We present nonrelativistic and relativistic benchmark databases (obtained by coupled cluster calculations) of 10 Zn−ligand bond distances, 8 dipole moments, and 12 bond dissociation energies in Zn coordination compounds with O, S, NH3, H2O, OH, SCH3, and H ligands. These are used to test the predictions of 39 density functionals, Hartree−Fock theory, and seven more approximate molecular orbital theories. In the nonrelativisitic case, the M05-2X, B97-2, and mPW1PW functionals emerge as the most accurate ones for this test data, with unitless balanced mean unsigned errors (BMUEs) of 0.33, 0.38, and 0.43, respectively. The best local functionals (i.e., functionals with no Hartree−Fock exchange) are M06-L and τ-HCTH with BMUEs of 0.54 and 0.60, respectively. The popular B3LYP functional has a BMUE of 0.51, only slightly better than the value of 0.54 for the best local functional, which is less expensive. Hartree−Fock theory itself has a BMUE of 1.22. The M05-2X functional has a mean unsigned error of 0.008 Å for bond lengths, 0.19 D for dipole moments, and 4.30 kcal/mol for bond energies. The X3LYP functional has a smaller mean unsigned error (0.007 Å) for bond lengths but has mean unsigned errors of 0.43 D for dipole moments and 5.6 kcal/mol for bond energies. The M06-2X functional has a smaller mean unsigned error (3.3 kcal/mol) for bond energies but has mean unsigned errors of 0.017 Å for bond lengths and 0.37 D for dipole moments. The best of the semiempirical molecular orbital theories are PM3 and PM6, with BMUEs of 1.96 and 2.02, respectively. The ten most accurate functionals from the nonrelativistic benchmark analysis are then tested in relativistic calculations against new benchmarks obtained with coupled-cluster calculations and a relativistic effective core potential, resulting in M05-2X (BMUE = 0.895), PW6B95 (BMUE = 0.90), and B97-2 (BMUE = 0.93) as the top three functionals. We find significant relativistic effects (∼0.01 Å in bond lengths, ∼0.2 D in dipole moments, and ∼4 kcal/mol in Zn−ligand bond energies) that cannot be neglected for accurate modeling, but the same density functionals that do well in all-electron nonrelativistic calculations do well with relativistic effective core potentials. Although most tests are carried out with augmented polarized triple-ζ basis sets, we also carried out some tests with an augmented polarized double-ζ basis set, and we found, on average, that with the smaller basis set DFT has no loss in accuracy for dipole moments and only ∼10% less accurate bond lengths.
In spite of the widespread use of perfluorinated solvents with amino and ether groups in a variety of application fields, the coordinative properties of these compounds are poorly known. It is generally assumed that the electron withdrawing perfluorinated moieties render these functional groups rather inert, but little is known quantitatively about the extent of their inertness. This paper reports on the interactions between inorganic monocations and perfluorotripentylamine and 2H-perfluoro-5,8,11-trimethyl-3,6,9,12-tetraoxapentadecane, as determined with fluorous liquid-membrane cationselective electrodes doped with tetrakis[3,5-bis(perfluorohexyl)phenyl]borate salts. The amine does not undergo measurable association with any ion tested, and its formal pK a is shown to be smaller than -0.5. This is consistent with the nearly planar structure of the amine at its nitrogen center, as obtained with density functional theory calculations. The tetraether interacts very weakly with Na + and Li + . Assuming 1:1 stoichiometry, formal association constants were determined to be 2.3 and 1.5 M -1 , respectively. This disproves an earlier proposition that the Lewis base character in such compounds may be non-existent. Due to the extremely low polarity of fluorous solvents and the resulting high extent of ion pair formation, a fluorophilic electrolyte salt with perfluoroalkyl substituents on both the cation and the anion had to be developed for these experiments. In its pure form, this first fluorophilic electrolyte salt is an ionic liquid with a glass transition temperature, T g , of -18.5 °C. Interestingly, the molar conductivity of solutions of this salt increases very steeply in the high concentration range, making it a particularly effective electrolyte salt.
We present benchmark databases of Zn-ligand bond distances, bond angles, dipole moments, and bond dissociation energies for Zn-containing small molecules and Zn coordination compounds with H, CH3, C2H5, NH3, O, OH, H2O, F, Cl, S, and SCH3 ligands. The test set also includes clusters with Zn-Zn bonds. In addition, we calculated dipole moments and binding energies for Zn centers in coordination environments taken from zinc metalloenzyme X-ray structures, representing both structural and catalytic zinc centers. The benchmark values are based on relativistic-core coupled cluster calculations. These benchmark calculations are used to test the predictions of four density functionals, namely B3LYP and the more recently developed M05-2X, M06, and M06-2X levels of theory, and six semiempirical methods, including neglect of diatomic differential overlap (NDDO) calculations incorporating the new PM3 parameter set for Zn called ZnB, developed by Brothers and co-workers, and the recent PM6 parametrization of Stewart. We found that the best DFT method to reproduce dipole moments and dissociation energies of our Zn compound database is M05-2X, which is consistent with a previous study employing a much smaller and less diverse database and a much larger set of density functionals. Here we show that M05-2X geometries and single-point coupled cluster calculations with M05-2X geometries can also be used as benchmarks for larger compounds, where coupled cluster optimization is impractical, and in particular we use this strategy to extend the geometry, binding energy, and dipole moment databases to additional molecules, and we extend the tests involving crystal-site coordination compounds to two additional proteins. We find that the most predictive NDDO methods for our training set are PM3 and MNDO/d. Notably, we also find large errors in B3LYP for the coordination compounds based on experimental X-ray geometries.
Arylamines (AA) and heterocyclic aromatic amines (HAA) are structurally related carcinogens formed during combustion of tobacco or cooking of meat. They undergo cytochrome P450 mediated N-hydroxylation to form metabolites which bind to DNA and lead to mutations. The N-hydroxylated metabolites of many AA also can undergo a co-oxidation reaction with oxy-hemolgobin (HbO2) to form methemoglobin (met-Hb) and the arylnitroso intermediates, which react with the β-Cys93 chain of Hb to form Hb-arylsulfinamide adducts. The biochemistry of arylamine metabolism has been exploited to biomonitor certain AAs through their Hb arylsulfinamide adducts in humans. We examined the reactivity of HbO2 with the N-hydroxylated metabolites of 4-aminobiphenyl (ABP, HONH-ABP), aniline (ANL, HONH-ANL), and the HAA 2-amino-9H-pyrido[2,3-b]indole (AαC, HONH-AαC), 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP, HONH-PhIP) and 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx, HONH-MeIQx). HONH-ABP, HO-ANL, and HONH-AαC induced methemoglobinemia and formed Hb sulfinamide adducts. However, HONH-MeIQx and HONH-PhIP did not react with the oxy-heme complex, and met-Hb formation and chemical modification of β-Cys93 residue was negligible. Molecular modeling studies showed that the distances between the H-ON-AA or H-ON-HAA substrates and the oxy-heme complex of HbO2 were too far away to induce methemoglobinemia. Different conformational changes in flexible helical and loop regions around the heme pocket induced by the H-ON-AA or H-ON-HAAs may explain the different proclivities of these chemicals to induce methemoglobinemia. Hb-Cys93β sulfinamide and sulfonamide adducts of ABP, ANL, and AαC were identified, by Orbitrap MS, following proteolysis of Hb with trypsin, Glu-C, or Lys-C. Hb sulfinamide and sulfonamide adducts of ABP were identified in blood of mice exposed to ABP, by Orbitrap MS. This is the first report of the identification of intact Hb sulfinamide adducts of carcinogenic AAs in vivo. The high reactivity of HONH-AαC with HbO2 suggests that the Hb sulfinamide adduct of AαC may be a promising biomarker of exposure to this HAA in humans.
Three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been obtained using comparative molecular field analysis (CoMFA) for a novel series of piperazine-based matrix metalloproteinase inhibitors (MMPIs). The crystal structure of stromelysin-1 (MMP-3) was used to identify regions of the enzyme and inhibitors where steric and electrostatic effects correlate strongly with biological activity. A training set composed of a subset of inhibitors (#10-35), which differed only with regards to the substituent (n-alkyl, amide, carbamide and sulfonamide) on the piperazine distal nitrogen, yielded the most predictive CoMFA model, with r(2) values of 0.592 (cross-validated) and 0.989 (conventional); this model was further validated using test compounds from two inhibitor subsets. Investigation of various ligand conformations, inhibitor subsets, alignment schemes and partial charge formalisms was required to obtain satisfactory models. The greatest success was achieved by incorporating inertial alignment together with manual adjustment of the enzyme-docked inhibitors to ensure complementarity between the inhibitors' substituent conformations and the structural characteristics of the MMP-3 S1-S2' binding pockets. Key insights into the structure-activity relationship (SAR) obtained from this analysis for this inhibitor set are in agreement with experimentally observed data on stromelysin-1 biological activity and binding-site topology. In particular, the present study sheds new light on the steric and electrostatic requirements for ligand binding to the partly solvent-exposed S1-S2' area.
There are many reported examples of small structural modifications to GPCR-targeted ligands leading to major changes in their functional activity, converting agonists into antagonists or vice versa. These shifts in functional activity are often accompanied by negligible changes in binding affinity. The current perspective focuses on outlining and analyzing various approaches that have been used to interconvert GPCR agonists, partial agonists, and antagonists in order to achieve the intended functional activity at a GPCR of therapeutic interest. An improved understanding of specific structural modifications that are likely to alter the functional activity of a GPCR ligand may be of use to researchers designing GPCR-targeted drugs and/or probe compounds, specifically in cases where a particular ligand exhibits good potency but not the preferred functional activity at the GPCR of choice.
Aberrant regulation of cap-dependent translation has been frequently observed in the development of cancer. Association of the cap binding protein eIF4E with N 7 -methylated guanosine capped mRNA is the rate limiting step governing translation initiation; and therefore represents an attractive process for cancer drug discovery. Previously, replacement of the 7-Me group of the Me 7 -guanosine monophosphate with a benzyl group has been found to increase binding affinity to eIF4E. Recent Xray crystallographic studies have revealed that the cap-dependent pocket undergoes a unique structural change in order to accommodate the benzyl group. To explore the structure activity relationships governing the affinity of N 7 -benzylated guanosine monophosphate (Bn 7 -GMP) for eIF4E, we virtually screened a library of 80 Bn 7 -GMP analogs utilizing CombiGlide as implemented in Schrodinger ® . A subset library of substituted Bn 7 -GMP analogs was synthesized and their dissociation constants (K d ) were determined. Due to the poor correlation between docking/scoring results and experimental binding affinities, three-dimensional quantitative structure-activity relationship (3D-QSAR) calculations were performed. Two highly predictive and self-consistent CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis) models were derived and optimized. These models may be useful for the future design of eIF4E cap-binding antagonists.
The secreted anthrax toxin consists of three components: the protective antigen (PA), edema factor (EF) and lethal factor (LF). LF, a zinc metalloproteinase, compromises the host immune system primarily by targeting mitogen-activated protein kinase kinases in macrophages. Peptide substrates and small-molecule inhibitors bind LF in the space between domains 3 and 4 of the hydrolase. Domain 3 is attached on a hinge to domain 2viaresidues Ile300 and Pro385, and can move through an angular arc of greater than 35° in response to the binding of different ligands. Here, multiple LF structures including five new complexes with co-crystallized inhibitors are compared and three frequently populated LF conformational states termed `bioactive', `open' and `tight' are identified. The bioactive position is observed with large substrate peptides and leaves all peptide-recognition subsites open and accessible. The tight state is seen in unliganded and small-molecule complex structures. In this state, domain 3 is clamped over certain substrate subsites, blocking access. The open position appears to be an intermediate state between these extremes and is observed owing to steric constraints imposed by specific bound ligands. The tight conformation may be the lowest-energy conformation among the reported structures, as it is the position observed with no bound ligand, while the open and bioactive conformations are likely to be ligand-induced.
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