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Abstract
Peptoid oligomers were initially developed as part of a larger basic research effort to accelerate the drug-discovery process in the biotech/biopharma industry. Their ease of synthesis, stability, and structural similarity to polypeptides made them ideal candidates for the combinatorial discovery of novel peptidomimetic drug candidates. Diverse libraries of short peptoid oligomers provided one of the first demonstrations in the mid-1990s that high-affinity ligands to pharmaceutically relevant receptors could be discovered from combinatorial libraries of synthetic compounds. The solid-phase submonomer method of peptoid synthesis was so efficient and general that it soon became possible to explore the properties of longer polypeptoid chains in a variety of areas beyond drug discovery (e.g., diagnostics, drug delivery, and materials science). Exploration into protein-mimetic materials soon followed, with the fundamental goal of folding a non-natural sequence-specific heteropolymer into defined secondary or tertiary structures. This effort first yielded the peptoid helix and much later the peptoid sheet, both of which are secondary-structure mimetics that are close relatives to their natural counterparts. These crucial discoveries have brought us closer to building proteinlike structure and function from a non-natural polymer and have provided great insight into the rules governing polymer and protein folding. The accessibility of peptoid synthesis to chemists and nonchemists alike, along with a lack of information-rich non-natural polymers available to study, has led to a rapid growth in the field of peptoid science by many new investigators. This work provides an overview of the initial discovery and early developments in the peptoid field.
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Affiliation(s)
- Ronald N Zuckermann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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2
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Batista-Viera F, Janson JC, Carlsson J. Affinity Chromatography. METHODS OF BIOCHEMICAL ANALYSIS 2011; 54:221-58. [DOI: 10.1002/9780470939932.ch9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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3
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Williams M. Challenges in developing P2 purinoceptor-based therapeutics. CIBA FOUNDATION SYMPOSIUM 2007; 198:309-21. [PMID: 8879833 DOI: 10.1002/9780470514900.ch18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Advances in the molecular cloning, expression and functional characterization of the P2 purinoceptor superfamily have provided a wealth of data to support a diverse functional role for ATP and related nucleotides in the regulation of tissue function. As with other receptor superfamilies, it is likely that distinct subtypes of each receptor will subserve discrete functions depending on tissue distribution and disease pathophysiology. At the present time, ATP is being evaluated as an anticancer agent and as an anaesthesia adjunct whereas UTP is studied as a novel treatment for cystic fibrosis. ARL67085 is a potent and selective P2T receptor antagonist that has potential as a novel antithrombotic agent. The key to exploiting the P2 purinoceptor area to enhance understanding of disease aetiology and concurrent therapeutic potential will be to focus efforts on the identification of novel pharmacophores that have potent and selective interactions with the various receptor subtypes as potential new leads. To this end, the use of high-throughput screening in conjunction with combinatorial chemical, conventional chemical and natural product library compound sources will be critical.
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Affiliation(s)
- M Williams
- Neuroscience Discovery, Abbott Laboratories, Abbott Park, IL 60064, USA
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4
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Lewis RA, Pickett SD, Clark DE. Computer-Aided Molecular Diversity Analysis and Combinatorial Library Design. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125939.ch1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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5
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Kappel JC, Yokum TS, Barany G. Parallel Solid-Phase Syntheses of 1,3,4-Thiadiazolium-2-Aminides. ACTA ACUST UNITED AC 2004; 6:746-52. [PMID: 15360209 DOI: 10.1021/cc049973b] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient and advantageous solid-phase strategy has been developed to synthesize 1,3,4-thiadiazolium-2-aminides. The title compounds were prepared in parallel fashion according to the following compact route: (i) anchoring of aromatic aldehydes to the solid support; (ii) solution preparation of 1,4-disubstituted thiosemicarbazides from hydrazines plus isothiocyanates; (iii) trimethylsilyl chloride-promoted cyclization between the resin-bound aldehydes and 1,4-disubstituted thiosemicarbazides; and (iv) removal of the products from the solid support by acid treatment. The products (17 made in all) were cleaved with high initial purities (90-98%) and obtained in generally good isolated yields (53-94%, with one exception).
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Affiliation(s)
- Joseph C Kappel
- Department of Chemistry, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455, USA
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Nam NH, Sardari S, Parang K. Reactions of solid-supported reagents and solid supports with alcohols and phenols through their hydroxyl functional group. JOURNAL OF COMBINATORIAL CHEMISTRY 2003; 5:479-546. [PMID: 12959554 DOI: 10.1021/cc020106l] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nguyen-Hai Nam
- Department of Biomedical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, USA.
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7
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Jia QI. Generating and Screening a Natural Product Library for CYclooxygenase and Lipoxygenase Dual Inhibitors. BIOACTIVE NATURAL PRODUCTS (PART J) 2003. [DOI: 10.1016/s1572-5995(03)80016-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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8
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Chen L, Deem MW. Monte Carlo methods for small molecule high-throughput experimentation. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2001; 41:950-7. [PMID: 11500111 DOI: 10.1021/ci000151l] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By analogy with Monte Carlo algorithms, we propose new strategies for design and redesign of small molecule libraries in high-throughput experimentation, or combinatorial chemistry. Several Monte Carlo methods are examined, including Metropolis, three types of biased schemes, and composite moves that include swapping or parallel tempering. Among them, the biased Monte Carlo schemes exhibit particularly high efficiency in locating optimal compounds. The Monte Carlo strategies are compared to a genetic algorithm approach. Although the best compounds identified by the genetic algorithm are comparable to those from the better Monte Carlo schemes, the diversity of favorable compounds identified is reduced by roughly 60%.
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Affiliation(s)
- L Chen
- Department of Chemical Engineering, University of California, Los Angeles, California 90095-1592, USA
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9
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Floyd CD, Leblanc C, Whittaker M. Combinatorial chemistry as a tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2000; 36:91-168. [PMID: 10818672 DOI: 10.1016/s0079-6468(08)70046-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The question 'will combinatorial chemistry deliver real medicines' has been posed [96]. First it is important to realise that the chemical part of the drug discovery process cannot stand alone; the integration of synthesis and biological assays is fundamental to the combinatorial approach. The results presented in Tables 3.1 to 3.8 suggest that so far smaller directed combinatorial libraries have obtained equivalent results to those obtained previously from traditional medicinal chemistry analogue programs. Unfortunately, because of the long time it takes to develop pharmaceutical drugs there are no examples yet of marketed drugs discovered by combinatorial methods. There are interesting examples where active leads have been discovered from the screening of the same library against multiple targets (e.g. libraries 13, 39, 43, 66, 71 and 76). It is now possible to handle much larger libraries of non-oligomeric structures and the chemistry required for such applications is becoming available. Whether combinatorial approaches can also be adapted to deal with all the other requirements of a successful pharmaceutical (lack of toxicity, bioavailability etc.) is open to question but there are already examples such as cassette dosing [235-237]. However we can still be optimistic about the possibility of larger libraries producing avenues of investigation for the medicinal chemist to develop into real drugs. Combinatorial chemistry is an important tool for the medicinal chemist.
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Affiliation(s)
- C D Floyd
- British Biotech Pharmaceuticals Limited, Oxford, U.K
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10
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Abstract
The combination of high-performance liquid chromatography and mass spectrometry (LC/MS) has had a significant impact on drug development over the past decade. Continual improvements in LC/MS interface technologies combined with powerful features for structure analysis, qualitative and quantitative, have resulted in a widened scope of application. These improvements coincided with breakthroughs in combinatorial chemistry, molecular biology, and an overall industry trend of accelerated development. New technologies have created a situation where the rate of sample generation far exceeds the rate of sample analysis. As a result, new paradigms for the analysis of drugs and related substances have been developed. The growth in LC/MS applications has been extensive, with retention time and molecular weight emerging as essential analytical features from drug target to product. LC/MS-based methodologies that involve automation, predictive or surrogate models, and open access systems have become a permanent fixture in the drug development landscape. An iterative cycle of "what is it?" and "how much is there?" continues to fuel the tremendous growth of LC/MS in the pharmaceutical industry. During this time, LC/MS has become widely accepted as an integral part of the drug development process. This review describes the utility of LC/MS techniques for accelerated drug development and provides a perspective on the significant changes in strategies for pharmaceutical analysis. Future applications of LC/MS technologies for accelerated drug development and emerging industry trends are also discussed.
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Affiliation(s)
- M S Lee
- Milestone Development Services, Pennington, New Jersey 08534-0813, USA
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11
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Abstract
Inorganic complexes have long been utilized for many therapeutic purposes. They were used or tried, perhaps because of the general notion that inorganic compounds (e.g., metal complexes) are toxic and a controlled use of such a compound may suppress some biological process. In this review, we briefly outline the properties of several selected groups of inorganic complexes and how they can affect biological systems and contribute to human pathologies.
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Affiliation(s)
- R Bakhtiar
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Castle Point on Hudson, Hoboken, New Jersey 07030, USA
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13
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Lim HK, Stellingweif S, Sisenwine S, Chan KW. Rapid drug metabolite profiling using fast liquid chromatography, automated multiple-stage mass spectrometry and receptor-binding. J Chromatogr A 1999; 831:227-41. [PMID: 10070764 DOI: 10.1016/s0021-9673(98)00956-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rapid drug metabolite profiling can be achieved using fast chromatographic separation and fast mass spectrometric scanning without compromising the separation efficiency. Fast chromatographic separations of drug and its metabolites can be achieved by eluting from a short narrow-bore guard cartridge column (20 x 2 mm I.D., 3 microns BDS Hypersil C8) at flow-rate of 1.0 ml/min and with a gradient volume greater than 90 column volumes. The need for chromatographic separation is important for automated data dependent multiple-stage mass spectrometry (MSn) experimentation. The total analysis time of 8 min permits profiling of metabolites in a 96-well plate in 13 h. The narrow chromatographic peaks resulting from the high flow-rate require the use of a mass spectrometer capable of fast scan speed due to the need to perform multiple MS experiments within the same chromatographic analysis. A method has been developed for screening potentially biologically active in vitro microsomal metabolites by affinity binding with a receptor. After separation by centrifugal ultrafiltration, the bound ligands are released and characterized by LC-MS. In vitro microsomal metabolites of tamoxifen, raloxifene and adatanserin were screened for potential biological activity using this method. The in vitro metabolites of tamoxifen captured by the receptor include N-demethyltamoxifen and three species of hydroxytamoxifen; these data are consistent with those from a conventional binding study and bioassay. In addition, both hydroxyraloxifene and dihydroxyraloxifene are also recognized by the receptor. The specificity of the molecular recognition process is illustrated by the absence of binding with control microsomal incubate and with adatanserin and its metabolites. Therefore, active metabolites can be rapidly profiled by fast LC, automated MSn, and receptor binding. This information can be obtained quickly and can add value to the drug discovery process.
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Affiliation(s)
- H K Lim
- Wyeth-Ayerst Research, Princeton, NJ 08543-8000, USA.
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14
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Spellmeyer DC, Grootenhuis PD. Chapter 28. Recent Developments in Molecular Diversity: Computational Approaches to Combinatorial Chemistry. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1999. [DOI: 10.1016/s0065-7743(08)60590-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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15
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16
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Multicomponent solution phase synthesis of dehydroamino acid derivatives based on the Passerini reaction. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)01522-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Robinson GM, Manica DP, Taylor EW, Smyth MR, Lunte CE. Development of a capillary electrophoretic separation of an N-(substituted)-glycine-peptoid combinatorial mixture. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1998; 707:247-55. [PMID: 9613957 DOI: 10.1016/s0378-4347(97)00596-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Capillary electrophoresis was used for the separation of a combinatorially synthesized N-(substituted)-glycine (NSG) peptoid mixture. This mixture consisted of 24 trimeric compounds sharing a common backbone structure but differing in the side chain attached at the N-terminal residue. Standards of the individual components were unavailable so that development of the separation was based on the mixture. A variety of buffer additives were investigated to enhance the CE resolution of this diverse mixture. Ion-pairing agents, cyclodextrins and organic modifiers were all evaluated as buffer additives. The best separations were achieved using a combination of buffer additives, each serving a different purpose in the separation. Heptane sulphonic acid (HSA) was used to reduce hydrophobic intramolecular interactions. Methyl-beta-cyclodextrin was used to provide host-guest interactions in order to resolve the very hydrophobic components of the NSG-peptoid mixture. The optimized run buffer consisted of 250 mM sodium phosphate buffer, pH 2.0, with 25 mM HSA and 40 mg/ml BCD and resulted in the resolution of 21 peaks for the 24 peptoids in the combinatorial mixture.
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Affiliation(s)
- G M Robinson
- Dublin City University, Glasnevin, Dublin, Ireland
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18
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Kim SW, Hong CY, Lee K, Lee EJ, Koh JS. Solid phase synthesis of benzylamine-derived sulfonamide library. Bioorg Med Chem Lett 1998; 8:735-8. [PMID: 9871532 DOI: 10.1016/s0960-894x(98)00114-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Using solid phase synthesis, a library has been constructed of benzylamine-derived sulfonamides which have strong inhibitory activity against the blood coagulant thrombin. The library compounds were obtained in good yield and high purity; four of these thrombin inhibitors showed nanomolar potency (Ki 600-10 nM).
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Affiliation(s)
- S W Kim
- Biotech Research Institute, LG Chemical Ltd./Research Park Science Town, Taejon, Korea
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19
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Zhao YZ, van Breemen RB, Nikolic D, Huang CR, Woodbury CP, Schilling A, Venton DL. Screening solution-phase combinatorial libraries using pulsed ultrafiltration/electrospray mass spectrometry. J Med Chem 1997; 40:4006-12. [PMID: 9406591 DOI: 10.1021/jm960729b] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A method is described whereby a family of homologues is synthesized in a one-pot reaction, without isolation or purification, and the reaction mixture is screened using a competitive binding assay based on pulsed ultrafiltration/electrospray mass spectrometry (PUF/ESMS) to tentatively identify those derivatives having the highest affinity for a target receptor. As a model system to test this approach, a synthetic scheme designed to prepare a series of analogues of the adenosine deaminase inhibitor erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA), as diastereomeric mixtures, was carried out. Pulsed ultrafiltration screening of the crude reaction mixture against controls without protein detected protonated molecules corresponding to EHNA-type derivatives and three of its linear, alkyl homologues but did not show protonated molecules for an isobutyl or benzylic EHNA derivative, suggesting the latter was inactive. To verify this conclusion, we prepared E/THNA, the linear homologues, and the benzylic derivative (each as a diastereomeric mixture) and bioassayed them for them adenosine deaminase inhibition index ([I]/[S]0.5). The bioassay results for the individually synthesized analogues were in good agreement with that predicted by the observed relative ion enhancement in the PUF experiments. Thus, the PUF protocol might be used as a general method to quickly provide direction to the chemist in search of drug candidates.
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Affiliation(s)
- Y Z Zhao
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago 60612-7231, USA
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Brown EG, Nuss JM. Alkylation of Rink's amide linker on polystyrene resin: A reductive amination approach to modified amine-linkers for the solid phase synthesis of N-substituted amide derivatives. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)10279-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Kim SW, Ahn SY, Koh JS, Lee JH, Ro S, Cho HY. Solid phase synthesis of hydantoin library using a novel cyclization and traceless cleavage step. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)00986-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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23
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van Breemen RB, Huang CR, Nikolic D, Woodbury CP, Zhao YZ, Venton DL. Pulsed ultrafiltration mass spectrometry: a new method for screening combinatorial libraries. Anal Chem 1997; 69:2159-64. [PMID: 9183179 DOI: 10.1021/ac970132j] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In response to the need for rapid screening of combinatorial libraries to identify new lead compounds during drug discovery, we have developed an on-line combination of ultrafiltration and electrospray mass spectrometry, called pulsed ultrafiltration mass spectrometry, which facilitates the identification of solution-phase ligands in library mixtures that bind to solution-phase receptors. After ligands contained in a library mixture were bound to a macromolecular receptor, e.g., human serum albumin or calf intestine adenosine deaminase, the ligand-receptor complexes were purified by ultrafiltration and then dissociated using methanol to elute the ligands into the electrospray mass spectrometer for detection. Ligands with dissociation constants in the micromolar to nanomolar range were successfully bound, released, and detected using this method, including warfarin, salicylate, furosemide, and thyroxine binding to human serum albumin, and erythro-9-(2-hydroxy-3-nonyl)adenine binding to calf intestine adenosine deaminase. Repetitive bind- and-release experiments demonstrated that the receptor could be reused. Thus, pulsed ultrafiltration mass spectrometry was shown to provide a simple and powerful new method for the screening of combinatorial libraries in support of new drug discovery.
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Affiliation(s)
- R B van Breemen
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago 60612-7231, USA
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24
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Affiliation(s)
- Wendy A. Warr
- Wendy Warr & Associates, 6 Berwick Court, Holmes Chapel, Cheshire, CW4 7HZ, England
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26
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Synthesekontrolle in der kombinatorischen Chemie durch Suspensions-1H-MAS-NMR-Untersuchungen an einzelnen Harzpartikeln. Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961082340] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Hill CL, Gall RD. The first combinatorially prepared and evaluated inorganic catalysts. Polyoxometalates for the aerobic oxidation of the mustard analog tetrahydrothiophene (THT). ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s1381-1169(96)00308-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Wess G, Bock K, Kleine H, Kurz M, Guba W, Hemmerle H, Lopez-Calle E, Baringhaus KH, Glombik H, Enhsen A, Kramer W. Design und Synthese eines Gerüstes aus Gallensäure für die kombinatorische Chemie. Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961081914] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Wilson-Lingardo L, Davis PW, Ecker DJ, Hébert N, Acevedo O, Sprankle K, Brennan T, Schwarcz L, Freier SM, Wyatt JR. Deconvolution of combinatorial libraries for drug discovery: experimental comparison of pooling strategies. J Med Chem 1996; 39:2720-6. [PMID: 8709102 DOI: 10.1021/jm960169g] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
An experimental evaluation of several different pooling strategies for combinatorial libraries was conducted using a library of 810 compounds and an enzyme inhibition assay (phospholipase A2). The library contained compounds with varying degrees of activity as well as inactive compounds. The compounds were synthesized in groups of three and pooled together in various formats to realize different pooling strategies. With one exception, all iterative deconvolution strategies and position scanning resulted in identification of the same compound. The results are in good agreement with the predicted outcome from theoretical and computational methods. These data support the tenet that active compounds for pharmaceutically relevant targets can be successfully identified from combinatorial libraries organized in mixtures.
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Pearlman DA, Murcko MA. CONCERTS: dynamic connection of fragments as an approach to de novo ligand design. J Med Chem 1996; 39:1651-63. [PMID: 8648605 DOI: 10.1021/jm950792l] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We have implemented and tested a new approach to de novo ligand design, CONCERTS (creation of novel compounds by evaluation of residues at target sites). In this method, each member of a user-defined set of fragments is allowed to move independently about a target active site during a molecular dynamics simulation. This allows the fragments to sample various low-energy orientations. When the geometry between proximal fragments is appropriate, bonds can be formed between the fragments. In this fashion, larger molecules can be built. The bonding arrangement can subsequently be changed-breaking bonds between chosen fragment pairs and forming them between other pairs-if the overall process creates lower energy molecules. We have tested this method with various mixes of fragments against the active sites of the FK506 binding protein (FKBP-12) and HIV-1 aspartyl protease. In several cases, CONCERTS suggests ligands which are in surprisingly good agreement with known inhibitors of these proteins.
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Affiliation(s)
- D A Pearlman
- Vertex Pharmaceuticals Incorporated, Cambridge, Massachusetts 02139-4211, USA
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33
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Gordon EM, Gallop MA, Patel DV. Strategy and Tactics in Combinatorial Organic Synthesis. Applications to Drug Discovery. Acc Chem Res 1996. [DOI: 10.1021/ar950170u] [Citation(s) in RCA: 207] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E. M. Gordon
- Affymax Research Institute, 4001 Miranda Avenue, Palo Alto, California 94304
| | - M. A. Gallop
- Affymax Research Institute, 4001 Miranda Avenue, Palo Alto, California 94304
| | - D. V. Patel
- Affymax Research Institute, 4001 Miranda Avenue, Palo Alto, California 94304
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34
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Affiliation(s)
- Lorin A. Thompson
- Department of Chemistry, University of California, Berkeley, California 94720
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35
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Structure-activity relationship of a novel peptide substrate for p60c-src protein tyrosine kinase. ACTA ACUST UNITED AC 1996. [DOI: 10.1007/bf00142241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Chen CL, Strop P, Lebl M, Lam KS. One bead-one compound combinatorial peptide library: different types of screening. Methods Enzymol 1996; 267:211-9. [PMID: 8743318 DOI: 10.1016/s0076-6879(96)67014-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- C L Chen
- Hoechst Marion Roussel, Tucson, Arizona 85737, USA
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37
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Chabala JC. Solid-phase combinatorial chemistry and novel tagging methods for identifying leads. Curr Opin Biotechnol 1995; 6:632-9. [PMID: 8527833 DOI: 10.1016/0958-1669(95)80104-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Encoded combinatorial chemical synthesis on solid phase is a new paradigm in organic chemistry that provides chemists with powers similar to those enjoyed by molecular biologists. Encoded chemical libraries will have a profound impact on all endeavors that seek to identify molecules with optimized properties and to understand the factors governing molecular interactions. In particular, the discovery and optimization of new therapeutic and diagnostic drug molecules, traditionally a slow manual process, will be greatly accelerated by this technology.
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Abstract
New technology is emerging that permits the chemical synthesis of large numbers of different compounds simultaneously. Combinatorial chemistry is heavily dependent upon the adaptation of organic synthesis to solid supports and has necessitated the development of appropriate analytical and chemical approaches to both monitor solid-phase reactions and release finished compounds into solution. Considerable progress has recently been made in all of these areas. Small-molecule libraries of medicinally important chemical classes, such as 1,4-benzodiazepines, mercaptopropionyl amino acids, and peptidyl phosphonates, have recently been reported. Encoded combinatorial libraries of dihydrobenzopyran-based and acylpiperidine-based pharmacophores have yielded potent inhibitors of carbonic anhydrase. Automated instrumentation is growing in importance for the synthesis of small-molecule libraries.
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Neustadt B, Wu A, Smith E, Nechuta T, Fawzi A, Zhang H, Ganguly A. A case study of combinatorial libraries: Endothelin receptor antagonist hexapeptides. Bioorg Med Chem Lett 1995. [DOI: 10.1016/0960-894x(95)00349-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
|
Miller SM, Simon RJ, Ng S, Zuckermann RN, Kerr JM, Moos WH. Comparison of the proteolytic susceptibilities of homologous L-amino acid, D-amino acid, and N-substituted glycine peptide and peptoid oligomers. Drug Dev Res 1995. [DOI: 10.1002/ddr.430350105] [Citation(s) in RCA: 334] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Synthetic combinatorial libraries: Views on techniques and their application. ACTA ACUST UNITED AC 1995. [DOI: 10.1007/bf02172067] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bruce JE, Anderson GA, Chen R, Cheng X, Gale DC, Hofstadler SA, Schwartz BL, Smith RD. Bio-affinity characterization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 1995; 9:644-650. [PMID: 7647362 DOI: 10.1002/rcm.1290090805] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A new approach, bio-affinity characterization mass spectrometry (BACMS), aimed at providing a more rapid, sensitive and potentially more flexible alternative to techniques presently employed for the characterization of noncovalent interactions in mixtures, such as would be encountered in combinatorial chemistry, in presented. BACMS avoids some of the difficulties and potential artifacts associated with affinity chromatography since the noncovalent associations occur in solution; thus, BACMS avoids the requirement of solid support media and the development of non-interfering linker species. This paper describes the conceptual basis for the methodology and its potential use in applications which include the screening of high affinity ligands in support of new drug development. BACMS exploits new Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry technologies which, when coupled to electrospray ionization (ESI), allow the investigation of specific noncovalent complexes formed in solution. BACMS utilizes the well-known attributes of FTICR, such as the high resolution mass analysis and (MS)n (n > or = 2) capabilities; however, it is even more directly a result of recently developed techniques involving quadrupolar excitation, such as selected-ion accumulation. These tools are demonstrated and the results illustrate the extraordinary sensitivity achievable (solution concentration of 1 x 10-9 M without the use of separations prior to ESI). Thus, the new capabilities demonstrated here, in conjunction with ESI, will be useful for the investigation of very low relative concentration noncovalent association directly from solution, and promote a faster alternative for combinatorial mixture screening and analysis.
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Affiliation(s)
- J E Bruce
- Chemical Sciences Department, Pacific Northwest Laboratory, Richland, Washington 99352, USA
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