DTNPD: A comprehensive database of drugs and targets for neurological and psychiatric disorders

In response to the shortcomings in data quality and coverage for neurological and psychiatric disorders (NPDs) in existing comprehensive databases, this paper introduces the DTNPD database, specifically designed for NPDs. DTNPD contains detailed information on 30 NPDs types, 1847 drugs, 514 drug targets, 64 drug combinations, and 61 potential target combinations, forming a network with 2389 drug-target associations. The database is user-friendly, offering open access and downloadable data, which is crucial for network pharmacology studies. The key strength of DTNPD lies in its robust networks of drug and target combinations, as well as drug-target networks, facilitating research and development in the field of NPDs. The development of the DTNPD database marks a significant milestone in understanding and treating NPDs. For accessing the DTNPD database, the primary URL is http://dtnpd.cnsdrug.com, complemented by a mirror site available at http://dtnpd.lyhbio.com.

Effective cryopreservation of human brain tissue and neural organoids

Human brain tissue models and organoids are vital for studying and modeling human neurological disease. However, the high cost of long-term cultured organoids inhibits their wide-ranging application. It is therefore urgent to develop methods for the cryopreservation of brain tissue and organoids. Here, we establish a method using methylcellulose, ethylene glycol, DMSO, and Y27632 (termed MEDY) for the cryopreservation of cortical organoids without disrupting the neural cytoarchitecture or functional activity. MEDY can be applied to multiple brain-region-specific organoids, including the dorsal/ventral forebrain, spinal cord, optic vesicle brain, and epilepsy patient-derived brain organoids. Additionally, MEDY enables the cryopreservation of human brain tissue samples, and pathological features are retained after thawing. Transcriptomic analysis shows that MEDY can protect synaptic function and inhibit the endoplasmic reticulum-mediated apoptosis pathway. MEDY will enable the large-scale and reliable storage of diverse neural organoids and living brain tissue and will facilitate wide-ranging research, medical applications, and drug screening.

Improvement in Grain Size Distribution Uniformity for Nuclear-Grade Austenitic Stainless Steel through Thermomechanical Treatment

In this work, thermomechanical treatment (single-pass rolling at 800 °C and solution treatment) was applied to nuclear-grade hot-rolled austenitic stainless steel to eliminate the mixed grain induced by the uneven hot-rolled microstructure. By employing high-temperature laser scanning confocal microscopy, microstructure evolution during solution treatment was observed in situ, and the effect of single-pass rolling reduction on it was investigated. In uneven hot-rolled microstructure, the millimeter-grade elongated grains (MEGs) possessed an extremely large size and a high Schmid factor for slip compared to the fine grains, which led to greater plastic deformation and increased dislocation density and deformation energy storage during single-pass rolling. During subsequent solution treatment, there were fewer nucleation sites for the new grain, and the grain boundary (GB) was the main nucleation site in MEGs at a lower rolling reduction. In contrast, at a higher reduction, increased uniformly distributed rolling deformation and more nucleation sites were developed in MEGs. As the reduction increased, the number of in-grain nucleation sites gradually exceeded that of GB nucleation sites, and in-grain nucleation preferentially occurred. This was beneficial for promoting the refinement of new recrystallized grains and a reduction in the size difference of new grains during recrystallization. The single-pass rolling reduction of 15-20% can effectively increase the nucleation sites and improve the uniformity of rolling deformation distribution in the MEGs, promote in-grain nucleation, and finally refine the abnormally coarse elongated grain, and eliminate the mixed-grain structure after solution treatment.

PROSCA: an online platform for humanized scaffold mining facilitating rational protein engineering

Protein scaffolds with small size, high stability and low immunogenicity show important applications in the field of protein engineering and design. However, no relevant computational platform has been reported yet to mining such scaffolds with the desired properties from massive protein structures in human body. Here, we developed PROSCA, a structure-based online platform dedicated to explore the space of the entire human proteome, and to discovery new privileged protein scaffolds with potential engineering value that have never been noticed. PROSCA accepts structure of protein as an input, which can be subsequently aligned with a certain class of protein structures (e.g. the human proteome either from experientially resolved or AlphaFold2 predicted structures, and the human proteins belonging to specific families or domains), and outputs humanized protein scaffolds which are structurally similar with the input protein as well as other related important information such as families, sequences, structures and expression level in human tissues. Through PROSCA, the user can also get excellent experience in visualizations of protein structures and expression overviews, and download the figures and tables of results which can be customized according to the user's needs. Along with the advanced protein engineering and selection technologies, PROSCA will facilitate the rational design of new functional proteins with privileged scaffolds. PROSCA is freely available at https://idrblab.org/prosca/.

CNSMolGen: A Bidirectional Recurrent Neural Network-Based Generative Model for De Novo Central Nervous System Drug Design

Central nervous system (CNS) drugs have had a significant impact on treating a wide range of neurodegenerative and psychiatric disorders. In recent years, deep learning-based generative models have shown great potential for accelerating drug discovery and improving efficacy. However, specific applications of these techniques in CNS drug discovery have not been widely reported. In this study, we developed the CNSMolGen model, which uses a framework of bidirectional recurrent neural networks (Bi-RNNs) for de novo molecular design of CNS drugs. Results showed that the pretrained model was able to generate more than 90% of completely new molecular structures, which possessed the properties of CNS drug molecules and were synthesizable. In addition, transfer learning was performed on small data sets with specific biological activities to evaluate the potential application of the model for CNS drug optimization. Here, we used drugs against the classical CNS disease target serotonin transporter (SERT) as a fine-tuned data set and generated a focused database against the target protein. The potential biological activities of the generated molecules were verified by using the physics-based induced-fit docking study. The success of this model demonstrates its potential in CNS drug design and optimization, which provides a new impetus for future CNS drug development.

JMJD2A mediates transcriptional activation of SFRP4 and regulates oxidative stress and mitochondrial dysfunction in heart failure

The importance of mitochondrial dysfunction and oxidative stress has been indicated in the progression of heart failure (HF). The molecular mechanisms, however, remain to be fully elucidated. This study aimed to explore the role and underlying mechanism of secreted frizzled-related protein 4 (SFRP4) in these two events in HF. Mice with HF were developed using transverse aortic constriction, and hematoxylin-eosin staining, MASSON staining, and Terminal deoxynucleotidyl transferase (TdT)-mediated 2'-Deoxyuridine 5'- Triphosphate nick end labeling (TUNEL assays) were conducted to detect morphological damage in the myocardial tissues of mice. HL-1 mouse cardiomyocytes were induced with isoproterenol (ISO), and cell viability and apoptosis were examined using cell counting kit-8 and TUNEL assays. SFRP4 and Jumonji domain-containing protein 2A (JMJD2A) were highly expressed in myocardial tissues. Suppression of SFRP4 alleviated apoptosis and fibrosis in myocardial tissues of mice. In addition, the extent of mitochondrial dysfunction and oxidative stress in damaged myocardial tissues and HL-1 cells was mitigated by SFRP4 inhibition as well. JMJD2A catalyzed demethylation modification of the SFRP4 promoter, thus promoting SFRP4 transcription in the development of HF. JMJD2A is responsible for SFRP4 transcription activation in the failing hearts of mice. Blockade of JMJD2A or SFRP4 might be a novel therapy effective in mitigating HF progression.

Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives

Solute carrier transporters (SLCs) are a class of important transmembrane proteins that are involved in the transportation of diverse solute ions and small molecules into cells. There are approximately 450 SLCs within the human body, and more than a quarter of them are emerging as attractive therapeutic targets for multiple complex diseases, e.g., depression, cancer, and diabetes. However, only 44 unique transporters (∼9.8% of the SLC superfamily) with 3D structures and specific binding sites have been reported. To design innovative and effective drugs targeting diverse SLCs, there are a number of obstacles that need to be overcome. However, computational chemistry, including physics-based molecular modeling and machine learning- and deep learning-based artificial intelligence (AI), provides an alternative and complementary way to the classical drug discovery approach. Here, we present a comprehensive overview on recent advances and existing challenges of the computational techniques in structure-based drug design of SLCs from three main aspects: (i) characterizing multiple conformations of the proteins during the functional process of transportation, (ii) identifying druggability sites especially the cryptic allosteric ones on the transporters for substrates and drugs binding, and (iii) discovering diverse small molecules or synthetic protein binders targeting the binding sites. This work is expected to provide guidelines for a deep understanding of the structure and function of the SLC superfamily to facilitate rational design of novel modulators of the transporters with the aid of state-of-the-art computational chemistry technologies including artificial intelligence.

Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine

Traditional Chinese medicine (TCM) has been extensively employed for the treatment of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is demand for discovering more SARS-CoV-2 Mpro inhibitors with diverse scaffolds to optimize anti-SARS-CoV-2 lead compounds. In this study, comprehensive in silico and in vitro assays were utilized to determine the potential inhibitors from TCM compounds against SARS-CoV-2 Mpro, which is an important therapeutic target for SARS-CoV-2. The ensemble docking analysis of 18263 TCM compounds against 15 SARS-CoV-2 Mpro conformations identified 19 TCM compounds as promising candidates. Further in vitro testing validated three compounds as inhibitors of SARS-CoV-2 Mpro and showed IC50 values of 4.64 ± 0.11, 7.56 ± 0.78, and 11.16 ± 0.26 μM, with EC50 values of 12.25 ± 1.68, 15.58 ± 0.77, and 29.32 ± 1.25 μM, respectively. Molecular dynamics (MD) simulations indicated that the three complexes remained stable over the last 100 ns of production run. An analysis of the binding mode revealed that the active compounds occupy different subsites (S1, S2, S3, and S4) of the active site of SARS-CoV-2 Mpro via specific poses through noncovalent interactions with key amino acids (e.g., HIS 41, ASN 142, GLY 143, MET 165, GLU 166, or GLN 189). Overall, this study provides evidence indicating that the three natural products obtained from TCM could be further used for anti-COVID-19 research, justifying the investigation of Chinese herbal medicinal ingredients as bioactive constituents for therapeutic targets.

Vegetation-fire feedbacks increase subtropical wildfire risk in scrubland and reduce it in forests

Climate dictates wildfire activity around the world. But East and Southeast Asia are an apparent exception as fire-activity variation there is unrelated to climatic variables. In subtropical China, fire activity decreased by 80% between 2003 and 2020 amid increased fire risks globally. Here, we assessed the fire regime, vegetation structure, fuel flammability and their interactions across subtropical Hubei, China. We show that tree basal area (TBA) and fuel flammability explained 60% of fire-frequency variance. Fire frequency and fuel flammability, in turn, explained 90% of TBA variance. These results reveal a novel system of scrubland-forest stabilized by vegetation-fire feedbacks. Frequent fires promote the persistence of derelict scrubland through positive vegetation-fire feedbacks; in forest, vegetation-fire feedbacks are negative and suppress fire. Thus, we attribute the decrease in wildfire activity to reforestation programs that concurrently increase forest coverage and foster negative vegetation-fire feedbacks that suppress wildfire.

MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics

Protein structure prediction is a longstanding issue crucial for identifying new drug targets and providing a mechanistic understanding of protein functions. To enhance the progress in this field, a spectrum of computational methodologies has been cultivated. AlphaFold2 has exhibited exceptional precision in predicting wild-type protein structures, with performance exceeding that of other methods. However, predicting the structures of missense mutant proteins using AlphaFold2 remains challenging due to the intricate and substantial structural alterations caused by minor sequence variations in the mutant proteins. Molecular dynamics (MD) has been validated for precisely capturing changes in amino acid interactions attributed to protein mutations. Therefore, for the first time, a strategy entitled 'MoDAFold' was proposed to improve the accuracy and reliability of missense mutant protein structure prediction by combining AlphaFold2 with MD. Multiple case studies have confirmed the superior performance of MoDAFold compared to other methods, particularly AlphaFold2.

SEPTIN2 suppresses an IFN-γ-independent, proinflammatory macrophage activation pathway

Interferon-gamma (IFN-γ) signaling is necessary for the proinflammatory activation of macrophages but IFN-γ-independent pathways, for which the initiating stimuli and downstream mechanisms are lesser known, also contribute. Here we identify, by high-content screening, SEPTIN2 (SEPT2) as a negative regulation of IFN-γ-independent macrophage autoactivation. Mechanistically, endoplasmic reticulum (ER) stress induces the expression of SEPT2, which balances the competition between acetylation and ubiquitination of heat shock protein 5 at position Lysine 327, thereby alleviating ER stress and constraining M1-like polarization and proinflammatory cytokine release. Disruption of this negative feedback regulation leads to the accumulation of unfolded proteins, resulting in accelerated M1-like polarization, excessive inflammation and tissue damage. Our study thus uncovers an IFN-γ-independent macrophage proinflammatory autoactivation pathway and suggests that SEPT2 may play a role in the prevention or resolution of inflammation during infection.

Jian Yun Qing Hua Decoction inhibits malignant behaviors of gastric carcinoma cells via COL12A1 mediated ferroptosis signal pathway

BACKGROUND

Jian Yun Qing Hua Decoction (JYQHD), a traditional Chinese medicine decoction, which has been applied in the treatment of gastric cancer (GC). We attempt to confirm the anti-gastric cancer effect of JYQHD and explore the mechanism of JYQHD.

METHODS

Acute toxicity test was used to understand the toxicity of JYQHD. We studied the expression and prognostic outcome of COL12A1 within GC tissues through the network databases. Using several web-based databases, we analyzed the major components and targets of JYQHD, as well as known therapeutic targets in gastric cancer. The Venn diagram was utilized to obtain the overlapped genes. Lentiviral vector, shRNAs and plasmids, were used to transfect GC cells. Cell counting kit-8 (CCK8), sphere formation, malondialdehyde (MDA), glutathione (GSH), reactive oxygen species (ROS), Fe2+, transmission electron microscopy (TEM), quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), Western-Blot (WB), and immunohistochemical (IHC) assays were employed to investigate the role and mechanism of COL12A1 and JYQHD in GC.

RESULTS

The results showed that JYQHD was non-toxic and safe. JYQHD inhibited growth and sphere formation ability through inducing the ferroptosis of GC cells, and suppressed the GC cells induced subcutaneous xenograft tumor growth. COL12A1 was highly expressed in gastric cancer tissues, indicating poor prognosis. COL12A1 specifically enhanced GC cell progression and stemness via suppressing ferroptosis. JYQHD down-regulated COL12A1 in order to suppress the stemness of GC cells via inducing ferroptosis.

CONCLUSION

COL12A1 inhibited ferroptosis and enhanced stemness in GC cells. JYQHD inhibited the development of GC cells by inhibiting cancer cell stemness via the ferroptosis pathway mediated by COL12A1.

Mapping synthetic binding proteins epitopes on diverse protein targets by protein structure prediction and protein-protein docking

Synthetic binding proteins (SBPs) are a class of artificial proteins engineered from privileged protein scaffolds, which can form highly specific molecular recognition interfaces with a variety of targets. Due to the characteristics of small size, high stability, and good tissue permeability, SBPs have important applications in biomedical research, disease diagnosis and treatment. However, knowledge of SBPs epitopes on the structures of target proteins is still limited, which hinder the development of novel SBPs. In this study, based on the currently available information of SBPs and their targets, 96 pairs of interacting proteins referring to 96 representative SBPs and 80 different targets, were systemically investigated using the state-of-the-art computational modeling techniques including AlphaFold2 protein structure prediction and Rosetta protein-protein docking. As a result, 71 out of the 96 pairs were successfully docked, of which 18, 33, and 20 pairs were defined as models with high, medium, and acceptable quality, respectively. In addition, the interface information was analyzed to decipher the interaction types driven SBPs and targets recognition. Overall, this work not only provides important structural information for understanding the mechanism of action of other SBPs with same protein scaffold, but also for aiding the rational protein engineering and to design of novel SBPs with biomedical applications.

Engineered human spinal cord-like tissues with dorsal and ventral neuronal progenitors for spinal cord injury repair in rats and monkeys

Transplanting human neural progenitor cells is a promising method of replenishing the lost neurons after spinal cord injury (SCI), but differentiating neural progenitor cells into the diverse types of mature functional spinal cord neurons in vivo is challenging. In this study, engineered human embryonic spinal cord-like tissues with dorsal and ventral neuronal characters (DV-SC) were generated by inducing human neural progenitor cells (hscNPCs) to differentiate into various types of dorsal and ventral neuronal cells on collagen scaffold in vitro. Transplantation of DV-SC into complete SCI models in rats and monkeys showed better therapeutic effects than undifferentiated hscNPCs, including pronounced cell survival and maturation. DV-SC formed a targeted connection with the host's ascending and descending axons, partially restored interrupted neural circuits, and improved motor evoked potentials and the hindlimb function of animals with SCI. This suggests that the transplantation of pre-differentiated hscNPCs with spinal cord dorsal and ventral neuronal characteristics could be a promising strategy for SCI repair.

Raddeanin A promotes autophagy-induced apoptosis by inactivating PI3K/AKT/mTOR pathway in lung adenocarcinoma cells

Non-small-cell lung cancer (NSCLC) is the most common cancer in the world. Previous studies have shown that Raddeanin A (RA) exhibited distinct antitumor properties in gastric and colon cancer. This study aimed to investigate the pharmacological actions and intrinsic mechanisms of RA in NSCLC. Through the application of network pharmacology, the potential targets of RA for NSCLC therapy such as SRC, MAPK1, and STAT3 were excavated. Enrichment analyses showed that these targets were concerned with the regulation of cell death, regulation of MAPK cascade, Ras signaling pathway, and PI3K/AKT signaling pathway. Meanwhile, 13 targets of RA were identified as autophagy-related genes. Our experiment data showed that RA effectively inhibited proliferation and induced apoptosis in lung cancer cells A549. We also found that RA could induce autophagy simultaneously. Furthermore, the autophagy induced by RA had a synergistic effect with apoptosis and contributed to cell death. Additionally, RA could downregulate the activity of the PI3K/AKT/mTOR pathway. Generally, our results indicated the antitumor effect and underlying mechanisms of RA on apoptosis and autophagy in A549 cells, suggesting that RA could be used as an effective antineoplastic agent.

The NSP4 T492I mutation increases SARS-CoV-2 infectivity by altering non-structural protein cleavage

The historically dominant SARS-CoV-2 Delta variant and the currently dominant Omicron variants carry a T492I substitution within the non-structural protein 4 (NSP4). Based on in silico analyses, we hypothesized that the T492I mutation increases viral transmissibility and adaptability, which we confirmed with competition experiments in hamster and human airway tissue culture models. Furthermore, we showed that the T492I mutation increases the replication capacity and infectiveness of the virus and improves its ability to evade host immune responses. Mechanistically, the T492I mutation increases the cleavage efficiency of the viral main protease NSP5 by enhancing enzyme-substrate binding, which increases production of nearly all non-structural proteins processed by NSP5. Importantly, the T492I mutation suppresses viral-RNA-associated chemokine production in monocytic macrophages, which may contribute to the attenuated pathogenicity of Omicron variants. Our results highlight the importance of NSP4 adaptation in the evolutionary dynamics of SARS-CoV-2.

Structure-Based Discovery of a Novel Allosteric Inhibitor against Human Dopamine Transporter

Human dopamine transporter (hDAT) regulates the reuptake of extracellular dopamine (DA) and is an essential therapeutic target for central nervous system (CNS) diseases. The allosteric modulation of hDAT has been identified for decades. However, the molecular mechanism underlying the transportation is still elusive, which hinders the rational design of allosteric modulators against hDAT. Here, a systematic structure-based method was performed to explore allosteric sites on hDAT in inward-open (IO) conformation and to screen compounds with allosteric affinity. First, the model of the hDAT structure was constructed based on the recently reported Cryo-EM structure of the human serotonin transporter (hSERT) and Gaussian-accelerated molecular dynamics (GaMD) simulation was further utilized for the identification of intermediate energetic stable states of the transporter. Then, with the potential druggable allosteric site on hDAT in IO conformation, virtual screening of seven enamine chemical libraries (∼440,000 compounds) was processed, resulting in 10 compounds being purchased for in vitro assay and with Z1078601926 discovered to allosterically inhibit hDAT (IC₅₀ = 0.527 [0.284; 0.988] μM) when nomifensine was introduced as an orthosteric ligand. Finally, the synergistic effect underlying the allosteric inhibition of hDAT by Z1078601926 and nomifensine was explored using additional GaMD simulation and postbinding free energy analysis. The hit compound discovered in this work not only provides a good starting point for lead optimization but also demonstrates the usability of the method for the structure-based discovery of novel allosteric modulators of other therapeutic targets.

Computational protein design - where it goes?

Proteins have been playing a critical role in the regulation of diverse biological processes related to human life. With the increasing demand, functional proteins are sparse in this immense sequence space. Therefore, protein design has become an important task in various fields, including medicine, food, energy, materials, etc. Directed evolution has recently led to significant achievements. Molecular modification of proteins through directed evolution technology has significantly advanced the fields of enzyme engineering, metabolic engineering, medicine, and beyond. However, it is impossible to identify desirable sequences from a large number of synthetic sequences alone. As a result, computational methods, including data-driven machine learning and physics-based molecular modeling, have been introduced to protein engineering to produce more functional proteins. This review focuses on recent advances in computational protein design, highlighting the applicability of different approaches as well as their limitations.

Proteomics profiles reveal the potential roles of proteins involved in chicken macrophages stimulated by Lipopolysaccharide

Lipopolysaccharide (LPS), a core part of gram-negative bacteria, is crucial for inducing an inflammatory response in living things. In the current study, we used LPS from Salmonella to stimulate chicken macrophages (HD11). Proteomics was used to investigate immune-related proteins and their roles further. Proteomics investigation revealed 31 differential expression proteins (DEPs) after 4 hours of LPS infection. 24 DEPs expressions were up-regulated, while seven were down-regulated. In this investigation, ten DEPs were mainly enriched in S. aureus infection, complement, and coagulation cascades, which were all implicated in the inflammatory response and clearance of foreign pathogens. Notably, complement C3 was shown to be up-regulated in all immune-related pathways, indicating that it is a potential protein in this study. This work contributes to a better understanding and clarification of the processes of Salmonella infection in chickens. It might bring up new possibilities for treating and breeding Salmonella-infected chickens.

Boosting the capacity and stability of a MoO3 cathode via valence regulation and polypyrrole coating for a rechargeable Zn ion battery

Molybdenum trioxide (MoO₃) is emerging as a hugely competitive cathode material for aqueous zinc ion batteries (ZIBs) for its high theoretical capacity and electrochemical activity. Nevertheless, owing to its undesirable electronic transport capability and poor structural stability, the practical capacity and cycling performance of MoO₃ are yet unsatisfactory, which greatly blocks its commercial use. In this work, we report an effective approach to first synthesise nanosized MoO_3-x materials to provide more active specific surface areas, while improving the capacity and cycle life of MoO₃ by introducing low valence Mo and coated polypyrrole (PPy). MoO₃ nanoparticles with low-valence-state Mo and PPy coating (denoted as MoO_3-x@PPy) are synthesized via a solvothermal method and subsequent electrodeposition process. The as-prepared MoO_3-x@PPy cathode delivers a high reversible capacity of 212.4 mA h g^-1 at 1 A g^-1 with good cycling life (more than 75% capacity retention after 500 cycles). In contrast, the original commercial MoO₃ sample only obtains a capacity of 99.3 mA h g^-1 at 1 A g^-1, and a cycling stability of 10% capacity retention over 500 cycles. Additionally, the fabricated Zn//MoO_3-x@PPy battery obtains a maximum energy density of 233.6 W h kg^-1 and a power density of 11.2 kW kg^-1. Our results provide an efficient and practical approach to enhance commercial MoO₃ materials as high-performance cathodes for AZIBs.

Multi-state Model-Based Identification of Cryptic Allosteric Sites on Human Serotonin Transporter

Serotonin transporter (SERT) plays a fundamental role in taking the synaptic cleft serotonin back to the presynaptic neuron. The discovery of allosteric SERT modulators represents the next-generation medication for psychiatric disorders such as depression. Here, based on the cryo-EM structures of ibogaine in complex with SERT in distinct conformations, the multiple functional structures of the transporter bound to serotonin, including outward-open (OO_holo), outward-occluded (OC_holo), and inward-open (IO_holo and IO_holo'), were carefully characterized by induced-fit docking Gaussian-accelerated molecular dynamics (IFD-GaMD) simulation and the free-energy landscape analysis. Further MM/GBSA binding free energy, per-residue contribution, and molecular interaction fingerprint calculations revealed the interaction variations of serotonin with SERT in functional structures, which confirmed the allostery of SERT during serotonin reuptake. Moreover, five unique cryptic allosteric sites, which are druggable and capable of targeting by small molecules, were identified on the characterized multistate structures. These results provide structural and energetic information for the molecular mechanism of serotonin reuptake and will provide opportunities for the development of novel therapeutics based on the identified new allosteric sites on SERT.

Sodium Ion Pre-Intercalation of δ-MnO2 Nanosheets for High Energy Density Aqueous Zinc-Ion Batteries

With the merits of low cost, environmental friendliness and rich resources, manganese dioxide is considered to be a promising cathode material for aqueous zinc-ion batteries (AZIBs). However, its low ion diffusion and structural instability greatly limit its practical application. Hence, we developed an ion pre-intercalation strategy based on a simple water bath method to grow in situ δ-MnO₂ nanosheets on flexible carbon cloth substrate (MnO₂), while pre-intercalated Na⁺ in the interlayer of δ-MnO₂ nanosheets (Na-MnO₂), which effectively enlarges the layer spacing and enhances the conductivity of Na-MnO₂. The prepared Na-MnO₂//Zn battery obtained a fairly high capacity of 251 mAh g^-1 at a current density of 2 A g^-1, a satisfactory cycle life (62.5% of its initial capacity after 500 cycles) and favorable rate capability (96 mAh g^-1 at 8 A g^-1). Furthermore, this study revealed that the pre-intercalation engineering of alkaline cations is an effective method to boost the properties of δ-MnO₂ zinc storage and provides new insights into the construction of high energy density flexible electrodes.

Unbiased molecular dynamics simulation of a first-in-class small molecule inhibitor binds to oncostatin M

Small molecule inhibitors (SMIs) targeting oncostatin M (OSM) signaling pathway represent new therapeutics to combat cancer, inflammatory bowel disease (IBD) and CNS disease. Recently, the first-in-class SMI named SMI-10B that target OSM and block its interaction with receptor (OSMR) were reported. However, the binding pocket and interaction mode of the compound on OSM remain poorly understood, which hampering the rational design of SMIs that target OSM. Here, using SMI-10B as a probe, the multiple pockets on OSM for small molecules binding were extensively explored by unbiased molecular dynamics (MD) simulations. Then, the near-native structure of the complex was identified by molecular mechanics generalized Born surface area (MM/GBSA) binding energy funnel. Moreover, the binding stabilities of the protein-ligand complexes in near- and non-native conformations were verified by additional independent MD runs and absolute free energy perturbation (FEP) calculation. In summary, the unique feature of SMI-10B spontaneously binds to OSM characterized here not only provide detailed information for understanding the molecular mechanism of SMI-10B binding to OSM, but also will facilitate the rational design of novel and more potent SMIs to block OSM signaling.

Unconventional secretion of unglycosylated ORF8 is critical for the cytokine storm during SARS-CoV-2 infection

Coronavirus disease 2019 is a respiratory infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Evidence on the pathogenesis of SARS-CoV-2 is accumulating rapidly. In addition to structural proteins such as Spike and Envelope, the functional roles of non-structural and accessory proteins in regulating viral life cycle and host immune responses remain to be understood. Here, we show that open reading frame 8 (ORF8) acts as messenger for inter-cellular communication between alveolar epithelial cells and macrophages during SARS-CoV-2 infection. Mechanistically, ORF8 is a secretory protein that can be secreted by infected epithelial cells via both conventional and unconventional secretory pathways. Conventionally secreted ORF8 is glycosylated and loses the ability to recognize interleukin 17 receptor A of macrophages, possibly due to the steric hindrance imposed by N-glycosylation at Asn78. However, unconventionally secreted ORF8 does not undergo glycosylation without experiencing the ER-Golgi trafficking, thereby activating the downstream NF-κB signaling pathway and facilitating a burst of cytokine release. Furthermore, we show that ORF8 deletion in SARS-CoV-2 attenuates inflammation and yields less lung lesions in hamsters. Our data collectively highlights a role of ORF8 protein in the development of cytokine storms during SARS-CoV-2 infection.

The Novel lncRNA RP9P Promotes Colorectal Cancer Progression by Modulating miR-133a-3p/FOXQ1 Axis

Background

The long non-coding RNA (lncRNA) RP9 pseudogene (RP9P) is a pseudogene-derived lncRNA that has never been reported in cancer, and its function underlying tumorigenesis in colorectal cancer (CRC) remains unknown.

Methods

RP9P and miR-133a-3p were filtered through bioinformatics analysis. The level of RP9P, miR-133a-3p, and FOXQ1 in CRC cell lines was detected by real-time PCR. Cell Counting Kit-8 and flow cytometric analyses were used to detect cell proliferation and apoptosis, respectively. Interactions between RP9P, miR-133a-3p, and FOXQ1 were confirmed by a dual-luciferase reporter assay.

Results

RP9P was overexpressed in CRC compared to normal control tissues and cells. Knockdown of RP9P inhibited CRC cell viability. RP9P directly interacted with miR-133a-3p, and miR-133a-3p downregulation abrogated the tumor-suppressing effect of RP9P knockdown. miR-133a-3p directly targeted FOXQ, which was positively regulated by RP9P. RP9P knockdown decreased FOXQ1 expression levels in CRC cells by directly targeting miR-133a-3p via a sponge mechanism. In addition, in vivo experiments in a xenograft model revealed that downregulated RP9P expression inhibited CRC cell tumorigenesis.

Conclusion

RP9P promotes colorectal cancer progression by regulating the miR-133a-3p/FOXQ1 axis.

Physicochemical and Biological Insights Into the Molecular Interactions Between Extracellular DNA and Exopolysaccharides in Myxococcus xanthus Biofilms

Extracellular DNA (eDNA) is a critical component in the extracellular matrix (ECM) of bacterial biofilms, while little is known about the mechanisms underlying how eDNA integrates into the ECM through potential macromolecular interactions. Myxococcus xanthus biofilm was employed as a suitable model for the investigation due to the co-distribution of eDNA and exopolysaccharides (EPS) owing to their direct interactions in the ECM. DNA is able to combine with M. xanthus EPS to form a macromolecular conjugate, which is dominated by the electrostatic forces participating in the polymer-polymer interactions. Without intercalation binding, DNA-EPS interactions exhibit a certain degree of reversibility. Acting as a strong extracellular framework during biofilm formation process, the eDNA-EPS complex not only facilitates the initial cell adhesion and subsequent establishment of ECM architecture, but also renders cells within biofilms stress resistances that are relevant to the survival of M. xanthus in some hostile environments. Furthermore, the EPS protects the conjugated DNA from the degradation by nucleic acid hydrolases, which leads to the continuous and stable existence of eDNA in the native ECM of M. xanthus biofilms. These results will shed light on developing prevention and treatment strategies against biofilm-related risks.

Increased odds ratio for erectile dysfunction in COVID-19 patients

PURPOSE

Erectile dysfunction and COVID-19 share similar risk factors, including vascular disruption of integrity, cytokine release, cardiovascular disease, diabetes and obesity. The aim of this study was to investigate the association between erectile dysfunction and COVID-19 patients.

METHODS

Odds ratio for erectile dysfunction in patients with a history of COVID-19 with and without comorbidities were calculated using a patients' registry platform i2b2. ICD-10 diagnoses codes were accessed for queries and data were analyzed using logistic regression.

RESULTS

Patients with COVID-19 were 3.3 times more likely to have erectile dysfunction with 95% CI (2.8, 3.8). The association became stronger with odds ratio 4.8 (95% CI (4.1, 5.7)) after adjusting for age groups. The odds ratio remained the same after adjusting for smoking status with 3.5 (95% CI (3.0, 4.1)). After adjusting for race, COVID-19 patients were 2.6 (95% CI (2.2, 3.1)) times more likely to have erectile dysfunction. The odds ratio were 1.6, 1.8, 1.9 and 2.3 after adjusting for respiratory disease, obesity, circulatory disease and diabetes, respectively.

CONCLUSION

COVID-19 and erectile dysfunction are strongly associated even after adjustment for known risk factors and demographics.

Molecular Mechanism for the Allosteric Inhibition of the Human Serotonin Transporter by Antidepressant Escitalopram

Human serotine transporter (hSERT) is one of the most influential drug targets, and its allosteric modulators (e.g., escitalopram) have emerged to be the next-generation medication for psychiatric disorders. However, the molecular mechanism underlying the allosteric modulation of hSERT is still elusive. Here, the simulation strategies of conventional (cMD) and steered (SMD) molecular dynamics were applied to investigate this molecular mechanism from distinct perspectives. First, cMD simulations revealed that escitalopram's binding to hSERT's allosteric site simultaneously enhanced its binding to the orthosteric site. Then, SMD simulation identified that the occupation of hSERT's allosteric site by escitalopram could also block its dissociation from the orthosteric site. Finally, by comparing the simulated structures of two hSERT-escitalopram complexes with and without allosteric modulation, a new conformational coupling between an extracellular (Arg104-Glu494) and an intracellular (Lys490-Glu494) salt bridge was identified. In summary, this study explored the mechanism underlying the allosteric modulation of hSERT by collectively applying two MD simulation strategies, which could facilitate our understanding of the allosteric modulations of not only hSERT but also other clinically important therapeutic targets.

Optimized, visible light-induced crosslinkable hybrid gelatin/hyaluronic acid scaffold promotes complete spinal cord injury repair

Severe microenvironmental changes after spinal cord injury (SCI) present serious challenges in neural regeneration and tissue repair. Gelatin (GL)- and hyaluronic acid (HA)-based hydrogels are attractive scaffolds because they are major components of the extracellular matrix and can provide a favorable adjustable microenvironment for neurogenesis and motor function recovery. In this study, three-dimensional hybrid GL/HA hydrogel scaffolds were prepared and optimized. The hybrid hydrogels could undergo in-situ gelation and fit the defects perfectly via visible light- induced crosslinking in the complete SCI rats. We found that the transplantation of the hybrid hydrogel scaffold significantly reduced the inflammatory responses and suppressed glial scar formation in an HA concentration-dependent manner. Moreover, the hybrid hydrogel with GL/HA ratios less than 8/2 effectively promoted endogenous neural stem cell migration and neurogenesis, as well as improved neuron maturation and axonal regeneration. The results showed locomotor function improved 60 days after transplantation, thus suggesting that GL/HA hydrogels can be considered as a promising scaffold for complete SCI repair.

SYNBIP: synthetic binding proteins for research, diagnosis and therapy

The success of protein engineering and design has extensively expanded the protein space, which presents a promising strategy for creating next-generation proteins of diverse functions. Among these proteins, the synthetic binding proteins (SBPs) are smaller, more stable, less immunogenic, and better of tissue penetration than others, which make the SBP-related data attracting extensive interest from worldwide scientists. However, no database has been developed to systematically provide the valuable information of SBPs yet. In this study, a database named ‘Synthetic Binding Proteins for Research, Diagnosis, and Therapy (SYNBIP)’ was thus introduced. This database is unique in (a) comprehensively describing thousands of SBPs from the perspectives of scaffolds, biophysical & functional properties, etc.; (b) panoramically illustrating the binding targets & the broad application of each SBP and (c) enabling a similarity search against the sequences of all SBPs and their binding targets. Since SBP is a human-made protein that has not been found in nature, the discovery of novel SBPs relied heavily on experimental protein engineering and could be greatly facilitated by in-silico studies (such as AI and computational modeling). Thus, the data provided in SYNBIP could lay a solid foundation for the future development of novel SBPs. The SYNBIP is accessible without login requirement at both official (https://idrblab.org/synbip/) and mirror (http://synbip.idrblab.net/) sites.

[Quantitative analysis of differential proteins in liver tissues of patients with non-alcoholic steatohepatitis using iTRAQ technology]

OBJECTIVE

To screen differentially expressed proteins (DSPs) in the liver tissues of patients with nonalcoholic steatohepatitis (NASH) using proteomic technologies to identify potential therapeutic targets of NASH.

METHODS

Liver tissue specimens were obtained from 3 patients with pathologically confirmed NASH and 3 normal control subjects. The total proteins were extracted from the specimens, and iTRAQ reagent was used to label the peptides for liquid chromatography tandem mass spectrometry (LC-MS/MS) detection. The DSPs were identified by comparing the data against UniProt protein database using Mascot2.3.02 software and were annotated and enriched using GO database; KEGG database was used for enrichment of the pathways involving these proteins. Real-time fluorescent quantitative PCR (qPCR) was performed to detect the mRNA expressions of the significant DSPs in NASH.

RESULTS

By the criteria that a DSP has >1.2 or < 0.8 fold difference between NASH group and the control group and with P < 0.05 as the threshold, a total of 648 significant DSPs in NASH were identified, including 246 up-regulated and 402 down-regulated proteins. GO functional enrichment analysis showed that the DSPs were involved mainly in small molecule metabolism, organic acid metabolism, oxygen acid metabolism and other biological processes, and were enriched in KEGG pathways including the metabolic pathways, complement coagulation cascades, and ribosomes. Among the 25 DEPs with a fold difference >2.0 or < 0.5 (P < 0.05), 6 proteins showed consistent results between qPCR verification and proteomic analysis, including 5 down-regulated proteins: Jumonji protein (JARID2), Lebasillinlike protein (LCA5L), synaptophysin 1 (SYN1) and collagen α-1 (XIII) chain (COL13A1), FYVE, RhoGEF and PH domain protein 5 (FGD5), and 1 upregulated protein glutathione S-transferase Mu 4 (GSTM4).

CONCLUSION

We identified 648 DEPs inthe liver tissue of patients NASH using iTRAQ technology and bioinformatics methods, and among them JARID2, SYN1, COL13A1, FGD5, and GSTM4 may serve as the key target proteins of NASH.

Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 Mpro

The continual spread of novel coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), posing a severe threat to the health worldwide. The main protease (Mpro, alias 3CLpro) of SARS-CoV-2 is a crucial enzyme for the maturation of viral particles and is a very attractive target for designing drugs to treat COVID-19. Here, we propose a multiple conformation-based virtual screening strategy to discover inhibitors that can target SARS-CoV-2 Mpro. Based on this strategy, nine Mpro structures and a protein mimetics library with 8960 commercially available compounds were prepared to carry out ensemble docking for the first time. Five of the nine structures are apo forms presented in different conformations, whereas the other four structures are holo forms complexed with different ligands. The surface plasmon resonance assay revealed that 6 out of 49 compounds had the ability to bind to SARS-CoV-2 Mpro. The fluorescence resonance energy transfer experiment showed that the biochemical half-maximal inhibitory concentration (IC50) values of the six compounds could hamper Mpro activities ranged from 0.69 ± 0.05 to 2.05 ± 0.92 μM. Evaluation of antiviral activity using the cell-based assay indicated that two compounds (Z1244904919 and Z1759961356) could strongly inhibit the cytopathic effect and reduce replication of the living virus in Vero E6 cells with the half-maximal effective concentrations (EC50) of 4.98 ± 1.83 and 8.52 ± 0.92 μM, respectively. The mechanism of the action for the two inhibitors were further elucidated at the molecular level by molecular dynamics simulation and subsequent binding free energy analysis. As a result, the discovered noncovalent reversible inhibitors with novel scaffolds are promising antiviral drug candidates, which may be used to develop the treatment of COVID-19.

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

Label-free quantification (LFQ) with a specific and sequentially integrated workflow of acquisition technique, quantification tool and processing method has emerged as the popular technique employed in metaproteomic research to provide a comprehensive landscape of the adaptive response of microbes to external stimuli and their interactions with other organisms or host cells. The performance of a specific LFQ workflow is highly dependent on the studied data. Hence, it is essential to discover the most appropriate one for a specific data set. However, it is challenging to perform such discovery due to the large number of possible workflows and the multifaceted nature of the evaluation criteria. Herein, a web server ANPELA (https://idrblab.org/anpela/) was developed and validated as the first tool enabling performance assessment of whole LFQ workflow (collective assessment by five well-established criteria with distinct underlying theories), and it enabled the identification of the optimal LFQ workflow(s) by a comprehensive performance ranking. ANPELA not only automatically detects the diverse formats of data generated by all quantification tools but also provides the most complete set of processing methods among the available web servers and stand-alone tools. Systematic validation using metaproteomic benchmarks revealed ANPELA's capabilities in 1 discovering well-performing workflow(s), (2) enabling assessment from multiple perspectives and (3) validating LFQ accuracy using spiked proteins. ANPELA has a unique ability to evaluate the performance of whole LFQ workflow and enables the discovery of the optimal LFQs by the comprehensive performance ranking of all 560 workflows. Therefore, it has great potential for applications in metaproteomic and other studies requiring LFQ techniques, as many features are shared among proteomic studies.

Copper (Cu2+) ion-induced misfolding of tau protein R3 peptide revealed by enhanced molecular dynamics simulation

Tau misfolding plays a significant role in some neurodegenerative diseases such as Alzheimer's disease (AD). It is intrinsically disordered and highly soluble under normal physiological conditions. While the protein will aggregate to form paired helical filaments (PHFs) under copper homeostasis at pathological conditions, which is the main substance of neurofibrillary tangles (NFTs) in the brain of AD patients. However, the molecular mechanism underlying the copper (Cu2+) ion-induced tau misfolding is not fully understood. In this study, using the 1/2 third repeat fragment (R3 peptide) of tau protein (residues 318-335: VTSKCGSLGNIHHKPGGG) as a model, a Gaussian accelerated molecular dynamics (GaMD) method followed by efficient trajectory analysis was carried out to investigate the influences of Cu2+ on the tau about the protein fold and the free energy landscape along the simulation. The two-dimensional potential of mean force (PMF) profiles obtained from reweighting of the GaMD simulations as well as clustering analysis revealed the Cu2+ ion induced α-helix fold R3 peptide located at the low-energy wells of free energy map, which is in agreement with the reported experimental result. In contrast, there is no α-helix fold of R3 peptide that appeared during the GaMD simulation without Cu2+ ion existing. Furthermore, the definition of secondary structure of protein (DSSP) analysis indicated that the R3 peptide with Cu2+ ion forms a stable structure of the helix (Lys321-His330 interval of the peptide) at between 400 and 500 ns. Therefore, the structures and free energy profiles from GaMD simulations proposed that Cu2+ triggers the aggregation of R3 peptide into toxic PHFs through a stable α-helix fold form.

MiR-342 controls Mycobacterium tuberculosis susceptibility by modulating inflammation and cell death

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb) that places a heavy strain on public health. Host susceptibility to Mtb is modulated by macrophages, which regulate the balance between cell apoptosis and necrosis. However, the role of molecular switches that modulate apoptosis and necrosis during Mtb infection remains unclear. Here, we show that Mtb-susceptible mice and TB patients have relatively low miR-342-3p expression, while mice with miR-342-3p overexpression are more resistant to Mtb. We demonstrate that the miR-342-3p/SOCS6 axis regulates anti-Mtb immunity by increasing the production of inflammatory cytokines and chemokines. Most importantly, the miR-342-3p/SOCS6 axis participates in the switching between Mtb-induced apoptosis and necrosis through A20-mediated K48-linked ubiquitination and RIPK3 degradation. Our findings reveal several strategies by which the host innate immune system controls intracellular Mtb growth via the miRNA-mRNA network and pave the way for host-directed therapies targeting these pathways.

Recent Advances in Computer-aided Antiviral Drug Design Targeting HIV-1 Integrase and Reverse Transcriptase Associated Ribonuclease H

Acquired immunodeficiency syndrome (AIDS) has been a chronic, life-threatening disease for a long time. However, a broad range of antiretroviral drug regimens are applicable for the successful suppression of virus replication in human immunodeficiency virus type 1 (HIV-1) infected people. The mutation-induced drug resistance problems during the treatment of AIDS forced people to continuously look for new antiviral agents. HIV-1 integrase (IN) and reverse transcriptase associated ribonuclease (RT-RNase H), two pivotal enzymes in HIV-1 replication progress, has gain popularity as drug-able targets for designing novel HIV-1 antiviral drugs. During the development of HIV-1 IN and/or RT-RNase H inhibitors, computer-aided drug design (CADD), including homology modeling, pharmacophore, docking, molecular dynamics (MD) simulation, and binding free energy calculation, represents a significant tool to accelerate the discovery of new drug candidates and reduce costs in antiviral drug development. In this review, we summarized the recent advances in the design of single-and dual-target inhibitors against HIV-1 IN or/and RT-RNase H as well as the prediction of mutation-induced drug resistance based on computational methods. We highlighted the results of the reported literature and proposed some perspectives on the design of novel and more effective antiviral drugs in the future.

Relationship between electrocardiographic changes and EPO level in stable CAD patients with autonomic nerve functional damage

OBJECTIVE

To investigate the relationship between electrocardiographic changes and erythropoietin (EPO) level in stable coronary artery disease (CAD) patients with autonomic nerve functional damage.

PATIENTS AND METHODS

Clinical data of 96 stable CAD patients who were treated in our hospital from January 2017 to December 2019 were retrospectively analyzed. All patients were grouped according to whether autonomic nerve function damage was combined; the baseline characteristic data and the morphological characteristics of ECG scattergram were compared between 2 groups, and the relationship between ECG scattergram and EPO level & autonomic nerve function was analyzed.

RESULTS

The levels of EPO and red cell volume distributing width (RDW) in stable CAD patients with autonomic nerve dysfunction were significantly higher than that of CAD patients without autonomic nerve dysfunction (p<0.05). The length of scattergram in stable CAD patients with autonomic nerve dysfunction was significantly shorter than that of those without autonomic nerve dysfunction (p<0.05). The cometary sign proportion of ECG scattergram in stable CAD patients with autonomic nerve dysfunction was significantly lower than that of stable CAD patients without autonomic nerve dysfunction (p<0.05). There was negative correlation between EPO levels and scattergram length in stable CAD patients with and without autonomic nerve dysfunction (r=0.44, p=0.02). There was no correlation between EPO levels and scatter width in stable CAD patients with and without autonomic nerve dysfunction (r=0.10, p=0.58). The results of binary logistic regression analysis showed that EPO level was the independent risk factor for the occurrence of autonomic dysfunction in patients with stable CAD (p<0.05). The length of scattergram was the independent protective factor of autonomic nerve function impairment in patients with stable CAD (p<0.05). The AUC of EPO level and scattergram was 0.74 and 0.72 respectively, both of which have similar prediction value.

CONCLUSIONS

The level of EPO in stable CAD patients with autonomic nerve dysfunction was related to the change of ECG; and the EPO level and scattergram length can be used to predict the occurrence risk of autonomic nerve dysfunction.

Understanding the Polypharmacological Profiles of Triple Reuptake Inhibitors by Molecular Simulation

The triple reuptake inhibitors (TRIs) class is a class of effective inhibitors of human monoamine transporters (hMATs), which includes dopamine, norepinephrine, and serotonin transporters (hDATs, hNETs, and hSERTs). Due to the high degree of structural homology of the binding sites of those transporters, it is a great challenge to design potent TRIs with fine-tuned binding profiles. The molecular determinants responsible for the binding selectivity of TRIs to hDATs, hNETs, and hSERTs remain elusive. In this study, the solved X-ray crystallographic structure of hSERT in complex with escitalopram was used as a basis for modeling nine complexes of three representative TRIs (SEP225289, NS2359, and EB1020) bound to their corresponding targets. Molecular dynamics (MD) and effective post-trajectory analysis were performed to estimate the drug binding free energies and characterize the selective profiles of each TRI to hMATs. The common binding mode of studied TRIs to hMATs was revealed by hierarchical clustering analysis of the per-residue energy. Furthermore, the combined protein-ligand interaction fingerprint and residue energy contribution analysis indicated that several conserved and nonconserved "Warm Spots" such as S149, V328, and M427 in hDAT, F317, F323, and V325 in hNET and F335, F341, and V343 in hSERT were responsible for the TRI-binding selectivity. These findings provided important information for rational design of a single drug with better polypharmacological profiles through modulating multiple targets.

Scar tissue removal-activated endogenous neural stem cells aid Taxol-modified collagen scaffolds in repairing chronic long-distance transected spinal cord injury

Scar tissue removal combined with biomaterial implantation is considered an effective measure to repair chronic transected spinal cord injury (SCI). However, whether more scar tissue removal surgeries could affect the treatment effects of biomaterial implantation still needs to be explored. In this study, we performed the first scar tissue removal surgery in the 3^rd month and the second in the 6^th month after completely removing 1 cm of spinal tissue in canines. We found that Taxol-modified linear ordered collagen scaffold (LOCS + Taxol) implantation could promote axonal regeneration, neurogenesis, and electrophysiological and functional recovery only in canines at the first scar tissue removal surgery, but not in canines at the second scar tissue removal surgery. Interestingly, we found that more endogenous neural stem cells (NSCs) around the injured site could be activated in canines with the first rather than the second scar tissue removal. Furthermore, we demonstrated that Taxol could promote the neuronal differentiation of NSCs in the myelin inhibition microenvironment through the p38 MAPK signaling pathway in vitro. Therefore, we speculated that endogenous NSC activation by the first scar tissue removal surgery and its further differentiation into neurons induced by Taxol may contribute to functional recovery in canines. Together, LOCS + Taxol implantation in combination with the first scar tissue removal provides a promising therapy for chronic long-distance transected SCI repair with the help of scar tissue removal activated endogenous NSCs.

Upregulation of Apol8 by Epothilone D facilitates the neuronal relay of transplanted NSCs in spinal cord injury

BACKGROUND

Microtubule-stabilizing agents have been demonstrated to modulate axonal sprouting during neuronal disease. One such agent, Epothilone D, has been used to treat spinal cord injury (SCI) by promoting axonal sprouting at the lesion site after SCI. However, the role of Epothilone D in the differentiation of neural stem cells (NSCs) in SCI repair is unknown. In the present study, we mainly explored the effects and mechanisms of Epothilone D on the neuronal differentiation of NSCs and revealed a potential new SCI treatment.

METHODS

In vitro differentiation assays, western blotting, and quantitative real-time polymerase chain reaction were used to detect the effects of Epothilone D on NSC differentiation. Retrograde tracing using a pseudotyped rabies virus was then used to detect neuronal circuit construction. RNA sequencing (RNA-Seq) was valuable for exploring the target gene involved in the neuronal differentiation stimulated by Epothilone D. In addition, lentivirus-induced overexpression and RNA interference technology were applied to demonstrate the function of the target gene. Last, an Apol8-NSC-linear ordered collagen scaffold (LOCS) graft was prepared to treat a mouse model of SCI, and functional and electrophysiological evaluations were performed.

RESULTS

We first revealed that Epothilone D promoted the neuronal differentiation of cultured NSCs and facilitated neuronal relay formation in the injured site after SCI. Furthermore, the RNA-Seq results demonstrated that Apol8 was upregulated during Epothilone D-induced neuronal relay formation. Lentivirus-mediated Apol8 overexpression in NSCs (Apol8-NSCs) promoted NSC differentiation toward neurons, and an Apol8 interference assay showed that Apol8 had a role in promoting neuronal differentiation under the induction of Epothilone D. Last, Apol8-NSC transplantation with LOCS promoted the neuronal differentiation of transplanted NSCs in the lesion site as well as synapse formation, thus improving the motor function of mice with complete spinal cord transection.

CONCLUSIONS

Epothilone D can promote the neuronal differentiation of NSCs by upregulating Apol8, which may provide a promising therapeutic target for SCI repair.