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As more and more protein structures are discovered, blind protein-ligand docking will play an important role in drug discovery because it can predict protein-ligand complex conformation without pocket information on the target proteins. Recently, deep learning-based methods have made significant advancements in blind protein-ligand docking, but their protein features are suboptimal because they do not fully consider the difference between potential pocket regions and non-pocket regions in protein feature extraction. In this work, we propose a pocket-guided strategy for guiding the ligand to dock to potential docking regions on a protein. To this end, we design a plug-and-play module to enhance the protein features, which can be directly incorporated into existing deep learning-based blind docking methods. The proposed module first estimates potential pocket regions on the target protein and then leverages a pocket-guided attention mechanism to enhance the protein features. Experiments are conducted on integrating our method with EquiBind and FABind, and the results show that their blind-docking performances are both significantly improved and new start-of-the-art performance is achieved by integration with FABind., (© The Author(s) 2024. Published by Oxford University Press.)

The introduction of AlphaFold 2 1 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design 2-6 . Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein-ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein-nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody-antigen prediction accuracy compared with AlphaFold-Multimer v.2.3 7,8 . Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework., (© 2024. The Author(s).)

The µ-opioid receptor (µOR) is an important target for pain management 1 and molecular understanding of drug action on µOR will facilitate the development of better therapeutics. Here we show, using double electron-electron resonance and single-molecule fluorescence resonance energy transfer, how ligand-specific conformational changes of µOR translate into a broad range of intrinsic efficacies at the transducer level. We identify several conformations of the cytoplasmic face of the receptor that interconvert on different timescales, including a pre-activated conformation that is capable of G-protein binding, and a fully activated conformation that markedly reduces GDP affinity within the ternary complex. Interaction of β-arrestin-1 with the μOR core binding site appears less specific and occurs with much lower affinity than binding of G i ., (© 2024. The Author(s).)

Cobalamin (vitamin B 12 , herein referred to as B 12 ) is an essential cofactor for most marine prokaryotes and eukaryotes 1,2 . Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics 2-4 . Here we show that two bacterial B 12 auxotrophs can salvage different B 12 building blocks and cooperate to synthesize B 12 . A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B 12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B 12 . Release of B 12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B 12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B 12 . These complex microbial interactions of ligand cross-feeding and joint B 12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B 12 producers. These findings add new players to our understanding of B 12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain that is linked via a cysteine-rich domain to their 7-transmembrane domain 1 . Upon activation, these receptors undergo a large conformational change to transmit the ligand binding signal from the extracellular ligand-binding domain to the G protein-coupling 7-transmembrane domain 2 . In this manuscript, we propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5. We present a series of structures in lipid nanodiscs, from inactive to fully active, including agonist-bound intermediate states. Further, using bulk and single-molecule fluorescence imaging, we reveal distinct receptor conformations upon allosteric modulator and G protein binding., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Ligand-based virtual screening (LBVS) methods are widely used to explore the vast chemical space in the search of novel compounds resorting to a variety of properties encoded in 1D, 2D or 3D descriptors. The success of 3D-LBVS is affected by the overlay of molecular pairs, thus making selection of the template compound, search of accessible conformational space and choice of the query conformation to be potential factors that modulate the successful retrieval of actives. This study examines the impact of adopting different choices for the query conformation of the template, paying also attention to the influence exerted by the structural similarity between templates and actives. The analysis is performed using PharmScreen, a 3D LBVS tool that relies on similarity measurements of the hydrophobic/philic pattern of molecules, and Phase Shape, which is based on the alignment of atom triplets followed by refinement of the volume overlap. The study is performed for the original DUD-E + database and a Morgan Fingerprint filtered version (denoted DUD-E + -Diverse; available in https://github.com/Pharmacelera/Query-models-to-3DLBVS ), which was prepared to minimize the 2D resemblance between template and actives. Although in most cases the query conformation exhibits a mild influence on the overall performance, a critical analysis is made to disclose factors, such as the content of structural features between template and actives and the induction of conformational strain in the template, that underlie the drastic impact of the query definition in the recovery of actives for certain targets. The findings of this research also provide valuable guidance for assisting the selection of the query definition in 3D LBVS campaigns., (© 2024. The Author(s).)

Many interactions involving a ligand and its molecular target are studied by rapid kinetics using a stopped-flow apparatus. Information obtained from these studies is often limited to a single, saturable relaxation that is insufficient to resolve all independent rate constants even for a two-step mechanism of binding obeying induced fit (IF) or conformational selection (CS). We introduce a simple method of general applicability where this limitation is overcome. The method accurately reproduces the rate constants for ligand binding to the serine protease thrombin determined independently from the analysis of multiple relaxations. Application to the inactive zymogen precursor of thrombin, prethrombin-2, resolves all rate constants for a binding mechanism of IF or CS from a single, saturable relaxation. Comparison with thrombin shows that the prethrombin-2 to thrombin conversion enhances ligand binding to the active site not by improving accessibility through the value of k on but by reducing the rate of dissociation k off . The conclusion holds regardless of whether binding is interpreted in terms of IF or CS and has general relevance for the mechanism of zymogen activation of serine proteases. The method also provides a simple test of the validity of IF and CS and indicates when more complex mechanisms of binding should be considered., Competing Interests: Conflict of interest The author declares that he has no conflict of interests with the contents of this article., (Copyright © 2024 The Author. Published by Elsevier Inc. All rights reserved.)

Riboswitches are broadly distributed regulatory elements most frequently found in the 5'-leader sequence of bacterial mRNAs that regulate gene expression in response to the binding of a small molecule effector. The occupancy status of the ligand-binding aptamer domain manipulates downstream information in the message that instructs the expression machinery. Currently, there are over 55 validated riboswitch classes, where each class is defined based on the identity of the ligand it binds and/or sequence and structure conservation patterns within the aptamer domain. This classification reflects an "aptamer-centric" perspective that dominates our understanding of riboswitches. In this review, we propose a conceptual framework that groups riboswitches based on the mechanism by which RNA manipulates information directly instructing the expression machinery. This scheme does not replace the established aptamer domain-based classification of riboswitches but rather serves to facilitate hypothesis-driven investigation of riboswitch regulatory mechanisms. Based on current bioinformatic, structural, and biochemical studies of a broad spectrum of riboswitches, we propose three major mechanistic groups: (1) "direct occlusion", (2) "interdomain docking", and (3) "strand exchange". We discuss the defining features of each group, present representative examples of riboswitches from each group, and illustrate how these RNAs couple small molecule binding to gene regulation. While mechanistic studies of the occlusion and docking groups have yielded compelling models for how these riboswitches function, much less is known about strand exchange processes. To conclude, we outline the limitations of our mechanism-based conceptual framework and discuss how critical information within riboswitch expression platforms can inform gene regulation., Competing Interests: Conflict of interest R. T. B. serves on the Scientific Advisory Boards of Expansion Therapeutics, SomaLogic and MeiraGTx. All other authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Cullin (CUL)-RING (Really Interesting New Gene) E3 ubiquitin (Ub) ligases (CRLs) are the largest E3 family. The E3 CRL core ligase is a subcomplex formed by the CUL C-terminal domain bound with the ROC1/RBX1 RING finger protein, which acts as a hub that mediates and organizes multiple interactions with E2, Ub, Nedd8, and the ARIH family protein, thereby resulting in Ub transfer to the E3-bound substrate. This report describes the modulation of CRL-dependent ubiquitination by small molecule compounds including KH-4-43, #33, and suramin, which target the CRL core ligases. We show that both KH-4-43 and #33 inhibit the ubiquitination of CK1α by CRL4 CRBN . However, either compound's inhibitory effect on this reaction is significantly reduced when a neddylated form of CRL4 CRBN is used. On the other hand, both #33 and KH-4-43 inhibit the ubiquitination of β-catenin by CRL1 β-TrCP and Nedd8-CRL1 β-TrCP almost equally. Thus, neddylation of CRL1 β-TrCP does not negatively impact the sensitivity to inhibition by #33 and KH-4-43. These findings suggest that the effects of neddylation to alter the sensitivity of CRL inhibition by KH-4-43/#33 is dependent upon the specific CRL type. Suramin, a compound that targets CUL's basic canyon, can effectively inhibit CRL1/4-dependent ubiquitination regardless of neddylation status, in contrast to the results observed with KH-4-43/#33. This observed differential drug sensitivity of KH-4-43/#33 appears to echo CUL-specific Nedd8 effects on CRLs as revealed by recent high-resolution structural biology efforts. The highly diversified CRL core ligase structures may provide opportunities for specific targeting by small molecule modulators., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Computing binding affinities is of great importance in drug discovery pipeline and its prediction using advanced machine learning methods still remains a major challenge as the existing datasets and models do not consider the dynamic features of protein-ligand interactions. To this end, we have developed PLAS-20k dataset, an extension of previously developed PLAS-5k, with 97,500 independent simulations on a total of 19,500 different protein-ligand complexes. Our results show good correlation with the available experimental values, performing better than docking scores. This holds true even for a subset of ligands that follows Lipinski's rule, and for diverse clusters of complex structures, thereby highlighting the importance of PLAS-20k dataset in developing new ML models. Along with this, our dataset is also beneficial in classifying strong and weak binders compared to docking. Further, OnionNet model has been retrained on PLAS-20k dataset and is provided as a baseline for the prediction of binding affinities. We believe that large-scale MD-based datasets along with trajectories will form new synergy, paving the way for accelerating drug discovery., (© 2024. The Author(s).)

Siglec-7 (sialic acid-binding immunoglobulin-like lectin 7) is a glycan-binding immune receptor that is emerging as a significant target of interest for cancer immunotherapy. The physiological ligands that bind Siglec-7, however, remain incompletely defined. In this study, we characterized the expression of Siglec-7 ligands on peripheral immune cell subsets and assessed whether Siglec-7 functionally regulates interactions between immune cells. We found that disialyl core 1 O-glycans are the major immune ligands for Siglec-7 and that these ligands are particularly highly expressed on naïve T-cells. Densely glycosylated sialomucins are the primary carriers of these glycans, in particular a glycoform of the cell-surface marker CD43. Biosynthesis of Siglec-7-binding glycans is dynamically controlled on different immune cell subsets through a genetic circuit involving the glycosyltransferase GCNT1. Siglec-7 blockade was found to increase activation of both primary T-cells and antigen-presenting dendritic cells in vitro, indicating that Siglec-7 binds T-cell glycans to regulate intraimmune signaling. Finally, we present evidence that Siglec-7 directly activates signaling pathways in T-cells, suggesting a new biological function for this receptor. These studies conclusively demonstrate the existence of a novel Siglec-7-mediated signaling axis that physiologically regulates T-cell activity. Going forward, our findings have significant implications for the design and implementation of therapies targeting immunoregulatory Siglec receptors., Competing Interests: Conflict of interest C. R. B. is a cofounder and Scientific Advisory Board member of Palleon Pharmaceuticals, Enable Bioscience, Redwood Biosciences (a subsidiary of Catalent), InterVenn Biosciences, Lycia Therapeutics, Virsti Therapeutics, OliLux Biosciences, and GanNA Bio. S. W. and C. R. B. are coinventors on a patent application related to work reviewed in this article held by Stanford University (grant no.: PCT/US2020/041603)., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

The success of colloidal semiconductor nanocrystals (NCs) in science and optoelectronics is inextricable from their surfaces. The functionalization of lead halide perovskite NCs 1-5 poses a formidable challenge because of their structural lability, unlike the well-established covalent ligand capping of conventional semiconductor NCs 6,7 . We posited that the vast and facile molecular engineering of phospholipids as zwitterionic surfactants can deliver highly customized surface chemistries for metal halide NCs. Molecular dynamics simulations implied that ligand-NC surface affinity is primarily governed by the structure of the zwitterionic head group, particularly by the geometric fitness of the anionic and cationic moieties into the surface lattice sites, as corroborated by the nuclear magnetic resonance and Fourier-transform infrared spectroscopy data. Lattice-matched primary-ammonium phospholipids enhance the structural and colloidal integrity of hybrid organic-inorganic lead halide perovskites (FAPbBr 3 and MAPbBr 3 (FA, formamidinium; MA, methylammonium)) and lead-free metal halide NCs. The molecular structure of the organic ligand tail governs the long-term colloidal stability and compatibility with solvents of diverse polarity, from hydrocarbons to acetone and alcohols. These NCs exhibit photoluminescence quantum yield of more than 96% in solution and solids and minimal photoluminescence intermittency at the single particle level with an average ON fraction as high as 94%, as well as bright and high-purity (about 95%) single-photon emission., (© 2023. The Author(s).)

Traditionally, drugs are monovalent, targeting only one site on the protein surface. This includes orthosteric and allosteric drugs, which bind the protein at orthosteric and allosteric sites, respectively. Orthosteric drugs are good in potency, whereas allosteric drugs have better selectivity and are solutions to classically undruggable targets. However, it would be difficult to simultaneously reach high potency and selectivity when targeting only one site. Also, both kinds of monovalent drugs suffer from mutation-caused drug resistance. To overcome these obstacles, dualsteric modulators have been proposed in the past twenty years. Compared to orthosteric or allosteric drugs, dualsteric modulators are bivalent (or bitopic) with two pharmacophores. Each of the two pharmacophores bind the protein at the orthosteric and an allosteric site, which could bring the modulator with special properties beyond monovalent drugs. In this study, we comprehensively review the current development of dualsteric modulators. Our main effort reason and illustrate the aims to apply the dualsteric approach, including a "double win" of potency and selectivity, overcoming mutation-caused drug resistance, developments of function-biased modulators, and design of partial agonists. Moreover, the strengths of the dualsteric technique also led to its application outside pharmacy, including the design of highly sensitive fluorescent tracers and usage as molecular rulers. Besides, we also introduced drug targets, designing strategies, and validation methods of dualsteric modulators. Finally, we detail the conclusions and perspectives.

Computational catalyst design requires identification of a metal and ligand that together result in the desired reaction reactivity and/or selectivity. A major impediment to translating computational designs to experiments is evaluating ligands that are likely to be synthesized. Here, we provide a solution to this impediment with our ReaLigands library that contains >30,000 monodentate, bidentate (didentate), tridentate, and larger ligands cultivated by dismantling experimentally reported crystal structures. Individual ligands from mononuclear crystal structures were identified using a modified depth-first search algorithm and charge was assigned using a machine learning model based on quantum-chemical calculated features. In the library, ligands are sorted based on direct ligand-to-metal atomic connections and on denticity. Representative principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) analyses were used to analyze several tridentate ligand categories, which revealed both the diversity of ligands and connections between ligand categories. We also demonstrated the utility of this library by implementing it with our building and optimization tools, which resulted in the very rapid generation of barriers for 750 bidentate ligands for Rh-hydride ethylene migratory insertion.

In this work, we investigate how spatial proximity of enzymes belonging to the same pathway (metabolon) affects metabolic flux. Using off-lattice Langevin dynamics simulations in tandem with a stochastic reaction-diffusion protocol and a semi-analytical reaction-diffusion model, we systematically explored how strength of protein-protein interactions, catalytic efficiency, and protein-ligand interactions affect metabolic flux through the metabolon. Formation of a metabolon leads to a greater speedup for longer pathways and especially for reaction-limited enzymes, whereas, for fully optimized diffusion-limited enzymes, the effect is negligible. Notably, specific cluster architectures are not a prerequisite for enhancing reaction flux. Simulations uncover the crucial role of optimal nonspecific protein-ligand interactions in enhancing catalytic efficiency of a metabolon. Our theory implies, and bioinformatics analysis confirms, that longer catalytic pathways are enriched in less optimal enzymes, whereas most diffusion-limited enzymes populate shorter pathways. Our findings point toward a plausible evolutionary strategy where enzymes compensate for less-than-optimal efficiency by increasing their local concentration in the clustered state., Competing Interests: Declaration of interests The authors declare that they have no competing interests., (Copyright © 2023 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Gathering information from multi-perspective graphs is an essential issue for many applications especially for protein-ligand-binding affinity prediction. Most of traditional approaches obtained such information individually with low interpretability. In this paper, we harness the rich information from multi-perspective graphs with a general model, which abstractly represents protein-ligand complexes with better interpretability while achieving excellent predictive performance. In addition, we specially analyze the protein-ligand-binding affinity problem, taking into account the heterogeneity of proteins and ligands. Experimental evaluations demonstrate the effectiveness of our data representation strategy on public datasets by fusing information from different perspectives. All codes are available in the https://github.com/Jthy-af/HaPPy ., (© 2023. International Association of Scientists in the Interdisciplinary Areas.)

Fast and accurate calculation of intermolecular interaction energies is desirable for understanding many chemical and biological processes, including the binding of small molecules to proteins. The Splinter ["Symmetry-adapted perturbation theory (SAPT0) protein-ligand interaction"] dataset has been created to facilitate the development and improvement of methods for performing such calculations. Molecular fragments representing commonly found substructures in proteins and small-molecule ligands were paired into >9000 unique dimers, assembled into numerous configurations using an approach designed to adequately cover the breadth of the dimers' potential energy surfaces while enhancing sampling in favorable regions. ~1.5 million configurations of these dimers were randomly generated, and a structurally diverse subset of these were minimized to obtain an additional ~80 thousand local and global minima. For all >1.6 million configurations, SAPT0 calculations were performed with two basis sets to complete the dataset. It is expected that Splinter will be a useful benchmark dataset for training and testing various methods for the calculation of intermolecular interaction energies., (© 2023. Springer Nature Limited.)

Cryptic pockets, or pockets absent in ligand-free, experimentally determined structures, hold great potential as drug targets. However, cryptic pocket openings are often beyond the reach of conventional biomolecular simulations because certain cryptic pocket openings involve slow motions. Here, we investigate whether AlphaFold can be used to accelerate cryptic pocket discovery either by generating structures with open pockets directly or generating structures with partially open pockets that can be used as starting points for simulations. We use AlphaFold to generate ensembles for 10 known cryptic pocket examples, including five that were deposited after AlphaFold's training data were extracted from the PDB. We find that in 6 out of 10 cases AlphaFold samples the open state. For plasmepsin II, an aspartic protease from the causative agent of malaria, AlphaFold only captures a partial pocket opening. As a result, we ran simulations from an ensemble of AlphaFold-generated structures and show that this strategy samples cryptic pocket opening, even though an equivalent amount of simulations launched from a ligand-free experimental structure fails to do so. Markov state models (MSMs) constructed from the AlphaFold-seeded simulations quickly yield a free energy landscape of cryptic pocket opening that is in good agreement with the same landscape generated with well-tempered metadynamics. Taken together, our results demonstrate that AlphaFold has a useful role to play in cryptic pocket discovery but that many cryptic pockets may remain difficult to sample using AlphaFold alone.

Protein A affinity chromatography is widely used for the large-scale purification of antibodies because of its high yield, selectivity, and compatibility with NaOH sanitation. A general platform to produce robust affinity capture ligands for proteins beyond antibodies would improve bioprocessing efficiency. We previously developed nanoCLAMPs (nano Clostridial Antibody Mimetic Proteins), a class of antibody mimetic proteins useful as lab-scale affinity capture reagents. This work describes a protein engineering campaign to develop a more robust nanoCLAMP scaffold compatible with harsh bioprocessing conditions. The campaign generated an improved scaffold with dramatically improved resistance to heat, proteases, and NaOH. To isolate additional nanoCLAMPs based on this scaffold, we constructed a randomized library of 1 × 10 10 clones and isolated binders to several targets. We then performed an in-depth characterization of nanoCLAMPs recognizing yeast SUMO, a fusion partner used for the purification of recombinant proteins. These second-generation nanoCLAMPs typically had a K d of <80 nM, a T m of >70 °C, and a t 1/2 in 0.1 mg/ml trypsin of >20 h. Affinity chromatography resins bearing these next-generation nanoCLAMPs enabled single-step purifications of SUMO fusions. Bound target proteins could be eluted at neutral or acidic pH. These affinity resins maintained binding capacity and selectivity over 20 purification cycles, each including 10 min of cleaning-in-place with 0.1 M NaOH, and remained functional after exposure to 100% DMF and autoclaving. The improved nanoCLAMP scaffold will enable the development of robust, high-performance affinity chromatography resins against a wide range of protein targets., Competing Interests: Conflict of interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: RJS and DMC are significant shareholders of Nectagen, Inc., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Molecular clustering analysis has been developed to facilitate visual inspection in the process of structure-based virtual screening. However, traditional methods based on molecular fingerprints or molecular descriptors limit the accuracy of selecting active hit compounds, which may be attributed to the lack of representations of receptor structural and protein-ligand interaction during the clustering. Here, a novel deep clustering framework named ClusterX is proposed to learn molecular representations of protein-ligand complexes and cluster the ligands. In ClusterX, the graph was used to represent the protein-ligand complex, and the joint optimisation can be used efficiently for learning the cluster-friendly features. Experiments on the KLIFs database show that the model can distinguish well between the binding modes of different kinase inhibitors. To validate the effectiveness of the model, the clustering results on the virtual screening dataset further demonstrated that ClusterX achieved better or more competitive performance against traditional methods, such as SIFt and extended connectivity fingerprints. This framework may provide a unique tool for clustering analysis and prove to assist computational medicinal chemists in visual decision-making., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

The κ-opioid receptor (KOR) represents a highly desirable therapeutic target for treating not only pain but also addiction and affective disorders 1 . However, the development of KOR analgesics has been hindered by the associated hallucinogenic side effects 2 . The initiation of KOR signalling requires the G i/o -family proteins including the conventional (G i1 , G i2 , G i3 , G oA and G oB ) and nonconventional (G z and G g ) subtypes. How hallucinogens exert their actions through KOR and how KOR determines G-protein subtype selectivity are not well understood. Here we determined the active-state structures of KOR in a complex with multiple G-protein heterotrimers-G i1 , G oA , G z and G g -using cryo-electron microscopy. The KOR-G-protein complexes are bound to hallucinogenic salvinorins or highly selective KOR agonists. Comparisons of these structures reveal molecular determinants critical for KOR-G-protein interactions as well as key elements governing G i/o -family subtype selectivity and KOR ligand selectivity. Furthermore, the four G-protein subtypes display an intrinsically different binding affinity and allosteric activity on agonist binding at KOR. These results provide insights into the actions of opioids and G-protein-coupling specificity at KOR and establish a foundation to examine the therapeutic potential of pathway-selective agonists of KOR., (© 2023. The Author(s).)

Photoaffinity ligands are best known as tools used to identify the specific binding sites of drugs to their molecular targets. However, photoaffinity ligands have the potential to further define critical neuroanatomic targets of drug action. In the brains of WT male mice, we demonstrate the feasibility of using photoaffinity ligands in vivo to prolong anesthesia via targeted yet spatially restricted photoadduction of azi- m -propofol (aziPm), a photoreactive analog of the general anesthetic propofol. Systemic administration of aziPm with bilateral near-ultraviolet photoadduction in the rostral pons, at the border of the parabrachial nucleus and locus coeruleus, produced a 20-fold increase in the duration of sedative and hypnotic effects compared with control mice without UV illumination. Photoadduction that missed the parabrachial-coerulean complex also failed to extend the sedative or hypnotic actions of aziPm and was indistinguishable from nonadducted controls. Paralleling the prolonged behavioral and EEG consequences of on target in vivo photoadduction, we conducted electrophysiologic recordings in rostral pontine brain slices. Using neurons within the locus coeruleus to further highlight the cellular consequences of irreversible aziPm binding, we demonstrate transient slowing of spontaneous action potentials with a brief bath application of aziPm that becomes irreversible on photoadduction. Together, these findings suggest that photochemistry-based strategies are a viable new approach for probing CNS physiology and pathophysiology. SIGNIFICANCE STATEMENT Photoaffinity ligands are drugs capable of light-induced irreversible binding, which have unexploited potential to identify the neuroanatomic sites of drug action. We systemically administer a centrally acting anesthetic photoaffinity ligand in mice, conduct localized photoillumination within the brain to covalently adduct the drug at its in vivo sites of action, and successfully enrich irreversible drug binding within a restricted 250 µm radius. When photoadduction encompassed the pontine parabrachial-coerulean complex, anesthetic sedation and hypnosis was prolonged 20-fold, thus illustrating the power of in vivo photochemistry to help unravel neuronal mechanisms of drug action., (Copyright © 2023 McKinstry-Wu, Wasilczuk et al.)

This dataset contains ligand conformations and docking scores for 1.4 billion molecules docked against 6 structural targets from SARS-CoV2, representing 5 unique proteins: MPro, NSP15, PLPro, RDRP, and the Spike protein. Docking was carried out using the AutoDock-GPU platform on the Summit supercomputer and Google Cloud. The docking procedure employed the Solis Wets search method to generate 20 independent ligand binding poses per compound. Each compound geometry was scored using the AutoDock free energy estimate, and rescored using RFScore v3 and DUD-E machine-learned rescoring models. Input protein structures are included, suitable for use by AutoDock-GPU and other docking programs. As the result of an exceptionally large docking campaign, this dataset represents a valuable resource for discovering trends across small molecule and protein binding sites, training AI models, and comparing to inhibitor compounds targeting SARS-CoV-2. The work also gives an example of how to organize and process data from ultra-large docking screens., (© 2023. UT-Battelle, LLC.)

We discuss how data unbiasing and simple methods such as protein-ligand Interaction FingerPrint (IFP) can overestimate virtual screening performance. We also show that IFP is strongly outperformed by target-specific machine-learning scoring functions, which were not considered in a recent report concluding that simple methods were better than machine-learning scoring functions at virtual screening.

Heparan sulfates (HS) proteoglycans are commonly found on the cell surface and mediate many processes. Binding of HS ligands is determined by the sulfation code on the HS chain that can be N-/2-O/6-O- or 3-O-sulfated, generating heterogenous sulfation patterns. 3-O sulfated HS (3S-HS) play a role in several (patho)physiological processes such as blood coagulation, viral pathogenesis and binding and internalization of tau in Alzheimer's disease. However, few 3S-HS-specific interactors are known. Thus, our insight into the role of 3S-HS in health and disease is limited, especially in the central nervous system. Using human CSF, we determined the interactome of synthetic HS with defined sulfation patterns. Our affinity-enrichment mass spectrometry studies expand the repertoire of proteins that may interact with (3S-)HS. Validating our approach, ATIII, a known 3S-HS interactor, was found to require GlcA-GlcNS6S3S for binding, similar to what has been reported. Our dataset holds novel, potential HS and 3S-HS protein ligands, that can be explored in future studies focusing on molecular mechanisms that depend on 3S-HS in (patho)physiological conditions., (© 2023. The Author(s).)

Adhesion G-protein-coupled receptors (aGPCRs) bear notable similarity to Notch proteins 1 , a class of surface receptors poised for mechano-proteolytic activation 2-4 , including an evolutionarily conserved mechanism of cleavage 5-8 . However, so far there is no unifying explanation for why aGPCRs are autoproteolytically processed. Here we introduce a genetically encoded sensor system to detect the dissociation events of aGPCR heterodimers into their constituent N-terminal and C-terminal fragments (NTFs and CTFs, respectively). An NTF release sensor (NRS) of the neural latrophilin-type aGPCR Cirl (ADGRL) 9-11 , from Drosophila melanogaster, is stimulated by mechanical force. Cirl-NRS activation indicates that receptor dissociation occurs in neurons and cortex glial cells. The release of NTFs from cortex glial cells requires trans-interaction between Cirl and its ligand, the Toll-like receptor Tollo (Toll-8) 12 , on neural progenitor cells, whereas expressing Cirl and Tollo in cis suppresses dissociation of the aGPCR. This interaction is necessary to control the size of the neuroblast pool in the central nervous system. We conclude that receptor autoproteolysis enables non-cell-autonomous activities of aGPCRs, and that the dissociation of aGPCRs is controlled by their ligand expression profile and by mechanical force. The NRS system will be helpful in elucidating the physiological roles and signal modulators of aGPCRs, which constitute a large untapped reservoir of drug targets for cardiovascular, immune, neuropsychiatric and neoplastic diseases 13 ., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Allosteric modulators are of prime interest in drug discovery. These drugs regulate the binding and function of endogenous ligands, with some advantages over orthosteric ligands. A typical pharmacological parameter in allosteric modulation is binding cooperativity. This property can yield unexpected but illuminating results when decomposed into its kinetic parameters. Using two reference models (the allosteric ternary complex receptor model and a heterodimer receptor model), a relationship has been derived for the cooperativity rate constant parameters. This relationship allows many combinations of the cooperativity kinetic parameters for a single binding cooperativity value obtained under equilibrium conditions. This assessment may help understand striking experimental results involving allosteric modulation and suggest further investigations in the field., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

A ligand-accessible space in the CYP2C19 active site was reconstituted as a fused grid-based Template with the use of structural data of the ligands. An evaluation system of CYP2C19-mediated metabolism has been developed on Template with the introduction of the idea of Trigger-residue initiated ligand-movement and fastening. Reciprocal comparison of the data of simulation on Template with experimental results suggested a unified way of the interaction of CYP2C19 and its ligands through the simultaneous plural-contact with Rear-wall of Template. CYP2C19 was expected to have a room for ligands between vertically standing parallel walls termed Facial-wall and Rear-wall, which were separated by a distance corresponding to 1.5-Ring (grid) diameter size. The ligand sittings were stabilized through contacts with Facial-wall and the left-side borders of Template including specific Position 29 or Left-end after Trigger-residue initiated ligand-movement. Trigger-residue movement is suggested to force ligands to stay firmly in the active site and then to initiate CYP2C19 reactions. Simulation experiments for over 450 reactions of CYP2C19 ligands supported the system established., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2022. Published by Elsevier Ltd.)

The paddlewheel [Ru 2 Cl(O 2 CCH 3 ) 4 ] complex was previously reported to react with the model protein hen egg white lysozyme (HEWL), forming adducts with two diruthenium moieties bound to Asp101 and Asp119 side chains upon the release of one acetate. To study the effect of the equatorial ligands on the reactivity with proteins of diruthenium compounds, X-ray structures of the adducts formed when HEWL reacts with [Ru 2 Cl(D- p -FPhF)(O 2 CCH 3 ) 3 ] [D- p -FPhF = N , N '-bis(4-fluorophenyl)formamidinate] under different conditions were solved. [Ru 2 Cl(D- p -FPhF)(O 2 CCH 3 ) 3 ] is bonded through their equatorial positions to the Asp side chains. Protein binding occurs cis or trans to D- p -FPhF. Lys or Arg side chains or even main-chain carbonyl groups can coordinate to the diruthenium core at the axial site. Data help to understand the reactivity of paddlewheel diruthenium complexes with proteins, providing useful information for the design of new artificial diruthenium-containing metalloenzymes with potential applications in the fields of catalysis, biomedicine, and biotechnology.

Carbenes with conjugatively connected redox system act as "auto-umpolung" ligands. Due to their electronic flexibility, they should also be particularly suitable to stabilize open-shell species. Herein, the first neutral radical of such sort is described in form of a dialkylamino-substituted bis(dicyanomethylene)cyclopropanide. Despite the absence of steric shielding, the radical is stable for an extended amount of time and was consequently characterized in solution via EPR measurements. These data and accompanying X-ray structural analyses indicate that the radical species is in equilibrium with aggregates (formed via π-stacking) and dimers (obtained via σ-bond formation between methylene carbons)., (© 2022 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Optimization of the catalyst structure to simultaneously improve multiple reaction objectives (e.g., yield, enantioselectivity, and regioselectivity) remains a formidable challenge. Herein, we describe a machine learning workflow for the multi-objective optimization of catalytic reactions that employ chiral bisphosphine ligands. This was demonstrated through the optimization of two sequential reactions required in the asymmetric synthesis of an active pharmaceutical ingredient. To accomplish this, a density functional theory-derived database of >550 bisphosphine ligands was constructed, and a designer chemical space mapping technique was established. The protocol used classification methods to identify active catalysts, followed by linear regression to model reaction selectivity. This led to the prediction and validation of significantly improved ligands for all reaction outputs, suggesting a general strategy that can be readily implemented for reaction optimizations where performance is controlled by bisphosphine ligands.

Unique π-cyclopentadienyl bridged dialanes are synthesized as complex salts with aluminate anions by comproportionation of aluminocenium cations [Al III (Cp)(Cp*)] + /[Al III Cp 2 ] + with [(Al I Cp*) 4 ]. Very short Al-Al bond lengths occur in positively charged Al 2 fragments. Intriguingly, the prepared asymmetric dialane shows a unique fluxional coordination of the cyclopentadienyl ligands.4+ fragments. Intriguingly, the prepared asymmetric dialane shows a unique fluxional coordination of the cyclopentadienyl ligands.

The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Photochemical studies on supramolecular hosts that can encapsulate small guest molecules commonly focus on three aspects: photoswitching the cage to release or trap the guest, the effect of the confining environment on the guest, and light-induced exciton or charge transfer within the cage structure. Here, we exploit ultrafast spectroscopy to address how the guest alters the photoswitching characteristics of the cage. For this, the impacts of three disparate guest compounds on ring-opening or ring-closure of a dithienylethene (DTE) ligand in a photoswitchable DTE-based coordination cage are juxtaposed. The guest modulates both outcome and timescale of the cage's photodynamics, by an interplay of structural strain, heavy-atom effect, and enhancement of charge-transfer processes exercised by the guest on the photo-excited cage. The approach might prove beneficial for attuning the applicability of photoswitchable nanocontainers and desired guest compounds., (© 2022 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Although parallel plate flow chamber assays are widely performed, extraction of kinetic parameters is limited to specialized labs with mathematical expertise and customized video-microscopy tracking tools. The recent development of Trackmate has increased researcher accessibility to tracking particles in video-microscopy experiments; however, there is a lack of tools that analyze this tracking information. We report a software tool, compatible with Trackmate, that extracts Receptor Ligand Non-Equilibrium Kinetic (RLNEK) parameters from video-microscopy data. This software should be of particular interest to the community of researchers and scientists interrogating the target-specific binding and release of immune cells., Competing Interests: Declaration of Competing Interest None., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Nanosized molecular clusters (MCs) composed of PbBr 2 and neutral ligand butylamine (BTYA) with unique optical properties in solution and solid states have been synthesized using ligand-assisted reprecipitation and spin-coating, separately. The studies of their optical properties using ultraviolet-visible (UV-vis) absorption and photoluminescence (PL) show the first electronic absorption and PL band of the MCs at 401 and 411 nm, respectively, for the solution and solid state samples that exhibit good stability under ambient conditions. Low-temperature PL spectra below 30 K show vibronic peaks indicative of a single size or a very narrow size distribution of the MCs. On the basis of Raman, X-ray diffraction, and transmission electron microscopy measurements, a layered structural model is proposed for the MCs with a BTYA ligand capping on the surface of the corner-shared tilted [PbBr 6 ] 4- octahedral framework. The stable and retained structure of MCs in the solid state is promising for photonics applications.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the deadly coronavirus disease 2019 (Covid-19) and is a concerning hazard to public health. This virus infects cells by establishing a contact between its spike protein (S-protein) and host human angiotensin-converting enzyme 2 (hACE2) receptor, subsequently initiating viral fusion. The inhibition of the interaction between the S-protein and hACE2 has immediately drawn attention amongst the scientific community, and the S-protein was considered the prime target to design vaccines and to develop affinity ligands for diagnostics and therapy. Several S-protein binders have been reported at a fast pace, ranging from antibodies isolated from immunised patients to de novo designed ligands, with some binders already yielding promising in vivo results in protecting against SARS-CoV-2. Natural, engineered and designed affinity ligands targeting the S-protein are herein summarised, focusing on molecular recognition aspects, whilst identifying preferred hot spots for ligand binding. This review serves as inspiration for the improvement of already existing ligands or for the design of new affinity ligands towards SARS-CoV-2 proteins. Lessons learnt from the Covid-19 pandemic are also important to consolidate tools and processes in protein engineering to enable the fast discovery, production and delivery of diagnostic, prophylactic, and therapeutic solutions in future pandemics., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

α2-adrenoceptors, (α2A, α2B and α2C-subtypes), are Gi-coupled receptors. Central activation of brain α2A and α2C-adrenoceptors is the main site for α2-agonist mediated clinical responses in hypertension, ADHD, muscle spasm and ITU management of sedation, reduction in opiate requirements, nausea and delirium. However, despite having the same Gi-potency in functional assays, some α2-agonists also stimulate Gs-responses whilst others do not. This was investigated. Agonist responses to 49 different α-agonists were studied (CRE-gene transcription, cAMP, ERK1/2-phosphorylation and binding affinity) in CHO cells stably expressing the human α2A, α2B or α2C-adrenoceptor, enabling ligand intrinsic efficacy to be determined (binding K D /Gi-IC 50 ). Ligands with high intrinsic efficacy (e.g., brimonidine and moxonidine at α2A) stimulated biphasic (Gi-Gs) concentration responses, however for ligands with low intrinsic efficacy (e.g., naphazoline), responses were monophasic (Gi-only). ERK1/2-phosphorylation responses appeared to be Gi-mediated. For Gs-mediated responses to be observed, both a system with high receptor reserve and high agonist intrinsic efficacy were required. From the Gi-mediated efficacy ratio, the degree of Gs-coupling could be predicted. The clinical relevance and precise receptor conformational changes that occur, given the structural diversity of compounds with high intrinsic efficacy, remains to be determined. Comparison with α1 and β1/β2-adrenoceptors demonstrated subclass affinity selectivity for some compounds (e.g., α2:dexmedetomidine, α1:A61603) whilst e.g., oxymetazoline had high affinity for both α2A and α1A-subtypes, compared to all others. Some compounds had subclass selectivity due to selective intrinsic efficacy (e.g., α2:brimonidine, α1:methoxamine/etilefrine). A detailed knowledge of these agonist characteristics is vital for improving computer-based deep-learning and drug design., (© 2022 The Authors. Pharmacology Research & Perspectives published by British Pharmacological Society and American Society for Pharmacology and Experimental Therapeutics and John Wiley & Sons Ltd.)

SARS-CoV-2 main protease is one of the major targets in drug development efforts against Covid-19. Even though several structures were reported to date, its dynamics is not understood well. In particular, impact of dimerization and ligand binding on the dynamics is an important issue to investigate. In this study, we performed molecular dynamics simulations of SARS-CoV and SARS-CoV-2 main proteases to investigate influence of dimerization on the dynamics by modeling monomeric and dimeric apo and holo forms. The dimerization causes an organization of the interdomain dynamics as well as some local structural changes. Moreover, we investigated impact of a peptide mimetic (N3) on the dynamics of SARS-CoV and SARS-CoV-2 Mpro. The ligand binding to the dimeric forms causes some key local changes at the dimer interface and it causes an allosteric interaction between the active sites of two protomers. Our results support the idea that only one protomer is active on SARS-CoV-2 due to this allosteric interaction. Additionally, we analyzed the molecular dynamics trajectories from graph theoretical perspective and found that the most influential residues - as measured by eigenvector centrality - are a group of residues in active site and dimeric interface of the protease. This study may form a bridge between what we know about the dynamics of SARS-CoV and SARS-CoV-2 Mpro. We think that enlightening allosteric communication of the active sites and the role of dimerization in SARS-CoV-2 Mpro can contribute to development of novel drugs against this global health problem as well as other similar proteases. Communicated by Ramaswamy H. Sarma.

Somatostatin and its analogues, known as somatostatin receptor ligands (SRLs), have been reported to attenuate weight gain in some clinical settings. However, their direct effects on preadipocytes are barely investigated. Therefore, this study aimed to evaluate the influence of SRLs on preadipocytes and to further explore the potential mechanisms. Cell Counting Kit-8 assay, Oil Red O staining, triglyceride contents measurements, quantitative polymerase chain reaction (qPCR) and western blot were used to investigate the effects of SRLs on preadipocytes. We found that three SRLs (octreotide, TT232 and pasireotide) inhibited cell viability after 8-48 h but not 4 h. Further western blot results showed that they significantly suppressed activation of PI3K/Akt pathway. Besides, lipid accumulation was also significantly inhibited by these SRLs. Moreover, mRNA levels of some critical adipogenic markers, including Pparg, Cebpa, Fasn, Fabp4, Acaca and Lpl, were downregulated by the treatments of all these SRLs. Consistently, the protein expression of peroxisome proliferator-activated receptor γ (PPARγ), CCAAT/enhancer binding protein α (C/EBPα) and fatty acid synthase (FAS) was also suppressed by SRLs. SRLs inhibit the proliferation and lipogenesis in preadipocytes. Their inhibitory effects on cell proliferation may be mediated by the downregulated PI3K/Akt pathway, and the suppressive actions on lipogenesis may be related to the decreased PPARγ and C/EBPα expression., (© 2022 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society). Published by John Wiley & Sons Ltd.)

G protein-coupled receptor (GPCR) signaling is ubiquitous. As an archetype of this signaling motif, rod phototransduction has provided many fundamental, quantitative details, including a dogma that one active GPCR molecule activates a substantial number of downstream G protein/enzyme effector complexes. However, rod phototransduction is light-activated, whereas GPCR pathways are predominantly ligand-activated. Here, we report a detailed study of the ligand-triggered GPCR pathway in mammalian olfactory transduction, finding that an odorant-receptor molecule when (one-time) complexed with its most effective odorants produces on average much less than one downstream effector. Further experiments gave a nominal success probability of tentatively ∼10 -4 (more conservatively, ∼10 -2 to ∼10 -5 ). This picture is potentially more generally representative of GPCR signaling than is rod phototransduction, constituting a paradigm shift.

A ligand-accessible space in the CYP2C9 active site was reconstituted as a fused grid-based Template with the use of structural data of the ligands. CYP2C9 Template generated has been developed as an evaluation system of CYP2C9 metabolism with the introduction of the idea of Trigger-residue initiated ligand-movement and fastening. Reciprocal comparison of the data of simulation on Template with experimental results suggested a unified way of the interaction of CYP2C9 and its ligands through the simultaneous plural-contact with Rear-wall of Template. CYP2C9 was expected to have a room for ligands between vertically standing parallel walls termed Facial-wall and Rear-wall. Both the walls were separated by a distance corresponding to 1.5-Ring (grid) diameter size, which was termed as Width-gauge. The results indicate that ligand sittings are stabilized through contacts with Facial-wall and the left-side border of Template including specific Position 29 or Left-end after Trigger-residue movement. In addition, Trigger-residue movement is suggested to force ligands to stay firmly in the active site and then initiate CYP2C9 reactions. Simulation experiments for over 500 reactions of CYP2C9 ligands supported the system established. Possible modes of enhanced catalyzes in bi-molecule bindings are also discussed., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2022 The Japanese Society for the Study of Xenobiotics. Published by Elsevier Ltd. All rights reserved.)

Function follows form in biology, and the binding of small molecules requires proteins with pockets that match the shape of the ligand. For design of binding to symmetric ligands, protein homo-oligomers with matching symmetry are advantageous as each protein subunit can make identical interactions with the ligand. Here, we describe a general approach to designing hyperstable C2 symmetric proteins with pockets of diverse size and shape. We first designed repeat proteins that sample a continuum of curvatures but have low helical rise, then docked these into C2 symmetric homodimers to generate an extensive range of C2 symmetric cavities. We used this approach to design thousands of C2 symmetric homodimers, and characterized 101 of them experimentally. Of these, the geometry of 31 were confirmed by small angle X-ray scattering and 2 were shown by crystallographic analyses to be in close agreement with the computational design models. These scaffolds provide a rich set of starting points for binding a wide range of C2 symmetric compounds.

Chalcogenide motifs are present as principal moieties in a vast array of natural products and complex molecules. Till date, the construction of these chalcogen motifs has been restricted to either the use of directing groups or the employment of a large excess of electronically activated arenes, typically employed as a cosolvent. Despite being highly effective, these methods have their own limitations in the step economy and the deployment of an excess amount of arenes. Herein, we report the evolution of a catalytic system employing arene-limited, nondirected thioarylation of arenes and heteroarenes using a complimentary dual-ligand approach. The reaction is controlled by a combination of steric and electronic factors, and the utilization of a suitable ligand enables the generation of products on a complimentary spectrum to that generated by classical methods. The combination of ligands remains imperative in the reaction protocol with theoretical calculations pointing towards a monoprotected amino acid ligand being crucial in the concerted metalation deprotonation (CMD) mechanism by a characteristic [5,6]-palladacyclic transition state, while the pyridine moiety assists in the active catalyst species formation and product release. Combined experimental and computational mechanistic investigations point toward the C-H activation step being both regio- and rate-determining. Interestingly, oxidative addition of the diphenyl disulfide substrate is found to be unlikely, and an alternative transmetalation-like mechanism involving the Pd-Ag heterometallic complex is proposed to be operative.

The rapid accumulation of molecular data motivates development of innovative approaches to computationally characterize sequences, structures and functions of biological and chemical molecules in an efficient, accessible and accurate manner. Notwithstanding several computational tools that characterize protein or nucleic acids data, there are no one-stop computational toolkits that comprehensively characterize a wide range of biomolecules. We address this vital need by developing a holistic platform that generates features from sequence and structural data for a diverse collection of molecule types. Our freely available and easy-to-use iFeatureOmega platform generates, analyzes and visualizes 189 representations for biological sequences, structures and ligands. To the best of our knowledge, iFeatureOmega provides the largest scope when directly compared to the current solutions, in terms of the number of feature extraction and analysis approaches and coverage of different molecules. We release three versions of iFeatureOmega including a webserver, command line interface and graphical interface to satisfy needs of experienced bioinformaticians and less computer-savvy biologists and biochemists. With the assistance of iFeatureOmega, users can encode their molecular data into representations that facilitate construction of predictive models and analytical studies. We highlight benefits of iFeatureOmega based on three research applications, demonstrating how it can be used to accelerate and streamline research in bioinformatics, computational biology, and cheminformatics areas. The iFeatureOmega webserver is freely available at http://ifeatureomega.erc.monash.edu and the standalone versions can be downloaded from https://github.com/Superzchen/iFeatureOmega-GUI/ and https://github.com/Superzchen/iFeatureOmega-CLI/., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Dye aggregates have attracted a great deal of attention due to their widespread applications in organic light-emitting devices, light-harvesting systems, etc. However, the strategies to precisely control chromophores with specific spatial arrangements still remain a great challenge. In this work, a series of double- and triple-decker supramolecular complexes are successfully constructed by coordination-driven self-assembly of carefully designed shape-complementary ligands, one claw-like tetraphenylethylene (TPE)-based host ligand and three tetratopic or ditopic guest ligands. The spatial configurations of these assemblies (one double-decker and three "S-shaped" or "X-shaped" triple-decker structures) depend on the angles of these TPE-derived ligands. Notably, the three triple-decker structures are geometric isomers. Furthermore, photophysical studies show that these complexes exhibit different ratios of radiative (k r ) and non-radiative (k nr ) rate constant due to the different spatial arrangements of TPE moieties. This study provides not only a unique strategy for the construction of multi-stacks with specific spatial arrangement, but also a promising platform for investigating the aggregation behavior of fluorescent chromophores., (© 2022 Wiley-VCH GmbH.)

Terpyridine (tpy)-based 3D discrete metallosupramolecular architectures, which are often inspired by polyhedral geometry and the biological structures found in nature, have drawn significant attention from the community of metallosupramolecular chemistry. Because of the linear tpy-M(II)-tpy connectivity, the creation of sophisticated 3D metallosupramolecules based on tpy remains a formidable synthetic challenge. Nevertheless, with recent advancement in ligand design and self-assembly, diverse 3D metallosupramolecular polyhedrons, such as Platonic solids, Archimedean solids, prims as well as Johnson solids, have been constructed and their potential applications have been explored. This review summarizes the progress on tpy-based discrete 3D metallosupramolecules, aiming to shed more light on the design and construction of novel discrete architectures with molecular-level precision through coordination-driven self-assembly., (© 2022 Wiley-VCH GmbH.)

In situ diffraction data collection using crystallization plates has been utilized for macromolecules to evaluate crystal quality without requiring additional sample treatment such as cryocooling. Although it is difficult to collect complete data sets using this technique due to the mechanical limitation of crystal rotation, recent advances in methods for data collection from multiple crystals have overcome this issue. At SPring-8, an in situ diffraction measurement system was constructed consisting of a goniometer for a plate, an articulated robot and plate storage. Using this system, complete data sets were obtained utilizing the small-wedge measurement method. Combining this system with an acoustic liquid handler to prepare protein-ligand complex crystals by applying fragment compounds to trypsin crystals for in situ soaking, binding was confirmed for seven out of eight compounds. These results show that the system functioned properly to collect complete data for structural analysis and to expand the capability for ligand screening in combination with a liquid dispenser., (open access.)