Gema Ballano

An electroactive and biologically responsive hybrid conjugate based on chemical similarity

Synthetic amino acids have become very important tools for the design of new materials. In this work, an electroactive polymer–amino acid hybrid material has been synthesized by conjugating poly(3,4-ethylenedioxythiophene) (PEDOT), a well known conducting polymer, with a synthetic amino acid bearing 3,4-ethylenedioxythiophene, which has been explicitly designed and prepared for such a purpose. Nanometric films have been electrochemically generated using a two-step procedure to evaluate the properties and potential applications of the resulting hybrid material. The successful incorporation of the amino acid as end-capping of the PEDOT chains has been proved by FTIR, energy dispersive X-ray and X-ray photoelectron spectroscopies. The fabrication of the hybrid material using an engineered tissue has allowed us to preserve not only morphological and structural characteristics of the conducting polymer but also, and most importantly, to preserve the electrical conductivity, electroactivity, electrochemical stability and specific capacitance. Finally, the behavior of the hybrid material as a cellular matrix has been compared with that of PEDOT using cellular adhesion and proliferation assays. Results obtained in this work represent the success of a new strategy for the preparation of peptide-conducting polymer hybrid materials, which is currently being improved upon by transforming the 3,4-ethylenedioxythiophene-containing amino acid into a cell adhesive peptide.

Self‐Assembly of Tetraphenylalanine Peptides

Three different tetraphenylalanine (FFFF) based peptides that differ at the N- and C-termini have been synthesized by using standard procedures to study their ability to form different nanoassemblies under a variety of conditions. The FFFF peptide assembles into nanotubes that show more structural imperfections at the surface than those formed by the diphenylalanine (FF) peptide under the same conditions. Periodic DFT calculations (M06L functional) were used to propose a model that consists of three FFFF molecules defining a ring through head-to-tail NH3(+)⋅⋅⋅(-)OOC interactions, which in turn stack to produce deformed channels with internal diameters between 12 and 16 Å. Depending on the experimental conditions used for the peptide incubation, N-fluorenylmethoxycarbonyl (Fmoc) protected FFFF self-assembles into a variety of polymorphs: ultra-thin nanoplates, fibrils, and star-like submicrometric aggregates. DFT calculations indicate that Fmoc-FFFF prefers a parallel rather than an antiparallel β-sheet assembly. Finally, coexisting multiple assemblies (up to three) were observed for Fmoc-FFFF-OBzl (OBzl = benzyl ester), which incorporates aromatic protecting groups at the two peptide terminals. This unusual and noticeable feature is attributed to the fact that the assemblies obtained by combining the Fmoc and OBzl groups contained in the peptide are isoenergetic.

Structural Analysis of a β-Helical Protein Motif Stabilized by Targeted Replacements with Conformationally Constrained Amino Acids

Here we study conformational stabilization induced in a beta-helical nanostructure by position-specific mutations. The nanostructure is constructed through the self-assembly of the beta-helical building block excised from E. coli galactoside acetyltransferase (PDB code 1krr , chain A; residues 131-165). The mutations involve substitutions by cyclic, conformationally constrained amino acids. Specifically, a complete structural analysis of the Pro-Xaa-Val sequence [with Xaa being Gly, Ac 3c (1-aminocyclopropane-1-carboxylic acid) and Ac 5c (1-aminocyclopentane-1-carboxylic acid)], corresponding to the 148-150 loop region in the wild-type (Gly) and mutated (Ac 3c and Ac 5c) 1krr , has been performed using Molecular Dynamics simulations and X-ray crystallography. Simulations have been performed for the wild-type and mutants of three different systems, namely the building block, the nanoconstruct and the isolated Pro-Xaa-Val tripeptide. Furthermore, the crystalline structures of five peptides of Pro-Xaa-Val or Xaa-Val sequences have been solved by X-ray diffraction analysis and compared with theoretical predictions. Both the theoretical and crystallographic studies indicate that the Pro-Ac n c-Val sequences exhibit a high propensity to adopt turn-like conformations, and this propensity is little affected by the chemical environment. Overall, the results indicate that replacement of Gly149 by Ac 3c or Ac 5c significantly reduce the conformational flexibility of the target site enhancing the structural specificity of the building block and the nanoconstruct derived from the 1krr beta-helical motif.

Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing

We present a chemical strategy to engineer analogs of the tumor-homing peptide CREKA (Cys-Arg-Glu-Lys-Ala), which binds to fibrin and fibrin-associated clotted plasma proteins in tumor vessels (Simberg et al. in Proc Natl Acad Sci USA 104:932–936, 2007) with improved ability to inhibit tumor growth. Computer modeling using a combination of simulated annealing and molecular dynamics were carried out to design targeted replacements aimed at enhancing the stability of the bioactive conformation of CREKA. Because this conformation presents a pocket-like shape with the charged groups of Arg, Glu and Lys pointing outward, non-proteinogenic amino acids α-methyl and N-methyl derivatives of Arg, Glu and Lys were selected, rationally designed and incorporated into CREKA analogs. The stabilization of the bioactive conformation predicted by the modeling for the different CREKA analogs matched the tumor fluorescence results, with tumor accumulation increasing with stabilization. Here we report the modeling, synthetic procedures, and new biological assays used to test the efficacy and utility of the analogs. Combined, our results show how studies based on multi-disciplinary collaboration can converge and lead to useful biomedical advances.

Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale

Departament d’Enginyeria Qui´mica, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Polite`cnica deCatalunya, Diagonal 647, Barcelona E-08028, Spain, Departamento de Qui´mica Orga´nica, Instituto de Cienciade Materiales de Arago´n, Universidad de Zaragoza - CSIC, 50009 Zaragoza, Spain, Departament de Qui´mica,Escola Polite`cnica Superior Universitat de Lleida, c/Jaume II No 69, Lleida E-25001, Spain, Department ofComputer Science, Rice University, Houston, Texas 77005, Departament d’Enginyeria Qui´mica, Facultat deQui´mica, Universitat de Barcelona, Marti´ Franque`s 1, Barcelona E-08028, Spain, Basic Research Program,SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, Maryland 21702,Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel, andCenter for Research in Nano-Engineering, Universitat Polite`cnica de Catalunya, Campus Sud, Edifici C’,C/Pasqual i Vila s/n, Barcelona E-08028, SpainReceived April 29, 20091. INTRODUCTIONOne of the major challenges that modern chemistry facesin the nanotechnological era is how to materialize ideasconceived in organic and inorganic chemistry laboratoriesto obtain

Design of hybrid conjugates based on chemical similarity

Conducting polymer–amino acid hybrid materials have been prepared by conjugating poly(3,4-ethylenedioxythiophene) (PEDOT) and an amino acid bearing a 3,4-ethylenedioxythiophene (EDOT) ring as a side group. Two amino acids have been designed, synthesized and characterized. These compounds differ in the presence or not of a methylene group between the EDOT ring and the backbone (i.e.I and II, respectively). The electrochemical properties of PEDOT and their conjugates with I and II (PEDOT-I and PEDOT-II) have been determined using cyclic voltammetry and electrochemical impedance spectroscopy, and subsequently compared. Incorporation of end capping amino acids has been found to increase the hydrophilicity of PEDOT surface, which is consistent with the better behaviour of the conjugates as the cellular matrix. The electronic properties of both the amino acids and the conjugates have been investigated by UV-vis spectroscopy. Results indicate that elimination of the methylene group of I provokes a reduction of 0.13 eV in the π–π* lowest transition energy (Eg) of the conjugate. This decrease is explained by the larger structural flexibility due to the methylene group in I. Calculations of the electronic properties of the two hybrids at the molecular level using quantum mechanical methods suggest that the end capping amino acids essentially affect the electronic intermolecular effects.

Structure of N,N′-bis(amino acids) in the solid state and in solution. A 13C and 15N CPMAS NMR study

Three bis(amino acids) linked by the amino groups have been prepared and structurally characterized. We have named them Gly-Gly, Ala-Ala and Gly-Ala (or Ala-Gly). These compounds have been characterized by NMR both in solution and in the solid state. They exist as zwitterions with the ammonium group proximal to the carboxylate anion. In the case of Gly-Ala, a dynamic situation is observed by CPMAS NMR ((13)C and (15)N) corresponding to a double proton migration between two proximal tautomers.

Effect of solvent choice on the self-assembly properties of a diphenylalanine amphiphile stabilized by an ion pair

A diphenylalanine (FF) amphiphile blocked at the C terminus with a benzyl ester (OBzl) and stabilized at the N terminus with a trifluoroacetate (TFA) anion was synthetized and characterized. Aggregation of peptide molecules was studied by considering a peptide solution in an organic solvent and adding pure water, a KCl solution, or another organic solvent as co-solvent. The choice of the organic solvent and co-solvent and the solvent/co-solvent ratio allowed the mixture to be tuned by modulating the polarity, the ionic strength, and the peptide concentration. Differences in the properties of the media used to dissolve the peptides resulted in the formation of different self-assembled microstructures (e.g. fibers, branched-like structures, plates, and spherulites). Furthermore, crystals of TFA⋅FF-OBzl were obtained from the aqueous peptide solutions for X-ray diffraction analysis. The results revealed a hydrophilic core constituted by carboxylate (from TFA), ester, and amide groups, and the core was found to be surrounded by a hydrophobic crown with ten aromatic rings. This segregated organization explains the assemblies observed in the different solvent mixtures as a function of the environmental polarity, ionic strength, and peptide concentration.

Electro‐biocompatibility of conjugates designed by chemical similarity

The roughness and thickness of films formed by hybrid conjugates prepared by coupling poly(3,4‐ethylenedioxythiophene) and synthetic amino acids bearing a 3,4‐ethylenedioxythiophene group in the side chain have been significantly increased using a new synthetic approach. This procedure also provoked a more effective incorporation of the amino acid at the end of the polymer chains, as has been reflected by the electronic and electrochemical properties. Although the surface polarity of all these materials is similar to that of formamide, the hydrophilicity of the conjugates is higher than that of the conducting polymer. The surface energy of all the investigated systems is dominated by the dispersive component, even though the role played by the polar contribution is more important for the conjugates than for the conducting polymer. On the other hand, all the prepared materials behave as bioactive matrices. The electrochemical response of the conjugates coated with cells reflects the electro‐compatibility of these two‐component substrates. Thus, the ability to exchange charge reversibly of all conjugates increases considerably when they are coated with cellular monolayers, which has attributed to favorable interactions at the interface formed by the conjugate surface and the cellular monolayer. Copyright