Detection and characterization of eravacycline heteroresistance in clinical bacterial isolates.

Eravacycline (ERV) has emerged as a therapeutic option for the treatment of carbapenem-resistant pathogens. However, the advent of heteroresistance (HR) to ERV poses a challenge to these therapeutic strategies. This study aimed to investigate ERV HR prevalence among common clinical isolates and further characterize ERV HR in carbapenem-resistant Klebsiella pneumoniae (CRKP). A total of 280 clinical pathogens from two centers were selected for HR and analyzed using population analysis profiling (PAP) and modified E-tests. The PAP assay revealed an overall ERV HR prevalence of 0.7% (2/280), with intermediate heterogeneity observed in 24.3% (68/280) of strains. The proportion of heteroresistant strains was 18.3% according to modified E-test results. A time-killing assay demonstrated that CRKP CFU increased significantly after 10 h of ERV treatment, contributing to the reduced bactericidal effect of ERV in vitro. Interestingly, dual treatment with ERV and polymyxin B effectively inhibited the total CFU, simultaneously reducing the required polymyxin B concentration. Furthermore, fitness cost measurements revealed a growth trade-off in CRKP upon acquiring drug resistance, highlighting fitness costs as crucial factors in the emergence of ERV HR in CRKP. Overall, the findings of the current study suggest that ERV HR in clinical strains presents a potential obstacle in its clinical application.

PTCH1 mutation as a potential predictive biomarker for immune checkpoint inhibitors in gastrointestinal cancer.

Immune checkpoint inhibitors (ICIs) have become prominent therapies for gastrointestinal cancer (GC). However, it is urgent to screen patients who can benefit from ICIs. Protein patched homolog 1 (PTCH1) is a frequently altered gene in GC. We attempt to explore the association between PTCH1 mutation and immunotherapy efficacy. The Memorial Sloan Kettering Cancer Center (MSKCC) cohort (n = 236) with GC (esophageal, gastric and colorectal cancers) patients receiving ICIs was used for discovery and the Peking University Cancer Hospital (PUCH) GC cohort (n = 92) was used for validation. Overall survival (OS) and tumor mutational burden (TMB) of the PTCH1 mutant-type (PTCH1-MUT) and PTCH1 wild-type (PTCH1-WT) groups were compared. Furthermore, GC data were collected from The Cancer Genome Atlas to assess the potential mechanisms. In the MSKCC cohort, PTCH1-MUT group showed significantly better OS (P = 0.017) and higher TMB. Multivariate analysis showed that PTCH1 mutation was associated with better OS. In the PUCH cohort, PTCH1-MUT group showed significantly longer OS (P = 0.036) and progression-free survival, and higher durable clinical benefit and TMB. Immune cell infiltration analysis revealed that PTCH1-MUT group had significantly higher distributions of CD8 T cells, CD4 T cells, NK cells, mast cells and M1 cells. The PTCH1-MUT group showed significantly higher expression of most immune-related genes. Gene set enrichment analysis showed that the PTCH1-MUT group had enriched INF-γ response, INF-α response, glycolysis and reactive oxygen species pathway gene sets. PTCH1 mutation may represent a potential biomarker for predicting ICIs response in GC. Nevertheless, prospective cohort studies should be performed to further validate our results.

POTEE mutation as a potential predictive biomarker for immune checkpoint inhibitors in lung adenocarcinoma.

Precise selection of patients who could benefit from immune checkpoint inhibitors (ICIs) is an important challenge for immunotherapy in lung cancer. POTEE (POTE Ankyrin Domain Family Member E) is a member of one primate-specific gene family which have been identified as cancer-related antigens and potential target for immunotherapy of cancer. Here, we investigated the correlation between POTEE mutation and the clinical outcome of ICIs treatment in non-small cell lung cancer (NSCLC). We merged three NSCLC cohorts (n = 165) to assess predictive value of POTEE mutation of immunotherapy efficacy in NSCLC. The prognostic analysis and the potential molecular mechanism exploration were conducted based on the data from The Cancer Genome Atlas (TCGA) database. In the merged cohort, patients with POTEE-mutation (POTEE-Mut) had a significantly higher objective response rate (ORR) (100% vs 27.7%; P < 0.001) and longer progression-free survival (PFS) (P = 0.001; HR 0.08; 95% CI 0.01 - 0.54) compared to patients with POTEE wild-type (POTEE-WT) in NSCLC. Also, patients with POTEE-Mut showed higher ORR (100% vs 27.2%; P < 0.001) and longer PFS (P = 0.001; HR 0.07; 95% CI 0.01 - 0.52) in lung adenocarcinoma (LUAD). POTEE mutation was significantly associated with higher tumor mutational burden (TMB) and higher neoantigen load (NAL), but not with PD-L1 expression in LUAD. Gene set enrichment analyses (GSEA) analysis revealed prominent enrichment of signatures related to DNA repair in POTEE-Mut group (P < 0.001) in LUAD. Our results indicate that POTEE mutation could serve as a potential predictive biomarker for ICIs in LUAD. However, prospective cohort studies are still needed for further validation.

Blood-Glucose-Depleting Hydrogel Dressing as an Activatable Photothermal/Chemodynamic Antibacterial Agent for Healing Diabetic Wounds.

Poorly healing and nonhealing diabetic wounds are challenging to treat as the rapid growth of bacteria due to the high local glucose content can lead to persistent inflammation and poor angiogenesis. Herein, a smart hydrogel dressing composed of 3,3',5,5'-tetramethylbenzidine/ferrous ion/Pluronic F-127/glucose oxidase (TMB/Fe2+/PF127/GOx) is designed and demonstrated to consume blood glucose while accelerating wound healing by generating antibacterial agents in situ. The loaded GOx degrades blood glucose to provide hydrogen peroxide (H2O2) and gluconic acid to support the Fe2+-based Fenton reaction, and the generated hydroxyl radical (·OH) facilitates the oxidation of TMB. The color change from colorless to green caused by the oxidation of TMB in the blood glucose range between 1 and 10 mM can be monitored visually. Simultaneously, this process induced chemodynamic therapy (CDT) by the specific generation of hydroxyl radical (·OH) for killing bacteria. Moreover, the oxidized TMB shows strong absorption in the near infrared (NIR) region so that NIR light can be converted into heat efficiently for photothermal therapy (PTT). As a result, nearly 100% of Staphylococcus aureus and Escherichia coli are killed by synergistic PTT/CDT, and the infected skin wounds undergo complete repair along with downregulation of interleukin-6 (IL-6) and upregulation of the vascular endothelial growth factor (VEGF) and matrix metallopeptidase-2 (MMP-2). Different from traditional wound dressings that can give rise to secondary injury, the excellent thermosensitive properties arising from the sol/gel phase transition render the hydrogel dressing materials injectable, self-reparable, and removable on demand. The multifunctional hydrogel with hypoglycemic, chemodynamic, photothermal, antibacterial, and on-demand thermosensitive properties has immense potential in the treatment of diabetic wounds.

Liquid biopsy using cell-free DNA in the early diagnosis of hepatocellular carcinoma.

Hepatocellular carcinoma ranks fourth in cancer-related causes of death worldwide and second in China. Patients with hepatocellular carcinoma (HCC) at the early stage have a better prognosis compared to HCC patients at the late stage. Therefore, early screening for HCC is critical for clinical treatment decisions and improving the prognosis of patients. Ultrasound (US), computed tomography (CT), and serum alpha fetoprotein (AFP) have been used to screen HCC, but HCC is still difficult to be diagnosed in the early stage due to the low sensitivity of the above methods. It is urgent to find a method with high sensitivity and specificity for the early diagnosis of HCC. Liquid biopsy is a noninvasive detection method using blood or other bodily fluids. Cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) are important biomarkers for liquid biopsy. Recently, HCC screening methods using the application of cfDNA and ctDNA have become the hot spot of early HCC diagnostics. In this mini review, we summarize the latest research progress of liquid biopsy based on blood cfDNA in early screening of HCC.

Mechanistic insights into the clinical Y96D mutation with acquired resistance to AMG510 in the KRASG12C.

Special oncogenic mutations in the RAS proteins lead to the aberrant activation of RAS and its downstream signaling pathways. AMG510, the first approval drug for KRAS, covalently binds to the mutated cysteine 12 of KRASG12C protein and has shown promising antitumor activity in clinical trials. Recent studies have reported that the clinically acquired Y96D mutation could severely affect the effectiveness of AMG510. However, the underlying mechanism of the drug-resistance remains unclear. To address this, we performed multiple microsecond molecular dynamics simulations on the KRASG12C-AMG510 and KRASG12C/Y96D-AMG510 complexes at the atomic level. The direct interaction between the residue 96 and AMG510 was impaired owing to the Y96D mutation. Moreover, the mutation yielded higher flexibility and more coupled motion of the switch II and α3-helix, which led to the departing motion of the switch II and α3-helix. The resulting departing motion impaired the interaction between the switch II and α3-helix and subsequently induced the opening and loosening of the AMG510 binding pocket, which further disrupted the interaction between the key residues in the pocket and AMG510 and induced an increased solvent exposure of AMG510. These findings reveal the resistance mechanism of AMG510 to KRASG12C/Y96D, which will help to offer guidance for the development of KRAS targeted drugs to overcome acquired resistance.

Mechanistic Insights into the Long-range Allosteric Regulation of KRAS Via Neurofibromatosis Type 1 (NF1) Scaffold Upon SPRED1 Loading.

Allosteric regulation is the most direct and efficient way of regulating protein function, wherein proteins transmit the perturbations at one site to another distinct functional site. Deciphering the mechanism of allosteric regulation is of vital importance for the comprehension of both physiological and pathological events in vivo as well as the rational allosteric drug design. However, it remains challenging to elucidate dominant allosteric signal transduction pathways, especially for large and multi-component protein machineries where long-range allosteric regulation exits. One of the quintessential examples having long-range allosteric regulation is the ternary complex, SPRED1-RAS-neurofibromin type 1 (NF1, a RAS GTPase-activating protein), in which SPRED1 facilitates RAS-GTP hydrolysis by interacting with NF1 at a distal, allosteric site from the RAS binding site. To address the underlying mechanism, we performed extensive Gaussian accelerated molecular dynamics simulations and Markov state model analysis of KRAS-NF1 complex in the presence and absence of SPRED1. Our findings suggested that SPRED1 loading allosterically enhanced KRAS-NF1 binding, but hindered conformational transformation of the NF1 catalytic center for RAS hydrolysis. Moreover, we unveiled the possible allosteric pathways upon SPRED1 binding through difference contact network analysis. This study not only provided an in-depth mechanistic insight into the allosteric regulation of KRAS by SPRED1, but also shed light on the investigation of long-range allosteric regulation among complex macromolecular systems.

Hydrogen sulfide treatment increases the antioxidant capacity of fresh Lingwu Long Jujube (Ziziphus jujuba cv. Mill) fruit during storage.

Hydrogen sulfide (H2S) has been identified as an important gaseous signal molecule in plants. Here, we investigated the effects of H2S on postharvest senescence and antioxidant metabolism of Lingwu Long Jujube (Ziziphus jujuba cv. Mill) fruits (LLJF). Fumigation of Jujube fruits with H2S released from 0.4 mm NaHS could significantly prolong the postharvest shelf life of jujube fruits, reduce the decay rate of fruit, the weight loss of fruit, and inhibit the fruit loss, hardness, color, soluble solids, and titratable acidity. Compared with the control group, exogenous H2S fumigation significantly decreased the loss of chlorophyll, carotenoids, soluble protein, ascorbic acid, phenols, and flavonoids in jujube fruits during post-harvest storage. At the same time, H2S could significantly delay the accumulation of malondialdehyde (MDA), hydrogen peroxide (H2O2) and superoxide anion (O2 ∙-) and promote catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX), peroxidase (POD) activity, and inhibit polyphenol oxidase (PPO) activity. To summarize, H2S can effectively alleviate postharvest senescence and decay of jujube fruits by regulating the ROS accumulation and antioxidant enzymes, and prolong the storage period of postharvest.

The clinical application value of phase angle of six parts in nutritional evaluation of tumor patients.

OBJECTIVES: The purpose of this study was to explore the clinical application value of phase angle (PA) of six parts in the nutritional evaluation and construct a prediction model for diagnosing malnutrition of tumor patients. METHODS: A total of 1129 patients with malignant tumors were analyzed retrospectively. The age, sex, tumor location and body mass index (BMI) of the patients were collected, and PA of six parts was measured. The Patient Subjective Global Assessment (PG-SGA) was used to evaluate the nutritional status of each patient. RESULTS: According to the PG-SGA, 66.5% (n = 750) of the patients were evaluated as malnourished. Patients under the age of 65 had higher PA values. The PA value of men was higher than that of women (except PA-RL). In different disease groups, the PA-RA and PA-TR values were significantly different. In our study, PA value increases with BMI and decreases with PG-SGA (except PG-SGA 0-1 group). Multivariate regression analysis indicates that the age (HR = 1.051, 95% CI 1.037-1.066, P < 0.001), BMI (HR = 0.885, 95% CI 0.849-0.924, P < 0.001), and PA-WB (HR = 0.615, 95% CI 0.546-0.692, P < 0.001) were independent significant predictors associated with malnutrition. The AUC of the prediction model is 0.7631 (p < 0.001), indicating that the model including age, BMI, and PA-WB has certain diagnostic value for the diagnosis of malnutrition. CONCLUSION: The PA-WB is an independent prognostic factor of malnutrition. The prediction model constructed by age, BMI, and PA-WB can be used as a useful tool for nutritional evaluation of tumor patients. TRIAL REGISTRATION: Clinical Trial No.: ChiCTR2100047858.

A simple assessment model based on phase angle for malnutrition and prognosis in hospitalized cancer patients.

BACKGROUND & AIMS: Malnutrition in cancer patients is a common but under-diagnosed condition that has negative effects on clinical outcomes. The development of an easy and reliable malnutrition assessment tool is thus critical for identification and nutritional support. We aimed to develop a phase angle (PA)-based prediction model of malnutrition and evaluate it in patient prognosis. METHODS: A retrospective cohort of data consisting of demographic, clinical parameter and PA test from 702 adult hospitalized cancer patients between June 2020 to February 2021 was analysed. PAs for 6 body sites were measured by a body composition analyser. Patient-generated subjective global assessment (PG-SGA) scale was used as the diagnostic standard of nutritional status (PG-SGA ≥ 4 points defined as malnutrition). Decision tree, mean decrease accuracy of random forest, stepAIC strategy and test of generalized likelihood ratio were employed to select important variables and develop models for predicting PG-SGA binary classification (PG-SGA < 4 or ≥ 4 as a split). Survival curves were plotted by using the Kaplan-Meier method. RESULTS: In all, 490 (69.8%) patients were malnourished according to their actual PG-SGA scores. Except for age, tumor type and body mass index (BMI), PA of the left arm was found to influence malnutrition classification and incorporated in the final predictive model. The model achieved good performance with an AUC of 0.813, 75.9% sensitivity and 73.3% specificity. The actual and predicted survival curves were almost overlapped. CONCLUSION: This study provides a simple nutritional assessment tool which may be used to facilitate oncology physicians to identify cancer patients at nutritional risk and potentially implement nutritional support. CLINICAL TRIAL NO: ChiCTR2100047858.

MicroRNA-483-5p accentuates cisplatin-induced acute kidney injury by targeting GPX3.

The ability of cisplatin (cis-diamminedichloroplatinum II) toxicity to induce acute kidney injury (AKI) has attracted attention and concern for a long time, but the molecular mechanism of action for cisplatin is not clear. MicroRNA-483 is involved in several diseases, such as tumorigenesis and osteoarthritis, but its renal target and potential role in AKI are unknown. In this study, we explored the pathogenic role and underlying mechanism of miR-483-5p in cisplatin-induced AKI, using transgenic mice, clinical specimen, and in vitro cell line. We found that miR-483-5p was significantly upregulated by cisplatin in a cisplatin-induced mouse model, in serum samples of patients who received cisplatin therapy, and in NRK-52E cells. Overexpression of miR-483-5p in mouse kidneys by stereotactic renal injection of lentiviruses mediated miR-483-5p or generation of conditional miR-483-overexpressing transgenic mice accentuated cisplatin-induced AKI by increasing oxidative stress, promoting apoptosis, and inhibiting autophagy of tubular cells. Furthermore, our results revealed miR-483-5p directly targeted to GPX3, overexpression of which rescued cisplatin-induced AKI by inhibiting oxidative stress and apoptosis of tubular cells, but not by regulating autophagy. Collectively, miR-483-5p is upregulated by cisplatin and exacerbates cisplatin-induced AKI via negative regulation of GPX3 and contributing oxidative stress and tubular cell apoptosis. These findings reveal a pathogenic role for miR-483-5p in cisplatin-induced AKI and suggest a novel target for the diagnosis and treatment of AKI.

Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins.

Ras undergoes interconversion between the active GTP-bound state and the inactive GDP-bound state. This GTPase cycle, which controls the activities of Ras, is accelerated by Ras GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (SOS). Oncogenic Ras mutations could affect the GTPase cycle and impair Ras functions. Additionally, Src-induced K-Ras Y32/64 dual phosphorylation has been reported to disrupt GTPase cycle and hinder Ras downstream signaling. However, the underlying mechanisms remain unclear. To address this, we performed molecular dynamics simulations (~30 µs in total) on unphosphorylated and phosphorylated K-Ras4B in GTP- and GDP-bound states, and on their complexes with GTPase cycle regulators (GAP and SOS) and the effector protein Raf. We found that K-Ras4B dual phosphorylation mainly alters the conformation at the nucleotide binding site and creates disorder at the catalytic site, resulting in the enlargement of GDP binding pocket and the retard of Ras-GTP intrinsic hydrolysis. We observed phosphorylation-induced shift in the distribution of Ras-GTP inactive-active sub-states and recognized potential druggable pockets in the phosphorylated Ras-GTP. Moreover, decreased catalytic competence or signal delivery abilities due to reduced binding affinities and/or distorted catalytic conformations of GAP, SOS and Raf were observed. In addition, the allosteric pathway from Ras/Raf interface to the distal Raf L4 loop was compromised by Ras phosphorylation. These results reveal the mechanisms by which phosphorylation influences the intrinsic or GAP/SOS catalyzed transformations between GTP- and GDP-bound states of Ras and its signal transduction to Raf. Our findings project Ras phosphorylation as a target for cancer drug discovery.

Conformational Selection Mechanism Provides Structural Insights into the Optimization of APC-Asef Inhibitors.

Metastasis is the major cause of death in colorectal cancer and it has been proven that inhibiting an interaction between adenomatous polyposis coli (APC) and Rho guanine nucleotide exchange factor 4 (Asef) efficaciously restrain metastasis. However, current inhibitors cannot achieve a satisfying effect in vivo and need to be optimized. In the present study, we applied molecular dynamics (MD) simulations and extensive analyses to apo and holo APC systems in order to reveal the inhibitor mechanism in detail and provide insights into optimization. MD simulations suggested that apo APC takes on a broad array of conformations and inhibitors stabilize conformation selectively. Representative structures in trajectories show specific APC-ligand interactions, explaining the different binding process. The stability and dynamic properties of systems elucidate the inherent factors of the conformation selection mechanism. Binding free energy analysis quantitatively confirms key interface residues and guide optimization. This study elucidates the conformation selection mechanism in APC-Asef inhibition and provides insights into peptide-based drug design.

Dual roles of ATP-binding site in protein kinases: Orthosteric inhibition and allosteric regulation.

Protein kinases use ATP to phosphorylate other proteins. Phosphorylation (p) universally orchestrates a fine-tuned network modulating a multitude of biological processes. Moreover, the start of networks, ATP-binding site, has been recognized dual roles to impact protein kinases function: (i) orthosteric inhibition, via being blocked to interference ATP occupying and (ii) allosteric regulation, via being altered first to induce further conformational changes. The above two terminologies are widely used in drug design, which has acquired quite a significant progress in the protein kinases field over the past 2 decades. Most small molecular inhibitors directly compete with ATP to implement orthosteric inhibition, still exhibiting irreplaceable and promising therapeutic effects. Additionally, numerous inhibitors can paradoxically lead protein kinases to hyperphosphorylation, even activation, indicative of the allosteric regulation role of the ATP-binding site. Here, we review the quintessential examples that apply for the dual roles in diverse ways. Our work provides an insight into the molecular mechanisms under the dual roles and will be promisingly instructive for future drug development.

Multifunctional bioactive Nd-Ca-Si glasses for fluorescence thermometry, photothermal therapy, and burn tissue repair.

Photothermal therapy (PTT), an emerging tumor treatment technology, has attracted tremendous interest, but excessive heat will cause damage to surrounding healthy tissues. Therefore, in situ temperature monitoring during PTT is of great importance to determine optimal treatment temperature and repair heat-damaged normal tissues. Here, we report the preparation of multifunctional Nd-Ca-Si silicate glasses and glass/alginate composite hydrogels that not only have photothermal property but also emit fluorescence under 808-nm laser irradiation, and its fluorescence intensity is linearly correlated with in situ temperature. With this feature, optimal PTT temperature for effective tumor treatment with minimal normal tissue damage can be obtained. In addition, because of the bioactive silicate components, the composite hydrogel has bioactivity to repair heat damage caused by PTT. This implantable multifunctional material with unique temperature monitoring, photothermal function, and wound healing bioactivity can be used for localized thermal therapy.

Surface plasmon resonance assay for exosomes based on aptamer recognition and polydopamine-functionalized gold nanoparticles for signal amplification.

A novel surface plasmon resonance (SPR) strategy is introduced for the specific determination of exosomes based on aptamer recognition and polydopamine-functionalized gold nanoparticle (Au@PDA NP)-assisted signal amplification. Exosomes derived from hepatic carcinoma SMMC-7721 were selected as the model target. SMMC-7721 exosomes can be specifically captured by the aptamer ZY-sls that was complementary to the DNA tetrahedron probes (DTPs), and then the CD63 aptamer-linked Au@PDA NPs recognized SMMC-7721 exosomes for signal amplification. The DTPs were modified on a Au film for preventing Au deposition on the surface during the introduction of HAuCl4, and PDA coated on the AuNPs was used to reduce HAuCl4 in situ without any reductant assistance. It results in a further enhanced SPR signal. The assay can clearly distinguish SMMC-7721 exosomes from others (HepG2 exosomes, Bel-7404 exosomes, L02 exosomes, MCF-7 exosomes, and SW480 exosomes, respectively). SMMC-7721 exosomes are specifically determined as low as 5.6 × 105 particles mL-1. The method has successfully achieved specific determination of SMMC-7721 exosomes even in 50% of human serum without any pretreatment. Graphical abstract A novel surface plasmon resonance (SPR) strategy was introduced for the specific determination of exosomes based on aptamer recognition and polydopamine functionalized gold nanoparticles (Au@PDA NPs). The SPR signal was improved using the Au@PDA NPs assisted amplification.

Parallel On-Target Derivatization for Mass Calibration and Rapid Profiling of N-Glycans by MALDI-TOF MS.

Glycosylation is an important post-translational modification of proteins, and abnormal glycosylation is involved in a variety of diseases. Accurate and rapid profiling of N-glycans by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is still technically challenging and hampered mainly by mass drift of instrument, manual identification of spectrum peaks, and poor cocrystallization with traditional matrices besides low ionization efficiency of analytes. In the present study, a parallel on-target derivatization strategy (POTDS), on the basis of two rationally combined matrices, i.e., 3-hydrazinobenzoic acid plus DHB (DHB/3HBA) and quinoline-3-carbohydrazide plus DHB (DHB/Q3CH), was proposed for mass calibration and rapid detection of reducing N-glycans. Both DHB/3HBA and DHB/Q3CH show high derivatization efficiency and can improve the ionization efficiency of reducing N-glycans significantly. For mass calibration, in combination with dextrans, DHB/3HBA and DHB/Q3CH prove to be highly sensitive matrices facilitating both MS and MS2 calibration for N-glycans in dual polarities. For rapid identification, the regular mass difference observed for each N-glycan labeled with Q3CH and 3HBA respectively can eliminate the occurrence of false positives and promote automated identification of N-glycans in complex samples. For relative quantitation, the acid-base pair of DHB/Q3CH generates a concentrated cocrystallization of glycan-matrix mixtures at the edge of the droplet uniformly, exhibiting good linearity (R2 > 0.998) and accuracy (RSD ≤ 10%). Furthermore, the established POTDS was successfully utilized to assess N-glycans of serum from HCC patients, revealing potential for biomarker discovery in clinical practice.

Insight into the mechanism of allosteric activation of PI3Kα by oncoprotein K-Ras4B.

Ras is a key member in the superfamily of small GTPase. Transforming between GTP-bound active state and GDP-bound inactive state in response to exogenous signals, Ras serves as a binary switch in various signaling pathways. One of its downstream effectors is phosphatidylinositol-4,5-bisphosphate 3-kinase α (PI3Kα), which phosphorylates phosphatidylinositol 4,5-bisphosphate into phosphatidylinositol 3,4,5-trisphosphate in the PI3K/Akt/mTOR pathway and mediates an array of important cellular activities including cell growth, migration and survival. Hyperactivation of PI3Kα induced by the Ras isoform K-Ras4B has been unveiled as a key event during the oncogenesis of pancreatic ductal adenocarcinoma, but the underlying mechanism of how K-Ras4B allosterically activates PI3Kα still remains largely unsolved. Here, we employed accelerated molecular dynamic simulations and allosteric pathway analysis to explore into the activation process of PI3Kα by K-Ras4B and unraveled the underlying structural mechanisms. We found that K-Ras4B binding induced more conformational dynamics within PI3Kα and triggered its step-wise transition from a self-inhibited state towards an activated state. Moreover, K-Ras4B binding markedly disrupted the interactions along the p110/p85 interface, especially the ones between nSH2 in p85 and its nearby functional domains in p110 like C2, helical, and kinase domains. The altered inter-domain interactions exposed the kinase domain, which promoted the membrane association and substrate phosphorylation of PI3Kα, thereby facilitating its activation. In particular, the community networks and allosteric pathways analysis further revealed that in PI3Kα/K-Ras4B system, allosteric signaling regulating p110/p85 interaction was rewired from the helical domain to the kinase domain and several important residues and their related allosteric pathways mediating PI3Kα autoinhibition were bypassed. The obtained structural mechanisms provide an in-depth mechanistic insight into the allosteric activation of PI3Kα by K-Ras4B as well as shed light on its drug discovery.

Investigation of the interaction between split aptamer and vascular endothelial growth factor 165 using single molecule force spectroscopy.

Understanding the binding of split aptamer/its target could become a breakthrough in the application of split aptamer. Herein, vascular endothelial growth factor (VEGF), a major biomarker of human diseases, was used as a model, and its interaction with split aptamer was explored with single molecule force spectroscopy (SMFS). SMFS demonstrated that the interaction force of split aptamer/VEGF165 was 169.44 ± 6.59 pN at the loading rate of 35.2 nN/s, and the binding probability of split aptamer/VEGF165 was dependent on the concentration of VEGF165 . On the basis of dynamic force spectroscopy results, one activation barrier in the dissociation process of split aptamer/VEGF165 complexes was revealed, which was similar to that of the intact aptamer/VEGF165 . Besides, the dissociation rate constant (koff ) of split aptamer/VEGF165 was close to that of intact aptamer/VEGF165 , and the interaction force of split aptamer/VEGF165 was higher than the force of intact aptamer/VEGF165 . It indicated that split aptamer also possessed high affinity with VEGF165 . The work can provide a new method for exploring the interaction of split aptamer/its targets at single-molecule level.

Unraveling allosteric landscapes of allosterome with ASD.

Allosteric regulation is one of the most direct and efficient ways to fine-tune protein function; it is induced by the binding of a ligand at an allosteric site that is topographically distinct from an orthosteric site. The Allosteric Database (ASD, available online at http://mdl.shsmu.edu.cn/ASD) was developed ten years ago to provide comprehensive information related to allosteric regulation. In recent years, allosteric regulation has received great attention in biological research, bioengineering, and drug discovery, leading to the emergence of entire allosteric landscapes as allosteromes. To facilitate research from the perspective of the allosterome, in ASD 2019, novel features were curated as follows: (i) >10 000 potential allosteric sites of human proteins were deposited for allosteric drug discovery; (ii) 7 human allosterome maps, including protease and ion channel maps, were built to reveal allosteric evolution within families; (iii) 1312 somatic missense mutations at allosteric sites were collected from patient samples from 33 cancer types and (iv) 1493 pharmacophores extracted from allosteric sites were provided for modulator screening. Over the past ten years, the ASD has become a central resource for studying allosteric regulation and will play more important roles in both target identification and allosteric drug discovery in the future.