Prediction of the binding site of 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine in acetylcholinesterase by docking studies with the SYSDOC program

Summary In the preceding paper we reported on a docking study with the SYSDOC program for predicting the binding sites of huperzine A in acetylcholinesterase (AChE) [Pang, Y.-P. and Kozikowski, A.P., J. Comput.-Aided Mol. Design, 8 (1994) 669]. Here we present a prediction of the binding sites of 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine (E2020) in AChE by the same method. E2020 is one of the most potent and selective reversible inhibitors of AChE, and this molecule has puzzled researchers, partly due to its flexible structure, in understanding how it binds to AChE. Based on the results of docking 1320 different conformers of E2020 into 69 different conformers of AChE and on the pharmacological data reported for E2020 and its analogs, we predict that both the R- and the S-isomer of E2020 span the whole binding cavity of AChE, with the ammonium group interacting mainly with Trp⁸⁴, Phe³³⁰ and Asp⁷², the phenyl group interacting mainly with Trp⁸⁴ and Phe³³⁰, and the indanone moiety interacting mainly with Tyr⁷⁰ and Trp²⁷⁹. The topography of the calculated E2020 binding sites provides insights into understanding the high potency of E2020 in the inhibition of AChE and provides hints as to possible structural modifications for identifying improved AChE inhibitors as potential therapeutics for the palliative treatment of Alzheimer's disease.     

Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics,thrombin and thermolysin inhibitors

Summary A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.     

Small molecules as inhibitors of cyclin-dependent kinases

Cell division (mitosis) is one of the basic requirements for multicellular oranisms. The capability of a cell to replicate enables a complex assembly to be created. Faulty regulation of the control mechanism in the cell cycle leads to an excessive cell proliferation and is the cause of cancer. The key position of the cyclin-dependent kinases (CDKs) and their direct partners, as well as the fact that the majority of malign illnesses show defects in at least one of these key players of the cell cycle, is of great interest for the development of low-molecular-weight CDK inhibitors. In this Review an overview of the different structural classes of ATP-competitive inhibitors of CDKs are given, whose devlopment was aimed at battling cancer. The Review shows how far the development of selective CDK inhibitors has progressed and to what extent the expectations for such drugs have so far been fulfilled.     

1H and 13C NMR characterization of hemiamidal isoniazid-NAD(H) adducts as possible inhibitors of InhA reductase of Mycobacterium tuberculosis

Isoniazid (INH) is easily oxidized with manganese(III) pyrophosphate, a chemical model of the KatG protein involved in activation of INH inside the bacteria Mycobacterium tuberculosis. Performed in the presence of NAD(+), this oxidation generates a family of isomeric INH-NAD(H) adducts, which have been shown to be effective inhibitors of InhA, an enzyme essential in mycolic acid biosynthesis. In this work, we fully characterized by (1)H and (13)C NMR spectroscopy four main species of INH-NAD(H) adducts that coexist in solution. Two of them are open diastereoisomers consisting of the covalent attachment of the isonicotinoyl radical at position four of the nicotinamide coenzyme. The other two result from a cyclization involving the amide group from the nicotinamide and the carbonyl group from the isonicotinoyl radical to give diastereoisomeric hemiamidals. Although an INH-NAD(H) adduct with a 4S configuration has been characterized within the active site of InhA from Xray crystallography and this bound adduct interpreted as an open form (Rozwarski et al., Science 1998, 279, 98-102), it is legitimate to raise the question about the effective active form(s), open or cyclic, of INH-NAD(H) adduct(s). Is there a single active form or are several forms able to inhibit the InhA activity with different levels of inhibitory potency?     

Synthesis and characterization of Cu,Ni and Zn binding capability of some amino- and imidazole hydroxamic acids: Effects of substitution of side chain amino-N for imidazole-N or hydroxamic-N-H for -N-CH3 on metal complexation

Solution equilibrium studies on Cu(II)-, Ni(II)- and Zn(II)-N-Me-β-Alaninehydroxamic acid (N-Me-β-Alaha), -N-Me-α-alaninehydroxamic acid (N-Me-α-Alaha), -Imidazole-4-carbohydroxamic acid (Im-4-Cha), -N-Me-imidazole-4-carbohydroxamic acid (N-Me-Im-4-Cha) and -Imidazole-4-acetohydroxamic acid (Im-4-Aha) systems have been performed by pH-potentiometry, UV–Vis spectrophotometry, EPR, CD, ESI-MS and ¹H NMR methods. According to the results: (i) the amino-N atoms are more basic in N-Me-α-Alaha and N-Me-β-Alaha than the hydroxamate function, but the trend is just the opposite between the imidazole-N(3) and hydroxamate. (ii) The metal ion anchor is always the hydroxamate part in the amino acid derivatives, while it is always the imidazole-N(3) in the studied imidazolehydroxamic acids. (iii) The three studied N-Me derivatives do not form metallacrowns. Only hydroxamate type chelate is formed with N-Me-β-Alaha, but with N-Me-α-Alaha a new type of coordination mode (via amino-N and hydroxamate-O) also exists. N-Me-Im-4-Cha also forms a dinuclear complex, [M₂L₃], with Cu(II) and Ni(II) (but not with Zn(II)). In this complex, one of the three ligands might bridge the two metal ions (five-membered hydroxamate-(O,O) plus five-membered (N_im, O_carb) bridging bis-chelating mode), while each of the additional two ligands binds to one metal. (iv) The two studied N–H derivatives, having dissociable proton on the hydroxamic-N, are able to form metallacrown species. A pentanuclear complex, [M₅L₄H₋₄], is exclusively formed above pH 4 between Cu(II) and Im-4-Aha. Interestingly, this 12-metallacrown-4 type complex, although together with various mononuclear binding isomers, appears also with Ni(II) and Zn(II). Unfortunately, the complexes of Im-4-Cha are not soluble in water at physiological pH at all.     

Rapid quantification of HIV protease inhibitors in human plasma by high-performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry

HIV protease inhibitors are important antiretroviral drugs which have substantially reduced the morbidity and mortality associated with HIV-1 infection. Recent data have shown relationships between plasma concentrations of the protease inhibitors and clinical response, which makes therapeutic drug monitoring valuable. We have developed and validated an assay, using liquid chromatography coupled with electrospray tandem mass spectrometry (LC/MS/MS), for the routine quantification of the six licensed protease inhibitors (amprenavir, indinavir, lopinavir, nelfinavir, ritonavir and saquinavir) and the pharmacologically active nelfinavir metabolite M8 in plasma. The sample pretreatment consisted of protein precipitation with a mixture of methanol and acetronitrile using only 100 microl of plasma. Chromatographic separation was performed on an Inertsil ODS3 column (50 x 2.0 mm i.d., particle size 5 microm), with a quick stepwise gradient using an acetate buffer (pH 5) and methanol, at a flow rate of 0.5 ml min(-1). The analytical run time was 5.5 min. The use of a 96-well plate autosampler allowed batch sizes up to 150 patient samples. The triple-quadrupole mass spectrometer was operated in the positive ion mode and multiple reaction monitoring was used for drug quantification. The method was validated over the concentration ranges 0.01-10 microg ml(-1) for indinavir and saquinavir, 0.1-10 microg ml(-1) for amprenavir, 0.05-10 microg ml(-1) for nelfinavir and ritonavir, 0.1-20 microg ml(-1) for lopinavir and 0.01-5 microg ml(-1) for M8. Saquinavir-d(5) and indinavir-d(6) were used as internal standards. The coefficients of variation were always <10% for both intra-day and inter-day precisions for each compound. Mean accuracies were also between the designated limits (+/-15%). The validated concentration ranges proved to be adequate in daily practice. This robust and fast LC/MS/MS assay is now successfully applied for routine therapeutic drug monitoring and pharmacokinetic studies in our hospital.     

西印度蔗螟聚集信息素次要组份合成方法的改进

2-甲基-4-庚醇和2-甲基-4-辛醇是西印度蔗螟(Metamasiushemipterus)聚集信息素的次要组份，本文以天然产物(S)-亮氨酸为原料合成出了2-甲基-4-庚醇及2-甲基-4-辛醇的所有对映异构体，其关键步骤是由(2S)-4-甲基-1,2-戊二醇合成出(2S)和(2R)-4-甲基-1,2-环氧戊烷两种重要中间体，目标产物光学纯度可达95%以上。     

Synthesis and biological activities of hydroxyl-protected fluorine-containing 4,4-dihydroxylmethyl-2-aryl-iminothiazolidines

Eight novel compounds were synthesized by a facile and mild method with high yields, and the structures of all the compounds were characterized by ¹H NMR IR mass and high resolution mass spectroscopy. Their inhibitory activity against insect-flight and trehalase in vitro were screened. Some target compounds have moderate inhibitory activity against trehalase, and show inhibition action to insect-flight.     

Emissive Annular Digold(I) Compounds Containing Diphosphine and Dithiolate Ligands

Molecular structures of three emissive annular digold compounds [Au₂(dmpm)(dtc)]Cl (dmpm = Me₂PCH₂PMe_2,dtc = S₂CNEt₂), 1 , [Au₂(dppm)(dtc)]PF₆, (dppm = Ph₂PCH₂PPh₂),₂,and [Au₂(dppe)(dtc)]-(PF₂) (dppe = Ph₂P(CH₂)₂PPh₂), 3, were determined. All three compounds are dimetallacycles having two gold atoms bridged by a dithiolate ligand and a diphosphine ligand, the geometry around each gold atom being almost linear. All the dimetal lacy die rings are slightly distorted from planarity with intramolecular Au-Au distances shorter than 3.0 Å. Compound 1 forms a polymeric chain through intermolecular Au-Au contacts (3.061 ? 3.135 Å). Compound 2 forms a tetramer through intermolecular Au-Au interactions (Au-Au distances ranging from 3.086 to 3.222 ). Compound 3 is monomeric. All of the compounds luminesce at 77 K in the solid state. Emissions originating from ³LMCT from dtc ligand to Au excited states are assigned. The emission maxima of 1 ? 3 are at 541,535 and 520 nm respectively and are blue shifted as the number of Au-Au interactions is decreased.