A genetic algorithm for structure-based de novo design

Genetic algorithms have properties which make them attractive in de novo drug design. Like other de novo design programs, genetic algorithms require a method to reduce the enormous search space of possible compounds. Most often this is done using information from known ligands. We have developed the ADAPT program, a genetic algorithm which uses molecular interactions evaluated with docking calculations as a fitness function to reduce the search space. ADAPT does not require information about known ligands. The program takes an initial set of compounds and iteratively builds new compounds based on the fitness scores of the previous set of compounds. We describe the particulars of the ADAPT algorithm and its application to three well-studied target systems. We also show that the strategies of enhanced local sampling and re-introducing diversity to the compound population during the design cycle provide better results than conventional genetic algorithm protocols.     

KINETIC STUDIES OF THE TWO LIGHT REACTIONS IN PHOTOSYNTHESIS

Abstract— The decay kinetics of the photo-induced absorbance changes in red and green algae are very sensitive to the wavelength of the actinic light. A four to tenfold increase in half-decay time is noted in going from short wavelength (550–650 mμ) to long wavelength (> 700 mμ) excitation. The slow decay rates produced by long wavelength light can be enhanced with a steady background of short wavelength light. A relationship between initial decay rates and O₂ evolution rates is described. This relationship allows a direct correspondence between these spectroscopic studies and the 'red-drop' and 'enhancement' experiments of Emerson.     

A simple and high‐resolution HPLC‐PDA method for simultaneous quantification of local anesthetics in in vitro buccal permeation enhancement studies

A simple, isocratic, high‐resolution and prompt HPLC‐PDA method was developed and validated for the simultaneous quantification of prilocaine (PCL) and lidocaine (LCL) hydrochlorides in in vitro buccal iontophoresis‐driven permeation studies. A reversed‐phase C₁₈ column (250 mm x 4.6 mm, 3μm, 110Å) was used for the chromatographic separation. The mobile phase contained acetonitrile: 0.1M sodium phosphate buffer, pH 7.0 (1:1, v/v), plus 0.05% (v/v) diethylamine. The isocratic flow rate was set at 1 mL/min and the detection wavelength was 203 nm. PCL and LCL eluted in 8.9 min and 13 min, respectively, and the system suitability parameters varied within an acceptable range. The method was selective, sensitive, precise, accurate and robust, producing a linear plot at the concentration range of 0.25 to 10 µg/mL. The application of this method was demonstrated by a significant enhancement of the permeation of PCL and LCL with the application of iontophoresis (1 mA/cm² per 1 h) through isolated porcine esophageal epithelium. The amount of the drug retained in the epithelium also increased with the application of an electrical current. Copyright © 2015 John Wiley & Sons, Ltd.     

Metal Assisted Synthesis of Cationic Sulfidobismuth Cubanes in Ionic Liquids

Bi₂S₃ was dissolved in the presence of either AuCl/PtCl₂ or AgCl in the ionic liquids [BMIm]Cl ⋅ xAlCl₃ (BMIm=1-n-butyl-3-methylimidazolium; x=4–4.3) through annealing the mixtures at 180 or 200 °C. Upon cooling to room temperature, orange, air-sensitive crystals of [BMIm](Bi₄S₄)[AlCl₄]₅ ( 1 ) or Ag(Bi₇S₈)[S(AlCl₃)₃]₂[AlCl₄]₂ ( 2 ) precipitated, respectively. 1 did not form in the absence of AuCl/PtCl₂, suggesting an essential role of the metal cations. X-ray diffraction on single-crystals of 1 revealed a monoclinic crystal structure that contains (Bi₄S₄)⁴⁺ heterocubanes and [AlCl₄]⁻ tetrahedra as well as [BMIm]⁺ cations. The intercalation of the ionic liquid was confirmed via solid state NMR spectroscopy, revealing unusual coupling behavior. The crystal structure of 2 consists of (Bi₇S₈)⁵⁺ spiro-dicubanes, [S(AlCl₃)₃]²⁻ tetrahedra triples, isolated [AlCl₄]⁻ tetrahedra, and heavily disordered silver(I) cations. No cation ordering took place in 2 upon slow cooling to 100 K.     

Preservation of Immunoreactivity in the Photolabeling of the B72.3 Human Antibody

Abstract— A mild and efficient method of linking a dihydroflavin to the C-17 carboxylic acid side chain of protochlorophyllide, without degradation of the sensitive E ring or loss of magnesium, is described. The appended dihydroflavin was shown to quench the fluorescence of protochlorophyllide. In contrast, a dihydronicotinamide moiety was unable to effect fluorescence quenching. The relevance of these findings to a possible mechanism of action of the enzyme protochlorophyllide reductase is discussed.     

Semi-empirical corrections to the mixing coefficients for the diatomics-in-molecules method

The diatomics-in-molecules (DIM) method requires information about the wavefunction (i.e. mixing coefficients) and the energy of various states of diatomic fragments. We show here that, if the diatomic energy is obtained from experiment, then it is also important to correct the mixing coefficients by making use of experimental atomic state energies. This point is illustrated by application to the OH⁺(³Σ^?) state manifold.     

The Complexed 1,3‐Diphospha‐2‐Arsaallyl Radical and Its Cationic and Anionic Derivatives

Photolysis of [Cp*As{W(CO)₅}₂] ( 1 a ) in the presence of Mes*P?PMes* (Mes*=2,4,6‐tri‐tert‐butylphenyl) leads to the novel 1,3‐diphospha‐2‐arsaallyl radical [(CO)₅W(μ,η²:η¹‐P₂AsMes*₂)W(CO)₄] ( 2 a ). The frontier orbitals of the radical 2 a are indicative of a stable π‐allylic system that is only marginally influenced by the d orbitals of the two tungsten atoms. The SOMO and the corresponding spin density distribution of the radical 2 a show that the unpaired electron is preferentially located at the two equivalent terminal phosphorus atoms, which has been confirmed by EPR spectroscopy. The protonated derivative of 2 a , the complex [(CO)₅W(μ,η²:η¹‐P₂As(H)Mes*₂)W(CO)₄] ( 6 a ) is formed during chromatographic workup, whereas the additional products [Mes*P?PMes*{W(CO)₅}] as the Z‐isomer ( 3 ) and the E‐isomer ( 4 ), and [As₂{W(CO)₅}₃] ( 5 ) are produced as a result of a decomposition reaction of radical 2 a . Reduction of radical 2 a yields the stable anion [(CO)₅W(μ,η²:η¹‐P₂AsMes*₂)W(CO)₄]^? in 7 a , whereas upon oxidation the corresponding cationic complex [(CO)₅W(μ,η²:η¹‐P₂AsMes*₂)W(CO)₄][SbF₆] ( 8 a ) is formed, which is only stable at low temperatures in solution. Compounds 2 a , 7 a , and 8 a represent the hitherto elusive complexed redox congeners of the diphospha‐arsa‐allyl system. The analogous oxidation of the triphosphaallyl radical [(CO)₅W(μ,η²:η¹‐ P₃Mes*₂)W(CO)₄] ( 2 b ) also leads to an allyl cation, which decomposes under CH activation to the phosphine derivative [(CO)₅W{μ,η²:η¹‐P₃(Mes*)(C₅H₂tBu₂C(CH₃)₂CH₂)}W(CO)₄] ( 9 ), in which a CH bond of a methyl group of the Mes* substituent has been activated. All new products have been characterized by NMR spectrometry and IR spectroscopy, and compounds 2 a , 3 , 6 a , 7 a , and 9 by X‐ray diffraction analysis.