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FitzGerald EA, Vagrys D, Opassi G, Klein HF, Hamilton DJ, Talibov VO, Abramsson M, Moberg A, Lindgren MT, Holmgren C, Davis B, O'Brien P, Wijtmans M, Hubbard RE, de Esch IJP, Danielson UH. Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:40-51. [PMID: 37714432 DOI: 10.1016/j.slasd.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery. However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads.
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Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Beactica Therapeutics AB, Virdings allé 2, Uppsala, Sweden
| | - Darius Vagrys
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Giulia Opassi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Hanna F Klein
- Department of Chemistry, University of York, York, United Kingdom
| | - David J Hamilton
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | | | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Ben Davis
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom
| | - Peter O'Brien
- Department of Chemistry, University of York, York, United Kingdom
| | - Maikel Wijtmans
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roderick E Hubbard
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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2
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Design, Synthesis, and Biological Evaluation of Benzimidazole Derivatives as Potential Lassa Virus Inhibitors. Molecules 2023; 28:molecules28041579. [PMID: 36838567 PMCID: PMC9963587 DOI: 10.3390/molecules28041579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
The Lassa virus (LASV) causes Lassa fever, a highly infectious and lethal agent of acute viral hemorrhagic fever. At present, there are still no effective treatments available, creating an urgent need to develop novel therapeutics. Some benzimidazole compounds targeting the arenavirus envelope glycoprotein complex (GPC) are promising inhibitors of LASV. In this study, we synthesized two series of LASV inhibitors based on the benzimidazole structure. Lentiviral pseudotypes bearing the LASV GPC were established to identify virus entry inhibitors. Surface plasmon resonance (SPR) was further used to verify the binding activities of the potential compounds. Compounds 7d-Z, 7h-Z, 13c, 13d, and 13f showed relatively excellent antiviral activities with IC50 values ranging from 7.58 to 15.46 nM and their SI values above 1251. These five representative compounds exhibited stronger binding affinity with low equilibrium dissociation constants (KD < 8.25 × 10-7 M) in SPR study. The compound 7h-Z displayed the most potent antiviral activity (IC50 = 7.58 nM) with a relatively high SI value (2496), which could be further studied as a lead compound. The structure-activity relationship indicated that the compounds with lipophilic and spatially larger substituents might possess higher antiviral activity and a much larger safety margin. This study will provide some good guidance for the development of highly active compounds with a novel skeleton against LASV.
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Cho Y, Pham Ba VA, Jeong JY, Choi Y, Hong S. Ion-Selective Carbon Nanotube Field-Effect Transistors for Monitoring Drug Effects on Nicotinic Acetylcholine Receptor Activation in Live Cells. SENSORS 2020; 20:s20133680. [PMID: 32630098 PMCID: PMC7374424 DOI: 10.3390/s20133680] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 12/23/2022]
Abstract
We developed ion-selective field-effect transistor (FET) sensors with floating electrodes for the monitoring of the potassium ion release by the stimulation of nicotinic acetylcholine receptors (nAChRs) on PC12 cells. Here, ion-selective valinomycin-polyvinyl chloride (PVC) membranes were coated on the floating electrode-based carbon nanotube (CNT) FETs to build the sensors. The sensors could selectively measure potassium ions with a minimum detection limit of 1 nM. We utilized the sensor for the real-time monitoring of the potassium ion released from a live cell stimulated by nicotine. Notably, this method also allowed us to quantitatively monitor the cell responses by agonists and antagonists of nAChRs. These results suggest that our ion-selective CNT-FET sensor has potential uses in biological and medical researches such as the monitoring of ion-channel activity and the screening of drugs.
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Affiliation(s)
- Youngtak Cho
- Department of Physics and Astronomy and Institute of Applied Physics, Seoul National University, Seoul 08826, Korea; (Y.C.); (V.A.P.B.); (J.-Y.J.); (Y.C.)
| | - Viet Anh Pham Ba
- Department of Physics and Astronomy and Institute of Applied Physics, Seoul National University, Seoul 08826, Korea; (Y.C.); (V.A.P.B.); (J.-Y.J.); (Y.C.)
- Department of Environmental Toxicology and Monitoring, Hanoi University of Natural Resources and Environment, Hanoi 11916, Vietnam
| | - Jin-Young Jeong
- Department of Physics and Astronomy and Institute of Applied Physics, Seoul National University, Seoul 08826, Korea; (Y.C.); (V.A.P.B.); (J.-Y.J.); (Y.C.)
| | - Yoonji Choi
- Department of Physics and Astronomy and Institute of Applied Physics, Seoul National University, Seoul 08826, Korea; (Y.C.); (V.A.P.B.); (J.-Y.J.); (Y.C.)
| | - Seunghun Hong
- Department of Physics and Astronomy and Institute of Applied Physics, Seoul National University, Seoul 08826, Korea; (Y.C.); (V.A.P.B.); (J.-Y.J.); (Y.C.)
- Correspondence: ; Tel.: +82-2-880-1343
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4
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Affiliation(s)
- Matthew D. Lloyd
- Drug & Target Development, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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5
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Guo H, Cheng K, Gao Y, Bai W, Wu C, He W, Li C, Li Z. A novel potent metal-binding NDM-1 inhibitor was identified by fragment virtual, SPR and NMR screening. Bioorg Med Chem 2020; 28:115437. [DOI: 10.1016/j.bmc.2020.115437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 01/25/2023]
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6
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Pourbasheer E, Azari Z, Ganjali MR. Recent Advances in Biosensors Based Nanostructure for Pharmaceutical Analysis. CURR ANAL CHEM 2019. [DOI: 10.2174/1573411014666180319152853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The development of novel nanostructures for pharmaceutical analysis has received
great attention. Biosensors are a class of analytical techniques competent in the rapid quantification
of drugs. Recently, the nanostructures have been applied for modification of biosensors.
Objective:
The goal of the present study is to review novel nanostructures for pharmaceutical analysis
by biosensors.
Method:
In this review, the application of different biosensors was extensively discussed.
Results:
Biosensors based nanostructures are a powerful alternative to conventional analytical techniques,
enabling highly sensitive, real-time, and high-frequency monitoring of drugs without extensive
sample preparation. Several examples of their application have been reported.
Conclusion:
The present paper reviews the recent advances on the pharmaceutical analysis of biosensor
based nanostructures.
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Affiliation(s)
- Eslam Pourbasheer
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran
| | - Zhila Azari
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
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Bergsdorf C, Wright SK. A Guide to Run Affinity Screens Using Differential Scanning Fluorimetry and Surface Plasmon Resonance Assays. Methods Enzymol 2018; 610:135-165. [PMID: 30390797 DOI: 10.1016/bs.mie.2018.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past 30 years, drug discovery has evolved from a pure phenotypic approach to an integrated target-based strategy. The implementation of high-throughput biochemical and cellular assays has enabled the screening of large compound libraries which has become an important and often times the main source of new chemical matter that serve as starting point for medicinal chemistry efforts. In addition, biophysical methods measuring the physical interaction (affinity) between a low molecular weight ligand and a target protein became an integral part of hit validation/optimization to rule out false positives due to assay artifacts. Recent advances in throughput, robustness, and sensitivity of biophysical affinity screening methods have broadened their application in hit identification and validation such that they can now complement classical functional readouts. As a result, new target classes can be accessed that have not been amenable to functional assays. In this chapter, two affinity screening methods, differential scanning fluorimetry and surface plasmon resonance, which are broadly utilized in both academia and pharmaceutical industry are discussed in respect to their use in hit identification and validation. These methods exemplify how assays which differ in complexity, throughput, and information content can support the hit identification/validation process. This chapter focuses on the practical aspects and caveats of these techniques in order to enable the reader to establish their own affinity-based screens in both formats.
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Affiliation(s)
| | - S Kirk Wright
- Novartis Institutes for BioMedical Research, Cambridge, MA, United States
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8
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Ferraro G, De Benedictis I, Malfitano A, Morelli G, Novellino E, Marasco D. Interactions of cisplatin analogues with lysozyme: a comparative analysis. Biometals 2017; 30:733-746. [DOI: 10.1007/s10534-017-0041-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
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9
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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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10
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Kaminski T, Gunnarsson A, Geschwindner S. Harnessing the Versatility of Optical Biosensors for Target-Based Small-Molecule Drug Discovery. ACS Sens 2017; 2:10-15. [PMID: 28722441 DOI: 10.1021/acssensors.6b00735] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Optical biosensors entered target-based small-molecule drug discovery more than two decades ago and have since transformed into a value-adding component in the decision-making process. Here, we briefly highlight the major application areas of optical biosensors and focus on desirable profiles of such platforms in order to ensure their effective use in small molecule drug discovery. Furthermore, we will emphasize current technology-based constraints and discuss experimental strategies to address these limitations as well as provide a view of necessary technology improvements for next generation platforms.
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Affiliation(s)
- Tim Kaminski
- Discovery Sciences, Innovative
Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, S-43183 Mölndal, Sweden
| | - Anders Gunnarsson
- Discovery Sciences, Innovative
Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, S-43183 Mölndal, Sweden
| | - Stefan Geschwindner
- Discovery Sciences, Innovative
Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, S-43183 Mölndal, Sweden
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11
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12
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Nothstein J, MacColl E, Zuck P, Cassaday J, Uebele VN, Hermes JD, Homsher MF. Dynamic Compound-Dependent Acoustic Transfer to Investigate Inhibitor Reversibility. SLAS Technol 2016; 22:485-492. [PMID: 28027447 DOI: 10.1177/2472630316684807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Automated mechanism of action studies are introducing the need for tailored compound delivery, which can be challenging for standard compound management procedures. Jump dilution assays investigating inhibitor reversibility require compound delivery at specific volumes to assay specific concentrations of 10 × IC50 for each inhibitor. Creating custom-made source plates with unique compound concentrations to dispense a uniform single volume can be prohibitively slow. A broadly applicable tool that enables on-the fly dispensing of variable amounts of stock concentrations was developed using the Acoustic Transfer System (ATS). The Dynamic Transfer Modification Program (DTMP) is an integrated LabVIEW program used to automate customized volume transfers from each well based on compound identity within a given source plate. A jump dilution investigating the time-dependent inhibition of the enzyme dipeptidyl peptidase-4 (DPP4) with multiple inhibitors is described here to demonstrate the delivery of specific volumes of various compounds in a high-throughput manner. The ability to automate this process allows for the characterization of inhibitor reversibility earlier in the drug discovery process, resulting in better informed lead candidate selection.
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Affiliation(s)
- Jennifer Nothstein
- 1 Screening and Protein Sciences, Merck Research Laboratories, North Wales, PA, USA
| | | | - Paul Zuck
- 1 Screening and Protein Sciences, Merck Research Laboratories, North Wales, PA, USA
| | - Jason Cassaday
- 1 Screening and Protein Sciences, Merck Research Laboratories, North Wales, PA, USA
| | - Victor N Uebele
- 1 Screening and Protein Sciences, Merck Research Laboratories, North Wales, PA, USA
| | - Jeffrey D Hermes
- 1 Screening and Protein Sciences, Merck Research Laboratories, North Wales, PA, USA
| | - Michelle F Homsher
- 1 Screening and Protein Sciences, Merck Research Laboratories, North Wales, PA, USA
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13
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Lerner C, Jakob-Roetne R, Buettelmann B, Ehler A, Rudolph M, Rodríguez Sarmiento RM. Design of Potent and Druglike Nonphenolic Inhibitors for Catechol O-Methyltransferase Derived from a Fragment Screening Approach Targeting the S-Adenosyl-l-methionine Pocket. J Med Chem 2016; 59:10163-10175. [PMID: 27685665 DOI: 10.1021/acs.jmedchem.6b00927] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A fragment screening approach designed to target specifically the S-adenosyl-l-methionine pocket of catechol O-methyl transferase allowed the identification of structurally related fragments of high ligand efficiency and with activity on the described orthogonal assays. By use of a reliable enzymatic assay together with X-ray crystallography as guidance, a series of fragment modifications revealed an SAR and, after several expansions, potent lead compounds could be obtained. For the first time nonphenolic and small low nanomolar potent, SAM competitive COMT inhibitors are reported. These compounds represent a novel series of potent COMT inhibitors that might be further optimized to new drugs useful for the treatment of Parkinson's disease, as adjuncts in levodopa based therapy, or for the treatment of schizophrenia.
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Affiliation(s)
- Christian Lerner
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Roland Jakob-Roetne
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Bernd Buettelmann
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andreas Ehler
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus Rudolph
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Rosa María Rodríguez Sarmiento
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
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14
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Label-enhanced surface plasmon resonance applied to label-free interaction analysis of small molecules and fragments. Anal Biochem 2016; 510:79-87. [DOI: 10.1016/j.ab.2016.06.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/24/2016] [Accepted: 06/06/2016] [Indexed: 12/30/2022]
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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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Lund BA, Christopeit T, Guttormsen Y, Bayer A, Leiros HKS. Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening. J Med Chem 2016; 59:5542-54. [PMID: 27165692 DOI: 10.1021/acs.jmedchem.6b00660] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The spread of antibiotic resistant bacteria is a global threat that shakes the foundations of modern healthcare. β-Lactamases are enzymes that confer resistance to β-lactam antibiotics in bacteria, and there is a critical need for new inhibitors of these enzymes for combination therapy together with an antibiotic. With this in mind, we have screened a library of 490 fragments to identify starting points for the development of new inhibitors of the class D β-lactamase oxacillinase-48 (OXA-48) through surface plasmon resonance (SPR), dose-rate inhibition assays, and X-ray crystallography. Furthermore, we have uncovered structure-activity relationships and used alternate conformations from a crystallographic structure to grow a fragment into a more potent compound with a KD of 50 μM and an IC50 of 18 μM.
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Affiliation(s)
- Bjarte Aarmo Lund
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway
| | - Tony Christopeit
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway
| | - Yngve Guttormsen
- Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway
| | - Annette Bayer
- Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway
| | - Hanna-Kirsti S Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway
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17
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Sheng C, Dong G, Miao Z, Zhang W, Wang W. State-of-the-art strategies for targeting protein-protein interactions by small-molecule inhibitors. Chem Soc Rev 2015; 44:8238-59. [PMID: 26248294 DOI: 10.1039/c5cs00252d] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Targeting protein-protein interactions (PPIs) has emerged as a viable approach in modern drug discovery. However, the identification of small molecules enabling us to effectively interrupt their interactions presents significant challenges. In the recent past, significant advances have been made in the development of new biological and chemical strategies to facilitate the discovery process of small-molecule PPI inhibitors. This review aims to highlight the state-of-the-art technologies and the achievements made recently in this field. The "hot spots" of PPIs have been proved to be critical for small molecules to bind. Three strategies including screening, designing, and synthetic approaches have been explored for discovering PPI inhibitors by targeting the "hot spots". Although the classic high throughput screening approach can be used, fragment screening, fragment-based drug design and newly improved virtual screening are demonstrated to be more effective in the discovery of PPI inhibitors. In addition to screening approaches, design strategies including anchor-based and small molecule mimetics of secondary structures involved in PPIs have become powerful tools as well. Finally, constructing new chemically spaced libraries with high diversity and complexity is becoming an important area of interest for PPI inhibitors. The successful cases from the recent five year studies are used to illustrate how these approaches are implemented to uncover and optimize small molecule PPI inhibitors and notably some of them have become promising therapeutics.
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Affiliation(s)
- Chunquan Sheng
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, P. R. China.
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18
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Fjellström O, Akkaya S, Beisel HG, Eriksson PO, Erixon K, Gustafsson D, Jurva U, Kang D, Karis D, Knecht W, Nerme V, Nilsson I, Olsson T, Redzic A, Roth R, Sandmark J, Tigerström A, Öster L. Creating novel activated factor XI inhibitors through fragment based lead generation and structure aided drug design. PLoS One 2015; 10:e0113705. [PMID: 25629509 PMCID: PMC4309560 DOI: 10.1371/journal.pone.0113705] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/27/2014] [Indexed: 11/19/2022] Open
Abstract
Activated factor XI (FXIa) inhibitors are anticipated to combine anticoagulant and profibrinolytic effects with a low bleeding risk. This motivated a structure aided fragment based lead generation campaign to create novel FXIa inhibitor leads. A virtual screen, based on docking experiments, was performed to generate a FXIa targeted fragment library for an NMR screen that resulted in the identification of fragments binding in the FXIa S1 binding pocket. The neutral 6-chloro-3,4-dihydro-1H-quinolin-2-one and the weakly basic quinolin-2-amine structures are novel FXIa P1 fragments. The expansion of these fragments towards the FXIa prime side binding sites was aided by solving the X-ray structures of reported FXIa inhibitors that we found to bind in the S1-S1'-S2' FXIa binding pockets. Combining the X-ray structure information from the identified S1 binding 6-chloro-3,4-dihydro-1H-quinolin-2-one fragment and the S1-S1'-S2' binding reference compounds enabled structure guided linking and expansion work to achieve one of the most potent and selective FXIa inhibitors reported to date, compound 13, with a FXIa IC50 of 1.0 nM. The hydrophilicity and large polar surface area of the potent S1-S1'-S2' binding FXIa inhibitors compromised permeability. Initial work to expand the 6-chloro-3,4-dihydro-1H-quinolin-2-one fragment towards the prime side to yield molecules with less hydrophilicity shows promise to afford potent, selective and orally bioavailable compounds.
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Affiliation(s)
- Ola Fjellström
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
- * E-mail:
| | - Sibel Akkaya
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Hans-Georg Beisel
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | | | - Karl Erixon
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - David Gustafsson
- Bioscience, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Ulrik Jurva
- Drug Metabolism and Pharmacokinetics, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Daiwu Kang
- Bioscience, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - David Karis
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Wolfgang Knecht
- Bioscience, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Viveca Nerme
- Bioscience, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Ingemar Nilsson
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Thomas Olsson
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Alma Redzic
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Robert Roth
- Discovery Sciences, AstraZeneca R&D, Mölndal, Sweden
| | | | | | - Linda Öster
- Discovery Sciences, AstraZeneca R&D, Mölndal, Sweden
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19
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Olaru A, Bala C, Jaffrezic-Renault N, Aboul-Enein HY. Surface Plasmon Resonance (SPR) Biosensors in Pharmaceutical Analysis. Crit Rev Anal Chem 2015; 45:97-105. [DOI: 10.1080/10408347.2014.881250] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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20
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Shepherd CA, Hopkins AL, Navratilova I. Fragment screening by SPR and advanced application to GPCRs. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:113-23. [PMID: 25301577 DOI: 10.1016/j.pbiomolbio.2014.09.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 09/25/2014] [Indexed: 12/31/2022]
Abstract
Surface plasmon resonance (SPR) is one of the primary biophysical methods for the screening of low molecular weight 'fragment' libraries, due to its low protein consumption and 'label-free' methodology. SPR biosensor interaction analysis is employed to both screen and confirm the binding of compounds in fragment screening experiments, as it provides accurate information on the affinity and kinetics of molecular interactions. The most advanced application of the use of SPR for fragment screening is against membrane protein drug targets, such G-protein coupled receptors (GPCRs). Biophysical GPCR assays using SPR have been validated with pharmacological measurements approximate to cell-based methods, yet provide the advantage of biophysical methods in their ability to measure the weak affinities of low molecular weight fragments. A number of SPR fragment screens against GPCRs have now been disclosed in the literature. SPR fragment screening is proving versatile to screen both thermostabilised GPCRs and solubilised wild type receptors. In this chapter, we discuss the state-of-the-art in GPCR fragment screening by SPR and the technical considerations in performing such experiments.
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Affiliation(s)
- Claire A Shepherd
- Division of Biological Chemistry and Drug Discovery, College of Life Science, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Andrew L Hopkins
- Division of Biological Chemistry and Drug Discovery, College of Life Science, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom.
| | - Iva Navratilova
- Division of Biological Chemistry and Drug Discovery, College of Life Science, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
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21
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Barile E, Pellecchia M. NMR-based approaches for the identification and optimization of inhibitors of protein-protein interactions. Chem Rev 2014; 114:4749-63. [PMID: 24712885 PMCID: PMC4027952 DOI: 10.1021/cr500043b] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Elisa Barile
- Sanford-Burnham Medical
Research Institute, 10901
North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maurizio Pellecchia
- Sanford-Burnham Medical
Research Institute, 10901
North Torrey Pines Road, La Jolla, California 92037, United States
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22
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Nero TL, Morton CJ, Holien JK, Wielens J, Parker MW. Oncogenic protein interfaces: small molecules, big challenges. Nat Rev Cancer 2014; 14:248-62. [PMID: 24622521 DOI: 10.1038/nrc3690] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Historically, targeting protein-protein interactions with small molecules was not thought possible because the corresponding interfaces were considered mostly flat and featureless and therefore 'undruggable'. Instead, such interactions were targeted with larger molecules, such as peptides and antibodies. However, the past decade has seen encouraging breakthroughs through the refinement of existing techniques and the development of new ones, together with the identification and exploitation of unexpected aspects of protein-protein interaction surfaces. In this Review, we describe some of the latest techniques to discover modulators of protein-protein interactions and how current drug discovery approaches have been adapted to successfully target these interfaces.
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Affiliation(s)
- Tracy L Nero
- Australian Cancer Research Foundation Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Craig J Morton
- Australian Cancer Research Foundation Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Jessica K Holien
- Australian Cancer Research Foundation Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Jerome Wielens
- 1] Australian Cancer Research Foundation Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia. [2] Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, Victoria 3065, Australia
| | - Michael W Parker
- 1] Australian Cancer Research Foundation Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia. [2] Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
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23
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Halogen-enriched fragment libraries as chemical probes for harnessing halogen bonding in fragment-based lead discovery. Future Med Chem 2014; 6:617-39. [DOI: 10.4155/fmc.14.20] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Halogen bonding has recently experienced a renaissance, gaining increased recognition as a useful molecular interaction in the life sciences. Halogen bonds are favorable, fairly directional interactions between an electropositive region on the halogen (the σ-hole) and a number of different nucleophilic interaction partners. Some aspects of halogen bonding are not yet understood well enough to take full advantage of its potential in drug discovery. We describe and present the concept of halogen-enriched fragment libraries. These libraries consist of unique chemical probes, facilitating the identification of favorable halogen bonds by sharing the advantages of classical fragment-based screening. Besides providing insights into the nature and applicability of halogen bonding, halogen-enriched fragment libraries provide smart starting points for hit-to-lead evolution.
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24
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Efficient screening of marine extracts for protease inhibitors by combining FRET based activity assays and surface plasmon resonance spectroscopy based binding assays. Mar Drugs 2013; 11:4279-93. [PMID: 24177674 PMCID: PMC3853728 DOI: 10.3390/md11114279] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 10/20/2013] [Accepted: 10/21/2013] [Indexed: 01/27/2023] Open
Abstract
The screening of extracts from marine organisms is a widely used strategy to discover new drug leads. A common problem in the screening process is the generation of false positive hits through unspecific effects from the complex chemical composition of the crude extracts. In this study, we explored a combination of a fluorescence resonance energy transfer (FRET) based activity assay and a surface plasmon resonance (SPR) based binding assay to avoid this problem. An aqueous extract was prepared from rest raw material of the Norwegian spring spawning herring, and further fractionated by methanol solubility and solid phase extraction. FRET based activity assays were used to determine the influence of each extract on the activity of different proteases. Several extracts showed more than 50% inhibition. The inhibition mechanisms were elucidated by SPR based competition experiments with known inhibitors. For the secreted aspartic proteases 1, 2, 3 and HIV-1 protease, the results indicated that some extracts contain inhibitors interacting specifically with the active site of the enzymes. The study shows that a combination of an activity assay and an SPR based binding assay is a powerful tool to identify potent inhibitors in marine extracts. Furthermore, the study shows that marine vertebrates offer an interesting source for new bioactive compounds, although they have rarely been explored for this purpose.
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25
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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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26
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Regnström K, Yan J, Nguyen L, Callaway K, Yang Y, Diep L, Xing W, Adhikari A, Beroza P, Hom RK, Riley B, Rudolph D, Jobling MF, Baker J, Johnston J, Konradi A, Bova MP, Artis DR. Label free fragment screening using surface plasmon resonance as a tool for fragment finding - analyzing parkin, a difficult CNS target. PLoS One 2013; 8:e66879. [PMID: 23861750 PMCID: PMC3702509 DOI: 10.1371/journal.pone.0066879] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/12/2013] [Indexed: 11/18/2022] Open
Abstract
Surface Plasmon Resonance (SPR) is rarely used as a primary High-throughput Screening (HTS) tool in fragment-based approaches. With SPR instruments becoming increasingly high-throughput it is now possible to use SPR as a primary tool for fragment finding. SPR becomes, therefore, a valuable tool in the screening of difficult targets such as the ubiquitin E3 ligase Parkin. As a prerequisite for the screen, a large number of SPR tests were performed to characterize and validate the active form of Parkin. A set of compounds was designed and used to define optimal SPR assay conditions for this fragment screen. Using these conditions, more than 5000 pre-selected fragments from our in-house library were screened for binding to Parkin. Additionally, all fragments were simultaneously screened for binding to two off target proteins to exclude promiscuous binding compounds. A low hit rate was observed that is in line with hit rates usually obtained by other HTS screening assays. All hits were further tested in dose responses on the target protein by SPR for confirmation before channeling the hits into Nuclear Magnetic Resonance (NMR) and other hit-confirmation assays.
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27
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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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28
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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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29
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Scott DE, Coyne AG, Hudson SA, Abell C. Fragment-Based Approaches in Drug Discovery and Chemical Biology. Biochemistry 2012; 51:4990-5003. [DOI: 10.1021/bi3005126] [Citation(s) in RCA: 324] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Duncan E. Scott
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Anthony G. Coyne
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Sean A. Hudson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Chris Abell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
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30
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Label-free monitoring of apoptosis by surface plasmon resonance detection of morphological changes. Apoptosis 2012; 17:916-25. [DOI: 10.1007/s10495-012-0737-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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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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32
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Sheng C, Zhang W. Fragment Informatics and Computational Fragment-Based Drug Design: An Overview and Update. Med Res Rev 2012; 33:554-98. [DOI: 10.1002/med.21255] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chunquan Sheng
- Department of Medicinal Chemistry; School of Pharmacy; Second Military Medical University; 325 Guohe Road Shanghai 200433 People's Republic of China
| | - Wannian Zhang
- Department of Medicinal Chemistry; School of Pharmacy; Second Military Medical University; 325 Guohe Road Shanghai 200433 People's Republic of China
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33
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Rich RL, Myszka DG. Survey of the 2009 commercial optical biosensor literature. J Mol Recognit 2012; 24:892-914. [PMID: 22038797 DOI: 10.1002/jmr.1138] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We took a different approach to reviewing the commercial biosensor literature this year by inviting 22 biosensor users to serve as a review committee. They set the criteria for what to expect in a publication and ultimately decided to use a pass/fail system for selecting which papers to include in this year's reference list. Of the 1514 publications in 2009 that reported using commercially available optical biosensor technology, only 20% passed their cutoff. The most common criticism the reviewers had with the literature was that "the biosensor experiments could have been done better." They selected 10 papers to highlight good experimental technique, data presentation, and unique applications of the technology. This communal review process was educational for everyone involved and one we will not soon forget.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT, USA
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34
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Zeder-Lutz G, Choulier L, Besse M, Cousido-Siah A, Figueras FXR, Didier B, Jung ML, Podjarny A, Altschuh D. Validation of surface plasmon resonance screening of a diverse chemical library for the discovery of protein tyrosine phosphatase 1b binders. Anal Biochem 2012; 421:417-27. [DOI: 10.1016/j.ab.2011.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/13/2011] [Accepted: 09/14/2011] [Indexed: 01/07/2023]
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35
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Emerging role of surface plasmon resonance in fragment-based drug discovery. Future Med Chem 2012; 3:1809-20. [PMID: 22004086 DOI: 10.4155/fmc.11.128] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Surface plasmon resonance (SPR) offers a method of biophysical fragment screening that is fast, efficient, cost effective and accurate. SPR is increasingly being adopted as a secondary assay to validate fragment hits. Recently, technical advances have resulted in the emergence of SPR as a primary screening methodology for fragment-based drug discovery. Moreover, SPR biosensor assays can be developed for a wide range of proteins, including membrane proteins, such as G-protein-coupled receptors. In this review, we discuss the advantages and limitations of SPR fragment screening including experimental consideration of reducing false positive and false negative rates to a minimum. We discuss how ligand efficiency can be used both as a method to eliminate false positives and to understand which fragments in a library may be a source of false negatives.
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36
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Hahn S, Achenbach J, Buscató E, Klingler FM, Schroeder M, Meirer K, Hieke M, Heering J, Barbosa-Sicard E, Loehr F, Fleming I, Doetsch V, Schubert-Zsilavecz M, Steinhilber D, Proschak E. Complementary Screening Techniques Yielded Fragments that Inhibit the Phosphatase Activity of Soluble Epoxide Hydrolase. ChemMedChem 2011; 6:2146-9. [DOI: 10.1002/cmdc.201100433] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Indexed: 01/30/2023]
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37
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Chung CW, Witherington J. Progress in the discovery of small-molecule inhibitors of bromodomain--histone interactions. ACTA ACUST UNITED AC 2011; 16:1170-85. [PMID: 21956175 DOI: 10.1177/1087057111421372] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bromodomains are structurally conserved protein modules present in a large number of chromatin-associated proteins and in many nuclear histone acetyltransferases. The bromodomain functions as an acetyl-lysine binding domain and has been shown to be pivotal in regulating protein-protein interactions in chromatin-mediated cellular gene transcription, cell proliferation, and viral transcriptional activation. Structural analyses of these modules in complex with acetyl-lysine peptide ligands provide insights into the molecular basis for recognition and ligand selectivity within this epigenetic reader family. However, there are significant challenges in configuring assays to identify inhibitors of these proteins. This review focuses on the progress made in developing methods to identify peptidic and small-molecule ligands using biophysical label-free and biochemical approaches. The advantage of each technique and the results reported are summarized, highlighting the potential applicably to other reader domains and the caveats in translation from simple in vitro systems to a biological context.
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38
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Molecular complexity and fragment-based drug discovery: ten years on. Curr Opin Chem Biol 2011; 15:489-96. [DOI: 10.1016/j.cbpa.2011.05.008] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 04/12/2011] [Accepted: 05/08/2011] [Indexed: 11/17/2022]
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39
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Abstract
A well-chosen set of fragments is able to cover a large chemical space using a small number of compounds. The actual size and makeup of the fragment set is dependent on the screening method since each technique has its own practical limits in terms of the number of compounds that can be screened and requirements for compound solubility. In this chapter, an overview of the general requirements for a fragment library is presented for different screening platforms. In the case of the FBDD work at Johnson & Johnson Pharmaceutical Research and Development, L.L.C., our main screening technology is X-ray crystallography. Since every soaked protein crystal needs to be diffracted and a protein structure determined to delineate if a fragment binds, the size of our initial screening library cannot be a rate-limiting factor. For this reason, we have chosen 900 as the appropriate primary fragment library size. To choose the best set, we have developed our own mix of simple property ("Rule of 3") and "bad" substructure filtering. While this gets one a long way in terms of limiting the fragment pool, there are still tens of thousands of compounds to choose from after this initial step. Many of the choices left at this stage are not drug-like, so we have developed an FBDD Score to help select a 900-compound set. The details of this score and the filtering are presented.
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Yamane J, Yao M, Zhou Y, Hiramatsu Y, Fujiwara K, Yamaguchi T, Yamaguchi H, Togame H, Tsujishita H, Takemoto H, Tanaka I. In-crystal affinity ranking of fragment hit compounds reveals a relationship with their inhibitory activities. J Appl Crystallogr 2011. [DOI: 10.1107/s0021889811017717] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Fragment-based drug discovery (FBDD), which is a molecular build-up strategy from small scaffolds, has recently become a promising approach for lead-compound generation. Although high-throughput protein crystallography is usually used to determine the protein–ligand complex structure and identify potential hit compounds, the relationship between the quality of theFo–Fcmaps of hit compounds and their inhibitory activities has rarely been examined. To address this issue, crystallographic competition experiments were carried out to determine the relative order of the in-crystal binding affinities using five hit compounds of bovine pancreatic trypsin inhibitors. Soaking experiments of all combinations of the five hit compounds were used to define the in-crystal affinity ranking. Based on characterization by a high-concentration bioassay, a clear correlation was observed between in-crystal binding affinities and the inhibitory activities in solution. Moreover, the correlation analysis revealed that X-ray-based screening can detect a weak hit compound with inhibitory activity below the limit of detection, even in a high-concentration assay. The proposed crystallographic competition method could function as a valuable tool, not only to select a plausible starting scaffold for subsequent synthetic efforts but also to access structure–activity relationships using fragment compounds with a wider detection limit than a biological assay. The crystallographic validation methodology described here will greatly accelerate the hit-to-lead process during fragment-based and structure-based drug design.
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Wang J, Zhu Z, Munir A, Zhou HS. Fe3O4 nanoparticles-enhanced SPR sensing for ultrasensitive sandwich bio-assay. Talanta 2011; 84:783-8. [PMID: 21482283 DOI: 10.1016/j.talanta.2011.02.020] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 02/07/2011] [Accepted: 02/09/2011] [Indexed: 10/18/2022]
Abstract
Magnetic nanoparticles (MNPs) have been receiving increasing attention because of its great potentials in bioseparation. However, the separation products are difficult to be detected by general method due to their extremely small size. Here, we demonstrate that MNPs can greatly enhance the signal of surface plasmon resonance spectroscopy (SPR). Features of MNPs-aptamer conjugates as a powerful amplification reagent for ultrasensitive immunoassay are reported in this work for the first time. In order to evaluate the sensing ability of MNPs-aptamer conjugates as an amplification reagent, a sandwich SPR sensor is constructed by using thrombin as model analyte. Thrombin, captured by immobilized anti-thrombin aptamer on SPR gold film, is sensitively detected by SPR spectroscopy with a lowest detection limit of 0.017 nM after MNPs-aptamer conjugates is used as amplification reagent. At the same time, the excellent selectivity of the present biosensor is also confirmed by using three kinds of proteins (BSA, human IgM and human IgE) as controls. These results confirm that MNPs is a powerful sandwich element and an excellent amplification reagent for SPR based sandwich immunoassay and SPR has a great potential for the detection of MNPs-based bioseparation products.
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Affiliation(s)
- Jianlong Wang
- Department of Chemical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
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Brandt P, Geitmann M, Danielson UH. Deconstruction of non-nucleoside reverse transcriptase inhibitors of human immunodeficiency virus type 1 for exploration of the optimization landscape of fragments. J Med Chem 2011; 54:709-18. [PMID: 21207958 DOI: 10.1021/jm101052g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This study has taken a closer look at the theoretical basis for protein-fragment interactions. The approach involved the deconstruction of 3 non-nucleoside inhibitors of HIV-1 reverse transcriptase and investigation of the interaction between 21 substructures and the enzyme. It focused on the concept of ligand efficiency and showed that ligand independent free energy fees (ΔG(ind)) are crucial for the understanding of the binding affinities of fragments. A value of 7.0 kcal mol(-1) for the ΔG(ind) term is shown to be a lower limit for the NNRTI binding pocket of HIV-1 RT. The addition of the ΔG(ind) term to the dissociation free energy in the calculation of a corrected ligand efficiency, in combination with the lack of an efficient ligand binding hot spot in the NNIBP, fully explains the existence of nonbinding NNRTI substructures. By applying the concept to a larger set of ligands, we could define a binding site profile that indicates the absence of an efficient fragment binding hot spot but an efficient binding of full-sized NNRTIs. The analysis explains some of the challenges in identifying fragments against flexible targets involving conformational changes and how fragments may be prioritized.
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Geitmann M, Elinder M, Seeger C, Brandt P, de Esch IJP, Danielson UH. Identification of a novel scaffold for allosteric inhibition of wild type and drug resistant HIV-1 reverse transcriptase by fragment library screening. J Med Chem 2011; 54:699-708. [PMID: 21207961 DOI: 10.1021/jm1010513] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A novel scaffold inhibiting wild type and drug resistant variants of human immunodeficiency virus type 1 reverse transcriptase (HIV-1RT) has been identified in a library consisting of 1040 fragments. The fragments were significantly different from already known non-nucleoside reverse transcriptase inhibitors (NNRTIs), as indicated by a Tversky similarity analysis. A screening strategy involving SPR biosensor-based interaction analysis and enzyme inhibition was used. Primary biosensor-based screening, using short concentration series, was followed by analysis of nevirapine competition and enzyme inhibition, thus identifying inhibitory fragments binding to the non-nucleoside reverse transcriptase inhibitor (NNRTI) binding site. Ten hits were discovered, and their affinities and resistance profiles were evaluated with wild type and three drug resistant enzyme variants (K103N, Y181C, and L100I). One fragment exhibited submillimolar K(D) and IC(50) values against all four tested enzyme variants. A substructure comparison between the fragment and 826 structurally diverse published NNRTIs confirmed that the scaffold was novel. The fragment is a bromoindanone with a ligand efficiency of 0.42 kcal/mol(-1).
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45
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Abstract
The fragment-based approach is now well established as an important component of modern drug discovery. A key part in establishing its position as a viable technique has been the development of a range of biophysical methodologies with sufficient sensitivity to detect the binding of very weakly binding molecules. X-ray crystallography was one of the first techniques demonstrated to be capable of detecting such weak binding, but historically its potential for screening was under-appreciated and impractical due to its relatively low throughput. In this chapter we discuss the various benefits associated with fragment-screening by X-ray crystallography, and describe the technical developments we have implemented to allow its routine use in drug discovery. We emphasize how this approach has allowed a much greater exploitation of crystallography than has traditionally been the case within the pharmaceutical industry, with the rapid and timely provision of structural information having maximum impact on project direction.
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Elinder M, Geitmann M, Gossas T, Källblad P, Winquist J, Nordström H, Hämäläinen M, Danielson UH. Experimental Validation of a Fragment Library for Lead Discovery Using SPR Biosensor Technology. ACTA ACUST UNITED AC 2010; 16:15-25. [DOI: 10.1177/1087057110389038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A new fragment library for lead discovery has been designed and experimentally validated for use in surface plasmon resonance (SPR) biosensor-based screening. The 930 compounds in the library were selected from 4.6 million commercially available compounds using a series of physicochemical and medicinal chemistry filters. They were screened against 3 prototypical drug targets: HIV-1 protease, thrombin and carbonic anhydrase, and a nontarget: human serum albumin. Compound solubility was not a problem under the conditions used for screening. The high sensitivity of the sensor surfaces allowed the detection of interactions for 35% to 97% of the fragments, depending on the target protein. None of the fragments was promiscuous (i.e., interacted with a stoichiometry ≥5:1 with all 4 proteins), and only 2 compounds dissociated slowly from all 4 proteins. The use of several targets proved valuable since several compounds would have been disqualified from the library on the grounds of promiscuity if fewer target proteins had been used. The experimental procedure allowed an efficient evaluation and exploration of the new fragment library and confirmed that the new library is suitable for SPR biosensor-based screening.
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Affiliation(s)
- Malin Elinder
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | | | | | | | - Johan Winquist
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | - Helena Nordström
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | | | - U. Helena Danielson
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
- Beactica AB, Uppsala, Sweden
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de Kloe GE, Retra K, Geitmann M, Källblad P, Nahar T, van Elk R, Smit AB, van Muijlwijk-Koezen JE, Leurs R, Irth H, Danielson UH, de Esch IJP. Surface Plasmon Resonance Biosensor Based Fragment Screening Using Acetylcholine Binding Protein Identifies Ligand Efficiency Hot Spots (LE Hot Spots) by Deconstruction of Nicotinic Acetylcholine Receptor α7 Ligands. J Med Chem 2010; 53:7192-201. [DOI: 10.1021/jm100834y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gerdien E. de Kloe
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Kim Retra
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of BioMolecular Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | | | | | - Tariq Nahar
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - René van Elk
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Jacqueline E. van Muijlwijk-Koezen
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Rob Leurs
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Hubertus Irth
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of BioMolecular Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - U. Helena Danielson
- Beactica AB, Box 567, SE-751 22 Uppsala, Sweden
- Department of Biochemistry and Organic Chemistry, Uppsala University, BMC, Box 576, SE-751 23, Uppsala, Sweden
| | - Iwan J. P. de Esch
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Hubbard RE. Structure-based drug discovery and protein targets in the CNS. Neuropharmacology 2010; 60:7-23. [PMID: 20673774 DOI: 10.1016/j.neuropharm.2010.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Accepted: 07/21/2010] [Indexed: 12/18/2022]
Abstract
Structure-based methods are having an increasing role and impact in drug discovery. The crystal structures of an increasing number of therapeutic targets are becoming available. These structures can transform our understanding of how these proteins perform their biological function and often provide insights into the molecular basis of disease. In addition, the structures can help the discovery process. Methods such as virtual screening and experimental fragment screening can provide starting hit compounds for a discovery project. Crystal structures of compounds bound to the protein can direct or guide the medicinal chemistry optimisation to improve drug-like properties - not only providing ideas on how to improve binding affinity or selectivity, but also showing where the compound can be modified in attempting to modulate physico-chemical properties and biological efficacy. The majority of drug discovery projects against globular protein targets now use these methods at some stage. This review provides a summary of the range of structure-based drug discovery methods that are in use and surveys the suitability of the methods for targets currently identified for CNS drugs. Until recently, structure-based discovery was difficult or unknown for these targets. The recent determination of the structures of a number of GPCR proteins, together with the steady increase in structures for other membrane proteins, is opening up the possibility for these structure-based methods to find increased use in drug discovery for CNS diseases and conditions.
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Holdgate GA, Anderson M, Edfeldt F, Geschwindner S. Affinity-based, biophysical methods to detect and analyze ligand binding to recombinant proteins: matching high information content with high throughput. J Struct Biol 2010; 172:142-57. [PMID: 20609391 DOI: 10.1016/j.jsb.2010.06.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 06/28/2010] [Accepted: 06/29/2010] [Indexed: 01/21/2023]
Abstract
Affinity-based technologies have become impactful tools to detect, monitor and characterize molecular interactions using recombinant target proteins. This can aid the understanding of biological function by revealing mechanistic details, and even more importantly, enables the identification of new improved ligands that can modulate the biological activity of those targets in a desired fashion. The selection of the appropriate technology is a key step in that process, as each one of the currently available technologies offers a characteristic type of biophysical information about the ligand-binding event. Alongside the indisputable advantages of each of those technologies they naturally display diverse restrictions that are quite frequently related to the target system to be studied but also to the affinity, solubility and molecular size of the ligands. This paper discusses some of the theoretical and experimental aspects of the most common affinity-based methods, what type of information can be gained from each one of those approaches, and what requirements as well as limitations are expected from working with recombinant proteins on those platforms and how those can be optimally addressed.
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Affiliation(s)
- Geoff A Holdgate
- Lead Generation Sciences, AstraZeneca R&D Alderley Park, Mereside, Alderley Park, United Kingdom
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50
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Algorithms for the automated selection of fragment-like molecules using single-point surface plasmon resonance measurements. Anal Biochem 2010; 402:179-84. [DOI: 10.1016/j.ab.2010.03.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 03/26/2010] [Accepted: 03/31/2010] [Indexed: 11/24/2022]
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