Hydrophobic Interaction Chromatography

DOTAD: A Database of Therapeutic Antibody Developability

The development of therapeutic antibodies is an important aspect of new drug discovery pipelines. The assessment of an antibody's developability-its suitability for large-scale production and therapeutic use-is a particularly important step in this process. Given that experimental assays to assess antibody developability in large scale are expensive and time-consuming, computational methods have been a more efficient alternative. However, the antibody research community faces significant challenges due to the scarcity of readily accessible data on antibody developability, which is essential for training and validating computational models. To address this gap, DOTAD (Database Of Therapeutic Antibody Developability) has been built as the first database dedicated exclusively to the curation of therapeutic antibody developability information. DOTAD aggregates all available therapeutic antibody sequence data along with various developability metrics from the scientific literature, offering researchers a robust platform for data storage, retrieval, exploration, and downloading. In addition to serving as a comprehensive repository, DOTAD enhances its utility by integrating a web-based interface that features state-of-the-art tools for the assessment of antibody developability. This ensures that users not only have access to critical data but also have the convenience of analyzing and interpreting this information. The DOTAD database represents a valuable resource for the scientific community, facilitating the advancement of therapeutic antibody research. It is freely accessible at http://i.uestc.edu.cn/DOTAD/ , providing an open data platform that supports the continuous growth and evolution of computational methods in the field of antibody development.

Purification and Quality Control of Recombinant Proteins Expressed in Mammalian Cells: A Practical Review

In the recent years, there has been a rapid development of new technologies and strategies when it comes to protein purification and quality control (QC), but the basic technologies for these processes go back a long way, with many improvements over the past few decades. The purpose of this chapter is to review these approaches, as well as some other topics such as the advantages and disadvantages of various purification methods for intracellular or extracellular proteins, the most effective and widely used genetically engineered affinity tags, solubility-enhancing tags, and specific proteases for removal of nontarget sequences. Affinity chromatography (AC), like Protein A or G resins for the recovery of antibodies or Fc fusion proteins or immobilized metals for the recovery of histidine-tagged proteins, will be discussed along with other conventional chromatography techniques: ion exchange (IEC), hydrophobic exchange (HEC), mixed mode (MMC), size exclusion (SEC), and ultrafiltration (UF) systems. How to select and combine these different technologies for the purification of any given protein and the minimal criteria for QC characterization of the purity, homogeneity, identity, and integrity of the final product will be presented.

Protein Hydrolysate from Underutilized Legumes: Unleashing the Potential for Future Functional Foods

Proteins play a vital role in human development, growth, and overall health. Traditionally, animal-derived proteins were considered the primary source of dietary protein. However, in recent years, there has been a remarkable shift in dietary consumption patterns, with a growing preference for plant-based protein sources. This shift has resulted in a significant increase in the production of plant proteins in the food sector. Consequently, there has been a surge in research exploring various plant sources, particularly wild, and underutilized legumes such as Canavalia, Psophocarpus, Cajanus, Lablab, Phaseolus, and Vigna, due to their exceptional nutraceutical value. This review presents the latest insights into innovative approaches used to extract proteins from underutilized legumes. Furthermore, it highlights the purification of protein hydrolysate using Fast Protein Liquid Chromatography. This review also covers the characterization of purified peptides, including their molecular weight, amino acid composition, and the creation of three-dimensional models based on amino acid sequences. The potential of underutilized legume protein hydrolysates as functional ingredients in the food industry is a key focus of this review. By incorporating these protein sources into food production, we can foster sustainable and healthy practices while minimizing environmental impact. The investigation of underutilized legumes offers exciting possibilities for future research and development in this area, further enhancing the utilization of plant-based protein sources.

1Progress, applications, challenges and prospects of protein purification technology

Protein is one of the most important biological macromolecules in life, which plays a vital role in cell growth, development, movement, heredity, reproduction and other life activities. High quality isolation and purification is an essential step in the study of the structure and function of target proteins. Therefore, the development of protein purification technologies has great theoretical and practical significance in exploring the laws of life activities and guiding production practice. Up to now, there is no forthcoming method to extract any proteins from a complex system, and the field of protein purification still faces significant opportunities and challenges. Conventional protein purification generally includes three steps: pretreatment, rough fractionation, and fine fractionation. Each of the steps will significantly affect the purity, yield and the activity of target proteins. The present review focuses on the principle and process of protein purification, recent advances, and the applications of these technologies in the life and health industry as well as their far-reaching impact, so as to promote the research of protein structure and function, drug development and precision medicine, and bring new insights to researchers in related fields.

Effect of M6A regulators on diagnosis, subtype classification, prognosis and novel therapeutic target development of idiopathic pulmonary fibrosis

Molecular biology studies show that RNA N6-methyladenosine (m6A) modifications may take part in the incidence and development of idiopathic pulmonary fibrosis (IPF). Nonetheless, the roles of m6A regulators in IPF are not fully demonstrated. In this study, 12 significant m6A regulators were filtered out between healthy controls and IPF patients using GSE33566 dataset. Random forest algorithm was used to identify 11 candidate m6A regulators to predict the incidence of IPF. The 11 candidate m6A regulators included leucine-rich PPR motif-containing protein (LRPPRC), methyltransferase-like protein 3, FTO alpha-ketoglutarate dependent dioxygenase (FTO), methyltransferase-like 14/16, zinc finger CCCH domain-containing protein 13, protein virilizer homolog, Cbl proto-oncogene like 1, fragile X messenger ribonucleoprotein 1 and YTH domain containing 1/2. A nomogram model was constructed based on 11 candidate m6A regulators and considered beneficial to IPF patients using decision curve analysis. Consensus clustering method was used to distinctly divide IPF patients into two m6A patterns (clusterA and clusterB) based on 12 significant m6A regulators. M6A scores of all IPF patients were obtained using principal component analysis to quantify the m6A patterns. Patients in clusterB had higher m6A scores than those in clusterA. Furthermore, patients in clusterB were correlated with Th17 and Treg cell infiltration, innate immunity and Th1 immunity, while those in clusterA were correlated with adaptive immunity and Th2 immunity. Patients in clusterB also had higher expressions of mesenchymal markers and regulatory factors of fibrosis but lower expressions of epithelial markers. Lastly and interestingly, two m6A regulators, LRPPRC (p = 0.011) and FTO (p = 0.042), were identified as novel prognostic genes in IPF patients for the first time using an external GSE93606 dataset. Both of them had a positive correlation with a better prognosis and may serve as therapy targets. Thus, we conducted virtual screening to discover potential drugs targeting LRPPRC and FTO in the treatment of IPF. In conclusion, m6A regulators are crucial to the onset, development and prognosis of IPF. Our study on m6A patterns may provide clues for clinical diagnosis, prognosis and targeted therapeutic drugs development for IPF.