In Silico Identification of Tripeptides as Lead Compounds for the Design of KOR Ligands

The kappa opioid receptor (KOR) represents an attractive target for the development of drugs as potential antidepressants, anxiolytics and analgesics. A robust computational approach may guarantee a reduction in costs in the initial stages of drug discovery, novelty and accurate results. In this work, a virtual screening workflow of a library consisting of ~6 million molecules was set up, with the aim to find potential lead compounds that could manifest activity on the KOR. This in silico study provides a significant contribution in the identification of compounds capable of interacting with a specific molecular target. The main computational techniques adopted in this experimental work include: (i) virtual screening; (ii) drug design and leads optimization; (iii) molecular dynamics. The best hits are tripeptides prepared via solution phase peptide synthesis. These were tested in vivo, revealing a good antinociceptive effect after subcutaneous administration. However, further work is due to delineate their full pharmacological profile, in order to verify the features predicted by the in silico outcomes.     

Ytterbium triflate catalysed Meerwein-Ponndorf-Verley (MPV) reduction

Ytterbium triflate was shown to be effective in promoting the reduction of substituted aromatic and aliphatic aldehydes and ketones using isopropanol as the solvent and the reducing agent. The whole process furnished the desired adducts in 22-98% yield.     

Rheoreversible polymeric organogels: the art of science for art conservation

A new category of gels where gelification and breaking of the gels are chemically induced is presented. In particular, the latent gellant polyallylamine produced stable gels with some organic solvents after reaction with CO2 at room temperature, giving the gellant polyallylammonium carbamate. The rheological behavior switches from solution-type to gel-type. After weak acid-catalyzed displacement of CO2, the gel character disappears in a few seconds, making these polymeric organogels rheoreversible by a simple chemical action. This "intelligent" chemical switch between solution-type and gel-type rheological behavior has been exploited to clean pictorial surfaces in art conservation. In fact, during the cleaning procedure, there is a need for the gel supporting the cleaning solvent to have a very high viscosity. After cleaning has been successful, there is a strong necessity to reduce the viscosity, to better eliminate traces of the gellant that must be completely removed from the work of art. In the present study, we show that the art of science, in the sense of designing new physicochemical systems exploiting the "science palette", can lead to an improvement in the techniques used to protect and conserve the results of the "artists' palette".     

Decoding two-dimensional polyacrylamide gel electrophoresis complex maps by autocovariance function: a simplified approach useful for proteomics

This paper describes a mathematical approach applied for decoding the complex signal of two-dimensional polyacrylamide gel electrophoresis maps of protein mixtures. The method is helpful in extracting analytical information since separation of all the proteins present in the sample is still far from being achieved and co-migrating proteins are generally present in the same spot. The simplified method described is based on the study of the 2-D autocovariance function (2D-ACVF) computed on an experimental digitized map. The first part of the 2D-ACVF allows for the estimation of the number of proteins present in the sample (2D-ACVF computed at the origin) and of the separation performance (mean spot size). Moreover, the 2D-ACVF plot is a powerful tool in identifying order in the spot position, and singling it out from the complex separation pattern. This method was validated on synthetic maps obtained by computer simulation to describe 2-D PAGE real maps and reference maps retrieved from the SWISS-2DPAGE database. The results obtained are discussed by focusing on specific information relevant in proteomics: sample complexity, separation performance, and identification of spot trains related to post-translational modifications.     

Symmetric Hubbard systems with superconducting magnetic response

In purely repulsive, C _4v -symmetric Hubbard clusters a correlation effect produces an effective two-body attraction and pairing; the key ingredient is the availability of W=0 pairs, that is, two-body solutions of appropriate symmetry. We study the tunneling of bound pairs in rings of 5-site units connected by weak intercell links; each unit has the topology of a CuO₄ cluster and a repulsive interaction is included on every site. Further, we test the superconducting nature of the response of this model to a threading magnetic field. We present a detailed numerical study of the two-unit ring filled with 6 particles and the three-unit ring with 8 particles; in both cases a lower filling yields normal behavior. In previous studies on 1d Hubbard chains, level crossings were reported (half-integer or fractional Aharonov-Bohm effect) which however cannot be due to superconducting pairs. In contrast, the nontrivial basis of clusters carrying W=0 pairs leads to genuine Superconducting Flux Quantization (SFQ). The data are understood in terms of a cell-perturbation theory scheme which is very accurate for weak links. This low-energy approach leads to an effective hard core boson Hamiltonian which naturally describes itinerant pairs and SFQ in mesoscopic rings. For the numerical calculations, we take advantage of a recently proposed exact diagonalization technique which can be generally applied to many-fermion problems and drastically reduces the size of the matrices to be handled.Received: 14 July 2003, Published online: 9 September 2003PACS: 71.27.+a Strongly correlated electron systems; heavy fermions - 74.20.Mn Nonconventional mechanisms - 73.22.-f Electronic structure of nanoscale materials: clusters, nanoparticles, nanotubes, and nanocrystals     

Pairing mechanism in the doped Hubbard antiferromagnet: the 4×4 model as a test case

We introduce a local formalism, in terms of eigenstates of number operators, having well defined point symmetry, to solve the Hubbard model at weak coupling on a N × N square lattice (for even N). The key concept is that of W = 0 states, that are the many-body eigenstates of the kinetic energy with vanishing Hubbard repulsion. At half filling, the wave function demonstrates an antiferromagnetic order, a lattice step translation being equivalent to a spin flip. Further, we state a general theorem which allows to find all the W = 0 pairs (two-body W = 0 singlet states). We show that, in special cases, this assigns the ground state symmetries at least in the weak coupling regime. The N = 4 case is discussed in detail. To study the doped half filled system, we enhance the group theory analysis of the 4×4 Hubbard model introducing an Optimal Group which explains all the degeneracies in the one-body and many-body spectra. We use the Optimal Group to predict the possible ground state symmetries of the 4×4 doped antiferromagnet by means of our general theorem and the results are in agreement with exact diagonalization data. Then we create W = 0 electron pairs over the antiferromagnetic state. We show analitycally that the effective interaction between the electrons of the pairs is attractive and forms bound states. Computing the corresponding binding energy we are able to definitely predict the exact ground state symmetry. Received 24 October 2000     

Preparation of Constrained Unnatural Aromatic Amino Acids via Unsaturated Diketopiperazine Intermediate

Unnatural aromatic amino acids are useful tools in drug discovery, since their insertion in bioactive peptide sequences can change the side chains spatial orientation, the backbone conformation and above all, their bioactivity. In this communication, we propose a straightforward method to synthesize 2′,6′‐dimethyl‐tyrosine and 2′,6′‐dimehylphenyl‐alanine derivatives as handling building blocks for peptide synthesis via unsaturated diketopiperazine (DKP) intermediate.     

Self‐assembling amphiphilic block copolymer from renewable δ‐decalactone and δ‐dodecalactone

Aliphatic polyesters have many applications in the biomedical field due to their properties and facile degradation. They are commonly synthesized via ring opening polymerization (ROP) with metal‐based catalysts, but as high temperatures are needed and the products contain metal, organocatalysts are now widely adopted to polymerize them at room temperature while also ensuring short reaction times. Here, 1,7,7‐triazabicyclo[4.4.0]‐dec‐5‐ene is used to polymerize less reactive but renewably‐derived lactones, namely δ‐decalactone and δ‐dodecalactone. These monomers were chosen in the attempt of creating renewable and highly lipophilic materials for drug delivery applications as alternatives to the more traditional, but non‐renewable δ‐valerolactone and ?‐caprolactone. A combination of ROP and living radical polymerization Reversible Addition‐Fragmentation Chain Transfer is proposed here to synthesize grafted block copolymers. They are able to self‐assemble in water, forming micelles where the lipophilic polyester core is able to entrap a lipophilic drug, thus making the system a good candidate for drug delivery. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55 , 3788–3797     

Nonadiabatic Van der Pol oscillations in molecular transport

The force exerted by the electrons on the nuclei of a current-carrying molecular junction can be manipulated to engineer nanoscale mechanical systems. In the adiabatic regime a peculiarity of these forces is negative friction, responsible for Van der Pol oscillations of the nuclear coordinates. In this work we study the robustness of the Van der Pol oscillations against high-frequency sources. For this purpose we go beyond the adiabatic approximation and perform full Ehrenfest dynamics simulations. The numerical scheme implements a mixed quantum-classical algorithm for open systems and is capable to deal with arbitrary time-dependent driving fields. We find that the Van der Pol oscillations are extremely stable. The nonadiabatic electron dynamics distorts the trajectory in the momentum-coordinate phase space but preserves the limit cycles in an average sense. We further show that high-frequency fields change both the oscillation amplitudes and the average nuclear positions. By switching the fields off at different times one obtains cycles of different amplitudes which attain the limit cycle only after considerably long times.     

Towards a description of the Kondo effect using time-dependent density-functional theory

We demonstrate that the zero-temperature conductance of the Anderson model can be calculated within the Landauer formalism combined with static density-functional theory. The proposed approximate functional is based on finite-temperature density-functional theory and yields the exact Kohn-Sham potential at the particle-hole symmetric point. Furthermore, in the limit of zero temperature it correctly exhibits a derivative discontinuity which is shown to be essential to reproduce the conductance plateau. On the other hand, at the Kondo temperature the exact Kohn-Sham conductance overestimates the real one by an order of magnitude. To understand the failure of density-functional theory, we resort to its time-dependent version and conclude that the suppression of the Kondo resonance must be attributed to dynamical exchange-correlation corrections.