A New Advanced Approach: Design and Screening of Affinity Peptide Ligands Using Computer Simulation Techniques.

Peptides acquire target affinity based on the combination of residues in their sequences and the conformation formed by their flexible folding, an ability that makes them very attractive biomaterials in therapeutic, diagnostic, and assay fields. With the development of computer technology, computer-aided design and screening of affinity peptides has become a more efficient and faster method. This review summarizes successful cases of computer-aided design and screening of affinity peptide ligands in recent years and lists the computer programs and online servers used in the process. In particular, the characteristics of different design and screening methods are summarized and categorized to help researchers choose between different methods. In addition, experimentally validated sequences are listed, and their applications are described, providing directions for the future development and application of computational peptide screening and design.

An AuNPs-based electrochemical aptasensor for the detection of 25-hydroxy vitamin D3.

Vitamin D3 (VD3) is the main form of vitamin D and an essential nutrient for maintaining human life. Currently, traditional methods for detecting 25-hydroxyvitamin D3(25(OH)D3) are complex and expensive. In this study, we constructed an accurate, sensitive, simple, and cost-effective label-free biosensor based on an aptamer for the detection of 25(OH)D3. The aptamer-modified sulfhydryl adopted self-assembly as a way to stably immobilize at the glassy carbon electrode (GCE) surface modified by gold nanoparticles (AuNPs). Upon 25(OH)D3 binding to the aptamer, the complexes inhibit electron transfer at the electrode surface, leading to reduced [Fe(CN)6]3-/4- redox peak current. Consequently, the quantity of 25(OH)D3 that interacts with the electrode-bound aptamer correlates with the observed electric current response values. The Aptamer/AuNPs/GCE aptasensor achieved direct and highly sensitive detection of 25(OH)D3 over a wide concentration range (1.0-1000 nM), with a limit of detection of 1.0 nM. At the same time, other molecules with a similar structure, such as 25(OH)D2, Vitamin D3, and Vitamin D2, had lower response interference than 25(OH)D3. Therefore, this biosensor has great potential to become a portable diagnostic device for 25(OH)D3.

Advances in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers.

Peptides and peptide aptamers have emerged as promising molecules for a wide range of biomedical applications due to their unique properties and versatile functionalities. The screening strategies for identifying peptides and peptide aptamers with desired properties are discussed, including high-throughput screening, display screening technology, and in silico design approaches. The synthesis methods for the efficient production of peptides and peptide aptamers, such as solid-phase peptide synthesis and biosynthesis technology, are described, along with their advantages and limitations. Moreover, various modification techniques are explored to enhance the stability, specificity, and pharmacokinetic properties of peptides and peptide aptamers. This includes chemical modifications, enzymatic modifications, biomodifications, genetic engineering modifications, and physical modifications. Furthermore, the review highlights the diverse biomedical applications of peptides and peptide aptamers, including targeted drug delivery, diagnostics, and therapeutic. This review provides valuable insights into the advancements in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. A comprehensive understanding of these aspects will aid researchers in the development of novel peptide-based therapeutics and diagnostic tools for various biomedical challenges.

Non-immobilized GO-SELEX screening of aptamers against cyclosporine A and its application in a AuNPs colorimetric aptasensor.

Cyclosporine A (CsA) is an immunosuppressive drug that is widely used in clinical practice. Due to its narrow therapeutic window and the significant differences between individuals, the therapeutic drug monitoring (TDM) of CsA is required to ensure patient safety. In this study, we screened a novel aptamer, named CsA7, which could specifically recognize CsA, and developed a AuNPs colorimetric aptasensor for the rapid detection of CsA. In the SELEX process, after eight rounds of screening, four aptamer candidate sequences were obtained and subjected to binding affinity and specificity tests. Finally, the CsA7 aptamer (Kd = 41.21 ng mL-1) showed the highest affinity for CsA. Based on CsA7, we also developed a AuNPs colorimetric aptasensor, which had a detection limit of 0.1 ng mL-1 and a quantitative range of 0.1-500 ng mL-1 and showed good selectivity among CsA and its analogs. According to the results, the CsA7 aptamer provides an alternative recognition molecule to the antibody in biosensor applications and shows great potential for the rapid and convenient detection of CsA.

Improving ADMET Prediction Accuracy for Candidate Drugs: Factors to Consider in QSPR Modeling Approaches.

Quantitative Structure-Property Relationship (QSPR) employs mathematical and statistical methods to reveal quantitative correlations between the pharmacokinetics of compounds and their molecular structures, as well as their physical and chemical properties. QSPR models have been widely applied in the prediction of drug absorption, distribution, metabolism, excretion, and toxicity (ADMET). However, the accuracy of QSPR models for predicting drug ADMET properties still needs improvement. Therefore, this paper comprehensively reviews the tools employed in various stages of QSPR predictions for drug ADMET. It summarizes commonly used approaches to building QSPR models, systematically analyzing the advantages and limitations of each modeling method to ensure their judicious application. We provide an overview of recent advancements in the application of QSPR models for predicting drug ADMET properties. Furthermore, this review explores the inherent challenges in QSPR modeling while also proposing a range of considerations aimed at enhancing model prediction accuracy. The objective is to enhance the predictive capabilities of QSPR models in the field of drug development and provide valuable reference and guidance for researchers in this domain.

Recent Advances in Computer-aided Virtual Screening and Docking Optimization for Aptamer.

Aptamers, as artificially synthesized short nucleotide sequences, have been widely used in protein analysis, gene engineering, and molecular diagnostics. Currently, the screening process of aptamers still relies on the traditional SELEX process, which is cumbersome and complex. Moreover, the success rate of aptamer screening through the SELEX process is not high, which has become a major challenge. In recent years, the development of computers has facilitated virtual screening, which can greatly accelerate the screening process of aptamers through computer-assisted screening. However, the accuracy and precision of current virtual screening software on the market vary. Therefore, this work summarizes the docking characteristics of four mainstream molecular docking software programs, including Auto dock, Auto dock Vina, MOE, and hex Dock, in recent years. Moreover, the accuracy and prediction performance of these four molecular docking software programs for aptamer docking based on experimental data is also evaluated. This will guide researchers in the selection of molecular docking software. Additionally, this review provides a detailed overview of the application of computer-aided virtual screening in aptamer screening, thus providing a direction for future development in this field.

A label-free fluorescent aptamer sensor for testosterone based on SYBR Green I.

Testosterone is a steroid hormone that plays an indispensable role in the normal metabolism of organisms. However, exogenous testosterone, even as low as nmol L-1, will harm the human body due to accumulation. In this study, we developed an unlabeled fluorescent sensor for testosterone based on SYBR Green I. SYBR Green I is a fluorescent dye that can be embedded into the G-quadruplex of the testosterone aptamer T5. The fluorescence quenching effect is utilized to achieve quantitative detection, which occurs by the competition between testosterone and SYBR Green I for the T5 aptamer binding sites. In this work, we optimized the detection conditions to make the fluorescent sensor more sensitive and verify the specificity, linear range, and detection ability in the buffer and real water samples. The sensor's LOD and LOQ values were 0.27 nmol L-1 and 0.91 nmol L-1, respectively, while the detection range was linear from 0.91 nmol L-1 to 2000 nmol L-1. According to the results, the sensor shows high specificity and good performance even in real sample detection such as tap water and river water, providing an alternative method for the quantitative detection of testosterone in the environment, which is more convenient and efficient.

Fusobacterium nucleatum, the communication with colorectal cancer.

Colorectal cancer (CRC) is the fourth most common cancer in 2018 with poor prognosis. Fusobacterium nucleatum (F.n), an anaerobe, is found to be enriched in both stools and tumor tissues of CRC patients. As surveys show, tumor initiates before the collection of F.n. In return, F.n helps cancer cells to build up tumor microenvironment and benefit for their chemo-resistant. The elements constituted the tumor environment, including neutrophils, macrophages and lymphocytes, contribute to the existing of tumor cells respectively. However, the integrated and interactive roles of those elements are poorly investigated. The intracellular molecular alteration MSI is a result of F.n infection and the microbiology-molecular pathological epidemiology (MPE) has become a new trend to analysis F.n and tumorigenesis. Chemoresistance of tumor cells is also affected by F.n induced microenvironment, or F.n achieves it directly. Finally, F.n could be a biomarker of CRC. All in all, our review will lay a foundation for the therapy of CRC through the interference of F.n and perspective to follow-up studies.

[Influence of auricular point sticking on incidence of nausea and vomiting and analgesia effect after gynecological laparoscopy].

OBJECTIVE: To observe the influence of auricular point sticking on incidence of nausea and vomiting and analgesia effect after gynecological laparoscopy, and provide evidence for clinical application of auricular point sticking. METHODS: One hundred and twenty cases of selective gynecological laparoscopy under general anesthesia were randomly divided into an auricular point sticking group and a placebo group, 60 cases in each group. In the auricular point sticking group, the auricular point sticking with vaccaria seeds was applied at Shenmen (TF 4), Wei (CO 4) and Jiaogan (AH 6a) before the operation and 1, 5, 9, 23 h after the operation, which were pressed 5 min each point each time. The two ears were proceeded at the same time. In the placebo group, the same point selection, sticking paste was used as the auricular point sticking group, but no sticking or pressing with vaccaria seeds was adopted. The incidence of nausea and vomiting, the usage rate of tropisetron and morphine within 24 hours of the operation, as well as the score of visual analogue scale (VAS) and other adverse reactions at 2, 6, 10, 24 h after the operation were observed respectively. RESULTS: Compared with the placebo group, the incidence of nausea and vomiting [31.7% (19/60), 16.7% (10/60) vs 58.3% (35/60), 35.0% (21/60)], the usage rate of tropisetron [21.7% (13/60) vs 48.3% (29/60)] and morphine [18.3% (11/60) vs 38.3% (23/60)], the VAS scores at all different time points in the auricular point sticking group were all decreased (all P < 0.05), and no adverse reaction was observed. CONCLUSION: The auricular point sticking could significantly decrease the incidence of nausea and vomiting in patients of gynecological laparoscopy and has positive analgesic effect.