Structural Basis of Substrate Recognition by the Postmitosane Modification Enzyme MitM in Mitomycin Biosynthesis.

Mitomycins make up a class of natural molecules produced by Streptomyces with strong antibacterial and antitumor activities. MitM is a key postmitosane modification enzyme involved in mitomycin biosynthesis in Streptomyces caespitosus. This protein was previously suggested to catalyze the aziridinium methylation of mitomycin A and the mitomycin intermediate 9a-demethyl-mitomycin A as an N-methyltransferase. The structural basis for MitM to recognize cofactor S-adenosyl-l-methionine (SAM) and substrate mitomycin A is unknown. Here, we determined the crystal structures of apo-MitM and MitM-mitomycin A-S-adenosylhomocysteine (SAH) ternary complexes with resolutions of 2.23 and 2.80 Å, respectively. We found that MitM adopts a class I SAM-dependent methyltransferase fold and forms a homodimer in solution. Conformational changes in a series of residues involved in the formation of active pockets assist MitM in binding SAH and mitomycin A. In particular, the 28ALGAASLGE36 loop changes most significantly. When mitomycin A binds, the bending direction of this loop is reversed, changing the entrance of the active site from open to closed. This study provides structural insights into MitM's involvement in the postmitosane stage of mitomycin biosynthesis and provides a template for the engineering of methyltransferases.

Specific glycine-dependent enzyme motion determines the potency of conformation selective inhibitors of threonyl-tRNA synthetase.

The function of proteins depends on their correct structure and proper dynamics. Understanding the dynamics of target proteins facilitates drug design and development. However, dynamic information is often hidden in the spatial structure of proteins. It is important but difficult to identify the specific residues that play a decisive role in protein dynamics. Here, we report that a critical glycine residue (Gly463) dominates the motion of threonyl-tRNA synthetase (ThrRS) and the sensitivity of the enzyme to antibiotics. Obafluorin (OB), a natural antibiotic, is a novel covalent inhibitor of ThrRS. The binding of OB induces a large conformational change in ThrRS. Through five crystal structures, biochemical and biophysical analyses, and computational simulations, we found that Gly463 plays an important role in the dynamics of ThrRS. Mutating this flexible residue into more rigid residues did not damage the enzyme's three-dimensional structure but significantly improved the thermal stability of the enzyme and suppressed its ability to change conformation. These mutations cause resistance of ThrRS to antibiotics that are conformationally selective, such as OB and borrelidin. This work not only elucidates the molecular mechanism of the self-resistance of OB-producing Pseudomonas fluorescens but also emphasizes the importance of backbone kinetics for aminoacyl-tRNA synthetase-targeting drug development.

Structure-guided conversion from an anaplastic lymphoma kinase inhibitor into Plasmodium lysyl-tRNA synthetase selective inhibitors.

Aminoacyl-tRNA synthetases (aaRSs) play a central role in the translation of genetic code, serving as attractive drug targets. Within this family, the lysyl-tRNA synthetase (LysRS) constitutes a promising antimalarial target. ASP3026, an anaplastic lymphoma kinase (ALK) inhibitor was recently identified as a novel Plasmodium falciparum LysRS (PfLysRS) inhibitor. Here, based on cocrystal structures and biochemical experiments, we developed a series of ASP3026 analogues to improve the selectivity and potency of LysRS inhibition. The leading compound 36 showed a dissociation constant of 15.9 nM with PfLysRS. The inhibitory efficacy on PfLysRS and parasites has been enhanced. Covalent attachment of L-lysine to compound 36 resulted in compound 36K3, which exhibited further increased inhibitory activity against PfLysRS but significantly decreased activity against ALK. However, its inhibitory activity against parasites did not improve, suggesting potential future optimization directions. This study presents a new example of derivatization of kinase inhibitors repurposed to inhibit aaRS.

Trading in catalytic power for sensing.

In this issue of Structure, Yin et al.1 present the CryoEM structure of the HisRS-like domain of human GCN2 and demonstrate that it is a pseudoenzyme, which binds uncharged tRNA in a different manner than HisRS and does not bind histidine and ATP.

Module-combinatorial design and screening of multifunctional polymers based on polyaspartic acid for DNA delivery.

It is crucial to develop non-viral gene vectors that can efficiently and safely transfect plasmid DNA into cells. Low transfection efficiency and high cytotoxicity of cationic polymers hinder their application as gene carriers. Modification of cationic polymers has emerged as an attractive strategy for efficient and safe nucleic acids delivery. In this study, a simple and rapid method is developed to synthesize a series of multifunctional polymers by utilizing biodegradable polyaspartic acid as the backbone and modifying it with three modules. This one-component polymer possesses capabilities for nucleic acid condensation, cellular uptake, and endosomal escape. Polymers containing imidazole, triazole, or pyridine group exhibited promising transfection activity. Substituted with dodecylamine or 2-hexyldecan-1-amine enhance cellular uptake and subsequent transfection. Furthermore, the influence of ionizable amine side chains on gene delivery is investigated. Two optimal polymers, combined with the avian encephalomyelitis virus (AEV) plasmid vaccine, induced robust specific antibody responses and cellular immune responses in mice and chickens. Through module-combination design and screening of polyaspartamide polymers, this study presents a paradigm for the development of gene delivery vectors.

Highly sulfonated poly ether ether ketone chelated with Cu2+ as a proton exchange membrane at sub-zero temperatures.

Improving the proton conductivity (σ) of proton exchange membranes at low temperatures is very important for expanding their application areas. Here, sulfonated poly ether ether ketone (SPEEK) membranes were prepared with different sulfonation degrees, and its maximum ion exchange capacity is 3.15 mmol/g for 10 h at 60 °C. Highly sulfonated SPEEK membrane exhibits ultra-high water uptake and excellent proton conductivity of 0.074 S/cm at -25 °C due to its abundant -SO3H. Nevertheless, its high swelling ratio and low mechanical strength are not conducive to the practical application of the membrane. Luckily, by employing the chelation of Cu2+ with -SO3- on the SPEEK chain, Cu2+-coordinated SPEEK membranes were prepared, and they not only retain high -SO3H content but also possess robust mechanical properties and good dimensional stability compared to pristine SPEEK membrane. Meanwhile, the σ of the SPEEK-Cu membrane reaches 0.054 S/cm at -25 °C, and its fuel cell maximum power (Wmax) reaches 0.42 W/cm2 at -10 °C, demonstrating superior low-temperature performance in comparison to other reported materials. Particularly, water states in the prepared membranes are quantified by low-temperature differential scanning calorimetry. Because much more water bound to the plentiful -SO3H and Cu2+ inside the membrane endows it with anti-freezing performance, the decay of the σ and the Wmax for the SPEEK-Cu membrane is retarded at sub-zero temperatures. It is envisioned that composite membranes comprising metal ions such as Cu2+-SPEEK have a high potential for sub-zero fuel cell applications.

Microwave-assisted synthesis of highly sulfated mannuronate glycans as potential inhibitors against SARS-CoV-2.

Algae-based marine carbohydrate drugs are typically decorated with negative ion groups such as carboxylate and sulfate groups. However, the precise synthesis of highly sulfated alginates is challenging, thus impeding their structure-activity relationship studies. Herein we achieve a microwave-assisted synthesis of a range of highly sulfated mannuronate glycans with up to 17 sulfation sites by overcoming the incomplete sulfation due to the electrostatic repulsion of crowded polyanionic groups. Although the partially sulfated tetrasaccharide had the highest affinity for the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, the fully sulfated octasaccharide showed the most potent interference with the binding of the RBD to angiotensin-converting enzyme 2 (ACE2) and Vero E6 cells, indicating that the sulfated oligosaccharides might inhibit the RBD binding to ACE2 in a length-dependent manner.

Leveraging Bilateral Correlations for Multi-Label Few-Shot Learning.

Multi-label few-shot learning (ML-FSL) refers to the task of tagging previously unseen images with a set of relevant labels, giving a small number of training examples. Modeling the correlations between instances and labels, formulated in the existing methods, allows us to extract more available knowledge from limited examples. However, they simply explore the instance and label correlations with a uniform importance assumption without considering the discrepancy of importance in different instances or labels, making the utilization of instance and label correlations a bottleneck for ML-FSL. To tackle the issue, we propose a unified framework named bilateral correlation reconstruction (BCR) to enable the network to effectively mine underlying instance and label correlations with varying importance information from both instance-to-label and label-to-instance perspectives. Specifically, from the instance-to-label perspective, we refine prototypes per category by reweighting each image with its specific instance-importance degree extracted from the similarity between the instance and the corresponding category. From the label-to-instance perspective, we smooth labels for each image by recovering latent label-importance with considering the integrated topology of all samples in a task. Experimental results on multiple benchmarks validate that BCR could outperform existing ML-FSL methods by large margins.

Efficient spatial separation of charge carriers over Sv-ZnIn2S4/NH2-MIL-88B(Fe) S-scheme heterojunctions for enhanced photocatalytic H2 evolution and antibiotics removal performance.

The exploration of highly efficient sunlight-assisted photocatalyst for photodegradation of organic contaminants or energy conversion is strongly encouraged. In this work, we designed a novel three-dimensional spindle-like Sv-ZIS@NMFe heterojunction made of amino functionalized NH2-MIL-88B(Fe) (NMFe) and ZnIn2S4 nanosheets with abundant sulfur vacancies (Sv-ZIS). The structural properties of NMFe materials, such as a clearly defined system of pores and cavities, were retained by the Sv-ZIS@NMFe composites. Additionally, the incorporation of sulfur vacancies, -NH2 functional groups, and well-matched energy level positions led to various synergistic effects that considerably enhanced internal electron transformation and migration, as well as improved adsorption performance. Consequently, under visible light irradiation, the optimized sample exhibited superior hydrogen production activity and tetracycline hydrochloride photodegradation performance. At last, density functional theory calculations was used to further elucidated the possible photoreactivity mechanism. This study demonstrates that the Sv-ZIS@NMFe heterojunction materials formed by ZnIn2S4 with suitable sulfur vacancies and amino functionalized Fe-MOFs have promising applications in photocatalysis.

Human lysyl-tRNA synthetase phosphorylation promotes HIV-1 proviral DNA transcription.

Human lysyl-tRNA synthetase (LysRS) was previously shown to be re-localized from its normal cytoplasmic location in a multi-aminoacyl-tRNA synthetase complex (MSC) to the nucleus of HIV-1 infected cells. Nuclear localization depends on S207 phosphorylation but the nuclear function of pS207-LysRS in the HIV-1 lifecycle is unknown. Here, we show that HIV-1 replication was severely reduced in a S207A-LysRS knock-in cell line generated by CRISPR/Cas9; this effect was rescued by S207D-LysRS. LysRS phosphorylation up-regulated HIV-1 transcription, as did direct transfection of Ap4A, an upstream transcription factor 2 (USF2) activator that is synthesized by pS207-LysRS. Overexpressing an MSC-derived peptide known to stabilize LysRS MSC binding inhibited HIV-1 replication. Transcription of HIV-1 proviral DNA and other USF2 target genes was reduced in peptide-expressing cells. We propose that nuclear pS207-LysRS generates Ap4A, leading to activation of HIV-1 transcription. Our results suggest a new role for nuclear LysRS in facilitating HIV-1 replication and new avenues for antiviral therapy.

Deep graph convolutional network for small-molecule retention time prediction.

The retention time (RT) is a crucial source of data for liquid chromatography-mass spectrometry (LCMS). A model that can accurately predict the RT for each molecule would empower filtering candidates with similar spectra but differing RT in LCMS-based molecule identification. Recent research shows that graph neural networks (GNNs) outperform traditional machine learning algorithms in RT prediction. However, all of these models use relatively shallow GNNs. This study for the first time investigates how depth affects GNNs' performance on RT prediction. The results demonstrate that a notable improvement can be achieved by pushing the depth of GNNs to 16 layers by the adoption of residual connection. Additionally, we also find that graph convolutional network (GCN) model benefits from the edge information. The developed deep graph convolutional network, DeepGCN-RT, significantly outperforms the previous state-of-the-art method and achieves the lowest mean absolute percentage error (MAPE) of 3.3% and the lowest mean absolute error (MAE) of 26.55 s on the SMRT test set. We also finetune DeepGCN-RT on seven datasets with various chromatographic conditions. The mean MAE of the seven datasets largely decreases 30% compared to previous state-of-the-art method. On the RIKEN-PlaSMA dataset, we also test the effectiveness of DeepGCN-RT in assisting molecular structure identification. By 30% lessening the number of potential structures, DeepGCN-RT is able to improve top-1 accuracy by about 11%.

MOF-Derived Spindle-Shaped Z-Scheme ZnO/ZnFe2O4 Heterojunction: A Magnetic Recovery Catalyst for Efficient Photothermal Degradation of Tetracycline Hydrochloride.

The development of photocatalysts with a wide spectral response and effective carrier separation capability is essential for the green degradation of tetracycline hydrochloride. In this study, a magnetic recyclable Z-scheme ZnO/ZnFe2O4 heterojunction (ZZF) was successfully constructed via the solid phase method, using MIL-88A(Fe)@Zn as the precursor. An appropriate band gap width and Z-scheme charge transfer mechanism provide ZZF with excellent visible light absorption performance, efficient charge separation, and a strong redox ability. Under visible light irradiation, the degradation efficiency of tetracycline hydrochloride for the optimal sample can reach 86.3% within 75 min in deionized water and 92.9% within 60 min in tap water, exhibiting superior stability and reusability after five cycles. Moreover, the catalyst in the water can be conveniently recovered by magnetic force. After visible light irradiation for 70 min, the temperature of the reaction system increased by 21.9 °C. Its degradation constant (35.53 × 10-3 min-1) increased to 5.1 times that at room temperature (6.95 × 10-3 min-1). Using thermal energy enhances the kinetic driving force of the reactants and facilitates carrier migration, meaning that more charge is available for the production of •O2- and •OH. This study provides a potential candidate for the efficient degradation of tetracycline hydrochloride by combining thermal catalysis with a photocatalytic heterojunction.

Curved Geometric Networks for Visual Anomaly Recognition.

Learning a latent embedding to understand the underlying nature of data distribution is often formulated in Euclidean spaces with zero curvature. However, the success of the geometry constraints, posed in the embedding space, indicates that curved spaces might encode more structural information, leading to better discriminative power and hence richer representations. In this work, we investigate the benefits of the curved space for analyzing anomalous, open-set, or out-of-distribution (OOD) objects in data. This is achieved by considering embeddings via three geometry constraints, namely, spherical geometry (with positive curvature), hyperbolic geometry (with negative curvature), or mixed geometry (with both positive and negative curvatures). Three geometric constraints can be chosen interchangeably in a unified design, given the task at hand. Tailored for the embeddings in the curved space, we also formulate functions to compute the anomaly score. Two types of geometric modules (i.e., geometric-in-one (GiO) and geometric-in-two (GiT) models) are proposed to plug in the original Euclidean classifier, and anomaly scores are computed from the curved embeddings. We evaluate the resulting designs under a diverse set of visual recognition scenarios, including image detection (multiclass OOD detection and one-class anomaly detection) and segmentation (multiclass anomaly segmentation and one-class anomaly segmentation). The empirical results show the effectiveness of our proposal through consistent improvement over various scenarios. The code is made available at https://github.com/JHome1/GiO-GiT.

Tetramerization of upstream stimulating factor USF2 requires the elongated bent leucine zipper of the bHLH-LZ domain.

Upstream stimulating factors (USFs), including USF1 and USF2, are key components of the transcription machinery that recruit coactivators and histone-modifying enzymes. Using the classic basic helix-loop-helix leucine zipper (bHLH-LZ) domain, USFs bind the E-box DNA and form tetramers that promote DNA looping for transcription initiation. The structural basis by which USFs tetramerize and bind DNA, however, remains unknown. Here, we report the crystal structure of the complete bHLH-LZ domain of USF2 in complex with E-box DNA. We observed that the leucine zipper (LZ) of USF2 is longer than that of other bHLH-LZ family transcription factors and that the C-terminus of USF2 forms an additional α-helix following the LZ region (denoted as LZ-Ext). We also found the elongated LZ-Ext facilitates compact tetramer formation. In addition to the classic interactions between the basic region and DNA, we show a highly conserved basic residue in the loop region, Lys271, participates in DNA interaction. Together, these findings suggest that USF2 forms a tetramer structure with a bent elongated LZ-Ext region, providing a molecular basis for its role as a key component of the transcription machinery.

Effects of albiflorin on oxidative stress and inflammatory responses in rats with acute spinal cord injury.

INTRODUCTION: Oxidative stress and inflammatory responses are often the predominant detrimental factors associated with spinal cord injury (SCI). This study investigates the potential therapeutic effects of albiflorin (AF) on alleviating inflammation and oxidative stress in the rat model with SCI. METHODS: Initially, the behavior of SCI-induced rats is examined by Basso-Beattie-Bresnahan score and the inclined plane examination. Then, the immunohistochemical staining of inflammasome-related protein (for instance, NACHT, LRR, and PYD domains-containing protein 3, NLRP3) is performed in combination with enzyme-linked immunosorbent assay (ELISA) of corresponding proinflammatory factors to assess the immunomodulatory effects of AF. Further, the markers involved in oxidative stress are examined by ELISA and western blot analysis analyses. RESULTS: These findings indicated that AF could alleviate motor dysfunction and the loss of neuron cells in SCI-induced rats. Mechanistically, AF could attenuate the inflammatory responses by reducing oxidative stress and activating nuclear erythroid-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) pathway in SCI rats. Depleting the antioxidant capacity by inhibiting glutathione biosynthesis could counteract the anti-inflammatory activity of AF in SCI rats. CONCLUSIONS: Together, our data suggested that AF could serve as a potential therapeutic agent against the aggravation of SCI in rats.

Development of Biaryl-Containing Aldo-Keto Reductase 1C3 (AKR1C3) Inhibitors for Reversing AKR1C3-Mediated Drug Resistance in Cancer Treatment.

Aldo-keto reductase 1C3 (AKR1C3) is correlated with tumor development and chemotherapy resistance. The catalytic activity of the enzyme has been recognized as one of the important factors in inducing anthracycline (ANT) resistance in cancer cells. Inhibition of AKR1C3 activity may provide a promising approach to restore the chemosensitivity of ANT-resistant cancers. Herein, a series of biaryl-containing AKR1C3 inhibitors has been developed. The best analogue S07-1066 selectively blocked AKR1C3-mediated reduction of doxorubicin (DOX) in MCF-7 transfected cell models. Furthermore, co-treatment of S07-1066 significantly synergized DOX cytotoxicity and reversed the DOX resistance in MCF-7 cells overexpressing AKR1C3. The potential synergism of S07-1066 over DOX cytotoxicity was demonstrated in vitro and in vivo. Our findings indicate that inhibition of AKR1C3 potentially enhances the therapeutic efficacy of ANTs and even suggests that AKR1C3 inhibitors may serve as effective adjuvants to overcome AKR1C3-mediated chemotherapy resistance in cancer treatment.

Structural Basis of Low-Molecular-Weight Thiol Glycosylation in Lincomycin A Biosynthesis.

The involvement of low-molecular-weight thiols in the biosynthesis of natural products is rarely reported. During lincomycin A biosynthesis, ergothioneine (EGT) is incorporated in the S-glycosylation catalyzed by LmbT. In contrast to the widely reported glycosylation of nitrogen and oxygen atoms, the glycosylation of sulfur atoms is less studied. In particular, the crystal structure of enzymes that glycosylate thiols on small molecules rather than peptides has not been reported. Here, we report the crystal structures of LmbT in apo form and in complex with GDP and EGT S-conjugated lincosamine. We found that LmbT has a characteristic glycosyltransferase type B fold, which forms a symmetric homotetramer. The substrates are bound deeply in the catalytic cleft. Consistent with the substrate structure, LmbT does not have the large peptide binding groove of the previously reported S-glycosyltransferase. Combined with site-directed mutagenesis, we propose a catalytic mechanism for the unusual EGT-mediated S-glycosylation in natural product biosynthesis.

Inhibiting autophagy before it starts.

Autophagy, an important cellular stress response mechanism, is often exploited by a variety of cancer cells to sustain rapid growth under stresses such as nutrient deprivation and hypoxia. Autophagy also plays a key role in tumor resistance to chemotherapy, radiotherapy or targeted therapy. Inhibition of autophagy is therefore a promising tumor treatment strategy. However, there is still a lack of effective autophagy inhibitors suitable for clinical use. Most drug development has focused on enzymes like the VPS34 and ULK1 kinases, or the cysteine protease ATG4B, which plays different roles in autophagy. We discovered a drug molecule Eltrombopag that inhibits the expression of autophagic lysosomal genes at the stage of transcriptional level, where the synthesis of these proteins has not really begun, by directly inhibiting the TFEB (transcription factor EB). This drug can improve the therapeutic effect of Temozolomide on glioblastoma treatment, further confirming the value of inhibiting autophagy in the treatment of cancer.Abbreviation: VPS34: vacuolar protein sorting 34; ULK1: unc-51 like autophagy activating kinase 1; TFEB: transcription factor EB; MITF: microphthalmia-associated transcription factor; TFE3: transcription factor E3; EO: Eltrombopag; ITC: isothermal titration calorimetry; bHLH-LZ: basic helix-loop-helix leucine zipper; LAMP1: lysosomal-associated membrane protein 1; CTSF: cathepsin F; HEXA: hexosaminidase subunit alpha.

Loss of threonyl-tRNA synthetase-like protein Tarsl2 has little impact on protein synthesis but affects mouse development.

Aminoacyl-tRNA synthetases (aaRSs) are essential components for mRNA translation. Two sets of aaRSs are required for cytoplasmic and mitochondrial translation in vertebrates. Interestingly, TARSL2 is a recently evolved duplicated gene of TARS1 (encoding cytoplasmic threonyl-tRNA synthetase) and represents the only duplicated aaRS gene in vertebrates. Although TARSL2 retains the canonical aminoacylation and editing activities in vitro, whether it is a true tRNA synthetase for mRNA translation in vivo is unclear. In this study, we showed that Tars1 is an essential gene since homozygous Tars1 KO mice were lethal. In contrast, when Tarsl2 was deleted in mice and zebrafish, neither the abundance nor the charging levels of tRNAThrs were changed, indicating that cells relied on Tars1 but not on Tarsl2 for mRNA translation. Furthermore, Tarsl2 deletion did not influence the integrity of the multiple tRNA synthetase complex, suggesting that Tarsl2 is a peripheral member of the multiple tRNA synthetase complex. Finally, we observed that Tarsl2-deleted mice exhibited severe developmental retardation, elevated metabolic capacity, and abnormal bone and muscle development after 3 weeks. Collectively, these data suggest that, despite its intrinsic activity, loss of Tarsl2 has little influence on protein synthesis but does affect mouse development.

Oxidase Heterotetramer Completes 1-Azabicyclo[3.1.0]hexane Formation with the Association of a Nonribosomal Peptide Synthetase.

Ficellomycin, azinomycins, and vazabitide A are nonribosomal peptide natural products characterized by an amino acid unit that contains a similar 1-azabicyclo[3.1.0]hexane (ABCH) pharmacophore. This unit is derived from diamino-dihydroxy-heptanic acid (DADH); however, the process through which linear DADH is cyclized to furnish an ABCH ring system remains poorly understood. Based on the reconstitution of the route of the ABCH-containing unit by blending genes/enzymes involved in the biosynthesis of ficellomycin and azinomycins, we report that ABCH formation is completed by an oxidase heterotetramer with the association of a nonribosomal peptide synthetase (NRPS). The DADH precursor was prepared in Escherichia coli to produce a conjugate subjected to in vitro enzymatic hydrolysis for offloading from an amino-group carrier protein. To furnish an aziridine ring, DADH was processed by C7-hydroxyl sulfonation and sulfate elimination-coupled cyclization. Further cyclization leading to an azabicyclic hexane pharmacophore was proved to occur in the NRPS, where the oxidase heterotetramer functions in trans and catalyzes α,ß-dehydrogenation to initiate the formation of a fused five-membered nitrogen heterocycle. The identity of ABCH was validated by utilization of the resultant ABCH-containing unit in the total biosynthesis of ficellomycin. Biochemical characterization, crystal structure, and site-specific mutagenesis rationalize the catalytic mechanism of the unusual oxidase heterotetramer.