Technical and practical aspects of (19) F NMR-based screening: toward sensitive high-throughput screening with rapid deconvolution

Use of Diethanolamine as a Viscous Solvent for Mixture Analysis by Multidimensional Heteronuclear ViscY NMR Experiments

Diethanolamine/DMSO-d₆ as a viscous binary solvent is first reported for the individualization of low-polarity mixture components by multidimensional heteronuclear ViscY NMR experiments under spin diffusion conditions. Solvent viscosity induces the slowing down of molecular tumbling, hence promoting magnetization transfer by dipolar longitudinal cross-relaxation. As a result, all ¹H nuclei resonances within the same molecule may correlate in a 2D nuclear Overhauser effect spectroscopy (NOESY) spectrum, giving access to mixture analysis. We offer a new way to analyze mixtures by considering 3D heteronuclear heteronuclear single-quantum coherence-NOESY (HSQC-NOESY) experiments under viscous conditions. We state the individualization of four low-polarity chemical compounds dissolved in the diethanolamine/DMSO-d₆ solvent blend using homonuclear selective 1D, 2D ¹H-¹H NOESY experiments and heteronuclear 1D, 2D ¹H-¹⁹F heteronuclear Overhauser effect spectroscopy, 2D ¹H-¹⁹F, ¹H-³¹P HSQC-NOESY, and 3D ¹H-¹⁹F-¹H, ¹H-³¹P-¹H HSQC-NOESY experiments by taking profit from spin diffusion.

Efficient Screening of Target-Specific Selected Compounds in Mixtures by 19F NMR Binding Assay with Predicted 19F NMR Chemical Shifts

Ligand-based 19 F NMR screening is a highly effective and well-established hit-finding approach. The high sensitivity to protein binding makes it particularly suitable for fragment screening. Different criteria can be considered for generating fluorinated fragment libraries. One common strategy is to assemble a large, diverse, well-designed and characterized fragment library which is screened in mixtures, generated based on experimental 19 F NMR chemical shifts. Here, we introduce a complementary knowledge-based 19 F NMR screening approach, named 19 Focused screening, enabling the efficient screening of putative active molecules selected by computational hit finding methodologies, in mixtures assembled and on-the-fly deconvoluted based on predicted 19 F NMR chemical shifts. In this study, we developed a novel approach, named LEFshift , for 19 F NMR chemical shift prediction using rooted topological fluorine torsion fingerprints in combination with a random forest machine learning method. A demonstration of this approach to a real test case is reported.

19F NMR viewed through two different lenses: ligand-observed and protein-observed 19F NMR applications for fragment-based drug discovery

19F NMR has emerged as a powerful tool in drug discovery, particularly in fragment-based screens. The favorable magnetic resonance properties of the fluorine-19 nucleus, the general absence of fluorine in biological settings, and its ready incorporation into both small molecules and biopolymers, has enabled multiple applications of 19F NMR using labeled small molecules and proteins in biophysical, biochemical, and cellular experiments. This review will cover developments in ligand-observed and protein-observed 19F NMR experiments tailored towards drug discovery with a focus on fragment screening. We also cover the key advances that have furthered the field in recent years, including quantitative, structural, and in-cell methodologies. Several case studies are described for each application to highlight areas for innovation and to further catalyze new NMR developments for using this versatile nucleus.

NMR Reporter Assays for the Quantification of Weak-Affinity Receptor-Ligand Interactions

Biophysical methods are widely employed in academia and the pharmaceutical industry to detect and quantify weak molecular interactions. Such methods find broad application in fragment-based drug discovery (FBDD). In an FBDD campaign, a suitable affinity determination method is key to advancing a project beyond the initial screening phase. Protein-observed (PO) nuclear magnetic resonance (NMR) finds widespread use due to its ability to sensitively detect very weak interactions at residue-level resolution. When there are issues precluding the use of PO-NMR, ligand-observed (LO) NMR reporter assays can be a useful alternative. Such assays can measure affinities in a similar range to PO-NMR while offering some distinct advantages, especially with regard to protein consumption and compound throughput. In this paper, we take a closer look at setting up such assays for routine use, with the aim of getting high-quality, accurate data and good throughput. We assess some of the key characteristics of these assays in the mathematical framework established for fluorescence polarization assays with which the readers may be more familiar. We also provide guidance on setting up such assays and compare their performance with other affinity determination methods that are commonly used in drug discovery.

Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation

The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between ¹H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).

Amyloid binding and beyond: a new approach for Alzheimer's disease drug discovery targeting Aβo-PrPC binding and downstream pathways

Amyloid β oligomers (Aβo) are the main toxic species in Alzheimer's disease, which have been targeted for single drug treatment with very little success. In this work we report a new approach for identifying functional Aβo binding compounds. A tailored library of 971 fluorine containing compounds was selected by a computational method, developed to generate molecular diversity. These compounds were screened for Aβo binding by a combined 19F and STD NMR technique. Six hits were evaluated in three parallel biochemical and functional assays. Two compounds disrupted Aβo binding to its receptor PrPC in HEK293 cells. They reduced the pFyn levels triggered by Aβo treatment in neuroprogenitor cells derived from human induced pluripotent stem cells (hiPSC). Inhibitory effects on pTau production in cortical neurons derived from hiPSC were also observed. These drug-like compounds connect three of the pillars in Alzheimer's disease pathology, i.e. prion, Aβ and Tau, affecting three different pathways through specific binding to Aβo and are, indeed, promising candidates for further development.

Applications of Solution NMR in Drug Discovery

During the past decades, solution nuclear magnetic resonance (NMR) spectroscopy has demonstrated itself as a promising tool in drug discovery. Especially, fragment-based drug discovery (FBDD) has benefited a lot from the NMR development. Multiple candidate compounds and FDA-approved drugs derived from FBDD have been developed with the assistance of NMR techniques. NMR has broad applications in different stages of the FBDD process, which includes fragment library construction, hit generation and validation, hit-to-lead optimization and working mechanism elucidation, etc. In this manuscript, we reviewed the current progresses of NMR applications in fragment-based drug discovery, which were illustrated by multiple reported cases. Moreover, the NMR applications in protein-protein interaction (PPI) modulators development and the progress of in-cell NMR for drug discovery were also briefly summarized.

CcpNmr AnalysisScreen, a new software programme with dedicated automated analysis tools for fragment-based drug discovery by NMR

Fragment-based drug discovery or FBDD is one of the main methods used by industry and academia for identifying drug-like candidates in early stages of drug discovery. NMR has a significant impact at any stage of the drug discovery process, from primary identification of small molecules to the elucidation of binding modes for guiding optimisations. The essence of NMR as an analytical tool, however, requires the processing and analysis of relatively large amounts of single data items, e.g. spectra, which can be daunting when managed manually. One bottleneck in FBDD by NMR is a lack of adequate and well-integrated resources for NMR data analysis that are freely available to the community. Thus, scientists typically resort to manually inspecting large datasets and relying predominantly on subjective interpretations. In this manuscript, we present CcpNmr AnalysisScreen, a software package that provides computational tools for automated analysis of FBDD data by NMR. We outline how the quality of collected spectra can be evaluated quickly, and how robust workflows can be optimised for reliable and rapid hit identification. With an intuitive graphical user interface and powerful algorithms, AnalysisScreen enables easy analysis of the large datasets needed in the early process of drug discovery by NMR.

Fluorine NMR functional screening: from purified enzymes to human intact living cells

The substrate- or cofactor-based fluorine NMR screening, also known as n-FABS (n fluorine atoms for biochemical screening), represents a powerful method for performing a direct functional assay in the search of inhibitors or enhancers of an enzymatic reaction. Although it suffers from the intrinsic low sensitivity compared to other biophysical techniques usually applied in functional assays, it has some distinctive features that makes it appealing for tackling complex chemical and biological systems. Its strengths are represented by the easy set-up, robustness, flexibility, lack of signal interference and rich information content resulting in the identification of bona fide inhibitors and reliable determination of their inhibitory strength. The versatility of the n-FABS allows its application to either purified enzymes, cell lysates or intact living cells. The principles, along with theoretical, technical and practical aspects, of the methodology are discussed. Furthermore, several applications of the technique to pharmaceutical projects are presented.

Fragments: where are we now?

Fragment-based drug discovery (FBDD) has become a mainstream technology for the identification of chemical hit matter in drug discovery programs. To date, the food and drug administration has approved four drugs, and over forty compounds are in clinical studies that can trace their origins to a fragment-based screen. The challenges associated with implementing an FBDD approach are many and diverse, ranging from the library design to developing methods for identifying weak affinity compounds. In this article, we give an overview of current progress in fragment library design, fragment to lead optimisation and on the advancement in techniques used for screening. Finally, we will comment on the future opportunities and challenges in this field.

Enantiodiscrimination by matrix-assisted DOSY NMR

High-resolution NMR is an essential technique for structure determination; however, stereochemistry assignment is still an obstacle. Several methods are known to overcome this limitation but usually at high costs or using derivatizations. Here we describe the use of different solvating agents to virtually discriminate the enantiomers of 15 analytes using 1H and 19F-{1H} DOSY NMR.

Current NMR Techniques for Structure-Based Drug Discovery

A variety of nuclear magnetic resonance (NMR) applications have been developed for structure-based drug discovery (SBDD). NMR provides many advantages over other methods, such as the ability to directly observe chemical compounds and target biomolecules, and to be used for ligand-based and protein-based approaches. NMR can also provide important information about the interactions in a protein-ligand complex, such as structure, dynamics, and affinity, even when the interaction is too weak to be detected by ELISA or fluorescence resonance energy transfer (FRET)-based high-throughput screening (HTS) or to be crystalized. In this study, we reviewed current NMR techniques. We focused on recent progress in NMR measurement and sample preparation techniques that have expanded the potential of NMR-based SBDD, such as fluorine NMR (¹⁹F-NMR) screening, structure modeling of weak complexes, and site-specific isotope labeling of challenging targets.

Non-invasive 19F NMR analysis of a protein-templated N-acylhydrazone dynamic combinatorial library

Dynamic combinatorial chemistry (DCC) is a powerful tool to identify ligands for biological targets.

19F multiple-quantum coherence NMR spectroscopy for probing protein–ligand interactions

A new ¹⁹F NMR method is presented which can be used to detect weak protein binding of small molecules with up to mM affinity. The method capitalizes on the synthetic availability of unique SF₅ containing compounds and the generation of five-quantum coherences (5QC). Given the high sensitivity of 5QC relaxation to exchange events (i.e. reversible protein binding) fragments which bind to the target with weak affinity can be identified. The utility of the method in early stage drug discovery programs is demonstrated with applications to two model proteins, the neurotoxic NGAL and the prominent tumor target β-catenin.

An NMR experiment is presented that allows identification of weak binders typically found in early stages of drug discovery programs.

19 F DOSY diffusion-NMR spectroscopy of fluoropolymers

A new pulse sequence for obtaining ¹⁹ F detected DOSY (diffusion ordered spectroscopy) spectra of fluorinated molecules is presented and used to study fluoropolymers based on vinylidene fluoride and chlorotrifluoroethylene. The performance of ¹⁹ F DOSY NMR experiments (and in general any type of NMR experiment) on fluoropolymers creates some unique complications that very often prevent detection of important signals. Factors that create these complications include: (1) the presence of many scalar couplings among ¹ H, ¹⁹ F and ¹³ C; (2) the large magnitudes of many ¹⁹ F homonuclear couplings (especially ² J_FF ); (3) the large ¹⁹ F chemical shift range; and (4) the low solubility of these materials (which requires that experiments be performed at high temperatures). A systematic study of the various methods for collecting DOSY NMR data, and the adaptation of these methods to obtain ¹⁹ F detected DOSY data, has been performed using a mixture of low molecular weight, fluorinated model compounds. The best pulse sequences and optimal experimental conditions have been determined for obtaining ¹⁹ F DOSY spectra. The optimum pulse sequences for acquiring ¹⁹ F DOSY NMR data have been determined for various circumstances taking into account the spectral dispersion, number and magnitude of couplings present, and experimental temperature. Pulse sequences and experimental parameters for optimizing these experiments for the study of fluoropolymers have been studied. Copyright © 2016 John Wiley & Sons, Ltd.

19 F NMR matrix-assisted DOSY: a versatile tool for differentiating fluorinated species in mixtures

NMR is the most versatile tool for the analysis of organic compounds and, in combination with Diffusion-Ordered Spectroscopy ('DOSY'), can give information on compounds in complex mixtures without the need for physical separation. In mixtures where the components' diffusion coefficients are nearly identical, for example because of similar sizes, Matrix-Assisted DOSY ('MAD') can help separate the signals of different constituents, resolving their spectra. Unfortunately, DOSY (including MAD) typically fails where signals overlap, as is common in ¹ H NMR. Using ¹⁹ F NMR avoids such problems, because the great sensitivity of the ¹⁹ F chemical shift to local environment leads to very well-dispersed spectra. Another advantage is the absence of any ¹⁹ F background signals from the matrices typically used, avoiding interference with the analyte signals. In this study, differentiation among fluorophenol and fluoroaniline isomers was evaluated using normal and reverse micelles-of sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB) and dioctyl sodium sulfosuccinate (AOT)-as matrices. These surfactants provide useful diffusion separation in these difficult mixtures, with all the solutes interacting with the matrices to different extents, in some cases leading to differences in diffusion coefficient of more than 30%. The best matrices for separating the signals of both acid and basic species were shown to be AOT and CTAB, which are useful over a wide range of surfactant concentration. Copyright © 2016 John Wiley & Sons, Ltd.

19 F NMR transverse and longitudinal relaxation filter experiments for screening: a theoretical and experimental analysis

Ligand-based ¹⁹ F NMR screening represents an efficient approach for performing binding assays. The high sensitivity of the methodology to receptor binding allows the detection of weak affinity ligands. The observable NMR parameters that are typically used are the ¹⁹ F transverse relaxation rate and isotropic chemical shift. However, there are few cases where the ¹⁹ F longitudinal relaxation rate should also be used. A theoretical and experimental analysis of the ¹⁹ F NMR transverse and longitudinal relaxation rates at different magnetic fields is presented along with proposed methods for improving the sensitivity and dynamic range of these experiments applied to fragment-based screening. Copyright © 2016 John Wiley & Sons, Ltd.

¹⁹F NMR indicator displacement assay using a synthetic receptor with appended paramagnetic relaxation agent

An admixture of zinc(II)-bis(dipicolylamine) receptor with covalently attached paramagnetic relaxation agent and fluorine-labeled phosphate indicator enables (19)F NMR detection of phosphorylated analytes with amplified switched-on signal intensity.

NMR approaches in structure-based lead discovery: recent developments and new frontiers for targeting multi-protein complexes

Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information on protein structure, dynamics and interaction at an atomic level in solution. Nowadays, in most ligand screening cascades, NMR-based methods are applied to identify and structurally validate small molecule binding. These can be high-throughput and are often used synergistically with other biophysical assays. Here, we describe current state-of-the-art in the portfolio of available NMR-based experiments that are used to aid early-stage lead discovery. We then focus on multi-protein complexes as targets and how NMR spectroscopy allows studying of interactions within the high molecular weight assemblies that make up a vast fraction of the yet untargeted proteome. Finally, we give our perspective on how currently available methods could build an improved strategy for drug discovery against such challenging targets.

¹⁹F NMR fingerprints: identification of neutral organic compounds in a molecular container

Improved methods for quickly identifying neutral organic compounds and differentiation of analytes with similar chemical structures are widely needed. We report a new approach to effectively "fingerprint" neutral organic molecules by using (19)F NMR and molecular containers. The encapsulation of analytes induces characteristic up- or downfield shifts of (19)F resonances that can be used as multidimensional parameters to fingerprint each analyte. The strategy can be achieved either with an array of fluorinated receptors or by incorporating multiple nonequivalent fluorine atoms in a single receptor. Spatial proximity of the analyte to the (19)F is important to induce the most pronounced NMR shifts and is crucial in the differentiation of analytes with similar structures. This new scheme allows for the precise and simultaneous identification of multiple analytes in a complex mixture.

19F DOSY NMR analysis for spin systems with nJFF couplings

NMR is a powerful method for identification and quantification of drug components and contaminations. These problems present themselves as mixtures, and here, one of the most powerful tools is DOSY. DOSY works best when there is no spectral overlap between components, so drugs containing fluorine substituents are well-suited for DOSY analysis as (19)F spectra are typically very sparse. Here, we demonstrate the use of a modified (19)F DOSY experiment (on the basis of the Oneshot sequences) for various fluorinated benzenes. For compounds with significant (n) JFF coupling constants, as is common, the undesirable J-modulation can be efficiently suppressed using the Oneshot45 pulse sequence. This investigation highlights (19)F DOSY as a valuable and robust method for analysis of molecular systems containing fluorine atoms even where there are large fluorine-fluorine couplings.

NMR and molecular recognition. The application of ligand-based NMR methods to monitor molecular interactions

NMR allows the monitoring of molecular recognition processes in solution. Nowadays, a plethora of NMR methods are available to deduce the key features of the interaction from both the ligand or the receptor points of view.

Design and generation of highly diverse fluorinated fragment libraries and their efficient screening with improved (19) F NMR methodology

Fragment screening performed with (19) F NMR spectroscopy is becoming increasingly popular in drug discovery projects. With this approach, libraries of fluorinated fragments are first screened using the direct-mode format of the assay. The choice of fluorinated motifs present in the library is fundamental in order to ensure a large coverage of chemical space and local environment of fluorine (LEF). Mono- and poly-fluorinated fragments to be included in the libraries for screening are selected from both in-house and commercial collections, and those that are ad hoc designed and synthesized. Additional fluorinated motifs to be included in the libraries derive from the fragmentation of compounds in development and launched on the market, and compounds contained in other databases (such as Integrity, PDB and ChEMBL). Complex mixtures of highly diverse fluorine motifs can be rapidly screened and deconvoluted in the same NMR tube with a novel on the fly combined procedure for the identification of the active molecule(s). Issues and problems encountered in the design, generation and screening of diverse fragment libraries of fluorinated compounds with (19) F NMR spectroscopy are analyzed and technical solutions are provided to overcome them. The versatile screening methodology described here can be efficiently applied in laboratories with limited NMR setup and could potentially lead to the increasing role of (19) F NMR in the hit identification and lead optimization phases of drug discovery projects.

Fluorine detected 2D NMR experiments for the practical determination of size and sign of homonuclear F-F and heteronuclear C-F multiple bond J-coupling constants in multiple fluorinated compounds

The use of fluorine in molecules obtained from chemical synthesis has become increasingly important within the pharmaceutical and agricultural industry. NMR characterization of these compounds is of great value with respect to their structure elucidation, their screening in metabolomics investigations and binding studies. The favorable NMR properties of the fluorine nucleus make NMR with fluorine detection of great value in this respect. A suite of NMR 2D F-F- and F-C-correlation experiments with fluorine detection was applied to the assignment of resonances, (n)J(CF)- and (n)J(FF)-couplings as well as the determination of their size and sign. The utilization of this experiment suite was exemplarily demonstrated for a highly fluorinated vinyl alkyl ether. Especially F-C HSQC and J-scaled F-C HMBC experiments allowed determining the size of the J-couplings of this compound. The relative sign of its homo- and heteronuclear couplings was achieved by different combinations of 2D NMR experiments, including non-selective and F2-selective F-C XLOC, F2-selective F-C HMQC, and F-F COSY. The F2-one/two-site selective F-C XLOC versions were found highly useful, as they led to simplifications of the common E.COSY patterns and resulted in a higher confidence level of the assignment by using selective excitation. The combination of F2-one/two-site selective F-C XLOC experiments with a F2-one-site selective F-C HMQC experiment provided the signs of all (n)J(CF)- and (n)J(FF)-couplings in the vinyl moiety of the test compound. Other combinations of experiments were found useful as well for special purposes when focusing for example on homonuclear couplings a combination of F-F COSY-10 with a F2-one-site selective F-C HMQC could be used. The E.COSY patterns in the spectra demonstrated were analyzed by use of the spin-selective displacement vectors, and in case of the XLOC also by use of the DQ- and ZQ-displacement vectors. The variety of experiments presented shall contribute to facilitate the interpretation of F-C correlations as well as to open alternative pathways for the determination of size and signs of homo- and heteronuclear couplings of multiply fluorinated small molecules.

The interaction of fatty acid amide hydrolase (FAAH) inhibitors with an anandamide carrier protein using (19)F-NMR

It has been reported that the endocannabinoid anandamide (AEA) binds to a class of fatty acid-binding proteins and serum albumin which can serve as carrier proteins and potentiate the cellular uptake of AEA and its intracellular translocation. Here, we employed (19)F nuclear magnetic resonance spectroscopy to study the interactions of serum albumin with two inhibitors of fatty acid amide hydrolase (FAAH), the enzyme involved in the deactivation of anandamide. We found that, for both inhibitors AM5206 and AM5207, the primary binding site on serum albumin is drug site 1 located at subdomain IIA. Neither inhibitor binds to drug site 2. While AM5207 binds exclusively to drug site 1, AM5206 also interacts with other fatty acid-binding sites on serum albumin. Additionally, AM5206 has an affinity for serum albumin approximately one order of magnitude higher than that of AM5207. The data suggest that interactions of FAAH inhibitors with albumin may provide added advantages for their ability to modulate endocannabinoid levels for a range of applications including analgesia, antiemesis, and neuroprotection.