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Elucidating Protein-Ligand Interactions Using High Throughput Biophysical Techniques

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Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design

Abstract

Proteins are large, complex molecules that functionally regulates almost all cellular and biochemical processes. As proteins are important component in cell physiology, their interaction with small molecules that modulates the function are clinically significant. Nearly, all essential biomolecular processes are highly sensitive and selective involving molecular recognition and binding of ligands/macromolecules to proteins. Hence, techniques that can reveal detailed information like binding energetics, kinetics, stoichiometry, thermodynamics, structural changes and conformational dynamics are of great importance. Current arsenal of techniques that enable characterization of these interactions have been well established and progressing towards advancement at a faster pace. The current chapter details four major biophysical techniques namely Nuclear Magnetic Resonance spectroscopy (NMR), Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC) and Fluorescence Spectroscopy that are vastly used in characterizing the thermodynamics and kinetics of protein-ligand interaction.

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References

  • Abboud, M. I., Hinchliffe, P., Brem, J., Macsics, R., Pfeffer, I., Makena, A., et al. (2017). 19F-NMR reveals the role of mobile loops in product and inhibitor binding by the São Paulo Metallo-β-lactamase. Angewandte Chemie International Edition, 56, 3862–3866.

    Google Scholar 

  • Abe, Y., Fukui, S., Koshiji, Y., Kobayashi, M., Shoji, T., Sugata, S., et al. (1999). Enantioselective binding sites on bovine serum albumin to dansyl amino acids. Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology, 1433, 188–197.

    Google Scholar 

  • Agarwal, N., Nair, M. S., Mazumder, A., & Poluri, K. M. (2018). Characterization of nanomaterials using nuclear magnetic resonance spectroscopy. In Characterization of nanomaterials (pp. 61–102). Amsterdam: Elsevier.

    Chapter  Google Scholar 

  • Aguirre, C., Cala, O., & Krimm, I. (2015). Overview of probing protein-ligand interactions using NMR. Current Protocols in Protein Science, 81, 17–18. 17.18. 11-17.18. 24.

    Article  PubMed  Google Scholar 

  • Ahmed-Belkacem, A., Colliandre, L., Ahnou, N., Nevers, Q., Gelin, M., Bessin, Y., et al. (2016). Fragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities. Nature Communications, 7, 1–11.

    Google Scholar 

  • Amano, R., Furukawa, T., & Sakamoto, T. (2019). ITC measurement for high-affinity aptamers binding to their target proteins. In Microcalorimetry of biological molecules (pp. 119–128). New York: Springer.

    Chapter  Google Scholar 

  • Aziz, A., Santhoshkumar, P., Sharma, K. K., & Abraham, E. C. (2007). Cleavage of the c-terminal serine of human αA-crystallin produces αA1-172 with increased chaperone activity and oligomeric size. Biochemistry, 46, 2510–2519.

    Article  CAS  PubMed  Google Scholar 

  • Balazs, A. Y. S., Carbajo, R. J., Davies, N. L., Dong, Y., Hird, A. W., Johannes, J. W., et al. (2019). Free ligand 1D NMR conformational signatures to enhance structure based drug design of a mcl-1 inhibitor (AZD5991) and other synthetic macrocycles. Journal of Medicinal Chemistry, 62, 9418–9437. https://doi.org/10.1021/acs.jmedchem.9b00716

  • Barelier, S., & Krimm, I. (2011). Ligand specificity, privileged substructures and protein druggability from fragment-based screening. Current Opinion in Chemical Biology, 15, 469–474.

    Article  CAS  PubMed  Google Scholar 

  • Bartoschek, S., Klabunde, T., Defossa, E., Dietrich, V., Stengelin, S., Griesinger, C., et al. (2010). Drug design for G-protein-coupled receptors by a ligand-based NMR method. Angewandte Chemie International Edition, 49, 1426–1429.

    Google Scholar 

  • Becker, W., Adams, L. A., Graham, B., Wagner, G. E., Zangger, K., Otting, G., et al. (2018). Trimethylsilyl tag for probing protein–ligand interactions by NMR. Journal of Biomolecular NMR, 70, 211–218.

    Google Scholar 

  • Billeter, M., Wagner, G., & Wüthrich, K. (2008). Solution NMR structure determination of proteins revisited. Journal of Biomolecular NMR, 42, 155–158.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bocquet N Markovic-Mueller, S., Cheng, R., Botte, M., AbdulRahman, W., Huber, S., et al. (2018) Structure based drug discovery on membrane protein targets.

    Google Scholar 

  • Boswell, Z. K., & Latham, M. P. (2018). Methyl-based NMR spectroscopy methods for uncovering structural dynamics in large proteins and protein complexes. Biochemistry, 58, 144–155.

    Article  PubMed  CAS  Google Scholar 

  • Bray, P., Emerson, J., Lee, D., Feller, S., Bain, D., & Feil, D. (1991). NMR and NQR studies of glass structure. Journal of Non-Crystalline Solids, 129, 240–248.

    Article  CAS  Google Scholar 

  • Breen, C. J., Raverdeau, M., & Voorheis, H. P. (2016). Development of a quantitative fluorescence-based ligand-binding assay. Scientific Reports, 6, 25769.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Burkhardt, M., & Schwille, P. (2006). Electron multiplying CCD based detection for spatially resolved fluorescence correlation spectroscopy. Optics Express, 14, 5013–5020.

    Article  PubMed  Google Scholar 

  • Burnouf, D., Ennifar, E., Guedich, S., Puffer, B., Hoffmann, G., Bec, G., et al. (2012). kinITC: A new method for obtaining joint thermodynamic and kinetic data by isothermal titration calorimetry. Journal of the American Chemical Society, 134, 559–565.

    Google Scholar 

  • Buurma, N. J., & Haq, I. (2007). Advances in the analysis of isothermal titration calorimetry data for ligand–DNA interactions. Methods, 42, 162–172.

    Article  CAS  PubMed  Google Scholar 

  • Buurma, N. J., & Haq, I. (2008). Calorimetric and spectroscopic studies of Hoechst 33258: Self-association and binding to non-cognate DNA. Journal of Molecular Biology, 381, 607–621.

    Article  CAS  PubMed  Google Scholar 

  • Cala, O., Guillière, F., & Krimm, I. (2014). NMR-based analysis of protein–ligand interactions. Analytical and Bioanalytical Chemistry, 406, 943–956.

    Article  CAS  PubMed  Google Scholar 

  • Cala, O., & Krimm, I. (2015). Ligand-orientation based fragment selection in STD NMR screening. Journal of Medicinal Chemistry, 58, 8739–8742.

    Article  CAS  PubMed  Google Scholar 

  • Capelli, D., Parravicini, C., Pochetti, G., Montanari, R., Temporini, C., Rabuffetti, M., et al. (2019). Surface Plasmon resonance as a tool for ligand binding investigation of engineered GPR17 receptor, a G protein coupled receptor involved in myelination. Frontiers in Chemistry, 7.

    Google Scholar 

  • Cengiz, N. (2020). Glutathione-responsive multifunctionalizable hydrogels via amine-epoxy “click” chemistry. European Polymer Journal, 123, 109441.

    Article  CAS  Google Scholar 

  • Chakraborty, S., Mohan, P. K., & Hosur, R. V. (2012). Residual structure and dynamics in DMSO-d6 denatured dynein light chain protein. Biochimie, 94, 231–241.

    Article  CAS  PubMed  Google Scholar 

  • Chandel, T. I., Zaman, M., Khan, M. V., Ali, M., Rabbani, G., Ishtikhar, M., et al. (2018). A mechanistic insight into protein-ligand interaction, folding, misfolding, aggregation and inhibition of protein aggregates: An overview. International Journal of Biological Macromolecules, 106, 1115–1129.

    Google Scholar 

  • Chappuis, Q., Milani, J., Vuichoud, B., Bornet, A., Gossert, A. D., Bodenhausen, G., et al. (2015). Hyperpolarized water to study protein–ligand interactions. The Journal of Physical Chemistry Letters, 6, 1674–1678.

    Article  CAS  PubMed  Google Scholar 

  • Chen, L., Wang, D., Lv, D., Wang, X., Liu, Y., Chen, X., et al. (2019). Identification of eupatilin and ginkgolide B as p38 ligands from medicinal herbs by surface plasmon resonance biosensor-based active ingredients recognition system. Journal of Pharmaceutical and Biomedical Analysis, 171, 35–42.

    Google Scholar 

  • Chen, X., Lin, Y., Liu, M., & Gilson, M. K. (2002). The binding database: Data management and interface design. Bioinformatics, 18, 130–139.

    Article  CAS  PubMed  Google Scholar 

  • Coates, C., Kerruth, S., Helassa, N., & Török, K. (2020). Kinetic mechanisms of fast glutamate sensing by fluorescent protein probes. Biophysical Journal, 118, 117–127.

    Article  CAS  PubMed  Google Scholar 

  • Cohen, Y., Avram, L., & Frish, L. (2005). Diffusion NMR spectroscopy in supramolecular and combinatorial chemistry: An old parameter—New insights. Angewandte Chemie International Edition, 44, 520–554.

    Article  CAS  PubMed  Google Scholar 

  • Collini, M., D'Alfonso, L., Molinari, H., Ragona, L., Catalano, M., & Baldini, G. (2003). Competitive binding of fatty acids and the fluorescent probe 1-8-anilinonaphthalene sulfonate to bovine β-lactoglobulin. Protein Science, 12, 1596–1603.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Croucher, D., Saunders, D. N., & Ranson, M. (2006). The Urokinase/PAI-2 complex a new high affinity ligand for the endocytosis receptor low density lipoprotein receptor-related proteiN. Journal of Biological Chemistry, 281, 10206–10213.

    Article  CAS  Google Scholar 

  • Dalvit, C., & Knapp, S. (2017). 19F NMR isotropic chemical shift for efficient screening of fluorinated fragments which are racemates and/or display multiple conformers. Magnetic Resonance in Chemistry, 55, 1091–1095.

    Article  CAS  PubMed  Google Scholar 

  • Dalvit, C., & Vulpetti, A. (2018). Ligand-based fluorine NMR screening: Principles and applications in drug discovery projects. Journal of Medicinal Chemistry, 62, 2218–2244.

    Article  PubMed  CAS  Google Scholar 

  • Damodaran, S., & Kinsella, J. E. (1981). The effects of neutral salts on the stability of macromolecules. A new approach using a protein-ligand binding system. Journal of Biological Chemistry, 256, 3394–3398.

    Article  CAS  Google Scholar 

  • Dansereau, S., Burz, D. S., & Shekhtman, A. (2019). Primary drug screening by in-cell NMR spectroscopy. In-cell NMR Spectroscopy, 249–271.

    Google Scholar 

  • Day, C. J., & Korolik, V. (2018). Identification of specific ligands for sensory receptors by small-molecule ligand arrays and surface plasmon resonance. In Bacterial chemosensing (pp. 303–317). New York: Springer.

    Google Scholar 

  • Deganutti, G., Zhukov, A., Deflorian, F., Federico, S., Spalluto, G., Cooke, R. M., et al. (2017). Impact of protein–ligand solvation and desolvation on transition state thermodynamic properties of adenosine a 2A ligand binding kinetics. In Silico Pharmacology, 5, 16.

    Google Scholar 

  • Diao, W., Tang, M., Ding, S., Li, X., Cheng, W., Mo, F., et al. (2018). Highly sensitive surface plasmon resonance biosensor for the detection of HIV-related DNA based on dynamic and structural DNA nanodevices. Biosensors and Bioelectronics, 100, 228–234.

    Google Scholar 

  • Ding, X., Cheng, W., Li, Y., Wu, J., Li, X., Cheng, Q., et al. (2017). An enzyme-free surface plasmon resonance biosensing strategy for detection of DNA and small molecule based on nonlinear hybridization chain reaction. Biosensors and Bioelectronics, 87, 345–351.

    Article  CAS  PubMed  Google Scholar 

  • Dolphin, A. C., & Lee, A. (2020). Presynaptic calcium channels: Specialized control of synaptic neurotransmitter release. Nature Reviews Neuroscience, 1–17.

    Google Scholar 

  • Dorion-Thibaudeau, J., St-Laurent, G., Raymond, C., De Crescenzo, G., & Durocher, Y. (2016). Biotinylation of the Fcγ receptor ectodomains by mammalian cell co-transfection: Application to the development of a surface plasmon resonance-based assay. Journal of Molecular Recognition, 29, 60–69.

    Article  CAS  PubMed  Google Scholar 

  • Douzi, B. (2017). Protein–protein interactions: Surface plasmon resonance. In Bacterial protein secretion systems (pp. 257–275). New York: Springer.

    Chapter  Google Scholar 

  • Drescher, D. G., Selvakumar, D., & Drescher, M. J. (2018). Analysis of protein interactions by surface plasmon resonance. In Advances in protein chemistry and structural biology (Vol. 110, pp. 1–30). Amsterdam: Elsevier.

    Google Scholar 

  • Dror, R. O., Pan, A. C., Arlow, D. H., Borhani, D. W., Maragakis, P., Shan, Y., et al. (2011). Pathway and mechanism of drug binding to G-protein-coupled receptors. Proceedings of the National Academy of Sciences, 108, 13118–13123.

    Google Scholar 

  • Du, J., & Strieter, E. R. (2018). A fluorescence polarization-based competition assay for measuring interactions between unlabeled ubiquitin chains and UCH37• RPN13. Analytical Biochemistry, 550, 84–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Du, X., Li, Y., Xia, Y.-L., Ai, S.-M., Liang, J., Sang, P., et al. (2016). Insights into protein–ligand interactions: Mechanisms, models, and methods. International Journal of Molecular Sciences, 17, 144.

    Google Scholar 

  • Dumas, P., Ennifar, E., Da Veiga, C., Bec, G., Palau, W., Di Primo, C., et al. (2016). Extending ITC to kinetics with kinITC. In Methods in enzymology (Vol. 567, pp. 157–180). Amsterdam: Elsevier.

    Google Scholar 

  • Eling, T., & DiAugustine, R. (1971). A role for phospholipids in the binding and metabolism of drugs by hepatic microsomes. Use of the fluorescent hydrophobic probe 1-anilinonaphthalene-8-sulphonate. Biochemical Journal, 123, 539–549.

    Article  CAS  PubMed Central  Google Scholar 

  • Enke, M., Jehle, F., Bode, S., Vitz, J., Harrington, M. J., Hager, M. D., et al. (2017). Histidine–zinc interactions investigated by Isothermal Titration Calorimetry (ITC) and their application in self-healing polymers. Macromolecular Chemistry and Physics, 218, 1600458.

    Google Scholar 

  • Eyring, H. (1935). The activated complex in chemical reactions. The Journal of Chemical Physics, 3, 107–115.

    Article  CAS  Google Scholar 

  • Falconer, R. J. (2016). Applications of isothermal titration calorimetry–the research and technical developments from 2011 to 2015. Journal of Molecular Recognition, 29, 504–515.

    Article  CAS  PubMed  Google Scholar 

  • Feng, C., Kovrigin, E. L., & Post, C. B. (2019). NmrLineGuru: standalone and user-friendly GUIs for fast 1D NMR lineshape simulation and analysis of multi-state equilibrium binding models. Scientific Reports, 9, 1–14.

    Article  CAS  Google Scholar 

  • Fielding, L. (2003). NMR methods for the determination of protein-ligand dissociation constants. Current Topics in Medicinal Chemistry, 3, 39–53.

    Article  CAS  PubMed  Google Scholar 

  • Fielding, L. (2007). NMR methods for the determination of protein–ligand dissociation constants. Progress in Nuclear Magnetic Resonance Spectroscopy, 51, 219–242.

    Article  CAS  Google Scholar 

  • Frederick, K. K., Marlow, M. S., Valentine, K. G., & Wand, A. J. (2007). Conformational entropy in molecular recognition by proteins. Nature, 448, 325–329.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Furukawa, A., Konuma, T., Yanaka, S., & Sugase, K. (2016). Quantitative analysis of protein–ligand interactions by NMR. Progress in Nuclear Magnetic Resonance Spectroscopy, 96, 47–57.

    Article  CAS  PubMed  Google Scholar 

  • Gao, J., Liang, E., Ma, R., Li, F., Liu, Y., Liu, J., et al. (2017). Fluorine pseudocontact shifts used for characterizing the protein–ligand interaction mode in the limit of NMR intermediate exchange. Angewandte Chemie International Edition, 56, 12982–12986.

    Google Scholar 

  • Garrett, A. B. (1962). The Bohr atomic model: Niels Bohr. Journal of Chemical Education, 39, 534.

    Article  Google Scholar 

  • Gasymov, O. K., Abduragimov, A. R., & Glasgow, B. J. (2008). Ligand binding site of tear lipocalin: Contribution of a trigonal cluster of charged residues probed by 8-anilino-1-naphthalenesulfonic acid. Biochemistry, 47, 1414–1424.

    Article  CAS  PubMed  Google Scholar 

  • Gee, C. T., Arntson, K. E., Koleski, E. J., Staebell, R. L., & Pomerantz, W. C. (2018). Dual labeling of the CBP/p300 KIX domain for 19F NMR leads to identification of a new small-molecule binding site. Chembiochem, 19, 963–969.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Geist, L., Mayer, M., Cockcroft, X.-L., Wolkerstorfer, B., Kessler, D., Engelhardt, H., et al. (2017). Direct NMR probing of hydration shells of protein ligand interfaces and its application to drug design. Journal of Medicinal Chemistry, 60, 8708–8715.

    Google Scholar 

  • Geuijen, K. P., van Wijk-Basten, D. E., Egging, D. F., Schasfoort, R. B., & Eppink, M. H. (2017). Rapid buffer and ligand screening for affinity chromatography by multiplexed surface Plasmon resonance imaging. Biotechnology Journal, 12, 1700154.

    Article  CAS  Google Scholar 

  • Ghatak, C., Rodnin, M. V., Vargas-Uribe, M., McCluskey, A. J., Flores-Canales, J. C., Kurnikova, M., et al. (2015). Role of acidic residues in helices TH8–TH9 in membrane interactions of the diphtheria toxin T domain. Toxins, 7, 1303–1323.

    Google Scholar 

  • Gohlke, A., Bower, J., Brown, P. N., Cameron, K. S., Drysdale, M., Goodwin, G., et al. (2018). A central role for biophysics in cancer drug discovery-development of candidate small molecule inhibitors in mutant KRas. Biophysical Journal, 114, 30a–31a.

    Google Scholar 

  • Gooley, P. R., Koay, A., & Mobbs, J. I. (2018). Applications of NMR and ITC for the study of the kinetics of carbohydrate binding by AMPK β-subunit carbohydrate-binding modules. In AMPK (pp. 87–98). New York: Springer.

    Chapter  Google Scholar 

  • Gordon, S. E., & Perugini, M. A. (2016). Protein-ligand interactions. In Analytical ultracentrifugation (pp. 329–353). New York: Springer.

    Chapter  Google Scholar 

  • Gossert, A. D., & Jahnke, W. (2016). NMR in drug discovery: A practical guide to identification and validation of ligands interacting with biological macromolecules. Progress in Nuclear Magnetic Resonance Spectroscopy, 97, 82–125.

    Article  CAS  PubMed  Google Scholar 

  • Gulati, K., Gangele, K., Kumar, D., & Poluri, K. M. (2019). An inter-switch between hydrophobic and charged amino acids generated druggable small molecule binding pocket in chemokine paralog CXCL3. Archives of Biochemistry and Biophysics, 662, 121–128.

    Article  CAS  PubMed  Google Scholar 

  • Gulati, K., & M Poluri, K. (2016). An overview of computational and experimental methods for designing novel proteins. Recent Patents on Biotechnology, 10, 235–263.

    Article  CAS  PubMed  Google Scholar 

  • Gulati, K., & Poluri, K. M. (2019). Role of engineered proteins as therapeutic formulations. In Pharmaceutical biocatalysis: Fundamentals, enzyme inhibitors, and enzymes in health and diseases (p. 159). Singapore: Jenny Stanford Publishing.

    Chapter  Google Scholar 

  • Guo, J., & Zhou, H.-X. (2016). Protein allostery and conformational dynamics. Chemical Reviews, 116, 6503–6515.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hansen, L. D., Transtrum, M. K., Quinn, C., & Demarse, N. (2016). Enzyme-catalyzed and binding reaction kinetics determined by titration calorimetry. Biochimica et Biophysica Acta (BBA)-General Subjects, 1860, 957–966.

    Article  CAS  Google Scholar 

  • Hao, C., Xu, G., Feng, Y., Lu, L., Sun, W., & Sun, R. (2017). Fluorescence quenching study on the interaction of ferroferric oxide nanoparticles with bovine serum albumin. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 184, 191–197.

    Article  CAS  Google Scholar 

  • Hatta, A., Suzuki, Y., & Suëtaka, W. (1984). Infrared absorption enhancement of monolayer species on thin evaporated Ag films by use of a Kretschmann configuration: Evidence for two types of enhanced surface electric fields. Applied Physics A, 35, 135–140.

    Article  Google Scholar 

  • Hevekerl, H., Tornmalm, J., & Widengren, J. (2016). Fluorescence-based characterization of non-fluorescent transient states of tryptophan–prospects for protein conformation and interaction studies. Scientific Reports, 6, 35052.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang, R., & Leung, I. K. (2016). Protein-directed dynamic combinatorial chemistry: A guide to protein ligand and inhibitor discovery. Molecules, 21, 910.

    Article  PubMed Central  CAS  Google Scholar 

  • Huang, R., & Leung, I. K. (2019). Protein–small molecule interactions by WaterLOGSY. In Methods in enzymology (Vol. 615, pp. 477–500). Amsterdam: Elsevier.

    Google Scholar 

  • Huber, S., Casagrande, F., Hug, M. N., Wang, L., Heine, P., Kummer, L., et al. (2017). SPR-based fragment screening with neurotensin receptor 1 generates novel small molecule ligands. PLoS One, 12.

    Google Scholar 

  • Jabar, S., Adams, L. A., Wang, Y., Aurelio, L., Graham, B., & Otting, G. (2017). Chemical tagging with tert-butyl and trimethylsilyl groups for measuring intermolecular nuclear overhauser effects in a large protein–ligand complex. Chemistry–A European Journal, 23, 13033–13036.

    Article  CAS  Google Scholar 

  • Jaiswal, N., Agarwal, N., Kaur, A., Tripathi, S., Gahlay, G. K., Arora, A., et al. (2019). Molecular interaction between human SUMO-I and histone like DNA binding protein of helicobacter pylori (Hup) investigated by NMR and other biophysical tools. International Journal of Biological Macromolecules, 123, 446–456.

    Google Scholar 

  • Johnson, O. T., Kaur, T., & Garner, A. L. (2019). A conditionally fluorescent peptide reporter of secondary structure modulation. Chembiochem, 20, 40–45.

    Article  CAS  PubMed  Google Scholar 

  • Jones, L. H., & Bunnage, M. E. (2017). Applications of chemogenomic library screening in drug discovery. Nature Reviews Drug Discovery, 16, 285.

    Article  CAS  PubMed  Google Scholar 

  • Joseph, P. R. B., Poluri, K. M., Sepuru, K. M., & Rajarathnam, K. (2015). Characterizing protein–glycosaminoglycan interactions using solution NMR spectroscopy. In Glycosaminoglycans (pp. 325–333). Amsterdam: Springer.

    Chapter  Google Scholar 

  • Joshi, U. M., Rao, P., Kodavanti, S., Lockard, V. G., & Mehendale, H. M. (1989). Fluorescence studies on binding of amphiphilic drugs to isolated lamellar bodies: Relevance to phospholipidosis. Biochimica et Biophysica Acta (BBA)-Lipids and Lipid Metabolism, 1004, 309–320.

    Article  CAS  Google Scholar 

  • Juhász, A., Csapó, E., Ungor, D., Tóth, G. K., Ls, V., & Dékány, I. (2016). Kinetic and thermodynamic evaluation of kynurenic acid binding to GluR1270–300 polypeptide by surface Plasmon resonance experiments. The Journal of Physical Chemistry B, 120, 7844–7850.

    Article  PubMed  CAS  Google Scholar 

  • Kaur, G., Paliwal, A., Tomar, M., & Gupta, V. (2016). Detection of Neisseria meningitidis using surface plasmon resonance based DNA biosensor. Biosensors and Bioelectronics, 78, 106–110.

    Article  CAS  PubMed  Google Scholar 

  • Kay, L. E. (2011). NMR studies of protein structure and dynamics-a look backwards and forwards. Journal of Magnetic Resonance (San Diego, Calif: 1997), 213, 492–494.

    Article  CAS  Google Scholar 

  • Keeler, J. (2011). Understanding NMR spectroscopy. Washington, D.C.: Wiley.

    Google Scholar 

  • Kirkpatrick, S. (1984). Optimization by simulated annealing: Quantitative studies. Journal of Statistical Physics, 34, 975–986.

    Article  Google Scholar 

  • Kivi, R., Solovjova, K., Haljasorg, T., Arukuusk, P., & Järv, J. (2016). Allosteric effect of adenosine triphosphate on peptide recognition by 3′ 5′-cyclic adenosine monophosphate dependent protein kinase catalytic subunits. The Protein Journal, 35, 459–466.

    Article  CAS  PubMed  Google Scholar 

  • Kollipara, M. R., Shadap, L., Banothu, V., Agarwal, N., Poluri, K. M., & Kaminsky, W. (2020). Fluorenone Schiff base derivative complexes of ruthenium, rhodium and iridium exhibiting efficient antibacterial activity and DNA-binding affinity. Journal of Organometallic Chemistry, 121246.

    Google Scholar 

  • Kooyman, R., De Bruijn, H., Eenink, R., & Greve, J. (1990). Surface plasmon resonance as a bioanalytical tool. Journal of Molecular Structure, 218, 345–350.

    Article  CAS  Google Scholar 

  • Korshunova, A., Lopanskaia, I., & Gudimchuk, N. (2019). Modern approaches to analysis of protein–ligand interactions. Biophysics, 64, 495–509.

    Article  CAS  Google Scholar 

  • Kozma, E., Jayasekara, P. S., Squarcialupi, L., Paoletta, S., Moro, S., Federico, S., et al. (2013). Fluorescent ligands for adenosine receptors. Bioorganic & Medicinal Chemistry Letters, 23, 26–36.

    Google Scholar 

  • Kubinyi, H. (2006). Chemogenomics in drug discovery. In Chemical genomics (pp. 1–19). New York: Springer.

    Google Scholar 

  • Kumar, P. K. (2017). Systematic screening of viral entry inhibitors using surface plasmon resonance. Reviews in Medical Virology, 27, e1952.

    Article  Google Scholar 

  • Kuzuyama, T., Takahashi, S., Takagi, M., & Seto, H. (2000). Characterization of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, an enzyme involved in isopentenyl diphosphate biosynthesis, and identification of its catalytic amino acid residues. Journal of Biological Chemistry, 275, 19928–19932.

    Article  CAS  Google Scholar 

  • Kyrychenko, A. (2015). Using fluorescence for studies of biological membranes: A review. Methods and Applications in Fluorescence, 3, 042003.

    Article  PubMed  CAS  Google Scholar 

  • Lakayan, D., Tuppurainen, J., Suutari, T. E., van Iperen, D. J., Somsen, G. W., & Kool, J. (2019). Design and evaluation of a multiplexed angular-scanning surface plasmon resonance system employing line-laser optics and CCD detection in combination with multi-ligand sensor chips. Sensors and Actuators B: Chemical, 282, 243–250.

    Article  CAS  Google Scholar 

  • Lampe, J. N., & Atkins, W. M. (2006). Time-resolved fluorescence studies of heterotropic ligand binding to cytochrome P450 3A4. Biochemistry, 45, 12204–12215.

    Article  CAS  PubMed  Google Scholar 

  • Larsson, T., Wedborg, M., & Turner, D. (2007). Correction of inner-filter effect in fluorescence excitation-emission matrix spectrometry using Raman scatter. Analytica Chimica Acta, 583, 357–363.

    Article  CAS  PubMed  Google Scholar 

  • Legchenko, A. (2013). The basics of NMR. In Magnetic resonance imaging for groundwater (pp. 15–44). New York: Wiley.

    Chapter  Google Scholar 

  • Li, D., DeRose, E. F., & London, R. E. (1999). The inter-ligand Overhauser effect: A powerful new NMR approach for mapping structural relationships of macromolecular ligands. Journal of Biomolecular NMR, 15, 71–76.

    Article  CAS  PubMed  Google Scholar 

  • Li, S., Yang, M., Zhou, W., Johnston, T. G., Wang, R., & Zhu, J. (2015). Dextran hydrogel coated surface plasmon resonance imaging (SPRi) sensor for sensitive and label-free detection of small molecule drugs. Applied Surface Science, 355, 570–576.

    Article  CAS  Google Scholar 

  • Liu, T., Lin, Y., Wen, X., Jorissen, R. N., & Gilson, M. K. (2007). BindingDB: A web-accessible database of experimentally determined protein–ligand binding affinities. Nucleic Acids Research, 35, D198–D201.

    Article  CAS  PubMed  Google Scholar 

  • Liu, X., Golden, L. C., Lopez, J. A., Shepherd, T. R., Yu, L., & Fuentes, E. J. (2019). Conformational dynamics and cooperativity drive the specificity of a protein-ligand interaction. Biophysical Journal, 116, 2314–2330.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu, X., Speckhard, D. C., Shepherd, T. R., Sun, Y. J., Hengel, S. R., Yu, L., et al. (2016). Distinct roles for conformational dynamics in protein-ligand interactions. Structure, 24, 2053–2066.

    Google Scholar 

  • Masson, J.-F. (2017). Surface plasmon resonance clinical biosensors for medical diagnostics. ACS Sensors, 2, 16–30.

    Article  CAS  PubMed  Google Scholar 

  • McClure, W. O., & Edelman, G. M. (1966). Fluorescent probes for conformational states of proteins. I. Mechanism of fluorescence of 2-p-toluidinylnaphthalene-6-sulfonate, a hydrophobic probe. Biochemistry, 5, 1908–1919.

    Article  CAS  PubMed  Google Scholar 

  • Meyer, B., da Veiga, C., Dumas, P., & Ennifar, E. (2019). Thermodynamics of molecular machines using incremental ITC. In Microcalorimetry of biological molecules (pp. 129–140). New York: Springer.

    Chapter  Google Scholar 

  • Meyer, B., & Peters, T. (2003). NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angewandte Chemie International Edition, 42, 864–890.

    Article  CAS  PubMed  Google Scholar 

  • Mobbs, J. I., Koay, A., Di Paolo, A., Bieri, M., Petrie, E. J., Gorman, M. A., et al. (2015). Determinants of oligosaccharide specificity of the carbohydrate-binding modules of AMP-activated protein kinase. Biochemical Journal, 468, 245–257.

    Google Scholar 

  • Mocz, G., & Ross, J. A. (2013). Fluorescence techniques in analysis of protein–ligand interactions. In Protein-ligand interactions (pp. 169–210). New York: Springer.

    Chapter  Google Scholar 

  • Mukherjee, S., Mohan, P. K., & Chary, K. V. (2007). Magnesium promotes structural integrity and conformational switching action of a calcium sensor protein. Biochemistry, 46, 3835–3845.

    Article  CAS  PubMed  Google Scholar 

  • Mureddu, L., & Vuister, G. W. (2019). Simple high-resolution NMR spectroscopy as a tool in molecular biology. The FEBS Journal, 286, 2035–2042.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nag, N., Ramreddy, T., Kombrabail, M., Mohan, P. K., D’souza, J., Rao, B., et al. (2006). Dynamics of DNA and portein-DNA complexes viewed through time-domain fluorescence. In Reviews in fluorescence 2006 (pp. 311–340). Springer.

    Google Scholar 

  • Nepravishta, R., Walpole, S., Tailford, L., Juge, N., & Angulo, J. (2019). Deriving ligand orientation in weak protein–ligand complexes by DEEP-STD NMR spectroscopy in the absence of protein chemical-shift assignment. Chembiochem, 20, 340–344.

    Article  CAS  PubMed  Google Scholar 

  • Nguyen, H. H., Park, J., Kang, S., & Kim, M. (2015). Surface plasmon resonance: A versatile technique for biosensor applications. Sensors, 15, 10481–10510.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nico, J., & Fischer, M. J. (2010). Surface plasmon resonance: A general introduction. In Surface Plasmon resonance (pp. 1–14). New York: Springer.

    Google Scholar 

  • Olsson, T. S., Williams, M. A., Pitt, W. R., & Ladbury, J. E. (2008). The thermodynamics of protein–ligand interaction and solvation: Insights for ligand design. Journal of Molecular Biology, 384, 1002–1017.

    Article  CAS  PubMed  Google Scholar 

  • Orts, J., Griesinger, C., & Carlomagno, T. (2009). The INPHARMA technique for pharmacophore mapping: A theoretical guide to the method. Journal of Magnetic Resonance, 200, 64–73.

    Article  CAS  PubMed  Google Scholar 

  • Pan, A. C., Borhani, D. W., Dror, R. O., & Shaw, D. E. (2013). Molecular determinants of drug–receptor binding kinetics. Drug Discovery Today, 18, 667–673.

    Article  CAS  PubMed  Google Scholar 

  • Panov, K., & Alsahafi, S. (2019). Investigation of molecular mechanisms of polymerase I (pol-l) inhibitor PMR-116 using isothermal titration Calorimetry (ITC). Access Microbiology, 1.

    Google Scholar 

  • Partlow, B. P., Bagheri, M., Harden, J. L., & Kaplan, D. L. (2016). Tyrosine templating in the self-assembly and crystallization of silk fibroin. Biomacromolecules, 17, 3570–3579.

    Article  CAS  PubMed  Google Scholar 

  • Pecht, I., Maron, E., Arnon, R., & Sela, M. (1971). Specific excitation energy transfer from antibodies to Dansyl-labeled antigen: Studies with the “loop” peptide of hen egg-white lysozyme. European Journal of Biochemistry, 19, 368–371.

    Article  CAS  PubMed  Google Scholar 

  • Pellecchia, M., Meininger, D., Dong, Q., Chang, E., Jack, R., & Sem, D. S. (2002). NMR-based structural characterization of large protein-ligand interactions. Journal of Biomolecular NMR, 22, 165–173.

    Article  CAS  PubMed  Google Scholar 

  • Perspicace, S., Banner, D., Benz, J., Müller, F., Schlatter, D., & Huber, W. (2009). Fragment-based screening using surface plasmon resonance technology. Journal of Biomolecular Screening, 14, 337–349.

    Article  CAS  PubMed  Google Scholar 

  • Piñeiro, Á., Muþoz, E., SabÚn, J., Costas, M., Bastos, M., VelÃzquez-Campoy, A., et al. (2019). AFFINImeter: A software to analyze molecular recognition processes from experimental data. Analytical Biochemistry, 577, 117–134.

    Google Scholar 

  • Plotnikova, O., Mel’Nikov, A., Mel’Nikov, G., & Gubina, T. (2016). Quenching of tryptophan fluorescence of bovine serum albumin under the effect of ions of heavy metals. Optics and Spectroscopy, 120, 65–69.

    Article  CAS  Google Scholar 

  • Poluri, K. M., & Gulati, K. (2016). Protein engineering techniques: Gateways to synthetic protein universe. Singapore: Springer.

    Google Scholar 

  • Poluri, K. M., & Gulati, K. (2017). World of proteins: Structure-function relationships and engineering techniques. In Protein engineering techniques (pp. 1–25). Singapore: Springer.

    Chapter  Google Scholar 

  • Poluri, K. M., Joseph, P. R. B., Sawant, K. V., & Rajarathnam, K. (2013). Molecular basis of glycosaminoglycan heparin binding to the chemokine CXCL1 dimer. Journal of Biological Chemistry, 288, 25143–25153.

    Article  CAS  Google Scholar 

  • Post, C. B. (2003). Exchange-transferred NOE spectroscopy and bound ligand structure determination. Current Opinion in Structural Biology, 13, 581–588.

    Article  CAS  PubMed  Google Scholar 

  • Prozeller, D., Morsbach, S., & Landfester, K. (2019). Isothermal titration calorimetry as a complementary method for investigating nanoparticle–protein interactions. Nanoscale, 11, 19265–19273.

    Article  CAS  PubMed  Google Scholar 

  • Radić, Z., Kirchhoff, P. D., Quinn, D. M., McCammon, J. A., & Taylor, P. (1997). Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase distinctions between active center ligands and fasciculin. Journal of Biological Chemistry, 272, 23265–23277.

    Article  Google Scholar 

  • Ràfols, C., Amézqueta, S., Fuguet, E., & Bosch, E. (2018). Molecular interactions between warfarin and human (HSA) or bovine (BSA) serum albumin evaluated by isothermal titration calorimetry (ITC), fluorescence spectrometry (FS) and frontal analysis capillary electrophoresis (FA/CE). Journal of Pharmaceutical and Biomedical Analysis, 150, 452–459.

    Article  PubMed  CAS  Google Scholar 

  • Ragona, L., Gasymov, O., Guliyeva, A. J., Aslanov, R. B., Zanzoni, S., Botta, C., et al. (2018). Rhodamine binds to silk fibroin and inhibits its self-aggregation. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1866, 661–667.

    Article  CAS  Google Scholar 

  • Raingeval, C., Cala, O., Brion, B., Le Borgne, M., Hubbard, R. E., & Krimm, I. (2019). 1D NMR WaterLOGSY as an efficient method for fragment-based lead discovery. Journal of Enzyme Inhibition and Medicinal Chemistry, 34, 1218–1225.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raj, R., Agarwal, N., Raghavan, S., Chakraborti, T., Poluri, K. M., & Kumar, D. (2020). Exquisite binding interaction of 18β-Glycyrrhetinic acid with histone like DNA binding protein of helicobacter pylori: A computational and experimental study. International Journal of Biological Macromolecules, 161, 231–246.

    Article  CAS  PubMed  Google Scholar 

  • Rao, A. B. P., Gulati, K., Joshi, N., Deb, D. K., Rambabu, D., Kaminsky, W., et al. (2017). Synthesis and biological studies of ruthenium, rhodium and iridium metal complexes with pyrazole-based ligands displaying unpredicted bonding modes. Inorganica Chimica Acta, 462, 223–235.

    Google Scholar 

  • Rayani, K., Muñoz, E., Spuches, A., Van Petegem, F., & Tibbits, G. (2018). Binding of calcium and magnesium to cardiac troponin C assessed through Isothermal Titration Calorimetry (ITC). Journal of Molecular and Cellular Cardiology, 124, 86.

    Article  Google Scholar 

  • Rega, M. F., Wu, B., Wei, J., Zhang, Z., Cellitti, J. F., & Pellecchia, M. (2011). SAR by interligand nuclear Overhauser effects (ILOEs) based discovery of acylsulfonamide compounds active against Bcl-xL and Mcl-1. Journal of Medicinal Chemistry, 54, 6000–6013.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rühmann, E., Betz, M., Fricke, M., Heine, A., Schäfer, M., & Klebe, G. (2015). Thermodynamic signatures of fragment binding: Validation of direct versus displacement ITC titrations. Biochimica et Biophysica Acta (BBA)-General Subjects, 1850, 647–656.

    Article  CAS  Google Scholar 

  • Saeed, I. Q., & Buurma, N. J. (2019). Analysis of isothermal titration calorimetry data for complex interactions using I2CITC. In Microcalorimetry of biological molecules (pp. 169–183). New York: Springer.

    Chapter  Google Scholar 

  • Sahni, N., Chaudhuri, R., Hickey, J. M., Manikwar, P., D’Souza, A., Metters, A., et al. (2017). Preformulation characterization, stabilization, and formulation design for the acrylodan-labeled glucose-binding protein SM4-AC. Journal of Pharmaceutical Sciences, 106, 1197–1210.

    Google Scholar 

  • Šakanovič, A., Hodnik, V., & Anderluh, G. (2019). Surface Plasmon resonance for measuring interactions of proteins with lipids and lipid membranes. In Lipid-protein interactions (pp. 53–70). Springer.

    Google Scholar 

  • Sánchez-Pedregal, V. M., Reese, M., Meiler, J., Blommers, M. J., Griesinger, C., & Carlomagno, T. (2005). The INPHARMA method: Protein-mediated interligand NOEs for pharmacophore mapping. Angewandte Chemie International Edition, 44, 4172–4175.

    Article  PubMed  CAS  Google Scholar 

  • Santofimia-Castaño, P., Rizzuti, B., Abián, O., Velázquez-Campoy, A., Iovanna, J. L., & Neira, J. L. (2018). Amphipathic helical peptides hamper protein-protein interactions of the intrinsically disordered chromatin nuclear protein 1 (NUPR1). Biochimica et Biophysica Acta (BBA)-General Subjects, 1862, 1283–1295.

    Article  CAS  Google Scholar 

  • Sarkar, I., & Mishra, A. K. (2018). Fluorophore tagged bio-molecules and their applications: A brief review. Applied Spectroscopy Reviews, 53, 552–601.

    Article  CAS  Google Scholar 

  • Sarkar, S., Gulati, K., Kairamkonda, M., Mishra, A., & Poluri, K. M. (2018). Elucidating protein-protein interactions through computational approaches and designing small molecule inhibitors against them for various diseases. Current Topics in Medicinal Chemistry, 18, 1719–1736.

    Article  CAS  PubMed  Google Scholar 

  • Sarkar, S., Gulati, K., Mishra, A., & Poluri, K. M. (2020). Protein nanocomposites: Special inferences to lysozyme based nanomaterials. International Journal of Biological Macromolecules, 151, 467–482.

    Article  CAS  PubMed  Google Scholar 

  • Sawant, K. V., Poluri, K. M., Dutta, A. K., Sepuru, K. M., Troshkina, A., Garofalo, R. P., et al. (2016). Chemokine CXCL1 mediated neutrophil recruitment: Role of glycosaminoglycan interactions. Scientific Reports, 6, 33123.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schasfoort, R., Abali, F., Stojanovic, I., Vidarsson, G., & Terstappen, L. W. (2018). Trends in SPR cytometry: Advances in label-free detection of cell parameters. Biosensors, 8, 102.

    Article  CAS  PubMed Central  Google Scholar 

  • Schmidtke, P., Luque, F. J., Murray, J. B., & Barril, X. (2011). Shielded hydrogen bonds as structural determinants of binding kinetics: Application in drug design. Journal of the American Chemical Society, 133, 18903–18910.

    Article  CAS  PubMed  Google Scholar 

  • Schuetz, D. A., de Witte, W. E. A., Wong, Y. C., Knasmueller, B., Richter, L., Kokh, D. B., et al. (2017). Kinetics for drug discovery: An industry-driven effort to target drug residence time. Drug Discovery Today, 22, 896–911.

    Google Scholar 

  • Shadap, L., Joshi, N., Poluri, K. M., Kollipara, M. R., & Kaminsky, W. (2018). Synthesis and structural characterization of arene d6 metal complexes of sulfonohydrazone and triazolo ligands: High potency of triazolo derivatives towards DNA binding. Polyhedron, 155, 302–312.

    Article  CAS  Google Scholar 

  • Shanehbandi, D., Majidi, J., Kazemi, T., Baradaran, B., Aghebati-Maleki, L., Fathi, F., et al. (2017). Immuno-biosensor for detection of CD20-positive cells using surface plasmon resonance. Advanced Pharmaceutical Bulletin, 7, 189.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sindrewicz, P., Li, X., Yates, E. A., Turnbull, J. E., Lian, L.-Y., & Yu, L.-G. (2019). Intrinsic tryptophan fluorescence spectroscopy reliably determines galectin-ligand interactions. Scientific Reports, 9, 1–12.

    Article  CAS  Google Scholar 

  • Śledź, P., & Caflisch, A. (2018). Protein structure-based drug design: From docking to molecular dynamics. Current Opinion in Structural Biology, 48, 93–102.

    Article  PubMed  CAS  Google Scholar 

  • Snyder, D. A., Chantova, M., & Chaudhry, S. (2015). Analysis of ligand–protein exchange by clustering of ligand diffusion coefficient pairs (CoLD-CoP). Journal of Magnetic Resonance, 255, 44–50.

    Article  CAS  PubMed  Google Scholar 

  • Szabo, A., Stolz, L., & Granzow, R. (1995). Surface plasmon resonance and its use in biomolecular interaction analysis (BIA). Current Opinion in Structural Biology, 5, 699–705.

    Article  CAS  PubMed  Google Scholar 

  • Taghipour, P., Zakariazadeh, M., Sharifi, M., Dolatabadi, J. E. N., & Barzegar, A. (2018). Bovine serum albumin binding study to erlotinib using surface plasmon resonance and molecular docking methods. Journal of Photochemistry and Photobiology B: Biology, 183, 11–15.

    Article  CAS  Google Scholar 

  • Tang, W., & Yengo, C. M. (2018). Inter-filament co-operativity is crucial for regulating muscle contraction. The Journal of Physiology, 596, 17.

    Article  CAS  PubMed  Google Scholar 

  • Umuhire Juru, A., Patwardhan, N. N., & Hargrove, A. E. (2019). Understanding the contributions of conformational changes, thermodynamics, and kinetics of RNA–small molecule interactions. ACS Chemical Biology, 14, 824–838.

    Article  CAS  PubMed  Google Scholar 

  • Usui, M., Furihata, K., Utsumi, H., Kato, T., & Tashiro, M. (2017). Applicability of the NMR-based screening methods with 19F detection to the fluorinated compound. J Res Anal, 3, 34–36.

    Google Scholar 

  • Van Der Merwe, P. A. (2001). Surface plasmon resonance. Protein-ligand interactions: hydrodynamics and calorimetry, 1, 137–170.

    Google Scholar 

  • Vargas-Uribe, M., Rodnin, M. V., øjemalm, K., Holgado, A., Kyrychenko, A., Nilsson, I., et al. (2015). Thermodynamics of membrane insertion and refolding of the diphtheria toxin T-domain. The Journal of Membrane Biology, 248, 383–394.

    Google Scholar 

  • Viegas, A., Manso, J., Nobrega, F. L., & Cabrita, E. J. (2011). Saturation-transfer difference (STD) NMR: A simple and fast method for ligand screening and characterization of protein binding. Journal of Chemical Education, 88, 990–994.

    Article  CAS  Google Scholar 

  • Vogel, M., & Suess, B. (2016). Label-free determination of the dissociation constant of small molecule-aptamer interaction by isothermal titration calorimetry. In Nucleic acid aptamers (pp. 113–125). San Diego, CA: Springer.

    Chapter  Google Scholar 

  • Wallerstein, J., & Akke, M. (2019). Minute additions of DMSO affect protein dynamics measurements by NMR relaxation experiments through significant changes in solvent viscosity. ChemPhysChem, 20, 326–332.

    Article  CAS  PubMed  Google Scholar 

  • Wang, Q., Liu, R., Yang, X., Wang, K., Zhu, J., He, L., et al. (2016). Surface plasmon resonance biosensor for enzyme-free amplified microRNA detection based on gold nanoparticles and DNA supersandwich. Sensors and Actuators B: Chemical, 223, 613–620.

    Article  CAS  Google Scholar 

  • Wang, Y., Huang, C.-J., Jonas, U., Wei, T., Dostalek, J., & Knoll, W. (2010). Biosensor based on hydrogel optical waveguide spectroscopy. Biosensors and Bioelectronics, 25, 1663–1668.

    Article  CAS  PubMed  Google Scholar 

  • Wang, Y. S., Liu, D., & Wyss, D. F. (2004). Competition STD NMR for the detection of high-affinity ligands and NMR-based screening. Magnetic Resonance in Chemistry, 42, 485–489.

    Article  CAS  PubMed  Google Scholar 

  • Waudby, C. A., Ramos, A., Cabrita, L. D., & Christodoulou, J. (2016). Two-dimensional NMR lineshape analysis. Scientific Reports, 6, 24826.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Winkie, M. L., So, J., Schlessman, J. L., & Smith, V. F. (2019). Characterization of protein-ligand interactions in MsrA from E. coli the. FASEB Journal, 33, 631.647–631.647.

    Article  Google Scholar 

  • Winter, G., Vogt, A., Glatting, G., Kletting, P., & Beer, A. (2018). Characterization of the receptor binding kinetics of PSMA-specific peptides by surface Plasmon resonance spectroscopy. Journal of Nuclear Medicine, 59, 1128–1128.

    Google Scholar 

  • Wiseman, T., Williston, S., Brandts, J. F., & Lin, L.-N. (1989). Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Analytical Biochemistry, 179, 131–137.

    Article  CAS  PubMed  Google Scholar 

  • Wolf, S., Amaral, M., Lowinski, M., VallÕe, F., Musil, D., Güldenhaupt, J., et al. (2019). Estimation of protein–ligand unbinding kinetics using non-equilibrium targeted molecular dynamics simulations. Journal of Chemical Information and Modeling, 59, 5135–5147.

    Google Scholar 

  • Wong, J. K.-H., Todd, M. H., & Rutledge, P. J. (2017). Recent advances in macrocyclic fluorescent probes for ion sensing. Molecules, 22, 200.

    Article  PubMed Central  CAS  Google Scholar 

  • Yamaoki, Y., Nagata, T., Sakamoto, T., & Katahira, M. (2020). Recent progress of in-cell NMR of nucleic acids in living human cells. Biophysical Reviews, 1–7.

    Google Scholar 

  • Yang, H., Huang, Y., He, J., Li, S., Tang, B., & Li, H. (2016). Interaction of lafutidine in binding to human serum albumin in gastric ulcer therapy: STD-NMR, WaterLOGSY-NMR, NMR relaxation times, Tr-NOESY, molecule docking, and spectroscopic studies. Archives of Biochemistry and Biophysics, 606, 81–89.

    Article  CAS  PubMed  Google Scholar 

  • Yang, L., Wang, J., L-z, Y., Hu, Z.-D., Wu, X., & Zheng, G. (2018). Characteristics of multiple Fano resonances in waveguide-coupled surface plasmon resonance sensors based on waveguide theory. Scientific Reports, 8, 1–10.

    CAS  Google Scholar 

  • Yu, Z., Li, P., & Merz Jr., K. M. (2017). Using ligand-induced protein chemical shift perturbations to determine protein–ligand structures. Biochemistry, 56, 2349–2362.

    Article  CAS  PubMed  Google Scholar 

  • Zare, H., Moosavi-Movahedi, A., Salami, M., Sheibani, N., Khajeh, K., & Habibi-Rezaei, M. (2016). Autolysis control and structural changes of purified ficin from Iranian fig latex with synthetic inhibitors. International Journal of Biological Macromolecules, 84, 464–471.

    Article  CAS  PubMed  Google Scholar 

  • Zhan, S., Shi, C., Ou, H., Song, H., & Wang, X. (2016). A real-time de-noising method applied for transient and weak biomolecular interaction analysis in surface plasmon resonance biosensing. Measurement Science and Technology, 27, 035702.

    Article  CAS  Google Scholar 

  • Zhang, J., & Nussinov, R. (2019). Protein allostery in drug discovery. Singapore: Springer.

    Book  Google Scholar 

  • Zhang, S., & Fitzpatrick, P. F. (2016). Identification of the allosteric site for phenylalanine in rat phenylalanine hydroxylase. Journal of Biological Chemistry, 291, 7418–7425.

    Article  CAS  Google Scholar 

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Acknowledgements

KMP acknowledge the receipt of Grants CRG/2018/001329 and SERB-SB/YS/LS-380/2013 from SERB-DST, and DBT-IYBA fellowship – BT/07/IYBA/2013-19. NA acknowledges the receipt of INSPIRE fellowship from Department of Science and Technology, India and VC is thankful to Department of Biotechnology (DBT-India) for JRF fellowship.

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  1. Nipanshu Agarwal and Vivek Chetry have contributed equally to this work.

Authors and Affiliations

  1. Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India

    Nipanshu Agarwal, Vivek Chetry & Krishna Mohan Poluri

  2. Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India

    Krishna Mohan Poluri

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    Sanjeev Kumar Singh

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Agarwal, N., Chetry, V., Poluri, K.M. (2021). Elucidating Protein-Ligand Interactions Using High Throughput Biophysical Techniques. In: Singh, S.K. (eds) Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design. Springer, Singapore. https://doi.org/10.1007/978-981-15-8936-2_9

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