Deep mutational scanning of proteins in mammalian cells

Protein mutagenesis is essential for unveiling the molecular mechanisms underlying protein function in health, disease, and evolution. In the past decade, deep mutational scanning methods have evolved to support the functional analysis of nearly all possible single-amino acid changes in a protein of interest. While historically these methods were developed in lower organisms such as E. coli and yeast, recent technological advancements have resulted in the increased use of mammalian cells, particularly for studying proteins involved in human disease. These advancements will aid significantly in the classification and interpretation of variants of unknown significance, which are being discovered at large scale due to the current surge in the use of whole-genome sequencing in clinical contexts. Here, we explore the experimental aspects of deep mutational scanning studies in mammalian cells and report the different methods used in each step of the workflow, ultimately providing a useful guide toward the design of such studies.

Advances in receptor modulation strategies for flexible, efficient, and enhanced antitumor efficacy

Tumor-sensitivity, effective transport, and precise delivery to tumor cells of nano drug delivery systems (NDDs) have been great challenges to cancer therapy in recent years. The conventional targeting approach involves actively installing the corresponding ligand on the nanocarriers, which is prone to recognize the antigen blasts overexpressed on the surface of tumor cells. However, there are some probable limitations for the active tumor-targeting systems in vivo as follows: a. the limited ligand amount of modifications; b. possible steric hindrance, which was likely to prevent ligand-receptor interaction during the delivery process. c. the restrained antigen saturation highly expressed on the cell membrane, will definitely decrease the specificity and often lead to "off-target" effects of NDDs; and d. water insolubility of nanocarriers due to excess of ligands modification. Obviously, any regulation of receptors on surface of tumor cells exerted an important influence on the delivery of targeting systems. Herein, receptor upregulation was mostly desired for enhancing targeted therapy from the cellular level. This technique with the amplification of receptors has the potential to enhance tumor sensitivity towards corresponding ligand-modified nanoparticles, and thereby increasing the effective therapeutic concentration as well as improving the efficacy of chemotherapy. The enhancement of positively expressed receptors on tumor cells and receptor-dependent therapeutic agents or NDDs with an assembled "self-promoting" effect contributes to increasing cell sensitivity to NPs, and will provide a basic platform for clinical therapeutic practice. In this review, we highlight the significance of modulating various receptors on different types of cancer cells for drug delivery and therapeutic benefits.

A Proliferation-Inducing Ligand Regulation in Polymorphonuclear Neutrophils by Panax ginseng

A proliferation-inducing ligand (APRIL) is a member of the tumor necrosis factor superfamily that was first identified as a factor favoring tumorigenesis. APRIL is important fitness and survival factors for B cells and plasma cells in the periphery. Considering this, as well as the quantitative predominance of neutrophils among the peripheral blood leukocytes, we carried out the first study assessing the influence of the transforming growth factor (TGF)-β signaling pathway on APRIL expression in these cells. Furthermore, as the Rb1 ginsenoside is known to exhibit multiple pharmacological activities, we verified if the saponin is capable of modulating the process. The present study shows that TGF-β increased the expression of APRIL and the level of phospho-p38, phospho-Akt(T308), and phospho-Akt(S473) in the cytoplasmic fraction, as well as the expression of Fra1, c-Fos, and c-Jun in the nuclear fraction, of neutrophils. However, exposure of these cells to Rb1 reduced the expression and level of the investigated proteins. No changes were found in the expression of APRIL and the level of p-p38 in the cytoplasmic fraction of neutrophils following the application of Rb1 alone, as well as in the neutrophils incubated first with Rb1 and then with TGF-β, whereas a higher level of phosphorylation was observed for Akt and PI3 kinases in the cells. Moreover, a higher expression of all the studied transcription factors was observed in the nuclear fraction of neutrophils. Based on the observed changes, it may be assumed that the expression of APRIL molecule in TGF-β-induced neutrophils and its regulation by Rb1 are associated with PI3K/AKT signaling pathways and transcription factors Fra-1, Fra-2, c-Jun, and c-Fos. Rb1 appears to be a favorable factor that may be potentially used in the modulation of tumor-promoting APRIL expression.

Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition

Vaccines and immunotherapies depend on the ability of antibodies to sensitively and specifically recognize particular antigens and specific epitopes on those antigens. As such, detailed characterization of antibody-antigen binding provides important information to guide development. Due to the time and expense required, high-resolution structural characterization techniques are typically used sparingly and late in a development process. Here, we show that antibody-antigen binding can be characterized early in a process for whole panels of antibodies by combining experimental and computational analyses of competition between monoclonal antibodies for binding to an antigen. Experimental "epitope binning" of monoclonal antibodies uses high-throughput surface plasmon resonance to reveal which antibodies compete, while a new complementary computational analysis that we call "dock binning" evaluates antibody-antigen docking models to identify why and where they might compete, in terms of possible binding sites on the antigen. Experimental and computational characterization of the identified antigenic hotspots then enables the refinement of the competitors and their associated epitope binding regions on the antigen. While not performed at atomic resolution, this approach allows for the group-level identification of functionally related monoclonal antibodies (i.e., communities) and identification of their general binding regions on the antigen. By leveraging extensive epitope characterization data that can be readily generated both experimentally and computationally, researchers can gain broad insights into the basis for antibody-antigen recognition in wide-ranging vaccine and immunotherapy discovery and development programs.

Informatics and Computational Methods in Natural Product Drug Discovery: A Review and Perspectives

The discovery of new pharmaceutical drugs is one of the preeminent tasks-scientifically, economically, and socially-in biomedical research. Advances in informatics and computational biology have increased productivity at many stages of the drug discovery pipeline. Nevertheless, drug discovery has slowed, largely due to the reliance on small molecules as the primary source of novel hypotheses. Natural products (such as plant metabolites, animal toxins, and immunological components) comprise a vast and diverse source of bioactive compounds, some of which are supported by thousands of years of traditional medicine, and are largely disjoint from the set of small molecules used commonly for discovery. However, natural products possess unique characteristics that distinguish them from traditional small molecule drug candidates, requiring new methods and approaches for assessing their therapeutic potential. In this review, we investigate a number of state-of-the-art techniques in bioinformatics, cheminformatics, and knowledge engineering for data-driven drug discovery from natural products. We focus on methods that aim to bridge the gap between traditional small-molecule drug candidates and different classes of natural products. We also explore the current informatics knowledge gaps and other barriers that need to be overcome to fully leverage these compounds for drug discovery. Finally, we conclude with a "road map" of research priorities that seeks to realize this goal.

A Proliferation Inducing Ligand (APRIL) targeted antibody is a safe and effective treatment of murine IgA nephropathy

IgA nephropathy (IgAN) is the most prevalent primary chronic glomerular disease for which no safe disease-specific therapies currently exist. IgAN is an autoimmune disease involving the production of autoantigenic, aberrantly O-glycosylated IgA1 and ensuing deposition of nephritogenic immune complexes in the kidney. A Proliferation Inducing Ligand (APRIL) has emerged as a key B-cell-modulating factor in this pathogenesis. Using a mouse anti-APRIL monoclonal antibody (4540), we confirm both the pathogenic role of APRIL in IgAN and the therapeutic efficacy of antibody-directed neutralization of APRIL in the grouped mouse ddY disease model. Treatment with 4540 directly translated to a reduction in relevant pathogenic mechanisms including suppressed serum IgA levels, reduced circulating immune complexes, significantly lower kidney deposits of IgA, IgG and C3, and suppression of proteinuria compared to mice receiving vehicle or isotype control antibodies. Furthermore, we translated these findings to the pharmacological characterization of VIS649, a highly potent, humanized IgG2κ antibody targeting and neutralizing human APRIL through unique epitope engagement, leading to inhibition of APRIL-mediated B-cell activities. VIS649 treatment of non-human primates showed dose-dependent reduction of serum IgA levels of up to 70%. A reduction of IgA⁺, IgM⁺, and IgG⁺ B cells was noted in the gut-associated mucosa of VIS649-treated animals. Population-based modeling predicted a favorable therapeutic dosing profile for subcutaneous administration of VIS649 in the clinical setting. Thus, our data highlight the potential therapeutic benefit of VIS649 for the treatment of IgAN.