Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase.

Nucleotide analog inhibitors, including broad-spectrum remdesivir and favipiravir, have shown promise in in vitro assays and some clinical studies for COVID-19 treatment, this despite an incomplete mechanistic understanding of the viral RNA-dependent RNA polymerase nsp12 drug interactions. Here, we examine the molecular basis of SARS-CoV-2 RNA replication by determining the cryo-EM structures of the stalled pre- and post- translocated polymerase complexes. Compared with the apo complex, the structures show notable structural rearrangements happening to nsp12 and its co-factors nsp7 and nsp8 to accommodate the nucleic acid, whereas there are highly conserved residues in nsp12, positioning the template and primer for an in-line attack on the incoming nucleotide. Furthermore, we investigate the inhibition mechanism of the triphosphate metabolite of remdesivir through structural and kinetic analyses. A transition model from the nsp7-nsp8 hexadecameric primase complex to the nsp12-nsp7-nsp8 polymerase complex is also proposed to provide clues for the understanding of the coronavirus transcription and replication machinery.

Crystal Structures of Membrane Transporter MmpL3, an Anti-TB Drug Target.

Despite intensive efforts to discover highly effective treatments to eradicate tuberculosis (TB), it remains as a major threat to global human health. For this reason, new TB drugs directed toward new targets are highly coveted. MmpLs (Mycobacterial membrane proteins Large), which play crucial roles in transporting lipids, polymers and immunomodulators and which also extrude therapeutic drugs, are among the most important therapeutic drug targets to emerge in recent times. Here, crystal structures of mycobacterial MmpL3 alone and in complex with four TB drug candidates, including SQ109 (in Phase 2b-3 clinical trials), are reported. MmpL3 consists of a periplasmic pore domain and a twelve-helix transmembrane domain. Two Asp-Tyr pairs centrally located in this domain appear to be key facilitators of proton-translocation. SQ109, AU1235, ICA38, and rimonabant bind inside the transmembrane region and disrupt these Asp-Tyr pairs. This structural data will greatly advance the development of MmpL3 inhibitors as new TB drugs.

Development of the nonreceptor tyrosine kinase FER-targeting PROTACs as a potential strategy for antagonizing ovarian cancer cell motility and invasiveness.

Aberrant overexpression of nonreceptor tyrosine kinase FER (Fps/Fes Related) has been reported in various ovarian carcinoma-derived tumor cells and is a poor prognosis factor for patient survival. It plays an essential role in tumor cell migration and invasion, acting concurrently in both kinase-dependent and -independent manners, which is not easily suppressed by conventional enzymatic inhibitors. Nevertheless, the PROteolysis-TArgeting Chimera (PROTAC) technology offers superior efficacy over traditional activity-based inhibitors by simultaneously targeting enzymatic and scaffold functions. Hence in this study, we report the development of two PROTAC compounds that promote robust FER degradation in a cereblon-dependent manner. Both PROTAC degraders outperform a Food and Drug Administration-approved drug, brigatinib, in ovarian cancer cell motility suppression. Importantly, these PROTAC compounds also degrade multiple oncogenic FER fusion proteins identified in human tumor samples. These results lay an experimental foundation to apply the PROTAC strategy to antagonize cell motility and invasiveness in ovarian and other types of cancers with aberrant expression of FER kinase and highlight PROTACs as a superior strategy for targeting proteins with multiple tumor-promoting functions.

SUMOylation of the ubiquitin ligase component KEAP1 at K39 upregulates NRF2 and its target function in lung cancer cell proliferation.

Nuclear Factor Erythroid 2-Related Factor 2 (NRF2) is important for the expression of genes associated with oxidative stress. The levels of NRF2 are controlled by Kelch-like ECH-associated protein 1 (KEAP1)-dependent degradation. Although oxidative stress is known to suppress KEAP1 activity to stabilize the levels of NRF2, the mechanism for this control is unclear. Here, we identify that KEAP1 is modified by SUMO1 at the lysine residue position 39 (K39). Arginine replacement of this lysine (K39R) in KEAP1 did not affect its stability, subcellular localization, or dimerization but promoted the formation of the Cullin 3 ubiquitin ligase and increased NRF2 ubiquitination. This was accompanied by decreased NRF2 expression. Gene reporter assays showed that the transcription of antioxidant response elements was heightened in KEAP1-WT cells compared to cells expressing the KEAP1-K39R SUMO1 substrate mutant. Consistent with this, chromatin immunoprecipitation assays revealed higher NRF2 binding to the promoter regions of antioxidant genes in cells expressing the KEAP1-WT compared to the KEAP1-K39R mutant protein in H1299 lung cancer cell. The significance of this suppression of KEAP1 activity by its SUMOylation was tested in a subcutaneous tumor model of H1299 lung cancer cell lines that differentially expressed the WT and K39R KEAP1 constructs. This model showed that mutating the SUMOylation site on KEAP1 altered the production of reactive oxygen species and suppressed tumor growth. Taken together, our study recognizes that NRF2-dependent redox control is regulated by the SUMOylation of KEAP1. These findings identify a potential new therapeutic option to counteract oxidative stress.

High-throughput computational materials screening of transition metal peroxides.

Semiconductor materials of abnormal stoichiometric ratio often exhibit unique properties, yet it is still a challenge to determine the structures of such materials in an efficient way. Herein, we propose a method for structurally biased screening according to the coordination numbers and the numbers of Wyckoff positions, balancing the atom local environment and the global symmetry of structures. Based on first-principles calculations, we have predicted two metastable peroxides P21/c-ScO2 and Pmmn-TiO3 with more than six coordination points. For these two structures, the most stable intrinsic defect is the oxygen vacancy (VO) at the peroxide anion (O2-2), which induces the absence of antibonding orbital formed by O2-2 near the valence band maximum. With the introduction of VO, the decrease of coordination numbers leads to charge recombination, and results in the appearance of an ordered phase TiO2.5 with stronger Ti-O orbital hybridization. The proposed method presents a promising and feasible approach for the screening of novel compounds.

HDAC6 inhibitor promotes reactive oxygen species-meditated clearance of Staphylococcus aureus in macrophage.

Staphylococcus aureus (S. aureus) pneumonia has become an increasingly important public health problem. Recent evidence suggests that epigenetic modifications are critical in the host immune defence against pathogen infection. In this study, we found that S. aureus infection induces the expression of histone deacetylase 6 (HDAC6) in a dose-dependent manner. Furthermore, by using a S. aureus pneumonia mouse model, we showed that the HDAC6 inhibitor, tubastatin A, demonstrates a protective effect in S. aureus pneumonia, decreasing the mortality and destruction of lung architecture, reducing the bacterial burden in the lungs and inhibiting inflammatory responses. Mechanistic studies in primary bone marrow-derived macrophages demonstrated that the HDAC6 inhibitors, tubastatin A and tubacin, reduced the intracellular bacterial load by promoting bacterial clearance rather than regulating phagocytosis. Finally, N-acetyl-L- cysteine, a widely used reactive oxygen species (ROS) scavenger, antagonized ROS production and significantly inhibited tubastatin A-induced S. aureus clearance. These findings demonstrate that HDAC6 inhibitors promote the bactericidal activity of macrophages by inducing ROS, an important host factor for S. aureus clearance and production. Our study identified HDAC6 as a suitable epigenetic modification target for preventing S. aureus infection, and tubastatin A as a useful compound in treating S. aureus pneumonia.

Generalized Octet Rule with Fractional Occupancies for Boron.

The octet rule is a fundamental theory in the chemical bonding of main-group elements, which achieve stable configurations by gaining, losing, or sharing electrons. However, the conventional octet rule, as depicted through Lewis structures, is inadequate for describing the electron delocalization in boron allotropes and boron-rich compounds due to the electron deficiency of boron. To address this, we introduce the concept of fractional electron occupancies, which more accurately reflect the electron delocalization in boron systems. Based on this, we propose a generalized octet rule that provides a more comprehensive understanding of the complex bonding configurations in boron allotropes and boron-rich compounds. Importantly, our predictions for α-B12 are validated by both first-principles calculations and existing experimental data. Beyond boron, this generalized octet rule is also applicable to systems with multiple resonance structures.

Damage-induced NAD release activates intestinal CD4+ and CD8+ T cell via P2X7R signaling.

BACKGROUND: Postoperative ileus (POI) is characterized by the activation of inflammation triggered by tissue damage. Damage-associated molecular patterns (DAMPs) reportedly induce local inflammation after injury. However, the impact of DAMPs on intestinal resident lymphocytes during POI remains poorly elucidated. METHODS: POI in mice was induced via intestinal manipulation (IM). The concentration of nicotinamide adenine dinucleotide (NAD) was detected after IM. The gastrointestinal motility of the mice was assessed after IM or NAD injection. Cytokine production and calcium influx in T cells were investigated after NAD stimulation using flow cytometry. RESULTS: The concentration of extracellular NAD significantly increased after IM administration, and NAD directly impaired gastrointestinal motility. Intraperitoneal injection of NAD promoted the expression of TNF-α in intestinal CD8+ and CD4+ T cells, but only IFN-γ production by CD8+ T cells was significantly promoted by NAD injection. Granzyme B production in CD8+ and CD4+ T cells decreased after administration. Concordantly, the same results were observed in NAD stimulation of intestinal CD3+ T cells in vitro. Blocking the P2X7R-related membrane enzyme ART2.2 significantly diminished the pro-inflammatory effect of NAD. CONCLUSION: IM includes the release of NAD derived from damaged tissues, consequently promoting pro-inflammatory cytokine production in intestinal CD4+ and CD8+ T lymphocytes. NAD-induced intestinal T cells activation may be associated with POI progression in the mouse.

BRCA genes as candidates for colorectal cancer genetic testing panel: systematic review and meta-analysis.

BACKGROUND: Breast cancer susceptibility gene (BRCA) mutation carriers are at an increased risk for breast, ovarian, prostate and pancreatic cancers. However, the role of BRCA is unclear in colorectal cancer; the results regarding the association between BRCA gene mutations and colorectal cancer risk are inconsistent and even controversial. This study aimed to investigate whether BRCA1 and BRCA2 gene mutations are associated with colorectal cancer risk. METHODS: In this systematic review, we searched PubMed/MEDLINE, Embase and Cochrane Library databases, adhering to PRISMA guidelines. Study quality was assessed using the Newcastle-Ottawa Scale (NOS). Unadjusted odds ratios (ORs) were used to estimate the probability of Breast Cancer Type 1 Susceptibility gene (BRCA1) and Breast Cancer Type 2 Susceptibility gene (BRCA2) mutations in colorectal cancer patients. The associations were evaluated using fixed effect models. RESULTS: Fourteen studies were included in the systematic review. Twelve studies, including seven case-control and five cohort studies, were included in the meta-analysis. A significant increase in the frequency of BRCA1 and BRCA2 mutations was observed in patients with colorectal cancer [OR = 1.34, 95% confidence interval (CI) = 1.02-1.76, P = 0.04]. In subgroup analysis, colorectal cancer patients had an increased odds of BRCA1 (OR = 1.48, 95% CI = 1.10-2.01, P = 0.01) and BRCA2 (OR = 1.56, 95% CI = 1.06-2.30, P = 0.02) mutations. CONCLUSIONS: BRCA genes are one of the genes that may increase the risk of developing colorectal cancer. Thus, BRCA genes could be potential candidates that may be included in the colorectal cancer genetic testing panel.

Diagnostic Value of Inflammation-Related Indicators in Distinguishing Early Colon Cancer and Adenomatous Polyps.

BACKGROUND: There are few clinical symptoms in early colorectal cancer, so it is necessary to find a simple and economical tumor detection index for auxiliary diagnosis. This study aims to explore the diagnostic value of preoperative inflammation-related indicators, such as neutrophil, lymphocyte, platelet count, platelet to lymphocyte ratio (PLA), neutrophil to lymphocyte ratio (NLR), and systemic immune-inflammation index (SII), for early colorectal cancer, and determine whether inflammation-related indicators can provide more accurate diagnostic judgment for patients. METHODS: This study was a retrospective study. Patients who were first diagnosed with colorectal cancer or colorectal adenomatous polyp at Beijing Friendship Hospital from October 2016 to October 2017 were retrospectively collected. According to inclusion and exclusion criteria, a total of 342 patients were included, including 216 patients with colorectal cancer and 126 patients with colorectal adenomatous polyp. Fasting venous blood and other clinical features were collected to compare the differences between colorectal cancer and colorectal adenoma. RESULTS: There were statistically significant differences in age, carcinoembryonic antigen, albumin, hemoglobin, mean platelet volume, lymphocyte, monocyte, NLR, PLA, SII, and mean platelet volume to platelet count ratio between colorectal cancer group and colorectal adenoma group (P < .05), and a Nomogram model was established. Using inflammatory markers to differentiate colorectal and colorectal polyps produced greater AUC than using tumor markers alone (.846 vs .695). CONCLUSION: Inflammation-related indicators, such as lymphocyte, monocyte, and mean platelet volume, may serve as potential indicators to assist in the diagnosis of early colorectal cancer.

Bridged Proteolysis Targeting Chimera (PROTAC) Enables Degradation of Undruggable Targets.

Proteolysis Targeting Chimeras (PROTACs) are attractive therapeutic modalities for degrading disease-causing proteins. While many PROTACs have been developed for numerous protein targets, current small-molecule PROTAC approaches cannot target undruggable proteins that do not have small-molecule binders. Here, we present a novel PROTAC approach, termed bridged PROTAC, which utilizes a small-molecule binder of the target protein's binding partner to recruit the protein complex into close proximity with an E3 ubiquitin ligase to target undruggable proteins. Applying this bridged PROTAC strategy, we discovered MS28, the first-in-class degrader of cyclin D1, which lacks a small-molecule binder. MS28 effectively degrades cyclin D1, with faster degradation kinetics and superior degradation efficiency than CDK4/6, through recruiting the CDK4/6-cyclin D1 complex to the von Hippel-Lindau E3 ligase. MS28 also suppressed the proliferation of cancer cells more effectively than CDK4/6 inhibitors and degraders. Altogether, the bridged PROTAC strategy could provide a generalizable platform for targeting undruggable proteins.

Camrelizumab combined with apatinib and S-1 as second-line treatment for patients with advanced gastric or gastroesophageal junction adenocarcinoma: a phase 2, single-arm, prospective study.

BACKGROUND: The current second-line treatment of advanced gastric or gastroesophageal junction adenocarcinoma remains unsatisfactory. Anti-PD-1 monoclonal antibody combined with anti-angiogenic therapy shows anti-tumor activity and synergistic effect. We aimed to assess the efficacy and safety of the combination therapy of camrelizumab, apatinib, and S-1 in patients with gastric or gastroesophageal junction adenocarcinoma. METHODS: In this open-label, single-arm, phase 2 trial, in each 21-day cycle, eligible patients received 200 mg intravenous camrelizumab in the first day, 500 mg oral apatinib once daily continuously, and specific dose oral S-1 in the first 14 days until the trial was discontinued disease progression, development of intolerable toxicity, or withdrawal of consent. The primary endpoint was objective response rate. The secondary endpoints were disease control rate, progression-free survival and overall survival, and safety. This study was registered at ClinicalTrials.gov, NCT04345783. RESULTS: Between May 2019 and August 2020, we enrolled a total of 24 patients in this trial. At the data cutoff (December 1, 2020), the median follow-up duration was 8.13 months. Seven of 24 (29.2%, 95%CI 14.9-49.2%) patients reached objective response. The median-progression-free survival was 6.5 months (95%CI 6.01-6.99) and the median overall survival was not reached. Grade 3 or 4 adverse events occurred in 6 (25.0%) patients, including elevated transaminase, thrombocytopenia, fatigue, proteinuria, and intestinal obstruction. No serious treatment-related adverse events or treatment-related deaths occurred. CONCLUSIONS: In this trial, the combination of camrelizumab, apatinib, and S-1 showed promising anti-tumor activity and manageable toxicity as a second-line therapy in patients with advanced gastric or gastroesophageal junction adenocarcinoma, regardless of PD-L1 expression. CLINICAL TRIAL REGISTRATION: NCT04345783.

Discovery of a first-in-class EZH2 selective degrader.

The enhancer of zeste homolog 2 (EZH2) is the main enzymatic subunit of the PRC2 complex, which catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to promote transcriptional silencing. EZH2 is overexpressed in multiple types of cancer including triple-negative breast cancer (TNBC), and high expression levels correlate with poor prognosis. Several EZH2 inhibitors, which inhibit the methyltransferase activity of EZH2, have shown promise in treating sarcoma and follicular lymphoma in clinics. However, EZH2 inhibitors are ineffective at blocking proliferation of TNBC cells, even though they effectively reduce the H3K27me3 mark. Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2.

Long non-coding RNA MFAT1 promotes skeletal muscle fibrosis by modulating the miR-135a-5p-Tgfbr2/Smad4 axis as a ceRNA.

Fibrosis after skeletal muscle injury is common in sports and can cause irreversible damage to the biomechanical properties of skeletal muscle. Long non-coding RNAs (lncRNAs) have been validated to act as important modulators in the fibrosis of various organs. Here, we reported a novel lncRNA (the skeletal muscle fibrosis-associated transcript 1, lnc-MFAT1), which was highly expressed in skeletal muscle fibrosis. We demonstrate that lnc-MFAT1 knockdown can reduce TGFß-induced fibrosis in vitro and attenuate skeletal muscle fibrosis after acute contusion in mice. Further study showed that lnc-MFAT1 acted as a competitive endogenous RNA of miR-135a-5p. Besides, the miR-135a-5p inhibition obviously promoted TGFß-induced fibrosis in vitro via enhancing its target genes Tgfbr2/Smad4. Moreover, we discovered that lnc-MFAT1 regulates Tgfbr2/Smad4 expression by sponging miR-135a-5p to exert competing endogenous RNA function, resulting in TGFß pathway activation. In conclusion, our study identified a crucial role of lnc-MFAT1-miR-135a-Tgfbr2/Smad4 axis in skeletal muscle fibrosis, providing a promising treatment option against skeletal muscle fibrosis.

Construction of an IMiD-based azide library as a kit for PROTAC research.

As a promising protein degradation strategy, PROTAC technology is increasingly becoming a new star in cancer treatment. Here we report the efficient construction of an IMiD-based azide library via a quick one-step conversion of the existing IMiD-based amine library. This new azide library can act as a kit to endow PROTAC libraries with triazole moieties for various POIs through a highly effective 'click reaction' and then help to rapidly screen out lead degraders that are valuable for drug development. Its power in fleetly identifying potent degraders has been verified on two oncogenic proteins, BCR-ABL and BET, the degraders of which showed comparable potency to or even higher potency than the reported PROTACs in degrading target proteins and effectively inhibiting cancer cell proliferation.

Prophylactic subcutaneous drainage reduces post-operative incisional infections in colorectal surgeries: a meta-analysis of randomized controlled trials.

BACKGROUND: Due to lack of high-level evidences, prophylactic subcutaneous drainage has so far not been recommended in relevant guidelines as a countermeasure against incisional infections. This meta-analysis aims to clarify the efficacy of subcutaneous drainage in reducing incisional infections in colorectal surgeries. METHODS: Cochrane Library, Embase, and PubMed were searched for randomized controlled trials comparing the incidence rate of incisional infections between patients receiving prophylactic subcutaneous drainage (interventions) and those not receiving (controls) after digestive surgeries. Results from included RCTs were pooled multiple times according to different surgical types. Heterogeneity, publication bias, and certainty of evidences were estimated. RESULTS: Eight randomized controlled trials were included. Three RCTs each included patients receiving all sorts of digestive surgeries (gastrointestinal, hepatobiliary, and pancreatic); pooled incisional infection rates between the drainage group and the control group were not significantly different (RR = 0.76, 95%CI: 0.48-1.21, p = 0.25). Four RCTs included patients receiving colorectal surgeries; pooled incisional infection rate in the drainage group was significantly lower than that in the control group (RR = 0.34, 95%CI: 0.19-0.61, p = 0.0004). Four RCTs included patients receiving upper GI and/or HBP surgeries; pooled incisional infection rates in the drainage group and the non-drainage group were not significantly different (RR = 0.85, 95%CI: 0.54-1.34, p = 0.49). CONCLUSIONS: Prophylactic subcutaneous drainage significantly reduces post-operative incisional infections in colorectal surgeries but was not efficacious in digestive surgeries in general.

Adsorption-Free Growth of Ultra-Thin Molybdenum Membranes with a Low-Symmetry Rectangular Lattice Structure.

Although low-symmetry lattice structure of 2D transition metals is highly anticipated for both fundamental research and potentially distinctive application, it still has not been experimentally realized, which greatly hinders the exploration of the unique properties. Here, ultra-thin body-centered-cubic (bcc) phase molybdenum (Mo) membranes are successfully synthesized with a low-symmetry rectangular (110) crystal face via an adsorption-free reaction. Through experimental and density functional theory studies, no foreign atoms being adsorbed is shown to be a key factor for the successful preparation of the bcc phase 2D transition metal with (110) faces. The realization of 2D Mo(110) with a low-symmetric rectangular lattice structure extends the scope of 2D structures and is also beneficial for the exploration and development of low-symmetry rectangular lattice-structured materials with unique properties.

Enhanced Transformation of Cr(VI) by Heterocyclic-N within Nitrogen-Doped Biochar: Impact of Surface Modulatory Persistent Free Radicals (PFRs).

Redox processes mediated by biochar(BC) enhanced the transformation of Cr(VI), which is largely dependent on the presence of PFRs as electron donors. Natural or artificial dopants in BC's could regulate inherent carbon configuration and PFRs. Until recently, the modulation of PFRs and transformation of Cr(VI) in BC by nonmetal-heterocyclic dopants was barely studied. In this study, changes in PFRs introduced by various nitrogen-dopants within BC are presented and the capacity for Cr(VI) transformation without light was investigated. It was found N-dopants were effectively embedded in carbon lattices through activated-Maillard reaction thus altering their charge and PFRs. Transformation of Cr(VI) in N doped biochar relied on mediated direct reduction by surface modulatory PFRs. The kinetic rate of transformation of Cr(VI) was increased 1.4-5 fold in N-BCs compared to nondoped BCs. Theortical calculation suggested a deficiency in surface electrons induced Lewis acid-base bonding which could acted as a bridge for electron transfer. Results of PCA and orbital energy indicated a colinear relationship between PFRs and pyrrolic N, as well as its dual-mode transformation of Cr(VI). This study provides an improved understanding of how N-doped BC contributes to the evolution of PFRs and their corresponding impacts on the transformation of Cr(VI) in environments.

Energy landscape of Au13: a global view of structure transformation.

It has long been a challenge in physics and chemistry to acquire a global picture of the energy landscape of a specific material, as well as the kinetic transformation process between configurations of interest. Here we have presented a comprehensive approach to deal with the structure transformation problem, along with the illustration of the energy landscape, as exemplified with the case of Au13. A configuration space based on interatomic distances was proposed and demonstrated to have a strong correlation between structure and energy, with application in structure analysis to screen for trial transition pathways. As several representative configurations and their transition pathways ascertained and by projecting on a plane, a visual two-dimensional contour map was sketched revealing the unique energy landscape of Au13. It shows that the 2D and 3D clusters form two funnels in the high-dimensional configuration space, with a transition pathway with a 0.976 eV barrier bridging them.

Motif based high-throughput structure prediction of superconducting monolayer titanium boride.

Two-dimensional boron structures, due to their diverse properties, have attracted great attention because of their potential applications in nanoelectronic devices. A series of TiBn (2 ≤ n ≤ 13) monolayers are efficiently constructed through our motif based method and theoretically investigated through high-throughput first-principles calculations. The configurations are generated based on the motifs of boron dimeric/triangular/quadrilateral fragments and multi-coordinate titanium-centered boron molecular wheels. Besides previously reported TiB4 and TiB9 which were discovered by the global search method, we predict that high symmetry monolayer TiB7 (Cmmm), which is octa-coordinate titanium boride, is dynamically stable. The TiB7 monolayer is a BCS superconductor with a transition temperature Tc of up to 8.3 K. The motif based approach is proved to be efficient in searching stable structures with prior knowledge so that the potentially stable transition metal monolayers can be quickly constructed by using basic cluster motifs. As an efficient way of discovering materials, the method is easily extended to predict other types of materials which have common characteristic patterns in the structure.