TY - JOUR
T1 - Discovery of lead natural products for developing pan-SARS-CoV-2 therapeutics
AU - Pérez-Vargas, Jimena
AU - Shapira, Tirosh
AU - Olmstead, Andrea D.
AU - Villanueva, Ivan
AU - Thompson, Connor A.H.
AU - Ennis, Siobhan
AU - Gao, Guang
AU - De Guzman, Joshua
AU - Williams, David E.
AU - Wang, Meng
AU - Chin, Aaleigha
AU - Bautista-Sánchez, Diana
AU - Agafitei, Olga
AU - Levett, Paul
AU - Xie, Xuping
AU - Nuzzo, Genoveffa
AU - Freire, Vitor F.
AU - Quintana-Bulla, Jairo I.
AU - Bernardi, Darlon I.
AU - Gubiani, Juliana R.
AU - Suthiphasilp, Virayu
AU - Raksat, Achara
AU - Meesakul, Pornphimol
AU - Polbuppha, Isaraporn
AU - Cheenpracha, Sarot
AU - Jaidee, Wuttichai
AU - Kanokmedhakul, Kwanjai
AU - Yenjai, Chavi
AU - Chaiyosang, Boonyanoot
AU - Teles, Helder Lopes
AU - Manzo, Emiliano
AU - Fontana, Angelo
AU - Leduc, Richard
AU - Boudreault, Pierre Luc
AU - Berlinck, Roberto G.S.
AU - Laphookhieo, Surat
AU - Kanokmedhakul, Somdej
AU - Tietjen, Ian
AU - Cherkasov, Artem
AU - Krajden, Mel
AU - Nabi, Ivan Robert
AU - Niikura, Masahiro
AU - Shi, Pei Yong
AU - Andersen, Raymond J.
AU - Jean, François
N1 - Funding Information:
Novel Coronavirus (COVID-19) Rapid Research Funding program of the Canadian Institutes of Health Research (CIHR) [OV3-170342 (FJ, RJA, PYS, IRN, AC, and NS)]; Novel Coronavirus (COVID-19) Rapid Research Funding program of the Canadian Institutes of Health Research (CIHR) [UBR 322812; VR3-172639 (RL, PLB, and FJ)]; Genome British Columbia /COVID-19 Rapid Response Funding Initiative [COV011 (FJ and RJA)]; NSERC Alliance COVID-19 Grant (AWD-015086 NSERC, 2020; IRN and FJ); Coronavirus Variants Rapid Response Network (CoVaRR-Net) grant (#175622 (FJ, ADO, NS, and IRN); and MITACS Inc. Accelerate Fellowship COVID-19 Award [IT18585 (TS, FJ)]. PYS was supported by NIH grants HHSN272201600013C, U01AI151801, and U19AI171413, and awards from the Sealy & Smith Foundation, the Kleberg Foundation , the John S. Dunn Foundation, the Amon G. Carter Foundation, the Gilson Longenbaugh Foundation, and the Summerfield Robert Foundation. RGSB is supported by FAPESP grant 2019/17721–9.
Funding Information:
Novel Coronavirus (COVID-19) Rapid Research Funding program of the Canadian Institutes of Health Research (CIHR) [OV3-170342 (FJ, RJA, PYS, IRN, AC, and NS)]; Novel Coronavirus (COVID-19) Rapid Research Funding program of the Canadian Institutes of Health Research (CIHR) [UBR 322812; VR3-172639 (RL, PLB, and FJ)]; Genome British Columbia/COVID-19 Rapid Response Funding Initiative [COV011 (FJ and RJA)]; NSERC Alliance COVID-19 Grant (AWD-015086 NSERC, 2020; IRN and FJ); Coronavirus Variants Rapid Response Network (CoVaRR-Net) grant (#175622 (FJ, ADO, NS, and IRN); and MITACS Inc. Accelerate Fellowship COVID-19 Award [IT18585 (TS, FJ)]. PYS was supported by NIH grants HHSN272201600013C, U01AI151801, and U19AI171413, and awards from the Sealy & Smith Foundation, the Kleberg Foundation, the John S. Dunn Foundation, the Amon G. Carter Foundation, the Gilson Longenbaugh Foundation, and the Summerfield Robert Foundation. RGSB is supported by FAPESP grant 2019/17721–9.The authors acknowledge the support of the CL3 facility (Facility for Infectious Disease and Epidemic Research (FINDER) of the Life Sciences Institute of the University of British Columbia founded by Dr. François Jean and its biosafety support staff including Dr. Bintou Ahidjo (Research Platform Manager) and T. Dean Airey (FINDER Senior Research Technician). Imaging was performed in the LSI Imaging Core Facility of the Life Sciences Institute at the University of British Columbia, supported by the Life Sciences Institute, the UBC GREx Biological Resilience Initiative. The infrastructure within LSI Imaging Core Facility is funded by the Canadian Foundation for Innovation, BC Knowledge Development Fund, Natural Sciences and Engineering Research Council of Canada Research Tools and Instruments, and UBC Research Facility Support Grants as well as a Strategic Investment Fund (Faculty of Medicine, UBC). We further thank Dr. Alex Ball, Jr. MD, Senior Scientist (GeneTex), for supplying the SARS-CoV-2 (COVID-19) nucleocapsid antibody [HL344] (GTX635679). We also acknowledge a generous donation towards the purchase of the CellInsight CX7 HCS system provided by the Vancouver General Hospital Foundation to Dr. Jean. We also thank Dr. Jill Kelly for proofreading the manuscript, Mike LeBlanc for technical assistance, and Dr. Carl Perez for administrative and logistic support during this study.
Funding Information:
The authors acknowledge the support of the CL3 facility (Facility for Infectious Disease and Epidemic Research (FINDER) of the Life Sciences Institute of the University of British Columbia founded by Dr. François Jean and its biosafety support staff including Dr. Bintou Ahidjo (Research Platform Manager) and T. Dean Airey (FINDER Senior Research Technician). Imaging was performed in the LSI Imaging Core Facility of the Life Sciences Institute at the University of British Columbia , supported by the Life Sciences Institute , the UBC GREx Biological Resilience Initiative. The infrastructure within LSI Imaging Core Facility is funded by the Canadian Foundation for Innovation, BC Knowledge Development Fund, Natural Sciences and Engineering Research Council of Canada Research Tools and Instruments, and UBC Research Facility Support Grants as well as a Strategic Investment Fund ( Faculty of Medicine , UBC ). We further thank Dr. Alex Ball, Jr., MD, Senior Scientist (GeneTex), for supplying the SARS-CoV-2 (COVID-19) nucleocapsid antibody [HL344] (GTX635679). We also acknowledge a generous donation towards the purchase of the CellInsight CX7 HCS system provided by the Vancouver General Hospital Foundation to Dr. Jean. We also thank Dr. Jill Kelly for proofreading the manuscript, Mike LeBlanc for technical assistance, and Dr. Carl Perez for administrative and logistic support during this study.
Publisher Copyright:
© 2022 The Authors
PY - 2023/1
Y1 - 2023/1
N2 - The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global public health crisis. The reduced efficacy of therapeutic monoclonal antibodies against emerging SARS-CoV-2 variants of concern (VOCs), such as omicron BA.5 subvariants, has underlined the need to explore a novel spectrum of antivirals that are effective against existing and evolving SARS-CoV-2 VOCs. To address the need for novel therapeutic options, we applied cell-based high-content screening to a library of natural products (NPs) obtained from plants, fungi, bacteria, and marine sponges, which represent a considerable diversity of chemical scaffolds. The antiviral effect of 373 NPs was evaluated using the mNeonGreen (mNG) reporter SARS-CoV-2 virus in a lung epithelial cell line (Calu-3). The screening identified 26 NPs with half-maximal effective concentrations (EC50) below 50 μM against mNG-SARS-CoV-2; 16 of these had EC50 values below 10 μM and three NPs (holyrine A, alotaketal C, and bafilomycin D) had EC50 values in the nanomolar range. We demonstrated the pan-SARS-CoV-2 activity of these three lead antivirals against SARS-CoV-2 highly transmissible Omicron subvariants (BA.5, BA.2 and BA.1) and highly pathogenic Delta VOCs in human Calu-3 lung cells. Notably, holyrine A, alotaketal C, and bafilomycin D, are potent nanomolar inhibitors of SARS-CoV-2 Omicron subvariants BA.5 and BA.2. The pan-SARS-CoV-2 activity of alotaketal C [protein kinase C (PKC) activator] and bafilomycin D (V-ATPase inhibitor) suggest that these two NPs are acting as host-directed antivirals (HDAs). Future research should explore whether PKC regulation impacts human susceptibility to and the severity of SARS-CoV-2 infection, and it should confirm the important role of human V-ATPase in the VOC lifecycle. Interestingly, we observed a synergistic action of bafilomycin D and N-0385 (a highly potent inhibitor of human TMPRSS2 protease) against Omicron subvariant BA.2 in human Calu-3 lung cells, which suggests that these two highly potent HDAs are targeting two different mechanisms of SARS-CoV-2 entry. Overall, our study provides insight into the potential of NPs with highly diverse chemical structures as valuable inspirational starting points for developing pan-SARS-CoV-2 therapeutics and for unravelling potential host factors and pathways regulating SARS-CoV-2 VOC infection including emerging omicron BA.5 subvariants.
AB - The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global public health crisis. The reduced efficacy of therapeutic monoclonal antibodies against emerging SARS-CoV-2 variants of concern (VOCs), such as omicron BA.5 subvariants, has underlined the need to explore a novel spectrum of antivirals that are effective against existing and evolving SARS-CoV-2 VOCs. To address the need for novel therapeutic options, we applied cell-based high-content screening to a library of natural products (NPs) obtained from plants, fungi, bacteria, and marine sponges, which represent a considerable diversity of chemical scaffolds. The antiviral effect of 373 NPs was evaluated using the mNeonGreen (mNG) reporter SARS-CoV-2 virus in a lung epithelial cell line (Calu-3). The screening identified 26 NPs with half-maximal effective concentrations (EC50) below 50 μM against mNG-SARS-CoV-2; 16 of these had EC50 values below 10 μM and three NPs (holyrine A, alotaketal C, and bafilomycin D) had EC50 values in the nanomolar range. We demonstrated the pan-SARS-CoV-2 activity of these three lead antivirals against SARS-CoV-2 highly transmissible Omicron subvariants (BA.5, BA.2 and BA.1) and highly pathogenic Delta VOCs in human Calu-3 lung cells. Notably, holyrine A, alotaketal C, and bafilomycin D, are potent nanomolar inhibitors of SARS-CoV-2 Omicron subvariants BA.5 and BA.2. The pan-SARS-CoV-2 activity of alotaketal C [protein kinase C (PKC) activator] and bafilomycin D (V-ATPase inhibitor) suggest that these two NPs are acting as host-directed antivirals (HDAs). Future research should explore whether PKC regulation impacts human susceptibility to and the severity of SARS-CoV-2 infection, and it should confirm the important role of human V-ATPase in the VOC lifecycle. Interestingly, we observed a synergistic action of bafilomycin D and N-0385 (a highly potent inhibitor of human TMPRSS2 protease) against Omicron subvariant BA.2 in human Calu-3 lung cells, which suggests that these two highly potent HDAs are targeting two different mechanisms of SARS-CoV-2 entry. Overall, our study provides insight into the potential of NPs with highly diverse chemical structures as valuable inspirational starting points for developing pan-SARS-CoV-2 therapeutics and for unravelling potential host factors and pathways regulating SARS-CoV-2 VOC infection including emerging omicron BA.5 subvariants.
KW - Host-directed antiviral
KW - Human protein kinase C
KW - Human TMPRSS2
KW - Human V-ATPase
KW - SARS-CoV-2 variants of concern
UR - http://www.scopus.com/inward/record.url?scp=85144436100&partnerID=8YFLogxK
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U2 - 10.1016/j.antiviral.2022.105484
DO - 10.1016/j.antiviral.2022.105484
M3 - Article
C2 - 36503013
AN - SCOPUS:85144436100
SN - 0166-3542
VL - 209
JO - Antiviral Research
JF - Antiviral Research
M1 - 105484
ER -