1
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G SK, N K, Elumalai E, Gupta KK. Identification of CXCR4 inhibitors as a key therapeutic small molecule in renal fibrosis. J Biomol Struct Dyn 2024; 42:8441-8453. [PMID: 37592737 DOI: 10.1080/07391102.2023.2246575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
The final stage of almost all chronic kidney diseases is renal fibrosis. Simple wounds or persistent inflammation can cause tissue inflammation, which, in the case of the kidney, results in scarring. Vascular sclerosis, tubulointerstitial fibrosis and glomerular fibrosis are all types of kidney fibrosis. Renal damage and fibrosis are caused by elevated expression of CXCR4. This study aimed to identify possible pharmacological agents which could bind to and inhibit isoform I of CXCR4 and determine their strength of interactions. The I-TASSER, Galaxyweb and Robetta were used to predict and refine the structure of the CXCR4 protein. ModBase was used to improve the loops, and then the quality was evaluated by using the ERRAT value (92.15) and Ramachandran plot. The improved 3D structure was subjected to small molecule database docking using Maestro (from Schrodinger) and the glide module. GROMACS was used to simulate molecules with the three top low glide scores and the best ADME properties. The best glide score was achieved by ligand ID 4990 (-11.5). Simulations, free energy landscape and residue decomposition analysis revealed that 4990 interacted more consistently with CXCR4 than the other two small molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Senthil Kumar G
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India
| | - Kishore N
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India
| | - Elakkiya Elumalai
- Centre for Bioinformatics, Pondicherry University, Pondicherry, India
| | - Krishna Kant Gupta
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India
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2
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Harms M, Haase A, Rodríguez-Alfonso A, Löffler J, Almeida-Hernández Y, Ruiz-Blanco YB, Albers D, Gilg A, von Bank F, Zech F, Groß R, Datta M, Jaikishan J, Draphoen B, Habib M, Ständker L, Wiese S, Lindén M, Winter G, Rasche V, Beer AJ, Jumaa H, Abadi AH, Kirchhoff F, Busch M, Dünker N, Sanchez-Garcia E, Münch J. Fatty acid conjugated EPI-X4 derivatives with increased activity and in vivo stability. J Control Release 2024; 373:583-598. [PMID: 39047872 DOI: 10.1016/j.jconrel.2024.07.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/09/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
Dysregulation of the CXCL12/CXCR4 axis is implicated in autoimmune, inflammatory, and oncogenic diseases, positioning CXCR4 as a pivotal therapeutic target. We evaluated optimized variants of the specific endogenous CXCR4 antagonist, EPI-X4, addressing existing challenges in stability and potency. Our structure-activity relationship study investigates the conjugation of EPI-X4 derivatives with long-chain fatty acids, enhancing serum albumin interaction and receptor affinity. Molecular dynamic simulations revealed that the lipid moieties stabilize the peptide-receptor interaction through hydrophobic contacts at the receptor's N-terminus, anchoring the lipopeptide within the CXCR4 binding pocket and maintaining essential receptor interactions. Accordingly, lipidation resulted in increased receptor affinities and antagonistic activities. Additionally, by interacting with human serum albumin lipidated EPI-X4 derivatives displayed sustained stability in human plasma and extended circulation times in vivo. Selected candidates showed significant therapeutic potential in human retinoblastoma cells in vitro and in ovo, with our lead derivative exhibiting higher efficacies compared to its non-lipidated counterpart. This study not only elucidates the optimization trajectory for EPI-X4 derivatives but also underscores the intricate interplay between stability and efficacy, crucial for delineating their translational potential in clinical applications.
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Affiliation(s)
- Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.
| | - André Haase
- Institute for Anatomy II, Department of Neuroanatomy, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany
| | - Armando Rodríguez-Alfonso
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm 89081, Germany; Core Unit Mass Spectrometry and Proteomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Jessica Löffler
- Department of Nuclear Medicine, Ulm University Medical Center, Ulm 89081, Germany
| | - Yasser Almeida-Hernández
- Computational Bioengineering, Department of Biochemical and Chemical Engineering, 44227 Dortmund, Germany
| | - Yasser B Ruiz-Blanco
- Computational Bioengineering, Department of Biochemical and Chemical Engineering, 44227 Dortmund, Germany
| | - Dan Albers
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Andrea Gilg
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Franziska von Bank
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Moumita Datta
- Institute of Immunology, Ulm University Medical Center, Ulm 89081, Germany
| | - Janeni Jaikishan
- Institute of Immunology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Monica Habib
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; Pharmaceutical Chemistry Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, Cairo, Egypt
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Mika Lindén
- Institute for Inorganic Chemistry II, 89081 Ulm, Germany
| | - Gordon Winter
- Department of Nuclear Medicine, Ulm University Medical Center, Ulm 89081, Germany
| | - Volker Rasche
- Experimental Cardiovascular Imaging (ExCaVI), Ulm University Medical Center, Ulm 89081, Germany
| | - Ambros J Beer
- Department of Nuclear Medicine, Ulm University Medical Center, Ulm 89081, Germany
| | - Hassan Jumaa
- Institute of Immunology, Ulm University Medical Center, Ulm 89081, Germany
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Maike Busch
- Institute for Anatomy II, Department of Neuroanatomy, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany
| | - Nicole Dünker
- Institute for Anatomy II, Department of Neuroanatomy, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Bioengineering, Department of Biochemical and Chemical Engineering, 44227 Dortmund, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
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3
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Sagini MN, Zepp M, Eyol E, Ali DM, Gromova S, Dahlmann M, Behrens D, Groeschel C, Tischmeier L, Hoffmann J, Berger MR, Forssmann WG. EPI-X4, a CXCR4 antagonist inhibits tumor growth in pancreatic cancer and lymphoma models. Peptides 2024; 175:171111. [PMID: 38036098 DOI: 10.1016/j.peptides.2023.171111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023]
Abstract
Endogenous peptide inhibitor for CXCR4 (EPI-X4) is a CXCR4 antagonist with potential for cancer therapy. It is a processed fragment of serum albumin from the hemofiltrate of dialysis patients. This study reports the efficacy of fifteen EPI-X4 derivatives in pancreatic cancer and lymphoma models. In vitro, the peptides were investigated for antiproliferation (cytotoxicity) by MTT assay. The mRNA expression for CXCR4 and CXCL12 was determined by RT-PCR, chip array and RNA sequencing. Chip array analysis yielded 634 genes associated with CXCR4/CXCL12 signaling. About 21% of these genes correlated with metastasis in the context of cell motility, proliferation, and survival. Expression levels of these genes were altered in pancreatic cancer (36%), lymphoma models (53%) and in patients' data (58%). EPI-X4 derivatives failed to inhibit cell proliferation due to low expression of CXCR4 in vitro, but inhibited tumor growth in the bioassays with significant efficacy. In the pancreatic cancer model, EPI-X4a, f and k inhibited mean tumor growth by > 50% and even caused complete remissions. In the lymphoma model, EPI-X4b, n and p inhibited mean tumor growth by > 70% and caused stable disease. Given the non-toxic and non-immunogenic properties of EPI-X4, these findings underscore its status as a promising therapy of pancreatic cancer and lymphoma and warrant further studies. SIMPLE SUMMARY: This study examined the value of chemokine receptor CXCR4 as an antineoplastic target for the endogenous peptide inhibitor of CXCR4 (EPI-X4), a 12-meric peptide derived from serum albumin. EPI-X4 inhibits CXCR4 interaction with its natural ligand, CXCL12 (SDF1). Therefore, malignancies (including pancreatic cancer and lymphoma) that depend on the CXCR4/CXCL12 pathway for progression can be targeted with EPI-X4. Of 634 genes that were linked to the CXCR4/CXCL12 pathway, 21% were associated with metastasis. In cultured human Suit2-007 pancreatic cancer cells, CXCR4 showed low to undetectable expression, which was why EPI-X4 did not inhibit pancreatic cancer cell proliferation. These findings were different in vivo, where CXCR4 was highly expressed and EPI-X4 inhibited tumor growth in rodents harboring pancreatic cancer or lymphoma. In the pancreatic cancer model, EPI-X4 derivatives a, f and k caused complete remissions, while in lymphomas EPI-X4 derivatives b, n and p caused stable disease.
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Affiliation(s)
- Micah N Sagini
- Toxicology and Chemotherapy Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Michael Zepp
- Toxicology and Chemotherapy Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Ergül Eyol
- Toxicology and Chemotherapy Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Doaa M Ali
- Toxicology and Chemotherapy Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Svetlana Gromova
- EPO, Experimental Pharmacology & Oncology Berlin-Buch GmbH, Germany
| | - Mathias Dahlmann
- EPO, Experimental Pharmacology & Oncology Berlin-Buch GmbH, Germany
| | - Diana Behrens
- EPO, Experimental Pharmacology & Oncology Berlin-Buch GmbH, Germany
| | - Christian Groeschel
- NeoPep Pharma GmbH & Co. KG., Hannover, Germany and Hannover Medical School, Department of Internal Medicine, Germany
| | - Linus Tischmeier
- NeoPep Pharma GmbH & Co. KG., Hannover, Germany and Hannover Medical School, Department of Internal Medicine, Germany
| | - Jens Hoffmann
- EPO, Experimental Pharmacology & Oncology Berlin-Buch GmbH, Germany
| | - Martin R Berger
- Toxicology and Chemotherapy Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany.
| | - Wolf-Georg Forssmann
- NeoPep Pharma GmbH & Co. KG., Hannover, Germany and Hannover Medical School, Department of Internal Medicine, Germany.
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4
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V J, M S, Wani A, Ahmad SF, Nadeem A, Sharma A, Ahmed SSSJ. Pharmacoscreening, molecular dynamics, and quantum mechanics of inermin from Panax ginseng: a crucial molecule inhibiting exosomal protein target associated with coronary artery disease progression. PeerJ 2023; 11:e16481. [PMID: 38077444 PMCID: PMC10710165 DOI: 10.7717/peerj.16481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Background Exosomes, microvesicles, carry and release several vital molecules across cells, tissues, and organs. Epicardial adipose tissue exosomes are critical in the development and progression of coronary artery disease (CAD). It is hypothesized that exosomes may transport causative molecules from inflamed tissue and deliver to the target tissue and progress CAD. Thus, identifying and inhibiting the CAD-associated proteins that are being transported to other cells via exosomes will help slow the progression of CAD. Methods This study uses a systems biological approach that integrates differential gene expression in the CAD, exosomal cargo assessment, protein network construction, and functional enrichment to identify the crucial exosomal cargo protein target. Meanwhile, absorption, distribution, metabolism, and excretion (ADME) screening of Panax ginseng-derived compounds was conducted and then docked against the protein target to identify potential inhibitors and then subjected to molecular dynamics simulation (MDS) to understand the behavior of the protein-ligand complex till 100 nanoseconds. Finally, density functional theory (DFT) calculation was performed on the ligand with the highest affinity with the target. Results Through the systems biological approach, Mothers against decapentaplegic homolog 2 protein (SMAD2) was determined as a potential target that linked with PI3K-Akt signaling, Ubiquitin mediated proteolysis, and the focal adhesion pathway. Further, screening of 190 Panax ginseng compounds, 27 showed drug-likeness properties. Inermin, a phytochemical showed good docking with -5.02 kcal/mol and achieved stability confirmation with SMAD2 based on MDS when compared to the known CAD drugs. Additionally, DFT analysis of inermin showed high chemical activity that significantly contributes to effective target binding. Overall, our computational study suggests that inermin could act against SMAD2 and may aid in the management of CAD.
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Affiliation(s)
- Janakiraman V
- Muti-omics and Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettnad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Sudhan M
- Muti-omics and Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettnad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Abubakar Wani
- Department of Immunology, St. Jude Children’s Research Hospital Memphis, TN, USA
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Nadeem
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ashutosh Sharma
- Centre of Bioengineering, NatProLab, Plant Innovation Lab, School of Engineering and Sciences, Tecnologico de Monterrey, Queretaro, Mexico
| | - Shiek S. S. J. Ahmed
- Muti-omics and Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettnad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
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5
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Harms M, Fabech Hansson R, Gilg A, Almeida-Hernández Y, Löffler J, Rodríguez-Alfonso A, Habib MMW, Albers D, Ahmed NS, Abadi AH, Winter G, Rasche V, Beer AJ, Weidinger G, Preising N, Ständker L, Wiese S, Sanchez-Garcia E, Zelikin AN, Münch J. Development of N-Terminally Modified Variants of the CXCR4-Antagonistic Peptide EPI-X4 for Enhanced Plasma Stability. J Med Chem 2023; 66:15189-15204. [PMID: 37940118 PMCID: PMC10682998 DOI: 10.1021/acs.jmedchem.3c01128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Indexed: 11/10/2023]
Abstract
EPI-X4, a natural peptide CXCR4 antagonist, shows potential for treating inflammation and cancer, but its short plasma stability limits its clinical application. We aimed to improve the plasma stability of EPI-X4 analogues without compromising CXCR4 antagonism. Our findings revealed that only the peptide N-terminus is prone to degradation. Consequently, incorporating d-amino acids or acetyl groups in this region enhanced peptide stability in plasma. Notably, EPI-X4 leads 5, 27, and 28 not only retained their CXCR4 binding and antagonism but also remained stable in plasma for over 8 h. Molecular dynamic simulations showed that these modified analogues bind similarly to CXCR4 as the original peptide. To further increase their systemic half-lives, we conjugated these stabilized analogues with large polymers and albumin binders. These advances highlight the potential of the optimized EPI-X4 analogues as promising CXCR4-targeted therapeutics and set the stage for more detailed preclinical assessments.
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Affiliation(s)
- Mirja Harms
- Institute
of Molecular Virology, Ulm University Medical
Center, Ulm 89081, Germany
| | - Rikke Fabech Hansson
- Department
of Chemistry and iNANO Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
| | - Andrea Gilg
- Institute
of Molecular Virology, Ulm University Medical
Center, Ulm 89081, Germany
| | - Yasser Almeida-Hernández
- Department
of Biochemical and Chemical Engineering, Computational Bioengineering, Emil-Figge Str. 66, Dortmund 44227, Germany
| | - Jessica Löffler
- Department
of Nuclear Medicine, Ulm University Medical
Center, Ulm 89081, Germany
| | - Armando Rodríguez-Alfonso
- Core
Facility Functional Peptidomics, Ulm University
Medical Center, Ulm 89081, Germany
- Core Unit
Mass Spectrometry and Proteomics, Ulm University
Medical Center, Ulm 89081, Germany
| | - Monica M. W. Habib
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
- Pharmaceutical
Chemistry Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic
Foundation, Cairo 11865, Egypt
| | - Dan Albers
- Institute
of Molecular Virology, Ulm University Medical
Center, Ulm 89081, Germany
| | - Nermin S. Ahmed
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Ashraf H. Abadi
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Gordon Winter
- Department
of Nuclear Medicine, Ulm University Medical
Center, Ulm 89081, Germany
| | - Volker Rasche
- Experimental
Cardiovascular Imaging (ExCaVI), Ulm University
Medical Center, Ulm 89081, Germany
| | - Ambros J. Beer
- Department
of Nuclear Medicine, Ulm University Medical
Center, Ulm 89081, Germany
| | - Gilbert Weidinger
- Institute
of Biochemistry and Molecular Biology, Ulm
University, Ulm 89081, Germany
| | - Nico Preising
- Core
Facility Functional Peptidomics, Ulm University
Medical Center, Ulm 89081, Germany
| | - Ludger Ständker
- Core
Facility Functional Peptidomics, Ulm University
Medical Center, Ulm 89081, Germany
| | - Sebastian Wiese
- Core Unit
Mass Spectrometry and Proteomics, Ulm University
Medical Center, Ulm 89081, Germany
| | - Elsa Sanchez-Garcia
- Department
of Biochemical and Chemical Engineering, Computational Bioengineering, Emil-Figge Str. 66, Dortmund 44227, Germany
| | - Alexander N. Zelikin
- Department
of Chemistry and iNANO Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
| | - Jan Münch
- Institute
of Molecular Virology, Ulm University Medical
Center, Ulm 89081, Germany
- Core
Facility Functional Peptidomics, Ulm University
Medical Center, Ulm 89081, Germany
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6
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M. S, V. J, Ahmad SF, Attia SM, Emran TB, Patil RB, Ahmed SSSJ. Structural Characteristics of PON1 with Leu55Met and Gln192Arg Variants Influencing Oxidative-Stress-Related Diseases: An Integrated Molecular Modeling and Dynamics Study. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:2060. [PMID: 38138163 PMCID: PMC10744641 DOI: 10.3390/medicina59122060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/04/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023]
Abstract
Background and Objectives: PON1 is a multi-functional antioxidant protein that hydrolyzes a variety of endogenous and exogenous substrates in the human system. Growing evidence suggests that the Leu55Met and Gln192Arg substitutions alter PON1 activity and are linked with a variety of oxidative-stress-related diseases. Materials and Methods: We implemented structural modeling and molecular dynamics (MD) simulation along with essential dynamics of PON1 and molecular docking with their endogenous (n = 4) and exogenous (n = 6) substrates to gain insights into conformational changes and binding affinity in order to characterize the specific functional ramifications of PON1 variants. Results: The Leu55Met variation had a higher root mean square deviation (0.249 nm) than the wild type (0.216 nm) and Gln192Arg (0.202 nm), implying increased protein flexibility. Furthermore, the essential dynamics analysis confirms the structural change in PON1 with Leu55Met vs. Gln192Arg and wild type. Additionally, PON1 with Leu55Met causes local conformational alterations at the substrate binding site, leading to changes in binding affinity with their substrates. Conclusions: Our findings highlight the structural consequences of the variants, which would increase understanding of the role of PON1 in the pathogenesis of oxidative-stress-related diseases, as well as the management of endogenous and exogenous chemicals in the treatment of diseases.
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Affiliation(s)
- Sudhan M.
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
| | - Janakiraman V.
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sabry M. Attia
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Societys, Sinhgad College of Pharmacy, Vadgaon (BK), Pune 411041, Maharashtra, India
| | - Shiek S. S. J. Ahmed
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
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7
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Jung CK, Münch J, Jacob T. Conformational States of the CXCR4 Inhibitor Peptide EPI-X4-A Theoretical Analysis. Int J Mol Sci 2023; 24:16229. [PMID: 38003419 PMCID: PMC10671355 DOI: 10.3390/ijms242216229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
EPI-X4, an endogenous peptide inhibitor, has exhibited potential as a blocker of CXCR4-a G protein-coupled receptor. This unique inhibitor demonstrates the ability to impede HIV-1 infection and halt CXCR4-dependent processes such as tumor cell migration and invagination. Despite its promising effects, a comprehensive understanding of the interaction between EPI-X4 and CXCR4 under natural conditions remains elusive due to experimental limitations. To bridge this knowledge gap, a simulation approach was undertaken. Approximately 150,000 secondary structures of EPI-X4 were subjected to simulations to identify thermodynamically stable candidates. This simulation process harnessed a self-developed reactive force field operating within the ReaxFF framework. The application of the Two-Phase Thermodynamic methodology to ReaxFF facilitated the derivation of crucial thermodynamic attributes of the EPI-X4 conformers. To deepen insights, an ab initio density functional theory calculation method was employed to assess the electrostatic potentials of the most relevant (i.e., stable) EPI-X4 structures. This analytical endeavor aimed to enhance comprehension of the inhibitor's structural characteristics. As a result of these investigations, predictions were made regarding how EPI-X4 interacts with CXCR4. Two pivotal requirements emerged. Firstly, the spatial conformation of EPI-X4 must align effectively with the CXCR4 receptor protein. Secondly, the functional groups present on the surface of the inhibitor's structure must complement the corresponding features of CXCR4 to induce attraction between the two entities. These predictive outcomes were based on a meticulous analysis of the conformers, conducted in a gaseous environment. Ultimately, this rigorous exploration yielded a suitable EPI-X4 structure that fulfills the spatial and functional prerequisites for interacting with CXCR4, thus potentially shedding light on new avenues for therapeutic development.
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Affiliation(s)
- Christoph Karsten Jung
- Helmholtz Institute Ulm (HIU) Electrochemical Energy Storage, Helmholtzstr. 11, D-89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), D-76021 Karlsruhe, Germany
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, D-89081 Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstr. 1, D-89081 Ulm, Germany
| | - Timo Jacob
- Helmholtz Institute Ulm (HIU) Electrochemical Energy Storage, Helmholtzstr. 11, D-89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), D-76021 Karlsruhe, Germany
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, D-89081 Ulm, Germany
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8
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Anirudhan A, Mahema S, Ahmad SF, Emran TB, Ahmed SSSJ, Paramasivam P. Screening of Crucial Cytosolicproteins Interconnecting the Endoplasmic Reticulum and Mitochondria in Parkinson's Disease and the Impact of Anti-Parkinson Drugs in the Preservation of Organelle Connectivity. Brain Sci 2023; 13:1551. [PMID: 38002511 PMCID: PMC10670093 DOI: 10.3390/brainsci13111551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Mitochondrial dysfunction is well-established in Parkinson's disease (PD); however, its dysfunctions associating with cell organelle connectivity remain unknown. We aimed to establish the crucial cytosolic protein involved in organelle connectivity between mitochondria and the endopalmic reticulum (ER) through a computational approach by constructing an organelle protein network to extract functional clusters presenting the crucial PD protein connecting organelles. Then, we assessed the influence of anti-parkinsonism drugs (n = 35) on the crucial protein through molecular docking and molecular dynamic simulation and further validated its gene expression in PD participants under, istradefylline (n = 25) and amantadine (n = 25) treatment. Based on our investigation, D-aspartate oxidase (DDO )protein was found to be the critical that connects both mitochondria and the ER. Further, molecular docking showed that istradefylline has a high affinity (-9.073 kcal/mol) against DDO protein, which may disrupt mitochondrial-ER connectivity. While amantadine (-4.53 kcal/mol) shows negligible effects against DDO that contribute to conformational changes in drug binding, Successively, DDO gene expression was downregulated in istradefylline-treated PD participants, which elucidated the likelihood of an istradefylline off-target mechanism. Overall, our findings illuminate the off-target effects of anti-parkinsonism medications on DDO protein, enabling the recommendation of off-target-free PD treatments.
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Affiliation(s)
- Athira Anirudhan
- Central Research Laboratory, Believers Church Medical College Hospital, Kuttapuzha, Thiruvalla 689101, Kerala, India
| | - S. Mahema
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Shiek S. S. J. Ahmed
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
| | - Prabu Paramasivam
- Madras Diabetes Research Foundation and Dr. Mohan’s Diabetes Specialities Centre, WHO Collaborating Centre for Non-Communicable Diseases Prevention and Control & IDF Centre of Education, Gopalapuram, Chennai 602105, Tamil Nadu, India
- Department of Neurology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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9
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Sudhan M, Janakiraman V, Patil R, Oyouni AAA, Hasan Mufti A, Ahmed SSSJ. Asn215Ser, Ala143Thr, and Arg112Cys variants in α-galactosidase A protein confer stability loss in Fabry's disease. J Biomol Struct Dyn 2023; 41:9840-9849. [PMID: 36420638 DOI: 10.1080/07391102.2022.2148001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022]
Abstract
Alpha galactosidase A (α-GalA) gene contains nine exons localized at the q-arm of the X chromosome. Generally, an α-GalA enzyme is involved in the removal of galactosyl moieties from the glycoproteins and glycolipids. Dysregulation results in the accumulation of glycoproteins as well as glycolipids in various organs leading to Fabry disease (FD). In this study, we examine the impact of Asn215Ser, Ala143Thr and Arg112Cys variants on the α-GalA protein structure contributing to functional dynamic changes in FD. The seven computational pathogenicity prediction methods were used to predict the effects of these variants on the α-GalA protein. The three-dimensional structure of α-GalA variants was modeled with the Swiss Model and Robetta server and validated using a variety of tools. Then, molecular dynamics (MD) simulation was performed to understand the stability and dynamic behavior of the wild-type and variants structures. Most of our analyzed pathogenicity prediction tools showed that Asn215Ser, Ala143Thr and Arg112Cys variants cause a deleterious effect on the α-GalA protein. Further, MD trajectory analysis showed the destabilizing effect of variants on α-GalA structure based on the root mean square deviation, root mean square fluctuation, solvent accessible surface area, the radius of gyration, hydrogen bond, cluster analysis and PCA analysis. This concludes that the presence of these variants could potentially affect the protein functional process of galactosyl moieties removal which might lead to Fabry disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- M Sudhan
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | - V Janakiraman
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | - Rajesh Patil
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy, Pune, India
| | | | - Ahmad Hasan Mufti
- Medical Genetics Department, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shiek S S J Ahmed
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
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10
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Schauenburg D, Zech F, Heck AJ, von Maltitz P, Harms M, Führer S, Alleva N, Münch J, Kuan SL, Kirchhoff F, Weil T. Peptide Bispecifics Inhibiting HIV-1 Infection by an Orthogonal Chemical and Supramolecular Strategy. Bioconjug Chem 2023; 34:1645-1652. [PMID: 37665137 PMCID: PMC10515486 DOI: 10.1021/acs.bioconjchem.3c00314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Viral infections pose a significant threat to human health, and effective antiviral strategies are urgently needed. Antiviral peptides have emerged as a promising class of therapeutic agents due to their unique properties and mechanisms of action. While effective on their own, combining antiviral peptides may allow us to enhance their potency and to prevent viral resistance. Here, we developed an orthogonal chemical strategy to prepare a heterodimeric peptide conjugate assembled on a protein-based nanoplatform. Specifically, we combined the optimized version of two peptides inhibiting HIV-1 by distinct mechanisms. Virus-inhibitory peptide (VIRIP) is a 20 amino acid fragment of α1-antitrypsin that inhibits HIV-1 by targeting the gp41 fusion peptide. Endogenous peptide inhibitor of CXCR4 (EPI-X4) is a 16-residue fragment of human serum albumin that prevents HIV-1 entry by binding to the viral CXCR4 co-receptor. Optimized forms of both peptides are assembled on supramolecular nanoplatforms through the streptavidin-biotin interaction. We show that the construct consisting of the two different peptides (SAv-VIR-102C9-EPI-X4 JM#173-C) shows increased activity against CCR5- and CXCR4-tropic HIV-1 variants. Our results are a proof of concept that peptides with different modes of action can be assembled on nanoplatforms to enhance their antiviral activity.
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Affiliation(s)
- Dominik Schauenburg
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstr. 1, 89081 Ulm, Germany
| | - Astrid Johanna Heck
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Pascal von Maltitz
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstr. 1, 89081 Ulm, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstr. 1, 89081 Ulm, Germany
| | - Siska Führer
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Nico Alleva
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstr. 1, 89081 Ulm, Germany
| | - Seah Ling Kuan
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstr. 1, 89081 Ulm, Germany
| | - Tanja Weil
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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11
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Grudzien P, Neufeld H, Ebe Eyenga M, Gaponenko V. Development of tolerance to chemokine receptor antagonists: current paradigms and the need for further investigation. Front Immunol 2023; 14:1184014. [PMID: 37575219 PMCID: PMC10420067 DOI: 10.3389/fimmu.2023.1184014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/27/2023] [Indexed: 08/15/2023] Open
Abstract
Chemokine G-protein coupled receptors are validated drug targets for many diseases, including cancer, neurological, and inflammatory disorders. Despite much time and effort spent on therapeutic development, very few chemokine receptor antagonists are approved for clinical use. Among potential reasons for the slow progress in developing chemokine receptor inhibitors, antagonist tolerance, a progressive reduction in drug efficacy after repeated administration, is likely to play a key role. The mechanisms leading to antagonist tolerance remain poorly understood. In many cases, antagonist tolerance is accompanied by increased receptor concentration on the cell surface after prolonged exposure to chemokine receptor antagonists. This points to a possible role of altered receptor internalization and presentation on the cell surface, as has been shown for agonist (primarily opioid) tolerance. In addition, examples of antagonist tolerance in the context of other G-protein coupled receptors suggest the involvement of noncanonical signal transduction in opposing the effects of the antagonists. In this review, we summarize the available progress and challenges in therapeutic development of chemokine receptor antagonists, describe the available knowledge about antagonist tolerance, and propose new avenues for future investigation of this important phenomenon. Furthermore, we highlight the modern methodologies that have the potential to reveal novel mechanisms leading to antagonist tolerance and to propel the field forward by advancing the development of potent "tolerance-free" antagonists of chemokine receptors.
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Affiliation(s)
| | | | | | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
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12
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Harms M, Smith N, Han M, Groß R, von Maltitz P, Stürzel C, Ruiz-Blanco YB, Almeida-Hernández Y, Rodriguez-Alfonso A, Cathelin D, Caspar B, Tahar B, Sayettat S, Bekaddour N, Vanshylla K, Kleipass F, Wiese S, Ständker L, Klein F, Lagane B, Boonen A, Schols D, Benichou S, Sanchez-Garcia E, Herbeuval JP, Münch J. Spermine and spermidine bind CXCR4 and inhibit CXCR4- but not CCR5-tropic HIV-1 infection. SCIENCE ADVANCES 2023; 9:eadf8251. [PMID: 37406129 DOI: 10.1126/sciadv.adf8251] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/01/2023] [Indexed: 07/07/2023]
Abstract
Semen is an important vector for sexual HIV-1 transmission. Although CXCR4-tropic (X4) HIV-1 may be present in semen, almost exclusively CCR5-tropic (R5) HIV-1 causes systemic infection after sexual intercourse. To identify factors that may limit sexual X4-HIV-1 transmission, we generated a seminal fluid-derived compound library and screened it for antiviral agents. We identified four adjacent fractions that blocked X4-HIV-1 but not R5-HIV-1 and found that they all contained spermine and spermidine, abundant polyamines in semen. We showed that spermine, which is present in semen at concentrations up to 14 mM, binds CXCR4 and selectively inhibits cell-free and cell-associated X4-HIV-1 infection of cell lines and primary target cells at micromolar concentrations. Our findings suggest that seminal spermine restricts sexual X4-HIV-1 transmission.
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Affiliation(s)
- Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Nikaïa Smith
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
- CNRS UMR-8601, Université Paris Cité, 75006 Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, 75014 Paris, France
| | - Mingyu Han
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, 75014 Paris, France
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Pascal von Maltitz
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christina Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
| | - Yasser Almeida-Hernández
- Computational Bioengineering, Department of Biochemical and Chemical Engineering, Emil-Figge Str. 66., 44227 Dortmund, Germany
| | - Armando Rodriguez-Alfonso
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081 Ulm, Germany
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Dominique Cathelin
- CNRS UMR-8601, Université Paris Cité, 75006 Paris, France
- Chemistry and Biology, Modeling and Immunology for Therapy (CBMIT), Paris, France
| | - Birgit Caspar
- CNRS UMR-8601, Université Paris Cité, 75006 Paris, France
- Chemistry and Biology, Modeling and Immunology for Therapy (CBMIT), Paris, France
| | - Bouceba Tahar
- Sorbonne University, CNRS, Institut de Biologie Paris-Seine (IBPS), Protein Engineering Platform, Molecular Interaction Service, F-75252 Paris, France
| | - Sophie Sayettat
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, 75014 Paris, France
| | - Nassima Bekaddour
- CNRS UMR-8601, Université Paris Cité, 75006 Paris, France
- Chemistry and Biology, Modeling and Immunology for Therapy (CBMIT), Paris, France
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Franziska Kleipass
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081 Ulm, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Bernard Lagane
- Infinity, Université de Toulouse, CNRS, INSERM, Toulouse, France
| | - Arnaud Boonen
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, P.O. Box 1030, 3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, P.O. Box 1030, 3000 Leuven, Belgium
| | - Serge Benichou
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, 75014 Paris, France
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
- Computational Bioengineering, Department of Biochemical and Chemical Engineering, Emil-Figge Str. 66., 44227 Dortmund, Germany
| | - Jean-Philippe Herbeuval
- CNRS UMR-8601, Université Paris Cité, 75006 Paris, France
- Chemistry and Biology, Modeling and Immunology for Therapy (CBMIT), Paris, France
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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13
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Gaonkar RH, Schmidt YT, Mansi R, Almeida-Hernanadez Y, Sanchez-Garcia E, Harms M, Münch J, Fani M. Development of a New Class of CXCR4-Targeting Radioligands Based on the Endogenous Antagonist EPI-X4 for Oncological Applications. J Med Chem 2023. [PMID: 37328158 DOI: 10.1021/acs.jmedchem.3c00131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The peptide fragment of human serum albumin that was identified as an inhibitor of C-X-C motif chemokine receptor 4 (CXCR4), termed EPI-X4, was investigated as a scaffold for the development of CXCR4-targeting radio-theragnostics. Derivatives of its truncated version JM#21 (ILRWSRKLPCVS) were conjugated to 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) and tested in Jurkat and Ghost-CXCR4 cells. Ligand-1, -2, -5, -6, -7, -8, and -9 were selected for radiolabeling. Molecular modeling indicated that 177Lu-DOTA incorporation C-terminally did not interfere with the CXCR4 binding. Lipophilicity, in vitro plasma stability, and cellular uptake hinted 177Lu-7 as superior. In Jurkat xenografts, all radioligands showed >90% washout from the body within an hour, with the exception of 177Lu-7 and 177Lu-9. 177Lu-7 demonstrated best CXCR4-tumor targeting. Ex vivo biodistribution and single-photon emission computed tomography (SPECT)/positron emission tomography (PET)/CT imaging of 177Lu-7/68Ga-7 showed the same distribution profile for both radioligands, characterized by very low uptake in all nontargeted organs except the kidneys. The data support the feasibility of CXCR4-targeting with EPI-X4-based radioligands and designate ligand-7 as a lead candidate for further optimization.
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Affiliation(s)
- Raghuvir Haridas Gaonkar
- Division of Radiopharmaceutical Chemistry, Department Theragnostics, University Hospital Basel, Basel 4031, Switzerland
| | - Yannik Tim Schmidt
- Division of Radiopharmaceutical Chemistry, Department Theragnostics, University Hospital Basel, Basel 4031, Switzerland
| | - Rosalba Mansi
- Division of Radiopharmaceutical Chemistry, Department Theragnostics, University Hospital Basel, Basel 4031, Switzerland
| | - Yasser Almeida-Hernanadez
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45117, Germany
- Computational Bioengineering, Faculty of Bio- and Chemical Engineering, Technical University Dortmund, Dortmund 44227, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45117, Germany
- Computational Bioengineering, Faculty of Bio- and Chemical Engineering, Technical University Dortmund, Dortmund 44227, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Melpomeni Fani
- Division of Radiopharmaceutical Chemistry, Department Theragnostics, University Hospital Basel, Basel 4031, Switzerland
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14
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Hartrampf PE, Kosmala A, Serfling SE, Bundschuh L, Higuchi T, Lapa C, Rowe SP, Matsusaka Y, Weich A, Buck AK, Bundschuh RA, Werner RA. Interobserver Agreement Rates on C-X-C Motif Chemokine Receptor 4-Directed Molecular Imaging and Therapy. Clin Nucl Med 2023; 48:483-488. [PMID: 36947793 PMCID: PMC10184817 DOI: 10.1097/rlu.0000000000004629] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/06/2023] [Indexed: 03/24/2023]
Abstract
BACKGROUND We aimed to evaluate the interobserver agreement rates in patients scanned with C-X-C motif chemokine receptor 4 (CXCR4)-directed PET/CT, including the rate of patients eligible for CXCR4-targeted radioligand therapy (RLT) based on scan results. METHODS Four independent observers reviewed 50 CXCR4-targeted [ 68 Ga]pentixafor PET/CT of patients with various solid cancers. On a visual level, the following items were assessed by each reader: overall scan impression, number of organ and lymph node (LN) metastases and number of affected organs and LN regions. For a quantitative investigation, readers had to choose a maximum of 3 target lesions, defined as largest in size and/or most intense uptake per organ compartment. Reference tissues were also quantified, including unaffected hepatic parenchyma and blood pool. Last, all observers had to decide whether patients were eligible for CXCR4-targeted RLT. Concordance rates were tested using intraclass correlation coefficients (ICCs). For interpretation, we applied the definition of Cicchetti (with 0.4-0.59 indicating fair; 0.6-0.74, good; 0.75-1, excellent agreement). RESULTS On a visual level, fair agreement was achieved for an overall scan impression (ICC, 0.58; 95% confidence interval, 0.45-0.71). Organ and LN involvement (ICC, ≥0.4) demonstrated fair, whereas CXCR4 density and number of LN and organ metastases showed good agreement rates (ICC, ≥0.65). Number of affected organs and affected LN areas, however, showed excellent concordance (ICC, ≥0.76). Quantification in LN and organ lesions also provided excellent agreement rates (ICC, ≥0.92), whereas quantified uptake in reference organs provided fair concordance (ICC, ≥0.54). Again, excellent agreement rates were observed when deciding on patients eligible for CXCR4-RLT (ICC, 0.91; 95% confidence interval, 0.85-0.95). CONCLUSIONS In patients scanned with CXCR4-targeted PET/CT, we observed fair to excellent agreement rates for both molecular imaging and therapy parameters, thereby favoring a more widespread adoption of [ 68 Ga]pentixafor in the clinic.
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Affiliation(s)
| | - Aleksander Kosmala
- From the Department of Nuclear Medicine, University Hospital Würzburg, Würzburg
| | | | - Lena Bundschuh
- Nuclear Medicine, Medical Faculty, University Hospital Augsburg, Augsburg, Germany
| | - Takahiro Higuchi
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Constantin Lapa
- Nuclear Medicine, Medical Faculty, University Hospital Augsburg, Augsburg, Germany
| | - Steven P. Rowe
- Johns Hopkins School of Medicine, The Russell H Morgan Department of Radiology and Radiological Sciences, Baltimore, MD
| | - Yohji Matsusaka
- From the Department of Nuclear Medicine, University Hospital Würzburg, Würzburg
| | - Alexander Weich
- Internal Medicine II, Gastroenterology, University Hospital Würzburg
- NET-Zentrum Würzburg, European Neuroendocrine Tumor Society Center of Excellence (ENETS CoE), University Hospital Würzburg, Würzburg, Germany
| | - Andreas K. Buck
- From the Department of Nuclear Medicine, University Hospital Würzburg, Würzburg
| | - Ralph A. Bundschuh
- Nuclear Medicine, Medical Faculty, University Hospital Augsburg, Augsburg, Germany
| | - Rudolf A. Werner
- From the Department of Nuclear Medicine, University Hospital Würzburg, Würzburg
- Johns Hopkins School of Medicine, The Russell H Morgan Department of Radiology and Radiological Sciences, Baltimore, MD
- NET-Zentrum Würzburg, European Neuroendocrine Tumor Society Center of Excellence (ENETS CoE), University Hospital Würzburg, Würzburg, Germany
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15
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Janakiraman V, Sudhan M, Patil S, Alzahrani KJ, Alzahrani FM, Halawani IF, Ahmed SSSJ. Rheumatoid arthritis treatment with zoledronic acid, a potentialinhibitorofGWAS-derived pharmacogenetics STAT3 and IL2 targets. Gene 2023; 866:147338. [PMID: 36889532 DOI: 10.1016/j.gene.2023.147338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/17/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
Rheumatoid arthritis (RA) is an inflammatory condition that primarily affects the joints and progress to affect other vital organs. Variety of drugs are being recommended to control the disease progression that benefits patients to perform day-to-day activities. Few of these RA drugs have noticeable side effects; therefore, it's crucial to choose the appropriate drug for treating RA with an understanding of the disease's pathophysiology. Herein, we investigated the RA genes from GWAS data to construct protein-protein interaction (PPI) network and to define appropriate drug targets for RA. The predicted drug targets were screened with the known RA drugs based on molecular docking. Further, the molecular dynamics simulations were performed to comprehend the conformational changes and stability of the targets upon binding of the selected top ranked RA drug. As a result, our constructed protein network from GWAS data revealed, STAT3 and IL2 could be potential pharmacogenetics targets that interlink most of the RA genes encoding proteins. These interlinked proteins of both the targets showed involvement in cell signaling, immune response, and TNF signaling pathway. Among the 192 RA drugs investigated, zoledronic acid had the lowest binding energy that inhibit both STAT3 (-6.307 kcal/mol) and IL2 (-6.231 kcal/mol). Additionally, STAT3 and IL2 trajectories on zoledronic acid binding exhibit notable differences in MD simulations as compared to a drug-free environment. Also, the in vitro assessment with the zoledronic acid confirms the outcome of our computational study. Overall, our study identify zoledronic acid could be potential inhibitor against these targets, that will benefits patients with RA. Comparative efficiency assessments between the RA drugs through clinical trials are needed to validate our findings in the treatment of RA.
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Affiliation(s)
- V Janakiraman
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
| | - M Sudhan
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT 84095, USA
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Fuad M Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ibrahim F Halawani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Shiek S S J Ahmed
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India.
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16
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Advanced EPI-X4 Derivatives Covalently Bind Human Serum Albumin Resulting in Prolonged Plasma Stability. Int J Mol Sci 2022; 23:ijms232315029. [PMID: 36499357 PMCID: PMC9735595 DOI: 10.3390/ijms232315029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022] Open
Abstract
Advanced derivatives of the Endogenous Peptide Inhibitor of CXCR4 (EPI-X4) have shown therapeutic efficacy upon topical administration in animal models of asthma and dermatitis. Here, we studied the plasma stability of the EPI-X4 lead compounds WSC02 and JM#21, using mass spectrometry to monitor the chemical integrity of the peptides and a functional fluorescence-based assay to determine peptide function in a CXCR4-antibody competition assay. Although mass spectrometry revealed very rapid disappearance of both peptides in human plasma within seconds, the functional assay revealed a significantly higher half-life of 9 min for EPI-X4 WSC02 and 6 min for EPI-X4 JM#21. Further analyses demonstrated that EPI-X4 WSC02 and EPI-X4 JM#21 interact with low molecular weight plasma components and serum albumin. Albumin binding is mediated by the formation of a disulfide bridge between Cys10 in the EPI-X4 peptides and Cys34 in albumin. These covalently linked albumin-peptide complexes have a higher stability in plasma as compared with the non-bound peptides and retain the ability to bind and antagonize CXCR4. Remarkably, chemically synthesized albumin-EPI-X4 conjugates coupled by non-breakable bonds have a drastically increased plasma stability of over 2 h. Thus, covalent coupling of EPI-X4 to albumin in vitro before administration or in vivo post administration may significantly increase the pharmacokinetic properties of this new class of CXCR4 antagonists.
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17
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Romero-Molina S, Ruiz-Blanco YB, Mieres-Perez J, Harms M, Münch J, Ehrmann M, Sanchez-Garcia E. PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity. J Proteome Res 2022; 21:1829-1841. [PMID: 35654412 PMCID: PMC9361347 DOI: 10.1021/acs.jproteome.2c00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Virtual screening
of protein–protein and protein–peptide
interactions is a challenging task that directly impacts the processes
of hit identification and hit-to-lead optimization in drug design
projects involving peptide-based pharmaceuticals. Although several
screening tools designed to predict the binding affinity of protein–protein
complexes have been proposed, methods specifically developed to predict
protein–peptide binding affinity are comparatively scarce.
Frequently, predictors trained to score the affinity of small molecules
are used for peptides indistinctively, despite the larger complexity
and heterogeneity of interactions rendered by peptide binders. To
address this issue, we introduce PPI-Affinity, a tool that leverages
support vector machine (SVM) predictors of binding affinity to screen
datasets of protein–protein and protein–peptide complexes,
as well as to generate and rank mutants of a given structure. The
performance of the SVM models was assessed on four benchmark datasets,
which include protein–protein and protein–peptide binding
affinity data. In addition, we evaluated our model on a set of mutants
of EPI-X4, an endogenous peptide inhibitor of the chemokine receptor
CXCR4, and on complexes of the serine proteases HTRA1 and HTRA3 with
peptides. PPI-Affinity is freely accessible at https://protdcal.zmb.uni-due.de/PPIAffinity.
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Affiliation(s)
- Sandra Romero-Molina
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Joel Mieres-Perez
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.,Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Michael Ehrmann
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
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18
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Caspar B, Cocchiara P, Melet A, Van Emelen K, Van der Aa A, Milligan G, Herbeuval JP. CXCR4 as a novel target in immunology: moving away from typical antagonists. FUTURE DRUG DISCOVERY 2022; 4:FDD77. [PMID: 35875591 PMCID: PMC9298491 DOI: 10.4155/fdd-2022-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
CXCR4 has been a target of interest in drug discovery for numerous years. However, so far, most if not all studies focused on finding antagonists of CXCR4 function. Recent studies demonstrate that targeting a minor allosteric pocket of CXCR4 induces an immunomodulating effect in immune cells expressing CXCR4, connected to the TLR pathway. Compounds binding in this minor pocket seem to be functionally selective with inverse agonistic properties in selected GPCR signaling pathways (Gi activation), but additional signaling pathways are likely to be involved in the immunomodulating effects. In depth research into these CXCR4-targeted immunomodulators could lead to novel treatment options for (auto)-immune diseases.
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Affiliation(s)
- Birgit Caspar
- CNRS UMR-8601, 45 Rue des Saints-Pères, Paris, F-75006, France
- Team Chemistry & Biology, Modelling & Immunology for Therapy, CBMIT, Paris, France
- Université Paris Cité, CNRS, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Paris, F-75006, France
| | - Pietro Cocchiara
- Centre for Translational Pharmacology, Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Armelle Melet
- CNRS UMR-8601, 45 Rue des Saints-Pères, Paris, F-75006, France
- Team Chemistry & Biology, Modelling & Immunology for Therapy, CBMIT, Paris, France
- Université Paris Cité, CNRS, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Paris, F-75006, France
| | - Kristof Van Emelen
- Ermium Therapeutics, Pépinière Paris Santé Cochin, 29 Rue du Faubourg Saint-Jacques, Paris, F-75014, France
| | - Annegret Van der Aa
- Ermium Therapeutics, Pépinière Paris Santé Cochin, 29 Rue du Faubourg Saint-Jacques, Paris, F-75014, France
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Jean-Philippe Herbeuval
- CNRS UMR-8601, 45 Rue des Saints-Pères, Paris, F-75006, France
- Team Chemistry & Biology, Modelling & Immunology for Therapy, CBMIT, Paris, France
- Université Paris Cité, CNRS, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Paris, F-75006, France
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19
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Harms M, Hansson RF, Carmali S, Almeida-Hernández Y, Sanchez-Garcia E, Münch J, Zelikin AN. Dimerization of the Peptide CXCR4-Antagonist on Macromolecular and Supramolecular Protraction Arms Affords Increased Potency and Enhanced Plasma Stability. Bioconjug Chem 2022; 33:594-607. [PMID: 35293739 DOI: 10.1021/acs.bioconjchem.2c00034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Peptides are prime drug candidates due to their high specificity of action but are disadvantaged by low proteolytic stability. Here, we focus on the development of stabilized analogues of EPI-X4, an endogenous peptide antagonist of CXCR4. We synthesized macromolecular peptide conjugates and performed side-by-side comparison with their albumin-binding counterparts and considered monovalent conjugates, divalent telechelic conjugates, and Y-shaped peptide dimers. All constructs were tested for competition with the CXCR4 antibody-receptor engagement, inhibition of receptor activation, and inhibition of the CXCR4-tropic human immunodeficiency virus infection. We found that the Y-shaped conjugates were more potent than the parent peptide and at the same time more stable in human plasma, with a favorable outlook for translational studies.
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Affiliation(s)
- Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Rikke Fabech Hansson
- Department of Chemistry and iNano Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
| | - Sheiliza Carmali
- Department of Chemistry and iNano Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
| | - Yasser Almeida-Hernández
- Computational Biochemistry, Center of Medical Biotechnology, University Duisburg-Essen, D-45141 Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University Duisburg-Essen, D-45141 Essen, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Alexander N Zelikin
- Department of Chemistry and iNano Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
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20
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Endogenous Peptide Inhibitors of HIV Entry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1366:65-85. [DOI: 10.1007/978-981-16-8702-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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