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Virard F, Giraud S, Bonnet M, Magadoux L, Martin L, Pham TH, Skafi N, Deneuve S, Frem R, Villoutreix BO, Sleiman NH, Reboulet J, Merabet S, Chaptal V, Chaveroux C, Hussein N, Aznar N, Fenouil T, Treilleux I, Saintigny P, Ansieau S, Manié S, Lebecque S, Renno T, Coste I. Targeting ERK-MYD88 interaction leads to ERK dysregulation and immunogenic cancer cell death. Nat Commun 2024; 15:7037. [PMID: 39147750 PMCID: PMC11327251 DOI: 10.1038/s41467-024-51275-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024] Open
Abstract
The quest for targeted therapies is critical in the battle against cancer. The RAS/MAP kinase pathway is frequently implicated in neoplasia, with ERK playing a crucial role as the most distal kinase in the RAS signaling cascade. Our previous research demonstrated that the interaction between ERK and MYD88, an adaptor protein in innate immunity, is crucial for RAS-dependent transformation and cancer cell survival. In this study, we examine the biological consequences of disrupting the ERK-MYD88 interaction through the ERK D-recruitment site (DRS), while preserving ERK's kinase activity. Our results indicate that EI-52, a small-molecule benzimidazole targeting ERK-MYD88 interaction induces an HRI-mediated integrated stress response (ISR), resulting in immunogenic apoptosis specific to cancer cells. Additionally, EI-52 exhibits anti-tumor efficacy in patient-derived tumors and induces an anti-tumor T cell response in mice in vivo. These findings suggest that inhibiting the ERK-MYD88 interaction may be a promising therapeutic approach in cancer treatment.
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Affiliation(s)
- François Virard
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
- University of Lyon, Faculté d'Odontologie, Hospices Civils de Lyon, Lyon, France
| | - Stéphane Giraud
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
- Center for Drug Discovery and Development, Synergy Lyon Cancer Foundation, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Mélanie Bonnet
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Léa Magadoux
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Laetitia Martin
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
- Center for Drug Discovery and Development, Synergy Lyon Cancer Foundation, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Thuy Ha Pham
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Najwa Skafi
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Sophie Deneuve
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Rita Frem
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Bruno O Villoutreix
- Université de Paris, NeuroDiderot, Inserm, Hôpital Robert Debré, 75019, Paris, France
| | - Nawal Hajj Sleiman
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242-CNRS/ENSL, Université Claude Bernard Lyon 1, Lyon, France
| | - Jonathan Reboulet
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242-CNRS/ENSL, Université Claude Bernard Lyon 1, Lyon, France
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242-CNRS/ENSL, Université Claude Bernard Lyon 1, Lyon, France
| | - Vincent Chaptal
- Drug Resistance & Membrane Proteins group, Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, Lyon, France
| | - Cédric Chaveroux
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Nader Hussein
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Nicolas Aznar
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Tanguy Fenouil
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
- University of Lyon, Faculté de Médecine, Hospices Civils de Lyon, Lyon, France
| | | | - Pierre Saintigny
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Stéphane Ansieau
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Serge Manié
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Serge Lebecque
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France
- University of Lyon, Faculté de Médecine, Hospices Civils de Lyon, Lyon, France
| | - Toufic Renno
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France.
| | - Isabelle Coste
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Lyon Cancer Research Center, Centre Léon Bérard, Lyon, France.
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2
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Sila T, Surasombatpattana S, Rajborirug S, Laochareonsuk W, Choochuen P, Kongkamol C, Ingviya T, Prompat N, Mahasirimongkol S, Sangkhathat S, Aiewsakun P. SARS-CoV-2 variant with the spike protein mutation F306L in the southern border provinces of Thailand. Sci Rep 2024; 14:7729. [PMID: 38565881 PMCID: PMC10987673 DOI: 10.1038/s41598-024-56646-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
The southernmost part of Thailand is a unique and culturally diverse region that has been greatly affected by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak during the coronavirus disease-2019 pandemic. To gain insights into this situation, we analyzed 1942 whole-genome sequences of SARS-CoV-2 obtained from the five southernmost provinces of Thailand between April 2021 and March 2022, together with those publicly available in the Global Initiative on Sharing All Influenza Data database. Our analysis revealed evidence for transboundary transmissions of the virus in and out of the five southernmost provinces during the study period, from both domestic and international sources. The most prevalent viral variant in our sequence dataset was the Delta B.1.617.2.85 variant, also known as the Delta AY.85 variant, with many samples carrying a non-synonymous mutation F306L in their spike protein. Protein-protein docking and binding interface analyses suggested that the mutation may enhance the binding between the spike protein and host cell receptor protein angiotensin-converting enzyme 2, and we found that the mutation was significantly associated with an increased fatality rate. This mutation has also been observed in other SARS-CoV-2 variants, suggesting that it is of particular interest and should be monitored.
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Affiliation(s)
- Thanit Sila
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Smonrapat Surasombatpattana
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Songyos Rajborirug
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Wison Laochareonsuk
- Division of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Pongsakorn Choochuen
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Chanon Kongkamol
- Department of Family Medicine and Preventive Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Thammasin Ingviya
- Department of Family Medicine and Preventive Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Napat Prompat
- Faculty of Medical Technology, Medical of Technology Service Center, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Surakameth Mahasirimongkol
- Department of Medical Sciences, Genetics Center, Medical Life Sciences Institute, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Surasak Sangkhathat
- Division of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
| | - Pakorn Aiewsakun
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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3
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Jin X, Hu X, Chen J, Shan L, Hao D, Zhang R. Electric field induced the changes in structure and function of human transforming growth factor beta receptor type I: from molecular dynamics to docking. J Biomol Struct Dyn 2024:1-12. [PMID: 38516997 DOI: 10.1080/07391102.2024.2329288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
The transforming growth factor beta (TGF-β) signaling pathway is believed to play essential roles in several physiological activities, including cancer. TGF-β receptor type I (TBR-I) is a key membrane receptor protein in the TGF-β signaling pathway, which relates to many intracellular biological effects. In recent years, cold atmospheric plasma (CAP) has been found to have promising prospects in selective anticancer therapy and has confirmed its essential role in the TGF-β signaling pathway. However, the ambiguous effect of CAP-induced electric field (EF) on TBR-I still limits the application of CAP in clinical therapy. Molecular dynamics is applied to assess the effect of EF on the structure of the extracellular domain of TBR-I using a series of indicators and methods, and then we discuss the ligand binding ability of TBR-I. Results show that moderate EF intensities' structural restraints may contribute to the structural stability and ligand-binding ability of TBR-I, but an EF higher than 0.1 V/nm will be harmful. What's more, EF induces a change in the docking interface of TBR-I, showing the conformation and position of special sequences of residues decide the ligand binding surface. The relevant results suggest that CAP-induced EF plays a crucial role in receptor-receptor interaction and provides significant guidelines for EF-related anticancer therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xinrui Jin
- School of Energy and Electrical Engineering, Chang'an University, Xi'an, China
| | - Xiaochuan Hu
- School of Energy and Electrical Engineering, Chang'an University, Xi'an, China
| | - Jiayu Chen
- School of Energy and Electrical Engineering, Chang'an University, Xi'an, China
| | - Lequn Shan
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Dingjun Hao
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Rui Zhang
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
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4
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Munna MMR, Islam MA, Shanta SS, Monty MA. Structural, functional, molecular docking analysis of a hypothetical protein from Talaromyces marneffei and its molecular dynamic simulation: an in-silico approach. J Biomol Struct Dyn 2024:1-20. [PMID: 38345137 DOI: 10.1080/07391102.2024.2314264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/29/2024] [Indexed: 03/01/2024]
Abstract
Telaromyces marneffei (formerly Penicillium marneffei) is an endemic pathogenic fungus in Southern China and Southeast Asia. It can cause disease in patients with travel-related exposure to this organism and high morbidity and mortality in acquired immune deficiency syndrome (AIDS). In this study, we analyzed the structure and function of a hypothetical protein from T. marneffei using several bioinformatics tools and servers to unveil novel pharmacological targets and design a peptide vaccine against specific epitopes. A total of seven functional epitopes were screened on the protein, and 'STGVDMWSV' was the most antigenic, non-allergenic and non-toxic. Molecular docking showed stronger affinity between the CTL epitope 'STGVDMWSV' and the MHC I allele HLA-A*02:01, a higher docking score -234.98 kcal/mol, revealed stable interactions during a 100 ns molecular dynamic simulation. Overall, the results of this study revealed that this hypothetical protein is crucial for comprehending biochemical, physiological pathways and identifying novel therapeutic targets for human health. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Masudur Rahman Munna
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md Ariful Islam
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, PR China
| | - Saima Sajnin Shanta
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Masuma Akter Monty
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, PR China
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5
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Jin Z, Wei Z. Molecular simulation for food protein-ligand interactions: A comprehensive review on principles, current applications, and emerging trends. Compr Rev Food Sci Food Saf 2024; 23:e13280. [PMID: 38284571 DOI: 10.1111/1541-4337.13280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 01/30/2024]
Abstract
In recent years, investigations on molecular interaction mechanisms between food proteins and ligands have attracted much interest. The interaction mechanisms can supply much useful information for many fields in the food industry, including nutrient delivery, food processing, auxiliary detection, and others. Molecular simulation has offered extraordinary insights into the interaction mechanisms. It can reflect binding conformation, interaction forces, binding affinity, key residues, and other information that physicochemical experiments cannot reveal in a fast and detailed manner. The simulation results have proven to be consistent with the results of physicochemical experiments. Molecular simulation holds great potential for future applications in the field of food protein-ligand interactions. This review elaborates on the principles of molecular docking and molecular dynamics simulation. Besides, their applications in food protein-ligand interactions are summarized. Furthermore, challenges, perspectives, and trends in molecular simulation of food protein-ligand interactions are proposed. Based on the results of molecular simulation, the mechanisms of interfacial behavior, enzyme-substrate binding, and structural changes during food processing can be reflected, and strategies for hazardous substance detection and food flavor adjustment can be generated. Moreover, molecular simulation can accelerate food development and reduce animal experiments. However, there are still several challenges to applying molecular simulation to food protein-ligand interaction research. The future trends will be a combination of international cooperation and data sharing, quantum mechanics/molecular mechanics, advanced computational techniques, and machine learning, which contribute to promoting food protein-ligand interaction simulation. Overall, the use of molecular simulation to study food protein-ligand interactions has a promising prospect.
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Affiliation(s)
- Zihan Jin
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zihao Wei
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, China
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6
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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7
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Lopez-Robles C, Scaramuzza S, Astorga-Simon EN, Ishida M, Williamson CD, Baños-Mateos S, Gil-Carton D, Romero-Durana M, Vidaurrazaga A, Fernandez-Recio J, Rojas AL, Bonifacino JS, Castaño-Díez D, Hierro A. Architecture of the ESCPE-1 membrane coat. Nat Struct Mol Biol 2023; 30:958-969. [PMID: 37322239 PMCID: PMC10352136 DOI: 10.1038/s41594-023-01014-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1), which rescues transmembrane proteins from the endolysosomal pathway for transport to the trans-Golgi network and the plasma membrane. This rescue entails the formation of recycling tubules through ESCPE-1 recruitment, cargo capture, coat assembly and membrane sculpting by mechanisms that remain largely unknown. Herein, we show that ESCPE-1 has a single-layer coat organization and suggest how synergistic interactions between ESCPE-1 protomers, phosphoinositides and cargo molecules result in a global arrangement of amphipathic helices to drive tubule formation. Our results thus define a key process of tubule-based endosomal sorting.
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Affiliation(s)
| | | | | | - Morié Ishida
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - David Gil-Carton
- CIC bioGUNE, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- BREM Basque Resource for Electron Microscopy, Leioa, Spain
| | - Miguel Romero-Durana
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | | | - Juan Fernandez-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | | | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Daniel Castaño-Díez
- BioEM Lab, Biozentrum, University of Basel, Basel, Switzerland.
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain.
| | - Aitor Hierro
- CIC bioGUNE, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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8
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Ni Q, Zhu B, Ji Y, Zheng Q, Liang X, Ma N, Jiang H, Zhang F, Shang Y, Wang Y, Xu S, Zhang E, Yuan Y, Chen T, Yin F, Cao H, Huang J, Xia J, Ding X, Qiu X, Ding K, Song C, Zhou W, Wu M, Wang K, Lui R, Lin Q, Chen W, Li Z, Cheng S, Wang X, Xie D, Li J. PPDPF Promotes the Development of Mutant KRAS-Driven Pancreatic Ductal Adenocarcinoma by Regulating the GEF Activity of SOS1. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2202448. [PMID: 36453576 PMCID: PMC9839844 DOI: 10.1002/advs.202202448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/11/2022] [Indexed: 06/17/2023]
Abstract
The guanine nucleotide exchange factor (GEF) SOS1 catalyzes the exchange of GDP for GTP on RAS. However, regulation of the GEF activity remains elusive. Here, the authors report that PPDPF functions as an important regulator of SOS1. The expression of PPDPF is significantly increased in pancreatic ductal adenocarcinoma (PDAC), associated with poor prognosis and recurrence of PDAC patients. Overexpression of PPDPF promotes PDAC cell growth in vitro and in vivo, while PPDPF knockout exerts opposite effects. Pancreatic-specific deletion of PPDPF profoundly inhibits tumor development in KRASG12D -driven genetic mouse models of PDAC. PPDPF can bind GTP and transfer GTP to SOS1. Mutations of the GTP-binding sites severely impair the tumor-promoting effect of PPDPF. Consistently, mutations of the critical amino acids mediating SOS1-PPDPF interaction significantly impair the GEF activity of SOS1. Therefore, this study demonstrates a novel model of KRAS activation via PPDPF-SOS1 axis, and provides a promising therapeutic target for PDAC.
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9
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Glycoprotein attachment with host cell surface receptor ephrin B2 and B3 in mediating entry of nipah and hendra virus: a computational investigation. J CHEM SCI 2022; 134:114. [DOI: 10.1007/s12039-022-02110-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/23/2022] [Accepted: 10/13/2022] [Indexed: 11/25/2022]
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10
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Pitsillou E, Liang JJ, Beh RC, Hung A, Karagiannis TC. Molecular dynamics simulations highlight the altered binding landscape at the spike-ACE2 interface between the Delta and Omicron variants compared to the SARS-CoV-2 original strain. Comput Biol Med 2022; 149:106035. [PMID: 36055162 PMCID: PMC9420038 DOI: 10.1016/j.compbiomed.2022.106035] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/15/2022] [Accepted: 08/20/2022] [Indexed: 11/21/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 variant (Omicron), represents a significant deviation in genetic makeup and function compared to previous variants. Following the BA.1 sublineage, the BA.2 and BA.3 Omicron subvariants became dominant, and currently the BA.4 and BA.5, which are quite distinct variants, have emerged. Using molecular dynamics simulations, we investigated the binding characteristics of the Delta and Omicron (BA.1) variants in comparison to wild-type (WT) at the interface of the spike protein receptor binding domain (RBD) and human angiotensin converting enzyme-2 (ACE2) ectodomain. The primary aim was to compare our molecular modelling systems with previously published observations, to determine the robustness of our approach for rapid prediction of emerging future variants. Delta and Omicron were found to bind to ACE2 with similar affinities (−39.4 and −43.3 kcal/mol, respectively) and stronger than WT (−33.5 kcal/mol). In line with previously published observations, the energy contributions of the non-mutated residues at the interface were largely retained between WT and the variants, with F456, F486, and Y489 having the strongest energy contributions to ACE2 binding. Further, residues N440K, Q498R, and N501Y were predicted to be energetically favourable in Omicron. In contrast to Omicron, which had the E484A and K417N mutations, intermolecular bonds were detected for the residue pairs E484:K31 and K417:D30 in WT and Delta, in accordance with previously published findings. Overall, our simplified molecular modelling approach represents a step towards predictive model systems for rapidly analysing arising variants of concern.
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Erausquin E, Serra P, Parras D, Santamaria P, López-Sagaseta J. Structural plasticity in I-Ag7 links autoreactivity to hybrid insulin peptides in type I diabetes. Front Immunol 2022; 13:924311. [PMID: 35967292 PMCID: PMC9365947 DOI: 10.3389/fimmu.2022.924311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
We recently provided evidence for promiscuous recognition of several different hybrid insulin peptides (HIPs) by the highly diabetogenic, I-Ag7-restricted 4.1-T cell receptor (TCR). To understand the structural determinants of this phenomenon, we solved the structure of an agonistic HIP/I-Ag7 complex, both in isolation as well as bound to the 4.1-TCR. We find that HIP promiscuity of the 4.1-TCR is dictated, on the one hand, by an amino acid sequence pattern that ensures I-Ag7 binding and, on the other hand, by the presence of three acidic residues at positions P5, P7 and P8 that favor an optimal engagement by the 4.1-TCR’s complementary determining regions. Surprisingly, comparison of the TCR-bound and unbound HIP/I-Ag7 structures reveals that 4.1-TCR binding triggers several novel and unique structural motions in both the I-Ag7 molecule and the peptide that are essential for docking. This observation indicates that the type 1 diabetes-associated I-Ag7 molecule is structurally malleable and that this plasticity allows the recognition of multiple peptides by individual TCRs that would otherwise be unable to do so.
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Affiliation(s)
- Elena Erausquin
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain
- Public University of Navarra (UPNA), Pamplona, Spain
- Navarra University Hospital, Pamplona, Spain
| | - Pau Serra
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Daniel Parras
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pere Santamaria
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- *Correspondence: Jacinto López-Sagaseta, ; Pere Santamaria,
| | - Jacinto López-Sagaseta
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain
- Public University of Navarra (UPNA), Pamplona, Spain
- Navarra University Hospital, Pamplona, Spain
- *Correspondence: Jacinto López-Sagaseta, ; Pere Santamaria,
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12
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Biswas S, Mahmud S, Mita MA, Afrose S, Hasan MR, Sultana Shimu MS, Saleh MA, Mostafa-Hedeab G, Alqarni M, Obaidullah AJ, Batiha GES. Molecular Docking and Dynamics Studies to Explore Effective Inhibitory Peptides Against the Spike Receptor Binding Domain of SARS-CoV-2. Front Mol Biosci 2022; 8:791642. [PMID: 35187069 PMCID: PMC8851422 DOI: 10.3389/fmolb.2021.791642] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/24/2021] [Indexed: 01/15/2023] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic due to the high transmission and mortality rate of this virus. The world health and economic sectors have been severely affected by this deadly virus, exacerbated by the lack of sufficient efficient vaccines. The design of effective drug candidates and their rapid development is necessary to combat this virus. In this study, we selected 23 antimicrobial peptides from the literature and predicted their structure using PEP-FOLD 3.5. In addition, we docked them to the SARS-CoV-2 spike protein receptor-binding domain (RBD) to study their capability to inhibit the RBD, which plays a significant role in virus binding, fusion and entry into the host cell. We used several docking programs including HDOCK, HPEPDOCK, ClusPro, and HawkDock to calculate the binding energy of the protein-peptide complexes. We identified four peptides with high binding free energy and docking scores. The docking results were further verified by molecular dynamics (MD) simulations to characterize the protein-peptide complexes in terms of their root-mean-square fluctuation (RMSF), root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond formation. Allergenicity and toxicity predictions suggested that the peptides we identified were non-allergenic and non-toxic. This study suggests that these four antimicrobial peptides could inhibit the RBD of SARS-CoV-2. Future in vitro and in vivo studies are necessary to confirm this.
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Affiliation(s)
- Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Md. Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Gomaa Mostafa-Hedeab
- Pharmacology Department and Health Research Unit-medical College, Jouf University, Jouf, Saudi Arabia
- Pharmacology Department, Faculty of Medicine, Beni-Suef University, Beni Suef, Egypt
| | - Mohammed Alqarni
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad J. Obaidullah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
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13
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Li H, Yan Y, Zhao X, Huang SY. Inclusion of Desolvation Energy into Protein–Protein Docking through Atomic Contact Potentials. J Chem Inf Model 2022; 62:740-750. [DOI: 10.1021/acs.jcim.1c01483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hao Li
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Yumeng Yan
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Xuejun Zhao
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
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14
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Kumar V. Molecular interactions between C9ORF72 and SMCR8: A local energetic frustration perspective. Biochem Biophys Res Commun 2021; 570:1-7. [PMID: 34256240 DOI: 10.1016/j.bbrc.2021.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/06/2021] [Indexed: 11/19/2022]
Abstract
The hexanucleotide repeat expansion in C9orf72 represents a major cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). C9orf72, together with SMCR8 and WDR41, can form a stable complex that regulates autophagy and membrane trafficking. Very recently, the cryo-EM structure of C9orf72-SMCR8-WDR41 helps in understanding the structure-function relationship of C9orf72. This protein complex is indispensable to several cellular processes and is strongly linked to familial ALS and FTD. Understanding the molecular basis of the C9orf72-SMCR8 protein-protein interaction is thus important to comprehend their function. To establish a basis for understanding the relationships between sequence, structure, and function of the C9orf72, this study reports a local frustration analysis on the C9orf72-SMCR8 complex structure. An analysis of local frustration profiles indicated that (1) the structural domains in C9orf72 are minimally-frustrated and relatively conserved, (2) high frustration patches on the protein-protein interface (3) increased frustration in the C-terminal helices involved in the dimerization of C9orf72 structures.
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Affiliation(s)
- Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, UP, 201303, India.
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15
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Villoutreix BO, Calvez V, Marcelin AG, Khatib AM. In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Int J Mol Sci 2021; 22:1695. [PMID: 33567580 PMCID: PMC7915722 DOI: 10.3390/ijms22041695] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 exploits angiotensin-converting enzyme 2 (ACE2) as a receptor to invade cells. It has been reported that the UK and South African strains may have higher transmission capabilities, eventually in part due to amino acid substitutions on the SARS-CoV-2 Spike protein. The pathogenicity seems modified but is still under investigation. Here we used the experimental structure of the Spike RBD domain co-crystallized with part of the ACE2 receptor, several in silico methods and numerous experimental data reported recently to analyze the possible impacts of three amino acid replacements (Spike K417N, E484K, N501Y) with regard to ACE2 binding. We found that the N501Y replacement in this region of the interface (present in both the UK and South African strains) should be favorable for the interaction with ACE2, while the K417N and E484K substitutions (South African strain) would seem neutral or even unfavorable. It is unclear if the N501Y substitution in the South African strain could counterbalance the K417N and E484K Spike replacements with regard to ACE2 binding. Our finding suggests that the UK strain should have higher affinity toward ACE2 and therefore likely increased transmissibility and possibly pathogenicity. If indeed the South African strain has a high transmission level, this could be due to the N501Y replacement and/or to substitutions in regions located outside the direct Spike-ACE2 interface but not so much to the K417N and E484K replacements. Yet, it should be noted that amino acid changes at Spike position 484 can lead to viral escape from neutralizing antibodies. Further, these amino acid substitutions do not seem to induce major structural changes in this region of the Spike protein. This structure-function study allows us to rationalize some observations made for the UK strain but raises questions for the South African strain.
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Affiliation(s)
- Bruno O. Villoutreix
- Integrative Computational Pharmacology and Data Mining, INSERM UMR 1141, NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de Virologie, F75013 Paris, France; (V.C.); (A.-G.M.)
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de Virologie, F75013 Paris, France; (V.C.); (A.-G.M.)
| | - Abdel-Majid Khatib
- Université de Bordeaux, INSERM, LAMC, U1029, F-33600 Pessac, France
- Institut Bergonié, 33000 Bordeaux, France
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