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Sun J, Shi M, Song Z, Hua F, Yan X, Zhang M, Duan H, Liu J. CD146-dependent macrophage infiltration promotes epidural fibrosis via the Erdr1/ERK/CCR2 pathway. Int Immunopharmacol 2024; 137:112528. [PMID: 38908086 DOI: 10.1016/j.intimp.2024.112528] [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: 02/02/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
Low back pain due to epidural fibrosis is a major complication after spine surgery. Macrophages infiltrate the wound area post laminectomy, but the role of macrophages in epidural fibrosis remains largely elusive. In a mouse model of laminectomy, macrophage depletion decreased epidural fibrosis. CD146, an adhesion molecule involved in cell migration, is expressed by macrophages. CD146-defective macrophages exhibited impaired migration, which was mediated by reduced expression of CCR2 and suppression of the MAPK/ERK signaling pathway. CD146-defective macrophages suppress the MAPK/ERK signaling pathway by increasing Erdr1. In vivo, CD146 deficiency decreased macrophage infiltration and reduced extracellular matrix deposition in wound tissues. Moreover, the anti-CD146 antibody AA98 suppressed macrophage infiltration and epidural fibrosis. Taken together, these findings demonstrated that CD146 deficiency alleviates epidural fibrosis by decreasing the migration of macrophages via the Erdr1/ERK/CCR2 pathway. Blocking CD146 and macrophage infiltration may help alleviate epidural fibrosis.
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Affiliation(s)
- Jinpeng Sun
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mohan Shi
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zeyuan Song
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Hua
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiyun Yan
- Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Nanozyme Laboratory in Zhongyuan, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan 451163, China
| | - Mingshun Zhang
- NHC Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Immunology, Nanjing Medical University, Nanjing, China.
| | - Hongxia Duan
- Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jun Liu
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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2
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Frasnetti E, Magni A, Castelli M, Serapian SA, Moroni E, Colombo G. Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence. Curr Opin Struct Biol 2024; 87:102835. [PMID: 38744148 DOI: 10.1016/j.sbi.2024.102835] [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: 01/23/2024] [Revised: 04/14/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Computational approaches can provide highly detailed insight into the molecular recognition processes that underlie drug binding, the assembly of protein complexes, and the regulation of biological functional processes. Classical simulation methods can bridge a wide range of length- and time-scales typically involved in such processes. Lately, automated learning and artificial intelligence methods have shown the potential to expand the reach of physics-based approaches, ushering in the possibility to model and even design complex protein architectures. The synergy between atomistic simulations and AI methods is an emerging frontier with a huge potential for advances in structural biology. Herein, we explore various examples and frameworks for these approaches, providing select instances and applications that illustrate their impact on fundamental biomolecular problems.
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Affiliation(s)
- Elena Frasnetti
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy
| | - Andrea Magni
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy
| | - Matteo Castelli
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy
| | - Stefano A Serapian
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy
| | | | - Giorgio Colombo
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy.
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3
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Condeminas M, Macias MJ. Overcoming challenges in structural biology with integrative approaches and nanobody-derived technologies. Curr Opin Struct Biol 2024; 84:102764. [PMID: 38215529 DOI: 10.1016/j.sbi.2023.102764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/24/2023] [Accepted: 12/11/2023] [Indexed: 01/14/2024]
Abstract
A full understanding of protein structure is key to unraveling how these systems work, how mutations affect their function, and discovering new hotspots for drug discovery. Research tackling this field began with the analysis of globular proteins. In recent years, as technology has improved, research efforts have broadened their focus to include the study of multidomain proteins and the analysis of conformational variability, flexibility, and dynamic systems. Here, we have selected five recent examples that integrate complementary structural methods to provide insight into the behavior of modular, flexible, and transient contacts. We also describe the structural application of domains derived from single-chain antibodies, which are instrumental in overcoming the size limitation of cryogenic electron microscopy (cryoEM) studies. As these methods are continuously developed, they will lead to the interrogation of more complex systems, revealing how large signaling and transcriptional machines are assembled in the context of health and disease.
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Affiliation(s)
- Miriam Condeminas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 10, Barcelona 08028, Spain; Department of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS-UPF), Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 10, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain.
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Holtzman MJ, Zhang Y, Wu K, Romero AG. Mitogen-activated protein kinase-guided drug discovery for post-viral and related types of lung disease. Eur Respir Rev 2024; 33:230220. [PMID: 38417971 PMCID: PMC10900067 DOI: 10.1183/16000617.0220-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/18/2024] [Indexed: 03/01/2024] Open
Abstract
Respiratory viral infections are a major public health problem, with much of their morbidity and mortality due to post-viral lung diseases that progress and persist after the active infection is cleared. This paradigm is implicated in the most common forms of chronic lung disease, such as asthma and COPD, as well as other virus-linked diseases including progressive and long-term coronavirus disease 2019. Despite the impact of these diseases, there is a lack of small-molecule drugs available that can precisely modify this type of disease process. Here we will review current progress in understanding the pathogenesis of post-viral and related lung disease with characteristic remodelling phenotypes. We will also develop how this data leads to mitogen-activated protein kinase (MAPK) in general and MAPK13 in particular as key druggable targets in this pathway. We will also explore recent advances and predict the future breakthroughs in structure-based drug design that will provide new MAPK inhibitors as drug candidates for clinical applications. Each of these developments point to a more effective approach to treating the distinct epithelial and immune cell based mechanisms, which better account for the morbidity and mortality of post-viral and related types of lung disease. This progress is vital given the growing prevalence of respiratory viruses and other inhaled agents that trigger stereotyped progression to acute illness and chronic disease.
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Affiliation(s)
- Michael J Holtzman
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
- NuPeak Therapeutics Inc., St. Louis, MO, USA
| | - Yong Zhang
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kangyun Wu
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Arthur G Romero
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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5
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Takarada JE, Cunha MR, Almeida VM, Vasconcelos SNS, Santiago AS, Godoi PH, Salmazo A, Ramos PZ, Fala AM, de Souza LR, Da Silva IEP, Bengtson MH, Massirer KB, Couñago RM. Discovery of pyrazolo[3,4-d]pyrimidines as novel mitogen-activated protein kinase kinase 3 (MKK3) inhibitors. Bioorg Med Chem 2024; 98:117561. [PMID: 38157838 DOI: 10.1016/j.bmc.2023.117561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
The dual-specificity protein kinase MKK3 has been implicated in tumor cell proliferation and survival, yet its precise role in cancer remains inconclusive. A critical step in elucidating the kinase's involvement in disease biology is the identification of potent, cell-permeable kinase inhibitors. Presently, MKK3 lacks a dedicated tool compound for these purposes, along with validated methods for the facile screening, identification, and optimization of inhibitors. In this study, we have developed a TR-FRET-based enzymatic assay for the detection of MKK3 activity in vitro and a BRET-based assay to assess ligand binding to this enzyme within intact human cells. These assays were instrumental in identifying hit compounds against MKK3 that share a common chemical scaffold, sourced from a library of bioactive kinase inhibitors. Initial hits were subsequently expanded through the synthesis of novel analogs. The resulting structure-activity relationship (SAR) was rationalized using molecular dynamics simulations against a homology model of MKK3. We expect our findings to expedite the development of novel, potent, selective, and bioactive inhibitors, thus facilitating investigations into MKK3's role in various cancers.
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Affiliation(s)
- Jéssica E Takarada
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Micael R Cunha
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Vitor M Almeida
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Stanley N S Vasconcelos
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - André S Santiago
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Paulo H Godoi
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Anita Salmazo
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Priscila Z Ramos
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Angela M Fala
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Lucas R de Souza
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Italo E P Da Silva
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Mario H Bengtson
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Katlin B Massirer
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Rafael M Couñago
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States.
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McGregor L, Acajjaoui S, Desfosses A, Saïdi M, Bacia-Verloop M, Schwarz JJ, Juyoux P, von Velsen J, Bowler MW, McCarthy AA, Kandiah E, Gutsche I, Soler-Lopez M. The assembly of the Mitochondrial Complex I Assembly complex uncovers a redox pathway coordination. Nat Commun 2023; 14:8248. [PMID: 38086790 PMCID: PMC10716376 DOI: 10.1038/s41467-023-43865-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The Mitochondrial Complex I Assembly (MCIA) complex is essential for the biogenesis of respiratory Complex I (CI), the first enzyme in the respiratory chain, which has been linked to Alzheimer's disease (AD) pathogenesis. However, how MCIA facilitates CI assembly, and how it is linked with AD pathogenesis, is poorly understood. Here we report the structural basis of the complex formation between the MCIA subunits ECSIT and ACAD9. ECSIT binding induces a major conformational change in the FAD-binding loop of ACAD9, releasing the FAD cofactor and converting ACAD9 from a fatty acid β-oxidation (FAO) enzyme to a CI assembly factor. We provide evidence that ECSIT phosphorylation downregulates its association with ACAD9 and is reduced in neuronal cells upon exposure to amyloid-β (Aβ) oligomers. These findings advance our understanding of the MCIA complex assembly and suggest a possible role for ECSIT in the reprogramming of bioenergetic pathways linked to Aβ toxicity, a hallmark of AD.
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Affiliation(s)
- Lindsay McGregor
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Samira Acajjaoui
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS (IBS), 38044, Grenoble, France
| | - Melissa Saïdi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS (IBS), 38044, Grenoble, France
| | - Jennifer J Schwarz
- European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Pauline Juyoux
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Jill von Velsen
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Andrew A McCarthy
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Eaazhisai Kandiah
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS (IBS), 38044, Grenoble, France.
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Montserrat Soler-Lopez
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France.
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