Structure-Based Identification of Kelch-like ECH-Associated Protein 1 as a Pharmacological Target of Electrophile-Containing Catechol-O-Methyltransferase Inhibitors.

Entacapone and nitecapone are electrophile-containing catechol-O-methyltransferase (COMT) inhibitors that are used to treat Parkinson's disease in combination with L-DOPA. It is desirable to investigate whether they can covalently bind to cellular protein targets using their reactive electrophilic warheads. We identified Kelch-like ECH-associated protein 1 (KEAP1), a sensor for oxidative and electrophilic stress, as a potential pharmacological target of both drugs by performing covalent-based reverse docking. We confirmed that both drugs activate nuclear factor erythroid 2-related factor 2 (NRF2) by reversibly modifying C151 on KEAP1. Both drugs can enhance the expression of growth differentiation factor 15 (GDF15) and NRF2 downstream antioxidant response element (ARE) genes, both in vitro and in vivo. Furthermore, both drugs exhibit anti-inflammatory effects in an NRF2-dependent acute gout model. Our findings suggest that these two drugs could be repurposed for the treatment of NRF2-modulated inflammatory diseases, and the 3-methylene-acetylacetone group of nitecapone could serve as a new reversible covalent warhead.

Precisely Engineering Asymmetric Atomic CoN4 by Electron Donating and Extracting for Oxygen Reduction Reaction.

The development of nonpyrolytic catalysts featuring precisely defined active sites represents an effective strategy for investigating the fundamental relationship between the catalytic activity of oxygen reduction reaction (ORR) catalysts and their local coordination environments. In this study, we have synthesized a series of model electrocatalysts with well-defined CoN4 centers and nonplanar symmetric coordination structures. These catalysts were prepared by a sequential process involving the chelation of cobalt salts and 1,10-phenanthroline-based ligands with various substituent groups (phen(X), where X=OH, CH3, H, Br, Cl) onto covalent triazine frameworks (CTFs). By modulating the electron-donating or electron-withdrawing properties of the substituent groups on the phen-based ligands, the electron density surrounding the CoN4 centers was effectively controlled. Our results demonstrated a direct correlation between the catalytic activity of the CoN4 centers and the electron-donating ability of the substituent group on the phenanthroline ligands. Notably, the catalyst denoted as BCTF-Co-phen(OH), featuring the electron-donating OH group, exhibited the highest ORR catalytic activity. This custom-crafted catalyst achieved a remarkable half-wave potential of up to 0.80 V vs. RHE and an impressive turnover frequency (TOF) value of 47.4×10-3 Hz at 0.80 V vs. RHE in an alkaline environment.

Reduction of Superoxide Radical Intermediate by Polydopamine for Efficient Hydrogen Peroxide Photosynthesis.

The synthesis of hydrogen peroxide through artificial photosynthesis is a green and promising technology with advantages in sustainability, economy and safety. However, superoxide radical (⋅O2 -), an important intermediate in photocatalytic oxygen reduction to H2O2 production, has strong oxidizing properties that potentially destabilize the catalyst. Therefore, avoiding the accumulation of ⋅O2 - for its rapid conversion to H2O2 is of paramount significance in improving catalyst stability and H2O2 yield. In this work, a strategy was developed to utilize protonated groups for the rapid depletion of converted ⋅O2 -, thereby the efficiency of photocatalytic synthesis of H2O2 from CN was successfully enhanced by 47-fold. The experimental findings demonstrated that polydopamine not only improved carrier separation efficiency, and more importantly, provided the adsorption reduction active site for ⋅O2 - for efficient H2O2 production. This work offers a versatile approach for synthesizing efficient and stable photocatalysts.

Structure-Based Identification of Organoruthenium Compounds as Nanomolar Antagonists of Cannabinoid Receptors.

Metal complexes exhibit a diverse range of coordination geometries, representing novel privileged scaffolds with convenient click types of preparation inaccessible for typical carbon-centered organic compounds. Herein, we explored the opportunity to identify biologically active organometallic complexes by reverse docking of a rigid, minimum-size octahedral organoruthenium scaffold against thousands of protein-binding pockets. Interestingly, cannabinoid receptor type 1 (CB1) was identified based on the docking scores and the degree of overlap between the docked organoruthenium scaffold and the hydrophobic scaffold of the cocrystallized ligand. Further structure-based optimization led to the discovery of organoruthenium complexes with nanomolar binding affinities and high selectivity toward CB2. Our work indicates that octahedral organoruthenium scaffolds may be advantageous for targeting the large and hydrophobic binding pockets and that the reverse docking approach may facilitate the discovery of novel privileged scaffolds, such as organometallic complexes, for exploring chemical space in lead discovery.

A High-Quality Data Set of Protein-Ligand Binding Interactions Via Comparative Complex Structure Modeling.

High-quality protein-ligand complex structures provide the basis for understanding the nature of noncovalent binding interactions at the atomic level and enable structure-based drug design. However, experimentally determined complex structures are scarce compared with the vast chemical space. In this study, we addressed this issue by constructing the BindingNet data set via comparative complex structure modeling, which contains 69,816 modeled high-quality protein-ligand complex structures with experimental binding affinity data. BindingNet provides valuable insights into investigating protein-ligand interactions, allowing visual inspection and interpretation of structural analogues' structure-activity relationships. It can also be used for evaluating machine-learning-based scoring functions. Our results indicate that machine learning models trained on BindingNet could reduce the bias caused by buried solvent-accessible surface area, as we previously found for models trained on the PDBbind data set. We also discussed strategies to improve BindingNet and its potential utilization for benchmarking the molecular docking methods and ligand binding free energy calculation approaches. The BindingNet complements PDBbind in constructing a sufficient and unbiased protein-ligand binding data set and is freely available at http://bindingnet.huanglab.org.cn.

Amorphous MnO2 Lamellae Encapsulated Covalent Triazine Polymer-Derived Multi-Heteroatoms-Doped Carbon for ORR/OER Bifunctional Electrocatalysis.

The intelligent construction of non-noble metal materials that exhibit reversible oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) with bifunctional electrocatalytic performance is greatly coveted in the realm of zinc-air batteries (ZABs). Herein, a crafted structure-amorphous MnO2 lamellae encapsulated covalent triazine polymer-derived N, S, P co-doped carbon sphere (A-MnO2 /NSPC) is designed using a self-doped pyrolysis coupled with an in situ encapsulation strategy. The customized A-MnO2 /NSPC-2 demonstrates a superior bifunctional electrocatalytic performance, confirmed by a small ΔE index of 0.64 V for ORR/OER. Experimental investigations, along with density functional theory calculations validate that predesigned amorphous MnO2 surface defects and abundant heteroatom catalytic active sites collectively enhance the oxygen electrocatalytic performance. Impressively, the A-MnO2 /NSPC-based rechargeable liquid ZABs show a large open-circuit potential of 1.54 V, an ultrahigh peak power density of 181 mW cm-2 , an enormous capacity of 816 mAh g-1 , and a remarkable stability for more than 1720 discharging/charging cycles. Additionally, the assembled flexible all-solid-state ZABs also demonstrate outstanding cycle stability, surpassing 140 discharging/charging cycles. Therefore, this highly operable synthetic strategy offers substantial understanding in the development of magnificent bifunctional electrocatalysts for various sustainable energy conversions and beyond.

Bimetallic-Coordinated Covalent Triazine Framework-Derived FeNi Alloy Nanoparticle-Decorated Coral-Like Nanocarbons for Oxygen Electrocatalysis.

It is highly desirable to fabricate transition bimetallic alloy-embedded porous nanocarbons with a unique nanoarchitecture for the oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) in rechargeable zinc-air batteries. In this work, we introduce a template-assisted in situ alloying synthesis of FeNi alloy nanoparticle-decorated coral-like nanocarbons (FeNi-CNCs) as efficient OER/ORR dual-functional electrocatalysts. The present materials are produced through polycondensation of a covalent triazine framework (CTF), the coordination of Ni and Fe ions, and sequential pyrolytic treatment. Through the pyrolysis process, the nanolamellar FeNi-CTF precursors can be facilely converted into FeNi alloy nanoparticle-decorated nanocarbons. These nanocarbons possess a distinctive three-dimensional (3D) coral-like nanostructure, which is favorable for the transport of oxygen and the diffusion of electrolyte. As a result, FeNi-CNC-800 with the highest efficiency exhibited remarkable electrocatalytic performance and great durability. Additionally, it also can be assembled into rechargeable zinc-air batteries that can be assembled in both liquid and solid forms, offering a superior peak power density, large specific capacity, and outstanding reusability during charging/discharging cycles (e.g., 5160 charging-and-discharging cycles at 10 mA cm-2 for the liquid forms). These traits make it a highly promising option in the burgeoning field of wearable energy conversion.

Specific binding of GPR174 by endogenous lysophosphatidylserine leads to high constitutive Gs signaling.

Many orphan G protein-coupled receptors (GPCRs) remain understudied because their endogenous ligands are unknown. Here, we show that a group of class A/rhodopsin-like orphan GPCRs including GPR61, GPR161 and GPR174 increase the cAMP level similarly to fully activated D1 dopamine receptor (D1R). We report cryo-electron microscopy structures of the GPR61‒Gs, GPR161‒Gs and GPR174‒Gs complexes without any exogenous ligands. The GPR174 structure reveals that endogenous lysophosphatidylserine (lysoPS) is copurified. While GPR174 fails to respond to exogenous lysoPS, likely owing to its maximal activation by the endogenous ligand, GPR174 mutants with lower ligand binding affinities can be specifically activated by lysoPS but not other lipids, in a dose-dependent manner. Moreover, GPR174 adopts a non-canonical Gs coupling mode. The structures of GPR161 and GPR61 reveal that the second extracellular loop (ECL2) penetrates into the orthosteric pocket, possibly contributing to constitutive activity. Our work definitively confirms lysoPS as an endogenous GPR174 ligand and suggests that high constitutive activity of some orphan GPCRs could be accounted for by their having naturally abundant ligands.

C-Dot-Embedded SiO2 Concentric Microspheres for Bright Fluorescent Photonic Pigments.

A simple yet powerful approach to obtain structural color is the amorphous assembly of colloidal spheres, which is also referred to as the amorphous photonic structure or photonic glasses (PGs). Additionally, the functionalization of the colloidal spheres as building blocks can further endow the resulting PGs with multifunctions. Herein, we have developed a facile strategy to prepare SiO2 colloidal spheres with concentrically embedded carbon dots (CDs). Notably, the CDs are prepared and silane-functionalized simultaneously, which enables the perfect incorporation of CDs into the Si-O network during the Stöber reaction and thus leads to the formation of a concentric SiO2/CD interlayer within the obtained SiO2 spheres. Moreover, the obtained SiO2/CD spheres can be applied as photonic pigments by assembling them into PGs, which exhibit structural color under daylight and fluorescence under UV illumination. With incorporation of carbon black, the structural color saturation and fluorescence intensity can be further manipulated. Owing to the combination of structural colored PGs and fluorescent CDs, our study can offer inspiration for color- and fluorescence-related applications such as sensing, in vivo imaging, LEDs, and anticounterfeiting.

Glucose-induced CRL4COP1-p53 axis amplifies glycometabolism to drive tumorigenesis.

The diabetes-cancer association remains underexplained. Here, we describe a glucose-signaling axis that reinforces glucose uptake and glycolysis to consolidate the Warburg effect and overcome tumor suppression. Specifically, glucose-dependent CK2 O-GlcNAcylation impedes its phosphorylation of CSN2, a modification required for the deneddylase CSN to sequester Cullin RING ligase 4 (CRL4). Glucose, therefore, elicits CSN-CRL4 dissociation to assemble the CRL4COP1 E3 ligase, which targets p53 to derepress glycolytic enzymes. A genetic or pharmacologic disruption of the O-GlcNAc-CK2-CSN2-CRL4COP1 axis abrogates glucose-induced p53 degradation and cancer cell proliferation. Diet-induced overnutrition upregulates the CRL4COP1-p53 axis to promote PyMT-induced mammary tumorigenesis in wild type but not in mammary-gland-specific p53 knockout mice. These effects of overnutrition are reversed by P28, an investigational peptide inhibitor of COP1-p53 interaction. Thus, glycometabolism self-amplifies via a glucose-induced post-translational modification cascade culminating in CRL4COP1-mediated p53 degradation. Such mutation-independent p53 checkpoint bypass may represent the carcinogenic origin and targetable vulnerability of hyperglycemia-driven cancer.

Emerging covalent triazine framework-based nanomaterials for electrochemical energy storage and conversion.

Recently, the increasing concerns regarding environmental and energy-related issues due to the use of fossil fuels have triggered extensive research on sustainable electrochemical energy storage and conversion (EESC). In this case, covalent triazine frameworks (CTFs) possess a large surface area, tailorable conjugated structures, electron donating-accepting/conducting moieties, and excellent chemical and thermal stabilities. These merits make them leading candidates for EESC. However, their poor electrical conductivity impedes electron and ion conduction, leading to unsatisfactory electrochemical performances, which limit their commercial applications. Thus, to overcome these challenges, CTF-based nanocomposites and their derivatives such as heteroatom-doped porous carbons, which inherit most of the merits of pristine CTFs, lead to excellent performances in the field of EESC. In this review, initially, we briefly highlight the existing strategies for the synthesis of CTFs with application-targeted properties. Next, we review the contemporary progress of CTFs and their derivatives related to electrochemical energy storage (supercapacitors, alkali-ion batteries, lithium-sulfur batteries, etc.) and conversion (oxygen reduction/evolution reaction, hydrogen evolution reaction, carbon dioxide reduction reaction, etc.). Finally, we discuss perspectives on current challenges and recommendations for the further development of CTF-based nanomaterials in burgeoning EESC research.

Solar-to-H2 O2 Energy Conversion by the Photothermal Effect of a Polymeric Photocatalyst via a Two-Channel Pathway.

With a view to using solar energy, the exploitation of near-infrared (NIR) light, which constitutes about 50 % of solar energy, in photocatalytic H2 O2 synthesis remains challenging. In this study, resorcinol-formaldehyde (RF), which has a relatively low bandgap and high conductivity, is introduced for photothermal catalytic generation of H2 O2 under ambient conditions. Owing to the promoted surface charge transfer rate under high temperature, the photosynthetic yield reaches roughly 2000 µm within 40 min under 400 mW cm-2 irradiation with a solar-to-chemical conversion (SCC) efficiency of up to 0.19 % at 338 K under ambient conditions, exceeding the rate of photocatalysis with a cooling system by a factor of about 2.5. Notably, the H2 O2 produced by RF during photothermal process was formed via a two-channel pathway, leading to the overall promotion of H2 O2 formation. The resultant H2 O2 can be applied in situ for pollutant removal. This work offers a sustainable and economical route for the efficient formation of H2 O2 .

In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein.

The spike protein of SARS-CoV-2 has been a promising target for developing vaccines and therapeutics due to its crucial role in the viral entry process. Previously reported cryogenic electron microscopy (cryo-EM) structures have revealed that free fatty acids (FFA) bind with SARS-CoV-2 spike protein, stabilizing its closed conformation and reducing its interaction with the host cell target in vitro. Inspired by these, we utilized a structure-based virtual screening approach against the conserved FFA-binding pocket to identify small molecule modulators of SARS-CoV-2 spike protein, which helped us identify six hits with micromolar binding affinities. Further evaluation of their commercially available and synthesized analogs enabled us to discover a series of compounds with better binding affinities and solubilities. Notably, our identified compounds exhibited similar binding affinities against the spike proteins of the prototypic SARS-CoV-2 and a currently circulating Omicron BA.4 variant. Furthermore, the cryo-EM structure of the compound SPC-14 bound spike revealed that SPC-14 could shift the conformational equilibrium of the spike protein toward the closed conformation, which is human ACE2 (hACE2) inaccessible. Our identified small molecule modulators targeting the conserved FFA-binding pocket could serve as the starting point for the future development of broad-spectrum COVID-19 intervention treatments.

A Comprehensive Survey of Prospective Structure-Based Virtual Screening for Early Drug Discovery in the Past Fifteen Years.

Structure-based virtual screening (SBVS), also known as molecular docking, has been increasingly applied to discover small-molecule ligands based on the protein structures in the early stage of drug discovery. In this review, we comprehensively surveyed the prospective applications of molecular docking judged by solid experimental validations in the literature over the past fifteen years. Herein, we systematically analyzed the novelty of the targets and the docking hits, practical protocols of docking screening, and the following experimental validations. Among the 419 case studies we reviewed, most virtual screenings were carried out on widely studied targets, and only 22% were on less-explored new targets. Regarding docking software, GLIDE is the most popular one used in molecular docking, while the DOCK 3 series showed a strong capacity for large-scale virtual screening. Besides, the majority of identified hits are promising in structural novelty and one-quarter of the hits showed better potency than 1 µM, indicating that the primary advantage of SBVS is to discover new chemotypes rather than highly potent compounds. Furthermore, in most studies, only in vitro bioassays were carried out to validate the docking hits, which might limit the further characterization and development of the identified active compounds. Finally, several successful stories of SBVS with extensive experimental validations have been highlighted, which provide unique insights into future SBVS drug discovery campaigns.

Pyrazole-containing pharmaceuticals: target, pharmacological activity, and their SAR studies.

Pyrazole is a five-membered heterocycle bearing two adjacent nitrogen atoms. Both pharmaceutical agents and natural products with pyrazole as a nucleus have exhibited a broad spectrum of biological activities. In the last few decades, more than 40 pyrazole-containing drugs have been approved by the FDA for the treatment of a broad range of clinical conditions including celecoxib (anti-inflammatory), CDPPB (antipsychotic), difenamizole (analgesic), etc. Owing to the unique physicochemical properties of the pyrazole core, pyrazole-containing drugs may exert better pharmacokinetics and pharmacological effects compared with drugs containing similar heterocyclic rings. The purpose of this paper is to provide an overview of all the existing drugs bearing a pyrazole nucleus that have been approved or in clinical trials, involving their pharmacological activities and SAR studies.

Systematic Investigation of Docking Failures in Large-Scale Structure-Based Virtual Screening.

In recent years, large-scale structure-based virtual screening has attracted increasing levels of interest for identification of novel compounds corresponding to potential drug targets. It is critical to understand the strengths and weaknesses of docking algorithms to increase the success rate in practical applications. Here, we systematically investigated the docking successes and failures of two representative docking programs: UCSF DOCK 3.7 and AutoDock Vina. DOCK 3.7 performed better in early enrichment on the Directory of Useful Decoys: Enhanced (DUD-E) data set, although both docking methods were roughly comparable in overall enrichment performance. DOCK 3.7 also showed superior computational efficiency. Intriguingly, the Vina scoring function showed a bias toward compounds with higher molecular weights. Both the tested docking approaches yielded incorrectly predicted ligand binding poses caused by the limitations of torsion sampling. Based on a careful analysis of docking results from six representative cases, we propose the reasons underlying docking failures; furthermore, we provide a few solutions, representing practical guidance for large-scale virtual screening campaigns and future docking algorithm development.

Assessment of the Generalization Abilities of Machine-Learning Scoring Functions for Structure-Based Virtual Screening.

In structure-based virtual screening (SBVS), it is critical that scoring functions capture protein-ligand atomic interactions. By focusing on the local domains of ligand binding pockets, a standardized pocket Pfam-based clustering (Pfam-cluster) approach was developed to assess the cross-target generalization ability of machine-learning scoring functions (MLSFs). Subsequently, 12 typical MLSFs were evaluated using random cross-validation (Random-CV), protein sequence similarity-based cross-validation (Seq-CV), and pocket Pfam-based cross-validation (Pfam-CV) methods. Surprisingly, all of the tested models showed decreased performances from Random-CV to Seq-CV to Pfam-CV experiments, not showing satisfactory generalization capacity. Our interpretable analysis suggested that the predictions on novel targets by MLSFs were dependent on buried solvent-accessible surface area (SASA)-related features of complex structures, with greater predicted binding affinities on complexes owning larger protein-ligand interfaces. By combining buried SASA-related features with target-specific patterns that were only shared among structurally similar compounds in the same cluster, the random forest (RF)-Score attained a good performance in the Random-CV test. Based on these findings, we strongly advise assessing the generalization ability of MLSFs with the Pfam-cluster approach and being cautious with the features learned by MLSFs.

Design, synthesis, and bioactivity evaluation of macrocyclic benzo[b]pyrido[4,3-e][1,4]oxazine derivatives as novel Pim-1 kinase inhibitors.

Pim-1 kinase is a serine/threonine kinase which is vital in many tumors. The Pim-1 inhibitor 10-DEBC and its derivatives discovered in our previous work were modified through macrocyclization strategy. A series of benzo[b]pyridine[4,3-e][1,4]oxazine macrocyclic compounds were designed, synthesized, and evaluated as novel Pim-1 kinase inhibitors. Among these compounds, compound H5 exhibited the highest activity with an IC50 value of 35 nM. In addition, the crystal complex structure of Pim-1 kinase bound with compound H3 was determined, and the structure-activity relationship of these macrocyclic compounds was analyzed, which provides the structural basis of further optimization of novel macrocyclic Pim-1 kinase inhibitors..

Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1.

The currently circulating Omicron sub-variants are the SARS-CoV-2 strains with the highest number of known mutations. Herein, we found that human angiotensin-converting enzyme 2 (hACE2) binding affinity to the receptor-binding domains (RBDs) of the four early Omicron sub-variants (BA.1, BA.1.1, BA.2, and BA.3) follows the order BA.1.1 > BA.2 > BA.3 ≈ BA.1. The complex structures of hACE2 with RBDs of BA.1.1, BA.2, and BA.3 reveal that the higher hACE2 binding affinity of BA.2 than BA.1 is related to the absence of the G496S mutation in BA.2. The R346K mutation in BA.1.1 majorly affects the interaction network in the BA.1.1 RBD/hACE2 interface through long-range alterations and contributes to the higher hACE2 affinity of the BA.1.1 RBD than the BA.1 RBD. These results reveal the structural basis for the distinct hACE2 binding patterns among BA.1.1, BA.2, and BA.3 RBDs.

Structural insights into G protein activation by D1 dopamine receptor.

G protein-coupled receptors (GPCRs) comprise the largest family of membrane receptors and are the most important drug targets. An agonist-bound GPCR engages heterotrimeric G proteins and triggers the exchange of guanosine diphosphate (GDP) with guanosine triphosphate (GTP) to promote G protein activation. A complete understanding of molecular mechanisms of G protein activation has been hindered by a lack of structural information of GPCR-G protein complex in nucleotide-bound states. Here, we report the cryo-EM structures of the D1 dopamine receptor and mini-Gs complex in the nucleotide-free and nucleotide-bound states. These structures reveal major conformational changes in Gα such as structural rearrangements of the carboxyl- and amino-terminal α helices that account for the release of GDP and the GTP-dependent dissociation of Gα from Gßγ subunits. As validated by biochemical and cellular signaling studies, our structures shed light into the molecular basis of the entire signaling events of GPCR-mediated G protein activation.