Design Of Ligands Research Articles

Automated design of multi-target ligands by generative deep learning

Generative deep learning models enable data-driven de novo design of molecules with tailored features. Chemical language models (CLM) trained on string representations of molecules such as SMILES have been successfully employed to design new chemical entities with experimentally confirmed activity on intended targets. Here, we probe the application of CLM to generate multi-target ligands for designed polypharmacology. We capitalize on the ability of CLM to learn from small fine-tuning sets of molecules and successfully bias the model towards designing drug-like molecules with similarity to known ligands of target pairs of interest. Designs obtained from CLM after pooled fine-tuning are predicted active on both proteins of interest and comprise pharmacophore elements of ligands for both targets in one molecule. Synthesis and testing of twelve computationally favored CLM designs for six target pairs reveals modulation of at least one intended protein by all selected designs with up to double-digit nanomolar potency and confirms seven compounds as designed dual ligands. These results corroborate CLM for multi-target de novo design as source of innovation in drug discovery.

Computational Design of Ligands for the Ir-Catalyzed C5-Borylation of Indoles through Tuning Dispersion Interactions.

The indole moiety is ubiquitous in natural products and pharmaceuticals. C-H borylation of the benzenoid moiety of indoles is a challenging task, especially at the C5 position. We have combined computational and experimental studies to introduce multiple noncovalent interactions, especially dispersion, between the substrate and catalytic ligand to realize C5-borylation of indoles with high reactivity and selectivity. The successful computational predictions of new ligands should be suitable for ligand design in other transition-metal catalyzed reactions.

Identity of the Silyl Ligand in an Iron Silyl Complex Influences Olefin Hydrogenation: An Experimental and Computational Study.

In this study, we explore the selective synthesis of iron silyl complexes using the reaction of an iron mesityl complex (MesCCC)FeMes(Py) with various hydrosilanes. These resulting iron silyl complexes, (MesCCC)Fe(SiH2Ph)(Py)(N2), (MesCCC)Fe(SiMe2Ph)(Py)(N2), and (MesCCC)Fe[SiMe(OSiMe3)2](Py)(N2), serve as effective precatalysts for olefin hydrogenation. The key to their efficiency in catalysis lies in the specific nature of the silyl ligand attached to the iron center. Experimental observations, supported by density functional theory (DFT) simulations, reveal that the catalytic performance correlates with the relative stability of dihydrogen and hydride species associated with each iron silyl complex. The stability of these intermediates is crucial for efficient hydrogen transfer during the catalytic cycle. The DFT simulations help to quantify these stability factors, showing a direct relationship between the silyl ligand's electronic and steric properties and the overall catalytic activity. Complexes with certain silyl ligands exhibit better performance due to the optimal balance between the stability and reactivity of the key active catalyst. This work highlights the importance of ligand design in the development of iron-based hydrogenation catalysts.

N-Glycosylation-Induced Pathologic Protein Conformations as a Tool to Guide the Selection of Biologically Active Small Molecules.

Post-translational modifications such as protein N-glycosylation, significantly influence cellular processes. Dysregulated N-glycosylation, exemplified in Grp94, a member of the Hsp90 family, leads to structural changes and the formation of epichaperomes, contributing to pathologies. Targeting N-glycosylation-induced conformations offers opportunities for developing selective chemical tools and drugs for these pathologic forms of chaperones. We here demonstrate how a specific Grp94 conformation induced by N-glycosylation, identified previously via molecular dynamics simulations, rationalizes the distinct behavior of similar ligands. Integrating dynamic ligand unbinding information with SAR development, we differentiate ligands productively engaging the pathologic Grp94 conformers from those that are not. Additionally, analyzing binding site stereoelectronic properties and QSAR models using cytotoxicity data unveils relationships between chemical, conformational properties, and biological activities. These findings facilitate the design of ligands targeting specific Grp94 conformations induced by abnormal glycosylation, selectively disrupting pathogenic protein networks while sparing normal mechanisms.

Partial to Total Generation of 3D Transition-Metal Complexes.

The design of transition-metal complexes (TMCs) has drawn much attention over the years because of their important applications as metallodrugs and functional materials. In this work, we present an extension of our recently reported approach, LigandDiff [Jin et al. J. Chem. Theory Comput. 20, 4377(2024)]. The new model, which we call multi-LigandDiff, is more flexible and greatly outperforms its predecessor. This scaffold-based diffusion model allows de novo ligand design with either existing ligands or without any ligand. Moreover, it allows users to predefine the denticity of the generated ligand. Our results indicate that multi-LigandDiff can generate well-defined ligands and is transferable to multiple transition metals and coordination geometries. In terms of its application, multi-LigandDiff successfully designed 338 Fe(II) spin-crossover (SCO) complexes from only 47 experimentally validated SCO complexes. And these generated complexes are configurationally diverse and structurally reasonable. Overall, the results show that multi-LigandDiff is an ideal tool to design novel TMCs from scratch.

Coordination Behaviors between Aryl Diamide Amine Ligands and Trivalent Lanthanides: A Spectroscopic and Structural Study

Investigating the complexation of organic ligands with trivalent lanthanides (Ln(III)) is crucial in various fields, particularly in the separation of actinides from lanthanides for spent fuel reprocessing. While alkyl diamide amine ligands have been extensively studied, aryl‐functionalized ligands are rarely reported. To understand the effect of substituents on the coordination mode of diamide amine ligands with Ln(III), two aryl‐substituted diamide amine ligands, 2,2'‐(p‐tolylazanediyl)bis(N‐ethyl‐N‐(p‐tolyl)acetamide) (L1) and 2,2'‐((2‐ethylhexyl)azanediyl)bis(N‐ethyl‐N‐(p‐tolyl)acetamide) (L2), were synthesized and systematically studied. 1H NMR titration showed that metal ion coordination affected the electron density of methylene groups near coordinating atoms more than that of aromatic rings, while fluorescence titration and single‐crystal analysis confirmed 1:1 ligand‐Ln(III) complexes. Compared to alkyl diamide amine ligands, aryl groups increased steric hindrance, enhancing torsional strain and preventing amine nitrogen from participating in complexation, leading to weaker coordination as only two carbonyl oxygen atoms coordinated with Ln(III) in a bidentate mode. This work provides insight into how substituents influence the complexation properties of diamide amine ligands with f‐elements, aiding in the design of new ligands with improved performance.

Benchtop-Stable Carbyl Iminopyridyl NiII Complexes for Olefin Polymerization.

Design of catalysts for Ni-catalyzed olefin polymerization predominantly focuses on ligand design rather than the activation process when attempting to achieve a broader scope of polyolefin micro- and macrostructures. Air-stable alkyl-or aryl-functionalized NiII precatalysts were designed which eliminate the need of in situ alkylating processes and are activated solely by halide abstraction to generate the cationic complex for olefin polymerization. These complexes represent an emerging class of olefin polymerization catalysts, enabling the study of various cocatalysts forming either inner- or outer-sphere ion pairs. It is demonstrated that an organoboron cocatalyst activation produces a well-defined ion pair, which in contrast to ill-defined organoaluminum cocatalysts, can directly activate the complex by halide abstraction to yield comparatively higher molecular weight homo/copolymers. Under high ethylene pressure, broader branching densities and the gradual incorporation of short-chain branches were achieved, circumventing the need for elaborate ligand design and copolymerization with α-olefins. The underlying chain-walking mechanism and ion pair interactions were further elucidated by DFT calculations. A phenyl group on the bridging carbon functioned as a rotational barrier, producing higher molecular weight polymers compared to methyl-substituted analogs. Here, we provide a perspective to manipulate the iminopyridyl NiII system, leveraging ion pair interactions and ligand design to govern polyolefin molecular weights and microstructures.

Tuning the Electronic Properties of Azophosphines as Ligands and Their Application in Base-Free Transfer Hydrogenation Catalysis.

The design and tuning of new ligands is crucial for unlocking new reactivity at transition metal centers. Azophosphines have recently emerged as a new class of 1,3-P,N ligands in ruthenium piano-stool complexes. This work shows that the azophosphine synthesis can tolerate N-aryl substituents with strongly electron-donating and electron-withdrawing para-R groups and that the nature of this R group can affect the spectroscopic and structural properties of the azophosphines, as measured by NMR spectroscopy, UV-vis spectroscopy, single-crystal X-ray diffraction, and DFT studies. Azophosphines are shown to be relatively weak phosphine donors, as shown by analysis of the 1 J P-Se coupling constants of the corresponding azophosphine selenides, but the donor properties can be fine tuned within this area of chemical space. Monodentate and bidentate Ru-azophosphine complexes were prepared, and their first use as a catalyst was probed. The Ru-azophosphine complexes were found to promote the transfer hydrogenation of acetophenone to 1-phenylethanol without the requirement of a harsh base additive, and the bidentate complex was more active than the monodentate analogue.

Coordination Site Selective Occupation Strategy for Tuning the Photosalient Effects of Photoactive Cd Complexes.

The application of photo responsive crystals to useful actuation demands a rational design to elicit controllable movement. The [2+2] photocycloaddition reaction triggers mechanical motion using associated photosalient (PS) effects. We herein report a coordination site selective occupation strategy to modulate the arrangement of C=C bonds and thereby tune the PS effect. Replacing or repositioning the donor atom at one end of the linear ligand allowed for a greater level of molecular structural flexibility, facilitating [2+2] photocycloaddition. The distance between photoreactive centres and coordination sites was adjusted by ligand design to regulate PS behaviour. This work suggests new avenues for modulating PS movement to achieve useful motion.

CLigOpt: controllable ligand design through target-specific optimization.

A key challenge in deep generative models for molecular design is to navigate random sampling of the vast molecular space, and produce promising molecules that strike a balance across multiple chemical criteria. Fragment-based drug design (FBDD), using fragments as starting points, is an effective way to constrain chemical space and improve generation of biologically active molecules. Furthermore, optimization approaches are often implemented with generative models to search through chemical space, and identify promising samples which satisfy specific properties. Controllable FBDD has promising potential in efficient target-specific ligand design. We propose a controllable FBDD model, CLigOpt, which can generate molecules with desired properties from a given fragment pair. CLigOpt is a variational autoencoder-based model which utilizes co-embeddings of node and edge features to fully mine information from molecular graphs, as well as a multi-objective Controllable Generation Module to generate molecules under property controls. CLigOpt achieves consistently strong performance in generating structurally and chemically valid molecules, as evaluated across six metrics. Applicability is illustrated through ligand candidates for hDHFR and it is shown that the proportion of feasible active molecules from the generated set is increased by 10%. Molecular docking and synthesizability prediction tasks are conducted to prioritize generated molecules to derive potential lead compounds. The source code is available via https://github.com/yutongLi1997/CLigOpt-Controllable-Ligand-Design-through-Target-Specific-Optimisation.

Theoretical Implications of Bifunctional Ligands to Improve Uranium Extraction Performance

Extraction of uranium from seawater is considered to be an effective way to solve the shortage of uranium resources, and the development of efficient adsorption functional groups is the key to uranium extraction. In this work, the complexation of uranyl cations with a series of diamidoxime and bifunctional (amidoximate‐carboxylate, amidoximate‐phosphate) ligands has been probed by quantum chemical calculations. For most of the uranyl complexes, the amidoxime groups adopt η2 mode to uranyl cations. Based on bonding analyses, we found that the uranyl complexes with methyl‐substituted ligands (H2L') possess stronger covalent interactions than those with phenyl‐substituted ligands (H2L). Consequently, the uranyl complexes with H2L' are more stable in the extraction process according to thermodynamic analysis. The amidoximate‐phosphate bifunctional ligand (H2L3') has stronger extraction capacity to uranyl cations than other ligands, which is related to the relatively lower decomposition energy, and it shows selectivity in seawater for uranyl cations over vanadium ions, which may be a potential ligand for uranium extraction. Therefore, the introduction of synergistic functional groups, i.e. the bifunctional ligands, enhance the extraction properties of uranyl cations. This work improves understanding of synergistic ligands, and may contribute to design and development of efficient ligands for recovery of uranium from seawater.

Metadynamics Study of Lipid-Mediated Antibacterial Toxin Binding to the EmrE Multiefflux Protein.

EmrE is a bacterial efflux protein in the small multidrug-resistant (SMR) family present in Escherichia coli. Due to its small size, 110 residues in each dimer subunit, it is an ideal model system to study ligand-protein-membrane interactions. Here in our work, we have calculated the free energy landscape of benzyltrimetylammonium (BTMA) and tetraphenyl phosphonium (TPP) binding to EmrE using the enhanced sampling method-multiple walker metadynamics. We estimate that the free energy of BTMA binding to EmrE is -21.2 ± 3.3 kJ/mol and for TPP is -43.6 ± 3.8 kJ/mol. BTMA passes through two metastable states to reach the binding pocket, while TPP has a more complex binding landscape with four metastable states and one main binding site. Our simulations show that the ligands interact with the membrane lipids at a distance 1 nm away from the binding site which forms a broad local minimum, consistent for both BTMA and TPP. This site can be an alternate entry point for ligands to partition from the membrane into the protein, especially for bulky and/or branched ligands. We also observed the membrane lipid and C-terminal 110HisA form salt-bridge interactions with the helix-1 residue 22LysB. Our free energy estimates and clusters are in close agreement with experimental data and give us an atomistic view of the ligand-protein-lipid interactions. Understanding the binding pathway of these ligands can guide us in future design of ligands that can alter or halt the function of EmrE.

6‐Hydroxy Picolinohydrazides Promoted Cu(I)‐Catalyzed Hydroxylation Reaction in Water: Machine‐Learning Accelerated Ligands Design and Reaction Optimization

Hydroxylated (hetero)arenes are privileged motifs in natural products, materials, small‐molecule pharmaceuticals and serve as versatile intermediates in synthetic organic chemistry. Herein, we report an efficient Cu(I)/6‐hydroxy picolinohydrazide‐catalyzed hydroxylation reaction of (hetero)aryl halides (Br, Cl) in water. By establishing machine learning (ML) models, the design of ligands and optimization of reaction conditions were effectively accelerated. L32 (6‐HPA‐DMCA) demonstrated high efficiency for (hetero)aryl bromides, promoting hydroxylation reactions with a minimal catalyst loading of 0.01 mol% (100 ppm) at 80 °C to reach 10000 TON or under near‐room temperature conditions for substrates containing sensitive functional groups (3.0 mol%); L42 (6‐HPA‐DTBCA) displayed superior reaction activity for chloride substrates, enabling hydroxylation reactions at 100 °C with 2‐3 mol% catalyst loading. These represent the state of art for both lowest catalyst loading and temperature in the copper‐catalyzed hydroxylation reactions. Furthermore, this method features a sustainable and environmentally friendly solvent system, accommodates a wide range of substrates, and shows potential for developing robust and scalable synthesis processes for key pharmaceutical intermediates.

6-Hydroxy Picolinohydrazides Promoted Cu(I)-Catalyzed Hydroxylation Reaction in Water: Machine-Learning Accelerated Ligands Design and Reaction Optimization.

Hydroxylated (hetero)arenes are privileged motifs in natural products, materials, small-molecule pharmaceuticals and serve as versatile intermediates in synthetic organic chemistry. Herein, we report an efficient Cu(I)/6-hydroxy picolinohydrazide-catalyzed hydroxylation reaction of (hetero)aryl halides (Br, Cl) in water. By establishing machine learning (ML) models, the design of ligands and optimization of reaction conditions were effectively accelerated. L32 (6-HPA-DMCA) demonstrated high efficiency for (hetero)aryl bromides, promoting hydroxylation reactions with a minimal catalyst loading of 0.01 mol% (100 ppm) at 80 °C to reach 10000 TON or under near-room temperature conditions for substrates containing sensitive functional groups (3.0 mol%); L42 (6-HPA-DTBCA) displayed superior reaction activity for chloride substrates, enabling hydroxylation reactions at 100 °C with 2-3 mol% catalyst loading. These represent the state of art for both lowest catalyst loading and temperature in the copper-catalyzed hydroxylation reactions. Furthermore, this method features a sustainable and environmentally friendly solvent system, accommodates a wide range of substrates, and shows potential for developing robust and scalable synthesis processes for key pharmaceutical intermediates.

Exploring the electronic influence on coordination complexes formed from appended pyrrolidine azothioformamide ligands and copper(I) salts

Redox-active arylazothioformamide (ATF) ligands have seen attention through their unique coordination complexes formed with salts of late transition metals and their known ability to oxidatively dissolve zerovalent metals. When mixed with Cu(I) salts, ATF ligands form both 2:1 and 2:2 coordination complexes remaining neutral without undergoing any redox event. Herein, a series of para-substituted pyrrolidine-ATFs were synthesized, incorporating both electron-donating groups (i.e., -OMe and -Me) as well as electron-withdrawing groups (i.e., -CF3, and -CN). These ligands were then mixed with Cu(I) salts, including CuBr, CuI, and [(CH3CN)4Cu](BF4) to form coordination complexes. The resulting complexes underwent thorough characterization, with several producing X-ray quality crystals for detailed structural analysis. Both strong and weak intermolecular interactions were found through Hirshfeld surface analysis and the redox activity of the complexes was probed using cyclic voltammetry in the voltage range of -1.8 to 1.8 V. Through a UV–Vis titration study, the binding interactions between the ligand host and Cu(I) metal salt guest molecules were determined and ranged from 4,000 – 100,000 M-1. Computational modeling was employed to calculate the change in Gibbs free energy (ΔG) for the formation of the complexes, revealing the optimal orientations between the ligand and the metal. These studies have confirmed that para-substituted pyrrolidine-ATFs containing electron-donating groups exhibit a higher binding affinity towards Cu(I) metal salts compared to those with electron-withdrawing groups. With a thorough understanding of ATF-metal coordination, further ligand design can lead to exciting new catalysts and/or selective metal dissolution agents.

Unearthing the Real-Time Excited State Dynamics from Antenna to Rare Earth Ions Using Ultrafast Transient Absorption.

The conventional energy transfer pathway in organic lanthanide complexes is purported to be from the excited singlet state of the chromophore to the triplet state and subsequently directly to the emitting state of the trivalent lanthanide ion. In this work, we found that the energy transfer occurs from the triplet state to the nearest energy level, instead of directly to the emitting state of the lanthanide ion. The triplet decay rate for different lanthanide ions follows an energy gap law from the triplet level to the receiving level of the lanthanide ion. Three different categories of complexes were synthesized and inspected using different techniques, demonstrating the universality of our findings. This work renews the insights to conventional findings, highlighting the importance of the energy gap between the triplet state and the nearest lanthanide energy level in optimization of light harvesting. The rationale of ligand design of chromophores should be reconsidered, leading to various applications of lanthanide complexes with enhanced quantum yield and brightness.

Highly Anisotropic Pd2Lab 2Lcc 2 and Pd2Lab 2Lcd 2 Type Cages by Heteromeric Completive Self-Sorting.

Pd(II)-based low-symmetry coordination cages possessing anisotropic cavities are of great interest. The common strategies employed to achieve such cages utilize either more than one type of symmetrical ligands (e.g., Laa, Lbb etc.) or only one type of unsymmetrical ligand (e.g., Lab). To significantly enhance the anisotropy, we have designed two unsymmetrical bidentate ligands i.e., Lab and Lcd, aiming at a low-symmetry Pd2Lab 2Lcd 2-type cage. It was accomplished by high-fidelity integrative self-sorting of two different low-symmetry cages having Pd2Lab 4 and Pd4Lcd 8-type architectures (homoleptic complexes of the designed ligands). Structural constraints and geometry complementarity in the ligand design drive the non-statistical exclusive self-assembly of the Pd2Lab 2Lcd 2-type cage. By taking advantage of the complemental geometries between ligands, a low-symmetry Pd2Lab 2Lcc 2-type cage was also obtained. Heteromeric completive self-sorting of three homoleptic assemblies (Pd2Lab 4, Pd4Lcc 8 and Pd4Lcd 8-type cages) into an exclusive mixture of Pd2Lab 2Lcd 2 and Pd2Lab 2Lcc 2-type mixed ligated assemblies was demonstrated through cage-to-cage transformations.

Highly Anisotropic Pd2Lab2Lcc2 and Pd2Lab2Lcd2 Type Cages by Heteromeric Completive Self‐Sorting

AbstractPd(II)‐based low‐symmetry coordination cages possessing anisotropic cavities are of great interest. The common strategies employed to achieve such cages utilize either more than one type of symmetrical ligands (e.g., Laa, Lbb etc.) or only one type of unsymmetrical ligand (e.g., Lab). To significantly enhance the anisotropy, we have designed two unsymmetrical bidentate ligands i.e., Lab and Lcd, aiming at a low‐symmetry Pd2Lab2Lcd2‐type cage. It was accomplished by high‐fidelity integrative self‐sorting of two different low‐symmetry cages having Pd2Lab4 and Pd4Lcd8‐type architectures (homoleptic complexes of the designed ligands). Structural constraints and geometry complementarity in the ligand design drive the non‐statistical exclusive self‐assembly of the Pd2Lab2Lcd2‐type cage. By taking advantage of the complemental geometries between ligands, a low‐symmetry Pd2Lab2Lcc2‐type cage was also obtained. Heteromeric completive self‐sorting of three homoleptic assemblies (Pd2Lab4, Pd4Lcc8 and Pd4Lcd8‐type cages) into an exclusive mixture of Pd2Lab2Lcd2 and Pd2Lab2Lcc2‐type mixed ligated assemblies was demonstrated through cage‐to‐cage transformations.

Metal-Organic Frameworks Derived Carbon-Supported Metal Electrocatalysts for Energy-Related Reduction Reactions.

Electrochemical reduction reactions, as cathodic processes in many energy-related devices, significantly impact the overall efficiency determined mainly by the performance of electrocatalysts. Metal-organic frameworks (MOFs) derived carbon-supported metal materials have become one of star electrocatalysts due to their tunable structure and composition through ligand design and metal screening. However, for different electroreduction reactions, the required active metal species vary in phase component, electronic state, and catalytic center configuration, hence requiring effective customization. From this perspective, this review comprehensively analyzes the structural design principles, metal loading strategies, practical electroreduction performance, and complex catalytic mechanisms, thereby providing insights and guidance for the future rational design of such electroreduction catalysts.

Metal–Organic Frameworks Derived Carbon‐Supported Metal Electrocatalysts for Energy‐Related Reduction Reactions

AbstractElectrochemical reduction reactions, as cathodic processes in many energy‐related devices, significantly impact the overall efficiency determined mainly by the performance of electrocatalysts. Metal–organic frameworks (MOFs) derived carbon‐supported metal materials have become one of star electrocatalysts due to their tunable structure and composition through ligand design and metal screening. However, for different electroreduction reactions, the required active metal species vary in phase component, electronic state, and catalytic center configuration, hence requiring effective customization. From this perspective, this review comprehensively analyzes the structural design principles, metal loading strategies, practical electroreduction performance, and complex catalytic mechanisms, thereby providing insights and guidance for the future rational design of such electroreduction catalysts.