Discovery of new inhibitor for the protein arginine deiminase type 4 (PAD4) by rational design of α-enolase-derived peptides

Rheumatoid arthritis (RA) is an inflammatory autoimmune disease affecting about 0.24 % of the world population. Protein arginine deiminase type 4 (PAD4) is believed to be responsible for the occurrence of RA by catalyzing citrullination of proteins. The citrullinated proteins act as autoantigens by stimulating an immune response. Citrullinated α-enolase has been identified as one of the autoantigens for RA. Hence, α-enolase serves as a suitable template for design of potential peptide inhibitors against PAD4. The binding affinity of α-enolase-derived peptides and PAD4 was virtually determined using PatchDock and HADDOCK docking programs. Synthesis of the designed peptides was performed using a solid phase peptide synthesis method. The inhibitory potential of each peptide was determined experimentally by PAD4 inhibition assay and IC₅₀ measurement. PAD4 assay data show that the N-P2 peptide is the most favourable substrate among all peptides. Further modification of N-P2 by changing the Arg residue to canavanine [P2 (Cav)] rendered it an inhibitor against PAD4 by reducing the PAD4 activity to 35 % with IC₅₀ 1.39 mM. We conclude that P2 (Cav) is a potential inhibitor against PAD4 and can serve as a starting point for the development of even more potent inhibitors.     

Development of new DMAP-related organocatalysts for use in the Michael addition reaction of β-ketoesters in water

A general and efficient protocol for the Michael addition reactions of β-ketoesters in pure water has been developed. The reactions are successfully catalyzed by newly designed DMAP-related organocatalysts such as 4-(didecylamino)pyridine, and the desired Michael adducts are obtained in good to high yields     

The reductionist paradox: are the laws of chemistry and physics sufficient for the discovery of new drugs?

Reductionism is alive and well in drug-discovery research. In that tradition, we continually improve experimental and computational methods for studying smaller and smaller aspects of biological systems. Although significant improvements continue to be made, are our efforts too narrowly focused? Suppose all error could be removed from these methods, would we then understand biological systems sufficiently well to design effective drugs? Currently, almost all drug research focuses on single targets. Should the process be expanded to include multiple targets? Recent efforts in this direction have lead to the emerging field of polypharmacology. This appears to be a move in the right direction, but how much polypharmacology is enough? As the complexity of the processes underlying polypharmacology increase will we be able to understand them and their inter-relationships? Is “new” mathematics unfamiliar in much of physics and chemistry research needed to accomplish this task? A number of these questions will be addressed in this paper, which focuses on issues and questions not answers to the drug-discovery conundrum.     

Radical Cations of Phenyl‐Substituted Aziridines: What Are the Conditions for Ring Opening?

Radical cations were generated from different phenyl-substituted aziridines by pulse radiolysis in aqueous solution containing TlOH.+, N3. or SO4.- as oxidants or in n-butyl chloride, by 60Co gamma radiolysis in Freon matrices at 77 K, and in some cases by flash photolysis in aqueous solution. Depending on the substitution pattern of the aziridines, two different types of radical cations are formed: if the N atom carries a phenyl ring, the aziridine appears to retain its structure after oxidation and the resulting radical cation shows an intense band at 440-480 nm, similar to that of the radical cation of dimethylaniline. Conversely, if the N atom carries an alkyl substituent while a phenyl ring is attached to a C-atom of the aziridine, oxidation results in spontaneous ring opening to yield azomethine ylide radical cations which have broad absorptions in the 500-800 nm range. In aqueous solution the two types of radical cations are quenched by O2 with different rates, whereas in n-butyl chloride, the ring-closed aziridine radical cations are not quenchable by O2. The results of quantum chemical calculations confirm the assignment of these species and allow to rationalize the different effects that phenyl rings have if they are attached in different positions of aziridines. In the pulse radiolysis experiments in aqueous solution, the primary oxidants can also be observed, whereas in n-butyl chloride a transient at 325 nm remains unidentified. In the laser flash experiments, both types of radical cations were also observed.     

Computational clues for a new mechanism in the glycosylase activity of the human DNA repair protein hOGG1. A generalized paradigm for purine-repairing systems?

A theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic cycle responsible for the glycosylase activity of the human DNA repair protein hOGG1: enzyme activation, cleavage of the glycosidic bond, and expulsion of the damaged base. An unprecedented large quantum mechanics (QM) model system has been used, which includes a complete oxoG molecule, the deoxyribose ring bonded to the phosphate groups, and most of the surrounding residues that simulate the protein binding pocket. It has been found that Asp268 does not play any role in Lys249 activation and that the oxoG basis acts as a coenzyme, triggering nucleophile activation by Lys249 deprotonation. An SN2 nucleophilic attack by Lys249 on the anomeric carbon then follows. This is the rate-determining step of the process with an activation barrier of 16.7 kcal mol(-1) in good agreement with the experimental value of 17.1 kcal mol(-1). The expelled oxoG plays again as an enzyme cofactor at the end of the process by activating (via proton transfer) ribose ring opening and Schiff base formation. This study suggests a recurring catalytic strategy in the enzymatic cleavage of purine nucleoside where the activation of the leaving group by protonation of the nucleoside base (via an enzymatic general acid) triggers the cleavage of the glycosidic bond.     

Structure and Bonding in First‐Row Transition‐Metal Dicarbides: Are They Related to the Stability of Met‐cars?

First-row transition-metal dicarbides MC(2) (M=Sc-Zn) have been investigated by using quantum-mechanical techniques. The competition between cyclic and linear isomers in these systems has been studied and the bonding scheme for these compounds is discussed through topological analysis of electron density. All of the systems have been found to prefer a C(2v)-symmetric arrangement, although for ZnC(2) the energy difference between this and the linear isomer is rather small. In most cases the C(2v)-symmetric structure corresponds to a T-shaped structure, with the exceptions of TiC(2), CoC(2), and NiC(2) which have been shown to be true rings. A detailed analysis of the variation of the energy of the system with geometry has been carried out. An analysis of the bonding, taking into account the main interactions between the valence orbitals of both fragments, the M atom and the C(2) molecule, has allowed the main features of these compounds to be interpreted. A clear correlation between the dissociation energies of the first-row transition-metal dicarbides and the bonding energies of the corresponding met-cars was observed.     

Can MM‐PBSA calculations predict the specificities of protein kinase inhibitors?

An application of the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) protocol to the prediction of protein kinase inhibitor selectivity is presented. Six different inhibitors are placed in equivalent orientations in each of six different receptors. Fully solvated molecular dynamics is then run for 1 ns on each of the 36 complexes, and the resulting trajectories scored, using the implicit solvent model. The results show some correlation with experimentally-determined specificities; anomalies may be attributed to a variety of causes, including difficulties in quantifying induced fit penalties and variabilities in normal modes calculations. Decomposing interaction energies on a per-residue basis yields more useful insights into the natures of the binding modes and suggests that the real value of such calculations lies in understanding interactions rather than outright prediction.     

Power‐to‐Syngas: An Enabling Technology for the Transition of the Energy System?

Power‐to‐X concepts promise a reduction of greenhouse gas emissions simultaneously guaranteeing a safe energy supply even at high share of renewable power generation, thus becoming a cornerstone of a sustainable energy system. Power‐to‐syngas, that is, the electrochemical conversion of steam and carbon dioxide with the use of renewably generated electricity to syngas for the production of synfuels and high‐value chemicals, offers an efficient technology to couple different energy‐intense sectors, such as “traffic and transportation” and “chemical industry”. Syngas produced by co‐electrolysis can thus be regarded as a key‐enabling step for a transition of the energy system, which offers additionally features of CO₂‐valorization and closed carbon cycles. Here, we discuss advantages and current limitations of low‐ and high‐temperature co‐electrolysis. Advances in both fundamental understanding of the basic reaction schemes and stable high‐performance materials are essential to further promote co‐electrolysis.     

Are cluster ion analysis beams good choices for hydrogen depth profiling using time‐of‐flight secondary ion mass spectrometry?

For more than three decades, time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) has been used for elemental depth profiling. In recent years, cluster primary ion sources (principally, C₆₀⁺, Bi_n⁺, and Au_n⁺) have become widely available, and they can greatly enhance the signal intensity of molecular ions (10–1000 times). Understanding the performance of cluster ion analysis beams used in elemental depth profiling can greatly assist normal ToF‐SIMS users in choosing the optimal analysis beam for depth profiling work. Presently, however, the experimental data are lacking, and such choices are difficult to make. In this paper, hydrogen and deuterium depth profiling were studied using six different analysis beams—25 keV Bi⁺, Bi₃⁺, Bi₅⁺, 50 keV Bi₃²⁺, 10 keV C₆₀⁺, and 20 keV C₆₀²⁺. The effort shows that cluster primary ions do enhance H^? and D^? yields, but the enhancement is only about 1.5–4.0 times when compared to atomic Bi⁺ ions. Because the currents of atomic ion analysis beams are much stronger than the currents of cluster ion analysis beams for most commercial ToF‐SIMS instruments, the atomic ion analysis beams can provide the strongest H^? and D^? signal intensities, and may be the best choices for hydrogen and deuterium depth profiling. In addition, two representative nuclides, ³⁰Si and ¹⁸O, were also studied and yielded results similar to those of H^? and D^?. Copyright © 2011 John Wiley & Sons, Ltd.     

Is there potential for use of the Hall effect in analytical science?

This article describes the basic principles of the Hall effect and how it has been applied in solid state applications to measure both the magnetic field and material properties. This is followed by an outline of research undertaken in aqueous ionic solutions as a possible precursor to application in chemical studies. However, previous research has shown that factors such as the Nernst effect have reduced the success of reliably measuring the Hall voltage under these conditions. The possibility of a multi-sensing approach using both electrical and acoustic Hall voltages to overcome these challenges is discussed. The article concludes with a brief look at some early efforts to detect biomolecular interactions.     

Tomocomd-Cardd, a novel approach for computer-aided ‘ rational’ drug design: I. Theoretical and experimental assessment of a promising method for computational screening and in silico design of new anthelmintic compounds

Summary In this work, the TOMOCOMD-CARDD approach has been applied to estimate the anthelmintic activity. Total and local (both atom and atom-type) quadratic indices and linear discriminant analysis were used to obtain a quantitative model that discriminates between anthelmintic and non-anthelmintic drug-like compounds. The obtained model correctly classified 90.37% of compounds in the training set. External validation processes to assess the robustness and predictive power of the obtained model were carried out. The QSAR model correctly classified 88.18% of compounds in this external prediction set. A second model was performed to outline some conclusions about the possible modes of action of anthelmintic drugs. This model permits the correct classification of 94.52% of compounds in the training set, and 80.00% of good global classification in the external prediction set. After that, the developed model was used in virtual in silicoscreening and several compounds from the Merck Index, Negwers handbook and Goodman and Gilman were identified by models as anthelmintic. Finally, the experimental assay of one organic chemical (G-1) by an in vivo test coincides fairly well (100) with model predictions. These results suggest that the proposed method will be a good tool for studying the biological properties of drug candidates during the early state of the drug-development process.     

First evidence for the use of organosilver compounds in Pd-catalyzed coupling reactions; a mechanistic rationale for the Pd/Ag-catalyzed enyne synthesis?

Silver acetylides have been prepared and used in Pd-catalyzed coupling reactions. Enynes have thus been obtained in good yields. This work demonstrates that organosilver compounds could enter the Pd catalytic cycle; it also supports the role of silver acetylides as intermediates in the new Pd/Ag-catalyzed coupling reaction.     

A Reevaluation of the Photolytic Properties of 2‐Hydroxybenzophenone‐Based UV Sunscreens: Are Chemical Sunscreens Inoffensive?

The excited states of a set of popular sunscreen agents (2‐hydroxybenzophenone, oxybenzone, and sulisobenzone) are studied by using femto‐ and nanosecond time‐resolved spectroscopy. Upon excitation, the compounds undergo an ultrafast excited‐state intramolecular proton transfer (ESIPT) reaction as the major energy‐wasting process and the rate constant of this reaction is k=2×10¹² s^?1. The ESIPT yields a keto conformer that undergoes a fast, picosecond internal conversion decay. However, a photodegradative pathway is a monophotonic H?O bond breakage that subsequently leads to trace yields of phenoxyl radicals. Because potentially harmful phenoxyl radicals are formed upon irradiation of sunscreen agents, care should be taken about their reactivity towards biologically relevant compounds.     

High‐resolution mass spectrometry for bioanalytical applications: Is this the new gold standard?

Liquid chromatography coupled to quadrupole‐based tandem mass spectrometry (QqQ) is termed the “gold standard” for bioanalytical applications because of its unpreceded selectivity, sensitivity, and the ruggedness of the technology. More recently, however, high‐resolution mass spectrometry (HRMS) has become increasingly popular for bioanalytical applications. Nonetheless, this technique is still viewed, either as a screening technology or as a research tool. Although HRMS is actively discussed during scientific conferences, it is yet to be widely utilised in routine laboratory settings and there remains a reluctance to use HRMS for quantitative measurements in regulated environments. This paper does not aim to comprehensively describe the potential of the latest HRMS technology, but rather, it focuses on what results can be obtained and outlines the author's experiences over a period of many years of the routine application of various forms of HRMS instrumentation. Fifteen years ago, some nine different QqQ methods were used in the author's laboratory to analyse a variety of different veterinary drug resides. Today, many more analytes are quantified by seven HRMS methods and just three QqQ methods remain in use for the analysis of a small set of compounds yet to be upgraded to HRMS analysis. This continual upgrading and migration of analytical methods were accompanied by regularly participating in laboratory proficiency tests (PTs). The PT reports (covering a range of analytes and analytical methods) were used to compare the accuracy of HRMS‐ versus QqQ‐based measurements. In the second part of this paper, the particular strengths and limitations of HRMS for both method development and routine measurements are critically discussed. This also includes some anecdotal experiences encountered when replacing QqQ assays with HRMS methods.     

What makes for a good catalytic cycle? A theoretical study of the SPhos ligand in the Suzuki-Miyaura reaction

The Suzuki-Miyaura cross-coupling reaction with the SPhos ligand was studied with DFT and analyzed within the energetic span model. With this information, we designed a modification to the SPhos (the "InPhos"), which theoretically corrects the deficiencies of the prior ligand.