Combinatorial synthesis of small-molecule libraries using 3-amino-5-hydroxybenzoic acid

Summary A non-peptide library of 2001 compounds has been prepared utilizing solid-phase techniques. The split/combine method was demonstrated to work well to form mixtures of compounds based on 3-amino-5-hydroxybenzoic acid as a core structure. The benzoic acid of the core structure served as the attachment point for the resin and the amino and hydroxy positions were variably substituted.     

Phosphorus-based combinatorial libraries: Use of amino acid derivatives as synthons

Summary Phosphorus has been used as a scaffold to prepare combinatorial libraries of phosphoramidates in which one of the diversity elements resulted from derivatives of amino acids. A small library was prepared for analytical and characterization purposes, followed by a larger library of approximately 8800 compounds. Libraries were assembled on solid supports using the conventional pool-and-divide method, followed by cleavage from the supports at the end of the synthesis. Mass spectrometry was used to confirm that library synthesis had been successful. Individual compounds were also prepared to study the stability of compounds of this type.     

Approaches for introducing high molecular diversity in scaffolds: Fast parallel synthesis of highly substituted 1H-quinolin-4-one libraries

We have developed a two steps strategy for the parallel synthesis of highly diversified quinolin-ones. In the first step we have combined and improved different synthetic methods for generating quinolin-4-ones bearing four different substitutions at specific positions using round bottomed flasks. The synthesis was assessed for a large number of substituted quinolin-4-ones. In the second step, the improved method was adapted to a parallel array synthesis using a 12 positions carrousel as demonstrated for the synthesis of 42-variable quinolin-4-ones. The first combinatorial library set 14(a-x) was obtained with a chemical purity of more than 95% without purification, the second library set 15(a-r), which included two synthetic steps, needed combinatorial purification using an innovative parallel purifier. The proposed approach contributes to a more extensive diversification of molecular scaffolds in general and provides access to highly substituted quinolinones in particular.     

Limitations of the Coupling of Amino Acid Mixtures for the Preparation of Equimolar Peptide Libraries

The standard method of peptide library synthesisinvolves coupling steps in which a single amino acidis reacted with a mixture of resin-bound amino acids.The more recently described positional scanningstrategy (in which each position in the peptide sequence is occupied in turn by a single residue) isdifferent since it involves the coupling of mixturesof amino acids to mixtures of resin-bound amino acids.In the present study, we analyze the compoundsproduced under these conditions measuring couplingrates and amounts of formed products, using mainly UV,HPLC, LC/MS and MS/MS techniques. Our data do notpermit to conclude that the resulting libraries arecomplete. Indeed, our analytical data indicate that alarge part of the di-, tri- and tetrapeptidessynthesized with this method are not present in thefinal mixture. Although chemical compensation (inwhich poor coupling kinetics is compensated by alarger excess of the incoming amino acid) has beenthought to counterbalance these biases, ourexperiments show that the compensation method does nottake into account the crucial influence of theresin-bound amino acid and that even the dipeptidelibraries obtained in this way are far fromcompleteness. The present work provides strong evidence that the coupling of mixtures of amino acidsto resin-bound residues, which is required by thepositional scanning strategy, results in incompleteand/or non-equimolar libraries. It also clearlyconfirms that coupling rates in solid-phase peptidesynthesis are dependent on the nature of both theincoming and the immobilized amino acid.     

Multicomponent synthesis of dihydrobenzoxazepinones,bearing four diversity points,as potential <Emphasis Type="Italic">α</Emphasis>-helix mimics

A very short convergent synthesis of dihydrobenzoxazepinones, bearing four diverse diversity points, based on coupling the Ugi reaction with a Mitsunobu cyclization, was developed. These compounds are potential α-helix mimics, where three of the four appendages are expected to imitate the residues in i, i + 4 and i + 7 positions. A library of 22 compounds bearing lipophilic substituents, designed to interact with the hydrophobic cleft of anti-apoptotic protein Bcl-xL, was synthesized. Preliminary biochemical tests, based on competitive binding, have already been carried out.     

A study of gas-sensitive properties of cobalt-modified polyacrylonitrile films by the methods of molecular modeling and quantum chemistry

The results of a theoretical study of the gas-sensitive properties of polyacrylonitrile (PAN) modified with cobalt compounds by using the methods of molecular modeling and quantum chemistry are presented. A surface cluster of cobalt-containing PAN formed by infrared heat treatment is simulated. The most stable configuration of the cluster has been determined, in which molecules of cobalt oxide and cobalt metahydroxide are located between two layers of PAN macromolecules without interacting with each other and with PAN molecules. This explains a composite structure of cobalt-containing PAN films. Molecular modeling demonstrated that the cobalt-modified PAN cluster is selectively sensitive to the molecules of chlorine, nitrogen dioxide, and carbon monoxide.     

Toward automated biochemotype annotation for large compound libraries

Summary Combinatorial chemistry allows scientists to probe large synthetically accessible chemical space. However, identifying the sub-space which is selectively associated with an interested biological target, is crucial to drug discovery and life sciences. This paper describes a process to automatically annotate biochemotypes of compounds in a library and thus to identify bioactivity related chemotypes (biochemotypes) from a large library of compounds. The process consists of two steps: (1) predicting all possible bioactivities for each compound in a library, and (2) deriving possible biochemotypes based on predictions. The Prediction of Activity Spectra for Substances program (PASS) was used in the first step. In second step, structural similarity and scaffold-hopping technologies are employed. These technologies are used to derive biochemotypes from bioactivity predictions and the corresponding annotated biochemotypes from MDL Drug Data Report (MDDR) database. About a one million (982,889) commercially available compound library (CACL) has been tested using this process. This paper demonstrates the feasibility of automatically annotating biochemotypes for large libraries of compounds. Nevertheless, some issues need to be considered in order to improve the process. First, the prediction accuracy of PASS program has no significant correlation with the number of compounds in a training set. Larger training sets do not necessarily increase the maximal error of prediction (MEP), nor do they increase the hit structural diversity. Smaller training sets do not necessarily decrease MEP, nor do they decrease the hit structural diversity. Second, the success of systematic bioactivity prediction relies on modeling, training data, and the definition of bioactivities (biochemotype ontology). Unfortunately, the biochemotype ontology was not well developed in the PASS program. Consequently, “ill-defined” bioactivities can reduce the quality of predictions. This paper suggests the ways in which the systematic bioactivities prediction program should be improved.     

Focused enumeration and assessing the structural diversity of scaffold libraries: conformationally restricted bicyclic secondary diamines

Comprehensive enumeration of conformationally restricted bicyclic secondary diamines (CRDA) was performed within defined structural limits, yielding a library of all theoretically possible compounds of this class, potentially useful as building blocks for drug design. In order to assess structural diversity of the generated library, molecular geometries of the library members were optimized using DFT calculations. It was shown that the distance between the amino groups and their relative orientation in space vary widely over the whole library, which might be beneficial for diversity-oriented conformational restriction approach in drug discovery. There are many representatives of "three-dimensional" scaffolds in the CRDA library. Selected literature data on biological activity of the known CRDA derivatives were discussed, demonstrating utility of the CRDA scaffold hopping in drug design.     

Synthesis of bis-peptides attached on poly[n]norbornene molecular scaffolds with well-defined relative positions and distances

This article describes novel synthetic approaches to polynorbornene molecular scaffolds substituted with peptides at various, well-defined positions. A library of norbornene building blocks with attached peptides was prepared. Alkene cyclobutane epoxide (ACE) coupling method was used as a key step reaction for the connection of two norbornene building blocks into bis-peptide scaffolds. Photodimerization of cyclobutene diesters offers an alternative route to polynorbornene bis-peptides. Pyrrolo-peptides were used for preparation of peptide-substituted 7-aza norbornenes. Asymmetrical bis-peptide scaffolds were prepared by ACE coupling of peptide-norbornane epoxide with another norbornene-peptide block. Chemical elaboration of bridgehead dimethyl esters of ACE products or epoxide ACE reagents was also used for peptide attachment.     

J酸分光光度法测定芳香族氨基化合物

综合考虑显色反应选择性、反应速度、灵敏度和偶氮化合物的水溶性等问题,通过对偶合组分分子结构的理论设计和实验筛选,研究了显色反应方法和条件,提出利用J酸(2-氨基-5-萘酚-7-磺酸)作为偶合试剂分光光度法测定水中芳香族氨基化合物。溴化钾催化,室温下,亚硝酸盐与芳香族氨基化合物在稀盐酸水溶液中发生重氮化反应,在碳酸钠水溶液中重氮盐与J酸偶合生成有色偶氮化合物,最大吸收波长480 nm。所测苯胺、4-氨基苯磺酸和1-萘胺的表观摩尔吸光系数分别为3.95×104,3.24×104和3.91×104 L·mol-1·cm-1。水中共存离子影响研究结果表明: 地表水中常见离子对测定结果不产生影响。采用J酸分光光度法测定了上海市复兴岛运河水样,同时,用标准加入法做回收实验,实验结果：苯胺回收率为98.5%～102.1%,相对标准偏差2.08%。J酸是一种常见有机试剂,易溶于水,挥发性低,其毒性大大低于盐酸萘乙二胺。J酸分光光度法测定芳香族氨基化合物具有灵敏度高、选择性好、操作简单快速、测定结果准确等优点,可用于环境水体中痕量芳香族氨基化合物的测定。     

利用Raman磁共振研究四极核对AX体系弛豫行为的影响

本文利用一维多量子Raman磁共振谱线的线宽测定了氯仿(CHCl₃)中碳氢体系的多量子的弛豫时间,由此得到第二类标量耦合弛豫起主导作用时的碳氢核自旋弛豫的交叉相关系数,氯核与碳和氢核的标量耦合常数,以及它们的相对符号。     

Bifunctional scaffolds as templates for synthetic combinatorial libraries

Summary A small-molecule synthetic combinatorial library was designed and synthesized that features potential pharmacophores attached to a variety of small cyclic scaffolds. The synthesis of the library involved randomization of three types of building blocks: 20 amino acids, 10 aromatic hydroxy acids and 21 alcohols, totaling a library complexity of 4200 compounds. Mitsunobu polymer-supported etherification was used in the last randomization. The library compounds were attached to beads via an ester-bond linkage enabling both on-bead as well as in-solution screening. When the library was tested against a model target, streptavidin, specific binders were found. The structures of the most active compounds were determined from the fragmentation pattern in MS/MS experiments.Abbreviations DCM dichloromethane - DEAD diethyl azodicarboxylate - DIAD diisopropyl azodicarboxylate - DIC diisopropyl carbodiimide - DMF dimethylformamide - Fmoc fluorenylmethyloxycarbonyl - HOBt N-hydroxybenzotriazole - MeOH methanol - PPh₃ triphenylphosphine - t-Bu tert-butyl - TFA trifluoroacetic acid - TG TentaGel-S-OH 130-m resin - THF tetrahydrofuran     

Investigation of electronic structure and associated nuclear quadrupole interaction of adsorbed fluorine atoms on silicon surface

The electronic energy levels and wave functions of fluorine and chlorine atoms adsorbed at the <111> surface of silicon are obtained by the Hartree-Fock procedure applied to clusters simulating the surface structure. Minimising the total energy with respect to the positions of the halogen atoms, the Si-Cl distance in the adsorbed system was found to be in good agreement with that from a recent SEXAFS measurement, there being no corresponding data presently available for fluorine on silicon surface. The calculated¹⁹ f ^* nuclear quadrupole coupling constants using the electronic wave functions for SiH₃F and the larger cluster Si₄H₉F, simulating the surface, differed substantially in contrast to the situation for the Si-F distance, indicating that the quadrupole coupling is a more sensitive indicator of the adequacy of the cluster chosen to represent the surface system. Experimental results for the coupling constants are awaited for comparison with theory.     

Determination of Organic Chlorine by Aluminium Monochloride Molecular Absorption Spectrometry Using Lead Atomic Line

The present study was conducted to investigate the molecular absorption by AlCl in a carbon rod furnace for determination of chlorine in organic compounds, by using the lead atomic line at 261.418 nm emitted from a Pb-hollow cathode lamp. A deuterium lamp was used for the simultaneous background correction. The method enables rapid and accurate determination of trace chlorine in varying organic samples with good precision. The method was tested on different organic chloro-coumpounds and α-pinene products.     

DasK-Röntgenemissionsspektrum des Chlors in freien Molekülen

TheKα andKβ spectra of chlorine in free molecules were studied using a special fluorescence X-ray tube and a high resolving curved crystal spectrograph with photoelectric registration. It was found that the wavelength shifts of ClKα₁ obtained for various gaseous compounds do not show the regularities observed with solid compounds of other 3rd period elements. — TheKβ spectrum consists of discrete lines the most intense of which result from transitions of the lonely pair electrons of the chlorine atoms. The spectra of HCl, Cl₂ and CH₃Cl can be explained using optical and betaspectroscopical data and MO calculations. The general structure of ClKβ of organic compounds seems to be determined by the hybridisation type of the carbon atoms bound to the chlorine atoms. Evidence is found for a contribution of molecular vibrational energy to the energies of the X-ray transitions.     

天然丰度的N-磷酰化氨基酸的15N NMR 研究

采用¹⁵N-¹H的2D HSQC、HMBC实验方法,测定了天然丰度的N-磷酰化氨基酸样品在溶液中的¹⁵N化学位移δ_N及偶合常数J_N-P,J_N-H. 实验表明：对于¹⁵N天然丰度样品,这是一种快速有效的实验方法. 研究发现：N-酰化后的氨基酸,其δ_N以及与氮原子直接相连的质子¹H的化学位移均发生十分明显的高场位移,而偶合常数¹J_N-P,¹J_N-H的变化与化合物构型相关联 .     

Elektronen-Kern-Doppelresonanz-Untersuchung vonU 2-Zentren in Kaliumchlorid

U ₂-centers in alkali halides are neutral hydrogen atoms in interstitial lattice sites, as has been shown by EPR measurements. The hyperfine interactions with the proton and with the four nearest halogen nuclei are resolved in the EPR spectrum. In order to resolve hyperfine interactions with further nuclei of the surrounding lattice ENDOR measurements have been performed onU ₂-centers in KCl at 77 °K. The analysis of the ENDOR spectra gave precise values for the hyperfine and quadrupole interaction constants of the nearest neighbour chlorine and potassium nuclei. The isotropic hyperfine constant of the chlorine neighbours is 24 times larger than that of the potassium neighbours although both nuclei are on equivalent first shell lattice positions. The hyperfine interactions of second shell potassium nuclei [(1/2, 1/2, 3/2)-position] show an unexpectedly large isotropic hyperfine constant. One expects a pure magnetic dipole-dipole interaction for the outer shell nuclei because of the concentrated hydrogen wave function. Two further chlorine shells could be approximately analysed. A theoretical estimate of the hyperfine and quadrupole interaction constants was made by orthogonalizing the 1s hydrogen wave function to the cores of the surrounding ions. If one takes into account the mutual overlap of neighbouring potassium and chlorine ions, one gets the right order of magnitude of the measured constants and a value of 10.4∶1 for the ratio of the isotropic hyperfine constants of the first shell chlorine and potassium nuclei. The relatively large isotropic constant of the second shell potassium nuclei can also be explained on this basis.     

Exploring antibody polyspecificity using synthetic combinatorial libraries

Summary Extensive mapping studies for seven antigen-antibody interactions have been carried out using both individual analogs and peptide libraries. With competitive ELISA, these studies have revealed that monoclonal antibodies exhibit a broad range of specificities, from antibodies that recognize only conservative substitutions for 1–2 positions of the antigenic determinant, to antibodies that recognize sequences that are completely unrelated to the parent antigen with comparable affinities. Synthetic combinatorial libraries, containing millions of peptide sequences, permit a more systematic and rapid evaluation of the extent of multiple-binding specificities of monoclonal antibodies than individual analogs. The peptide libraries used here comprise mixtures of compounds having specifically defined positions and mixture positions. The same diversity of sequences in different formats, which differ by the numbers of positions singularly defined and different locations defined within the sequence, can be examined. Comparison of the screening results, selection criteria of the most active mixtures, and different approaches used for the deconvolution of active individual compounds are discussed. Synthetic combinatorial libraries greatly facilitate the understanding of antigen-antibody interactions at the amino acid level and will assist in the development of improved immunodiagnostics.     

Description and Performance Analysis of an Infrared Library Search System

Abstract

An infrared library search system is described. The spectral library consists of 608 FT-IR spectra represented with a data point every 4 cm^?1 in the 3700–500 cm^?1 range. Four different similarity measures for spectral search were implemented. Performance analysis was carried out in order to estimate the ability of the system to identify organic compounds on the basis of their IR spectra.     

Statistical molecular design of peptoid libraries

Statistical experimental design provides an efficient approach for selecting the building blocks to span the structural space and increase the information content in a combinatorial library. A set of renin-inhibitors, hexapeptoids, is used to illustrate the approach. Multivariate quantitative structure-activity relationships (MQSARs) were developed relating renin inhibition to the peptoid sequences variation, parametrized by the z-scales. By using the information from the models, the number of building block sets could be reduced from six to three. Using a statistical molecular design (SMD) reduces the number of compounds from more than 100 000 down to 90. A second SMD was used for comparison, based on less prior knowledge. This gave a reduction from over 2 billion to 120 compounds.