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Lau J, Rousseau E, Kwon D, Lin KS, Bénard F, Chen X. Insight into the Development of PET Radiopharmaceuticals for Oncology. Cancers (Basel) 2020; 12:E1312. [PMID: 32455729 PMCID: PMC7281377 DOI: 10.3390/cancers12051312] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
While the development of positron emission tomography (PET) radiopharmaceuticals closely follows that of traditional drug development, there are several key considerations in the chemical and radiochemical synthesis, preclinical assessment, and clinical translation of PET radiotracers. As such, we outline the fundamentals of radiotracer design, with respect to the selection of an appropriate pharmacophore. These concepts will be reinforced by exemplary cases of PET radiotracer development, both with respect to their preclinical and clinical evaluation. We also provide a guideline for the proper selection of a radionuclide and the appropriate labeling strategy to access a tracer with optimal imaging qualities. Finally, we summarize the methodology of their evaluation in in vitro and animal models and the road to clinical translation. This review is intended to be a primer for newcomers to the field and give insight into the workflow of developing radiopharmaceuticals.
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Affiliation(s)
- Joseph Lau
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Etienne Rousseau
- Department of Nuclear Medicine and Radiobiology, University of Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
| | - Daniel Kwon
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (D.K.); (K.-S.L.); (F.B.)
| | - Kuo-Shyan Lin
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (D.K.); (K.-S.L.); (F.B.)
| | - François Bénard
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (D.K.); (K.-S.L.); (F.B.)
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA;
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Lee J, Purushothaman B, Song JM. Inkjet Bioprinting on Parchment Paper for Hit Identification from Small Molecule Libraries. ACS OMEGA 2020; 5:588-596. [PMID: 31956806 PMCID: PMC6964283 DOI: 10.1021/acsomega.9b03169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
In this study, an inkjet bioprinting-based high-throughput screening (HTS) system was designed and applied for the first time to a catecholpyrimidine-based small molecule library to find hit compounds that inhibit c-Jun NH2-terminal kinase1 (JNK1). JNK1 kinase, inactivated MAPKAPK2, and specific fluorescent peptides along with bioink were printed on parchment paper under optimized printing conditions that did not allow rapid evaporation of printed media based on Triton-X and glycerol. Subsequently, different small compounds were printed and tested against JNK1 kinase to evaluate their degree of phosphorylation inhibition. After printing and incubation, fluorescence intensities from the phosphorylated/nonphosphorylated peptide were acquired for the % phosphorylation analysis. The IM50 (inhibitory mole 50) value was determined as 1.55 × 10-15 mol for the hit compound, 22. Thus, this work demonstrated that inkjet bioprinting-based HTS can potentially be adopted for the drug discovery process using small molecule libraries, and cost-effective HTS can be expected to be established based on its low nano- to picoliter printing volume.
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Guo X, Wang L, Hu J, Zhang M. CuI nanoparticle-catalyzed synthesis of tetracyclic benzo[ e]benzo[4,5]imidazo[1,2- c][1,3]thiazin-6-imine heterocycles by S NAr-type C-S, C-N bond formation from isothiocyanatobenzenes and benzimidazoles. RSC Adv 2018; 8:22259-22267. [PMID: 35541714 PMCID: PMC9081286 DOI: 10.1039/c8ra02552e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 06/04/2018] [Indexed: 11/21/2022] Open
Abstract
In this paper, a simple and practical synthesis of benzo[e]benzo[4,5]imidazo[1,2-c][1,3]thiazin-6-imine tetracyclic heterocycles via a CuI nanoparticle-catalyzed intramolecular C(sp2)-S coupling reaction is presented. This strategy provides a straightforward method for synthesizing analogs of the anti-HIV drug 3,4-dihydro-2H,6H-pyrimido[1,2-c][1,3]benzothiazin-6-imine (PD 404182). The reaction rate and yield were increased by employing CuI nanoparticles.
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Affiliation(s)
- Xiaolong Guo
- Department of Chemistry, Capital Normal University Beijing 100048 China
| | - Luyao Wang
- Department of Chemistry, Capital Normal University Beijing 100048 China
| | - Jing Hu
- Department of Chemistry, Capital Normal University Beijing 100048 China
| | - Mengmeng Zhang
- Department of Chemistry, Capital Normal University Beijing 100048 China
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Kowalczyk W, Sanchez J, Kraaz P, Hutt OE, Haylock DN, Duggan PJ. The binding of boronated peptides to low affinity mammalian saccharides. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.23101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Julie Sanchez
- CSIRO Manufacturing, Bag 10; Clayton South Victoria 3169 Australia
- Institut de Recherche de Chimie Paris, CNRS - Chimie ParisTech, 11 rue Pierre et Marie Curie; Paris 75005 France
| | - Phillipe Kraaz
- CSIRO Manufacturing, Bag 10; Clayton South Victoria 3169 Australia
| | - Oliver E. Hutt
- CSIRO Manufacturing, Bag 10; Clayton South Victoria 3169 Australia
| | - David N. Haylock
- CSIRO Manufacturing, Bag 10; Clayton South Victoria 3169 Australia
| | - Peter J. Duggan
- CSIRO Manufacturing, Bag 10; Clayton South Victoria 3169 Australia
- School of Chemical and Physical Sciences; Flinders University; Adelaide South Australia 5042 Australia
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Kowalczyk W, Sanchez J, Kraaz P, Hutt OE, Haylock DN, Duggan PJ. The binding of boronated peptides to low affinity mammalian saccharides. Biopolymers 2018:e23101. [PMID: 29381187 DOI: 10.1002/bip.23101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 11/09/2022]
Abstract
A 54-member library of boronated octapeptides, with all but the boronated residue being proteinogenic, was tested for affinity to a set of saccharides commonly found on the terminus of mammalian glycans. After experimentation with a high-throughput dye-displacement assay, attention was focused on isothermal titration calorimetry as a tool to provide reliable affinity data, including enthalpy and entropy of binding. A small number of boronated peptides showed higher affinity and significant selectivity for N-acetylneuraminic acid over methyl-α-d-galactopyranoside, methyl-α/β-l-fucopyranoside and N-acetyl-d-glucosamine. Thermodynamic data showed that for most of the boronated peptides studied, saccharide binding was associated with a significant increase in entropy, presumably resulting from the displacement of semiordered water molecules from around the sugar and/or peptide.
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Affiliation(s)
- Wioleta Kowalczyk
- CSIRO Manufacturing, Bag 10, Clayton South, Victoria, 3169, Australia
| | - Julie Sanchez
- CSIRO Manufacturing, Bag 10, Clayton South, Victoria, 3169, Australia
- Institut de Recherche de Chimie Paris, CNRS - Chimie ParisTech, 11 rue Pierre et Marie Curie, Paris, 75005, France
| | - Phillipe Kraaz
- CSIRO Manufacturing, Bag 10, Clayton South, Victoria, 3169, Australia
| | - Oliver E Hutt
- CSIRO Manufacturing, Bag 10, Clayton South, Victoria, 3169, Australia
| | - David N Haylock
- CSIRO Manufacturing, Bag 10, Clayton South, Victoria, 3169, Australia
| | - Peter J Duggan
- CSIRO Manufacturing, Bag 10, Clayton South, Victoria, 3169, Australia
- School of Chemical and Physical Sciences, Flinders University, Adelaide, South Australia, 5042, Australia
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Zhu W, Chen H, Wang Y, Wang J, Peng X, Chen X, Gao Y, Li C, He Y, Ai J, Geng M, Zheng M, Liu H. Design, Synthesis, and Pharmacological Evaluation of Novel Multisubstituted Pyridin-3-amine Derivatives as Multitargeted Protein Kinase Inhibitors for the Treatment of Non-Small Cell Lung Cancer. J Med Chem 2017; 60:6018-6035. [PMID: 28714692 DOI: 10.1021/acs.jmedchem.7b00076] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A novel series of pyridin-3-amine derivatives were designed, synthesized, and evaluated as multitargeted protein kinase inhibitors for the treatment of non-small cell lung cancer (NSCLC). Hit 1 was first disclosed by in silico screening against fibroblast growth factor receptors (FGFR), which was subsequently validated by in vitro experiments. The structure-activity relationship (SAR) of its analogues was then explored to afford novel FGFR inhibitors 2a-2p and 3a-3q. Among them, 3m showed potent inhibition against FGFR1, 2, and 3. Interestingly, compound 3m not only inhibited various phosphorylation and downstream signaling across different oncogenic forms in FGFR-overactivated cancer cells but also showed nanomolar level inhibition against several other NSCLC-related oncogene kinases, including RET, EGFR, EGFR/T790M/L858R, DDR2, and ALK. Finally, in vivo pharmacology evaluations of 3m showed significant antitumor activity (TGI = 66.1%) in NCI-H1581 NSCLC xenografts with a good pharmacokinetic profile.
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Affiliation(s)
- Wei Zhu
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Hui Chen
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Yulan Wang
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Jiang Wang
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Xia Peng
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Xianjie Chen
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Yinglei Gao
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Chunpu Li
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Yulong He
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Jing Ai
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Meiyu Geng
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Mingyue Zheng
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Hong Liu
- University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
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Wang Z, Sun H, Yao X, Li D, Xu L, Li Y, Tian S, Hou T. Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power. Phys Chem Chem Phys 2016; 18:12964-75. [PMID: 27108770 DOI: 10.1039/c6cp01555g] [Citation(s) in RCA: 563] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
As one of the most popular computational approaches in modern structure-based drug design, molecular docking can be used not only to identify the correct conformation of a ligand within the target binding pocket but also to estimate the strength of the interaction between a target and a ligand. Nowadays, as a variety of docking programs are available for the scientific community, a comprehensive understanding of the advantages and limitations of each docking program is fundamentally important to conduct more reasonable docking studies and docking-based virtual screening. In the present study, based on an extensive dataset of 2002 protein-ligand complexes from the PDBbind database (version 2014), the performance of ten docking programs, including five commercial programs (LigandFit, Glide, GOLD, MOE Dock, and Surflex-Dock) and five academic programs (AutoDock, AutoDock Vina, LeDock, rDock, and UCSF DOCK), was systematically evaluated by examining the accuracies of binding pose prediction (sampling power) and binding affinity estimation (scoring power). Our results showed that GOLD and LeDock had the best sampling power (GOLD: 59.8% accuracy for the top scored poses; LeDock: 80.8% accuracy for the best poses) and AutoDock Vina had the best scoring power (rp/rs of 0.564/0.580 and 0.569/0.584 for the top scored poses and best poses), suggesting that the commercial programs did not show the expected better performance than the academic ones. Overall, the ligand binding poses could be identified in most cases by the evaluated docking programs but the ranks of the binding affinities for the entire dataset could not be well predicted by most docking programs. However, for some types of protein families, relatively high linear correlations between docking scores and experimental binding affinities could be achieved. To our knowledge, this study has been the most extensive evaluation of popular molecular docking programs in the last five years. It is expected that our work can offer useful information for the successful application of these docking tools to different requirements and targets.
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Affiliation(s)
- Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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A Multimodal Data Analysis Approach for Targeted Drug Discovery Involving Topological Data Analysis (TDA). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 899:253-68. [PMID: 27325272 DOI: 10.1007/978-3-319-26666-4_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In silico drug discovery refers to a combination of computational techniques that augment our ability to discover drug compounds from compound libraries. Many such techniques exist, including virtual high-throughput screening (vHTS), high-throughput screening (HTS), and mechanisms for data storage and querying. However, presently these tools are often used independent of one another. In this chapter, we describe a new multimodal in silico technique for the hit identification and lead generation phases of traditional drug discovery. Our technique leverages the benefits of three independent methods-virtual high-throughput screening, high-throughput screening, and structural fingerprint analysis-by using a fourth technique called topological data analysis (TDA). We describe how a compound library can be independently tested with vHTS, HTS, and fingerprint analysis, and how the results can be transformed into a topological data analysis network to identify compounds from a diverse group of structural families. This process of using TDA or similar clustering methods to identify drug leads is advantageous because it provides a mechanism for choosing structurally diverse compounds while maintaining the unique advantages of already established techniques such as vHTS and HTS.
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Abstract
Natural products have traditionally been a major source of leads in the drug discovery process. However, the development of high-throughput screening led to an increased interest in synthetic methods that enabled the rapid construction of large libraries of molecules. This resulted in the termination or downscaling of many natural product research programs, but the chemical libraries did not necessarily produce a larger amount of drug leads. On one hand, this chapter explores the current state of natural product research within the drug discovery process. On the other hand it evaluates the efforts made to increase the amount of leads generated from chemical libraries and considers what role natural products could play here.
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Affiliation(s)
- Eric F van Herwerden
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Roderich D Süssmuth
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 124, 10623, Berlin, Germany.
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10
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Leeson PD, Davis AM, Steele J. Drug-like properties: guiding principles for design - or chemical prejudice? DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 1:189-95. [PMID: 24981484 DOI: 10.1016/j.ddtec.2004.11.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The concepts of 'drug-like' and 'lead-like' chemical properties are having a major influence on the selection of compounds for high-throughput screening, and in the design of lead generation libraries. Medicinal chemists are recycling 'privileged' drug-like structures, whilst aiming to seek optimal physical properties for oral delivery. This approach biases the chemical profiles of compound screening collections towards known structures. Novel library synthesis, creating new chemical classes to address intellectual property, toxicity issues, and less chemically tractable targets, though considered risky, is warranted.:
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Affiliation(s)
- Paul D Leeson
- Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leics, UK LE11 5RH.
| | - Andrew M Davis
- Department of Physical and Metabolic Science, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leics, UK LE11 5RH
| | - John Steele
- Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leics, UK LE11 5RH
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Sharpless KB, Manetsch R. In situ click chemistry: a powerful means for lead discovery. Expert Opin Drug Discov 2013; 1:525-38. [PMID: 23506064 DOI: 10.1517/17460441.1.6.525] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combinatorial chemistry and parallel synthesis are important and regularly applied tools for lead identification and optimisation, although they are often accompanied by challenges related to the efficiency of library synthesis and the purity of the compound library. In the last decade, novel means of lead discovery approaches have been investigated where the biological target is actively involved in the synthesis of its own inhibitory compound. These fragment-based approaches, also termed target-guided synthesis (TGS), show great promise in lead discovery applications by combining the synthesis and screening of libraries of low molecular weight compounds in a single step. Of all the TGS methods, the kinetically controlled variant is the least well known, but it has the potential to emerge as a reliable lead discovery method. The kinetically controlled TGS approach, termed in situ click chemistry, is discussed in this article.
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Affiliation(s)
- K Barry Sharpless
- WM Keck Professor, Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC-315 La Jolla, CA 92037, USA.
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12
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Baghbanzadeh M, Pilger C, Kappe CO. Palladium-Catalyzed Direct Arylation of Heteroaromatic Compounds: Improved Conditions Utilizing Controlled Microwave Heating. J Org Chem 2011; 76:8138-42. [DOI: 10.1021/jo201516v] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mostafa Baghbanzadeh
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University, Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | | | - C. Oliver Kappe
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University, Graz, Heinrichstrasse 28, 8010 Graz, Austria
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Simmons KJ, Chopra I, Fishwick CWG. Structure-based discovery of antibacterial drugs. Nat Rev Microbiol 2011; 8:501-10. [PMID: 20551974 DOI: 10.1038/nrmicro2349] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The modern era of antibacterial chemotherapy began in the 1930s, and the next four decades saw the discovery of almost all the major classes of antibacterial agents that are currently in use. However, bacterial resistance to many of these drugs is becoming an increasing problem. As such, the discovery of drugs with novel modes of action will be vital to meet the threats created by the emergence of resistance. Success in discovering inhibitors using high-throughput screening of chemical libraries is rare. In this Review we explore the exciting opportunities for antibacterial-drug discovery arising from structure-based drug design.
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Affiliation(s)
- Katie J Simmons
- Antimicrobial Research Centre, University of Leeds, Leeds, UK
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Computational medicinal chemistry in fragment-based drug discovery: what, how and when. Future Med Chem 2011; 3:95-134. [DOI: 10.4155/fmc.10.277] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The use of fragment-based drug discovery (FBDD) has increased in the last decade due to the encouraging results obtained to date. In this scenario, computational approaches, together with experimental information, play an important role to guide and speed up the process. By default, FBDD is generally considered as a constructive approach. However, such additive behavior is not always present, therefore, simple fragment maturation will not always deliver the expected results. In this review, computational approaches utilized in FBDD are reported together with real case studies, where applicability domains are exemplified, in order to analyze them, and then, maximize their performance and reliability. Thus, a proper use of these computational tools can minimize misleading conclusions, keeping the credit on FBDD strategy, as well as achieve higher impact in the drug-discovery process. FBDD goes one step beyond a simple constructive approach. A broad set of computational tools: docking, R group quantitative structure–activity relationship, fragmentation tools, fragments management tools, patents analysis and fragment-hopping, for example, can be utilized in FBDD, providing a clear positive impact if they are utilized in the proper scenario – what, how and when. An initial assessment of additive/non-additive behavior is a critical point to define the most convenient approach for fragments elaboration.
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Mizuhara T, Oishi S, Fujii N, Ohno H. Efficient Synthesis of Pyrimido[1,2-c] [1,3]benzothiazin-6-imines and Related Tricyclic Heterocycles by SNAr-Type C−S, C−N, or C−O Bond Formation with Heterocumulenes. J Org Chem 2009; 75:265-8. [DOI: 10.1021/jo902327n] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tsukasa Mizuhara
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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18
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Malo S. The contribution of (not so) public research to commercial innovations in the field of combinatorial chemistry. RESEARCH POLICY 2009. [DOI: 10.1016/j.respol.2009.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Vriamont N, Govaerts B, Grenouillet P, de Bellefon C, Riant O. Design of a Genetic Algorithm for the Simulated Evolution of a Library of Asymmetric Transfer Hydrogenation Catalysts. Chemistry 2009; 15:6267-78. [DOI: 10.1002/chem.200802192] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sakamoto S, Kabe Y, Hatakeyama M, Yamaguchi Y, Handa H. Development and application of high-performance affinity beads: Toward chemical biology and drug discovery. CHEM REC 2009; 9:66-85. [DOI: 10.1002/tcr.20170] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Sladojevich F, Trabocchi A, Guarna A. Stereoselective cyclopropanation of serine- and threonine-derived oxazines to access new morpholine-based scaffolds. Org Biomol Chem 2008; 6:3328-36. [PMID: 18802639 DOI: 10.1039/b808895k] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general strategy for the synthesis of novel, orthogonally protected scaffolds based on the unique 2-oxa-5-azabicyclo[4.1.0]heptane structure is presented. The described reaction sequence takes advantage of easily available starting materials such as serine and threonine and leads to stereochemically dense structures in few, high-yielding synthetic steps. We show how the stereochemistry can be easily tuned by starting from different beta-hydroxy-alpha-amino acids and also by means of a transition metal-catalyzed cyclopropanation step. The compounds find application as constrained templates for the construction of geometrically diversified libraries of compounds.
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Affiliation(s)
- Filippo Sladojevich
- Department of Organic Chemistry Ugo Schiff, University of Florence, Polo Scientifico e Tecnologico, Via della Lastruccia 13, I-50019, Sesto Fiorentino (FI), Italy
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Srinivasan R, Tan LP, Wu H, Yao SQ. Solid-Phase Assembly and In Situ Screening of Protein Tyrosine Phosphatase Inhibitors. Org Lett 2008; 10:2295-8. [DOI: 10.1021/ol8006875] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajavel Srinivasan
- Departments of Chemistry and Biological Sciences, NUS MedChem Program of the Office of Life Sciences, National University of Singapore, Singapore 117543
| | - Lay Pheng Tan
- Departments of Chemistry and Biological Sciences, NUS MedChem Program of the Office of Life Sciences, National University of Singapore, Singapore 117543
| | - Hao Wu
- Departments of Chemistry and Biological Sciences, NUS MedChem Program of the Office of Life Sciences, National University of Singapore, Singapore 117543
| | - Shao Q. Yao
- Departments of Chemistry and Biological Sciences, NUS MedChem Program of the Office of Life Sciences, National University of Singapore, Singapore 117543
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Liu Z, Mu Y, Song Z. Solid Phase Synthesis of 4,5-disubstituted 1,2,4-triazol-3-one Derivatives from resin-bound Acylhydrazines. JOURNAL OF CHEMICAL RESEARCH 2008. [DOI: 10.3184/030823408x314725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A new strategy for solid-phase synthesis of 4,5-disubstituted 2,4-dihydro-3 H-1,2,4-triazol-3-ones has been developed. The 4-substituted 5-(4-hydroxyphenyl)-1,2,4-triazol-3-one derivatives were synthesised from resin-bound acylhydrazines in several steps, in good overall yields and purity.
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Affiliation(s)
- Zhanxiang Liu
- Department of Chemistry, Zhejiang University (Campus Xixi), Hangzhou 310028, P.R. China
| | - Yuanyuan Mu
- Department of Chemistry, Zhejiang University (Campus Xixi), Hangzhou 310028, P.R. China
| | - Zhaosheng Song
- Department of Chemistry, Zhejiang University (Campus Xixi), Hangzhou 310028, P.R. China
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24
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Development of a chemical screening system using aqueorin-fused protein. Biochem Biophys Res Commun 2008; 368:600-5. [DOI: 10.1016/j.bbrc.2008.01.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 01/22/2008] [Indexed: 11/22/2022]
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25
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Pearlman DA, Rao BG, Charifson P. FURSMASA: A new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data. Proteins 2008; 71:1519-38. [DOI: 10.1002/prot.21991] [Citation(s) in RCA: 6] [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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26
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27
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Jones JO, Diamond MI. Design and implementation of cell-based assays to model human disease. ACS Chem Biol 2007; 2:718-24. [PMID: 18030988 DOI: 10.1021/cb700177u] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cell-based assays, if appropriately designed, can be used to rapidly identify molecular mechanisms of human disease and develop novel therapeutics. In the last 20 years, many genes that cause or contribute to diverse disorders, including cancer and neurodegenerative disease, have been identified. With such genes in hand, scientists have created numerous model systems to dissect the molecular mechanisms of basic cellular and developmental biology. Meanwhile, techniques for high-throughput screening that use large chemical libraries have been developed, as have cDNA and RNA interference libraries that cover the entire human genome. By combining cell-based assays with chemical and genetic screens, we now have vastly improved our ability to dissect molecular mechanisms of disease and to identify therapeutic targets and therapeutic lead compounds. However, cell-based screening systems have yet to yield many fundamental insights into disease pathogenesis, and the development of therapeutic leads is frustratingly slow. This may be due to a failure of such assays to accurately reflect key aspects of pathogenesis. This Review attempts to guide the design of productive cellular models of human disease that may be used in high-throughput chemical and genetic screens. We emphasize two points: (i) model systems should use quantifiable molecular indicators of a pathogenic process, and (ii) small chemical libraries that include molecules with known biological activity and/or acceptable safety profiles are very useful.
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Affiliation(s)
- Jeremy O. Jones
- Departments of Neurology and Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143-2280
| | - Marc I. Diamond
- Departments of Neurology and Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143-2280
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28
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Williams DR, Lee MR, Song YA, Ko SK, Kim GH, Shin I. Synthetic small molecules that induce neurogenesis in skeletal muscle. J Am Chem Soc 2007; 129:9258-9. [PMID: 17622149 DOI: 10.1021/ja072817z] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Griffiths-Jones CM, Hopkin MD, Jönsson D, Ley SV, Tapolczay DJ, Vickerstaffe E, Ladlow M. Fully automated flow-through synthesis of secondary sulfonamides in a binary reactor system. ACTA ACUST UNITED AC 2007; 9:422-30. [PMID: 17348713 DOI: 10.1021/cc060152b] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A fully automated flow-through process for the production of secondary sulfonamides is presented. Primary sulfonamides were monoalkylated using a two-step "catch and release" protocol to generate library products of high purity. The automated flow synthesis platform incorporates four independent reactor columns and is able to perform automated column regeneration. A 48-member sulfonamide library was prepared as two 24-member sublibraries, affording library compounds in good yields and high purities without the need for further column chromatographic purification.
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Affiliation(s)
- Charlotte M Griffiths-Jones
- GlaxoSmithKline Cambridge Technology Centre, University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
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31
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Goodnow RA, Gillespie P. 1Hit and Lead Identification: Efficient Practices for Drug Discovery. PROGRESS IN MEDICINAL CHEMISTRY 2007; 45:1-61. [PMID: 17280901 DOI: 10.1016/s0079-6468(06)45501-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Robert A Goodnow
- Discovery Chemistry, Roche Research Center, Nutley, NJ 07110-1199, USA
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32
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Kou BB, Zhang F, Yang TM, Liu G. Simultaneous Solid-Phase Synthesis of Quinoxalinone and Benzimidazole Scaffold Libraries. ACTA ACUST UNITED AC 2006; 8:841-7. [PMID: 17096573 DOI: 10.1021/cc060074s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article describes a method for simultaneous solid-phase synthesis of a quinoxalinone and benzimidazole scaffold library that consists of 240 members. The library was generated by using the solid-phase "split-and-pool" approach and the IRORI sorting system.
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Affiliation(s)
- Bin-Bin Kou
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 1 Xian Nong Tan Street, Beijing 100050, PR China
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33
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Portal CF, Bradley M. High-Throughput Physical Organic Chemistry Hammett Parameter Evaluation. Anal Chem 2006; 78:4931-7. [PMID: 16841913 DOI: 10.1021/ac060596u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-throughput analysis techniques were developed to allow the rapid assessment of a range of Hammett parameters utilizing positive electrospray mass spectrometry (ESI+ -MS) as the sole quantitative tool, with the core of the approach being a so-called "analytical construct". Hammett substituent parameters were determined for a range of meta- and para-substituted anilines by high-throughput (HT) assessment of relative reaction rates for competitive amide bond formation reaction with up to five parameters determined in a single pot reaction. Sensitivity of the reaction to substituents' effects (materialized by Hammett's rho parameter) was determined in the first instance, with HT Hammett's sigma substituent parameter assessment then carried out successfully for over 30 anilines, with excellent correlation observed between the HT ESI+ -MS method of determination and literature values.
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Affiliation(s)
- Christophe F Portal
- Combinatorial Centre of Excellence, School of Chemistry, The University of Edinburgh, Edinburgh EH9 3JJ, UK
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Liu Z, Zhao J, Huang X. Solid-phase synthesis of 1,3,4-oxadiazoline-5-thione derivatives from resin-bound acylhydrazines. Bioorg Med Chem Lett 2006; 16:1828-30. [PMID: 16442286 DOI: 10.1016/j.bmcl.2006.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Revised: 12/16/2005] [Accepted: 01/05/2006] [Indexed: 11/30/2022]
Abstract
A new strategy for solid-phase synthesis of 2,5-disubstituted 1,3,4-oxadiazoles has been developed. The 1,3,4-oxadiazoline-5-thione derivatives were synthesized from resin-bound acylhydrazines in several steps providing 78-88% overall yields and excellent purity.
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Affiliation(s)
- Zhanxiang Liu
- Department of Chemistry, Zhejiang University (Campus Xixi), Hangzhou 310028, People's Republic of China.
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35
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Abstract
Novel starting points for drug discovery projects are generally found either by screening large collections of compounds or smaller more-focused libraries. Ideally, hundreds or even thousands of actives are initially found, and these need to be reduced to a handful of promising lead series. In several sequential steps, many actives are dropped and only some are followed up. Computational chemistry tools are used in this context to predict properties, cluster hits, design focused libraries and search for close analogues to explore the potential of hit series. At the end of hit-to-lead, the project must commit to one, or preferably a few, lead series that will be refined during lead optimization and hopefully produce a drug candidate. Striving for the best possible decision is crucial because choosing the wrong series is a costly one-way street.
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Affiliation(s)
- Volker Schnecke
- Computational Lead Discovery, Department of Medicinal Chemistry, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden.
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36
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Gombosuren N, Novák Z, Kotschy A, Mincsovics E, Dibó G. A multidimensional overpressured layer chromatographic method for the characterization of tetrazine libraries. ACTA ACUST UNITED AC 2006; 69:239-49. [PMID: 16516973 DOI: 10.1016/j.jbbm.2005.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 11/22/2005] [Accepted: 12/04/2005] [Indexed: 11/20/2022]
Abstract
The recent combinatorial approach in synthetic organic chemistry started a new age in drug discovery. The generation of compound libraries in combination with high-throughput screening has become the method of choice for the production of new pharmacological leads for chemical optimization. Characterization and separation of such pool of compounds have been lagging behind the synthetic and screening methodologies. Overpressured layer chromatography (OPLC) is an instrumentalized planar liquid chromatographic technique associated with the use of optimized layers prepared from particles of narrow particle size distribution and small diameter. On one hand, uni-directional OPLC allows the simultaneous separation of large number of samples in minutes. On the other hand, two-dimensional OPLC offers multidimensional separation on a single layer. This paper shows the complete multidimensional separation of a tetrazine library prepared by parallel combinatorial synthesis. In general, this approach may become the method of choice for the characterization of compound libraries.
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Affiliation(s)
- Naran Gombosuren
- Eötvös Loránd University, Department of Organic Chemistry, Pázmány sétány 1/A, H-1117 Budapest, Hungary
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37
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Koch MA, Waldmann H. Protein structure similarity clustering and natural product structure as guiding principles for chemical genomics. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2006:89-109. [PMID: 16709001 DOI: 10.1007/978-3-540-37635-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The majority of all proteins are modularly built from a limited set of approximately 1,000 structural domains. The knowledge of a common protein fold topology in the ligand-sensing cores of protein domains can be exploited for the design of small-molecule libraries in the development of inhibitors and ligands. Thus, a novel strategy of clustering protein domain cores based exclusively on structure similarity considerations (protein structure similarity clustering, PSSC) has been successfully applied to the development of small-molecule inhibitors of acetylcholinesterase and the 11beta-hydroxysteroid dehydrogenases based on the structure of a naturally occurring Cdc25 inhibitor. The efficiency of making use of the scaffolds of natural products as biologically prevalidated starting points for the design of compound libraries is further highlighted by the development of benzopyran-based FXR ligands.
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Affiliation(s)
- M A Koch
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Dortmund, Germany
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38
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Koukoulitsa C, Geromichalos GD, Skaltsa H. VolSurf analysis of pharmacokinetic properties for several antifungal sesquiterpene lactones isolated from Greek Centaurea sp. J Comput Aided Mol Des 2005; 19:617-23. [PMID: 16254688 DOI: 10.1007/s10822-005-9018-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Accepted: 09/20/2005] [Indexed: 11/25/2022]
Abstract
Sesquiterpene lactones are terpenoid compounds characteristic of the Asteraceae (Compositae) possessing a variety of biological activities, such as cytotoxic, antitumor, antibacterial, and antifungal. The prediction of the pharmacokinetic profile of several antifungal sesquiterpene lactones, isolated from Greek taxa of Centaurea sp., was undertaken in this study using the VolSurf procedure. The molecules were projected on the following pre-calculated ADME models: Caco-2 cell permeability, plasma protein affinity, blood-brain barrier permeation and thermodynamic solubility. The in silico projection revealed a non optimal pharmacokinetic profile for the studied compounds. ADME in silico screening of a semi-synthetic derivatives virtual library has been performed in order to optimize the pharmacokinetic properties. A number of derivatives were proposed as it was predicted to have higher Caco-2 cell permeability, while the pharmacokinetic behaviour regarding BBB penetration, protein binding and solubility was mainly preserved.
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Affiliation(s)
- Catherine Koukoulitsa
- Department of Pharmacognosy & Chemistry of Natural Products, School of Pharmacy, University of Athens, Panepistimiopolis, Zografou, GR-157 71, Athens, Greece.
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39
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Yan SF, Asatryan H, Li J, Zhou Y. Novel Statistical Approach for Primary High-Throughput Screening Hit Selection. J Chem Inf Model 2005; 45:1784-90. [PMID: 16309285 DOI: 10.1021/ci0502808] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The standard activity threshold-based method (the "top X" approach), currently widely used in the high-throughput screening (HTS) data analysis, is ineffective at identifying good-quality hits. We have proposed a novel knowledge-based statistical approach, driven by the hidden structure-activity relationship (SAR) within a screening library, for primary hit selection. Application to an in-house ultrahigh-throughput screening (uHTS) campaign has demonstrated it can directly identify active scaffolds containing valuable SAR information with a greatly improved confirmation rate compared to the standard "top X" method (from 55% to 85%). This approach may help produce high-quality leads and expedite the hit-to-lead process in drug discovery.
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Affiliation(s)
- S Frank Yan
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA.
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40
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Jose J, Betscheider D, Zangen D. Bacterial surface display library screening by target enzyme labeling: Identification of new human cathepsin G inhibitors. Anal Biochem 2005; 346:258-67. [PMID: 16225837 DOI: 10.1016/j.ab.2005.08.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 07/21/2005] [Accepted: 08/08/2005] [Indexed: 11/21/2022]
Abstract
The aim of this study was to establish a new tool for screening surface displayed peptide libraries based on the idea that cells expressing an enzyme inhibitor at the surface can be specifically labeled by the target enzyme. For this purpose peptide P15, exhibiting a K(i) value of 0.25 microM toward human cathepsin G, was expressed on the Escherichia coli cell surface by the use of Autodisplay. Purified cathepsin G was coupled to biotin and incubated with cells expressing the inhibitor. After addition of streptavidin-fluorescein isothiocyanate, these cells could be clearly differentiated from control cells by whole-cell fluorescence using flow cytometer analysis. To determine whether this protocol can be used for the sorting of single cells, a mixed population of cells with and without inhibitor was treated accordingly. Single cells were selected by increased fluorescence and sorted using fluorescence-activated cell sorting (FACS). Single cell clones were obtained and subjected to DNA sequence analysis. It turned out that the bacteria selected by this protocol displayed the correct peptide inhibitor at the cell surface. The protocol was then used to screen random peptide libraries, expressed at the cell surface, and a new lead structure for human cathepsin G (IC50 = 11.7 microM) was identified. The new drug discovery tool presented here consists of three steps: (a) surface display of peptide libraries, (b) selection of single cells with inhibiting structures by using the inherent affinity of the target enzyme, and (c) sorting of single cells, which were labeled by FACS.
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Affiliation(s)
- Joachim Jose
- Bioanalytics, Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Universitaetsstr. 1, 40225 Duesseldorf, Germany.
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41
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Gonthier E, Breinbauer R. Solid-supported reagents and catalysts for the preparation of large ring compounds. Mol Divers 2005; 9:51-62. [PMID: 15789552 DOI: 10.1007/s11030-005-1308-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Parallel combinatorial synthesis in solution using immobilized reagents, catalysts, and scavengers has emerged as a powerful technique for the preparation of diverse libraries of compounds. This technique has only recently been applied to the synthesis of large-ring compounds. In this comprehensive review several strategies are presented and discussed, including Pd-catalyzed allylic alkylation, Stille-coupling, macrolactonization and macrolactamization using solid supported reagents and catalysts. In several cases site isolation has allowed operation, of these macrocyclization reactions in concentrated solution (pseudo-dilution effect).
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42
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Portal C, Launay D, Merritt A, Bradley M. High Throughput Physical Organic Chemistry: Analytical Constructs for Monomer Reactivity Profiling. ACTA ACUST UNITED AC 2005; 7:554-60. [PMID: 16004498 DOI: 10.1021/cc050013e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A polymer-supported analytical construct was used to quantify the reactivity of a range of monomers in the Ugi four-component condensation using positive electrospray ionization mass spectrometry (MS) as a quantitative analytical tool. The construct incorporated a bromo group to act as a peak splitter and a quaternary ammonium to act as a MS sensitizer and ionization leveler, thereby allowing direct quantitation of the cleaved adducts by MS. The relative reactivities of 10 carboxylic acids were quantified by the relative levels of product generated as determined by MS and 10 isonitriles, and 10 aldehydes were investigated in the same way. The effect of concentration variations on monomers reactivity and product profiles were rapidly determined using this approach, and the method opens up the way for studying, in a single pot, multiple reactions with a broad range of monomers under identical and self-consistent reaction conditions.
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Affiliation(s)
- Christophe Portal
- Combinatorial Centre of Excellence, School of Chemistry, The University of Edinburgh, Edinburgh EH9 3JJ, UK
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43
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Jönsson D, Warrington BH, Ladlow M. Automated flow-through synthesis of heterocyclic thioethers. ACTA ACUST UNITED AC 2005; 6:584-95. [PMID: 15244420 DOI: 10.1021/cc0499486] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The fully automated, sequential flow-through synthesis of a 44-member array of thioethers 10[1-4,1-11] employing a resin "capture and release" reactor column is described. The array incorporates four different heterocyclic scaffolds, and the synthesis was performed using a custom-built robotic synthesizer that is able to (i) load and regenerate the reactor column and (ii) array each product into a single vial using UV threshold detection. All the compounds were obtained in high yield (>75%) and excellent purity (>95%) without the need for further purification.
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Affiliation(s)
- Daniel Jönsson
- GlaxoSmithKline Cambridge Technology Centre, University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
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44
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Vickerstaffe E, Warrington BH, Ladlow M, Ley SV. A Highly Automated, Polymer-Assisted Strategy for the Preparation of 2-Alkylthiobenzimidazoles andN,N‘-Dialkylbenzimidazolin-2-ones. ACTA ACUST UNITED AC 2005; 7:385-97. [PMID: 15877467 DOI: 10.1021/cc049832+] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A multistep, polymer-assisted solution phase strategy for the highly automated (auto-PASP) synthesis of 2-alkylthiobenzimidazole and N,N'-dialkylbenzimidazolin-2-one libraries is presented. The approach incorporates in-line purification techniques to afford library products directly with high purities and is exemplified by the preparation of a 96-member 2-alkylthiobenzimidazoline library 1[1-12,1-8] and a 72-member N,N'-dialkylbenzimidazolin-2-one library 9[1-12,1-6].
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Affiliation(s)
- Emma Vickerstaffe
- GlaxoSmithKline Cambridge Technology Centre, University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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45
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Zajdel P, Subra G, Bojarski AJ, Duszyńska B, Pawłowski M, Martinez J. Parallel solid-phase synthesis and characterization of new sulfonamide and carboxamide proline derivatives as potential CNS agents. Bioorg Med Chem 2005; 13:3029-35. [PMID: 15781412 DOI: 10.1016/j.bmc.2005.01.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Revised: 01/24/2005] [Accepted: 01/31/2005] [Indexed: 10/25/2022]
Abstract
A solid-phase synthesis of the 64-member library of novel sulfonamide and carboxamide proline derivatives, focused on the 5-HT7 receptor antagonist SB-258741, was described. The final compounds were obtained in good yields and high purity upon cleavage from SynPhase Lanterns, functionalized by a BAL linker. The library representatives were screened for 5-HT7, 5-HT1A and D2 receptors to explore the impact of a tertiary amine moiety, the length of an alkylene spacer and the aryl fragment on the receptor affinity. The preliminary biological results provided data for further investigation aimed at a search for 5-HT7 receptor agents, and permitted the identification of several compounds with significant 5-HT1A receptor affinity.
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Affiliation(s)
- Paweł Zajdel
- Laboratoire des Aminoacides, Peptides et Protéines (LAPP), UMR 5810, Faculté de Pharmacie, Université Montpellier I et II, 15 avenue Charles Flahault, 34060 Montpellier, France.
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46
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Abstract
The automation of all aspects of manual solution-phase synthesis into one integrated, efficient, and reliable system could be regarded as something of an unmet challenge in organic chemistry. The requirements for modern solution-phase libraries in mainstream drug discovery is typically 50-250 high-purity compounds on a 10-100-mg scale, whether for target class libraries or lead optimization, and short cycle time in combination with high capacity is critical. To achieve these goals, in a codevelopment between Aventis and Accelab GmbH, Kusterdingen, Germany, we designed a completely novel system of independent workstations connected by a shuttle transfer system produced by Montech, Derendingen, Switzerland. Seven modular workstations process four reactions on each shuttle in parallel, with the ability to perform synthesis (temperature control and liquid reagent handling), filtration, liquid-liquid extraction, evaporation, weighing, solid-phase extraction, and HPLC/MS analysis. The modular design enables the continuous loading of shuttles at any time, and each shuttle can have its own workflow. The design also allows easy expansion for future needs. The result is a combination of high flexibility and high throughput.
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Affiliation(s)
- Angelika Weber
- Chemical Scaffold and Automated Synthesis Unit, Aventis Pharma Deutschland GmbH, a company of the sanofi-aventis group, 65926 Frankfurt am Main, Germany
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47
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Koch MA, Waldmann H. Protein domain fold similarity and natural product structure as guiding principles for compound library design. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2005:1-18. [PMID: 15645714 DOI: 10.1007/3-540-27055-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Affiliation(s)
- M A Koch
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology and Fachbereich Organische Chemie, University of Dortmund, Germany
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48
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Wong D, Robertson G. Applying combinatorial chemistry and biology to food research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2004; 52:7187-7198. [PMID: 15563194 DOI: 10.1021/jf040140i] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In the past decade combinatorial chemistry has become a major focus of research activity in the pharmaceutical industry for accelerating the development of novel therapeutic compounds. The same combinatorial strategies could be applied to a broad spectrum of areas in agricultural and food research, including food safety and nutrition, development of product ingredients, and processing and conversion of natural products. In contrast to "rational design", the combinatorial approach relies on molecular diversity and high-throughput screening. The capability of exploring the structural and functional limits of a vast population of diverse chemical and biochemical molecules makes it possible to expedite the creation and isolation of compounds of desirable and useful properties. Several studies in recent years have demonstrated the utility of combinatorial methods for food research. These include the discovery of synthetic antimicrobial, antioxidative, and aflatoxin-binding peptides, the identification and analysis of unique flavor compounds, the generation of new enzyme inhibitors, the development of therapeutic antibodies for botulinum neurotoxins, the synthesis of unnatural polyketides and carotenoids, and the modification of food enzymes with novel properties. The results of such activities could open a large area of applications with potential benefits to the food industry. This review describes the current techniques of combinatorial chemistry and their applications, with emphasis on examples in food science research.
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Affiliation(s)
- Dominic Wong
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA.
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49
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Koch MA, Wittenberg LO, Basu S, Jeyaraj DA, Gourzoulidou E, Reinecke K, Odermatt A, Waldmann H. Compound library development guided by protein structure similarity clustering and natural product structure. Proc Natl Acad Sci U S A 2004; 101:16721-6. [PMID: 15548605 PMCID: PMC534721 DOI: 10.1073/pnas.0404719101] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To identify biologically relevant and drug-like protein ligands for medicinal chemistry and chemical biology research the grouping of proteins according to evolutionary relationships and conservation of molecular recognition is an established method. We propose to employ structure similarity clustering of the ligand-sensing cores of protein domains (PSSC) in conjunction with natural product guided compound library development as a synergistic approach for the identification of biologically prevalidated ligands with high fidelity. This is supported by the concepts that (i) in nature spatial structure is more conserved than amino acid sequence, (ii) the number of fold types characteristic for all protein domains is limited, and (iii) the underlying frameworks of natural product classes with multiple biological activities provide evolutionarily selected starting points in structural space. On the basis of domain core similarity considerations and irrespective of sequence similarity, Cdc25A phosphatase, acetylcholinesterase, and 11beta-hydroxysteroid dehydrogenases type 1 and type 2 were grouped into a similarity cluster. A 147-member compound collection derived from the naturally occurring Cdc25A inhibitor dysidiolide yielded potent and selective inhibitors of the other members of the similarity cluster with a hit rate of 2-3%. Protein structure similarity clustering may provide an experimental opportunity to identify supersites in proteins.
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Affiliation(s)
- Marcus A Koch
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
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Spiegel PC, Kaiser SM, Simon JA, Stoddard BL. Disruption of Protein-Membrane Binding and Identification of Small-Molecule Inhibitors of Coagulation Factor VIII. ACTA ACUST UNITED AC 2004; 11:1413-22. [PMID: 15489168 DOI: 10.1016/j.chembiol.2004.08.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Revised: 08/03/2004] [Accepted: 08/04/2004] [Indexed: 11/16/2022]
Abstract
Factor VIII is a critical member of the blood coagulation cascade. It binds to the membrane surfaces of activated platelets at the site of vascular injury via a highly specific interaction between factor VIII's carboxy-terminal C2 domain and their phosphatidylserine-rich lipid bilayer. We have identified small-molecule inhibitors of factor VIII's membrane binding activity that have IC50 values as low as 2.5 microM. This interaction is approximately 10(3)-fold tighter than that of free o-phospho-L-serine. These compounds also inhibit factor VIII-dependent activation of factor X, indicating that disruption of membrane lipid binding leads to inhibition of the intrinsic coagulation pathway. The tightest binding inhibitor is specific and does not prevent membrane binding by the closely related coagulation factor V. These results indicate that this and related compounds may be used as leads to develop novel antithrombotic agents.
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Affiliation(s)
- P Clint Spiegel
- Graduate Program in Biomolecular Structure and Design, University of Washington, Seattle, Washington 98195, USA
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