Showing papers in "ACS Combinatorial Science in 1999"

A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases.

Abstract: The discovery of various protein/receptor targets from genomic research is expanding rapidly. Along with the automation of organic synthesis and biochemical screening, this is bringing a major change in the whole field of drug discovery research. In the traditional drug discovery process, the industry tests compounds in the thousands. With automated synthesis, the number of compounds to be tested could be in the millions. This two-dimensional expansion will lead to a major demand for resources, unless the chemical libraries are made wisely. The objective of this work is to provide both quantitative and qualitative characterization of known drugs which will help to generate “drug-like” libraries. In this work we analyzed the Comprehensive Medicinal Chemistry (CMC) database and seven different subsets belonging to different classes of drug molecules. These include some central nervous system active drugs and cardiovascular, cancer, inflammation, and infection disease states. A quantitative characterization ...

Beyond Mere Diversity: Tailoring Combinatorial Libraries for Drug Discovery

Abstract: Combinatorial library design attempts to choose the best set of substituents for a combinatorial synthetic scheme to maximize the chances of finding a useful compound, such as a drug lead. Initial efforts were focused primarily on maximizing diversity, perhaps allowing some bias by the inclusion of a small, fixed set of pharmacophoric substituents. However, many factors besides diversity impact good library design for drug discovery. A library can be better “tailored” by assigning the candidate substituents to categories such as polar, pharmacophoric, rigid, low molecular weight, and expensive. Stratified sampling by successive steps of D-optimal design generates diverse designs which are also consistent with desirable profiles of these properties. Comparing the diversity scores among design profiles reveals the tradeoffs between diversity, physical property distributions, synthetic difficulty, expense, and pharmacophoric bias. The diversity scores can be calibrated by scoring the best designs from subset...

Parallel personal comments on "classical" papers in combinatorial chemistry

Abstract: It is appropriate to start this new journal with an article about the history of this particular fieldsespecially when the field is so new that even the basic terminology is not completely defined.† When I was asked to write an article about the history of combinatorial chemistry, I believed that it would not be too difficult since I was engaged in this exciting new technology from the start of the first combinatorial chemistry company, Selectide Corporation in Tucson.‡ To make this historical retrospective more objective, I decided to consult with several scientists who published in this field at the early stages and whose articles may be considered as having formed the new way of thinking about the techniques used to develop new drugs and catalysts and an unlimited variety of materials. After reading the responses of my colleagues, it was clear that when we were building Selectide in 1991, there were scientists already heavily engaged in creating and using diversity in various forms. Some people were exploring this new field without even realizing it. I can document this fact from my own experience. In 1988, we published a paper with Giorgio Fassina and Irwin Chaiken1 in which we synthesized a mixture of analogues of oxytocin by coupling a mixture of amino acids in one step of the synthesis and applying this mixture to the column with immobilized neurophysin. The analogues with an affinity toward neurophysin were retained on the column, and after elution their structures were analyzed. None of us realized the potential of this technique for the development of new drugs; at that time we were “entrenched” in the approach of making one compound at a time, analyzing it, and evaluating it biologically. However, even in the 1990s the world was not ready to accept the idea of building libraries of organic molecules and screening them to find interesting compounds. It took another several years before an academic course of combinatorial chemistry was offered to students at The University of Louisville in 1996 by Professor Arno Spatola. The new chemists graduating from schools in the next couple of years will not be surprised when asked to prepare a couple hundred thousand compounds for the screening project next week. Just seven short years ago the response at a presentation to a major pharmaceutical company to the exposure of the library technology was not only skepticism but absolute certainty that this technique may never work and that it will never be applied in a pharmaceutical industry. There is no serious company today who would not have its own group of chemists, or even a department, working in this area. Combinatorial chemistry, however, even though somewhat fashionable today, will become an absolutely routine technique tomorrow and will be applied in situations where its application is optimal. These special groups and departments will eventually get dissolved into medicinal chemistry, lead discovery, and lead optimization, just as NMR spectroscopy grew from specialized laboratories into freely accessible instruments available for day to day research. Back when we were discussing the question of “Who is the father of molecular diversity?” in the rather controversial review article written with Viktor Krchňak2 (one referee suggested that this type of article should never be published in a scientific journal, the second referee recommended the publication with high priority), we concluded that there is no “father of diversity”. However, there is a “Mother of diversity”sMother Nature. Well, she did not publish Her findings anywhere, but maybe this is due to the fact that the experiment is not finished yet. What can be a better way of * Tel: (619) 550-9636. Fax: (619) 550-9666. E-mail: michal@5z.com. † Today, the term “combinatorial chemistry” is used for techniques to synthesize, in parallel, more than one compound. This is obviously not correct, since to make something combinatorial, one should perform at least one combinatorial step in the synthesis (i.e., a step in which the number of processed compartments (reaction vessels) is lower than the number of prepared compounds). (Ed. Note: This opinion does not reflect JCC’s current Guidelines.) ‡ I thought that I would be writing about how we hired inexpensive labor, bought used laboratory equipment from Bilinski’s shop in the middle of the desert, built the laboratories from kitchen furniture, how the purchase of the major equipment was decided by the result of the tennis match, how the decapeptide sequenced in the evening was synthesized and HPLCpurified during one night, how the technology was believed to be so unique that it should not even be patented, or how the seed capital of $100,000 turned into 22 times more (even though company was less than one week from the “brick wall” in the process). 3 J. Comb. Chem. 1999, 1, 3-24

Fluorescence-Quenched Solid Phase Combinatorial Libraries in the Characterization of Cysteine Protease Substrate Specificity†

Abstract: To map the substrate specificity of cysteine proteases, two combinatorial peptide libraries were synthesized and screened using the archetypal protease, papain. The use of PEGA resin as the solid support for library synthesis facilitated the application of an on-resin fluorescence-quenched assay. Results from the screening of library 2 indicated a preference for Pro or Val in the S3 subsite and hydrophobic residues in S2; the most prevalent residue not being Phe but Val. The S1 subsite exhibited a dual specificity for both small, nonpolar residues, Ala or Gly, as well as larger, Gln, and charged residues, Arg. Small residues predominated in the S1‘−S4‘ subsites. Active peptides from the libraries and variations thereof were resynthesized and their kinetics of hydrolysis by papain assessed in solution phase assays. Generally, there was a good correlation between the extent of substrate cleavage on solid phase and the kcat/KM's obtained in solution phase assays. Several good substrates for papain were obtai...

On the Development of New Poly(styrene-oxyethylene) Graft Copolymer Resin Supports for Solid-Phase Organic Synthesis

Abstract: With the aim of creating new, improved solid supports for organic synthesis, a series of poly(styrene-oxyethylene) graft copolymers 6a - d was synthesized by anionic polymerization of ethylene oxide from a polystyrene-supported 1,3-diol 5b. Graft lengths were varied from 29 to 58 repeat units (67-82 wt % polyoxyethylene). The so-formed alcohols 6a - d were further transformed into chlorides 7a - d, amines 8a - d, and two commonly used linkers, Wang 9a - d and HMPB 10a - d. These functional group interconversions were efficiently monitored using gel-phase 13C NMR, and the solid-state properties of all copolymers were characterized by differential scanning calorimetry. Thermal properties of these materials were found to be dominated by the polyoxyethylene composition. A correlation between the melting point associated with the graft lengths and the physical properties of the resins was observed. The optimum graft copolymer composition, determined by balancing the degree of functional group loading with resi...

Matrix assisted synthetic transformations: a mosaic of diverse contributions. I. The pattern emerges.

Abstract: This Perspective is the first of two parts compiled from contributions elicited from many of the originators of different matrices which have been used for synthetic transformations. The idea has been to include personal recollections not normally encouraged in traditional reviews, incidentally bringing to the reader's attention the varied connections which bind all together.

A combinatorial approach to recognition of chirality: preparation of highly enantioselective aryl-dihydropyrimidine selectors for chiral HPLC.

Abstract: A parallel library of 108 4-aryl-1,4-dihydropyrimidine (DHPM) enantiomers, which are potential selectors for chiral HPLC separations, was synthesized using the single-step Biginelli multicomponent condensation. The individual compounds were screened by observing the enantioselectivity for resolution on a “brush-type” l-(3,5-dinitrobenzoyl)leucine-based chiral stationary phase, and separation factors α up to 12 were achieved. The best candidates from the library contained an ortho-substituted aromatic group at C4 carbon atom of the pyrimidine ring and an alkyl substituent at N1 nitrogen atom. Resolution of the enantiomers of the lead compound, 4-(9-phenanthryl)-DHPM 8, using semipreparative chiral HPLC followed by attachment to monodisperse macroporous aminomethacrylate beads, provided the novel polymer based chiral stationary phase with good enantioselectivities in the resolution of several π-acidic aryl-dihydropyrimidines and derivatized profens. In addition, 3,5-dinitrobenzamido derivatives of α-amino a...

Determining affinity-selected ligands and estimating binding affinities by online size exclusion chromatography/liquid chromatography-mass spectrometry.

Abstract: Size exclusion chromatography (SEC) isolation of affinity-selected ligands combined with reverse phase liquid chromatography−mass spectrometry (LC-MS) is an effective means for identifying members of mixtures which form tightly bound noncovalent complexes with target proteins. A potential liability of the approach is that the SEC isolation is carried out under nonequilibrium conditions favoring protein/ligand complex dissociation. At long SEC isolation times and/or for complexes with fast off-rates the extent of dissociation can jeopardize the ability to detect the affinity-selected components. Additionally, equilibrium binding affinities cannot be exactly determined from the measured distribution of isolated ligands. We present here an online SEC/LC-MS system for determining affinity-selected members of active mixtures which reduces this liability. A kinetic model of the SEC isolation process is developed to determine the practical limits for the application of the method and to extrapolate equilibrium b...

Toward Designing Drug-Like Libraries: A Novel Computational Approach for Prediction of Drug Feasibility of Compounds

Abstract: Prediction of the degree of drug-like character in small molecules is of great industrial interest. The major barrier, however, is the lack of a definition for drug-like character. We used the concept of the multilevel chemical compatibility (MLCC) between a compound and a drug library as a measure of the drug-like character of a compound. The rationale is that the local chemical environment of each atom or group of atoms in a compound largely contributes to the stability, toxicity, and metabolism in vivo. A systematic comparison of the local environments within a compound and those within the existing drugs provides a basis for determining whether and how much a compound is drug-like. We applied the MLCC calculations to four test sets: top selling drugs, compounds under biological testing prior to the preclinical test, anticancer drugs, and compounds known to have poor drug-like character. The following conclusions were obtained: (1) A convergent number of unique local structure types were found in the...

Matrix assisted synthetic transformations: a mosaic of diverse contributions. II. The pattern is completed.

Abstract: in which the originators of many gel-type matrixes have described the development of their materials. In Part II, the story continues to unfold in the same manner. The focus of Part I was the introductory section by Bruce Merrifield; that of Part II is provided by a personal perspective from the other “father” of this field, Robert Letsinger, who independently conceived of solid-phase synthesis and pursued the concept, as applied to DNA synthesis, with equal vigor. His efforts provide the foundation for much of today’s biotechnology. Truly we do stand on the shoulders of giants, 2 who dreamed of things that never were and made those dreams reality. Table 1 summarizes some reasons why there has been so much interest in the development of new supports. Tables 2 and 3 provide an overview of the content of the two parts. Note, however, that the second contribution to Part II is a description of traditional gel form PS beads made with some novel technological improvements. Each section is introduced by personal remarks (D.H. comments). The final section consists of a discussion by Bing Yan and myself on a topic dear to our hearts: we know from the few studies that have been done that the rates and yields of particular transformations are highly dependent on the nature of the matrix. These studies provide some clues as to which would be the best selection for any reaction series. As with Part I, all contributors were given similar instructions: to prepare a personal account of their support development work, focusing on how the structure of the support influences its suitability. 3 The opinions and comments provided by the contributors are, obviously, their own, and occasionally they are in conflict with statements by myself and others (since no contributor has had access to other contributions). I have on several occasions had to suggest modifications to authors, but I have never sought to influence their opinions; differences of opinion are not uncommon in this field and are part of its considerable fascination. I do, however, take full responsibility for encouraging candor, humor, and personal comments; attributes rarely found in conventional reviews! * E-mail: dhudson@solidphase.com. © Copyright 1999 by the American Chemical Society

Parallel synthesis of prostaglandin E1 analogues.

Abstract: The first demonstration of the rapid parallel synthesis of diverse prostaglandin derivatives is reported. Upper (α-) side chain diversity was introduced to core 1 via the parallel Suzuki coupling of hydroborated alkenes. Conversion to the enones 3 and 9 was followed by the addition of the lower (ω-) side chains as higher-order cuprates 4. Upper side chains incorporating an N-acylsulfonamide protecting group were further transformed into prostaglandin amide analogues. Cleavage from support with HF/pyridine followed by scavenging provided 26 prostaglandin E1 analogues in high purity.

A Comparison of Various FTIR and FT Raman Methods: Applications in the Reaction Optimization Stage of Combinatorial Chemistry

Abstract: Four different FTIR methodssingle-bead FTIR, beam condenser, macro attenuated total reflection (macro-ATR), and KBr pellet methodsand macro and single-bead FT Raman methods have been investigated, and the relative utility was compared for the analysis of resin-bound organic compounds and the monitoring of solid-phase organic reactions. Furthermore, the comparison includes two additional methods from the literature: diffuse reflectance infrared Fourier transform spectroscopy and photoacoustic spectroscopy. While all of these methods have some utility for solid-phase sample analysis, the relative merits of these methods vary particularly in such areas as the information content, spectral quality, sensitivity, speed, sample requirement, and the instrument cost. Both single-bead FTIR and beam condenser FTIR methods have been found to be superb methods in each of these aspects. In the following way, these methods meet many of the essential requirements for a thin layer chromatography (TLC) equivalent for soli...

Designing Diverse and Focused Combinatorial Libraries of Synthetic Polymers

Abstract: Molecular topology and genetic algorithm optimized quantitative structure−property relationships (QSPR) have been used to design diverse and focused libraries of synthetic biodegradable polymers. A diverse subset (17 polymers) of a 112-member virtual polymer library was selected based on the molecular topology of the repeat unit using a stochastic diversity method (SimSearch-SCA). These 17 polymers were shown to be highly representative of the two-dimensional property space for the full library where the properties of interest are glass transition temperature (Tg) and hydrophobicity as measured by the air−water contact angle (CA). The 17 polymers in the diverse library were used to derive QSPR equations for Tg and CA by using a genetic algorithm to select molecular topology descriptors for linear regression. High quality models were derived for both Tg and CA. These QSPR models were tested by comparing the computed and experimental Tg and CA values for the 95 polymers that were not included in the trainin...

Improved Methods for Encoding and Decoding Dialkylamine-Encoded Combinatorial Libraries

Abstract: Optimized methods for utilizing and analyzing dialkylamine tags in encoded combinatorial chemistry are reported. A previously described LC/fluorescence method has been shortened from over 1 h to 6 min. A novel ion exchange LC/MS method for decoding has been developed which is both fast and rugged. The use of quantitative encoding schemes is described. These new techniques have allowed a simplified, automated sample preparation scheme, and over 300 encoded bead samples can be read in a day.

Comparison of resin and solution screening methodologies in combinatorial chemistry and the identification of a 100 nM inhibitor of trypanothione reductase.

Abstract: Two identical polyamine peptide conjugate libraries were screened against the parasitic enzyme trypanothione reductase. One of these libraries was in a solution format, while the other was resin-based and was used in two resin-based screens (a diminution assay and a direct bead screening). Potent inhibitors (100 nM) of trypanothione reductase were identified both in the solution screen and in the resin-based screens when using the PEGA resin of Meldal. Resin screening of both types failed to work with TentaGel resin. Importantly there was excellent agreement between the solution and resin-based assays, suggesting both methods are reliable for the screening of combinatorial libraries.

Solid-Phase Synthesis of β-Keto Esters via Sequential Baylis−Hillman and Heck Reactions

Abstract: Acrylic acid was immobilized on polystyrene−Wang resin, followed by Baylis−Hillman reaction with aldehydes using DABCO as catalyst. Addition of 1 equiv of lanthanum(III) trifluoromethanesulfonate was found to improve yields, as in solution phase. After the Baylis−Hillman step, Heck reaction with aryl halides resulted in α-substituted β-keto esters, which were cleaved from the resin by acid hydrolysis with concomitant decarboxylation to afford aryl ketone products. Overall yields of 0−49% were obtained with 26 examples.

High-Throughput 1H NMR and HPLC Characterization of a 96-Member Substituted Methylene Malonamic Acid Library

Abstract: A solid phase organic synthesis method has been developed for the preparation of substituted methylene malonamic acids and malonic ester mono acids 5 Two substituents are introduced into the core molecule 5 by preparation of unsymmetrical malonic acid derivatives 2, followed by Knoevenagel condensation with aromatic or aliphatic aldehydes, giving resin-bound 4 Evaluation of the scope of these reactions led to the preparation of a 96-member library from a set of eight amines/alcohols (seven amines and one alcohol) and 11 aldehydes leading to 88 substituted methylene malonamic/malonate mono acids 5 and eight unsymmetrical malonamic/malonate mono acids 3 Structural validation and quantitation for every member of the library was obtained by evaluation of 1H NMR and HPLC, respectively The 1H NMR data were obtained using automated delivery of DMSO solutions of every library member from a 96-deep well microtiter plate to a flow probe-equipped NMR spectrometer HPLC data were used for determination of the ext

Solid-Phase Synthesis of Trisubstituted 2-Imidazolidones and 2-Imidazolidinethiones

Abstract: An efficient method for the solid-phase synthesis of 1,3,4-trisubstituted-2-imidazolidones and 1,3,4-trisubstituted-2-imidazolidinethiones from reduced N-acylated dipeptides is described. The complete reduction of the amide bonds of an N-acylated dipeptide with borane in THF results in two secondary and one tertiary amine. Reaction of the resulting resin-bound polyamine 4 with carbonyldiimidazole or thiocarbonyldiimidazole affords, respectively, cyclic ureas 6 and cyclic thioureas 7 in high yield and purity. Details on the selection of the building blocks and characterization of the controls for the libraries' synthesis will be presented. These procedures have also been used to generate parallel arrays and mixture-based combinatorial libraries of cyclic ureas and thioureas.

Solid-Phase Synthesis of 2,4,6-Trisubstituted Pyridines

Abstract: A new solid-phase synthesis of 2,4,6-trisubstituted pyridines from hydroxyacetophenones is described. The synthesis includes Claisen−Schmidt and Michael reactions on Wang resin to produce 1,5-diketones, which are then cyclized with ammonium acetate. The pyridine substituents are introduced independently and are derived from readily available, diverse sets of starting materials. The method is suitable for the synthesis of arrays of compounds.

New Chemoselective Metalating Agents for Solid-Phase Synthesis

Abstract: Development of new soluble, chemoselective metalating reagents is essential for exploring solid-phase organometallic chemistry. Cuprates and zincates were expected to be potentially usable for solid-phase chemistry, and we started to investigate chemoselective solid-phase halogen−metal exchange reactions using ate complexes. At 0 °C, the halogen−zinc exchange reactions proceeded smoothly in the presence of 2.2 equiv of LTBZ, and the subsequent reaction with an electrophile followed by cleavage with NaOMe/MeOH-THF gave the desired product in an excellent yield. The immobilized organozincate on polymer support was also transformed into the immobilized organocuprate by treatment with lithium cyanothienylcuprate. The palladium-catalyzed cross-coupling reaction of the immobilized organozincate with iodobenzene proceeded smoothly at room temperature to give an unsymmetrical biaryl. This methodology is considered to provide a new chemoselective method for solid-phase carbon−carbon bond formation.

A combinatorial approach toward the discovery of non-peptide, subtype-selective somatostatin receptor ligands.

Abstract: The tetradecapeptide somatostatin is widely distributed throughout the body and is thought to be involved with a variety of regulatory functions. Recently, five human somatostatin receptors (hSSTR1-5) have been cloned and characterized. Several selective peptidal agonists of the hSSTR receptors are known, and we sought to apply this information to the design of novel non-peptide small molecule ligands for each receptor. Initial computational methods identified a 200 nM murine SSTR2 active compound via a database search of our sample collection. A combinatorial library was designed around the structural class of the compound with the goal of rapidly developing this initial lead into the desired subtype-selective small molecules in order to characterize the pharmacology of each of the receptor subtypes. The library was synthesized using the resin-archive, iterative deconvolution format. The total number of unique compounds in the library was expected to be 131 670, present in 79 mixtures of 1330 or 2660 com...

Solid-Supported Benzotriazoles: Synthetic Auxiliaries and Traceless Linkers for the Combinatorial Synthesis of Amine Libraries1

Abstract: This paper describes the successful transfer of benzotriazole-based chemistry on solid support. The strategy followed to anchor this peculiar heterocycle on solid phase and the full analytical characterization of the various supported benzotriazoles are herein described. The chemistry assessment process on solid phase, the preparation of discrete libraries by parallel synthesis, the semiautomated purification procedures, and the complete analytical characterization of the library components are also presented and discussed.

Polystyrene grafted fluoropolymer microtubes: New supports for solid-phase organic synthesis with useful performance at high temperature

Abstract: New solid supports for organic synthesis have been developed by radiolytically grafting polystyrene onto inert fluoropolymer tubes. The grafted tubes have been functionalized and utilized in two solid-phase organic reactions performed at high temperatures.

Parallel Synthesis of Aminomethylphosphine Ligands

Abstract: Aminomethylphosphines (RaRbPCHRcNRdRe) were prepared by condensation of RaRbPH, RcCHO, and RdReNH in THF at ambient temperature. A 96-member library of aminomethylphosphines was prepared in paralle...

A combined parallel synthesis and screening of macrocyclic lanthanide complexes for the cleavage of phospho di- and triesters and double-stranded DNA.

Abstract: A parallel synthesis of macrocyclic lanthanide-ligand complexes 4Ln has been developed in conjunction with a parallel screening of these ligands for catalysis of phosphate ester hydrolysis. Complexes 4Ln were screened on a 96-well plate reader for their ability to catalyze the hydrolysis of a variety of phosphate esters efficiently. The hydrolysis of bis(4-nitrophenyl) phosphate (BNPP) 5 and p-nitrophenylethyl phosphate 6 was accelerated by up to 150-fold in the presence of the complex 4cGd. The cleavage of a double-stranded DNA plasmid with this same complex obeyed saturation kinetics following a Michaelian model (K(m) = 7.4 microM, kcat = 4.5 x 10(-3) min-1). Our findings demonstrate how a combination of parallel synthesis and screening can expedite compound access, accelerate catalyst identification, and thereby dramatically increase the speed of finding good ligand-metal combinations.

Synthesis and Characterization of a Mixture-Based Library of Oxime Ethers Based on a Common Aromatic Scaffold

Abstract: A mixture-based library of oxime ethers of general structure 4 (Scheme 2) has been prepared and characterized. Synthesis of the aromatic scaffold 3 (Scheme 1) containing two aromatic aminooxy groups followed by its reaction with 55 pairwise combinations of 11 aromatic aldehydes A−K in separate wells results in the formation of a library of sublibraries each containing four major oxime ether components. Extensive characterization of the sublibraries by LC−MS and NMR shows formation of all of the expected products in comparable amounts. The library compositions show little sensitivity of the oximation reaction to the aldehyde structure. This synthetically simple procedure provides a rapid approach to covering diversity space for this class of compounds and has implications for their use in dynamic combinatorial libraries.

Solid-phase synthesis of a combinatorial array of 1,3-bis(acylamino)-2-butanones, inhibitors of the cysteine proteases cathepsins K and L.

Abstract: To more rapidly prepare members of the 1,3-bis(acylamino)-2-butanone class of cysteine protease inhibitors, a solid-phase synthesis was developed. 1-Azido-3-amino-2,2-dimethoxybutane (4), which has the two amino groups differentiated and the ketone protected as a a ketal, served as a surrogate for the 1,3-diamino-2-butanone core. Amine (4) was coupled to the BAL-resin-linked carboxylic acids derived from alpha-amino acid esters. Evaluation of a small combinatorial array by measuring inhibition constants (Ki,appS) against cathepsins K, L, and B provided some structure-activity relationship trends with respect to selectivity and potency. Novel, potent inhibitors of cathepsins K and L were identified.