With the advances in medicine, people have deeply understood the complex pathogenesis of diseases. Revealing the mechanism of action and therapeutic effect of drugs from an overall perspective has become the top priority of drug design. However, the traditional drug design methods cannot meet the current needs. In recent years, with the rapid development of systems biology, a variety of new technologies including metabolomics, genomics, and proteomics have been used in drug research and development. As a bridge between traditional pharmaceutical theory and modern science, computer-aided drug design(CADD) can shorten the drug development cycle and improve the success rate of drug design. The application of systems biology and CADD provides a methodological basis and direction for revealing the mechanism and action of drugs from an overall perspective. This paper introduces the research and application of systems biology in CADD from different perspectives and proposes the development direction, providing reference for promoting the application.
Humans ; Systems Biology ; Drug Design ; Drug Development ; Genomics ; Medicine

It is among the goals in metabolic engineering to construct microbial cell factories producing high-yield and high value-added target products, and an important solution is to design efficient synthetic pathway for the target products. However, due to the difference in metabolic capacity among microbial chassises, the available substrate and the yielded products are limited. Therefore, it is urgent to design related metabolic pathways to improve the production capacity. Existing metabolic engineering approaches to designing heterologous pathways are mainly based on biological experience, which are inefficient. Moreover, the yielded results are in no way comprehensive. However, systems biology provides new methods for heterologous pathway design, particularly the graph-based and constraint-based methods. Based on the databases containing rich metabolism information, they search for and uncover possible metabolic pathways with designated strategy (graph-based method) or algorithm (constraint-based method) and then screen out the optimal pathway to guide the modification of strains. In this paper, we reviewed the databases and algorithms for pathway design, and the applications in metabolic engineering and discussed the strengths and weaknesses of existing algorithms in practical application, hoping to provide a reference for the selection of optimal methods for the design of product synthesis pathway.
Algorithms ; Biosynthetic Pathways ; Metabolic Engineering ; Metabolic Networks and Pathways/genetics* ; Systems Biology

Since its establishment 30 years ago, the discipline of metabolic engineering has developed rapidly based on its deep integration with molecular biology, systems biology and synthetic biology successively, which has greatly contributed to advancing and upgrading biotechnology industry. This review firstly analyzes the current status of academic research and China's competence in the area of metabolic engineering according to the data of papers published in SCI-indexed journals in the past 30 years. Subsequently, the article summarizes the development of systems biology methods and enabling technologies of synthetic biology and their applications in metabolic engineering in the past 10 years. Finally, the major challenges and future perspectives for the development of metabolic engineering are briefly discussed.
Biotechnology ; Industry ; Metabolic Engineering ; Synthetic Biology ; Systems Biology

In 1990s, Bailey and Stephanopoulos put forward the concept of classic metabolic engineering, aiming to use DNA recombination technology to rewire metabolic network to achieve improved cell performance and increased target products. In the last 30 years since the birth of metabolic engineering, life science have flourished, and new disciplines such as genomics, systems biology and synthetic biology have emerged, injecting new connotations and vitality into the development of metabolic engineering. Classic metabolic engineering research has entered into an unprecedented stage of systems metabolic engineering. The application of synthetic biology tools and strategies, such as omics technology, genomic-scale metabolic model, parts assembly, circuits design, dynamic control, genome editing and many others, have greatly improved the design, build, and rewiring capabilities of complex metabolism. The intervention of machine learning and the combination of evolutionary engineering and metabolic engineering will further promote the development of systems metabolic engineering. This paper analyzes the development of metabolic engineering in the past 30 years and summarizes the novel theories, techniques, strategies, and applications of metabolic engineering that have emerged over the past 30 years.
Gene Editing ; Metabolic Engineering ; Metabolic Networks and Pathways/genetics* ; Synthetic Biology ; Systems Biology

With Chinese medicine (CM) gaining popularity in recent years, researchers and clinicians have put in much interest and effort into the makings and effects of it, especially after the recent announcement of World Health Orgnitation's incorporation of CM into mainstream medical compendium. Individual herb has complex properties, coming from its pharmacological properties and the Chinese medical principles of organ-directed, taste and dynamic orientational behaviours. The use of individual herb in CM is rare, where various herbs/ingredients are mostly found in a prescribed formula. To fully reveal the effects of CM is a great challenge. The complexity of various herbs in combined effect, the absorption and utility rate by the body, uniqueness of individual physique, sub-types of pathological behaviors and time-line progression of the healing process add on to the complication of understanding the full effect of CM. Various theories such as pathophysiology guidance, pharmacokinetic-pharmacodynamic compatibility method, and Global Systems Biology for Integrative Genomics, Proteomics and Metabolomics, which interactively provide a wider scope, more details, with the consideration of development timeline, may shed more light to revealing the full picture of the effects of compatibility prescription.
Drugs, Chinese Herbal/pharmacology* ; Medicine, Chinese Traditional ; Prescriptions ; Systems Biology

Metabonomics is the branch of systems biology. It has been widely used in the fields of diagnostic markers discovery, disease prognosis, drug action mechanism, drug efficacy and toxicity evaluation, traditional Chinese medicine syndromes differentiation. There are shortcomings in the conventional metabonomics research. Microdialysis technology is a new type of biosampling technology, and metabonomics research based on microdialysis technology is in the ascendant. In view of the particularity of microdialysis technology and its great differences from traditional sampling and pretreatment methods, the metabonomics process based on microdialysis technology has certain similarities with traditional metabonomics research, and its basic process has some particularity. Advantages and basic strategies of metabonomics research by microdialysis technology are systematically summarized for researchers' reference.
Medicine, Chinese Traditional ; Metabolomics ; Microdialysis ; Research Design ; Systems Biology

In industrial biotechnology, microbial cell factories utilize renewable resources to produce energy, materials and chemicals. Industrial biotechnology plays an increasingly important role in solving the resource, energy and environmental problems. Systems biology has shed new light on industrial biotechnology, deepening our understanding of industrial microbial cell factories and their bioprocess from "Black-box" to "White-box". Systems-wide profiling of genome, transcriptome, proteome, metabolome, and fluxome has proven valuable to better unveil network operation and regulation on the genome scale. System biology has been successfully applied to create microbial cell factories for numerous products and derive attractive industrial processes, which has constantly expedited the development of industrial biotechnology. This review focused on the recent advance and applications of omics and trans-omics in industrial biotechnology, including genomics, transcriptomics, proteomics, metabolomics, fluxomics and genome scale modeling, and so on. Furthermore, this review also discussed the potential and promise of systems biology in industrial biotechnology.
Biotechnology ; Genomics ; Industrial Microbiology ; Metabolic Engineering ; Metabolomics ; Systems Biology

To quickly and efficiently understand the intracellular metabolic characteristics of industrial microorganisms, and to find potential metabolic engineering targets, genome-scale metabolic network models (GSMMs) as a systems biology tool, are attracting more and more attention. We review here the 20-year history of metabolic network model, analyze the research status and development of GSMMs, summarize the methods for model construction and analysis, and emphasize the applications of metabolic network model for analyzing intracellular metabolic activity of microorganisms from cellular phenotypes, and metabolic engineering. Furthermore, we indicate future development trend of metabolic network model.
Industrial Microbiology ; Metabolic Engineering ; Metabolic Networks and Pathways ; genetics ; Models, Biological ; Systems Biology

BACKGROUND: Exosomes are membrane-enclosed extracellular vesicles implicated in cell-cell communication. Exosomes contain proteins, mRNAs, non-coding RNAs (miRNAs and lncRNAs) and lipids that are derived from producing cells. These nano-sized vesicles are present in biofluids including blood, urine, saliva, amniotic fluid, semen and conditioned media of cultured cells. METHODS: This review summarizes current progress on the strategies of development of diagnostic biomarkers and drug loading onto exosomes for overcoming cancer progression. RESULTS: A number of studies indicate that the exosome appears to be a key player in tissue repair and regeneration of in a number of animal disease models. In addition, alterations of the molecular profiles in exosomes are known to be correlated with the disease progression including cancer, suggesting their usefulness in disease diagnosis and prognosis. Studies utilizing engineered exosomes either by chemical or biological methods have demonstrated promising results in a number of animal models with cancer. CONCLUSION: Understanding the molecular and cellular properties of exosomes offer benefits for cancer diagnosis by liquid biopsy and for their application in therapeutic drug delivery systems. Studies have shown that genetic or molecular engineering of exosomes augmented their target specificity and anticancer activity with less toxicity. Thus, deeper understanding of exosome biology will facilitate their therapeutic potential as an innovative drug delivery system for cancer.
Amniotic Fluid ; Biology ; Biomarkers ; Biopsy ; Cells, Cultured ; Culture Media, Conditioned ; Diagnosis ; Disease Models, Animal ; Disease Progression ; Drug Delivery Systems ; Exosomes ; Extracellular Vesicles ; Female ; Models, Animal ; Prognosis ; Regeneration ; RNA, Messenger ; RNA, Untranslated ; Saliva ; Semen ; Sensitivity and Specificity

Genetically engineered mouse models are used in high-throughput phenotyping screens to understand genotype-phenotype associations and their relevance to human diseases. However, not all mutant mouse lines with detectable phenotypes are associated with human diseases. Here, we propose the “Target gene selection system for Genetically engineered mouse models” (TarGo). Using a combination of human disease descriptions, network topology, and genotype-phenotype correlations, novel genes that are potentially related to human diseases are suggested. We constructed a gene interaction network using protein-protein interactions, molecular pathways, and co-expression data. Several repositories for human disease signatures were used to obtain information on human disease-related genes. We calculated disease- or phenotype-specific gene ranks using network topology and disease signatures. In conclusion, TarGo provides many novel features for gene function prediction.
Animals ; Computational Biology ; Genes, vif ; Genetic Association Studies ; Humans ; Mice ; Phenotype ; Systems Biology