Research_Takumi Ueda

Ongoing Studies

• Quantitative elucidation of the biofunction-related conformational dynamics of drug-target proteins

  Drug-target proteins exert their biofunctions with continuously changing their conformations.
  In relation to this point, NMR methods provide quantitative spatiotemporal information
  on proteins under conformational equilibria, including the structure of each state, exchange rate, and population.

  We are proceeding with studies on the elucidation of function-related
  conformational equilibria of drug-target proteins, including G protein-coupled receptors (GPCRs).

  These studies promote our understanding of the biological events and drug development.
  

• Development of mid-size molecules that regulate activities of drug-target proteins using NMR

  Mid-size molecules, such as atypical peptides, are promising drug modality potentially capable of targeting intracellular protein-protein interactions,
  which are difficult targets for conventional small-size drugs and antibodies.

  We utilize NMR to clarify their conformational �gchameleonicity�h: flexibly changing their dynamic conformation to adapt their environments,
  including aqueous solution, hydrophobic membrane, and the complex with the receptor, which determines their membrane permeability and affinity for the receptor.
  

• Clarification of overall biological events by integrating multi-level experimental information using NMR

  We are exploring methods for constructing models of biological events by integrating multi-scale experimental data,
  including atom-level precise structural information of drug-target proteins (by X-ray crystallography and cryo-electron microscopy)
  and cell biological real-time observation, by utilizing quantitative information on the function-related conformational equilibria
  obtained from NMR and exchange Monte-Carlo method, which can realize the comprehensive and effective optimization of multiple parameters in the model.

  Our study, which can be referred to as �gQuantitative structural life science�h, will establish novel approach for
  understanding biological events and accelerating drug development.

Outline of the previous studies

NMR studies of GPCRs are challenging, because of their large molecular weight and low stability, resulting in limited information.
We have overcome these bottlenecks through the development of novel analytical methods, measurement techniques, and sample preparation methods.
(J. Biomol. NMR 2018, J. Biomol. NMR 2015, J. Biomol. NMR 2012, etc.)

For example, by using exchange Monte Carlo method, a machine learning approach, we maximized the information obtained from NMR signals and
quantitatively extracted the population and exchange rates of the conformational equilibria (Nat. Chem. Biol. 2020).

We employed the developed methods to reveal that GPCRs exist in dynamic equilibrium states between multiple inactive and active structures,
and that the population of the active conformations determine the efficacy and functional selectivity of the GPCR drugs.
(Proc. Natl. Acad. Sci. 2022, Angew. Chem. Int. Ed. 2015, Nat. Commun. 2012)

Furthermore, by utilizing nanodiscs, we successfully analyzed GPCRs in lipid bilayers by NMR,
elucidating mechanisms underlying the arrestin activation and modulation of the GPCR activity by lipids.
(Angew. Chem. Int. Ed. 2014, Nat. Commun. 2021, Nat. Commun. 2018, Sci. Adv. 2020)

We also uncovered the two-step ligand recognition mechanism of chemokine receptors.
(J. Biomol. NMR 2015, J. Am. Chem. Soc. 2010, J. Biol. Chem. 2009)

These function-related conformational equilibria of GPCRs provide biologically and pharmacologically important insights
not attainable by other structural biology methods, leading to requests for several review articles.

(Nat. Rev. Drug Discov. 2019, J. Magn. Reson. 2022, Biophys. Rev. 2019, etc.) In addition to GPCRs, we also utilized NMR to clarify the functions of the following drug-target proteins.

• Partial activation mechanism of the ATP-gated ion channel P2X4 receptor (Proc. Natl. Acad. Sci. 2016)
• Electron transport mechanisms of photosynthetic membrane proteins (Plant Cell 2012)
• Regulatory mechanisms of the thermotaxis control protein CheA-CheY (Sci. Rep. 2016)
• UV-damaged DNA repair mechanism of photolyase �iJ. Biol. Chem. 2005, J. Biol. Chem. 2004a, J. Biol. Chem. 2004b�j