Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?

Structure-activity relationship (SAR) and/or quantitative structure-activity relationship (QSAR) studies play an important role in a lead optimization of drug discovery research. When there is a lack of ligand-bound protein structural information, one of the assumptions in SAR and QSAR studies is that similar analogs bind to the same binding site in a similar binding mode. In such studies, outliers have often been observed, especially in QSAR. However, most of these studies have focused their attention on the development of QSAR and left outliers unattended. We searched ligand-bound X-ray crystal structures from the protein structure database to find evidences that could indicate a possible source of outliers in SAR or QSAR. Our results showed the possibility of conformational changes in a flexible binding site as one possible source of outliers. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

X-ray crystal structure of arsenite-inhibited xanthine oxidase: μ-sulfido,μ-oxo double bridge between molybdenum and arsenic in the active site

Xanthine oxidoreductase is a molybdenum-containing enzyme that catalyzes the hydroxylation reaction of sp(2)-hybridized carbon centers of a variety of substrates, including purines, aldehydes, and other heterocyclic compounds. The complex of arsenite-inhibited xanthine oxidase has been characterized previously by UV-vis, electron paramagnetic resonance, and X-ray absorption spectroscopy (XAS), and the catalytically essential sulfido ligand of the square-pyrimidal molybdenum center has been suggested to be involved in arsenite binding through either a μ-sulfido,μ-oxo double bridge or a single μ-sulfido bridge. However, this is contrary to the crystallographically observed single μ-oxo bridge between molybdenum and arsenic in the desulfo form of aldehyde oxidoreductase from Desulfovibrio gigas (an enzyme closely related to xanthine oxidase), whose molybdenum center has an oxo ligand replacing the catalytically essential sulfur, as seen in the functional form of xanthine oxidase. Here we use X-ray crystallography to characterize the molybdenum center of arsenite-inhibited xanthine oxidase and solve the structures of the oxidized and reduced inhibition complexes at 1.82 and 2.11 ? resolution, respectively. We observe μ-sulfido,μ-oxo double bridges between molybdenum and arsenic in the active sites of both complexes. Arsenic is four-coordinate with a distorted trigonal-pyramidal geometry in the oxidized complex and three-coordinate with a distorted trigonal-planar geometry in the reduced complex. The doubly bridged binding mode is in agreement with previous XAS data indicating that the catalytically essential sulfur is also essential for the high affinity of reduced xanthine oxidoreductase for arsenite.     

Density functional theory on the larger active site models for [NiFe] hydrogenases: Two-state reactivity?

The mechanism for H₂ activation catalyzed by [NiFe] hydrogenases is investigated with a series of models for the Ni(II) and Ni(III) forms in both high-spin (HS) and low-spin (LS) states by density functional theory (DFT/B3LYP) calculations. The geometry optimizations include unconstrained models, partially constrained (to the crystal structure parameters) models and models with addition of nearby protein residues. Several uncertainties concerning the mechanism are addressed in our study: (1) the oxidation state of the active species that binds and cleaves H₂; (2) the structures and spin states prevalent in active site forms; (3) the influence of the surrounding protein environments on the active site. Adding the nearby protein residues to a fairly rigid active site framework stablizes the LS Ni(II) species. Although models for Ni–SI forms, with a vacant binding site, still prefer HS, addition of H₂ or CO stablizes the LS form. Thus, access to this LS state and two-state reactivity may play a role in the mechanism. Furthermore, the more complete protein models show that the energetic preference for the binding site for both H₂ and CO changes from Fe to Ni. This change brings the computational results in closer accord with the experimental ones.     

Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds?

Computational scaffold hopping aims to identify core structure replacements in active compounds. To evaluate scaffold hopping potential from a principal point of view, regardless of the computational methods that are applied, a global analysis of conventional scaffolds in analog series from compound activity classes was carried out. The majority of analog series was found to contain multiple scaffolds, thus enabling the detection of intra-series scaffold hops among closely related compounds. More than 1000 activity classes were found to contain increasing proportions of multi-scaffold analog series. Thus, using such activity classes for scaffold hopping analysis is likely to overestimate the scaffold hopping (core structure replacement) potential of computational methods, due to an abundance of artificial scaffold hops that are possible within analog series.     

Aerobic oxidation of alcohol by model complexes relevant to metal site galactose oxidase: role of copper(I) intermediate,evidence for the generation of end-on copper(II)–OOH species and catalytic promiscuity for oxidation of benzyl alcohol,catechol and o-aminophenol

Transition Metal Chemistry - Tridentate ligands having meridional NNO donor centres were designed and synthesized mimicking the copper coordination in the metal site of galactose oxidase enzyme....     

The Effect of a Covalent and a Noncovalent Small-Molecule Inhibitor on the Structure of Abg β-Glucosidase in the Gas-Phase

The effects of binding two small-molecule inhibitors to Agrobacterium sp. strain ATCC 21400 (Abg) β-glucosidase on the conformations and stability of gas-phase ions of Abg have been investigated. Biotin-iminosugar conjugate (BIC) binds noncovalently to Abg while 2,4-dinitro-2-deoxy-2-fluoro-β-d-glucopyranoside (2FG-DNP) binds covalently with loss of DNP. In solution, Abg is a dimer. Mass spectra show predominantly dimer ions, provided care is taken to avoid dissociation of dimers in solution and dimer ions in the ion sampling interface. When excess inhibitor, either covalent or noncovalent, is added to solutions of Abg, mass spectra show peaks almost entirely from 2:2 inhibitor-enzyme dimer complexes. Tandem mass spectrometry experiments show similar dissociation channels for the apo-enzyme and 2FG-enzyme dimers. The +21 dimer produces +10 and +11 monomers. The internal energy required to dissociate the +21 2FG-enzyme to its monomers (767?±?30 eV) is about 36 eV higher than that for the apo-enzyme dimer (731?±?6 eV), reflecting the stabilization of the free enzyme dimer by the 2FG inhibitor. The primary dissociation channels for the noncovalent BIC-enzyme dimer are loss of neutral and charged BIC. The internal energy required to induce loss of BIC is 482?±?8 eV, considerably less than that required to dissociate the dimers. For a given charge state, ions of the covalent and noncovalent complexes have about 15 % and 25 % lower cross sections, respectively, compared with the apo-enzyme. Thus, binding the inhibitors causes the gas-phase protein to adopt more compact conformations. Noncovalent binding surprisingly produces the greatest change in protein ion conformation, despite the weaker inhibitor binding.

Quantum cluster size and solvent polarity effects on the geometries and Mössbauer properties of the active site model for ribonucleotide reductase intermediate X: a density functional theory study

In studying the properties of metalloproteins using ab initio quantum mechanical methods, one has to focus on the calculations on the active site. The bulk protein and solvent environment is often neglected, or is treated as a continuum dielectric medium with a certain dielectric constant. The size of the quantum cluster of the active site chosen for calculations can vary by including only the first-shell ligands which are directly bound to the metal centers, or including also the second-shell residues which are adjacent to and normally have H-bonding interactions with the first-shell ligands, or by including also further hydrogen bonding residues. It is not well understood how the size of the quantum cluster and the value of the dielectric constant chosen for the calculations will influence the calculated properties. In this paper, we have studied three models (A, B, and C) of different sizes for the active site of the ribonucleotide reductase intermediate X, using density functional theory (DFT) OPBE functional with broken-symmetry methodology. Each model is studied in gas-phase and in the conductor-like screening (COSMO) solvation model with different dielectric constants ε = 4, 10, 20, and 80, respectively. All the calculated Fe-ligand geometries, Heisenberg J coupling constants, and the Mössbauer isomer shifts, quadrupole splittings, and the ⁵⁷Fe, ¹H, and ¹⁷O hyperfine tensors are compared. We find that the calculated isomer shifts are very stable. They are virtually unchanged with respect to the size of the cluster and the dielectric constant of the environment. On the other hand, certain Fe-ligand distances are sensitive to both the size of the cluster and the value of ε. ε = 4, which is normally used for the protein environment, appears too small when studying the diiron active site geometry with only the first-shell ligands as seen by comparisons with larger models.     

Thiolate-bridged nickel-copper complexes: a binuclear model for the catalytic site of acetyl coenzyme a synthase?

Reaction of the nickel metalloligands [EtN2S2]Ni (EtN2S2, N,N'-diethyl-3,7-diazanonane-1,9-dithiolate) or K2[Ni(phmi)] (phmi, N,N'-1,2-phenylenebis(2-sulfanyl-2-methylpropionamide)) with [Cu(CH3CN)4]BF4 yields polynuclear complexes in which two copper(I) ions are bridged by the nickel metalloligands. Alternatively, reaction with the Cu(I) source, [(PhTttBu)Cu] (PhTttBu, phenyltris((tert-butylthio)methyl)borate), generates discrete binuclear NiCu complexes that may serve as models of the acetyl coenzyme A synthase active site. The binuclear species react reversibly with CO via rupture of the thiolate bridges.     

Solution structure of the sheep prion PrP〚142-166〛: a possible site for the conformational conversion of prion protein

In order to get deeper insight into the molecular forces responsible for prion pathogenic conversion, conformational properties of a synthetic linear peptide derived from the globular core of sheep prion protein were studied by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. The studied peptide encompassing the 〚142–166〛 (in human numbering) region of sheep prion protein, folds in physiological conditions into a β-hairpin like tertiary structure, whereas, in the non-pathogenic form of protein and in trifuoroethanol (TFE), the region is engaged in largely α-helical conformation. Such structural duality of the fragment indicates a possible transconformational site within prion protein and may explain one of the early structural causes of prion diseases.     

Perspective: Do macromolecules play a role in the mechanisms of nerve stimulation and nervous transmission?

Fibrillar macromolecular networks are ubiquitous in biological systems, from cellular cytoskeletons to tissues such as muscle and tendon. The presence of such networks in neuronal tissue is known, for example, in the cytoskeleton and extracellular matrix in and around neuronal and glial cells, but their function is believed to be principally mechanical/structural in nature. However, there has long been speculation regarding a broader role for neuronal fibrillar macromolecules, which are anionic polyelectrolytes, specifically regarding their participation in nervous stimulation and transmission. This Perspective reviews literature that spans more than a century, including very recent work, and attempts to build a case for considering a multifunctional role for such macromolecules that includes participation in not only nervous activity but also in diverse phenomena including electric communication within and between cells and mechanisms of anesthetic action. Perhaps the creation and utilization of “artificial axons” is within reach with design rules coming at least in part from fundamental considerations of macromolecular science. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 7–14     

Critical comparison of equations correlating valence and length of a chemical bond. Evaluation of the parameters R1 and B for the MoO bond in MoO6 octahedra

The most commonly used equations correlating bond valence and bond length have been critically compared. It has been shown that the Zachariasen equation is more accurate than the Brown–Shannon equation. Doubts already voiced about the universality of the constant B in the Brown–Altermatt equation with a value of 0.37 Å have been hereby confirmed. Moreover, by a method based on the comparison of formal oxidation states and valences of molybdenum in suitable oxides, the parameters relative to the Zachariasen equation have been accurately determined for the MoO bond in MoO₆ octahedra. Their values are R₁=1.8790 and B=0.3048 Å in the 3–6 v.u. range.     

MO investigations on lignin model compounds: IX. A PCILO study of the hydrogen bond O-H…O and O-H…N type formed by phenol with some proton acceptors

A systematic PCILO study has been carried out on the intermolecular hydrogen bond formed by phenol with proton acceptors such as acetone, ether, p-benzoquinone, N,N-dimethylformamide, trimethylamine, pyridine, acetonitrile and acrylonitrile. The complexes studied form hydrogen bonds with energy intervals of 20 − 45 kJ mol⁻¹ at distances R_O…Y = 0.265 − 0.300 nm (Y=N,0). For the system phenol-pyridine both the 1:1 complex PhPy and the 2:1 complex Ph₂Py were also studied. The calculated hydrogen bond energies are compared and discussed with experimental data from the literature. The calculated hydrogen bond and O-H stretching force constants are in range expected.     

Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers?

A lead optimization is usually carried out by structure-activity relationship (SAR) and/or quantitative structure-activity relationship (QSAR) studies. One of the assumptions in SAR and QSAR studies is that similar analogs bind to the same binding site in a similar binding mode. One often observes that there are outliers, especially in QSAR. However, most QSAR studies are carried out focusing their attention to the development of QSAR and leave the outliers without much attention. We searched a number of ligand-bound X-ray crystal structures from the protein structure database to find evidences that could indicate a possible source of outliers in SAR or QSAR. Our results show that unusual binding mode could be a source of outliers. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

On the possible catalytic role of a single water molecule in the acetone + OH gas phase reaction: a theoretical pseudo-second-order kinetics study

In this work, we have revisited the mechanism of the acetone + OH radical reaction assisted by a single water molecule simulating atmospheric conditions. Density functional methods are employed in conjunction with CCSD(T) and large basis sets to explore the potential energy surface of this radical-molecule reaction. Computational kinetics calculations in a pseudo-second order mechanism have been performed, taking into account average atmospheric water concentrations and temperatures. We have used this method recently to study the single-water molecule-assisted H-abstraction in acetaldehyde (Iuga et al. in J Phys Chem Lett 1:3112, 2010) and in glyoxal (Iuga et al. in Chem Phys Lett 501:11, 2010) by OH radicals, and we showed that the initial water complexation step is essential in the rate constant calculation. In both cases, the amount of complex formed is only about 0.01% of the total organic molecule concentration, and as a consequence, water does not accelerate the reaction. In the acetone reaction with OH radicals under atmospheric conditions, we also find that the water–acetone complex concentration is much too small to be relevant, and thus, the rate constant of the water-assisted mechanism is orders of magnitude smaller than the water-free corresponding value.     

Competitive electron transfers from a tyrosyl side-chain and peptide bond in the photodegradation of N-tosyl alpha-aminomethylamides: an insight into photosynthesis and photodamage in the biological oxidation of water?

Photo-excited N-tosyl derivatives of phenylalanyl- and, more particularly, O-methyltyrosylmethylamides undergo electron transfer from aryl to tosyl groups whereas the photo-degradation of aliphatic analogues is initiated by electron transfer from the peptide bond, suggesting the latter as one possible reason for the rapid turnover of the D1 protein in biological water oxidation when the essential mediating role of tyrosine 116 in the PSII complex is inhibited.     

Effect of pulegone and pulegone oxide on the corrosion of steel in 1?M HCl

The inhibitive action of pulegone and pulegone oxide toward acid corrosion of steel in molar hydrochloric acid was studied by weight loss measurements, potentiodynamic polarization, and impedance spectroscopy (EIS) methods. The pulegone is extracted starting from oil of Pennyroyal Mint (Mentha pulegium). The natural compound was found to delay the corrosion rate. The pulegone oxide is prepared by oxidation of pulegone. The inhibition efficiency was found to increase with the inhibitor content to attain 81 and 75% at 5 g dm⁻³ for pulegone and pulegone oxide. The increase in temperature leads to an increase in the inhibition efficiency of the natural compared.