Vibrational analysis of amino acids and short peptides in hydrated media. 3. Successive KL repeats induce highly stable beta-strands capable of forming non-H-bonded aggregates

Circular dichroism (CD) and Raman scattering were applied to the aqueous solution of minimalist LK peptides constructed with successive KL repeats leading to the following generic primary sequence: (KL)nK. Three peptides of this family, a 3-mer (n=1), a 9-mer (n=4), and a 15-mer (n=7), are analyzed in this report. Raman spectra of the 3-mer (KLK, a random chain) and its labile-hydrogen deuterated species yield a set of interesting information for analyzing longer peptides of this series. Although the CD spectrum of the 9-mer (KLKLKLKLK) reveals a signal traditionally assigned to a random structure, the corresponding Raman spectrum allows finding a mixture of conformations in solution, adopting predominantly beta-type structures. This fact proves the utility of Raman spectroscopy to eliminate eventual ambiguity concerning conformational assignments in peptides based only on the use of CD technique. Finally, the 15-mer (KLKLKLKLKLKLKLK) gives rise to CD and Raman spectra clearly assignable to a beta-type structure. On the basis of all the observed results on the 15-mer, we can confirm that this peptide may exist as isolated beta-strands at low concentration (sub-micromolar), flat-oriented at the air/water interface, whereas at high concentrations (millimolar), non-H-bonded immersible aggregates might be formed. A hypothetical model for these beta-strand aggregates could be proposed as stabilized by an interior hydrophobic core and a hydrophilic external face, formed by leucine and lysine side chains, respectively.     

Effect of permodified β‐cyclodextrin on the photophysical properties of poly[2,7‐(9,9‐dioctylfluorene)‐alt‐(5,5′‐bithiophene)] main chain polyrotaxanes

The photophysical properties of two polyrotaxanes ( PFBTh?PSβCD and PFBTh?PMeβCD ) composed of fluorene and bithiophene encapsulated into permodified β‐cyclodextrin cavities have been investigated and compared with those of the reference PFBTh . Rotaxane formation results in improvements of the thermal stability, solubility in common organic solvents, as well as better film forming ability combined with a high transparency. As expected PFBTh and its encapsulated forms absorb at wavelengths beyond 510 nm, and time‐resolved photoluminescence (PL) in solution shows a well‐define vibronic structures with a predominance of the 0‐0 transitions and an energy difference of 0.16 eV. The fluorescence lifetimes follow a monoexponential decay with a value τ = 630 ± 30 ps. Atomic force microscopy, AFM, indicated a tendency of polyrotaxanes to organize into fibers. The advancing contact angles indicated higher surface hydrophobicity and lower surface free‐energy values for polyrotaxanes compared with their unthreaded analogues. The device based on PFBTh?PSβCD: PCBM in a 1/1 w/w ratio under simulated AM 1.5G illumination at 100 mW cm^?2 exhibited improved photovoltaic parameters of cells, resulted in high V_oc (0.68 V), J_sc (1.65 mA cm^?2), FF (31.6%), and PCE (0.35) values, compared with PFBTh or PFBTh?PMeβCD , respectively. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 460–471     

Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins

In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple‐scattering EXAFS analysis performed within the rigid‐body refinement scheme, non‐muffin‐tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye–Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K‐edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.     

Evaluation of methoxy polyethylene glycol‐polylactide diblock copolymers as additive in hypromellose film coating

This paper deals with a new application of diblock methoxy polyethylene glycol‐polylactide block copolymers, a class of synthetic biomaterials largely studied in the pharmaceutical and biomedical fields owing to their favorable properties such as biocompatibility, biodegradability, low immunogenicity, and good mechanical properties. In this work, these materials were evaluated as additives for gastro‐soluble pharmaceutical coating aimed to reduce film stiffness and water permeability. Two copolymers with different polylactide chain lengths were synthesized and characterized in term of molecular weight and solid‐state properties. A series of free films with different hypromellose/copolymers ratio were prepared and characterized in terms of appearance, components miscibility, plasticity, and water vapor permeability. The obtained results demonstrate that copolymers effectively influence hypromellose film properties according to their concentration and molecular weight. Specifically, the addition of the copolymer with a molecular weight of 6.5 kDa in a ratio hypromellose:polymer 5:1, allowed to obtain films with good appearance, improved plasticization, and water permeability properties. For higher molecular weight, copolymer or different ratios was not possible to observe the improvement of all the properties at the same time. The results also make possible to define the critical features to improve in order to use block copolymers as additive in hypromellose film coating. The availability of new water‐soluble additives able to work as plasticizer and moisture sealer in polymeric films represents an important progress not only in the field of pharmaceutical coating but also in that of food coatings, as for example in the formulation of edible films. Copyright © 2013 John Wiley & Sons, Ltd.     

Cycloolefin Copolymers by Early and Late Transition Metal Catalysts

The complex [Pd(κ²‐P,O‐{2‐(2‐MeOC₆H₄)₂P}C₆H₄SO₃)Me(dmso)] ( 1 ) is investigated for the copolymerization of (E) with norbornene (N) and functionalized N derivatives affording P(E‐co‐N) in excellent yields. Copolymer molar masses are higher than those of PE and increase with N concentration. In addition, the complex [Ti(κ²‐N,O‐{2,6‐F₂C₆H₃N = C(Me)C(H) = C(CF₃)O})₂Cl₂] ( 2 ) is evaluated as catalyst for living E‐co‐N copolymerization upon activation with dried methylaluminoxane between 25 and 90 °C. Copolymerization at different [N]/[E] feed ratios affords stereoirregular alternating high molar mass P(E‐co‐N) with narrow molar mass distribution. P(E‐co‐N) living copolymerization is demonstrated by kinetics at 50 °C. Block copolymers are synthesized and fully characterized.

     

Mechanistic Aspects of Gas‐Phase Hydrogen‐Atom Transfer from Methane to [CO].+ and [SiO].+: Why Do They Differ?

The reactivity of the two diatomic congeneric systems [CO]^.+ and [SiO]^.+ towards methane has been investigated by means of mass spectrometry and quantum‐chemical calculations. While [CO]^.+ gives rise to three different reaction channels, [SiO]^.+ reacts only by hydrogen‐atom transfer (HAT) from methane under thermal conditions. A theoretical analysis of the respective HAT processes reveals two distinctly different mechanistic pathways for [CO]^.+ and [SiO]^.+, and a comparison to the higher metal oxides of Group 14 emphasizes the particular role of carbon as a second‐row p element.     

Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease

The 3CL-Protease appears to be a very promising medicinal target to develop anti-SARS-CoV-2 agents. The availability of resolved structures allows structure-based computational approaches to be carried out even though the lack of known inhibitors prevents a proper validation of the performed simulations. The innovative idea of the study is to exploit known inhibitors of SARS-CoV 3CL-Pro as a training set to perform and validate multiple virtual screening campaigns. Docking simulations using four different programs (Fred, Glide, LiGen, and PLANTS) were performed investigating the role of both multiple binding modes (by binding space) and multiple isomers/states (by developing the corresponding isomeric space). The computed docking scores were used to develop consensus models, which allow an in-depth comparison of the resulting performances. On average, the reached performances revealed the different sensitivity to isomeric differences and multiple binding modes between the four docking engines. In detail, Glide and LiGen are the tools that best benefit from isomeric and binding space, respectively, while Fred is the most insensitive program. The obtained results emphasize the fruitful role of combining various docking tools to optimize the predictive performances. Taken together, the performed simulations allowed the rational development of highly performing virtual screening workflows, which could be further optimized by considering different 3CL-Pro structures and, more importantly, by including true SARS-CoV-2 3CL-Pro inhibitors (as learning set) when available.