Reverse-QTY code design of active human serum albumin self-assembled amphiphilic nanoparticles for effective anti-tumor drug doxorubicin release in mice.

Human serum albumin (HSA) is a highly water-soluble protein with 67% alpha-helix content and three distinct domains (I, II, and III). HSA offers a great promise in drug delivery with enhanced permeability and retention effect. But it is hindered by protein denaturation during drug entrapment or conjugation that result in distinct cellular transport pathways and reduction of biological activities. Here we report using a protein design approach named reverse-QTY (rQTY) code to convert specific hydrophilic alpha-helices to hydrophobic to alpha-helices. The designed HSA undergo self-assembly of well-ordered nanoparticles with highly biological actives. The hydrophilic amino acids, asparagine (N), glutamine (Q), threonine (T), and tyrosine (Y) in the helical B-subdomains of HSA were systematically replaced by hydrophobic leucine (L), valine (V), and phenylalanine (F). HSArQTY nanoparticles exhibited efficient cellular internalization through the cell membrane albumin binding protein GP60, or SPARC (secreted protein, acidic and rich in cysteine)-mediated pathways. The designed HSArQTY variants displayed superior biological activities including: i) encapsulation of drug doxorubicin, ii) receptor-mediated cellular transport, iii) tumor cell targeting, and iv) antitumor efficiency compare to denatured HSA nanoparticles. HSArQTY nanoparticles provided superior tumor targeting and antitumor therapeutic effects compared to the albumin nanoparticles fabricated by antisolvent precipitation method. We believe that the rQTY code is a robust platform for specific hydrophobic modification of functional hydrophilic proteins with clear-defined binding interfaces.

Hiding in plain sight: three chemically distinct α-helix types.

Linus Pauling in 1950 published a three-dimensional model for a universal protein secondary structure motif which he initially called the alpha-spiral. Jack Dunitz, then a postdoc in Pauling's lab suggested to Pauling that the term helix is more accurate than spiral when describing the right-handed peptide and protein coiled structures. Pauling agreed, hence the rise of the alpha-helix, and, by extension, the 'double helix' structure of DNA. Although structural biologists and protein chemists are familiar with varying polar and apolar characters of amino acids in alpha-helices, to non-experts the three chemically distinct alpha-helix types classified here may hide in plain sight.

QTY code designed antibodies for aggregation prevention: A structural bioinformatic and computational study.

Therapeutic monoclonal antibodies are the most rapidly growing class of molecular medicine, and they are beneficial to the treatment of a broad spectrum of human diseases. However, the aggregation of antibodies during the process of manufacture, distribution, and storage poses significant challenges, potentially compromising efficacy and inducing adverse immune responses. We previously conceived a QTY (glutamine, threonine, tyrosine) code, a simple tool for enhancing protein water-solubility by systematically pairwise replacing hydrophobic residues L (leucine), V (valine)/I (isoleucine), and F (phenylalanine). The QTY code offers a promising alternative to traditional methods of controlling aggregation in integral transmembrane proteins. In this study, we designed variants of four antibodies applying the QTY code, changing only the ß-sheets. Through the structure-based aggregation analysis, we found that these QTY antibody variants demonstrated significantly decreased aggregation propensity compared to their wild-type counter parts. Our results of molecular dynamics simulations showed that the design by QTY code is capable of maintaining the antigen-binding affinity and structural stability. Our structural informatic and computational study suggests that the QTY code offers a significant potential in mitigating antibody aggregation.

Molecular Dynamic Simulations Reveal that Water-Soluble QTY-Variants of Glutamate Transporters EAA1, EAA2 and EAA3 Retain the Conformational Characteristics of Native Transporters.

OBJECTIVE: Glutamate transporters play a crucial role in neurotransmitter homeostasis, but studying their structure and function is challenging due to their membrane-bound nature. This study aims to investigate whether water-soluble QTY-variants of glutamate transporters EAA1, EAA2 and EAA3 retain the conformational characteristics and dynamics of native membrane-bound transporters. METHODS: Molecular dynamics simulations and comparative genomics were used to analyze the structural dynamics of both native transporters and their QTY-variants. Native transporters were simulated in lipid bilayers, while QTY-variants were simulated in aqueous solution. Lipid distortions, relative solvent accessibilities, and conformational changes were examined. Evolutionary conservation profiles were correlated with structural dynamics. Statistical analyses included multivariate analysis to account for confounding variables. RESULTS: QTY-variants exhibited similar residue-wise conformational dynamics to their native counterparts, with correlation coefficients of 0.73 and 0.56 for EAA1 and EAA3, respectively (p < 0.001). Hydrophobic interactions of native helices correlated with water interactions of QTY- helices (rs = 0.4753, p < 0.001 for EAA1). QTY-variants underwent conformational changes resembling the outward-to-inward transition of native transporters. CONCLUSIONS: Water-soluble QTY-variants retain key structural properties of native glutamate transporters and mimic aspects of native lipid interactions, including conformational flexibility. This research provides valuable insights into the conformational changes and molecular mechanisms of glutamate transport, potentially offering a new approach for studying membrane protein dynamics and drug interactions.

Protein Design: From the Aspect of Water Solubility and Stability.

Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.

Discovery of Dehydroabietylamine Derivatives as Antibacterial and Antifungal Agents.

A diverse array of biologically active derivatives was derived by modifying the chemically active sites of dehydroabietylamine. Herein, we describe the synthesis of a new series of C-19-arylated dehydroabietylamine derivatives using a palladium-catalyzed C(sp3)-H activation reaction. Five analogues (3b, 3d, 3h, 3n, and 4a) exhibited antibacterial activity against Escherichia coli. Compound 4a exhibited strong inhibitory activity against DNA Topo II and Topo IV. Molecular docking modeling indicated that it can bind effectively to the target through interactions with amino acid residues. The synthesized compounds were tested in vitro for their antifungal activity against six common phytopathogenic fungi. The mechanism of action of compound 4c against Rhizoctorzia solani was investigated, revealing that it disrupts the morphology of the mycelium and enhances cell membrane permeability.

Effect of Ultrasound on Thrombus debris during Sonothrombolysis in a Microfluidic device.

Microbubble-mediated sonothrombolysis has been proven to be a non-invasive and efficient method for thrombolysis. Nevertheless, there is a potential risk that the thrombus debris generated during the dissolution of the original thrombus are too large and can lead to hazardous emboli. Using a sonothrombolysis microfluidic platform, we investigated the effects of ultrasound power, thrombolytic agent and microbubble concentration on the size of thrombus debris with the example of microbubble-mediated sonothrombolysis of arterial thrombus. Additionally, we studied the effects of ultrasound power on the size and shape of thrombus debris produced by acute and chronic arterial sonothrombolysis. In acute arterial sonothrombolysis, ultrasound power has significant effect on the size of thrombus debris and steadily increases with the increase of ultrasound power. Conversely, in chronic arterial sonothrombolysis, the size of thrombus debris is minimally affected by ultrasound power. Using the sonothrombolysis microfluidic platform, the relationship between ultrasound power and the safety of sonothrombolysis has been illustrated, and the sonothrombolysis microfluidic platform is demonstrated to be a promising tool for further studies on the process of sonothrombolysis.

Percutaneous Mechanical Thrombectomy Using the AcoStream Thrombus Aspiration System for Acute Superior Mesenteric Artery Embolism.

BACKGROUND: This study was performed to summarize our experience in treating acute superior mesenteric artery embolism (SMAE) by percutaneous mechanical thrombectomy (PMT). METHODS: Between January 2023 and October 2023, 18 patients presenting with acute mesenteric ischemia were admitted to our center, including 11 cases of SMAE, 3 cases of superior mesenteric artery thrombosis, and 4 cases of superior mesenteric vein thrombosis. We retrospectively reviewed 8 patients (4 males and 4 females; range, 51-79 years; mean, 62.50 ± 9.67 years) who underwent treatment of acute SMAE using the AcoStream system. The patients had no obvious evidence of intestinal necrosis as shown by peritoneal puncture or computed tomography. Thrombectomy was performed on the superior mesenteric artery (SMA) using an 8F AcoStream thrombus aspiration system (Acotec, China). The demographics, risk factors, therapeutic effect, complications, mortality, and follow-up of the study population were assessed. RESULTS: The technical success rate was 100%. After 1-3 passes (2.38 ± 0.92) and aspiration thrombectomy, complete thrombus removal was achieved in 7 (87.50%) patients. One patient received an adjunctive catheter-directed thrombolysis due to partial thrombus removal. Thrombolysis was conducted for 2 days, resulting in complete resolution of the thrombus. The other 7 patients did not receive adjunctive endovascular intervention due to complete thrombus removal and no residual stenosis. No distal embolization or device-related complications were noted during the procedure. After the procedure, sufficient clinical improvement was seen in 6 patients within 1-2 days. Two patients showed no significant improvement of their symptoms. Laparotomy was performed on day 1 and day 2 after thrombectomy in patients 3 and 7, respectively. Intestinal necrosis was diagnosed operatively and intestinal resection was performed. All patients were discharged 6-15 days (9.50 ± 3.07) after admission without perioperative complication or death. The mean follow-up period was 5.00 ± 3.30 months (range, 1-10 months), and the follow-up rate was 100%. During the follow-up, all patients remained symptom-free. Computed tomography angiography images showed good flow in the trunk and branches of the SMA in all patients. CONCLUSIONS: PMT using the AcoStream system is a minimally invasive, safe, and effective technique for acute SMAE. Early application of PMT can achieve immediate revascularization of the SMA and have the potential advantage of avoiding laparotomy or reducing the extension of enterectomy, as it could theoretically restore intestinal perfusion in less time than open revascularization. If the symptoms do not improve after PMT, exploratory laparotomy should be scheduled as soon as possible. Further studies are necessary on this field to confirm these findings.

THE CLINICAL VALUE OF ß-D-GLUCAN TESTING AND NEXT-GENERATION METAGENOMIC SEQUENCING FOR THE DIAGNOSIS OF FUNGAL ENDOPHTHALMITIS.

PURPOSE: To explore the clinical value of ß-D-glucan (BDG) testing and metagenomic next-generation sequencing (mNGS) for detecting the pathogens of fungal endophthalmitis (FE). METHODS: This study included 32 cases (32 eyes) with FE and 20 cases (20 eyes) with intraocular inflammation caused by other etiologies. All patients underwent extraction of aqueous humor or vitreous fluid samples for BDG testing and mNGS. The diagnostic performance and total clinical concordance rate of BDG testing and mNGS for FE were evaluated and calculated based on the results of the clinical diagnosis. RESULTS: Among the clinically diagnosed FE, the positivity rates of BDG testing and mNGS (90.63%) were both significantly higher ( P < 0.001) than that of microbial cultures (53.13%). There was 100% consistency in pathogen identification using mNGS and culture identification for culture-positive cases. The area under the curve was 0.927 for BDG testing and 0.853 for mNGS. When the two tests were combined, sensitivity (93.75%), specificity (100.00%), and total clinical concordance rate (96.15%) were all improved, compared with the single tests. CONCLUSION: The positive rates of BDG test and mNGS were markedly higher than those of cultures in FE identification. The combination of these two tests showed improved performance when compared with individual tests.

CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs.

Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. Although gene profiling can identify their cancer-specific signatures, systematic correlations between protein functions and tumor-related mechanisms are still unclear. We present here the CrMP-Sol database ( https://bio-gateway.aigene.org.cn/g/CrMP ), which aims to breach the gap between the two. Machine learning was used to extract key functional descriptions for protein visualization in the 3D-space, where spatial distributions provide function-based predictive connections between proteins and cancer types. CrMP-Sol also presents QTY-enabled water-soluble designs to facilitate native membrane protein studies despite natural hydrophobicity. Five examples with varying transmembrane helices in different categories were used to demonstrate the feasibility. Native and redesigned proteins exhibited highly similar characteristics, predicted structures and binding pockets, and slightly different docking poses against known ligands, although task-specific designs are still required for proteins more susceptible to internal hydrogen bond formations. The database can accelerate therapeutic developments and biotechnological applications of cancer-related membrane proteins.

The exact phenomenon and early signaling events of the endothelial cytoskeleton response to ultrasound.

Low-intensity ultrasound can be applied for medical imaging and disease treatment in clinical and experimental studies. However, the biological effects of ultrasound on blood vessels, especially endothelial cells (ECs) are still unclear. In this study, the laws of endothelial cytoskeleton changes under ultrasound induction are investigated. ECs are exposed to low-intensity ultrasound, and the cytoskeletal morphology is analyzed by a filamentous (F)-actin staining technique. We further analyze the characteristics of cytoskeleton rupture using indirect immunofluorescence techniques and cytoskeleton electron microscopy. Finally, the biological effects induced by ultrasound at the tissue level are investigated in an ex vivo blood-vessel model. Significant changes in cytoskeletal structure are detected when induced by ultrasound, including cytoskeletal rupture, blebbing and apoptosis. Moreover, a temporal threshold of ECs injury under different ultrasonic intensities is established. This study illustrates a pattern of significant changes in the cytoskeletal structure of ECs induced by ultrasound. The finding serves as a guide for selecting a safe threshold for clinical ultrasound applications.

Polymyxin B therapy based on therapeutic drug monitoring in carbapenem-resistant organisms sepsis: the PMB-CROS randomized clinical trial.

BACKGROUND: The appropriate administration regimen of polymyxin B is yet controversial. The present study aimed to explore the optimal dose of polymyxin B under therapeutic drug monitoring (TDM) guidance. METHODS: In China's Henan province, 26 hospitals participated in a randomized controlled trial. We included patients with sepsis caused by carbapenem-resistant Gram-negative bacteria (CR-GNB) susceptible to polymyxin B. The patients were randomly divided into a high-dose (HD) group or a low-dose (LD) group and received 150 mg loading dose, 75 mg every 12 h and 100 mg loading dose, 50 mg every 12 h, respectively. TDM was employed to determine if the dose of polymyxin B needs adjustment based on the area under the concentration-time curve across 24 h at a steady state (ssAUC0-24) of 50-100 mg h/L. The primary outcome was the 14-day clinical response, and the secondary outcomes included 28- and 14-day mortality. RESULTS: This trial included 311 patients, with 152 assigned to the HD group and 159 assigned to the LD group. Intention-to-treat analysis showed that the 14-day clinical response was non-significant (p = 0.527): 95/152 (62.5%) in the HD group and 95/159 (59.7%) in the LD group. Kaplan-Meier's 180-day survival curve showed survival advantage in the HD group than in the LD group (p = 0.037). More patients achieved the target ssAUC0-24 in the HD than in the LD group (63.8% vs. 38.9%; p = 0.005) and in the septic shock subgroup compared to all subjects (HD group: 71.4% vs. 63.8%, p = 0.037; LD group: 58.3% vs. 38.9%, p = 0.0005). Also, the target AUC compliance was not correlated with clinical outcomes but with acute kidney injury (AKI) (p = 0.019). Adverse events did not differ between the HD and LD groups. CONCLUSION: A fixed polymyxin B loading dose of 150 mg and a maintenance dose of 75 mg every 12 h was safe for patients with sepsis caused by CR-GNB and improves long-term survival. The increased AUC was associated with increased incidence of AKI, and TDM results were valued to prevent AKI. Trial registration Trial registration ClinicalTrials.gov: ChiCTR2100043208, Registration date: January 26, 2021.

Guanxinping ameliorates atherosclerosis via MAPK/NF-κB signaling pathway in ApoE-/- mice.

BACKGROUND: Atherosclerosis (AS), one of the leading causes of deaths and disabilities, is a kind of vascular disease of lipid disorders and chronic inflammation. Guanxinping (GXP) has been administrated in the treatment of AS for nearly 20 years with satisfying clinical response. This study aimed to explore its underlying mechanisms of anti-atherosclerotic effect in AS. METHODS: Male ApoE-/- mice were randomized into five groups and fed with either standard diet (control group, CON) or high-fat diet (HFD) for 12 weeks. HFD mice were further divided randomly and either fed continually with HFD as a model group, or atorvastatin (ATO), or low-dose GXP (LGXP), or high-dose GXP (HGXP). After 12 weeks, the body weight, serum triglyceride (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-c), and low-density lipoprotein cholesterol (LDL-c) were detected. Moreover, serum inflammation cytokines including tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and interleukin-1ß (IL-1ß) concentrations were measured. The structure of aortic tissues was examined by hematoxylin-eosin staining. The mRNA expression of TNF-α, IL-6, and IL-1ß were assessed by qPCR. The protein expressions of ICAM-1, VCAM-1, MCP-1, IL-6, IL-1ß, p38MAPK, ERK1/2, JNK, IκB-α, and NF-κBp65 in the aorta were also detected. RESULTS: GXP treatment reduced serum TG, TC, and LDL-c levels in ApoE-/- mice. Moreover, GXP reduced lipid accumulation in the aorta of ApoE-/- mice, induced by HFD. Furthermore, GXP ameliorated the aorta morphological damage and reduced the serum TNF-α, IL-6, and IL-1ß levels. GXP also attenuated the protein expression of ICAM-1, VCAM-1, MCP-1, IL-6, IL-1ß, p38MAPK, ERK1/2, JNK, and NF-κBp65, whereas it increased the IκBα level in aortic tissues of ApoE-/- mice. CONCLUSIONS: Our results show that GXP could ameliorate atherosclerosis, which is mediated by inhibition of the MAPK/NF-κB signaling pathway in ApoE-/- mice. This study provides evidence that GXP might be a promising drug for the treatment of AS.

Dynamic Dimerization of Chemokine Receptors and Potential Inhibitory Role of Their Truncated Isoforms Revealed through Combinatorial Prediction.

Chemokine receptors play crucial roles in fundamental biological processes. Their malfunction may result in many diseases, including cancer, autoimmune diseases, and HIV. The oligomerization of chemokine receptors holds significant functional implications that directly affect their signaling patterns and pharmacological responses. However, the oligomerization patterns of many chemokine receptors remain poorly understood. Furthermore, several chemokine receptors have highly truncated isoforms whose functional role is not yet clear. Here, we computationally show homo- and heterodimerization patterns of four human chemokine receptors, namely CXCR2, CXCR7, CCR2, and CCR7, along with their interaction patterns with their respective truncated isoforms. By combining the neural network-based AlphaFold2 and physics-based protein-protein docking tool ClusPro, we predicted 15 groups of complex structures and assessed the binding affinities in the context of atomistic molecular dynamics simulations. Our results are in agreement with previous experimental observations and support the dynamic and diverse nature of chemokine receptor dimerization, suggesting possible patterns of higher-order oligomerization. Additionally, we uncover the strong potential of truncated isoforms to block homo- and heterodimerization of chemokine receptors, also in a dynamic manner. Our study provides insights into the dimerization patterns of chemokine receptors and the functional significance of their truncated isoforms.

Synthesis of Pillar[5]arene- and Phosphazene-Linked Porous Organic Polymers for Highly Efficient Adsorption of Uranium.

It is crucial to design efficient adsorbents for uranium from natural seawater with wide adaptability, effectiveness, and environmental safety. Porous organic polymers (POPs) provide superb tunable porosity and stability among developed porous materials. In this work, two new POPs, i.e., HCCP-P5-1 and HCCP-P5-2 were rationally designed and constructed by linked with macrocyclic pillar[5]arene as the monomer and hexachlorophosphate as the core via a macrocycle-to-framework strategy. Both pillar[5]arene-containing POPs exhibited high uranium adsorption capacity compared with previously reported macrocycle-free counterparts. The isothermal adsorption curves and kinetic studies showed that the adsorption of POPs on uranium was consistent with the Langmuir model and the pseudo-second-order kinetic model. Especially, HCCP-P5-1 has reached 537.81 mg/g, which is greater than most POPs that have been reported. Meanwhile, the comparison between both HCCP-P5-1 and HCCP-P5-2 can illustrate that the adsorption capacity and stability could be adjusted by the monomer ratio. This work provides a new idea for the design and construction of uranium adsorbents from macrocycle-derived POPs.

Ned Seeman and the prediction of amino acid-basepair motifs mediating protein-nucleic acid recognition.

Fifty years ago, the first atomic-resolution structure of a nucleic acid double helix, the mini-duplex (ApU)2, revealed details of basepair geometry, stacking, sugar conformation, and backbone torsion angles, thereby superseding earlier models based on x-ray fiber diffraction, including the original DNA double helix proposed by Watson and Crick. Just 3 years later, in 1976, Ned Seeman, John Rosenberg, and Alex Rich leapt from their structures of mini-duplexes and H-bonding motifs between bases in small-molecule structures and transfer RNA to predicting how proteins could sequence specifically recognize double helix nucleic acids. They proposed interactions between amino acid side chains and nucleobases mediated by two hydrogen bonds in the major or minor grooves. One of these, the arginine-guanine pair, emerged as the most favored amino acid-base interaction in experimental structures of protein-nucleic acid complexes determined since 1986. In this brief review we revisit the pioneering work by Seeman et al. and discuss the importance of the arginine-guanine pairing motif.

The Association between Dietary Protein Intake and the Risk of Pancreatic Cancer: Evidence from 14 Publications.

Many studies have been published to assess the association about dietary protein intake on the risk of pancreatic cancer, but with inconsistent result. This meta-analysis aimed to evaluate whether protein intake could affect the risk of pancreatic cancer. A systematic literature search was performed in PubMed, EMBASE and Web of Science up to October 1, 2019. Pooled relative risks (RR) and 95% confidence intervals (CI) were calculated using a random-effect model. A total of 14 studies (12 case-control studies and two cohort studies) were included. Overall, total protein intake had no significant association on the risk of pancreatic cancer (RR = 1.02, 95%CI= 0.85-1.22, I2=45.7%). Subgroup analyses showed such relationships were almost not influenced by study design and geographic location. Interestingly, when we performed the subgroup analysis by protein type, the opposite association was found in animal protein intake (RR = 1.37, 95%CI= 0.93-2.01) and vegetable protein intake (RR = 0.78, 95%CI= 0.54-1.14), although these two groups were not statistically significant. In conclusion, this meta-analysis indicated that dietary total protein intake may be not associated with the risk of pancreatic cancer. However, protein type may be affecting the result which was found from our research. Therefore, studies with detailed information, especially protein type, are warranted to further confirm these findings.

Self-Assembling Peptide EAK16 and RADA16 Nanofiber Scaffold Hydrogel.

Short peptides are ubiquitous in nature. They are found as hormones, pheromones, antibacterial and antifungal agents in innate immunity systems, toxins, and pesticides. But no one seriously considered that peptides could be useful as scaffold hydrogel materials. There has been a significant change since 1990 after the discovery of an ionic self-complementary peptide as a very interesting repeating segment in a yeast protein. It is now recognized that self-assembling peptides made from 20 natural amino acids have real material properties. Currently, many diverse applications have been developed from these simple and designer self-assembling peptide scaffold hydrogels and are commercially available. Examples include: (1) real 3D tissue cell cultures of diverse tissue cells and various stem cells, (2) reparative and regenerative medicine as well as tissue engineering, (3) 3D tissue printing, (4) sustained releases of small molecules, growth factors, and monoclonal antibodies, and (5) accelerated wound healings of skin and diabetic ulcers as well as instant hemostatic applications in surgery. Self-assembling peptide nanobiotechnology will likely continue to expand in many directions in the coming years.