Prediction of allosteric druggable pockets of cyclin-dependent kinases.

Cyclin-dependent kinase (Cdk) proteins play crucial roles in the cell cycle progression and are thus attractive drug targets for therapy against such aberrant cell cycle processes as cancer. Since most of the available Cdk inhibitors target the highly conserved catalytic ATP pocket and their lack of specificity often lead to side effects, it is imperative to identify and characterize less conserved non-catalytic pockets capable of interfering with the kinase activity allosterically. However, a systematic analysis of these allosteric druggable pockets is still in its infancy. Here, we summarize the existing Cdk pockets and their selectivity. Then, we outline a network-based pocket prediction approach (NetPocket) and illustrate its utility for systematically identifying the allosteric druggable pockets with case studies. Finally, we discuss potential future directions and their challenges.

Dynamic geometry design of cyclic peptide architectures for RNA structure.

Designing inhibitors for RNA is still challenging due to the bottleneck of maintaining the binding interaction of inhibitor-RNA accompanied by subtle RNA flexibility. Thus, the current approach usually needs to screen thousands of candidate inhibitors for binding. Here, we propose a dynamic geometry design approach to enrich the hits with only a tiny pool of designed geometrically compatible scaffold candidates. First, our method uses graph-based tree decomposition to explore the complementarity rigid binding cyclic peptide and design the amino acid side chain length and charge to fit the RNA pocket. Then, we perform an energy-based dynamical network algorithm to optimize the inhibitor-RNA hydrogen bonds. Dynamic geometry-guided design yields successful inhibitors with low micromolar binding affinity scaffolds and experimentally competes with the natural RNA chaperone. The results indicate that the dynamic geometry method yields higher efficiency and accuracy than traditional methods. The strategy could be further optimized to design the length and chirality by adopting nonstandard amino acids and facilitating RNA engineering for biological or medical applications.

Co0 -Coδ+ Interface Double-Site-Mediated C-C Coupling for the Photothermal Conversion of CO2 into Light Olefins.

Solar-driven CO2 hydrogenation into multi-carbon products is a highly desirable, but challenging reaction. The bottleneck of this reaction lies in the C-C coupling of C1 intermediates. Herein, we construct the C-C coupling centre for C1 intermediates via the in situ formation of Co0 -Coδ+ interface double sites on MgAl2 O4 (Co-CoOx /MAO). Our experimental and theoretical prediction results confirmed the effective adsorption and activation of CO2 by the Co0 site to produce C1 intermediates, while the introduction of the electron-deficient state of Coδ+ can effectively reduce the energy barrier of the key CHCH* intermediates. Consequently, Co-CoOx /MAO exhibited a high C2-4 hydrocarbons production rate of 1303 µmol g-1 h-1 ; the total organic carbon selectivity of C2-4 hydrocarbons is 62.5 % under light irradiation with a high ratio (≈11) of olefin to paraffin. This study provides a new approach toward the design of photocatalysts used for CO2 conversion into C2+ products.

DLSSAffinity: protein-ligand binding affinity prediction via a deep learning model.

Evaluating the protein-ligand binding affinity is a substantial part of the computer-aided drug discovery process. Most of the proposed computational methods predict protein-ligand binding affinity using either limited full-length protein 3D structures or simple full-length protein sequences as the input features. Thus, protein-ligand binding affinity prediction remains a fundamental challenge in drug discovery. In this study, we proposed a novel deep learning-based approach, DLSSAffinity, to accurately predict the protein-ligand binding affinity. Unlike the existing methods, DLSSAffinity uses the pocket-ligand structural pairs as the local information to predict short-range direct interactions. Besides, DLSSAffinity also uses the full-length protein sequence and ligand SMILES as the global information to predict long-range indirect interactions. We tested DLSSAffinity on the PDBbind benchmark. The results showed that DLSSAffinity achieves Pearson's R = 0.79, RMSE = 1.40, and SD = 1.35 on the test set. Comparing DLSSAffinity with the existing state-of-the-art deep learning-based binding affinity prediction methods, the DLSSAffinity model outperforms other models. These results demonstrate that combining global sequence and local structure information as the input features of a deep learning model can improve the accuracy of protein-ligand binding affinity prediction.

Phosphorus doped and defect modified graphitic carbon nitride for boosting photocatalytic hydrogen production.

The enhancement of photogenerated carrier separation efficiency is a significant factor in the improvement of photocatalyst performance in photocatalytic hydrogen evolution. Heteroatom doping and defect construction have been considered valid methods to boost the photocatalytic activity of graphitic carbon nitride. Herein, we report graphitic carbon nitride modified with P doping and N defects (PCNx), and the effects of doping and defects were investigated in photocatalytic H2 evolution. Its hydrogen evolution rate can reach up to about 59.1 µmol h-1, which is more than 123.1 times higher than pristine graphitic carbon nitride under visible light irradiation. Importantly, the apparent quantum efficiency reaches 8.73% at 420 nm. The excellent performance of the PCNx photocatalyst was attributed to the following aspects: (I) the large BET surface area of PCNx affords more active sites for H2 production and (II) the introduction of P and N defects can accelerate the charge carrier separation and transfer efficiency, leading to more efficient photocatalytic hydrogen production. The photocatalyst showed obviously enhanced activities.

Carbon Nitride Photocatalysts with Integrated Oxidation and Reduction Atomic Active Centers for Improved CO2 Conversion.

Single-atom active-site catalysts have attracted significant attention in the field of photocatalytic CO2 conversion. However, designing active sites for CO2 reduction and H2 O oxidation simultaneously on a photocatalyst and combining the corresponding half-reaction in a photocatalytic system is still difficult. Here, we synthesized a bimetallic single-atom active-site photocatalyst with two compatible active centers of Mn and Co on carbon nitride (Mn1 Co1 /CN). Our experimental results and density functional theory calculations showed that the active center of Mn promotes H2 O oxidation by accumulating photogenerated holes. In addition, the active center of Co promotes CO2 activation by increasing the bond length and bond angle of CO2 molecules. Benefiting from the synergistic effect of the atomic active centers, the synthesized Mn1 Co1 /CN exhibited a CO production rate of 47 µmol g-1 h-1 , which is significantly higher than that of the corresponding single-metal active-site photocatalyst.

The TAR binding dynamics and its implication in Tat degradation mechanism.

Human immunodeficiency virus (HIV) is a retrovirus that progressively attacks the human immune system. It is known that the HIV viral protein Tat recruits the host elongation factor, positive transcription elongation factor b (P-TEFb), onto the nascent HIV viral transactivation response element (TAR) RNA to overcome the elongation pause for active transcription of the entire viral genome. Interestingly, there exists an amplifying feedback loop between Tat and TAR-a reduction in Tat increases the elongation pause, resulting in more TAR RNA fragments instead of the entire viral genome transcript, and the TAR fragments as a scaffold for PRC2 complex in turn promote Tat ubiquitination and degradation. In this study, the structural ensembles and binding dynamics of various interfaces in the Tat/TAR/P-TEFb complex are probed by all-atom accelerated sampling molecular dynamics simulations. The results show that a protein-binding inhibitor F07#13 targeting the Tat/P-TEFb interface initiates the above feedback loop and shuts down the active transcription. Another RNA binding inhibitor, JB181, targeting the Tat/TAR interface, can prevent TAR from pulling down the Tat from P-TEFb protein and further reducing Tat degradation. The detailed mechanism of the complex dynamics helps elucidate how Tat and TAR coordinate the regulation between HIV genome transcription versus possible HIV latency.

The regulation mechanism of phosphorylation and mutations in intrinsically disordered protein 4E-BP2.

Eukaryotic translation initiation factor 4E binding protein 2 (4E-BP2) is an inhibitor of mRNA cap-dependent translations. Wild-type (WT) 4E-BP2 is intrinsically disordered under physiological conditions, while phosphorylation converts the disordered fragments 18-62 into a four-stranded ß-sheet structure. The regulation mechanism of phosphorylation on 4E-BP2 still remains ambiguous. In this study, replica-exchange molecular dynamics (REMD) simulations were utilized to sample the conformation spaces of WT, phosphorylated WT (pWT), and phosphorylated mutated (pMT) 4E-BP2. Starting from extended structures, the folded structures were only observed in pWT simulations. The folding pathway shows that the folded structures of pWT are formed in the order of ß1/ß4, ß3, and ß2. The formation of ß-turns on pWT, which are driven by hydrogen bonds between the phosphorylated residues and adjacent residues, are the rate-limiting steps in the folding process. The long-range electrostatic interactions contribute toward the stabilization of the folded structures. Moreover, the disruption of ß-turn structures induced by mutations would prevent the folding of pMT 4E-BP2. Our finding is helpful in understanding the regulation of the structural ensembles of intrinsically disordered proteins.

Up-regulation of plasma lncRNA CACS15 distinguished early-stage oral squamous cell carcinoma patient.

OBJECTIVE: To study the role of LncRNA CASC15 in oral squamous cell carcinoma. RESULTS: In the present study, we showed that plasma CASC15 was up-regulated in stage I and II oral squamous cell carcinoma patients than in oral ulcer patients and healthy controls, while no significant correlation was found between oral ulcer patients and healthy controls. Up-regulation of plasma CASC15 distinguished oral squamous cell carcinoma patients from oral ulcer patients and healthy controls. LncRNA MEG3 was inversely correlated with CASC15 in oral squamous cell carcinoma tissues. In oral squamous cell carcinoma cells, CASC15 over-expression led to the inhibited expression of MEG3, and MEG3 over-expression did not alter CASC15 expression. MEG3 over-expression decreased, while CASC15 over-expression increased the proliferation rate of oral squamous cell carcinoma cells. In addition, MEG3 over-expression attenuated the effects of CASC15 over-expression. CONCLUSION: Therefore, CASC15 over-expression may serve as a potential diagnostic biomarker for oral squamous cell carcinoma, and CASC15 may promote oral squamous cell carcinoma cell proliferation by down-regulating MEG3.

Solar-Driven Water-Gas Shift Reaction over CuOx /Al2 O3 with 1.1 % of Light-to-Energy Storage.

Hydrogen production from coal gasification provides a cleaning approach to convert coal resource into chemical energy, but the key procedures of coal gasification and thermal catalytic water-gas shift (WGS) reaction in this energy technology still suffer from high energy cost. We herein propose adopting a solar-driven WGS process instead of traditional thermal catalysis, with the aim of greatly decreasing the energy consumption. Under light irradiation, the CuOx /Al2 O3 delivers excellent catalytic activity (122 µmol gcat -1 s-1 of H2 evolution and >95 % of CO conversion) which is even more efficient than noble-metal-based catalysts (Au/Al2 O3 and Pt/Al2 O3 ). Importantly, this solar-driven WGS process costs no electric/thermal power but attains 1.1 % of light-to-energy storage. The attractive performance of the solar-driven WGS reaction over CuOx /Al2 O3 can be attributed to the combined photothermocatalysis and photocatalysis.

Nanostructured Materials for Photothermal Carbon Dioxide Hydrogenation: Regulating Solar Utilization and Catalytic Performance.

Converting carbon dioxide (CO2) into value-added fuels or chemicals through photothermal catalytic CO2 hydrogenation is a promising approach to alleviate the energy shortage and global warming. Understanding the nanostructured material strategies in the photothermal catalytic CO2 hydrogenation process is vital for designing photothermal devices and catalysts and maximizing the photothermal CO2 hydrogenation performance. In this Perspective, we first describe several essential nanomaterial design concepts to enhance sunlight absorption and utilization in photothermal CO2 hydrogenation. Subsequently, we review the latest progress in photothermal CO2 hydrogenation into C1 (e.g., CO, CH4, and CH3OH) and multicarbon hydrocarbon (C2+) products. Finally, the relevant challenges and opportunities in this exciting research realm are discussed. This perspective provides a comprehensive understanding for the light-heat synergy over nanomaterials and instruction for rational photothermal catalyst design for CO2 utilization.

HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules.

The HIV-1 transactivator protein Tat interacts with the transactivation response element (TAR) at the three-nucleotide UCU bulge to facilitate the recruitment of transcription elongation factor-b (P-TEFb) and induce the transcription of the integrated proviral genome. Therefore, the Tat-TAR interaction, unique to the virus, is a promising target for developing antiviral therapeutics. Currently, there are no FDA-approved drugs against HIV-1 transcription, suggesting the need to develop novel inhibitors that specifically target HIV-1 transcription. We have identified potential candidates that effectively inhibit viral transcription in myeloid and T cells without apparent toxicity. Among these candidates, two molecules showed inhibition of viral protein expression. A molecular docking and simulation approach was used to determine the binding dynamics of these small molecules on TAR RNA in the presence of the P-TEFb complex, which was further validated by a biotinylated RNA pulldown assay. Furthermore, we examined the effect of these molecules on transcription factors, including the SWI/SNF complex (BAF or PBAF), which plays an important role in chromatin remodeling near the transcription start site and hence regulates virus transcription. The top candidates showed significant viral transcription inhibition in primary cells infected with HIV-1 (98.6). Collectively, our study identified potential transcription inhibitors that can potentially complement existing cART drugs to address the current therapeutic gap in current regimens. Additionally, shifting of the TAR RNA loop towards Cyclin T1 upon molecule binding during molecular simulation studies suggested that targeting the TAR loop and Tat-binding UCU bulge together should be an essential feature of TAR-binding molecules/inhibitors to achieve complete viral transcription inhibition.

Isomerized Green Solid Additive Engineering for Thermally Stable and Eco-Friendly All-Polymer Solar Cells with Approaching 19% Efficiency.

Laboratory-scale all-polymer solar cells (all-PSCs) have exhibited remarkable power conversion efficiencies (PCEs) exceeding 19%. However, the utilization of hazardous solvents and nonvolatile liquid additives poses challenges for eco-friendly commercialization, resulting in the trade-off between device efficiency and operation stability. Herein, an innovative approach based on isomerized solid additive engineering is proposed, employing volatile dithienothiophene (DTT) isomers to modulate intermolecular interactions and facilitate molecular stacking within the photoactive layers. Through elucidating the underlying principles of the DTT-induced polymer assembly on molecular level, a PCE of 18.72% is achieved for devices processed with environmentally benign solvents, ranking it among the highest record values for eco-friendly all-PSCs. Significantly, such superiorities of the DTT-isomerized strategy afford excellent compatibility with large-area blade-coating techniques, offering a promising pathway for industrial-scale manufacturing of all-PSCs. Moreover, these devices demonstrate enhanced thermal stability with a promising extrapolated T80 lifetime of 14 000 h, further bolstering their potential for sustainable technological advancement.

The auto-inhibition mechanism of transcription factor Ets-1 induced by phosphorylation on the intrinsically disordered region.

As the most abundant post-translation modifications (PTMs), the phosphorylation usually occurred on the intrinsically disordered regions (IDRs). The regulation on the structures and interactions of IDRs induced by phosphorylation is critical to the function performing. The eukaryotic transcription factor 1 (Ets-1) is a member of transcription factor family, which participates in many important biological processes. The DNA-binding ability of Ets-1 is auto-inhibited by a disordered serine-rich region (SRR) on the Ets-1. The inhibition ability of SRR is greatly enhanced by the phosphorylation of the serine on the SRR. Nevertheless, the molecular mechanisms of the phosphorylation regulation on the structure and activity of Ets-1 are still unclear and under debates. By using both of the molecular simulations and biochemical experiments, we studied the molecule mechanism of phosphorylation regulation on the auto-inhibition of the Ets-1. The reasons of stabilization of Ets-1 core by phosphorylation on SRR region were elucidated. More important, the free energy landscapes (FEL) show that both of the steric hindrance and allosteric regulation are responsible for the DNA-binding inhibitory induced by phosphorylation, but the steric effects contribute greater than the allosteric regulation. The phosphorylation not only enhances the electrostatic interactions to facilitate the steric impedance, but also promotes the formation of hydrophobic residue clusters, which provide major driven force for the allosteric regulation. The structural basis of auto-inhibition of Ets-1 induced by the phosphorylation revealed in this study would great help the developing of inhibitor for the cancer therapy.

Phosphorylation regulates the binding of intrinsically disordered proteins via a flexible conformation selection mechanism.

Phosphorylation is one of the most common post-translational modifications. The phosphorylation of the kinase-inducible domain (KID), which is an intrinsically disordered protein (IDP), promotes the folding of KID and binding with the KID-interacting domain (KIX). However, the regulation mechanism of the phosphorylation on KID is still elusive. In this study, the structural ensembles and binding process of pKID and KIX are studied by all-atom enhanced sampling technologies. The results show that more hydrophobic interactions are formed in pKID, which promote the formation of the special hydrophobic residue cluster (HRC). The pre-formed HRC promotes binding to the correct sites of KIX and further lead the folding of pKID. Consequently, a flexible conformational selection model is proposed to describe the binding and folding process of intrinsically disordered proteins. The binding mechanism revealed in this work provides new insights into the dynamic interactions and phosphorylation regulation of proteins.

Performance of protein-ligand docking with CDK4/6 inhibitors: a case study.

It is widely believed that tertiary protein-ligand interactions are essential in determining protein function. Currently, the structure sampling and scoring function in traditional docking methods still have limitations. Therefore, new methods for protein-ligand docking are desirable. The accurate docking can speed up the early-stage development of new drugs. Here we present a multi-source information-based protein-ligand docking approach (pmDock). In the CDK4/6 inhibitor case study, pmDock produces a substantial accuracy increases between the predicted geometry centers of ligands and experiments compared to AutoDock and SwissDock alone. Also, pmDock improves predictions for critical binding sites and captures more tertiary binding interactions. Our results demonstrate that pmDock is a reliable docking method for accurate protein-ligand prediction.

Photoinduced Defect Engineering: Enhanced Photothermal Catalytic Performance of 2D Black In2 O3- x Nanosheets with Bifunctional Oxygen Vacancies.

Photothermal CO2 reduction technology has attracted tremendous interest as a solution for the greenhouse effect and energy crisis, and thereby it plays a critical role in solving environmental problems and generating economic benefits. In2 O3- x has emerged as a potential photothermal catalyst for CO2 conversion into CO via the light-driven reverse water gas shift reaction. However, it is still a challenge to modulate the structural and electronic characteristics of In2 O3 to enhance photothermocatalytic activity synergistically. In this work, a novel route to activate inert In(OH)3 into 2D black In2 O3- x nanosheets via photoinduced defect engineering is proposed. Theoretical calculations and experimental results verify the existence of bifunctional oxygen vacancies in the 2D black In2 O3- x nanosheets host, which enhances light harvesting and chemical adsorption of CO2 molecules dramatically, achieving 103.21 mmol gcat -1 h-1 with near-unity selectivity for CO generation and meanwhile excellent stability. This study reveals an exciting phenomenon that light is an ideal external stimulus on the layered In2 O3 system, and its electronic structure can be adjusted efficiently through photoinduced defect engineering; it can be anticipated that this synthesis strategy can be extended to wider application fields.

A Virulence-Associated Glycolipid with Distinct Conformational Attributes: Impact on Lateral Organization of Host Plasma Membrane, Autophagy, and Signaling.

Mycobacterium tuberculosis (Mtb) serves as the epitome of how lipids-next to proteins-are utilized as central effectors in pathogenesis. It synthesizes an arsenal of structurally atypical lipids (C60-C90) to impact various membrane-dependent steps involved in host interactions. There is a growing precedent to support insertion of these exposed lipids into the host membrane as part of their mode of action. However, the vital role of specific virulence-associated lipids in modulating cellular functions by altering the host membrane organization and associated signaling pathways remain unanswered questions. Here, we combined chemical synthesis, biophysics, cell biology, and molecular dynamics simulations to elucidate host membrane structure modifications and modulation of membrane-associated signaling using synthetic Mycobacterium tuberculosis sulfoglycolipids (Mtb SL). We reveal that Mtb SL reorganizes the host cell plasma membrane domains while showing higher preference for fluid membrane regions. This rearrangement is governed by the distinct conformational states sampled by SL acyl chains. Physicochemical assays with SL analogues reveal insights into their structure-function relationships, highlighting specific roles of lipid acyl chains and headgroup, along with effects on autophagy and cytokine profiles. Our findings uncover a mechanism whereby Mtb uses specific chemical moieties on its lipids to fine-tune host lipid interactions and confer control of the downstream functions by modifying the cell membrane structure and function. These findings will inspire development of chemotherapeutics against Mtb by counteracting their effects on the host-cell membrane.

Characterization of a New Cyclohexylamine Oxidase From Acinetobacter sp. YT-02.

Cyclohexylamine (CHAM) is widely used in various industries, but it is harmful to human beings and the environment. Acinetobacter sp. YT-02 can degrade CHAM via cyclohexanone as an intermediate. In this study, the cyclohexylamine oxidase (CHAO) gene from Acinetobacter sp. YT-02 was cloned. Amino acid sequence alignment indicated that the cyclohexylamine oxidase (CHAOYT-02) was 48% identical to its homolog from Brevibacterium oxydans IH-35A (CHAOIH-35). The enzyme was expressed in Escherichia coli BL21 (DE3), and purified to apparent homogeneity by Ni-affinity chromatography. The purified enzyme was proposed to be a dimer of molecular mass of approximately 91 kDa. The enzyme exhibited its maximum activity at 50°C and at pH 7.0. The enzyme was thermolabile as demonstrated by loss of important percentage of its maximal activity after 30 min incubation at 50°C. Metal ions Mg2+, Co2+, and K+ had certain inhibitory effect on the enzyme activity. The kinetic parameters K m and V max were 0.25 ± 0.02 mM and 4.3 ± 0.083 µM min-1, respectively. The biochemical properties, substrate specificities, and three-dimensional structures of CHAOYT-02 and CHAOIH-35 were compared. Our results are helpful to elucidate the mechanism of microbial degradation of CHAM in the strain YT-02. In addition, CHAOYT-02, as a potential biocatalyst, is promising in controlling CHAM pollution and deracemization of chiral amines.

Large-scale preparation of heterometallic chalcogenide MnSb2S4 monolayer nanosheets with a high visible-light photocatalytic activity for H2 evolution.

Free standing MnSb2S4 2D monolayer nanosheets were developed by a simple calcination of the neutral hydrazine molecule bridged chalcogenide, and were found to display a highly efficient and stable activity for photocatalytic hydrogen evolution from water under visible light irradiation (420-730 nm).