Step-by-step design of proteins for small molecule interaction: A review on recent milestones.

Protein design is the field of synthetic biology that aims at developing de novo custom-made proteins and peptides for specific applications. Despite exploring an ambitious goal, recent computational advances in both hardware and software technologies have paved the way to high-throughput screening and detailed design of novel folds and improved functionalities. Modern advances in the field of protein design for small molecule targeting are described in this review, organized in a step-by-step fashion: from the conception of a new or upgraded active binding site, to scaffold design, sequence optimization, and experimental expression of the custom protein. In each step, contemporary examples are described, and state-of-the-art software is briefly explored.

Production of highly efficient activated carbons from industrial wastes for the removal of pharmaceuticals from water-A full factorial design.

The wide occurrence of pharmaceuticals in aquatic environments urges the development of cost-effective solutions for their removal from water. In a circular economy context, primary paper mill sludge (PS) was used to produce activated carbon (AC) aiming the adsorptive removal of these contaminants. The use of low-cost precursors for the preparation of ACs capable of competing with commercial ACs continues to be a challenge. A full factorial design of four factors (pyrolysis temperature, residence time, precursor/activating agent ratio, and type of activating agent) at two levels was applied to the production of AC using PS as precursor. The responses analysed were the yield of production, percentage of adsorption for three pharmaceuticals (sulfamethoxazole, carbamazepine, and paroxetine), specific surface area (SBET), and total organic carbon (TOC). Statistical analysis was performed to evaluate influencing factors in the responses and to determine the most favourable production conditions. Four ACs presented very good responses, namely on the adsorption of the pharmaceuticals under study (average adsorption percentage around 78%, which is above that of commercial AC), and SBET between 1389 and 1627 m2 g-1. A desirability analysis pointed out 800 °C for 60 min and a precursor/KOH ratio of 1:1 (w/w) as the optimal production conditions.

Paper pulp-based adsorbents for the removal of pharmaceuticals from wastewater: A novel approach towards diversification.

In this work, two pulps, bleached (BP) and raw pulp (RP), derived from the paper production process, were used as precursors of non-activated and activated carbons (ACs). In the case of non-ACs, the production involved either pyrolysis or pyrolysis followed by acid washing. For ACs production, the pulps were impregnated with K2CO3 or H3PO4, and then pyrolysed and acid washed. After production, the materials were physically and chemically characterized. Then, batch adsorption tests on the removal of two pharmaceuticals (the anti-epileptic carbamazepine (CBZ) and the antibiotic sulfamethoxazole (SMX)) from ultra-pure water and from Waste Water Treatment Plant (WWTP) effluents were performed. In ultra-pure water, non-ACs were not able to adsorb CBZ or SMX while ACs showed good adsorption capacities. In WWTP effluents, although ACs satisfactorily adsorbed CBZ and SMX, they showed lower adsorption capacities for the latter. Tests with WWTP effluents revealed that the best adsorption capacities were achieved by carbons produced from BP and activated with H3PO4: 92±19mgg-1 for CBZ and 13.0±0.6mgg-1 for SMX. These results indicate the potential of paper pulps as precursors for ACs that can be applied in wastewater treatment.

Cholinium-based Good's buffers ionic liquids as remarkable stabilizers and recyclable preservation media for recombinant small RNAs.

RNA is a biopolymer of high relevance in the biopharmaceuticals field and in fundamental and applied research; however, the preservation of the RNA stability is still a remarkable challenge. Herein, we demonstrate the enhanced potential of aqueous solutions of self-buffering cholinium-based Good's buffers ionic liquids (GB-ILs), at 20 and 50 % (w/w), as alternative preservation media of recombinant small RNAs. The thermal stability of RNA is highly enhanced by GB-ILs, with an increase of 14 °C in the biopolymer melting temperature - the highest increase observed up to date with ILs. Most GB-ILs investigated improve the stability of RNA at least up to 30-days, both at 25 °C and at 4 °C, without requiring the typical samples freezing. Molecular dynamics simulations were applied to better understand the molecular-level mechanisms responsible for the observed RNA improved stability. The number of IL cations surrounding the RNA chain is similar, yet with differences found for the IL anions, which are responsible for the overall charge of the biopolymer first solvation sphere. No cytotoxicity of the studied solutions containing RNA and ILs at 20 % (w/w) was observed onto two distinct human cell lines, reinforcing their potential to act as preservation media when foreseeing biopharmaceutical applications. Finally, RNA was successfully recovered from the ILs aqueous solutions, without changes in its structural integrity, and the ILs successfully recycled and reused.

Recent Advances on Mass Spectrometry Analysis of Nitrated Phospholipids.

In recent years, there has been an increasing interest in nitro fatty acids (NO2-FA) as signaling molecules formed under nitroxidative stress. NO2-FA were detected in vivo in a free form, although it is assumed that they may also be esterified to phospholipids (PL). Nevertheless, insufficient discussion about the nature, origin, or role of nitro phospholipids (NO2-PL) was reported up to now. The aim of this study was to develop a mass spectrometry (MS) based approach which allows identifying nitroalkenes derivatives of three major PL classes found in living systems: phosphatidylcholines (PCs), phosphatidylethanolamine (PEs), and phosphatidylserines (PSs). NO2-PLs were generated by NO2BF4 in hydrophobic environment, mimicking biological systems. The NO2-PLs were then detected by electrospray ionization (ESI-MS) and ESI-MS coupled to hydrophilic interaction liquid chromatography (HILIC). Identified NO2-PLs were further analyzed by tandem MS in positive (as [M + H](+) ions for all PL classes) and negative-ion mode (as [M - H](-) ions for PEs and PSs and [M + OAc](-) ions for PCs). Typical MS/MS fragmentation pattern of all NO2-PL included a neutral loss of HNO2, product ions arising from the combined loss of polar headgroup and HNO2, [NO2-FA + H](+) and [NO2-FA - H](-) product ions, and cleavages on the fatty acid backbone near the nitro group, allowing its localization within the FA akyl chain. Developed MS method was used to identify NO2-PL in cardiac mitochondria from a well-characterized animal model of type 1 diabetes mellitus. We identified nine NO2-PCs and one NO2-PE species. The physiological relevance of these findings is still unknown.

An unusual highly emissive water-soluble iridium lissamine-alanine complex and its use in a molecular logic gate.

The interaction of iridium(iii) with a new lissamine rhodamine B sulfonyl derivative, bearing alanine as a building block, (1) with an orange emission in water results in a green highly emissive Ir@1 complex at room temperature. The new Ir@1 complex can sense the toxic Hg(2+) metal ion and cysteine. Based on such properties, a new sophisticated molecular logic gate with three inputs was designed.

Diazole-based powdered cocrystal featuring a helical hydrogen-bonded network: structure determination from PXRD, solid-state NMR and computer modeling.

We present the structure of a new equimolar 1:1 cocrystal formed by 3,5-dimethyl-1H-pyrazole (dmpz) and 4,5-dimethyl-1H-imidazole (dmim), determined by means of powder X-ray diffraction data combined with solid-state NMR that provided insight into topological details of hydrogen bonding connectivities and weak interactions such as CH···π contacts. The use of various 1D/2D (13)C, (15)N and (1)H high-resolution solid-state NMR techniques provided structural insight on local length scales revealing internuclear proximities and relative orientations between the dmim and dmpz molecular building blocks of the studied cocrystal. Molecular modeling and DFT calculations were also employed to generate meaningful structures. DFT refinement was able to decrease the figure of merit R(F(2)) from ~11% (PXRD only) to 5.4%. An attempt was made to rationalize the role of NH···N and CH···π contacts in stabilizing the reported cocrystal. For this purpose four imidazole derivatives with distinct placement of methyl substituents were reacted with dmpz to understand the effect of methylation in blocking or enabling certain intermolecular contacts. Only one imidazole derivative (dmim) was able to incorporate into the dmpz trimeric motif thus resulting in a cocrystal, which contains both hydrophobic (methyl groups) and hydrophilic components that self-assemble to form an atypical 1D network of helicoidal hydrogen bonded pattern, featuring structural similarities with alpha-helix arrangements in proteins. The 1:1 dmpz···dmim compound I is the first example of a cocrystal formed by two different azoles.

Rhodamine-Appended Bipyridine: XOR and OR Logic Operations Integrated in an Example of Controlled Metal Migration.

A new bipyridyl derivative 1 bearing rhodamine B as visible fluorophore was designed, synthesized and characterized as a fluorescent and colorimetric sensor for metal ions. Interaction with Cu(2+), Zn(2+), Cd(2+), Hg(+), and Hg(2+) ions was followed by UV/Vis and emission spectroscopy. Upon addition of these metal ions, different colorimetric and fluorescent responses were observed. "Off-on-off" (Cu(2+), Zn(2+), and Hg(2+)) and "off-on" (Hg(+) and Cd(2+)) systems were obtained. Probe 1 was explored to mimic XOR and OR logic operations for the simultaneous detection of Hg(+)-Cu(2+) and Hg(+)-Zn(2+) pairs, respectively. DFT calculations were also performed to gain insight into the lowest-energy gas-phase conformation of free receptor 1 as well as the atomistic details of the coordination modes of the various metal ions.

Synthesis, spectroscopy studies, and theoretical calculations of new fluorescent probes based on pyrazole containing porphyrins for Zn(II), Cd(II), and Hg(II) optical detection.

New pyrazole-porphyrin conjugates were successfully prepared from a reaction of ß-porphyrin-chalcone derivatives with phenylhydrazine in acetic acid followed by an oxidative step. This fast and efficient synthetic approach provided the expected compounds in yields up to 82%. The sensing ability of the new porphyrin-pyrazole derivatives to detect the metal ions Ag(+), Na(+), K(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Hg(2+), Pb(2+), and Cr(3+) was studied by spectrophotometric and spectrofluorimetric titrations. In the presence of Zn(2+), the conjugates exhibit changes in the emission spectra that are desired for a ratiometric-type fluoroionophoric detection probe. The studies were extended to gas phase, where the pyrazole-porphyrin conjugates show ability to sense metal ions with high selectivity toward Cu(2+) and Ag(+), and in poly(methyl methacrylate) doped films with promising results for Zn(2+) detection.

Production of adsorbents by pyrolysis of paper mill sludge and application on the removal of citalopram from water.

This work describes the production of alternative adsorbents from industrial residues and their application for the removal of a highly consumed antidepressant (citalopram) from water. The adsorbents were produced by pyrolysis of both primary and biological paper mill sludge at different temperatures and residence times. The original sludge and the produced chars were fully characterized by elemental and proximate analyses, total organic carbon, specific surface area (BET), N2 isotherms, FTIR, (13)C and (1)H solid state NMR and SEM. Batch kinetic and equilibrium experiments were carried out to describe the adsorption of citalopram onto the produced materials. The fastest kinetics and the highest adsorption capacity were obtained using primary sludge pyrolysed at 800 °C during 150 min. The use of pyrolysed paper mill sludge for the remediation of contaminated waters might constitute an interesting application for the valorization of those wastes.

A new 3,5-bisporphyrinylpyridine derivative as a fluorescent ratiometric probe for zinc ions.

A new 3,5-disubstituted pyridine with two porphyrin moieties was prepared through an efficient synthetic approach involving 2-formyl-5,10,15,20-tetraphenylporphyrin (1), piperidine, and catalytic amounts of [La(OTf)3]. 3,5-Bis(5,10,15,20-tetraphenylporphyrin-2-ylmethyl)pyridine (2) was fully characterized and its sensing ability towards Zn(2+), Cu(2+), Hg(2+), Cd(2+), and Ag(+) was evaluated in solution by absorption and fluorescence spectroscopy and in gas phase by using matrix-assisted laser desorption/ionization (MALDI)-TOF mass spectrometry. Strong changes in the ground and excited state were detected in the case of the soft metal ions Zn(2+), Cd(2+), Hg(2+), and Cu(2+). A three-metal-per-ligand molar ratio was obtained in all cases and a significant ratiometric behavior was observed in the presence of Zn(2+) with the appearance of a new band at 608 nm, which can be assigned to a metal-to-ligand charge transfer. The system was able to quantify 79 ppb of Zn(2+) and the theoretical calculations are in accordance with the stoichiometry observed in solution. The gas-phase sensorial ability of compound 2 towards all metal ions was confirmed by using MALDI-TOF MS and in solid state by using polymeric films of polymethylmethacrylate (PMMA) doped with ligand 2. The results showed that compound 2 can be analytically used to develop new colorimetric molecular devices that are able to discriminate between Hg(2+) and Zn(2+) in solid phase. The crystal structure of Zn(II) complex of 3,5-bisporphyrinylpyridine was unequivocally elucidated by using single-crystal X-ray diffraction studies.

Inulavosin and its benzo-derivatives, melanogenesis inhibitors, target the copper loading mechanism to the active site of tyrosinase.

Tyrosinase, a melanosomal membrane protein containing copper, is a key enzyme for melanin synthesis in melanocytes. Inulavosin inhibits melanogenesis by enhancing a degradation of tyrosinase in lysosomes. However, the mechanism by which inulavosin redirects tyrosinase to lysosomes is yet unknown. The analyses of structure-activity relationship of inulavosin and its benzo-derivatives reveal that the hydroxyl and the methyl groups play a critical role in their inhibitory activity. Intriguingly, the docking studies to tyrosinase suggest that the compounds showing inhibitory activity bind through hydrophobic interactions to the cavity of tyrosinase below which the copper-binding sites are located. This cavity is proposed to be required for the association with a chaperon that assists in copper loading to tyrosinase in Streptomyces antibioticus. Inulavosin and its benzo-derivatives may compete with the copper chaperon and result in a lysosomal mistargeting of apo-tyrosinase that has a conformational defect.

Corrole and corrole functionalized silica nanoparticles as new metal ion chemosensors: a case of silver satellite nanoparticles formation.

Corrole macrocycles are very appealing dyes for incorporation into light harvesting devices. This work shows the sensorial ability of 5,10,15-tris(pentafluorophenyl)corrole 1 and its monoanionic species toward Na(+), Ca(2+), Cu(2+), Cd(2+), Pb(2+), Hg(2+), Ag(+), and Al(3+) metal ions in toluene and acetonitrile. The photophysical studies toward metal ions were carried out by absorption and emission spectroscopy. From all metal ions studied, corrole 1 shows to be colorimetric for Hg(2+) allowing a naked-eye detection of Hg(2+) through a change of color from purple to blue in acetonitrile and from green to yellow in toluene. In addition a new ß-imine corrole 4 was successful synthesized and further functionalized with 3-isocyanatopropyl-trimethoxysilane resulting in an alkoxysilane derivative 5. The grafting of alkoxysilane derivative 5 with optically transparent silica nanoparticles (SiNPs) was achieved succesfully. The new-coated silica nanoparticles with corrole 5 were studied in the presence of Cu(2+), Hg(2+), and Ag(+) as metal ion probes. Interestingly, upon addition of Ag(+), groups of satellite AgNPs were formed around the SiNPs and were checked by transmission electron microscopy (TEM). At same time, a change of color from green to yellow was observed.

meso-Tetraphenylbenzoporphyrin-2(2),2(3)-dicarboxylic anhydride: a platform to benzoporphyrin derivatives.

A method to synthesize meso-tetraphenylbenzoporphyrin-2(2),2(3)-dicarboxylic anhydride is reported. This compound reacts with alkylamines and arylamines to afford the corresponding "phthalimides" in moderate to excellent yields. The reaction of the title compound with benzene-1,4-diamine or with benzene-1,3-diamine yields the corresponding N,N'-(phenylene)bisphthalimides, whereas with benzene-1,2-diamine or naphthalene-1,8-diamine it affords heterocyclic-fused porphyrins. Molecular mechanics simulations elucidates the multiplicity of signals observed in the NMR spectra of the N,N'-(1,4-phenylene)bisphthalimide 11. This molecule exhibits two preferential conformations corresponding to a coplanar and an almost perpendicular arrangement of the benzoporphyrin units relative to the central benzenic ring.

Glycophthalocyanines: structural differentiation and isomeric differentiation by matrix-assisted laser desorption/ionization tandem mass spectrometry.

RATIONALE: Glycophthalocyanines have a great promising potential in many scientific areas. However, their structural characterization is not an easy task. To overcome this drawback, it is urgent to develop simple and efficient methodologies to characterize this type of compounds. In this work, we describe the use of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and MALDI-MS/MS of the [M+H](+) to distinguish between two isomeric glycophatholocyanines bearing four galactose units with protected (1a and 2a) or unprotected hydroxyl groups (1b and 2b). METHODS: The MALDI-MS and MALDI-MS/MS spectra were acquired using a MALDI-TOF/TOF Applied Biosystems 4800 Proteomics Analyzer instrument equipped with a nitrogen laser and using dithranol as matrix. Computational studies were performed in order to gain insights into the mechanisms underlying the different fragmentation pathways observed for the isomeric species. RESULTS: The fragmentation pattern observed in MALDI-MS/MS spectra of the [M+H](+) ion was dependent on the peripheral distribution of the sugar units. Phthalocyanines (Pcs) with a sugar unit in each isoindole ring show the typical loss of sugar units (cleavage of C6-O bond) while Pcs with the four sugar units linked to the same isoindole ring show a major and unusual fragmentation pathway corresponding to the cleavage of the C5-C6 bond of the sugar units. This type of fragmentation is not usually observed in the MS/MS of oligosaccharides. CONCLUSIONS: MALDI-MS is a valuable tool for the structural characterization/differentiation of isomeric glycophthalocyanines.

Functionalized Porphyrins as Red Fluorescent Probes for Metal Cations: Spectroscopic, MALDI-TOF Spectrometry, and Doped-Polymer Studies.

Invited for this month's cover are groups from the University of Aveiro and the University NOVA of Lisbon/Bioscope. The cover picture of the lighthouses of Barra (Aveiro) and Cabo Espichel (Lisbon) in Portugal represents the remarkable sensing ability of benzoporphyrin derivatives for Hg2+ metal ions. These systems have high potential for use as chromogenic and fluorogenic sensors. Read the full text of the article on page 1230.

Functionalized Porphyrins as Red Fluorescent Probes for Metal Cations: Spectroscopic, MALDI-TOF Spectrometry, and Doped-Polymer Studies.

The sensing ability of benzoporphyrins 1-5 and porphyrin-2-ylpyridines 6-10 towards different metal ions Na+ , K+ , Ca2+ , Mg2+ , Pb2+ , Cu2+ , Ni2+ , Zn2+ , Cd2+ , Hg2+ , and Cr3+ was explored in solution by absorption and fluorescence spectroscopy. Strong changes in the ground and excited state were detected only in the case of the soft metal ions Zn2+ , Cd2+ , Hg2+ , and Cu2+ . A one metal per ligand molar ratio was obtained in all cases for compounds 1-5. In addition, a remarkable increase of the emission intensity for 1-5 was observed in the presence of Hg2+ . In this series the highest association constant was obtained for compound 1 (log Kass =(8.71±4.81)×10-3 ), which was able to quantify 32 ppb of Hg2+ . For compounds 6-10 containing an additional pyridine unit, a metal-to-ligand stoichiometry of 1:2 was determined. The gas-phase detection abilities of compounds 1-10 using MALDI-TOF-MS spectrometry confirmed that their sensorial ability and theoretical calculations are in accordance with the stoichiometry observed. Our preliminary studies show that some of the compounds supported in polymethylmethacrylate (PMMA) films can be used as promising metal-ion solid chemosensors; it was found that compound 1 in PMMA is able to distinguish between Zn2+ and Hg2+ in the solid phase.

Combining multinuclear high-resolution solid-state MAS NMR and computational methods for resonance assignment of glutathione tripeptide.

We present a complete set of experimental approaches for the NMR assignment of powdered tripeptide glutathione at natural isotopic abundance, based on J-coupling and dipolar NMR techniques combined with (1)H CRAMPS decoupling. To fully assign the spectra, two-dimensional (2D) high-resolution methods, such as (1)H-(13)C INEPT-HSQC/PRESTO heteronuclear correlations (HETCOR), (1)H-(1)H double-quantum (DQ), and (1)H-(14)N D-HMQC correlation experiments, have been used. To support the interpretation of the experimental data, periodic density functional theory calculations together with the GIPAW approach have been used to calculate the (1)H and (13)C chemical shifts. It is found that the shifts calculated with two popular plane wave codes (CASTEP and Quantum ESPRESSO) are in excellent agreement with the experimental results.

Packing interactions in hydrated and anhydrous forms of the antibiotic Ciprofloxacin: a solid-state NMR, X-ray diffraction, and computer simulation study.

We present an experimental NMR, X-ray diffraction (XRD), and computational study of the supramolecular assemblies of two crystalline forms of Ciprofloxacin: one anhydrate and one hydrate forming water wormholes. The resonance assignment of up to 51 and 54 distinct (13)C and (1)H resonances for the hydrate is reported. The effect of crystal packing, identified by XRD, on the (1)H and (13)C chemical shifts including weak interionic H-bonds, is quantified; (1)H chemical shift changes up to ∼-3.5 ppm for CH···π contacts and ∼+2 ppm (CH···O((-))); ∼+4.7 ppm (((+))NH···O((-))) for H-bonds. Water intake induces chemical shift changes up to 2 and 5 ppm for (1)H and (13)C nuclei, respectively. Such chemical shifts are found to be sensitive detectors of hydration/dehydration in highly insoluble hydrates.

Molecular dynamics study of a heteroditopic-calix[4]diquinone-assisted transfer of KCl and dopamine through a water-chloroform liquid-liquid interface.

The ability of two heteroditopic calix[4]diquinone receptors to transport a KCl ion-pair and a dopamine zwitterion through a water-chloroform interface was investigated via molecular dynamics (MD) simulations. Gas-phase conformational analysis has been carried on KCl and dopamine receptor binding associations and the lowest energy structures found in both cases show that the recognition of KCl and dopamine zwitterion occurs through multiple and cooperative N-H...anion and O...cation bonding interactions, with the receptor adopting equivalent folded conformations stabilized by pi-stacking interactions. The unconstrained MD simulations performed on KCl and dopamine complexes inserted in either the chloroform or water phase revealed that receptors are preferentially located at the interface with the hydrophobic tert-butyl groups of the calix[4]diquinone moiety immersed in the chloroform bulk while the polar anion binding cavity is directed toward the water phase. When the KCl complex is placed in chloroform, the release of the ion-pair occurs only after the first contact with the water interface, being a nonsimultaneous event, with the chloride anion leaving the receptor before the potassium cation. The dopamine, via the -NH(3)(+) binding entity, remains bound to the receptor during the entire time of the MD simulation (10 ns). In contrast, when both complexes were inserted in the water bulk, the full release of KCl and dopamine are fast events. The potentials of mean force (PMFs), associated with the migration of the complexes from chloroform to water through the interface, were calculated from steered molecular dynamics (SMD) simulations. The PMFs for the free KCl and zwitterionic dopamine migrations were also obtained for comparison purposes. The transport of KCl from water to chloroform (the reverse path) mediated by the receptor has a free energy barrier estimated in 6.50 kcal mol(-1), which is 3.0 kcal mol(-1) smaller than that found for the free KCl. The transport of dopamine complex along the reverse path is characterized by downhill energy profile, with a small free energy barrier of 6.56 kcal mol(-1).