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Hönig SMN, Flachsenberg F, Ehrt C, Neumann A, Schmidt R, Lemmen C, Rarey M. SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces. J Comput Aided Mol Des 2024; 38:13. [PMID: 38493240 PMCID: PMC10944417 DOI: 10.1007/s10822-024-00551-7] [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: 12/18/2023] [Accepted: 02/13/2024] [Indexed: 03/18/2024]
Abstract
The growing size of make-on-demand chemical libraries is posing new challenges to cheminformatics. These ultra-large chemical libraries became too large for exhaustive enumeration. Using a combinatorial approach instead, the resource requirement scales approximately with the number of synthons instead of the number of molecules. This gives access to billions or trillions of compounds as so-called chemical spaces with moderate hardware and in a reasonable time frame. While extremely performant ligand-based 2D methods exist in this context, 3D methods still largely rely on exhaustive enumeration and therefore fail to apply. Here, we present SpaceGrow: a novel shape-based 3D approach for ligand-based virtual screening of billions of compounds within hours on a single CPU. Compared to a conventional superposition tool, SpaceGrow shows comparable pose reproduction capacity based on RMSD and superior ranking performance while being orders of magnitude faster. Result assessment of two differently sized subsets of the eXplore space reveals a higher probability of finding superior results in larger spaces highlighting the potential of searching in ultra-large spaces. Furthermore, the application of SpaceGrow in a drug discovery workflow was investigated in four examples involving G protein-coupled receptors (GPCRs) with the aim to identify compounds with similar binding capabilities and molecular novelty.
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Affiliation(s)
- Sophia M N Hönig
- BioSolveIT, An der Ziegelei 79, 53757, Sankt Augustin, Germany
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany
| | | | - Christiane Ehrt
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany
| | | | - Robert Schmidt
- BioSolveIT, An der Ziegelei 79, 53757, Sankt Augustin, Germany
| | | | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany.
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2
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DeRatt LG, Pietsch EC, Cisar JS, Jacoby E, Kazmi F, Matico R, Shaffer P, Tanner A, Wang W, Attar R, Edwards JP, Kuduk SD. Discovery of Alternative Binding Poses through Fragment-Based Identification of DHODH Inhibitors. ACS Med Chem Lett 2024; 15:381-387. [PMID: 38505861 PMCID: PMC10945543 DOI: 10.1021/acsmedchemlett.3c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 03/21/2024] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a mitochondrial enzyme that affects many aspects essential to cell proliferation and survival. Recently, DHODH has been identified as a potential target for acute myeloid leukemia therapy. Herein, we describe the identification of potent DHODH inhibitors through a scaffold hopping approach emanating from a fragment screen followed by structure-based drug design to further improve the overall profile and reveal an unexpected novel binding mode. Additionally, these compounds had low P-gp efflux ratios, allowing for applications where exposure to the brain would be required.
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Affiliation(s)
- Lindsey G. DeRatt
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - E. Christine Pietsch
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Justin S. Cisar
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Edgar Jacoby
- Janssen
Pharmaceutical Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Faraz Kazmi
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Rosalie Matico
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Paul Shaffer
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Alexandra Tanner
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Weixue Wang
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Ricardo Attar
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - James P. Edwards
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Scott D. Kuduk
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
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3
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What Makes GPCRs from Different Families Bind to the Same Ligand? Biomolecules 2022; 12:biom12070863. [PMID: 35883418 PMCID: PMC9313020 DOI: 10.3390/biom12070863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/09/2022] [Accepted: 06/19/2022] [Indexed: 12/10/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of cell-surface receptor proteins with important functions in signal transduction and often serve as therapeutic drug targets. With the rapidly growing public data on three dimensional (3D) structures of GPCRs and GPCR-ligand interactions, computational prediction of GPCR ligand binding becomes a convincing option to high throughput screening and other experimental approaches during the beginning phases of ligand discovery. In this work, we set out to computationally uncover and understand the binding of a single ligand to GPCRs from several different families. Three-dimensional structural comparisons of the GPCRs that bind to the same ligand revealed local 3D structural similarities and often these regions overlap with locations of binding pockets. These pockets were found to be similar (based on backbone geometry and side-chain orientation using APoc), and they correlate positively with electrostatic properties of the pockets. Moreover, the more similar the pockets, the more likely a ligand binding to the pockets will interact with similar residues, have similar conformations, and produce similar binding affinities across the pockets. These findings can be exploited to improve protein function inference, drug repurposing and drug toxicity prediction, and accelerate the development of new drugs.
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4
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Grosjean H, Işık M, Aimon A, Mobley D, Chodera J, von Delft F, Biggin PC. SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. J Comput Aided Mol Des 2022; 36:291-311. [PMID: 35426591 PMCID: PMC9010448 DOI: 10.1007/s10822-022-00452-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/22/2022] [Indexed: 11/01/2022]
Abstract
A novel crystallographic fragment screening data set was generated and used in the SAMPL7 challenge for protein-ligands. The SAMPL challenges prospectively assess the predictive power of methods involved in computer-aided drug design. Application of various methods to fragment molecules are now widely used in the search for new drugs. However, there is little in the way of systematic validation specifically for fragment-based approaches. We have performed a large crystallographic high-throughput fragment screen against the therapeutically relevant second bromodomain of the Pleckstrin-homology domain interacting protein (PHIP2) that revealed 52 different fragments bound across 4 distinct sites, 47 of which were bound to the pharmacologically relevant acetylated lysine (Kac) binding site. These data were used to assess computational screening, binding pose prediction and follow-up enumeration. All submissions performed randomly for screening. Pose prediction success rates (defined as less than 2 Å root mean squared deviation against heavy atom crystal positions) ranged between 0 and 25% and only a very few follow-up compounds were deemed viable candidates from a medicinal-chemistry perspective based on a common molecular descriptors analysis. The tight deadlines imposed during the challenge led to a small number of submissions suggesting that the accuracy of rapidly responsive workflows remains limited. In addition, the application of these methods to reproduce crystallographic fragment data still appears to be very challenging. The results show that there is room for improvement in the development of computational tools particularly when applied to fragment-based drug design.
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Affiliation(s)
- Harold Grosjean
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, South Parks Road, OX1 3QU, Oxford, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, OX11 0QX, Didcot, UK
| | - Mehtap Işık
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 10065, New York, NY, USA
| | - Anthony Aimon
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, OX11 0QX, Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA, Didcot, UK
| | - David Mobley
- Department of Pharmaceutical Sciences, Department of Chemistry, University of California, 92617, Irvine, California, USA
| | - John Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 10065, New York, NY, USA
| | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, OX11 0QX, Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA, Didcot, UK
- Centre for Medicines Discovery, University of Oxford, Old Road Campus, Roosevelt Drive, OX3 7DQ, Headington, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, OX3 7DQ, Headington, UK
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, South Parks Road, OX1 3QU, Oxford, UK.
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5
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Leveraging nonstructural data to predict structures and affinities of protein-ligand complexes. Proc Natl Acad Sci U S A 2021; 118:2112621118. [PMID: 34921117 PMCID: PMC8713799 DOI: 10.1073/pnas.2112621118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 01/02/2023] Open
Abstract
Structure-based drug design depends on the ability to predict both the three-dimensional structures of candidate molecules bound to their targets and the associated binding affinities. We demonstrate that one can substantially improve the accuracy of these predictions using easily obtained data about completely different molecules that bind to the same target without requiring any target-bound structures of these molecules. The approach we developed to integrate physical and data-driven modeling may find a variety of applications in the rapidly growing field of artificial intelligence for drug discovery. Over the past five decades, tremendous effort has been devoted to computational methods for predicting properties of ligands—i.e., molecules that bind macromolecular targets. Such methods, which are critical to rational drug design, fall into two categories: physics-based methods, which directly model ligand interactions with the target given the target’s three-dimensional (3D) structure, and ligand-based methods, which predict ligand properties given experimental measurements for similar ligands. Here, we present a rigorous statistical framework to combine these two sources of information. We develop a method to predict a ligand’s pose—the 3D structure of the ligand bound to its target—that leverages a widely available source of information: a list of other ligands that are known to bind the same target but for which no 3D structure is available. This combination of physics-based and ligand-based modeling improves pose prediction accuracy across all major families of drug targets. Using the same framework, we develop a method for virtual screening of drug candidates, which outperforms standard physics-based and ligand-based virtual screening methods. Our results suggest broad opportunities to improve prediction of various ligand properties by combining diverse sources of information through customized machine-learning approaches.
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6
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Imrie F, Hadfield TE, Bradley AR, Deane CM. Deep generative design with 3D pharmacophoric constraints. Chem Sci 2021; 12:14577-14589. [PMID: 34881010 PMCID: PMC8580048 DOI: 10.1039/d1sc02436a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/18/2021] [Indexed: 12/30/2022] Open
Abstract
Generative models have increasingly been proposed as a solution to the molecular design problem. However, it has proved challenging to control the design process or incorporate prior knowledge, limiting their practical use in drug discovery. In particular, generative methods have made limited use of three-dimensional (3D) structural information even though this is critical to binding. This work describes a method to incorporate such information and demonstrates the benefit of doing so. We combine an existing graph-based deep generative model, DeLinker, with a convolutional neural network to utilise physically-meaningful 3D representations of molecules and target pharmacophores. We apply our model, DEVELOP, to both linker and R-group design, demonstrating its suitability for both hit-to-lead and lead optimisation. The 3D pharmacophoric information results in improved generation and allows greater control of the design process. In multiple large-scale evaluations, we show that including 3D pharmacophoric constraints results in substantial improvements in the quality of generated molecules. On a challenging test set derived from PDBbind, our model improves the proportion of generated molecules with high 3D similarity to the original molecule by over 300%. In addition, DEVELOP recovers 10× more of the original molecules compared to the baseline DeLinker method. Our approach is general-purpose, readily modifiable to alternate 3D representations, and can be incorporated into other generative frameworks. Code is available at https://github.com/oxpig/DEVELOP.
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Affiliation(s)
- Fergus Imrie
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford Oxford OX1 3LB UK
| | - Thomas E Hadfield
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford Oxford OX1 3LB UK
| | - Anthony R Bradley
- Exscientia Ltd The Schrödinger Building, Oxford Science Park Oxford OX4 4GE UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford Oxford OX1 3LB UK
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7
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Chan HTH, Moesser MA, Walters RK, Malla TR, Twidale RM, John T, Deeks HM, Johnston-Wood T, Mikhailov V, Sessions RB, Dawson W, Salah E, Lukacik P, Strain-Damerell C, Owen CD, Nakajima T, Świderek K, Lodola A, Moliner V, Glowacki DR, Spencer J, Walsh MA, Schofield CJ, Genovese L, Shoemark DK, Mulholland AJ, Duarte F, Morris GM. Discovery of SARS-CoV-2 M pro peptide inhibitors from modelling substrate and ligand binding. Chem Sci 2021; 12:13686-13703. [PMID: 34760153 PMCID: PMC8549791 DOI: 10.1039/d1sc03628a] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/05/2021] [Indexed: 12/22/2022] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and crystallographic data and an array of biomolecular simulation techniques, including automated docking, molecular dynamics (MD) and interactive MD in virtual reality, QM/MM, and linear-scaling DFT, to investigate the molecular features underlying recognition of the natural Mpro substrates. We extensively analysed the subsite interactions of modelled 11-residue cleavage site peptides, crystallographic ligands, and docked COVID Moonshot-designed covalent inhibitors. Our modelling studies reveal remarkable consistency in the hydrogen bonding patterns of the natural Mpro substrates, particularly on the N-terminal side of the scissile bond. They highlight the critical role of interactions beyond the immediate active site in recognition and catalysis, in particular plasticity at the S2 site. Building on our initial Mpro-substrate models, we used predictive saturation variation scanning (PreSaVS) to design peptides with improved affinity. Non-denaturing mass spectrometry and other biophysical analyses confirm these new and effective 'peptibitors' inhibit Mpro competitively. Our combined results provide new insights and highlight opportunities for the development of Mpro inhibitors as anti-COVID-19 drugs.
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Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Marc A Moesser
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
| | - Rebecca K Walters
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tika R Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Helen M Deeks
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tristan Johnston-Wood
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - William Dawson
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - C David Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Takahito Nakajima
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Katarzyna Świderek
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - Alessio Lodola
- Food and Drug Department, University of Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Vicent Moliner
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - David R Glowacki
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - James Spencer
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Martin A Walsh
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Luigi Genovese
- Univ. Grenoble Alpes, CEA, IRIG-MEM-L_Sim 38000 Grenoble France
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Garrett M Morris
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
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8
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Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallogr D Struct Biol 2021; 77:1168-1182. [PMID: 34473087 PMCID: PMC8411975 DOI: 10.1107/s2059798321008196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/09/2021] [Indexed: 11/10/2022] Open
Abstract
In recent years, crystallographic fragment screening has matured into an almost routine experiment at several modern synchrotron sites. The hits of the screening experiment, i.e. small molecules or fragments binding to the target protein, are revealed along with their 3D structural information. Therefore, they can serve as useful starting points for further structure-based hit-to-lead development. However, the progression of fragment hits to tool compounds or even leads is often hampered by a lack of chemical feasibility. As an attractive alternative, compound analogs that embed the fragment hit structurally may be obtained from commercial catalogs. Here, a workflow is reported based on filtering and assessing such potential follow-up compounds by template docking. This means that the crystallographic binding pose was integrated into the docking calculations as a central starting parameter. Subsequently, the candidates are scored on their interactions within the binding pocket. In an initial proof-of-concept study using five starting fragments known to bind to the aspartic protease endothiapepsin, 28 follow-up compounds were selected using the designed workflow and their binding was assessed by crystallography. Ten of these compounds bound to the active site and five of them showed significantly increased affinity in isothermal titration calorimetry of up to single-digit micromolar affinity. Taken together, this strategy is capable of efficiently evolving the initial fragment hits without major synthesis efforts and with full control by X-ray crystallography.
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Affiliation(s)
- Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Steffen Glöckner
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Niki Messini
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Simon Huber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Ahmed Merabet
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Hans-Dieter Gerber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
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9
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Computational Modeling to Explain Why 5,5-Diarylpentadienamides are TRPV1 Antagonists. Molecules 2021; 26:molecules26061765. [PMID: 33801115 PMCID: PMC8004144 DOI: 10.3390/molecules26061765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/14/2021] [Accepted: 03/18/2021] [Indexed: 11/29/2022] Open
Abstract
Several years ago, the crystallographic structures of the transient receptor potential vanilloid 1 (TRPV1) in the presence of agonists and antagonists were reported, providing structural information about its chemical activation and inactivation. TRPV1’s activation increases the transport of calcium and sodium ions, leading to the excitation of sensory neurons and the perception of pain. On the other hand, its antagonistic inactivation has been explored to design analgesic drugs. The interactions between the antagonists 5,5-diarylpentadienamides (DPDAs) and TRPV1 were studied here to explain why they inactivate TRPV1. The present work identified the structural features of TRPV1–DPDA complexes, starting with a consideration of the orientations of the ligands inside the TRPV1 binding site by using molecular docking. After this, a chemometrics analysis was performed (i) to compare the orientations of the antagonists (by using LigRMSD), (ii) to describe the recurrent interactions between the protein residues and ligand groups in the complexes (by using interaction fingerprints), and (iii) to describe the relationship between topological features of the ligands and their differential antagonistic activities (by using a quantitative structure–activity relationship (QSAR) with 2D autocorrelation descriptors). The interactions between the DPDA groups and the residues Y511, S512, T550, R557, and E570 (with a recognized role in the binding of classic ligands), and the occupancy of isoquinoline or 3-hydroxy-3,4-dihydroquinolin-2(1H)-one groups of the DPDAs in the vanilloid pocket of TRPV1 were clearly described. Based on the results, the structural features that explain why DPDAs inactivate TRPV1 were clearly exposed. These features can be considered for the design of novel TRPV1 antagonists.
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10
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Abstract
INTRODUCTION Molecular docking has been consolidated as one of the most important methods in the molecular modeling field. It has been recognized as a prominent tool in the study of protein-ligand complexes, to describe intermolecular interactions, to accurately predict poses of multiple ligands, to discover novel promising bioactive compounds. Molecular docking methods have evolved in terms of their accuracy and reliability; but there are pending issues to solve for improving the connection between the docking results and the experimental evidence. AREAS COVERED In this article, the author reviews very recent innovative molecular docking applications with special emphasis on reverse docking, treatment of protein flexibility, the use of experimental data to guide the selection of docking poses, the application of Quantum mechanics(QM) in docking, and covalent docking. EXPERT OPINION There are several issues being worked on in recent years that will lead to important breakthroughs in molecular docking methods in the near future These developments are related to more efficient exploration of large datasets and receptor conformations, advances in electronic description, and the use of structural information for guiding the selection of results.
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Affiliation(s)
- Julio Caballero
- Departamento De Bioinformática, Centro De Bioinformática, Simulación Y Modelado (CBSM), Facultad De Ingeniería, Universidad De Talca, Talca, Chile
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11
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Flachsenberg F, Meyder A, Sommer K, Penner P, Rarey M. A Consistent Scheme for Gradient-Based Optimization of Protein -Ligand Poses. J Chem Inf Model 2020; 60:6502-6522. [PMID: 33258376 DOI: 10.1021/acs.jcim.0c01095] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Scoring and numerical optimization of protein-ligand poses is an integral part of docking tools. Although many scoring functions exist, many of them are not continuously differentiable and they are rarely explicitly analyzed with respect to their numerical optimization behavior. Here, we present a consistent scheme for pose scoring and gradient-based pose optimization. It consists of a novel variant of the BFGS algorithm enabling step-length control, named LSL-BFGS (limited step length BFGS), and the empirical JAMDA scoring function designed for pose prediction and good numerical optimizability. The JAMDA scoring function shows a high pose prediction performance in the CASF-2016 docking power benchmark, top-ranking a pose with an RMSD of ≤2 Å in about 89% of the cases. The combination of JAMDA scoring with the LSL-BFGS algorithm shows a significantly higher optimization locality (i.e., no excessive movement of poses) than with the classical BFGS algorithm while retaining the characteristically low number of scoring function evaluations. The JAMDA scoring and optimization scheme is freely available for noncommercial use and academic research.
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Affiliation(s)
- Florian Flachsenberg
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Agnes Meyder
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Kai Sommer
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Patrick Penner
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
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12
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Penner P, Martiny V, Gohier A, Gastreich M, Ducrot P, Brown D, Rarey M. Shape-Based Descriptors for Efficient Structure-Based Fragment Growing. J Chem Inf Model 2020; 60:6269-6281. [PMID: 33196169 DOI: 10.1021/acs.jcim.0c00920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structure-based fragment growing is one of the key techniques in fragment-based drug design. Fragment growing is commonly practiced based on structural and biophysical data. Computational workflows are employed to predict which fragment elaborations could lead to high-affinity binders. Several such workflows exist but many are designed to be long running noninteractive systems. Shape-based descriptors have been proven to be fast and perform well at virtual-screening tasks. They could, therefore, be applied to the fragment-growing problem to enable an interactive fragment-growing workflow. In this work, we describe and analyze the use of specific shape-based directional descriptors for the task of fragment growing. The performance of these descriptors that we call ray volume matrices (RVMs) is evaluated on two data sets containing protein-ligand complexes. While the first set focuses on self-growing, the second measures practical performance in a cross-growing scenario. The runtime of screenings using RVMs as well as their robustness to three dimensional perturbations is also investigated. Overall, it can be shown that RVMs are useful to prefilter fragment candidates. For up to 84% of the 3299 generated self-growing cases and for up to 66% of the 326 generated cross-growing cases, RVMs could create poses with less than 2 Å root-mean-square deviation to the crystal structure with average query speeds of around 30,000 conformations per second. This opens the door for fast explorative screenings of fragment libraries.
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Affiliation(s)
- Patrick Penner
- ZBH-Center for Bioinformatics, Universität Hamburg, Bundesstr. 43, 20146 Hamburg, Germany
| | - Virginie Martiny
- Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France
| | - Arnaud Gohier
- Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France
| | - Marcus Gastreich
- BioSolveIT GmbH, An der Ziegelei 79, 53757 Sankt Augustin, Germany
| | - Pierre Ducrot
- Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France
| | - David Brown
- Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France
| | - Matthias Rarey
- ZBH-Center for Bioinformatics, Universität Hamburg, Bundesstr. 43, 20146 Hamburg, Germany
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13
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Varela-Rial A, Majewski M, Cuzzolin A, Martínez-Rosell G, De Fabritiis G. SkeleDock: A Web Application for Scaffold Docking in PlayMolecule. J Chem Inf Model 2020; 60:2673-2677. [PMID: 32407111 DOI: 10.1021/acs.jcim.0c00143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SkeleDock is a scaffold docking algorithm which uses the structure of a protein-ligand complex as a template to model the binding mode of a chemically similar system. This algorithm was evaluated in the D3R Grand Challenge 4 pose prediction challenge, where it achieved competitive performance. Furthermore, we show that if crystallized fragments of the target ligand are available then SkeleDock can outperform rDock docking software at predicting the binding mode. This Application Note also addresses the capacity of this algorithm to model macrocycles and deal with scaffold hopping. SkeleDock can be accessed at https://playmolecule.org/SkeleDock/.
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Affiliation(s)
- Alejandro Varela-Rial
- Acellera Labs, Doctor Trueta 183, Barcelona, Spain.,Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
| | - Maciej Majewski
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
| | | | | | - Gianni De Fabritiis
- Acellera Labs, Doctor Trueta 183, Barcelona, Spain.,Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, Barcelona, Spain
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14
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Rachman M, Bajusz D, Hetényi A, Scarpino A, Merő B, Egyed A, Buday L, Barril X, Keserű GM. Discovery of a novel kinase hinge binder fragment by dynamic undocking. RSC Med Chem 2020; 11:552-558. [PMID: 33479656 PMCID: PMC7593776 DOI: 10.1039/c9md00519f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/11/2020] [Indexed: 12/17/2022] Open
Abstract
A virtual screening workflow for fragment-sized kinase inhibitors is presented, along with a newly identified and validated hinge binder fragment.
One of the key motifs of type I kinase inhibitors is their interactions with the hinge region of ATP binding sites. These interactions contribute significantly to the potency of the inhibitors; however, only a tiny fraction of the available chemical space has been explored with kinase inhibitors reported in the last twenty years. This paper describes a workflow utilizing docking with rDock and dynamic undocking (DUck) for the virtual screening of fragment libraries in order to identify fragments that bind to the kinase hinge region. We have identified 8-amino-2H-isoquinolin-1-one (MR1), a novel and potent hinge binding fragment, which was experimentally tested on a diverse set of kinases, and is hereby suggested for future fragment growing or merging efforts against various kinases, particularly MELK. Direct binding of MR1 to MELK was confirmed by STD-NMR, and its binding to the ATP-pocket was confirmed by a new competitive binding assay based on microscale thermophoresis.
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Affiliation(s)
- Moira Rachman
- Facultat de Farmàcia and Institut de Biomedicina , Universitat de Barcelona , Av. Joan XXIII 27-31 , 08028 Barcelona , Spain.,Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary .
| | - Dávid Bajusz
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary .
| | - Anasztázia Hetényi
- Department of Medical Chemistry , University of Szeged , Dóm tér 8 , H-6720 Szeged , Hungary
| | - Andrea Scarpino
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary .
| | - Balázs Merő
- Signal Transduction and Functional Genomics Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary
| | - Attila Egyed
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary .
| | - László Buday
- Signal Transduction and Functional Genomics Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary
| | - Xavier Barril
- Facultat de Farmàcia and Institut de Biomedicina , Universitat de Barcelona , Av. Joan XXIII 27-31 , 08028 Barcelona , Spain.,Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys 23 , 08010 Barcelona , Spain
| | - György M Keserű
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary .
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15
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Abramyan TM, An Y, Kireev D. Off-Pocket Activity Cliffs: A Puzzling Facet of Molecular Recognition. J Chem Inf Model 2019; 60:152-161. [PMID: 31790251 DOI: 10.1021/acs.jcim.9b00731] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
While accurate quantitative prediction of ligand-protein binding affinity remains an elusive goal, high-affinity ligands to therapeutic targets are being designed through heuristic optimization of ligand-protein contacts. However, herein, through large-scale data mining and analyses, we demonstrate that a ligand's binding can also be strongly affected through modifying its solvent-exposed portion that does not make contacts with the protein, thus resulting in "off-pocket activity cliffs" (OAC). We then exposed the roots of the OAC phenomenon by means of molecular dynamics (MD) simulations and MD data analyses. We expect OAC to extend our knowledge of molecular recognition and enhance the drug designer's toolkit.
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Affiliation(s)
- Tigran M Abramyan
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , 27599-7363
| | - Yi An
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , 27599-7363
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , 27599-7363
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16
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Majewski M, Ruiz-Carmona S, Barril X. An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder. Commun Chem 2019. [DOI: 10.1038/s42004-019-0205-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
The predominant view in structure-based drug design is that small-molecule ligands, once bound to their target structures, display a well-defined binding mode. However, structural stability (robustness) is not necessary for thermodynamic stability (binding affinity). In fact, it entails an entropic penalty that counters complex formation. Surprisingly, little is known about the causes, consequences and real degree of robustness of protein-ligand complexes. Since hydrogen bonds have been described as essential for structural stability, here we investigate 469 such interactions across two diverse structure sets, comprising of 79 drug-like and 27 fragment ligands, respectively. Completely constricted protein-ligand complexes are rare and may fulfill a functional role. Most complexes balance order and disorder by combining a single anchoring point with looser regions. 25% do not contain any robust hydrogen bond and may form loose structures. Structural stability analysis reveals a hidden layer of complexity in protein-ligand complexes that should be considered in ligand design.
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17
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Pandey VK, Singh VK, Chandra S, Hasan SH. Coordination polymeric fluorescent gel: effect of removal of branch substituents of the central core over properties. J COORD CHEM 2019. [DOI: 10.1080/00958972.2019.1606908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Vinay Kumar Pandey
- Department of Chemistry, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, India
| | - Vikas Kumar Singh
- Department of Chemistry, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, India
| | - Subhash Chandra
- Department of Chemistry, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, India
| | - Syed Hadi Hasan
- Department of Chemistry, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, India
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18
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Bai N, Roder H, Dickson A, Karanicolas J. Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities. Sci Rep 2019; 9:2650. [PMID: 30804351 PMCID: PMC6389909 DOI: 10.1038/s41598-018-37072-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/30/2018] [Indexed: 01/20/2023] Open
Abstract
Differential scanning fluorimetry (DSF), also known as ThermoFluor or Thermal Shift Assay, has become a commonly-used approach for detecting protein-ligand interactions, particularly in the context of fragment screening. Upon binding to a folded protein, most ligands stabilize the protein; thus, observing an increase in the temperature at which the protein unfolds as a function of ligand concentration can serve as evidence of a direct interaction. While experimental protocols for this assay are well-developed, it is not straightforward to extract binding constants from the resulting data. Because of this, DSF is often used to probe for an interaction, but not to quantify the corresponding binding constant (Kd). Here, we propose a new approach for analyzing DSF data. Using unfolding curves at varying ligand concentrations, our "isothermal" approach collects from these the fraction of protein that is folded at a single temperature (chosen to be temperature near the unfolding transition). This greatly simplifies the subsequent analysis, because it circumvents the complicating temperature dependence of the binding constant; the resulting constant-temperature system can then be described as a pair of coupled equilibria (protein folding/unfolding and ligand binding/unbinding). The temperature at which the binding constants are determined can also be tuned, by adding chemical denaturants that shift the protein unfolding temperature. We demonstrate the application of this isothermal analysis using experimental data for maltose binding protein binding to maltose, and for two carbonic anhydrase isoforms binding to each of four inhibitors. To facilitate adoption of this new approach, we provide a free and easy-to-use Python program that analyzes thermal unfolding data and implements the isothermal approach described herein ( https://sourceforge.net/projects/dsf-fitting ).
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Heinrich Roder
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Alex Dickson
- Department of Biochemistry & Molecular Biology and Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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19
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Sommer K, Flachsenberg F, Rarey M. NAOMInext – Synthetically feasible fragment growing in a structure-based design context. Eur J Med Chem 2019; 163:747-762. [DOI: 10.1016/j.ejmech.2018.11.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022]
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20
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Adlere I, Sun S, Zarca A, Roumen L, Gozelle M, Viciano CP, Caspar B, Arimont M, Bebelman JP, Briddon SJ, Hoffmann C, Hill SJ, Smit MJ, Vischer HF, Wijtmans M, de Graaf C, de Esch IJP, Leurs R. Structure-based exploration and pharmacological evaluation of N-substituted piperidin-4-yl-methanamine CXCR4 chemokine receptor antagonists. Eur J Med Chem 2018; 162:631-649. [PMID: 30476826 DOI: 10.1016/j.ejmech.2018.10.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/23/2018] [Accepted: 10/27/2018] [Indexed: 01/20/2023]
Abstract
Using the available structural information of the chemokine receptor CXCR4, we present hit finding and hit exploration studies that make use of virtual fragment screening, design, synthesis and structure-activity relationship (SAR) studies. Fragment 2 was identified as virtual screening hit and used as a starting point for the exploration of 31 N-substituted piperidin-4-yl-methanamine derivatives to investigate and improve the interactions with the CXCR4 binding site. Additionally, subtle structural ligand changes lead to distinct interactions with CXCR4 resulting in a full to partial displacement of CXCL12 binding and competitive and/or non-competitive antagonism. Three-dimensional quantitative structure-activity relationship (3D-QSAR) and binding model studies were used to identify important hydrophobic interactions that determine binding affinity and indicate key ligand-receptor interactions.
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Affiliation(s)
- I Adlere
- Griffin Discoveries BV, Amsterdam, the Netherlands
| | - S Sun
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - A Zarca
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - L Roumen
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - M Gozelle
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06560, Ankara, Turkey
| | - C Perpiñá Viciano
- Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich-Schiller University Jena, Hans-Knöll-Strasse 2, 07745, Jena, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078, Würzburg, Germany
| | - B Caspar
- Division of Pharmacology, Physiology and Neuroscience and Centre of Membrane Proteins and Receptors (COMPARE), School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - M Arimont
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - J P Bebelman
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - S J Briddon
- Division of Pharmacology, Physiology and Neuroscience and Centre of Membrane Proteins and Receptors (COMPARE), School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - C Hoffmann
- Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich-Schiller University Jena, Hans-Knöll-Strasse 2, 07745, Jena, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078, Würzburg, Germany
| | - S J Hill
- Division of Pharmacology, Physiology and Neuroscience and Centre of Membrane Proteins and Receptors (COMPARE), School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - M J Smit
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - H F Vischer
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - M Wijtmans
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - C de Graaf
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - I J P de Esch
- Griffin Discoveries BV, Amsterdam, the Netherlands; Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - R Leurs
- Griffin Discoveries BV, Amsterdam, the Netherlands; Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.
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21
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Drwal MN, Bret G, Perez C, Jacquemard C, Desaphy J, Kellenberger E. Structural Insights on Fragment Binding Mode Conservation. J Med Chem 2018; 61:5963-5973. [PMID: 29906118 DOI: 10.1021/acs.jmedchem.8b00256] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Aiming at a deep understanding of fragment binding to ligandable targets, we performed a large scale analysis of the Protein Data Bank. Binding modes of 1832 drug-like ligands and 1079 fragments to 235 proteins were compared. We observed that the binding modes of fragments and their drug-like superstructures binding to the same protein are mostly conserved, thereby providing experimental evidence for the preservation of fragment binding modes during molecular growing. Furthermore, small chemical changes in the fragment are tolerated without alteration of the fragment binding mode. The exceptions to this observation generally involve conformational variability of the molecules. Our data analysis also suggests that, provided enough fragments have been crystallized within a protein, good interaction coverage of the binding pocket is achieved. Last, we extended our study to 126 crystallization additives and discuss in which cases they provide information relevant to structure-based drug design.
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Affiliation(s)
- Malgorzata N Drwal
- Laboratoire d'Innovation Thérapeutique , UMR7200, Université de Strasbourg , 74 Route du Rhin , 67401 Illkirch , France
| | - Guillaume Bret
- Laboratoire d'Innovation Thérapeutique , UMR7200, Université de Strasbourg , 74 Route du Rhin , 67401 Illkirch , France
| | - Carlos Perez
- Eli Lilly Research Laboratories , Avenida de la Industria, 30 , 28108 Alcobendas , Madrid , Spain
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique , UMR7200, Université de Strasbourg , 74 Route du Rhin , 67401 Illkirch , France
| | - Jérémy Desaphy
- Lilly Research Laboratories, Eli Lilly and Company , Lilly Corporate Center , Indianapolis , Indiana 46285 , United States
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique , UMR7200, Université de Strasbourg , 74 Route du Rhin , 67401 Illkirch , France
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22
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Fu D, Meiler J. RosettaLigandEnsemble: A Small-Molecule Ensemble-Driven Docking Approach. ACS OMEGA 2018; 3:3655-3664. [PMID: 29732444 PMCID: PMC5928483 DOI: 10.1021/acsomega.7b02059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 03/20/2018] [Indexed: 05/27/2023]
Abstract
RosettaLigand is a protein-small-molecule (ligand) docking software capable of predicting binding poses and is used for virtual screening of medium-sized ligand libraries. Structurally similar small molecules are generally found to bind in the same pose to one binding pocket, despite some prominent exceptions. To make use of this information, we have developed RosettaLigandEnsemble (RLE). RLE docks a superimposed ensemble of congeneric ligands simultaneously. The program determines a well-scoring overall pose for this superimposed ensemble before independently optimizing individual protein-small-molecule interfaces. In a cross-docking benchmark of 89 protein-small-molecule co-crystal structures across 20 biological systems, we found that RLE improved sampling efficiency in 62 cases, with an average change of 18%. In addition, RLE generated more consistent docking results within a congeneric series and was capable of rescuing the unsuccessful docking of individual ligands, identifying a nativelike top-scoring model in 10 additional cases. The improvement in RLE is driven by a balance between having a sizable common chemical scaffold and meaningful modifications to distal groups. The new ensemble docking algorithm will work well in conjunction with medicinal chemistry structure-activity relationship (SAR) studies to more accurately recapitulate protein-ligand interfaces. We also tested whether optimizing the rank correlation of RLE-binding scores to SAR data in the refinement step helps the high-resolution positioning of the ligand. However, no significant improvement was observed.
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23
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Kaiser CE, Rincon Pabon JP, Khowsathit J, Castaldi MP, Kazmirski SL, Weis DD, Zhang AX, Karanicolas J. Modulating Antibody Structure and Function through Directed Mutations and Chemical Rescue. ACS Synth Biol 2018; 7:1152-1162. [PMID: 29609459 DOI: 10.1021/acssynbio.8b00124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Monoclonal antibody therapeutics have revolutionized the treatment of diseases such as cancer and autoimmune disorders, and also serve as research reagents for diverse and unparalleled applications. To extend their utility in both contexts, we have begun development of tunable antibodies, whose activity can be controlled by addition of a small molecule. Conceptually, we envision that incorporating cavity-forming mutations into an antibody can disrupt its structure, thereby reducing its affinity for antigen; addition of a small molecule may then restore the active structure, and thus rescue antigen binding. As a first proof of concept toward implementing this strategy, we have incorporated individual tryptophan to glycine mutations into FITC-E2, an anti-fluorescein single-chain variable fragment (scFv). We find that these can disrupt the protein structure and diminish antigen binding, and further that both structure and function can be rescued by addition of indole to complement the deleted side chain. While the magnitude of the affinity difference triggered by indole is modest in this first model system, it nonetheless provides a framework for future mutation/ligand pairs that may induce more dramatic responses. Disrupting and subsequently rescuing antibody activity, as exemplified by this first example, may represent a new approach to "design in" fine-tuned control of antibody activity for a variety of future applications.
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Affiliation(s)
- Christine E. Kaiser
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Juan Pablo Rincon Pabon
- Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Jittasak Khowsathit
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| | - M. Paola Castaldi
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Steven L. Kazmirski
- Structure and Biophysics, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - David D. Weis
- Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Andrew X. Zhang
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - John Karanicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
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24
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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.
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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
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Fu DY, Meiler J. Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review. J Chem Inf Model 2018; 58:225-233. [PMID: 29286651 DOI: 10.1021/acs.jcim.7b00418] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Incorporating experimental restraints is a powerful method of increasing accuracy in computational protein small molecule docking simulations. Different algorithms integrate distinct forms of biochemical data during the docking and/or scoring stages. These so-called hybrid methods make use of receptor-based information such as nuclear magnetic resonance (NMR) restraints or small molecule-based information such as structure-activity relationships (SARs). A third class of methods directly interrogates contacts between the protein receptor and the small molecule. This work reviews the current state of using such restraints in docking simulations, evaluates their feasibility across broad systems, and identifies potential areas of algorithm development.
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Affiliation(s)
- Darwin Y Fu
- Department of Chemistry Vanderbilt University Nashville, Tennessee 37235, United States
| | - Jens Meiler
- Department of Chemistry Vanderbilt University Nashville, Tennessee 37235, United States
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The versatility of boron in biological target engagement. Nat Chem 2017; 9:731-742. [DOI: 10.1038/nchem.2814] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/12/2017] [Indexed: 12/20/2022]
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Drwal MN, Bret G, Kellenberger E. Multi-target Fragments Display Versatile Binding Modes. Mol Inform 2017; 36. [PMID: 28691374 DOI: 10.1002/minf.201700042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/30/2017] [Indexed: 11/10/2022]
Abstract
Promiscuity is an interesting concept in fragment-based drug design as fragments with low specificity can be advantageous for finding many screening hits. We present a PDB-wide analysis of multi-target fragments and their binding mode conservation. Focussing on multi-target fragments, we found that the majority shows non-conserved binding modes, even if they bind in a similar conformation or similar protein targets. Surprisingly, fragment properties alone are not able to predict whether a fragment will exhibit a versatile or conserved binding mode, emphasizing the interplay between protein and fragment features during a binding event and the importance of structure-based modelling.
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Affiliation(s)
- Malgorzata N Drwal
- UMR 7200 - Laboratoire d'Innovation Thérapeutique, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France phone: +33 3 68 85 42 21 fax: +33 3 68 85 43 10
| | - Guillaume Bret
- UMR 7200 - Laboratoire d'Innovation Thérapeutique, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France phone: +33 3 68 85 42 21 fax: +33 3 68 85 43 10
| | - Esther Kellenberger
- UMR 7200 - Laboratoire d'Innovation Thérapeutique, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France phone: +33 3 68 85 42 21 fax: +33 3 68 85 43 10
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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.
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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
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