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Torres SV, Valle MB, Mackessy SP, Menzies SK, Casewell NR, Ahmadi S, Burlet NJ, Muratspahić E, Sappington I, Overath MD, Rivera-de-Torre E, Ledergerber J, Laustsen AH, Boddum K, Bera AK, Kang A, Brackenbrough E, Cardoso IA, Crittenden EP, Edge RJ, Decarreau J, Ragotte RJ, Pillai AS, Abedi M, Han HL, Gerben SR, Murray A, Skotheim R, Stuart L, Stewart L, Fryer TJA, Jenkins TP, Baker D. De novo designed proteins neutralize lethal snake venom toxins. RESEARCH SQUARE 2024:rs.3.rs-4402792. [PMID: 38798548 PMCID: PMC11118692 DOI: 10.21203/rs.3.rs-4402792/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Snakebite envenoming remains a devastating and neglected tropical disease, claiming over 100,000 lives annually and causing severe complications and long-lasting disabilities for many more1,2. Three-finger toxins (3FTx) are highly toxic components of elapid snake venoms that can cause diverse pathologies, including severe tissue damage3 and inhibition of nicotinic acetylcholine receptors (nAChRs) resulting in life-threatening neurotoxicity4. Currently, the only available treatments for snakebite consist of polyclonal antibodies derived from the plasma of immunized animals, which have high cost and limited efficacy against 3FTxs5,6,7. Here, we use deep learning methods to de novo design proteins to bind short- and long-chain α-neurotoxins and cytotoxins from the 3FTx family. With limited experimental screening, we obtain protein designs with remarkable thermal stability, high binding affinity, and near-atomic level agreement with the computational models. The designed proteins effectively neutralize all three 3FTx sub-families in vitro and protect mice from a lethal neurotoxin challenge. Such potent, stable, and readily manufacturable toxin-neutralizing proteins could provide the basis for safer, cost-effective, and widely accessible next-generation antivenom therapeutics. Beyond snakebite, our computational design methodology should help democratize therapeutic discovery, particularly in resource-limited settings, by substantially reducing costs and resource requirements for development of therapies to neglected tropical diseases.
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Affiliation(s)
- Susana Vázquez Torres
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA
| | - Melisa Benard Valle
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stephen P. Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, 80639, USA
| | - Stefanie K. Menzies
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Biomedical & Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom LA1 4YG8
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Shirin Ahmadi
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nick J. Burlet
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Edin Muratspahić
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Isaac Sappington
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA
| | - Max D. Overath
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Esperanza Rivera-de-Torre
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jann Ledergerber
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kim Boddum
- Sophion Bioscience, DK-2750 Ballerup, Denmark
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Evans Brackenbrough
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Iara A. Cardoso
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Edouard P. Crittenden
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Rebecca J. Edge
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Robert J. Ragotte
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Arvind S. Pillai
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mohamad Abedi
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah L. Han
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Stacey R. Gerben
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Analisa Murray
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Rebecca Skotheim
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lynda Stuart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Thomas J. A. Fryer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105,USA
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Arunrungvichian K, Vajragupta O, Hayakawa Y, Pongrakhananon V. Targeting Alpha7 Nicotinic Acetylcholine Receptors in Lung Cancer: Insights, Challenges, and Therapeutic Strategies. ACS Pharmacol Transl Sci 2024; 7:28-41. [PMID: 38230275 PMCID: PMC10789132 DOI: 10.1021/acsptsci.3c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 01/18/2024]
Abstract
Alpha7 nicotinic acetylcholine receptor (α7 nAChR) is an ion-gated calcium channel that plays a significant role in various aspects of cancer pathogenesis, particularly in lung cancer. Preclinical studies have elucidated the molecular mechanism underlying α7 nAChR-associated lung cancer proliferation, chemotherapy resistance, and metastasis. Understanding and targeting this mechanism are crucial for developing therapeutic interventions aimed at disrupting α7 nAChR-mediated cancer progression and improving treatment outcomes. Drug research and discovery have determined natural compounds and synthesized chemical antagonists that specifically target α7 nAChR. However, approved α7 nAChR antagonists for clinical use are lacking, primarily due to challenges related to achieving the desired selectivity, efficacy, and safety profiles required for effective therapeutic intervention. This comprehensive review provided insights into the molecular mechanisms associated with α7 nAChR and its role in cancer progression, particularly in lung cancer. Furthermore, it presents an update on recent evidence about α7 nAChR antagonists and addresses the challenges encountered in drug research and discovery in this field.
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Affiliation(s)
- Kuntarat Arunrungvichian
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Unit
of Compounds Library for Drug Discovery, Mahidol University, Bangkok 10400, Thailand
| | - Opa Vajragupta
- Research
Affairs, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yoshihiro Hayakawa
- Institute
of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Varisa Pongrakhananon
- Department
of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Preclinical
Toxicity and Efficacy Assessment of Medicines and Chemicals Research
Unit, Chulalongkorn University, Bangkok 10330, Thailand
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Regalado L, Sario S, Mendes RJ, Valle J, Harvey PJ, Teixeira C, Gomes P, Andreu D, Santos C. Towards a Sustainable Management of the Spotted-Wing Drosophila: Disclosing the Effects of Two Spider Venom Peptides on Drosophila suzukii. INSECTS 2023; 14:533. [PMID: 37367349 DOI: 10.3390/insects14060533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2023]
Abstract
The spotted-wing drosophila (Drosophila suzukii) is a polyphagous pest that causes severe damage and economic losses to soft-skinned fruit production. Current control methods are dominated by inefficient cultural practices and broad-spectrum insecticides that, in addition to having toxic effects on non-target organisms, are becoming less effective due to acquired resistance. The increasing awareness of the real impact of insecticides on health and the environment has promoted the exploration of new insecticidal compounds, addressing novel molecular targets. This study explores the efficacy of two orally delivered spider venom peptides (SVPs), J-atracotoxin-Hv1c (Hv1c) and µ-theraphotoxin-Hhn2b (TRTX), to manage D. suzukii, through survival assays and the evaluation of gene expression associated with detoxification pathways. Treatment with TRTX at 111.5 µM for 48 h enhanced fly longevity compared with the control group. Gene expression analysis suggests that detoxification and stress-related mechanisms, such as expression of P450 proteins and apoptotic stimuli signaling, are triggered in D. suzukii flies in response to these treatments. Our results highlight the potential interest of SVPs to control this pest, shedding light on how to ultimately develop improved target-specific formulations.
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Affiliation(s)
- Laura Regalado
- iB2, Biology Department, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
- LAQV-REQUIMTE, Faculty of Sciences, University of Porto, 4050-453 Porto, Portugal
| | - Sara Sario
- iB2, Biology Department, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
- LAQV-REQUIMTE, Faculty of Sciences, University of Porto, 4050-453 Porto, Portugal
| | - Rafael J Mendes
- iB2, Biology Department, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
- LAQV-REQUIMTE, Faculty of Sciences, University of Porto, 4050-453 Porto, Portugal
| | - Javier Valle
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08002 Barcelona, Spain
| | - Peta J Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cátia Teixeira
- LAQV-REQUIMTE, Faculty of Sciences, University of Porto, 4050-453 Porto, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Faculty of Sciences, University of Porto, 4050-453 Porto, Portugal
| | - David Andreu
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08002 Barcelona, Spain
| | - Conceição Santos
- iB2, Biology Department, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
- LAQV-REQUIMTE, Faculty of Sciences, University of Porto, 4050-453 Porto, Portugal
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Brogna C, Cristoni S, Brogna B, Bisaccia DR, Marino G, Viduto V, Montano L, Piscopo M. Toxin-like Peptides from the Bacterial Cultures Derived from Gut Microbiome Infected by SARS-CoV-2-New Data for a Possible Role in the Long COVID Pattern. Biomedicines 2022; 11:biomedicines11010087. [PMID: 36672595 PMCID: PMC9855837 DOI: 10.3390/biomedicines11010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/18/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023] Open
Abstract
It has been 3 years since the beginning of the SARS-CoV-2 outbreak, however it is as yet little known how to care for the acute COVID-19 and long COVID patients. COVID-19 clinical manifestations are of both pulmonary and extra-pulmonary types. Extra-pulmonary ones include extreme tiredness (fatigue), shortness of breath, muscle aches, hyposmia, dysgeusia, and other neurological manifestations. In other autoimmune diseases, such as Parkinson's disease (PD) or Alzheimer's Disease (AD), it is well known that role of acetylcholine is crucial in olfactory dysfunction. We have already observed the presence of toxin-like peptides in plasma, urine, and faecal samples from COVID-19 patients, which are very similar to molecules known to alter acetylcholine signaling. After observing the production of these peptides in bacterial cultures, we have performed additional proteomics analyses to better understand their behavior and reported the extended data from our latest in vitro experiment. It seems that the gut microbiome continues to produce toxin-like peptides also after the decrease of RNA SARS-CoV-2 viral load at molecular tests. These toxicological interactions between the gut/human microbiome bacteria and the virus suggest a new scenario in the study of the clinical symptoms in long COVID and also in acute COVID-19 patients. It is discussed that in the bacteriophage similar behavior, the presence of toxins produced by bacteria continuously after viral aggression can be blocked using an appropriate combination of certain drugs.
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Affiliation(s)
- Carlo Brogna
- Department of Research, Craniomed Group Facility Srl., 20091 Bresso, Italy
- Correspondence: (C.B.); (M.P.)
| | | | - Barbara Brogna
- Department of Radiology, Moscati Hospital, Contrada Amoretta, 83100 Avellino, Italy
| | | | - Giuliano Marino
- Marsanconsulting Srl. Public Health Company, Via dei Fiorentini, 80133 Napoli, Italy
| | | | - Luigi Montano
- Andrology Unit and Service of Life Style Medicine in Uro-Andrology, Local Health Authority (ASL), 84124 Salerno, Italy
| | - Marina Piscopo
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
- Correspondence: (C.B.); (M.P.)
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