Exploring the state- and allele-specific conformational landscapes of Ras: understanding their respective druggabilities.

Recent advances in direct inhibition of Ras benefit from the protein's intrinsic dynamic nature that derives therapeutically vulnerable conformers bearing transiently formed cryptic pockets. Hotspot mutants of Ras are major tumor drivers and are hyperactivated in cells at variable levels, which may require allele-specific strategies for effective targeting. However, it remains unclear how the prevalent oncogenic mutations and activation states perturb the free energy landscape governing the protein dynamics and druggability. Here we characterized the nucleotide state- and allele-dependent alterations of Ras conformational dynamics using a combined NMR experimental and computational approach and constructed quantitative ensembles revealing the conservation of the cryptic SI/II-P and SII-P pockets in different states and alleles. Highly local but critical conformational reorganizations that undermine the SII-P accessibility to residue 12 have been identified as a common mechanism resulting in the low reactivities of Ras·GTP as well as Ras(G12D)·GDP with covalent SII-P inhibitors. Our results strongly support the conformational selection scenario for interactions between Ras and the previously reported binders and offer insights for the future development of state- and allele-specific, as well as pan-Ras, inhibitors.

Broadly resistant HIV-1 against CD4-binding site neutralizing antibodies.

Recently identified broadly neutralizing antibodies (bnAbs) show great potential for clinical interventions against HIV-1 infection. However, resistant strains may impose substantial challenges. Here, we report on the identification and characterization of a panel of HIV-1 strains with broad and potent resistance against a large number of bnAbs, particularly those targeting the CD4-binding site (CD4bs). Site-directed mutagenesis revealed that several key epitope mutations facilitate resistance and are located in the inner domain, loop D, and ß23/loop V5/ß24 of HIV-1 gp120. The resistance is largely correlated with binding affinity of antibodies to the envelope trimers expressed on the cell surface. Our results therefore demonstrate the existence of broadly resistant HIV-1 strains against CD4bs neutralizing antibodies. Treatment strategies based on the CD4bs bnAbs must overcome such resistance to achieve optimal clinical outcomes.

An enriched simulation environment for evaluation of closed-loop anesthesia.

To simulate and evaluate the administration of anesthetic agents in the clinical setting, many pharmacology models have been proposed and validated, which play important roles for in silico testing of closed-loop control methods. However, to the authors' best knowledge, there is no anesthesia simulator incorporating closed-loop feedback control of anesthetic agent administration freely available and accessible to the public. Consequently, many necessary but time consuming procedures, such as selecting models from the available literatures and establishing new simulator algorithms, will be repeated by different researchers who intend to explore a novel control algorithm for closed-loop anesthesia. To address this issue, an enriched anesthesia simulator was devised in our laboratory and made freely available to the anesthesia community. This simulator was built by using MATLAB(®) (The MathWorks, Natick, MA). The GUI technology embedded in MATLAB was chosen as the tool to develop a human-machine interface. This simulator includes four types of anesthetic models, and all have been wildly used in closed-loop anesthesia studies. For each type of model, 24 virtual patients were created with significant diversity. In addition, the platform also provides a model identification module and a control method library. For the model identification module, the least square method and particle swarm optimization were presented. In the control method library, a proportional-integral-derivative control and a model predictive control were provided. Both the model identification module and the control method library are extensive and readily accessible for users to add user-defined functions. This simulator could be a benchmark-testing platform for closed-loop control of anesthesia, which is of great value and has significant development potential. For convenience, this simulator is termed as Wang's Simulator, which can be downloaded from http://www.AutomMed.org .

Combined Hydroxyethyl Starch Luteolin Nanocrystals for Effective Anti-Hyperuricemia Effect in Mice Model.

Introduction: Although flavonoid compounds exhibit various pharmacological activities, their clinical applications are restricted by low oral bioavailability owing to their poor solubility. Nanocrystals (NCs) represent an excellent strategy for enhancing the oral bioavailability of flavonoids. Hydroxyethyl starch (HES), a biomaterial compound used as a plasma expander, could be an ideal stabilizer material for preparing flavonoid NCs. Methods: HES was used to stabilize flavonoid nanocrystals (NCs), using luteolin (LUT) as a model drug. After full characterization, the freeze-drying and storage stability, solubility, intestinal absorption, pharmacokinetics, and in vivo anti-hyperuricemic effect of the optimized HES-stabilized LUT NCs (LUT-HES NCs) were investigated. Results: Uniformed LUT-HES NCs were prepared with mean particle size of 191.1±16.8 nm, zeta potential of about -23 mV, drug encapsulation efficiency of 98.52 ± 1.01%, and drug loading of 49.26 ± 0.50%. The freeze-dried LUT-HES NCs powder showed good re-dispersibility and storage stability for 9 months. Notably, compared with the coarse drug, LUT-HES NCs exhibited improved saturation solubility (7.49 times), increased drug dissolution rate, enhanced Caco-2 cellular uptake (2.78 times) and oral bioavailability (Fr=355.7%). Pharmacodynamic studies showed that LUT-HES NCs remarkably lowered serum uric acid levels by 69.93% and ameliorated renal damage in hyperuricemic mice. Conclusion: HES is a potential stabilizer for poorly soluble flavonoid NCs and provides a promising strategy for the clinical application of these compounds. LUT-HES NCs may be an alternative or complementary strategy for hyperuricemia treatment.

Causal Relationship between Immune Cells and Gynecological Cancers through Bidirectional and Multivariable Mendelian Randomization Analyses.

Background: Evidence suggests potential associations between gynecological malignancies and various immune cell chemicals and systems. However, establishing a causal relationship remains uncertain. Methods: This work employed Wald ratio for one single-nucleotide polymorphism (SNP) or the inverse-variance weighted method (IVW) for multiple SNPs to conduct bidirectional two-sample Mendelian randomization (MR) analysis by utilizing genome-wide association study (GWAS) data. We employed supplementary methods, including MR-Egger and weighted median methods, to detect and correct for the influence of horizontal pleiotropy. In addition, we also use colocalization analysis for further validation. Results: In IVW analysis, increases in relative count of circulating CD11c+ HLA-DR++ conventional dendritic cells (cDC) were associated with an elevated risk of breast cancer (OR [95% CI], 1.1295 [1.0632-1.2000], P = 8.044 × 10-5), while elevated levels of HLA-DR on plasmacytoid dendritic cells (DC) and HLA-DR on DC were protective against breast cancer. In addition, actual count of CD39+ resting Treg AC was also shown to be causally associated with the development of ovarian cancer, whereas a high relative count of CD28+ CD45RA- CD8+ T cells reduced the risk of cervical cancer. Sensitivity analysis revealed almost no evidence of bias in the current study. Multivariable MR (MVMR) analyses further confirmed a direct impact of the CD11c+ HLA-DR++ cDC immune phenotype on breast cancer. Colocalization analysis showed the lead SNP, rs780094, suggesting HLA-DR GWAS shared a common genetic mechanism with breast cancer. Conclusions: The MR study identified significant causal relationships between multiple immunophenotypes and breast cancer, aiming to provide clinicians with some reference for cancer prediction and explore further potential associations between immune phenotypes and gynecologic tumors.

Multimodal Autonomous Locomotion of Liquid Crystal Elastomer Soft Robot.

Self-oscillation phenomena observed in nature serve as extraordinary inspiration for designing synthetic autonomous moving systems. Converting self-oscillation into designable self-sustained locomotion can lead to a new generation of soft robots that require minimal/no external control. However, such locomotion is typically constrained to a single mode dictated by the constant surrounding environment. In this study, a liquid crystal elastomer (LCE) robot capable of achieving self-sustained multimodal locomotion, with the specific motion mode being controlled via substrate adhesion or remote light stimulation is presented. Specifically, the LCE is mechanically trained to undergo repeated snapping actions to ensure its self-sustained rolling motion in a constant gradient thermal field atop a hotplate. By further fine-tuning the substrate adhesion, the LCE robot exhibits reversible transitions between rolling and jumping modes. In addition, the rolling motion can be manipulated in real time through light stimulation to perform other diverse motions including turning, decelerating, stopping, backing up, and steering around complex obstacles. The principle of introducing an on-demand gate control offers a new venue for designing future autonomous soft robots.

Photoswitchable optoelectronic properties of 2D MoSe2/diarylethene hybrid structures.

The ability to modulate optical and electrical properties of two-dimensional (2D) semiconductors has sparked considerable interest in transition metal dichalcogenides (TMDs). Herein, we introduce a facile strategy for modulating optoelectronic properties of monolayer MoSe2 with external light. Photochromic diarylethene (DAE) molecules formed a 2-nm-thick uniform layer on MoSe2, switching between its closed- and open-form isomers under UV and visible irradiation, respectively. We have discovered that the closed DAE conformation under UV has its lowest unoccupied molecular orbital energy level lower than the conduction band minimum of MoSe2, which facilitates photoinduced charge separation at the hybrid interface and quenches photoluminescence (PL) from monolayer flakes. In contrast, open isomers under visible light prevent photoexcited electron transfer from MoSe2 to DAE, thus retaining PL emission properties. Alternating UV and visible light repeatedly show a dynamic modulation of optoelectronic signatures of MoSe2. Conductive atomic force microscopy and Kelvin probe force microscopy also reveal an increase in conductivity and work function of MoSe2/DAE with photoswitched closed-form DAE. These results may open new opportunities for designing new phototransistors and other 2D optoelectronic devices.

Advances in Two-Dimensional Magnetic Semiconductors via Substitutional Doping of Transition Metal Dichalcogenides.

Transition metal dichalcogenides (TMDs) are two-dimensional (2D) materials with remarkable electrical, optical, and chemical properties. One promising strategy to tailor the properties of TMDs is to create alloys through a dopant-induced modification. Dopants can introduce additional states within the bandgap of TMDs, leading to changes in their optical, electronic, and magnetic properties. This paper overviews chemical vapor deposition (CVD) methods to introduce dopants into TMD monolayers, and discusses the advantages, limitations, and their impacts on the structural, electrical, optical, and magnetic properties of substitutionally doped TMDs. The dopants in TMDs modify the density and type of carriers in the material, thereby influencing the optical properties of the materials. The magnetic moment and circular dichroism in magnetic TMDs are also strongly affected by doping, which enhances the magnetic signal in the material. Finally, we highlight the different doping-induced magnetic properties of TMDs, including superexchange-induced ferromagnetism and valley Zeeman shift. Overall, this review paper provides a comprehensive summary of magnetic TMDs synthesized via CVD, which can guide future research on doped TMDs for various applications, such as spintronics, optoelectronics, and magnetic memory devices.

Comparative Study of the Preparation of High-Molecular-Weight Fibroin by Degumming Silk with Several Neutral Proteases.

Removing sericin from the periphery of silk without damage to silk fibroin (SF) to obtain high-molecular-weight SF is a major challenge in the field of SF-based biomaterials. In this study, four neutral proteases, subtilisin, trypsin, bromelain and papain, were used to degum silk, and the degumming efficiency of the proteases and their influence on the molecular weight (MW) of regenerated silk fibroin were studied. The results indicated that all four neutral proteases could remove sericin from silk almost completely, and they caused less damage to SF fibers than Na2CO3 degumming did. The degumming efficiency of trypsin and papain was strong, but they caused relatively high damage to SF, whereas bromelain caused the least damage. The results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis, gel permeation chromatography and shear viscosity showed that the MWs of regenerated SF derived from neutral protease degumming were significantly higher than that of SF derived from Na2CO3 degumming. The MW of regenerated SF derived from bromelain degumming was the highest, while the MWs of regenerated SF derived from papain and trypsin degumming were relatively low. This study provides an efficient and environmentally friendly biological degumming method for obtaining high-molecular-weight silk fibroin.

Silk Fibroin-Modified Liposome/Gene Editing System Knocks out the PLK1 Gene to Suppress the Growth of Lung Cancer Cells.

Polo-like protein kinase 1 (PLK1) plays a key role in lung cancer cell mitosis. The knockout of PLK1 gene by the CRISPR-Cas9 system can effectively inhibit the proliferation of tumor cells, but there is no suitable vector for in vivo delivery. In this study, CRISPR-Cas9 gene knockout plasmids encoding sgRNA, Cas9 and green fluorescent protein were constructed. Then, the plasmids were packaged with liposome (Lip) and cholesterol-modified Antheraea pernyi silk fibroin (CASF) to obtain the CASF/Lip/pDNA ternary complex. The CASF/Lip/pDNA complex was transfected into lung cancer cells A549 to investigate the transfection efficiency, the PLK1 gene knockout effect and the inhibitory effect on lung cancer cells. The results showed that the transfection efficiency of the CASF/Lip/pDNA complex was significantly higher than that of the Lip/pDNA binary complex, and the expression of PLK1 in cells transfected with CASF/Lip/pDNA complexes was significantly lower than that in cells transfected with Lip/pDNA complexes. The CASF/Lip/pDNA complex significantly increased the apoptosis rate and decreased the proliferation activity of lung cancer cells compared with Lip/pDNA complexes. The cytotoxicity of the complexes was evaluated by coculture with the human bronchial epithelial cells BEAS2B. The results showed that CASF/Lip/pDNA complexes exhibited lower cytotoxicity than Lip/pDNA complexes. The fibroin-modified liposome/PLK1 gene knockout system not only effectively inhibited the growth of lung cancer cells but also showed no obvious toxicity to normal cells, showing potential for clinical application in lung cancer therapy.

Preparation and Properties of Antibacterial Silk Fibroin Scaffolds.

The development of a wound dressing with both antibacterial and healing-guiding functions is a major concern in the treatment of open and infected wounds. In this study, poly(hexamethylene biguanide) hydrochloride (PHMB) was loaded into a 3D silk fibroin (SF) scaffold based on electrostatic interactions between PHMB and SF, and PHMB/SF hybrid scaffolds were prepared via freeze-drying. The effects of the PHMB/SF ratio on the antibacterial activity and cytocompatibility of the hybrid scaffold were investigated. The results of an agar disc diffusion test and a bacteriostasis rate examination showed that when the mass ratio of PHMB/SF was greater than 1/100, the scaffold exhibited obvious antibacterial activity against E. coli and S. aureus. L-929 cells were encapsulated in the PHMB/SF scaffolds and cultured in vitro. SEM, laser scanning confocal microscopy, and CCK-8 assay results demonstrated that hybrid scaffolds with a PHMB/SF ratio of less than 2/100 significantly promoted cell adhesion, spreading, and proliferation. In conclusion, a hybrid scaffold with a PHMB/SF ratio of approximately 2/100 not only effectively inhibited bacterial reproduction but also showed good cytocompatibility and is expected to be usable as a functional antibacterial dressing for wound repair.

Preclinical characterization of amubarvimab and romlusevimab, a pair of non-competing neutralizing monoclonal antibody cocktail, against SARS-CoV-2.

Monoclonal antibodies (mAbs) targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein have demonstrated clinical efficacy in preventing or treating coronavirus disease 2019 (COVID-19), resulting in the emergency use authorization (EUA) for several SARS-CoV-2 targeting mAb by regulatory authority. However, the continuous virus evolution requires diverse mAb options to combat variants. Here we describe two fully human mAbs, amubarvimab (BRII-196) and romlusevimab (BRII-198) that bind to non-competing epitopes on the receptor binding domain (RBD) of spike protein and effectively neutralize SARS-CoV-2 variants. A YTE modification was introduced to the fragment crystallizable (Fc) region of both mAbs to prolong serum half-life and reduce effector function. The amubarvimab and romlusevimab combination retained activity against most mutations associated with reduced susceptibility to previously authorized mAbs and against variants containing amino acid substitutions in their epitope regions. Consistently, the combination of amubarvimab and romlusevimab effectively neutralized a wide range of viruses including most variants of concern and interest in vitro. In a Syrian golden hamster model of SARS-CoV-2 infection, animals receiving combination of amubarvimab and romlusevimab either pre- or post-infection demonstrated less weight loss, significantly decreased viral load in the lungs, and reduced lung pathology compared to controls. These preclinical findings support their development as an antibody cocktail therapeutic option against COVID-19 in the clinic.

Ultrafast Digital Fabrication of Designable Architectured Liquid Crystalline Elastomer.

The muscle-like activities of liquid crystalline elastomers (LCEs) offer great potential for designing future soft machines. Their motion complexity, however, relies on inflexible and cumbersome mesogen alignment techniques. Here, a digital photocuring method for ultrafast template-free fabrication of LCE artificial muscles capable of designable complex motions is reported. This method utilizes the intrinsic light attenuation in the through-plane direction to create mesogen alignment for reversible bending action. To turn this simple actuation into complex motions, the principles of muscles are borrowed which realize diverse motions through the cooperative actions of otherwise simple contraction/expansion of individual muscle bundles. Specifically, the spatiotemporal digital light is utilized to design LCE architectures composed of strategically arranged bending modules. As such, LCE capable of highly designable motions can be fabricated within 25 s light curing without employing any physical alignment templates, which offers an attractive option toward designing functionally diverse soft machines.

A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants.

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge and spread around the world, antibodies and vaccines to confer broad and potent neutralizing activity are urgently needed. Through the isolation and characterization of monoclonal antibodies (mAbs) from individuals infected with SARS-CoV-2, we identified one antibody, P36-5D2, capable of neutralizing the major SARS-CoV-2 variants of concern. Crystal and electron cryo-microscopy (cryo-EM) structure analyses revealed that P36-5D2 targeted to a conserved epitope on the receptor-binding domain of the spike protein, withstanding the three key mutations-K417N, E484K, and N501Y-found in the variants that are responsible for escape from many potent neutralizing mAbs, including some already approved for emergency use authorization (EUA). A single intraperitoneal (IP) injection of P36-5D2 as a prophylactic treatment completely protected animals from challenge of infectious SARS-CoV-2 Alpha and Beta. Treated animals manifested normal body weight and were devoid of infection-associated death up to 14 days. A substantial decrease of the infectious virus in the lungs and brain, as well as reduced lung pathology, was found in these animals compared to the controls. Thus, P36-5D2 represents a new and desirable human antibody against the current and emerging SARS-CoV-2 variants.

Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2.

Neutralizing antibodies (nAbs) to SARS-CoV-2 hold powerful potentials for clinical interventions against COVID-19 disease. However, their common genetic and biologic features remain elusive. Here we interrogate a total of 165 antibodies from eight COVID-19 patients, and find that potent nAbs from different patients have disproportionally high representation of IGHV3-53/3-66 usage, and therefore termed as public antibodies. Crystal structural comparison of these antibodies reveals they share similar angle of approach to RBD, overlap in buried surface and binding residues on RBD, and have substantial spatial clash with receptor angiotensin-converting enzyme-2 (ACE2) in binding to RBD. Site-directed mutagenesis confirms these common binding features although some minor differences are found. One representative antibody, P5A-3C8, demonstrates extraordinarily protective efficacy in a golden Syrian hamster model against SARS-CoV-2 infection. However, virus escape analysis identifies a single natural mutation in RBD, namely K417N found in B.1.351 variant from South Africa, abolished the neutralizing activity of these public antibodies. The discovery of public antibodies and shared escape mutation highlight the intricate relationship between antibody response and SARS-CoV-2, and provide critical reference for the development of antibody and vaccine strategies to overcome the antigenic variation of SARS-CoV-2.

A pathogen-like antigen-based vaccine confers immune protection against SARS-CoV-2 in non-human primates.

Activation of nucleic acid sensing Toll-like receptors (TLRs) in B cells is involved in antiviral responses by promoting B cell activation and germinal center responses. In order to take advantage of this natural pathway for vaccine development, synthetic pathogen-like antigens (PLAs) constructed of multivalent antigens with encapsulated TLR ligands can be used to activate B cell antigen receptors and TLRs in a synergistic manner. Here we report a PLA-based coronavirus disease 2019 (COVID-19) vaccine candidate designed by combining a phage-derived virus-like particle carrying bacterial RNA as TLR ligands with the receptor-binding domain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S protein as the target antigen. This PLA-based vaccine candidate induces robust neutralizing antibodies in both mice and non-human primates (NHPs). Using a NHP infection model, we demonstrate that the viral clearance is accelerated in vaccinated animals. In addition, the PLA-based vaccine induces a T helper 1 (Th1)-oriented response and a durable memory, supporting its potential for further clinical development.