1
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Małecki PH, Fassauer GM, Rüger N, Schulig L, Link A, Krylova O, Heinemann U, Weiss MS. Structure-based mapping of the histone-binding pocket of KDM4D using functionalized tetrazole and pyridine core compounds. Eur J Med Chem 2024; 276:116642. [PMID: 38981336 DOI: 10.1016/j.ejmech.2024.116642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024]
Abstract
KDM4 histone demethylases became an exciting target for inhibitor development as the evidence linking them directly to tumorigenesis mounts. In this study, we set out to better understand the binding cavity using an X-ray crystallographic approach to provide a detailed landscape of possible interactions within the under-investigated region of KDM4. Our design strategy was based on utilizing known KDM binding motifs, such as nicotinic acid and tetrazolylhydrazides, as core motifs that we decided to enrich with flexible tails to map the distal histone binding site. The resulting X-ray structures of the novel compounds bound to KDM4D, a representative of the KDM4 family, revealed the interaction pattern with distal residues in the histone-binding site. The most prominent protein rearrangement detected upon ligand binding is the loop movement that blocks the accessibility to the histone binding site. Apart from providing new sites that potential inhibitors can target, the novel compounds may prove helpful in exploring the capacity of ligands to bind in sites distal to the cofactor-binding site of other KDMs or 2-oxoglutarate (2OG)-dependent oxygenases. The case study proves that combining a strong small binding motif with flexible tails to probe the binding pocket will facilitate lead discovery in classical drug-discovery campaigns, given the ease of accessing X-ray quality crystals.
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Affiliation(s)
- Piotr H Małecki
- Macromolecular Structure and Interaction, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany; Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489, Berlin, Germany; Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego-Str. 12/14, 61-704, Poznań, Poland.
| | - Georg M Fassauer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Universität Greifswald, Friedrich-Ludwig-Jahn-Straße 17, 17489, Greifswald, Germany
| | - Nicole Rüger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Universität Greifswald, Friedrich-Ludwig-Jahn-Straße 17, 17489, Greifswald, Germany
| | - Lukas Schulig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Universität Greifswald, Friedrich-Ludwig-Jahn-Straße 17, 17489, Greifswald, Germany
| | - Andreas Link
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Universität Greifswald, Friedrich-Ludwig-Jahn-Straße 17, 17489, Greifswald, Germany
| | - Oxana Krylova
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Udo Heinemann
- Macromolecular Structure and Interaction, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489, Berlin, Germany
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2
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Bennett GM, Starczewski J, dela Cerna MVC. In silico identification of putative druggable pockets in PRL3, a significant oncology target. Biochem Biophys Rep 2024; 39:101767. [PMID: 39050014 PMCID: PMC11267023 DOI: 10.1016/j.bbrep.2024.101767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/19/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Protein tyrosine phosphatases (PTP) have emerged as targets in diseases characterized by aberrant phosphorylations such as cancers. The activity of the phosphatase of regenerating liver 3, PRL3, has been linked to several oncogenic and metastatic pathways, particularly in breast, ovarian, colorectal, and blood cancers. Development of small molecules that directly target PRL3, however, has been challenging. This is partly due to the lack of structural information on how PRL3 interacts with its inhibitors. Here, computational methods are used to bridge this gap by evaluating the druggability of PRL3. In particular, web-based pocket prediction tools, DoGSite3 and FTMap, were used to identify binding pockets using structures of PRL3 currently available in the Protein Data Bank. Druggability assessment by molecular dynamics simulations with probes was also performed to validate these results and to predict the strength of binding in the identified pockets. While several druggable pockets were identified, those in the closed conformation show more promise given their volume and depth. These two pockets flank the active site loops and roughly correspond to pockets predicted by molecular docking in previous papers. Notably, druggability simulations predict the possibility of low nanomolar affinity inhibitors in these sites implying the potential to identify highly potent small molecule inhibitors for PRL3. Putative pockets identified here can be leveraged for high-throughput virtual screening to further accelerate the drug discovery against PRL3 and development of PRL3-directed therapeutics.
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Affiliation(s)
- Grace M. Bennett
- Department of Biochemistry, Chemistry, and Physics, Georgia Southern University, Savannah, GA, 31419, USA
| | - Julia Starczewski
- Department of Biochemistry, Chemistry, and Physics, Georgia Southern University, Savannah, GA, 31419, USA
| | - Mark Vincent C. dela Cerna
- Department of Biochemistry, Chemistry, and Physics, Georgia Southern University, Savannah, GA, 31419, USA
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3
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Xie S, Liang Y, Song Y, Li T, Jia J. Repurposing Anidulafungin for Alzheimer's Disease via Fragment-Based Drug Discovery. ACS Chem Neurosci 2024; 15:2995-3008. [PMID: 39096284 PMCID: PMC11342299 DOI: 10.1021/acschemneuro.4c00150] [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: 03/15/2024] [Revised: 06/19/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024] Open
Abstract
The misfolding and aggregation of beta-amyloid (Aβ) peptides have been implicated as key pathogenic events in the early stages of Alzheimer's disease (AD). Inhibiting Aβ aggregation represents a potential disease-modifying therapeutic approach to AD treatment. Previous studies have identified various molecules that inhibit Aβ aggregation, some of which share common chemical substructures (fragments) that may be key to their inhibitory activity. Employing fragment-based drug discovery (FBDD) methods may facilitate the identification of these fragments, which can subsequently be used to screen new inhibitors and provide leads for further drug development. In this study, we used an in silico FBDD approach to identify 17 fragment clusters that are significantly enriched among Aβ aggregation inhibitors. These fragments were then used to screen anti-infective agents, a promising drug class for repurposing against amyloid aggregation. This screening process identified 16 anti-infective drugs, 5 of which were chosen for further investigation. Among the 5 candidates, anidulafungin, an antifungal compound, showed high efficacy in inhibiting Aβ aggregation in vitro. Kinetic analysis revealed that anidulafungin selectively blocks the primary nucleation step of Aβ aggregation, substantially delaying Aβ fibril formation. Cell viability assays demonstrated that anidulafungin can reduce the toxicity of oligomeric Aβ on BV2 microglia cells. Molecular docking simulations predicted that anidulafungin interacted with various Aβ species, including monomers, oligomers, and fibrils, potentially explaining its activity against Aβ aggregation and toxicity. This study suggests that anidulafungin is a potential drug to be repurposed for AD, and FBDD is a promising approach for discovering drugs to combat Aβ aggregation.
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Affiliation(s)
- Siqi Xie
- Innovation
Center for Neurological Disorders and Department of Neurology, Xuanwu
Hospital, Capital Medical University, National
Clinical Research Center for Geriatric Diseases, Beijing 100053, P. R. China
| | - Yumei Liang
- Innovation
Center for Neurological Disorders and Department of Neurology, Xuanwu
Hospital, Capital Medical University, National
Clinical Research Center for Geriatric Diseases, Beijing 100053, P. R. China
| | - Yang Song
- Innovation
Center for Neurological Disorders and Department of Neurology, Xuanwu
Hospital, Capital Medical University, National
Clinical Research Center for Geriatric Diseases, Beijing 100053, P. R. China
| | - Tingting Li
- Innovation
Center for Neurological Disorders and Department of Neurology, Xuanwu
Hospital, Capital Medical University, National
Clinical Research Center for Geriatric Diseases, Beijing 100053, P. R. China
| | - Jianping Jia
- Innovation
Center for Neurological Disorders and Department of Neurology, Xuanwu
Hospital, Capital Medical University, National
Clinical Research Center for Geriatric Diseases, Beijing 100053, P. R. China
- Beijing
Key Laboratory of Geriatric Cognitive Disorders, Beijing 100053, P. R. China
- Clinical
Center for Neurodegenerative Disease and Memory Impairment, Capital Medical University, Beijing 100053, P. R. China
- Center
of Alzheimer’s Disease, Beijing Institute of Brain Disorders,
Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing 100053, P. R. China
- Key
Laboratory of Neurodegenerative Diseases, Ministry of Education, Beijing 100053, P. R. China
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4
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Ábrányi-Balogh P, Bajusz D, Orgován Z, Keeley AB, Petri L, Péczka N, Szalai TV, Pálfy G, Gadanecz M, Grant EK, Imre T, Takács T, Ranđelović I, Baranyi M, Marton A, Schlosser G, Ashraf QF, de Araujo ED, Karancsi T, Buday L, Tóvári J, Perczel A, Bush JT, Keserű GM. Mapping protein binding sites by photoreactive fragment pharmacophores. Commun Chem 2024; 7:168. [PMID: 39085342 PMCID: PMC11292009 DOI: 10.1038/s42004-024-01252-w] [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: 06/01/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024] Open
Abstract
Fragment screening is a popular strategy of generating viable chemical starting points especially for challenging targets. Although fragments provide a better coverage of chemical space and they have typically higher chance of binding, their weak affinity necessitates highly sensitive biophysical assays. Here, we introduce a screening concept that combines evolutionary optimized fragment pharmacophores with the use of a photoaffinity handle that enables high hit rates by LC-MS-based detection. The sensitivity of our screening protocol was further improved by a target-conjugated photocatalyst. We have designed, synthesized, and screened 100 diazirine-tagged fragments against three benchmark and three therapeutically relevant protein targets of different tractability. Our therapeutic targets included a conventional enzyme, the first bromodomain of BRD4, a protein-protein interaction represented by the oncogenic KRasG12D protein, and the yet unliganded N-terminal domain of the STAT5B transcription factor. We have discovered several fragment hits against all three targets and identified their binding sites via enzymatic digestion, structural studies and modeling. Our results revealed that this protocol outperforms screening traditional fully functionalized and photoaffinity fragments in better exploration of the available binding sites and higher hit rates observed for even difficult targets.
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Affiliation(s)
- Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Aaron B Keeley
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - László Petri
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Nikolett Péczka
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Tibor Viktor Szalai
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology & HUN-REN-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
| | - Márton Gadanecz
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Laboratory of Structural Chemistry and Biology & HUN-REN-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | | | - Tímea Imre
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- MS Metabolomics Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Takács
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Signal Transduction and Functional Genomics Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ivan Ranđelović
- National Tumor Biology Laboratory and Department of Experimental Pharmacology, National Institute of Oncology, Budapest, Hungary
- KINETO Lab Ltd, Budapest, Hungary
| | - Marcell Baranyi
- KINETO Lab Ltd, Budapest, Hungary
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - András Marton
- Department of Chemical and Environmental Process Engineering, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Waters Research Center, Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Eötvös Loránd University, Budapest, Hungary
| | - Qirat F Ashraf
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Elvin D de Araujo
- Centre for Medicinal Chemistry, University of Toronto at Mississauga, Mississauga, ON, Canada
| | - Tamás Karancsi
- Department of Chemical and Environmental Process Engineering, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Waters Research Center, Budapest, Hungary
| | - László Buday
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Signal Transduction and Functional Genomics Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - József Tóvári
- National Tumor Biology Laboratory and Department of Experimental Pharmacology, National Institute of Oncology, Budapest, Hungary
| | - András Perczel
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Laboratory of Structural Chemistry and Biology & HUN-REN-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
| | | | - György M Keserű
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
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5
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Labrecque C, Fuglestad B. Ligandability at the Membrane Interface of GPx4 Revealed through a Reverse Micelle Fragment Screening Platform. JACS AU 2024; 4:2676-2686. [PMID: 39055139 PMCID: PMC11267533 DOI: 10.1021/jacsau.4c00427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
While they account for a large portion of drug targets, membrane proteins present a unique challenge for drug discovery. Peripheral membrane proteins (PMPs), a class of water-soluble proteins that bind to membranes, are also difficult targets, particularly those that function only when bound to membranes. The protein-membrane interface in PMPs is often where functional interactions and catalysis occur, making it a logical target for inhibition. However, protein-membrane interfaces are underexplored spaces in inhibitor design, and there is a need for enhanced methods for small-molecule ligand discovery. In an effort to better initiate drug discovery efforts for PMPs, this study presents a screening methodology using membrane-mimicking reverse micelles (mmRM) and NMR-based fragment screening to assess ligandability at the protein-membrane interface. The proof-of-principle target, glutathione peroxidase 4 (GPx4), is a lipid hydroperoxidase that is essential for the oxidative protection of membranes and thereby the prevention of ferroptosis. GPx4 inhibition is promising for therapy-resistant cancer therapy, but current inhibitors are generally covalent ligands with limited clinical utility. Presented here is the discovery of noncovalent small-molecule ligands for membrane-bound GPx4 revealed through the mmRM fragment screening methodology. The fragments were tested against GPx4 under bulk aqueous conditions and displayed little to no binding to the protein without embedment into the membrane. The 9 hits had varying affinities and partitioning coefficients and revealed properties of fragments that bind within the protein-membrane interface. Additionally, a secondary screen confirmed the potential to progress the fragments by enhancing the affinity from >200 to ∼15 μM with the addition of certain hydrophobic groups. This study presents an advancement of screening capabilities for membrane-associated proteins, reveals ligandability within the GPx4 protein-membrane interface, and may serve as a starting point for developing noncovalent inhibitors of GPx4.
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Affiliation(s)
- Courtney
L. Labrecque
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Brian Fuglestad
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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6
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Sternicki LM, Poulsen SA. Fragment-based drug discovery campaigns guided by native mass spectrometry. RSC Med Chem 2024; 15:2270-2285. [PMID: 39026646 PMCID: PMC11253872 DOI: 10.1039/d4md00273c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/19/2024] [Indexed: 07/20/2024] Open
Abstract
Native mass spectrometry (nMS) is well established as a biophysical technique for characterising biomolecules and their interactions with endogenous or investigational small molecule ligands. The high sensitivity mass measurements make nMS particularly well suited for applications in fragment-based drug discovery (FBDD) screening campaigns where the detection of weakly binding ligands to a target biomolecule is crucial. We first reviewed the contributions of nMS to guiding FBDD hit identification in 2013, providing a comprehensive perspective on the early adoption of nMS for fragment screening. Here we update this initial progress with a focus on contributions of nMS that have guided FBDD for the period 2014 until end of 2023. We highlight the development of nMS adoption in FBDD in the context of other biophysical fragment screening techniques. We also discuss the roadmap for increased adoption of nMS for fragment screening beyond soluble proteins, including for guiding the discovery of fragments supporting advances in PROTAC discovery, RNA-binding small molecules and covalent therapeutic drug discovery.
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Affiliation(s)
- Louise M Sternicki
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
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7
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Klett T, Schwer M, Ernst LN, Engelhardt MU, Jaag SJ, Masberg B, Knappe C, Lämmerhofer M, Gehringer M, Boeckler FM. Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53. Drug Des Devel Ther 2024; 18:2653-2679. [PMID: 38974119 PMCID: PMC11226190 DOI: 10.2147/dddt.s466829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN). Methods After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5'-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS). Results In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53. Conclusion The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and -9.1 °C.
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Affiliation(s)
- Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Martin Schwer
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Larissa N Ernst
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Marc U Engelhardt
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Simon J Jaag
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Benedikt Masberg
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Matthias Gehringer
- Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Medicinal Chemistry, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
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8
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Holder L, Yuce E, Oriomah G, Jenkins AP, Reynisson J, Winter A, Cosgrove SC. Accessing Active Fragments for Drug Discovery Utilising Nitroreductase Biocatalysis. Chembiochem 2024:e202400428. [PMID: 38940076 DOI: 10.1002/cbic.202400428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 06/29/2024]
Abstract
Biocatalysis has played a limited role in the early stages of drug discovery. This is often attributed to the limited substrate scope of enzymes not affording access to vast areas of novel chemical space. Here, we have shown a promiscuous nitroreductase enzyme (NR-55) can be used to produce a panel of functionalised anilines from a diverse panel of aryl nitro starting materials. After screening on analytical scale, we show that sixteen substrates could be scaled to 1 mmol scale, with several poly-functional anilines afforded with ease under the standard conditions. The aniline products were also screened for activity against several cell lines of interest, with modest activity observed for one compound. This study demonstrates the potential for nitroreductase biocatalysis to provide access to functional fragments under benign conditions.
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Affiliation(s)
- Lauren Holder
- School of Chemical and Physical Sciences & Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Eda Yuce
- School of Life Sciences, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Gabriel Oriomah
- School of Life Sciences, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Aimee-Page Jenkins
- School of Chemical and Physical Sciences & Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Jóhannes Reynisson
- School of Life Sciences, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
- School of Pharmacy, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Anja Winter
- School of Life Sciences, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Sebastian C Cosgrove
- School of Chemical and Physical Sciences & Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
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9
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McCarthy WJ, Thomas SE, Olaleye T, Boland JA, Floto RA, Williams G, Blundell TL, Coyne AG, Abell C. A Fragment-Based Competitive 19F LB-NMR Platform For Hotspot-Directed Ligand Profiling. Angew Chem Int Ed Engl 2024:e202406846. [PMID: 38896426 DOI: 10.1002/anie.202406846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/19/2024] [Accepted: 06/19/2024] [Indexed: 06/21/2024]
Abstract
Ligand binding hotspots are regions of protein surfaces that form particularly favourable interactions with small molecule pharmacophores. Targeting interactions with these hotspots maximises the efficiency of ligand binding. Existing methods are capable of identifying hotspots but often lack assays to quantify ligand binding and direct elaboration at these sites. Herein, we describe a fragment-based competitive 19F Ligand Based NMR (LB-NMR) screening platform that enables routine, quantitative ligand profiling focused at ligand-binding hotspots. As a proof of concept, the method was applied to 4'-phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium abscessus (Mabs). X-ray crystallographic characterisation of the hits from a 960-member fragment screen identified three ligand-binding hotspots across the PPAT active site. From the fragment hits a collection of 19F reporter candidates were designed and synthesised. By rigorous prioritisation and use of optimisation workflows, a single 19F reporter molecule was generated for each hotspot. Profiling the binding of a set of structurally characterised ligands by competitive 19F LB-NMR with this suite of 19F reporters recapitulated the binding affinity and site ID assignments made by ITC and X-ray crystallography. This quantitative mapping of ligand binding events at hotspot level resolution establishes the utility of the fragment-based competitive 19F LB-NMR screening platform for hotspot-directed ligand profiling.
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Affiliation(s)
- William J McCarthy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
- Present Address: Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, UK, NW1 1AT
| | - Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK, CB2 1GA
- Present Address: Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK, CB2 1PD
| | - Tayo Olaleye
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Jennifer A Boland
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - R Andres Floto
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK, CB2 0QH
- VPD Heart Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK, CB2 0BB
| | - Glyn Williams
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK, CB2 1GA
- VPD Heart Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK, CB2 0BB
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
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10
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Huyen NTT, Phuc BV, Huyen TT, Hong TT, Nguyen H, Nguyen VH, Nguyen MT, Hung TQ, Dinh CP, Dang TT. Design and Synthesis of Novel β-Carboline-Bisindole Hybrids as Potential Anticancer Agents. ChemMedChem 2024:e202400316. [PMID: 38856518 DOI: 10.1002/cmdc.202400316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
We are reporting a short and convenient pathway for the synthesis of novel β-carboline-bisindole hybrid compounds from relatively cheap and commercially available chemicals such as tryptamine, dialdehydes and indoles. These newly designed compounds can also be prepared in high yields with the tolerance of many functional groups under mild conditions. Notably, these β-carboline-bisindole hybrid compounds exhibited some promising applications as anticancer agents against the three common cancer cell lines MCF-7 (breast cancer), SK-LU-1 (lung cancer), and HepG2 (liver cancer). The two best compounds 5 b and 5 g inhibited the aforementioned cell lines with the same IC50 range of the reference Ellipticine at less than 2 μM. A molecular docking study to gain more information about the interactions between the synthesized molecules and the kinase domain of the EGFR was performed. Therefore, this finding can have significant impacts on the development of future research in medicinal chemistry and drug discovery.
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Affiliation(s)
- Nguyen Thi Thanh Huyen
- Faculty of Chemistry, VNU-Ha Noi University of Science, 19 Le Thanh Tong, Phan Chu Trinh, Hoan Kiem, Hanoi, Vietnam
| | - Ban Van Phuc
- Institute of Chemistry, Vietnamese Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Tran Thi Huyen
- Faculty of Chemistry, VNU-Ha Noi University of Science, 19 Le Thanh Tong, Phan Chu Trinh, Hoan Kiem, Hanoi, Vietnam
| | - Tran Thi Hong
- Faculty of Chemistry, VNU-Ha Noi University of Science, 19 Le Thanh Tong, Phan Chu Trinh, Hoan Kiem, Hanoi, Vietnam
| | - Hien Nguyen
- Faculty of Chemistry, Hanoi National University of Education (HNUE), Vietnam
| | - Van Ha Nguyen
- Faculty of Chemistry, VNU-Ha Noi University of Science, 19 Le Thanh Tong, Phan Chu Trinh, Hoan Kiem, Hanoi, Vietnam
| | - Minh Tho Nguyen
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Tran Quang Hung
- Institute of Chemistry, Vietnamese Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Vietnam
| | - Chau Phi Dinh
- NuChem Sciences, a Sygnature Discovery Business, 480 rue Perreault, Lévis, QC, G6 W 7 V6, Canada
| | - Tuan Thanh Dang
- Faculty of Chemistry, VNU-Ha Noi University of Science, 19 Le Thanh Tong, Phan Chu Trinh, Hoan Kiem, Hanoi, Vietnam
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11
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Herbst C, Endres S, Würz R, Sotriffer C. Assessment of fragment docking and scoring with the endothiapepsin model system. Arch Pharm (Weinheim) 2024; 357:e2400061. [PMID: 38631672 DOI: 10.1002/ardp.202400061] [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: 01/23/2024] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Fragment-based screening has become indispensable in drug discovery. Yet, the weak binding affinities of these small molecules still represent a challenge for the reliable detection of fragment hits. The extent of this issue was illustrated in the literature for the aspartic protease endothiapepsin: When seven biochemical and biophysical in vitro screening methods were applied to screen a library of 361 fragments, very poor overlap was observed between the hit fragments identified by the individual approaches, resulting in high levels of false positive and/or false negative results depending on the mutually compared methods. Here, the reported in vitro findings are juxtaposed with the results from in silico docking and scoring approaches. The docking programs GOLD and Glide were considered with the scoring functions ASP, ChemScore, ChemPLP, GoldScore, DSXCSD, and GlideScore. First, the ranking power and scoring power were assessed for the named scoring functions. Second, the capability of reproducing the crystallized fragment binding modes was tested in a structure-based redocking approach. The redocking success notably depended on the ligand efficiency of the considered fragments. Third, a blinded virtual screening approach was employed to evaluate whether in silico screening can compete with in vitro methods in the enrichment of fragment databases.
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Affiliation(s)
- Carina Herbst
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Sara Endres
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Rebecca Würz
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
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12
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Zhao G, Zhu M, Li Y, Zhang G, Li Y. Using DNA-encoded libraries of fragments for hit discovery of challenging therapeutic targets. Expert Opin Drug Discov 2024; 19:725-740. [PMID: 38753553 DOI: 10.1080/17460441.2024.2354287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION The effectiveness of Fragment-based drug design (FBDD) for targeting challenging therapeutic targets has been hindered by two factors: the small library size and the complexity of the fragment-to-hit optimization process. The DNA-encoded library (DEL) technology offers a compelling and robust high-throughput selection approach to potentially address these limitations. AREA COVERED In this review, the authors propose the viewpoint that the DEL technology matches perfectly with the concept of FBDD to facilitate hit discovery. They begin by analyzing the technical limitations of FBDD from a medicinal chemistry perspective and explain why DEL may offer potential solutions to these limitations. Subsequently, they elaborate in detail on how the integration of DEL with FBDD works. In addition, they present case studies involving both de novo hit discovery and full ligand discovery, especially for challenging therapeutic targets harboring broad drug-target interfaces. EXPERT OPINION The future of DEL-based fragment discovery may be promoted by both technical advances and application scopes. From the technical aspect, expanding the chemical diversity of DEL will be essential to achieve success in fragment-based drug discovery. From the application scope side, DEL-based fragment discovery holds promise for tackling a series of challenging targets.
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Affiliation(s)
- Guixian Zhao
- Chongqing University FuLing Hospital, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Mengping Zhu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
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13
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Liang Z, Candib A, Soriano-Castell D, Fischer W, Finley K, Maher P. Fragment-based drug discovery and biological evaluation of novel cannabinol-based inhibitors of oxytosis/ferroptosis for neurological disorders. Redox Biol 2024; 72:103138. [PMID: 38581858 PMCID: PMC11002867 DOI: 10.1016/j.redox.2024.103138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024] Open
Abstract
The oxytosis/ferroptosis regulated cell death pathway is an emerging field of research owing to its pathophysiological relevance to a wide range of neurological disorders, including Alzheimer's and Parkinson's diseases and traumatic brain injury. Developing novel neurotherapeutics to inhibit oxytosis/ferroptosis offers exciting opportunities for the treatment of these and other neurological diseases. Previously, we discovered cannabinol (CBN) as a unique, potent inhibitor of oxytosis/ferroptosis by targeting mitochondria and modulating their function in neuronal cells. To further elucidate which key pharmacophores and chemical space are essential to the beneficial effects of CBN, we herein introduce a fragment-based drug discovery strategy in conjunction with cell-based phenotypic screens using oxytosis/ferroptosis to determine the structure-activity relationship of CBN. The resulting information led to the development of four new CBN analogs, CP1-CP4, that not only preserve the sub-micromolar potency of neuroprotection and mitochondria-modulating activities seen with CBN in neuronal cell models but also have better druglike properties. Moreover, compared to CBN, the analog CP1 shows improved in vivo efficacy in the Drosophila model of mild traumatic brain injury. Together these studies identify the key molecular scaffolds of cannabinoids that contribute to neuroprotection against oxytosis/ferroptosis. They also highlight the advantageous approach of combining in vitro cell-based assays and rapid in vivo studies using Drosophila models for evaluating new therapeutic compounds.
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Affiliation(s)
- Zhibin Liang
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, United States.
| | - Alec Candib
- Shiley Bioscience Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, United States
| | - David Soriano-Castell
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, United States
| | - Wolfgang Fischer
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, United States
| | - Kim Finley
- Shiley Bioscience Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, United States
| | - Pamela Maher
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, United States.
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14
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Li GC, Castro MA, Ukwaththage T, Sanders CR. Optimizing NMR fragment-based drug screening for membrane protein targets. J Struct Biol X 2024; 9:100100. [PMID: 38883400 PMCID: PMC11176934 DOI: 10.1016/j.yjsbx.2024.100100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/05/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024] Open
Abstract
NMR spectroscopy has played a pivotal role in fragment-based drug discovery by coupling detection of weak ligand-target binding with structural mapping of the binding site. Fragment-based screening by NMR has been successfully applied to many soluble protein targets, but only to a limited number of membrane proteins, despite the fact that many drug targets are membrane proteins. This is partly because of difficulties preparing membrane proteins for NMR-especially human membrane proteins-and because of the inherent complexity associated with solution NMR spectroscopy on membrane protein samples, which require the inclusion of membrane-mimetic agents such as micelles, nanodiscs, or bicelles. Here, we developed a generalizable protocol for fragment-based screening of membrane proteins using NMR. We employed two human membrane protein targets, both in fully protonated detergent micelles: the single-pass C-terminal domain of the amyloid precursor protein, C99, and the tetraspan peripheral myelin protein 22 (PMP22). For both we determined the optimal NMR acquisition parameters, protein concentration, protein-to-micelle ratio, and upper limit to the concentration of D6-DMSO in screening samples. Furthermore, we conducted preliminary screens of a plate-format molecular fragment mixture library using our optimized conditions and were able to identify hit compounds that selectively bound to the respective target proteins. It is hoped that the approaches presented here will be useful in complementing existing methods for discovering lead compounds that target membrane proteins.
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Affiliation(s)
- Geoffrey C Li
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
| | - Manuel A Castro
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
| | - Thilini Ukwaththage
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
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15
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Zhu S, Huang W, Liu S, Yu R, Ma Y, Wang H, Zhang R, Liu B, Lan Y, Shen R. Synthesis of benzooxepane-fused cyclobutene derivatives via Pd-catalyzed cascade reactions of haloarenes and diynylic ethers. Chem Commun (Camb) 2024; 60:5707-5710. [PMID: 38738645 DOI: 10.1039/d4cc00999a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
A tandem palladium-catalyzed Sonogashira coupling, propargyl-allenyl isomerization, and [2+2] cycloaddition sequence between electron-deficient haloarenes and 1,8-diynylic ethers is developed. The reaction shows good functional tolerance and proceeds under mild conditions to provide a new profile of benzooxepane-fused cyclobutene derivatives in moderate to high yields with high selectivity. The reaction mechanism is validated both by experimental studies and DFT calculations.
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Affiliation(s)
- Shugao Zhu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China.
| | - Wenliang Huang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China.
| | - Shihan Liu
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 400030, China.
| | - Rongjing Yu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China.
| | - Yufeng Ma
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China.
| | - Hong Wang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China.
| | - Rui Zhang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China.
| | - Bin Liu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China.
| | - Yu Lan
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 400030, China.
- College of Chemistry and Institute of Green Catalysis, Zhengzhou University, Zhengzhou 450001, China
| | - Ruwei Shen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 211800, China
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16
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Muller J, Marchisio L, Attia R, Zedet A, Maradan R, Vallet M, Aebischer A, Harakat D, Senejoux F, Ramseyer C, Foley S, Cardey B, Girard C, Pudlo M. A colorimetric assay adapted to fragment screening revealing aurones and chalcones as new arginase inhibitors. RSC Med Chem 2024; 15:1722-1730. [PMID: 38784454 PMCID: PMC11110760 DOI: 10.1039/d3md00713h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/23/2024] [Indexed: 05/25/2024] Open
Abstract
Arginase, a difficult-to-target metalloenzyme, is implicated in a wide range of diseases, including cancer, infectious, and cardiovascular diseases. Despite the medical need, existing inhibitors have limited structural diversity, consisting predominantly of amino acids and their derivatives. The search for innovative arginase inhibitors has now extended to screening approaches. Due to the small and narrow active site of arginase, screening must meet the criteria of fragment-based screening. However, the limited binding capacity of fragments requires working at high concentrations, which increases the risk of interference and false positives. In this study, we investigated three colorimetric assays and selected one based on interference for screening under these challenging conditions. The subsequent adaptation and application to the screening a library of metal chelator fragments resulted in the identification of four compounds with moderate activity. The synthesis and evaluation of a series of compounds from one of the hits led to compound 21a with an IC50 value of 91.1 μM close to the reference compound piceatannol. Finally, molecular modelling supports the potential binding of aurones and chalcones to the active site of arginase, suggesting them as new candidates for the development of novel arginase inhibitors.
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Affiliation(s)
- Jason Muller
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Luca Marchisio
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Rym Attia
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Andy Zedet
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Robin Maradan
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Maxence Vallet
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Alison Aebischer
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Dominique Harakat
- URCATech, ICMR, CNRS UMR 7312 URCA Bât 18, BP 1039, Cedex 2 51687 Reims France
| | - François Senejoux
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Christophe Ramseyer
- Chrono-environnement UMR6249, CNRS Université de Franche-Comté F-25000 Besançon France
| | - Sarah Foley
- Chrono-environnement UMR6249, CNRS Université de Franche-Comté F-25000 Besançon France
| | - Bruno Cardey
- Chrono-environnement UMR6249, CNRS Université de Franche-Comté F-25000 Besançon France
| | - Corine Girard
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Marc Pudlo
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
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17
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Labrecque CL, Fuglestad B. Ligandability at the membrane interface of GPx4 revealed through a reverse micelle fragment screening platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593437. [PMID: 38766018 PMCID: PMC11100811 DOI: 10.1101/2024.05.09.593437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
While they account for a large portion of drug targets, membrane proteins (MPs) present a unique challenge for drug discovery. Peripheral membrane proteins (PMPs), a class of proteins that bind reversibly to membranes, are also difficult targets, particularly those that function only while bound to membranes. The protein-membrane interface in PMPs is often where functional interactions and catalysis occur, making it a logical target for inhibition. However, interfaces are underexplored spaces in inhibitor design and there is a need for enhanced methods for small-molecule ligand discovery. In an effort to better initiate drug discovery efforts for PMPs, this study presents a screening methodology using membrane-mimicking reverse micelles (mmRM) and NMR-based fragment screening to assess ligandability in the protein-membrane interface. The proof-of-principle target, glutathione peroxidase 4 (GPx4), is a lipid hydroperoxidase which is essential for the oxidative protection of membranes and thereby the prevention of ferroptosis. GPx4 inhibition is promising for therapy-resistant cancer therapy, but current inhibitors are generally covalent ligands with limited clinical utility. Presented here is the discovery of non-covalent small-molecule ligands for membrane-bound GPx4 revealed through the mmRM fragment screening methodology. The fragments were tested against GPx4 in bulk aqueous conditions and displayed little to no binding to the protein without embedment into the membrane. The 9 hits had varying affinities and partitioning coefficients and revealed properties of fragments that bind within the protein-membrane interface. Additionally, a secondary screen confirmed the potential to progress the fragments by enhancing the affinity from > 200 μM to ~15 μM with the addition of certain hydrophobic groups. This study presents an advancement of screening capabilities for membrane associated proteins, reveals ligandability within the GPx4 protein-membrane interface, and may serve as a starting point for developing non-covalent inhibitors of GPx4.
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Affiliation(s)
- Courtney L. Labrecque
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 22384, United States
| | - Brian Fuglestad
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 22384, United States
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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18
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Schmitz B, Frieg B, Homeyer N, Jessen G, Gohlke H. Extracting binding energies and binding modes from biomolecular simulations of fragment binding to endothiapepsin. Arch Pharm (Weinheim) 2024; 357:e2300612. [PMID: 38319801 DOI: 10.1002/ardp.202300612] [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: 10/20/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Fragment-based drug discovery (FBDD) aims to discover a set of small binding fragments that may be subsequently linked together. Therefore, in-depth knowledge of the individual fragments' structural and energetic binding properties is essential. In addition to experimental techniques, the direct simulation of fragment binding by molecular dynamics (MD) simulations became popular to characterize fragment binding. However, former studies showed that long simulation times and high computational demands per fragment are needed, which limits applicability in FBDD. Here, we performed short, unbiased MD simulations of direct fragment binding to endothiapepsin, a well-characterized model system of pepsin-like aspartic proteases. To evaluate the strengths and limitations of short MD simulations for the structural and energetic characterization of fragment binding, we predicted the fragments' absolute free energies and binding poses based on the direct simulations of fragment binding and compared the predictions to experimental data. The predicted absolute free energies are in fair agreement with the experiment. Combining the MD data with binding mode predictions from molecular docking approaches helped to correctly identify the most promising fragments for further chemical optimization. Importantly, all computations and predictions were done within 5 days, suggesting that MD simulations may become a viable tool in FBDD projects.
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Affiliation(s)
- Birte Schmitz
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Nadine Homeyer
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gisela Jessen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
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19
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Stillman NH, Joseph JA, Ahmed J, Baysah CZ, Dohoney RA, Ball TD, Thomas AG, Fitch TC, Donnelly CM, Kumar S. Protein mimetic 2D FAST rescues alpha synuclein aggregation mediated early and post disease Parkinson's phenotypes. Nat Commun 2024; 15:3658. [PMID: 38688913 PMCID: PMC11061149 DOI: 10.1038/s41467-024-47980-4] [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: 07/13/2022] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Abberent protein-protein interactions potentiate many diseases and one example is the toxic, self-assembly of α-Synuclein in the dopaminergic neurons of patients with Parkinson's disease; therefore, a potential therapeutic strategy is the small molecule modulation of α-Synuclein aggregation. In this work, we develop an Oligopyridylamide based 2-dimensional Fragment-Assisted Structure-based Technique to identify antagonists of α-Synuclein aggregation. The technique utilizes a fragment-based screening of an extensive array of non-proteinogenic side chains in Oligopyridylamides, leading to the identification of NS132 as an antagonist of the multiple facets of α-Synuclein aggregation. We further identify a more cell permeable analog (NS163) without sacrificing activity. Oligopyridylamides rescue α-Synuclein aggregation mediated Parkinson's disease phenotypes in dopaminergic neurons in early and post disease Caenorhabditis elegans models. We forsee tremendous potential in our technique to identify lead therapeutics for Parkinson's disease and other diseases as it is expandable to other oligoamide scaffolds and a larger array of side chains.
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Affiliation(s)
- Nicholas H Stillman
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Johnson A Joseph
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Jemil Ahmed
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
- Molecular and Cellular Biophysics Program, Boettcher West, Room 228, 2050 E. Iliff Ave, University of Denver, Denver, CO, 80210, USA
| | - Charles Zuwu Baysah
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Ryan A Dohoney
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Tyler D Ball
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Alexandra G Thomas
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Tessa C Fitch
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Courtney M Donnelly
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Sunil Kumar
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA.
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA.
- Molecular and Cellular Biophysics Program, Boettcher West, Room 228, 2050 E. Iliff Ave, University of Denver, Denver, CO, 80210, USA.
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20
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Li J, Chandgude AL, Zheng Q, Dömling A. Innovative synthesis of drug-like molecules using tetrazole as core building blocks. Beilstein J Org Chem 2024; 20:950-958. [PMID: 38711589 PMCID: PMC11070966 DOI: 10.3762/bjoc.20.85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024] Open
Abstract
Tetrazole is widely utilized as a bioisostere for carboxylic acid in the field of medicinal chemistry and drug development, enhancing the drug-like characteristics of various molecules. Typically, tetrazoles are introduced from their nitrile precursors through late-stage functionalization. In this work, we propose a novel strategy involving the use of diversely protected, unprecedented tetrazole aldehydes as building blocks. This approach facilitates the incorporation of the tetrazole group into multicomponent reactions or other chemistries, aiding in the creation of a variety of complex, drug-like molecules. These innovative tetrazole building blocks are efficiently and directly synthesized using a Passerini three-component reaction (PT-3CR), employing cost-effective and readily available materials. We further showcase the versatility of these new tetrazole building blocks by integrating the tetrazole moiety into various multicomponent reactions (MCRs), which are already significantly employed in drug discovery. This technique represents a unique and complementary method to existing tetrazole synthesis processes. It aims to meet the growing demand for tetrazole-based compound libraries and novel scaffolds, which are challenging to synthesize through other methods.
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Affiliation(s)
- Jingyao Li
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ajay L Chandgude
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Qiang Zheng
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackӯ University in Olomouc, Olomouc, Czech Republic
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21
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Lanka G, Banerjee S, Adhikari N, Ghosh B. Fragment-based discovery of new potential DNMT1 inhibitors integrating multiple pharmacophore modeling, 3D-QSAR, virtual screening, molecular docking, ADME, and molecular dynamics simulation approaches. Mol Divers 2024:10.1007/s11030-024-10837-5. [PMID: 38637479 DOI: 10.1007/s11030-024-10837-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
DNA methyl transferases (DNMTs) are one of the crucial epigenetic modulators associated with a wide variety of cancer conditions. Among the DNMT isoforms, DNMT1 is correlated with bladder, pancreatic, and breast cancer, as well as acute myeloid leukemia and esophagus squamous cell carcinoma. Therefore, the inhibition of DNMT1 could be an attractive target for combating cancers and other metabolic disorders. The disadvantages of the existing nucleoside and non-nucleoside DNMT1 inhibitors are the main motive for the discovery of novel promising inhibitors. Here, pharmacophore modeling, 3D-QSAR, and e-pharmacophore modeling of DNMT1 inhibitors were performed for the large fragment database screening. The resulting fragments with high dock scores were combined into molecules. The current study revealed several constitutional pharmacophoric features that can be essential for selective DNMT1 inhibition. The fragment docking and virtual screening identified 10 final hit molecules that exhibited good binding affinities in terms of docking score, binding free energies, and acceptable ADME properties. Also, the modified lead molecules (GL1b and GL2b) designed in this study showed effective binding with DNMT1 confirmed by their docking scores, binding free energies, 3D-QSAR predicted activities and acceptable drug-like properties. The MD simulation studies also suggested that leads (GL1b and GL2b) formed stable complexes with DNMT1. Therefore, the findings of this study can provide effective information for the development/identification of novel DNMT1 inhibitors as effective anticancer agents.
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Affiliation(s)
- Goverdhan Lanka
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
- Computer Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata, West Bengal, 700032, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata, West Bengal, 700032, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India.
- Computer Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India.
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22
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Baldini L, Lenci E, Faggi C, Trabocchi A. Identification of BACE-1 inhibitors through directed C(sp 3)-H activation on 5-oxo-pyrrolidine-3-carboxylic acid derivatives. Org Biomol Chem 2024; 22:2754-2763. [PMID: 38488214 DOI: 10.1039/d3ob02117c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Convenient synthesis of stereochemically dense 5-oxo-pyrrolidines was obtained from succinic anyhdride and imines by combining the Castagnoli-Cushman reaction with directed Pd-catalyzed C(sp3)-H functionalization, taking advantage of the developing carboxylic group properly derivatized with 8-aminoquinoline as a directing group. These fully substituted 5-oxopyrrolidines were found to be able to inhibit BACE-1 enzyme with sub-micromolar activity, thanks to the interaction of the key aryl appendage introduced by C(sp3)-H activation within BACE-1 S2' subsite.
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Affiliation(s)
- Lorenzo Baldini
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy.
| | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy.
| | - Cristina Faggi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy.
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy.
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23
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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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24
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Utgés JS, MacGowan SA, Ives CM, Barton GJ. Classification of likely functional class for ligand binding sites identified from fragment screening. Commun Biol 2024; 7:320. [PMID: 38480979 PMCID: PMC10937669 DOI: 10.1038/s42003-024-05970-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Fragment screening is used to identify binding sites and leads in drug discovery, but it is often unclear which binding sites are functionally important. Here, data from 37 experiments, and 1309 protein structures binding to 1601 ligands were analysed. A method to group ligands by binding sites is introduced and sites clustered according to profiles of relative solvent accessibility. This identified 293 unique ligand binding sites, grouped into four clusters (C1-4). C1 includes larger, buried, conserved, and population missense-depleted sites, enriched in known functional sites. C4 comprises smaller, accessible, divergent, missense-enriched sites, depleted in functional sites. A site in C1 is 28 times more likely to be functional than one in C4. Seventeen sites, which to the best of our knowledge are novel, in 13 proteins are identified as likely to be functionally important with examples from human tenascin and 5-aminolevulinate synthase highlighted. A multi-layer perceptron, and K-nearest neighbours model are presented to predict cluster labels for ligand binding sites with an accuracy of 96% and 100%, respectively, so allowing functional classification of sites for proteins not in this set. Our findings will be of interest to those studying protein-ligand interactions and developing new drugs or function modulators.
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Affiliation(s)
- Javier S Utgés
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Stuart A MacGowan
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Callum M Ives
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Geoffrey J Barton
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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25
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Cebi E, Lee J, Subramani VK, Bak N, Oh C, Kim KK. Cryo-electron microscopy-based drug design. Front Mol Biosci 2024; 11:1342179. [PMID: 38501110 PMCID: PMC10945328 DOI: 10.3389/fmolb.2024.1342179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024] Open
Abstract
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.
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Affiliation(s)
| | | | | | | | - Changsuk Oh
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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26
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Barnes L, Birkinshaw TN, Senior AJ, Brügge OS, Lewis W, Argent SP, Moody CJ, Nortcliffe A. Iodoetherification as a strategy towards sp 3-rich scaffolds for drug discovery. Bioorg Med Chem 2024; 101:117636. [PMID: 38354458 DOI: 10.1016/j.bmc.2024.117636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024]
Abstract
Functionalised tetrahydropyran and spirooxepane scaffolds were prepared utilising an iodoetherification strategy and elaborated to demonstrate their potential use in library synthesis. The iodoetherification products could be readily transformed to the corresponding azides that could be further functionalised via copper-catalysed azide-alkyne cycloaddition or reduction to the amine. The lead-likeness and three-dimensionality of the scaffolds were examined and compared to commercial libraries.
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Affiliation(s)
- Lydia Barnes
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Timothy N Birkinshaw
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Aaron J Senior
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Oscar Siles Brügge
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - William Lewis
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Stephen P Argent
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Christopher J Moody
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Andrew Nortcliffe
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.
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27
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Shyam M, Kumar S, Singh V. Unlocking Opportunities for Mycobacterium leprae and Mycobacterium ulcerans. ACS Infect Dis 2024; 10:251-269. [PMID: 38295025 PMCID: PMC10862552 DOI: 10.1021/acsinfecdis.3c00371] [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: 07/31/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
In the recent decade, scientific communities have toiled to tackle the emerging burden of drug-resistant tuberculosis (DR-TB) and rapidly growing opportunistic nontuberculous mycobacteria (NTM). Among these, two neglected mycobacteria species of the Acinetobacter family, Mycobacterium leprae and Mycobacterium ulcerans, are the etiological agents of leprosy and Buruli ulcer infections, respectively, and fall under the broad umbrella of neglected tropical diseases (NTDs). Unfortunately, lackluster drug discovery efforts have been made against these pathogenic bacteria in the recent decade, resulting in the discovery of only a few countable hits and majorly repurposing anti-TB drug candidates such as telacebec (Q203), P218, and TB47 for current therapeutic interventions. Major ignorance in drug candidate identification might aggravate the dramatic consequences of rapidly spreading mycobacterial NTDs in the coming days. Therefore, this Review focuses on an up-to-date account of drug discovery efforts targeting selected druggable targets from both bacilli, including the accompanying challenges that have been identified and are responsible for the slow drug discovery. Furthermore, a succinct discussion of the all-new possibilities that could be alternative solutions to mitigate the neglected mycobacterial NTD burden and subsequently accelerate the drug discovery effort is also included. We anticipate that the state-of-the-art strategies discussed here may attract major attention from the scientific community to navigate and expand the roadmap for the discovery of next-generation therapeutics against these NTDs.
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Affiliation(s)
- Mousumi Shyam
- Department
of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mersa, Ranchi, Jharkhand 835215, India
| | - Sumit Kumar
- Holistic
Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
| | - Vinayak Singh
- Holistic
Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, University of Cape Town, Rondebosch 7701, South Africa
- Institute
of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Observatory 7925, Cape Town, South Africa
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28
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Jinsong S, Qifeng J, Xing C, Hao Y, Wang L. Molecular fragmentation as a crucial step in the AI-based drug development pathway. Commun Chem 2024; 7:20. [PMID: 38302655 PMCID: PMC10834946 DOI: 10.1038/s42004-024-01109-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
The AI-based small molecule drug discovery has become a significant trend at the intersection of computer science and life sciences. In the pursuit of novel compounds, fragment-based drug discovery has emerged as a novel approach. The Generative Pre-trained Transformers (GPT) model has showcased remarkable prowess across various domains, rooted in its pre-training and representation learning of fundamental linguistic units. Analogous to natural language, molecular encoding, as a form of chemical language, necessitates fragmentation aligned with specific chemical logic for accurate molecular encoding. This review provides a comprehensive overview of the current state of the art in molecular fragmentation. We systematically summarize the approaches and applications of various molecular fragmentation techniques, with special emphasis on the characteristics and scope of applicability of each technique, and discuss their applications. We also provide an outlook on the current development trends of molecular fragmentation techniques, including some potential research directions and challenges.
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Affiliation(s)
- Shao Jinsong
- Nantong University, School of Information Science and Technology, Nantong, China
| | - Jia Qifeng
- Nantong University, School of Information Science and Technology, Nantong, China
| | - Chen Xing
- Nantong University, School of Information Science and Technology, Nantong, China
| | - Yajie Hao
- Nantong University, School of Information Science and Technology, Nantong, China
| | - Li Wang
- Nantong University, Research Center for Intelligence Information Technology, Nantong, China.
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29
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Kovachka S, Panosetti M, Grimaldi B, Azoulay S, Di Giorgio A, Duca M. Small molecule approaches to targeting RNA. Nat Rev Chem 2024; 8:120-135. [PMID: 38278932 DOI: 10.1038/s41570-023-00569-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/28/2024]
Abstract
The development of innovative methodologies to identify RNA binders has attracted enormous attention in chemical biology and drug discovery. Although antibiotics targeting bacterial ribosomal RNA have been on the market for decades, the renewed interest in RNA targeting reflects the need to better understand complex intracellular processes involving RNA. In this context, small molecules are privileged tools used to explore the biological functions of RNA and to validate RNAs as therapeutic targets, and they eventually are to become new drugs. Despite recent progress, the rational design of specific RNA binders requires a better understanding of the interactions which occur with the RNA target to reach the desired biological response. In this Review, we discuss the challenges to approaching this underexplored chemical space, together with recent strategies to bind, interact and affect biologically relevant RNAs.
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Affiliation(s)
- Sandra Kovachka
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Marc Panosetti
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
- Molecular Medicine Research Line, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Benedetto Grimaldi
- Molecular Medicine Research Line, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Stéphane Azoulay
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France.
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30
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Exertier C, Salerno A, Antonelli L, Fiorillo A, Ocello R, Seghetti F, Caciolla J, Uliassi E, Masetti M, Fiorentino E, Orsini S, Di Muccio T, Ilari A, Bolognesi ML. Fragment Merging, Growing, and Linking Identify New Trypanothione Reductase Inhibitors for Leishmaniasis. J Med Chem 2024; 67:402-419. [PMID: 38164929 PMCID: PMC10788915 DOI: 10.1021/acs.jmedchem.3c01439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/30/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
Trypanothione reductase (TR) is a suitable target for drug discovery approaches against leishmaniasis, although the identification of potent inhibitors is still challenging. Herein, we harnessed a fragment-based drug discovery (FBDD) strategy to develop new TR inhibitors. Previous crystallographic screening identified fragments 1-3, which provided ideal starting points for a medicinal chemistry campaign. In silico investigations revealed critical hotspots in the TR binding site, guiding our structure- and ligand-based structure-actvity relationship (SAR) exploration that yielded fragment-derived compounds 4-14. A trend of improvement in Leishmania infantum TR inhibition was detected along the optimization and confirmed by the crystal structures of 9, 10, and 14 in complex with Trypanosoma brucei TR. Compound 10 showed the best TR inhibitory profile (Ki = 0.2 μM), whereas 9 was the best one in terms of in vitro and ex vivo activity. Although further fine-tuning is needed to improve selectivity, we demonstrated the potentiality of FBDD on a classic but difficult target for leishmaniasis.
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Affiliation(s)
- Cécile Exertier
- Institute of Molecular Biology and Pathology (IBPM) of the National Research Council of Italy (CNR), c/o Department of Biochemical Sciences, Sapienza University of Rome, Piazzale A. Moro 5, Roma 00185, Italy
| | - Alessandra Salerno
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Lorenzo Antonelli
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Piazzale A. Moro 5, Roma 00185, Italy
| | - Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Piazzale A. Moro 5, Roma 00185, Italy
| | - Riccardo Ocello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Francesca Seghetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Jessica Caciolla
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Elisa Uliassi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Eleonora Fiorentino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, Roma 00161, Italy
| | - Stefania Orsini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, Roma 00161, Italy
| | - Trentina Di Muccio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, Roma 00161, Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology (IBPM) of the National Research Council of Italy (CNR), c/o Department of Biochemical Sciences, Sapienza University of Rome, Piazzale A. Moro 5, Roma 00185, Italy
| | - Maria Laura Bolognesi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
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31
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Melancon K, Pliushcheuskaya P, Meiler J, Künze G. Targeting ion channels with ultra-large library screening for hit discovery. Front Mol Neurosci 2024; 16:1336004. [PMID: 38249296 PMCID: PMC10796734 DOI: 10.3389/fnmol.2023.1336004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 01/23/2024] Open
Abstract
Ion channels play a crucial role in a variety of physiological and pathological processes, making them attractive targets for drug development in diseases such as diabetes, epilepsy, hypertension, cancer, and chronic pain. Despite the importance of ion channels in drug discovery, the vastness of chemical space and the complexity of ion channels pose significant challenges for identifying drug candidates. The use of in silico methods in drug discovery has dramatically reduced the time and cost of drug development and has the potential to revolutionize the field of medicine. Recent advances in computer hardware and software have enabled the screening of ultra-large compound libraries. Integration of different methods at various scales and dimensions is becoming an inevitable trend in drug development. In this review, we provide an overview of current state-of-the-art computational chemistry methodologies for ultra-large compound library screening and their application to ion channel drug discovery research. We discuss the advantages and limitations of various in silico techniques, including virtual screening, molecular mechanics/dynamics simulations, and machine learning-based approaches. We also highlight several successful applications of computational chemistry methodologies in ion channel drug discovery and provide insights into future directions and challenges in this field.
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Affiliation(s)
- Kortney Melancon
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | | | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- Medical Faculty, Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, Leipzig, Germany
| | - Georg Künze
- Medical Faculty, Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
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32
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Zhao Y, Li X, Deng WH, Wu B, Liao RZ, Zhou YG. Dearomatization of [2.2]Paracyclophane-Derived N-Sulfonylimines through Cyclopropanation with Sulfur Ylides. J Org Chem 2024; 89:321-329. [PMID: 38086000 DOI: 10.1021/acs.joc.3c02052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
An unprecedented dearomatization of [2.2]paracyclophane-derived cyclic N-sulfonylimines was conducted through cyclopropanation with sulfur ylides, giving a series of dearomative cyclopropanes with good yields. DFT calculations suggested that the dearomatization was attributed to the relatively weak aromaticity of [2.2]paracyclophane derivatives that resulted from the effect of the unique [2.2]paracyclophane skeleton and the electron-withdrawing N-sulfonyl group. Some downstream elaborations of the products were demonstrated.
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Affiliation(s)
- Yang Zhao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, P. R. China
| | - Xiang Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, P. R. China
| | - Wen-Hao Deng
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 116024, P. R. China
| | - Bo Wu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, P. R. China
| | - Rong-Zhen Liao
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 116024, P. R. China
| | - Yong-Gui Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, P. R. China
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33
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Powers A, Yu HH, Suriana P, Koodli RV, Lu T, Paggi JM, Dror RO. Geometric Deep Learning for Structure-Based Ligand Design. ACS CENTRAL SCIENCE 2023; 9:2257-2267. [PMID: 38161364 PMCID: PMC10755842 DOI: 10.1021/acscentsci.3c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024]
Abstract
A pervasive challenge in drug design is determining how to expand a ligand-a small molecule that binds to a target biomolecule-in order to improve various properties of the ligand. Adding single chemical groups, known as fragments, is important for lead optimization tasks, and adding multiple fragments is critical for fragment-based drug design. We have developed a comprehensive framework that uses machine learning and three-dimensional protein-ligand structures to address this challenge. Our method, FRAME, iteratively determines where on a ligand to add fragments, selects fragments to add, and predicts the geometry of the added fragments. On a comprehensive benchmark, FRAME consistently improves predicted affinity and selectivity relative to the initial ligand, while generating molecules with more drug-like chemical properties than docking-based methods currently in widespread use. FRAME learns to accurately describe molecular interactions despite being given no prior information on such interactions. The resulting framework for quality molecular hypothesis generation can be easily incorporated into the workflows of medicinal chemists for diverse tasks, including lead optimization, fragment-based drug discovery, and de novo drug design.
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Affiliation(s)
- Alexander
S. Powers
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Helen H. Yu
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Patricia Suriana
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Rohan V. Koodli
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
- Biomedical
Informatics Program, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Tianyu Lu
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Joseph M. Paggi
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ron O. Dror
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
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He B, Hu Y, Chen W, He X, Zhang E, Hu M, Zhang P, Yan W, Ye Y. Design, Synthesis, and Antifungal Activity of N-(alkoxy)-Diphenyl Ether Carboxamide Derivates as Novel Succinate Dehydrogenase Inhibitors. Molecules 2023; 29:83. [PMID: 38202666 PMCID: PMC10780015 DOI: 10.3390/molecules29010083] [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: 11/15/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024] Open
Abstract
Succinate dehydrogenase (SDH, EC 1.3.5.1) is one of the most promising targets for fungicide development and has attracted great attention worldwide. However, existing commercial fungicides targeting SDH have led to the increasingly prominent problem of pathogen resistance, so it is necessary to develop new fungicides. Herein, we used a structure-based molecular design strategy to design and synthesize a series of novel SDHI fungicides containing an N-(alkoxy)diphenyl ether carboxamide skeleton. The mycelial growth inhibition experiment showed that compound M15 exhibited a very good control effect against four plant pathogens, with inhibition rates of more than 60% at a dose of 50 μg/mL. A structure-activity relationship study found that N-O-benzyl-substituted derivatives showed better antifungal activity than others, especially the introduction of a halogen on the benzyl. Furthermore, the molecular docking results suggested that π-π interactions with Trp35 and hydrogen bonds with Tyr33 and Trp173 were crucial interaction sites when inhibitors bound to SDH. Morphological observation of mycelium revealed that M15 could inhibit the growth of mycelia. Moreover, in vivo and in vitro tests showed that M15 not only inhibited the enzyme activity of SDH but also effectively protected rice from damage due to R. solani infection, with a result close to that of the control at a concentration of 200 μg/mL. Thus, the N-(alkoxy)diphenyl ether carboxamide skeleton is a new starting point for the discovery of new SDH inhibitors and is worthy of further investigation.
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Affiliation(s)
- Bo He
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (B.H.); (Y.H.); (W.C.); (X.H.); (E.Z.); (M.H.); (W.Y.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Yanhao Hu
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (B.H.); (Y.H.); (W.C.); (X.H.); (E.Z.); (M.H.); (W.Y.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Wang Chen
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (B.H.); (Y.H.); (W.C.); (X.H.); (E.Z.); (M.H.); (W.Y.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Xu He
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (B.H.); (Y.H.); (W.C.); (X.H.); (E.Z.); (M.H.); (W.Y.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Enpei Zhang
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (B.H.); (Y.H.); (W.C.); (X.H.); (E.Z.); (M.H.); (W.Y.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Mengxu Hu
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (B.H.); (Y.H.); (W.C.); (X.H.); (E.Z.); (M.H.); (W.Y.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Pu Zhang
- Research & Development Center, Jiangsu Flag Chemical Industry Co., Ltd., Nanjing 210095, China;
| | - Wei Yan
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (B.H.); (Y.H.); (W.C.); (X.H.); (E.Z.); (M.H.); (W.Y.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Yonghao Ye
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (B.H.); (Y.H.); (W.C.); (X.H.); (E.Z.); (M.H.); (W.Y.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
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Heitmann T, Liao G, de León P, Ernst G, Buchler I, Wei H, Shlevkov E, Brown D, Fitzek M, Collier M, Smith DM, Barrow JC. Fragment-Based Screening Identifies New Quinazolinone-Based Inositol Hexakisphosphate Kinase (IP6K) Inhibitors. ACS Med Chem Lett 2023; 14:1760-1766. [PMID: 38116421 PMCID: PMC10726443 DOI: 10.1021/acsmedchemlett.3c00409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023] Open
Abstract
A high-throughput fragment-based screen has been employed to discover a series of quinazolinone inositol hexakisphosphate kinase (IP6K) inhibitors. IP6Ks have been studied for their role in glucose homeostasis, metabolic disease, fatty liver disease, chronic kidney disease, blood coagulation, neurological development, and psychiatric disease. IP6Ks phosphorylate inositol hexakisphosphate (IP6) to form pyrophosphate 5-diphospho-1,2,3,4,6-pentakisphosphate (IP7). Molecular docking studies and investigation of structure-activity relationships around the quinazolinone core resulted in compounds with submicromolar potency and interesting selectivity for IP6K1 versus the closely related IP6K2 and IP6K3 isoforms.
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Affiliation(s)
- Tyler Heitmann
- Lieber
Institute for Brain Development, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Gangling Liao
- Lieber
Institute for Brain Development, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Pablo de León
- Lieber
Institute for Brain Development, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Glen Ernst
- Lieber
Institute for Brain Development, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Ingrid Buchler
- Lieber
Institute for Brain Development, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Huijun Wei
- Lieber
Institute for Brain Development, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Evgeny Shlevkov
- Lieber
Institute for Brain Development, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Dean Brown
- Hit
Discovery, Discovery Sciences, R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Martina Fitzek
- Hit
Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield SK10 4TG, U.K.
| | - Matthew Collier
- Hit
Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield SK10 4TG, U.K.
| | - David M. Smith
- Emerging
Innovations Unit, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | - James C. Barrow
- Lieber
Institute for Brain Development, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
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36
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Wranik M, Kepa MW, Beale EV, James D, Bertrand Q, Weinert T, Furrer A, Glover H, Gashi D, Carrillo M, Kondo Y, Stipp RT, Khusainov G, Nass K, Ozerov D, Cirelli C, Johnson PJM, Dworkowski F, Beale JH, Stubbs S, Zamofing T, Schneider M, Krauskopf K, Gao L, Thorn-Seshold O, Bostedt C, Bacellar C, Steinmetz MO, Milne C, Standfuss J. A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers. Nat Commun 2023; 14:7956. [PMID: 38042952 PMCID: PMC10693631 DOI: 10.1038/s41467-023-43523-5] [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: 02/23/2023] [Accepted: 11/10/2023] [Indexed: 12/04/2023] Open
Abstract
Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we describe a multi-reservoir, high viscosity extruder as a step towards automation of sample delivery at XFELs. Compared to a standard single extruder, sample exchange time was halved and the workload of users was greatly reduced. In-built temperature control of samples facilitated optimal extrusion and supported sample stability. After commissioning the device with lysozyme crystals, we collected time-resolved data using crystals of a membrane-bound, light-driven sodium pump. Static data were also collected from the soluble protein tubulin that was soaked with a series of small molecule drugs. Using these data, we identify low occupancy (as little as 30%) ligands using a minimal amount of data from a serial crystallography experiment, a result that could be exploited for structure-based drug design.
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Affiliation(s)
- Maximilian Wranik
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland.
| | - Michal W Kepa
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland.
| | - Emma V Beale
- Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Daniel James
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Quentin Bertrand
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Hannah Glover
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Dardan Gashi
- Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Melissa Carrillo
- Laboratory of Nanoscale Biology, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Yasushi Kondo
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Robin T Stipp
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Georgii Khusainov
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Karol Nass
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Dmitry Ozerov
- Scientific Computing, Theory and Data Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Claudio Cirelli
- Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Philip J M Johnson
- Laboratory for Nonlinear Optics, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Florian Dworkowski
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - John H Beale
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Scott Stubbs
- Large Research Facilities Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Thierry Zamofing
- Large Research Facilities Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Marco Schneider
- Large Research Facilities Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Kristina Krauskopf
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, Munich, 81377, Germany
| | - Li Gao
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, Munich, 81377, Germany
| | - Oliver Thorn-Seshold
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, Munich, 81377, Germany
| | - Christoph Bostedt
- Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
- LUXS Laboratory for Ultrafast X-ray Sciences, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Camila Bacellar
- Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Christopher Milne
- Femtosecond X-ray Experiments Instrument, European XFEL GmbH, Schenefeld, Germany
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
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37
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Proj M, Hrast M, Bajc G, Frlan R, Meden A, Butala M, Gobec S. Discovery of a fragment hit compound targeting D-Ala:D-Ala ligase of bacterial peptidoglycan biosynthesis. J Enzyme Inhib Med Chem 2023; 38:387-397. [PMID: 36446617 PMCID: PMC9718554 DOI: 10.1080/14756366.2022.2149745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Bacterial resistance is an increasing threat to healthcare systems, highlighting the need for discovering new antibacterial agents. An established technique, fragment-based drug discovery, was used to target a bacterial enzyme Ddl involved in the biosynthesis of peptidoglycan. We assembled general and focused fragment libraries that were screened in a biochemical inhibition assay. Screening revealed a new fragment-hit inhibitor of DdlB with a Ki value of 20.7 ± 4.5 µM. Binding to the enzyme was confirmed by an orthogonal biophysical method, surface plasmon resonance, making the hit a promising starting point for fragment development.
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Affiliation(s)
- Matic Proj
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Martina Hrast
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Bajc
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Rok Frlan
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Anže Meden
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Butala
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia,CONTACT Stanislav Gobec Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, 1000Ljubljana, Slovenia
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38
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Acquasaliente L, Pierangelini A, Pagotto A, Pozzi N, De Filippis V. From haemadin to haemanorm: Synthesis and characterization of full-length haemadin from the leech Haemadipsa sylvestris and of a novel bivalent, highly potent thrombin inhibitor (haemanorm). Protein Sci 2023; 32:e4825. [PMID: 37924304 PMCID: PMC10683372 DOI: 10.1002/pro.4825] [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: 06/16/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Hirudin from Hirudo medicinalis is a bivalent α-Thrombin (αT) inhibitor, targeting the enzyme active site and exosite-I, and is currently used in anticoagulant therapy along with its simplified analogue hirulog. Haemadin, a small protein (57 amino acids) isolated from the land-living leech Haemadipsa sylvestris, selectively inhibits αT with a potency identical to that of recombinant hirudin (KI = 0.2 pM), with which it shares a common disulfide topology and overall fold. At variance with hirudin, haemadin targets exosite-II and therefore (besides the free protease) it also blocks thrombomodulin-bound αT without inhibiting the active intermediate meizothrombin, thus offering potential advantages over hirudin. Here, we produced in reasonably high yields and pharmaceutical purity (>98%) wild-type haemadin and the oxidation resistant Met5 → nor-Leucine analogue, both inhibiting αT with a KI of 0.2 pM. Thereafter, we used site-directed mutagenesis, spectroscopic, ligand-displacement, and Hydrogen/Deuterium Exchange-Mass Spectrometry techniques to map the αT regions relevant for the interaction with full-length haemadin and with the synthetic N- and C-terminal peptides Haem(1-10) and Haem(45-57). Haem(1-10) competitively binds to/inhibits αT active site (KI = 1.9 μM) and its potency was enhanced by 10-fold after Phe3 → β-Naphthylalanine exchange. Conversely to full-length haemadin, haem(45-57) displays intrinsic affinity for exosite-I (KD = 1.6 μM). Hence, we synthesized a peptide in which the sequences 1-9 and 45-57 were joined together through a 3-Glycine spacer to yield haemanorm, a highly potent (KI = 0.8 nM) inhibitor targeting αT active site and exosite-I. Haemanorm can be regarded as a novel class of hirulog-like αT inhibitors with potential pharmacological applications.
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Affiliation(s)
- Laura Acquasaliente
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Andrea Pierangelini
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Anna Pagotto
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Nicola Pozzi
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
- Department of Biochemistry and Molecular Biology, Edward A. Doisy Research CenterSaint Louis UniversitySt. LouisMissouriUSA
| | - Vincenzo De Filippis
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
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Martinelli M, Giorgiutti C, Fessard T, Lefebvre Q. Introducing covalent warheads on spirocyclic sp 2-sp 3 fragments by innate C-H functionalization. Org Biomol Chem 2023; 21:9230-9235. [PMID: 37965862 DOI: 10.1039/d3ob01746j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Sp2-sp3 fragments play a vital role in fragment-based drug design (FBDD). Strategies to chemically modify them and efficiently access libraries of these compounds have been goals of the highest priority in the last decades. In this work, a series of sp2-sp3 fragments was synthesized and validated for that purpose, based on their measured physical-chemical properties. Selective C-H cyanation and allylation of these fragments was demonstrated by simple heating in presence of an appropriate hydrogen-atom transfer reagent and a radical acceptor. These conditions enabled a streamlined access to covalent fragments in a single step, by direct introduction of the desired covalent binder. Preliminary results on vinylation, as well as late-stage functionalization of a drug analogue were disclosed.
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Affiliation(s)
- Matteo Martinelli
- Department of Chemistry, University of Pavia, Viale Taramelli, Pavia 27100, Italy
- SpiroChem AG, Mattenstrasse 22, 4058 Basel, Switzerland.
| | | | - Thomas Fessard
- SpiroChem AG, Mattenstrasse 22, 4058 Basel, Switzerland.
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40
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Usman FO, Gogoi AR, Mixdorf JC, Gutierrez O, Nguyen HM. Rhodium-Catalyzed Asymmetric Synthesis of 1,2-Disubstituted Allylic Fluorides. Angew Chem Int Ed Engl 2023; 62:e202314843. [PMID: 37856668 PMCID: PMC11069351 DOI: 10.1002/anie.202314843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/21/2023]
Abstract
Although there are many methods for the asymmetric synthesis of monosubstituted allylic fluorides, construction of enantioenriched 1,2-disubstituted allylic fluorides has not been reported. To address this gap, we report an enantioselective synthesis of 1,2-disubstituted allylic fluorides using chiral diene-ligated rhodium catalyst, Et3 N ⋅ 3HF as a source of fluoride, and Morita Baylis Hillman (MBH) trichloroacetimidates. Kinetic studies show that one enantiomer of racemic MBH substrate reacts faster than the other. Computational studies reveal that both syn and anti π-allyl complexes are formed upon ionization of allylic substrate, and the syn complexes are slightly energetically favorable. This is in contrast to our previous observation for formation of monosubstituted π-allyl intermediates, in which the syn π-allyl conformation is strongly preferred. In addition, the presence of an electron-withdrawing group at C2 position of racemic MBH substrate renders 1,2-disubstituted π-allyl intermediate formation endergonic and reversible. To compare, formation of monosubstituted π-allyl intermediates was exergonic and irreversible. DFT calculations and kinetic studies support a dynamic kinetic asymmetric transformation process wherein the rate of isomerization of the 1,2-disubstituted π-allylrhodium complexes is faster than that of fluoride addition onto the more reactive intermediate. The 1,2-disubstituted allylic fluorides were obtained in good yields, enantioselectivity, and branched selectivity.
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Affiliation(s)
- Fuad O Usman
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Achyut R Gogoi
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Jason C Mixdorf
- Department of Medical Physics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Osvaldo Gutierrez
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Hien M Nguyen
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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Hocking B, Armstrong A, Mann DJ. Covalent fragment libraries in drug discovery-Design, synthesis, and screening methods. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:105-146. [PMID: 37981350 DOI: 10.1016/bs.pmch.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
As the development of drugs with a covalent mode of action is becoming increasingly popular, well-validated covalent fragment-based drug discovery (FBDD) methods have been comparatively slow to keep up with the demand. In this chapter the principles of covalent fragment reactivity, library design, synthesis, and screening methods are explored in depth, focussing on literature examples with direct applications to practical covalent fragment library design and screening. Further, questions about the future of the field are explored and potential useful advances are proposed.
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Affiliation(s)
- Brad Hocking
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - David J Mann
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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42
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Wang H, Zhao G, Zhang T, Li Y, Zhang G, Li Y. Comparative Study of DNA Barcode Integrity Evaluation Approaches in the Early-Stage Development of DNA-Compatible Chemical Transformation. ACS Pharmacol Transl Sci 2023; 6:1724-1733. [PMID: 37974618 PMCID: PMC10644510 DOI: 10.1021/acsptsci.3c00181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Indexed: 11/19/2023]
Abstract
DNA-encoded libraries (DEL) have emerged as an important drug discovery technical platform for target-based compound library selection. The success rate of DEL depends on both the chemical diversity of combinatorial libraries and the accuracy of DNA barcoding. Therefore, it is critical that the chemistry applied to library construction should efficiently transform on a wide range of substrates while preserving the integrity of DNA tags. Although several analytical methods have been developed to measure DNA damage caused by DEL chemical reactions, efficient and cost-effective evaluation criteria for DNA damage detection are still demanding. Herein, we set standards for evaluating the DNA compatibility of chemistry development at the laboratory level. Based on four typical DNA damage models of three different DEL formats, we evaluated the detection capabilities of four analytical methods, including ultraperformance liquid chromatography (UPLC-MS), electrophoresis, quantitative polymerase chain reaction (qPCR), and Sanger sequencing. This work systematically revealed the scope and capability of different analytical methods in assessing DNA damages caused by chemical transformation. Based on the results, we recommended UPLC-MS and qPCR as efficient methods for DNA barcode integrity analysis in the early-stage development of DNA-compatible chemistry. Meanwhile, we identified that Sanger sequencing was unreliable to assess DNA damage in this application.
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Affiliation(s)
- Huicong Wang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Guixian Zhao
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Tianyang Zhang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical
Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical
Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical
Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Beijing
National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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43
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Cuellar ME, Yang M, Karavadhi S, Zhang YQ, Zhu H, Sun H, Shen M, Hall MD, Patnaik S, Ashe KH, Walters MA, Pockes S. An electrophilic fragment screening for the development of small molecules targeting caspase-2. Eur J Med Chem 2023; 259:115632. [PMID: 37453329 PMCID: PMC10529632 DOI: 10.1016/j.ejmech.2023.115632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/04/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
Recent Alzheimer's research has shown increasing interest in the caspase-2 (Casp2) enzyme. However, the available Casp2 inhibitors, which have been pentapeptides or peptidomimetics, face challenges for use as CNS drugs. In this study, we successfully screened a 1920-compound chloroacetamide-based, electrophilic fragment library from Enamine. Our two-point dose screen identified 64 Casp2 hits, which were further evaluated in a ten-point dose-response study to assess selectivity over Casp3. We discovered compounds with inhibition values in the single-digit micromolar and sub-micromolar range, as well as up to 32-fold selectivity for Casp2 over Casp3. Target engagement analysis confirmed the covalent-irreversible binding of the selected fragments to Cys320 at the active site of Casp2. Overall, our findings lay a strong foundation for the future development of small-molecule Casp2 inhibitors.
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Affiliation(s)
- Matthew E Cuellar
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, 55414, USA
| | - Mu Yang
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, 55414, USA
| | - Surendra Karavadhi
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Ya-Qin Zhang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Hu Zhu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Samarjit Patnaik
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Karen H Ashe
- Department of Neurology, University of Minnesota, 2101 6th Street SE, Minneapolis, MN, 55455, USA
| | - Michael A Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, 55414, USA.
| | - Steffen Pockes
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, 55414, USA; Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
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44
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Arachchi MK, Schaugaard RN, Schlegel HB, Nguyen HM. Scope and Mechanistic Probe into Asymmetric Synthesis of α-Trisubstituted-α-Tertiary Amines by Rhodium Catalysis. J Am Chem Soc 2023; 145:19642-19654. [PMID: 37651695 PMCID: PMC10581542 DOI: 10.1021/jacs.3c04211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Asymmetric reactions that convert racemic mixtures into enantioenriched amines are of significant importance due to the prevalence of amines in pharmaceuticals, with about 60% of drug candidates containing tertiary amines. Although transition-metal catalyzed allylic substitution processes have been developed to provide access to enantioenriched α-disubstituted allylic amines, enantioselective synthesis of sterically demanding α-tertiary amines with a tetrasubstituted carbon stereocenter remains a major challenge. Herein, we report a chiral diene-ligated rhodium-catalyzed asymmetric substitution of racemic tertiary allylic trichloroacetimidates with aliphatic secondary amines to afford α-trisubstituted-α-tertiary amines. Mechanistic investigation is conducted using synergistic experimental and computational studies. Density functional theory calculations show that the chiral diene-ligated rhodium promotes the ionization of tertiary allylic substrates to form both anti and syn π-allyl intermediates. The anti π-allyl pathway proceeds through a higher energy than the syn π-allyl pathway. The rate of conversion of the less reactive π-allyl intermediate to the more reactive isomer via π-σ-π interconversion was faster than the rate of nucleophilic attack onto the more reactive intermediate. These data imply that the Curtin-Hammett conditions are met in the amination reaction, leading to dynamic kinetic asymmetric transformation. Computational studies also show that hydrogen bonding interactions between β-oxygen of allylic substrate and amine-NH greatly assist the delivery of amine nucleophile onto more hindered internal carbon of the π-allyl intermediate. The synthetic utility of the current methodology is showcased by efficient preparation of α-trisubstituted-α-tertiary amines featuring pharmaceutically relevant secondary amine cores with good yields and excellent selectivities (branched-linear >99:1, up to 99% enantiomeric excess).
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Affiliation(s)
- Madhawee K Arachchi
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Richard N Schaugaard
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Hien M Nguyen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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45
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Uppuladinne MVN, Achalere A, Sonavane U, Joshi R. Probing the structure of human tRNA 3Lys in the presence of ligands using docking, MD simulations and MSM analysis. RSC Adv 2023; 13:25778-25796. [PMID: 37655355 PMCID: PMC10467029 DOI: 10.1039/d3ra03694d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023] Open
Abstract
The tRNA3Lys, which acts as a primer for human immunodeficiency virus type 1 (HIV-1) reverse transcription, undergoes structural changes required for the formation of a primer-template complex. Small molecules have been targeted against tRNA3Lys to inhibit the primer-template complex formation. The present study aims to understand the kinetics of the conformational landscape spanned by tRNA3Lys in apo form using molecular dynamics simulations and Markov state modeling. The study is taken further to investigate the effect of small molecules like 1,4T and 1,5T on structural conformations and kinetics of tRNA3Lys, and comparative analysis is presented. Markov state modeling of tRNA3Lys apo resulted in three metastable states where the conformations have shown the non-canonical structures of the anticodon loop. Based on analyses of ligand-tRNA3Lys interactions, crucial ion and water mediated H-bonds and free energy calculations, it was observed that the 1,4-triazole more strongly binds to the tRNA3Lys compared to 1,5-triazole. However, the MSM analysis suggest that the 1,5-triazole binding to tRNA3Lys has brought rigidity not only in the binding pocket (TΨC arm, D-TΨC loop) but also in the whole structure of tRNA3Lys. This may affect the easy opening of primer tRNA3Lys required for HIV-1 reverse transcription.
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Affiliation(s)
- Mallikarjunachari V N Uppuladinne
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Archana Achalere
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Uddhavesh Sonavane
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Rajendra Joshi
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
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46
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Bourougaa L, Ouassaf M, Shtaiwi A. Discovery of novel potent drugs for influenza by inhibiting the vital function of neuraminidase via fragment-based drug design (FBDD) and molecular dynamics simulation strategies. J Biomol Struct Dyn 2023:1-15. [PMID: 37640004 DOI: 10.1080/07391102.2023.2251065] [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: 07/10/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023]
Abstract
The current work describes a fragment linking methodology to generate new neuraminidase inhibitors. A total number of 28,977 fragments from Zinc 20 have been obtained and screened for neuraminidase receptor affinity. Using Schrödinger software, the highest-scoring 270 fragment hits (with scores greater than -7.6) were subjected to fragment combining to create 100 new molecules. These 100 novel compounds were studied using XP docking to evaluate the molecular interaction modes and their binding affinity to neuraminidase receptor. The top ten molecules were selected, for ADMET, drug-likeness features. Based on these characteristics, the best four developed molecules and Zanamivir were submitted to a molecular dynamics simulation investigation to estimate their dynamics within the neuraminidase receptor using Gromacs software. All MD simulation findings show that the generated complexes are very stable when compared to the clinical inhibitor (Zanamivir). In addition, the four designed neuraminidase inhibitors formed very stable complexes with neuraminidase receptor (with total binding energies ranging from -83.50 to -107.85 Kj/mol) according to the total binding energy calculated by MM-PBSA. For the objective of developing new influenza medications, these novel molecules have the potential to be further evaluated in vitro and in vivo for influenza drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lotfi Bourougaa
- Group of Computational and Medicinal Chemistry, Laboratory of Molecular Chemistry and Environment, University of Biskra, Biskra, Algeria
| | - Mebarka Ouassaf
- Group of Computational and Medicinal Chemistry, Laboratory of Molecular Chemistry and Environment, University of Biskra, Biskra, Algeria
| | - Amneh Shtaiwi
- Faculty of Pharmacy, Middle East University Amman, Amman, Jordan
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47
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Salvini CLA, Darlot B, Davison J, Martin MP, Tudhope SJ, Turberville S, Kawamura A, Noble MEM, Wedge SR, Crawford JJ, Waring MJ. Fragment expansion with NUDELs - poised DNA-encoded libraries. Chem Sci 2023; 14:8288-8294. [PMID: 37564419 PMCID: PMC10411621 DOI: 10.1039/d3sc01171b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Optimisation of the affinity of lead compounds is a critical challenge in the identification of drug candidates and chemical probes and is a process that takes many years. Fragment-based drug discovery has become established as one of the methods of choice for drug discovery starting with small, low affinity compounds. Due to their low affinity, the evolution of fragments to desirable levels of affinity is often a key challenge. The accepted best method for increasing the potency of fragments is by iterative fragment growing, which can be very time consuming and complex. Here, we introduce a paradigm for fragment hit optimisation using poised DNA-encoded chemical libraries (DELs). The synthesis of a poised DEL, a partially constructed library that retains a reactive handle, allows the coupling of any active fragment for a specific target protein, allowing rapid discovery of potent ligands. This is illustrated for bromodomain-containing protein 4 (BRD4), in which a weakly binding fragment was coupled to a 42-member poised DEL via Suzuki-Miyaura cross coupling resulting in the identification of an inhibitor with 51 nM affinity in a single step, representing an increase in potency of several orders of magnitude from an original fragment. The potency of the compound was shown to arise from the synergistic combination of substructures, which would have been very difficult to discover by any other method and was rationalised by X-ray crystallography. The compound showed attractive lead-like properties suitable for further optimisation and demonstrated BRD4-dependent cellular pharmacology. This work demonstrates the power of poised DELs to rapidly optimise fragments, representing an attractive generic approach to drug discovery.
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Affiliation(s)
- Catherine L A Salvini
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
| | - Benoit Darlot
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
- Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Jack Davison
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
| | - Mathew P Martin
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Susan J Tudhope
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Shannon Turberville
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Akane Kawamura
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
- Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Martin E M Noble
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Stephen R Wedge
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - James J Crawford
- Genentech Inc. 1 DNA Way South San Francisco California 94080 USA
| | - Michael J Waring
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
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48
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Mojanaga OO, Acharya KR, Lloyd MD. Recombinant protein production for structural and kinetic studies: A case study using M. tuberculosis α-methylacyl-CoA racemase (MCR). Methods Enzymol 2023; 690:1-37. [PMID: 37858526 DOI: 10.1016/bs.mie.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Modern drug discovery is a target-driven approach in which a particular protein such as an enzyme is implicated in the disease process. Commonly, small-molecule drugs are identified using screening, rational design, and structural biology approaches. Drug screening, testing and optimization is typically conducted in vitro, and copious amounts of protein are required. The advent of recombinant DNA technologies has resulted in a rise in proteins purified by affinity techniques, typically by incorporating an "affinity tag" at the N- or C-terminus. Use of these tagged proteins and affinity techniques comes with a host of issues. This chapter describes the production of an untagged enzyme, α-methylacyl-CoA racemase (MCR) from Mycobacterium tuberculosis, using a recombinant E. coli system. Purification of the enzyme on a 100 mg scale using tandem anion-exchange chromatographies (DEAE-sepharose and RESOURCE-Q columns), and size-exclusion chromatographies is described. A modified protocol allowing the purification of cationic proteins is also described, based on tandem cation-exchange chromatographies (using CM-sepharose and RESOURCE-S columns) and size-exclusion chromatographies. The resulting MCR protein is suitable for biochemical and structural biology applications. The described protocols have wide applicability to the purification of other recombinant proteins and enzymes without using affinity chromatography.
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Affiliation(s)
- Otsile O Mojanaga
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - K Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
| | - Matthew D Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
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Brooke H, Ghoshray M, Ibrahim A, Lloyd MD. Steady-state kinetic analysis of reversible enzyme inhibitors: A case study on calf intestine alkaline phosphatase. Methods Enzymol 2023; 690:39-84. [PMID: 37858536 DOI: 10.1016/bs.mie.2023.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Enzymes are important drug targets and inhibition of enzymatic activity is an important therapeutic strategy. Enzyme assays measuring catalytic activity are utilized in both the discovery and development of new drugs. Colorimetric assays based on the release of 4-nitrophenol from substrates are commonly used. 4-Nitrophenol is only partly ionized to 4-nitrophenolate under typical assay conditions (pH 7-9) leading to under-estimation of product formation rates due to the much lower extinction coefficient of 4-nitrophenol compared to 4-nitrophenolate. Determination of 4-nitrophenol pKa values based on absorbance at 405 nm as a function of experimental pH values is reported, allowing for calculation of a corrected extinction coefficient at the assay pH. Characterization of inhibitor properties using steady-state enzyme kinetics is demonstrated using calf intestine alkaline phosphatase and 4-nitrophenyl phosphate as substrate at pH ∼8.2. The following kinetic parameters were determined: Km= 40±3 µM; Vmax= 72.8±1.2 µmolmin-1mg protein-1; kcat= 9.70±0.16 s-1; kcat/Km= 2.44±0.16 × 105 M-1s-1 (mean± SEM, N = 4). Sodium orthovanadate and EDTA were used as model inhibitors and the following pIC50 values were measured using dose-response curves: 6.61±0.08 and 3.07±0.03 (mean±SEM, N = 4). Rapid dilution experiments determined that inhibition was reversible for sodium orthovanadate and irreversible for EDTA. A Ki value for orthovanadate of 51±8 nM (mean±SEM, N = 3) was determined. Finally, data analysis and statistical design of experiments are discussed.
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Affiliation(s)
- Henry Brooke
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - Meghna Ghoshray
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - Archad Ibrahim
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - Matthew D Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
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Bryan DR, Kulp JL, Mahapatra MK, Bryan RL, Viswanathan U, Carlisle MN, Kim S, Schutte WD, Clarke KV, Doan TT, Kulp JL. BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation. J Chem Inf Model 2023; 63:4229-4236. [PMID: 37406353 DOI: 10.1021/acs.jcim.3c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Fragment-based drug design uses data about where, and how strongly, small chemical fragments bind to proteins, to assemble new drug molecules. Over the past decade, we have been successfully using fragment data, derived from thermodynamically rigorous Monte Carlo fragment-protein binding simulations, in dozens of preclinical drug programs. However, this approach has not been available to the broader research community because of the cost and complexity of doing simulations and using design tools. We have developed a web application, called BMaps, to make fragment-based drug design widely available with greatly simplified user interfaces. BMaps provides access to a large repository (>550) of proteins with 100s of precomputed fragment maps, druggable hot spots, and high-quality water maps. Users can also employ their own structures or those from the Protein Data Bank and AlphaFold DB. Multigigabyte data sets are searched to find fragments in bondable orientations, ranked by a binding-free energy metric. The designers use this to select modifications that improve affinity and other properties. BMaps is unique in combining conventional tools such as docking and energy minimization with fragment-based design, in a very easy to use and automated web application. The service is available at https://www.boltzmannmaps.com.
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Affiliation(s)
- Daniel R Bryan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - John L Kulp
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
- Zymergen, Inc., 430 E. 29th Street, Suite 625, New York, New York 10016, United States
| | - Manoj K Mahapatra
- Kanak Manjari Institute of Pharmaceutical Sciences, Rourkela 769015, Odisha, India
| | - Richard L Bryan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Usha Viswanathan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Micah N Carlisle
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Surim Kim
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
- Zymergen, Inc., 430 E. 29th Street, Suite 625, New York, New York 10016, United States
| | - William D Schutte
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Kevaughn V Clarke
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Tony T Doan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - John L Kulp
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
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