Comprehensive and High-Throughput Exploration of Chemical Space Using Broadband 19 F NMR-Based Screening

Optimal control pulses for the 1.2-GHz (28.2-T) NMR spectrometers

The ability to measure nuclear magnetic resonance (NMR) spectra with a large sample volume is crucial for concentration-limited biological samples to attain adequate signal-to-noise (S/N) ratio. The possibility to measure with a 5-mm cryoprobe is currently absent at the 1.2-GHz NMR instruments due to the exceedingly high radio frequency power demands, which is four times compared to 600-MHz instruments. Here, we overcome the high-power demands by designing optimal control (OC) pulses with up to 20 times lower power requirements than currently necessary at a 1.2-GHz spectrometer. We show that multidimensional biomolecular NMR experiments constructed using these OC pulses can bestow improvement in the S/N ratio of up to 26%. With the expected power limitations of a 5-mm cryoprobe, we observe an enhancement in the S/N ratio of more than 240% using our OC sequences. This motivates the development of a cryoprobe with a larger volume than the current 3-mm cryoprobes.

Discovery of a selective and biologically active low-molecular weight antagonist of human interleukin-1β

Human interleukin-1β (hIL-1β) is a pro-inflammatory cytokine involved in many diseases. While hIL-1β directed antibodies have shown clinical benefit, an orally available low-molecular weight antagonist is still elusive, limiting the applications of hIL-1β-directed therapies. Here we describe the discovery of a low-molecular weight hIL-1β antagonist that blocks the interaction with the IL-1R1 receptor. Starting from a low affinity fragment-based screening hit 1, structure-based optimization resulted in a compound (S)-2 that binds and antagonizes hIL-1β with single-digit micromolar activity in biophysical, biochemical, and cellular assays. X-ray analysis reveals an allosteric mode of action that involves a hitherto unknown binding site in hIL-1β encompassing two loops involved in hIL-1R1/hIL-1β interactions. We show that residues of this binding site are part of a conformationally excited state of the mature cytokine. The compound antagonizes hIL-1β function in cells, including primary human fibroblasts, demonstrating the relevance of this discovery for future development of hIL-1β directed therapeutics.

Fragment-based drug discovery supports drugging 'undruggable' protein-protein interactions

Protein-protein interactions (PPIs) have important roles in various cellular processes, but are commonly described as 'undruggable' therapeutic targets due to their large, flat, featureless interfaces. Fragment-based drug discovery (FBDD) has achieved great success in modulating PPIs, with more than ten compounds in clinical trials. Here, we highlight the progress of FBDD in modulating PPIs for therapeutic development. Targeting hot spots that have essential roles in both fragment binding and PPIs provides a shortcut for the development of PPI modulators via FBDD. We highlight successful cases of cracking the 'undruggable' problems of PPIs using fragment-based approaches. We also introduce new technologies and future trends. Thus, we hope that this review will provide useful guidance for drug discovery targeting PPIs.

Tools shaping drug discovery and development

Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.

TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules

Chaperones tapasin and transporter associated with antigen processing (TAP)-binding protein related (TAPBPR) associate with the major histocompatibility complex (MHC)-related protein 1 (MR1) to promote trafficking and cell surface expression. However, the binding mechanism and ligand dependency of MR1/chaperone interactions remain incompletely characterized. Here in vitro, biochemical and computational studies reveal that, unlike MHC-I, TAPBPR recognizes MR1 in a ligand-independent manner owing to the absence of major structural changes in the MR1 α2-1 helix between empty and ligand-loaded molecules. Structural characterization using paramagnetic nuclear magnetic resonance experiments combined with restrained molecular dynamics simulations reveals that TAPBPR engages conserved surfaces on MR1 to induce similar adaptations to those seen in MHC-I/TAPBPR co-crystal structures. Finally, nuclear magnetic resonance relaxation dispersion experiments using 19F-labeled diclofenac show that TAPBPR can affect the exchange kinetics of noncovalent metabolites with the MR1 groove, serving as a catalyst. Our results support a role of chaperones in stabilizing nascent MR1 molecules to enable loading of endogenous or exogenous cargo.

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.

SORDOR pulses: expansion of the Böhlen-Bodenhausen scheme for low-power broadband magnetic resonance

A novel type of efficient broadband pulse, called second-order phase dispersion by optimised rotation (SORDOR), has recently been introduced. In contrast to adiabatic excitation, SORDOR-90 pulses provide effective transverse 90∘ rotations throughout their bandwidth, with a quadratic offset dependence of the phase in the x , y plane. Together with phase-matched SORDOR-180 pulses, this enables the Böhlen-Bodenhausen broadband refocusing approach for linearly frequency-swept pulses to be extended to any type of 90∘ /180∘ pulse-delay sequence. Example pulse shapes are characterised in theory and experiment, and an example application is given with a 19 F -PROJECT experiment for measuring relaxation times with reduced distortions due to J -coupling evolution.

Practical Considerations and Guidelines for Spectral Referencing for Fluorine NMR Ligand Screening

Fluorine (¹⁹F) NMR strategies are increasingly being employed for evaluating ligand binding to macromolecules, among many other uses. ¹⁹F NMR offers many advantages as a result of its sensitive spin 1/2 nucleus, 100% natural abundance, and wide chemical shift range. Moreover, because of its absence from biological samples, one can directly monitor ligand binding without background interference from the macromolecule. Therefore, all these aforementioned features make it an attractive approach for screening compounds. However, the detection of ligand binding, especially those with weak affinities, can require interpretations of minor changes in chemical shifts. Thus, chemical shift referencing is critical for accurate measurements and interpretations. Unfortunately, one cannot rely on spectrometer indirect referencing alone, and internal chemical references have sample-dependent issues. Here, we evaluated 10 potential candidate compounds that could serve as ¹⁹F NMR chemical references. Multiple factors were systematically evaluated for each candidate to monitor the suitability for ¹⁹F NMR screening purposes. These factors include aqueous solubility, buffer compatibility, salt compatibility, aqueous stability, tolerability to pH changes, temperature changes, and compound pooling. It was concluded that there was no ideal candidate, but five compounds had properties that met the screening requirements.

Improved design of frequency-swept pulse sequences

Frequency-swept pulses are extensively used in magnetic resonance spectroscopic techniques for the robust manipulation of spins across wide ranges of offset frequencies in the presence of B₁ field variations. Nevertheless, designing pulse sequences consisting of multiple frequency-swept pulses can be challenging, as they often require specific timings and parameter tweaking. In the present work we discuss a simple and general approach for constructing such sequences. We present new and improved pulse sequences for applications including broadband B₁-tolerant CPMG (CHORUS-CPMG), broadband chirped excitation with suppression of homonuclear J-modulation (PROCHORUS), and the further compression of frequency-swept pulse sequences by superposition of pulses which reduces pulse sequence durations by 25-40%. All sequence design strategies are accompanied by mathematical presentations, experimental results, and supporting simulations.

Concurrent J-evolving refocusing pulses

Conventional refocusing pulses are optimised for a single spin without considering any type of coupling. However, despite the fact that most couplings will result in undesired distortions, refocusing in delay-pulse-delay-type sequences with desired heteronuclear coherence transfer might be enhanced considerably by including coupling evolution into pulse design. We provide a proof of principle study for a Hydrogen-Carbon refocusing pulse sandwich with inherent J-evolution following the previously reported ICEBERG-principle with improved performance in terms of refocusing performance and/or overall effective coherence transfer time. Pulses are optimised using optimal control theory with a newly derived quality factor and z-controls as an efficient tool to speed up calculations. Pulses are characterised in theory and experiment and compared to conventional concurrent refocusing pulses, clearly showing an improvement for the J-evolving pulse sandwich. As a side-product, also efficient J-compensated resfocusing pulse sandwiches - termed BUBU pulses following the nomenclature of previous J-compensated BUBI and BEBE^tr pulse sandwiches - have been optimised.

Fragment-to-Lead Medicinal Chemistry Publications in 2020

Fragment-based drug discovery (FBDD) continues to evolve and make an impact in the pharmaceutical sciences. We summarize successful fragment-to-lead studies that were published in 2020. Having systematically analyzed annual scientific outputs since 2015, we discuss trends and best practices in terms of fragment libraries, target proteins, screening technologies, hit-optimization strategies, and the properties of hit fragments and the leads resulting from them. As well as the tabulated Fragment-to-Lead (F2L) programs, our 2020 literature review identifies several trends and innovations that promise to further increase the success of FBDD. These include developing structurally novel screening fragments, improving fragment-screening technologies, using new computer-aided design and virtual screening approaches, and combining FBDD with other innovative drug-discovery technologies.

Synergistic Lewis acid and Pd active sites of metal–organic frameworks for highly efficient carbonylation of methyl nitrite to dimethyl carbonate

We for the first time systematically investigated a MOF UiO-66 based catalyst showing the synergistic effect of Lewis acid sites and Pd(ii) for highly efficient methyl nitrite (MN) carbonylation to dimethyl carbonate (DMC).

Visible light-mediated radical fluoromethylation via halogen atom transfer activation of fluoroiodomethane

Incorporation of the fluoromethyl group can profoundly influence the physicochemical properties of organic molecules, offering a promising strategy for the discovery of novel pharmaceutical agents. Direct fluoromethylation of unfunctionalized C(sp2) centres can be achieved using fluoromethyl radicals, but current methods for their generation usually rely on the activation of non-commercial or expensive radical precursors via inefficient single electron transfer pathways, which limits their synthetic application. Here we report the development of a fluoromethylation strategy based on the generation of fluoromethyl radicals from commercially available fluoroiodomethane via halogen atom transfer. This mode of activation is orchestrated by visible light and tris(trimethylsilyl)silane, which serves as both a hydrogen- and halogen atom transfer reagent to facilitate the formation of C(sp3)-CH2F bonds via a radical chain process. The utility of this metal- and photocatalyst-free transformation is demonstrated through the multicomponent synthesis of complex α-fluoromethyl amines and amino acid derivatives via radical addition to in situ-formed iminium ions, and the construction of β-fluoromethyl esters and amides from electron-deficient alkene acceptors. These complex fluoromethylated products, many of which are inaccessible via previously reported methods, may serve as useful building blocks or fragments in synthetic and medicinal chemistry both in academia and industry.

Heteropore covalent organic framework-based composite membrane prepared by in situ growth on non-woven fabric for sample pretreatment of food non-targeted analysis

A heteropore covalent organic framework (COF)-based composite membrane material was prepared and proved to have a satisfactory effect on the pretreatment of vegetable samples. The composite membrane was fabricated by in situ growth of a dual-pore COF on the surface of polydopamine (PDA)-aminated non-woven (NW) fabric. Due to the difference in the strength of the interaction between the phytochromes/COF and the pesticides/COF, the removal of phytochromes and the recovery of pesticides can be achieved by adjusting the composition of the solution. Through a simple immersion or filtration operation, NW@PDA@COF composite membrane can quickly and almost completely remove interfering phytochromes in the samples. The recovery of pesticides was determined by HPLC-MS/MS, and the recovery efficiencies were 72.3~101.7% and 67.3~106.7% for immersion and filtration modes of five different vegetable samples, respectively; the RSD is between 1.1 and 19% (n = 3). The limits of detection and quantification for the 13 pesticides investigated were 0.08 μg·L^-1 and 0.23 μg·L^-1, respectively. A wide linear range of 1~1000 μg·L^-1 was observed with R² values from 0.9774 to 0.9998. The membrane can be repeatedly used for at least 10 times by using a facile elution treatment. Compared to other commonly used sample pretreatment materials, heteropore COF-based composite membrane is superior in terms of sorbent amount, treatment time, operation simplicity, and material reusability.

Hydrogen Bond Acceptor Propensity of Different Fluorine Atom Types: An Analysis of Experimentally and Computationally Derived Parameters

The propensity of organic fluorine acting as a weak hydrogen bond acceptor (HBA) in intermolecular and intramolecular interactions has been the subject of many experimental and theoretical studies often reaching different conclusions. Over the last few years, new and stronger evidences have emerged for the direct involvement of fluorine in weak hydrogen bond (HB) formation. However, not all the fluorine atom types can act as weak HBA. In this work, the differential HBA propensity of various types of fluorine atoms was analyzed with a particular emphasis for the different types of alkyl fluorides. This was carried out by evaluating ab initio computed parameters, experimental ¹⁹ F NMR chemical shifts and small molecule crystallographic structures (extracted from the CSD database). According to this analysis, shielded (with reference to the ¹⁹ F NMR chemical shift) alkyl mono-fluorinated motifs display the highest HBA propensity in agreement with solution studies. Although much weaker than other well-characterized HB complexes, the fragile HBs formed by these fluorinated motifs have important implications for the chemical-physical and structural properties of the molecules, chemical reactions, and protein-ligand recognition.

Optimization of phase dispersion enables broadband excitation without homonuclear coupling artifacts

In NMR spectroscopy, many specialized shaped pulses are available for broadband excitation, beyond the bandwidth of conventional high-powered hard pulses. These shaped pulses typically have long duration. However, long-duration pulses are unsuitable for spectra containing significant homonuclear couplings, such as polyfluorinated compounds in 19F NMR. J-coupling evolution during the excitation pulse leads to spectral artifacts and incorrect peak integrals. Here, we report an approach to optimal control pulse design which significantly reduces the pulse length required to excite large bandwidths of chemical shift frequencies. The target state phase is not chosen beforehand but is instead only constrained to be linearly dependent on offset frequency. The first-order phase of the target state is then treated as a free-variable, to be optimized at the same time as the RF waveform itself. The resulting spectra are easily phased using standard NMR processing software. We observe that the required pulse length is significantly shorter than for currently available in-phase excitation schemes. Spectral artifacts from homonuclear couplings are avoided. We also demonstrate that pure in-phase excitation can be obtained over the same bandwidth by appending two inversion pulses, at the expense of increased overall duration.

Application of Fragment-Based Drug Discovery to Versatile Targets

Fragment-based drug discovery (FBDD) is a powerful method to develop potent small-molecule compounds starting from fragments binding weakly to targets. As FBDD exhibits several advantages over high-throughput screening campaigns, it becomes an attractive strategy in target-based drug discovery. Many potent compounds/inhibitors of diverse targets have been developed using this approach. Methods used in fragment screening and understanding fragment-binding modes are critical in FBDD. This review elucidates fragment libraries, methods utilized in fragment identification/confirmation, strategies applied in growing the identified fragments into drug-like lead compounds, and applications of FBDD to different targets. As FBDD can be readily carried out through different biophysical and computer-based methods, it will play more important roles in drug discovery.

A Practical Perspective on the Roles of Solution NMR Spectroscopy in Drug Discovery

Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to study structures and dynamics of biomolecules under physiological conditions. As there are numerous NMR-derived methods applicable to probe protein–ligand interactions, NMR has been widely utilized in drug discovery, especially in such steps as hit identification and lead optimization. NMR is frequently used to locate ligand-binding sites on a target protein and to determine ligand binding modes. NMR spectroscopy is also a unique tool in fragment-based drug design (FBDD), as it is able to investigate target-ligand interactions with diverse binding affinities. NMR spectroscopy is able to identify fragments that bind weakly to a target, making it valuable for identifying hits targeting undruggable sites. In this review, we summarize the roles of solution NMR spectroscopy in drug discovery. We describe some methods that are used in identifying fragments, understanding the mechanism of action for a ligand, and monitoring the conformational changes of a target induced by ligand binding. A number of studies have proven that ¹⁹F-NMR is very powerful in screening fragments and detecting protein conformational changes. In-cell NMR will also play important roles in drug discovery by elucidating protein-ligand interactions in living cells.