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Gantla MR, Tsigelny IF, Kouznetsova VL. Repurposing of drugs for combined treatment of COVID-19 cytokine storm using machine learning. Med Drug Discov 2023; 17:100148. [PMID: 36466363 PMCID: PMC9706997 DOI: 10.1016/j.medidd.2022.100148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 12/02/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) induced cytokine storm is the major cause of COVID-19 related deaths. Patients have been treated with drugs that work by inhibiting a specific protein partly responsible for the cytokines production. This approach provided very limited success, since there are multiple proteins involved in the complex cell signaling disease mechanisms. We targeted five proteins: Angiotensin II receptor type 1 (AT1R), A disintegrin and metalloprotease 17 (ADAM17), Nuclear Factor‑Kappa B (NF‑κB), Janus kinase 1 (JAK1) and Signal Transducer and Activator of Transcription 3 (STAT3), which are involved in the SARS‑CoV‑2 induced cytokine storm pathway. We developed machine-learning (ML) models for these five proteins, using known active inhibitors. After developing the model for each of these proteins, FDA-approved drugs were screened to find novel therapeutics for COVID‑19. We identified twenty drugs that are active for four proteins with predicted scores greater than 0.8 and eight drugs active for all five proteins with predicted scores over 0.85. Mitomycin C is the most active drug across all five proteins with an average prediction score of 0.886. For further validation of these results, we used the PyRx software to conduct protein-ligand docking experiments and calculated the binding affinity. The docking results support findings by the ML model. This research study predicted that several drugs can target multiple proteins simultaneously in cytokine storm-related pathway. These may be useful drugs to treat patients because these therapies can fight cytokine storm caused by the virus at multiple points of inhibition, leading to synergistically effective treatments.
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Key Words
- 1D 2D 3D, one- two- three-dimensional
- ADAM17, A disintegrin and metalloprotease 17
- ARDS, acute respiratory distress syndrome
- AT1R, Angiotensin II receptor type 1
- AUROC, Area under receiver operator characteristic curve
- COVID-19
- COVID-19, coronavirus disease 2019
- CRS, cytokine release syndrome
- CXCL10, CXC-chemokine ligand 10
- Docking
- FDA, Food and Drug Administration
- G-CSF, granulocyte colony stimulating factor
- IC50, half maximal inhibitory concentration
- ICU, intensive care unit
- IL, interleukin
- JAK1, Janus kinase 1
- MCP1, monocyte chemoattractant protein-1
- MIP1α, macrophage inflammatory protein 1
- ML, machine learning
- Machine learning
- Multi-targeted drug discovery
- NF-κB, Nuclear Factor-Kappa B
- PDB, Protein Data Bank
- PaDEL, Pharmaeutical data exploration laboratory
- ROC, receiver operator characteristic curve
- SARS-CoV-2
- SMILES, Simplified Molecular-Input Line-Entry System
- STAT3, signal transducer and activator of transcription 3
- Screening of FDA-approved drugs
- TNFα, tumor necrosis factor α
- WEKA, Waikato Environment for Knowledge Analysis
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Affiliation(s)
| | - Igor F Tsigelny
- San Diego Supercomputer Center, UC San Diego, Calif, USA
- BiAna, La Jolla, Calif, USA
- Dept. of Neurosciences, UC San Diego, Calif, USA
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Bousquet J, Le Moing V, Blain H, Czarlewski W, Zuberbier T, de la Torre R, Pizarro Lozano N, Reynes J, Bedbrook A, Cristol JP, Cruz AA, Fiocchi A, Haahtela T, Iaccarino G, Klimek L, Kuna P, Melén E, Mullol J, Samolinski B, Valiulis A, Anto JM. Efficacy of broccoli and glucoraphanin in COVID-19: From hypothesis to proof-of-concept with three experimental clinical cases. World Allergy Organ J 2021; 14:100498. [PMID: 33425204 PMCID: PMC7770975 DOI: 10.1016/j.waojou.2020.100498] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
COVID-19 is described in a clinical case involving a patient who proposed the hypothesis that Nuclear factor (erythroid-derived 2)-like 2 (Nrf2)-interacting nutrients may help to prevent severe COVID-19 symptoms. Capsules of broccoli seeds containing glucoraphanin were being taken before the onset of SARS-CoV-2 infection and were continued daily for over a month after the first COVID-19 symptoms. They were found to reduce many of the symptoms rapidly and for a duration of 6-12 h by repeated dosing. When the patient was stable but still suffering from cough and nasal obstruction when not taking the broccoli capsules, a double-blind induced cough challenge confirmed the speed of onset of the capsules (less than 10 min). A second clinical case with lower broccoli doses carried out during the cytokine storm confirmed the clinical benefits already observed. A third clinical case showed similar effects at the onset of symptoms. In the first clinical trial, we used a dose of under 600 μmol per day of glucoraphanin. However, such a high dose may induce pharmacologic effects that require careful examination before the performance of any study. It is likely that the fast onset of action is mediated through the TRPA1 channel. These experimental clinical cases represent a proof-of-concept confirming the hypothesis that Nrf2-interacting nutrients are effective in COVID-19. However, this cannot be used in practice before the availability of further safety data, and confirmation is necessary through proper trials on efficacy and safety.
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Key Words
- ACE, Angiotensin converting enzyme
- AT1R, Angiotensin II receptor type 1
- BMI, Body mass index
- Broccoli
- Broccoli, Broccoli seed capsules
- COVID-19
- COVID-19, Coronavirus 19 disease
- Cough challenge
- NAPQI, N-acetyl-p-benzoquinone imine
- Nrf2
- Nrf2, Nuclear factor (erythroid-derived 2)-like 2
- SARS, Severe acute respiratory syndrome
- SARS-Cov-2, Severe acute respiratory syndrome coronavirus 2
- TRP, Transient receptor potential
- TRPA1
- TRPA1, Transient receptor potential ankyrin 1
- TRPV1
- TRPV1, Transient receptor potential vanillin 1
- VAS, Visual analogue scale
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Affiliation(s)
- Jean Bousquet
- Charité, Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Comprehensive Allergy Center, Department of Dermatology and Allergy, Berlin, Germany
- MACVIA France, University Hospital, Montpellier, France
| | | | - Hubert Blain
- Department of Geriatrics, Montpellier University Hospital, Montpellier, France
| | | | - Torsten Zuberbier
- Charité, Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Comprehensive Allergy Center, Department of Dermatology and Allergy, Berlin, Germany
| | - Rafael de la Torre
- CIBER Fisiopatologia de La Obesidad y Nutrición (CIBEROBN), Madrid, Spain
- IMIM (Hospital del Mar Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Jacques Reynes
- Maladies Infectiouses et Tropicales, CHU Montpellier, France
| | - Anna Bedbrook
- MACVIA France, University Hospital, Montpellier, France
- MASK-air, Montpellier, France
| | - Jean-Paul Cristol
- Laboratoire de Biochimie et Hormonologie, PhyMedExp, Université de Montpellier, INSERM, CNRS, CHU de Montpellier, France
| | - Alvaro A. Cruz
- Fundação ProAR, Federal University of Bahia and GARD/WHO Planning Group, Salvador, Brazil
| | - Alessandro Fiocchi
- Division of Allergy, Department of Pediatric Medicine - The Bambino Gesù Children's Research Hospital Holy see, Rome, Italy
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, And University of Helsinki, Helsinki, Finland
| | - Guido Iaccarino
- Department of Advanced Biomedical Sciences, Federico II University, Napoli, Italy
| | - Ludger Klimek
- Center for Rhinology and Allergology, Wiesbaden, Germany
| | - Piotr Kuna
- Division of Internal Medicine, Asthma and Allergy, Barlicki University Hospital, Medical University of Lodz, Poland
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet and Sachs' Children's Hospital, Stockholm, Sweden
| | - Joaquim Mullol
- Rhinology Unit & Smell Clinic, ENT Department, Hospital Clinic - Clinical & Experimental Respiratory Immunoallergy, IDIBAPS, CIBERES, Universitat de Barcelona, Barcelona, Spain
| | - Boleslaw Samolinski
- Department of Prevention of Environmental Hazards and Allergology, Medical University of Warsaw, Poland
| | - Arunas Valiulis
- Vilnius University Faculty of Medicine, Institute of Clinical Medicine & Institute of Health Sciences, Vilnius, Lithuania
| | - Josep M. Anto
- IMIM (Hospital del Mar Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- ISGlobal. ISGlobAL, Barcelona, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
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