1
|
FitzGerald EA, Vagrys D, Opassi G, Klein HF, Hamilton DJ, Talibov VO, Abramsson M, Moberg A, Lindgren MT, Holmgren C, Davis B, O'Brien P, Wijtmans M, Hubbard RE, de Esch IJP, Danielson UH. Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:40-51. [PMID: 37714432 DOI: 10.1016/j.slasd.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery. However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads.
Collapse
Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Beactica Therapeutics AB, Virdings allé 2, Uppsala, Sweden
| | - Darius Vagrys
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Giulia Opassi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Hanna F Klein
- Department of Chemistry, University of York, York, United Kingdom
| | - David J Hamilton
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | | | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Ben Davis
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom
| | - Peter O'Brien
- Department of Chemistry, University of York, York, United Kingdom
| | - Maikel Wijtmans
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roderick E Hubbard
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
2
|
Vester K, Metz A, Huber S, Loll B, Wahl MC. Conformation-dependent ligand hot spots in the spliceosomal RNA helicase BRR2. Acta Crystallogr D Struct Biol 2023; 79:304-317. [PMID: 36974964 PMCID: PMC10071561 DOI: 10.1107/s2059798323001778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/26/2023] [Indexed: 03/29/2023] Open
Abstract
The conversion of hits to leads in drug discovery involves the elaboration of chemical core structures to increase their potency. In fragment-based drug discovery, low-molecular-weight compounds are tested for protein binding and are subsequently modified, with the tacit assumption that the binding mode of the original hit will be conserved among the derivatives. However, deviations from binding mode conservation are rather frequently observed, but potential causes of these alterations remain incompletely understood. Here, two crystal forms of the spliceosomal RNA helicase BRR2 were employed as a test case to explore the consequences of conformational changes in the target protein on the binding behaviour of fragment derivatives. The initial fragment, sulfaguanidine, bound at the interface between the two helicase cassettes of BRR2 in one crystal form. Second-generation compounds devised by structure-guided docking were probed for their binding to BRR2 in a second crystal form, in which the original fragment-binding site was altered due to a conformational change. While some of the second-generation compounds retained binding to parts of the original site, others changed to different binding pockets of the protein. A structural bioinformatics analysis revealed that the fragment-binding sites correspond to predicted binding hot spots, which strongly depend on the protein conformation. This case study offers an example of extensive binding-mode changes during hit derivatization, which are likely to occur as a consequence of multiple binding hot spots, some of which are sensitive to the flexibility of the protein.
Collapse
Affiliation(s)
- Karen Vester
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Alexander Metz
- Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Simon Huber
- Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Bernhard Loll
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Markus C. Wahl
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein Strasse 15, 12489 Berlin, Germany
| |
Collapse
|
3
|
FitzGerald EA, Butko MT, Boronat P, Cederfelt D, Abramsson M, Ludviksdottir H, van Muijlwijk-Koezen JE, de Esch IJP, Dobritzsch D, Young T, Danielson UH. Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor. RSC Adv 2021; 11:7527-7537. [PMID: 35423271 PMCID: PMC8694943 DOI: 10.1039/d0ra09844b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/28/2021] [Indexed: 01/13/2023] Open
Abstract
Biophysical screening of compound libraries for the identification of ligands that interact with a protein is efficient, but does typically not reveal if (or how) ligands may interfere with its functional properties. For this a biochemical/functional assay is required. But for proteins whose function is dependent on a conformational change, such assays are typically complex or have low throughput. Here we have explored a high-throughput second-harmonic generation (SHG) biosensor to detect fragments that induce conformational changes upon binding to a protein in real time and identify dynamic regions. Multiwell plate format SHG assays were developed for wild-type and six engineered single-cysteine mutants of acetyl choline binding protein (AChBP), a homologue to ligand gated ion channels (LGICs). They were conjugated with second harmonic-active labels via amine or maleimide coupling. To validate the assay, it was confirmed that the conformational changes induced in AChBP by nicotinic acetyl choline receptor (nAChR) agonists and antagonists were qualitatively different. A 1056 fragment library was subsequently screened against all variants and conformational modulators of AChBP were successfully identified, with hit rates from 9-22%, depending on the AChBP variant. A subset of four hits was selected for orthogonal validation and structural analysis. A time-resolved grating-coupled interferometry-based biosensor assay confirmed the interaction to be a reversible 1-step 1 : 1 interaction, and provided estimates of affinities and interaction kinetic rate constants (K D = 0.28-63 μM, k a = 0.1-6 μM-1 s-1, k d = 1 s-1). X-ray crystallography of two of the fragments confirmed their binding at a previously described conformationally dynamic site, corresponding to the regulatory site of LGICs. These results reveal that SHG has the sensitivity to identify fragments that induce conformational changes in a protein. A selection of fragment hits with a response profile different to known LGIC regulators was characterized and confirmed to bind to dynamic regions of the protein.
Collapse
Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
- Beactica Therapeutics Virdings allé 2 Uppsala 754 40 Sweden
| | | | - Pierre Boronat
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Daniela Cederfelt
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | | | - Jacqueline E van Muijlwijk-Koezen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Doreen Dobritzsch
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | - Tracy Young
- Biodesy, Inc. 170 Harbor Way South San Francisco 94080 CA USA
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
- Science for Life Laboratory, Uppsala University Sweden
| |
Collapse
|
4
|
Prati F, Zuccotto F, Fletcher D, Convery MA, Fernandez‐Menendez R, Bates R, Encinas L, Zeng J, Chung C, De Dios Anton P, Mendoza‐Losana A, Mackenzie C, Green SR, Huggett M, Barros D, Wyatt PG, Ray PC. Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA. ChemMedChem 2018; 13:672-677. [PMID: 29399991 PMCID: PMC5915743 DOI: 10.1002/cmdc.201700774] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Indexed: 11/17/2022]
Abstract
Our findings reported herein provide support for the benefits of including functional group complexity (FGC) within fragments when screening against protein targets such as Mycobacterium tuberculosis InhA. We show that InhA fragment actives with FGC maintained their binding pose during elaboration. Furthermore, weak fragment hits with functional group handles also allowed for facile fragment elaboration to afford novel and potent InhA inhibitors with good ligand efficiency metrics for optimization.
Collapse
Affiliation(s)
- Federica Prati
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Fabio Zuccotto
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Daniel Fletcher
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Maire A. Convery
- Platform Technology and SciencesMedicines Research Centre, GlaxoSmithKlineGunnels Wood RoadStevenage HertsSG1 2NYHertfordshireUK
| | - Raquel Fernandez‐Menendez
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Robert Bates
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Lourdes Encinas
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Jingkun Zeng
- Platform Technology and SciencesMedicines Research Centre, GlaxoSmithKlineGunnels Wood RoadStevenage HertsSG1 2NYHertfordshireUK
| | - Chun‐wa Chung
- Platform Technology and SciencesMedicines Research Centre, GlaxoSmithKlineGunnels Wood RoadStevenage HertsSG1 2NYHertfordshireUK
| | - Paco De Dios Anton
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Alfonso Mendoza‐Losana
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Claire Mackenzie
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Simon R. Green
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Margaret Huggett
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - David Barros
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Paul G. Wyatt
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Peter C. Ray
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| |
Collapse
|
5
|
Drwal MN, Jacquemard C, Perez C, Desaphy J, Kellenberger E. Do Fragments and Crystallization Additives Bind Similarly to Drug-like Ligands? J Chem Inf Model 2017; 57:1197-1209. [PMID: 28414463 DOI: 10.1021/acs.jcim.6b00769] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The success of fragment-based drug design (FBDD) hinges upon the optimization of low-molecular-weight compounds (MW < 300 Da) with weak binding affinities to lead compounds with high affinity and selectivity. Usually, structural information from fragment-protein complexes is used to develop ideas about the binding mode of similar but drug-like molecules. In this regard, crystallization additives such as cryoprotectants or buffer components, which are highly abundant in crystal structures, are frequently ignored. Thus, the aim of this study was to investigate the information present in protein complexes with fragments as well as those with additives and how they relate to the binding modes of their drug-like counterparts. We present a thorough analysis of the binding modes of crystallographic additives, fragments, and drug-like ligands bound to four diverse targets of wide interest in drug discovery and highly represented in the Protein Data Bank: cyclin-dependent kinase 2, β-secretase 1, carbonic anhydrase 2, and trypsin. We identified a total of 630 unique molecules bound to the catalytic binding sites, among them 31 additives, 222 fragments, and 377 drug-like ligands. In general, we observed that, independent of the target, protein-fragment interaction patterns are highly similar to those of drug-like ligands and mostly cover the residues crucial for binding. Crystallographic additives are also able to show conserved binding modes and recover the residues important for binding in some of the cases. Moreover, we show evidence that the information from fragments and drug-like ligands can be applied to rescore docking poses in order to improve the prediction of binding modes.
Collapse
Affiliation(s)
- Malgorzata N Drwal
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
| | - Carlos Perez
- Eli Lilly Research Laboratories , Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | - Jérémy Desaphy
- Lilly Research Laboratories, Eli Lilly and Company , Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
| |
Collapse
|
6
|
Ranganathan A, Heine P, Rudling A, Plückthun A, Kummer L, Carlsson J. Ligand Discovery for a Peptide-Binding GPCR by Structure-Based Screening of Fragment- and Lead-Like Chemical Libraries. ACS Chem Biol 2017; 12:735-745. [PMID: 28032980 DOI: 10.1021/acschembio.6b00646] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Peptide-recognizing G protein-coupled receptors (GPCRs) are promising therapeutic targets but often resist drug discovery efforts. Determination of crystal structures for peptide-binding GPCRs has provided opportunities to explore structure-based methods in lead development. Molecular docking screens of two chemical libraries, containing either fragment- or lead-like compounds, against a neurotensin receptor 1 crystal structure allowed for a comparison between different drug development strategies for peptide-binding GPCRs. A total of 2.3 million molecules were screened computationally, and 25 fragments and 27 leads that were top-ranked in each library were selected for experimental evaluation. Of these, eight fragments and five leads were confirmed as ligands by surface plasmon resonance. The hit rate for the fragment screen (32%) was thus higher than for the lead-like library (19%), but the affinities of the fragments were ∼100-fold lower. Both screens returned unique scaffolds and demonstrated that a crystal structure of a stabilized peptide-binding GPCR can guide the discovery of small-molecule agonists. The complementary advantages of exploring fragment- and lead-like chemical space suggest that these strategies should be applied synergistically in structure-based screens against challenging GPCR targets.
Collapse
Affiliation(s)
- Anirudh Ranganathan
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Philipp Heine
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Axel Rudling
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Andreas Plückthun
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lutz Kummer
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- G7 Therapeutics AG, Grabenstrasse
11a, 8952 Schlieren, Switzerland
| | - Jens Carlsson
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC,
Box 596, SE-751 24 Uppsala, Sweden
| |
Collapse
|
7
|
Kavanagh ME, Gray JL, Gilbert SH, Coyne AG, McLean KJ, Davis HJ, Munro AW, Abell C. Substrate Fragmentation for the Design of M. tuberculosis CYP121 Inhibitors. ChemMedChem 2016; 11:1924-35. [PMID: 27432475 PMCID: PMC5026067 DOI: 10.1002/cmdc.201600248] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/24/2016] [Indexed: 11/11/2022]
Abstract
The cyclo-dipeptide substrates of the essential M. tuberculosis (Mtb) enzyme CYP121 were deconstructed into their component fragments and screened against the enzyme. A number of hits were identified, one of which exhibited an unexpected inhibitor-like binding mode. The inhibitory pharmacophore was elucidated, and fragment binding affinity was rapidly improved by synthetic elaboration guided by the structures of CYP121 substrates. The resulting inhibitors have low micromolar affinity, good predicted physicochemical properties and selectivity for CYP121 over other Mtb P450s. Spectroscopic characterisation of the inhibitors' binding mode provides insight into the effect of weak nitrogen-donor ligands on the P450 heme, an improved understanding of factors governing CYP121-ligand recognition and speculation into the biological role of the enzyme for Mtb.
Collapse
Affiliation(s)
- Madeline E Kavanagh
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Janine L Gray
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sophie H Gilbert
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Anthony G Coyne
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of LifeSciences, The University of Manchester, Manchester, M1 7DN, UK
| | - Holly J Davis
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of LifeSciences, The University of Manchester, Manchester, M1 7DN, UK
| | - Chris Abell
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| |
Collapse
|
8
|
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
| |
Collapse
|
9
|
Ligand deconstruction: Why some fragment binding positions are conserved and others are not. Proc Natl Acad Sci U S A 2015; 112:E2585-94. [PMID: 25918377 DOI: 10.1073/pnas.1501567112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fragment-based drug discovery (FBDD) relies on the premise that the fragment binding mode will be conserved on subsequent expansion to a larger ligand. However, no general condition has been established to explain when fragment binding modes will be conserved. We show that a remarkably simple condition can be developed in terms of how fragments coincide with binding energy hot spots--regions of the protein where interactions with a ligand contribute substantial binding free energy--the locations of which can easily be determined computationally. Because a substantial fraction of the free energy of ligand binding comes from interacting with the residues in the energetically most important hot spot, a ligand moiety that sufficiently overlaps with this region will retain its location even when other parts of the ligand are removed. This hypothesis is supported by eight case studies. The condition helps identify whether a protein is suitable for FBDD, predicts the size of fragments required for screening, and determines whether a fragment hit can be extended into a higher affinity ligand. Our results show that ligand binding sites can usefully be thought of in terms of an anchor site, which is the top-ranked hot spot and dominates the free energy of binding, surrounded by a number of weaker satellite sites that confer improved affinity and selectivity for a particular ligand and that it is the intrinsic binding potential of the protein surface that determines whether it can serve as a robust binding site for a suitably optimized ligand.
Collapse
|
10
|
Abstract
Allostery is the most direct and efficient way for regulation of biological macromolecule function, ranging from the control of metabolic mechanisms to signal transduction pathways. Allosteric modulators target to allosteric sites, offering distinct advantages compared to orthosteric ligands that target to active sites, such as greater specificity, reduced side effects, and lower toxicity. Allosteric modulators have therefore drawn increasing attention as potential therapeutic drugs in the design and development of new drugs. In recent years, advancements in our understanding of the fundamental principles underlying allostery, coupled with the exploitation of powerful techniques and methods in the field of allostery, provide unprecedented opportunities to discover allosteric proteins, detect and characterize allosteric sites, design and develop novel efficient allosteric drugs, and recapitulate the universal features of allosteric proteins and allosteric modulators. In the present review, we summarize the recent advances in the repertoire of allostery, with a particular focus on the aforementioned allosteric compounds.
Collapse
Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai, China
| | | | | |
Collapse
|
11
|
Bauman JD, Patel D, Dharia C, Fromer MW, Ahmed S, Frenkel Y, Vijayan RSK, Eck JT, Ho WC, Das K, Shatkin AJ, Arnold E. Detecting allosteric sites of HIV-1 reverse transcriptase by X-ray crystallographic fragment screening. J Med Chem 2013; 56:2738-46. [PMID: 23342998 PMCID: PMC3906421 DOI: 10.1021/jm301271j] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
HIV-1 reverse transcriptase (RT) undergoes a series of conformational changes during viral replication and is a central target for antiretroviral therapy. The intrinsic flexibility of RT can provide novel allosteric sites for inhibition. Crystals of RT that diffract X-rays to better than 2 Å resolution facilitated the probing of RT for new druggable sites using fragment screening by X-ray crystallography. A total of 775 fragments were grouped into 143 cocktails, which were soaked into crystals of RT in complex with the non-nucleoside drug rilpivirine (TMC278). Seven new sites were discovered, including the Incoming Nucleotide Binding, Knuckles, NNRTI Adjacent, and 399 sites, located in the polymerase region of RT, and the 428, RNase H Primer Grip Adjacent, and 507 sites, located in the RNase H region. Three of these sites (Knuckles, NNRTI Adjacent, and Incoming Nucleotide Binding) are inhibitory and provide opportunities for discovery of new anti-AIDS drugs.
Collapse
Affiliation(s)
- Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - Disha Patel
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Medicinal Chemistry, Rutgers University, Piscataway, New Jersey
| | - Chhaya Dharia
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - Marc W. Fromer
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - Sameer Ahmed
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - Yulia Frenkel
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - R. S. K. Vijayan
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - J. Thomas Eck
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - William C. Ho
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - Aaron J. Shatkin
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
- Department of Medicinal Chemistry, Rutgers University, Piscataway, New Jersey
| |
Collapse
|
12
|
Bisignano P, Lambruschini C, Bicego M, Murino V, Favia AD, Cavalli A. In silico deconstruction of ATP-competitive inhibitors of glycogen synthase kinase-3β. J Chem Inf Model 2012. [PMID: 23198830 DOI: 10.1021/ci300355p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fragment-based methods have emerged in the last two decades as alternatives to traditional high throughput screenings for the identification of chemical starting points in drug discovery. One arguable yet popular assumption about fragment-based design is that the fragment binding mode remains conserved upon chemical expansion. For instance, the question of the binding conservation upon fragmentation of a molecule is still unclear. A number of papers have challenged this hypothesis by means of experimental techniques, with controversial results, "underlining" the idea that a simple generalization, maybe, is not possible. From a computational standpoint, the issue has been rarely addressed and mostly to test novel protocols on limited data sets. To fill this gap, we here report on a computational retrospective study concerned with the in silico deconstruction of leadlike compounds, active on the pharmaceutically relevant enzyme glycogen synthase kinase-3β.
Collapse
Affiliation(s)
- Paola Bisignano
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, Italy
| | | | | | | | | | | |
Collapse
|
13
|
Murray CW, Verdonk ML, Rees DC. Experiences in fragment-based drug discovery. Trends Pharmacol Sci 2012; 33:224-32. [PMID: 22459076 DOI: 10.1016/j.tips.2012.02.006] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 11/17/2022]
Abstract
Fragment-based drug discovery (FBDD) has become established in both industry and academia as an alternative approach to high-throughput screening for the generation of chemical leads for drug targets. In FBDD, specialised detection methods are used to identify small chemical compounds (fragments) that bind to the drug target, and structural biology is usually employed to establish their binding mode and to facilitate their optimisation. In this article, we present three recent and successful case histories in FBDD. We then re-examine the key concepts and challenges of FBDD with particular emphasis on recent literature and our own experience from a substantial number of FBDD applications. Our opinion is that careful application of FBDD is living up to its promise of delivering high quality leads with good physical properties and that in future many drug molecules will be derived from fragment-based approaches.
Collapse
Affiliation(s)
- Christopher W Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.
| | | | | |
Collapse
|
14
|
Krimm I, Lancelin JM, Praly JP. Binding evaluation of fragment-based scaffolds for probing allosteric enzymes. J Med Chem 2012; 55:1287-95. [PMID: 22229710 DOI: 10.1021/jm201439b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fragment-based drug discovery has become a powerful method for the generation of drug leads against therapeutic targets. Beyond the identification of novel and effective starting points for drug design, fragments have emerged as reliable tools for assessing protein druggability and identifying protein hot spots. Here, we have examined fragments resulting from the deconstruction of known inhibitors from the glycogen phosphorylase enzyme, a therapeutic target against type 2 diabetes, with two motivations. First, we have analyzed the fragment binding to the multiple binding sites of the glycogen phosphorylase, and then we have investigated the use of fragments to study allosteric enzymes. The work we report illustrates the power of fragmentlike ligands not only for probing the various binding pockets of proteins, but also for uncovering cooperativity between these various binding sites.
Collapse
Affiliation(s)
- Isabelle Krimm
- Institut des Sciences Analytiques, UMR CNRS 5280, Université de Lyon, Université Claude Bernard Lyon 1, Bât. CPE Lyon, Domaine scientifique de la Doua, F-69622 Villeurbanne, France.
| | | | | |
Collapse
|
15
|
Geitmann M, Elinder M, Seeger C, Brandt P, de Esch IJP, Danielson UH. Identification of a novel scaffold for allosteric inhibition of wild type and drug resistant HIV-1 reverse transcriptase by fragment library screening. J Med Chem 2011; 54:699-708. [PMID: 21207961 DOI: 10.1021/jm1010513] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A novel scaffold inhibiting wild type and drug resistant variants of human immunodeficiency virus type 1 reverse transcriptase (HIV-1RT) has been identified in a library consisting of 1040 fragments. The fragments were significantly different from already known non-nucleoside reverse transcriptase inhibitors (NNRTIs), as indicated by a Tversky similarity analysis. A screening strategy involving SPR biosensor-based interaction analysis and enzyme inhibition was used. Primary biosensor-based screening, using short concentration series, was followed by analysis of nevirapine competition and enzyme inhibition, thus identifying inhibitory fragments binding to the non-nucleoside reverse transcriptase inhibitor (NNRTI) binding site. Ten hits were discovered, and their affinities and resistance profiles were evaluated with wild type and three drug resistant enzyme variants (K103N, Y181C, and L100I). One fragment exhibited submillimolar K(D) and IC(50) values against all four tested enzyme variants. A substructure comparison between the fragment and 826 structurally diverse published NNRTIs confirmed that the scaffold was novel. The fragment is a bromoindanone with a ligand efficiency of 0.42 kcal/mol(-1).
Collapse
|
16
|
Abstract
Fragment screening has proven to be a powerful alternative to traditional methods for drug discovery. Biophysical methods, such as X-ray crystallography, NMR spectroscopy, and surface plasmon resonance, are used to screen a diverse library of small molecule compounds. Although compounds identified via this approach have relatively weak affinity, they provide a good platform for lead development and are highly efficient binders with respect to their size. Fragment screening has been utilized for a wide range of targets, including HIV-1 proteins. Here, we review the fragment screening studies targeting HIV-1 proteins using X-ray crystallography or surface plasmon resonance. These studies have successfully detected binding of novel fragments to either previously established or new sites on HIV-1 protease and reverse transcriptase. In addition, fragment screening against HIV-1 reverse transcriptase has been used as a tool to better understand the complex nature of ligand binding to a flexible target.
Collapse
Affiliation(s)
- Joseph D Bauman
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | | | | |
Collapse
|