The cardiac glycosides ouabain and digitoxin, established Na+/K+ ATPase inhibitors, were found to inhibit MDA-MB-231 breast cancer cell migration through an unbiased chemical genetics screen for cell motility. The Na+/K+ ATPase acts both as an ion-transporter and a receptor for cardiac glycosides. To delineate which function is related to breast cancer cell migration, structure-activity relationship (SAR) profiles of cardiac glycosides were established at the cellular (cell migration inhibition), molecular (Na+/K+ ATPase inhibition), and atomic (computational docking) levels. The SAR of cardiac glycosides and their analogs revealed a similar profile - a decrease in potency when the parent cardiac glycoside structure was modified - for each activity investigated. Since assays were done at the cellular, molecular and atomic levels, correlation of SAR profiles across these multiple assays established links between cellular activity and specific protein-small molecule interactions. The observed antimigratory effects in breast cancer cells are directly related to the inhibition of Na+/K+ transport. Specifically, the orientation of cardiac glycosides at the putative cation permeation path formed by transmembrane helices ?M1-M6 correlates with the Na+ pump activity and cell migration. Other Na+/K+ ATPase inhibitors that are structurally distinct from cardiac glycosides also exhibit antimigratory activity, corroborating the conclusion that the antiport function of Na+/K+ ATPase, and not the receptor function is important for supporting the motility of MDA-MB-231 breast cancer cells. Correlative SAR can establish new relationships between specific biochemical functions and higher-level cellular processes, particularly for proteins with multiple functions and small molecules with unknown or various modes of action.
Collaboration between pharmacists and physicians in the care of patients with chronic kidney disease (CKD) may improve the quality of drug dosage regimens that require adjustment according to the renal function.
Establishing methods to accurately assess and model the binding strength of surfactants around a given-chirality single-walled carbon nanotube (SWNT) are crucial for selective enrichment, targeted functionalization, and spectrally sharp nanodevices. Unlike surfactant exchange, which is subject to interferences from the second surfactant, we herein introduce a thermal dissociation method based on reversible H(+)/O2 doping to determine SWNT/surfactant thermodynamic stability values with greater fidelity. Thermodynamic values were reproduced using molecular mechanics augmented by ab initio calculations in order to better assess ?-? interactions. This afforded detailed quantification of the flavin binding strength in terms of ?-? stacking (55-58%), with the remaining portion roughly split 3:1 between electrostatic plus van der Waals flavin mononucleotide (FMN) interdigitation and H-bonding interactions, respectively. Quasi-epitaxial ?-? alignment between the near-armchair FMN helix and the underlying nanotube lattice plays a crucial role in stabilizing these assemblies. The close resemblance of the thermal dissociation method to helix-coil and ligand-binding transitions of DNA opens up a unique insight into the molecular engineering of self-organizing surfactants around various-chirality nanotubes.
X-ray crystallography has been fundamental in discovering fine structural features of ultrasmall gold clusters capped by thiolated ligands. For still unknown structures, however, new tools capable of providing relevant structural information are sought. We prepared a 25-gold atom nanocluster protected by the smallest ligand ever used, ethanethiol. This cluster displays the electrochemistry, mass spectrometry, and UV-vis absorption spectroscopy features of similar Au25 clusters protected by 18 thiolated ligands. The anionic and the neutral form of Au25(SEt)18 were fully characterized by (1)H and (13)C NMR spectroscopy, which confirmed the monolayer's properties and the paramagnetism of neutral Au25(SEt)18(0). X-ray crystallography analysis of the latter provided the first known structure of a gold cluster protected by a simple, linear alkanethiolate. Here, we also report the direct observation by electron nuclear double resonance (ENDOR) of hyperfine interactions between a surface-delocalized unpaired electron and the gold atoms of a nanocluster. The advantages of knowing the exact molecular structure and having used such a small ligand allowed us to compare the experimental values of hyperfine couplings with DFT calculations unaffected by structure's approximations or omissions.
The first rearrangement of 2-methyleneoxetanes to ?,?-unsaturated methylketones is reported. It is proposed that when these substrates are heated, the corresponding oxetenes are formed and subsequently undergo electrocyclic ring-opening to methyl vinylketones. In particular, ?-silyl-?,?-unsaturated methylketones were isolated in moderate to high yields and with high stereoselectivities. Based on the proposed mechanism, density functional theory explains the differential kinetics and stereoselectivities among substrates.
Au25(SR)18 (R = -CH2-CH2-Ph) is a molecule-like nanocluster displaying distinct electrochemical and optical features. Although it is often taken as an example of a particularly well-understood cluster, very recent literature has provided a quite unclear or even a controversial description of its properties. We prepared monodisperse Au25(SR)18(0) and studied by cyclic voltammetry, under particularly controlled conditions, the kinetics of its reduction or oxidation to a series of charge states, -2, -1, +1, +2, and +3. For each electrode process, we determined the standard heterogeneous electron-transfer (ET) rate constants and the reorganization energies. The latter points to a relatively large inner reorganization. Reduction to form Au25(SR)18(2-) and oxidation to form Au25(SR)18(2+) and Au25(SR)18(3+) are chemically irreversible. The corresponding decay rate constants and lifetimes are incompatible with interpretations of very recent literature reports. The problem of how ET affects the Au25 magnetism was addressed by comparing the continuous-wave electron paramagnetic resonance (cw-EPR) behaviors of radical Au25(SR)18(0) and its oxidation product, Au25(SR)18(+). As opposed to recent experimental and computational results, our study provides compelling evidence that the latter is a diamagnetic species. The DFT-computed optical absorption spectra and density of states of the -1, 0, and +1 charge states nicely reproduced the experimentally estimated dependence of the HOMO-LUMO energy gap on the actual charge carried by the cluster. The conclusions about the magnetism of the 0 and +1 charge states were also reproduced, stressing that the three HOMOs are not virtually degenerate as routinely assumed: In particular, the splitting of the HOMO manifold in the cation species is severe, suggesting that the usefulness of the superatom interpretation is limited. The electrochemical, EPR, and computational results thus provide a self-consistent picture of the properties of Au25(SR)18 as a function of its charge state and may furnish a methodology blueprint for understanding the redox and magnetic behaviors of similar molecule-like gold nanoclusters.
We synthesized two molecular systems, in which an endofullerene C60 , incarcerating one hydrogen molecule (H2 @C60 ) and a nitroxide radical are connected by a folded 310 -helical peptide. The difference between the two molecules is the direction of the peptide orientation. The nuclear spin relaxation rates and the para ? ortho conversion rate of the incarcerated hydrogen molecule were determined by (1) H NMR spectroscopy. The experimental results were analyzed using DFT-optimized molecular models. The relaxation rates and the conversion rates of the two peptides fall in the expected distance range. One of the two peptides is particularly rigid and thus ideal to keep the H2 @C60 /nitroxide separation, r, as large and controlled as possible, which results in particularly low relaxation and conversion rates. Despite the very similar optimized distance, however, the rates measured with the other peptide are considerably higher and thus are compatible with a shorter effective distance. The results strengthen the outcome of previous investigations that while the para ? ortho conversion rates satisfactorily obey the Wigners theory, the nuclear spin relaxation rates are in excellent agreement with the Solomon-Bloembergen equation predicting a 1/r(6) dependence.
A number of novel fused thiophene derivatives have been prepared and identified as potent inhibitors of MEK. The SAR data of selected examples and the in vivo profiling of compound 13 h demonstrates the functional activity of this class of compounds in HT-29 PK/PD models.
Monodisperse Au(25)L(18)(0) (L = S(CH(2))(2)Ph) and [n-Oct(4)N(+)][Au(25)L(18)(-)] clusters were synthesized in tetrahydrofuran. An original strategy was then devised to oxidize them: in the presence of bis(pentafluorobenzoyl) peroxide, the neutral or the negatively charged clusters react as efficient electron donors in a dissociative electron-transfer (ET) process, in the former case yielding [Au(25)L(18)(+)][C(6)F(5)CO(2)(-)]. As opposed to other reported redox methods, this dissociative ET approach is irreversible, easily controllable, and clean, particularly for NMR purposes, as no hydrogen atoms are introduced. By using this approach, the -1, 0, and +1 charge states of Au(25)L(18) could be fully characterized by (1)H and (13)C NMR spectroscopy, using one- and two-dimensional techniques, in various solvents, and as a function of temperature. For all charge states, the NMR results and analysis nicely match recent structural findings about the presence of two different ligand populations in the capping monolayer, each resonance of the two ligand families displaying distinct NMR patterns. The radical nature of Au(25)L(18)(0) is particularly evident in the (1)H and (13)C NMR patterns of the inner ligands. The NMR behavior of radical Au(25)L(18)(0) was also simulated by DFT calculations, and the interplay between theory and experiments revealed a fundamental paramagnetic contribution coming from Fermi contact shifts. Interestingly, the NMR patterns of Au(25)L(18)(-) and Au(25)L(18)(+) were found to be quite similar, pointing to the latter cluster form as a diamagnetic species.
Raf kinase inhibitor protein (RKIP) interacts with a number of different proteins and regulates multiple signaling pathways. Here, we show that locostatin, a small molecule that covalently binds RKIP, not only disrupts interactions of RKIP with Raf-1 kinase, but also with G protein-coupled receptor kinase 2. In contrast, we found that locostatin does not disrupt binding of RKIP to two other proteins: inhibitor of ?B kinase ? and transforming growth factor ?-activated kinase 1. These results thus imply that different proteins interact with different regions of RKIP. Locostatins mechanism of action involves modification of a nucleophilic residue on RKIP. We observed that after binding RKIP, part of locostatin is slowly hydrolyzed, leaving a smaller RKIP-butyrate adduct. We identified the residue alkylated by locostatin as His86, a highly conserved residue in RKIPs ligand-binding pocket. Computational modeling of the binding of locostatin to RKIP suggested that the recognition interaction between small molecule and protein ensures that locostatins electrophilic site is poised to react with His86. Furthermore, binding of locostatin would sterically hinder binding of other ligands in the pocket. These data provide a basis for understanding how locostatin disrupts particular interactions of RKIP with RKIP-binding proteins and demonstrate its utility as a probe of specific RKIP interactions and functions.
Modeling chemical events inside proteins often require the incorporation of solvent effects via continuum polarizable models. One of these approaches is based on the assumption that the interface between solute and solvent acts as a conductor. Image charges are added on the molecular surface to satisfy the appropriate conductor boundary conditions in the presence of solute charges. As in the case of other polarizable continuum models that are based on surface tessellation, the simplest implementation of this approach is often limited to several hundred atoms due to a matrix inversion, which scales as the cube of the number or tesserae. For larger systems, approaches that use iterative matrix solvers coupled to fast summation methods must be used. In the present work, we develop a self-consistent approach to obtain conductor-like screening charges suitable for applications in proteins. The approach is based on a density fragmentation of a graphical surface tessellation. This method, although approximate, provides a straightforward scheme of parallelization, which can in principle be added to existing linear scaling implementations of conductor-like models. We implement this method in conjunction with a fixed charge model for the protein, as well as with a moving domain QM/MM description of the protein. In the latter case, the overall result leads to a charge distribution within the protein determined by self-polarization and polarization due to solvent.
Structure-energy relationships for a small group of pyranose and septanose mono-saccharide ligands are developed for binding to Concanavalin A (ConA). The affinity of ConA for methyl "manno"?-septanoside 7 was found to be higher than any of the previously reported mono-septanoside ligands. Isothermal titration calorimetry (ITC) in conjunction with docking simulations and quantum mechanics/molecular mechanics (QM/MM) modeling established the specific role of binding enthalpy in the structure-energy relations of ConA bound to natural mono-saccharides and unnatural mono-septanosides. An important aspect in the differential binding among ligands is the deformation energy required to reorganize internal hydroxyl groups upon binding of the ligand to ConA.
An unanticipated cleavage of 2-azido-2-(hydroxymethyl)oxetanes is reported. In attempts to oxidize the title oxetanyl alcohols to the corresponding carboxylic acids with RuO4, cleaved nitriles were formed as the sole isolable products, while a closely related tetrahydrofuran gave solely the expected carboxylic acid. Quantum chemical calculations suggest that the divergent outcomes are governed by conformational differences in the azidoalcohols.
Azobenzene undergoes reversible cis<-->trans photoisomerization upon irradiation. Substituents often change the isomerization behavior of azobenzene, but not always in a predictive manner. The synthesis and properties of three azobenzene derivatives, AzoAMP-1, -2, and -3, are reported. AzoAMP-1 (2,2-bis[N-(2-pyridyl)methyl]diaminoazobenzene), which possesses two aminomethylpyridine groups ortho to the azo group, exhibits minimal trans-->cis photoisomerization and extremely rapid cis-->trans thermal recovery. AzoAMP-1 adopts a planar conformation in the solid state and is much more emissive (Phi(fl) = 0.003) than azobenzene when frozen in a matrix of 1:1 diethylether/ethanol at 77 K. Two strong intramolecular hydrogen bonds between anilino protons and pyridyl and azo nitrogen atoms are responsible for these unusual properties. Computational data predict AzoAMP-1 should not isomerize following S(2)<--S(0) excitation because of the presence of an energy barrier in the S(1) state. When potential energy curves are recalculated with methyl groups in place of anilino protons, the barrier to isomerization disappears. The dimethylated analogue AzoAMP-2 was independently synthesized, and the photoisomerization predicted by calculations was confirmed experimentally. AzoAMP-2, when irradiated at 460 nm, photoisomerizes with a quantum yield of 0.19 and has a much slower rate of thermal isomerization back to the trans form compared to that of AzoAMP-1. Its emission intensity at 77 K is comparable to that of azobenzene. Confirmation that the AzoAMP-1 and -2 retain excited state photochemistry analogous to azobenzene was provided by ultrafast transient absorption spectroscopy of both compounds in the visible spectral region. The isomerization of azobenzene occurs via a concerted inversion mechanism where both aryl rings must adopt a collinear arrangement prior to inversion. The hydrogen bonding in AzoAMP-1 prevents both aryl rings from adopting this conformation. To further probe the mechanism of isomerization, AzoAMP-3, which has only one anilinomethylpyridine substituent for hydrogen bonding, was prepared and characterized. AzoAMP-3 does not isomerize and exhibits emission (Phi(fl) = 0.0008) at 77 K. The hydrogen bonding motif in AzoAMP-1 and AzoAMP-3 provides the first example where inhibiting the concerted inversion pathway in an azobenzene prevents isomerization. These molecules provide important supporting evidence for the spectroscopic and computational studies aimed at elucidating the isomerization mechanism in azobenzene.
Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids). These methods are highly efficient, since they implement quantum chemistry techniques for modeling only the small part of the system (QM layer) that undergoes chemical modifications, charge transfer, etc., under the influence of the surrounding environment. The rest of the system (MM layer) is described in terms of molecular mechanics force fields, assuming that its influence on the QM layer can be roughly decomposed in terms of electrostatic interactions and steric hindrance. Common limitations of QM/MM methods include inaccuracies in the MM force fields, when polarization effects are not explicitly considered, and the approximate treatment of electrostatic interactions at the boundaries between QM and MM layers. This article reviews recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in extended systems beyond the common limitations of QM/MM hybrid methods. We focus on the moving-domain QM/MM (MoD-QM/MM) methodology that partitions the system into many molecular domains and obtains the electrostatic and structural properties of the whole system from an iterative self-consistent treatment of the constituent molecular fragments. We illustrate the MoD-QM/MM method as applied to the description of photosystem II as well as in conjunction with the application of spectroscopically constrained QM/MM optimization methods, based on high-resolution spectroscopic data (extended X-ray absorption fine structure spectra, and exchange coupling constants).
A series of 4-azaindole inhibitors of c-Met kinase is described. The postulated binding mode was confirmed by an X-ray crystal structure and series optimisation was performed on the basis of this structure. Future directions for series development are discussed.
A series of quinoxaline inhibitors of c-Met kinase is described. The postulated binding mode was confirmed by an X-ray crystal structure and optimisation of the series was performed on the basis of this structure. Future directions for development of the series are discussed together with the identification of a novel quinoline scaffold.
8,5-Cyclopurine deoxynucleosides are unique tandem lesions containing an additional covalent bond between the base and the sugar. These mutagenic and genotoxic lesions are repaired only by nucleotide excision repair. The N-glycosidic (or C1-N9) bond of 2-deoxyguanosine (dG) derivatives is usually susceptible to acid hydrolysis, but even after cleavage of this bond of the cyclopurine lesions, the base would remain attached to the sugar. Here, the stability of the N-glycosidic bond and the products formed by formic acid hydrolysis of (5S)-8,5-cyclo-2-deoxyguanosine (S-cdG) were investigated. For comparison, the stability of the N-glycosidic bond of 8,5-cyclo-2,5-dideoxyguanosine (ddcdG), 8-methyl-2-deoxyguanosine (8-Me-dG), 7,8-dihydro-8-oxo-2-deoxyguanosine (8-Oxo-dG), and dG was also studied. In various acid conditions, S-cdG and ddcdG exhibited similar stability to hydrolysis. Likewise, 8-Me-dG and dG showed comparable stability, but the half-lives of the cyclic dG lesions were at least 5-fold higher than those of dG or 8-Me-dG. NMR studies were carried out to investigate the products formed after the cleavage of the C1-N9 bond. 2-Deoxyribose generated ? and ? anomers of deoxyribopyranose and deoxyribopyranose oligomers following acid treatment. S-cdG gave ?- and ?-deoxyribopyranose linked guanine as the major products, but ? and ? anomers of deoxyribofuranose linked guanine and other products were also detected. The N-glycosidic bond of 8-Oxo-dG was found exceptionally stable in acid. Computational studies determined that both the protonation of the N7 atom and the rate constant in the bond breaking step control the overall kinetics of hydrolysis, but both varied for the molecules studied indicating a delicate balance between the two steps. Nevertheless, the computational approach successfully predicted the trend observed experimentally. For 8-Oxo-dG, the low pK(a) of O(8) and N3 prevented appreciable protonation, making the free energy for N-glycosidic bond cleavage in the subsequent step very high.
In order to truly unlock advanced applications of single-walled carbon nanotubes (SWNTs), one needs to separate them according to both chirality and handedness. Here we show that the chiral D-ribityl phosphate chain of flavin mononucleotide (FMN) induces a right-handed helix that enriches the left-handed SWNTs for all suspended (n,m) species. Such enantioselectivity stems from the sp(3) hybridization of the N atom anchoring the sugar moiety to the flavin ring. This produces two FMN conformations (syn and anti) analogous to DNA. Electrostatic interactions between the neighboring uracil moiety and the 2-OH group of the side chain provide greater stability to the anti-FMN conformation that leads to a right-handed FMN helix. The right-handed twist that the FMN helix imposes to the underlying nanotube, similar to "Indian burn", causes diameter dilation of only the left-handed SWNTs, whose improved intermolecular interactions with the overlaying FMN helix, impart enantioselection.
The present work is aimed to provide detail on the binding process between Raf kinase inhibitor protein (RKIP) and locostatin, the only exogenous compound known to alter the function of RKIP. Understanding the basis of RKIP inhibition for use in pharmacological applications is of considerable interest, as dysregulated RKIP expression has the potential to contribute to pathophysiological processes. Herein, we report a series of atomistic models to describe the protein-ligand recognition step and the subsequent reactivity steps. Modeling approaches include ligand docking, molecular dynamics, and quantum mechanics/molecular mechanics calculations. We expect that such a computational assay will serve to study similar complexes in which potency is associated with recognition and reactivity. Although previous data suggested a single amino acid residue (His86) to be involved in the binding of locostatin, the actual ligand conformation and the steps involved in the reactivity process remain elusive from a detailed atomistic description. We show that the first reaction step, consisting of a nucleophilic attack of the nitrogen (N?) of His86 at the sp(2)-hybridized carbon (C2) of locostatin, presents a late transition state (almost identical to the product). The reaction is followed by a hydrogen abstraction and hydrolysis. The theoretically predicted overall rate constant (6 M(-1) s(-1)) is in a very good agreement with the experimentally determined rate constant (13 M(-1) s(-1)).
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