Amino acids functionalized graphene oxide for enhanced hydrophilicity and antifouling property of poly(vinylidene fluoride) membranes

LLM4THP: a computing tool to identify tumor homing peptides by molecular and sequence representation of large language model based on two-layer ensemble model strategy

Tumor homing peptides (THPs) have a distinctive capacity to specifically attach to tumor cells, providing a promising approach for targeted cancer treatment and detection. Although THPs have the potential for significant impact, their detection by conventional methods is both time-consuming and expensive. To tackle this issue, we provide LLM4THP, an innovative computational approach that utilizes large language models (LLMs) to quickly and effectively detect THPs. LLM4THP utilizes two protein LLMs, ESM2 and Prot_T5_XL_UniRef50, to encode peptide sequences. This allows for the capture of complex patterns and relationships within the peptide data. In addition, we utilize inherent sequence characteristics such as Amino Acid Composition (AAC), Pseudo Amino Acid Composition (PAAC), Amphiphilic Pseudo Amino Acid Composition (APAAC), and Composition, Transition, and Distribution (CTD) to improve the representation of peptides. The RDKitDescriptors feature representation approach transforms peptide sequences into molecular objects and computes chemical characteristics, resulting in enhanced THP identification. The LLM4THP ensemble strategy incorporates various features into a two-layer learning architecture. The first layer consists of LightGBM, XGBoost, Random Forest, and Extremely Randomized Trees, which generate a set of meta results. The second layer utilizes Logistic Regression to further refine the identification of sequences as either THP or non-THP. LLM4THP exhibits exceptional performance compared to the most advanced methods, showcasing enhancements in accuracy, Matthew's correlation coefficient, F1 score, area under the curve, and average precision. The source code and dataset can be accessed at the following URL: https://github.com/abcair/LLM4THP.

Biocompatibility of graphene oxide nanosheets functionalized with various amino acids towards mesenchymal stem cells

Graphene and its derivatives have gained popularity due to their numerous applications in various fields, such as biomedicine. Recent reports have revealed the severe toxic effects of these nanomaterials on cells and organs. In general, the chemical composition and surface chemistry of nanomaterials affect their biocompatibility. Therefore, the purpose of the present study was to evaluate the cytotoxicity and genotoxicity of graphene oxide (GO) synthesized by Hummer's method and functionalized by different amino acids such as lysine, methionine, aspartate, and tyrosine. The obtained nanosheets were identified by FT-IR, EDX, RAMAN, FE-SEM, and DLS techniques. In addition, trypan blue and Alamar blue methods were used to assess the cytotoxicity of mesenchymal stem cells extracted from human embryonic umbilical cord Wharton jelly (WJ-MSCs). The annexin V staining procedure was used to determine apoptotic and necrotic death. In addition, COMET and karyotyping techniques were used to assess the extent of DNA and chromosome damage. The results of the cytotoxicity assay showed that amino acid modifications significantly reduced the concentration-dependent cytotoxicity of GO to varying degrees. The GO modified with aspartic acid had the lowest cytotoxicity. There was no evidence of chromosomal damage in the karyotyping method, but in the comet assay, the samples modified with tyrosine and lysine showed the greatest DNA damage and rate of apoptosis. Overall, the aspartic acid-modified GO caused the least cellular and genetic damage to WJ-MSCs, implying its superior biomedical applications such as cell therapy and tissue engineering over GO.

Theoretical study of glycine amino acid adsorption on graphene oxide

The non-dissociative and dissociative adsorptions of zwitterionic Gly on graphene oxide (GO) was studied in the framework of DFT using a cluster model approach. In this work, the interaction with an epoxy group of GO basal plane was mainly considered. As a comparison, the non-dissociative and dissociative adsorptions of neutral Gly were also taken into account. The non-dissociative adsorption modes for zwitterionic and neutral Gly conformers show binding energies of 12.2 and 14.4 kcal mol^-1, respectively. These molecules are thought to remain over the GO surface due to attractive noncovalent interactions. Two dissociative adsorption modes, for Z-Gly and N-Gly, show smaller binding energies of 7.2 and 8.4 kcal mol^-1, where the deprotonated species links strongly through a C-O or C-N covalent bond to the GO surface. The results obtained in the present theoretical approach to the glycine/graphene oxide system support the fact that glycine can be attached to epoxy groups of graphene oxide basal planes in addition to the anchoring on edge oxidation groups. In summary, we conclude that glycine can be used as a reducing agent as well as a functionalizer of GO sheets.

Selenium-containing polyurethane with elevated catalytic stability for sustained nitric oxide release

Stable and controllable nitric oxide (NO) release at the physiological level from biomedical materials remains a challenge for NO-based therapy. NO-generating polymers have great potential to achieve this goal because they can catalytically decompose endogenous S-nitrosothiols (RSNOs) into NO. However, the current catalytic surfaces based on such polymers often suffer from loss of catalytic sites, which can influence the stability of NO release in their long-term application. In this work, we proposed a novel strategy to enhance the catalytic stability of NO-catalytic materials by incorporating catalytic sites into the polymer backbone. Selenium-containing polyurethane (PU-Se) was synthesized by using the catalyst 2,2'-diselenodiethanol (SeDO) as the chain extender. A series of PU/PU-Se blend films were prepared to investigate the effect of PU-Se content on the catalytic properties. The blend films exhibited excellent catalytic activity, and also showed outstanding catalytic stability in comparison with PU coated by diselenide/dopamine (PU-PDA-Se). Among these blend films, PU-Se-10 exhibited a stable NO release rate of 5.05 × 10^-10 mol cm^-2 min^-1 after exposure to PBS buffer for 30 days. Moreover, the PU/PU-Se films exhibited decreased platelet activation/adhesion, low hemolysis ratio, excellent biocompatibility, and similar mechanical properties to PU. It is expected that the newly designed PU-Se has great potential in generating stable NO release at the physiological level for the long-term application of blood-contacting medical devices.