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The synthesis and biological annotation of small molecules from underexplored chemical space will play a central role in the development of drugs for challenging targets currently being identified in frontier areas of biological research such as human genetics. 相似文献
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《Cell cycle (Georgetown, Tex.)》2013,12(18)
Comment on: Trego KS, et al. Cell Cycle 2011; 10:1998-2007. 相似文献
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Grossman R Kasturi P Hamelberg D Liu B 《Journal of bioinformatics and computational biology》2004,2(1):155-171
In this paper, we introduce an algorithm that assigns an essentially unique key called the Universal Chemical Key (UCK) to molecular structures. The molecular structures are represented as labeled graphs whose nodes abstract atoms and whose edges abstract bonds. The algorithm was tested on 236,917 compounds obtained from the National Cancer Institute (NCI) database of chemical compounds. On this database, the UCK algorithm assigned unique keys for chemicals with distinct molecular structures. 相似文献
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Molecular dynamics simulations of triclinic hen egg white lysozyme in aqueous solution were performed to calculate the intrinsic pKas of 14 ionizable residues. An all-atom model was used for both solvent and solute, and a single 180 ps simulation in conjunction with a Gaussian fluctuation analysis method was used. An advantage of the Gaussian fluctuation method is that it only requires a single simulation of the system in a reference state to calculate all the pKas in the protein, in contrast to multiple simulations for the free energy perturbation method. pKint shifts with respect to reference titratable residues were evaluated and compared to results obtained using a finite difference Poisson-Boltzmann (FDPB) method with a continuum solvent model; overall agreement with the direction of the shifts was generally observed, though the magnitude of the shifts was typically larger with the explicit solvent model. The contribution of the first solvation shell to the total charging free energies of the titratable groups was explicitly evaluated and found to be significant. Dielectric shielding between pairs of titratable groups was examined and found to be smaller than expected. The effect of the approximations used to treat the long-range interactions on the pKint shifts is discussed. © 1994 Wiley-Liss, Inc. 相似文献
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Just as complex electronic circuits are built from simple Boolean gates, diverse biological functions, including signal transduction, differentiation, and stress response, frequently use biochemical switches as a functional module. A relatively small number of such switches have been described in the literature, and these exhibit considerable diversity in chemical topology. We asked if biochemical switches are indeed rare and if there are common chemical motifs and family relationships among such switches. We performed a systematic exploration of chemical reaction space by generating all possible stoichiometrically valid chemical configurations up to 3 molecules and 6 reactions and up to 4 molecules and 3 reactions. We used Monte Carlo sampling of parameter space for each such configuration to generate specific models and checked each model for switching properties. We found nearly 4,500 reaction topologies, or about 10% of our tested configurations, that demonstrate switching behavior. Commonly accepted topological features such as feedback were poor predictors of bistability, and we identified new reaction motifs that were likely to be found in switches. Furthermore, the discovered switches were related in that most of the larger configurations were derived from smaller ones by addition of one or more reactions. To explore even larger configurations, we developed two tools: the “bistabilizer,” which converts almost-bistable systems into bistable ones, and frequent motif mining, which helps rank untested configurations. Both of these tools increased the coverage of our library of bistable systems. Thus, our systematic exploration of chemical reaction space has produced a valuable resource for investigating the key signaling motif of bistability. 相似文献
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Macromolecular interactions (i.e. protein-protein or DNA/RNA-protein interactions) play important cellular roles, including cellular communication and programmed cell death. Small-molecule chemical probes are crucial for dissecting these highly organized interactions, for mapping their function at the molecular level and developing new therapeutics. The lack of ideal chemical probes required to understand macromolecular interactions is the missing link in the next step of dissecting such interactions. Unfortunately, the classical combinatorial-chemistry community has not successfully provided the required probes (i.e. natural product inspired chemical probes that are rich in stereochemical and three-dimensional structural diversity) to achieve these goals. The emerging area of diversity-oriented synthesis (DOS) is beginning to provide natural product-like chemical probes that may be useful in this arena. 相似文献
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Nature represents a vast source of chemical diversity, which is supposed to cover broader areas of chemical space than synthetically obtained substances typical of medicinal chemistry. With regard to drug discovery from nature, the terrestrial environment has been the most and longest studied source, while the investigation of compounds produced by marine organisms is still in its infancy. With the objective of demonstrating the enormous chemical diversity of nature, in particular that of the marine environment, we used the chemical space navigation tool ChemGPS-NP to compare sets of marine, terrestrial and synthetic compounds with respect to physico-chemical properties and their occupation of the biologically relevant chemical space. Despite considerable overlap, the three datasets clearly differ from each other by occupying and extending into different, specific, regions in chemical space. Synthetic compounds are e.g. comparably small, with some of them being highly flexible, while marine and terrestrial products are larger and characterised by higher and lower molecular flexibility, respectively, with increasing size. Moreover, the three datasets differ to some degree in polarity, aromaticity and heteroatom content. Taken together, ChemGPS-NP has been proven to be a useful tool for navigating large volumes of biologically relevant chemical space. In this study we demonstrated the chemical uniqueness and differences of large sets of natural products, with particular emphasis on marine substances. The hence de-veiled differences further underline the relevance of natural products, of both marine and terrester origin, for future drug discovery. 相似文献
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pH dependence of amide chemical shifts in natively disordered polypeptides detects medium-range interactions with ionizable residues
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A growing number of natively disordered proteins undergo a folding/binding process that is essential for their biological function. An interesting question is whether these proteins have incompletely solvated regions that drive the folding/binding process. Although the presence of predominantly hydrophobic buried regions can be easily ascertained by high-sensitivity differential scanning calorimetry analysis, the identification of those residues implicated in the burial requires NMR analysis. We have selected a partially solvated natively disordered fragment of Escherichia coli, thioredoxin, C37 (38-108), for full NMR spectral assignment. The secondary chemical shifts, temperature coefficients, and relaxation rates (R(1) and R(2)) of this fragment indicate the presence of a flexible backbone without a stable hydrogen bond network near neutral pH. (1)H-(15)N heteronuclear single quantum coherence analysis of the pH dependence of amide chemical shifts in fragment C37 within pH 2.0 and 7.0 suggests the presence of interactions between nonionizable residues and the carboxylate groups of four Asp and four Glu residues. The pH midpoints (pH(m)) of the amides in the ionizable residues (Asp or Glu) and, consequently, the shifts in the pH(m) (DeltapH(m)) of these residues with respect to model tetrapeptides, are sequence-dependent; and the nonionizable residues that show pH dependence cluster around the ionizable ones. The same pH dependence has been observed in two fragments: M37 (38-73) and C73 (74-108), ruling out the participation of long-range interactions. Our studies indicate the presence of a 15-residue pH-dependent segment with the highest density of ionizable sites in the disordered ensembles of fragments C37 and M37. The observed correlations between ionizable and nonionizable residues in this segment suggest the organization of the backbone and side chains through local and medium-range interactions up to nine residues apart, in contrast to only a few interactions in fragment C73. These results agree qualitatively with the predominantly hydrophobic buried surface detected only in fragments C37 and M37 by highly sensitive differential scanning calorimetry analysis. This work offers a sensitive and rapid new tool to obtain clues about local and nonlocal interactions between ionizable and nonionizable residues in the growing family of natively disordered small proteins with full NMR assignments. 相似文献
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It is demonstrated that complexation between the ferric cation and the Z-chalcone of the naturally occurring anthocyanin malvin takes place in acidic aqueous solutions. The flexible open cavity of the Z-chalcone best fits the steric and electronic requirements of the ferric ion in water. 相似文献
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R. L. Braam R. J. Walhout W. Jaarsma H. W. van Es B. J. Rensing 《Netherlands heart journal》2008,16(4):137-138
A 70-year-old man presented to the urology department because of haematuria. Computed tomography performed to visualise the kidneys unexpectedly revealed an abnormal aspect of the lateral wall of the left ventricle (LV) (figure 1). He was subsequently referred to our cardiology department. He had suffered from an inferior wall myocardial infarction 21 years earlier. Coronary artery bypass grafting was performed six years later using two venous grafts and the left internal mammary artery. Afterwards the patient was in an excellent clinical condition. He denied having had any cardiac symptoms during his visits to the outpatient clinic. Physical examination revealed no abnormalities. 相似文献
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Some aspects of the strategy of initial search of biologically active compounds at mass tests of chemical compounds have been discussed. Different approaches to pre-experimental estimation of biological activity using mathematical statistics and computer analysis have been analysed. 相似文献
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In routine guaiacol assays for thyroid peroxidase and lactoperoxidase employing a newly purchased bottle of guaiacol from Aldrich Chemical Co., we were surprised to find the formation of a blue color instead of the expected amber color classically associated with this assay. This was observed also with horseradish, myelo-, and cytochrome c peroxidase. The blue color (Amax approximately 650 nm) was not formed with guaiacol reagents obtained from two other chemical companies, nor was it seen with a bottle of old Aldrich guaiacol that had been in use in the laboratory for more than 10 years. In the present investigation we provide evidence that formation of the blue color is closely associated with the presence of a low concentration of catechol (approximately 0.5 mol%) in the new Aldrich guaiacol reagent. Catechol itself, even in much higher concentration, is a very weak donor for peroxidase, forming a light pink color. The blue color in Aldrich new guaiacol is not formed to the exclusion of 470-nm-absorbing product(s). Formation of the latter is, however, inhibited, and use of Aldrich new guaiacol for assay leads to low values for peroxidase activity. Other dihydroxyphenols (resorcinol and hydroquinone) do not mimic the action of catechol in formation of the blue color. Resorcinol is a very potent inhibitor of peroxidation of guaiacol. Possible schemes are proposed for formation of the products that may be associated with the amber and blue colors. 相似文献
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