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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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2
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Jin X, Zhu T, Zhang JZH, He X. Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes. Front Chem 2018; 6:150. [PMID: 29868556 PMCID: PMC5952040 DOI: 10.3389/fchem.2018.00150] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/16/2018] [Indexed: 01/13/2023] Open
Abstract
In this study, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method was applied for NMR chemical shift calculations of protein-ligand complexes. In the AF-QM/MM approach, the protein binding pocket is automatically divided into capped fragments (within ~200 atoms) for density functional theory (DFT) calculations of NMR chemical shifts. Meanwhile, the solvent effect was also included using the Poission-Boltzmann (PB) model, which properly accounts for the electrostatic polarization effect from the solvent for protein-ligand complexes. The NMR chemical shifts of neocarzinostatin (NCS)-chromophore binding complex calculated by AF-QM/MM accurately reproduce the large-sized system results. The 1H chemical shift perturbations (CSP) between apo-NCS and holo-NCS predicted by AF-QM/MM are also in excellent agreement with experimental results. Furthermore, the DFT calculated chemical shifts of the chromophore and residues in the NCS binding pocket can be utilized as molecular probes to identify the correct ligand binding conformation. By combining the CSP of the atoms in the binding pocket with the Glide scoring function, the new scoring function can accurately distinguish the native ligand pose from decoy structures. Therefore, the AF-QM/MM approach provides an accurate and efficient platform for protein-ligand binding structure prediction based on NMR derived information.
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Affiliation(s)
- Xinsheng Jin
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
| | - Tong Zhu
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
| | - John Z. H. Zhang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- Department of Chemistry, New York University, New York, NY, United States
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- National Engineering Research Centre for Nanotechnology, Shanghai, China
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3
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NMR in structure-based drug design. Essays Biochem 2017; 61:485-493. [PMID: 29118095 DOI: 10.1042/ebc20170037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 12/13/2022]
Abstract
NMR spectroscopy is a powerful technique that can provide valuable structural information for drug discovery endeavors. Here, we discuss the strengths (and limitations) of NMR applications to structure-based drug discovery, highlighting the different levels of resolution and throughput obtainable. Additionally, the emerging field of paramagnetic NMR in drug discovery and recent developments in approaches to speed up and automate protein-observed NMR data collection and analysis are discussed.
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Lesovoy DM, Mineev KS, Bragin PE, Bocharova OV, Bocharov EV, Arseniev AS. NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 69:165-179. [PMID: 29063258 DOI: 10.1007/s10858-017-0146-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
In the case of soluble proteins, chemical shift mapping is used to identify the intermolecular interfaces when the NOE-based calculations of spatial structure of the molecular assembly are impossible or impracticable. However, the reliability of the membrane protein interface mapping based on chemical shifts or other relevant parameters was never assessed. In the present work, we investigate the predictive power of various NMR parameters that can be used for mapping of helix-helix interfaces in dimeric TM domains. These parameters are studied on a dataset containing three structures of helical dimers obtained for two different proteins in various membrane mimetics. We conclude that the amide chemical shifts have very little predictive value, while the methyl chemical shifts could be used to predict interfaces, though with great care. We suggest an approach based on conversion of the carbon NMR relaxation parameters of methyl groups into parameters of motion, and one of such values, the characteristic time of methyl rotation, appears to be a reliable sensor of interhelix contacts in transmembrane domains. The carbon NMR relaxation parameters of methyl groups can be measured accurately and with high sensitivity and resolution, making the proposed parameter a useful tool for investigation of protein-protein interfaces even in large membrane proteins. An approach to build the models of transmembrane dimers based on perturbations of methyl parameters and TMDOCK software is suggested.
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Affiliation(s)
- D M Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
| | - K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
| | - P E Bragin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Lomonosov Moscow State University, Leninskiye Gory, 1, Moscow, Russian Federation, 119991
| | - O V Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
| | - E V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997.
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700.
- National Research Centre "Kurchatov Institute", Kurchatov Complex of NBICS-technologies, Akad. Kurchatova Sqr., 1, Moscow, Russian Federation, 123182.
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
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Yu Z, Li P, Merz KM. Using Ligand-Induced Protein Chemical Shift Perturbations To Determine Protein–Ligand Structures. Biochemistry 2017; 56:2349-2362. [DOI: 10.1021/acs.biochem.7b00170] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Zhuoqin Yu
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Pengfei Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Kenneth M. Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
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Khattri RB, Morris DL, Davis CM, Bilinovich SM, Caras AJ, Panzner MJ, Debord MA, Leeper TC. An NMR-Guided Screening Method for Selective Fragment Docking and Synthesis of a Warhead Inhibitor. Molecules 2016; 21:molecules21070846. [PMID: 27438815 PMCID: PMC6274284 DOI: 10.3390/molecules21070846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 02/07/2023] Open
Abstract
Selective hits for the glutaredoxin ortholog of Brucella melitensis are determined using STD NMR and verified by trNOE and (15)N-HSQC titration. The most promising hit, RK207, was docked into the target molecule using a scoring function to compare simulated poses to experimental data. After elucidating possible poses, the hit was further optimized into the lead compound by extension with an electrophilic acrylamide warhead. We believe that focusing on selectivity in this early stage of drug discovery will limit cross-reactivity that might occur with the human ortholog as the lead compound is optimized. Kinetics studies revealed that lead compound 5 modified with an ester group results in higher reactivity than an acrylamide control; however, after modification this compound shows little selectivity for bacterial protein versus the human ortholog. In contrast, hydrolysis of compound 5 to the acid form results in a decrease in the activity of the compound. Together these results suggest that more optimization is warranted for this simple chemical scaffold, and opens the door for discovery of drugs targeted against glutaredoxin proteins-a heretofore untapped reservoir for antibiotic agents.
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Affiliation(s)
- Ram B Khattri
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Daniel L Morris
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Caroline M Davis
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Stephanie M Bilinovich
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Andrew J Caras
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Matthew J Panzner
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Michael A Debord
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Thomas C Leeper
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
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7
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Frank AT. Can Holo NMR Chemical Shifts be Directly Used to Resolve RNA–Ligand Poses? J Chem Inf Model 2016; 56:368-76. [DOI: 10.1021/acs.jcim.5b00593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Aaron T. Frank
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Onila I, ten Brink T, Fredriksson K, Codutti L, Mazur A, Griesinger C, Carlomagno T, Exner TE. On-the-Fly Integration of Data from a Spin-Diffusion-Based NMR Experiment into Protein-Ligand Docking. J Chem Inf Model 2015; 55:1962-72. [PMID: 26226383 DOI: 10.1021/acs.jcim.5b00235] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
INPHARMA (interligand nuclear Overhauser enhancement for pharmacophore mapping) determines the relative orientation of two competitive ligands in the protein binding pocket. It is based on the observation of interligand transferred NOEs mediated by spin diffusion through protons of the protein and is, therefore, sensitive to the specific interactions of each of the two ligands with the protein. We show how this information can be directly included into a protein-ligand docking program to guide the prediction of the complex structures. Agreement between the experimental and back-calculated spectra based on the full relaxation matrix approach is translated into a score contribution that is combined with the scoring function ChemPLP of our docking tool PLANTS. This combined score is then used to predict the poses of five weakly bound cAMP-dependent protein kinase (PKA) ligands. After optimizing the setup, which finally also included trNOE data and optimized protonation states, very good success rates were obtained for all combinations of three ligands. For one additional ligand, no conclusive results could be obtained due to the ambiguous electron density of the ligand in the X-ray structure, which does not disprove alternative ligand poses. The failures of the remaining ligand are caused by suboptimal locations of specific protein side chains. Therefore, side-chain flexibility should be included in an improved INPHARMA-PLANTS version. This will reduce the strong dependence on the used protein input structure leading to improved scores overall, not only for this last ligand.
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Affiliation(s)
- Ionut Onila
- Institute of Pharmacy, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz , 78457 Konstanz, Germany
| | - Tim ten Brink
- Department of Chemistry and Zukunftskolleg, Universität Konstanz , 78457 Konstanz, Germany
| | - Kai Fredriksson
- Institute of Pharmacy, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz , 78457 Konstanz, Germany
| | - Luca Codutti
- Structural and Computational Biology Unit, EMBL , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Adam Mazur
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Teresa Carlomagno
- Structural and Computational Biology Unit, EMBL , Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Thomas E Exner
- Institute of Pharmacy, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz , 78457 Konstanz, Germany
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Aguirre C, Cala O, Krimm I. Overview of Probing Protein‐Ligand Interactions Using NMR. ACTA ACUST UNITED AC 2015; 81:17.18.1-17.18.24. [DOI: 10.1002/0471140864.ps1718s81] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Clémentine Aguirre
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
| | - Olivier Cala
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
| | - Isabelle Krimm
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
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