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ISSN (Print): 1872-2083
ISSN (Online): 2212-4012

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Research Article

Finding Appropriate Signal Peptides for Secretory Production of Recombinant Glucarpidase: An In Silico Method

Author(s): Omid Vakili, Seyyed Hossein Khatami, Amir Maleksabet, Ahmad Movahedpour, Saeed Ebrahimi Fana, Rasoul Sadegh, Amir Hossein Salmanzadeh, Hadi Razeghifam, Sajjad Nourdideh, Sadra Samavarchi Tehrani* and Mortaza Taheri-Anganeh*

Volume 15, Issue 4, 2021

Published on: 20 September, 2021

Page: [302 - 315] Pages: 14

DOI: 10.2174/1872208315666210921095420

Price: $65

Abstract

Background: Methotrexate (MTX) is a general chemotherapeutic agent utilized to treat a variety of malignancies, woefully, its high doses can cause nephrotoxicity and subsequent defect in the process of MTX excretion. The recombinant form of glucarpidase is produced by engineered E. coli and is a confirmed choice to overcoming this problem.

Objective: In the present study, in silico analyses were performed to select suitable SPs for the secretion of recombinant glucarpidase in E. coli.

Methods: The signal peptide website and UniProt database were employed to collect the SPs and protein sequences. In the next step, SignalP-5.0 helped us to predict the SPs and the position of cleavage sites. Moreover, physicochemical properties and solubility were evaluated using Prot- Param and Protein-sol online software, and finally, ProtCompB was used to predict the final subcellular localization.

Results: Luckily, all SPs could form soluble fusion proteins. At last, it was found that PPB and TIBA could translocate the glucarpidase into the extracellular compartment.

Conclusion: This study showed that there are only 2 applicable SPs for the extracellular translocation of glucarpidase. Although the findings were remarkable with high degrees of accuracy and precision based on the utilization of bioinformatics analyses, additional experimental assessments are required to confirm and validate it. Recent patents revealed several inventions related to the clinical aspects of vaccine peptides against human disorders.

Keywords: Methotrexate, recombinant protein, biopharmaceuticals, glucarpidase, bioinformatics, malignancies.

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[1]
Araújo JR, Martel F, Borges N, Araújo JM, Keating E. Folates and aging: role in mild cognitive impairment, dementia and depression. Ageing Res Rev 2015; 22: 9-19.
[http://dx.doi.org/10.1016/j.arr.2015.04.005] [PMID: 25939915]
[2]
Obeid R, Holzgreve W, Pietrzik K. Is 5-methyltetrahydrofolate an alternative to folic acid for the prevention of neural tube defects? J Perinat Med 2013; 41(5): 469-83.
[http://dx.doi.org/10.1515/jpm-2012-0256] [PMID: 23482308]
[3]
Duthie SJ. Folic acid deficiency and cancer: mechanisms of DNA instability. Br Med Bull 1999; 55(3): 578-92.
[http://dx.doi.org/10.1258/0007142991902646] [PMID: 10746348]
[4]
Hagner N, Joerger M. Cancer chemotherapy: targeting folic acid synthesis. Cancer Manag Res 2010; 2: 293-301.
[PMID: 21301589]
[5]
Kantarjian H, Thomas D, O’Brien S, et al. Long-term follow-up results of hyperfractionated cyclophosphamide, vincristine, doxorubicin, and dexamethasone (Hyper-CVAD), a dose-intensive regimen, in adult acute lymphocytic leukemia. Cancer 2004; 101(12): 2788-801.
[http://dx.doi.org/10.1002/cncr.20668] [PMID: 15481055]
[6]
Bonadonna G, Valagussa P, Moliterni A, Zambetti M, Brambilla C. Adjuvant cyclophosphamide, methotrexate, and fluorouracil in node-positive breast cancer: the results of 20 years of follow-up. N Engl J Med 1995; 332(14): 901-6.
[http://dx.doi.org/10.1056/NEJM199504063321401] [PMID: 7877646]
[7]
Ferreri AJ, Reni M, Dell’Oro S, et al. Combined treatment with high-dose methotrexate, vincristine and procarbazine, without intrathecal chemotherapy, followed by consolidation radiotherapy for primary central nervous system lymphoma in immunocompetent patients. Oncology 2001; 60(2): 134-40.
[http://dx.doi.org/10.1159/000055310] [PMID: 11244328]
[8]
Green JM. Glucarpidase to combat toxic levels of methotrexate in patients. Ther Clin Risk Manag 2012; 8: 403-13.
[http://dx.doi.org/10.2147/TCRM.S30135] [PMID: 23209370]
[9]
Widemann BC, Balis FM, Kim A, et al. Glucarpidase, leucovorin, and thymidine for high-dose methotrexate-induced renal dysfunction: clinical and pharmacologic factors affecting outcome. J Clin Oncol 2010; 28(25): 3979-86.
[http://dx.doi.org/10.1200/JCO.2009.25.4540] [PMID: 20679598]
[10]
Rader RA. Redefining biopharmaceutical. Nat Biotechnol 2008; 26(7): 743-51.
[http://dx.doi.org/10.1038/nbt0708-743] [PMID: 18612293]
[11]
Buchen S, Ngampolo D, Melton RG, et al. Carboxypeptidase G2 rescue in patients with methotrexate intoxication and renal failure. Br J Cancer 2005; 92(3): 480-7.
[http://dx.doi.org/10.1038/sj.bjc.6602337] [PMID: 15668713]
[12]
Levêque D, Santucci R, Gourieux B, Herbrecht R. Pharmacokinetic drug-drug interactions with methotrexate in oncology. Expert Rev Clin Pharmacol 2011; 4(6): 743-50.
[http://dx.doi.org/10.1586/ecp.11.57] [PMID: 22111860]
[13]
Tuffaha HW, Al Omar S. Glucarpidase for the treatment of life-threatening methotrexate overdose. Drugs Today 2012; 48(11): 705-11.
[http://dx.doi.org/10.1358/dot.2012.48.11.1871575] [PMID: 23170306]
[14]
Widemann BC, Sung E, Anderson L, et al. Pharmacokinetics and metabolism of the methotrexate metabolite 2, 4-diamino-N(10)-methylpteroic acid. J Pharmacol Exp Ther 2000; 294(3): 894-901.
[PMID: 10945838]
[15]
Schwartz S, Borner K, Müller K, et al. Glucarpidase (carboxypeptidase g2) intervention in adult and elderly cancer patients with renal dysfunction and delayed methotrexate elimination after high-dose methotrexate therapy. Oncologist 2007; 12(11): 1299-308.
[http://dx.doi.org/10.1634/theoncologist.12-11-1299] [PMID: 18055849]
[16]
Ramsey LB, Balis FM, O’Brien MM, et al. Consensus guideline for use of glucarpidase in patients with high-dose methotrexate induced acute kidney injury and delayed methotrexate clearance. Oncologist 2018; 23(1): 52-61.
[http://dx.doi.org/10.1634/theoncologist.2017-0243] [PMID: 29079637]
[17]
Phillips M, Smith W, Balan G, Ward S. Pharmacokinetics of glucarpidase in subjects with normal and impaired renal function. J Clin Pharmacol 2008; 48(3): 279-84.
[http://dx.doi.org/10.1177/0091270007311571] [PMID: 18192538]
[18]
DeAngelis LM, Tong WP, Lin S, Fleisher M, Bertino JR. Carboxypeptidase G2 rescue after high-dose methotrexate. J Clin Oncol 1996; 14(7): 2145-9.
[http://dx.doi.org/10.1200/JCO.1996.14.7.2145] [PMID: 8683248]
[19]
Kesik-Brodacka M. Progress in biopharmaceutical development. Biotechnol Appl Biochem 2018; 65(3): 306-22.
[http://dx.doi.org/10.1002/bab.1617] [PMID: 28972297]
[20]
Taheri-Anganeh M, Khatami SH, Jamali Z, et al. LytU-SH3b fusion protein as a novel and efficient enzybiotic against methicillin-resistant Staphylococcus aureus. Mol Biol Res Commun 2019; 8(4): 151-8.
[PMID: 32042832]
[21]
Kim M-J, Park HS, Seo KH, Yang H-J, Kim S-K, Choi J-H. Complete solubilization and purification of recombinant human growth hormone produced in Escherichia coli. PLoS One 2013; 8(2): e56168.
[http://dx.doi.org/10.1371/journal.pone.0056168] [PMID: 23409149]
[22]
Thanassi DG, Hultgren SJ. Multiple pathways allow protein secretion across the bacterial outer membrane. Curr Opin Cell Biol 2000; 12(4): 420-30.
[http://dx.doi.org/10.1016/S0955-0674(00)00111-3] [PMID: 10873830]
[23]
Slouka C, Kopp J, Spadiut O, Herwig C. Perspectives of inclusion bodies for bio-based products: curse or blessing? Appl Microbiol Biotechnol 2019; 103(3): 1143-53.
[http://dx.doi.org/10.1007/s00253-018-9569-1] [PMID: 30569219]
[24]
Tehrani SS, Goodarzi G, Naghizadeh M, et al. In silico evaluation of suitable signal peptides for secretory production of recombinant granulocyte colony stimulating factor in Escherichia coli. Recent Pat Biotechnol 2020; 14(4): 269-310.
[http://dx.doi.org/10.2174/1872208314999200730115018]
[25]
Khatami SH, Taheri-Anganeh M, Arianfar F, et al. Analyzing signal peptides for secretory production of recombinant diagnostic antigen B8/1 from Echinococcus granulosus: an in silico approach. Mol Biol Res Commun 2020; 9(1): 1-10.
[PMID: 32582787]
[26]
Kaur J, Kumar A, Kaur J. Strategies for optimization of heterologous protein expression in E. coli: Roadblocks and reinforcements. Int J Biol Macromol 2018; 106: 803-22.
[http://dx.doi.org/10.1016/j.ijbiomac.2017.08.080] [PMID: 28830778]
[27]
Dastjerdeh MS, Marashiyan M, Boroujeni MB, Golkar M, Shokrgozar MA, Rahimi H. In silico analysis of different signal peptides for the secretory production of recombinant human keratinocyte growth factor in Escherichia coli. Comput Biol Chem 2019; 80: 225-33.
[http://dx.doi.org/10.1016/j.compbiolchem.2019.03.003] [PMID: 30999249]
[28]
Choi JH, Lee SY. Secretory and extracellular production of recombinant proteins using Escherichia coli. Appl Microbiol Biotechnol 2004; 64(5): 625-35.
[http://dx.doi.org/10.1007/s00253-004-1559-9] [PMID: 14966662]
[29]
Zamani M, Nezafat N, Negahdaripour M, Dabbagh F, Ghasemi Y. In silico evaluation of different signal peptides for the secretory production of human growth hormone in E. coli. Int J Pept Res Ther 2015; 21(3): 261-8.
[http://dx.doi.org/10.1007/s10989-015-9454-z]
[30]
Asadia M, Taheri-Anganeha M, Jamalib Z, et al. In silico analysis of signal peptides for secretory production of a-amylase in Bacillus subtilis. Asia Pac J Mol Biol Biotechnol 2019; 27(3): 113-24.
[http://dx.doi.org/10.35118/apjmbb.2019.027.3.11]
[31]
Zarei M, Nezafat N, Morowvat MH, Ektefaie M, Ghasemi Y. In silico analysis of different signal peptides for secretory production of arginine deiminase in Escherichia coli. Recent Pat Biotechnol 2019; 13(3): 217-27.
[http://dx.doi.org/10.2174/1872208313666190101114602] [PMID: 30621572]
[32]
Chang CCH, Song J, Tey BT, Ramanan RN. Bioinformatics approaches for improved recombinant protein production in Escherichia coli: protein solubility prediction. Brief Bioinform 2014; 15(6): 953-62.
[http://dx.doi.org/10.1093/bib/bbt057] [PMID: 23926206]
[33]
Asadi M, Gharibi S, Khatami SH, et al. Analysis of suitable signal peptides for designing a secretory thermostable cyanide degrading nitrilase: An in silico approach. J Environ Treat Tech 2019; 7: 506-13.
[34]
Taheri-Anganeh M, Khatami SH, Jamali Z, Savardashtaki A, Ghasemi Y, Mostafavi-Pour Z. In silico analysis of suitable signal peptides for secretion of a recombinant alcohol dehydrogenase with a key role in atorvastatin enzymatic synthesis. Mol Biol Res Commun 2019; 8(1): 17-26.
[PMID: 31528640]
[35]
Gallo E. High-throughput generation of in silico derived synthetic antibodies via one-step enzymatic DNA assembly of fragments. Mol Biotechnol 2020; 62(2): 142-50.
[http://dx.doi.org/10.1007/s12033-019-00232-z] [PMID: 31894513]
[36]
Kamble A, Srinivasan S, Singh H. In-silico bioprospecting: finding better enzymes. Mol Biotechnol 2019; 61(1): 53-9.
[http://dx.doi.org/10.1007/s12033-018-0132-1] [PMID: 30406439]
[37]
Chakraborty N, Besra A, Basak J. Molecular cloning of an amino acid permease gene and structural characterization of the protein in common bean (Phaseolus vulgaris L.). Mol Biotechnol 2020; 62(3): 210-7.
[http://dx.doi.org/10.1007/s12033-020-00240-4] [PMID: 32036550]
[38]
Negahdaripour M, Nezafat N, Hajighahramani N, Soheil Rahmatabadi S, Hossein Morowvat M, Ghasemi Y. In silico study of different signal peptides for secretory production of interleukin-11 in Escherichia coli. Curr Proteomics 2017; 14(2): 112-21.
[http://dx.doi.org/10.2174/1570164614666170106110848]
[39]
Vafadar A, Taheri-Anganeh M, Movahedpour A, et al. In silico design and evaluation of scfv-cdtb as a novel immunotoxin for breast cancer treatment. Int J Cancer Manag 2020; 13(1): 1-8.
[http://dx.doi.org/10.5812/ijcm.96094]
[40]
Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: signal P 3.0. J Mol Biol 2004; 340(4): 783-95.
[http://dx.doi.org/10.1016/j.jmb.2004.05.028] [PMID: 15223320]
[41]
Choo KH, Tan TW, Ranganathan S, Eds. A comprehensive assessment of N-terminal signal peptides prediction methods.Bmc Bioinformatics 2009; 10(15): 1-12.
[42]
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A. Protein identification and analysis tools on the expasy server. In: The proteomics protocols handbook. Walker JM. Heidelberg: Springer 2005; pp. 571-607.
[http://dx.doi.org/10.1385/1-59259-890-0:571]
[43]
Walker JM. The proteomics protocols handbook Heidelberg Springer. 2005; p. 98.
[http://dx.doi.org/10.1385/1592598900]
[44]
Hebditch M, Carballo-Amador MA, Charonis S, Curtis R, Warwicker J. Protein-Sol: a web tool for predicting protein solubility from sequence. Bioinformatics 2017; 33(19): 3098-100.
[http://dx.doi.org/10.1093/bioinformatics/btx345] [PMID: 28575391]
[45]
Zeng R, Gao S, Xu L, Liu X, Dai F. Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici. BMC Microbiol 2018; 18(1): 191.
[http://dx.doi.org/10.1186/s12866-018-1329-y] [PMID: 30458731]
[46]
Ferlay J, Steliarova-Foucher E, Lortet-Tieulent J, et al. Cancer incidence and mortality patterns in Europe: estimates for 40 countries in 2012. Eur J Cancer 2013; 49(6): 1374-403.
[http://dx.doi.org/10.1016/j.ejca.2012.12.027] [PMID: 23485231]
[47]
Collaborators GRF. Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990-2015: a systematic analysis for the global burden of disease study 2015. Lancet 2016; 388(10053): 1659-724.
[http://dx.doi.org/10.1016/S0140-6736(16)31679-8] [PMID: 27733284]
[48]
Wishart DS. Bioinformatics in drug development and assessment. Drug Metab Rev 2005; 37(2): 279-310.
[http://dx.doi.org/10.1081/DMR-55225] [PMID: 15931766]
[49]
Taheri-Anganeh M, Amiri A, Movahedpour A, et al. In silico evaluation of PLAC1-fliC as a chimeric vaccine against breast cancer. Iran Biomed J 2020; 24(3): 173-82.
[http://dx.doi.org/10.29252/ibj.24.3.173] [PMID: 31952435]
[50]
Yousefi T, Mir SM, Asadi J, et al. In silico analysis of non-synonymous single nucleotide polymorphism in a human KLK-2 gene associated with prostate cancer. Meta Gene 2019; 21: 100578.
[http://dx.doi.org/10.1016/j.mgene.2019.100578]
[51]
Mohammadi S, Mostafavi-Pour Z, Ghasemi Y, et al. In silico analysis of different signal peptides for the excretory production of recombinant NS3-GP96 fusion protein in Escherichia coli. Int J Pept Res Ther 2019; 25(4): 1279-90.
[http://dx.doi.org/10.1007/s10989-018-9775-9]
[52]
Baumgarten T, Ytterberg AJ, Zubarev RA, de Gier J-W. Optimizing recombinant protein production in the Escherichia coli periplasm alleviates stress. Appl Environ Microbiol 2018; 84(12): e00270-18.
[http://dx.doi.org/10.1128/AEM.00270-18] [PMID: 29654183]
[53]
Owji H, Nezafat N, Negahdaripour M, Hajiebrahimi A, Ghasemi Y. A comprehensive review of signal peptides: structure, roles, and applications. Eur J Cell Biol 2018; 97(6): 422-41.
[http://dx.doi.org/10.1016/j.ejcb.2018.06.003] [PMID: 29958716]
[54]
Low KO, Muhammad Mahadi N, Md Illias R. Optimisation of signal peptide for recombinant protein secretion in bacterial hosts. Appl Microbiol Biotechnol 2013; 97(9): 3811-26.
[http://dx.doi.org/10.1007/s00253-013-4831-z] [PMID: 23529680]
[55]
Nezafat N, Karimi Z, Eslami M, Mohkam M, Zandian S, Ghasemi Y. Designing an efficient multi-epitope peptide vaccine against Vibrio choleraevia combined immunoinformatics and protein interaction based approaches. Comput Biol Chem 2016; 62: 82-95.
[http://dx.doi.org/10.1016/j.compbiolchem.2016.04.006] [PMID: 27107181]
[56]
Mousavi P, Mostafavi-Pour Z, Morowvat MH, et al. In silico analysis of several signal peptides for the excretory production of reteplase in Escherichia coli. Curr Proteomics 2017; 14(4): 326-35.
[http://dx.doi.org/10.2174/1570164614666170809144446]
[57]
Goda SK, Rashidi FAB, Fakharo AA, Al-Obaidli A. Functional overexpression and purification of a codon optimized synthetic glucarpidase (carboxypeptidase G2) in Escherichia coli. Protein J 2009; 28(9-10): 435-42.
[http://dx.doi.org/10.1007/s10930-009-9211-2] [PMID: 19911261]
[58]
Minton NP, Atkinson T, Sherwood RF. Molecular cloning of the Pseudomonas carboxypeptidase G2 gene and its expression in Escherichia coli and Pseudomonas putida. J Bacteriol 1983; 156(3): 1222-7.
[http://dx.doi.org/10.1128/jb.156.3.1222-1227.1983] [PMID: 6358192]
[59]
Sherwood RF, Melton RG, Alwan SM, Hughes P. Purification and properties of carboxypeptidase G2 from Pseudomonas sp. strain RS-16. Use of a novel triazine dye affinity method. Eur J Biochem 1985; 148(3): 447-53.
[http://dx.doi.org/10.1111/j.1432-1033.1985.tb08860.x] [PMID: 3838935]
[60]
van Dijl J, Hecker M. Bacillus subtilis: from soil bacterium to super-secreting cell factory. BioMed Central 2013; 12: 1-6.
[61]
Freudl R. Signal peptides for recombinant protein secretion in bacterial expression systems. Microb Cell Fact 2018; 17(1): 52.
[http://dx.doi.org/10.1186/s12934-018-0901-3] [PMID: 29598818]
[62]
Mergulhão FJ, Summers DK, Monteiro GA. Recombinant protein secretion in Escherichia coli. Biotechnol Adv 2005; 23(3): 177-202.
[http://dx.doi.org/10.1016/j.biotechadv.2004.11.003] [PMID: 15763404]
[63]
Yarabbi H, Mortazavi SA, Yavarmanesh M, Javadmanesh A. In silico study of different signal peptides to express recombinant glutamate decarboxylase in the outer membrane of Escherichia coli. Int J Pept Res Ther 2019; 1-13.
[http://dx.doi.org/10.1007/s10989-019-09986-1]
[64]
Bahrami AA, Payandeh Z, Khalili S, Zakeri A, Bandehpour M. Immunoinformatics: in silico approaches and computational design of a multi-epitope, immunogenic protein. Int Rev Immunol 2019; 38(6): 307-22.
[http://dx.doi.org/10.1080/08830185.2019.1657426] [PMID: 31478759]
[65]
Chan P, Curtis RA, Warwicker J. Soluble expression of proteins correlates with a lack of positively-charged surface. Sci Rep 2013; 3(1): 3333.
[http://dx.doi.org/10.1038/srep03333] [PMID: 24276756]
[66]
Kramer RM, Shende VR, Motl N, Pace CN, Scholtz JM. Toward a molecular understanding of protein solubility: increased negative surface charge correlates with increased solubility. Biophys J 2012; 102(8): 1907-15.
[http://dx.doi.org/10.1016/j.bpj.2012.01.060] [PMID: 22768947]
[67]
AlQahtani AD, Al-Mansoori L, Bashraheel SS, et al. Production of “biobetter” glucarpidase variants to improve drug detoxification and antibody directed enzyme prodrug therapy for cancer treatment. Eur J Pharm Sci 2019; 127: 79-91.
[http://dx.doi.org/10.1016/j.ejps.2018.10.014] [PMID: 30343151]
[68]
Palmer T, Berks BC. The twin-arginine translocation (Tat) protein export pathway. Nat Rev Microbiol 2012; 10(7): 483-96.
[http://dx.doi.org/10.1038/nrmicro2814] [PMID: 22683878]
[69]
Denks K, Vogt A, Sachelaru I, Petriman N-A, Kudva R, Koch H-G. The Sec translocon mediated protein transport in prokaryotes and eukaryotes. Mol Membr Biol 2014; 31(2-3): 58-84.
[http://dx.doi.org/10.3109/09687688.2014.907455] [PMID: 24762201]

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