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Yahiro I, Barnuevo KDE, Sato O, Mohapatra S, Toyoda A, Itoh T, Ohno K, Matsuyama M, Chakraborty T, Ohta K. Modeling the SDF-1/CXCR4 protein using advanced artificial intelligence and antagonist screening for Japanese anchovy. Front Physiol 2024; 15:1349119. [PMID: 38370015 PMCID: PMC10869568 DOI: 10.3389/fphys.2024.1349119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
SDF-1/CXCR4 chemokine signaling are indispensable for cell migration, especially the Primordial Germ Cell (PGC) migration towards the gonadal ridge during early development. We earlier found that this signaling is largely conserved in the Japanese anchovy (Engraulis japonicus, EJ), and a mere treatment of CXCR4 antagonist, AMD3100, leads to germ cell depletion and thereafter gonad sterilization. However, the effect of AMD3100 was limited. So, in this research, we scouted for CXCR4 antagonist with higher potency by employing advanced artificial intelligence deep learning-based computer simulations. Three potential candidates, AMD3465, WZ811, and LY2510924, were selected and in vivo validation was conducted using Japanese anchovy embryos. We found that seven transmembrane motif of EJ CXCR4a and EJ CXCR4b were extremely similar with human homolog while the CXCR4 chemokine receptor N terminal (PF12109, essential for SDF-1 binding) was missing in EJ CXCR4b. 3D protein analysis and cavity search predicted the cavity in EJ CXCR4a to be five times larger (6,307 ų) than that in EJ CXCR4b (1,241 ų). Docking analysis demonstrated lower binding energy of AMD3100 and AMD3465 to EJ CXCR4a (Vina score -9.6) and EJ CXCR4b (Vina score -8.8), respectively. Furthermore, we observed significant PGC mismigration in microinjected AMD3465 treated groups at 10, 100 and 1 × 105 nM concentration in 48 h post fertilized embryos. The other three antagonists showed various degrees of PGC dispersion, but no significant effect compared to their solvent control at tested concentrations was observed. Cumulatively, our results suggests that AMD3645 might be a better candidate for abnormal PGC migration in Japanese anchovy and warrants further investigation.
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Affiliation(s)
- Issei Yahiro
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | | | - Oga Sato
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Sipra Mohapatra
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Aqua-Bioresource Innovation Center, Kyushu University, Saga, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Takehiko Itoh
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Kaoru Ohno
- National Institute for Basic Biology (NIBB), Aichi, Japan
| | | | - Tapas Chakraborty
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Aqua-Bioresource Innovation Center, Kyushu University, Saga, Japan
| | - Kohei Ohta
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Aqua-Bioresource Innovation Center, Kyushu University, Saga, Japan
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2
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Sonawani A, Naglekar A, Kharche S, Sengupta D. Assessing Protein-Protein Docking Protocols: Case Studies of G-Protein-Coupled Receptor Interactions. Methods Mol Biol 2024; 2780:257-280. [PMID: 38987472 DOI: 10.1007/978-1-0716-3985-6_13] [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] [Indexed: 07/12/2024]
Abstract
The interactions of G-protein-coupled receptors (GPCRs) with other proteins are critical in several cellular processes but resolving their structural dynamics remains challenging. An increasing number of GPCR complexes have been experimentally resolved but others including receptor variants are yet to be characterized, necessitating computational predictions of their interactions. Although integrative approaches with multi-scale simulations would provide rigorous estimates of their conformational dynamics, protein-protein docking remains a first tool of choice of many researchers due to the availability of open-source programs and easy to use web servers with reasonable predictive power. Protein-protein docking algorithms have limited ability to consider protein flexibility, environment effects, and entropy contributions and are usually a first step towards more integrative approaches. The two critical steps of docking: the sampling and scoring algorithms have improved considerably and their performance has been validated against experimental data. In this chapter, we provide an overview and generalized protocol of a few docking protocols using GPCRs as test cases. In particular, we demonstrate the interactions of GPCRs with extracellular protein ligands and an intracellular protein effectors (G-protein) predicted from docking approaches and test their limitations. The current chapter will help researchers critically assess docking protocols and predict experimentally testable structures of GPCR complexes.
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Affiliation(s)
- Archana Sonawani
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, Navi Mumbai, India
| | - Amit Naglekar
- CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - Durba Sengupta
- CSIR-National Chemical Laboratory, Pune, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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3
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Ma L, Zhang S, Liang Q, Huang W, Wang H, Pan E, Xu P, Zhang S, Tao F, Tang J, Qing R. CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs. BMC Bioinformatics 2023; 24:360. [PMID: 37743473 PMCID: PMC10518928 DOI: 10.1186/s12859-023-05477-9] [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: 01/25/2023] [Accepted: 09/12/2023] [Indexed: 09/26/2023] Open
Abstract
Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. Although gene profiling can identify their cancer-specific signatures, systematic correlations between protein functions and tumor-related mechanisms are still unclear. We present here the CrMP-Sol database ( https://bio-gateway.aigene.org.cn/g/CrMP ), which aims to breach the gap between the two. Machine learning was used to extract key functional descriptions for protein visualization in the 3D-space, where spatial distributions provide function-based predictive connections between proteins and cancer types. CrMP-Sol also presents QTY-enabled water-soluble designs to facilitate native membrane protein studies despite natural hydrophobicity. Five examples with varying transmembrane helices in different categories were used to demonstrate the feasibility. Native and redesigned proteins exhibited highly similar characteristics, predicted structures and binding pockets, and slightly different docking poses against known ligands, although task-specific designs are still required for proteins more susceptible to internal hydrogen bond formations. The database can accelerate therapeutic developments and biotechnological applications of cancer-related membrane proteins.
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Affiliation(s)
- Lina Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sitao Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qi Liang
- Zhejiang Lab, Research Center for Intelligent Computing Platforms, Hangzhou, 311121, Zhejiang, China
| | - Wenting Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Emily Pan
- The Lawrenceville School, 2500 Main Street, Lawrenceville, NJ, 08648, USA
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuguang Zhang
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jin Tang
- Zhejiang Lab, Research Center for Intelligent Computing Platforms, Hangzhou, 311121, Zhejiang, China.
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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4
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Kumar V, Ozguney B, Vlachou A, Chen Y, Gazit E, Tamamis P. Peptide Self-Assembled Nanocarriers for Cancer Drug Delivery. J Phys Chem B 2023; 127:1857-1871. [PMID: 36812392 PMCID: PMC10848270 DOI: 10.1021/acs.jpcb.2c06751] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/24/2022] [Indexed: 02/24/2023]
Abstract
The design of novel cancer drug nanocarriers is critical in the framework of cancer therapeutics. Nanomaterials are gaining increased interest as cancer drug delivery systems. Self-assembling peptides constitute an emerging novel class of highly attractive nanomaterials with highly promising applications in drug delivery, as they can be used to facilitate drug release and/or stability while reducing side effects. Here, we provide a perspective on peptide self-assembled nanocarriers for cancer drug delivery and highlight the aspects of metal coordination, structure stabilization, and cyclization, as well as minimalism. We review particular challenges in nanomedicine design criteria and, finally, provide future perspectives on addressing a portion of the challenges via self-assembling peptide systems. We consider that the intrinsic advantages of such systems, along with the increasing progress in computational and experimental approaches for their study and design, could possibly lead to novel classes of single or multicomponent systems incorporating such materials for cancer drug delivery.
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Affiliation(s)
- Vijay
Bhooshan Kumar
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Busra Ozguney
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Anastasia Vlachou
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Yu Chen
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ehud Gazit
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department
of Materials Science and Engineering, Iby and Aladar Fleischman Faculty
of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol
School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Phanourios Tamamis
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Department
of Materials Science and Engineering, Texas
A&M University, College
Station, Texas 77843-3003, United States
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5
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Wu X, Qian L, Zhao H, Lei W, Liu Y, Xu X, Li J, Yang Z, Wang D, Zhang Y, Zhang Y, Tang R, Yang Y, Tian Y. CXCL12/CXCR4: An amazing challenge and opportunity in the fight against fibrosis. Ageing Res Rev 2023; 83:101809. [PMID: 36442720 DOI: 10.1016/j.arr.2022.101809] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 11/26/2022]
Abstract
Fibrosis is a pathological process caused by abnormal wound healing response, which often leads to excessive deposition of extracellular matrix, distortion of organ architecture, and loss of organ function. Aging is an important risk factor for the development of organ fibrosis. C-X-C receptor 4 (CXCR4) is the predominant chemokine receptor on fibrocytes, C-X-C motif ligand 12 (CXCL12) is the only ligand of CXCR4. Accumulated evidence have confirmed that CXCL12/CXCR4 can be involved in multiple pathological mechanisms in fibrosis, such as inflammation, immunity, epithelial-mesenchymal transition, and angiogenesis. In addition, CXCL12/CXCR4 have also been shown to improve fibrosis levels in many organs including the heart, liver, lung and kidney; thus, they are promising targets for anti-fibrotic therapy. Notably, inhibitors of CXCL12 or CXCR4 also play an important role in various fibrosis-related diseases. In summary, this review systematically summarizes the role of CXCL12/CXCR4 in fibrosis, and this information is of great significance for understanding CXCL12/CXCR4. This will also contribute to the design of further studies related to CXCL12/CXCR4 and fibrosis, and shed light on potential therapies for fibrosis.
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Affiliation(s)
- Xue Wu
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Lu Qian
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Huadong Zhao
- Department of General Surgery, Tangdu Hospital, The Airforce Medical University, Xi'an, China
| | - Wangrui Lei
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Yanqing Liu
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Xiaoling Xu
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Jiawen Li
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Zhi Yang
- Department of General Surgery, Tangdu Hospital, The Airforce Medical University, Xi'an, China
| | - Du Wang
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Yuchen Zhang
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Yan Zhang
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Ran Tang
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Yang Yang
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China.
| | - Ye Tian
- Deparment of Neurology, Xi'an No.3 Hospital, Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China.
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6
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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7
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Allosteric modulation of the chemokine receptor-chemokine CXCR4-CXCL12 complex by tyrosine sulfation. Int J Biol Macromol 2022; 206:812-822. [PMID: 35306016 DOI: 10.1016/j.ijbiomac.2022.03.078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 11/21/2022]
Abstract
The chemokine receptor CXCR4 and its cognate ligand CXCL12 mediate pathways that lead to cell migration and chemotaxis. Although the structural details of related receptor-ligand complexes have been resolved, the roles of the N-terminal domain of the receptor and post-translational sulfation that are determinants of ligand selectivity and affinity remain unclear. Here, we analyze the structural dynamics induced by receptor sulfation by combining molecular dynamics, docking and network analysis. The sulfotyrosine residues, 7YsN-term, 12YsN-term and 21YsN-term allow the N-terminal domain of the apo-sulfated receptor to adopt an "open" conformation that appears to facilitate ligand binding. The overall topology of the CXCR4-CXCL12 complex is independent of the sulfation state, but an extensive network of protein-protein interactions characterizes the sulfated receptor, in line with its increased ligand affinity. The altered interactions of sulfotyrosine residues, such as 21YsN-term-47RCXCL12 replacing the 21YN-term-13FCXCL12 interaction, propagate via allosteric pathways towards the receptor lumen. In particular, our results suggest that the experimentally-reported receptor-ligand interactions 262D6.58-8RCXCL12 and 277E7.28-12RCXCL12 could be dependent on the sulfation state of the receptor and need to be carefully analyzed. Our work is an important step in understanding chemokine-receptor interactions and how post-translational modifications could modulate receptor-ligand complexes.
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8
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Identify potential prognostic indicators and tumor-infiltrating immune cells in pancreatic adenocarcinoma. Biosci Rep 2022; 42:230704. [PMID: 35083488 PMCID: PMC8859426 DOI: 10.1042/bsr20212523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/12/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Pancreatic adenocarcinoma (PAAD) is a kind of highly malignant tumor and lacks early diagnosis method and effective treatment. Tumor microenvironment (TME) is of great importance for the occurrence and development of PAAD. Thus, a comprehensive overview of genes and tumor-infiltrating immune cells (TICs) related to TME dynamic changes conduce to develop novel therapeutic targets and prognostic indicators. Methods: We used MAlignant Tumors using Expression data (ESTIMATE) algorithm to analyze the transcriptome RNA-seq data of 182 PAAD cases on The Cancer Genome Atlas (TCGA) platform. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein–protein interaction (PPI) network, COX regression analysis and gene set enrichment analysis (GSEA) were carried out to get the hub genes related to the prognosis of PAAD patients. These core genes were validated in GEPIA. CXCL10 expression as a poor prognostic indicator was validated in GEO database. Finally, CIBERSORT algorithm was applied to understand the status of TICs. Results: A total of 715 up-regulated differential expression genes (DEGs) and 57 down-regulated DEGs were found simultaneously in stromal and immune groups. These DEGs were mainly enriched in immune recognition, activation and response processes. CD4, CXCL12, CXCL10, CCL5 and CXCL9 were the top five core genes. Then, the validation of these genes showed that CD4, CXCL10, CXCL5, CXCL9 were up-regulated in PAAD. Among the core genes, CXCL10 had a negative correlation with the survival time of PAAD patients. CD8+ T cells, CD4+ T cells memory activated, macrophages M1 had positive correlation of CXCL10 expression, whereas regulatory T cells (Tregs), macrophages M0 and B cells memory had negative correlation. Conclusion: We generated a series of genes related to TME with prognostic implications and TICs in PAAD, which have the potential to be novel immunotherapy targets and prognostic markers. The data showed that CXCL10 was favorable as a poor prognostic indicator in PAAD patients.
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Single-Cell Sequencing Demonstrates Complex Resistance Landscape in CLL and MCL Treated with BTK and BCL2 Inhibitors. Blood Adv 2021; 6:503-508. [PMID: 34861696 PMCID: PMC8791563 DOI: 10.1182/bloodadvances.2021006211] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/15/2021] [Indexed: 11/23/2022] Open
Abstract
Therapy resistance to both individual and sequential BTK and BCL2 inhibition is clonally complex and most commonly oligoclonal. Single-agent resistance mutations occur in mutually exclusive clones; resistance mutations to sequential monotherapies variably co-occur.
The genomic landscape of resistance to targeted agents (TAs) used as monotherapy in chronic lymphocytic leukemia (CLL) is complex and often heterogeneous at the patient level. To gain insight into the clonal architecture of acquired genomic resistance to Bruton tyrosine kinase (BTK) inhibitors and B-cell lymphoma 2 (BCL2) inhibitors in CLL, particularly in patients carrying multiple resistance mutations, we performed targeted single-cell DNA sequencing of 8 patients who developed progressive disease (PD) on TAs (either class). In all cases, analysis of single-cell architecture revealed mutual exclusivity between multiple resistance mutations to the same TA class, variable clonal co-occurrence of multiple mutations affecting different TAs in patients exposed to both classes, and a phenomenon of multiple independent emergences of identical nucleotide changes leading to canonical resistance mutations. We also report the first observation of established BCL2 resistance mutations in a patient with mantle cell lymphoma (MCL) following PD on sequential monotherapy, implicating BCL2 as a venetoclax resistance mechanism in MCL. Taken together, these data reveal the significant clonal complexity of CLL and MCL progression on TAs at the nucleotide level and confirm the presence of multiple, clonally independent, mechanisms of TA resistance within each individual disease context.
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10
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Spiller S, Wippold T, Bellmann-Sickert K, Franz S, Saalbach A, Anderegg U, Beck-Sickinger AG. Protease-Triggered Release of Stabilized CXCL12 from Coated Scaffolds in an Ex Vivo Wound Model. Pharmaceutics 2021; 13:pharmaceutics13101597. [PMID: 34683890 PMCID: PMC8539926 DOI: 10.3390/pharmaceutics13101597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
Biomaterials are designed to improve impaired healing of injured tissue. To accomplish better cell integration, we suggest to coat biomaterial surfaces with bio-functional proteins. Here, a mussel-derived surface-binding peptide is used and coupled to CXCL12 (stromal cell-derived factor 1α), a chemokine that activates CXCR4 and consequently recruits tissue-specific stem and progenitor cells. CXCL12 variants with either non-releasable or protease-mediated-release properties were designed and compared. Whereas CXCL12 was stabilized at the N-terminus for protease resistance, a C-terminal linker was designed that allowed for specific cleavage-mediated release by matrix metalloproteinase 9 and 2, since both enzymes are frequently found in wound fluid. These surface adhesive CXCL12 derivatives were produced by expressed protein ligation. Functionality of the modified chemokines was assessed by inositol phosphate accumulation and cell migration assays. Increased migration of keratinocytes and primary mesenchymal stem cells was demonstrated. Immobilization and release were studied for bioresorbable PCL-co-LC scaffolds, and accelerated wound closure was demonstrated in an ex vivo wound healing assay on porcine skin grafts. After 24 h, a significantly improved CXCL12-specific growth stimulation of the epithelial tips was already observed. The presented data display a successful application of protein-coated biomaterials for skin regeneration.
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Affiliation(s)
- Sabrina Spiller
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; (S.S.); (K.B.-S.)
| | - Tom Wippold
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
| | - Kathrin Bellmann-Sickert
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; (S.S.); (K.B.-S.)
| | - Sandra Franz
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
| | - Anja Saalbach
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
| | - Ulf Anderegg
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
- Correspondence: (U.A.); (A.G.B.-S.); Tel.: +49-341-972-5881 (U.A.); +49-341-973-6900 (A.G.B.-S.); Fax: +49-341-972-5878 (U.A.); +49-341-973-6909 (A.G.B.-S.)
| | - Annette G. Beck-Sickinger
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; (S.S.); (K.B.-S.)
- Correspondence: (U.A.); (A.G.B.-S.); Tel.: +49-341-972-5881 (U.A.); +49-341-973-6900 (A.G.B.-S.); Fax: +49-341-972-5878 (U.A.); +49-341-973-6909 (A.G.B.-S.)
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11
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Wang Y, Tan J, Li J, Chen H, Wang W. ING5 Inhibits Migration and Invasion of Esophageal Cancer Cells by Downregulating the IL-6/CXCL12 Signaling Pathway. Technol Cancer Res Treat 2021; 20:15330338211039940. [PMID: 34520285 PMCID: PMC8445537 DOI: 10.1177/15330338211039940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common cancer in East Asia and in other parts of the world and exhibits a poor prognosis. Growth inhibitor 5 (ING5) is a new member of the growth inhibitor (ING) protein family and is involved in many important cellular functions, such as the cell cycle, apoptosis, and chromatin remodeling. As a newly discovered tumor suppressor, ING5 has been shown to inhibit lung cancer proliferation and distant metastasis through the AKT pathway. In lung cancer tumors, ING5 can attenuate the ability of cancer cells to invade normal tumor-adjacent tissues. However, ING5 has rarely been studied in ESCC. Here, we found that in ESCC EC-109 cancer cells, ING5 overexpression inhibited cell proliferation and tumor invasion, whereas, in ESCC TE-1 cancer cells, ING5 knockdown promoted cell invasion. In a nude mouse xenograft model, ING5 overexpression inhibited tumor growth and the invasion ability of ESCC cells. Further studies revealed that ING5 overexpression inhibited IL-6/CXCL12 expression at both the mRNA and protein levels as well as morphological changes. We found for the first time that ING5 inhibits ESCC cell migration and invasion by downregulating the IL-6/CXCL12 signaling pathway.
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Affiliation(s)
- Yali Wang
- Henan Provincial Chest Hospital, Zhengzhou, P.R. China
| | - Jiao Tan
- Henan Provincial Chest Hospital, Zhengzhou, P.R. China
| | - Jing Li
- Henan Provincial Chest Hospital, Zhengzhou, P.R. China
| | - Huihui Chen
- Henan Provincial Chest Hospital, Zhengzhou, P.R. China
| | - Wei Wang
- Henan Provincial Chest Hospital, Zhengzhou, P.R. China
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12
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Qing R, Tao F, Chatterjee P, Yang G, Han Q, Chung H, Ni J, Suter BP, Kubicek J, Maertens B, Schubert T, Blackburn C, Zhang S. Non-full-length Water-Soluble CXCR4 QTY and CCR5 QTY Chemokine Receptors: Implication for Overlooked Truncated but Functional Membrane Receptors. iScience 2020; 23:101670. [PMID: 33376963 PMCID: PMC7756140 DOI: 10.1016/j.isci.2020.101670] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/12/2020] [Accepted: 10/08/2020] [Indexed: 01/06/2023] Open
Abstract
It was posited that functionalities of GPCRs require full-length sequences that are negated by residue deletions. Here we report that significantly truncated nfCCR5QTY and nfCXCR4QTY still bind native ligands. Receptor-ligand interactions were discovered from yeast 2-hybrid screening and confirmed by mating selection. Two nfCCR5QTY (SZ218a, SZ190b) and two nfCXCR4QTY (SZ158a, SZ146a) were expressed in E. coli. Synthesized receptors exhibited α-helical structures and bound respective ligands with reduced affinities. SZ190b and SZ158a were reconverted into non-QTY forms and expressed in HEK293T cells. Reconverted receptors localized on cell membranes and functioned as negative regulators for ligand-induced signaling when co-expressed with full-length receptors. CCR5-SZ190b individually can perform signaling at a reduced level with higher ligand concentration. Our findings provide insight into essential structural components for CCR5 and CXCR4 functionality, while raising the possibility that non-full-length receptors may be resulted from alternative splicing and that pseudo-genes in genomes may be present and functional in living organisms. Y2H screening reveals ligand interaction from truncated CXCR4 and CCR5 in QTY form Truncated CCR5QTY and CXCR4QTY can be produced in E. coli and bind native ligands Reconverted receptors localize on membranes and regulate cell signaling in HEK293 Our finding indicates potential presence and function for truncated receptors
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Affiliation(s)
- Rui Qing
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Fei Tao
- Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Pranam Chatterjee
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,The Center for Bits and Atoms, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gaojie Yang
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qiuyi Han
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Haeyoon Chung
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jun Ni
- Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Bernhard P Suter
- Next Interactions, Inc., 2600 Hilltop Drive, Building B, C332, Richmond, CA 94806, USA
| | - Jan Kubicek
- Cube Biotech, GmbH, Creative Campus, Alfred-Nobel Strasse 10, 40789 Monheim, Germany
| | - Barbara Maertens
- Cube Biotech, GmbH, Creative Campus, Alfred-Nobel Strasse 10, 40789 Monheim, Germany
| | | | - Camron Blackburn
- The Center for Bits and Atoms, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Shuguang Zhang
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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13
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Internal water channel formation in CXCR4 is crucial for G i-protein coupling upon activation by CXCL12. Commun Chem 2020; 3:133. [PMID: 36703316 PMCID: PMC9814148 DOI: 10.1038/s42004-020-00383-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/15/2020] [Indexed: 01/29/2023] Open
Abstract
Chemokine receptor CXCR4 is a major drug target for numerous diseases because of its involvement in the regulation of cell migration and the developmental process. In this study, atomic-level molecular dynamics simulations were used to determine the activation mechanism and internal water formation of CXCR4 in complex with chemokine CXCL12 and Gi-protein. The results indicated that CXCL12-bound CXCR4 underwent transmembrane 6 (TM6) outward movement and a decrease in tyrosine toggle switch by eliciting the breakage of hydrophobic layer to form a continuous internal water channel. In the GDP-bound Gαi-protein state, the rotation and translation of the α5-helix of Gαi-protein toward the cytoplasmic pocket of CXCR4 induced an increase in interdomain distance for GDP leaving. Finally, an internal water channel formation model was proposed based on our simulations for CXCL12-bound CXCR4 in complex with Gαi-protein upon activation for downstream signaling. This model could be useful in anticancer drug development.
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14
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Stephens BS, Ngo T, Kufareva I, Handel TM. Functional anatomy of the full-length CXCR4-CXCL12 complex systematically dissected by quantitative model-guided mutagenesis. Sci Signal 2020; 13:eaay5024. [PMID: 32665413 PMCID: PMC7437921 DOI: 10.1126/scisignal.aay5024] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Because of their prominent roles in development, cancer, and HIV, the chemokine receptor CXCR4 and its ligand CXCL12 have been the subject of numerous structural and functional studies, but the determinants of ligand binding, selectivity, and signaling are still poorly understood. Here, building on our latest structural model, we used a systematic mutagenesis strategy to dissect the functional anatomy of the CXCR4-CXCL12 complex. Key charge swap mutagenesis experiments provided evidence for pairwise interactions between oppositely charged residues in the receptor and chemokine, confirming the accuracy of the predicted orientation of the chemokine relative to the receptor and providing insight into ligand selectivity. Progressive deletion of N-terminal residues revealed an unexpected contribution of the receptor N terminus to chemokine signaling. This finding challenges a longstanding "two-site" hypothesis about the essential features of the receptor-chemokine interaction in which the N terminus contributes only to binding affinity. Our results suggest that although the interaction of the chemokine N terminus with the receptor-binding pocket is the key driver of signaling, the signaling amplitude depends on the extent to which the receptor N terminus binds the chemokine. Together with systematic characterization of other epitopes, these data enable us to propose an experimentally consistent structural model for how CXCL12 binds CXCR4 and initiates signal transmission through the receptor transmembrane domain.
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Affiliation(s)
- Bryan S Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tony Ngo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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15
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Ngo T, Stephens BS, Gustavsson M, Holden LG, Abagyan R, Handel TM, Kufareva I. Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity. PLoS Biol 2020; 18:e3000656. [PMID: 32271748 PMCID: PMC7173943 DOI: 10.1371/journal.pbio.3000656] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 04/21/2020] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
Chemokines and their receptors are orchestrators of cell migration in humans. Because dysregulation of the receptor-chemokine system leads to inflammation and cancer, both chemokines and receptors are highly sought therapeutic targets. Yet one of the barriers for their therapeutic targeting is the limited understanding of the structural principles behind receptor-chemokine recognition and selectivity. The existing structures do not include CXC subfamily complexes and lack information about the receptor distal N-termini, despite the importance of the latter in signaling, regulation, and bias. Here, we report the discovery of the geometry of the complex between full-length CXCR4, a prototypical CXC receptor and driver of cancer metastasis, and its endogenous ligand CXCL12. By comprehensive disulfide cross-linking, we establish the existence and the structure of a novel interface between the CXCR4 distal N-terminus and CXCL12 β1-strand, while also recapitulating earlier findings from nuclear magnetic resonance, modeling and crystallography of homologous receptors. A cross-linking-informed high-resolution model of the CXCR4-CXCL12 complex pinpoints the interaction determinants and reveals the occupancy of the receptor major subpocket by the CXCL12 proximal N terminus. This newly found positioning of the chemokine proximal N-terminus provides a structural explanation of CXC receptor-chemokine selectivity against other subfamilies. Our findings challenge the traditional two-site understanding of receptor-chemokine recognition, suggest the possibility of new affinity and signaling determinants, and fill a critical void on the structural map of an important class of therapeutic targets. These results will aid the rational design of selective chemokine-receptor targeting small molecules and biologics with novel pharmacology.
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Affiliation(s)
- Tony Ngo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Bryan S. Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Lauren G. Holden
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tracy M. Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
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16
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Gonzalez-Rivera JC, Orr AA, Engels SM, Jakubowski JM, Sherman MW, O'Connor KN, Matteson T, Woodcock BC, Contreras LM, Tamamis P. Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding. Comput Struct Biotechnol J 2020; 18:137-152. [PMID: 31988703 PMCID: PMC6965710 DOI: 10.1016/j.csbj.2019.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 12/02/2022] Open
Abstract
The oxidation of RNA has been implicated in the development of many diseases. Among the four ribonucleotides, guanosine is the most susceptible to oxidation, resulting in the formation of 8-oxo-7,8-dihydroguanosine (8-oxoG). Despite the limited knowledge about how cells regulate the detrimental effects of oxidized RNA, cellular factors involved in its regulation have begun to be identified. One of these factors is polynucleotide phosphorylase (PNPase), a multifunctional enzyme implicated in RNA turnover. In the present study, we have examined the interaction of PNPase with 8-oxoG in atomic detail to provide insights into the mechanism of 8-oxoG discrimination. We hypothesized that PNPase subunits cooperate to form a binding site using the dynamic SFF loop within the central channel of the PNPase homotrimer. We evolved this site using a novel approach that initially screened mutants from a library of beneficial mutations and assessed their interactions using multi-nanosecond Molecular Dynamics simulations. We found that evolving this single site resulted in a fold change increase in 8-oxoG affinity between 1.2 and 1.5 and/or selectivity between 1.5 and 1.9. In addition to the improvement in 8-oxoG binding, complementation of K12 Δpnp with plasmids expressing mutant PNPases caused increased cell tolerance to H2O2. This observation provides a clear link between molecular discrimination of RNA oxidation and cell survival. Moreover, this study provides a framework for the manipulation of modified-RNA protein readers, which has potential application in synthetic biology and epitranscriptomics.
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Affiliation(s)
- Juan C. Gonzalez-Rivera
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
| | - Sean M. Engels
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
| | - Joseph M. Jakubowski
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
| | - Mark W. Sherman
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX 78712, United States
| | - Katherine N. O'Connor
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
| | - Tomas Matteson
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX 78712, United States
| | - Brendan C. Woodcock
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX 78712, United States
- Corresponding authors at: McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States (L.M. Contreras).
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
- Corresponding authors at: McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States (L.M. Contreras).
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17
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Jakubowski J, Orr AA, Le DA, Tamamis P. Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:289-305. [PMID: 31809572 PMCID: PMC7732148 DOI: 10.1021/acs.jcim.9b00561] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Indexed: 12/24/2022]
Abstract
The aggregation of amyloid-β (Aβ) peptides into senile plaques is a hallmark of Alzheimer's disease (AD) and is hypothesized to be the primary cause of AD related neurodegeneration. Previous studies have shown the ability of curcumin to both inhibit the aggregation of Aβ peptides into oligomers or fibrils and reduce amyloids in vivo. Despite the promise of curcumin and its derivatives to serve as diagnostic, preventative, and potentially therapeutic AD molecules, the mechanism by which curcumin and its derivatives bind to and inhibit Aβ fibrils' formation remains elusive. Here, we investigated curcumin and a set of curcumin derivatives in complex with a hexamer peptide model of the Aβ1-42 fibril using nearly exhaustive docking, followed by multi-ns molecular dynamics simulations, to provide atomistic-detail insights into the molecules' binding and inhibitory properties. In the vast majority of the simulations, curcumin and its derivatives remain firmly bound in complex with the fibril through primarily three different principle binding modes, in which the molecules interact with residue domain 17LVFFA21, in line with previous experiments. In a small subset of these simulations, the molecules partly dissociate the outermost peptide of the Aβ1-42 fibril by disrupting β-sheets within the residue domain 12VHHQKLVFF20. A comparison between binding modes leading or not leading to partial dissociation of the outermost peptide suggests that the latter is attributed to a few subtle key structural and energetic interaction-based differences. Interestingly, partial dissociation appears to be either an outcome of high affinity interactions or a cause leading to high affinity interactions between the molecules and the fibril, which could partly serve as a compensation for the energy loss in the fibril due to partial dissociation. In conjunction with this, we suggest a potential inhibition mechanism of Αβ1-42 aggregation by the molecules, where the partially dissociated 16KLVFF20 domain of the outermost peptide could either remain unstructured or wrap around to form intramolecular interactions with the same peptide's 29GAIIG33 domain, while the molecules could additionally act as a patch against the external edge of the second outermost peptide's 16KLVFF20 domain. Thereby, individually or concurrently, these could prohibit fibril elongation.
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Affiliation(s)
| | | | - Doan A. Le
- Artie McFerrin Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Phanourios Tamamis
- Artie McFerrin Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
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18
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Kokotidou C, Jonnalagadda SVR, Orr AA, Vrentzos G, Kretsovali A, Tamamis P, Mitraki A. Designer Amyloid Cell-Penetrating Peptides for Potential Use as Gene Transfer Vehicles. Biomolecules 2019; 10:E7. [PMID: 31861408 PMCID: PMC7023140 DOI: 10.3390/biom10010007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
Cell-penetrating peptides are used extensively to deliver molecules into cells due to their unique characteristics such as rapid internalization, charge, and non-cytotoxicity. Amyloid fibril biomaterials were reported as gene transfer or retroviral infection enhancers; no cell internalization of the peptides themselves is reported so far. In this study, we focus on two rationally and computationally designed peptides comprised of β-sheet cores derived from naturally occurring protein sequences and designed positively charged and aromatic residues exposed at key residue positions. The β-sheet cores bestow the designed peptides with the ability to self-assemble into amyloid fibrils. The introduction of positively charged and aromatic residues additionally promotes DNA condensation and cell internalization by the self-assembled material formed by the designed peptides. Our results demonstrate that these designer peptide fibrils can efficiently enter mammalian cells while carrying packaged luciferase-encoding plasmid DNA, and they can act as a protein expression enhancer. Interestingly, the peptides additionally exhibited strong antimicrobial activity against the enterobacterium Escherichia coli.
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Affiliation(s)
- Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Grete, Greece;
- Institute of Electronic Structure and Laser (IESL) FORTH, 70013 Heraklion, Crete, Greece
| | - Sai Vamshi R. Jonnalagadda
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - George Vrentzos
- Institute of Molecular Biology and Biotechnology (IMBB) FORTH, 70013 Heraklion, Crete, Greece; (G.V.); (A.K.)
| | - Androniki Kretsovali
- Institute of Molecular Biology and Biotechnology (IMBB) FORTH, 70013 Heraklion, Crete, Greece; (G.V.); (A.K.)
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Grete, Greece;
- Institute of Electronic Structure and Laser (IESL) FORTH, 70013 Heraklion, Crete, Greece
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19
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Orr AA, Yang J, Sule N, Chawla R, Hull KG, Zhu M, Romo D, Lele PP, Jayaraman A, Manson MD, Tamamis P. Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr. Biophys J 2019; 118:492-504. [PMID: 31839263 DOI: 10.1016/j.bpj.2019.11.3382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/05/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
The attractant chemotaxis response of Escherichia coli to norepinephrine requires that it be converted to 3,4-dihydroxymandelic acid (DHMA) by the monoamine oxidase TynA and the aromatic aldehyde dehydrogenase FeaB. DHMA is sensed by the serine chemoreceptor Tsr, and the attractant response requires that at least one subunit of the periplasmic domain of the Tsr homodimer (pTsr) has an intact serine-binding site. DHMA that is generated in vivo by E. coli is expected to be a racemic mixture of the (R) and (S) enantiomers, so it has been unclear whether one or both chiral forms are active. Here, we used a combination of state-of-the-art tools in molecular docking and simulations, including an in-house simulation-based docking protocol, to investigate the binding properties of (R)-DHMA and (S)-DHMA to E. coli pTsr. Our studies computationally predicted that (R)-DHMA should promote a stronger attractant response than (S)-DHMA because of a consistently greater-magnitude piston-like pushdown of the pTsr α-helix 4 toward the membrane upon binding of (R)-DHMA than upon binding of (S)-DHMA. This displacement is caused primarily by interaction of DHMA with Tsr residue Thr156, which has been shown by genetic studies to be critical for the attractant response to L-serine and DHMA. These findings led us to separate the two chiral species and test their effectiveness as chemoattractants. Both the tethered cell and motility migration coefficient assays validated the prediction that (R)-DHMA is a stronger attractant than (S)-DHMA. Our study demonstrates that refined computational docking and simulation studies combined with experiments can be used to investigate situations in which subtle differences between ligands may lead to diverse chemotactic responses.
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Affiliation(s)
- Asuka A Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Jingyun Yang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Nitesh Sule
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Kenneth G Hull
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Mingzhao Zhu
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Daniel Romo
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Michael D Manson
- Department of Biology, Texas A&M University, College Station, Texas.
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.
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20
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QTY code designed thermostable and water-soluble chimeric chemokine receptors with tunable ligand affinity. Proc Natl Acad Sci U S A 2019; 116:25668-25676. [PMID: 31776256 DOI: 10.1073/pnas.1909026116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chemokine receptors are of great interest as they play a critical role in many immunological and pathological processes. The ability to study chemokine receptors in aqueous solution without detergent would be significant because natural receptors require detergents to become soluble. We previously reported using the QTY code to design detergent-free chemokine receptors. We here report the design of 2 detergent-free chimeric chemokine receptors that were experimentally unattainable in detergent solution. We designed chimeric receptors by switching the N terminus and 3 extracellular (EC) loops between different receptors. Specifically, we replaced the N terminus and 3 EC loops of CCR5QTY with the N terminus and 3 EC loops of CXCR4. The ligand for CXCR4; namely CXCL12, binds to the chimeric receptor CCR5QTY (7TM)-CXCR4 (N terminus+3 EC loops), but with lower affinity compared to CXCR4; the CCL5 ligand of CCR5 binds the chimeric receptor with ∼20× lower affinity. The chimeric design helps to elucidate the mechanism of native receptor-ligand interaction. We also show that all detergent-free QTY-designed chemokine receptors, expressed in Escherichia coli, bind to their respective chemokines with affinities in the nanomolar (nM) range, similar to the affinities of native receptors and SF9-produced QTY variants. These QTY-designed receptors exhibit remarkable thermostability in the presence of arginine and retain ligand-binding activity after heat treatment at 60 °C for 4 h and 24 h, and at 100 °C for 10 min. Our design approach enables affordable scale-up production of detergent-free QTY variant chemokine receptors with tunable functionality for various uses.
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21
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Park H, Jin UH, Orr AA, Echegaray SP, Davidson LA, Allred CD, Chapkin RS, Jayaraman A, Lee K, Tamamis P, Safe S. Isoflavones as Ah Receptor Agonists in Colon-Derived Cell Lines: Structure-Activity Relationships. Chem Res Toxicol 2019; 32:2353-2364. [PMID: 31621310 DOI: 10.1021/acs.chemrestox.9b00352] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many of the protective responses observed for flavonoids in the gastrointestinal track resemble aryl hydrocarbon receptor (AhR)-mediated effects. Therefore, we examined the structure-activity relationships of isoflavones and isomeric flavone and flavanones as AhR ligands on the basis of their induction of CYP1A1, CYP1B1, and UGT1A1 gene expression in colon cancer Caco2 cells and young adult mouse colonocyte (YAMC) cells. Caco2 cells were significantly more Ah-responsive than YAMC cells, and this was due, in part, to flavonoid-induced cytotoxicity in the latter cell lines. The structure-activity relationships for the flavonoids were complex and both response and cell context specific; however, there was significant variability in the AhR activities of the isomeric substituted isoflavones and flavones. For example, 4',5,7-trihydroxyisoflavone (genistein) was AhR-inactive whereas 4',5,7-trihydroxyflavone (apigenin) induced CYP1A1, CYP1B1, and UGT1A1 in Caco2 cells. In contrast, both 5,7-dihydroxy-4-methoxy substituted isoflavone (biochanin A) and flavone (acacetin) induced all three AhR-responsive genes; 4',5,7-trimethoxyisoflavone was a potent AhR agonist, and the isomeric flavone was AhR-inactive. These results coupled with simulation studies modeling flavonoid interaction within the AhR binding pocket demonstrate that the orientation of the substituted phenyl ring at C-2 (flavones) or C-3 (isoflavones) on the common 4-H-chromen-4-one ring strongly influences the activities of isoflavones and flavones as AhR agonists.
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Affiliation(s)
- Hyejin Park
- Department of Veterinary Physiology and Pharmacology , Texas A&M University , College Station , Texas 77843 , United States
| | - Un-Ho Jin
- Department of Veterinary Physiology and Pharmacology , Texas A&M University , College Station , Texas 77843 , United States
| | - Asuka A Orr
- Artie McFerrin Department of Chemical Engineering , Texas A&M University , College Station , Texas 77840 , United States
| | - Stephanie P Echegaray
- Artie McFerrin Department of Chemical Engineering , Texas A&M University , College Station , Texas 77840 , United States
| | - Laurie A Davidson
- Department of Nutrition and Food Science , Texas A&M University , College Station , Texas 77843 , United States
| | - Clinton D Allred
- Department of Nutrition and Food Science , Texas A&M University , College Station , Texas 77843 , United States
| | - Robert S Chapkin
- Department of Nutrition and Food Science , Texas A&M University , College Station , Texas 77843 , United States
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering , Texas A&M University , College Station , Texas 77840 , United States
| | - Kyongbum Lee
- Department of Chemical and Biological Engineering , Tufts University , Medford , Massachusetts 02155 , United States
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering , Texas A&M University , College Station , Texas 77840 , United States
| | - Stephen Safe
- Department of Veterinary Physiology and Pharmacology , Texas A&M University , College Station , Texas 77843 , United States
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22
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Yi J, Gao ZF. MicroRNA-9-5p promotes angiogenesis but inhibits apoptosis and inflammation of high glucose-induced injury in human umbilical vascular endothelial cells by targeting CXCR4. Int J Biol Macromol 2019; 130:1-9. [PMID: 30716366 DOI: 10.1016/j.ijbiomac.2019.02.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 02/08/2023]
Abstract
High glucose (HG) has the potential to cause vascular endothelial cell injury, while microRNAs (miRNAs) play a key role in treating endothelial cell injury. CXC chemokine receptor-4 (CXCR4) is reported to be expressed in vascular endothelial cells. Hence, this study investigated role of miR-9-5p in the angiogenesis and apoptosis of HG-induced human umbilical vascular endothelial cells (HUVECs) injury. Dual luciferase reporter gene assay verified that miR-9-5p targeted CXCR4. RT-qPCR and western blot analysis revealed that miR-9-5p was down-regulated, meanwhile CXCR4 was up-regulated in the HG-induced HUVECs. HUVECs were cultured in 30 mmol/L HG in vitro, and then transfected with miR-9-5p mimic or CXCR4 siRNA to identify the effect of miR-9-5p on cell activity, angiogenesis, apoptosis, and inflammation of HG-induced HUVECs. The results suggested that overexpression of miR-9-5p or silencing of CXCR4 in HG-induced HUVECs increased cell proliferation and tubule length, while decreasing the apoptosis rate and the expression of inflammatory factors. Furthermore, miR-9-5p inhibited the phosphorylation of extracellular regulated protein kinases (ERK), protein kinase B (AKT), and Mammalian Target of Rapamycin (mTOR) proteins via downregulation of CXCR4. Therefore, overexpression of miR-9-5p suppressed the mitogen-activated protein kinase (MAPK)/ERK and the PI3K/AKT/mTOR pathway by inhibiting CXCR4, thereby reducing HG-induced injury in HUVECs.
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Affiliation(s)
- Jun Yi
- Department of Anesthesiology, Beijing Jishuitan Hospital, Beijing 100035, PR China
| | - Zhi-Feng Gao
- Department of Anesthesiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, PR China.
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23
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Hitchinson B, Eby JM, Gao X, Guite-Vinet F, Ziarek JJ, Abdelkarim H, Lee Y, Okamoto Y, Shikano S, Majetschak M, Heveker N, Volkman BF, Tarasova NI, Gaponenko V. Biased antagonism of CXCR4 avoids antagonist tolerance. Sci Signal 2018; 11:11/552/eaat2214. [PMID: 30327409 DOI: 10.1126/scisignal.aat2214] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Repeated dosing of drugs targeting G protein-coupled receptors can stimulate antagonist tolerance, which reduces their efficacy; thus, strategies to avoid tolerance are needed. The efficacy of AMD3100, a competitive antagonist of the chemokine receptor CXCR4 that mobilizes leukemic blasts from the bone marrow into the blood to sensitize them to chemotherapy, is reduced after prolonged treatment. Tolerance to AMD3100 increases the abundance of CXCR4 on the surface of leukemic blasts, which promotes their rehoming to the bone marrow. AMD3100 inhibits both G protein signaling by CXCR4 and β-arrestin1/2-dependent receptor endocytosis. We demonstrated that biased antagonists of G protein-dependent chemotaxis but not β-arrestin1/2 recruitment and subsequent receptor endocytosis avoided tolerance. The peptide antagonist X4-2-6, which is derived from transmembrane helix 2 and extracellular loop 1 of CXCR4, limited chemotaxis and signaling but did not promote CXCR4 accumulation on the cell surface or cause tolerance. The activity of X4-2-6 was due to its distinct mechanism of inhibition of CXCR4. The peptide formed a ternary complex with the receptor and its ligand, the chemokine CXCL12. Within this complex, X4-2-6 released the portion of CXCL12 critical for receptor-mediated activation of G proteins but enabled the rest of the chemokine to recruit β-arrestins to the receptor. In contrast, AMD3100 displaced all components of the chemokine responsible for CXCR4 activation. We further identified a small molecule with similar biased antagonist properties to those of X4-2-6, which may provide a viable alternative to patients when antagonist tolerance prevents drugs from reaching efficacy.
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Affiliation(s)
- Ben Hitchinson
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Jonathan M Eby
- Department of Surgery, Burn and Shock Trauma Research Institute, Loyola University Chicago, Chicago, IL, USA
| | - Xianlong Gao
- Department of Surgery, Burn and Shock Trauma Research Institute, Loyola University Chicago, Chicago, IL, USA.,Department of Surgery, Morsani College of Medicine, University of South Florida, College of Medicine, Tampa, FL, USA
| | - Francois Guite-Vinet
- Department of Biochemistry, Research Centre, Sainte-Justine Hospital, Montréal, Quebec, Canada
| | - Joshua J Ziarek
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hazem Abdelkarim
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Youngshim Lee
- Division of Bioscience and Biotechnology, Biomolecular Informatics Center, Konkuk University, Seoul 05029, Republic of Korea
| | - Yukari Okamoto
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Sojin Shikano
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Matthias Majetschak
- Department of Surgery, Burn and Shock Trauma Research Institute, Loyola University Chicago, Chicago, IL, USA.,Department of Surgery, Morsani College of Medicine, University of South Florida, College of Medicine, Tampa, FL, USA
| | - Nikolaus Heveker
- Department of Biochemistry, Research Centre, Sainte-Justine Hospital, Montréal, Quebec, Canada
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nadya I Tarasova
- Cancer and Inflammation Program, National Cancer Institute, P.O. Box B, Frederick, MD, USA
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.
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24
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CXCR3 expression in colorectal cancer cells enhanced invasion through preventing CXCR4 internalization. Exp Cell Res 2018; 371:162-174. [DOI: 10.1016/j.yexcr.2018.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/03/2018] [Accepted: 08/05/2018] [Indexed: 01/09/2023]
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25
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Terheyden-Keighley D, Zhang X, Brand-Saberi B, Theiss C. CXCR4/SDF1 signalling promotes sensory neuron clustering in vitro. Biol Open 2018; 7:bio.035568. [PMID: 30135081 PMCID: PMC6176946 DOI: 10.1242/bio.035568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
During the development of the peripheral nervous system, a subgroup of neural crest cells migrate away from the neural tube and coalesce into clusters of sensory neurons (ganglia). Mechanisms involved in the formation of the dorsal root ganglia (DRG) from neural crest cells are currently unclear. Mice carrying mutations in Cxcr4, which is known to control neural crest migration, exhibit malformed DRG. In order to investigate this phenomenon, we modelled sensory neuron differentiation in vitro by directing the differentiation of human induced pluripotent stem cells into sensory neurons under SDF1 (agonist), AMD3100 (antagonist) or control conditions. There we could show a marked effect on the clustering activity of the neurons in vitro, suggesting that CXCR4 signalling is involved in facilitating DRG condensation. Summary: The signalling mechanisms directing sensory neuron gangliogenesis are not well understood. Here, we model this process through stem cell differentiation and show that CXCR4 signalling facilitates neural clustering.
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Affiliation(s)
- Daniel Terheyden-Keighley
- Institute of Anatomy, Department of Cytology, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Xiaoqing Zhang
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, 200092 Shanghai, China
| | - Beate Brand-Saberi
- Institute of Anatomy, Department of Anatomy and Molecular Embryology, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Carsten Theiss
- Institute of Anatomy, Department of Cytology, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
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26
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Orr AA, Gonzalez-Rivera JC, Wilson M, Bhikha PR, Wang D, Contreras LM, Tamamis P. A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins. Methods 2018; 143:34-47. [DOI: 10.1016/j.ymeth.2018.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/14/2018] [Accepted: 01/26/2018] [Indexed: 12/25/2022] Open
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27
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Sahoo AR, Mishra R, Rana S. The Model Structures of the Complement Component 5a Receptor (C5aR) Bound to the Native and Engineered hC5a. Sci Rep 2018; 8:2955. [PMID: 29440703 PMCID: PMC5811428 DOI: 10.1038/s41598-018-21290-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
The interaction of hC5a with C5aR, previously hypothesized to involve a “two-site” binding, (i) recognition of the bulk of hC5a by the N-terminus (NT) of C5aR (“site1”), and (ii) recognition of C-terminus (CT) of hC5a by the extra cellular surface (ECS) of the C5aR (“site2”). However, the pharmacological landscapes of such recognition sites are yet to be illuminated at atomistic resolution. In the context, unique model complexes of C5aR, harboring pharmacophores of diverse functionality at the “site2” has recently been described. The current study provides a rational illustration of the “two-site” binding paradigm in C5aR, by recruiting the native agonist hC5a and engineered antagonist hC5a(A8). The hC5a-C5aR and hC5a(A8)-C5aR complexes studied over 250 ns of molecular dynamics (MD) each in POPC bilayer illuminate the hallmark of activation mechanism in C5aR. The intermolecular interactions in the model complexes are well supported by the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) based binding free energy calculation, strongly correlating with the reported mutational studies. Exemplified in two unique and contrasting molecular complexes, the study provides an exceptional understanding of the pharmacological divergence observed in C5aR, which will certainly be useful for search and optimization of new generation “neutraligands” targeting the hC5a-C5aR interaction.
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Affiliation(s)
- Amita Rani Sahoo
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha, 752050, India
| | - Richa Mishra
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha, 752050, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha, 752050, India.
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28
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Abstract
Docking algorithms have been widely used to elucidate ligand:receptor interactions that are important in biological function. Here, we introduce an in-house developed docking-refinement protocol that combines the following innovative features. (1) The use of multiple short molecular dynamics (MD) docking simulations, with residues within the binding pocket of the receptor unconstrained, so that the binding modes of the ligand in the binding pocket may be exhaustively examined. (2) The initial positioning of the ligand within the binding pocket based on complementary shape, and the use of both harmonic and quartic spherical potentials to constrain the ligand in the binding pocket during multiple short docking simulations. (3) The selection of the most probable binding modes generated by the short docking simulations using interaction energy calculations, as well as the subsequent application of all-atom MD simulations and physical-chemistry based free energy calculations to elucidate the most favorable binding mode of the ligand in complex with the receptor. In this chapter, we provide step-by-step instructions on how to computationally investigate the binding of small-molecule ligands to protein receptors by examining as control and test cases, respectively, the binding of L-serine and R-3,4-dihydroxymandelic acid (R-DHMA) to the Escherichia coli chemoreceptor Tsr. Similar computational strategies can be used for the molecular modeling of a series of ligand:protein receptor interactions.
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29
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Badr HS, El-Gendy FM, Helwa MA. Serum stromal-derived-factor-1 (CXCL12) and its alpha chemokine receptor (CXCR4) as biomarkers in neonatal sepsis. J Matern Fetal Neonatal Med 2017; 31:2209-2215. [PMID: 28562124 DOI: 10.1080/14767058.2017.1336760] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND Neonatal sepsis remains one of the leading causes of morbidity and mortality both among term and preterm infants. Advances in neonatal care improved survival and reduced complications in preterm infants. Chemokines are chemotactic cytokines that give directional guidance for leukocyte migration during inflammatory process. The chemokine CXCL12 and its receptor CXCR4 are now known to play an important role in inflammatory states. However, its value as a biomarker in neonatal sepsis is unclear. OBJECTIVES To assess the value of measuring the serum levels of alpha-chemokine receptor type 4 (CXCR-4) and stromal-derived-factor-1 (CXCL12) in diagnosis of late onset neonatal sepsis. SUBJECT AND METHODS Serum levels of CXCL12 and CXCR4 were determined in 38 full term neonates, 23 cases of late onset sepsis (13 males and 10 female), and 15 healthy neonates as control (six males and nine females) by ELISA technique and flow-cytometry. RESULTS Serum levels of CXCR4 and CXCL12 were significantly higher in neonates with late onset sepsis compared with the non-septic ones. The sensitivity, the specificity, and the overall accuracy of CXCL12 were 100%. The sensitivity of CXCR4 was 87%; the specificity was 80% and the overall accuracy was 84%. CONCLUSIONS Serum CXCR4 and CXCL12 levels increase significantly in septic neonates and they are valuable marker in diagnosis of neonatal sepsis. Serum concentrations of both chemokines represent promising novel biomarkers for neonatal sepsis.
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Affiliation(s)
- Hassan S Badr
- a Department of Pediatrics , Menoufia University , Shibin El Kom , Egypt
| | - Fady M El-Gendy
- a Department of Pediatrics , Menoufia University , Shibin El Kom , Egypt
| | - Mohamed A Helwa
- b Clinical Pathology, Faculty of Medicine , Menoufia University , Shibin El Kom , Egypt
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30
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Xu J, Liang J, Meng YM, Yan J, Yu XJ, Liu CQ, Xu L, Zhuang SM, Zheng L. Vascular CXCR4 Expression Promotes Vessel Sprouting and Sensitivity to Sorafenib Treatment in Hepatocellular Carcinoma. Clin Cancer Res 2017; 23:4482-4492. [DOI: 10.1158/1078-0432.ccr-16-2131] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 09/14/2016] [Accepted: 02/16/2017] [Indexed: 11/16/2022]
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31
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Kieckens E, Rybarczyk J, Li RW, Vanrompay D, Cox E. Potential immunosuppressive effects of Escherichia coli O157:H7 experimental infection on the bovine host. BMC Genomics 2016; 17:1049. [PMID: 28003017 PMCID: PMC5178093 DOI: 10.1186/s12864-016-3374-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 12/05/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Enterohaemorrhagic Escherichia coli (EHEC), like E. coli O157:H7 are frequently detected in bovine faecal samples at slaughter. Cattle do not show clinical symptoms upon infection, but for humans the consequences after consuming contaminated beef can be severe. The immune response against EHEC in cattle cannot always clear the infection as persistent colonization and shedding in infected animals over a period of months often occurs. In previous infection trials, we observed a primary immune response after infection which was unable to protect cattle from re-infection. These results may reflect a suppression of certain immune pathways, making cattle more prone to persistent colonization after re-infection. To test this, RNA-Seq was used for transcriptome analysis of recto-anal junction tissue and ileal Peyer's patches in nine Holstein-Friesian calves in response to a primary and secondary Escherichia coli O157:H7 infection with the Shiga toxin (Stx) negative NCTC12900 strain. Non-infected calves served as controls. RESULTS In tissue of the recto-anal junction, only 15 genes were found to be significantly affected by a first infection compared to 1159 genes in the ileal Peyer's patches. Whereas, re-infection significantly changed the expression of 10 and 17 genes in the recto-anal junction tissue and the Peyer's patches, respectively. A significant downregulation of 69 immunostimulatory genes and a significant upregulation of seven immune suppressing genes was observed. CONCLUSIONS Although the recto-anal junction is a major site of colonization, this area does not seem to be modulated upon infection to the same extent as ileal Peyer's patches as the changes in gene expression were remarkably higher in the ileal Peyer's patches than in the recto-anal junction during a primary but not a secondary infection. We can conclude that the main effect on the transcriptome was immunosuppression by E. coli O157:H7 (Stx-) due to an upregulation of immune suppressive effects (7/12 genes) or a downregulation of immunostimulatory effects (69/94 genes) in the ileal Peyer's patches. These data might indicate that a primary infection promotes a re-infection with EHEC by suppressing the immune function.
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Affiliation(s)
- E. Kieckens
- Laboratory of Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
- Laboratory of Immunology and Animal Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - J. Rybarczyk
- Laboratory of Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
- Laboratory of Immunology and Animal Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - R. W. Li
- USDA-ARS, Bovine Functional Genomics Laboratory, Beltsville, MD USA
| | - D. Vanrompay
- Laboratory of Immunology and Animal Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - E. Cox
- Laboratory of Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
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32
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Orr AA, Wördehoff MM, Hoyer W, Tamamis P. Uncovering the Binding and Specificity of β-Wrapins for Amyloid-β and α-Synuclein. J Phys Chem B 2016; 120:12781-12794. [DOI: 10.1021/acs.jpcb.6b08485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Michael M. Wördehoff
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
- Institute
of Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
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33
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Cheng Y, Jin UH, Davidson LA, Chapkin RS, Jayaraman A, Tamamis P, Orr A, Allred C, Denison MS, Soshilov A, Weaver E, Safe S. Editor's Highlight: Microbial-Derived 1,4-Dihydroxy-2-naphthoic Acid and Related Compounds as Aryl Hydrocarbon Receptor Agonists/Antagonists: Structure-Activity Relationships and Receptor Modeling. Toxicol Sci 2016; 155:458-473. [PMID: 27837168 DOI: 10.1093/toxsci/kfw230] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
1,4-Dihydroxy-2-naphthoic acid (1,4-DHNA) is a bacterial-derived metabolite that binds the aryl hydrocarbon receptor (AhR) and exhibits anti-inflammatory activity in the gut. The structure-dependent AhR activity of hydroxyl/carboxy-substituted naphthoic acids (NAs) was determined in young adult mouse colonic (YAMC) cells and human Caco2 colon cancer cells using CYP1A1/CYP1B1 mRNAs as Ah-responsive genes. Compounds used in this study include 1,4-, 3,5-, and 3,7-DHNA, 1,4-dimethoxy-2-naphthoic acid (1,4-DMNA), 1- and 4-hydroxy-2-naphthoic acid (1-HNA, 4-HNA), 1- and 2-naphthoic acid (1-NA, 2-NA), and 1- and 2-naphthol (1-NOH, 2-NOH). 1,4-DHNA was the most potent compound among hydroxyl/carboxy naphthalene derivatives, and the fold induction response for CYP1A1 and CYP1B1 was similar to that observed for 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in YAMC and Caco2 cells. 1- and 4-HNA were less potent than 1,4-DHNA but induced maximal (TCDD-like) response for CYP1B1 (both cell lines) and CYP1A1 (Caco2 cells). With the exception of 1- and 2-NA, all compounds significantly induced Cyp1b1 in YAMC cells and these responses were not observed in AhR-deficient YAMC cells generated using CRISPR/Cas9 technology. In addition, we also observed that 1- and 2-NOH (and 1,4-DHNA) were weak AhR agonists, and 1- and 2-NOH also exhibited partial AhR antagonist activity. Structure-activity relationship studies for CYP1A1 but not CYP1B1 were similar in both cell lines, and CYP1A1 induction required one or both 1,4-dihydroxy substituents and activity was significantly enhanced by the 2-carboxyl group. We also used computational analysis to show that 1,4-DHNA and TCDD share similar interactions within the AhR binding pocket and differ primarily due to the negatively charged group of 1,4-DHNA.
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Affiliation(s)
- Yating Cheng
- Department of Veterinary Physiology and Pharmacology
| | - Un-Ho Jin
- Department of Veterinary Physiology and Pharmacology
| | | | | | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843
| | - Asuka Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843
| | | | - Michael S Denison
- Department of Environmental Toxicology, University of California, Davis, California 95616
| | - Anatoly Soshilov
- Department of Environmental Toxicology, University of California, Davis, California 95616
| | - Evelyn Weaver
- Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Stephen Safe
- Department of Veterinary Physiology and Pharmacology
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34
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Cutolo P, Basdevant N, Bernadat G, Bachelerie F, Ha-Duong T. Interaction of chemokine receptor CXCR4 in monomeric and dimeric state with its endogenous ligand CXCL12: coarse-grained simulations identify differences. J Biomol Struct Dyn 2016; 35:399-412. [PMID: 26813575 DOI: 10.1080/07391102.2016.1145142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Despite the recent resolutions of the crystal structure of the chemokine receptor CXCR4 in complex with small antagonists or viral chemokine, a description at the molecular level of the interactions between the full-length CXCR4 and its endogenous ligand, the chemokine CXCL12, in relationship with the receptor recognition and activation, is not yet completely elucidated. Moreover, since CXCR4 is able to form dimers, the question of whether the CXCR4-CXCL12 complex has a 1:1 or 2:1 preferential stoichiometry is still an open question. We present here results of coarse-grained protein-protein docking and molecular dynamics simulations of CXCL12 in association with CXCR4 in monomeric and dimeric states. Our proposed models for the 1:1 and 2:1 CXCR4-CXCL12 quaternary structures are consistent with recognition and activation motifs of both partners provided by the available site-directed mutagenesis data. Notably, we observed that in the 2:1 complex, the chemokine N-terminus makes more steady contacts with the receptor residues critical for binding and activation than in the 1:1 structure, suggesting that the 2:1 stoichiometry would favor the receptor signaling activity with respect to the 1:1 association.
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Affiliation(s)
- Pasquale Cutolo
- a UMR996 - Inflammation, Chemokines and Immunopathology , Inserm, Université Paris-Sud, Université Paris-Saclay , Clamart , France
| | - Nathalie Basdevant
- b LAMBE - UMR 8587, Université d'Evry-Val-d'Essonne, CNRS , Evry , France
| | - Guillaume Bernadat
- c BioCIS - UMR 8076, Université Paris-Sud, CNRS, Université Paris-Saclay , Châtenay-Malabry , France
| | - Françoise Bachelerie
- a UMR996 - Inflammation, Chemokines and Immunopathology , Inserm, Université Paris-Sud, Université Paris-Saclay , Clamart , France
| | - Tâp Ha-Duong
- c BioCIS - UMR 8076, Université Paris-Sud, CNRS, Université Paris-Saclay , Châtenay-Malabry , France
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Liebick M, Schläger C, Oppermann M. Analysis of Chemokine Receptor Trafficking by Site-Specific Biotinylation. PLoS One 2016; 11:e0157502. [PMID: 27310579 PMCID: PMC4911081 DOI: 10.1371/journal.pone.0157502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/31/2016] [Indexed: 12/17/2022] Open
Abstract
Chemokine receptors undergo internalization and desensitization in response to ligand activation. Internalized receptors are either preferentially directed towards recycling pathways (e.g. CCR5) or sorted for proteasomal degradation (e.g. CXCR4). Here we describe a method for the analysis of receptor internalization and recycling based on specific Bir A-mediated biotinylation of an acceptor peptide coupled to the receptor, which allows a more detailed analysis of receptor trafficking compared to classical antibody-based detection methods. Studies on constitutive internalization of the chemokine receptors CXCR4 (12.1% ± 0.99% receptor internalization/h) and CCR5 (13.7% ± 0.68%/h) reveals modulation of these processes by inverse (TAK779; 10.9% ± 0.95%/h) or partial agonists (Met-CCL5; 15.6% ± 0.5%/h). These results suggest an actively driven internalization process. We also demonstrate the advantages of specific biotinylation compared to classical antibody detection during agonist-induced receptor internalization, which may be used for immunofluorescence analysis as well. Site-specific biotinylation may be applicable to studies on trafficking of transmembrane proteins, in general.
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MESH Headings
- Amides/pharmacology
- Animals
- Antibodies, Monoclonal/biosynthesis
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/isolation & purification
- Basophils/cytology
- Basophils/drug effects
- Basophils/metabolism
- Biotin/chemistry
- Biotin/metabolism
- Biotinylation
- CCR5 Receptor Antagonists/pharmacology
- Carbon-Nitrogen Ligases/genetics
- Carbon-Nitrogen Ligases/metabolism
- Cell Line, Tumor
- Chemokine CCL5/pharmacology
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Mice
- Protein Transport/drug effects
- Quaternary Ammonium Compounds/pharmacology
- Rats
- Receptors, CXCR4/antagonists & inhibitors
- Receptors, CXCR4/genetics
- Receptors, CXCR4/metabolism
- Receptors, CXCR5/antagonists & inhibitors
- Receptors, CXCR5/genetics
- Receptors, CXCR5/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Transfection
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Affiliation(s)
- Marcel Liebick
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Niedersachsen, Germany
| | - Christian Schläger
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Niedersachsen, Germany
| | - Martin Oppermann
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Niedersachsen, Germany
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36
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Parravicini C, Daniele S, Palazzolo L, Trincavelli ML, Martini C, Zaratin P, Primi R, Coppolino G, Gianazza E, Abbracchio MP, Eberini I. A promiscuous recognition mechanism between GPR17 and SDF-1: Molecular insights. Cell Signal 2016; 28:631-42. [PMID: 26971834 DOI: 10.1016/j.cellsig.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/29/2016] [Accepted: 03/06/2016] [Indexed: 01/19/2023]
Abstract
Recent data and publications suggest a promiscuous behaviour for GPR17, a class-A GPCR operated by different classes of ligands, such as uracil nucleotides, cysteinyl-leukotrienes and oxysterols. This observation, together with the ability of several class-A GPCRs to form homo- and hetero-dimers, is likely to unveil new pathophysiological roles and novel emerging pharmacological properties for some of these GPCRs, including GPR17. This receptor shares structural, phylogenetic and functional properties with some chemokine receptors, CXCRs. Both GPR17 and CXCR2 are operated by oxysterols, and both GPR17 and CXCR ligands have been demonstrated to have a role in orchestrating inflammatory responses and oligodendrocyte precursor cell differentiation to myelinating cells in acute and chronic diseases of the central nervous system. Here, by combining in silico modelling data with in vitro validation in (i) a classical reference pharmacological assay for GPCR activity and (ii) a model of maturation of primary oligodendrocyte precursor cells, we demonstrate that GPR17 can be activated by SDF-1, a ligand of chemokine receptors CXCR4 and CXCR7, and investigate the underlying molecular recognition mechanism. We also demonstrate that cangrelor, a GPR17 orthosteric antagonist, can block the SDF-1-mediated activation of GPR17 in a concentration-dependent manner. The ability of GPR17 to respond to different classes of GPCR ligands suggests that this receptor modifies its function depending on the extracellular mileu changes occurring under specific pathophysiological conditions and advocates it as a strategic target for neurodegenerative diseases with an inflammatory/immune component.
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Affiliation(s)
- Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Simona Daniele
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy; Dipartimento di Farmacia, Università degli Studi di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy.
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | | | - Claudia Martini
- Dipartimento di Farmacia, Università degli Studi di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy.
| | - Paola Zaratin
- Fondazione Italiana Sclerosi Multipla, Via Operai 40, 16149 Genova, Italy.
| | - Roberto Primi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Giusy Coppolino
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Maria P Abbracchio
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy; Dipartimento di Scienze Biomediche e Cliniche "L. Sacco", Università degli Studi di Milano, Via Gian Battista Grassi 74, 20157 Milano, Italy.
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37
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Jiang Y, Yuan Y, Zhang X, Liang T, Guo Y, Li M, Pu X. Use of network model to explore dynamic and allosteric properties of three GPCR homodimers. RSC Adv 2016. [DOI: 10.1039/c6ra18243g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We used an elastic network model and protein structure network to study three class A GPCR homodimers.
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Affiliation(s)
- Yuanyuan Jiang
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu 610064
- P. R. China
| | - Xi Zhang
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Tao Liang
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Yanzhi Guo
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Menglong Li
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Xumei Pu
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
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38
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Sand L, Scotlandi K, Berghuis D, Snaar-Jagalska B, Picci P, Schmidt T, Szuhai K, Hogendoorn P. CXCL14, CXCR7 expression and CXCR4 splice variant ratio associate with survival and metastases in Ewing sarcoma patients. Eur J Cancer 2015; 51:2624-33. [DOI: 10.1016/j.ejca.2015.08.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/05/2015] [Accepted: 08/21/2015] [Indexed: 11/26/2022]
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39
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Sand LGL, Jochemsen AG, Beletkaia E, Schmidt T, Hogendoorn PCW, Szuhai K. Novel splice variants of CXCR4 identified by transcriptome sequencing. Biochem Biophys Res Commun 2015; 466:89-94. [PMID: 26321665 DOI: 10.1016/j.bbrc.2015.08.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
Abstract
Chemokine receptor CXCR4 is involved in tumor growth, angiogenesis and metastasis. Its function is regulated in many ways and one of them is alternative splicing. We identified two novel coding splice variants (CXCR4-3 and CXCR4-4) of CXCR4 in Ewing sarcoma (EWS) cell lines by whole transcriptome sequencing and validated these with reverse transcriptase- PCR and Sanger sequencing. The novel splice variants were expressed at RNA level in Ewing sarcoma samples and in other tumor cell lines and placenta, but not in lung. Due to inclusion of an additional exon the new isoforms have a 70 and 33 amino acid elongation of the N-terminal end of CXCR4. For validation at protein and functional level, the identified isoforms and normal CXCR4 were cloned into an EYFP tagged vector and ectopically expressed in HEK293T cell line and EWS cell line A673. Of the novel isoforms CXCR4-3 showed cell membrane localization and a functional response after addition of CXCR4 ligand CXCL12a. CXCR4-4 showed strong cytoplasmic accumulation and no response to ligand treatment. The role of the newly discovered isoforms in CXCR4 signaling is likely to be limited. Our data stresses the importance of functional validation of newly identified isoforms.
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Affiliation(s)
- L G L Sand
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - A G Jochemsen
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - E Beletkaia
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - T Schmidt
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - P C W Hogendoorn
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - K Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.
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40
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Progress toward rationally designed small-molecule peptide and peptidomimetic CXCR4 antagonists. Future Med Chem 2015; 7:1261-83. [DOI: 10.4155/fmc.15.64] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Over the last 5 years, X-ray structures of CXCR4 in complex with three different ligands (the small-molecule antagonist IT1t, the polypeptide antagonist CVX15 and the viral chemokine antagonist vMIP-II) have been released. In addition to the inherent scientific value of these specific X-ray structures, they provide a reliable structural foundation for studies of the molecular interactions between CXCR4 and its key peptide ligands (CXCL12 and HIV-1 gp120), and serve as valuable templates for further development of small-molecule CXCR4 antagonists with therapeutic potential. We here review recent computational studies of the molecular interactions between CXCR4 and its peptide ligands – based on the X-ray structures of CXCR4 – and the current status of small-molecule peptide and peptidomimetic CXCR4 antagonists.
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41
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Wu CH, Wang CJ, Chang CP, Cheng YC, Song JS, Jan JJ, Chou MC, Ke YY, Ma J, Wong YC, Hsieh TC, Tien YC, Gullen EA, Lo CF, Cheng CY, Liu YW, Sadani AA, Tsai CH, Hsieh HP, Tsou LK, Shia KS. Function-oriented development of CXCR4 antagonists as selective human immunodeficiency virus (HIV)-1 entry inhibitors. J Med Chem 2015; 58:1452-65. [PMID: 25584630 DOI: 10.1021/jm501772w] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Motivated by the pivotal role of CXCR4 as an HIV entry co-receptor, we herein report a de novo hit-to-lead effort on the identification of subnanomolar purine-based CXCR4 antagonists against HIV-1 infection. Compound 24, with an EC50 of 0.5 nM against HIV-1 entry into host cells and an IC50 of 16.4 nM for inhibition of radioligand stromal-derived factor-1α (SDF-1α) binding to CXCR4, was also found to be highly selective against closely related chemokine receptors. We rationalized that compound 24 complementarily interacted with the critical CXCR4 residues that are essential for binding to HIV-1 gp120 V3 loop and subsequent viral entry. Compound 24 showed a 130-fold increase in anti-HIV activity compared to that of the marketed CXCR4 antagonist, AMD3100 (Plerixafor), whereas both compounds exhibited similar potency in mobilization of CXCR4(+)/CD34(+) stem cells at a high dose. Our study offers insight into the design of anti-HIV therapeutics devoid of major interference with SDF-1α function.
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Affiliation(s)
- Chien-Huang Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes , Miaoli County 35053, Taiwan, R.O.C
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42
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Lv ZD, Kong B, Liu XP, Dong Q, Niu HT, Wang YH, Li FN, Wang HB. CXCL12 chemokine expression suppresses human breast cancer growth and metastasis in vitro and in vivo. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:6671-6678. [PMID: 25400746 PMCID: PMC4230065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 09/15/2014] [Indexed: 06/04/2023]
Abstract
Chemokine receptors are now known to play an important role in cancer growth and metastasis. However, there is little information regarding chemokine expression in breast cancer. The aim of this study was to evaluate CXCL12 expression in breast cancer and to investigate the question of whether reduced expression of CXCL12 may have any pathological significance in breast cancer development or progression. In this study, we performed western blotting and immunohistochemistry to evaluate the expression of CXCL12 and relevance with clinicopathological factors in the invasive ductal carcinoma. Reduction of CXCL12 was significantly correlated with tumor size, lymph node metastasis, TNM stage and Her-2 expression in breast cancer. Patients with negative CXCL12 expression had significantly lower cumulative postoperative 5 year survival rate than those with positive CXCL12 expression. In addition, we demonstrated that upregulation of CXCL12 expression by infection with an adenovirus containing a CXCL12 vector significantly inhibited cell growth and reduced the migration of breast cancer cells. Furthermore, animal studies revealed that nude mice injected with the Ad-CXCL12 cell lines featured a lighter weight than the control cell lines. These data suggest that CXCL12 plays an important role in cell growth and invasion in human breast cancer and it appears to be a potential prognostic marker for patients with breast cancer.
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MESH Headings
- Animals
- Breast Neoplasms/genetics
- Breast Neoplasms/immunology
- Breast Neoplasms/metabolism
- Breast Neoplasms/mortality
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/immunology
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/mortality
- Carcinoma, Ductal, Breast/secondary
- Cell Proliferation
- Chemokine CXCL12/genetics
- Chemokine CXCL12/metabolism
- Female
- Humans
- Kaplan-Meier Estimate
- MCF-7 Cells
- Mice, Nude
- Middle Aged
- Neoplasm Invasiveness
- Signal Transduction
- Time Factors
- Transfection
- Tumor Burden
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Affiliation(s)
- Zhi-Dong Lv
- Department of Breast Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266003, P. R. China
| | - Bin Kong
- Department of Breast Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266003, P. R. China
| | - Xiang-Ping Liu
- Central Laboratory of Molecular Biology, The Affiliated Hospital of Qingdao UniversityQingdao 266003, P. R. China
| | - Qian Dong
- Department of Pediatric Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266003, P. R. China
| | - Hai-Tao Niu
- Department of Urology Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266003, P. R. China
| | - Yong-Hua Wang
- Department of Urology Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266003, P. R. China
| | - Fu-Nian Li
- Department of Breast Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266003, P. R. China
| | - Hai-Bo Wang
- Department of Breast Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266003, P. R. China
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Tamamis P, Kieslich CA, Nikiforovich GV, Woodruff TM, Morikis D, Archontis G. Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking. BMC BIOPHYSICS 2014; 7:5. [PMID: 25170421 PMCID: PMC4141665 DOI: 10.1186/2046-1682-7-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/30/2014] [Indexed: 01/31/2023]
Abstract
Background The complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases. The cyclic hexapeptide PMX53 (sequence Ace-Phe-[Orn-Pro-dCha-Trp-Arg]) is a full C5aR antagonist of nanomolar potency, and is widely used to study C5aR function in disease. Results We construct for the first time molecular models for the C5aR:PMX53 complex without the a priori use of experimental constraints, via a computational framework of molecular dynamics (MD) simulations, docking, conformational clustering and free energy filtering. The models agree with experimental data, and are used to propose important intermolecular interactions contributing to binding, and to develop a hypothesis for the mechanism of PMX53 antagonism. Conclusion This work forms the basis for the design of improved C5aR antagonists, as well as for atomic-detail mechanistic studies of complement activation and function. Our computational framework can be widely used to develop GPCR-ligand structural models in membrane environments, peptidomimetics and other chemical compounds with potential clinical use.
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Affiliation(s)
- Phanourios Tamamis
- Department of Physics, University of Cyprus, PO 20537, CY1678 Nicosia, Cyprus
| | - Chris A Kieslich
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
| | | | - Trent M Woodruff
- School of Biomedical Sciences, the University of Queensland, St Lucia 4072, Australia
| | - Dimitrios Morikis
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
| | - Georgios Archontis
- Department of Physics, University of Cyprus, PO 20537, CY1678 Nicosia, Cyprus
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44
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Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5. Sci Rep 2014; 4:5447. [PMID: 24965094 PMCID: PMC4894430 DOI: 10.1038/srep05447] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/05/2014] [Indexed: 01/01/2023] Open
Abstract
CCL5 (RANTES) is an inflammatory chemokine which binds to chemokine receptor CCR5 and induces signaling. The CCL5:CCR5 associated chemotactic signaling is of critical biological importance and is a potential HIV-1 therapeutic axis. Several studies provided growing evidence for the expression of CCL5 and CCR5 in non-hematological malignancies. Therefore, the delineation of the CCL5:CCR5 complex structure can pave the way for novel CCR5-targeted drugs. We employed a computational protocol which is primarily based on free energy calculations and molecular dynamics simulations, and report, what is to our knowledge, the first computationally derived CCL5:CCR5 complex structure which is in excellent agreement with experimental findings and clarifies the functional role of CCL5 and CCR5 residues which are associated with binding and signaling. A wealth of polar and non-polar interactions contributes to the tight CCL5:CCR5 binding. The structure of an HIV-1 gp120 V3 loop in complex with CCR5 has recently been derived through a similar computational protocol. A comparison between the CCL5 : CCR5 and the HIV-1 gp120 V3 loop : CCR5 complex structures depicts that both the chemokine and the virus primarily interact with the same CCR5 residues. The present work provides insights into the blocking mechanism of HIV-1 by CCL5.
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45
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Tamamis P, Floudas CA. Molecular recognition of CCR5 by an HIV-1 gp120 V3 loop. PLoS One 2014; 9:e95767. [PMID: 24763408 PMCID: PMC3999033 DOI: 10.1371/journal.pone.0095767] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/29/2014] [Indexed: 12/04/2022] Open
Abstract
The binding of protein HIV-1 gp120 to coreceptors CCR5 or CXCR4 is a key step of the HIV-1 entry to the host cell, and is predominantly mediated through the V3 loop fragment of HIV-1 gp120. In the present work, we delineate the molecular recognition of chemokine receptor CCR5 by a dual tropic HIV-1 gp120 V3 loop, using a comprehensive set of computational tools predominantly based on molecular dynamics simulations and free energy calculations. We report, what is to our knowledge, the first complete HIV-1 gp120 V3 loop : CCR5 complex structure, which includes the whole V3 loop and the N-terminus of CCR5, and exhibits exceptional agreement with previous experimental findings. The computationally derived structure sheds light into the functional role of HIV-1 gp120 V3 loop and CCR5 residues associated with the HIV-1 coreceptor activity, and provides insights into the HIV-1 coreceptor selectivity and the blocking mechanism of HIV-1 gp120 by maraviroc. By comparing the binding of the specific dual tropic HIV-1 gp120 V3 loop with CCR5 and CXCR4, we observe that the HIV-1 gp120 V3 loop residues 13-21, which include the tip, share nearly identical structural and energetic properties in complex with both coreceptors. This result paves the way for the design of dual CCR5/CXCR4 targeted peptides as novel potential anti-AIDS therapeutics.
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Affiliation(s)
- Phanourios Tamamis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
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