1
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Hardie A, Cossins BP, Lovera S, Michel J. Deconstructing allostery by computational assessment of the binding determinants of allosteric PTP1B modulators. Commun Chem 2023; 6:125. [PMID: 37322137 DOI: 10.1038/s42004-023-00926-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023] Open
Abstract
Fragment-based drug discovery is an established methodology for finding hit molecules that can be elaborated into lead compounds. However it is currently challenging to predict whether fragment hits that do not bind to an orthosteric site could be elaborated into allosteric modulators, as in these cases binding does not necessarily translate into a functional effect. We propose a workflow using Markov State Models (MSMs) with steered molecular dynamics (sMD) to assess the allosteric potential of known binders. sMD simulations are employed to sample protein conformational space inaccessible to routine equilibrium MD timescales. Protein conformations sampled by sMD provide starting points for seeded MD simulations, which are combined into MSMs. The methodology is demonstrated on a dataset of protein tyrosine phosphatase 1B ligands. Experimentally confirmed allosteric inhibitors are correctly classified as inhibitors, whereas the deconstructed analogues show reduced inhibitory activity. Analysis of the MSMs provide insights into preferred protein-ligand arrangements that correlate with functional outcomes. The present methodology may find applications for progressing fragments towards lead molecules in FBDD campaigns.
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Affiliation(s)
- Adele Hardie
- EaStChem School of Chemistry, Joseph Black Building, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Benjamin P Cossins
- UCB Pharma, 216 Bath Road, Slough, UK
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, UK
| | - Silvia Lovera
- UCB Pharma, Chemin du Foriest 1, 1420, Braine-l'Alleud, Belgium
| | - Julien Michel
- EaStChem School of Chemistry, Joseph Black Building, University of Edinburgh, Edinburgh, EH9 3FJ, UK.
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2
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Steffek M, Helgason E, Popovych N, Rougé L, Bruning JM, Li KS, Burdick DJ, Cai J, Crawford T, Xue J, Decurtins W, Fang C, Grubers F, Holliday MJ, Langley A, Petersen A, Satz AL, Song A, Stoffler D, Strebel Q, Tom JYK, Skelton N, Staben ST, Wichert M, Mulvihill MM, Dueber EC. A Multifaceted Hit-Finding Approach Reveals Novel LC3 Family Ligands. Biochemistry 2023; 62:633-644. [PMID: 34985287 DOI: 10.1021/acs.biochem.1c00682] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Autophagy-related proteins (Atgs) drive the lysosome-mediated degradation pathway, autophagy, to enable the clearance of dysfunctional cellular components and maintain homeostasis. In humans, this process is driven by the mammalian Atg8 (mAtg8) family of proteins comprising the LC3 and GABARAP subfamilies. The mAtg8 proteins play essential roles in the formation and maturation of autophagosomes and the capture of specific cargo through binding to the conserved LC3-interacting region (LIR) sequence within target proteins. Modulation of interactions of mAtg8 with its target proteins via small-molecule ligands would enable further interrogation of their function. Here we describe unbiased fragment and DNA-encoded library (DEL) screening approaches for discovering LC3 small-molecule ligands. Both strategies resulted in compounds that bind to LC3, with the fragment hits favoring a conserved hydrophobic pocket in mATG8 proteins, as detailed by LC3A-fragment complex crystal structures. Our findings demonstrate that the malleable LIR-binding surface can be readily targeted by fragments; however, rational design of additional interactions to drive increased affinity proved challenging. DEL libraries, which combine small, fragment-like building blocks into larger scaffolds, yielded higher-affinity binders and revealed an unexpected potential for reversible, covalent ligands. Moreover, DEL hits identified possible vectors for synthesizing fluorescent probes or bivalent molecules for engineering autophagic degradation of specific targets.
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Affiliation(s)
- Micah Steffek
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Elizabeth Helgason
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Lionel Rougé
- Structure Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - John M Bruning
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ke Sherry Li
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel J Burdick
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jianping Cai
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Terry Crawford
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jing Xue
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Willy Decurtins
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Chunlin Fang
- WuXi AppTec (Wuhan) Company, Ltd., No. 666 GaoXin Road, WuHan East Lake High-tech Development Zone, Hubei 430075, China
| | - Felix Grubers
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Michael J Holliday
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Allyson Langley
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ann Petersen
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Alexander Lee Satz
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Aimin Song
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel Stoffler
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Quentin Strebel
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jeffrey Y K Tom
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Skelton
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Steven T Staben
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Moreno Wichert
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Melinda M Mulvihill
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Erin C Dueber
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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3
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Moinul M, Khatun S, Amin SA, Jha T, Gayen S. Recent trends in fragment-based anticancer drug design strategies against different targets: A mini-review. Biochem Pharmacol 2022; 206:115301. [DOI: 10.1016/j.bcp.2022.115301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
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4
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Furka Á. Forty years of combinatorial technology. Drug Discov Today 2022; 27:103308. [PMID: 35760283 DOI: 10.1016/j.drudis.2022.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Combinatorial technology has been facilitating the synthesis and screening of large molecular libraries containing millions of organic compounds ever since its introduction 40 years ago. It has changed the paradigms of pharmaceutical research from focusing on single compounds to focusing on immense collections of compounds. It inspired the development of dynamic combinatorial libraries, fragment-based drug discovery and virtual library screening. Combinatorial technology was revitalized by the development of DNA encoding. Amplification of DNA oligomers plus next-generation sequencing has made it possible to successfully screen billions of compounds in a single process.
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Affiliation(s)
- Árpád Furka
- Eötvös Loránd University Budapest Hungary, 1077 Rozsa u. 23-25, Budapest, Hungary.
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5
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Arney JW, Weeks KM. RNA-Ligand Interactions Quantified by Surface Plasmon Resonance with Reference Subtraction. Biochemistry 2022; 61:1625-1632. [PMID: 35802500 PMCID: PMC9357220 DOI: 10.1021/acs.biochem.2c00177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structured RNAs bind ligands and are attractive targets for small-molecule drugs. A wide variety of analytical methods have been used to characterize RNA-ligand interactions, but our experience is that most have significant limitations in terms of material requirements and applicability to complex RNAs. Surface plasmon resonance (SPR) potentially overcomes these limitations, but we find that the standard experimental framework measures notable nonspecific electrostatic-mediated interactions, frustrating analysis of weak RNA binders. SPR measurements are typically quantified relative to a non-target reference channel. Here, we show that referencing to a channel containing a non-binding control RNA enables subtraction of nonspecific binding contributions, allowing measurements of accurate and specific binding affinities. We validated this approach for small-molecule binders of two riboswitch RNAs with affinities ranging from nanomolar to millimolar, including low-molecular-mass fragment ligands. SPR implemented with reference subtraction reliably discriminates specific from nonspecific binding, uses RNA and ligand material efficiently, and enables rapid exploration of the ligand-binding landscape for RNA targets.
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Affiliation(s)
- J. Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
27599-3290
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6
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Abstract
The emerging risk of viral diseases has triggered the search for preventive and therapeutic agents. Since the beginning of the COVID-19 pandemic, greater efforts have been devoted to investigating virus entry mechanisms into host cells. The feasibility of plasmonic sensing technologies for screening interactions of small molecules in real time, while providing the pharmacokinetic drug profiling of potential antiviral compounds, offers an advantageous approach over other biophysical methods. This review summarizes recent advancements in the drug discovery process of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) inhibitors using Surface Plasmon Resonance (SPR) biosensors. A variety of SPR assay formats are discussed according to the binding kinetics and drug efficacies of both natural products and repurposed drugs. Special attention has been given to the targeting of antiviral agents that block the receptor binding domain of the spike protein (RBD-S) and the main protease (3CLpro) of SARS-CoV-2. The functionality of plasmonic biosensors for high-throughput screening of entry virus inhibitors was also reviewed taking into account experimental parameters (binding affinities, selectivity, stability), potential limitations and future applications.
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7
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Naik A, Misra SK. Modern Sensing Approaches for Predicting Toxicological Responses of Food- and Drug-Based Bioactives on Microbiomes of Gut Origin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6396-6413. [PMID: 34081444 DOI: 10.1021/acs.jafc.1c02736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent scientific findings have correlated the gut microbes with homeostasis of human health by delineating their role in pathogen resistance, bioactive metabolization, and immune responses. Foreign materials, like xenobiotics, that induce an altering effect to the human body also influence the gut microbiome to some extent and often limit their use as a result of significant side effects. Investigating the xenobiotic effect of new therapeutic material or edible could be quite painstaking and economically non-viable. Thus, the use of predictive toxicology methods can be an innovative strategy in the food, pharma, and agriculture industries. There are reported in silico, ex vivo, in vitro, and in vivo methods to evaluate such effects but with added drawbacks, such as lower predictability, physiological dissimilarities, and high cost of associated invasive procedures. This review highlights the current and future possibilities with newer modern sensing approaches of economic and time-scale advantages for predicting toxicological responses on gut microbiomes.
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Affiliation(s)
- Aishwarya Naik
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kalyanpur, Uttar Pradesh 208016, India
| | - Santosh K Misra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kalyanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kalyanpur, Uttar Pradesh 208016, India
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8
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Moreira-Filho JT, Silva AC, Dantas RF, Gomes BF, Souza Neto LR, Brandao-Neto J, Owens RJ, Furnham N, Neves BJ, Silva-Junior FP, Andrade CH. Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. Front Immunol 2021; 12:642383. [PMID: 34135888 PMCID: PMC8203334 DOI: 10.3389/fimmu.2021.642383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022] Open
Abstract
Schistosomiasis is a parasitic disease caused by trematode worms of the genus Schistosoma and affects over 200 million people worldwide. The control and treatment of this neglected tropical disease is based on a single drug, praziquantel, which raises concerns about the development of drug resistance. This, and the lack of efficacy of praziquantel against juvenile worms, highlights the urgency for new antischistosomal therapies. In this review we focus on innovative approaches to the identification of antischistosomal drug candidates, including the use of automated assays, fragment-based screening, computer-aided and artificial intelligence-based computational methods. We highlight the current developments that may contribute to optimizing research outputs and lead to more effective drugs for this highly prevalent disease, in a more cost-effective drug discovery endeavor.
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Affiliation(s)
- José T. Moreira-Filho
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Arthur C. Silva
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Rafael F. Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Barbara F. Gomes
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lauro R. Souza Neto
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Didcot, United Kingdom
- Research Complex at Harwell, Didcot, United Kingdom
| | - Raymond J. Owens
- The Rosalind Franklin Institute, Harwell, United Kingdom
- Division of Structural Biology, The Wellcome Centre for Human Genetic, University of Oxford, Oxford, United Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bruno J. Neves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Floriano P. Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina H. Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
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9
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Wang Q, Zhu G, Liu Z. Establishment of inhibitor screening and validation system for tryptophanyl tRNA synthetase using surface plasmon resonance. Anal Biochem 2021; 623:114183. [PMID: 33798474 DOI: 10.1016/j.ab.2021.114183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 11/28/2022]
Abstract
With the increase in throughput and sensitivity, biophysical technology has become a major component of the early drug discovery phase. Surface plasmon resonance technology (SPR) is one of the most widely used biophysical technologies. It has the advantages of circumventing labeling, molecular weight limitations, and neglect of low affinity interactions, etc., and provides a robust platform for hit to lead discovery and optimization. Here, we successfully established a reliable and repeatable tryptophanyl tRNA synthetase (TrpRS) SPR high-throughput screening and validation system by optimizing the TrpRS tag, TrpRS immobilization methodology, and the buffer conditions. When TrpRS was immobilized on Streptavidin (SA) sensor chip, the substrate competitive inhibitor indolmycin exhibited the best binding affinity in HBS-P (10 mM HEPES, 150 mM NaCl, 0.05% surfactant P-20, pH 7.4), 1 mM ATP and MgCl2, with a KD (dissociation equilibrium constant) value of 0.6 ± 0.1 μM. The Z-factor values determined in the screening assays were all larger than 0.9. We hope that our proposed research ideas and methods may provide a scientific basis for establishing SPR analysis of other drug targets, accelerate the discovery and optimization of target lead compounds, and assist the clinical application of next-generation drugs.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | - Guiwang Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
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10
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Tiwari PB, Bencheqroun C, Lemus M, Shaw T, Kouassi-Brou M, Alaoui A, Üren A. SPRD: a surface plasmon resonance database of common factors for better experimental planning. BMC Mol Cell Biol 2021; 22:17. [PMID: 33676410 PMCID: PMC7937274 DOI: 10.1186/s12860-021-00354-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
Background Surface plasmon resonance is a label-free biophysical technique that is widely used in investigating biomolecular interactions, including protein-protein, protein-DNA, and protein-small molecule binding. Surface plasmon resonance is a very powerful tool in different stages of small molecule drug development and antibody characterization. Both academic institutions and pharmaceutical industry extensively utilize this method for screening and validation studies involving direct molecular interactions. In most applications of the surface plasmon resonance technology, one of the studied molecules is immobilized on a microchip, while the second molecule is delivered through a microfluidic system over the immobilized molecules. Changes in total mass on the chip surface is recorded in real time as an indicator of the molecular interactions. Main body Quality and accuracy of the surface plasmon resonance data depend on experimental variables, including buffer composition, type of sensor chip, coupling chemistry of molecules on the sensor surface, and surface regeneration conditions. These technical details are generally included in materials and methods sections of published manuscripts and are not easily accessible using the common internet browser search engines or PubMed. Herein, we introduce a surface plasmon resonance database, www.sprdatabase.info that contains technical details extracted from 5140 publications with surface plasmon resonance data. We also provide an analysis of experimental conditions preferred by different laboratories. These experimental variables can be searched within the database and help future users of this technology to design better experiments. Conclusion Amine coupling and CM5 chips were the most common methods used for immobilizing proteins in surface plasmon resonance experiments. However, number of different chips, capture methods and buffer conditions were used by multiple investigators. We predict that the database will significantly help the scientific community using this technology and hope that users will provide feedback to improve and expand the database indefinitely. Publicly available information in the database can save a great amount of time and resources by assisting initial optimization and troubleshooting of surface plasmon resonance experiments.
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Affiliation(s)
| | - Camelia Bencheqroun
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington, DC, 20057, USA
| | - Mario Lemus
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA
| | - Taryn Shaw
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA
| | - Marilyn Kouassi-Brou
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA.,Geisel School of Medicine, Dartmouth College, NH, 03755, Hanover, USA
| | - Adil Alaoui
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington, DC, 20057, USA
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA.
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11
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Kumar PKR. Systematic Screening of Viral Entry Inhibitors Using Surface Plasmon Resonance. Methods Mol Biol 2020; 2089:131-145. [PMID: 31773651 DOI: 10.1007/978-1-0716-0163-1_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Surface plasmon resonance (SPR) analytical method was initially used as biosensor for analyzing diverse biomolecular interactions and recently gained important place in the drug discovery. Here, I describe the procedures for screening of inhibitors against the viral proteins using the SPR. Using the described procedures, in the past, we were able to identify several antiviral products that interfere viral-host receptor proteins interactions.
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Affiliation(s)
- Penmetcha K R Kumar
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba City, Ibaraki, Japan.
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12
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Canning P, Birchall K, Kettleborough CA, Merritt A, Coombs PJ. Fragment-based target screening as an empirical approach to prioritising targets: a case study on antibacterials. Drug Discov Today 2020; 25:S1359-6446(20)30339-1. [PMID: 32920060 DOI: 10.1016/j.drudis.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/27/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022]
Abstract
Here, we describe a novel workflow combining informatic and experimental approaches to enable evidence-based prioritising of targets from large sets in parallel. High-throughput protein production and biophysical fragment screening is used to identify those targets that are tractable and ligandable. As proof of concept we have applied this to a set of antibacterial targets comprising 146 essential genes. Of these targets, 51 were selected and 38 delivered results that allowed us to rank them by ligandability. The data obtained against these derisked targets have enabled rapid progression into structurally enabled drug discovery projects, demonstrating the practical value of the fragment-based target screening workflow.
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Affiliation(s)
- Peter Canning
- Centre for Therapeutics Discovery, LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Kristian Birchall
- Centre for Therapeutics Discovery, LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Catherine A Kettleborough
- Centre for Therapeutics Discovery, LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Andy Merritt
- Centre for Therapeutics Discovery, LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Peter J Coombs
- Centre for Therapeutics Discovery, LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK.
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13
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Targeting the Initiator Protease of the Classical Pathway of Complement Using Fragment-Based Drug Discovery. Molecules 2020; 25:molecules25174016. [PMID: 32899120 PMCID: PMC7504721 DOI: 10.3390/molecules25174016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/23/2022] Open
Abstract
The initiating protease of the complement classical pathway, C1r, represents an upstream and pathway-specific intervention point for complement-related autoimmune and inflammatory diseases. Yet, C1r-targeted therapeutic development is currently underrepresented relative to other complement targets. In this study, we developed a fragment-based drug discovery approach using surface plasmon resonance (SPR) and molecular modeling to identify and characterize novel C1r-binding small-molecule fragments. SPR was used to screen a 2000-compound fragment library for binding to human C1r. This led to the identification of 24 compounds that bound C1r with equilibrium dissociation constants ranging between 160–1700 µM. Two fragments, termed CMP-1611 and CMP-1696, directly inhibited classical pathway-specific complement activation in a dose-dependent manner. CMP-1611 was selective for classical pathway inhibition, while CMP-1696 also blocked the lectin pathway but not the alternative pathway. Direct binding experiments mapped the CMP-1696 binding site to the serine protease domain of C1r and molecular docking and molecular dynamics studies, combined with C1r autoactivation assays, suggest that CMP-1696 binds within the C1r active site. The group of structurally distinct fragments identified here, along with the structure–activity relationship profiling of two lead fragments, form the basis for future development of novel high-affinity C1r-binding, classical pathway-specific, small-molecule complement inhibitors.
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14
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Liu X, Zhang X, Lv D, Yuan Y, Zheng G, Zhou D. Assays and technologies for developing proteolysis targeting chimera degraders. Future Med Chem 2020; 12:1155-1179. [PMID: 32431173 PMCID: PMC7333641 DOI: 10.4155/fmc-2020-0073] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023] Open
Abstract
Targeted protein degradation by small-molecule degraders represents an emerging mode of action in drug discovery. Proteolysis targeting chimeras (PROTACs) are small molecules that can recruit an E3 ligase and a protein of interest (POI) into proximity, leading to induced ubiquitination and degradation of the POI by the proteasome system. To date, the design and optimization of PROTACs remain empirical due to the complicated mechanism of induced protein degradation. Nevertheless, it is increasingly appreciated that profiling step-by-step along the ubiquitin-proteasome degradation pathway using biochemical and biophysical assays are essential in understanding the structure-activity relationship and facilitating the rational design of PROTACs. This review aims to summarize these assays and to discuss the potential of expanding the toolbox with other new techniques.
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Affiliation(s)
- Xingui Liu
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
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15
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Zhou M, Li W, Li J, Xie L, Wu R, Wang L, Fu S, Su W, Hu J, Wang J, Li P. Phase-separated condensate-aided enrichment of biomolecular interactions for high-throughput drug screening in test tubes. J Biol Chem 2020; 295:11420-11434. [PMID: 32461254 DOI: 10.1074/jbc.ra120.012981] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
Modification-dependent and -independent biomolecular interactions, including protein-protein, protein-DNA/RNA, protein-sugar, and protein-lipid interactions, play crucial roles in all cellular processes. Dysregulation of these biomolecular interactions or malfunction of the associated enzymes results in various diseases; therefore, these interactions and enzymes are attractive targets for therapies. High-throughput screening can greatly facilitate the discovery of drugs for these targets. Here, we describe a biomolecular interaction detection method, called phase-separated condensate-aided enrichment of biomolecular interactions in test tubes (CEBIT). The readout of CEBIT is the selective recruitment of biomolecules into phase-separated condensates harboring their cognate binding partners. We tailored CEBIT to detect various biomolecular interactions and activities of biomolecule-modifying enzymes. Using CEBIT-based high-throughput screening assays, we identified known inhibitors of the p53/MDM2 (MDM2) interaction and of the histone methyltransferase, suppressor of variegation 3-9 homolog 1 (SUV39H1), from a compound library. CEBIT is simple and versatile, and is likely to become a powerful tool for drug discovery and basic biomedical research.
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Affiliation(s)
- Min Zhou
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Weiping Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jian Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Leiming Xie
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Rongbo Wu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Liang Wang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shuai Fu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei Su
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jianyang Hu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing Wang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
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16
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Coyle J, Walser R. Applied Biophysical Methods in Fragment-Based Drug Discovery. SLAS DISCOVERY 2020; 25:471-490. [PMID: 32345095 DOI: 10.1177/2472555220916168] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fragment-based drug discovery (FBDD) has come of age in the last decade with the FDA approval of four fragment-derived drugs. Biophysical methods are at the heart of hit discovery and validation in FBDD campaigns. The three most commonly used methods, thermal shift, surface plasmon resonance, and nuclear magnetic resonance, can be daunting for the novice user. We aim here to provide the nonexpert user of these methods with a summary of problems and challenges that might be faced, but also highlight the potential gains that each method can contribute to an FBDD project. While our view on FBDD is slightly biased toward enabling structure-guided drug discovery, most of the points we address in this review are also valid for non-structure-focused FBDD.
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Affiliation(s)
- Joe Coyle
- Astex Pharmaceuticals, Cambridge, UK
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17
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Fragments: where are we now? Biochem Soc Trans 2020; 48:271-280. [PMID: 31985743 DOI: 10.1042/bst20190694] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/30/2022]
Abstract
Fragment-based drug discovery (FBDD) has become a mainstream technology for the identification of chemical hit matter in drug discovery programs. To date, the food and drug administration has approved four drugs, and over forty compounds are in clinical studies that can trace their origins to a fragment-based screen. The challenges associated with implementing an FBDD approach are many and diverse, ranging from the library design to developing methods for identifying weak affinity compounds. In this article, we give an overview of current progress in fragment library design, fragment to lead optimisation and on the advancement in techniques used for screening. Finally, we will comment on the future opportunities and challenges in this field.
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18
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Tsopelas F, Tsantili-Kakoulidou A. Advances with weak affinity chromatography for fragment screening. Expert Opin Drug Discov 2019; 14:1125-1135. [DOI: 10.1080/17460441.2019.1648425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fotios Tsopelas
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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19
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Lu Y, Qin S, Zhang B, Dai A, Cai X, Ma M, Gao ZG, Yang D, Stevens RC, Jacobson KA, Wang MW, Shui W. Accelerating the Throughput of Affinity Mass Spectrometry-Based Ligand Screening toward a G Protein-Coupled Receptor. Anal Chem 2019; 91:8162-8169. [PMID: 31094506 DOI: 10.1021/acs.analchem.9b00477] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Affinity mass spectrometry (MS) enables rapid screening of compound mixtures for ligands bound to a specific protein target, yet its current throughput is limited to individually assay pools of 400-2000 compounds. Typical affinity MS screens implemented in pharmaceutical industry laboratories identify putative ligands based on qualitative analysis of compound binding to the target whereas no quantitative information is acquired to discriminate high- and low-affinity ligands in the screening phase. Furthermore, these screens require purification of a stabilized form of the protein target, which poses a great challenge for membrane receptor targets. Here, we describe a new, potentially general affinity MS strategy that allows screening of 20,000 compounds in one pool for highly efficient ligand discovery toward a G protein-coupled receptor (GPCR) target. Quantitative measurement of compound binding to the receptor enables high-affinity ligand selection using both the purified receptor and receptor-embedded cell membranes. This high-throughput, label-free and quantitative affinity MS screen resulted in discovery of three new antagonists of the A2A adenosine receptor.
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Affiliation(s)
- Yan Lu
- iHuman Institute , ShanghaiTech University , 201210 Shanghai , China.,School of Life Science and Technology , ShanghaiTech University , 201210 Shanghai , China.,University of Chinese Academy of Sciences , 100049 Beijing , China
| | - Shanshan Qin
- iHuman Institute , ShanghaiTech University , 201210 Shanghai , China
| | - Bingjie Zhang
- iHuman Institute , ShanghaiTech University , 201210 Shanghai , China
| | - Antao Dai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 Shanghai , China
| | - Xiaoqing Cai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 Shanghai , China
| | - Mengna Ma
- iHuman Institute , ShanghaiTech University , 201210 Shanghai , China.,School of Life Science and Technology , ShanghaiTech University , 201210 Shanghai , China.,University of Chinese Academy of Sciences , 100049 Beijing , China
| | - Zhan-Guo Gao
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) , National Institutes of Health , Bethesda , Maryland 20892 United States
| | - Dehua Yang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 Shanghai , China
| | - Raymond C Stevens
- iHuman Institute , ShanghaiTech University , 201210 Shanghai , China.,School of Life Science and Technology , ShanghaiTech University , 201210 Shanghai , China
| | - Kenneth A Jacobson
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) , National Institutes of Health , Bethesda , Maryland 20892 United States
| | - Ming-Wei Wang
- University of Chinese Academy of Sciences , 100049 Beijing , China.,The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 Shanghai , China.,School of Pharmacy , Fudan University , 201203 Shanghai , China
| | - Wenqing Shui
- iHuman Institute , ShanghaiTech University , 201210 Shanghai , China.,School of Life Science and Technology , ShanghaiTech University , 201210 Shanghai , China
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20
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Ralph EC, Hall J. An SPR-based analysis of cGAS substrate K D and steady-state K M values. Methods Enzymol 2019; 625:61-76. [PMID: 31455537 DOI: 10.1016/bs.mie.2019.04.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Surface plasmon resonance (SPR) is a standard method for evaluating direct protein-small molecule binding. While studying the catalytic mechanism of cyclic GMP-AMP synthase (cGAS), we developed an SPR-based method to measure steady-state KM values that complements traditional SPR affinity measurements. The method relies on refractive changes to detect protein interaction with substrates and products, and takes advantage of stimulator of type 1 interferon genes (STING) binding to the cGAS product, 2',3'-cGAMP. The specific method described here uses co-immobilization of cGAS and double-stranded DNA through a biotin tag; it should be generally applicable to other proteins and protein complexes.
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Affiliation(s)
- Erik C Ralph
- Worldwide Medicinal Chemistry, Pfizer, Groton, CT, United States.
| | - Justin Hall
- Worldwide Medicinal Chemistry, Pfizer, Groton, CT, United States
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21
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Small-molecule inhibitors of lysine methyltransferases SMYD2 and SMYD3: current trends. Future Med Chem 2019; 11:901-921. [DOI: 10.4155/fmc-2018-0380] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Lysine methyltransferases SMYD2 and SMYD3 are involved in the epigenetic regulation of cell differentiation and functioning. Overexpression and deregulation of these enzymes have been correlated to the insurgence and progression of different tumors, making them promising molecular targets in cancer therapy even if their role in tumors is not yet fully understood. In this light, selective small-molecule inhibitors are required to fully understand and validate these enzymes, as this is a prerequisite for the development of successful targeted therapeutic strategies. The present review gives a systematic overview of the chemical probes developed to selectively target SMYD2 and SMYD3, with particular focus on the structural features important for high inhibitory activity, on the mode of inhibition and on the efficacy in cell-based and in in vivo models.
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22
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Robson-Tull J. Biophysical screening in fragment-based drug design: a brief overview. ACTA ACUST UNITED AC 2019. [DOI: 10.1093/biohorizons/hzy015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Jacob Robson-Tull
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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23
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Zhang W, Chen ST, He QY, Huang LQ, Li X, Lai XP, Zhan SF, Huang HT, Liu XH, Wu J, Li G. Asprellcosides B of Ilex asprella Inhibits Influenza A Virus Infection by Blocking the Hemagglutinin- Mediated Membrane Fusion. Front Microbiol 2019; 9:3325. [PMID: 30728818 PMCID: PMC6351491 DOI: 10.3389/fmicb.2018.03325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 12/21/2018] [Indexed: 01/26/2023] Open
Abstract
Ilex asprella is routinely used in China as a traditional medicinal herb to treat influenza (Flu). However, its specific antiviral activity and underlying molecular mechanism have not yet been determined. In this study, we sought to determine the antiviral activity and mechanism of Asprellcosides B, an active component extracted from Ilex asprella, and used against the influenza A virus cell culture. We also performed a computer-assisted structural modeling analysis and carried out surface plasmon resonance (SPR) experiments in the hope of determining the viral target of Asprellcosides B. Results from our studies show that Asprellcosides B reduced virus replication by up to 63% with an IC50 of about 9 μM. It also decreased the low pH-induced and virus-mediated hemolysis by 71% in vitro. Molecular docking simulation analysis suggested a possible binding of Asprellcosides B to the hemagglutinin (HA), which was confirmed by a surface plasmon resonance (SPR) assay. Altogether, our findings demonstrate that Asprellcosides B inhibits the influenza A virus, through a specific binding to the HA, resulting in the blockade of the HA-mediated membrane fusion.
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Affiliation(s)
- Wen Zhang
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Si-Tai Chen
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiu-Yan He
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Li-Quan Huang
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiong Li
- Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Xiao-Ping Lai
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Dongguan Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Traditional Chinese Medicine, Dongguan, China
| | - Shao-Feng Zhan
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hui-Ting Huang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiao-Hong Liu
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianguo Wu
- Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China.,Guangdong Longfan Biological Science and Technology Company, Ltd., Foshan, China
| | - Geng Li
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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24
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Assessing molecular interactions with biophysical methods using the validation cross. Biochem Soc Trans 2018; 47:63-76. [DOI: 10.1042/bst20180271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 11/17/2022]
Abstract
Abstract
There are numerous methods for studying molecular interactions. However, each method gives rise to false negative- or false positive binding results, stemming from artifacts of the scientific equipment or from shortcomings of the experimental format. To validate an initial positive binding result, additional methods need to be applied to cover the shortcomings of the primary experiment. The aim of such a validation procedure is to exclude as many artifacts as possible to confirm that there is a true molecular interaction that meets the standards for publishing or is worth investing considerable resources for follow-up activities in a drug discovery project. To simplify this validation process, a graphical scheme — the validation cross — can be used. This simple graphic is a powerful tool for identifying blind spots of a binding hypothesis, for selecting the most informative combination of methods to reveal artifacts and, in general, for understanding more thoroughly the nature of a validation process. The concept of the validation cross was originally introduced for the validation of protein–ligand interactions by NMR in drug discovery. Here, an attempt is made to expand the concept to further biophysical methods and to generalize it for binary molecular interactions.
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25
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Abstract
Experimental screening for protein-ligand interactions is a central task in drug discovery. Nuclear magnetic resonance (NMR) spectroscopy enables the determination of binding affinities, as well as the measurement of structural and dynamic parameters governing the interaction. With traditional liquid-state NMR relying on a nuclear spin polarization on the order of 10-5, hyperpolarization methods such as dissolution dynamic nuclear polarization (D-DNP) can increase signals by several orders of magnitude. The resulting increase in sensitivity has the potential to reduce requirements for the concentration of protein and ligands, improve the accuracy of the detection of interaction by allowing the use of near-stoichiometric conditions, and increase throughput. This chapter introduces a selection of basic techniques for the application of D-DNP to screening. Procedures for hyperpolarization are briefly reviewed, followed by the description of NMR methods for detection of binding through changes in chemical shift and relaxation parameters. Experiments employing competitive binding with a known ligand are shown, which can be used to determine binding affinity or yield structural information on the pharmacophore. The specific challenges of working with nonrenewable hyperpolarization are reviewed, and solutions including the use of multiplexed NMR detection are described. Altogether, the methods summarized in this chapter are intended to allow for the efficient detection of binding affinity, structure, and dynamics facilitated through substantial signal enhancements provided by hyperpolarization.
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Affiliation(s)
- Yaewon Kim
- Chemistry Department, Texas A&M University, College Station, TX, United States
| | - Christian Hilty
- Chemistry Department, Texas A&M University, College Station, TX, United States.
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26
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Dobrev VS, Fred LM, Gerhart KP, Metallo SJ. Characterization of the Binding of Small Molecules to Intrinsically Disordered Proteins. Methods Enzymol 2018; 611:677-702. [PMID: 30471704 DOI: 10.1016/bs.mie.2018.09.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered proteins (IDPs) comprise a large fraction of eukaryotic proteomes. IDPs are prevalent in cellular regulation, signaling networks, and disease pathways. The abundance and activity of IDPs is tightly controlled at multiple levels, and their dysregulation is associated with disease. Because of the importance of IDPs in both normal and disease states of the cell, IDPs are attractive targets for modulation by small molecules both to understand their biology and to provide potential drug leads. Multiple screens have successfully identified small molecules that bind to IDPs. Here, we describe how surface plasmon resonance, NMR, and fluorescence methods can be used to characterize the direct binding affinity between small molecules and IDPs. We describe how these techniques can contribute to identifying previously unknown small-molecule binding sites on IDPs.
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Affiliation(s)
- Veselin S Dobrev
- Department of Chemistry, Georgetown University, Washington, DC, United States
| | - Lisette M Fred
- Department of Chemistry, Georgetown University, Washington, DC, United States
| | - Kaitlyn P Gerhart
- Department of Chemistry, Georgetown University, Washington, DC, United States
| | - Steven J Metallo
- Department of Chemistry, Georgetown University, Washington, DC, United States; Institute for Soft Matter Synthesis and Metrology, Georgetown University, Washington, DC, United States.
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27
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Nagatoishi S, Caaveiro JMM, Tsumoto K. Biophysical Analysis of the Protein-Small Molecule Interactions to Develop Small Molecule Drug Discovery. YAKUGAKU ZASSHI 2018; 138:1033-1041. [DOI: 10.1248/yakushi.17-00211-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | | | - Kouhei Tsumoto
- School of Engineering, The University of Tokyo
- The Institute of Medical Science, The University of Tokyo
- Drug Discovery Initiative, The University of Tokyo
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28
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Lamoree B, Hubbard RE. Using Fragment-Based Approaches to Discover New Antibiotics. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2018; 23:495-510. [PMID: 29923463 PMCID: PMC6024353 DOI: 10.1177/2472555218773034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/16/2018] [Accepted: 04/05/2018] [Indexed: 12/29/2022]
Abstract
Fragment-based lead discovery has emerged over the past two decades as a successful approach to generate novel lead candidates in drug discovery programs. The two main advantages over conventional high-throughput screening (HTS) are more efficient sampling of chemical space and tighter control over the physicochemical properties of the lead candidates. Antibiotics are a class of drugs with particularly strict property requirements for efficacy and safety. The development of novel antibiotics has slowed down so much that resistance has now evolved against every available antibiotic drug. Here we give an overview of fragment-based approaches in screening and lead discovery projects for new antibiotics. We discuss several successful hit-to-lead development examples. Finally, we highlight the current challenges and opportunities for fragment-based lead discovery toward new antibiotics.
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Affiliation(s)
- Bas Lamoree
- YSBL, Department of Chemistry, University of York, Heslington, York, UK
| | - Roderick E. Hubbard
- YSBL, Department of Chemistry, University of York, Heslington, York, UK
- Vernalis Research, Granta Park, Abington, Cambridge, UK
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29
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Quinn JG, Pitts KE, Steffek M, Mulvihill MM. Determination of Affinity and Residence Time of Potent Drug-Target Complexes by Label-free Biosensing. J Med Chem 2018; 61:5154-5161. [PMID: 29772180 DOI: 10.1021/acs.jmedchem.7b01829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prolonged drug-target occupancy has become increasingly important in lead optimization, and biophysical assays that measure residence time are in high demand. Here we report a practical label-free assay methodology that provides kinetic and affinity measurements suitable for most target classes without long preincubations and over comparatively short sample contact times. The method, referred to as a "chaser" assay, has been applied to three sets of unrelated kinase/inhibitor panels in order to measure the residence times, where correlation with observed efficacy was suspected. A lower throughput chaser assay measured a residence time of 3.6 days ±3.4% (95% CI) and provided single digit pM sensitivity. A higher throughput chaser methodology enabled a maximum capacity of 108 compounds in duplicate/day with an upper residence time limit of 9 h given an assay dissociation time of 34 min.
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Affiliation(s)
- John G Quinn
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Keith E Pitts
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Micah Steffek
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Melinda M Mulvihill
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
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30
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Proudfoot A, Bussiere DE, Lingel A. High-Confidence Protein–Ligand Complex Modeling by NMR-Guided Docking Enables Early Hit Optimization. J Am Chem Soc 2017; 139:17824-17833. [DOI: 10.1021/jacs.7b07171] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Andrew Proudfoot
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Dirksen E. Bussiere
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Andreas Lingel
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
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31
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Current perspectives in fragment-based lead discovery (FBLD). Essays Biochem 2017; 61:453-464. [PMID: 29118093 PMCID: PMC5869234 DOI: 10.1042/ebc20170028] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/23/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023]
Abstract
It is over 20 years since the first fragment-based discovery projects were disclosed. The methods are now mature for most ‘conventional’ targets in drug discovery such as enzymes (kinases and proteases) but there has also been growing success on more challenging targets, such as disruption of protein–protein interactions. The main application is to identify tractable chemical startpoints that non-covalently modulate the activity of a biological molecule. In this essay, we overview current practice in the methods and discuss how they have had an impact in lead discovery – generating a large number of fragment-derived compounds that are in clinical trials and two medicines treating patients. In addition, we discuss some of the more recent applications of the methods in chemical biology – providing chemical tools to investigate biological molecules, mechanisms and systems.
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32
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Kumar PKR. Systematic screening of viral entry inhibitors using surface plasmon resonance. Rev Med Virol 2017; 27. [PMID: 29047180 DOI: 10.1002/rmv.1952] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 08/02/2017] [Accepted: 09/07/2017] [Indexed: 12/12/2022]
Abstract
Viral binding and entry into host cells for various viruses have been studied extensively, yielding a detailed understanding of the overall viral entry process. As cell entry is an essential and requisite process by which a virus initiates infection, it is an attractive target for therapeutic intervention. The advantages of targeting viral entry are an extracellular target site, relatively easy access for biological interventions, and lower toxicity. Several cell-based strategies and biophysical techniques have been used to screen compounds that block viral entry. These studies led to the discovery of inhibitors against HIV, HCV, influenza, Ebola, and RSV. In recent years, several compounds screened by fragment-based drug discovery have been approved as drugs or are in the final stages of clinical trials. Among fragment screening technologies, surface plasmon resonance has been widely used because it provides accurate information on binding kinetics, allows real-time monitoring of ligand-drug interactions, requires very small sample amounts to perform analyses, and requires no modifications to or labeling of ligands. This review focuses on surface plasmon resonance-based schemes for screening viral entry inhibitors.
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Affiliation(s)
- Penmetcha K R Kumar
- National Institute of Advanced Industrial Science and Technology, Tsukuba City, Ibaraki, Japan
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33
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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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34
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Lusvarghi S, Ghirlando R, Davison JR, Bewley CA. Chemical and Biophysical Approaches for Complete Characterization of Lectin-Carbohydrate Interactions. Methods Enzymol 2017; 598:3-35. [PMID: 29306440 PMCID: PMC6141027 DOI: 10.1016/bs.mie.2017.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lectins are carbohydrate-binding proteins unrelated to antibodies or enzymes. While carbohydrates are present on all cells and pathogens, lectins are also ubiquitous in nature and their interactions with glycans mediate countless biological and physical interactions. Due to the multivalency found in both lectins and their glycan-binding partners, complete characterization of these interactions can be complex and typically requires the use of multiple complimentary techniques. In this chapter, we provide a general strategy and protocols for chemical and biophysical approaches that can be used to characterize carbohydrate-mediated interactions in the context of individual oligosaccharides, as part of a glycoprotein, and ending with visualization of interactions with whole virions.
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Affiliation(s)
- Sabrina Lusvarghi
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jack R Davison
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States.
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Abstract
Small-molecule drug discovery has traditionally focused on occupancy of a binding site that directly affects protein function, and this approach typically precludes targeting proteins that lack such amenable sites. Furthermore, high systemic drug exposures may be needed to maintain sufficient target inhibition in vivo, increasing the risk of undesirable off-target effects. Induced protein degradation is an alternative approach that is event-driven: upon drug binding, the target protein is tagged for elimination. Emerging technologies based on proteolysis-targeting chimaeras (PROTACs) that exploit cellular quality control machinery to selectively degrade target proteins are attracting considerable attention in the pharmaceutical industry owing to the advantages they could offer over traditional small-molecule strategies. These advantages include the potential to reduce systemic drug exposure, the ability to counteract increased target protein expression that often accompanies inhibition of protein function and the potential ability to target proteins that are not currently therapeutically tractable, such as transcription factors, scaffolding and regulatory proteins.
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Affiliation(s)
| | - Craig M. Crews
- Departments of Molecular, Cellular & Developmental Biology; Chemistry; Pharmacology, Yale University, New Haven, CT 06511, USA
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37
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Jones AM, Westwood IM, Osborne JD, Matthews TP, Cheeseman MD, Rowlands MG, Jeganathan F, Burke R, Lee D, Kadi N, Liu M, Richards M, McAndrew C, Yahya N, Dobson SE, Jones K, Workman P, Collins I, van Montfort RLM. A fragment-based approach applied to a highly flexible target: Insights and challenges towards the inhibition of HSP70 isoforms. Sci Rep 2016; 6:34701. [PMID: 27708405 PMCID: PMC5052559 DOI: 10.1038/srep34701] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/15/2016] [Indexed: 12/13/2022] Open
Abstract
The heat shock protein 70s (HSP70s) are molecular chaperones implicated in many cancers and of significant interest as targets for novel cancer therapies. Several HSP70 inhibitors have been reported, but because the majority have poor physicochemical properties and for many the exact mode of action is poorly understood, more detailed mechanistic and structural insight into ligand-binding to HSP70s is urgently needed. Here we describe the first comprehensive fragment-based inhibitor exploration of an HSP70 enzyme, which yielded an amino-quinazoline fragment that was elaborated to a novel ATP binding site ligand with different physicochemical properties to known adenosine-based HSP70 inhibitors. Crystal structures of amino-quinazoline ligands bound to the different conformational states of the HSP70 nucleotide binding domain highlighted the challenges of a fragment-based approach when applied to this particular flexible enzyme class with an ATP-binding site that changes shape and size during its catalytic cycle. In these studies we showed that Ser275 is a key residue in the selective binding of ATP. Additionally, the structural data revealed a potential functional role for the ATP ribose moiety in priming the protein for the formation of the ATP-bound pre-hydrolysis complex by influencing the conformation of one of the phosphate binding loops.
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Affiliation(s)
- Alan M Jones
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Isaac M Westwood
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom.,Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - James D Osborne
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Thomas P Matthews
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Matthew D Cheeseman
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Martin G Rowlands
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Fiona Jeganathan
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Diane Lee
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Nadia Kadi
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Manjuan Liu
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Meirion Richards
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Craig McAndrew
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Norhakim Yahya
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Sarah E Dobson
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom.,Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Keith Jones
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Rob L M van Montfort
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom.,Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom
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38
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Strelow JM. A Perspective on the Kinetics of Covalent and Irreversible Inhibition. SLAS DISCOVERY 2016; 22:3-20. [PMID: 27703080 DOI: 10.1177/1087057116671509] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The clinical and commercial success of covalent drugs has prompted a renewed and more deliberate pursuit of covalent and irreversible mechanisms within drug discovery. A covalent mechanism can produce potent inhibition in a biochemical, cellular, or in vivo setting. In many cases, teams choose to focus on the consequences of the covalent event, defined by an IC50 value. In a biochemical assay, the IC50 may simply reflect the target protein concentration in the assay. What has received less attention is the importance of the rate of covalent modification, defined by kinact/KI. The kinact/KI is a rate constant describing the efficiency of covalent bond formation resulting from the potency (KI) of the first reversible binding event and the maximum potential rate (kinact) of inactivation. In this perspective, it is proposed that the kinact/KI should be employed as a critical parameter to identify covalent inhibitors, interpret structure-activity relationships (SARs), translate activity from biochemical assays to the cell, and more accurately define selectivity. It is also proposed that a physiologically relevant kinact/KI and an (unbound) AUC generated from a pharmacokinetic profile reflecting direct exposure of the inhibitor to the target protein are two critical determinants of in vivo covalent occupancy. A simple equation is presented to define this relationship and improve the interpretation of covalent and irreversible kinetics.
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Affiliation(s)
- John M Strelow
- 1 Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
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39
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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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40
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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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41
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Abstract
After 20 years of sometimes quiet growth, fragment-based drug discovery (FBDD) has become mainstream. More than 30 drug candidates derived from fragments have entered the clinic, with two approved and several more in advanced trials. FBDD has been widely applied in both academia and industry, as evidenced by the large number of papers from universities, non-profit research institutions, biotechnology companies and pharmaceutical companies. Moreover, FBDD draws on a diverse range of disciplines, from biochemistry and biophysics to computational and medicinal chemistry. As the promise of FBDD strategies becomes increasingly realized, now is an opportune time to draw lessons and point the way to the future. This Review briefly discusses how to design fragment libraries, how to select screening techniques and how to make the most of information gleaned from them. It also shows how concepts from FBDD have permeated and enhanced drug discovery efforts.
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42
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Ferruz N, De Fabritiis G. Binding Kinetics in Drug Discovery. Mol Inform 2016; 35:216-26. [PMID: 27492236 DOI: 10.1002/minf.201501018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/20/2016] [Indexed: 12/19/2022]
Abstract
Over the last years, researchers have increasingly become interested in measuring and understanding drugs' binding kinetics, namely the time in which drug and its target associate and dissociate. Historically, drug discovery programs focused on the optimization of target affinity as a proxy of in-vivo efficacy. However, often the efficacy of a ligand is not appropriately described by the in-vitro measured drug-receptor affinity, but rather depends on the lifetime of the in-vivo drug-receptor interaction. In this review we review recent works that highlight the importance of binding kinetics, molecular determinants for rational optimization and the recent emergence of computational methods as powerful tools in measuring and understanding binding kinetics.
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Affiliation(s)
- Noelia Ferruz
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra,Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain.,Acellera, Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain
| | - Gianni De Fabritiis
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra,Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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43
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Bauer U, Breeze AL. “Ligandability” of Drug Targets: Assessment of Chemical Tractability via Experimental and
In Silico
Approaches. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/9783527677047.ch03] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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44
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Christopeit T, Leiros HKS. Fragment-based discovery of inhibitor scaffolds targeting the metallo-β-lactamases NDM-1 and VIM-2. Bioorg Med Chem Lett 2016; 26:1973-7. [DOI: 10.1016/j.bmcl.2016.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/11/2022]
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45
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Fragment Screening of Human Aquaporin 1. Int J Mol Sci 2016; 17:449. [PMID: 27023529 PMCID: PMC4848905 DOI: 10.3390/ijms17040449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 11/17/2022] Open
Abstract
Aquaporins (AQPs) are membrane proteins that enable water transport across cellular plasma membranes in response to osmotic gradients. Phenotypic analyses have revealed important physiological roles for AQPs, and the potential for AQP water channel modulators in various disease states has been proposed. For example, AQP1 is overexpressed in tumor microvessels, and this correlates with higher metastatic potential and aggressiveness of the malignancy. Chemical modulators would help in identifying the precise contribution of water channel activity in these disease states. These inhibitors would also be important therapeutically, e.g., in anti-cancer treatment. This perceived importance contrasts with the lack of success of high-throughput screens (HTS) to identify effective and specific inhibitors of aquaporins. In this paper, we have screened a library of 1500 "fragments", i.e., smaller than molecules used in HTS, against human aquaporin (hAQP1) using a thermal shift assay and surface plasmon resonance. Although these fragments may not inhibit their protein target, they bound to and stabilized hAQP1 (sub mM binding affinities (KD), with an temperature of aggregation shift ΔTagg of +4 to +50 °C) in a concentration-dependent fashion. Chemically expanded versions of these fragments should follow the determination of their binding site on the aquaporin surface.
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Abstract
INTRODUCTION Fragment-based approaches have played an increasing role alongside high-throughput screening in drug discovery for 15 years. The label-free biosensor technology based on surface plasmon resonance (SPR) is now sensitive and informative enough to serve during primary screens and validation steps. AREAS COVERED In this review, the authors discuss the role of SPR in fragment screening. After a brief description of the underlying principles of the technique and main device developments, they evaluate the advantages and adaptations of SPR for fragment-based drug discovery. SPR can also be applied to challenging targets such as membrane receptors and enzymes. EXPERT OPINION The high-level of immobilization of the protein target and its stability are key points for a relevant screening that can be optimized using oriented immobilized proteins and regenerable sensors. Furthermore, to decrease the rate of false negatives, a selectivity test may be performed in parallel on the main target bearing the binding site mutated or blocked with a low-off-rate ligand. Fragment-based drug design, integrated in a rational workflow led by SPR, will thus have a predominant role for the next wave of drug discovery which could be greatly enhanced by new improvements in SPR devices.
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Affiliation(s)
- Alain Chavanieu
- a Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 , Université de Montpellier, CNRS, ENSCM , Montpellier Cedex 5, France
| | - Martine Pugnière
- b IRCM , Institut de Recherche en Cancérologie de Montpellier , Montpellier , France.,c INSERM, U1194 , Université Montpellier , Montpellier , France.,d ICM , Institut Régional du Cancer , Montpellier , France
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Woods LA, Dolezal O, Ren B, Ryan JH, Peat TS, Poulsen SA. Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination. J Med Chem 2016; 59:2192-204. [PMID: 26882437 DOI: 10.1021/acs.jmedchem.5b01940] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fragment-based drug discovery (FBDD) is contingent on the development of analytical methods to identify weak protein-fragment noncovalent interactions. Herein we have combined an underutilized fragment screening method, native state mass spectrometry, together with two proven and popular fragment screening methods, surface plasmon resonance and X-ray crystallography, in a fragment screening campaign against human carbonic anhydrase II (CA II). In an initial fragment screen against a 720-member fragment library (the "CSIRO Fragment Library") seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. A further 70 compounds that comprised the initial hit chemotypes were subsequently sourced from the full CSIRO compound collection and screened. The fragment results were extremely well correlated across the three methods. Our findings demonstrate that there is a tremendous opportunity to apply native state mass spectrometry as a complementary fragment screening method to accelerate drug discovery.
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Affiliation(s)
- Lucy A Woods
- Griffith University , Eskitis Institute for Drug Discovery, Brisbane, Queensland Australia
| | - Olan Dolezal
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Bin Ren
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - John H Ryan
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Thomas S Peat
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Sally-Ann Poulsen
- Griffith University , Eskitis Institute for Drug Discovery, Brisbane, Queensland Australia
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48
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Bains W. Low potency toxins reveal dense interaction networks in metabolism. BMC SYSTEMS BIOLOGY 2016; 10:19. [PMID: 26897366 PMCID: PMC4761184 DOI: 10.1186/s12918-016-0262-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 01/29/2016] [Indexed: 11/13/2022]
Abstract
BACKGROUND The chemicals of metabolism are constructed of a small set of atoms and bonds. This may be because chemical structures outside the chemical space in which life operates are incompatible with biochemistry, or because mechanisms to make or utilize such excluded structures has not evolved. In this paper I address the extent to which biochemistry is restricted to a small fraction of the chemical space of possible chemicals, a restricted subset that I call Biochemical Space. I explore evidence that this restriction is at least in part due to selection again specific structures, and suggest a mechanism by which this occurs. RESULTS Chemicals that contain structures that our outside Biochemical Space (UnBiological groups) are more likely to be toxic to a wide range of organisms, even though they have no specifically toxic groups and no obvious mechanism of toxicity. This correlation of UnBiological with toxicity is stronger for low potency (millimolar) toxins. I relate this to the observation that most chemicals interact with many biological structures at low millimolar toxicity. I hypothesise that life has to select its components not only to have a specific set of functions but also to avoid interactions with all the other components of life that might degrade their function. CONCLUSIONS The chemistry of life has to form a dense, self-consistent network of chemical structures, and cannot easily be arbitrarily extended. The toxicity of arbitrary chemicals is a reflection of the disruption to that network occasioned by trying to insert a chemical into it without also selecting all the other components to tolerate that chemical. This suggests new ways to test for the toxicity of chemicals, and that engineering organisms to make high concentrations of materials such as chemical precursors or fuels may require more substantial engineering than just of the synthetic pathways involved.
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Affiliation(s)
- William Bains
- Earth, Atmospheric and Planetary Sciences Department, MIT, 77 Mass Avenue, Cambridge, MA, 02139, USA.
- Rufus Scientific Ltd., 37 The Moor, Melbourn, Royston, Herts, SG8 6ED, UK.
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49
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Hanley RP, Horvath S, An J, Hof F, Wulff JE. Salicylates are interference compounds in TR-FRET assays. Bioorg Med Chem Lett 2016; 26:973-977. [DOI: 10.1016/j.bmcl.2015.12.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/12/2015] [Accepted: 12/15/2015] [Indexed: 12/20/2022]
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50
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Hubbard RE. The Role of Fragment-based Discovery in Lead Finding. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch01] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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