a visual dictionary that aims to provide another layer of structural representations.TALAIA offers a visual grammar that combines simple representations of amino acids while retaining their general geometry and physicochemical properties. It uses unique objects, with differentiated shapes and colors to represent amino acids. It makes easier to spot crucial molecular information, including patches of amino acids or key interactions between side chains. Most conventions used in TALAIA are standard in chemistry and biochemistry, so experimentalists and modelers can rapidly grasp the meaning of any TALAIA depiction. RESULTS We propose TALAIA as a tool that renders protein structures and encodes structure and physicochemical aspects as a simple visual grammar. The approach is fast, highly informative, and intuitive, allowing the identification of possible interactions, hydrophobic patches, and other characteristic structural features at first glance. The first implementation of TALAIA can be found at https://github.com/insilichem/talaia.
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Affiliation(s)
- Mercè Alemany-Chavarria
- Insilichem, Department of chemistry, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Jaime Rodríguez-Guerra
- Insilichem, Department of chemistry, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Jean-Didier Maréchal
- Insilichem, Department of chemistry, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
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2
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Sánchez-Aparicio JE, Sciortino G, Mates-Torres E, Lledós A, Maréchal JD. Successes and challenges in multiscale modelling of artificial metalloenzymes: the case study of POP-Rh 2 cyclopropanase. Faraday Discuss 2022; 234:349-366. [PMID: 35147145 DOI: 10.1039/d1fd00069a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular modelling applications in metalloenzyme design are still scarce due to a series of challenges. On top of that, the simulations of metal-mediated binding and the identification of catalytic competent geometries require both large conformational exploration and simulation of fine electronic properties. Here, we demonstrate how the incorporation of new tools in multiscale strategies, namely substrate diffusion exploration, allows taking a step further. As a showcase, the enantioselective profiles of the most outstanding variants of an artificial Rh2-based cyclopropanase (GSH, HFF and RFY) developed by Lewis and co-workers (Nat. Commun., 2015, 6, 7789 and Nat. Chem., 2018, 10, 318-324) have been rationalized. DFT calculations on the free-cofactor-mediated process identify the carbene insertion and the cyclopropanoid formation as crucial events, the latter being the enantiodetermining step, which displays up to 8 competitive orientations easily altered by the protein environment. The key intermediates of the reaction were docked into the protein scaffold showing that some mutated residues have direct interaction with the cofactor and/or the co-substrate. These interactions take the form of a direct coordination of Rh in GSH and HFF and a strong hydrophobic patch with the carbene moiety in RFY. Posterior molecular dynamics sustain that the cofactor induces global re-arrangements of the protein. Finally, massive exploration of substrate diffusion, based on the GPathFinder approach, defines this event as the origin of the enantioselectivity in GSH and RFY. For HFF, fine molecular dockings suggest that it is likely related to local interactions upon diffusion. This work shows how modelling of long-range mutations on the catalytic profiles of metalloenzymes may be unavoidable and software simulating substrate diffusion should be applied.
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Affiliation(s)
| | - Giuseppe Sciortino
- InSiliChem, Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Eric Mates-Torres
- InSiliChem, Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Agustí Lledós
- InSiliChem, Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Jean-Didier Maréchal
- InSiliChem, Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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3
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Bonczidai-Kelemen D, Sciortino G, May NV, Garribba E, Fábián I, Lihi N. Introducing the penicillamine moiety into a metallopeptide mimicking the NiSOD enzyme: electronic and kinetic effects. Inorg Chem Front 2022. [DOI: 10.1039/d1qi01025e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The novel NiSOD related metallopeptide incorporates penicillamine moiety in the active center which alters both the electronic and kinetic features.
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Affiliation(s)
- Dóra Bonczidai-Kelemen
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
| | - Giuseppe Sciortino
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Technology, 43007 Tarragona, Spain
| | - Nóra V. May
- Centre for Structural Science, Research Centre for Natural Sciences, H-1117, Budapest, Hungary
| | - Eugenio Garribba
- Dipartimento di Scienze Mediche, Chirurgiche e Sperimentali, Università di Sassari, I-07100 Sassari, Italy
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032, Debrecen, Hungary
| | - Norbert Lihi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032, Debrecen, Hungary
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4
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Illa O, Ospina J, Sánchez-Aparicio JE, Pulido X, Abengozar MÁ, Gaztelumendi N, Carbajo D, Nogués C, Rivas L, Maréchal JD, Royo M, Ortuño RM. Hybrid Cyclobutane/Proline-Containing Peptidomimetics: The Conformational Constraint Influences Their Cell-Penetration Ability. Int J Mol Sci 2021; 22:ijms22105092. [PMID: 34065025 PMCID: PMC8151717 DOI: 10.3390/ijms22105092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 01/22/2023] Open
Abstract
A new family of hybrid β,γ-peptidomimetics consisting of a repetitive unit formed by a chiral cyclobutane-containing trans-β-amino acid plus a Nα-functionalized trans-γ-amino-l-proline joined in alternation were synthesized and evaluated as cell penetrating peptides (CPP). They lack toxicity on the human tumoral cell line HeLa, with an almost negligible cell uptake. The dodecapeptide showed a substantial microbicidal activity on Leishmania parasites at 50 µM but with a modest intracellular accumulation. Their previously published γ,γ-homologues, with a cyclobutane γ-amino acid, showed a well-defined secondary structure with an average inter-guanidinium distance of 8–10 Å, a higher leishmanicidal activity as well as a significant intracellular accumulation. The presence of a very rigid cyclobutane β-amino acid in the peptide backbone precludes the acquisition of a defined conformation suitable for their cell uptake ability. Our results unveiled the preorganized charge-display as a relevant parameter, additional to the separation among the charged groups as previously described. The data herein reinforce the relevance of these descriptors in the design of CPPs with improved properties.
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Affiliation(s)
- Ona Illa
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
- Correspondence: (O.I.); (M.R.); (R.M.O.)
| | - Jimena Ospina
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
| | - José-Emilio Sánchez-Aparicio
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
| | - Ximena Pulido
- Institut de Recerca Biomèdica, c/Baldiri Reixac 10, 08028 Barcelona, Spain;
- Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), c/ Jordi Girona 18–26, 08034 Barcelona, Spain
- Departamento de Química, Universidad del Tolima, Santa Helena Parte Alta, Ibagué 730006299, Tolima, Colombia
| | - María Ángeles Abengozar
- Centro de Investigaciones Biológicas Margarita Salas, c/ Ramiro de Maeztu 9, CSIC, 28040 Madrid, Spain; (M.Á.A.); (L.R.)
| | - Nerea Gaztelumendi
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.G.); (C.N.)
| | - Daniel Carbajo
- Institut de Química Avançada de Catalunya (IQAC-CSIC), c/ Jordi Girona, 18-26, 08034 Barcelona, Spain;
| | - Carme Nogués
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.G.); (C.N.)
| | - Luis Rivas
- Centro de Investigaciones Biológicas Margarita Salas, c/ Ramiro de Maeztu 9, CSIC, 28040 Madrid, Spain; (M.Á.A.); (L.R.)
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
| | - Miriam Royo
- Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), c/ Jordi Girona 18–26, 08034 Barcelona, Spain
- Institut de Química Avançada de Catalunya (IQAC-CSIC), c/ Jordi Girona, 18-26, 08034 Barcelona, Spain;
- Correspondence: (O.I.); (M.R.); (R.M.O.)
| | - Rosa M. Ortuño
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
- Correspondence: (O.I.); (M.R.); (R.M.O.)
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Sciortino G, Aureliano M, Garribba E. Rationalizing the Decavanadate(V) and Oxidovanadium(IV) Binding to G-Actin and the Competition with Decaniobate(V) and ATP. Inorg Chem 2021; 60:334-344. [PMID: 33253559 PMCID: PMC8016201 DOI: 10.1021/acs.inorgchem.0c02971] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The experimental data collected over the past 15 years on the interaction of decavanadate(V) (V10O286-; V10), a polyoxometalate (POM) with promising anticancer and antibacterial action, with G-actin, were rationalized by using several computational approaches (docking, density functional theory (DFT), and molecular dynamics (MD)). Moreover, a comparison with the isostructural and more stable decaniobate(V) (Nb10O286-; Nb10) was carried out. Four binding sites were identified, named α, β, γ, and δ, the site α being the catalytic nucleotide site located in the cleft of the enzyme at the interface of the subdomains II and IV. It was observed that the site α is preferred by V10, whereas Nb10 is more stable at the site β; this indicates that, differently from other proteins, G-actin could contemporaneously bind the two POMs, whose action would be synergistic. Both decavanadate and decaniobate induce conformational rearrangements in G-actin, larger for V10 than Nb10. Moreover, the binding mode of oxidovanadium(IV) ion, VIVO2+, formed upon the reduction of decavanadate(V) by the -SH groups of accessible cysteine residues, is also found in the catalytic site α with (His161, Asp154) coordination; this adduct overlaps significantly with the region where ATP is bound, accounting for the competition between V10 and its reduction product VIVO2+ with ATP, as previously observed by EPR spectroscopy. Finally, the competition with ATP was rationalized: since decavanadate prefers the nucleotide site α, Ca2+-ATP displaces V10 from this site, while the competition is less important for Nb10 because this POM shows a higher affinity for β than for site α. A relevant consequence of this paper is that other metallodrug-protein systems, in the absence or presence of eventual inhibitors and/or competition with molecules of the organism, could be studied with the same approach, suggesting important elements for an explanation of the biological data and a rational drug design.
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Affiliation(s)
- Giuseppe Sciortino
- Dipartimento
di Chimica e Farmacia, Università
di Sassari, Via Vienna 2, I-07100 Sassari, Italy
- Institute
of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans, 16, 43007 Tarragona, Spain
- (G.S.) Phone +34 977 920229. Email
| | - Manuel Aureliano
- CCMar,
FCT, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 8000-139 Faro, Portugal
- (M.A.) Phone +351 289 800977. Email
| | - Eugenio Garribba
- Dipartimento
di Chimica e Farmacia, Università
di Sassari, Via Vienna 2, I-07100 Sassari, Italy
- (E.G.) Phone +39 079 229487. Email
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6
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Sciortino G, Maréchal JD, Garribba E. Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01507e] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An integrated instrumental/computational approach to characterize metallodrug–protein adducts at the molecular level is reviewed. A series of applications are described, focusing on potential vanadium drugs with a generalization to other metals.
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Affiliation(s)
- Giuseppe Sciortino
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Jean-Didier Maréchal
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia
- Università di Sassari
- 07100 Sassari
- Italy
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7
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Sánchez-Aparicio JE, Tiessler-Sala L, Velasco-Carneros L, Roldán-Martín L, Sciortino G, Maréchal JD. BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization. J Chem Inf Model 2020; 61:311-323. [PMID: 33337144 DOI: 10.1021/acs.jcim.0c00827] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With a large amount of research dedicated to decoding how metallic species bind to proteins, in silico methods are interesting allies for experimental procedures. To date, computational predictors mostly work by identifying the best possible sequence or structural match of the target protein with metal-binding templates. These approaches are fundamentally focused on the first coordination sphere of the metal. Here, we present the BioMetAll predictor that is based on a different postulate: the formation of a potential metal-binding site is related to the geometric organization of the protein backbone. We first report the set of convenient geometric descriptors of the backbone needed for the algorithm and their parameterization from a statistical analysis. Then, the successful benchmark of BioMetAll on a set of more than 90 metal-binding X-ray structures is presented. Because BioMetAll allows structural predictions regardless of the exact geometry of the side chains, it appears extremely valuable for systems whose structures (either experimental or theoretical) are not optimal for metal-binding sites. We report here its application on three different challenging cases: (i) the modulation of metal-binding sites during conformational transition in human serum albumin, (ii) the identification of possible routes of metal migration in hemocyanins, and (iii) the prediction of mutations to generate convenient metal-binding sites for de novo biocatalysts. This study shows that BioMetAll offers a versatile platform for numerous fields of research at the interface between inorganic chemistry and biology and allows to highlight the role of the preorganization of the protein backbone as a marker for metal binding. BioMetAll is an open-source application available at https://github.com/insilichem/biometall.
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Affiliation(s)
- José-Emilio Sánchez-Aparicio
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Laura Tiessler-Sala
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Lorea Velasco-Carneros
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Lorena Roldán-Martín
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Giuseppe Sciortino
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain.,Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
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Fahmy SA, Ponte F, Fawzy IM, Sicilia E, Bakowsky U, Azzazy HMES. Host-Guest Complexation of Oxaliplatin and Para-Sulfonatocalix[n]Arenes for Potential Use in Cancer Therapy. Molecules 2020; 25:E5926. [PMID: 33327642 PMCID: PMC7765097 DOI: 10.3390/molecules25245926] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 01/25/2023] Open
Abstract
P-sulfonatocalix[n]arenes have demonstrated a great potential for encapsulation of therapeutic drugs via host-guest complexation to improve solubility, stability, and bioavailability of encapsulated drugs. In this work, guest-host complexes of a third-generation anticancer drug (oxaliplatin) and p-4-sulfocalix[n]arenes (n = 4 and 6; p-SC4 and p-SC6, respectively) were prepared and investigated, using 1H NMR, UV, Job's plot analysis, and DFT calculations, for use as cancer therapeutics. The peak amplitude of the prepared host-guest complexes was linearly proportional to the concentration of oxaliplatin in the range of 1.0 × 10-5 M-1 to 2.1 × 10-4 M-1. The reaction stoichiometry between either p-SC4 or p-SC6 and oxaliplatin in the formed complexes was 1:1. The stability constants for the complexes were 5.07 × 104 M-1 and 6.3 × 104 M-1. These correspond to complexation free energy of -6.39 and -6.52 kcal/mol for p-SC4 and p-SC6, respectively. Complexation between oxaliplatin and p-SC4 or p-SC6 was found to involve hydrogen bonds. Both complexes exhibited enhanced biological and high cytotoxic activities against HT-29 colorectal cells and MCF-7 breast adenocarcinoma compared to free oxaliplatin, which warrants further investigation for cancer therapy.
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Affiliation(s)
- Sherif Ashraf Fahmy
- Department of Chemistry, School of Sciences & Engineering, The American University in Cairo, AUC Avenue, P.O. Box 74, New Cairo 11835, Egypt;
| | - Fortuna Ponte
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.P.); (E.S.)
| | - Iten M. Fawzy
- Pharmaceutical Chemistry Department, Faculty of Pharmaceutical Sciences and Pharmaceutical Industries, Future University in Egypt, Cairo 12311, Egypt;
| | - Emilia Sicilia
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.P.); (E.S.)
| | - Udo Bakowsky
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, 35037 Marburg, Germany
| | - Hassan Mohamed El-Said Azzazy
- Department of Chemistry, School of Sciences & Engineering, The American University in Cairo, AUC Avenue, P.O. Box 74, New Cairo 11835, Egypt;
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Illa O, Olivares JA, Gaztelumendi N, Martínez-Castro L, Ospina J, Abengozar MÁ, Sciortino G, Maréchal JD, Nogués C, Royo M, Rivas L, Ortuño RM. Chiral Cyclobutane-Containing Cell-Penetrating Peptides as Selective Vectors for Anti- Leishmania Drug Delivery Systems. Int J Mol Sci 2020; 21:E7502. [PMID: 33053805 PMCID: PMC7590151 DOI: 10.3390/ijms21207502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 02/04/2023] Open
Abstract
Two series of new hybrid γ/γ-peptides, γ-CC and γ-CT, formed by (1S,2R)-3-amino-2,2,dimethylcyclobutane-1-carboxylic acid joined in alternation to a Nα-functionalized cis- or trans-γ-amino-l-proline derivative, respectively, have been synthesized and evaluated as cell penetrating peptides (CPP) and as selective vectors for anti-Leishmania drug delivery systems (DDS). They lacked cytotoxicity on the tumoral human cell line HeLa with a moderate cell-uptake on these cells. In contrast, both γ-CC and γ-CT tetradecamers were microbicidal on the protozoan parasite Leishmania beyond 25 μM, with significant intracellular accumulation. They were conjugated to fluorescent doxorubicin (Dox) as a standard drug showing toxicity beyond 1 μM, while free Dox was not toxic. Intracellular accumulation was 2.5 higher than with Dox-TAT conjugate (TAT = transactivator of transcription, taken as a standard CPP). The conformational structure of the conjugates was approached both by circular dichroism spectroscopy and molecular dynamics simulations. Altogether, computational calculations predict that the drug-γ-peptide conjugates adopt conformations that bury the Dox moiety into a cavity of the folded peptide, while the positively charged guanidinium groups face the solvent. The favorable charge/hydrophobicity balance in these CPP improves the solubility of Dox in aqueous media, as well as translocation across cell membranes, making them promising candidates for DDS.
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Affiliation(s)
- Ona Illa
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.I.); (J.-A.O.); (L.M.-C.); (J.O.); (G.S.); (J.-D.M.)
| | - José-Antonio Olivares
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.I.); (J.-A.O.); (L.M.-C.); (J.O.); (G.S.); (J.-D.M.)
| | - Nerea Gaztelumendi
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain;
| | - Laura Martínez-Castro
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.I.); (J.-A.O.); (L.M.-C.); (J.O.); (G.S.); (J.-D.M.)
| | - Jimena Ospina
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.I.); (J.-A.O.); (L.M.-C.); (J.O.); (G.S.); (J.-D.M.)
| | - María-Ángeles Abengozar
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, c/Ramiro de Maeztu, 9, 28040 Madrid, Spain;
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.I.); (J.-A.O.); (L.M.-C.); (J.O.); (G.S.); (J.-D.M.)
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.I.); (J.-A.O.); (L.M.-C.); (J.O.); (G.S.); (J.-D.M.)
| | - Carme Nogués
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain;
| | - Míriam Royo
- Institut de Química Avançada de Catalunya (IQAC-CSIC), c/Jordi Girona, 18–26, 08034 Barcelona, Spain;
- Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), c/Jordi Girona, 18–26, 08034 Barcelona, Spain
| | - Luis Rivas
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, c/Ramiro de Maeztu, 9, 28040 Madrid, Spain;
| | - Rosa M. Ortuño
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.I.); (J.-A.O.); (L.M.-C.); (J.O.); (G.S.); (J.-D.M.)
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10
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Janoš P, Spinello A, Magistrato A. All-atom simulations to studying metallodrugs/target interactions. Curr Opin Chem Biol 2020; 61:1-8. [PMID: 32781390 DOI: 10.1016/j.cbpa.2020.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/03/2020] [Accepted: 07/12/2020] [Indexed: 12/16/2022]
Abstract
Metallodrugs are extensively used to treat and diagnose distinct disease types. The unique physical-chemical properties of metal ions offer tantalizing opportunities to tailor effective scaffolds for selectively targeting specific biomolecules. Modern experimental techniques have collected a large body of structural data concerning the interactions of metallodrugs with their biomolecular targets, although being unable to exhaustively assess the molecular basis of their mechanism of action. In this scenario, the complementary use of accurate computational methods allows uncovering the minutiae of metallodrugs/targets interactions and their underlying mechanism of action at an atomic-level of detail. This knowledge is increasingly perceived as an invaluable requirement to rationally devise novel and selective metallodrugs. Building on literature studies, selected largely from the last 2 years, this compendium encompasses a cross-section of the current role, advances, and challenges met by computer simulations to decipher the mechanistic intricacies of prototypical metallodrugs.
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Affiliation(s)
- Pavel Janoš
- CNR-IOM c/o SISSA, Via Bonomea 265, 34136, Trieste, Italy
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