1
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Yang X, Yang G, Chu J. GraphCL-DTA: A Graph Contrastive Learning With Molecular Semantics for Drug-Target Binding Affinity Prediction. IEEE J Biomed Health Inform 2024; 28:4544-4552. [PMID: 38190664 DOI: 10.1109/jbhi.2024.3350666] [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: 01/10/2024]
Abstract
Drug-target binding affinity prediction plays an important role in the early stages of drug discovery, which can infer the strength of interactions between new drugs and new targets. However, the performance of previous computational models is limited by the following drawbacks. The learning of drug representation relies only on supervised data without considering the information in the molecular graph itself. Moreover, most previous studies tended to design complicated representation learning modules, while uniformity used to measure representation quality is ignored. In this study, we propose GraphCL-DTA, a graph contrastive learning with molecular semantics for drug-target binding affinity prediction. This graph contrastive learning framework replaces the dropout-based data augmentation strategy by performing data augmentation in the embedding space, thereby better preserving the semantic information of the molecular graph. A more essential and effective drug representation can be learned through this graph contrastive framework without additional supervised data. Next, we design a new loss function that can be directly used to adjust the uniformity of drug and target representations. By directly optimizing the uniformity of representations, the representation quality of drugs and targets can be improved. The effectiveness of the above innovative elements is verified on two real datasets, KIBA and Davis. Compared with the GraphDTA model, the relative improvement of the GraphCL-DTA model on the two datasets is 2.7% and 4.5%. The graph contrastive learning framework and uniformity function in the GraphCL-DTA model can be embedded into other computational models as independent modules to improve their generalization capability.
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2
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Radka CD, Grace CR, Hasdemir HS, Li Y, Rodriguez CC, Rodrigues P, Oldham ML, Qayyum MZ, Pitre A, MacCain WJ, Kalathur RC, Tajkhorshid E, Rock CO. The carboxy terminus causes interfacial assembly of oleate hydratase on a membrane bilayer. J Biol Chem 2024; 300:105627. [PMID: 38211817 PMCID: PMC10847778 DOI: 10.1016/j.jbc.2024.105627] [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: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
The soluble flavoprotein oleate hydratase (OhyA) hydrates the 9-cis double bond of unsaturated fatty acids. OhyA substrates are embedded in membrane bilayers; OhyA must remove the fatty acid from the bilayer and enclose it in the active site. Here, we show that the positively charged helix-turn-helix motif in the carboxy terminus (CTD) is responsible for interacting with the negatively charged phosphatidylglycerol (PG) bilayer. Super-resolution microscopy of Staphylococcus aureus cells expressing green fluorescent protein fused to OhyA or the CTD sequence shows subcellular localization along the cellular boundary, indicating OhyA is membrane-associated and the CTD sequence is sufficient for membrane recruitment. Using cryo-electron microscopy, we solved the OhyA dimer structure and conducted 3D variability analysis of the reconstructions to assess CTD flexibility. Our surface plasmon resonance experiments corroborated that OhyA binds the PG bilayer with nanomolar affinity and we found the CTD sequence has intrinsic PG binding properties. We determined that the nuclear magnetic resonance structure of a peptide containing the CTD sequence resembles the OhyA crystal structure. We observed intermolecular NOE from PG liposome protons next to the phosphate group to the CTD peptide. The addition of paramagnetic MnCl2 indicated the CTD peptide binds the PG surface but does not insert into the bilayer. Molecular dynamics simulations, supported by site-directed mutagenesis experiments, identify key residues in the helix-turn-helix that drive membrane association. The data show that the OhyA CTD binds the phosphate layer of the PG surface to obtain bilayer-embedded unsaturated fatty acids.
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Affiliation(s)
- Christopher D Radka
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA; Department of Host Microbe Interactions, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
| | - Christy R Grace
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Hale S Hasdemir
- Theoretical and Computational Biophysics Group, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yupeng Li
- Theoretical and Computational Biophysics Group, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Carlos C Rodriguez
- Theoretical and Computational Biophysics Group, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Patrick Rodrigues
- Hartwell Center of Biotechnology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael L Oldham
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - M Zuhaib Qayyum
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Aaron Pitre
- Cell and Tissue Imaging Center, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - William J MacCain
- Department of Host Microbe Interactions, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ravi C Kalathur
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Charles O Rock
- Department of Host Microbe Interactions, St Jude Children's Research Hospital, Memphis, Tennessee, USA
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3
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Osborne MJ, Sulekha A, Culjkovic-Kraljacic B, Gasiorek J, Ruediger E, Jolicouer E, Marinier A, Assouline S, Borden KLB. Medicinal Chemistry and NMR Driven Discovery of Novel UDP-glucuronosyltransferase 1A Inhibitors That Overcome Therapeutic Resistance in Cells. J Mol Biol 2024; 436:168378. [PMID: 38043731 PMCID: PMC10841659 DOI: 10.1016/j.jmb.2023.168378] [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: 10/04/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023]
Abstract
The UDP glucuronosyltransferases (UGT) deactivate many therapeutics via glucuronidation while being required for clearance of normal metabolites and xenobiotics. There are 19 UGT enzymes categorized into UGT1A and UGT2B families based on sequence conservation. This presents a challenge in terms of targeting specific UGTs to overcome drug resistance without eliciting overt toxicity. Here, we identified for the first time that UGT1A4 is highly elevated in acute myeloid leukemia (AML) patients and its reduction corresponded to objective clinical responses. To develop inhibitors to UGT1A4, we leveraged previous NMR-based fragment screening data against the C-terminal domain of UGT1A (UGT1A-C). NMR and medicinal chemistry strategies identified novel chemical matter based on fragment compounds with the capacity to bind ∼20 fold more tightly to UGT1A-C (Kd ∼ 600 μM vs ∼30 μM). Some compounds differentially inhibited UGT1A4 versus UGT1A1 enzyme activity and restored drug sensitivity in resistant human cancer cells. NMR-based NOE experiments revealed these novel compounds recognised a region distal to the catalytic site suggestive of allosteric regulation. This binding region is poorly conserved between UGT1A and UGT2B C-terminal sequences, which otherwise exhibit high similarity. Consistently, these compounds did not bind to the C-terminal domain of UGT2B7 nor a triple mutant of UGT1A-C replaced with UGT2B7 residues in this region. Overall, we discovered a site on UGTs that can be leveraged to differentially target UGT1As and UGT2Bs, identified UGT1A4 as a therapeutic target, and found new chemical matter that binds the UGT1A C-terminus, inhibits glucuronidation and restores drug sensitivity.
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Affiliation(s)
- Michael J Osborne
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
| | - Anamika Sulekha
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
| | - Jadwiga Gasiorek
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
| | - Edward Ruediger
- Drug Discovery Unit, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Eric Jolicouer
- Drug Discovery Unit, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Anne Marinier
- Drug Discovery Unit, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Sarit Assouline
- Jewish General Hospital and McGill University, 3755 Cote Ste Catherine, Montreal, Quebec H3T1E2, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
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4
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Wang TY, Ji H, Everton D, Le ATH, Krylova SM, Fournier R, Krylov SN. Fundamental Determinants of the Accuracy of Equilibrium Constants for Affinity Complexes. Anal Chem 2023; 95:15826-15832. [PMID: 37831482 DOI: 10.1021/acs.analchem.3c03557] [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: 10/14/2023]
Abstract
The equilibrium constant of a chemical reaction is arguably the key thermodynamic parameter in chemistry; we naturally expect that equilibrium constants are determined accurately. The majority of equilibrium constants determined today are those of binding reactions that form affinity complexes, such as protein-protein, protein-DNA, and protein-small molecule. There is growing awareness that the determination of equilibrium constants for highly stable affinity complexes may be very inaccurate. However, fundamental (i.e., method-independent) determinants of accuracy are poorly understood. Here, we present a study that explicitly shows what the accuracy of equilibrium constants of affinity complexes depends on. This study reveals the critical importance of the choice of concentration of interacting components and creates a theoretical foundation for improving the accuracy of the equilibrium constants. The predicted influence of concentrations on accuracy was confirmed experimentally. The results of this fundamental study provide instructive guidance for experimentalists independently on the method they use.
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Affiliation(s)
- Tong Ye Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Hongchen Ji
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Daniel Everton
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - An T H Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - René Fournier
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
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5
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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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6
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Larda S, Ayotte Y, Denk MM, Coote P, Heffron G, Bendahan D, Shahout F, Girard N, Iddir M, Bouchard P, Bilodeau F, Woo S, Farmer LJ, LaPlante SR. Robust Strategy for Hit-to-Lead Discovery: NMR for SAR. J Med Chem 2023; 66:13416-13427. [PMID: 37732695 PMCID: PMC10578354 DOI: 10.1021/acs.jmedchem.3c00656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Indexed: 09/22/2023]
Abstract
Establishing robust structure-activity relationships (SARs) is key to successful drug discovery campaigns, yet it often remains elusive due to screening and hit validation artifacts (false positives and false negatives), which frequently result in unproductive downstream expenditures of time and resources. To address this issue, we developed an integrative biophysics-driven strategy that expedites hit-to-lead discovery, mitigates false positives/negatives and common hit validation errors, and provides a robust approach to obtaining accurate binding and affinity measurements. The advantage of this method is that it vastly improves the clarity and reproducibility for affinity-driven SAR by monitoring and eliminating confounding factors. We demonstrate the ease at which high-quality micromolar binders can be generated from the initial millimolar fragment screening hits against an "undruggable" protein target, HRas.
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Affiliation(s)
| | - Yann Ayotte
- NMX
Research and Solutions Inc., Laval H7V 5B7, Canada
- INRS
− Centre Armand-Frappier Santé Biotechnologie, Laval H7V 1B7, Canada
| | - Maria M. Denk
- NMX
Research and Solutions Inc., Laval H7V 5B7, Canada
- INRS
− Centre Armand-Frappier Santé Biotechnologie, Laval H7V 1B7, Canada
| | - Paul Coote
- NMX
Research and Solutions Inc., Laval H7V 5B7, Canada
- Harvard
Medical School, Boston, Massachusetts 02115, United States
- Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Gregory Heffron
- NMX
Research and Solutions Inc., Laval H7V 5B7, Canada
- Harvard
Medical School, Boston, Massachusetts 02115, United States
| | - David Bendahan
- INRS
− Centre Armand-Frappier Santé Biotechnologie, Laval H7V 1B7, Canada
| | - Fatma Shahout
- INRS
− Centre Armand-Frappier Santé Biotechnologie, Laval H7V 1B7, Canada
| | | | - Mustapha Iddir
- INRS
− Centre Armand-Frappier Santé Biotechnologie, Laval H7V 1B7, Canada
| | | | | | - Simon Woo
- NMX
Research and Solutions Inc., Laval H7V 5B7, Canada
- INRS
− Centre Armand-Frappier Santé Biotechnologie, Laval H7V 1B7, Canada
| | - Luc J. Farmer
- NMX
Research and Solutions Inc., Laval H7V 5B7, Canada
- INRS
− Centre Armand-Frappier Santé Biotechnologie, Laval H7V 1B7, Canada
| | - Steven R. LaPlante
- NMX
Research and Solutions Inc., Laval H7V 5B7, Canada
- INRS
− Centre Armand-Frappier Santé Biotechnologie, Laval H7V 1B7, Canada
- Harvard
Medical School, Boston, Massachusetts 02115, United States
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7
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Shukla VK, Siemons L, Hansen DF. Intrinsic structural dynamics dictate enzymatic activity and inhibition. Proc Natl Acad Sci U S A 2023; 120:e2310910120. [PMID: 37782780 PMCID: PMC10576142 DOI: 10.1073/pnas.2310910120] [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: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 10/04/2023] Open
Abstract
Enzymes are known to sample various conformations, many of which are critical for their biological function. However, structural characterizations of enzymes predominantly focus on the most populated conformation. As a result, single-point mutations often produce structures that are similar or essentially identical to those of the wild-type enzyme despite large changes in enzymatic activity. Here, we show for mutants of a histone deacetylase enzyme (HDAC8) that reduced enzymatic activities, reduced inhibitor affinities, and reduced residence times are all captured by the rate constants between intrinsically sampled conformations that, in turn, can be obtained independently by solution NMR spectroscopy. Thus, for the HDAC8 enzyme, the dynamic sampling of conformations dictates both enzymatic activity and inhibitor potency. Our analysis also dissects the functional role of the conformations sampled, where specific conformations distinct from those in available structures are responsible for substrate and inhibitor binding, catalysis, and product dissociation. Precise structures alone often do not adequately explain the effect of missense mutations on enzymatic activity and drug potency. Our findings not only assign functional roles to several conformational states of HDAC8 but they also underscore the paramount role of dynamics, which will have general implications for characterizing missense mutations and designing inhibitors.
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Affiliation(s)
- Vaibhav Kumar Shukla
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Lucas Siemons
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - D. Flemming Hansen
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
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8
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Monaco S, Angulo J, Wallace M. Imaging Saturation Transfer Difference (STD) NMR: Affinity and Specificity of Protein-Ligand Interactions from a Single NMR Sample. J Am Chem Soc 2023. [PMID: 37487192 PMCID: PMC10401705 DOI: 10.1021/jacs.3c02218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
We have combined saturation transfer difference NMR (STD NMR) with chemical shift imaging (CSI) and controlled concentration gradients of small molecule ligands to develop imaging STD NMR, a new tool for the assessment of protein-ligand interactions. Our methodology allows the determination of protein-ligand dissociation constants (KD) and assessment of the binding specificity in a single NMR tube, avoiding time-consuming titrations. We demonstrate the formation of suitable and reproducible concentration gradients of ligand along the vertical axis of the tube, against homogeneous protein concentration, and present a CSI pulse sequence for the acquisition of STD NMR experiments at different positions along the sample tube. Compared to the conventional methodology in which the [ligand]/[protein] ratio is increased manually, we can perform STD NMR experiments at a greater number of ratios and construct binding epitopes in a fraction (∼20%) of the experimental time. Second, imaging STD NMR also allows us to screen for non-specific binders, by monitoring any variation of the binding epitope map at increasing [ligand]/[protein] ratios. Hence, the proposed method does carry the potential to speed up and smooth out the drug discovery process.
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Affiliation(s)
- Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Jesus Angulo
- Instituto de Investigaciones Químicas (IIQ), Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, Sevilla 41092, Spain
| | - Matthew Wallace
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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9
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Jakubec M, Rylandsholm FG, Rainsford P, Silk M, Bril'kov M, Kristoffersen T, Juskewitz E, Ericson JU, Svendsen JSM. Goldilocks Dilemma: LPS Works Both as the Initial Target and a Barrier for the Antimicrobial Action of Cationic AMPs on E. coli. Biomolecules 2023; 13:1155. [PMID: 37509189 PMCID: PMC10377513 DOI: 10.3390/biom13071155] [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: 06/22/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial peptides (AMPs) are generally membrane-active compounds that physically disrupt bacterial membranes. Despite extensive research, the precise mode of action of AMPs is still a topic of great debate. This work demonstrates that the initial interaction between the Gram-negative E. coli and AMPs is driven by lipopolysaccharides (LPS) that act as kinetic barriers for the binding of AMPs to the bacterial membrane. A combination of SPR and NMR experiments provide evidence suggesting that cationic AMPs first bind to the negatively charged LPS before reaching a binding place in the lipid bilayer. In the event that the initial LPS-binding is too strong (corresponding to a low dissociation rate), the cationic AMPs cannot effectively get from the LPS to the membrane, and their antimicrobial potency will thus be diminished. On the other hand, the AMPs must also be able to effectively interact with the membrane to exert its activity. The ability of the studied cyclic hexapeptides to bind LPS and to translocate into a lipid membrane is related to the nature of the cationic charge (arginine vs. lysine) and to the distribution of hydrophobicity along the molecule (alternating vs. clumped tryptophan).
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Affiliation(s)
- Martin Jakubec
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019 Tromsø, Norway
| | - Fredrik G Rylandsholm
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019 Tromsø, Norway
| | - Philip Rainsford
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019 Tromsø, Norway
| | - Mitchell Silk
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019 Tromsø, Norway
| | - Maxim Bril'kov
- Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019 Tromsø, Norway
| | - Tone Kristoffersen
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019 Tromsø, Norway
| | - Eric Juskewitz
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019 Tromsø, Norway
| | - Johanna U Ericson
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019 Tromsø, Norway
| | - John Sigurd M Svendsen
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019 Tromsø, Norway
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10
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Shortridge MD, Chaubey B, Zhang HJ, Pavelitz T, Vidadala V, Tang C, Olsen GL, Calin GA, Varani G. Drug-Like Small Molecules That Inhibit Expression of the Oncogenic MicroRNA-21. ACS Chem Biol 2023; 18:237-250. [PMID: 36727622 PMCID: PMC10593481 DOI: 10.1021/acschembio.2c00502] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We report the discovery of drug-like small molecules that bind specifically to the precursor of the oncogenic and pro-inflammatory microRNA-21 with mid-nanomolar affinity. The small molecules target a local structure at the Dicer cleavage site and induce distinctive structural changes in the RNA, which correlate with specific inhibition of miRNA processing. Structurally conservative single nucleotide substitutions eliminate the conformational change induced by the small molecules, which is also not observed in other miRNA precursors. The most potent of these compounds reduces cellular proliferation and miR-21 levels in cancer cell lines without inhibiting kinases or classical receptors, while closely related compounds without this specific binding activity are inactive in cells. These molecules are highly ligand-efficient (MW < 330) and display specific biochemical and cellular activity by suppressing the maturation of miR-21, thereby providing an avenue toward therapeutic development in multiple diseases where miR-21 is abnormally expressed.
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Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bhawna Chaubey
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Huanyu J Zhang
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Thomas Pavelitz
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Venkata Vidadala
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gregory L Olsen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - George A Calin
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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11
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Marteau R, Ravez S, Mazhari Dorooee D, Bouchaoui H, Porte K, Devedjian JC, Melnyk P, Devos D, Frédérick R, El Bakali J. Repositioning of FDA-Approved antifungal agents to interrogate Acyl-CoA synthetase long chain family member 4 (ACSL4) in ferroptosis. Biochem Pharmacol 2022; 204:115239. [PMID: 36075462 DOI: 10.1016/j.bcp.2022.115239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 01/06/2023]
Abstract
Ferroptosis, first coined in 2012, is an iron-dependent regulated cell death (RCD) characterized by the accumulation of lipid peroxides to toxic levels. This mechanism is currently being evaluated as a target for a variety of diseases offering new opportunities for drug design and development. Recent reports uncovered acyl-CoA synthetase long-chain 4 (ACSL4) as a critical contributor to ferroptosis execution. Therefore, ACSL4 inhibitors are emerging as attractive anti-ferroptotic agents. Herein, we developed a robust screening cascade with orthogonal biophysical and biochemical techniques to identify original human ACSL4 inhibitors. By screening an FDA-approved drug library, we were able to identify and validate new inhibitors with micromolar-range activities against ACSL4. With an IC50 of 280 nM against hACSL4, antifungal agent sertaconazole is to our knowledge, the most potent ACSL4 inhibitor identified so far. In addition, sertaconazole significantly reduced lipid peroxidation and ferroptosis in human differentiated dopaminergic neurons (Lund human mesencephalic LUHMES cells), demonstrating that it is a valuable chemical tool for further investigating the role of ACSL4 in ferroptosis. This study highlights the phenethyl-imidazole scaffold as a novel and promising starting point for the development of anti-ferroptotic agents targeting ACSL4.
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Affiliation(s)
- Romain Marteau
- Medicinal Chemistry Research Group (CMFA), Louvain Drug Research Institute (LDRI), Université catholique de Louvain (UCLouvain), 73 Avenue Mounier, B1.73.10, 1200 Bruxelles, Belgium
| | - Séverine Ravez
- Univ. Lille, Inserm, CHU Lille, UMR-S-U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Darius Mazhari Dorooee
- Medicinal Chemistry Research Group (CMFA), Louvain Drug Research Institute (LDRI), Université catholique de Louvain (UCLouvain), 73 Avenue Mounier, B1.73.10, 1200 Bruxelles, Belgium
| | - Hind Bouchaoui
- Univ. Lille, Inserm, CHU Lille, UMR-S-U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Karine Porte
- Medicinal Chemistry Research Group (CMFA), Louvain Drug Research Institute (LDRI), Université catholique de Louvain (UCLouvain), 73 Avenue Mounier, B1.73.10, 1200 Bruxelles, Belgium
| | - Jean-Christophe Devedjian
- Univ. Lille, Inserm, CHU Lille, UMR-S-U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France; Université du Littoral Côte d'Opale-1, place de l'Yser, BP 72033, 59375 Dunkerque Cedex, France
| | - Patricia Melnyk
- Univ. Lille, Inserm, CHU Lille, UMR-S-U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France
| | - David Devos
- Univ. Lille, Inserm, CHU Lille, UMR-S-U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Raphaël Frédérick
- Medicinal Chemistry Research Group (CMFA), Louvain Drug Research Institute (LDRI), Université catholique de Louvain (UCLouvain), 73 Avenue Mounier, B1.73.10, 1200 Bruxelles, Belgium.
| | - Jamal El Bakali
- Univ. Lille, Inserm, CHU Lille, UMR-S-U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France.
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12
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Sasikumar PG, Ramachandra M. Small Molecule Agents Targeting PD-1 Checkpoint Pathway for Cancer Immunotherapy: Mechanisms of Action and Other Considerations for Their Advanced Development. Front Immunol 2022; 13:752065. [PMID: 35585982 PMCID: PMC9108255 DOI: 10.3389/fimmu.2022.752065] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/29/2022] [Indexed: 12/20/2022] Open
Abstract
Pioneering success of antibodies targeting immune checkpoints such as programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) has changed the outlook of cancer therapy. Although these antibodies show impressive durable clinical activity, low response rates and immune-related adverse events are becoming increasingly evident in antibody-based approaches. For further strides in cancer immunotherapy, novel treatment strategies including combination therapies and alternate therapeutic modalities are highly warranted. Towards this discovery and development of small molecule, checkpoint inhibitors are actively being pursued, and the efforts have culminated in the ongoing clinical testing of orally bioavailable checkpoint inhibitors. This review focuses on the small molecule agents targeting PD-1 checkpoint pathway for cancer immunotherapy and highlights various chemotypes/scaffolds and their characterization including binding and functionality along with reported mechanism of action. The learnings from the ongoing small molecule clinical trials and crucial points to be considered for their clinical development are also discussed.
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13
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Structural and mechanistic insights into modulation of α-Synuclein fibril formation by aloin and emodin. Biochim Biophys Acta Gen Subj 2022; 1866:130151. [DOI: 10.1016/j.bbagen.2022.130151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/02/2022] [Accepted: 04/08/2022] [Indexed: 11/20/2022]
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14
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LeBlanc RM, Mesleh MF. A drug discovery toolbox for Nuclear Magnetic Resonance (NMR) characterization of ligands and their targets. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 37:51-60. [PMID: 34895655 DOI: 10.1016/j.ddtec.2020.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/22/2020] [Accepted: 11/27/2020] [Indexed: 10/22/2022]
Abstract
Information about the structure, dynamics, and ligand-binding properties of biomolecules can be derived from Nuclear Magnetic Resonance (NMR) spectroscopy and provides valuable information for drug discovery. A multitude of experimental approaches provides a wealth of information that can be tailored to the system of interest. Methods to study the behavior of ligands upon target binding enable the identification of weak binders in a robust manner that is critical for the identification of truly novel binding interactions. This is particularly important for challenging targets. Observing the solution behavior of biomolecules yields information about their structure, dynamics, and interactions. This review describes the breadth of approaches that are available, many of which are under-utilized in a drug-discovery environment, and focuses on recent advances that continue to emerge.
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Affiliation(s)
- Regan M LeBlanc
- Structural Biology and Biophysics, Vertex Pharmaceuticals Inc., Boston, MA, 02210, United States
| | - Michael F Mesleh
- Structural Biology and Biophysics, Vertex Pharmaceuticals Inc., Boston, MA, 02210, United States.
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15
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Liu S, Abboud MI, John T, Mikhailov V, Hvinden I, Walsby-Tickle J, Liu X, Pettinati I, Cadoux-Hudson T, McCullagh JSO, Schofield CJ. Roles of metal ions in the selective inhibition of oncogenic variants of isocitrate dehydrogenase 1. Commun Biol 2021; 4:1243. [PMID: 34725432 PMCID: PMC8560763 DOI: 10.1038/s42003-021-02743-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 10/04/2021] [Indexed: 12/29/2022] Open
Abstract
Cancer linked isocitrate dehydrogenase (IDH) 1 variants, notably R132H IDH1, manifest a 'gain-of-function' to reduce 2-oxoglutarate to 2-hydroxyglutarate. High-throughput screens have enabled clinically useful R132H IDH1 inhibitors, mostly allosteric binders at the dimer interface. We report investigations on roles of divalent metal ions in IDH substrate and inhibitor binding that rationalise this observation. Mg2+/Mn2+ ions enhance substrate binding to wt IDH1 and R132H IDH1, but with the former manifesting lower Mg2+/Mn2+ KMs. The isocitrate-Mg2+ complex is the preferred wt IDH1 substrate; with R132H IDH1, separate and weaker binding of 2-oxoglutarate and Mg2+ is preferred. Binding of R132H IDH1 inhibitors at the dimer interface weakens binding of active site Mg2+ complexes; their potency is affected by the Mg2+ concentration. Inhibitor selectivity for R132H IDH1 over wt IDH1 substantially arises from different stabilities of wt and R132H IDH1 substrate-Mg2+ complexes. The results reveal the importance of substrate-metal ion complexes in wt and R132H IDH1 catalysis and the basis for selective R132H IDH1 inhibition. Further studies on roles of metal ion complexes in TCA cycle and related metabolism, including from an evolutionary perspective, are of interest.
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Affiliation(s)
- Shuang Liu
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Department of Natural Sciences, Lebanese American University, Byblos/Beirut, Lebanon
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ingvild Hvinden
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Xiao Liu
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ilaria Pettinati
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom Cadoux-Hudson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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16
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Shortridge MD, Varani G. Efficient NMR Screening Approach to Discover Small Molecule Fragments Binding Structured RNA. ACS Med Chem Lett 2021; 12:1253-1260. [PMID: 34413954 DOI: 10.1021/acsmedchemlett.1c00109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/07/2021] [Indexed: 01/27/2023] Open
Abstract
We describe a scalable nuclear magnetic resonance (NMR) screening approach to identify and prioritize small molecule fragments that bind to structured RNAs. This approach is target agnostic and, therefore, amenable to many RNA structures and libraries, and it provides initial hits for further synthetic elaboration and structure-based drug discovery efforts. We demonstrate the approach on the pre-miR-21 stem-loop, which is of significant interest in oncology and metabolic diseases. We screened the pre-miR-21 hairpin using a small (420 compounds) commercially available fragment library and identified 18 hits in the first round of triage screening. This was further refined to four fragments which passed all screening cascade filters. Among these four hits, a thiadiazole fragment was demonstrated to bind the Dicer cleavage site of pre-miR-21 by target-detected NMR experiments and through the observation of clear intermolecular NOEs.
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Affiliation(s)
- Matthew D. Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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17
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Mass OA, Tuccinardi J, Woodbury L, Wolf CL, Grantham B, Holdaway K, Pu X, King MD, Warner DL, Jorcyk CL, Warner LR. Bioactive recombinant human oncostatin M for NMR-based screening in drug discovery. Sci Rep 2021; 11:16174. [PMID: 34376712 PMCID: PMC8355150 DOI: 10.1038/s41598-021-95424-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
Oncostatin M (OSM) is a pleiotropic, interleukin-6 family inflammatory cytokine that plays an important role in inflammatory diseases, including inflammatory bowel disease, rheumatoid arthritis, and cancer progression and metastasis. Recently, elevated OSM levels have been found in the serum of COVID-19 patients in intensive care units. Multiple anti-OSM therapeutics have been investigated, but to date no OSM small molecule inhibitors are clinically available. To pursue a high-throughput screening and structure-based drug discovery strategy to design a small molecule inhibitor of OSM, milligram quantities of highly pure, bioactive OSM are required. Here, we developed a reliable protocol to produce highly pure unlabeled and isotope enriched OSM from E. coli for biochemical and NMR studies. High yields (ca. 10 mg/L culture) were obtained in rich and minimal defined media cultures. Purified OSM was characterized by mass spectrometry and circular dichroism. The bioactivity was confirmed by induction of OSM/OSM receptor signaling through STAT3 phosphorylation in human breast cancer cells. Optimized buffer conditions yielded 1H, 15N HSQC NMR spectra with intense, well-dispersed peaks. Titration of 15N OSM with a small molecule inhibitor showed chemical shift perturbations for several key residues with a binding affinity of 12.2 ± 3.9 μM. These results demonstrate the value of bioactive recombinant human OSM for NMR-based small molecule screening.
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Affiliation(s)
- Olga A. Mass
- grid.184764.80000 0001 0670 228XBiomoleculer Research Center, Boise State University, Boise, ID 83725 USA
| | - Joseph Tuccinardi
- grid.184764.80000 0001 0670 228XDepartment of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, ID 83725 USA
| | - Luke Woodbury
- grid.184764.80000 0001 0670 228XBiomoleculer Research Center, Boise State University, Boise, ID 83725 USA
| | - Cody L. Wolf
- grid.184764.80000 0001 0670 228XBiomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725 USA ,grid.184764.80000 0001 0670 228XDepartment of Biological Sciences, Boise State University, Boise, ID 83725 USA
| | - Bri Grantham
- grid.184764.80000 0001 0670 228XBiomoleculer Research Center, Boise State University, Boise, ID 83725 USA
| | - Kelsey Holdaway
- grid.184764.80000 0001 0670 228XDepartment of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, ID 83725 USA
| | - Xinzhu Pu
- grid.184764.80000 0001 0670 228XBiomoleculer Research Center, Boise State University, Boise, ID 83725 USA ,grid.184764.80000 0001 0670 228XBiomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725 USA
| | - Matthew D. King
- grid.184764.80000 0001 0670 228XDepartment of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, ID 83725 USA ,grid.184764.80000 0001 0670 228XBiomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725 USA
| | - Don L. Warner
- grid.184764.80000 0001 0670 228XDepartment of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, ID 83725 USA ,grid.184764.80000 0001 0670 228XBiomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725 USA
| | - Cheryl L. Jorcyk
- grid.184764.80000 0001 0670 228XBiomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725 USA ,grid.184764.80000 0001 0670 228XDepartment of Biological Sciences, Boise State University, Boise, ID 83725 USA
| | - Lisa R. Warner
- grid.184764.80000 0001 0670 228XBiomoleculer Research Center, Boise State University, Boise, ID 83725 USA ,grid.184764.80000 0001 0670 228XDepartment of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, ID 83725 USA ,grid.184764.80000 0001 0670 228XBiomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725 USA
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18
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Investigating the Disordered and Membrane-Active Peptide A-Cage-C Using Conformational Ensembles. Molecules 2021; 26:molecules26123607. [PMID: 34204651 PMCID: PMC8231226 DOI: 10.3390/molecules26123607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
The driving forces and conformational pathways leading to amphitropic protein-membrane binding and in some cases also to protein misfolding and aggregation is the subject of intensive research. In this study, a chimeric polypeptide, A-Cage-C, derived from α-Lactalbumin is investigated with the aim of elucidating conformational changes promoting interaction with bilayers. From previous studies, it is known that A-Cage-C causes membrane leakages associated with the sporadic formation of amorphous aggregates on solid-supported bilayers. Here we express and purify double-labelled A-Cage-C and prepare partially deuterated bicelles as a membrane mimicking system. We investigate A-Cage-C in the presence and absence of these bicelles at non-binding (pH 7.0) and binding (pH 4.5) conditions. Using in silico analyses, NMR, conformational clustering, and Molecular Dynamics, we provide tentative insights into the conformations of bound and unbound A-Cage-C. The conformation of each state is dynamic and samples a large amount of overlapping conformational space. We identify one of the clusters as likely representing the binding conformation and conclude tentatively that the unfolding around the central W23 segment and its reorientation may be necessary for full intercalation at binding conditions (pH 4.5). We also see evidence for an overall elongation of A-Cage-C in the presence of model bilayers.
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19
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Jakubec M, Bariås E, Furse S, Govasli ML, George V, Turcu D, Iashchishyn IA, Morozova-Roche LA, Halskau Ø. Cholesterol-containing lipid nanodiscs promote an α-synuclein binding mode that accelerates oligomerization. FEBS J 2021; 288:1887-1905. [PMID: 32892498 DOI: 10.1111/febs.15551] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 07/28/2020] [Accepted: 09/01/2020] [Indexed: 01/09/2023]
Abstract
Dysregulation of the biosynthesis of cholesterol and other lipids has been implicated in many neurological diseases, including Parkinson's disease. Misfolding of α-synuclein (α-Syn), the main actor in Parkinson's disease, is associated with changes in a lipid environment. However, the exact molecular mechanisms underlying cholesterol effect on α-Syn binding to lipids as well as α-Syn oligomerization and fibrillation remain elusive, as does the relative importance of cholesterol compared to other factors. We probed the interactions and fibrillation behaviour of α-Syn using styrene-maleic acid nanodiscs, containing zwitterionic and anionic lipid model systems with and without cholesterol. Surface plasmon resonance and thioflavin T fluorescence assays were employed to monitor α-Syn binding, as well as fibrillation in the absence and presence of membrane models. 1 H-15 N-correlated NMR was used to monitor the fold of α-Syn in response to nanodisc binding, determining individual residue apparent affinities for the nanodisc-contained bilayers. The addition of cholesterol inhibited α-Syn interaction with lipid bilayers and, however, significantly promoted α-Syn fibrillation, with a more than a 20-fold reduction of lag times before fibrillation onset. When α-Syn bilayer interactions were analysed at an individual residue level by solution-state NMR, we observed two different effects of cholesterol. In nanodiscs made of DOPC, the addition of cholesterol modulated the NAC part of α-Syn, leading to stronger interaction of this region with the lipid bilayer. In contrast, in the nanodiscs comprising DOPC, DOPE and DOPG, the NAC part was mostly unaffected by the presence of cholesterol, while the binding of the N and the C termini was both inhibited.
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Affiliation(s)
- Martin Jakubec
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
| | - Espen Bariås
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
| | - Samuel Furse
- Department of Molecular Biology, University of Bergen, Norway
| | - Morten L Govasli
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
- Division of Infection and Immunity, University College London, London, UK
| | - Vinnit George
- Department of Chemistry, University of Bergen, Norway
| | - Diana Turcu
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
| | - Igor A Iashchishyn
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden
| | | | - Øyvind Halskau
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
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20
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Fedorenko M, Alesio J, Fedorenko A, Slitt A, Bothun GD. Dominant entropic binding of perfluoroalkyl substances (PFASs) to albumin protein revealed by 19F NMR. CHEMOSPHERE 2021; 263:128083. [PMID: 33297081 PMCID: PMC8479757 DOI: 10.1016/j.chemosphere.2020.128083] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 05/05/2023]
Abstract
Mechanistic insight into protein binding by poly- and perfluoroalkyl substances (PFASs) is critical to understanding how PFASs distribute and accumulate within the body and to developing predictive models within and across classes of PFASs. Fluorine nuclear magnetic resonance spectroscopy (19F NMR) has proven to be a powerful, yet underutilized tool to study PFAS binding; chemical shifts of each fluorine group reflect the local environment along the length of the PFAS molecule. Using bovine serum albumin (BSA), we report dissociation constants, Kd, for four common PFASs well below reported critical micelle concentrations (CMCs) - perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorohexanesulfonic acid (PFHxS), and perfluorooctanesulfonic acid (PFOS) - as a function of temperature in phosphate buffered saline. Kd values were determined based on the difluoroethyl group adjacent to the anionic headgroups and the terminal trifluoromethyl groups. Our results indicate that the hydrophobic tails exhibit greater binding affinity relative to the headgroup, and that the binding affinities are generally consistent with previous results showing that greater PFAS hydrophobicity leads to greater protein binding. However, the binding mechanism was dominated by entropic hydrophobic interactions attributed to desolvation of the PFAS tails within the hydrophobic cavities of the protein and on the surface of the protein. In addition, PFNA appears to form hemimicelles on the protein surfaces below reported CMC values. This work provides a renewed approach to utilizing 19F NMR for PFAS-protein binding studies and a new perspective on the role of solvent entropy.
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Affiliation(s)
- Michael Fedorenko
- Department of Chemical Engineering, University of Rhode Island, 2 East Alumni Ave, Kingston, RI, 02881, USA
| | - Jessica Alesio
- Department of Chemical Engineering, University of Rhode Island, 2 East Alumni Ave, Kingston, RI, 02881, USA
| | - Anatoliy Fedorenko
- Department of Chemical Engineering, University of Rhode Island, 2 East Alumni Ave, Kingston, RI, 02881, USA
| | - Angela Slitt
- Department of Biomedical & Pharmaceutical Sciences, University of Rhode Island, 7 Greenhouse Rd, Kingston, RI, 02881, USA
| | - Geoffrey D Bothun
- Department of Chemical Engineering, University of Rhode Island, 2 East Alumni Ave, Kingston, RI, 02881, USA.
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21
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Diethelm-Varela B. Using NMR Spectroscopy in the Fragment-Based Drug Discovery of Small-Molecule Anticancer Targeted Therapies. ChemMedChem 2020; 16:725-742. [PMID: 33236493 DOI: 10.1002/cmdc.202000756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/21/2020] [Indexed: 12/19/2022]
Abstract
Against the challenge of providing personalized cancer care, the development of targeted therapies stands as a promising approach. The discovery of these agents can benefit from fragment-based drug discovery (FBDD) methods that help guide ligand design and provide key structural information on the targets of interest. In particular, nuclear magnetic resonance spectroscopy is a promising biophysical tool in fragment discovery due to its detection capabilities and versatility. This review provides an overview of FBDD, describes the basis of NMR-based fragment screening, summarizes some exciting technical advances reported over the past decades, and closes with a discussion of selected case studies where this technique has been used as part of drug discovery campaigns to produce lead compounds towards the design of anti-cancer targeted therapies.
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Affiliation(s)
- Benjamin Diethelm-Varela
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD 21201, USA
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22
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Emwas AH, Szczepski K, Poulson BG, Chandra K, McKay RT, Dhahri M, Alahmari F, Jaremko L, Lachowicz JI, Jaremko M. NMR as a "Gold Standard" Method in Drug Design and Discovery. Molecules 2020; 25:E4597. [PMID: 33050240 PMCID: PMC7594251 DOI: 10.3390/molecules25204597] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Kacper Szczepski
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Benjamin Gabriel Poulson
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Kousik Chandra
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada;
| | - Manel Dhahri
- Biology Department, Faculty of Science, Taibah University, Yanbu El-Bahr 46423, Saudi Arabia;
| | - Fatimah Alahmari
- Nanomedicine Department, Institute for Research and Medical, Consultations (IRMC), Imam Abdulrahman Bin Faisal University (IAU), Dammam 31441, Saudi Arabia;
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, Università di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
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23
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Wallace M, Lam K, Kuraite A, Khimyak YZ. Rapid Determination of the Acidity, Alkalinity and Carboxyl Content of Aqueous Samples by 1H NMR with Minimal Sample Quantity. Anal Chem 2020; 92:12789-12794. [PMID: 32897055 DOI: 10.1021/acs.analchem.0c02594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The titratable acidity, alkalinity, and carboxylate content are fundamental properties required for the understanding of aqueous chemical systems. Here, we present a set of new methods that allow these properties to be determined directly by 1H NMR without the labor, cost, and sample quantity associated with running separate potentiometric or conductometric titrations. Our methods require only the measurement of the pH-sensitive 1H chemical shifts of indicator molecules and do not require the tedious titration of reagents into a sample. To determine the titratable acidity, an excess of 2-methylimidazole (2MI) is added to a sample and the quantity of protons absorbed by 2MI is determined from its 1H chemical shifts. The titratable alkalinity of a sample can be similarly determined using acetic acid. To determine the concentration of deprotonated carboxylates, a sample is acidified with HCl, and the quantity of H+ absorbed is determined from the 1H chemical shift of methylphosphonic acid. We validate our methods by demonstrating the measurement of the acidity of fruit-flavored drinks, the alkalinity of tap water, and the carboxylate content of nanocellulose dispersions.
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Affiliation(s)
- Matthew Wallace
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Kevin Lam
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Agne Kuraite
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Yaroslav Z Khimyak
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
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24
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Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL. Target-Directed Approaches for Screening Small Molecules against RNA Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:869-894. [PMID: 32419578 PMCID: PMC7442623 DOI: 10.1177/2472555220922802] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules have a variety of cellular functions that can drive disease pathologies. They are without a doubt one of the most intriguing yet controversial small-molecule drug targets. The ability to widely target RNA with small molecules could be revolutionary, once the right tools, assays, and targets are selected, thereby defining which biomolecules are targetable and what constitutes drug-like small molecules. Indeed, approaches developed over the past 5-10 years have changed the face of small molecule-RNA targeting by addressing historic concerns regarding affinity, selectivity, and structural dynamics. Presently, selective RNA-protein complex stabilizing drugs such as branaplam and risdiplam are in clinical trials for the modulation of SMN2 splicing, compounds identified from phenotypic screens with serendipitous outcomes. Fully developing RNA as a druggable target will require a target engagement-driven approach, and evolving chemical collections will be important for the industrial development of this class of target. In this review we discuss target-directed approaches that can be used to identify RNA-binding compounds and the chemical knowledge we have today of small-molecule RNA binders.
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Affiliation(s)
- Hafeez S. Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Laurent Knerr
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
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25
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Competition NMR for Detection of Hit/Lead Inhibitors of Protein-Protein Interactions. Molecules 2020; 25:molecules25133017. [PMID: 32630327 PMCID: PMC7412237 DOI: 10.3390/molecules25133017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Screening for small-molecule fragments that can lead to potent inhibitors of protein–protein interactions (PPIs) is often a laborious step as the fragments cannot dissociate the targeted PPI due to their low μM–mM affinities. Here, we describe an NMR competition assay called w-AIDA-NMR (weak-antagonist induced dissociation assay-NMR), which is sensitive to weak μM–mM ligand–protein interactions and which can be used in initial fragment screening campaigns. By introducing point mutations in the complex’s protein that is not targeted by the inhibitor, we lower the effective affinity of the complex, allowing for short fragments to dissociate the complex. We illustrate the method with the compounds that block the Mdm2/X-p53 and PD-1/PD-L1 oncogenic interactions. Targeting the PD-/PD-L1 PPI has profoundly advanced the treatment of different types of cancers.
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26
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Miyazaki Y, Ono N, Huang M, Altaf‐Ul‐Amin M, Kanaya S. Comprehensive Exploration of Target-specific Ligands Using a Graph Convolution Neural Network. Mol Inform 2020; 39:e1900095. [PMID: 31815371 PMCID: PMC7050504 DOI: 10.1002/minf.201900095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/08/2019] [Indexed: 11/10/2022]
Abstract
Machine learning approaches are widely used to evaluate ligand activities of chemical compounds toward potential target proteins. Especially, exploration of highly selective ligands is important for the development of new drugs with higher safety. One difficulty in constructing well-performing model predicting such a ligand activity is the absence of data on true negative ligand-protein interactions. In other words, in many cases we can access to plenty of information on ligands that bind to specific protein, but less or almost no information showing that compounds don't bind to proteins of interest. In this paper, we suggested an approach to comprehensively explore candidates for ligands specifically targeting toward proteins without using information on the true negative interaction. The approach consists of 4 steps: 1) constructing a model that distinguishes ligands for the target proteins of interest from those targeting proteins that cause off-target effects, by using graph convolution neural network (GCNN); 2) extracting feature vectors after convolution/pooling processes and mapping their principal components in two dimensions; 3) specifying regions with higher density for two ligand groups through kernel density estimation; and 4) investigating the distribution of compounds for exploration on the density map using the same classifier and decomposer. If compounds for exploration are located in higher-density regions of ligand compounds, these compounds can be regarded as having relatively high binding affinity to the major target or off-target proteins compared with other compounds. We applied the approach to the exploration of ligands for β-site amyloid precursor protein [APP]-cleaving enzyme 1 (BACE1), a major target for Alzheimer Disease (AD), with less off-target effect toward cathepsin D. We demonstrated that the density region of BACE1 and cathepsin D ligands are well-divided, and a group of natural compounds as a target for exploration of new drug candidates also has significantly different distribution on the density map.
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Affiliation(s)
- Yu Miyazaki
- Division of Information Science, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
| | - Naoaki Ono
- Division of Information Science, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
- Data Science Center, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
| | - Ming Huang
- Division of Information Science, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
| | - Md. Altaf‐Ul‐Amin
- Division of Information Science, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
| | - Shigehiko Kanaya
- Division of Information Science, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
- Data Science Center, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
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27
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Huang L, Li X, Li Y, Yin X, Li Y, Wu B, Mo H, Liao CJ, Mengiste T, Guo W, Dai M, Zhang C. Endosidin2-14 Targets the Exocyst Complex in Plants and Fungal Pathogens to Inhibit Exocytosis. PLANT PHYSIOLOGY 2019; 180:1756-1770. [PMID: 31072814 PMCID: PMC6752926 DOI: 10.1104/pp.18.01457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/29/2019] [Indexed: 05/29/2023]
Abstract
The evolutionarily conserved octameric exocyst complex tethers secretory vesicles to the site of membrane fusion during exocytosis. The plant exocyst complex functions in cell wall biosynthesis, polarized growth, stress responses, and hormone signaling. In fungal pathogens, the exocyst complex is required for growth, development, and pathogenesis. Endosidin2 (ES2) is known to inhibit exocytosis in plant and mammalian cells by targeting the EXO70 subunit of the exocyst complex. Here we show that an analog of ES2, ES2-14, targets plant and two fungal EXO70s. A lower dosage of ES2-14 than of ES2 is required to inhibit plant growth, plant exocytic trafficking, and fungal growth. ES2-14 treatments inhibit appressorium formation and reduce lesion sizes caused by Magnaporthe oryzae Inhibition of EXO70 by ES2-14 in Botrytis cinerea also reduces its virulence in Arabidopsis (Arabidopsis thaliana). Interestingly, ES2-14 did not affect EXO70 localization or transferrin recycling in mammalian cells. Overall, our results indicate that a minor change in ES2 affects its specificity in targeting EXO70s in different organisms and they demonstrate the potential of using ES2-14 to study the mechanisms of plant and fungal exocytosis and the roles of exocytosis in fungus-plant interactions.
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Affiliation(s)
- Lei Huang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Xiaohui Li
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Yang Li
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Xianglin Yin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Yong Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Bin Wu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Huaping Mo
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907
| | - Chao-Jan Liao
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Wei Guo
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Mingji Dai
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Chunhua Zhang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
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28
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Nshogoza G, Liu Y, Gao J, Liu M, Moududee SA, Ma R, Li F, Zhang J, Wu J, Shi Y, Ruan K. NMR Fragment-Based Screening against Tandem RNA Recognition Motifs of TDP-43. Int J Mol Sci 2019; 20:ijms20133230. [PMID: 31262091 PMCID: PMC6651732 DOI: 10.3390/ijms20133230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 01/10/2023] Open
Abstract
The TDP-43 is originally a nuclear protein but translocates to the cytoplasm in the pathological condition. TDP-43, as an RNA-binding protein, consists of two RNA Recognition Motifs (RRM1 and RRM2). RRMs are known to involve both protein-nucleotide and protein-protein interactions and mediate the formation of stress granules. Thus, they assist the entire TDP-43 protein with participating in neurodegenerative and cancer diseases. Consequently, they are potential therapeutic targets. Protein-observed and ligand-observed nuclear magnetic resonance (NMR) spectroscopy were used to uncover the small molecule inhibitors against the tandem RRM of TDP-43. We identified three hits weakly binding the tandem RRMs using the ligand-observed NMR fragment-based screening. The binding topology of these hits is then depicted by chemical shift perturbations (CSP) of the 15N-labeled tandem RRM and RRM2, respectively, and modeled by the CSP-guided High Ambiguity Driven biomolecular DOCKing (HADDOCK). These hits mainly bind to the RRM2 domain, which suggests the druggability of the RRM2 domain of TDP-43. These hits also facilitate further studies regarding the hit-to-lead evolution against the TDP-43 RRM domain.
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Affiliation(s)
- Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yaqian Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Jia Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Mingqing Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Sayed Ala Moududee
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
- CAS, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China
| | - Ke Ruan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
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29
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Maity S, Gundampati RK, Suresh Kumar TK. NMR Methods to Characterize Protein-Ligand Interactions. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19849296] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Structural information pertaining to the interactions between biological macromolecules and ligands is of potential significance for understanding of molecular mechanisms in key biological processes. Recently, nuclear magnetic resonance (NMR) spectroscopic techniques has come of age and has widened its scope to characterize binding interactions of small molecules with biological macromolecules especially, proteins. NMR spectroscopy-based techniques are versatile due to their ability to examine weak binding interactions and for rapid screening the binding affinities of ligands with proteins at atomic resolution. In this review, we provide a broad overview of some of the important NMR approaches to investigate interactions of small organic molecules with proteins.
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Affiliation(s)
- Sanhita Maity
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Ravi Kumar Gundampati
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
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30
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Dalvit C, Parent A, Vallée F, Mathieu M, Rak A. Fast NMR Methods for Measuring in the Direct and/or Competition Mode the Dissociation Constants of Chemical Fragments Interacting with a Receptor. ChemMedChem 2019; 14:1115-1127. [DOI: 10.1002/cmdc.201900152] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Indexed: 12/16/2022]
Affiliation(s)
| | - Annick Parent
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
| | - Francois Vallée
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
| | - Magali Mathieu
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
| | - Alexey Rak
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
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31
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A novel method using nuclear magnetic resonance for plasma protein binding assessment in drug discovery programs. J Pharm Biomed Anal 2019; 167:21-29. [DOI: 10.1016/j.jpba.2019.01.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 11/19/2022]
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32
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Monolith weak affinity chromatography for μg-protein-ligand interaction study. J Pharm Biomed Anal 2019; 166:164-173. [DOI: 10.1016/j.jpba.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 11/17/2022]
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33
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Chae H, Kwak DK, Lee MK, Chi SW, Kim KB. Solid-state nanopore analysis on conformation change of p53TAD-MDM2 fusion protein induced by protein-protein interaction. NANOSCALE 2018; 10:17227-17235. [PMID: 30191243 DOI: 10.1039/c8nr06423g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Although protein-protein interactions (PPIs) are emerging therapeutic targets for human diseases, development of high-throughput screening (HTS) technologies against PPI targets remains challenging. In this study, we propose a protein complex structure to effectively detect conformational changes of protein resulting from PPI using solid-state nanopore for a novel, widely-applicable drug screening method against various PPI targets. To effectively detect conformational changes resulting from PPI, we designed a fusion protein MLP (MDM2-linker-p53TAD), where p53TAD and MDM2 are connected by a 16 amino acid linker. The globular conformation of MLP exhibited a single-peak translocation event, whereas the dumbbell-like conformation of nutlin-3-bound MLP revealed as a double-peak signal. The proportion of double-peak to single-peak signals increased from 9.3% to 23.0% as nutlin-3 concentration increased. The translocation kinetics of the two different MLP conformations with varied applied voltage were analyzed. Further, the fractional current of the intra-peak of the double-peak signal was analyzed, probing the structure of our designed protein complex. This approach of nanopore sensing may be extendedly employed in screening of PPI inhibitors and protein conformation studies.
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Affiliation(s)
- Hongsik Chae
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea.
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34
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Becker W, Bhattiprolu KC, Gubensäk N, Zangger K. Investigating Protein-Ligand Interactions by Solution Nuclear Magnetic Resonance Spectroscopy. Chemphyschem 2018; 19:895-906. [PMID: 29314603 PMCID: PMC5915746 DOI: 10.1002/cphc.201701253] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/04/2018] [Indexed: 12/13/2022]
Abstract
Protein-ligand interactions are of fundamental importance in almost all processes in living organisms. The ligands comprise small molecules, drugs or biological macromolecules and their interaction strength varies over several orders of magnitude. Solution NMR spectroscopy offers a large repertoire of techniques to study such complexes. Here, we give an overview of the different NMR approaches available. The information they provide ranges from the simple information about the presence of binding or epitope mapping to the complete 3 D structure of the complex. NMR spectroscopy is particularly useful for the study of weak interactions and for the screening of binding ligands with atomic resolution.
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Affiliation(s)
- Walter Becker
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | | | - Nina Gubensäk
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | - Klaus Zangger
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
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35
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36
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Ángeles Canales M, Félix Espinosa J. Ligand-detected NMR Methods in Drug Discovery. BIOPHYSICAL TECHNIQUES IN DRUG DISCOVERY 2017. [DOI: 10.1039/9781788010016-00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This book chapter describes the basic principles of NMR-based techniques for detecting ligand binding and uses examples of the application of these techniques in drug discovery programs for screening, hit validation and optimization to illustrate their utility in characterizing ligand–protein interactions. The binding of small molecules to biological receptors can be observed directly by detecting changes in a particular NMR parameter when the protein is added to a sample containing the ligand, or indirectly, using a “spy” molecule in competitive NMR experiments. Combinations of different NMR experiments can be used to confirm binding and also to obtain structural information that can be used to guide medicinal chemistry decisions. Ligand-observed NMR methods are able to identify weak affinity ligands that cannot be detected by other biophysical techniques, which means that NMR-based methods are extremely valuable tools for fragment-based drug discovery approaches.
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Affiliation(s)
- María Ángeles Canales
- Department of Química Orgánica I, Universidad Complutense de Madrid Avd. Complutense s/n 28040 Madrid Spain
| | - Juan Félix Espinosa
- Centro de Investigación Lilly Avda. de la Industria 30 28108, Alcobendas, Madrid Spain
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37
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Ponnusamy S, Coss CC, Thiyagarajan T, Watts K, Hwang DJ, He Y, Selth LA, McEwan IJ, Duke CB, Pagadala J, Singh G, Wake RW, Ledbetter C, Tilley WD, Moldoveanu T, Dalton JT, Miller DD, Narayanan R. Novel Selective Agents for the Degradation of Androgen Receptor Variants to Treat Castration-Resistant Prostate Cancer. Cancer Res 2017; 77:6282-6298. [PMID: 28978635 DOI: 10.1158/0008-5472.can-17-0976] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/08/2017] [Accepted: 09/22/2017] [Indexed: 01/01/2023]
Abstract
Androgen receptor (AR) mediates the growth of prostate cancer throughout its course of development, including in abnormal splice variants (AR-SV)-driven advanced stage castration-resistant disease. AR stabilization by androgens makes it distinct from other steroid receptors, which are typically ubiquitinated and degraded by proteasomes after ligand binding. Thus, targeting AR in advanced prostate cancer requires the development of agents that can sustainably degrade variant isoforms for effective therapy. Here we report the discovery and characterization of potent selective AR degraders (SARD) that markedly reduce the activity of wild-type and splice variant isoforms of AR at submicromolar doses. Three SARDs (UT-69, UT-155, and (R)-UT-155) bind the amino-terminal transcriptional activation domain AF-1, which has not been targeted for degradation previously, with two of these SARD (UT-69 and UT-155) also binding the carboxy-terminal ligand binding domain. Despite different mechanisms of action, all three SARDs degraded wild-type AR and inhibited AR function, exhibiting greater inhibitory potency than the approved AR antagonists. Collectively, our results introduce a new candidate class of next-generation therapeutics to manage advanced prostate cancer. Cancer Res; 77(22); 6282-98. ©2017 AACR.
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MESH Headings
- Alternative Splicing
- Androgen Receptor Antagonists/chemistry
- Androgen Receptor Antagonists/pharmacology
- Anilides/chemistry
- Anilides/pharmacology
- Animals
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Proliferation/genetics
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Indoles/chemistry
- Indoles/pharmacology
- Male
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Molecular Structure
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Suriyan Ponnusamy
- Department of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee
| | | | - Thirumagal Thiyagarajan
- Department of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Kate Watts
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Dong-Jin Hwang
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Yali He
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories, School of Medicine, The University of Adelaide, South Australia
- Freemasons Foundation Centre for Men's Health, School of Medicine, The University of Adelaide, South Australia
| | - Iain J McEwan
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Charles B Duke
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Jayaprakash Pagadala
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Geetika Singh
- St. Jude Children's Hospital and Research Center, Memphis, Tennessee
| | - Robert W Wake
- Department of Urology, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Christopher Ledbetter
- Department of Urology, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, School of Medicine, The University of Adelaide, South Australia
- Freemasons Foundation Centre for Men's Health, School of Medicine, The University of Adelaide, South Australia
| | - Tudor Moldoveanu
- St. Jude Children's Hospital and Research Center, Memphis, Tennessee
| | | | - Duane D Miller
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Ramesh Narayanan
- Department of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee.
- West Cancer Center, Memphis, Tennessee
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38
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Li Y, Kang C. Solution NMR Spectroscopy in Target-Based Drug Discovery. Molecules 2017; 22:E1399. [PMID: 28832542 PMCID: PMC6151424 DOI: 10.3390/molecules22091399] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 12/14/2022] Open
Abstract
Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
| | - Congbao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
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39
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Beeram S, Bi C, Zheng X, Hage DS. Chromatographic studies of drug interactions with alpha 1-acid glycoprotein by ultrafast affinity extraction and peak profiling. J Chromatogr A 2017; 1497:92-101. [PMID: 28366566 DOI: 10.1016/j.chroma.2017.03.056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 03/11/2017] [Accepted: 03/21/2017] [Indexed: 12/28/2022]
Abstract
Interactions with serum proteins such as alpha1-acid glycoprotein (AGP) can have a significant effect on the behavior and pharmacokinetics of drugs. Ultrafast affinity extraction and peak profiling were used with AGP microcolumns to examine these processes for several model drugs (i.e., chlorpromazine, disopyramide, imipramine, lidocaine, propranolol and verapamil). The association equilibrium constants measured for these drugs with soluble AGP by ultrafast affinity extraction were in the general range of 104-106M-1 at pH 7.4 and 37°C and gave good agreement with literature values. Some of these values were dependent on the relative drug and protein concentrations that were present when using a single-site binding model; these results suggested a more complex mixed-mode interaction was actually present, which was also then used to analyze the data. The apparent dissociation rate constants that were obtained by ultrafast affinity extraction when using a single-site model varied from 0.14 to 7.0s-1 and were dependent on the relative drug and protein concentrations. Lower apparent dissociation rate constants were obtained by this approach as the relative amount of drug versus protein was decreased, with the results approaching those measured by peak profiling at low drug concentrations. This information should be useful in better understanding how these and other drugs interact with AGP in the circulation. In addition, the chromatographic approaches that were optimized and used in this report to examine these systems can be adapted for the analysis of other solute-protein interactions of biomedical interest.
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Affiliation(s)
- Sandya Beeram
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Cong Bi
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Xiwei Zheng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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40
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Haft DH, Pierce PG, Mayclin SJ, Sullivan A, Gardberg AS, Abendroth J, Begley DW, Phan IQ, Staker BL, Myler PJ, Marathias VM, Lorimer DD, Edwards TE. Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors. Sci Rep 2017; 7:41074. [PMID: 28120876 PMCID: PMC5264612 DOI: 10.1038/srep41074] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/12/2016] [Indexed: 01/08/2023] Open
Abstract
During human infection, Mycobacterium tuberculosis (Mtb) survives the normally bacteriocidal phagosome of macrophages. Mtb and related species may be able to combat this harsh acidic environment which contains reactive oxygen species due to the mycobacterial genomes encoding a large number of dehydrogenases. Typically, dehydrogenase cofactor binding sites are open to solvent, which allows NAD/NADH exchange to support multiple turnover. Interestingly, mycobacterial short chain dehydrogenases/reductases (SDRs) within family TIGR03971 contain an insertion at the NAD binding site. Here we present crystal structures of 9 mycobacterial SDRs in which the insertion buries the NAD cofactor except for a small portion of the nicotinamide ring. Line broadening and STD-NMR experiments did not show NAD or NADH exchange on the NMR timescale. STD-NMR demonstrated binding of the potential substrate carveol, the potential product carvone, the inhibitor tricyclazol, and an external redox partner 2,6-dichloroindophenol (DCIP). Therefore, these SDRs appear to contain a non-exchangeable NAD cofactor and may rely on an external redox partner, rather than cofactor exchange, for multiple turnover. Incidentally, these genes always appear in conjunction with the mftA gene, which encodes the short peptide MftA, and with other genes proposed to convert MftA into the external redox partner mycofactocin.
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Affiliation(s)
- Daniel H Haft
- National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Phillip G Pierce
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Amy Sullivan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA.,University of Washington, Department of Medical Education and Biomedical Informatics &Department of Global Health, Seattle WA 98195, USA
| | - Vasilios M Marathias
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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41
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Karki I, Christen MT, Spiriti J, Slack RL, Oda M, Kanaori K, Zuckerman DM, Ishima R. Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg 2+ Titration Analysis for HIV-1 Ribonuclease H Domain. J Phys Chem B 2016; 120:12420-12431. [PMID: 27973819 DOI: 10.1021/acs.jpcb.6b08323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This article communicates our study to elucidate the molecular determinants of weak Mg2+ interaction with the ribonuclease H (RNH) domain of HIV-1 reverse transcriptase in solution. As the interaction is weak (a ligand-dissociation constant >1 mM), nonspecific Mg2+ interaction with the protein or interaction of the protein with other solutes that are present in the buffer solution can confound the observed Mg2+-titration data. To investigate these indirect effects, we monitored changes in the chemical shifts of backbone amides of RNH by recording NMR 1H-15N heteronuclear single-quantum coherence spectra upon titration of Mg2+ into an RNH solution. We performed the titration under three different conditions: (1) in the absence of NaCl, (2) in the presence of 50 mM NaCl, and (3) at a constant 160 mM Cl- concentration. Careful analysis of these three sets of titration data, along with molecular dynamics simulation data of RNH with Na+ and Cl- ions, demonstrates two characteristic phenomena distinct from the specific Mg2+ interaction with the active site: (1) weak interaction of Mg2+, as a salt, with the substrate-handle region of the protein and (2) overall apparent lower Mg2+ affinity in the absence of NaCl compared to that in the presence of 50 mM NaCl. A possible explanation may be that the titrated MgCl2 is consumed as a salt and interacts with RNH in the absence of NaCl. In addition, our data suggest that Na+ increases the kinetic rate of the specific Mg2+ interaction at the active site of RNH. Taken together, our study provides biophysical insight into the mechanism of weak metal interaction on a protein.
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Affiliation(s)
- Ichhuk Karki
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Martin T Christen
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Justin Spiriti
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Ryan L Slack
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Masayuki Oda
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Kenji Kanaori
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Daniel M Zuckerman
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Rieko Ishima
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
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42
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Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA. J Med Chem 2016; 59:11148-11160. [PMID: 28002966 DOI: 10.1021/acs.jmedchem.6b01450] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Small molecules that bind to RNA potently and specifically are relatively rare. The study of molecules that bind to the HIV-1 transactivation response (TAR) hairpin, a cis-acting HIV genomic element, has long been an important model system for the chemistry of targeting RNA. Here we report the synthesis, biochemical, and structural evaluation of a series of molecules that bind to HIV-1 TAR RNA. A promising analogue, 15, retained the TAR binding affinity of the initial hit and displaced a Tat-derived peptide with an IC50 of 40 μM. NMR characterization of a soluble analogue, 2, revealed a noncanonical binding mode for this class of compounds. Finally, evaluation of 2 and 15 by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) indicates specificity in binding to TAR within the context of an in vitro-synthesized 365-nt HIV-1 5'-untranslated region (UTR). Thus, these compounds exhibit a novel and specific mode of interaction with TAR, providing important suggestions for RNA ligand design.
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43
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Conformational modulation of the farnesoid X receptor by prenylflavonoids: Insights from hydrogen deuterium exchange mass spectrometry (HDX-MS), fluorescence titration and molecular docking studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1667-1677. [PMID: 27596062 DOI: 10.1016/j.bbapap.2016.08.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 12/20/2022]
Abstract
We report on the molecular interactions of the farnesoid X receptor (FXR) with prenylflavonoids, an emerging class of FXR modulators. FXR is an attractive therapeutic target for mitigating metabolic syndromes (MetS) because FXR activates the inhibitory nuclear receptor, small heterodimer partner (SHP), thereby inhibiting both gluconeogenesis and de novo lipogenesis. We and others have shown that xanthohumol (XN), the principal prenylflavonoid of the hop plant (Humulus lupulus L.), is a FXR agonist based on its ability to affect lipid and glucose metabolism in vivo and to induces FXR target genes in biliary carcinoma cells and HEK293 cells. However, studies are currently lacking to rationalize the molecular mechanisms of FXR modulation by prenylflavonoids. We addressed this deficiency and report the first systematic study of FXR prenylflavonoid interactions. We combined hydrogen deuterium exchange mass spectrometry (HDX-MS) with computational studies for dissecting molecular recognition and conformational impact of prenylflavonoid interactions on the ligand binding domain (LBD) of human FXR. Four prenylflavonoids were tested: xanthohumol, a prenylated chalcone, two prenylated flavonones, namely isoxanthohumol (IX) and 8-prenylnaringenin (8PN), and a semisynthetic prenylflavonoid derivative, tetrahydroxanthohumol (TX). Enhancement of the HDX protection profile data by in silico predicted models of FXR prenylflavonoid complexes resulted in mapping of the prenylflavonoid interactions within the canonical ligand binding pocket. Our findings provide a foundation for the exploration of the chemical scaffolds of prenylated chalcones and flavanones as leads for future structure activity studies of this important nuclear receptor with potential relevance for ameliorating lipid metabolic disorders associated with obesity and MetS.
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44
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Conte M, Hippler M. Dynamic NMR and Quantum-Chemical Study of the Stereochemistry and Stability of the Chiral MoO2(acac)2 Complex in Solution. J Phys Chem A 2016; 120:6677-87. [PMID: 27510306 DOI: 10.1021/acs.jpca.6b03563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The stereochemistry and dynamics of MoO2(acac)2 in benzene, chloroform, and toluene were investigated by variable temperature (1)H NMR, density functional theory (SOGGA11-X, B3LYP), and ab initio (MP2) methods. In solution, an equilibrium between two chiral enantiomers with C2 symmetry was identified, Λ-cis-MoO2(acac)2 and Δ-cis-MoO2(acac)2. The two enantiomers are connected via achiral cis transition states that switch the enantiomeric conformations via a Ray-Dutt, Bailar, and a newly described racemization twisting mechanism. All three mechanisms have similar calculated activation energies. Activation parameters Ea, ΔH(‡), and ΔS(‡) were experimentally determined for the exchange process, with a small, negative ΔS(‡), and a positive ΔH(‡) of 68.1 kJ mol(-1) in benzene, 54.9 kJ mol(-1) in chloroform, and 60.6 kJ mol(-1) in toluene, in reasonable general agreement with the calculations. Trans configurations of MoO2(acac)2 are very much higher in energy than cis and are not relevant in the temperature range experimentally studied, 243-340 K. The enantiomers interconvert within seconds near room temperature and much faster at elevated temperatures. Racemization will thus prevent the use of enantiomerically pure MoO2(acac)2 for chiral catalysis under practical conditions.
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Affiliation(s)
- Marco Conte
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, United Kingdom
| | - Michael Hippler
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, United Kingdom
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45
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Abstract
Evidence is presented that binding isotherms, simple or biphasic, can be extracted directly from noninterpreted, complex 2D NMR spectra using principal component analysis (PCA) to reveal the largest trend(s) across the series. This approach renders peak picking unnecessary for tracking population changes. In 1:1 binding, the first principal component captures the binding isotherm from NMR-detected titrations in fast, slow, and even intermediate and mixed exchange regimes, as illustrated for phospholigand associations with proteins. Although the sigmoidal shifts and line broadening of intermediate exchange distorts binding isotherms constructed conventionally, applying PCA directly to these spectra along with Pareto scaling overcomes the distortion. Applying PCA to time-domain NMR data also yields binding isotherms from titrations in fast or slow exchange. The algorithm readily extracts from magnetic resonance imaging movie time courses such as breathing and heart rate in chest imaging. Similarly, two-step binding processes detected by NMR are easily captured by principal components 1 and 2. PCA obviates the customary focus on specific peaks or regions of images. Applying it directly to a series of complex data will easily delineate binding isotherms, equilibrium shifts, and time courses of reactions or fluctuations.
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Affiliation(s)
- Jia Xu
- Department of Biochemistry, University of Missouri , 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Steven R Van Doren
- Department of Biochemistry, University of Missouri , 117 Schweitzer Hall, Columbia, Missouri 65211, United States
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46
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Nikolaev YV, Kochanowski K, Link H, Sauer U, Allain FHT. Systematic Identification of Protein-Metabolite Interactions in Complex Metabolite Mixtures by Ligand-Detected Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2016; 55:2590-600. [PMID: 27065204 DOI: 10.1021/acs.biochem.5b01291] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-metabolite interactions play a vital role in the regulation of numerous cellular processes. Consequently, identifying such interactions is a key prerequisite for understanding cellular regulation. However, the noncovalent nature of the binding between proteins and metabolites has so far hampered the development of methods for systematically mapping protein-metabolite interactions. The few available, largely mass spectrometry-based, approaches are restricted to specific metabolite classes, such as lipids. In this study, we address this issue and show the potential of ligand-detected nuclear magnetic resonance (NMR) spectroscopy, which is routinely used in drug development, to systematically identify protein-metabolite interactions. As a proof of concept, we selected four well-characterized bacterial and mammalian proteins (AroG, Eno, PfkA, and bovine serum albumin) and identified metabolite binders in complex mixes of up to 33 metabolites. Ligand-detected NMR captured all of the reported protein-metabolite interactions, spanning a full range of physiologically relevant Kd values (low micromolar to low millimolar). We also detected a number of novel interactions, such as promiscuous binding of the negatively charged metabolites citrate, AMP, and ATP, as well as binding of aromatic amino acids to AroG protein. Using in vitro enzyme activity assays, we assessed the functional relevance of these novel interactions in the case of AroG and show that l-tryptophan, l-tyrosine, and l-histidine act as novel inhibitors of AroG activity. Thus, we conclude that ligand-detected NMR is suitable for the systematic identification of functionally relevant protein-metabolite interactions.
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Affiliation(s)
- Yaroslav V Nikolaev
- Institute of Molecular Biology & Biophysics, ETH Zürich , CH-8093 Zürich, Switzerland
| | - Karl Kochanowski
- Institute of Molecular Systems Biology, ETH Zürich , CH-8093 Zürich, Switzerland.,Life Science Zurich PhD Program on Systems Biology , Zurich, Switzerland
| | - Hannes Link
- Institute of Molecular Systems Biology, ETH Zürich , CH-8093 Zürich, Switzerland.,Max-Planck Institute for Terrestrial Microbiology , Marburg, Germany
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich , CH-8093 Zürich, Switzerland
| | - Frederic H-T Allain
- Institute of Molecular Biology & Biophysics, ETH Zürich , CH-8093 Zürich, Switzerland
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47
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Khan A, Leśniak RK, Brem J, Rydzik AM, Choi H, Leung IKH, McDonough MA, Schofield CJ, Claridge TDW. Development and application of ligand-based NMR screening assays for γ-butyrobetaine hydroxylase. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00004e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 1H NMR based dual-reporter binding assay for γ-butyrobetaine hydroxylase (BBOX) reveals unexpected structure–activity relationships for isoquinoline-derived inhibitors.
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Affiliation(s)
- A. Khan
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - R. K. Leśniak
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - J. Brem
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - A. M. Rydzik
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - H. Choi
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - I. K. H. Leung
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - M. A. McDonough
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - C. J. Schofield
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - T. D. W. Claridge
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
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48
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Souard F, Perrier S, Noël V, Fave C, Fiore E, Peyrin E, Garcia J, Vanhaverbeke C. Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H NMR Spectroscopy and Molecular Modeling. Chemistry 2015; 21:15740-8. [PMID: 26356596 DOI: 10.1002/chem.201501527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/25/2022]
Abstract
Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.
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Affiliation(s)
- Florence Souard
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
| | - Sandrine Perrier
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Emmanuelle Fiore
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Eric Peyrin
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Julian Garcia
- DCM, Université Grenoble Alpes, Grenoble, 38000 (France).,DCM, CNRS, Grenoble, 38000 (France)
| | - Cécile Vanhaverbeke
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
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49
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Zheng X, Bi C, Li Z, Podariu M, Hage DS. Analytical methods for kinetic studies of biological interactions: A review. J Pharm Biomed Anal 2015; 113:163-80. [PMID: 25700721 PMCID: PMC4516701 DOI: 10.1016/j.jpba.2015.01.042] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 01/13/2023]
Abstract
The rates at which biological interactions occur can provide important information concerning the mechanism and behavior of these processes in living systems. This review discusses several analytical methods that can be used to examine the kinetics of biological interactions. These techniques include common or traditional methods such as stopped-flow analysis and surface plasmon resonance spectroscopy, as well as alternative methods based on affinity chromatography and capillary electrophoresis. The general principles and theory behind these approaches are examined, and it is shown how each technique can be utilized to provide information on the kinetics of biological interactions. Examples of applications are also given for each method. In addition, a discussion is provided on the relative advantages or potential limitations of each technique regarding its use in kinetic studies.
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Affiliation(s)
- Xiwei Zheng
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Cong Bi
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Zhao Li
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Maria Podariu
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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Worley B, Sisco NJ, Powers R. Statistical removal of background signals from high-throughput (1)H NMR line-broadening ligand-affinity screens. JOURNAL OF BIOMOLECULAR NMR 2015; 63:53-58. [PMID: 26156049 PMCID: PMC4577452 DOI: 10.1007/s10858-015-9962-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/30/2015] [Indexed: 06/04/2023]
Abstract
NMR ligand-affinity screens are vital to drug discovery, are routinely used to screen fragment-based libraries, and used to verify chemical leads from high-throughput assays and virtual screens. NMR ligand-affinity screens are also a highly informative first step towards identifying functional epitopes of unknown proteins, as well as elucidating the biochemical functions of protein-ligand interaction at their binding interfaces. While simple one-dimensional (1)H NMR experiments are capable of indicating binding through a change in ligand line shape, they are plagued by broad, ill-defined background signals from protein (1)H resonances. We present an uncomplicated method for subtraction of protein background in high-throughput ligand-based affinity screens, and show that its performance is maximized when phase-scatter correction is applied prior to subtraction.
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Affiliation(s)
- Bradley Worley
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA
| | - Nicholas J Sisco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287, USA
- Magnetic Resonance Research Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA.
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