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Roy A, Shi L, Chang A, Dong X, Fernandez A, Kraft JC, Li J, Le VQ, Winegar RV, Cherf GM, Slocum D, Poulson PD, Casper GE, Vallecillo-Zúniga ML, Valdoz JC, Miranda MC, Bai H, Kipnis Y, Olshefsky A, Priya T, Carter L, Ravichandran R, Chow CM, Johnson MR, Cheng S, Smith M, Overed-Sayer C, Finch DK, Lowe D, Bera AK, Matute-Bello G, Birkland TP, DiMaio F, Raghu G, Cochran JR, Stewart LJ, Campbell MG, Van Ry PM, Springer T, Baker D. De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8. Nat Commun 2023; 14:5660. [PMID: 37704610 PMCID: PMC10500007 DOI: 10.1038/s41467-023-41272-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023] Open
Abstract
The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between homologous αvβ6 and αvβ8 and other RGD integrins, stabilize specific conformational states, and have high thermal stability could have considerable therapeutic utility. Existing small molecule and antibody inhibitors do not have all these properties, and hence new approaches are needed. Here we describe a generalized method for computationally designing RGD-containing miniproteins selective for a single RGD integrin heterodimer and conformational state. We design hyperstable, selective αvβ6 and αvβ8 inhibitors that bind with picomolar affinity. CryoEM structures of the designed inhibitor-integrin complexes are very close to the computational design models, and show that the inhibitors stabilize specific conformational states of the αvβ6 and the αvβ8 integrins. In a lung fibrosis mouse model, the αvβ6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity.
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Affiliation(s)
- Anindya Roy
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lei Shi
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Encodia Inc, 5785 Oberlin Drive, San Diego, CA, 92121, USA
| | - Ashley Chang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Xianchi Dong
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China
| | - Andres Fernandez
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - John C Kraft
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Jing Li
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
| | - Viet Q Le
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
| | - Rebecca Viazzo Winegar
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Gerald Maxwell Cherf
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Denali Therapeutics, South San Francisco, CA, USA
| | - Dean Slocum
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
| | - P Daniel Poulson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Garrett E Casper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | | | - Jonard Corpuz Valdoz
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Marcos C Miranda
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Hua Bai
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Yakov Kipnis
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Audrey Olshefsky
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Tanu Priya
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Lauren Carter
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cameron M Chow
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Max R Johnson
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Suna Cheng
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - McKaela Smith
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Catherine Overed-Sayer
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Bioscience COPD/IPF, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Donna K Finch
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Alchemab Therapeutics Ltd, Cambridge, UK
| | - David Lowe
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Evox Therapeutics Limited, Oxford Science Park, Medawar Centre, East Building, Robert Robinson Avenue, Oxford, OX4 4HG, England
| | - Asim K Bera
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Gustavo Matute-Bello
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Timothy P Birkland
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ganesh Raghu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Dept of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Lance J Stewart
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Melody G Campbell
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
| | - Pam M Van Ry
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.
| | - Timothy Springer
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA.
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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3
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Hua L, Ju L, Xu H, Li C, Sun S, Zhang Q, Cao J, Ding R. Outdoor air pollution exposure and the risk of asthma and wheezing in the offspring. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:14165-14189. [PMID: 36149565 DOI: 10.1007/s11356-022-23094-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
According to the "fetal origin of disease" hypothesis, air pollution exposure in pregnancy may play an important role in stimulating the early programming of asthma and allergies. However, previous studies reported inconsistent findings. The aim of this meta-analysis was to provide higher grade evidence and quantitatively analyze the link between prenatal exposure to outdoor air pollutants and childhood asthma and wheezing. Databases (Web of Science and PubMed) were extensively searched for articles published from the start of the database to September 15, 2021. Either random-effect model or fixed-effect model was used to estimate the disease-specific relative risks (RR) with the corresponding 95% confidence intervals (CIs) to estimate the association. Newcastle-Ottawa Quality Score (NOS) was used to assess the quality of studies. This study finally included 13 cohort studies, and the findings showed that NO2 and SO2 exposure during entire pregnancy was significantly associated with wheezing (RR = 1.032, 95% CI: 1.000, 1.066) and asthma (RR = 1.114, 95% CI: 1.066, 1.164), respectively. Further analyses showed that PM2.5 were positively associated with asthma in the second (RR = 1.194, 95% CI: 1.143, 1.247) and third trimester (RR = 1.050, 95% CI: 1.007, 1.094), while NO2 (RR = 1.060, 95% CI: 1.021, 1.101) and SO2 (RR = 1.067, 95% CI: 1.013, 1.123) were shown positively associated with asthma only in the second trimester. The relationship between wheezing and outdoor air pollutants was not significant in any of the pregnancy subgroups. This study suggests that prenatal exposure of outdoor air pollution may increase the asthma and wheezing risk in the offspring and that the second trimester may be a sensitive period for air pollution exposure. But the interpretation of the causal association is hampered by limited number of studies on dose response.
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Affiliation(s)
- Lei Hua
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Liangliang Ju
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Hanbing Xu
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Changlian Li
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Shu Sun
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Qi Zhang
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Jiyu Cao
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- Department of Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Rui Ding
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China.
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5
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Shamsollahi HR, Jahanbin B, Rafieian S, Yunesian M. Particulates induced lung inflammation and its consequences in the development of restrictive and obstructive lung diseases: a systematic review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:25035-25050. [PMID: 33779901 DOI: 10.1007/s11356-021-13559-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/16/2021] [Indexed: 05/13/2023]
Abstract
Particulate matters (PMs) are significant components of air pollution in the urban environment. PMs with aerodynamic diameter less than 2.5 μm (PM2.5) can penetrate to the alveolar area and introduce numerous compounds to the pneumocystis that can initiate inflammatory response. There are several questions about this exposure as follows: does PM2.5-induced inflammation lead to a specific disease? If yes, what is the form of the progressed disease? This systematic review was designed and conducted to respond to these questions. Four databases, including Web of Science, Scopus, PubMed, and Embase, were reviewed systematically to find the related articles. According to the included articles, the only available data on the inflammatory effects of PM2.5 comes from either in vitro or animal studies. Both types of studies have shown that the induced inflammation is type I and includes secretion of proinflammatory cytokines. The exposure duration of longer than 28 weeks was not observed in any of the reviewed studies. However, as there is not a specific antigenic component in the urban particulate matters and based on the available evidence, the antigen-presenting is not a common process in the inflammatory responses to PM2.5. Therefore, neither signaling to repair cells such as fibroblasts nor over-secretion of extracellular matrix (ECM) proteins can occur following PM2.5-induced inflammation. These pieces of evidence weaken the probability of the development of fibrotic diseases. On the other hand, permanent inflammation induces the destruction of ECM and alveolar walls by over-secretion of protease enzymes and therefore results in progressive obstructive effects.
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Affiliation(s)
- Hamid Reza Shamsollahi
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Behnaz Jahanbin
- Department of Pathology, Cancer Research Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahab Rafieian
- General Thoracic Surgery Ward, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Masud Yunesian
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
- Center for Air Pollution Research (CAPR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, Tehran, Iran.
- Department of Research Methodology and Data Analysis, Institute for Environmental Research (IER), Tehran University of Medical Sciences, Tehran, Iran.
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6
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Gibbs JL, Dallon BW, Lewis JB, Walton CM, Arroyo JA, Reynolds PR, Bikman BT. Diesel Exhaust Particle Exposure Compromises Alveolar Macrophage Mitochondrial Bioenergetics. Int J Mol Sci 2019; 20:ijms20225598. [PMID: 31717476 PMCID: PMC6888061 DOI: 10.3390/ijms20225598] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/29/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
Diesel exhaust particles (DEPs) are known pathogenic pollutants that constitute a significant quantity of air pollution. Given the ubiquitous presence of macrophages throughout the body, including the lungs, as well as their critical role in tissue and organismal metabolic function, we sought to determine the effect of DEP exposure on macrophage mitochondrial function. Following daily DEP exposure in mice, pulmonary macrophages were isolated for mitochondrial analyses, revealing reduced respiration rates and dramatically elevated H2O2 levels. Serum ceramides and inflammatory cytokines were increased. To determine the degree to which the changes in mitochondrial function in macrophages were not dependent on any cross-cell communication, primary pulmonary murine macrophages were used to replicate the DEP exposure in a cell culture model. We observed similar changes as seen in pulmonary macrophages, namely diminished mitochondrial respiration, but increased H2O2 production. Interestingly, when treated with myriocin to inhibit ceramide biosynthesis, these DEP-induced mitochondrial changes were mitigated. Altogether, these data suggest that DEP exposure may compromise macrophage mitochondrial and whole-body function via pathologic alterations in macrophage ceramide metabolism.
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Affiliation(s)
- Jonathan L. Gibbs
- Metabolism Research Lab, Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Blake W. Dallon
- Metabolism Research Lab, Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Joshua B. Lewis
- Lung and Placental Research Lab, Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Chase M. Walton
- Metabolism Research Lab, Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Juan A. Arroyo
- Lung and Placental Research Lab, Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Paul R. Reynolds
- Lung and Placental Research Lab, Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Benjamin T. Bikman
- Metabolism Research Lab, Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
- Correspondence:
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