1
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Schüttel M, Will E, Sangouard G, Zarda A, Habeshian S, Nielsen AL, Heinis C. Solid-phase peptide synthesis in 384-well plates. J Pept Sci 2024; 30:e3555. [PMID: 38220145 DOI: 10.1002/psc.3555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/31/2023] [Accepted: 11/03/2023] [Indexed: 01/16/2024]
Abstract
Newer solid-phase peptide synthesis and release strategies enable the production of short peptides with high purity, allowing direct screening for desired bioactivity without prior chromatographic purification. However, the maximum number of peptides that can currently be synthesized per microplate reactor is 96, allowing the parallel synthesis of 384 peptides in modern devices that have space for 4 microplate reactors. To synthesize larger numbers of peptides, we modified a commercially available peptide synthesizer to enable the production of peptides in 384-well plates, which allows the synthesis of 1,536 peptides in one run (4 × 384 peptides). We report new hardware components and customized software that allowed for the synthesis of 1,536 short peptides in good quantity (average > 0.5 μmol), at high concentration (average > 10 mM), and decent purity without purification (average > 80%). The high-throughput peptide synthesis, which we developed with peptide drug development in mind, may be widely used for peptide library synthesis and screening, antibody epitope scanning, epitope mimetic development, or protease/kinase substrate screening.
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Affiliation(s)
- Mischa Schüttel
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Edward Will
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gontran Sangouard
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anne Zarda
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sevan Habeshian
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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2
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Isakova AM, Kovalenko AA, Skorb EV, Shityakov S. NeuroClick: software for mimicking click reaction to generate drug-like molecules permeating the blood-brain barrier. Future Med Chem 2024; 16:389-398. [PMID: 38372134 DOI: 10.4155/fmc-2023-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
Background: Traditional methods for chemical library generation in virtual screening often impose limitations on the accessible chemical space or produce synthetically irrelevant structures. Incorporating common chemical reactions into generative algorithms could offer significant benefits. Materials & methods: In this study, we developed NeuroClick, a graphical user interface software designed to perform in silico azide-alkyne cycloaddition, a widely utilized synthetic approach in modern medicinal chemistry. Results & conclusion: NeuroClick facilitates the generation and filtering of large combinatorial libraries at a remarkable rate of 10,000 molecules per minute. Moreover, the generated products can be filtered to identify subsets of pharmaceutically relevant compounds based on Lipinski's rule of five and blood-brain barrier permeability prediction. We demonstrate the utility of NeuroClick by generating and filtering several thousand molecules for dopamine D3 receptor ligand screening.
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Affiliation(s)
- Anastasiia M Isakova
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russian Federation
| | - Alexander A Kovalenko
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russian Federation
| | - Ekaterina V Skorb
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russian Federation
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russian Federation
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3
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Blanc A, Todorovic M, Dude I, Merkens H, Bénard F, Perrin DM. Toward tryptathionine-stapled one-bead-one-compound (OBOC) libraries: solid phase synthesis of a bioactive octretoate analog. Org Biomol Chem 2023; 21:8112-8116. [PMID: 37772608 DOI: 10.1039/d3ob01378b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
New somatostatin analogs are highly desirable for diagnosing and treating neuroendocrine tumors (NETs). Here we describe the solid-phase synthesis of a new octreotate (TATE) analog where the disulfide bond is replaced with a tryptathionine (Ttn) staple as part of an effort to prototyping a one-bead-one-compound (OBOC) library of Ttn-stapled peptides. Library design provides the potential for on- and off-bead screening. To validate our method, we labelled Ttn-TATE with a fluorescent dye to demonstrate binding to soluble somatostatin receptor subtype-2 and staining of Ar42J rat prostate cancer cells. By exploring this staple in the context of a ligand of known affinity, this method paves the way for an OBOC library construction of bioactive octreotate analogs and, more broadly speaking, tryptathionine-staped peptide macrocycles.
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Affiliation(s)
- Antoine Blanc
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, V6T-1Z1, Canada.
| | - Mihajlo Todorovic
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, V6T-1Z1, Canada.
| | - Iulia Dude
- Molecular Oncology, British Columbia Cancer Agency Research Centre, 675 West10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Helen Merkens
- Molecular Oncology, British Columbia Cancer Agency Research Centre, 675 West10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - François Bénard
- Molecular Oncology, British Columbia Cancer Agency Research Centre, 675 West10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - David M Perrin
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, V6T-1Z1, Canada.
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4
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Li YJ, Zhang L, Yang PP, Zhang K, Gong XF, Hou DY, Cao H, Wu XC, Liu R, Lam KS, Wang L. Bioinspired Screening of Anti-Adhesion Peptides against Blood Proteins for Intravenous Delivery of Nanomaterials. Nano Lett 2022; 22:8076-8085. [PMID: 36135098 DOI: 10.1021/acs.nanolett.2c02243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nanomaterials (NMs) inevitably adsorb proteins in blood and form "protein corona" upon intravenous administration as drug carriers, potentially changing the biological properties and intended functions. Inspired by anti-adhesion properties of natural proteins, herein, we employed the one-bead one-compound (OBOC) combinatorial peptide library method to screen anti-adhesion peptides (AAPs) against proteins. The library beads displaying random peptides were screened with three fluorescent-labeled plasma proteins. The nonfluorescence beads, presumed to have anti-adhesion property against the proteins, were isolated for sequence determination. These identified AAPs were coated on gold nanorods (GNRs), enabling significant extension of the blood circulating half-life of these GNRs in mice to 37.8 h, much longer than that (26.6 h) of PEG-coated GNRs. In addition, such AAP coating was found to alter the biodistribution profile of GNRs in mice. The bioinspired screening strategy and resulting peptides show great potential for enhancing the delivery efficiency and targeting ability of NMs.
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Affiliation(s)
- Yi-Jing Li
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Lingze Zhang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Pei-Pei Yang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Kuo Zhang
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Xue-Feng Gong
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Da-Yong Hou
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Hui Cao
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Xiao-Chun Wu
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, UC Davis NCI-designated Comprehensive Cancer Center, University of California Davis, Sacramento, California 95817, United States
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, UC Davis NCI-designated Comprehensive Cancer Center, University of California Davis, Sacramento, California 95817, United States
- Division of Hematology and Oncology, Department of Internal Medicine, School of Medicine, University of California Davis, Sacramento, California 95817, United States
| | - Lei Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
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5
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Suay-García B, Bueso-Bordils JI, Falcó A, Antón-Fos GM, Alemán-López PA. Virtual Combinatorial Chemistry and Pharmacological Screening: A Short Guide to Drug Design. Int J Mol Sci 2022; 23:ijms23031620. [PMID: 35163543 PMCID: PMC8836228 DOI: 10.3390/ijms23031620] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Traditionally, drug development involved the individual synthesis and biological evaluation of hundreds to thousands of compounds with the intention of highlighting their biological activity, selectivity, and bioavailability, as well as their low toxicity. On average, this process of new drug development involved, in addition to high economic costs, a period of several years before hopefully finding a drug with suitable characteristics to drive its commercialization. Therefore, the chemical synthesis of new compounds became the limiting step in the process of searching for or optimizing leads for new drug development. This need for large chemical libraries led to the birth of high-throughput synthesis methods and combinatorial chemistry. Virtual combinatorial chemistry is based on the same principle as real chemistry—many different compounds can be generated from a few building blocks at once. The difference lies in its speed, as millions of compounds can be produced in a few seconds. On the other hand, many virtual screening methods, such as QSAR (Quantitative Sturcture-Activity Relationship), pharmacophore models, and molecular docking, have been developed to study these libraries. These models allow for the selection of molecules to be synthesized and tested with a high probability of success. The virtual combinatorial chemistry–virtual screening tandem has become a fundamental tool in the process of searching for and developing a drug, as it allows the process to be accelerated with extraordinary economic savings.
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Affiliation(s)
- Beatriz Suay-García
- ESI International @ UCHCEU, Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera—CEU, CEU Universities San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain;
- Correspondence:
| | - Jose I. Bueso-Bordils
- Departamento de Farmacia, Universidad Cardenal Herrera—CEU, CEU Universities, C/Ramón y Cajal s/n, Alfara del Patriarca, 46115 Valencia, Spain; (G.M.A.-F.); (P.A.A.-L.); (J.I.B.-B.)
| | - Antonio Falcó
- ESI International @ UCHCEU, Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera—CEU, CEU Universities San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain;
| | - Gerardo M. Antón-Fos
- Departamento de Farmacia, Universidad Cardenal Herrera—CEU, CEU Universities, C/Ramón y Cajal s/n, Alfara del Patriarca, 46115 Valencia, Spain; (G.M.A.-F.); (P.A.A.-L.); (J.I.B.-B.)
| | - Pedro A. Alemán-López
- Departamento de Farmacia, Universidad Cardenal Herrera—CEU, CEU Universities, C/Ramón y Cajal s/n, Alfara del Patriarca, 46115 Valencia, Spain; (G.M.A.-F.); (P.A.A.-L.); (J.I.B.-B.)
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6
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Abstract
Large structurally diverse peptidomimetic chemical libraries have been very useful tools in chemical biology and drug discovery for the identification of therapeutically important compounds with higher affinity and improved pharmacological properties against different protein targets.Here we describe a simple and general method for the submonomer solid phase synthesis of large one bead-one compound (OBOC) peptidomimetic libraries of structurally diverse compounds that can be encoded by mass or genetic methods.
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7
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Abstract
DNA-encoded library synthesis is an evolved combinatorial synthesis, using a split-and-pool strategy in 96-well plates, libraries containing millions to billions of compounds can be prepared by a combination of chemical and enzymatic synthesis. Here we describe the analytics methods used in the library synthesis with one cycle of synthesis as an example.
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Affiliation(s)
- Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA.
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8
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Abstract
DNA-encoded library (DEL) links the powers of genetics and chemicals via high-efficient enzymatic ligation of DNA barcodes and the "split and pool" combinatorial synthesis. Natural products (NPs) are evolutionary optimized compounds that have played a key role in the history of human drug discovery. Herein, we describe a method for functionality-independent annotation of complex natural products with amplifiable DNA barcodes to generate a DNA-encoded natural product library (nDEL). This method provides a simple and practical solution to leverage natural products by DNA barcoding.
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Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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9
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Albuquerque HMT, Pinto DCGA, Silva AMS. Microwave Irradiation: Alternative Heating Process for the Synthesis of Biologically Applicable Chromones, Quinolones, and Their Precursors. Molecules 2021; 26:molecules26206293. [PMID: 34684877 PMCID: PMC8541360 DOI: 10.3390/molecules26206293] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Microwave irradiation has become a popular heating technique in organic synthesis, mainly due to its short reaction times, solventless reactions, and, sometimes, higher yields. Additionally, microwave irradiation lowers energy consumption and, consequently, is ideal for optimization processes. Moreover, there is evidence that microwave irradiation can improve the regioselectivity and stereoselectivity aspects of vital importance in synthesizing bioactive compounds. These crucial features of microwave irradiation contribute to its inclusion in green chemistry procedures. Since 2003, the use of microwave-assisted organic synthesis has become common in our laboratory, making our group one of the first Portuguese research groups to implement this heating source in organic synthesis. Our achievements in the transformation of heterocyclic compounds, such as (E/Z)-3-styryl-4H-chromen-4-ones, (E)-3-(2-hydroxyphenyl)-4-styryl-1H-pyrazole, (E)-2-(4-arylbut-1-en-3-yn-1-yl)-4H-chromen-4-ones, or (E)-2-[2-(5-aryl-2-methyl-2H-1,2,3-triazol-4-yl)vinyl]-4H-chromen-4-ones, will be discussed in this review, highlighting the benefits of microwave irradiation use in organic synthesis.
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10
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Baudis S, Behl M. High-Throughput and Combinatorial Approaches for the Development of Multifunctional Polymers. Macromol Rapid Commun 2021; 43:e2100400. [PMID: 34460146 DOI: 10.1002/marc.202100400] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/18/2021] [Indexed: 01/22/2023]
Abstract
High-throughput (HT) development of new multifunctional polymers is accomplished by the combination of different HT tools established in polymer sciences in the last decade. Important advances are robotic/HT synthesis of polymer libraries, the HT characterization of polymers, and the application of spatially resolved polymer library formats, explicitly microarray and gradient libraries. HT polymer synthesis enables the generation of material libraries with combinatorial design motifs. Polymer composition, molecular weight, macromolecular architecture, etc. may be varied in a systematic, fine-graded manner to obtain libraries with high chemical diversity and sufficient compositional resolution as model systems for the screening of these materials for the functions aimed. HT characterization allows a fast assessment of complementary properties, which are employed to decipher quantitative structure-properties relationships. Moreover, these methods facilitate the HT determination of important surface parameters by spatially resolved characterization methods, including time-of-flight secondary ion mass spectrometry and X-ray photoelectron spectroscopy. Here current methods for the high-throughput robotic synthesis of multifunctional polymers as well as their characterization are presented and advantages as well as present limitations are discussed.
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Affiliation(s)
- Stefan Baudis
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513, Teltow, Germany
| | - Marc Behl
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513, Teltow, Germany
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11
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Abstract
Click chemistry, proposed nearly 20 years ago, promised access to novel chemical space by empowering combinatorial library synthesis with a "few good reactions". These click reactions fulfilled key criteria (broad scope, quantitative yield, abundant starting material, mild reaction conditions, and high chemoselectivity), keeping the focus on molecules that would be easy to make, yet structurally diverse. This philosophy bears a striking resemblance to DNA-encoded library (DEL) technology, the now-dominant combinatorial chemistry paradigm. This review highlights the similarities between click and DEL reaction design and deployment in combinatorial library settings, providing a framework for the design of new DEL synthesis technologies to enable next-generation drug discovery.
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Affiliation(s)
- Patrick R Fitzgerald
- Skaggs Doctoral Program in the Chemical and Biological Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M Paegel
- Departments of Pharmaceutical Sciences, Chemistry, & Biomedical Engineering, University of California, Irvine, 101 Theory Suite 100, Irvine, California 92617, United States
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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12
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Wang S, Yan X, Su G, Yan B. Cytotoxicity Induction by the Oxidative Reactivity of Nanoparticles Revealed by a Combinatorial GNP Library with Diverse Redox Properties. Molecules 2021; 26:3630. [PMID: 34198523 PMCID: PMC8231810 DOI: 10.3390/molecules26123630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
It is crucial to establish relationship between nanoparticle structures (or properties) and nanotoxicity. Previous investigations have shown that a nanoparticle's size, shape, surface and core materials all impact its toxicity. However, the relationship between the redox property of nanoparticles and their toxicity has not been established when all other nanoparticle properties are identical. Here, by synthesizing an 80-membered combinatorial gold nanoparticle (GNP) library with diverse redox properties, we systematically explored this causal relationship. The compelling results revealed that the oxidative reactivity of GNPs, rather than their other physicochemical properties, directly caused cytotoxicity via induction of cellular oxidative stress. Our results show that the redox diversity of nanoparticles is regulated by GNPs modified with redox reactive ligands.
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Affiliation(s)
- Shenqing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China;
| | - Xiliang Yan
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Institute of Environmental Research at Greater Bay, Ministry of Education, Guangzhou University, Guangzhou 510006, China;
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong 226001, China;
| | - Bing Yan
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Institute of Environmental Research at Greater Bay, Ministry of Education, Guangzhou University, Guangzhou 510006, China;
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13
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Hunter JH, Prendergast L, Valente LF, Madin A, Pairaudeau G, Waring MJ. High Fidelity Suzuki-Miyaura Coupling for the Synthesis of DNA Encoded Libraries Enabled by Micelle Forming Surfactants. Bioconjug Chem 2020; 31:149-155. [PMID: 31873005 DOI: 10.1021/acs.bioconjchem.9b00838] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA encoded chemical libraries provide a highly efficient means of screening vast numbers of small molecules against an immobilized protein target. Their potential is currently restricted by the constraints of carrying out library synthesis in the presence of attached DNA tags, for which a limited number of reactions and substrates can be used. Even established reactions, such as Suzuki-Miyaura couplings, do not give efficient coupling reactions across a wide range of substrates and can lead to significant DNA degradation. We developed an efficient protocol for carrying out Suzuki-Miyaura couplings on DNA tagged substrates that proceeds with unprecedented efficiency to the desired biaryl products (>98% on average with no detectable DNA degradation) across a wide range of drug-like substrates using a micellar promoted process with commercial TPGS-750-M surfactant. We have demonstrated the applicability of this method in DEL synthesis by preparing a prototypical two-dimensional 36-member library employing the Suzuki-Miyaura coupling methodology as the final library synthesis step. This work shows, for the first time, that standard micellar surfactants can promote reactions for encoded library synthesis, leading to libraries of exceptional fidelity, and demonstrates the potential to expand the range of accessible DNA compatible chemistry.
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Affiliation(s)
- James H Hunter
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Lisa Prendergast
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4AD , U.K
| | - Louis F Valente
- JMP Division , SAS Institute Inc. , 100 SAS Campus Drive , Cary , North Carolina 27513 , United States
| | - Andrew Madin
- Discovery Sciences IMED Biotech Unit , AstraZeneca , 310 Cambridge Science Park, Milton Road , Cambridge CB4 0WG , U.K
| | - Garry Pairaudeau
- Discovery Sciences IMED Biotech Unit , AstraZeneca , 310 Cambridge Science Park, Milton Road , Cambridge CB4 0WG , U.K
| | - Michael J Waring
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
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14
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Abstract
During the last decade, genome sequence databases of many species have been more and more completed so that it has become possible to further develop a recently established technique of FISH (Fluorescence In Situ Hybridization) called COMBO-FISH (COMBinatorial Oligo FISH). In contrast to standard FISH techniques, COMBO-FISH makes use of a bioinformatic search in sequence databases for probe design, so that it can be done for any species so far sequenced. In the original approach, oligonucleotide stretches of typical lengths of 15-30 nucleotides were selected in such a way that they only co-localize at the given genome target. Typical probe sets of about 20-40 stretches were used to label about 50-250 kb specifically. The probes of different lengths can be composed of purines and pyrimidines, but were often restricted to homo-purine or homo-pyrimidine probe sets because of the experimental advantage of using a protocol omitting denaturation of the target strand and triple strand binding of the probes. This allows for a better conservation of the 3D folding and arrangement of the genome. With an improved, rigorous genome sequence database analysis and sequence search according to statistical frequency and uniqueness, a novel family of probes repetitively binding to characteristic genome features like SINEs (Short Interspersed Nuclear Elements, e.g., ALU elements), LINEs (Long Interspersed Nuclear Elements, e.g., L1), or centromeres has been developed. These probes can be synthesized commercially as DNA or PNA probes with high purity and labeled by fluorescent dye molecules. Here, new protocols are described for purine-pyrimidine probes omitting heat treatment for denaturation of the target so that oligonucleotide labeling can also be combined with immune-staining by specific antibodies. If the dyes linked to the oligonucleotide stretches undergo reversible photo-bleaching (laser-induced slow blinking), the labeled cell nuclei can be further subjected to super-resolution localization microscopy for complex chromatin architecture research.
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Affiliation(s)
- Michael Hausmann
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany.
| | - Jin-Ho Lee
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Matthias Krufczik
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
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15
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Boschetti E, Righetti PG. Detection of Plant Low-Abundance Proteins by Means of Combinatorial Peptide Ligand Library Methods. Methods Mol Biol 2020; 2139:381-404. [PMID: 32462601 DOI: 10.1007/978-1-0716-0528-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The detection and identification of low-abundance proteins from plant tissues is still a major challenge. Among the reasons are the low protein content, the presence of few very high-abundance proteins, and the presence of massive amounts of other biochemical compounds. In the last decade numerous technologies have been devised to resolve the situation, in particular with methods based on solid-phase combinatorial peptide ligand libraries. This methodology, allowing for an enhancement of low-abundance proteins, has been extensively applied with the advantage of deciphering the proteome composition of various plant organs. This general methodology is here described extensively along with a number of possible variations. Specific guidelines are suggested to cover peculiar situations or to comply with other associated analytical methods.
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16
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Flood DT, Asai S, Zhang X, Wang J, Yoon L, Adams ZC, Dillingham BC, Sanchez BB, Vantourout JC, Flanagan ME, Piotrowski DW, Richardson P, Green SA, Shenvi RA, Chen JS, Baran PS, Dawson PE. Expanding Reactivity in DNA-Encoded Library Synthesis via Reversible Binding of DNA to an Inert Quaternary Ammonium Support. J Am Chem Soc 2019; 141:9998-10006. [PMID: 31136164 PMCID: PMC7033622 DOI: 10.1021/jacs.9b03774] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA Encoded Libraries have proven immensely powerful tools for lead identification. The ability to screen billions of compounds at once has spurred increasing interest in DEL development and utilization. Although DEL provides access to libraries of unprecedented size and diversity, the idiosyncratic and hydrophilic nature of the DNA tag severely limits the scope of applicable chemistries. It is known that biomacromolecules can be reversibly, noncovalently adsorbed and eluted from solid supports, and this phenomenon has been utilized to perform synthetic modification of biomolecules in a strategy we have described as reversible adsorption to solid support (RASS). Herein, we present the adaptation of RASS for a DEL setting, which allows reactions to be performed in organic solvents at near anhydrous conditions opening previously inaccessible chemical reactivities to DEL. The RASS approach enabled the rapid development of C(sp2)-C(sp3) decarboxylative cross-couplings with broad substrate scope, an electrochemical amination (the first electrochemical synthetic transformation performed in a DEL context), and improved reductive amination conditions. The utility of these reactions was demonstrated through a DEL-rehearsal in which all newly developed chemistries were orchestrated to afford a compound rich in diverse skeletal linkages. We believe that RASS will offer expedient access to new DEL reactivities, expanded chemical space, and ultimately more drug-like libraries.
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Affiliation(s)
- Dillon T. Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shota Asai
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Xuejing Zhang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jie Wang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Leonard Yoon
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Zoë C. Adams
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Blythe C. Dillingham
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Brittany B. Sanchez
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Julien C. Vantourout
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Mark E. Flanagan
- Pfizer Medicinal Chemistry, Eastern Point Road, Groton, CT 06340, United States
| | - David W. Piotrowski
- Pfizer Medicinal Chemistry, Eastern Point Road, Groton, CT 06340, United States
| | - Paul Richardson
- Pfizer Medicinal Chemistry, 10578 Science Center Drive, San Diego, CA 92121, United States
| | - Samantha A. Green
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryan A. Shenvi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jason S. Chen
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Phil S. Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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17
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Yoneyama K, Suzuki R, Kuramochi Y, Satake A. A Candidate for Multitopic Probes for Ligand Discovery in Dynamic Combinatorial Chemistry. Molecules 2019; 24:E2166. [PMID: 31181809 PMCID: PMC6600254 DOI: 10.3390/molecules24112166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/30/2019] [Accepted: 06/07/2019] [Indexed: 11/26/2022] Open
Abstract
Multifunctionalized materials are expected to be versatile probes to find specific interactions between a ligand and a target biomaterial. Thus, efficient methods to prepare possible combinations of the functionalities is desired. The concept of dynamic combinatorial chemistry (DCC) is ideal for the generation of any possible combination, as well as screening for target biomaterials. Here, we propose a new molecular design of multitopic probes for ligand discovery in DCC. We synthesized a new Gable Porphyrin, GP1, having prop-2-yne groups as a scaffold to introduce various functional groups. GP1 is a bis(imidazolylporphyrinatozinc) compound connected through a 1,3-phenylene moiety, and it gives macrocycles spontaneously and quantitatively by strong imidazole-to-zinc complementary coordination. Some different types of functional groups were introduced into GP1 in high yields. Formation of heterogeneous macrocycles composed of GP1 derivatives having different types of substituents was accomplished under equilibrium conditions. These results promise that enormous numbers of macrocycles having various functional groups can be provided when the kinds of GP components increase. These features are desirable for DCC, and the present system using GP1 is a potential candidate to provide a dynamic combinatorial library of multitopic probes to discover specific interactions between a ligand and a biomaterial.
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Affiliation(s)
- Keiko Yoneyama
- Graduate School of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Rina Suzuki
- Graduate School of Chemical Sciences and Technology, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Yusuke Kuramochi
- Department of Chemistry, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Akiharu Satake
- Department of Chemistry, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
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18
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Abstract
miR-155 plays key promoting roles in several cancers and emerges as an important anticancer therapeutic target. However, the discovery of small molecules that target RNAs is challenging. Peptidomimetics have been shown to be a rich source for discovering novel ligands to regulate cellular proteins. However, the potential of using peptidomimetics for RNA targeting is relatively unexplored. To this end, we designed and synthesized members of a novel 320 000 compound macrocyclic peptidomimetic library. An affinity-based screening protocol led to the identification of a pre-miR-155 binder that inhibits oncogenic miR-155 maturation in vitro and in cell and induces cancer cell apoptosis. The results of this investigation demonstrate that macrocyclic peptidomimetics could serve as a new scaffold for RNA targeting.
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Affiliation(s)
- Hao Yan
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
| | - Mi Zhou
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Umesh Bhattarai
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
| | - Yabin Song
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
| | - Mengmeng Zheng
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
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19
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Das M, Yang T, Dong J, Prasetya F, Xie Y, Wong KHQ, Cheong A, Woon ECY. Multiprotein Dynamic Combinatorial Chemistry: A Strategy for the Simultaneous Discovery of Subfamily-Selective Inhibitors for Nucleic Acid Demethylases FTO and ALKBH3. Chem Asian J 2018; 13:2854-2867. [PMID: 29917331 DOI: 10.1002/asia.201800729] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/12/2018] [Indexed: 12/18/2022]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful supramolecular approach for discovering ligands for biomolecules. To date, most, if not all, biologically templated DCC systems employ only a single biomolecule to direct the self-assembly process. To expand the scope of DCC, herein, a novel multiprotein DCC strategy has been developed that combines the discriminatory power of a zwitterionic "thermal tag" with the sensitivity of differential scanning fluorimetry. This strategy is highly sensitive and could differentiate the binding of ligands to structurally similar subfamily members. Through this strategy, it was possible to simultaneously identify subfamily-selective probes against two clinically important epigenetic enzymes: FTO (7; IC50 =2.6 μm) and ALKBH3 (8; IC50 =3.7 μm). To date, this is the first report of a subfamily-selective ALKBH3 inhibitor. The developed strategy could, in principle, be adapted to a broad range of proteins; thus it is of broad scientific interest.
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MESH Headings
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/antagonists & inhibitors
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/chemistry
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics
- AlkB Homolog 5, RNA Demethylase/antagonists & inhibitors
- AlkB Homolog 5, RNA Demethylase/chemistry
- AlkB Homolog 5, RNA Demethylase/genetics
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/antagonists & inhibitors
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/chemistry
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics
- Catalysis
- Combinatorial Chemistry Techniques/methods
- Enzyme Inhibitors/chemistry
- Fluorometry/methods
- Humans
- Hydrazones/chemistry
- Kinetics
- Ligands
- Molecular Structure
- Oxidoreductases, O-Demethylating/antagonists & inhibitors
- Oxidoreductases, O-Demethylating/chemistry
- Oxidoreductases, O-Demethylating/genetics
- Peptides/chemistry
- Peptides/genetics
- Protein Denaturation
- Protein Engineering
- Protein Structure, Secondary
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Transition Temperature
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Affiliation(s)
- Mohua Das
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Tianming Yang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Jinghua Dong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Fransisca Prasetya
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Yiming Xie
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Kendra H Q Wong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Adeline Cheong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Esther C Y Woon
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
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20
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Bhaskaruni SVHS, Maddila S, van Zyl WE, Jonnalagadda SB. Ag₂O on ZrO₂ as a Recyclable Catalyst for Multicomponent Synthesis of Indenopyrimidine Derivatives. Molecules 2018; 23:E1648. [PMID: 29976914 PMCID: PMC6100188 DOI: 10.3390/molecules23071648] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022] Open
Abstract
We describe the synthesis of silver loaded on zirconia and its use as an efficient catalyst for a one-pot three-component reaction to synthesize 11 indenopyrimidine derivatives, of which 7 are new compounds. The procedure involves substituted benzaldehydes, indane-1,3-dione, and guanidinium hydrochloride, with ethanol as solvent. The proposed green protocol at room temperature is simple and efficient, giving excellent yields (90⁻96%) in short reaction times (<30 min). The protocol works well according to the green chemistry principles with respect to high atom economy, no need for column separation, and reusability of the catalyst, which are attractive features. XRD, TEM, SEM, and BET analysis were used to characterize the catalyst materials.
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Affiliation(s)
- Sandeep V H S Bhaskaruni
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Chiltern Hills, Durban 4000, South Africa.
| | - Suresh Maddila
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Chiltern Hills, Durban 4000, South Africa.
| | - Werner E van Zyl
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Chiltern Hills, Durban 4000, South Africa.
| | - Sreekantha B Jonnalagadda
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Chiltern Hills, Durban 4000, South Africa.
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21
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Ziegler RE, Desai BK, Jee J, Gupton BF, Roper TD, Jamison TF. 7-Step Flow Synthesis of the HIV Integrase Inhibitor Dolutegravir. Angew Chem Int Ed Engl 2018; 57:7181-7185. [PMID: 29756689 PMCID: PMC6033037 DOI: 10.1002/anie.201802256] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/30/2018] [Indexed: 01/09/2023]
Abstract
Dolutegravir (DTG), an important active pharmaceutical ingredient (API) used in combination therapy for the treatment of HIV, has been synthesized in continuous flow. By adapting the reported GlaxoSmithKline process chemistry batch route for Cabotegravir, DTG was produced in 4.5 h in sequential flow operations from commercially available materials. Key features of the synthesis include rapid manufacturing time for pyridone formation, one-step direct amidation of a functionalized pyridone, and telescoping of multiple steps to avoid isolation of intermediates and enable for greater throughput.
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Affiliation(s)
- Robert E. Ziegler
- Department of ChemistryMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
| | - Bimbisar K. Desai
- Department of Chemical and Life Science EngineeringVirginia Commonwealth University, Biotech 8737 N. 5 StreetRichmondVA23219USA
| | - Jo‐Ann Jee
- Department of Chemical and Life Science EngineeringVirginia Commonwealth University, Biotech 8737 N. 5 StreetRichmondVA23219USA
| | - B. Frank Gupton
- Department of Chemical and Life Science EngineeringVirginia Commonwealth University, Biotech 8737 N. 5 StreetRichmondVA23219USA
| | - Thomas D. Roper
- Department of Chemical and Life Science EngineeringVirginia Commonwealth University, Biotech 8737 N. 5 StreetRichmondVA23219USA
| | - Timothy F. Jamison
- Department of ChemistryMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
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22
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Gilormini PA, Lion C, Vicogne D, Guérardel Y, Foulquier F, Biot C. Chemical glycomics enrichment: imaging the recycling of sialic acid in living cells. J Inherit Metab Dis 2018; 41:515-523. [PMID: 29294191 PMCID: PMC5959963 DOI: 10.1007/s10545-017-0118-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/28/2017] [Accepted: 11/20/2017] [Indexed: 01/10/2023]
Abstract
The development of metabolic oligosaccharide engineering (MOE) over the past two decades enabled the bioimaging studies of glycosylation processes in physio-pathological contexts. Herein, we successfully applied the chemical reporter strategy to image the fate of sialylated glycoconjugates in healthy and sialin-deficient patient fibroblasts. This chemical glycomics enrichment is a powerful tool for tracking sialylated glycoconjugates and probing lysosomal recycling capacities. Thus, such strategies appear fundamental for the characterization of lysosomal storage diseases.
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Affiliation(s)
- Pierre André Gilormini
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Cédric Lion
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Dorothée Vicogne
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Yann Guérardel
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - François Foulquier
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.
| | - Christophe Biot
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.
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23
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Patil P, Mishra B, Sheombarsing G, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Library-to-Library Synthesis of Highly Substituted α-Aminomethyl Tetrazoles via Ugi Reaction. ACS Comb Sci 2018; 20:70-74. [PMID: 29215263 PMCID: PMC5813278 DOI: 10.1021/acscombsci.7b00137] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/21/2017] [Indexed: 12/26/2022]
Abstract
α-Aminomethyl tetrazoles, recently made accessible by an Ugi multicomponent reaction (MCR), were shown to be excellent starting materials for a further Ugi MCR, yielding substituted N-methyl-2-(((1-methyl-1H-tetrazol-5-yl)methyl)amino)acetamides having four points of diversity in a library-to-library approach. The scope and limitations of the two-step sequence was explored by conducting more than 50 reactions. Irrespective of electron-rich and electron-deficient oxo-components and the nature of the isocyanide component, the reactions give excellent yields. Sterically less hindered α-aminomethyl tetrazoles give better yields of in further Ugi MCR. The target scaffold has four points of diversity and is finding applications to fill screening decks for high-throughput screening (HTS) in the European Lead Factory and in structure-based drug design.
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Affiliation(s)
- Pravin Patil
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Bhupendra Mishra
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Gitanjali Sheombarsing
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian
University, Faculty of Chemistry, Department
of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Ingardena 3, 30-060 Kraków, Poland
| | - Justyna Kalinowska-Tłuścik
- Jagiellonian
University, Faculty of Chemistry, Department
of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Ingardena 3, 30-060 Kraków, Poland
| | - Alexander Dömling
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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24
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Saleh D, Degterev A. Chemical Library Screens to Identify Pharmacological Modulators of Necroptosis. Methods Mol Biol 2018; 1857:19-33. [PMID: 30136227 DOI: 10.1007/978-1-4939-8754-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Necroptosis is mediated by the formation of the detergent-insoluble necrosome complex between Ser/Thr kinases RIPK1 and RIPK3, which mediates RIPK3-dependent phosphorylation and activation of the critical necroptosis effector MLKL. Small molecule screens have been instrumental in the development of new chemical probes for this pathway. In this chapter, we describe several cellular assays that are readily amendable for the identification of new modulators of necroptosis as well as secondary assays to facilitate initial characterization of the mode of activity of small molecule hits.
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Affiliation(s)
- Danish Saleh
- Medical Scientist Training Program, Program in Neuroscience, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Alexei Degterev
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
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25
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Vinogradov AA, Gates ZP, Zhang C, Quartararo AJ, Halloran KH, Pentelute BL. Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries. ACS Comb Sci 2017; 19:694-701. [PMID: 28892357 PMCID: PMC5818986 DOI: 10.1021/acscombsci.7b00109] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.
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Affiliation(s)
| | - Zachary P. Gates
- Department of Chemistry, Massachusetts Institute of Technology, 18-563, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 18-563, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Anthony J. Quartararo
- Department of Chemistry, Massachusetts Institute of Technology, 18-563, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Kathryn H. Halloran
- Department of Chemistry, Massachusetts Institute of Technology, 18-563, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 18-563, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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26
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Medyouni R, Elgabsi W, Naouali O, Romerosa A, Sulaiman Al-Ayed A, Baklouti L, Hamdi N. One-pot three-component Biginelli-type reaction to synthesize 3,4-dihydropyrimidine-2-(1H)-ones catalyzed by Co phthalocyanines: Synthesis, characterization, aggregation behavior and antibacterial activity. Spectrochim Acta A Mol Biomol Spectrosc 2016; 167:165-174. [PMID: 27287623 DOI: 10.1016/j.saa.2016.04.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 04/24/2016] [Accepted: 04/25/2016] [Indexed: 06/06/2023]
Abstract
The synthesis of a novel phthalonitrile derivative with pyridine-2-thiol and 2,4,6-trimethylphenylamine substituents functionalized groups and its peripherally tetrasubstituted cobalt phthalocyanine and cationic phthalocyanines complexes were reported. The aggregation investigations carried out in different concentrations indicate that Co Phthalocyanines compounds 3,4 do not have any aggregation behavior for the concentration range of 6×10(-4)-14×10(-6)M in DMSO. The ion binding properties of Co Phthalocyanines compounds 3,4 show the formation of stable complex with Co(2+). In addition 3,4-Dihydropyrimidin-2(1H)-one derivatives were synthesized by modified Biginelli cyclocondensation reaction catalyzed by MPc as Lewis base. The structures of the synthesized compounds have been successfully characterized by the spectroscopic methods (IR, (1)H NMR, (13C)NMR, UV-Vis, mass spectrometry, elemental analysis and NMR 2D). The influence of substrate/catalyst ratio, solvent was also investigated to find optimal reaction on this synthesis for getting the highest conversion. Different parameters were examined for finding optimal conditions of catalysis. In addition; the compounds 3-11 were investigated for antimicrobial activity. Most of them exhibited important antimicrobial activity.
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Affiliation(s)
- Rawdha Medyouni
- Heterocyclic and Organometallic Chemistry Laboratory, Higher Institute of Environmental Sciences and Technology, University of Carthage, Hammam-Lif, 2050, Tunisia
| | - Wissal Elgabsi
- Heterocyclic and Organometallic Chemistry Laboratory, Higher Institute of Environmental Sciences and Technology, University of Carthage, Hammam-Lif, 2050, Tunisia
| | - Olfa Naouali
- Laboratory of Applied Chemistry and Natural Substances Resources and Environment, Faculty of Sciences, University of Carthage, Zarzouna-Bizerta, 7021, Tunisia
| | - Antonio Romerosa
- Área de Química Inorgánica, Universidad d'Almeria 04120, Almería, Spain
| | - Abdullah Sulaiman Al-Ayed
- Chemistry Department, College of Science and Arts, Qassim University, Al-Rass, Kingdom of Saudi Arabia
| | - Lasaad Baklouti
- Chemistry Department, College of Science and Arts, Qassim University, Al-Rass, Kingdom of Saudi Arabia; Laboratory of Applied Chemistry and Natural Substances Resources and Environment, Faculty of Sciences, University of Carthage, Zarzouna-Bizerta, 7021, Tunisia
| | - Naceur Hamdi
- Heterocyclic and Organometallic Chemistry Laboratory, Higher Institute of Environmental Sciences and Technology, University of Carthage, Hammam-Lif, 2050, Tunisia; Chemistry Department, College of Science and Arts, Qassim University, Al-Rass, Kingdom of Saudi Arabia.
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27
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Abstract
This review focuses on recent progress in noncomputational methods to introduce catalytic function into proteins, peptides, and peptide assemblies. We discuss various approaches to creating catalytic activity and classification of noncomputational methods into rational and combinatorial classes. The section on rational design covers recent progress in the development of short peptides and oligomeric peptide assemblies for various natural and unnatural reactions. The section on combinatorial design describes recent advances in the discovery of catalytic peptides. We present the future prospects of these and other new approaches in a broader context, including implications for functional material design.
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Affiliation(s)
- Yoshiaki Maeda
- Department of Chemistry, City University of New York-Hunter College, New York, New York 10065;
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, Syracuse, New York 13244;
| | - Hiroshi Matsui
- Department of Chemistry, City University of New York-Hunter College, New York, New York 10065;
- Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021
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Delle Fratte S, Piubelli C, Domenici E. Development of a High-Throughput Scintillation Proximity Assay for the Identification of C-Domain Translational Initiation Factor 2 Inhibitors. ACTA ACUST UNITED AC 2016; 7:541-6. [PMID: 14599352 DOI: 10.1177/1087057102238628] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Translational initiation factor 2 (IF2) is the largest of the 3 factors required for translation initiation in prokaryotes and has been shown to be essential in Escherichia coli. It stimulates the binding of fMet-tRNAfMet to the 30S ribosomal subunit in the presence of GTP. The selectivity is achieved through specific recognition of the tRNAfMet blocked α-amino group. IF2 is composed of 3 structural domains: N-domain, whose function is not known; G-domain, which contains the GTP/GDP binding site and the GTPase catalytic center; and C-domain, which recognizes and binds fMet-tRNAfMet. Its activity is strictly bacteria specific and highly conserved among prokaryotes. So far, antibiotics targeting IF2 function are not known, and this makes it an ideal target for new drugs with mechanisms of resistance not yet developed. A few assays have been developed in the past, which allow the detection of IF2 activity either directly or indirectly. In both instances, the assays are based on radioactive detection and do not allow for high throughput because of the need for separation or solvent extraction steps. The authors describe a novel biochemical assay for IF2 that exploits the molecular recognition of fMet-tRNAfMet by the C-domain. The assay is based on the incubation of biotinyl-IF2 with fMet-tRNAfMet and the subsequent capture of the radiolabeled complex by streptavidin-coated beads, exploiting the scintillation proximity assay (SPA) technology. The assay has been designed in an automatable, homogeneous, miniaturized fashion suitable for high-throughput screening and is rapid, sensitive, and robust to dimethyl sulfoxide (DMSO) up to 10% v/v. The assay, used to screen a limited chemical collection of about 5000 compounds and a subset of compounds originated by a 2-D substructural search, has shown to be able to detect potential IF2 inhibitors.
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29
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Guenat S, Rouleau N, Bielmann C, Bedard J, Maurer F, Allaman-Pillet N, Nicod P, Bielefeld-Sévigny M, Beckmann JS, Bonny C, Bossé R, Roduit R. Homogeneous and Nonradioactive High-Throughput Screening Platform for the Characterization of Kinase Inhibitors in Cell Lysates. ACTA ACUST UNITED AC 2016; 11:1015-26. [PMID: 17092917 DOI: 10.1177/1087057106294697] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Protein kinases are directly implicated in many human diseases; therefore, kinase inhibitors show great promises as new therapeutic drugs. In an effort to facilitate the screening and the characterization of kinase inhibitors, a novel application of the AlphaScreen technology was developed to monitor JNK activity from (1) purified kinase preparations and (2) endogenous kinase from cell lysates preactivated with different cytokines. The authors confirmed that both adenosine triphosphate (ATP) competitive as well as peptide-based JNK inhibitors were able to block the activity of both recombinant and HepG2 endogenous JNK activity. Using the same luminescence technique adapted for binding studies, the authors characterized peptide inhibitor mechanisms by measuring the binding affinity of the inhibitors for JNK. Because of the versatility of the technology, this cell-based JNK kinase assay could be adapted to other kinases and would represent a powerful tool to evaluate endogenous kinase activity and test a large number of potential inhibitors in a more physiologically relevant environment.
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Affiliation(s)
- Sylvie Guenat
- Service of Medical Genetics, CHUV, Lausanne, Switzerland
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30
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Abstract
Components within synthetic chemical and natural product extract libraries often interfere with fluorescence-based assays. Fluorescence interference can result when the intrinsic spectral properties of colored compounds overlap with the fluorescent probes. Typically, fluorescence-based protease assays use peptide amidomethylcoumarin derivatives as substrates. However, because many organic compounds absorb in the ultraviolet region, they can interfere with coumarin-based fluorescence assays. Red-shifted fluorescent dyes such as peptidyl rhodamine derivatives are useful because there is generally less interference from organic compounds outside the ultraviolet wavelengths. In this report, rhodamine-based fluorogenic substrates, such as bis-(Leu)2-Rhod110 and bis-(Ala-Pro)2-Rhod110, were developed for leucine aminopeptidase and dipeptidyl aminopeptidase. Novel, tandem rhodamine substrates such as Ala-Pro-Rhod110-Leu were designed with 2 protease cleavage sites and used to assay 2 proteases in a multiplex format. General endpoint high-throughput screening (HTS) assays were also developed for leucine aminopeptidase, dipeptidyl aminopeptidase, and trypsin that incorporated both amidomethylcoumarin and rhodamine-based fluorogenic substrates into a single screening format. These dual-substrate assays allowed for the successful screening of the LOPAC™ collection and natural product extracts despite high levels of fluorescence interference.
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Affiliation(s)
- Stephan K Grant
- Department of Human and Animal Infectious Disease Research, Merck and Co., Rahway, NJ, USA
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31
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Chen Y, Diener K, Patel IR, Kawooya JK, Martin GA, Yamdagni P, Zhang X, Sandrasalphaa A, Sahasrabudhe S, Busch SJ. Phage Display of Functional Human TNF-α Converting Enzyme Catalytic Domain: A Rapid Method for the Production of Stabilized Proteolytic Proteins for Assay Development and High-Throughput Screening. ACTA ACUST UNITED AC 2016; 7:433-40. [PMID: 14599359 DOI: 10.1177/108705702237675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The catalytic domain of human tumor necrosis factor-α (TNF-α) converting enzyme (TACE) was expressed in a phage display system to determine whether stable and active enzyme could be made for high-throughput screening (HTS). This would address many issues around screening of proteases in this class. The phage-displayed TACE catalytic domain (PDT) properly cleaved the fusion protein of glutathione S-transferase (GST)-pro-TNF-α to generate the mature TNF-α in vitro. To determine the utility of the PDT in HTS, the authors further demonstrated that PDT was able to generate a strong reproducible fluorescence signal by cleaving a fluorogenic TNF-α-specific peptide in vitro. More important, the catalytic activity of the PDT was inhibited by a broad-spectrum matrix metalloprotease (MMP) inhibitor but not by an MMP-I specific inhibitor, illustrating the potential utility of PDT for HTS. The PDT was also compared with baculovirus-expressed TACE (BET) in these assays to establish the relative efficacy of PDT. Both PDT and BET showed a similar specific cleavage profile against the defined substrates. Activity of the BET, however, was stable at 4 °C for less than 24 h. In contrast, the PDT exhibited remarkable stability, losing very little activity even after 2 years at 4 °C. On the basis of these results, the authors concluded that the phage display system might be a useful tool for expressing proteins that have stability issues related to auto-proteolytic activity. Furthermore, the ease and low cost of large-scale production of phage should make it suitable for assay development and HTS.
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Affiliation(s)
- Yangde Chen
- Department of Functional Genomics, Aventis Pharmaceuticals, Inc., Bridgewater, NJ, USA
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32
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Hajduk PJ, Betz SF, Mack J, Ruan X, Towne DL, Lerner CG, Beutel BA, Fesik SW. A Strategy for High-Throughput Assay Development Using Leads Derived from Nuclear Magnetic Resonance-Based Screening. ACTA ACUST UNITED AC 2016; 7:429-32. [PMID: 14599358 DOI: 10.1177/108705702237674] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A strategy is described for the development of high-throughput screening assays against targets of unknown function that involves the use of nuclear magnetic resonance (NMR) spectroscopy. Using this approach, molecules that bind to the protein target are identified from an NMR-based screen of a library of substrates, cofactors, and other compounds that are known to bind to many proteins and enzymes. Once a ligand has been discovered, a fluorescent or radiolabeled analog of the ligand is synthesized that can be used in a high-throughput screen. The approach is illustrated in the development of a high-throughput screening assay against HI-0033, a conserved protein from Haemophilus influenzae whose function is currently unknown. Adenosine was found to bind to HI-0033 by NMR, and fluorescent analogs were rapidly identified that bound to HI-0033 in the submicromolar range. Using these fluorescent compounds, a fluorescence polarization assay was developed that is suitable for high-throughput screening and obtaining detailed structure-activity relationships for lead optimization.
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Affiliation(s)
- Philip J Hajduk
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL, USA
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Gearhart TL, Montelaro RC, Schurdak ME, Pilcher CD, Rinaldo CR, Kodadek T, Park Y, Islam K, Yurko R, Marques ETA, Burke DS. Selection of a potential diagnostic biomarker for HIV infection from a random library of non-biological synthetic peptoid oligomers. J Immunol Methods 2016; 435:85-9. [PMID: 27182050 PMCID: PMC4947968 DOI: 10.1016/j.jim.2016.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/10/2016] [Accepted: 05/02/2016] [Indexed: 12/05/2022]
Abstract
Non-biological synthetic oligomers can serve as ligands for antibodies. We hypothesized that a random combinatorial library of synthetic poly-N-substituted glycine oligomers, or peptoids, could represent a random “shape library” in antigen space, and that some of these peptoids would be recognized by the antigen-binding pocket of disease-specific antibodies. We synthesized and screened a one bead one compound combinatorial library of peptoids, in which each bead displayed an 8-mer peptoid with ten possible different amines at each position (108 theoretical variants). By screening one million peptoid/beads we found 112 (approximately 1 in 10,000) that preferentially bound immunoglobulins from human sera known to be positive for anti-HIV antibodies. Reactive peptoids were then re-synthesized and rigorously evaluated in plate-based ELISAs. Four peptoids showed very good, and one showed excellent, properties for establishing a sero-diagnosis of HIV. These results demonstrate the feasibility of constructing sero-diagnostic assays for infectious diseases from libraries of random molecular shapes. In this study we sought a proof-of-principle that we could identify a potential diagnostic antibody ligand biomarker for an infectious disease in a random combinatorial library of 100 million peptoids. We believe that this is the first evidence that it is possible to develop sero-diagnostic assays – for any infectious disease – based on screening random libraries of non-biological molecular shapes.
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Affiliation(s)
- Tricia L Gearhart
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA, 15261, United States
| | - Ronald C Montelaro
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA, 15261, United States
| | - Mark E Schurdak
- Drug Discovery Institute, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA 15261, United States
| | - Chris D Pilcher
- Center for AIDS Research, University of California, 1001 Potrero Ave, SFGH 80, San Francisco, CA 94110, United States
| | - Charles R Rinaldo
- Graduate School of Public Health, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA, United States
| | - Thomas Kodadek
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yongseok Park
- Graduate School of Public Health, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA, United States
| | - Kazi Islam
- Peptide Synthesis Facility, University of Pittsburgh, 300 Technology Drive, Pittsburgh, PA 15219, United States
| | - Raymond Yurko
- Peptide Synthesis Facility, University of Pittsburgh, 300 Technology Drive, Pittsburgh, PA 15219, United States
| | - Ernesto T A Marques
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA, 15261, United States; Graduate School of Public Health, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA, United States
| | - Donald S Burke
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA, 15261, United States; Graduate School of Public Health, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA, United States.
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Le NNT, Zorn S, Schmitt SK, Gopalan P, Murphy WL. Hydrogel arrays formed via differential wettability patterning enable combinatorial screening of stem cell behavior. Acta Biomater 2016; 34:93-103. [PMID: 26386315 PMCID: PMC4794413 DOI: 10.1016/j.actbio.2015.09.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/03/2015] [Accepted: 09/15/2015] [Indexed: 01/12/2023]
Abstract
Here, we have developed a novel method for forming hydrogel arrays using surfaces patterned with differential wettability. Our method for benchtop array formation is suitable for enhanced-throughput, combinatorial screening of biochemical and biophysical cues from chemically defined cell culture substrates. We demonstrated the ability to generate these arrays without the need for liquid handling systems and screened the combinatorial effects of substrate stiffness and immobilized cell adhesion peptide concentration on human mesenchymal stem cell (hMSC) behavior during short-term 2-dimensional cell culture. Regardless of substrate stiffness, hMSC initial cell attachment, spreading, and proliferation were linearly correlated with immobilized CRGDS peptide concentration. Increasing substrate stiffness also resulted in increased hMSC initial cell attachment, spreading, and proliferation; however, examination of the combinatorial effects of CRGDS peptide concentration and substrate stiffness revealed potential interplay between these distinct substrate signals. Maximal hMSC proliferation seen on substrates with either high stiffness or high CRGDS peptide concentration suggests that some baseline level of cytoskeletal tension was required for hMSC proliferation on hydrogel substrates and that multiple substrate signals could be engineered to work in synergy to promote mechanosensing and regulate cell behavior. STATEMENT OF SIGNIFICANCE Our novel array formation method using surfaces patterned with differential wettability offers the advantages of benchtop array formation for 2-dimensional cell cultures and enhanced-throughput screening without the need for liquid handling systems. Hydrogel arrays formed via our method are suitable for screening the influence of chemical (e.g. cell adhesive ligands) and physical (stiffness, size, shape, and thickness) substrate properties on stem cell behavior. The arrays are also fully compatible with commercially available micro-array add-on systems, which allows for simultaneous control of the insoluble and soluble cell culture environment. This study used hydrogel arrays to demonstrate that synergy between cell adhesion and mechanosensing can be used to regulate hMSC behavior.
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Affiliation(s)
- Ngoc Nhi T Le
- Materials Science Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Stefan Zorn
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Samantha K Schmitt
- Materials Science Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Padma Gopalan
- Materials Science Program, University of Wisconsin-Madison, Madison, WI, USA; Department of Material Science and Engineering, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - William L Murphy
- Materials Science Program, University of Wisconsin-Madison, Madison, WI, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA; Department of Material Science and Engineering, University of Wisconsin-Madison, Madison, WI, USA; Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI, USA.
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35
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Dalecki AG, Malalasekera AP, Schaaf K, Kutsch O, Bossmann SH, Wolschendorf F. Combinatorial phenotypic screen uncovers unrecognized family of extended thiourea inhibitors with copper-dependent anti-staphylococcal activity. Metallomics 2016; 8:412-21. [PMID: 26935206 PMCID: PMC4838501 DOI: 10.1039/c6mt00003g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The continuous rise of multi-drug resistant pathogenic bacteria has become a significant challenge for the health care system. In particular, novel drugs to treat infections of methicillin-resistant Staphylococcus aureus strains (MRSA) are needed, but traditional drug discovery campaigns have largely failed to deliver clinically suitable antibiotics. More than simply new drugs, new drug discovery approaches are needed to combat bacterial resistance. The recently described phenomenon of copper-dependent inhibitors has galvanized research exploring the use of metal-coordinating molecules to harness copper's natural antibacterial properties for therapeutic purposes. Here, we describe the results of the first concerted screening effort to identify copper-dependent inhibitors of Staphylococcus aureus. A standard library of 10 000 compounds was assayed for anti-staphylococcal activity, with hits defined as those compounds with a strict copper-dependent inhibitory activity. A total of 53 copper-dependent hit molecules were uncovered, similar to the copper independent hit rate of a traditionally executed campaign conducted in parallel on the same library. Most prominent was a hit family with an extended thiourea core structure, termed the NNSN motif. This motif resulted in copper-dependent and copper-specific S. aureus inhibition, while simultaneously being well tolerated by eukaryotic cells. Importantly, we could demonstrate that copper binding by the NNSN motif is highly unusual and likely responsible for the promising biological qualities of these compounds. A subsequent chemoinformatic meta-analysis of the ChEMBL chemical database confirmed the NNSNs as an unrecognized staphylococcal inhibitor, despite the family's presence in many chemical screening libraries. Thus, our copper-biased screen has proven able to discover inhibitors within previously screened libraries, offering a mechanism to reinvigorate exhausted molecular collections.
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Affiliation(s)
- Alex G Dalecki
- Department of Medicine, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA.
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Peng X, Yang G, Fan X, Bai Y, Ren X, Zhou Y. Controlled methyl-esterification of pectin catalyzed by cation exchange resin. Carbohydr Polym 2016; 137:650-656. [PMID: 26686175 DOI: 10.1016/j.carbpol.2015.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 11/18/2022]
Abstract
This study developed a new method to methyl-esterify pectin using a cation exchange resin. Homogalacturonan (HG)-type pectin (WGPA-3-HG) and rhamnogalacturonan (RG)-I-type pectin (AHP-RG) obtained from the roots of Panax ginseng and sunflower heads, respectively, were used as models. Compared to commonly used methyl-esterification methods that use either methyl iodide or acidified methanol, the developed method can methyl-esterify both HG- and RG-I-type pectins without degrading their structures via β-elimination or acid hydrolysis. In addition, by modifying reaction conditions, including the mass ratio of resin to pectin, reaction time, and temperature, the degree of esterification can be controlled. Moreover, the resin and methanol can be recycled to conserve resources, lower costs, and reduce environmental pollution. This new methodology will be highly useful for industrial esterification of pectin.
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Affiliation(s)
- Xiaoxia Peng
- Jilin Province Key Laboratory on Chemistry and Biology of Natural Drugs in Changbai Mountain, School of Life Sciences, Northeast Normal University, Changchun 130024, PR China
| | - Guang Yang
- Jilin Province Key Laboratory on Chemistry and Biology of Natural Drugs in Changbai Mountain, School of Life Sciences, Northeast Normal University, Changchun 130024, PR China
| | - Xingchen Fan
- Jilin Province Key Laboratory on Chemistry and Biology of Natural Drugs in Changbai Mountain, School of Life Sciences, Northeast Normal University, Changchun 130024, PR China
| | - Yeming Bai
- Jilin Province Key Laboratory on Chemistry and Biology of Natural Drugs in Changbai Mountain, School of Life Sciences, Northeast Normal University, Changchun 130024, PR China
| | - Xiaomeng Ren
- Jilin Province Key Laboratory on Chemistry and Biology of Natural Drugs in Changbai Mountain, School of Life Sciences, Northeast Normal University, Changchun 130024, PR China
| | - Yifa Zhou
- Jilin Province Key Laboratory on Chemistry and Biology of Natural Drugs in Changbai Mountain, School of Life Sciences, Northeast Normal University, Changchun 130024, PR China.
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Houghten RA, Ganno ML, McLaughlin JP, Dooley C, Eans SO, Santos RG, LaVoi T, Nefzi A, Welmaker G, Giulianotti MA, Toll L. Direct Phenotypic Screening in Mice: Identification of Individual, Novel Antinociceptive Compounds from a Library of 734,821 Pyrrolidine Bis-piperazines. ACS Comb Sci 2016; 18:51-64. [PMID: 26651386 PMCID: PMC4710894 DOI: 10.1021/acscombsci.5b00126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/09/2015] [Indexed: 12/04/2022]
Abstract
The hypothesis in the current study is that the simultaneous direct in vivo testing of thousands to millions of systematically arranged mixture-based libraries will facilitate the identification of enhanced individual compounds. Individual compounds identified from such libraries may have increased specificity and decreased side effects early in the discovery phase. Testing began by screening ten diverse scaffolds as single mixtures (ranging from 17,340 to 4,879,681 compounds) for analgesia directly in the mouse tail withdrawal model. The "all X" mixture representing the library TPI-1954 was found to produce significant antinociception and lacked respiratory depression and hyperlocomotor effects using the Comprehensive Laboratory Animal Monitoring System (CLAMS). The TPI-1954 library is a pyrrolidine bis-piperazine and totals 738,192 compounds. This library has 26 functionalities at the first three positions of diversity made up of 28,392 compounds each (26 × 26 × 42) and 42 functionalities at the fourth made up of 19,915 compounds each (26 × 26 × 26). The 120 resulting mixtures representing each of the variable four positions were screened directly in vivo in the mouse 55 °C warm-water tail-withdrawal assay (ip administration). The 120 samples were then ranked in terms of their antinociceptive activity. The synthesis of 54 individual compounds was then carried out. Nine of the individual compounds produced dose-dependent antinociception equivalent to morphine. In practical terms what this means is that one would not expect multiexponential increases in activity as we move from the all-X mixture, to the positional scanning libraries, to the individual compounds. Actually because of the systematic formatting one would typically anticipate steady increases in activity as the complexity of the mixtures is reduced. This is in fact what we see in the current study. One of the final individual compounds identified, TPI 2213-17, lacked significant respiratory depression, locomotor impairment, or sedation. Our results represent an example of this unique approach for screening large mixture-based libraries directly in vivo to rapidly identify individual compounds.
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Affiliation(s)
- Richard A. Houghten
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Michelle L. Ganno
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Jay P. McLaughlin
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Colette
T. Dooley
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Shainnel O. Eans
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Radleigh G. Santos
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Travis LaVoi
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Adel Nefzi
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Greg Welmaker
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Marc A. Giulianotti
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Lawrence Toll
- Torrey Pines Institute for
Molecular Studies, 11350
Southwest Village Parkway, Port St. Lucie, Florida 34987, United States
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Gulati K, Poluri KM. An Overview of Computational and Experimental Methods for Designing Novel Proteins. Recent Pat Biotechnol 2016; 10:235-263. [PMID: 27745543 DOI: 10.2174/1872208310666161013152249] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/15/2016] [Accepted: 09/19/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Unraveling the comprehensive networks of molecular signaling in various cellular processes and redesign/rewire them as per human wish is the ultimate dream of the biomedical researchers. Recent advances in the experimental and computational biophysics have provided us with enormous amount of protein sequences and a wide variety of structural information. Protein engineering is a fledging field and a creative process to design the target proteins or signaling networks with desirable structure and functions. OBJECTIVE Protein engineering has been a powerful tool in bioengineering for last couple of decades for generating vast numbers of useful enzymes/proteins that possess huge therapeutic and industrial potential. Now it is the high time to review the existing technologies and tune these methods for a desirable purpose as per the demand of biotechnological/biomedical applications. RESULTS Numerous engineering approaches have been developed to generate synthetic protein universe with desired specificity and enhanced performance in comparison to their natural counterparts. The current review provides a glimpse of several of the important computational and experimental methods that are being widely used under the categories of rational design, de novo design, directed evolution and combinatorial approach. CONCLUSIONS This review shed light on the technicalities, advantages and pitfalls of the existing methodologies along with their applications, recent patents obtained using the engineered proteins and the current and future perspectives of protein engineering techniques.
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Affiliation(s)
| | - Krishna M Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee- 247667, Uttarakhand, India
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Váradi A, Palmer TC, Notis Dardashti R, Majumdar S. Isocyanide-Based Multicomponent Reactions for the Synthesis of Heterocycles. Molecules 2015; 21:E19. [PMID: 26703561 PMCID: PMC4782750 DOI: 10.3390/molecules21010019] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/02/2015] [Accepted: 12/17/2015] [Indexed: 11/16/2022] Open
Abstract
Multicomponent reactions (MCRs) are extremely popular owing to their facile execution, high atom-efficiency and the high diversity of products. MCRs can be used to access various heterocycles and highly functionalized scaffolds, and thus have been invaluable tools in total synthesis, drug discovery and bioconjugation. Traditional isocyanide-based MCRs utilize an external nucleophile attacking the reactive nitrilium ion, the key intermediate formed in the reaction of the imine and the isocyanide. However, when reactants with multiple nucleophilic groups (bisfunctional reactants) are used in the MCR, the nitrilium intermediate can be trapped by an intramolecular nucleophilic attack to form various heterocycles. The implications of nitrilium trapping along with widely applied conventional isocyanide-based MCRs in drug design are discussed in this review.
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Affiliation(s)
- András Váradi
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Travis C Palmer
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | | | - Susruta Majumdar
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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Abstract
Small molecule receptors are attractive potential sensors of post-translational modifications, including methylated lysine and methylated arginine. Using dynamic combinatorial chemistry (DCC), our lab previously identified a suite of receptors that bind to Kme3 with a range of affinities ranging from low micromolar to high nanomolar, each with a unique selectivity for Kme3 over the lower methylation states. To enable these receptors to have broad application as Kme3 sensors, we have developed a method for their late-stage modification, which we used to synthesize biotinylated derivatives of A2B, A2D, and A2G in a single step. For our most attractive receptor for applications, A2N, we needed to develop an alternative method for its selective functionalization, which we achieved by "activating" the carboxylic acids on the constituent monomer A or N by pre-functionalizing them with glycine (Gly). Using the resulting Gly-A and Gly-N monomers, we synthesized the novel A2N variants A2Gly-N, Gly-A2N, and Gly-A2Gly-N, which enabled the late stage biotinylation of A2N wherever Gly was incorporated. Finally, we performed ITC and NMR binding experiments to study the effect that carboxylate spacing has on the affinity and selectivity of A2Gly-N and Gly-A2N for KmeX guests compared to A2N. These studies revealed the proximity of the carboxylates to play a complex role in the molecular recognition event, despite their positioning on the outside of the receptor.
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Affiliation(s)
- Nicholas K Pinkin
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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41
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Liguori R, Ionata E, Marcolongo L, Vandenberghe LPDS, La Cara F, Faraco V. Optimization of Arundo donax Saccharification by (Hemi)cellulolytic Enzymes from Pleurotus ostreatus. Biomed Res Int 2015; 2015:951871. [PMID: 26634214 PMCID: PMC4652331 DOI: 10.1155/2015/951871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/17/2015] [Accepted: 10/01/2015] [Indexed: 11/26/2022]
Abstract
An enzymatic mixture of cellulases and xylanases was produced by Pleurotus ostreatus using microcrystalline cellulose as inducer, partially characterized and tested in the statistical analysis of Arundo donax bioconversion. The Plackett-Burman screening design was applied to identify the most significant parameters for the enzymatic hydrolysis of pretreated A. donax. As the most significant influence during the enzymatic hydrolysis of A. donax was exercised by the temperature (°C), pH, and time, the combined effect of these factors in the bioconversion by P. ostreatus cellulase and xylanase was analyzed by a 3(3) factorial experimental design. It is worth noting that the best result of 480.10 mg of sugars/gds, obtained at 45 °C, pH 3.5, and 96 hours of incubation, was significant also when compared with the results previously reached by process optimization with commercial enzymes.
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Affiliation(s)
- Rossana Liguori
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - Elena Ionata
- Institute of Agro-Environment and Forest Biology, National Research Council (CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Loredana Marcolongo
- Institute of Agro-Environment and Forest Biology, National Research Council (CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luciana Porto de Souza Vandenberghe
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Coronel Francisco H. dos Santos Avenue 210, 81531-990 Curitiba, PR, Brazil
| | - Francesco La Cara
- Institute of Agro-Environment and Forest Biology, National Research Council (CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Vincenza Faraco
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
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42
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Popova B, Schubert S, Bulla I, Buchwald D, Kramer W. A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules. PLoS One 2015; 10:e0136778. [PMID: 26355961 PMCID: PMC4565649 DOI: 10.1371/journal.pone.0136778] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/08/2015] [Indexed: 11/19/2022] Open
Abstract
A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis.
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Affiliation(s)
- Blagovesta Popova
- Department Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Department Molecular Genetics and Preparative Molecular Biology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- * E-mail:
| | - Steffen Schubert
- Department Molecular Genetics and Preparative Molecular Biology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Department Dermatology, Venereology and Allergology, University Medical Center, Göttingen, Germany
- Information Network of Departments of Dermatology (IVDK), Göttingen, Germany
| | - Ingo Bulla
- Theoretical Biology and Biophysics, Group T-6, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Institute for Mathematics and Informatics, Universität Greifswald, Greifswald, Germany
- Department Bioinformatics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Daniela Buchwald
- Department Bioinformatics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Neurobiology Laboratory, German Primate Center GmbH, Göttingen, Germany
| | - Wilfried Kramer
- Department Molecular Genetics and Preparative Molecular Biology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Department Molecular Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
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43
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Drożdż W, Kołodziejski M, Markiewicz G, Jenczak A, Stefankiewicz AR. Generation of a Multicomponent Library of Disulfide Donor-Acceptor Architectures Using Dynamic Combinatorial Chemistry. Int J Mol Sci 2015; 16:16300-12. [PMID: 26193265 PMCID: PMC4519951 DOI: 10.3390/ijms160716300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 11/16/2022] Open
Abstract
We describe here the generation of new donor-acceptor disulfide architectures obtained in aqueous solution at physiological pH. The application of a dynamic combinatorial chemistry approach allowed us to generate a large number of new disulfide macrocyclic architectures together with a new type of [2]catenanes consisting of four distinct components. Up to fifteen types of structurally-distinct dynamic architectures have been generated through one-pot disulfide exchange reactions between four thiol-functionalized aqueous components. The distribution of disulfide products formed was found to be strongly dependent on the structural features of the thiol components employed. This work not only constitutes a success in the synthesis of topologically- and morphologically-complex targets, but it may also open new horizons for the use of this methodology in the construction of molecular machines.
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Affiliation(s)
- Wojciech Drożdż
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
- Centre for Advanced Technologies, Adam Mickiewicz University, Umultowska 89c, 61-614 Poznań, Poland.
| | - Michał Kołodziejski
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
- Centre for Advanced Technologies, Adam Mickiewicz University, Umultowska 89c, 61-614 Poznań, Poland.
| | - Grzegorz Markiewicz
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
- Centre for Advanced Technologies, Adam Mickiewicz University, Umultowska 89c, 61-614 Poznań, Poland.
| | - Anna Jenczak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
- Centre for Advanced Technologies, Adam Mickiewicz University, Umultowska 89c, 61-614 Poznań, Poland.
| | - Artur R Stefankiewicz
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
- Centre for Advanced Technologies, Adam Mickiewicz University, Umultowska 89c, 61-614 Poznań, Poland.
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Torrades F, García-Hortal JA, García-Montaño J. Mineralization of hetero bi-functional reactive dye in aqueous solution by Fenton and photo-Fenton reactions. Environ Technol 2015; 36:2035-2042. [PMID: 25687801 DOI: 10.1080/09593330.2015.1019931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This study focused on the advanced oxidation of the hetero bi-functional reactive dye Sumifix Supra Yellow 3RF (CI Reactive Yellow 145) using dark Fenton and photo-Fenton conditions in a lab-scale experiment. A 2(3) factorial design was used to evaluate the effects of the three key factors: temperature, Fe(II) and H2O2 concentrations, for a dye concentration of 250 mg L(-1) with chemical oxygen demand (COD) of 172 mg L(-1) O2 at pH=3. The response function was the COD reduction. This methodology lets us find the effects and interactions of the studied variables and their roles in the efficiency of the treatment process. In the optimization, the correlation coefficients for the model (R2) were 0.948 and 0.965 for Fenton and photo-Fenton treatments, respectively. Under optimized reaction conditions: pH=3, temperature=298 K, [H2O2]=11.765 mM and [Fe(II)]=1.075 mM; 60 min of treatment resulted in a 79% and 92.2% decrease in COD, for the dye taken as the model organic compound, after Fenton and photo-Fenton treatments, respectively.
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Affiliation(s)
- Francesc Torrades
- a Departament d'Enginyeria Química, ETSEIA de Terrassa , Universitat Politècnica de Catalunya , C/Colom 11, Terrassa (Barcelona) E-08222 , Spain
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45
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Yao S, Nie S, Yuan Y, Wang S, Qin C. Efficient extraction of bagasse hemicelluloses and characterization of solid remainder. Bioresour Technol 2015; 185:21-7. [PMID: 25746474 DOI: 10.1016/j.biortech.2015.02.052] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 05/11/2023]
Abstract
To reduce the degradation of cellulose and obtain high molecular weight of hemicellulose from the extracts, pH pre-corrected hot water pretreatment was developed by employing sodium hydroxide (3.9mol/L). The response surface model was established to optimize the extraction process. The species composition and purity of hemicellulose extract was analyzed by High Performance Liquid Chromatography (HPLC). The obtained solid remainder was analyzed by FTIR and SEM. The results showed that the component of xylose in hemicellulose extract was similar with commercial xylan. FTIR and SEM were shown to be able to evaluate solid remainder composition and surface characterization of the bagasse. The biggest balance between solid remainder and dissolved solid was obtained. Not only the yield of dissolved solid was improved, but the structure of solid remainder was also proved, which was beneficial to pulping and papermaking.
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Affiliation(s)
- Shuangquan Yao
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, PR China
| | - Shuangxi Nie
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, PR China; Department of Chemical Engineering, University of New Brunswick, Fredericton, NB E3B5A3, Canada
| | - Yue Yuan
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, PR China
| | - Shuangfei Wang
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, PR China
| | - Chengrong Qin
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, PR China.
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Benito-Peña E, Navarro-Villoslada F, Carrasco S, Jockusch S, Ottaviani MF, Moreno-Bondi MC. Experimental mixture design as a tool for the synthesis of antimicrobial selective molecularly imprinted monodisperse microbeads. ACS Appl Mater Interfaces 2015; 7:10966-10976. [PMID: 25942541 DOI: 10.1021/acsami.5b02238] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The effect of the cross-linker on the shape and size of molecular imprinted polymer (MIP) beads prepared by precipitation polymerization has been evaluated using a chemometric approach. Molecularly imprinted microspheres for the selective recognition of fluoroquinolone antimicrobials were prepared in a one-step precipitation polymerization procedure using enrofloxacin (ENR) as the template molecule, methacrylic acid as functional monomer, 2-hydroxyethyl methacrylate as hydrophilic comonomer, and acetonitrile as the porogen. The type and amount of cross-linker, namely ethylene glycol dimethacrylate, divinylbenzene or trimethylolpropane trimethacrylate, to obtain monodispersed MIP spherical beads in the micrometer range was optimized using a simplex lattice design. Particle size and morphology were assessed by scanning electron microscopy, dynamic light scattering, and nitrogen adsorption measurements. Electron paramagnetic resonance spectroscopy in conjunction with a nitroxide as spin probe revealed information about the microviscosity and polarity of the binding sites in imprinted and nonimprinted polymer beads.
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Affiliation(s)
- Elena Benito-Peña
- †Chemical Optosensors and Applied Photochemistry Group, Dept. of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense, E-28040 Madrid, Spain
| | - Fernando Navarro-Villoslada
- †Chemical Optosensors and Applied Photochemistry Group, Dept. of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense, E-28040 Madrid, Spain
| | - Sergio Carrasco
- †Chemical Optosensors and Applied Photochemistry Group, Dept. of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense, E-28040 Madrid, Spain
| | - Steffen Jockusch
- ‡Department of Chemistry, Columbia University, New York, 3000 Broadway, New York, New York 10027, United States
| | - M Francesca Ottaviani
- §Department of Earth, Life and Environment Sciences (DiSTeVA), Loc. Crocicchia, I 61029 Urbino, Italy
| | - Maria C Moreno-Bondi
- †Chemical Optosensors and Applied Photochemistry Group, Dept. of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense, E-28040 Madrid, Spain
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Isidro-Llobet A, Hadje Georgiou K, Galloway WRJD, Giacomini E, Hansen MR, Méndez-Abt G, Tan YS, Carro L, Sore HF, Spring DR. A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds. Org Biomol Chem 2015; 13:4570-80. [PMID: 25778821 PMCID: PMC4441267 DOI: 10.1039/c5ob00371g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/11/2015] [Indexed: 01/23/2023]
Abstract
Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity.
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Affiliation(s)
- Albert Isidro-Llobet
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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48
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Özdemir M, Sönmez M, Şen F, Dinçer M, Özdemir N. A novel one-pot synthesis of heterocyclic compound (4-benzoyl-5-phenyl-2-(pyridin-2-yl)-3,3a-dihydropyrazolo[1,5-c]pyrimidin-7(6H)-one): structural (X-ray and DFT) and spectroscopic (FT-IR, NMR, UV-Vis and Mass) characterization studies. Spectrochim Acta A Mol Biomol Spectrosc 2015; 137:1304-1314. [PMID: 25305624 DOI: 10.1016/j.saa.2014.08.131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 08/27/2014] [Accepted: 08/31/2014] [Indexed: 06/04/2023]
Abstract
In this study, the title compound named as 4-benzoyl-5-phenyl-2-(pyridin-2-yl)-3,3a-dihydropyrazolo[1,5-c]pyrimidin-7(6H)-one (C24H18N4O2) was both experimentally and theoretically investigated. The compound was synthesized and characterized by FT-IR, NMR ((1)H NMR, (13)C NMR and HETCOR-NMR), Mass spectroscopies and single-crystal X-ray diffraction methods. The compound crystallizes in the monoclinic space group P2(1)/n with a=6.1402 (3) Å, b=21.4470 (15) Å, c=15.0049 (8) Å and β=97.407 (4)°. The molecular geometry was obtained from the X-ray structure determination optimized using density functional theory (DFT/B3LYP) method with the 6-31+G(d, p) basis set in ground state. From the optimized structure, geometric parameters, vibrational wavenumbers and chemical shifts of molecule were obtained. Experimental measurements were compared with its corresponding the calculated data. An excellent harmony between the two data was ascertained. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMOs) and non-linear optical (NLO) properties of the title molecule were investigated by theoretical calculations at the B3LYP/6-31+G(d, p) level.
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Affiliation(s)
- Mecit Özdemir
- Kilis 7 Aralık University, Arts and Sciences Faculty, Department of Chemistry, 79000 Kilis, Turkey.
| | - Mehmet Sönmez
- Gaziantep University, Arts and Sciences Faculty, Department of Chemistry, 27310 Gaziantep, Turkey
| | - Fatih Şen
- Kilis 7 Aralık University, Vocational High School of Health Services, Department of Opticianry, 79000 Kilis, Turkey
| | - Muharrem Dinçer
- Ondokuz Mayıs University, Arts and Sciences Faculty, Department of Physics, 55139 Samsun, Turkey
| | - Namık Özdemir
- Ondokuz Mayıs University, Arts and Sciences Faculty, Department of Physics, 55139 Samsun, Turkey
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49
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Kona R, Fahmy RM, Claycamp G, Polli JE, Martinez M, Hoag SW. Quality-by-design III: application of near-infrared spectroscopy to monitor roller compaction in-process and product quality attributes of immediate release tablets. AAPS PharmSciTech 2015; 16:202-16. [PMID: 25319052 PMCID: PMC4309813 DOI: 10.1208/s12249-014-0180-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 07/15/2014] [Indexed: 11/30/2022] Open
Abstract
The objective of this study is to use near-infrared spectroscopy (NIRS) coupled with multivariate chemometric models to monitor granule and tablet quality attributes in the formulation development and manufacturing of ciprofloxacin hydrochloride (CIP) immediate release tablets. Critical roller compaction process parameters, compression force (CFt), and formulation variables identified from our earlier studies were evaluated in more detail. Multivariate principal component analysis (PCA) and partial least square (PLS) models were developed during the development stage and used as a control tool to predict the quality of granules and tablets. Validated models were used to monitor and control batches manufactured at different sites to assess their robustness to change. The results showed that roll pressure (RP) and CFt played a critical role in the quality of the granules and the finished product within the range tested. Replacing binder source did not statistically influence the quality attributes of the granules and tablets. However, lubricant type has significantly impacted the granule size. Blend uniformity, crushing force, disintegration time during the manufacturing was predicted using validated PLS regression models with acceptable standard error of prediction (SEP) values, whereas the models resulted in higher SEP for batches obtained from different manufacturing site. From this study, we were able to identify critical factors which could impact the quality attributes of the CIP IR tablets. In summary, we demonstrated the ability of near-infrared spectroscopy coupled with chemometrics as a powerful tool to monitor critical quality attributes (CQA) identified during formulation development.
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Affiliation(s)
- Ravikanth Kona
- />School of Pharmacy, University of Maryland, 20 N. Pine Street, Baltimore, Maryland 21201 USA
| | - Raafat M. Fahmy
- />Office of New Animal Drug Evaluation, Center for Veterinary Medicine, FDA, Rockville, Maryland 20855 USA
| | - Gregg Claycamp
- />Office of New Animal Drug Evaluation, Center for Veterinary Medicine, FDA, Rockville, Maryland 20855 USA
| | - James E. Polli
- />School of Pharmacy, University of Maryland, 20 N. Pine Street, Baltimore, Maryland 21201 USA
| | - Marilyn Martinez
- />Office of New Animal Drug Evaluation, Center for Veterinary Medicine, FDA, Rockville, Maryland 20855 USA
| | - Stephen W. Hoag
- />School of Pharmacy, University of Maryland, 20 N. Pine Street, Baltimore, Maryland 21201 USA
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50
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Abstract
If used in an optimized manner, the technology of combinatorial peptide solid-phase libraries can easily improve the analytical determinations of proteomes by several factors. The discovery of novel species and of early stage biomarkers becomes thus reachable with a simple sample treatment. This report describes the most important point to consider (overloading and full recovery) along with a minimum scientific background and gives then detailed recipes to laboratory technicians. Orientations for optional routes are also given according to the objective of the experimental investigations. This covers different approaches to capture proteins of very low abundance. Total protein harvestings to prevent partial losses are also described such as single exhaustive desorption and fractionated elutions for more detailed analyses. Documented results are also reported demonstrating the capability of the technology well beyond what is the common assumption.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milan, 20131, Italy
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