1
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Hanson GSM, Coxon CR. Fluorinated Tags to Study Protein Conformation and Interactions Using 19F NMR. Chembiochem 2024; 25:e202400195. [PMID: 38744671 DOI: 10.1002/cbic.202400195] [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: 03/01/2024] [Revised: 04/19/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
The incorporation of fluorine atoms into a biomacromolecule provides a background-free and environmentally sensitive reporter of structure, conformation and interactions using 19F NMR. There are several methods to introduce the 19F reporter - either by synthetic incorporation via solid phase peptide synthesis; by suppressing the incorporation or biosynthesis of a natural amino acid and supplementing the growth media with a fluorinated counterpart during protein expression; and by genetic code expansion to add new amino acids to the amino acid alphabet. This review aims to discuss progress in the field of introducing fluorinated handles into biomolecules for NMR studies by post-translational bioconjugation or 'fluorine-tagging'. We will discuss the range of chemical tagging 'warheads' that have been used, explore the applications of fluorine tags, discuss ways to enhance reporter sensitivity and how the signal to noise ratios can be boosted. Finally, we consider some key challenges of the field and offer some ideas for future directions.
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Affiliation(s)
- George S M Hanson
- EaStChem School of Chemistry, University of Edinburgh, Joseph Black Building, Kings Buildings, West Mains Road, EH9 3FJ, Edinburgh, UK
| | - Christopher R Coxon
- EaStChem School of Chemistry, University of Edinburgh, Joseph Black Building, Kings Buildings, West Mains Road, EH9 3FJ, Edinburgh, UK
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2
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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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3
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Toyama Y, Shimada I. Quantitative analysis of the slow exchange process by 19F NMR in the presence of scalar and dipolar couplings: applications to the ribose 2'- 19F probe in nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00446-7. [PMID: 38918317 DOI: 10.1007/s10858-024-00446-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024]
Abstract
Solution NMR spectroscopy is a particularly powerful technique for characterizing the functional dynamics of biomolecules, which is typically achieved through the quantitative characterization of chemical exchange processes via the measurement of spin relaxation rates. In addition to the conventional nuclei such as 15N and 13C, which are abundant in biomolecules, fluorine-19 (19F) has recently garnered attention and is being widely used as a site-specific spin probe. While 19F offers the advantages of high sensitivity and low background, it can be susceptible to artifacts in quantitative relaxation analyses due to a multitude of dipolar and scalar coupling interactions with nearby 1H spins. In this study, we focused on the ribose 2'-19F spin probe in nucleic acids and investigated the effects of 1H-19F spin interactions on the quantitative characterization of slow exchange processes on the millisecond time scale. We demonstrated that the 1H-19F dipolar coupling can significantly affect the interpretation of 19F chemical exchange saturation transfer (CEST) experiments when 1H decoupling is applied, while the 1H-19F interactions have a lesser impact on Carr-Purcell-Meiboom-Gill relaxation dispersion applications. We also proposed a modified CEST scheme to alleviate these artifacts along with experimental verifications on self-complementary RNA systems. The theoretical framework presented in this study can be widely applied to various 19F spin systems where 1H-19F interactions are operative, further expanding the utility of 19F relaxation-based NMR experiments.
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Affiliation(s)
- Yuki Toyama
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Ichio Shimada
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima, 739-8528, Japan.
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4
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Conti Nibali S, De Siervi S, Luchinat E, Magrì A, Messina A, Brocca L, Mantovani S, Oliviero B, Mondelli MU, De Pinto V, Turato C, Arrigoni C, Lolicato M. VDAC1-interacting molecules promote cell death in cancer organoids through mitochondrial-dependent metabolic interference. iScience 2024; 27:109853. [PMID: 38784007 PMCID: PMC11112339 DOI: 10.1016/j.isci.2024.109853] [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: 11/23/2023] [Revised: 03/06/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
The voltage-dependent anion-selective channel isoform 1 (VDAC1) is a pivotal component in cellular metabolism and apoptosis with a prominent role in many cancer types, offering a unique therapeutic intervention point. Through an in-silico-to-in-vitro approach we identified a set of VA molecules (VDAC Antagonists) that selectively bind to VDAC1 and display specificity toward cancer cells. Biochemical characterization showed that VA molecules can directly interact with VDAC1 with micromolar affinity by competing with the endogenous ligand NADH for a partially shared binding site. NADH displacement results in mitochondrial distress and reduced cell proliferation, especially when compared to non-cancerous cells. Experiments performed on organoids derived from intrahepatic cholangiocarcinoma patients demonstrated a dose-dependent reduction in cell viability upon treatment with VA molecules with lower impact on healthy cells than conventional treatments like gemcitabine. VA molecules are chemical entities representing promising candidates for further optimization and development as cancer therapy strategies through precise metabolic interventions.
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Affiliation(s)
| | - Silvia De Siervi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Enrico Luchinat
- Department of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, 50019 Firenze, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine – CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Andrea Magrì
- Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Angela Messina
- Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Lorenza Brocca
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Stefania Mantovani
- Research Department, Division of Clinical Immunology—Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Barbara Oliviero
- Research Department, Division of Clinical Immunology—Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mario U. Mondelli
- Research Department, Division of Clinical Immunology—Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, Section of Biology & Genetics, University of Catania, Catania, Italy
| | - Cristian Turato
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Marco Lolicato
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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5
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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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6
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Ang EWJ, Djordjevic I, Solic I, Goh CY, Steele TWJ. Tougher Bioadhesives through Dual Stimulation Strategies. Adv Healthc Mater 2024; 13:e2303666. [PMID: 38431774 DOI: 10.1002/adhm.202303666] [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: 11/29/2023] [Revised: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Carbene-based bioadhesives have favourable attributes for tissue adhesion, including non-specific bonding to wet and dry tissues, but suffer from relatively weak fracture strength after photocuring. Light irradiation of carbene-precursor (diazirine) also creates inert side products that are absent under thermal activation. Herein, a dual activation method combines light irradiation at elevated temperatures for the evaluation of diazirine depletion and effects on cohesive properties. A customized photo/thermal-rheometer evaluates viscoelastic properties, correlated to the kinetics of carbene:diazoalkane ratios via 19F NMR). The latter exploits the sensitive -CF3 functional group to determine joule-based light/temperature kinetics on trifluoroaryl diazirine consumption. The combination of heat and photoactivation produced bioadhesives that are 3× tougher compared to control. Dual thermal/light irradiation may be a strategy to improve viscoelastic dissipation and toughness of photo-activated adhesive resins.
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Affiliation(s)
- Elwin W J Ang
- Nanyang Environment and Water Research Institute, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, 637553, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Ivan Djordjevic
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Ivan Solic
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Chen Yee Goh
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Terry W J Steele
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
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7
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Singh A, Jain N, Shankar U, Sharma TK, Kumar A. Characterization of G-quadruplex structures in genes involved in survival and pathogenesis of Acinetobacter baumannii as a potential drug target. Int J Biol Macromol 2024; 269:131806. [PMID: 38670179 DOI: 10.1016/j.ijbiomac.2024.131806] [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: 12/13/2023] [Revised: 03/21/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024]
Abstract
Acinetobacter baumannii is a notorious pathogen that commonly thrives in hospital environments and is responsible for numerous nosocomial infections in humans. The burgeoning multi-drug resistance leaves relatively minimal options for treating the bacterial infection, posing a significant problem and prompting the identification of new approaches for tackling the same. This motivated us to focus on non-canonical nucleic acid structures, mainly G-quadruplexes, as drug targets. G-quadruplexes have recently been gaining attention due to their involvement in multiple bacterial and viral pathogenesis. Herein, we sought to explore conserved putative G-quadruplex motifs in A. baumannii. In silico analysis revealed the presence of eight conserved motifs in genes involved in bacterial survival and pathogenesis. The biophysical and biomolecular analysis confirmed stable G-quadruplex formation by the motifs and showed a high binding affinity with the well-reported G-quadruplex binding ligand, BRACO-19. BRACO-19 exposure also decreased the growth of bacteria and downregulated the expression of G-quadruplex-harboring genes. The biofilm-forming ability of the bacteria was also affected by BRACO-19 addition. Taking all these observations into account, we have shown here for the first time the potential of G-quadruplex structures as a promising drug target in Acinetobacter baumannii, for addressing the challenges posed by this infamous pathogen.
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Affiliation(s)
- Aakriti Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Neha Jain
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Tarun Kumar Sharma
- Department of Medical Biotechnology, Gujarat Biotechnology University, Gandhinagar 382355, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India.
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8
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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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9
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Chai Z, Li C. In-Cell 19F NMR of Proteins: Recent Progress and Future Opportunities. Chemistry 2024; 30:e202303988. [PMID: 38269421 DOI: 10.1002/chem.202303988] [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] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
In vitro, 19F NMR methodology is preferably selected as a complementary and straightforward method for unveiling the conformations, dynamics, and interactions of biological molecules. Its effectiveness in vivo has seen continuous improvement, addressing challenges faced by conventional heteronuclear NMR experiments on structured proteins, such as severe line broadening, low signal-to-noise ratio, and background signals. Herein, we summarize the distinctive advantages of 19F NMR, along with recent progress in sample preparation and applications within the realm of in-cell NMR. Additionally, we offer insights into the future directions and prospects of this methodology based on our understanding.
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Affiliation(s)
- Zhaofei Chai
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
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10
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Loh YY, Anantharajan J, Huang Q, Xu W, Fulwood J, Ng HQ, Ng EY, Gea CY, Choong ML, Tan QW, Koh X, Lim WH, Nacro K, Cherian J, Baburajendran N, Ke Z, Kang C. Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening. Protein Sci 2024; 33:e4904. [PMID: 38358126 PMCID: PMC10868430 DOI: 10.1002/pro.4904] [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: 11/13/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
UBE2T is an attractive target for drug development due to its linkage with several types of cancers. However, the druggability of ubiquitin-conjugating E2 (UBE2T) is low because of the lack of a deep and hydrophobic pocket capable of forming strong binding interactions with drug-like small molecules. Here, we performed fragment screening using 19 F-nuclear magnetic resonance (NMR) and validated the hits with 1 H-15 N-heteronuclear single quantum coherence (HSQC) experiment and X-ray crystallographic studies. The cocrystal structures obtained revealed the binding modes of the hit fragments and allowed for the characterization of the fragment-binding sites. Further screening of structural analogues resulted in the identification of a compound series with inhibitory effect on UBE2T activity. Our current study has identified two new binding pockets in UBE2T, which will be useful for the development of small molecules to regulate the function of this protein. In addition, the compounds identified in this study can serve as chemical starting points for the development of UBE2T modulators.
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Affiliation(s)
- Yong Yao Loh
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jothi Anantharajan
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Qiwei Huang
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Weijun Xu
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Justina Fulwood
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Hui Qi Ng
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Elizabeth Yihui Ng
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Chong Yu Gea
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Meng Ling Choong
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Qian Wen Tan
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Xiaoying Koh
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Wan Hsin Lim
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Kassoum Nacro
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Joseph Cherian
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Zhiyuan Ke
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
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11
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Bhat AP, Pomerantz WCK, Arnold WA. Fluorinated Pharmaceutical and Pesticide Photolysis: Investigating Reactivity and Identifying Fluorinated Products by Combining Computational Chemistry, 19F NMR, and Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 38340057 PMCID: PMC10883306 DOI: 10.1021/acs.est.3c09341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Fluorinated breakdown products from photolysis of pharmaceuticals and pesticides are of environmental concern due to their potential persistence and toxicity. While mass spectrometry workflows have been shown to be useful in identifying products, they fall short for fluorinated products and may miss up to 90% of products. Studies have shown that 19F NMR measurements assist in identifying and quantifying reaction products, but this protocol can be further developed by incorporating computations. Density functional theory was used to compute 19F NMR shifts for parent and product structures in photolysis reactions. Computations predicted NMR spectra of compounds with an R2 of 0.98. Computed shifts for several isolated product structures from LC-HRMS matched the experimental shifts with <0.7 ppm error. Multiple products including products that share the same shift that were not previously reported were identified and quantified using computational shifts, including aliphatic products in the range of -80 to -88 ppm. Thus, photolysis of fluorinated pharmaceuticals and pesticides can result in compounds that are polyfluorinated alkyl substances (PFAS), including aliphatic-CF3 or vinyl-CF2 products derived from heteroaromatic-CF3 groups. C-F bond-breaking enthalpies and electron densities around the fluorine motifs agreed well with the experimentally observed defluorination of CF3 groups. Combining experimental-computational 19F NMR allows quantification of products identified via LC-HRMS without the need for authentic standards. These results have applications for studies of environmental fate and analysis of fluorinated pharmaceuticals and pesticides in development.
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Affiliation(s)
- Akash P Bhat
- Department of Civil, Environmental, and Geo- Engineering University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - William A Arnold
- Department of Civil, Environmental, and Geo- Engineering University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, Minnesota 55455, United States
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12
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Caceres-Cortes J, Falk B, Mueller L, Dhar TGM. Perspectives on Nuclear Magnetic Resonance Spectroscopy in Drug Discovery Research. J Med Chem 2024; 67:1701-1733. [PMID: 38290426 DOI: 10.1021/acs.jmedchem.3c02389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The drug discovery landscape has undergone a significant transformation over the past decade, owing to research endeavors in a wide range of areas leading to strategies for pursuing new drug targets and the emergence of novel drug modalities. NMR spectroscopy has been a technology of fundamental importance to these research pursuits and has seen its use expanded both within and outside of traditional medicinal chemistry applications. In this perspective, we will present advancement of NMR-derived methods that have facilitated the characterization of small molecules and novel drug modalities including macrocyclic peptides, cyclic dinucleotides, and ligands for protein degradation. We will discuss innovations in NMR spectroscopy at the chemistry and biology interface that have broadened NMR's utility from hit identification through lead optimization activities. We will also discuss the promise of emerging NMR approaches in bridging our understanding and addressing challenges in the pursuit of the therapeutic agents of the future.
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Affiliation(s)
- Janet Caceres-Cortes
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Bradley Falk
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Luciano Mueller
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - T G Murali Dhar
- Discovery Chemistry, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 085401, United States
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13
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Frere GA, Hasabnis A, Francisco CB, Suleiman M, Alimowska O, Rahmatullah R, Gould J, Su CYC, Voznyy O, Gunning PT, Basso EA, Prosser RS. Next-Generation Tags for Fluorine Nuclear Magnetic Resonance: Designing Amplification of Chemical Shift Sensitivity. J Am Chem Soc 2024; 146:3052-3064. [PMID: 38279916 DOI: 10.1021/jacs.3c09730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
Fluorine NMR is a highly sensitive technique for delineating the conformational states of biomolecules and has shown great utility in drug screening and in understanding protein function. Current fluorinated protein tags leverage the intrinsic chemical shift sensitivity of the 19F nucleus to detect subtle changes in protein conformation and topology. This chemical shift sensitivity can be amplified by embedding the fluorine or trifluoromethyl reporter within a pyridone. Due to their polarizability and rapid tautomerization, pyridones exhibit a greater range of electron delocalization and correspondingly greater 19F NMR chemical shift dispersion. To assess the chemical shift sensitivity of these tautomeric probes to the local environment, 19F NMR spectra of all possible monofluorinated and trifluoromethyl-tagged versions of 2-pyridone were recorded in methanol/water mixtures ranging from 100% methanol to 100% water. 4-Fluoro-2-pyridone and 6-(trifluoromethyl)-2-pyridone (6-TFP) displayed the greatest sensitivity of the monofluorinated and trifluoromethylated pyridones, exceeding that of known conventional CF3 reporters. To evaluate the utility of tautomeric pyridone tags for 19F NMR of biomolecules, the alpha subunit of the stimulatory G protein (Gsα) and human serum albumin (HSA) were each labeled with a thiol-reactive derivative of 6-TFP and the spectra were recorded as a function of various adjuvants and drugs. The tautomeric tag outperformed the conventional tag, 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide through the improved resolution of several functional states.
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Affiliation(s)
- Geordon A Frere
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Advait Hasabnis
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Camila B Francisco
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
- Department of Chemistry, State University of Maringá, 5790, Maringá 87020-900, Brazil
| | - Motasem Suleiman
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Olga Alimowska
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Rima Rahmatullah
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Jerome Gould
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Celia Yi-Chia Su
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Oleksandr Voznyy
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Patrick T Gunning
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Ernani A Basso
- Department of Chemistry, State University of Maringá, 5790, Maringá 87020-900, Brazil
| | - Robert S Prosser
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
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14
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Lewis R, Huang CH, White JC, Haynes CL. Using 19F NMR to Investigate Cationic Carbon Dot Association with Per- and Polyfluoroalkyl Substances (PFAS). ACS NANOSCIENCE AU 2023; 3:408-417. [PMID: 37868224 PMCID: PMC10588439 DOI: 10.1021/acsnanoscienceau.3c00022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 10/24/2023]
Abstract
There is much concern about per- and polyfluoroalkyl substances (PFAS) based on their environmental persistence and toxicity, resulting in an urgent need for remediation technologies. This study focused on determining if nanoscale polymeric carbon dots are a viable sorbent material for PFAS and developing fluorine nuclear magnetic resonance spectroscopy (19F NMR) methods to probe interactions between carbon dots and PFAS at the molecular scale. Positively charged carbon dots (PEI-CDs) were synthesized using branched polyethyleneimine to target anionic PFAS by promoting electrostatic interactions. PEI-CDs were exposed to perfluorooctanoic acid (PFOA) to assess their potential as a PFAS sorbent material. After exposure to PFOA, the average size of the PEI-CDs increased (1.6 ± 0.5 to 7.8 ± 1.8 nm) and the surface charge decreased (+38.6 ± 1.1 to +26.4 ± 0.8 mV), both of which are consistent with contaminant sorption. 19F NMR methods were developed to gain further insight into PEI-CD affinity toward PFAS without any complex sample preparation. Changes in PFOA peak intensity and chemical shift were monitored at various PEI-CD concentrations to establish binding curves and determine the chemical exchange regime. 19F NMR spectral analysis indicates slow-intermediate chemical exchange between PFOA and CDs, demonstrating a high-affinity interaction. The α-fluorine had the greatest change in chemical shift and highest affinity, suggesting electrostatic interactions are the dominant sorption mechanism. PEI-CDs demonstrated affinity for a wide range of analytes when exposed to a mixture of 24-PFAS, with a slight preference toward perfluoroalkyl sulfonates. Overall, this study shows that PEI-CDs are an effective PFAS sorbent material and establishes 19F NMR as a suitable method to screen for novel sorbent materials and elucidate interaction mechanisms.
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Affiliation(s)
- Riley
E. Lewis
- Department
of Chemistry, University of Minnesota-Twin
Cities, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Cheng-Hsin Huang
- Department
of Chemistry, University of Minnesota-Twin
Cities, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Jason C. White
- The
Connecticut Agricultural Experiment Station, The Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, Connecticut 06511, United States
| | - Christy L. Haynes
- Department
of Chemistry, University of Minnesota-Twin
Cities, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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15
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Buchholz C, Sneddon MS, McPherson JE, Das S, Gee CT, Grillo MJ, Chai SC, Lee RE, Chen T, Harki DA, Shelat AA, Pomerantz WCK. Fragment-Based NMR Screening of the BPTF PHD Finger Methyl Lysine Reader Leads to the First Small-Molecule Inhibitors. ACS Med Chem Lett 2023; 14:1441-1447. [PMID: 37849548 PMCID: PMC10577693 DOI: 10.1021/acsmedchemlett.3c00343] [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: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
Methyl lysine readers, specifically PHD fingers, are emerging epigenetic targets in human diseases. For example, several PHD finger fusions are implicated in clinical cases of acute myeloid leukemia, highlighting the potential for PHD inhibitors in disease regulation. However, limited chemical matter targeting PHD fingers exists. Here we report the first fragment-based screen against the BPTF PHD to identify several of the first reported BPTF PHD-targeting small-molecule ligands. We used ligand-observed NMR to first screen a fragment library, followed by biophysical validation to prioritize two scaffolds, pyrrolidine- and pyridazine-containing fragments. Structural predictions show that these respective scaffolds may engage two distinct subpockets on the protein. The demonstrated ligandability of the BPTF PHD supports the future development of methyl lysine reader chemical probes to study their oncogenic functions.
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Affiliation(s)
- Caroline
R. Buchholz
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Molly S. Sneddon
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Joseph E. McPherson
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sourav Das
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Clifford T. Gee
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Michael J. Grillo
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sergio C. Chai
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Richard E. Lee
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Taosheng Chen
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Daniel A. Harki
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Anang A. Shelat
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - William C. K. Pomerantz
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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16
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Wilson DJD. Extreme NMR shielding in fluoro-nitrogen cations. Phys Chem Chem Phys 2023; 25:25420-25434. [PMID: 37706351 DOI: 10.1039/d3cp03399f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
The structure and NMR shielding of a set of N-F containing cations is reported to near-quantitative accuracy from extensive ab initio calculations. Currently, the shortest experimentally confirmed N-F bond is 1.2461(10) Å in NNF+, however CCSD(T)-F12b/cc-pVQZ-F12 optimised geometries suggest that even shorter N-F bonds are possible for both monocations (1.236 Å, HNF+) and dications (1.098 Å, NF2+). NMR shielding constants have been calculated in a composite manner with individual components from coupled-cluster expansions up to CCSDTQP and basis sets up to aug-cc-pCV8Z, together with vibrational and relativistic corrections. 15N and 19F NMR chemical shifts correlate well with available experimental data. Extreme 19F chemical shifts are predicted for HNF+ (1628.9 ppm) and NH2F2+ (1298.0 ppm), which are by far the largest 19F chemical shifts ever reported and well outside the known range of +865 ppm (F2O2) to -448 ppm (ClF). The 15N chemical shift of -1283.07 ppm in HNF+ is similarly extreme, being well outside the known range of 15N chemical shifts of -730 to 260 ppm (CH3NO2 reference). This work highlights the application of state-of-the-art theoretical techniques, and provides accurate NMR properties of both isolated and yet unknown N-F cations, which can serve to guide and supplement NMR experimentation.
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Affiliation(s)
- David J D Wilson
- Department of Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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17
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Lysak DH, Grisi M, Marable K, Conley GM, Michal CA, Moxley-Paquette V, Wolff WW, Downey K, Kock FVC, Costa PM, Ronda K, Moraes TB, Steiner K, Colnago LA, Simpson AJ. Exploring the Potential of Broadband Complementary Metal Oxide Semiconductor Micro-Coil Nuclear Magnetic Resonance for Environmental Research. Molecules 2023; 28:5080. [PMID: 37446742 PMCID: PMC10343494 DOI: 10.3390/molecules28135080] [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: 06/01/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
With sensitivity being the Achilles' heel of nuclear magnetic resonance (NMR), the superior mass sensitivity offered by micro-coils can be an excellent choice for tiny, mass limited samples such as eggs and small organisms. Recently, complementary metal oxide semiconductor (CMOS)-based micro-coil transceivers have been reported and demonstrate excellent mass sensitivity. However, the ability of broadband CMOS micro-coils to study heteronuclei has yet to be investigated, and here their potential is explored within the lens of environmental research. Eleven nuclei including 7Li, 19F, 31P and, 205Tl were studied and detection limits in the low to mid picomole range were found for an extended experiment. Further, two environmentally relevant samples (a sprouting broccoli seed and a D. magna egg) were successfully studied using the CMOS micro-coil system. 13C NMR was used to help resolve broad signals in the 1H spectrum of the 13C enriched broccoli seed, and steady state free precession was used to improve the signal-to-noise ratio by a factor of six. 19F NMR was used to track fluorinated contaminants in a single D. magna egg, showing potential for studying egg-pollutant interactions. Overall, CMOS micro-coil NMR demonstrates significant promise in environmental research, especially when the future potential to scale to multiple coil arrays (greatly improving throughput) is considered.
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Affiliation(s)
- Daniel H. Lysak
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Marco Grisi
- Annaida Technologies, Innovation Park, 1015 Lausanne, Switzerland
| | - Kathryn Marable
- Annaida Technologies, Innovation Park, 1015 Lausanne, Switzerland
| | | | - Carl A. Michal
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | | | - William W. Wolff
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Katelyn Downey
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Flavio V. C. Kock
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Peter M. Costa
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Kiera Ronda
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Tiago B. Moraes
- Departamento Engenharia de Biossistemas, Universidade de São Paulo/ESALQ, Av. Páduas Dias, 11, Piracicaba 13418-900, SP, Brazil
| | - Katrina Steiner
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Luiz A. Colnago
- Embrapa Instrumentação, Rua XV de Novembro 1452, São Carlos 13560-970, SP, Brazil
| | - Andre J. Simpson
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
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18
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Huang Y, Reddy KD, Bracken C, Qiu B, Zhan W, Eliezer D, Boudker O. Environmentally Ultrasensitive Fluorine Probe to Resolve Protein Conformational Ensembles by 19F NMR and Cryo-EM. J Am Chem Soc 2023; 145:8583-8592. [PMID: 37023263 PMCID: PMC10119980 DOI: 10.1021/jacs.3c01003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Indexed: 04/08/2023]
Abstract
Limited chemical shift dispersion represents a significant barrier to studying multistate equilibria of large membrane proteins by 19F NMR. We describe a novel monofluoroethyl 19F probe that dramatically increases the chemical shift dispersion. The improved conformational sensitivity and line shape enable the detection of previously unresolved states in one-dimensional (1D) 19F NMR spectra of a 134 kDa membrane transporter. Changes in the populations of these states in response to ligand binding, mutations, and temperature correlate with population changes of distinct conformations in structural ensembles determined by single-particle cryo-electron microscopy (cryo-EM). Thus, 19F NMR can guide sample preparation to discover and visualize novel conformational states and facilitate image analysis and three-dimensional (3D) classification.
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Affiliation(s)
- Yun Huang
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Krishna D. Reddy
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Clay Bracken
- Department
of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Biao Qiu
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Wenhu Zhan
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - David Eliezer
- Department
of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Olga Boudker
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
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19
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Exploring the Antitubercular Activity of Anthranilic Acid Derivatives: From MabA (FabG1) Inhibition to Intrabacterial Acidification. Pharmaceuticals (Basel) 2023; 16:ph16030335. [PMID: 36986435 PMCID: PMC10057394 DOI: 10.3390/ph16030335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Mycobacterium tuberculosis, the pathogen that causes tuberculosis, is responsible for the death of 1.5 million people each year and the number of bacteria resistant to the standard regimen is constantly increasing. This highlights the need to discover molecules that act on new M. tuberculosis targets. Mycolic acids, which are very long-chain fatty acids essential for M. tuberculosis viability, are synthesized by two types of fatty acid synthase (FAS) systems. MabA (FabG1) is an essential enzyme belonging to the FAS-II cycle. We have recently reported the discovery of anthranilic acids as MabA inhibitors. Here, the structure–activity relationships around the anthranilic acid core, the binding of a fluorinated analog to MabA by NMR experiments, the physico-chemical properties and the antimycobacterial activity of these inhibitors were explored. Further investigation of the mechanism of action in bacterio showed that these compounds affect other targets than MabA in mycobacterial cells and that their antituberculous activity is due to the carboxylic acid moiety which induces intrabacterial acidification.
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20
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Audsley G, Carpenter H, Essien NB, Lai-Morrice J, Al-Hilaly Y, Serpell LC, Akien GR, Tizzard GJ, Coles SJ, Ulldemolins CP, Kostakis GE. Chiral Co 3Y Propeller-Shaped Chemosensory Platforms Based on 19F-NMR. Inorg Chem 2023; 62:2680-2693. [PMID: 36716401 PMCID: PMC9930122 DOI: 10.1021/acs.inorgchem.2c03737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Two propeller-shaped chiral CoIII3YIII complexes built from fluorinated ligands are synthesized and characterized by single-crystal X-ray diffraction (SXRD), IR, UV-vis, circular dichroism (CD), elemental analysis, thermogravimetric analysis (TGA), electron spray ionization mass spectroscopy (ESI-MS), and NMR (1H, 13C, and 19F). This work explores the sensing and discrimination abilities of these complexes, thus providing an innovative sensing method using a 19F NMR chemosensory system and opening new directions in 3d/4f chemistry. Control experiments and theoretical studies shed light on the sensing mechanism, while the scope and limitations of this method are discussed and presented.
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Affiliation(s)
- Gabrielle Audsley
- Department
of Chemistry, School of Life Sciences, University
of Sussex, Brighton BN1 9QJ, UK
| | - Harry Carpenter
- Department
of Chemistry, School of Life Sciences, University
of Sussex, Brighton BN1 9QJ, UK
| | - Nsikak B. Essien
- Department
of Chemistry, School of Life Sciences, University
of Sussex, Brighton BN1 9QJ, UK
| | - James Lai-Morrice
- Department
of Chemistry, School of Life Sciences, University
of Sussex, Brighton BN1 9QJ, UK
| | - Youssra Al-Hilaly
- Sussex
Neuroscience, School of Life Sciences, University
of Sussex, Brighton BN1 9QG, UK,Chemistry
Department, College of Science, Mustansiriyah
University, Baghdad 10001, Iraq
| | - Louise C. Serpell
- Sussex
Neuroscience, School of Life Sciences, University
of Sussex, Brighton BN1 9QG, UK
| | - Geoffrey R. Akien
- Department
of Chemistry, Lancaster University, Lancaster LA1 4YB, UK
| | - Graham J. Tizzard
- UK
National Crystallography Service, Chemistry, University of Southampton, Southampton SO1 71BJ, UK
| | - Simon J. Coles
- UK
National Crystallography Service, Chemistry, University of Southampton, Southampton SO1 71BJ, UK
| | | | - George E. Kostakis
- Department
of Chemistry, School of Life Sciences, University
of Sussex, Brighton BN1 9QJ, UK,
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21
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Lete MG, Franconetti A, Bertuzzi S, Delgado S, Azkargorta M, Elortza F, Millet O, Jiménez-Osés G, Arda A, Jiménez-Barbero J. NMR Investigation of Protein-Carbohydrate Interactions: The Recognition of Glycans by Galectins Engineered with Fluorotryptophan Residues. Chemistry 2023; 29:e202202208. [PMID: 36343278 PMCID: PMC10107428 DOI: 10.1002/chem.202202208] [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: 07/14/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
Fluorine (19 F) incorporation into glycan-binding proteins (lectins) has been achieved and exploited to monitor the binding to carbohydrate ligands by nuclear magnetic resonance (NMR) spectroscopy. Galectins are a family of lectins that bind carbohydrates, generally with weak affinities, through a combination of intermolecular interactions including a key CH-π stacking involving a conserved tryptophan residue. Herein, Galectin-3 (Gal3) and Galectin-8 (Gal8) with one and two carbohydrate recognition domains (CRDs), respectively, were selected. Gal3 contains one Trp, whereas Gal8 contains three, one at each binding site and a third one not involved in sugar binding; these were substituted by the corresponding F-Trp analogues. The presence of fluorine did not significantly modify the affinity for glycan binding, which was in slow exchange on the 19 F NMR chemical-shift timescale, even for weak ligands, and allowed binding events taking place at two different binding sites within the same lectin to be individualized.
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Affiliation(s)
- Marta G Lete
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Antonio Franconetti
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Sara Bertuzzi
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Sandra Delgado
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Félix Elortza
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Oscar Millet
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Gonzalo Jiménez-Osés
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain
| | - Ana Arda
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain.,Department of Organic Chemistry II Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940, Leioa, Spain.,Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain
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22
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Gerothanassis IP. Ligand-observed in-tube NMR in natural products research: A review on enzymatic biotransformations, protein-ligand interactions, and in-cell NMR spectroscopy. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2022.104536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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23
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Lu Y, Sun M, Xi N. Effects of fluorine bonding and nonbonding interactions on 19F chemical shifts. RSC Adv 2022; 12:32082-32096. [PMID: 36415555 PMCID: PMC9644289 DOI: 10.1039/d2ra06660b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 11/03/2023] Open
Abstract
19F-NMR signals are sensitive to local electrostatic fields and are useful in probing protein structures and dynamics. Here, we used chemically identical ortho-F nuclei in N-phenyl γ-lactams to investigate the relationship between 19F NMR chemical shifts and local environments. By varying the structures at the C5- and C7-substituents, we demonstrated that 19F shifts and Hammett coefficients in Hammett plots follow typical relationships in bonding interactions, while manifesting reverse correlations in nonbonding contacts. Quantum mechanics calculations revealed that one of the ortho-F nuclei engages in n → π* orbital delocalization between F lone pair electrons (n) and a C[double bond, length as m-dash]O/Ar[double bond, length as m-dash]N antibonding orbital (π*), and the other ortho-F nucleus exhibits n ↔ σ orbital polarization between the n electrons and the C-H σ bonding orbital. As 19F NMR spectroscopy find increasing use in molecular sensors and biological sciences, our findings are valuable for designing sensitive probes, elucidating molecular structures, and quantifying analytes.
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Affiliation(s)
- Yang Lu
- Institute of Drug Discovery Technology, Ningbo University Ningbo Zhejiang 315211 P. R. China
| | - Mingming Sun
- Department of Chemistry, Nanchang University 999 Xuefu Avenue Nanchang 330031 P. R. China
| | - Ning Xi
- Institute of Drug Discovery Technology, Ningbo University Ningbo Zhejiang 315211 P. R. China
- School of Medicine, Ningbo University Ningbo Zhejiang 315211 P. R. China
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24
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Peacock DM, Kelly MJS, Shokat KM. Probing the KRas Switch II Groove by Fluorine NMR Spectroscopy. ACS Chem Biol 2022; 17:2710-2715. [PMID: 36166818 PMCID: PMC9594042 DOI: 10.1021/acschembio.2c00566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
While there has been recent success in the development of KRasG12C inhibitors, unmet needs for selective inhibitors of KRasG12D and the remaining oncogenic KRas proteins remain. Here, we applied trifluoromethyl-containing ligands of KRas proteins as competitive probe ligands to assay the occupancy of the switch II pocket by 19F NMR spectroscopy. Structure-activity-relationship studies of probe ligands increased the sensitivity of the assay and identified structures that differentially detected each nucleotide state of KRasG12D. These differences in selectivity, combined with the high resolution of 19F NMR spectroscopy, enabled this method to be expanded to assay both nucleotide states of the protein simultaneously.
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Affiliation(s)
- D. Matthew Peacock
- Department
of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Mark J. S. Kelly
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San
Francisco, California 94158, United States
| | - Kevan M. Shokat
- Department
of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States,Howard
Hughes Medical Institute, San Francisco, California 94158, United States,E-mail:
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25
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Olson NM, Johnson JA, Peterson KE, Henisch SC, Marshall AP, Smanski MJ, Carlson EE, Pomerantz WC. Development of a single culture E. coli expression system for the enzymatic synthesis of fluorinated tyrosine and its incorporation into proteins. J Fluor Chem 2022; 261-262. [PMID: 37197608 PMCID: PMC10187777 DOI: 10.1016/j.jfluchem.2022.110014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Current experiments that rely on biosynthetic metabolic protein labeling with 19F often require fluorinated amino acids, which in the case of 2- and 3-fluorotyrosine can be expensive. However, using these amino acids has provided valuable insight into protein dynamics, structure, and function. Here, we develop a new in-cell method for fluorinated tyrosine generation from readily available substituted phenols and subsequent metabolic labeling of proteins in a single bacterial expression culture. This approach uses a dual-gene plasmid encoding for a model protein BRD4(D1) and a tyrosine phenol lyase from Citrobacter freundii, which catalyzes the formation of tyrosine from phenol, pyruvate, and ammonium. Our system demonstrated both enzymatic fluorotyrosine production and expression of 19F-labeled proteins as analyzed by 19F NMR and LC-MS methods. Further optimization of our system should provide a cost-effective alternative to a variety of traditional protein-labeling strategies.
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26
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Stadler KA, Becker W, Darnhofer B, Birner-Gruenberger R, Zangger K. Overexpression of recombinant proteins containing non-canonical amino acids in Vibrio natriegens: p-azido-L-phenylalanine as coupling site for 19F-tags. Amino Acids 2022; 54:1041-1053. [PMID: 35419750 PMCID: PMC9217835 DOI: 10.1007/s00726-022-03148-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/27/2022] [Indexed: 11/26/2022]
Abstract
Vibrio natriegens is the fastest growing organism identified so far. The minimum doubling time of only 9.4 min, the ability to utilize over 60 different carbon sources and its non-pathogenic properties make it an interesting alternative to E. coli as a new production host for recombinant proteins. We investigated the ability of the engineered V. natriegens strain, Vmax™ Express, to incorporate the non-canonical amino acid (ncAA) p-azido-L-phenylalanine (AzF) into recombinant proteins for NMR applications. AzF was incorporated into enhanced yellow fluorescent protein (EYFP) and MlaC, an intermembrane transport protein, by stop codon suppression. AzF incorporation into EYFP resulted in an improved suppression efficiency (SE) of up to 35.5 ± 0.8% and a protein titer of 26.7 ± 0.7 mg/L. The expression levels of MlaC-AzF even exceeded those of E. coli BL21 cells. For the recording of 1H-15N and 19F NMR spectra, EYFP-AzF was expressed and isotopically labeled in minimal medium and the newly introduced azido-group was used as coupling site for NMR sensitive 19F-tags. Our findings show that Vmax is a flexible expression host, suitable for the incorporation of ncAAs in recombinant proteins with the potential to surpass protein yields of E. coli. The presented method suggests the implementation of V. natriegens for expression of isotopically labeled proteins containing ncAAs, which can be chemically modified for the application in protein-observed 19F-NMR.
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Affiliation(s)
- Karina A Stadler
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Walter Becker
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 17177, Stockholm, Sweden
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
| | - Ruth Birner-Gruenberger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Technische Universität Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - Klaus Zangger
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
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27
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Xu Z, Gu S, Li Y, Wu J, Zhao Y. Recognition-Enabled Automated Analyte Identification via 19F NMR. Anal Chem 2022; 94:8285-8292. [PMID: 35622989 DOI: 10.1021/acs.analchem.2c00642] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nuclear magnetic resonance (NMR) is an indispensable tool for structural elucidation and noninvasive analysis. Automated identification of analytes with NMR is highly pursued in metabolism research and disease diagnosis; however, this process is often complicated by the signal overlap and the sample matrix. We herein report a detection scheme based on 19F NMR spectroscopy and dynamic recognition, which effectively simplifies the detection signal and mitigates the influence of the matrix on the detection. It is demonstrated that this approach can not only detect and differentiate capsaicin and dihydrocapsaicin in complex real-world samples but also quantify the ibuprofen content in sustained-release capsules. Based on the 19F signals obtained in the detection using a set of three 19F probes, automated analyte identification is achieved, effectively reducing the odds of misrecognition caused by structural similarity.
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Affiliation(s)
- Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Siyi Gu
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yipeng Li
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Jian Wu
- Instrumental Analysis Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China.,Key Laboratory of Energy Regulation Materials, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
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28
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Vulpetti A, Lingel A, Dalvit C, Schiering N, Oberer L, Henry C, Lu Y. Efficient Screening of Target-Specific Selected Compounds in Mixtures by 19F NMR Binding Assay with Predicted 19F NMR Chemical Shifts. ChemMedChem 2022; 17:e202200163. [PMID: 35475323 DOI: 10.1002/cmdc.202200163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/26/2022] [Indexed: 11/06/2022]
Abstract
Ligand-based 19 F NMR screening is a highly effective and well-established hit-finding approach. The high sensitivity to protein binding makes it particularly suitable for fragment screening. Different criteria can be considered for generating fluorinated fragment libraries. One common strategy is to assemble a large, diverse, well-designed and characterized fragment library which is screened in mixtures, generated based on experimental 19 F NMR chemical shifts. Here, we introduce a complementary knowledge-based 19 F NMR screening approach, named 19 Focused screening, enabling the efficient screening of putative active molecules selected by computational hit finding methodologies, in mixtures assembled and on-the-fly deconvoluted based on predicted 19 F NMR chemical shifts. In this study, we developed a novel approach, named LEFshift , for 19 F NMR chemical shift prediction using rooted topological fluorine torsion fingerprints in combination with a random forest machine learning method. A demonstration of this approach to a real test case is reported.
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Affiliation(s)
- Anna Vulpetti
- Novartis Pharma AG, Global Discovery Chemistry, Novartis Campus, 4002, Basel, SWITZERLAND
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Claudio Dalvit
- Novartis Institutes for BioMedical Research Basel, Protease Platform, SWITZERLAND
| | - Nikolaus Schiering
- Novartis Institutes for BioMedical Research Basel, Protease Platform, SWITZERLAND
| | - Lukas Oberer
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Chrystelle Henry
- Novartis Institutes for BioMedical Research Basel, Protein Science, SWITZERLAND
| | - Yipin Lu
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
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29
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Yang D, Gronenborn AM, Chong LT. Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field. J Phys Chem A 2022; 126:2286-2297. [PMID: 35352936 PMCID: PMC9014858 DOI: 10.1021/acs.jpca.2c00255] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/15/2022] [Indexed: 12/27/2022]
Abstract
We developed force field parameters for fluorinated, aromatic amino acids enabling molecular dynamics (MD) simulations of fluorinated proteins. These parameters are tailored to the AMBER ff15ipq protein force field and enable the modeling of 4, 5, 6, and 7F-tryptophan, 3F- and 3,5F-tyrosine, and 4F- or 4-CF3-phenylalanine. The parameters include 181 unique atomic charges derived using the implicitly polarized charge (IPolQ) scheme in the presence of SPC/Eb explicit water molecules and 9 unique bond, angle, or torsion terms. Our simulations of benchmark peptides and proteins maintain expected conformational propensities on the μs time scale. In addition, we have developed an open-source Python program to calculate fluorine relaxation rates from MD simulations. The extracted relaxation rates from protein simulations are in good agreement with experimental values determined by 19F NMR. Collectively, our results illustrate the power and robustness of the IPolQ lineage of force fields for modeling the structure and dynamics of fluorine-containing proteins at the atomic level.
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Affiliation(s)
- Darian
T. Yang
- Molecular
Biophysics and Structural Biology Graduate Program, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, Pennsylvania 15260, United States
- Department
of Structural Biology, University of Pittsburgh
School of Medicine, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Angela M. Gronenborn
- Department
of Structural Biology, University of Pittsburgh
School of Medicine, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Lillian T. Chong
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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30
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Shanina E, Kuhaudomlarp S, Lal K, Seeberger PH, Imberty A, Rademacher C. Allosterische, Wirkstoff‐zugängliche Bindestellen in β‐Propeller‐Lektinen. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202109339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Elena Shanina
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
| | - Sakonwan Kuhaudomlarp
- University Grenoble Alpes CNRS CERMAV 38000 Grenoble Frankreich
- Department of Biochemistry Faculty of Science Mahidol University 10400 Bangkok Thailand
- Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University 10400 Bangkok Thailand
| | - Kanhaya Lal
- University Grenoble Alpes CNRS CERMAV 38000 Grenoble Frankreich
- Dipartimento di Chimica via Golgi 19 Università degli Studi di Milano 20133 Milano Italien
| | - Peter H. Seeberger
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
| | - Anne Imberty
- University Grenoble Alpes CNRS CERMAV 38000 Grenoble Frankreich
| | - Christoph Rademacher
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
- Department of Pharmaceutical Chemistry University of Vienna Althanstraße 14 1080 Wien Österreich
- Department of Microbiology, Immunobiology and Genetics Max F. Perutz Labs Campus Vienna Biocenter 5 1030 Wien Österreich
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31
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Shanina E, Kuhaudomlarp S, Lal K, Seeberger PH, Imberty A, Rademacher C. Druggable Allosteric Sites in β-Propeller Lectins. Angew Chem Int Ed Engl 2022; 61:e202109339. [PMID: 34713573 PMCID: PMC9298952 DOI: 10.1002/anie.202109339] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/05/2021] [Indexed: 12/24/2022]
Abstract
Carbohydrate‐binding proteins (lectins) are auspicious targets in drug discovery to combat antimicrobial resistance; however, their non‐carbohydrate drug‐like inhibitors are still unavailable. Here, we present a druggable pocket in a β‐propeller lectin BambL from Burkholderia ambifaria as a potential target for allosteric inhibitors. This site was identified employing 19F NMR fragment screening and a computational pocket prediction algorithm SiteMap. The structure–activity relationship study revealed the most promising fragment with a dissociation constant of 0.3±0.1 mM and a ligand efficiency of 0.3 kcal mol−1 HA−1 that affected the orthosteric site. This effect was substantiated by site‐directed mutagenesis in the orthosteric and secondary pockets. Future drug‐discovery campaigns that aim to develop small molecule inhibitors can benefit from allosteric sites in lectins as a new therapeutic approach against antibiotic‐resistant pathogens.
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Affiliation(s)
- Elena Shanina
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Sakonwan Kuhaudomlarp
- University Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France.,Department of Biochemistry, Faculty of Science, Mahidol University, 10400, Bangkok, Thailand.,Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 10400, Bangkok, Thailand
| | - Kanhaya Lal
- University Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France.,Dipartimento di Chimica via Golgi 19, Universita" degli Studi di Milano, 20133, Milano, Italy
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Anne Imberty
- University Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany.,Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1080, Vienna, Austria.,Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Labs, Campus Vienna Biocenter 5, 1030, Vienna, Austria
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32
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Pantoja CF, Zweckstetter M, Rezaei-Ghaleh N. Dynamical Component Exchange in a Model Phase Separating System: an NMR-based Approach. Phys Chem Chem Phys 2022; 24:6169-6175. [DOI: 10.1039/d2cp00042c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biomolecular phase separation plays a key role in spatial organization of cellular activities. Dynamic formation and rapid component exchange between phase separated cellular bodies and their environment are crucial for...
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33
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Bella G, Milone M, Bruno G, Santoro A. Which DFT factors influence the accuracy of 1H, 13C and 195Pt NMR chemical shift predictions in organopolymetallic square-planar complexes? New scaling parameters for homo- and hetero-multimetallic compounds and their direct applications. Phys Chem Chem Phys 2022; 24:26642-26658. [DOI: 10.1039/d2cp02773a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Because of their chemical heterogeneity, stereochemical complexity and the presence of heavy atoms involving orbitals with high quantum number L, organopolymetallic complexes require considerable focus during their NMR spectral interpretation.
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Affiliation(s)
- Giovanni Bella
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
- Department of Health Science, University of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Marco Milone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Giuseppe Bruno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Antonio Santoro
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
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