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Bhayani JA, Ballicora MA. Determination of dissociation constants of protein ligands by thermal shift assay. Biochem Biophys Res Commun 2021; 590:1-6. [PMID: 34959191 DOI: 10.1016/j.bbrc.2021.12.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022]
Abstract
The thermal shift assay (TSA) is a powerful tool used to detect molecular interactions between proteins and ligands. Using temperature as a physical denaturant and an extrinsic fluorescent dye, the TSA tracks protein unfolding. This method precisely determines the midpoint of the unfolding transition (Tm), which can shift upon the addition of a ligand. Though experimental protocols have been well developed, the thermal shift assay data traditionally yielded qualitative results. Quantitative methods for Kd determination relied either on empirical and inaccurate usage of Tm or on isothermal approaches, which do not take full advantage of the melting point precision provided by the TSA. We present a new analysis method based on a model that relies on the equilibrium system between the native and molten globule state of the protein using the van't Hoff equation. We propose the Kd can be determined by plotting Tm values versus the logarithm of ligand concentrations and fitting the data to an equation we derived. After testing this procedure with the monomeric maltose-binding protein and an allosterically regulated homotetrameric enzyme (ADP-glucose pyrophosphorylase), we observed that binding results correlated very well with previously established parameters. We demonstrate how this method could potentially offer a broad applicability to a wide range of protein classes and the ability to detect both active and allosteric site binding compounds.
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Affiliation(s)
- Jaina A Bhayani
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, IL, 60660, USA
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, IL, 60660, USA.
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2
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Ramos J, Laux V, Haertlein M, Boeri Erba E, McAuley KE, Forsyth VT, Mossou E, Larsen S, Langkilde AE. Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme. IUCRJ 2021; 8:372-386. [PMID: 33953924 PMCID: PMC8086161 DOI: 10.1107/s2052252521001299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
This structural and biophysical study exploited a method of perdeuterating hen egg-white lysozyme based on the expression of insoluble protein in Escherichia coli followed by in-column chemical refolding. This allowed detailed comparisons with perdeuterated lysozyme produced in the yeast Pichia pastoris, as well as with unlabelled lysozyme. Both perdeuterated variants exhibit reduced thermal stability and enzymatic activity in comparison with hydrogenated lysozyme. The thermal stability of refolded perdeuterated lysozyme is 4.9°C lower than that of the perdeuterated variant expressed and secreted in yeast and 6.8°C lower than that of the hydrogenated Gallus gallus protein. However, both perdeuterated variants exhibit a comparable activity. Atomic resolution X-ray crystallographic analyses show that the differences in thermal stability and enzymatic function are correlated with refolding and deuteration effects. The hydrogen/deuterium isotope effect causes a decrease in the stability and activity of the perdeuterated analogues; this is believed to occur through a combination of changes to hydrophobicity and protein dynamics. The lower level of thermal stability of the refolded perdeuterated lysozyme is caused by the unrestrained Asn103 peptide-plane flip during the unfolded state, leading to a significant increase in disorder of the Lys97-Gly104 region following subsequent refolding. An ancillary outcome of this study has been the development of an efficient and financially viable protocol that allows stable and active perdeuterated lysozyme to be more easily available for scientific applications.
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Affiliation(s)
- Joao Ramos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Valerie Laux
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Elisabetta Boeri Erba
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale, Université de Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Katherine E. McAuley
- Diamond Light Source, Didcot OX11 0DE, United Kingdom
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Estelle Mossou
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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3
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Rainard JM, Pandarakalam GC, McElroy SP. Using Microscale Thermophoresis to Characterize Hits from High-Throughput Screening: A European Lead Factory Perspective. SLAS DISCOVERY 2019; 23:225-241. [PMID: 29460707 PMCID: PMC5824829 DOI: 10.1177/2472555217744728] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
High-throughput screening (HTS) is a proven method for discovering new lead matter for drug discovery and chemical biology. To maximize the likelihood of identifying genuine binders to a molecular target, and avoid wasting resources following up compounds with unproductive/nonspecific mechanisms of action, it is important to employ a range of assays during an HTS campaign that build confidence of target engagement for hit compounds. Biophysical methods that measure direct target/compound engagement have established themselves as key techniques in generating this confidence, and they are now integral to the latter stages of HTS triage at the European Lead Factory (ELF). One relatively new technique that the ELF is using is microscale thermophoresis (MST), which measures the differences in rate of movement through a temperature gradient that are caused when single molecular species form complexes. Here we provide an overview of the MST assay development workflow that the ELF employs and a perspective of our experience to date of using MST to triage the output of HTS campaigns and how it compares and contrasts with the use of other biophysical techniques.
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Affiliation(s)
- Julie M Rainard
- 1 European Screening Centre Newhouse, Biocity Scotland, University of Dundee, Newhouse, UK
| | - George C Pandarakalam
- 1 European Screening Centre Newhouse, Biocity Scotland, University of Dundee, Newhouse, UK
| | - Stuart P McElroy
- 1 European Screening Centre Newhouse, Biocity Scotland, University of Dundee, Newhouse, UK
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Bai N, Roder H, Dickson A, Karanicolas J. Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities. Sci Rep 2019; 9:2650. [PMID: 30804351 PMCID: PMC6389909 DOI: 10.1038/s41598-018-37072-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/30/2018] [Indexed: 01/20/2023] Open
Abstract
Differential scanning fluorimetry (DSF), also known as ThermoFluor or Thermal Shift Assay, has become a commonly-used approach for detecting protein-ligand interactions, particularly in the context of fragment screening. Upon binding to a folded protein, most ligands stabilize the protein; thus, observing an increase in the temperature at which the protein unfolds as a function of ligand concentration can serve as evidence of a direct interaction. While experimental protocols for this assay are well-developed, it is not straightforward to extract binding constants from the resulting data. Because of this, DSF is often used to probe for an interaction, but not to quantify the corresponding binding constant (Kd). Here, we propose a new approach for analyzing DSF data. Using unfolding curves at varying ligand concentrations, our "isothermal" approach collects from these the fraction of protein that is folded at a single temperature (chosen to be temperature near the unfolding transition). This greatly simplifies the subsequent analysis, because it circumvents the complicating temperature dependence of the binding constant; the resulting constant-temperature system can then be described as a pair of coupled equilibria (protein folding/unfolding and ligand binding/unbinding). The temperature at which the binding constants are determined can also be tuned, by adding chemical denaturants that shift the protein unfolding temperature. We demonstrate the application of this isothermal analysis using experimental data for maltose binding protein binding to maltose, and for two carbonic anhydrase isoforms binding to each of four inhibitors. To facilitate adoption of this new approach, we provide a free and easy-to-use Python program that analyzes thermal unfolding data and implements the isothermal approach described herein ( https://sourceforge.net/projects/dsf-fitting ).
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Heinrich Roder
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Alex Dickson
- Department of Biochemistry & Molecular Biology and Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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Mosquito-larvicidal BinA toxin displays affinity for glycoconjugates: Proposal for BinA mediated cytotoxicity. J Invertebr Pathol 2018; 156:29-40. [PMID: 30003921 DOI: 10.1016/j.jip.2018.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/05/2018] [Accepted: 07/07/2018] [Indexed: 11/20/2022]
Abstract
Lysinibacillus sphaericus parasporal BinAB toxin displays mosquito larvicidal activity against Culex and Anopheles, but several Aedes species are refractory. Recently reported crystal structure of BinAB revealed the presence of N-terminal lectin-like domain in BinA. Hemagglutination and hemolytic activities were not observed for BinA in the present studies. We attempted to characterize carbohydrate specificity of BinA by high-throughput approaches using extrinsic fluorescence and thermofluor shift assay. A total of 34 saccharides (mono-, di- and polysaccharides, and glycoproteins) were used for initial high-throughput screening. The promising glycans were identified based on significant change in the fluorescence intensity. Surface plasmon resonance revealed differential binding of BinA with glycoproteins (fetuin, asialofetuin and thyroglobulin) and affinity for simple sugars, l-fucose and l-arabinose. In the limited carbohydrate competition assay, arabinose, fucose and fetuin inhibited BinA toxicity towards Culex larvae. This study for the first time provides direct evidence that BinA is competent to bind diverse and structurally different glycosylated proteins. This activity may be linked to its intracellular cytotoxicity, as protein N-glycosylation is thought to be critical for development and survival of insect larvae. The glycoproteins do not form stable complexes with BinA, however, as observed in the pull-down assay using affinity immobilized BinA and in native-PAGE analysis. As BinA displays only mild affinity with receptor polypeptide, we hypothesize that toxin-receptor specificity of BinA in Culex may be mediated by dual interaction of BinA with glycan core of GPI anchor and receptor polypeptide. The study shall be useful for refining strategies for improving larvicidal activity and for broadening target specificity of BinAB toxin.
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Santofimia-Castaño P, Rizzuti B, Abián O, Velázquez-Campoy A, Iovanna JL, Neira JL. Amphipathic helical peptides hamper protein-protein interactions of the intrinsically disordered chromatin nuclear protein 1 (NUPR1). Biochim Biophys Acta Gen Subj 2018. [DOI: 10.1016/j.bbagen.2018.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Synthesis, biophysical and functional studies of two BP100 analogues modified by a hydrophobic chain and a cyclic peptide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1502-1516. [PMID: 29750913 DOI: 10.1016/j.bbamem.2018.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/02/2018] [Accepted: 05/07/2018] [Indexed: 12/22/2022]
Abstract
Antimicrobial peptides (AMPs) work as a primary defense against pathogenic microorganisms. BP100, (KKLFKKILKYL-NH2), a rationally designed short, highly cationic AMP, acts against many bacteria, displaying low toxicity to eukaryotic cells. Previously we found that its mechanism of action depends on membrane surface charge and on peptide-to-lipid ratio. Here we present the synthesis of two BP100 analogs: BP100‑alanyl‑hexadecyl‑1‑amine (BP100-Ala-NH-C16H33) and cyclo(1‑4)‑d‑Cys1, Ile2, Leu3, Cys4-BP100 (Cyclo(1‑4)‑cILC-BP100). We examined their binding to large unilamellar vesicles (LUV), conformational and functional properties, and compared with those of BP100. The analogs bound to membranes with higher affinity and a lesser dependence on electrostatic forces than BP100. In the presence of LUV, BP100 and BP100-Ala-NH-C16H33 acquired α-helical conformation, while Cyclo(1‑4)‑cILC-BP100) was partly α-helical and partly β-turn. Taking in conjunction: 1. particle sizes and zeta potential, 2. effects on lipid flip-flop, 3. leakage of LUVs internal contents, and 4. optical microscopy of giant unilamellar vesicles, we concluded that at high concentrations, all three peptides acted by a carpet mechanism, while at low concentrations the peptides acted by disorganizing the lipid bilayer, probably causing membrane thinning. The higher activity and lesser membrane surface charge dependence of the analogs was probably due to their greater hydrophobicity. The MIC values of both analogs towards Gram-positive and Gram-negative bacteria were similar to those of BP100 but both analogues were more hemolytic. Confocal microscopy showed Gram-positive B. subtilis killing with concomitant extensive membrane damage suggestive of lipid clustering, or peptide-lipid aggregation. These results were in agreement with those found in model membranes.
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Kaiser CE, Rincon Pabon JP, Khowsathit J, Castaldi MP, Kazmirski SL, Weis DD, Zhang AX, Karanicolas J. Modulating Antibody Structure and Function through Directed Mutations and Chemical Rescue. ACS Synth Biol 2018; 7:1152-1162. [PMID: 29609459 DOI: 10.1021/acssynbio.8b00124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Monoclonal antibody therapeutics have revolutionized the treatment of diseases such as cancer and autoimmune disorders, and also serve as research reagents for diverse and unparalleled applications. To extend their utility in both contexts, we have begun development of tunable antibodies, whose activity can be controlled by addition of a small molecule. Conceptually, we envision that incorporating cavity-forming mutations into an antibody can disrupt its structure, thereby reducing its affinity for antigen; addition of a small molecule may then restore the active structure, and thus rescue antigen binding. As a first proof of concept toward implementing this strategy, we have incorporated individual tryptophan to glycine mutations into FITC-E2, an anti-fluorescein single-chain variable fragment (scFv). We find that these can disrupt the protein structure and diminish antigen binding, and further that both structure and function can be rescued by addition of indole to complement the deleted side chain. While the magnitude of the affinity difference triggered by indole is modest in this first model system, it nonetheless provides a framework for future mutation/ligand pairs that may induce more dramatic responses. Disrupting and subsequently rescuing antibody activity, as exemplified by this first example, may represent a new approach to "design in" fine-tuned control of antibody activity for a variety of future applications.
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Affiliation(s)
- Christine E. Kaiser
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Juan Pablo Rincon Pabon
- Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Jittasak Khowsathit
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| | - M. Paola Castaldi
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Steven L. Kazmirski
- Structure and Biophysics, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - David D. Weis
- Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Andrew X. Zhang
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - John Karanicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
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Holdgate GA, Meek TD, Grimley RL. Mechanistic enzymology in drug discovery: a fresh perspective. Nat Rev Drug Discov 2017; 17:115-132. [PMID: 29192286 DOI: 10.1038/nrd.2017.219] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Given the therapeutic and commercial success of small-molecule enzyme inhibitors, as exemplified by kinase inhibitors in oncology, a major focus of current drug-discovery and development efforts is on enzyme targets. Understanding the course of an enzyme-catalysed reaction can help to conceptualize different types of inhibitor and to inform the design of screens to identify desired mechanisms. Exploiting this information allows the thorough evaluation of diverse compounds, providing the knowledge required to efficiently optimize leads towards differentiated candidate drugs. This review highlights the rationale for conducting high-quality mechanistic enzymology studies and considers the added value in combining such studies with orthogonal biophysical methods.
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Affiliation(s)
- Geoffrey A Holdgate
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - Thomas D Meek
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Rachel L Grimley
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
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Yang SC, Yen FL, Wang PW, Aljuffali IA, Weng YH, Tseng CH, Fang JY. Naphtho[1,2-b]furan-4,5-dione is a potent anti-MRSA agent against planktonic, biofilm and intracellular bacteria. Future Microbiol 2017; 12:1059-1073. [DOI: 10.2217/fmb-2017-0044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Aim: Naphtho[1,2-b]furan-4,5-dione (N12D) and naphtho[2,3-b]furan-4,9-dione (N23D) are furanonaphthoquinone derivatives from natural resources. We examined the antimicrobial activity of N12D and N23D against drug-resistant Staphylococcus aureus. Materials & methods: Minimum inhibitory concentration, minimum bactericidal concentration, bacterial viability and agar diffusion assay were conducted against methicillin-resistant S. aureus (MRSA) and clinical isolates of vancomycin-resistant S. aureus. Results & conclusion: The minimum inhibitory concentration of N12D and N23D against MRSA was 4.9–9.8 and 39 μM, respectively. With regard to the agar diffusion test, the inhibition zone of the quinone compounds was threefold larger than that of oxacillin. N12D was found to inhibit MRSA biofilm thickness from 24 to 16 μm as observed by confocal microscopy. N12D showed a significant reduction of the intracellular MRSA burden without decreasing the macrophage viability. The antibacterial mechanisms of N12D may be bacterial wall/membrane damage and disturbance of gluconeogenesis and the tricarboxylic acid cycle.
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Affiliation(s)
- Shih-Chun Yang
- Pharmaceutics Laboratory, Graduate Institute of Natural Products, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Feng-Lin Yen
- Department of Fragrance & Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Pei-Wen Wang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 404, Taiwan
| | - Ibrahim A Aljuffali
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Yi-Han Weng
- Pharmaceutics Laboratory, Graduate Institute of Natural Products, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Chih-Hua Tseng
- Department of Fragrance & Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Natural Products & Drug Development, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Infectious Disease & Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jia-You Fang
- Pharmaceutics Laboratory, Graduate Institute of Natural Products, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
- Chinese Herbal Medicine Research Team, Healthy Aging Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
- Research Center for Food & Cosmetic Safety & Research Center for Chinese Herbal Medicine, Chang Gung University of Science & Technology, Taoyuan 333, Taiwan
- Department of Anesthesiology, Chang Gung Memorial Hospital, Kweishan, Taoyuan 333, Taiwan
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Chilton M, Clennell B, Edfeldt F, Geschwindner S. Hot-Spotting with Thermal Scanning: A Ligand- and Structure-Independent Assessment of Target Ligandability. J Med Chem 2017; 60:4923-4931. [PMID: 28537726 DOI: 10.1021/acs.jmedchem.7b00208] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Evaluating the ligandability of a protein target is a key component when defining hit-finding strategies or when prioritize among drug targets. Computational as well as biophysical approaches based on nuclear magnetic resonance (NMR) fragment screening are powerful approaches but suffer from specific constraints that limit their usage. Here, we demonstrate the applicability of high-throughput thermal scanning (HTTS) as a simple and generic biophysical fragment screening method to reproduce assessments from NMR-based screening. By applying this method to a large set of proteins we can furthermore show that the assessment is predictive of the success of high-throughput screening (HTS). The few divergences for targets of low ligandability originate from the sensitivity differences of the orthogonal biophysical methods. We thus applied a new strategy making use of modulations in the solvent structure to improve assay sensitivity. This novel approach enables improved ligandability assessments in accordance with NMR-based assessments and more importantly positions the methodology as a valuable option for biophysical fragment screening.
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Affiliation(s)
- Molly Chilton
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
| | - Ben Clennell
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
| | - Fredrik Edfeldt
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
| | - Stefan Geschwindner
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
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12
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Leite FHA, Froes TQ, da Silva SG, de Souza EIM, Vital-Fujii DG, Trossini GHG, Pita SSDR, Castilho MS. An integrated approach towards the discovery of novel non-nucleoside Leishmania major pteridine reductase 1 inhibitors. Eur J Med Chem 2017; 132:322-332. [DOI: 10.1016/j.ejmech.2017.03.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/18/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022]
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13
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Dahl G, Steigele S, Hillertz P, Tigerström A, Egnéus A, Mehrle A, Ginkel M, Edfeldt F, Holdgate G, O'Connell N, Kappler B, Brodte A, Rawlins PB, Davies G, Westberg EL, Folmer RHA, Heyse S. Unified Software Solution for Efficient SPR Data Analysis in Drug Research. SLAS DISCOVERY 2016; 22:203-209. [PMID: 27789754 PMCID: PMC5302086 DOI: 10.1177/1087057116675316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Surface plasmon resonance (SPR) is a powerful method for obtaining detailed molecular interaction parameters. Modern instrumentation with its increased throughput has enabled routine screening by SPR in hit-to-lead and lead optimization programs, and SPR has become a mainstream drug discovery technology. However, the processing and reporting of SPR data in drug discovery are typically performed manually, which is both time-consuming and tedious. Here, we present the workflow concept, design and experiences with a software module relying on a single, browser-based software platform for the processing, analysis, and reporting of SPR data. The efficiency of this concept lies in the immediate availability of end results: data are processed and analyzed upon loading the raw data file, allowing the user to immediately quality control the results. Once completed, the user can automatically report those results to data repositories for corporate access and quickly generate printed reports or documents. The software module has resulted in a very efficient and effective workflow through saved time and improved quality control. We discuss these benefits and show how this process defines a new benchmark in the drug discovery industry for the handling, interpretation, visualization, and sharing of SPR data.
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Affiliation(s)
- Göran Dahl
- 1 Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden
| | | | - Per Hillertz
- 3 R&D Information, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden
| | - Anna Tigerström
- 1 Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden
| | - Anders Egnéus
- 3 R&D Information, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden
| | | | | | - Fredrik Edfeldt
- 1 Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden
| | - Geoff Holdgate
- 4 Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, UK
| | - Nichole O'Connell
- 5 Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, Waltham, MA, USA
| | | | | | - Philip B Rawlins
- 4 Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, UK
| | - Gareth Davies
- 6 Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, Macclesfield, Cheshire, UK
| | - Eva-Lotta Westberg
- 3 R&D Information, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden
| | - Rutger H A Folmer
- 1 Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden
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14
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Rogez-Florent T, Goossens L, Drucbert AS, Duban-Deweer S, Six P, Depreux P, Danzé PM, Goossens JF, Foulon C. Amine coupling versus biotin capture for the assessment of sulfonamide as ligands of hCA isoforms. Anal Biochem 2016; 511:42-51. [DOI: 10.1016/j.ab.2016.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/08/2016] [Accepted: 07/29/2016] [Indexed: 12/11/2022]
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15
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Renaud JP, Chung CW, Danielson UH, Egner U, Hennig M, Hubbard RE, Nar H. Biophysics in drug discovery: impact, challenges and opportunities. Nat Rev Drug Discov 2016; 15:679-98. [PMID: 27516170 DOI: 10.1038/nrd.2016.123] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.
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Affiliation(s)
- Jean-Paul Renaud
- NovAliX, Boulevard Sébastien Brant, 67405 Illkirch Cedex, France.,Institut de Génétique et Biologie Moléculaire et Cellulaire, CNRS UMR7104/INSERM U964/Université de Strasbourg, 1 rue Laurent Fries - BP10142, 67404 Illkirch Cedex, France.,RiboStruct, 15 rue Neuve, 67540 Ostwald, France
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - U Helena Danielson
- Department of Chemistry - BMC and Science for Life Laboratory, Drug Discovery &Development Platform, Uppsala University, SE-751 05 Uppsala, Sweden.,Beactica AB, Uppsala Business Park, 754 50 Uppsala, Sweden
| | - Ursula Egner
- Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin, Germany
| | - Michael Hennig
- Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland.,leadXpro AG, PARK INNOVAARE, CH-5234 Villigen, Switzerland
| | - Roderick E Hubbard
- University of York, Heslington, York, YO10 5DD, UK.,Vernalis (R&D), Granta Park, Cambridge, CB21 6GB, UK
| | - Herbert Nar
- Boehringer Ingelheim GmbH &Co. KG, Birkendorfer Strasse 65, 88400 Biberach, Germany
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16
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Leite FHA, Santiago PBGDS, Froes TQ, da Silva Filho J, da Silva SG, Ximenes RM, de Faria AR, Brondani DJ, de Albuquerque JFC, Castilho MS. Structure-guided discovery of thiazolidine-2,4-dione derivatives as a novel class of Leishmania major pteridine reductase 1 inhibitors. Eur J Med Chem 2016; 123:639-648. [PMID: 27517809 DOI: 10.1016/j.ejmech.2016.07.060] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 07/20/2016] [Accepted: 07/24/2016] [Indexed: 10/21/2022]
Abstract
Leishmania major, as other protozoan parasites, plague human kind since pre-historic times but it remains a worldwide ailment for which the therapeutic arsenal remains scarce. Although L. major is pteridine- and purine-auxotroph, well-established folate biosynthesis inhibitors, such as methotrexate, have poor effect over the parasite survival. The lack of efficiency is related to an alternative biochemical pathway in which pteridine reductase 1 (PTR1) plays a major role. For this reason, this enzyme has been considered a promising target for anti-leishmanial drug development and several inhibitors that share the substrate scaffold have been reported. In order to design a novel class of PTR1 inhibitors, we employed the thiazolidinone ring as a bioisosteric replacement for pteridine/purine ring. Among seven novel thiazolidine-2,4-dione derivatives reported herein, 2d was identified as the most promising lead by thermal shift assays (ΔTm = 11 °C, p = 0,01). Kinetic assays reveal that 2d has IC50 = 44.67 ± 1.74 μM and shows a noncompetitive behavior. This information guided docking studies and molecular dynamics simulations (50 000 ps) that supports 2d putative binding profile (H-bonding to Ser-111 and Leu-66) and shall be useful to design more potent inhibitors.
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Affiliation(s)
- Franco Henrique A Leite
- Programa de Pós-graduação em Biotecnologia - PPGBiotec, Universidade Estadual de Feira de Santana, Brazil
| | | | | | | | | | - Rafael M Ximenes
- Departamento de Antibióticos, Universidade Federal de Pernambuco, Brazil
| | | | | | | | - Marcelo Santos Castilho
- Programa de Pós-graduação em Biotecnologia - PPGBiotec, Universidade Estadual de Feira de Santana, Brazil; Faculdade de Farmácia, Universidade Federal da Bahia, Brazil.
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17
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Integrating biophysics with HTS-driven drug discovery projects. Drug Discov Today 2016; 21:491-8. [PMID: 26826422 DOI: 10.1016/j.drudis.2016.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/04/2016] [Accepted: 01/20/2016] [Indexed: 12/13/2022]
Abstract
Over the past decade biophysics has become an established discipline in HTS hit triaging, owing to its high fidelity in detecting protein-ligand interactions. Many pharma companies are using biophysical techniques to filter HTS output for false positives, as will be discussed in this review. Moreover, I will demonstrate how the earlier application of biophysics, already at the HTS assay development stage, is potentially even more impactful. Two key areas here are early mode-of-action studies and ensuring that the HTS assay and subsequent cascade are fit for purpose. Top-level results from 20 in-house projects are shown to underpin the impact of these studies.
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18
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Fuchigami T, Yamashita Y, Kawasaki M, Ogawa A, Haratake M, Atarashi R, Sano K, Nakagaki T, Ubagai K, Ono M, Yoshida S, Nishida N, Nakayama M. Characterisation of radioiodinated flavonoid derivatives for SPECT imaging of cerebral prion deposits. Sci Rep 2015; 5:18440. [PMID: 26669576 PMCID: PMC4680881 DOI: 10.1038/srep18440] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/18/2015] [Indexed: 12/22/2022] Open
Abstract
Prion diseases are fatal neurodegenerative diseases characterised by deposition of amyloid plaques containing abnormal prion protein aggregates (PrP(Sc)). This study aimed to evaluate the potential of radioiodinated flavonoid derivatives for single photon emission computed tomography (SPECT) imaging of PrP(Sc). In vitro binding assays using recombinant mouse PrP (rMoPrP) aggregates revealed that the 4-dimethylamino-substituted styrylchromone derivative (SC-NMe2) had higher in vitro binding affinity (Kd = 24.5 nM) and capacity (Bmax = 36.3 pmol/nmol protein) than three other flavonoid derivatives (flavone, chalcone, and aurone). Fluorescent imaging using brain sections from mouse-adapted bovine spongiform encephalopathy (mBSE)-infected mice demonstrated that SC-NMe2 clearly labelled PrP(Sc)-positive prion deposits in the mice brain. Two methoxy SC derivatives, SC-OMe and SC-(OMe)2, also showed high binding affinity for rMoPrP aggregates with Ki values of 20.8 and 26.6 nM, respectively. In vitro fluorescence and autoradiography experiments demonstrated high accumulation of [(125)I]SC-OMe and [(125)I]SC-(OMe)2 in prion deposit-rich regions of the mBSE-infected mouse brain. SPECT/computed tomography (CT) imaging and ex vivo autoradiography demonstrated that [(123)I]SC-OMe showed consistent brain distribution with the presence of PrP(Sc) deposits in the mBSE-infected mice brain. In conclusion, [(123)I]SC-OMe appears a promising SPECT radioligand for monitoring prion deposit levels in the living brain.
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Affiliation(s)
- Takeshi Fuchigami
- Department of Hygienic Chemistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yuki Yamashita
- Department of Hygienic Chemistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Masao Kawasaki
- Department of Hygienic Chemistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Ayaka Ogawa
- Department of Hygienic Chemistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Mamoru Haratake
- Department of Hygienic Chemistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.,Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | - Ryuichiro Atarashi
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Kazunori Sano
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Takehiro Nakagaki
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Kaori Ubagai
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Masahiro Ono
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sakura Yoshida
- Department of Hygienic Chemistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Morio Nakayama
- Department of Hygienic Chemistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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19
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Buckton LK, Wahyudi H, McAlpine SR. The first report of direct inhibitors that target the C-terminal MEEVD region on heat shock protein 90. Chem Commun (Camb) 2015; 52:501-4. [PMID: 26528929 DOI: 10.1039/c5cc03245h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Sixteen linear and cyclic peptides were designed de novo to target the C-terminus of heat shock protein 90 (Hsp90). Protein binding data indicates that three compounds directly block co-chaperone access to Hsp90's C-terminus and luciferase renaturation assays confirm Hsp90-mediated protein folding is disrupted. This is the first report of an inhibitor that binds directly to the C-terminal MEEVD region of Hsp90.
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Affiliation(s)
- L K Buckton
- School of Chemistry, Gate 2 High Street, Dalton 219, University of New South Wales, Sydney, Australia.
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20
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Cesa LC, Mapp AK, Gestwicki JE. Direct and Propagated Effects of Small Molecules on Protein-Protein Interaction Networks. Front Bioeng Biotechnol 2015; 3:119. [PMID: 26380257 PMCID: PMC4547496 DOI: 10.3389/fbioe.2015.00119] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/05/2015] [Indexed: 12/15/2022] Open
Abstract
Networks of protein–protein interactions (PPIs) link all aspects of cellular biology. Dysfunction in the assembly or dynamics of PPI networks is a hallmark of human disease, and as such, there is growing interest in the discovery of small molecules that either promote or inhibit PPIs. PPIs were once considered undruggable because of their relatively large buried surface areas and difficult topologies. Despite these challenges, recent advances in chemical screening methodologies, combined with improvements in structural and computational biology have made some of these targets more tractable. In this review, we highlight developments that have opened the door to potent chemical modulators. We focus on how allostery is being used to produce surprisingly robust changes in PPIs, even for the most challenging targets. We also discuss how interfering with one PPI can propagate changes through the broader web of interactions. Through this analysis, it is becoming clear that a combination of direct and propagated effects on PPI networks is ultimately how small molecules re-shape biology.
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Affiliation(s)
- Laura C Cesa
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA
| | - Anna K Mapp
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA ; Department of Chemistry, University of Michigan , Ann Arbor, MI , USA
| | - Jason E Gestwicki
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA ; Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Diseases, University of California San Francisco , San Francisco, CA , USA
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21
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Edfeldt F, Evenäs J, Lepistö M, Ward A, Petersen J, Wissler L, Rohman M, Sivars U, Svensson K, Perry M, Feierberg I, Zhou XH, Hansson T, Narjes F. Identification of indole inhibitors of human hematopoietic prostaglandin D2 synthase (hH-PGDS). Bioorg Med Chem Lett 2015; 25:2496-500. [DOI: 10.1016/j.bmcl.2015.04.065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/19/2015] [Accepted: 04/20/2015] [Indexed: 11/25/2022]
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22
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Determining binding sites of polycyclic aromatic small molecule-based amyloid-beta peptide aggregation modulators using sequence-specific antibodies. Anal Biochem 2015; 470:61-70. [DOI: 10.1016/j.ab.2014.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/21/2014] [Accepted: 10/27/2014] [Indexed: 12/22/2022]
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23
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Development and validation of an LC-ESI-MS/MS method for the triple reuptake inhibitor indatraline enabling its quantification in MS Binding Assays. Anal Bioanal Chem 2014; 407:471-85. [DOI: 10.1007/s00216-014-8312-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
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24
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Si Mehand M, De Crescenzo G, Srinivasan B. On-line kinetic model discrimination for optimized surface plasmon resonance experiments. J Mol Recognit 2014; 27:276-84. [PMID: 24700594 DOI: 10.1002/jmr.2358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 12/19/2013] [Indexed: 01/15/2023]
Abstract
In order to improve the throughput of surface plasmon resonance-based biosensors, an on-line iterative optimization algorithm has been presented aiming at reducing experimental time and material consumption without any loss of confidence on kinetic parameters [De Crescenzo (2008) J. Mol Recognit., 21, 256-66.]. This algorithm was based on a simple Langmuirian model to compute the confidence and predict optimal injections. However, this kinetic model is not suitable for all interactions, as it does not include mass transfer limitation that may occur for fast interaction kinetics. If a simple model was to be used when this phenomenon influenced the interactions, kinetic parameters would be biased. On the other hand, we show in this paper that data analysis with a kinetic model including a mass transfer limitation step would lead to longer experiments and poorer confidence if the interactions were simple. So, in this manuscript, we present an on-line model discrimination and optimization approach to increase the throughput of surface plasmon resonance biosensors.
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Affiliation(s)
- Massinissa Si Mehand
- Department of Chemical Engineering, École Polytechnique de Montréal, PO Box 6079, Centre-ville Station, H3C 3A7, Montréal, Québec, Canada
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25
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Richter I, Fidler AE. Marine invertebrate xenobiotic-activated nuclear receptors: their application as sensor elements in high-throughput bioassays for marine bioactive compounds. Mar Drugs 2014; 12:5590-618. [PMID: 25421319 PMCID: PMC4245547 DOI: 10.3390/md12115590] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 10/31/2014] [Accepted: 11/11/2014] [Indexed: 02/07/2023] Open
Abstract
Developing high-throughput assays to screen marine extracts for bioactive compounds presents both conceptual and technical challenges. One major challenge is to develop assays that have well-grounded ecological and evolutionary rationales. In this review we propose that a specific group of ligand-activated transcription factors are particularly well-suited to act as sensors in such bioassays. More specifically, xenobiotic-activated nuclear receptors (XANRs) regulate transcription of genes involved in xenobiotic detoxification. XANR ligand-binding domains (LBDs) may adaptively evolve to bind those bioactive, and potentially toxic, compounds to which organisms are normally exposed to through their specific diets. A brief overview of the function and taxonomic distribution of both vertebrate and invertebrate XANRs is first provided. Proof-of-concept experiments are then described which confirm that a filter-feeding marine invertebrate XANR LBD is activated by marine bioactive compounds. We speculate that increasing access to marine invertebrate genome sequence data, in combination with the expression of functional recombinant marine invertebrate XANR LBDs, will facilitate the generation of high-throughput bioassays/biosensors of widely differing specificities, but all based on activation of XANR LBDs. Such assays may find application in screening marine extracts for bioactive compounds that could act as drug lead compounds.
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Affiliation(s)
- Ingrid Richter
- Environmental Technology Group, Cawthron Institute, Private Bag 2, Nelson 7012, New Zealand.
| | - Andrew E Fidler
- Environmental Technology Group, Cawthron Institute, Private Bag 2, Nelson 7012, New Zealand.
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26
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Rogez-Florent T, Duhamel L, Goossens L, Six P, Drucbert AS, Depreux P, Danzé PM, Landy D, Goossens JF, Foulon C. Label-free characterization of carbonic anhydrase-novel inhibitor interactions using surface plasmon resonance, isothermal titration calorimetry and fluorescence-based thermal shift assays. J Mol Recognit 2014; 27:46-56. [PMID: 24375583 DOI: 10.1002/jmr.2330] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 09/19/2013] [Accepted: 09/28/2013] [Indexed: 11/06/2022]
Abstract
This work describes the development of biophysical unbiased methods to study the interactions between new designed compounds and carbonic anhydrase II (CAII) enzyme. These methods have to permit both a screening of a series of sulfonamide derivatives and the identification of a lead compound after a thorough study of the most promising molecules. Interactions data were collected using surface plasmon resonance (SPR) and thermal shift assay (TSA). In the first step, experiments were performed with bovine CAII isoform and were extended to human CAII. Isothermal titration calorimetry (ITC) experiments were also conducted to obtain thermodynamics parameters necessary for the processing of the TSA data. Results obtained with this reference methodology demonstrate the effectiveness of SPR and TSA. KD values obtained from SPR data were in perfect accordance with ITC. For TSA, despite the fact that the absolute values of KD were quite different, the same affinity scale was obtained for all compounds. The binding affinities of the analytes studied vary by more than 50 orders of magnitude; for example, the KD value determined by SPR were 6 ± 4 and 299 ± 25 nM for compounds 1 and 3, respectively. This paper discusses some of the theoretical and experimental aspects of the affinity-based methods and evaluates the protein consumption to develop methods for the screening of further new compounds. The double interest of SPR, that is, for screening and for the quick thorough study of the interactions parameters (ka , kd , and KD ), leads us to choose this methodology for the study of new potential inhibitors.
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Affiliation(s)
- Tiphaine Rogez-Florent
- Université Lille Nord de France, F-59000, Lille, France; UDSL, EA-4481, UFR Pharmacie, Université Lille Nord de France, F-59000, Lille, France
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27
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Orwig SD, Chi PV, Du Y, Hill SE, Cavitt MA, Suntharalingam A, Turnage KC, Dickey CA, France S, Fu H, Lieberman RL. Ligands for glaucoma-associated myocilin discovered by a generic binding assay. ACS Chem Biol 2014; 9:517-25. [PMID: 24279319 DOI: 10.1021/cb4007776] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mutations in the olfactomedin domain of myocilin (myoc-OLF) are the strongest link to inherited primary open angle glaucoma. In this recently identified protein misfolding disorder, aggregation-prone disease variants of myocilin hasten glaucoma-associated elevation of intraocular pressure, leading to vision loss. Despite its well-documented pathogenic role, myocilin remains a domain of unknown structure or function. Here we report the first small-molecule ligands that bind to the native state of myoc-OLF. To discover these molecules, we designed a general label-free, mix-and-measure, high throughput chemical assay for restabilization (CARS), which is likely readily adaptable to discover ligands for other proteins. Of the 14 hit molecules identified from screening myoc-OLF against the Sigma-Aldrich Library of Pharmacologically Active Compounds using CARS, surface plasmon resonance binding studies reveal three are stoichiometric ligand scaffolds with low micromolar affinity. Two compounds, GW5074 and apigenin, inhibit myoc-OLF amyloid formation in vitro. Structure-activity relationship-based soluble derivatives reduce aggregation in vitro as well as enhance secretion of full-length mutant myocilin in a cell culture model. Our compounds set the stage for a new chemical probe approach to clarify the biological function of wild-type myocilin and represent lead therapeutic compounds for diminishing intracellular sequestration of toxic mutant myocilin.
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Affiliation(s)
- Susan D. Orwig
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Pamela V. Chi
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Yuhong Du
- Department
of Pharmacology, Emory University School of Medicine, 1510 Clifton
Road, Atlanta, Georgia 30322, United States
| | - Shannon E. Hill
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Marchello A. Cavitt
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Amrithaa Suntharalingam
- Department
of Molecular Medicine and Byrd Alzheimer’s Research Institute, University of South Florida, 4001 E. Fletcher Ave. Tampa, Florida 33613, United States
| | - Katherine C. Turnage
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Chad A. Dickey
- Department
of Molecular Medicine and Byrd Alzheimer’s Research Institute, University of South Florida, 4001 E. Fletcher Ave. Tampa, Florida 33613, United States
| | - Stefan France
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Haian Fu
- Department
of Pharmacology, Emory University School of Medicine, 1510 Clifton
Road, Atlanta, Georgia 30322, United States
| | - Raquel L. Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
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28
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Label-enhanced surface plasmon resonance: a new concept for improved performance in optical biosensor analysis. SENSORS 2013; 13:15348-63. [PMID: 24217357 PMCID: PMC3871110 DOI: 10.3390/s131115348] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 10/29/2013] [Accepted: 11/02/2013] [Indexed: 11/20/2022]
Abstract
Surface plasmon resonance (SPR) is a well-established optical biosensor technology with many proven applications in the study of molecular interactions as well as in surface and material science. SPR is usually applied in the label-free mode which may be advantageous in cases where the presence of a label may potentially interfere with the studied interactions per se. However, the fundamental challenges of label-free SPR in terms of limited sensitivity and specificity are well known. Here we present a new concept called label-enhanced SPR, which is based on utilizing strongly absorbing dye molecules in combination with the evaluation of the full shape of the SPR curve, whereby the sensitivity as well as the specificity of SPR is significantly improved. The performance of the new label-enhanced SPR method was demonstrated by two simple model assays: a small molecule assay and a DNA hybridization assay. The small molecule assay was used to demonstrate the sensitivity enhancement of the method, and how competitive assays can be used for relative affinity determination. The DNA assay was used to demonstrate the selectivity of the assay, and the capabilities in eliminating noise from bulk liquid composition variations.
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29
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Choulier L, Nominé Y, Zeder-Lutz G, Charbonnier S, Didier B, Jung ML, Altschuh D. Chemical Library Screening Using a SPR-Based Inhibition in Solution Assay: Simulations and Experimental Validation. Anal Chem 2013; 85:8787-95. [DOI: 10.1021/ac4019445] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Laurence Choulier
- Biotechnologie et Signalisation
Cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412 Illkirch,
France
| | - Yves Nominé
- Biotechnologie et Signalisation
Cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412 Illkirch,
France
| | - Gabrielle Zeder-Lutz
- Biotechnologie et Signalisation
Cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412 Illkirch,
France
| | - Sebastian Charbonnier
- Biotechnologie et Signalisation
Cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412 Illkirch,
France
| | - Bruno Didier
- Prestwick Chemical, Bd Gonthier d’Andernach, Parc d’Innovation,
67400
Illkirch, France
| | - Marie-Louise Jung
- Prestwick Chemical, Bd Gonthier d’Andernach, Parc d’Innovation,
67400
Illkirch, France
| | - Danièle Altschuh
- Biotechnologie et Signalisation
Cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412 Illkirch,
France
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30
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Makley LN, Gestwicki JE. Expanding the number of 'druggable' targets: non-enzymes and protein-protein interactions. Chem Biol Drug Des 2013; 81:22-32. [PMID: 23253128 DOI: 10.1111/cbdd.12066] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Following sequencing and assembly of the human genome, the preferred methods for identification of new drug targets have changed dramatically. Modern tactics such as genome-wide association studies (GWAS) and deep sequencing are fundamentally different from the pharmacology-guided approaches used previously, in which knowledge of small molecule ligands acting at their cellular targets was the primary discovery engine. A consequence of the 'target-first, pharmacology-second' strategy is that many predicted drug targets are non-enzymes, such as scaffolding, regulatory or structural proteins, and their activities are often dependent on protein-protein interactions (PPIs). These types of targets create unique challenges to drug discovery efforts because enzymatic turnover cannot be used as a convenient surrogate for compound potency. Moreover, it is often challenging to predict how ligand binding to non-enzymes might affect changes in protein function and/or pathobiology. Thus, in the postgenomic era, targets might be strongly implicated by molecular biology-based methods, yet they often later earn the designation of 'undruggable'. Can the scope of available targets be widened to include these promising, but challenging, non-enzymes? In this review, we discuss advances in high-throughput screening (HTS) technology and chemical library design that are emerging to deal with these challenges.
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Affiliation(s)
- Leah N Makley
- Departments of Pathology, Biological Chemistry and the Interdisciplinary Program in Medicinal Chemistry, The Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
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New direction for glaucoma therapeutics: focus on the olfactomedin domain of myocilin. Future Med Chem 2013. [PMID: 23190098 DOI: 10.4155/fmc.12.132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Geschwindner S, Dekker N, Horsefield R, Tigerström A, Johansson P, Scott CW, Albert JS. Development of a Plate-Based Optical Biosensor Fragment Screening Methodology to Identify Phosphodiesterase 10A Inhibitors. J Med Chem 2013; 56:3228-34. [DOI: 10.1021/jm301665y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Niek Dekker
- Discovery Sciences, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Rob Horsefield
- Discovery Sciences, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Anna Tigerström
- Discovery Sciences, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Patrik Johansson
- Discovery Sciences, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Clay W. Scott
- CNS Discovery Research, AstraZeneca
Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, Delaware
19850, United States
| | - Jeffrey S. Albert
- CNS Discovery Research, AstraZeneca
Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, Delaware
19850, United States
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Holdgate G, Geschwindner S, Breeze A, Davies G, Colclough N, Temesi D, Ward L. Biophysical methods in drug discovery from small molecule to pharmaceutical. Methods Mol Biol 2013; 1008:327-355. [PMID: 23729258 DOI: 10.1007/978-1-62703-398-5_12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Biophysical methods have become established in many areas of drug discovery. Application of these methods was once restricted to a relatively small number of scientists using specialized, low throughput technologies and methods. Now, automated high-throughput instruments are to be found in a growing number of laboratories. Many biophysical methods are capable of measuring the equilibrium binding constants between pairs of molecules crucial for molecular recognition processes, encompassing protein-protein, protein-small molecule, and protein-nucleic acid interactions, and several can be used to measure the kinetic or thermodynamic components controlling these biological processes. For a full characterization of a binding process, determinations of stoichiometry, binding mode, and any conformational changes associated with such interactions are also required. The suite of biophysical methods that are now available represents a powerful toolbox of techniques which can effectively deliver this full characterization.The aim of this chapter is to provide the reader with an overview of the drug discovery process and how biophysical methods, such as surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), nuclear magnetic resonance, mass spectrometry (MS), and thermal unfolding methods can answer specific questions in order to influence project progression and outcomes. The selection of these examples is based upon the experiences of the authors at AstraZeneca, and relevant approaches are highlighted where they have utility in a particular drug discovery scenario.
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Fang Y, Xu W, Meng XL, Ye XY, Wu J, Xu ZK. Poly(2-hydroxyethyl methacrylate) brush surface for specific and oriented adsorption of glycosidases. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:13318-13324. [PMID: 22921196 DOI: 10.1021/la302738s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We present a detailed picture to screen general ligands from simple chemicals for fabricating affinity surface to glycosidase enzymes. The surface was constructed by grafting poly(2-hydroxyethyl methacrylate) (PHEMA) brush on SPR gold chip via surface-initiated atom-transfer radical polymerization, after which poly(methoxyethyl methacrylate) (PMEMA) and poly(oligo(ethylene glycol) methacrylate) (POEGMA) brushes were also prepared for comparison. SPR measurements were adopted to monitor the early-stage adsorption of two glycosidases and three other typical proteins. PHEMA resists the adsorption of lysozyme, bovine serum albumin, and fibrinogen, while it is capable of specifically adsorbing β-glucosidase (GLU) and β-galactosidase (GAL). These are quite different from the nonspecific adsorption of PMEMA and the anti-nonspecific adsorption of POEGMA to the studied proteins, because PHEMA is the acceptor substrate of the glycosidases. About 69.6 and 93.7 ng/cm(2) of GAL and GLU are adsorbed on the PHEMA brush surface, of which more than 49.6 ng/cm(2) is remained after washing with PBS. The specific adsorption process is appropriately described by Freundlich isothermal model rather than Langmuir one, and is also indicated to be spontaneous, endothermic, and entropy driven through thermodynamic studies. Taking into account all stated results above, we propose that molecular recognition takes place between the hydroxyl groups of PHEMA and the active sites of glycosidases, which subsequently enables the oriented adsorption of glycosidases on the brush surface. The adsorbed enzyme can be effectively eluted with 1.0 M aqueous solution of ethanol. Our findings open the door to the further development in the design of novel acceptor substrate-ligand affinity chromatography for enzyme purification.
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Affiliation(s)
- Yan Fang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
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Moumné R, Catala M, Larue V, Micouin L, Tisné C. Fragment-based design of small RNA binders: Promising developments and contribution of NMR. Biochimie 2012; 94:1607-19. [DOI: 10.1016/j.biochi.2012.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/01/2012] [Indexed: 02/06/2023]
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Haruki H, Gonzalez MR, Johnsson K. Exploiting ligand-protein conjugates to monitor ligand-receptor interactions. PLoS One 2012; 7:e37598. [PMID: 22701522 PMCID: PMC3365113 DOI: 10.1371/journal.pone.0037598] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 04/23/2012] [Indexed: 01/12/2023] Open
Abstract
We introduce three assays for analyzing ligand-receptor interactions based on the specific conjugation of ligands to SNAP-tag fusion proteins. Conjugation of ligands to different SNAP-tag fusions permits the validation of suspected interactions in cell extracts and fixed cells as well as the establishment of high-throughput assays. The different assays allow the analysis of strong and weak interactions. Conversion of ligands into SNAP-tag substrates thus provides access to a powerful toolbox for the analysis of their interactions with proteins.
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Affiliation(s)
- Hirohito Haruki
- École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research (NCCR) in Chemical Biology, Lausanne, Switzerland
| | - Monica Rengifo Gonzalez
- École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research (NCCR) in Chemical Biology, Lausanne, Switzerland
| | - Kai Johnsson
- École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research (NCCR) in Chemical Biology, Lausanne, Switzerland
- * E-mail:
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Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. J Mol Recognit 2012; 25:32-52. [PMID: 22213449 DOI: 10.1002/jmr.1167] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.
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Affiliation(s)
- Rajesh Ghai
- Institute for Molecular Bioscience (IMB), University of Queensland, St. Lucia, Queensland, 4072, Australia
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Geschwindner S, Carlsson JF, Knecht W. Application of optical biosensors in small-molecule screening activities. SENSORS 2012; 12:4311-23. [PMID: 22666031 PMCID: PMC3355412 DOI: 10.3390/s120404311] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 03/20/2012] [Accepted: 03/23/2012] [Indexed: 11/16/2022]
Abstract
The last two decades have seen remarkable progress and improvements in optical biosensor systems such that those are currently seen as an important and value-adding component of modern drug screening activities. In particular the introduction of microplate-based biosensor systems holds the promise to match the required throughput without compromising on data quality thus representing a sought-after complement to traditional fluidic systems. This article aims to highlight the application of the two most prominent optical biosensor technologies, namely surface plasmon resonance (SPR) and optical waveguide grating (OWG), in small-molecule screening and will present, review and discuss the advantages and disadvantages of different assay formats on these platforms. A particular focus will be on the specific advantages of the inhibition in solution assay (ISA) format in contrast to traditional direct binding assays (DBA). Furthermore we will discuss different application areas for both fluidic as well as plate-based biosensor systems by considering the individual strength of the platforms.
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Affiliation(s)
- Stefan Geschwindner
- Discovery Sciences, AstraZeneca R&D Mölndal, 43183 Mölndal, Sweden; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (S.G.); (W.K.); Tel.: +46-31-776-2197 (S.G.); Tel.: +46-31-706-5341 (W.K.)
| | - Johan F. Carlsson
- Discovery Sciences, AstraZeneca R&D Mölndal, 43183 Mölndal, Sweden; E-Mail:
| | - Wolfgang Knecht
- CVGI iMed, Bioscience, AstraZeneca R&D Mölndal, 43183 Mölndal, Sweden
- Authors to whom correspondence should be addressed; E-Mails: (S.G.); (W.K.); Tel.: +46-31-776-2197 (S.G.); Tel.: +46-31-706-5341 (W.K.)
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Coan KED, Swann MJ, Ottl J. Measurement and Differentiation of Ligand-Induced Calmodulin Conformations by Dual Polarization Interferometry. Anal Chem 2012; 84:1586-91. [DOI: 10.1021/ac202844e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristin E. D. Coan
- Novartis Institutes for BioMedical
Research Basel, CPC/LFP/Label-free Technologies, Novartis Pharma AG, Basel, Switzerland
| | - Marcus J. Swann
- Farfield Group Ltd., West Wing 7, Voyager, Chicago Avenue, Manchester
Airport, Manchester, M90 3DQ, United Kingdom
| | - Johannes Ottl
- Novartis Institutes for BioMedical
Research Basel, CPC/LFP/Label-free Technologies, Novartis Pharma AG, Basel, Switzerland
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Cuyvers S, Dornez E, Abou Hachem M, Svensson B, Hothorn M, Chory J, Delcour JA, Courtin CM. Isothermal titration calorimetry and surface plasmon resonance allow quantifying substrate binding to different binding sites of Bacillus subtilis xylanase. Anal Biochem 2011; 420:90-2. [PMID: 21964501 PMCID: PMC4854199 DOI: 10.1016/j.ab.2011.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/22/2011] [Accepted: 09/05/2011] [Indexed: 10/17/2022]
Abstract
Isothermal titration calorimetry and surface plasmon resonance were tested for their ability to study substrate binding to the active site (AS) and to the secondary binding site (SBS) of Bacillus subtilis xylanase A separately. To this end, three enzyme variants were compared. The first was a catalytically incompetent enzyme that allows substrate binding to both the AS and SBS. In the second enzyme, binding to the SBS was impaired by site-directed mutagenesis, whereas in the third enzyme, the AS was blocked using a covalent inhibitor. Both techniques were able to show that AS and SBS have a similar binding affinity.
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Affiliation(s)
- Sven Cuyvers
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre, Katholieke Universiteit Leuven, Leuven 3001, Belgium.
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Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol 2011; 21:150-60. [PMID: 21349700 DOI: 10.1016/j.sbi.2011.01.011] [Citation(s) in RCA: 389] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 01/25/2011] [Accepted: 01/27/2011] [Indexed: 11/23/2022]
Abstract
Improved rational drug design methods are needed to lower the cost and increase the success rate of drug discovery and development. Alchemical binding free energy calculations, one potential tool for rational design, have progressed rapidly over the past decade, but still fall short of providing robust tools for pharmaceutical engineering. Recent studies, especially on model receptor systems, have clarified many of the challenges that must be overcome for robust predictions of binding affinity to be useful in rational design. In this review, inspired by a recent joint academic/industry meeting organized by the authors, we discuss these challenges and suggest a number of promising approaches for overcoming them.
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Combining biophysical screening and X-ray crystallography for fragment-based drug discovery. Top Curr Chem (Cham) 2011; 317:115-43. [PMID: 21837555 DOI: 10.1007/128_2011_225] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Over the past decade, fragment-based drug discovery (FBDD) has gained importance for the generation of novel ideas to inspire synthetic chemistry. In order to identify small molecules that bind to a target protein, multiple approaches have been utilized by various groups in the pharmaceutical industry and by academic groups. The combination of fragment screening by biophysical methods and in particular with surface plasmon resonance technologies (SPR) together with the visualization of the binding properties by X-ray crystallography offers a number of benefits. Screening by SPR identifies ligands for a target protein as well as provides an assessment of the binding properties with respect to affinity, stoichiometry, and specificity of the interaction. Despite the huge technology advances of the past years, X-ray crystallography is still a resource-intensive technology, and SPR binding data provides excellent measures to prioritize X-ray experiments and consequently enable a better success rate in obtaining structural information. Information on the chemical structures of fragments binding to a protein can be used to perform similarity searches in compound libraries in order to establish structure-activity relationships as well as to explore particular scaffolds. At Roche we have applied this workflow for a number of targets and the experiences will be outlined in this review.
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