tetano
Editor, Senior Moderator
Front Immunol
. 2024 Feb 13:14:1282859.
doi: 10.3389/fimmu.2023.1282859. eCollection 2023. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches
Anna Niarakis[SUP] 1 2 [/SUP], Marek Ostaszewski[SUP] 3 [/SUP], Alexander Mazein[SUP] 3 [/SUP], Inna Kuperstein[SUP] 4 5 6 [/SUP], Martina Kutmon[SUP] 7 [/SUP], Marc E Gillespie[SUP] 8 9 [/SUP], Akira Funahashi[SUP] 10 [/SUP], Marcio Luis Acencio[SUP] 3 [/SUP], Ahmed Hemedan[SUP] 3 [/SUP], Michael Aichem[SUP] 11 [/SUP], Karsten Klein[SUP] 11 [/SUP], Tobias Czauderna[SUP] 12 [/SUP], Felicia Burtscher[SUP] 3 [/SUP], Takahiro G Yamada[SUP] 10 [/SUP], Yusuke Hiki[SUP] 13 [/SUP], Noriko F Hiroi[SUP] 14 15 [/SUP], Finterly Hu[SUP] 7 16 [/SUP], Nhung Pham[SUP] 7 16 [/SUP], Friederike Ehrhart[SUP] 16 [/SUP], Egon L Willighagen[SUP] 16 [/SUP], Alberto Valdeolivas[SUP] 17 [/SUP], Aurelien Dugourd[SUP] 17 [/SUP], Francesco Messina[SUP] 18 [/SUP], Marina Esteban-Medina[SUP] 19 20 [/SUP], Maria Peña-Chilet[SUP] 19 20 21 [/SUP], Kinza Rian[SUP] 19 [/SUP], Sylvain Soliman[SUP] 2 [/SUP], Sara Sadat Aghamiri[SUP] 22 [/SUP], Bhanwar Lal Puniya[SUP] 22 [/SUP], Aurélien Naldi[SUP] 2 [/SUP], Tomáš Helikar[SUP] 22 [/SUP], Vidisha Singh[SUP] 1 [/SUP], Marco Fariñas Fernández[SUP] 23 [/SUP], Viviam Bermudez[SUP] 23 [/SUP], Eirini Tsirvouli[SUP] 23 [/SUP], Arnau Montagud[SUP] 24 [/SUP], Vincent Noël[SUP] 4 5 6 [/SUP], Miguel Ponce-de-Leon[SUP] 24 [/SUP], Dieter Maier[SUP] 25 [/SUP], Angela Bauch[SUP] 25 [/SUP], Benjamin M Gyori[SUP] 26 [/SUP], John A Bachman[SUP] 26 [/SUP], Augustin Luna[SUP] 27 28 [/SUP], Janet Piñero[SUP] 29 30 [/SUP], Laura I Furlong[SUP] 29 30 [/SUP], Irina Balaur[SUP] 3 [/SUP], Adrien Rougny[SUP] 31 32 [/SUP], Yohan Jarosz[SUP] 3 [/SUP], Rupert W Overall[SUP] 33 [/SUP], Robert Phair[SUP] 34 [/SUP], Livia Perfetto[SUP] 35 [/SUP], Lisa Matthews[SUP] 36 [/SUP], Devasahayam Arokia Balaya Rex[SUP] 37 [/SUP], Marija Orlic-Milacic[SUP] 8 [/SUP], Luis Cristobal Monraz Gomez[SUP] 4 5 6 [/SUP], Bertrand De Meulder[SUP] 38 [/SUP], Jean Marie Ravel[SUP] 4 5 6 [/SUP], Bijay Jassal[SUP] 8 [/SUP], Venkata Satagopam[SUP] 3 39 [/SUP], Guanming Wu[SUP] 40 [/SUP], Martin Golebiewski[SUP] 41 [/SUP], Piotr Gawron[SUP] 3 [/SUP], Laurence Calzone[SUP] 4 5 6 [/SUP], Jacques S Beckmann[SUP] 42 [/SUP], Chris T Evelo[SUP] 16 [/SUP], Peter D'Eustachio[SUP] 36 [/SUP], Falk Schreiber[SUP] 11 43 [/SUP], Julio Saez-Rodriguez[SUP] 17 [/SUP], Joaquin Dopazo[SUP] 19 20 21 44 [/SUP], Martin Kuiper[SUP] 23 [/SUP], Alfonso Valencia[SUP] 24 45 [/SUP], Olaf Wolkenhauer[SUP] 46 47 [/SUP], Hiroaki Kitano[SUP] 48 [/SUP], Emmanuel Barillot[SUP] 4 5 6 [/SUP], Charles Auffray[SUP] 38 [/SUP], Rudi Balling[SUP] 49 [/SUP], Reinhard Schneider[SUP] 3 [/SUP]; COVID-19 Disease Map Community
Affiliations
Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing.
Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors.
Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19.
Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.
Keywords: SARS-CoV-2; disease maps; dynamic models; large-scale community effort; mechanistic models; systems biology; systems medicine.
. 2024 Feb 13:14:1282859.
doi: 10.3389/fimmu.2023.1282859. eCollection 2023. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches
Anna Niarakis[SUP] 1 2 [/SUP], Marek Ostaszewski[SUP] 3 [/SUP], Alexander Mazein[SUP] 3 [/SUP], Inna Kuperstein[SUP] 4 5 6 [/SUP], Martina Kutmon[SUP] 7 [/SUP], Marc E Gillespie[SUP] 8 9 [/SUP], Akira Funahashi[SUP] 10 [/SUP], Marcio Luis Acencio[SUP] 3 [/SUP], Ahmed Hemedan[SUP] 3 [/SUP], Michael Aichem[SUP] 11 [/SUP], Karsten Klein[SUP] 11 [/SUP], Tobias Czauderna[SUP] 12 [/SUP], Felicia Burtscher[SUP] 3 [/SUP], Takahiro G Yamada[SUP] 10 [/SUP], Yusuke Hiki[SUP] 13 [/SUP], Noriko F Hiroi[SUP] 14 15 [/SUP], Finterly Hu[SUP] 7 16 [/SUP], Nhung Pham[SUP] 7 16 [/SUP], Friederike Ehrhart[SUP] 16 [/SUP], Egon L Willighagen[SUP] 16 [/SUP], Alberto Valdeolivas[SUP] 17 [/SUP], Aurelien Dugourd[SUP] 17 [/SUP], Francesco Messina[SUP] 18 [/SUP], Marina Esteban-Medina[SUP] 19 20 [/SUP], Maria Peña-Chilet[SUP] 19 20 21 [/SUP], Kinza Rian[SUP] 19 [/SUP], Sylvain Soliman[SUP] 2 [/SUP], Sara Sadat Aghamiri[SUP] 22 [/SUP], Bhanwar Lal Puniya[SUP] 22 [/SUP], Aurélien Naldi[SUP] 2 [/SUP], Tomáš Helikar[SUP] 22 [/SUP], Vidisha Singh[SUP] 1 [/SUP], Marco Fariñas Fernández[SUP] 23 [/SUP], Viviam Bermudez[SUP] 23 [/SUP], Eirini Tsirvouli[SUP] 23 [/SUP], Arnau Montagud[SUP] 24 [/SUP], Vincent Noël[SUP] 4 5 6 [/SUP], Miguel Ponce-de-Leon[SUP] 24 [/SUP], Dieter Maier[SUP] 25 [/SUP], Angela Bauch[SUP] 25 [/SUP], Benjamin M Gyori[SUP] 26 [/SUP], John A Bachman[SUP] 26 [/SUP], Augustin Luna[SUP] 27 28 [/SUP], Janet Piñero[SUP] 29 30 [/SUP], Laura I Furlong[SUP] 29 30 [/SUP], Irina Balaur[SUP] 3 [/SUP], Adrien Rougny[SUP] 31 32 [/SUP], Yohan Jarosz[SUP] 3 [/SUP], Rupert W Overall[SUP] 33 [/SUP], Robert Phair[SUP] 34 [/SUP], Livia Perfetto[SUP] 35 [/SUP], Lisa Matthews[SUP] 36 [/SUP], Devasahayam Arokia Balaya Rex[SUP] 37 [/SUP], Marija Orlic-Milacic[SUP] 8 [/SUP], Luis Cristobal Monraz Gomez[SUP] 4 5 6 [/SUP], Bertrand De Meulder[SUP] 38 [/SUP], Jean Marie Ravel[SUP] 4 5 6 [/SUP], Bijay Jassal[SUP] 8 [/SUP], Venkata Satagopam[SUP] 3 39 [/SUP], Guanming Wu[SUP] 40 [/SUP], Martin Golebiewski[SUP] 41 [/SUP], Piotr Gawron[SUP] 3 [/SUP], Laurence Calzone[SUP] 4 5 6 [/SUP], Jacques S Beckmann[SUP] 42 [/SUP], Chris T Evelo[SUP] 16 [/SUP], Peter D'Eustachio[SUP] 36 [/SUP], Falk Schreiber[SUP] 11 43 [/SUP], Julio Saez-Rodriguez[SUP] 17 [/SUP], Joaquin Dopazo[SUP] 19 20 21 44 [/SUP], Martin Kuiper[SUP] 23 [/SUP], Alfonso Valencia[SUP] 24 45 [/SUP], Olaf Wolkenhauer[SUP] 46 47 [/SUP], Hiroaki Kitano[SUP] 48 [/SUP], Emmanuel Barillot[SUP] 4 5 6 [/SUP], Charles Auffray[SUP] 38 [/SUP], Rudi Balling[SUP] 49 [/SUP], Reinhard Schneider[SUP] 3 [/SUP]; COVID-19 Disease Map Community
Affiliations
- PMID: 38414974
- PMCID: PMC10897000
- DOI: 10.3389/fimmu.2023.1282859
Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing.
Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors.
Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19.
Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.
Keywords: SARS-CoV-2; disease maps; dynamic models; large-scale community effort; mechanistic models; systems biology; systems medicine.