1
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Stegmann DP, Steuber J, Fritz G, Wojdyla JA, Sharpe ME. Fast fragment and compound screening pipeline at the Swiss Light Source. Methods Enzymol 2023; 690:235-284. [PMID: 37858531 DOI: 10.1016/bs.mie.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Crystallography-based fragment screening is a highly effective technique employed in structure-based drug discovery to expand the range of lead development opportunities. It allows screening and sorting of weakly binding, low molecular mass fragments, which can be developed into larger high-affinity lead compounds. Technical improvements at synchrotron beamlines, design of innovative libraries mapping chemical space efficiently, effective soaking methods and enhanced data analysis have enabled the implementation of high-throughput fragment screening pipelines at multiple synchrotron facilities. This widened access to CBFS beyond the pharma industry has allowed academic users to rapidly screen large quantities of fragment-soaked protein crystals. The positive outcome of a CBFS campaign is a set of structures that present the three-dimensional arrangement of fragment-protein complexes in detail, thereby providing information on the location and the mode of interaction of bound fragments. Through this review, we provide users with a comprehensive guide that sets clear expectations before embarking on a crystallography-based fragment screening campaign. We present a list of essential pre-requirements that must be assessed, including the suitability of your current crystal system for a fragment screening campaign. Furthermore, we extensively discuss the available methodological options, addressing their limitations and providing strategies to overcome them. Additionally, we provide a brief perspective on how to proceed once hits are obtained. Notably, we emphasize the solutions we have implemented for instrumentation and software development within our Fast Fragment and Compound Screening pipeline. We also highlight third-party software options that can be utilized for rapid refinement and hit assessment.
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Affiliation(s)
| | - Julia Steuber
- Institute of Biology, Department of Cellular Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Günter Fritz
- Institute of Biology, Department of Cellular Microbiology, University of Hohenheim, Stuttgart, Germany.
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2
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Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:life12091438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying “magic bullets” amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand–target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural–energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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3
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Shi B, Zhou Y, Li X. Recent advances in DNA-encoded dynamic libraries. RSC Chem Biol 2022; 3:407-419. [PMID: 35441147 PMCID: PMC8985084 DOI: 10.1039/d2cb00007e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/16/2022] [Indexed: 11/21/2022] Open
Abstract
The DNA-encoded chemical library (DEL) has emerged as a powerful technology platform in drug discovery and is also gaining momentum in academic research. The rapid development of DNA-/DEL-compatible chemistries has greatly expanded the chemical space accessible to DELs. DEL technology has been widely adopted in the pharmaceutical industry and a number of clinical drug candidates have been identified from DEL selections. Recent innovations have combined DELs with other legacy and emerging techniques. Among them, the DNA-encoded dynamic library (DEDL) introduces DNA encoding into the classic dynamic combinatorial libraries (DCLs) and also integrates the principle of fragment-based drug discovery (FBDD), making DEDL a novel approach with distinct features from static DELs. In this Review, we provide a summary of the recently developed DEDL methods and their applications. Future developments in DEDLs are expected to extend the application scope of DELs to complex biological systems with unique ligand-discovery capabilities.
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Affiliation(s)
- Bingbing Shi
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Jining Medical University Jining Shandong 272067 P. R. China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission Units 1503-1511 15/F. Building 17W Hong Kong SAR China
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4
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Revillo Imbernon J, Jacquemard C, Bret G, Marcou G, Kellenberger E. Comprehensive analysis of commercial fragment libraries. RSC Med Chem 2022; 13:300-310. [PMID: 35434627 PMCID: PMC8942207 DOI: 10.1039/d1md00363a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
Screening of fragment libraries is a valuable approach to the drug discovery process. The quality of the library is one of the keys to success, and more particularly the design or choice of a library has to meet the specificities of the research program. In this study, we made an inventory of the commercial fragment libraries and we established a methodology which allows any library to be positioned in relation to the complete offer currently on the market, by addressing the following questions: does this chemical library look like another chemical library? What is the coverage of the current chemical space by this chemical library? What are the characteristic structural features of the fragments of this chemical library? We based our analysis on 2D and 3D chemical descriptors, framework class generation and the generative topographic map. We identified 59 270 scaffolds, which can be searched in a dedicated web site (https://gtmfrag.drugdesign.unistra.fr) and developed a model which accounts for fragment diversity while being easy to interpret (download at 10.5281/zenodo.5534434).
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Affiliation(s)
- Julia Revillo Imbernon
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Guillaume Bret
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Gilles Marcou
- Laboratory of Chemoinformatics, UMR7177 CNRS Université de StrasbourgStrasbourgFrance
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
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5
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Rahal A, Sharma DK, Kumar A, Sharma N, Dayal D. In silico to In vivo development of a polyherbal against Haemonchus contortus. Heliyon 2022; 8:e08789. [PMID: 35106389 PMCID: PMC8789534 DOI: 10.1016/j.heliyon.2022.e08789] [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: 07/27/2021] [Revised: 08/09/2021] [Accepted: 01/13/2022] [Indexed: 10/25/2022] Open
Abstract
Haemonchus contortus is a major constraint in the development of small ruminant subsector due to significant production losses incurred by it. The present study explores the antiparasitic potential of three anthelmintic plants (Butea monosperma, Vitex negundo and Catharanthus roseus (L.) G.Don) against H. contortus taking albendazole as the standard. In silico molecular docking and pharmacokinetic prediction studies were conducted with known bioactive molecules of these plants (palasonin, vinblastine, vincristine, betulinic acid and ursolic acid) against Glutamate Dehydrogenase (GDH) and tubulin molecules of the parasite. Methanolic extracts of these herbs were fractionated (hexane, ethyl acetate, chloroform and methanol) and used in in vitro larvicidal studies. Based on the in vitro data, two herbal prototypes were developed and clinically tested. All the 5 ligand molecules showed better binding affnity for GDH and tubulin protein as compared with albendazole and shared similar binding site in the core of the GDH hexamer with slight variations. Albendazole approximately stacked against GLY190A residue, showing hydrophobic interactions with PRO157A and a Pi-cation electrostatic interaction with ARG390 along with four hydrogen bonds. Vincristine formed 2 pi-anionic electrostatic bonds with ASP158 of B and C subunits alongwith hydrogen bonding and hydrophobic interaction and an additional pi-anion electrostatic interaction at ASP158A for vinblastine. Albendazole bound to α-tubulin next to colchicine site whereas vinblastine is bound at the nearby laulimalide/peloruside site of the dimer. Betulinic acid showed lateral interaction between the H2-H3 loop of one alpha subunit and H10 of the adjacent alpha subunit of two tubulin dimers. Ursolic acid and palasonin bound at the intradimer N site of microtubulin involving the H1-H7 and H1-H2 zone, respectively. The in vitro studies demonstrated good dose dependent anthelmintic potential. Both the prototypes were quite efficacious in clearing the infection, keeping it to a minimal for more than 5 months, probably, through direct anthelmintic effect through GDH, tubulin depolymerization and uncoupling as well as indirectly through immunomodulation along with antioxidant and anti-inflammatory properties.
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Affiliation(s)
- Anu Rahal
- Division of Animal Health, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, 281122, UP, India
| | - D K Sharma
- Division of Animal Health, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, 281122, UP, India
| | - Ashok Kumar
- Division of Animal Health, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, 281122, UP, India
| | - Nitika Sharma
- Division of Animal Health, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, 281122, UP, India
| | - Deen Dayal
- Division of Animal Health, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, 281122, UP, India
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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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7
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Bajusz D, Wade WS, Satała G, Bojarski AJ, Ilaš J, Ebner J, Grebien F, Papp H, Jakab F, Douangamath A, Fearon D, von Delft F, Schuller M, Ahel I, Wakefield A, Vajda S, Gerencsér J, Pallai P, Keserű GM. Exploring protein hotspots by optimized fragment pharmacophores. Nat Commun 2021; 12:3201. [PMID: 34045440 PMCID: PMC8159961 DOI: 10.1038/s41467-021-23443-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
Fragment-based drug design has introduced a bottom-up process for drug development, with improved sampling of chemical space and increased effectiveness in early drug discovery. Here, we combine the use of pharmacophores, the most general concept of representing drug-target interactions with the theory of protein hotspots, to develop a design protocol for fragment libraries. The SpotXplorer approach compiles small fragment libraries that maximize the coverage of experimentally confirmed binding pharmacophores at the most preferred hotspots. The efficiency of this approach is demonstrated with a pilot library of 96 fragment-sized compounds (SpotXplorer0) that is validated on popular target classes and emerging drug targets. Biochemical screening against a set of GPCRs and proteases retrieves compounds containing an average of 70% of known pharmacophores for these targets. More importantly, SpotXplorer0 screening identifies confirmed hits against recently established challenging targets such as the histone methyltransferase SETD2, the main protease (3CLPro) and the NSP3 macrodomain of SARS-CoV-2.
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Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | | | - Grzegorz Satała
- Maj Institute of Pharmacology Polish Academy of Sciences, Kraków, Poland
| | - Andrzej J Bojarski
- Maj Institute of Pharmacology Polish Academy of Sciences, Kraków, Poland
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Jessica Ebner
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Henrietta Papp
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Centre for Medicines Discovery, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Amanda Wakefield
- Department of Chemistry, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Sándor Vajda
- Department of Chemistry, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | | | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary.
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Water-soluble inhibitors of ABCG2 (BCRP) - A fragment-based and computational approach. Eur J Med Chem 2020; 210:112958. [PMID: 33199153 DOI: 10.1016/j.ejmech.2020.112958] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 12/13/2022]
Abstract
A good balance between hydrophilicity and lipophilicity is a prerequisite for all bioactive compounds. If the hydrophilicity of a compound is low, its solubility in water will be meager. Many drug development failures have been attributed to poor aqueous solubility. ABCG2 inhibitors are especially prone to be insoluble since they have to address the extremely large and hydrophobic multidrug binding site in ABCG2. For instance, our previous, tariquidar-related ABCG2 inhibitor UR-MB108 (1) showed high potency (79 nM), but very low aqueous solubility (78 nM). To discover novel potent ABCG2 inhibitors with improved solubility we pursued a fragment-based approach. Substructures of 1 were optimized and the fragments 'enlarged' to obtain inhibitors, supported by molecular docking studies. Synthesis was achieved, i.a., via Sonogashira coupling, click chemistry and amide coupling. A kinetic solubility assay revealed that 1 and most novel inhibitors did not precipitate during the short time period of the applied biological assays. The solubility of the compounds in aqueous media at equilibrium was investigated in a thermodynamic solubility assay, where UR-Ant116 (40), UR-Ant121 (41), UR-Ant131 (48) and UR-Ant132 (49) excelled with solubilities between 1 μM and 1.5 μM - an up to 19-fold improvement compared to 1. Moreover, these novel N-phenyl-chromone-2-carboxamides inhibited ABCG2 in a Hoechst 33342 transport assay with potencies in the low three-digit nanomolar range, reversed MDR in cancer cells, were non-toxic and proved stable in blood plasma. All properties make them attractive candidates for in vitro assays requiring long-term incubation and in vivo studies, both needing sufficient solubility at equilibrium. 41 and 49 were highly ABCG2-selective, a precondition for developing PET tracers. The triple ABCB1/C1/G2 inhibitor 40 qualifies for potential therapeutic applications, given the concerted role of the three transporter subtypes at many tissue barriers, e.g. the BBB.
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Chen JL, Zhang P, Abe M, Aikawa H, Zhang L, Frank AJ, Zembryski T, Hubbs C, Park H, Withka J, Steppan C, Rogers L, Cabral S, Pettersson M, Wager TT, Fountain MA, Rumbaugh G, Childs-Disney JL, Disney MD. Design, Optimization, and Study of Small Molecules That Target Tau Pre-mRNA and Affect Splicing. J Am Chem Soc 2020; 142:8706-8727. [PMID: 32364710 PMCID: PMC7357857 DOI: 10.1021/jacs.0c00768] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Approximately 95% of human genes are alternatively spliced, and aberrant splicing events can cause disease. One pre-mRNA that is alternatively spliced and linked to neurodegenerative diseases is tau (microtubule-associated protein tau), which can cause frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17) and can contribute to Alzheimer's disease. Here, we describe the design of structure-specific lead small molecules that directly target tau pre-mRNA from sequence. This was followed by hit expansion and analogue synthesis to further improve upon these initial lead molecules. The emergent compounds were assessed for functional activity in a battery of assays, including binding assays and an assay that mimics molecular recognition of tau pre-mRNA by a U1 small nuclear ribonucleoprotein (snRNP) splicing factor. Compounds that emerged from these studies had enhanced potency and selectivity for the target RNA relative to the initial hits, while also having significantly improved drug-like properties. The compounds are shown to directly target tau pre-mRNA in cells, via chemical cross-linking and isolation by pull-down target profiling, and to rescue disease-relevant splicing of tau pre-mRNA in a variety of cellular systems, including primary neurons. More broadly, this study shows that lead, structure-specific compounds can be designed from sequence and then further optimized for their physicochemical properties while at the same time enhancing their activity.
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Affiliation(s)
- Jonathan L. Chen
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Peiyuan Zhang
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Masahito Abe
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Haruo Aikawa
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Liying Zhang
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Alexander J. Frank
- Department of Chemistry & Biochemistry, State University of New York at Fredonia, Fredonia, New York 14063, United States
| | - Timothy Zembryski
- Department of Chemistry & Biochemistry, State University of New York at Fredonia, Fredonia, New York 14063, United States
| | - Christopher Hubbs
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - HaJeung Park
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jane Withka
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Claire Steppan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Lucy Rogers
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Shawn Cabral
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Martin Pettersson
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Travis T. Wager
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Matthew A. Fountain
- Department of Chemistry & Biochemistry, State University of New York at Fredonia, Fredonia, New York 14063, United States
| | - Gavin Rumbaugh
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter
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10
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Kirsch P, Hartman AM, Hirsch AKH, Empting M. Concepts and Core Principles of Fragment-Based Drug Design. Molecules 2019; 24:molecules24234309. [PMID: 31779114 PMCID: PMC6930586 DOI: 10.3390/molecules24234309] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/11/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
In this review, a general introduction to fragment-based drug design and the underlying concepts is given. General considerations and methodologies ranging from library selection/construction over biophysical screening and evaluation methods to in-depth hit qualification and subsequent optimization strategies are discussed. These principles can be generally applied to most classes of drug targets. The examples given for fragment growing, merging, and linking strategies at the end of the review are set in the fields of enzyme-inhibitor design and macromolecule–macromolecule interaction inhibition. Building upon the foundation of fragment-based drug discovery (FBDD) and its methodologies, we also highlight a few new trends in FBDD.
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Affiliation(s)
- Philine Kirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
| | - Alwin M. Hartman
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-988-062-031
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11
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Ferenczy GG, Keserű GM. Thermodynamic profiling for fragment-based lead discovery and optimization. Expert Opin Drug Discov 2019; 15:117-129. [PMID: 31741402 DOI: 10.1080/17460441.2020.1691166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The enthalpic and entropic components of the ligand-protein binding free energy reflect the type and quality of the interactions and relate to the physicochemical properties of the ligands. These findings have significance in medicinal chemistry optimizations since they suggest that the thermodynamic profiling of the binding may help monitor and control the unfavorable size and hydrophobicity increase typically accompanying affinity improvements and leading to suboptimal pharmacokinetic properties.Areas covered: This review describes the ligand-protein binding event in terms of elementary steps, their associated interactions, and their enthalpic and entropic consequences. The relationships among the breaking and forming interactions, the binding thermodynamic profile, and the physicochemical properties of the ligands are also discussed.Expert opinion: Analysis of the size dependence of available affinity and favorable enthalpy highlights the limitation of the simultaneous optimization of these quantities. Indeed, moderate, rather than very high affinities can be conciliated with favorable physicochemical and pharmacokinetic profiles as it is supported by the affinity range of historical oral drugs. Although thermodynamic quantities are not suitable endpoints for medicinal chemistry optimizations owing to the complexity of the binding thermodynamics, thermodynamic profiling together with structural studies can be advantageously used to understand the details of the binding process and to optimize it.
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Affiliation(s)
- György G Ferenczy
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest, Hungary
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12
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Giordanetto F, Jin C, Willmore L, Feher M, Shaw DE. Fragment Hits: What do They Look Like and How do They Bind? J Med Chem 2019; 62:3381-3394. [PMID: 30875465 PMCID: PMC6466478 DOI: 10.1021/acs.jmedchem.8b01855] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
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A “fragment hit”, a
molecule of low molecular weight
that has been validated to bind to a target protein, can be an effective
chemical starting point for a drug discovery project. Our ability
to find and progress fragment hits could potentially be improved by
enhancing our understanding of their binding properties, which to
date has largely been based on tacit knowledge and reports from individual
projects. In the work reported here, we systematically analyzed the
molecular and binding properties of fragment hits using 489 published
protein–fragment complexes. We identified a number of notable
features that these hits tend to have in common, including preferences
in buried surface area upon binding, hydrogen bonding and other directional
interactions with the protein targets, structural topology, functional-group
occurrence, and degree of carbon saturation. In the future, taking
account of these preferences in designing and selecting fragments
to screen against protein targets may increase the chances of success
in fragment screening campaigns.
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Affiliation(s)
| | - Chentian Jin
- D. E. Shaw Research , New York , New York 10036 , United States
| | | | - Miklos Feher
- D. E. Shaw Research , New York , New York 10036 , United States
| | - David E Shaw
- D. E. Shaw Research , New York , New York 10036 , United States.,Department of Biochemistry and Molecular Biophysics , Columbia University , New York , New York 10032 , United States
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13
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Zhou Y, Li C, Peng J, Xie L, Meng L, Li Q, Zhang J, Li XD, Li X, Huang X, Li X. DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery. J Am Chem Soc 2018; 140:15859-15867. [DOI: 10.1021/jacs.8b09277] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yu Zhou
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Chen Li
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
| | - Jianzhao Peng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Liangxu Xie
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water
Bay, Kowloon, Hong Kong, Hong Kong
| | - Ling Meng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Qingrong Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Jianfu Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water
Bay, Kowloon, Hong Kong, Hong Kong
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
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14
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Szilágyi B, Kovács P, Ferenczy GG, Rácz A, Németh K, Visy J, Szabó P, Ilas J, Balogh GT, Monostory K, Vincze I, Tábi T, Szökő É, Keserű GM. Discovery of isatin and 1H-indazol-3-ol derivatives as d-amino acid oxidase (DAAO) inhibitors. Bioorg Med Chem 2018; 26:1579-1587. [DOI: 10.1016/j.bmc.2018.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/27/2018] [Accepted: 02/03/2018] [Indexed: 01/23/2023]
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15
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Orgován Z, Ferenczy GG, Steinbrecher T, Szilágyi B, Bajusz D, Keserű GM. Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of D-amino acid oxidase inhibitors. J Comput Aided Mol Des 2018; 32:331-345. [PMID: 29335871 DOI: 10.1007/s10822-018-0097-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/06/2018] [Indexed: 01/16/2023]
Abstract
Optimization of fragment size D-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.
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Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | | | - Bence Szilágyi
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary.
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16
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Fragment-based drug discovery and its application to challenging drug targets. Essays Biochem 2017; 61:475-484. [PMID: 29118094 DOI: 10.1042/ebc20170029] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 11/17/2022]
Abstract
Fragment-based drug discovery (FBDD) is a technique for identifying low molecular weight chemical starting points for drug discovery. Since its inception 20 years ago, FBDD has grown in popularity to the point where it is now an established technique in industry and academia. The approach involves the biophysical screening of proteins against collections of low molecular weight compounds (fragments). Although fragments bind to proteins with relatively low affinity, they form efficient, high quality binding interactions with the protein architecture as they have to overcome a significant entropy barrier to bind. Of the biophysical methods available for fragment screening, X-ray protein crystallography is one of the most sensitive and least prone to false positives. It also provides detailed structural information of the protein-fragment complex at the atomic level. Fragment-based screening using X-ray crystallography is therefore an efficient method for identifying binding hotspots on proteins, which can then be exploited by chemists and biologists for the discovery of new drugs. The use of FBDD is illustrated here with a recently published case study of a drug discovery programme targeting the challenging protein-protein interaction Kelch-like ECH-associated protein 1:nuclear factor erythroid 2-related factor 2.
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17
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Jaegle M, Wong EL, Tauber C, Nawrotzky E, Arkona C, Rademann J. Proteintemplat-gesteuerte Fragmentligationen - von der molekularen Erkennung zur Wirkstofffindung. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 129:7464-7485. [PMID: 32313319 PMCID: PMC7159557 DOI: 10.1002/ange.201610372] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Indexed: 12/28/2022]
Abstract
AbstractProteintemplat‐gesteuerte Fragmentligationen sind ein neuartiges Konzept zur Unterstützung der Wirkstofffindung und können dazu beitragen, die Wirksamkeit von Proteinliganden zu verbessern. Es handelt sich dabei um chemische Reaktionen zwischen niedermolekularen Verbindungen (“Fragmenten”), die die Oberfläche eines Proteins als Reaktionsgefäß verwenden, um die Bildung eines Proteinliganden mit erhöhter Bindungsaffinität zu katalysieren. Die Methode nutzt die molekulare Erkennung kleiner reaktiver Fragmente durch die Proteine sowohl zur Assemblierung der Liganden als auch zur Identifizierung bioaktiver Fragmentkombinationen. Chemische Synthese und Bioassay werden dabei in einem Schritt vereint. Dieser Aufsatz diskutiert die biophysikalischen Grundlagen der reversiblen und irreversiblen Fragmentligationen und gibt einen Überblick über die Methoden, mit denen die durch das Proteintemplat gebildeten Ligationsprodukte detektiert werden können. Der chemische Reaktionsraum und aktuelle Anwendungen wie auch die Bedeutung dieses Konzeptes für die Wirkstofffindung werden erörtert.
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Affiliation(s)
- Mike Jaegle
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Ee Lin Wong
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Carolin Tauber
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Eric Nawrotzky
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Christoph Arkona
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Jörg Rademann
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
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18
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Jaegle M, Wong EL, Tauber C, Nawrotzky E, Arkona C, Rademann J. Protein-Templated Fragment Ligations-From Molecular Recognition to Drug Discovery. Angew Chem Int Ed Engl 2017; 56:7358-7378. [PMID: 28117936 PMCID: PMC7159684 DOI: 10.1002/anie.201610372] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Indexed: 12/14/2022]
Abstract
Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed.
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Affiliation(s)
- Mike Jaegle
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Ee Lin Wong
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Carolin Tauber
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Eric Nawrotzky
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Christoph Arkona
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Jörg Rademann
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
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19
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Chilton M, Clennell B, Edfeldt F, Geschwindner S. Hot-Spotting with Thermal Scanning: A Ligand- and Structure-Independent Assessment of Target Ligandability. J Med Chem 2017; 60:4923-4931. [PMID: 28537726 DOI: 10.1021/acs.jmedchem.7b00208] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Evaluating the ligandability of a protein target is a key component when defining hit-finding strategies or when prioritize among drug targets. Computational as well as biophysical approaches based on nuclear magnetic resonance (NMR) fragment screening are powerful approaches but suffer from specific constraints that limit their usage. Here, we demonstrate the applicability of high-throughput thermal scanning (HTTS) as a simple and generic biophysical fragment screening method to reproduce assessments from NMR-based screening. By applying this method to a large set of proteins we can furthermore show that the assessment is predictive of the success of high-throughput screening (HTS). The few divergences for targets of low ligandability originate from the sensitivity differences of the orthogonal biophysical methods. We thus applied a new strategy making use of modulations in the solvent structure to improve assay sensitivity. This novel approach enables improved ligandability assessments in accordance with NMR-based assessments and more importantly positions the methodology as a valuable option for biophysical fragment screening.
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Affiliation(s)
- Molly Chilton
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
| | - Ben Clennell
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
| | - Fredrik Edfeldt
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
| | - Stefan Geschwindner
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
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20
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Williams G, Ferenczy GG, Ulander J, Keserű GM. Binding thermodynamics discriminates fragments from druglike compounds: a thermodynamic description of fragment-based drug discovery. Drug Discov Today 2016; 22:681-689. [PMID: 27916639 DOI: 10.1016/j.drudis.2016.11.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/12/2016] [Accepted: 11/24/2016] [Indexed: 01/18/2023]
Abstract
Small is beautiful - reducing the size and complexity of chemical starting points for drug design allows better sampling of chemical space, reveals the most energetically important interactions within protein-binding sites and can lead to improvements in the physicochemical properties of the final drug. The impact of fragment-based drug discovery (FBDD) on recent drug discovery projects and our improved knowledge of the structural and thermodynamic details of ligand binding has prompted us to explore the relationships between ligand-binding thermodynamics and FBDD. Information on binding thermodynamics can give insights into the contributions to protein-ligand interactions and could therefore be used to prioritise compounds with a high degree of specificity in forming key interactions.
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Affiliation(s)
- Glyn Williams
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, UK
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Johan Ulander
- CVMD Innovative Medicines, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
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21
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Lipinski CA. Rule of five in 2015 and beyond: Target and ligand structural limitations, ligand chemistry structure and drug discovery project decisions. Adv Drug Deliv Rev 2016; 101:34-41. [PMID: 27154268 DOI: 10.1016/j.addr.2016.04.029] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/22/2016] [Accepted: 04/27/2016] [Indexed: 12/13/2022]
Abstract
The rule of five (Ro5), based on physicochemical profiles of phase II drugs, is consistent with structural limitations in protein targets and the drug target ligands. Three of four parameters in Ro5 are fundamental to the structure of both target and drug binding sites. The chemical structure of the drug ligand depends on the ligand chemistry and design philosophy. Two extremes of chemical structure and design philosophy exist; ligands constructed in the medicinal chemistry synthesis laboratory without input from natural selection and natural product (NP) metabolites biosynthesized based on evolutionary selection. Exceptions to Ro5 are found mostly among NPs. Chemistry chameleon-like behavior of some NPs due to intra-molecular hydrogen bonding as exemplified by cyclosporine A is a strong contributor to NP Ro5 outliers. The fragment derived, drug Navitoclax is an example of the extensive expertise, resources, time and key decisions required for the rare discovery of a non-NP Ro5 outlier.
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22
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Keserű GM, Erlanson DA, Ferenczy GG, Hann MM, Murray CW, Pickett SD. Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia. J Med Chem 2016; 59:8189-206. [DOI: 10.1021/acs.jmedchem.6b00197] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- György M. Keserű
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Daniel A. Erlanson
- Carmot Therapeutics, Inc. 409 Illinois Street, San Francisco, California 94158, United States
| | - György G. Ferenczy
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Michael M. Hann
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Stephen D. Pickett
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
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