Site specific polarization transfer from a hyperpolarized ligand of dihydrofolate reductase

Screening of Protein-Ligand Binding Using a SABRE Hyperpolarized Reporter

Hyperpolarization through signal amplification by reversible exchange (SABRE) provides a facile means to enhance nuclear magnetic resonance (NMR) signals of small molecules containing an N-heterocycle or other binding site for a polarization transfer catalyst. A purpose-designed reporter ligand, which is capable of binding both to a target protein and to the catalyst, makes the sensitivity enhancement by this technique compatible with the measurement of a range of biomolecular interactions. The ¹H polarization of the reporter ligand 4-amidinopyridine, which is targeting trypsin, is used to screen ligands that are not themselves hyperpolarizable by SABRE. The respective protein-ligand dissociation constants (K_D) are determined by an observed change in the R₂ relaxation rate of the reporter. A calculation of expected signal changes indicates that the accessible ligand K_D values extend over several orders of magnitude, while the concentrations of target proteins and ligands can be reduced considering the sensitivity gains from hyperpolarization. In general, the design of a single, weakly binding ligand for a target protein enables the use of SABRE hyperpolarization for ligand screening or other biophysical studies involving macromolecular interactions.

Challenges and Advances in the Application of Dynamic Nuclear Polarization to Liquid-State NMR Spectroscopy

Nuclear magnetic resonance (NMR) spectroscopy is a powerful method to study the molecular structure and dynamics of materials. The inherently low sensitivity of NMR spectroscopy is a consequence of low spin polarization. Hyperpolarization of a spin ensemble is defined as a population difference between spin states that far exceeds what is expected from the Boltzmann distribution for a given temperature. Dynamic nuclear polarization (DNP) can overcome the relatively low sensitivity of NMR spectroscopy by using a paramagnetic matrix to hyperpolarize a nuclear spin ensemble. Application of DNP to NMR can result in sensitivity gains of up to four orders of magnitude compared to NMR without DNP. Although DNP NMR is now more routinely utilized for solid-state (ss) NMR spectroscopy, it has not been exploited to the same degree for liquid-state samples. This Review will consider challenges and advances in the application of DNP NMR to liquid-state samples. The Review is organized into four sections: (i) mechanisms of DNP NMR relevant to hyperpolarization of liquid samples; (ii) applications of liquid-state DNP NMR; (iii) available detection schemes for liquid-state samples; and (iv) instrumental challenges and outlook for liquid-state DNP NMR.

Amplification of Nuclear Overhauser Effect Signals by Hyperpolarization for Screening of Ligand Binding to Immobilized Target Proteins

Immobilization of a target protein enhances the cross-relaxation rates for transfer of nuclear spin polarization but reduces the accessible target concentration. Hyperpolarization of ligand spins by dissolution dynamic nuclear polarization (D-DNP) is shown to increase sensitivity for observing the intraligand nuclear Overhauser effect (NOE). This effect, also known as the transferred NOE (trNOE), can be used for detection of binding and for obtaining binding-related structural information. The measurement of hyperpolarized trNOE signals is demonstrated for the ligand 4'-hydroxyazobenzene-2-carboxylic acid interacting with avidin protein immobilized on polystyrene beads. In a sample containing 63.5 μM ligands and 0.83 μM accessible protein binding sites, the signal enhancement provided by D-DNP leads to single-scan detection of the NOE buildup, despite that this signal peaks at only 2% of the total ligand signal. These buildup curves allow the confirmation of binding through a change in the sign of the NOE and the quantitative determination of cross-relaxation rates. The combination of the D-DNP technique and protein immobilization may facilitate the identification of intraligand NOEs in ligand screening for drug discovery. The same method may be applied to in vivo characterization of ligand interactions with cell surface proteins.

Determination of protein-ligand binding modes using fast multi-dimensional NMR with hyperpolarization

Elucidation of small molecule-protein interactions provides essential information for understanding biological processes such as cellular signaling, as well as for rational drug development. Here, multi-dimensional NMR with sensitivity enhancement by dissolution dynamic nuclear polarization (D-DNP) is shown to allow the determination of the binding epitope of folic acid when complexed with the target dihydrofolate reductase. Protein signals are selectively enhanced by polarization transfer from the hyperpolarized ligand. A pseudo three-dimensional data acquisition with ligand-side Hadamard encoding results in protein-side [13C, 1H] chemical shift correlations that contain intermolecular nuclear Overhauser effect (NOE) information. A scoring function based on this data is used to select pre-docked ligand poses. The top five poses are within 0.76 Å root-mean-square deviation from a reference structure for the encoded five protons, showing improvements compared with the poses selected by an energy-based scoring function without experimental inputs. The sensitivity enhancement provided by the D-DNP combined with multi-dimensional NMR increases the speed and potentially the selectivity of structure elucidation of ligand binding epitopes.

Determination of Ligand Binding Epitope Structures Using Polarization Transfer from Hyperpolarized Ligands

Drug discovery processes require the determination of the protein binding site structure, which can be achieved via nuclear magnetic resonance (NMR) spectroscopy. While traditional NMR spectroscopy suffers from low sensitivity, NMR signals can be significantly enhanced through hyperpolarization of nuclear spins. Here, folic acid is hyperpolarized by dissolution dynamic nuclear polarization (D-DNP). Polarization transfer to dihydrofolate reductase is compared to signal evolution predicted for docking-derived structures. The results demonstrate that a scoring function derived from the experimental data improves the ranking of structures. With data from six methyl groups, Spearman's correlation coefficient of the experimental scoring function to the root-mean-square deviation from a reference structure is 0.88 for five individually addressed ligand protons and 0.59 for the entire ligand, while the same correlation coefficient of the energy calculated from docking alone is 0.49. D-DNP NMR-derived ranking, therefore, is capable of determining the ligand structure with a small number of individually addressed source spins.

Applications of Dissolution-DNP for NMR Screening

Experimental screening for protein-ligand interactions is a central task in drug discovery. Nuclear magnetic resonance (NMR) spectroscopy enables the determination of binding affinities, as well as the measurement of structural and dynamic parameters governing the interaction. With traditional liquid-state NMR relying on a nuclear spin polarization on the order of 10-5, hyperpolarization methods such as dissolution dynamic nuclear polarization (D-DNP) can increase signals by several orders of magnitude. The resulting increase in sensitivity has the potential to reduce requirements for the concentration of protein and ligands, improve the accuracy of the detection of interaction by allowing the use of near-stoichiometric conditions, and increase throughput. This chapter introduces a selection of basic techniques for the application of D-DNP to screening. Procedures for hyperpolarization are briefly reviewed, followed by the description of NMR methods for detection of binding through changes in chemical shift and relaxation parameters. Experiments employing competitive binding with a known ligand are shown, which can be used to determine binding affinity or yield structural information on the pharmacophore. The specific challenges of working with nonrenewable hyperpolarization are reviewed, and solutions including the use of multiplexed NMR detection are described. Altogether, the methods summarized in this chapter are intended to allow for the efficient detection of binding affinity, structure, and dynamics facilitated through substantial signal enhancements provided by hyperpolarization.

Applications of dissolution dynamic nuclear polarization in chemistry and biochemistry

Sensitivity of detection is one of the most limiting aspects when applying NMR spectroscopy to current problems in the molecular sciences. A number of hyperpolarization methods exist for increasing the population difference between nuclear spin Zeeman states and enhance the signal-to-noise ratio by orders of magnitude. Among these methods, dissolution dynamic nuclear polarization (D-DNP) is unique in its capability of providing high spin polarization for many types of molecules in the liquid state. Originally proposed for biomedical applications including in vivo imaging, applications in high resolution NMR spectroscopy are now emerging. These applications are the focus of the present review. Using D-DNP, a small sample aliquot is first hyperpolarized as a frozen solid at low temperature, followed by dissolution into the liquid state. D-DNP extends the capabilities of liquid state NMR spectroscopy towards shorter timescales and enables the study of nonequilibrium processes, such as the kinetics and mechanisms of reactions. It allows the determination of intermolecular interactions, in particular based on spin relaxation parameters. At the same time, a challenge in the application of this hyperpolarization method is that spin polarization is nonrenewable. Substantial effort has been devoted to develop methods for enabling rapid correlation spectroscopy, the measurement of time-dependent signals, and the extension of the observable time window. With these methods, D-DNP has the potential to open new application areas in the chemical and biochemical sciences.

Intermolecular interactions determined by NOE build-up in macromolecules from hyperpolarized small molecules

The nuclear Overhauser effect (NOE) is a primary means to characterize intermolecular interactions using modern NMR spectroscopy. Multiple experiments measured using different mixing time can be used for quantifying NOE buildup and measuring cross-relaxation rates. However, this approach using conventional multi-dimensional NMR is time consuming. Hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) can generate deviations from equilibrium spin polarization by orders of magnitude, thereby enhancing signals and allowing to characterize NOE build up in real-time. Since most small molecules can be hyperpolarized using D-DNP, this method is applicable to the study of intermolecular interactions between small molecules and macromolecules. This application is demonstrated using a model system for host-guest interactions including the third generation polyamidoamine dendrimer (G3 PAMAM) and the pharmaceutical phenylbutazone (PBZ). After mixing ¹H hyperpolarized PBZ with PAMAM, the NOE build up is directly observed at different sites of the dendrimer in series of one-dimensional NMR spectra. Cross-relaxation rates specific to individual source and target spins are determined from the build up curves. Further, the polarization enhancement is shown to be sufficiently large to allow identification of cross-peaks not observed in a conventional 2D-NOESY spectrum. The improved signal-to-noise ratio provided by hyperpolarization allows for characterizing the intermolecular interaction in an almost instantaneous measurement, opening an application to macromolecular and biomacromolecular NMR.

In-Vitro Dissolution Dynamic Nuclear Polarization for Sensitivity Enhancement of NMR with Biological Molecules

Dissolution dynamic nuclear polarization (D-DNP) is a technique to prepare hyperpolarized nuclear spin states, yielding a signal enhancement of several orders of magnitude for liquid-state NMR. Here, we describe experimental procedures for the application of D-DNP in high-resolution NMR of biochemical compounds, to determine the time evolution of biochemical processes and intermolecular interactions.

Modeling of Polarization Transfer Kinetics in Protein Hydration Using Hyperpolarized Water

Water-protein interactions play a central role in protein structure, dynamics, and function. These interactions, traditionally, have been studied using nuclear magnetic resonance (NMR) by measuring chemical exchange and nuclear Overhauser effect (NOE). Polarization transferred from hyperpolarized water can result in substantial transient signal enhancements of protein resonances due to these processes. Here, we use dissolution dynamic nuclear polarization and flow-NMR for measuring the pH dependence of transferred signals to the protein trypsin. A maximum enhancement of 20 is visible in the amide proton region of the spectrum at pH 6.0, and of 47 at pH 7.5. The aliphatic region is enhanced up to 2.3 times at pH 6.0 and up to 2.5 times at pH 7.5. The time dependence of these observed signals can be modeled quantitatively using rate equations incorporating chemical exchange to amide sites and, optionally, intramolecular NOE to aliphatic protons. On the basis of these two- and three-site models, average exchange (k_ex) and cross-relaxation rates (σ) obtained were k_ex = 12 s^-1, σ = -0.33 s^-1 for pH 7.5 and k_ex = 1.8 s^-1, σ = -0.72 s^-1 for pH 6.0 at a temperature of 304 K. These values were validated using conventional EXSY and NOESY measurements. In general, a rapid measurement of exchange and cross-relaxation rates may be of interest for the study of structural changes of the protein occurring on the same time scale. Besides protein-water interactions, interactions with cosolvent or solutes can further be investigated using the same methods.