Challenges in Leveraging Functional Information to Evaluate Predicted Protein-Ligand Interactions
Explore the source record for details and available documents.
SEARCH · Search NASA
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Explore the source record for details and available documents.
Near-infrared (NIR) luminescent materials are pivotal for advanced optoelectronic and biomedical applications, yet attaining efficient emission in the NIR-II region (950-1400 nm) remains challenging. Here, we introduce a ligand cationization strategy for designing copper(i) iodide-organic hybrid materials that emit in the NIR-II region (920-1120 nm) with PLQYs up to 8.58%. By incorporating rigid cationic ligands with CuI modules, we synergistically achieve bandgap narrowing (to 1.51 eV) and structural rigidification via ionic-dative bonding, effectively suppressing non-radiative decay while extending emission beyond 1100 nm. Coupled with solution processability-enabled by the successful synthesis of nanometer-sized nanoparticles in various shapes-and excellent thermal stability (≥210 °C), this work establishes ligand cationization as a universal approach for designing efficient NIR-II emitters.
Facile sintering of atomically dispersed supported noble metal catalysts at catalytically relevant temperatures, particularly under reducing conditions, poses a challenge for their practical applications. Some ligands, such as carbonyls, aid in improving the stability at the expense of severely suppressing the catalytic activity. In this work, we demonstrate that substitution of the carbonyl ligands with reactive acetylene ligands can maintain the atomic dispersion of the supported mononuclear rhodium complex under harsh reducing conditions (>573 K), as confirmed by in-situ X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopies. In contrast, the supported rhodium carbonyl complex aggregates into nanoclusters under identical conditions. Furthermore, our results indicate that the acetylene ligands provide this anti-sintering ability while retaining the hydrogenation activity.
Tetraphenylethene-based ligands with lowered symmetry are promising building blocks for the construction of novel luminescent metal–organic frameworks (MOFs). However, few examples have been reported, and predicting the ligand conformation and the dimensionality of the resulting MOF remains challenging. In order to uncover how synthetic conditions and accessible ligand conformations may affect the resulting MOF structure, four new MOF structures were synthesized under solvothermal conditions using the meta-coordinated tetraphenylethene-based ligand m-ETTC and paddlewheel SBUs composed of Co(II), Cu(II), and Zn(II). WSU-10 (WSU = Washington State University) is formed with either Zn or Cu comprising stacked psuedo-2D layers. The dimensionality of WSU-10 can be intentionally increased through the addition of pyrazine as a pillar ligand into the synthesis, forming the 3D structure WSU-11. The third structure, WSU-20, is formed by the combination of Zn or Co with m-ETTC and is intrinsically 3D without the use of a pillar ligand; interestingly, this is the result of a distortion in the paddlewheel SBU. Finally, Cu was also found to form a new structure (WSU-12), which displays an m-ETTC conformation unique from that found in the other isolated MOFs. Structural features are compared across the series and a mechanistic relationship between WSU-10 and -20 is proposed, providing insight into the factors that can encourage the generation of frameworks with increased dimensionality.
Two atomic layer etching (ALE) methods were studied for crystalline GaN, based on oxidation, fluorination, and ligand exchange. Etching was performed on unintentionally doped GaN grown by hydride vapor phase epitaxy. For the first step, the GaN surfaces were oxidized using either water vapor or remote O 2 -plasma exposure to produce a thin oxide layer. Removal of the surface oxide was addressed using alternating exposures of hydrogen fluoride (HF) and trimethylgallium (TMG) via fluorination and ligand exchange, respectively. Several HF and TMG super cycles were implemented to remove the surface oxide. Each ALE process was monitored in situ using multiwavelength ellipsometry. X-ray photoelectron spectroscopy was employed for the characterization of surface composition and impurity states. Additionally, the thermal and plasma-enhanced ALE methods were performed on patterned wafers and transmission electron microscopy (TEM) was used to measure the surface change. The x-ray photoelectron spectroscopy measurements indicated that F and O impurities remained on etched surfaces for both ALE processes. Ellipsometry indicated a slight reduction in thickness. TEM indicated a removal rate that was less than predicted. In conclusion, we suggest that the etch rates were reduced due to the ordered structure of the oxide formed on crystalline GaN surfaces.
Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.
Extractive diglycolamide (DGA) resins are used in several state-of-the-art techniques for purifying 225 Ac, a promising radiometal for targeted alpha therapy. Unfortunately, separation processes that rely on resins are often limited to slow flow rates, high elution volumes, and long processing times. Membrane adsorbers functionalized with DGA ligands are an alternative separation material that may overcome these challenges. This work presents (1) the synthesis of an aminated tetrahexyldiglycolamide ligand, (2) the covalent tethering of the ligand to electrospun poly(vinylbenzyl chloride) fiber mats, and (3) the adsorption and desorption of La(III) and 225 Ac. Chemical and physical characterization supports the covalent tethering of the ligand to the fiber mat, as well as the preservation of the fiber surface area and porosity after functionalization. Equilibrium adsorption experiments were performed with stable La(III) and radioactive 225 Ac. Trends in affinity are consistent between commercial resins and the synthesized membrane adsorbers; however, the Langmuir constants and the maximum binding capacity of the membrane adsorbers were generally lower than the resins. Despite these differences, the modeled selectivity for an equimolar solution of La(III)/ 225 Ac in 10 M nitric acid is 57. Furthermore, 225 Ac is rapidly desorbed from the fibers in 10 M nitric acid (<20 min). The La(III)/ 225 Ac selectivity and rapid 225 Ac desorption indicate this class of materials is promising for rapid radioanalytical separations.
Achieving stable, selective single-atom catalysts is challenging because localsurface-site structures are difficult to control. Surface organometallic chemistry and organic−inorganic hybrid materials offer partial solutions, but applications to supporting zero-valent metals are limited. We demonstrate that well-defined, ionically bound N-heterocyclic phosphenium ([NHP] + ) ligands can be generated on silylium-functionalized sulfated zirconia ([ i Pr 3 Si][SZO]). These surface-bound [NHP][SZO] ligands coordinate Pt(0) centers, forming [(NHP)Pt(0)L][SZO] precatalysts that are highly active for alkyne hydrosilylation. Systematic studies reveal that sterically bulky aromatic ligands enhance regioselectivity, achieving performances comparable to molecular Pt catalysts. Further, more-coordinating anions support more-regioselective precatalysts; therefore, SZO supports more-selective species than weaker-coordinating Al(OC(CF 3 ) 3 ) 3 - functionalized silica, a trend confirmed by molecular analogues. These results demonstrate that both the ligand and support control catalytic behavior and enable solid-state structure− activity relationships.
Investigation of Uranyl Perchlorate Anion Complexes in the Gas Phase via Infrared Multiphoton Dissociation and Collision Induced Dissociation Brittany D. M. Hodges, Christopher A. Zarzana, JungSoo Kim, Jonathan Martens, and W. C. M. Berden Introduction (120 words max) Effects of electronic structure on chemical bonding and reactivity play critical roles shaping the chemical bonding and reactivity behaviors of heavy elements. Understanding the role of f electrons in bond formation between the actinide-series elements like uranium with other ligands is critical for solving technical challenges associated with these heavy elements, important to nuclear fuel cycles, efficient separations of rare earth metals, and understanding the chemistry of stored nuclear fuels and related environmental management sites. In this study, we further examine the interactions between uranyl and the perchlorate ion in order to understand the structures of these ions through the use of IRMPD. Here we report the IRMPD spectra of [UO2(ClO4)3]-, [UO3(ClO4)2]-, and a proposed transition state. Methods (120 word max) IRMPD spectra and CID spectra were acquired using a Bruker amaZon QIT/MS instrument at the Free-Electron Lasers for Infrared eXperiments (FELIX) laboratory at Radboud University. The FELIX QIT/MS is modified to allow for the high-intensity tunable IR beam from FELIX to be directed into the ion packet, resulting in multiphoton dissociation that is measured only when the IR frequency is in resonance with an adequately high absorption vibrational mode of the mass-selected complex. DFT geometry optimizations and frequency calculations using the Gaussian suite of programs were performed using B3LYP, TPSSh, and PBE0 level of theory with 6-31+G(d) basis for the O, C, H, and N atoms and the SDD basis set for U. The SDD basis set employs the Stuttgart/Dresden effective core potential. Preliminary Data or Plenary Speakers Abstract (300 words max) Metal ion clusters of uranyl perchlorate were formed via direct electrospray ionization. For each metal ligand complex of interest, the parent ion was isolated and collision induced dissociation fragmentation and Infrared Multiphoton Dissociation (IRMPD) fragmentation spectra were acquired. Results presented here are the first look at the IRMPD spectra of [UO3(ClO4)2]-, [UO2(ClO4)3]-. Structures were examined using Gaussian at different levels of theory B3LYP level of theory, TPPSh and PBE0 levels, to reflect the behaviors of uranium metal ligand complexes most accurately. In these structures, we identified an overlap between each of these uranyl stretches resulting in their largely being obscured by a perchlorate mode. The CID product spectra agree with similar structures reported by Groenewold for uranyl nitrate in 2006 (10.1021/ja058106n).
Rare-earth elements (REEs) are present in a broad range of critical materials. The development of solid adsorbents for REE capture could enable the cost-effective recycling of REE-containing magnets and electronics. In this context, covalent organic frameworks (COFs) are promising candidates for REE adsorption due to their exceptionally high surface area. Despite having attractive physical properties, COFs are heavily underutilized for REE capture applications due to their limited lifecycle in aqueous acidic environments, as well as synthetic challenges associated with the incorporation of ligands suitable for REE capture. Here, in this work, we show how the Ugi multicomponent reaction can be leveraged to postsynthetically modify imine-based COFs for the introduction of a diglycolic acid (DGA) moiety, an efficient scaffold for REE capture. The adsorption capacity of the DGA-functionalized COF was found to be more than 40 times higher than that of the pristine imine COF precursor and more than four times higher than that of the next-best reported DGA-functionalized solid support. This rationally designed COF has appealing characteristics of high adsorption capacity, fast and efficient capture and release of the REE ions, and reliable recyclability, making it one of the most promising adsorbents for solid–liquid REE ion extractions reported to date.
The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein–ligand docking have recently been introduced, so far no previous works have systematically studied the behaviour of the latest docking and structure prediction methods within the broadly applicable context of: (1) using predicted (apo) protein structures for docking (for example, for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (for example, for enzyme design); and (3) having no previous knowledge of binding pockets (for example, for generalization to unknown pockets). To enable a deeper understanding of the real-world utility of docking methods, we introduce PoseBench, a comprehensive benchmark for broadly applicable protein–ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein–ligand docking and protein–ligand structure prediction using both primary ligand and multiligand benchmark datasets, the latter of which we introduce to the DL community. Empirically, using PoseBench, we find that: (1) DL cofolding methods generally outperform comparable conventional and DL docking baseline algorithms, but popular methods such as AlphaFold 3 are still challenged by prediction targets with new protein–ligand binding poses; (2) certain DL cofolding methods are highly sensitive to their input multiple sequence alignments, whereas others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting new or multiligand protein targets.
Selective ion separations are central to technologies spanning water purification, resource recovery, and clean energy. Conventional polymer membranes, which rely on steric hindrance or Donnan exclusion, struggle to discriminate between chemically similar ions in high-ionic-strength environments. Ligand-functionalized membranes offer a transformative strategy by embedding molecular recognition directly into polymer matrices, enabling selective complexation and transport. Here, this Viewpoint highlights the structure–function relationships underlying ligand-mediated ion separation, emphasizing the interplay of dehydration penalties, ligand coordination, and nanoscale confinement. We discuss design principles, denticity, donor identity, rigidity, and spatial organization, alongside the permeability–selectivity trade-off, multicomponent effects, and stability challenges. Finally, we outline emerging strategies, from bioinspired ligands to computationally guided design, that chart a path toward next-generation membranes for precise and energy-efficient ion separations.
The separation of trivalent lanthanides and actinides is challenging because of their similar sizes and charge densities. S-donating extractants have shown significant selectivity for trivalent actinides over lanthanides, with single-stage americium/ lanthanide separation efficiencies for some thiol-based extractants reported at >99.999%. While such separations could transform the nuclear waste management landscape, these systems are often limited by the hydrolytic and radiolytic stability of the extractant. Progress away from thiol-based systems is limited by the poorly understood and complex interactions of these extractants in organic phases, where molecular aggregation and micelle formation obfuscates assessment of the metal–extractant coordination environment. Because S-donating thioethers are generally more resistant to hydrolysis and oxidation and the aqueous phase coordination chemistry is anticipated to lack complications brought on by micelle formation, we have considered three thioethers, 2,2'-thiodiacetic acid (TDA), (2R,5S)- tetrahydrothiophene-2,5-dicarboxylic acid, and 2,5-thiophenedicarboxylic acid (TPA), as possible trivalent actinide selective reagents. Formation constants, extended X-ray absorption fine structure spectroscopy, and computational studies were completed for thioether complexes with a variety of trivalent lanthanides and actinides including Nd, Eu, Tb, Am, Cm, Bk, and Cf. TPA was found to have moderately higher selectivity for the actinides because of its ability to bind actinides in a different manner than lanthanides, but the utility of TPA is limited by poor water solubility and high rigidity. While significant competition with water for the metal center limits the efficacy of aqueous-based thioethers for separations, the characterization of these solution-phase, S-containing lanthanide and actinide complexes is the most comprehensively available in the literature to date. Here, this is due to the breadth of lanthanides and actinides considered as well as the techniques deployed and serves as a platform for the further development of Scontaining reagents for actinide separations. Additionally, this paper reports on the first bond lengths for Cf and Bk with a neutral S donor.
Phospholipid bilayers formed at solid-liquid interfaces have garnered interest as mimics of cell-membranes to model association reactions of proteins with lipid-bilayer-tethered ligands. Despite the importance of understanding how ligand density in a lipid bilayer impacts the protein-ligand association response, relating the ligand-modified lipid fraction to the absolute density of solution-accessible ligands in a lipid bilayer remains a challenge in interfacial quantitative analysis. In this work, confocal-Raman microscopy is employed to quantify the association of anti-biotin IgG with a small fraction of biotinylated lipids dispersed in either gel-phase or liquid-crystalline supported lipid bilayers, deposited on the interior surfaces of wide-pore silica surfaces. We examine the question whether inter-leaflet lipid translocation contributes to the population of solution-accessible biotin ligands on the distal leaflet of a supported lipid bilayer by comparing their protein accumulation response with ligands dispersed in lipid monolayers on nitrile-derivatized silica surfaces. The binding of antibody to biotin ligands dispersed in gel-phase bilayers exhibited an equivalent biotin-coverage response as the accumulation of IgG onto gel-phase monolayers, indicating that gel-phase bilayer symmetry was preserved. This result contrasts with the ~60% greater anti-biotin capture observed at fluid-phase bilayers compared to fluid-phase monolayers prepared at equivalent biotin fractions. This enhanced protein capture is attributed to biotin-capped lipids being transferred from the surface-associated proximal leaflet of the bilayer to the solution-exposed distal leaflet by the inter-leaflet exchange or lipid flip-flop, a facile process in fluid-phase supported lipid bilayers. Here, the results suggest caution in interpreting the results of quantitative studies of protein binding to lipid-tethered ligands dispersed in fluid-phase phospholipid bilayers.
Electrical activity in the brain and heart depends on rhythmic generation of action potentials by pacemaker ion channels (HCN) whose activity is regulated by cAMP binding. Previous work has uncovered evidence for both positive and negative cooperativity in cAMP binding, but such bulk measurements suffer from limited parameter resolution. Efforts to eliminate this ambiguity using single-molecule techniques have been hampered by the inability to directly monitor binding of individual ligand molecules to membrane receptors at physiological concentrations. Here we overcome these challenges using nanophotonic zero-mode waveguides4 to directly resolve binding dynamics of individual ligands to multimeric HCN1 and HCN2 ion channels. We show that cAMP binds independently to all four subunits when the pore is closed, despite a subsequent conformational isomerization to a flip state at each site. The different dynamics in binding and isomerization are likely to underlie physiologically distinct responses of each isoform to cAMP and provide direct validation of the ligand-induced flip-state model. Furthermore, this approach for observing stepwise binding in multimeric proteins at physiologically relevant concentrations can directly probe binding allostery at single-molecule resolution in other intact membrane proteins and receptors.
Conspectus The variability of chemical bonding in open-shell transition-metal complexes not only motivates their study as functional materials and catalysts but also challenges conventional computational modeling tools. Here, tailoring ligand chemistry can alter preferred spin or oxidation states as well as electronic structure properties and reactivity, creating vast regions of chemical space to explore when designing new materials atom by atom. Although first-principles density functional theory (DFT) remains the workhorse of computational chemistry in mechanism deduction and property prediction, it is of limited use here. DFT is both far too computationally costly for widespread exploration of transition-metal chemical space and also prone to inaccuracies that limit its predictive performance for localized d electrons in transition-metal complexes. These challenges starkly contrast with the well-trodden regions of small-organic-molecule chemical space, where the analytical forms of molecular mechanics force fields and semiempirical theories have for decades accelerated the discovery of new molecules, accurate DFT functional performance has been demonstrated, and gold-standard methods from correlated wavefunction theory can predict experimental results to chemical accuracy. The combined promise of transition-metal chemical space exploration and lack of established tools has mandated a distinct approach. In this Account, we outline the path we charted in exploration of transition-metal chemical space starting from the first machine learning (ML) models (i.e., artificial neural network and kernel ridge regression) and representations for the prediction of open-shell transition-metal complex properties. The distinct importance of the immediate coordination environment of the metal center as well as the lack of low-level methods to accurately predict structural properties in this coordination environment first motivated and then benefited from these ML models and representations. Once developed, the recipe for prediction of geometric, spin state, and redox potential properties was straightforwardly extended to a diverse range of other properties, including in catalysis, computational “feasibility”, and the gas separation properties of periodic metal–organic frameworks. Interpretation of selected features most important for model prediction revealed new ways to encapsulate design rules and confirmed that models were robustly mapping essential structure–property relationships. Encountering the special challenge of ensuring that good model performance could generalize to new discovery targets motivated investigation of how to best carry out model uncertainty quantification. Distance-based approaches, whether in model latent space or in carefully engineered feature space, provided intuitive measures of the domain of applicability. With all of these pieces together, ML can be harnessed as an engine to tackle the large-scale exploration of transition-metal chemical space needed to satisfy multiple objectives using efficient global optimization methods. In practical terms, bringing these artificial intelligence tools to bear on the problems of transition-metal chemical space exploration has resulted in ML-model assessments of large, multimillion compound spaces in minutes and validated new design leads in weeks instead of decades.
Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery. Here, we develop Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screen a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures – four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone – as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identifies biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design shows shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we develop cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid and scalable design of new biosensors, overcoming constraints of natural biosensors.
Isoreticular chemistry, which enables property optimization by changing compositions without changing topology, is a powerful synthetic strategy. One of the biggest challenges facing isoreticular chemistry is to extend it to ligands with strongly coordinating substituent groups such as unbound –COOH, because competitive interactions between such groups and metal ions can derail isoreticular chemistry. It is even more challenging to have an isoreticular series of carboxyl-functionalized MOFs capable of encompassing chemically disparate metal ions. Furthermore, with the simultaneous introduction of carboxyl functionalization and pore space partition, a family of carboxyl-functionalized materials is developed in diverse compositions from homometallic Cr 3+ and Ni 2+ to heterometallic Co 2+ /V 3+ , Ni 2+ /V 3+ , Co 2+ /In 3+ , Co 2+ /Ni 2+ . Cr-MOFs remain highly crystalline in boiling water. Unprecedentedly, one Cr-MOF can withstand the treatment cycle with 10m NaOH and 12m HCl, allowing reversible inter-conversion between unbound –COOH acid form and –COO – base form. These materials exhibit excellent sorption properties such as high uptake capacity for CO 2 (100.2 cm 3 g –1 ) and hydrocarbon gases (e.g., 142.1 cm 3 g –1 for C 2 H 2 , 110.5 cm 3 g –1 for C 2 H 4 ) at 1 bar and 298K, high benzene/cyclohexane selectivity (up to ≈40), and promising separation performance for gas mixtures such as C 2 H 2 /CO 2 and C 2 H 2 /C 2 H 4 .