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Ya’u Sabo Ajingi, Nujarin Jongruja. Antimicrobial Peptide Engineering: Rational Design, Synthesis, and Synergistic Effect. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Fine J, Lackner R, Samudrala R, Chopra G. Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications. Sci Rep 2019; 9:13155. [PMID: 31511563 PMCID: PMC6739337 DOI: 10.1038/s41598-019-49515-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 07/31/2019] [Indexed: 12/17/2022] Open
Abstract
We have developed the Computational Analysis of Novel Drug Opportunities (CANDO) platform to infer homology of drug behaviour at a proteomic level by constructing and analysing structural compound-proteome interaction signatures of 3,733 compounds with 48,278 proteins in a shotgun manner. We applied the CANDO platform to predict putative therapeutic properties of 428 psychoactive compounds that belong to the phenylethylamine, tryptamine, and cannabinoid chemical classes for treating mental health indications. Our findings indicate that these 428 psychoactives are among the top-ranked predictions for a significant fraction of mental health indications, demonstrating a significant preference for treating such indications over non-mental health indications, relative to randomized controls. Also, we analysed the use of specific tryptamines for the treatment of sleeping disorders, bupropion for substance abuse disorders, and cannabinoids for epilepsy. Our innovative use of the CANDO platform may guide the identification and development of novel therapies for mental health indications and provide an understanding of their causal basis on a detailed mechanistic level. These predictions can be used to provide new leads for preclinical drug development for mental health and other neurological disorders.
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Affiliation(s)
- Jonathan Fine
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Rachel Lackner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ram Samudrala
- Department of Biomedical Informatics, SUNY, Buffalo, NY, USA.
| | - Gaurav Chopra
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- Purdue Institute for Drug Discovery, Purdue Institute for Integrative Neuroscience, Purdue Institute for Integrative Neuroscience, Purdue Institute for Immunology, Inflammation and Infectious Disease, Integrative Data Science Initiative, Purdue Center for Cancer Research, West Lafayette, IN, USA.
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Gupta N, Pandya P, Verma S. Computational Predictions for Multi-Target Drug Design. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2018. [DOI: 10.1007/7653_2018_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Chopra G, Samudrala R. Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform. Curr Pharm Des 2017; 22:3109-23. [PMID: 27013226 DOI: 10.2174/1381612822666160325121943] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/01/2015] [Indexed: 01/05/2023]
Abstract
BACKGROUND Traditional drug discovery approaches focus on a limited set of target molecules for treatment against specific indications/diseases. However, drug absorption, dispersion, metabolism, and excretion (ADME) involve interactions with multiple protein systems. Drugs approved for particular indication(s) may be repurposed as novel therapeutics for others. The severely declining rate of discovery and increasing costs of new drugs illustrate the limitations of the traditional reductionist paradigm in drug discovery. METHODS We developed the Computational Analysis of Novel Drug Opportunities (CANDO) platform based on a hypothesis that drugs function by interacting with multiple protein targets to create a molecular interaction signature that can be exploited for therapeutic repurposing and discovery. We compiled a library of compounds that are human ingestible with minimal side effects, followed by an 'all-compounds' vs 'all-proteins' fragment-based multitarget docking with dynamics screen to construct compound-proteome interaction matrices that were then analyzed to determine similarity of drug behavior. The proteomic signature similarity of drugs is then ranked to make putative drug predictions for all indications in a shotgun manner. RESULTS We have previously applied this platform with success in both retrospective benchmarking and prospective validation, and to understand the effect of druggable protein classes on repurposing accuracy. Here we use the CANDO platform to analyze and determine the contribution of multitargeting (polypharmacology) to drug repurposing benchmarking accuracy. Taken together with the previous work, our results indicate that a large number of protein structures with diverse fold space and a specific polypharmacological interactome is necessary for accurate drug predictions using our proteomic and evolutionary drug discovery and repurposing platform. CONCLUSION These results have implications for future drug development and repurposing in the context of polypharmacology.
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Affiliation(s)
- Gaurav Chopra
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
| | - Ram Samudrala
- Department of Biomedical Informatics, SUNY, Buffalo, NY, USA.
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5
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Combating Ebola with Repurposed Therapeutics Using the CANDO Platform. Molecules 2016; 21:molecules21121537. [PMID: 27898018 PMCID: PMC5958544 DOI: 10.3390/molecules21121537] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/23/2016] [Accepted: 10/28/2016] [Indexed: 12/20/2022] Open
Abstract
Ebola virus disease (EVD) is extremely virulent with an estimated mortality rate of up to 90%. However, the state-of-the-art treatment for EVD is limited to quarantine and supportive care. The 2014 Ebola epidemic in West Africa, the largest in history, is believed to have caused more than 11,000 fatalities. The countries worst affected are also among the poorest in the world. Given the complexities, time, and resources required for a novel drug development, finding efficient drug discovery pathways is going to be crucial in the fight against future outbreaks. We have developed a Computational Analysis of Novel Drug Opportunities (CANDO) platform based on the hypothesis that drugs function by interacting with multiple protein targets to create a molecular interaction signature that can be exploited for rapid therapeutic repurposing and discovery. We used the CANDO platform to identify and rank FDA-approved drug candidates that bind and inhibit all proteins encoded by the genomes of five different Ebola virus strains. Top ranking drug candidates for EVD treatment generated by CANDO were compared to in vitro screening studies against Ebola virus-like particles (VLPs) by Kouznetsova et al. and genetically engineered Ebola virus and cell viability studies by Johansen et al. to identify drug overlaps between the in virtuale and in vitro studies as putative treatments for future EVD outbreaks. Our results indicate that integrating computational docking predictions on a proteomic scale with results from in vitro screening studies may be used to select and prioritize compounds for further in vivo and clinical testing. This approach will significantly reduce the lead time, risk, cost, and resources required to determine efficacious therapies against future EVD outbreaks.
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Farrokhi V, Bajrami B, Nemati R, McShane AJ, Rueckert F, Wells B, Yao X. Development of Structural Marker Peptides for Cystic Fibrosis Transmembrane Conductance Regulator in Cell Plasma Membrane by Reversed-Footprinting Mass Spectrometry. Anal Chem 2015; 87:8603-7. [DOI: 10.1021/acs.analchem.5b01962] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | | | | | | | - Franz Rueckert
- Department
of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Barrett Wells
- Department
of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
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7
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Kim H, Yoo SJ, Kang HA. Yeast synthetic biology for the production of recombinant therapeutic proteins. FEMS Yeast Res 2015; 866:1-9. [PMID: 25130199 DOI: 10.1007/978-1-61779-770-5_1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
The production of recombinant therapeutic proteins is one of the fast-growing areas of molecular medicine and currently plays an important role in treatment of several diseases. Yeasts are unicellular eukaryotic microbial host cells that offer unique advantages in producing biopharmaceutical proteins. Yeasts are capable of robust growth on simple media, readily accommodate genetic modifications, and incorporate typical eukaryotic post-translational modifications. Saccharomyces cerevisiae is a traditional baker's yeast that has been used as a major host for the production of biopharmaceuticals; however, several nonconventional yeast species including Hansenula polymorpha, Pichia pastoris, and Yarrowia lipolytica have gained increasing attention as alternative hosts for the industrial production of recombinant proteins. In this review, we address the established and emerging genetic tools and host strains suitable for recombinant protein production in various yeast expression systems, particularly focusing on current efforts toward synthetic biology approaches in developing yeast cell factories for the production of therapeutic recombinant proteins.
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Affiliation(s)
- Hyunah Kim
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Su Jin Yoo
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, Korea
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8
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Bill RM. Recombinant protein subunit vaccine synthesis in microbes: a role for yeast? J Pharm Pharmacol 2014; 67:319-28. [DOI: 10.1111/jphp.12353] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/18/2014] [Indexed: 12/14/2022]
Abstract
Abstract
Objectives
Recombinant protein subunit vaccines are formulated using protein antigens that have been synthesized in heterologous host cells. Several host cells are available for this purpose, ranging from Escherichia coli to mammalian cell lines. This article highlights the benefits of using yeast as the recombinant host.
Key findings
The yeast species, Saccharomyces cerevisiae and Pichia pastoris, have been used to optimize the functional yields of potential antigens for the development of subunit vaccines against a wide range of diseases caused by bacteria and viruses. Saccharomyces cerevisiae has also been used in the manufacture of 11 approved vaccines against hepatitis B virus and one against human papillomavirus; in both cases, the recombinant protein forms highly immunogenic virus-like particles.
Summary
Advances in our understanding of how a yeast cell responds to the metabolic load of producing recombinant proteins will allow us to identify host strains that have improved yield properties and enable the synthesis of more challenging antigens that cannot be produced in other systems. Yeasts therefore have the potential to become important host organisms for the production of recombinant antigens that can be used in the manufacture of subunit vaccines or in new vaccine development.
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Affiliation(s)
- Roslyn M Bill
- School of Life and Health Sciences, Aston University, Birmingham, UK
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9
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Bill RM. Playing catch-up with Escherichia coli: using yeast to increase success rates in recombinant protein production experiments. Front Microbiol 2014; 5:85. [PMID: 24634668 PMCID: PMC3942658 DOI: 10.3389/fmicb.2014.00085] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/17/2014] [Indexed: 11/13/2022] Open
Abstract
Several host systems are available for the production of recombinant proteins, ranging from Escherichia coli to mammalian cell-lines. This article highlights the benefits of using yeast, especially for more challenging targets such as membrane proteins. On account of the wide range of molecular, genetic, and microbiological tools available, use of the well-studied model organism, Saccharomyces cerevisiae, provides many opportunities to optimize the functional yields of a target protein. Despite this wealth of resources, it is surprisingly under-used. In contrast, Pichia pastoris, a relative new-comer as a host organism, is already becoming a popular choice, particularly because of the ease with which high biomass (and hence recombinant protein) yields can be achieved. In the last few years, advances have been made in understanding how a yeast cell responds to the stress of producing a recombinant protein and how this information can be used to identify improved host strains in order to increase functional yields. Given these advantages, and their industrial importance in the production of biopharmaceuticals, I argue that S. cerevisiae and P. pastoris should be considered at an early stage in any serious strategy to produce proteins.
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Affiliation(s)
- Roslyn M Bill
- School of Life and Health Sciences, Aston University Birmingham, UK
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10
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Vogl T, Thallinger GG, Zellnig G, Drew D, Cregg JM, Glieder A, Freigassner M. Towards improved membrane protein production in Pichia pastoris: general and specific transcriptional response to membrane protein overexpression. N Biotechnol 2014; 31:538-52. [PMID: 24594271 DOI: 10.1016/j.nbt.2014.02.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/20/2014] [Accepted: 02/23/2014] [Indexed: 01/13/2023]
Abstract
Membrane proteins are the largest group of human drug targets and are also used as biocatalysts. However, due to their complexity, efficient expression remains a bottleneck for high level production. In recent years, the methylotrophic yeast Pichia pastoris has emerged as one of the most commonly used expression systems for membrane protein production. Here, we have analysed the transcriptomes of P. pastoris strains producing different classes of membrane proteins (mitochondrial, ER/Golgi and plasma membrane localized) to understand the cellular response and to identify targets to engineer P. pastoris towards an improved chassis for membrane protein production. Microarray experiments revealed varying transcriptional responses depending on the enzymatic activity, subcellular localization and physiological role of the membrane proteins. While an alternative oxidase evoked primarily a response within the mitochondria, the overexpression of transporters entering the secretory pathway had a wide effect on lipid metabolism and induced the upregulation of the UPR (unfolded protein response) transcription factor Hac1p. Coexpression of P. pastoris endogenous HAC1 increased the levels of ER-resident membrane proteins 1.5- to 2.1-fold. Subsequent transcriptome analysis of HAC1 coexpression revealed an upregulation of the folding machinery correlating with an expansion of the ER membrane capacity, thus boosting membrane protein production. Hence, our study has helped to elucidate the cellular response of P. pastoris to the expression of different classes of membrane proteins and led specifically to new insights into the effect of PpHac1p on membrane proteins entering the secretory pathway.
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Affiliation(s)
- Thomas Vogl
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Gerhard G Thallinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/5, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8036 Graz, Austria; Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/5, 8010 Graz, Austria
| | - Guenther Zellnig
- Institute of Plant Sciences, University of Graz, Schubertstrasse 51, 8010 Graz, Austria
| | - David Drew
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - James M Cregg
- Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA
| | - Anton Glieder
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/5, 8010 Graz, Austria
| | - Maria Freigassner
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria.
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11
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Öberg F, Hedfalk K. Recombinant production of the human aquaporins in the yeastPichia pastoris(Invited Review). Mol Membr Biol 2012; 30:15-31. [DOI: 10.3109/09687688.2012.665503] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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12
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Faisal S, Ullah F, Maity PK, Rolfe A, Samarakoon TB, Porubsky P, Neuenswander B, Lushington GH, Basha FZ, Organ MG, Hanson PR. Facile (triazolyl)methylation of MACOS-derived benzofused sultams utilizing ROMP-derived OTP reagents. ACS COMBINATORIAL SCIENCE 2012; 14:268-72. [PMID: 22384820 DOI: 10.1021/co2001839] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A combination of MACOS scale-out and ROMP-derived oligomeric triazole phosphates (OTP(n)) have been successfully utilized for the preparation of a 106-member library of triazole containing benzothiaoxazepine-1,1-dioxides. This report demonstrates the utilization of a suite of soluble OTP(n) reagents for facile (triazolyl)methylation of 10 MACOS-derived sultam scaffolds in purification-free process for parallel synthesis of small molecule collections for HTS.
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Affiliation(s)
- Saqib Faisal
- Department
of Chemistry, University of Kansas, 1251
Wescoe Hall Drive, Lawrence,
Kansas 66045-7582, United States
- H. E. J. Research
Institute
of Chemistry, International Center for Chemical and Biological Science, University of Karachi, Karachi, Pakistan
| | - Farman Ullah
- Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J
1P3, Canada
| | - Pradip K. Maity
- Department
of Chemistry, University of Kansas, 1251
Wescoe Hall Drive, Lawrence,
Kansas 66045-7582, United States
| | - Alan Rolfe
- Department
of Chemistry, University of Kansas, 1251
Wescoe Hall Drive, Lawrence,
Kansas 66045-7582, United States
| | - Thiwanka B. Samarakoon
- Department
of Chemistry, University of Kansas, 1251
Wescoe Hall Drive, Lawrence,
Kansas 66045-7582, United States
| | - Patrick Porubsky
- The University of Kansas Center for Chemical Methodologies and Library Development (KU-CMLD), 2034 Becker Drive, Del Shankel Structural
Biology Center, Lawrence, Kansas 66047, United States
| | - Benjamin Neuenswander
- The University of Kansas Center for Chemical Methodologies and Library Development (KU-CMLD), 2034 Becker Drive, Del Shankel Structural
Biology Center, Lawrence, Kansas 66047, United States
| | - Gerald H. Lushington
- Department
of Chemistry, University of Kansas, 1251
Wescoe Hall Drive, Lawrence,
Kansas 66045-7582, United States
- The University of Kansas Center for Chemical Methodologies and Library Development (KU-CMLD), 2034 Becker Drive, Del Shankel Structural
Biology Center, Lawrence, Kansas 66047, United States
| | - Fatima Z. Basha
- H. E. J. Research
Institute
of Chemistry, International Center for Chemical and Biological Science, University of Karachi, Karachi, Pakistan
| | - Michael G. Organ
- The University of Kansas Center for Chemical Methodologies and Library Development (KU-CMLD), 2034 Becker Drive, Del Shankel Structural
Biology Center, Lawrence, Kansas 66047, United States
- Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J
1P3, Canada
| | - Paul R. Hanson
- Department
of Chemistry, University of Kansas, 1251
Wescoe Hall Drive, Lawrence,
Kansas 66045-7582, United States
- The University of Kansas Center for Chemical Methodologies and Library Development (KU-CMLD), 2034 Becker Drive, Del Shankel Structural
Biology Center, Lawrence, Kansas 66047, United States
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Steen A, Wiederhold E, Gandhi T, Breitling R, Slotboom DJ. Physiological adaptation of the bacterium Lactococcus lactis in response to the production of human CFTR. Mol Cell Proteomics 2011; 10:M000052MCP200. [PMID: 21742800 DOI: 10.1074/mcp.m000052-mcp200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Biochemical and biophysical characterization of CFTR (the cystic fibrosis transmembrane conductance regulator) is thwarted by difficulties to obtain sufficient quantities of correctly folded and functional protein. Here we have produced human CFTR in the prokaryotic expression host Lactococcus lactis. The full-length protein was detected in the membrane of the bacterium, but the yields were too low (< 0.1% of membrane proteins) for in vitro functional and structural characterization, and induction of the expression of CFTR resulted in growth arrest. We used isobaric tagging for relative and absolute quantitation based quantitative proteomics to find out why production of CFTR in L. lactis was problematic. Protein abundances in membrane and soluble fractions were monitored as a function of induction time, both in CFTR expression cells and in control cells that did not express CFTR. Eight hundred and forty six proteins were identified and quantified (35% of the predicted proteome), including 163 integral membrane proteins. Expression of CFTR resulted in an increase in abundance of stress-related proteins (e.g. heat-shock and cell envelope stress), indicating the presence of misfolded proteins in the membrane. In contrast to the reported consequences of membrane protein overexpression in Escherichia coli, there were no indications that the membrane protein insertion machinery (Sec) became overloaded upon CFTR production in L. lactis. Nutrients and ATP became limiting in the control cells as the culture entered the late exponential and stationary growth phases but this did not happen in the CFTR expressing cells, which had stopped growing upon induction. The different stress responses elicited in E. coli and L. lactis upon membrane protein production indicate that different strategies are needed to overcome low expression yields and toxicity.
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Affiliation(s)
- Anton Steen
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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Baumann M, Baxendale IR, Kuratli C, Ley SV, Martin RE, Schneider J. Synthesis of a drug-like focused library of trisubstituted pyrrolidines using integrated flow chemistry and batch methods. ACS COMBINATORIAL SCIENCE 2011; 13:405-13. [PMID: 21528880 DOI: 10.1021/co2000357] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A combination of flow and batch chemistries has been successfully applied to the assembly of a series of trisubstituted drug-like pyrrolidines. This study demonstrates the efficient preparation of a focused library of these pharmaceutically important structures using microreactor technologies, as well as classical parallel synthesis techniques, and thus exemplifies the impact of integrating innovative enabling tools within the drug discovery process.
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Affiliation(s)
- Marcus Baumann
- Innovative Technology Centre, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Ian R. Baxendale
- Innovative Technology Centre, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Christoph Kuratli
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, Chemistry Technology and Innovation, 4070 Basel, Switzerland
| | - Steven V. Ley
- Innovative Technology Centre, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Rainer E. Martin
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, Chemistry Technology and Innovation, 4070 Basel, Switzerland
| | - Josef Schneider
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, Chemistry Technology and Innovation, 4070 Basel, Switzerland
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15
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Steen A, Wiederhold E, Gandhi T, Breitling R, Slotboom DJ. Physiological Adaptation of the Bacterium Lactococcus lactis in Response to the Production of Human CFTR. Mol Cell Proteomics 2011. [DOI: 10.1074/mcp.m000052-mcp201] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Bill RM, Henderson PJF, Iwata S, Kunji ERS, Michel H, Neutze R, Newstead S, Poolman B, Tate CG, Vogel H. Overcoming barriers to membrane protein structure determination. Nat Biotechnol 2011; 29:335-40. [PMID: 21478852 DOI: 10.1038/nbt.1833] [Citation(s) in RCA: 275] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new approaches to solving membrane protein structures based on recent technological advances. Rational approaches to overcoming the bottlenecks in the field are urgently required as membrane proteins, which typically comprise ~30% of the proteomes of organisms, are dramatically under-represented in the structural database of the Protein Data Bank.
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Affiliation(s)
- Roslyn M Bill
- School of Life and Health Sciences, Aston University, Birmingham, UK
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17
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Ashe MP, Bill RM. Mapping the yeast host cell response to recombinant membrane protein production: Relieving the biological bottlenecks. Biotechnol J 2011; 6:707-14. [DOI: 10.1002/biot.201000333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 01/28/2011] [Accepted: 02/11/2011] [Indexed: 11/12/2022]
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Altamura N, Calamita G. Systems for Production of Proteins for Biomimetic Membrane Devices. BIOLOGICAL AND MEDICAL PHYSICS, BIOMEDICAL ENGINEERING 2011. [DOI: 10.1007/978-94-007-2184-5_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Baumann K, Carnicer M, Dragosits M, Graf AB, Stadlmann J, Jouhten P, Maaheimo H, Gasser B, Albiol J, Mattanovich D, Ferrer P. A multi-level study of recombinant Pichia pastoris in different oxygen conditions. BMC SYSTEMS BIOLOGY 2010; 4:141. [PMID: 20969759 PMCID: PMC2987880 DOI: 10.1186/1752-0509-4-141] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 10/22/2010] [Indexed: 12/24/2022]
Abstract
Background Yeasts are attractive expression platforms for many recombinant proteins, and there is evidence for an important interrelation between the protein secretion machinery and environmental stresses. While adaptive responses to such stresses are extensively studied in Saccharomyces cerevisiae, little is known about their impact on the physiology of Pichia pastoris. We have recently reported a beneficial effect of hypoxia on recombinant Fab secretion in P. pastoris chemostat cultivations. As a consequence, a systems biology approach was used to comprehensively identify cellular adaptations to low oxygen availability and the additional burden of protein production. Gene expression profiling was combined with proteomic analyses and the 13C isotope labelling based experimental determination of metabolic fluxes in the central carbon metabolism. Results The physiological adaptation of P. pastoris to hypoxia showed distinct traits in relation to the model yeast S. cerevisiae. There was a positive correlation between the transcriptomic, proteomic and metabolic fluxes adaptation of P. pastoris core metabolism to hypoxia, yielding clear evidence of a strong transcriptional regulation component of key pathways such as glycolysis, pentose phosphate pathway and TCA cycle. In addition, the adaptation to reduced oxygen revealed important changes in lipid metabolism, stress responses, as well as protein folding and trafficking. Conclusions This systems level study helped to understand the physiological adaptations of cellular mechanisms to low oxygen availability in a recombinant P. pastoris strain. Remarkably, the integration of data from three different levels allowed for the identification of differences in the regulation of the core metabolism between P. pastoris and S. cerevisiae. Detailed comparative analysis of the transcriptomic data also led to new insights into the gene expression profiles of several cellular processes that are not only susceptible to low oxygen concentrations, but might also contribute to enhanced protein secretion.
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Affiliation(s)
- Kristin Baumann
- Department of Chemical Engineering, Autonomous University of Barcelona, Spain
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20
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The flow synthesis of heterocycles for natural product and medicinal chemistry applications. Mol Divers 2010; 15:613-30. [PMID: 20960230 DOI: 10.1007/s11030-010-9282-1] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 09/14/2010] [Indexed: 10/18/2022]
Abstract
This article represents an overview of recent research from the Innovative Technology Centre in the field of flow chemistry which was presented at the FROST2 meeting in Budapest in October 2009. After a short introduction of this rapidly expanding field, we discuss some of our results with a main focus on the synthesis of heterocyclic compounds which we use in various natural product and medicinal chemistry programmes.
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Ferndahl C, Bonander N, Logez C, Wagner R, Gustafsson L, Larsson C, Hedfalk K, Darby RAJ, Bill RM. Increasing cell biomass in Saccharomyces cerevisiae increases recombinant protein yield: the use of a respiratory strain as a microbial cell factory. Microb Cell Fact 2010; 9:47. [PMID: 20565740 PMCID: PMC2901257 DOI: 10.1186/1475-2859-9-47] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 06/17/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recombinant protein production is universally employed as a solution to obtain the milligram to gram quantities of a given protein required for applications as diverse as structural genomics and biopharmaceutical manufacture. Yeast is a well-established recombinant host cell for these purposes. In this study we wanted to investigate whether our respiratory Saccharomyces cerevisiae strain, TM6*, could be used to enhance the productivity of recombinant proteins over that obtained from corresponding wild type, respiro-fermentative strains when cultured under the same laboratory conditions. RESULTS Here we demonstrate at least a doubling in productivity over wild-type strains for three recombinant membrane proteins and one recombinant soluble protein produced in TM6* cells. In all cases, this was attributed to the improved biomass properties of the strain. The yield profile across the growth curve was also more stable than in a wild-type strain, and was not further improved by lowering culture temperatures. This has the added benefit that improved yields can be attained rapidly at the yeast's optimal growth conditions. Importantly, improved productivity could not be reproduced in wild-type strains by culturing them under glucose fed-batch conditions: despite having achieved very similar biomass yields to those achieved by TM6* cultures, the total volumetric yields were not concomitantly increased. Furthermore, the productivity of TM6* was unaffected by growing cultures in the presence of ethanol. These findings support the unique properties of TM6* as a microbial cell factory. CONCLUSIONS The accumulation of biomass in yeast cell factories is not necessarily correlated with a proportional increase in the functional yield of the recombinant protein being produced. The respiratory S. cerevisiae strain reported here is therefore a useful addition to the matrix of production hosts currently available as its improved biomass properties do lead to increased volumetric yields without the need to resort to complex control or cultivation schemes. This is anticipated to be of particular value in the production of challenging targets such as membrane proteins.
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Affiliation(s)
- Cecilia Ferndahl
- Chemical and Biological Engineering/Molecular Biotechnology, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Nicklas Bonander
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Christel Logez
- UMR 7175 - LC1, Dpt Récepteurs et Protéines Membranaires, ESBS, Blvd Sébastien Brant, BP 10413, 67412 Illkirch Cedex, France
| | - Renaud Wagner
- UMR 7175 - LC1, Dpt Récepteurs et Protéines Membranaires, ESBS, Blvd Sébastien Brant, BP 10413, 67412 Illkirch Cedex, France
| | - Lena Gustafsson
- Chemical and Biological Engineering/Molecular Biotechnology, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Christer Larsson
- Chemical and Biological Engineering/Molecular Biotechnology, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Kristina Hedfalk
- Department of Chemistry/Biochemistry, Göteborg University, Box 462, 405 30 Göteborg, Sweden
| | - Richard AJ Darby
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Roslyn M Bill
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
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Venturoni F, Nikbin N, Ley SV, Baxendale IR. The application of flow microreactors to the preparation of a family of casein kinase I inhibitors. Org Biomol Chem 2010; 8:1798-806. [DOI: 10.1039/b925327k] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Freigassner M, Pichler H, Glieder A. Tuning microbial hosts for membrane protein production. Microb Cell Fact 2009; 8:69. [PMID: 20040113 PMCID: PMC2807855 DOI: 10.1186/1475-2859-8-69] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 12/29/2009] [Indexed: 12/22/2022] Open
Abstract
The last four years have brought exciting progress in membrane protein research. Finally those many efforts that have been put into expression of eukaryotic membrane proteins are coming to fruition and enable to solve an ever-growing number of high resolution structures. In the past, many skilful optimization steps were required to achieve sufficient expression of functional membrane proteins. Optimization was performed individually for every membrane protein, but provided insight about commonly encountered bottlenecks and, more importantly, general guidelines how to alleviate cellular limitations during microbial membrane protein expression. Lately, system-wide analyses are emerging as powerful means to decipher cellular bottlenecks during heterologous protein production and their use in microbial membrane protein expression has grown in popularity during the past months. This review covers the most prominent solutions and pitfalls in expression of eukaryotic membrane proteins using microbial hosts (prokaryotes, yeasts), highlights skilful applications of our basic understanding to improve membrane protein production. Omics technologies provide new concepts to engineer microbial hosts for membrane protein production.
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Affiliation(s)
- Maria Freigassner
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
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