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      Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook

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          ABSTRACT

          The bioengineering tools have significant advantages through less time-consuming and utilized as a promising stage for the production of pharmaceutical bioproducts under the single platform. This review highlighted the advantages and current improvement in the plant, animal and microbial bioengineering tools and outlines feasible approaches by biological and process’s bioengineering levels for advancing the economic feasibility of pharmaceutical’s production. The critical analysis results revealed that system biology and synthetic biology along with advanced bioengineering tools like transcriptome, proteome, metabolome and nano bioengineering tools have shown a promising impact on the development of pharmaceutical’s bioproducts. Tools to overcome and resolve the accompanying encounters of pharmaceutical’s production that include nano bioengineering tools are also discussed. As a summary and prospect, it also gives new insight into the challenges and possible breakthrough of the development of pharmaceutical’s bioproducts through bioengineering tools.

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          Most cited references123

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          KEGG: kyoto encyclopedia of genes and genomes.

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          KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).
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            Direct multiplexed measurement of gene expression with color-coded probe pairs.

            We describe a technology, the NanoString nCounter gene expression system, which captures and counts individual mRNA transcripts. Advantages over existing platforms include direct measurement of mRNA expression levels without enzymatic reactions or bias, sensitivity coupled with high multiplex capability, and digital readout. Experiments performed on 509 human genes yielded a replicate correlation coefficient of 0.999, a detection limit between 0.1 fM and 0.5 fM, and a linear dynamic range of over 500-fold. Comparison of the NanoString nCounter gene expression system with microarrays and TaqMan PCR demonstrated that the nCounter system is more sensitive than microarrays and similar in sensitivity to real-time PCR. Finally, a comparison of transcript levels for 21 genes across seven samples measured by the nCounter system and SYBR Green real-time PCR demonstrated similar patterns of gene expression at all transcript levels.
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              ExPASy: The proteomics server for in-depth protein knowledge and analysis.

              The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.
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                Author and article information

                Journal
                Bioengineered
                Bioengineered
                KBIE
                kbie20
                Bioengineered
                Taylor & Francis
                2165-5979
                2165-5987
                2019
                26 October 2019
                : 10
                : 1
                : 469-492
                Affiliations
                [a ]Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, China
                [b ]Bioresource Institute for Healthy Utilization, Zunyi Medical University , Zunyi, China
                [c ]College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing, China
                Author notes
                CONTACT Jingshan Shi shijs@ 123456zmu.edu.cn Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi 563003, China
                Jishuang Chen BIHU_ZMU@ 123456zmu.edu.cn Bioresource Institute for Healthy Utilization, Zunyi Medical University , Zunyi 563003, China
                Author information
                http://orcid.org/0000-0002-0850-8592
                http://orcid.org/0000-0002-2537-1751
                http://orcid.org/0000-0002-9359-0163
                Article
                1682108
                10.1080/21655979.2019.1682108
                6844412
                31656120
                a02eaacb-0c14-4409-bbc0-9782e3539903
                © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 27 July 2019
                : 8 September 2019
                : 11 October 2019
                Page count
                Figures: 4, Tables: 2, References: 130, Pages: 24
                Funding
                Funded by: Guizhou Science and Technology Corporation Platform Talents Fund
                Award ID: Grant No.: [2017]5733-001 & CK-1130-002)
                The authors are grateful for the financial support under Distinguished High-Level Talents Research Grant from a Guizhou Science and Technology Corporation Platform Talents Fund (Grant No.: [2017]5733-001 & CK-1130-002) and Zunyi Medical University, China for their support. We are also thanks to our all laboratory colleagues for their constructive help.
                Categories
                Review

                Biomedical engineering
                bioengineered tools,bioproducts,genomics,metabolomics,pharmaceuticals,proteomics

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