Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site

Eg5, a mitotic kinesin exclusively involved in the formation and function of the mitotic spindle has attracted interest as an anticancer drug target. Eg5 is co-crystallized with several inhibitors bound to its allosteric binding pocket. Each of these occupies a pocket formed by loop 5/helix α2 (L5/α2). Recently designed inhibitors additionally occupy a hydrophobic pocket of this site. The goal of the present study was to explore this hydrophobic pocket with our MED-SuMo fragment-based protocol, and thus discover novel chemical structures that might bind as inhibitors. The MED-SuMo software is able to compare and superimpose similar interaction surfaces upon the whole protein data bank (PDB). In a fragment-based protocol, MED-SuMo retrieves MED-Portions that encode protein-fragment binding sites and are derived from cross-mining protein-ligand structures with libraries of small molecules. Furthermore we have excluded intra-family MED-Portions derived from Eg5 ligands that occupy the hydrophobic pocket and predicted new potential ligands by hybridization that would fill simultaneously both pockets. Some of the latter having original scaffolds and substituents in the hydrophobic pocket are identified in libraries of synthetically accessible molecules by the MED-Search software. Ksenia Oguievetskaia and Laetitia Martin-Chanas contributed equally to this work.     

Transmission of polar substituent effects across the cubane ring system: 19F substituent chemical shifts (SCS) of 4‐substituted (X) cub‐1‐yl fluorides revisited

¹⁹F NMR shieldings of 4‐substituted (X) cub‐1‐yl fluorides ( 4 ) for a set of substituents (X?H, NO₂, CN, NC, CF₃, COOH, F, Cl, HO, NH₂, CH₃, Si(CH₃)₃, Li, O^? and NH) covering a wide range of electronic substituent effects were calculated using the DFT‐GIAO theoretical model. The level of theory, B3LYP/6‐311+G(2d,p), provided ¹⁹F substituent chemical shifts (SCS) in good agreement with experimental values where known. By means of NBO analysis, various molecular parameters were obtained from the optimized geometries. Linear regression analysis was employed to explore the relationship between the calculated ¹⁹F SCS and polar field, resonance and group electronegativity substituent constants (σ_F, σ_R and σ_x, respectively) and also the NBO derived molecular parameters (fluorine natural charges (Q_n), electron occupancies on fluorine of lone pairs (n_F) and occupation number of the C? F antibonding orbital (σ_CF*)). The key determining parameters appear to be n_F and σ_CF*(occup). Both factors are a function of the electrostatic field influence of the substituent (σ_F effect) but are counteractive in their influence on the shifts. No evidence for a significant resonance effect influence on the shifts could be identified. Copyright © 2009 John Wiley & Sons, Ltd.     

Transmission of polar substituent effects in bicycloalkane systems as probed by fluorine-19 nuclear magnetic resonance

The results of a correlative analysis indicate that the ¹⁹F substituent chemical shifts (SCS) of 4-substituted bicyclo[2.2.1]hept-1-y1 fluorides are essentially a manifestation of electronegativity effects which are $\text{opposite}$ in sign to those previously disclosed for the corresponding 4-substituted bicyclo[2.2.2]oct-1-y1 fluorides.     

Peptide backbone reconstruction using dead-end elimination and a knowledge-based forcefield

A novel, yet simple and automated, protocol for reconstruction of complete peptide backbones from C(alpha) coordinates only is described, validated, and benchmarked. The described method collates a set of possible backbone conformations for each set of residue triads from a structural library derived from the PDB. The optimal permutation of these three residue segments of backbone conformations is determined using the dead-end elimination (DEE) algorithm. Putative conformations are evaluated using a pairwise-additive knowledge-based forcefield term and a fragment overlap term. The protocol described in this report is able to restore the full backbone coordinates to within 0.2-0.6 A of the actual crystal structure from C(alpha) coordinates only. In addition, it is insensitive to errors in the input C(alpha) coordinates with RMSDs of 3.0 A, and this is illustrated through application to deliberately distorted C(alpha) traces. The entire process, as described, is rapid, requiring of the order of a few minutes for a typical protein on a typical desktop PC. Approximations enable this to be reduced to a few seconds, although this is at the expense of prediction accuracy. This compares very favorably to previously published methods, being sufficiently fast for general use and being one of the most accurate methods. Because the method is not restricted to the reconstruction from only C(alpha) coordinates, reconstruction based on C(beta) coordinates is also demonstrated.     

Some group IVB derivatives of 1,6-methano[10]annulene. Synthesis, substituent effects and reactivity

Certain Group IVB derivatives of 1,6-methano[10]annulene have been synthesised, and their ¹³C nuclear magnetic resonance spectra recorded and assigned, to provide a measure of the substituent effects exerted by metalloid-containing groups in this non-benzenoid aromatic system. Comparisons are made with the corresponding naphthalene and some anthracene derivatives. Protiodemetallations of a number of arylsilanes and -stannanes have been examined, and in protiodestannylation by CH₃CO₂H/dioxane at 27°C (an electrophilic aromatic substitution) the - (or 2-) position of 1,6-methano[10]annulene is ca. 35 times as reactive as the (or 1-) position of naphthalene, whereas in protiodesilylation by CF₃CO₂H/CH₃CO₂H at 27°C it is ca. 700 times the more reactive.     

Determination of glyphosate mono-isopropylamine salt in process samples using flow injection analysis with tris(2,2'-bipyridyl)ruthenium(II) chemiluminescence detection

The mono-isopropylamine salt of glyphosate was selectively determined directly in industrial and commercial formulations using flow injection analysis with tris(2,2′-bipyridyl)ruthenium(II) chemiluminescence detection without the need for separation. Glyphosate and its mono-isopropylamine salt furnished detection limits of 7×10⁻⁹ and 3.5×10⁻¹⁰ M and relative standard deviations of 0.4% at 1×10⁻⁷ M and 0.8% at 5×10⁻⁸ M, respectively. The methodology is robust and reliable with samples subjected only to aqueous dilution prior to analysis.     

Nucleophilic substitution at the bridgehead of 1,4-dihalobicyclo[2.2.2]octanes : An abnormal leaving group mobility order

Stannylation of 1-bromo- and 1-chloro-4-iodobicyclo[2.2.2]octane with (trimethyltin) lithium indicate an abnormal leaving group mobility (Br>I>Cl).