The SARS-CoV-2 M pro Dimer-Based Screening System: A Synthetic Biology Tool for Identifying Compounds with Dimerization Inhibitory Potential

The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could b...

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Published inACS synthetic biology Vol. 13; no. 2; pp. 509 - 520
Main Authors Giri-Rachman, Ernawati Arifin, Effendy, Vergio V, Azmi, Muhammad H S, Yamahoki, Nicholas, Stephanie, Rebecca, Agustiyanti, Dian F, Wisnuwardhani, Popi H, Angelina, Marissa, Rubiyana, Yana, Aditama, Reza, Ningrum, Ratih A, Wardiana, Andri, Fibriani, Azzania
Format Journal Article
LanguageEnglish
Published United States 16.02.2024
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Abstract The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could be utilized at lower biosafety levels remains essential. This study aimed to develop a novel SARS-CoV-2 main protease (M ) dimer-based screening system (DBSS) utilizing synthetic biology in BL21(DE3). We linked the SARS-CoV-2 M with the DNA-binding domain of AraC regulatory protein, which regulates the reporter gene expression. Protein modeling and molecular docking showed that saquinavir could bind to AraC-M both in its monomer and dimer forms. The constructed DBSS assay indicated the screening system could detect saquinavir inhibitory activity at a concentration range of 4-10 μg/mL compared to the untreated control ( ≤ 0.05). The Vero E6 cell assay validated the DBSS result that saquinavir at 4-10 μg/mL exhibited antiviral activity against SARS-CoV-2. Our DBSS could be used for preliminary screening of numerous drug candidates that possess a dimerization inhibitor activity of SARS-CoV-2 M and also minimize the use of a high biosafety level laboratory.
AbstractList The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could be utilized at lower biosafety levels remains essential. This study aimed to develop a novel SARS-CoV-2 main protease (M ) dimer-based screening system (DBSS) utilizing synthetic biology in BL21(DE3). We linked the SARS-CoV-2 M with the DNA-binding domain of AraC regulatory protein, which regulates the reporter gene expression. Protein modeling and molecular docking showed that saquinavir could bind to AraC-M both in its monomer and dimer forms. The constructed DBSS assay indicated the screening system could detect saquinavir inhibitory activity at a concentration range of 4-10 μg/mL compared to the untreated control ( ≤ 0.05). The Vero E6 cell assay validated the DBSS result that saquinavir at 4-10 μg/mL exhibited antiviral activity against SARS-CoV-2. Our DBSS could be used for preliminary screening of numerous drug candidates that possess a dimerization inhibitor activity of SARS-CoV-2 M and also minimize the use of a high biosafety level laboratory.
Author Fibriani, Azzania
Azmi, Muhammad H S
Ningrum, Ratih A
Giri-Rachman, Ernawati Arifin
Rubiyana, Yana
Stephanie, Rebecca
Wisnuwardhani, Popi H
Aditama, Reza
Wardiana, Andri
Agustiyanti, Dian F
Yamahoki, Nicholas
Effendy, Vergio V
Angelina, Marissa
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CitedBy_id crossref_primary_10_1016_j_bpc_2024_107258
Cites_doi 10.1186/s12985-020-01457-0
10.1007/s11030-020-10130-1
10.3390/ijms232012240
10.1016/S0076-6879(06)22019-6
10.1016/j.csbj.2022.06.023
10.1093/bioinformatics/btp599
10.1007/s43440-020-00155-6
10.1016/j.febslet.2005.02.056
10.1128/CMR.00109-21
10.3389/fmicb.2014.00172
10.1021/acscombsci.0c00058
10.17567/ataunidfd.1030475
10.1016/j.antiviral.2009.06.004
10.1093/nar/gkz268
10.1016/j.heliyon.2018.e01023
10.1093/nar/gky430
10.1093/nar/gkz424
10.1080/14756366.2020.1850710
10.1002/0471140864.ps0524s61
10.1038/s41467-022-31570-3
10.3390/v13071352
10.1021/acs.jcim.0c00575
10.1128/JVI.02680-07
10.1021/bi0616302
10.1016/j.heliyon.2021.e07962
10.1038/s41467-020-16954-7
10.1038/s41467-020-18709-w
10.1007/978-1-0716-2111-0_22
10.1080/07391102.2021.1910571
10.1016/j.jmb.2015.09.014
10.1016/0092-8674(87)90563-0
10.1016/j.jep.2005.01.004
10.17713/ajs.v36i3.329
10.1080/07391102.2021.1970626
10.1021/bi1002585
10.1007/s00894-020-04600-4
10.1093/nar/gki387
10.1016/j.imu.2020.100461
10.1016/S1473-3099(20)30120-1
10.1126/science.abj8754
10.1093/nar/gky473
10.3390/pharmaceutics15030925
10.1002/jps.2600580708
10.3390/biom12070944
10.1002/iub.2465
10.1107/S0907444913001315
10.1002/jcc.21256
10.3389/fchem.2021.622898
10.1111/j.1742-4658.2006.05130.x
10.3382/ps/pez465
10.1126/science.abb3405
10.1021/acsptsci.0c00108
10.1038/s42003-022-03090-9
10.1186/s12906-017-2005-8
10.1093/nar/gki376
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Keywords COVID-19
dimer-based screening system
protease inhibitor
antivirus
drug discovery
main protease
Language English
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References ref9/cit9
ref3/cit3
ref27/cit27
ref63/cit63
ref56/cit56
Fibriani A. (ref12/cit12) 2018; 14
ref16/cit16
ref52/cit52
ref23/cit23
ref8/cit8
ref59/cit59
ref2/cit2
Giri-Rachman E. A. (ref11/cit11) 2017
ref37/cit37
ref20/cit20
ref48/cit48
ref60/cit60
ref17/cit17
ref10/cit10
ref35/cit35
ref53/cit53
ref19/cit19
ref21/cit21
ref42/cit42
ref46/cit46
ref49/cit49
ref13/cit13
ref61/cit61
ref67/cit67
ref24/cit24
ref38/cit38
ref50/cit50
ref54/cit54
ref6/cit6
ref36/cit36
ref18/cit18
ref25/cit25
ref29/cit29
Giri-Rachman E. A. (ref45/cit45) 2021
ref39/cit39
ref14/cit14
ref57/cit57
ref5/cit5
ref51/cit51
ref28/cit28
ref68/cit68
ref40/cit40
ref55/cit55
ref69/cit69
ref15/cit15
ref62/cit62
ref66/cit66
ref41/cit41
ref58/cit58
ref22/cit22
ref33/cit33
ref4/cit4
ref30/cit30
ref47/cit47
ref1/cit1
ref44/cit44
ref7/cit7
References_xml – ident: ref68/cit68
  doi: 10.1186/s12985-020-01457-0
– ident: ref13/cit13
  doi: 10.1007/s11030-020-10130-1
– ident: ref66/cit66
– ident: ref55/cit55
– ident: ref67/cit67
  doi: 10.3390/ijms232012240
– ident: ref10/cit10
  doi: 10.1016/S0076-6879(06)22019-6
– ident: ref24/cit24
  doi: 10.1016/j.csbj.2022.06.023
– ident: ref51/cit51
  doi: 10.1093/bioinformatics/btp599
– ident: ref4/cit4
  doi: 10.1007/s43440-020-00155-6
– ident: ref9/cit9
  doi: 10.1016/j.febslet.2005.02.056
– ident: ref2/cit2
  doi: 10.1128/CMR.00109-21
– ident: ref36/cit36
  doi: 10.3389/fmicb.2014.00172
– ident: ref18/cit18
  doi: 10.1021/acscombsci.0c00058
– ident: ref39/cit39
  doi: 10.17567/ataunidfd.1030475
– ident: ref38/cit38
  doi: 10.1016/j.antiviral.2009.06.004
– ident: ref57/cit57
  doi: 10.1093/nar/gkz268
– ident: ref8/cit8
  doi: 10.1016/j.heliyon.2018.e01023
– ident: ref48/cit48
  doi: 10.1093/nar/gky430
– ident: ref49/cit49
  doi: 10.1093/nar/gkz424
– ident: ref17/cit17
  doi: 10.1080/14756366.2020.1850710
– ident: ref35/cit35
  doi: 10.1002/0471140864.ps0524s61
– ident: ref7/cit7
  doi: 10.1038/s41467-022-31570-3
– ident: ref60/cit60
  doi: 10.3390/v13071352
– ident: ref29/cit29
  doi: 10.1021/acs.jcim.0c00575
– ident: ref25/cit25
  doi: 10.1128/JVI.02680-07
– ident: ref33/cit33
  doi: 10.1021/bi0616302
– ident: ref69/cit69
  doi: 10.1016/j.heliyon.2021.e07962
– ident: ref19/cit19
  doi: 10.1038/s41467-020-16954-7
– ident: ref23/cit23
  doi: 10.1038/s41467-020-18709-w
– ident: ref61/cit61
  doi: 10.1007/978-1-0716-2111-0_22
– ident: ref28/cit28
  doi: 10.1080/07391102.2021.1910571
– ident: ref53/cit53
  doi: 10.1016/j.jmb.2015.09.014
– ident: ref37/cit37
  doi: 10.1016/0092-8674(87)90563-0
– ident: ref42/cit42
  doi: 10.1016/j.jep.2005.01.004
– ident: ref54/cit54
– ident: ref62/cit62
  doi: 10.17713/ajs.v36i3.329
– ident: ref30/cit30
  doi: 10.1080/07391102.2021.1970626
– ident: ref22/cit22
  doi: 10.1021/bi1002585
– ident: ref14/cit14
  doi: 10.1007/s00894-020-04600-4
– ident: ref47/cit47
  doi: 10.1093/nar/gki387
– ident: ref15/cit15
  doi: 10.1016/j.imu.2020.100461
– ident: ref1/cit1
  doi: 10.1016/S1473-3099(20)30120-1
– ident: ref46/cit46
  doi: 10.1126/science.abj8754
– ident: ref50/cit50
  doi: 10.1093/nar/gky473
– ident: ref44/cit44
  doi: 10.3390/pharmaceutics15030925
– volume-title: Plasmid Vektor Ekspresi Rekombinan untuk Penapisan Cepat Kandididat Obat Anti-SARS-CoV-2 yang Menarget Sisi Dimerisasi dari Protomer Main Protease SARS-COV-2 [Recombinant Expression Vector Plasmid for Rapid Screening of Anti-SARS-CoV-2 Drug Candidates Targeting the Dimerization Side of SARS-CoV-2 Main Protease Protomer]
  year: 2021
  ident: ref45/cit45
  contributor:
    fullname: Giri-Rachman E. A.
– volume-title: Produk Bakteri Escherichia coli yang Dimodifikasi secara Genetik untuk Penapisan Cepat Kandidat Obat Antituberkulosis Baru [Product of genetically modified Escherichia coli bacteria for rapid screening of new antituberculosis drug candidates]
  year: 2017
  ident: ref11/cit11
  contributor:
    fullname: Giri-Rachman E. A.
– ident: ref58/cit58
  doi: 10.1002/jps.2600580708
– ident: ref3/cit3
  doi: 10.3390/biom12070944
– ident: ref20/cit20
  doi: 10.1002/iub.2465
– ident: ref21/cit21
  doi: 10.1107/S0907444913001315
– ident: ref52/cit52
  doi: 10.1002/jcc.21256
– ident: ref63/cit63
– ident: ref5/cit5
  doi: 10.3389/fchem.2021.622898
– ident: ref27/cit27
  doi: 10.1111/j.1742-4658.2006.05130.x
– volume: 14
  start-page: 166
  issue: 3
  year: 2018
  ident: ref12/cit12
  publication-title: Biotechnol Ind. J.
  contributor:
    fullname: Fibriani A.
– ident: ref59/cit59
  doi: 10.3382/ps/pez465
– ident: ref6/cit6
  doi: 10.1126/science.abb3405
– ident: ref16/cit16
  doi: 10.1021/acsptsci.0c00108
– ident: ref40/cit40
  doi: 10.1038/s42003-022-03090-9
– ident: ref41/cit41
  doi: 10.1186/s12906-017-2005-8
– ident: ref56/cit56
  doi: 10.1093/nar/gki376
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Snippet The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability...
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Title The SARS-CoV-2 M pro Dimer-Based Screening System: A Synthetic Biology Tool for Identifying Compounds with Dimerization Inhibitory Potential
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