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Gonzalez-Llerena JL, Espinosa-Rodriguez BA, Treviño-Almaguer D, Mendez-Lopez LF, Carranza-Rosales P, Gonzalez-Barranco P, Guzman-Delgado NE, Romo-Mancillas A, Balderas-Renteria I. Cordycepin Triphosphate as a Potential Modulator of Cellular Plasticity in Cancer via cAMP-Dependent Pathways: An In Silico Approach. Int J Mol Sci 2024; 25:5692. [PMID: 38891880 PMCID: PMC11171877 DOI: 10.3390/ijms25115692] [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: 04/05/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Cordycepin, or 3'-deoxyadenosine, is an adenosine analog with a broad spectrum of biological activity. The key structural difference between cordycepin and adenosine lies in the absence of a hydroxyl group at the 3' position of the ribose ring. Upon administration, cordycepin can undergo an enzymatic transformation in specific tissues, forming cordycepin triphosphate. In this study, we conducted a comprehensive analysis of the structural features of cordycepin and its derivatives, contrasting them with endogenous purine-based metabolites using chemoinformatics and bioinformatics tools in addition to molecular dynamics simulations. We tested the hypothesis that cordycepin triphosphate could bind to the active site of the adenylate cyclase enzyme. The outcomes of our molecular dynamics simulations revealed scores that are comparable to, and superior to, those of adenosine triphosphate (ATP), the endogenous ligand. This interaction could reduce the production of cyclic adenosine monophosphate (cAMP) by acting as a pseudo-ATP that lacks a hydroxyl group at the 3' position, essential to carry out nucleotide cyclization. We discuss the implications in the context of the plasticity of cancer and other cells within the tumor microenvironment, such as cancer-associated fibroblast, endothelial, and immune cells. This interaction could awaken antitumor immunity by preventing phenotypic changes in the immune cells driven by sustained cAMP signaling. The last could be an unreported molecular mechanism that helps to explain more details about cordycepin's mechanism of action.
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Affiliation(s)
- Jose Luis Gonzalez-Llerena
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
- Center for Research on Nutrition and Public Health, School of Public Health and Nutrition, Autonomous University of Nuevo Leon, Monterrey 66460, Mexico;
| | - Bryan Alejandro Espinosa-Rodriguez
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
| | - Daniela Treviño-Almaguer
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
| | - Luis Fernando Mendez-Lopez
- Center for Research on Nutrition and Public Health, School of Public Health and Nutrition, Autonomous University of Nuevo Leon, Monterrey 66460, Mexico;
| | - Pilar Carranza-Rosales
- Laboratory of Cell Biology, Northeast Biomedical Research Center, Mexican Social Security Institute, Monterrey 64720, Mexico;
| | - Patricia Gonzalez-Barranco
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
| | - Nancy Elena Guzman-Delgado
- Health Research Division, High Specialty Medical Unit, Cardiology Hospital N. 34. Mexican Social Security Institute, Monterrey 64360, Mexico;
| | - Antonio Romo-Mancillas
- Computer Aided Drug Design and Synthesis Group, School of Chemistry, Autonomous University of Queretaro, Queretaro 76010, Mexico
| | - Isaias Balderas-Renteria
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
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Liang Z, Zhang K, Guo H, Tang X, Chen M, Shi J, Yang J. Cordycepin alleviates hepatic fibrosis in association with the inhibition of glutaminolysis to promote hepatic stellate cell senescence. Int Immunopharmacol 2024; 132:111981. [PMID: 38565039 DOI: 10.1016/j.intimp.2024.111981] [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: 02/21/2024] [Revised: 03/18/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
Cordycepin (CRD) is an active component derived from Cordyceps militaris, which possesses multiple biological activities and uses in liver disease. However, whether CRD improves liver fibrosis by regulating hepatic stellate cell (HSC) activation has remained unknown. The study aims further to clarify the activities of CRD on liver fibrosis and elucidate the possible mechanism. Our results demonstrated that CRD significantly relieved hepatocyte injury and inhibited HSC activation, alleviating hepatic fibrogenesis in the Diethyl 1,4-dihydro-2,4,6-trimethyl-3,5-pyridinedicarboxylate (DDC)-induced mice model. In vitro, CRD exhibited dose-dependent repress effects on HSC proliferation, migration, and pro-fibrotic function in TGF-β1-activated LX-2 and JS-1 cells. The functional enrichment analysis of RNA-seq data indicated that the pathway through which CRD alleviates HSC activation involves cellular senescence and cell cycle-related pathways. Furthermore, it was observed that CRD accumulated the number of senescence-associated a-galactosidase positive cells and the levels of senescencemarker p21, and provoked S phasearrestof activated HSC. Remarkably, CRD treatment abolished TGF-β-induced yes-associated protein (YAP) nuclear translocation that acts upstream of glutaminolysis in activated HSC. On the whole, CRD significantly inhibited glutaminolysis of activated-HSC and induced cell senescence through the YAP signaling pathway, consequently alleviating liver fibrosis, which may be a valuable supplement for treating liver fibrosis.
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Affiliation(s)
- Zhu Liang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Keyan Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Hongli Guo
- Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xujiao Tang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Mingzhu Chen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Jinsong Shi
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Jing Yang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China.
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Chen M, Luo J, Jiang W, Chen L, Miao L, Han C. Cordycepin: A review of strategies to improve the bioavailability and efficacy. Phytother Res 2023; 37:3839-3858. [PMID: 37329165 DOI: 10.1002/ptr.7921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 06/18/2023]
Abstract
Cordycepin is a bioactive compound extracted from Cordyceps militaris. As a natural antibiotic, cordycepin has a wide variety of pharmacological effects. Unfortunately, this highly effective natural antibiotic is proved to undergo rapid deamination by adenosine deaminase (ADA) in vivo and, as a consequence, its half-life is shortened and bioavailability is decreased. Therefore, it is of critical importance to work out ways to slow down the deamination so as to increase its bioavailability and efficacy. This study reviews recent researches on a series of aspects of cordycepin such as the bioactive molecule's pharmacological action, metabolism and transformation as well as the underlying mechanism, pharmacokinetics and, particularly, the methods for reducing the degradation to improve the bioavailability and efficacy. It is drawn that there are three methods that can be applied to improve the bioavailability and efficacy: to co-administrate an ADA inhibitor and cordycepin, to develop more effective derivatives via structural modification, and to apply new drug delivery systems. The new knowledge can help optimize the application of the highly potent natural antibiotic-cordycepin and develop novel therapeutic strategies.
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Affiliation(s)
- Min Chen
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
- School of Medicine, Linyi University, Linyi, China
| | - Jiahao Luo
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wenming Jiang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lijing Chen
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Longxing Miao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chunchao Han
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
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Chotpatiwetchkul W, Sittiwanichai S, Niramitranon J, Pongprayoon P. What make malarial adenosine deaminase from PLASMODIUM VIVAX recognise adenosine and 5'-methylthioadenosine: simulation studies. J Biomol Struct Dyn 2023; 41:1437-1444. [PMID: 34994283 DOI: 10.1080/07391102.2021.2021989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Malaria is a life-threatening disease in humans caused by Plasmodium parasites. Plasmodium vivax (P. vivax) is one of the prevalent species found worldwide. An increase in an anti-malarial drug resistance suggests the urgent need for new drugs. Zn2+-containing adenosine deaminase (ADA) is a promising drug target because the ADA inhibition is fatal to the parasite. Malarial ADA accepts both adenosine (ADN) and 5'-methylthioadenosine (MTA) as substrates. The understanding of the substrate binding becomes crucial for an anti-malarial drug development. In this work, ADA from P. vivax (pvADA) is of interest due to its prevalence worldwide. The binding of ADN and MTA are studied here using Molecular Dynamics (MD) simulations. Upon binding, the open and closed states of pvADA are captured. The displacement of α7, linking loops of β3/α12, β4/α13, β5/α15, and α10/α11 is involved in the cavity closure and opening. Also, the inappropriate substrate orientation induces a failure in a complete cavity closure. Interactions with D46, D172, S280, D310, and D311 are important for ADN binding, whereas only hydrogen bonds with D172 and D311 are sufficient to anchor MTA inside the pocket. No Zn2+-coordinated histidine residues is acquired for substrate binding. D172 is found to play a role in ribose moiety recognition, while D311 is crucial for trapping the amine group of an adenine ring towards the Zn2+ site. Comparing between ADN and MTA, the additional interaction between D310 and an amine nitrogen on ADN supports a tighter fit that may facilitate the deamination.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Warot Chotpatiwetchkul
- Applied Computational Chemistry Research Unit, Department of Chemistry, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sirin Sittiwanichai
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Jitti Niramitranon
- Department of Computer Engineering, Faculty of Engineering, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand.,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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Schwenzer H, De Zan E, Elshani M, van Stiphout R, Kudsy M, Morris J, Ferrari V, Um IH, Chettle J, Kazmi F, Campo L, Easton A, Nijman S, Serpi M, Symeonides S, Plummer R, Harrison DJ, Bond G, Blagden SP. The Novel Nucleoside Analogue ProTide NUC-7738 Overcomes Cancer Resistance Mechanisms In Vitro and in a First-In-Human Phase I Clinical Trial. Clin Cancer Res 2021; 27:6500-6513. [PMID: 34497073 PMCID: PMC9401491 DOI: 10.1158/1078-0432.ccr-21-1652] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/04/2021] [Accepted: 09/02/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Nucleoside analogues form the backbone of many therapeutic regimens in oncology and require the presence of intracellular enzymes for their activation. A ProTide is comprised of a nucleoside fused to a protective phosphoramidate cap. ProTides are easily incorporated into cells whereupon the cap is cleaved and a preactivated nucleoside released. 3'-Deoxyadenosine (3'-dA) is a naturally occurring adenosine analogue with established anticancer activity in vitro but limited bioavailability due to its rapid in vivo deamination by the circulating enzyme adenosine deaminase, poor uptake into cells, and reliance on adenosine kinase for its activation. In order to overcome these limitations, 3'-dA was chemically modified to create the novel ProTide NUC-7738. EXPERIMENTAL DESIGN We describe the synthesis of NUC-7738. We determine the IC50 of NUC-7738 using pharmacokinetics (PK) and conduct genome-wide analyses to identify its mechanism of action using different cancer model systems. We validate these findings in patients with cancer. RESULTS We show that NUC-7738 overcomes the cancer resistance mechanisms that limit the activity of 3'-dA and that its activation is dependent on ProTide cleavage by the enzyme histidine triad nucleotide-binding protein 1. PK and tumor samples obtained from the ongoing first-in-human phase I clinical trial of NUC-7738 further validate our in vitro findings and show NUC-7738 is an effective proapoptotic agent in cancer cells with effects on the NF-κB pathway. CONCLUSIONS Our study provides proof that NUC-7738 overcomes cellular resistance mechanisms and supports its further clinical evaluation as a novel cancer treatment within the growing pantheon of anticancer ProTides.
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Affiliation(s)
- Hagen Schwenzer
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Erica De Zan
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mustafa Elshani
- School of Medicine, University of St Andrews, St. Andrews, United Kingdom
| | - Ruud van Stiphout
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mary Kudsy
- School of Medicine, University of St Andrews, St. Andrews, United Kingdom
| | - Josephine Morris
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Valentina Ferrari
- School of Pharmacy and Pharmaceutical Sciences, University of Cardiff, Cardiff, United Kingdom
| | - In Hwa Um
- School of Medicine, University of St Andrews, St. Andrews, United Kingdom
| | - James Chettle
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Farasat Kazmi
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Leticia Campo
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Alistair Easton
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Sebastian Nijman
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, University of Cardiff, Cardiff, United Kingdom
| | - Stefan Symeonides
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Ruth Plummer
- Northern Centre for Cancer Care, Newcastle Hospitals NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne, United Kingdom
| | - David J Harrison
- School of Medicine, University of St Andrews, St. Andrews, United Kingdom
- NuCana PLC, Edinburgh, United Kingdom
| | - Gareth Bond
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sarah P Blagden
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom.
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Pongprayoon P, Kaewhom P, Kaewmongkol S, Suwan E, Stich RW, Wiriya B, Jittapalapong S. Structural dynamics of Rhipicephalus microplus serpin-3. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1962011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| | - Paitoon Kaewhom
- Faculty of Agricultural Technology, Burapha University, Sakaeo Campus, Sakaeo, Thailand
| | - Sarawan Kaewmongkol
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies for Agriculture and Food (CASAF), Food and Agricultural Industries, Kasetsart University Institute for Advanced Studies (NRU-KU), Bangkok, Thailand
| | - Eukote Suwan
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Roger W. Stich
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Benjamaporn Wiriya
- Center for Advanced Studies for Agriculture and Food (CASAF), Food and Agricultural Industries, Kasetsart University Institute for Advanced Studies (NRU-KU), Bangkok, Thailand
| | - Sathaporn Jittapalapong
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies for Agriculture and Food (CASAF), Food and Agricultural Industries, Kasetsart University Institute for Advanced Studies (NRU-KU), Bangkok, Thailand
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Tian W, Liu X, Wang L, Zheng B, Jiang K, Fu G, Feng W. Deciphering the selective binding mechanisms of anaplastic lymphoma kinase-derived neuroblastoma tumor neoepitopes to human leukocyte antigen. J Mol Model 2021; 27:134. [PMID: 33899124 DOI: 10.1007/s00894-021-04754-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 04/15/2021] [Indexed: 12/14/2022]
Abstract
Neuroblastoma (NB), as a metastatic form of solid tumor, has a high fatality rate found in early childhood. The two anaplastic lymphoma kinase (ALK) neoepitopes nonamer and decamer used in cancer immunotherapy against NB cancer can selectively bind to the human leukocyte antigen (HLA-B*15:01) groove with high affinities, whereas the native self-peptide is unable to interact with the HLA-B*15:01. Here, we performed molecular dynamics (MD) simulations and subsequent molecular mechanics-generalized born surface area (MM-GBSA) binding free energy calculations to explore the selective binding mechanisms of nonamer and decamer to the HLA-B*15:01 against the self-peptide. MD simulations revealed the significant conformational dynamics of the self-peptide in the HLA-B*15:01 groove against the nonamer and decamer. Binding free energy calculations showed that the binding affinities of HLA-B*15:01-neoepitope complexes were followed in the order decamer > nonamer > self-peptide. Detailed analysis of HLA-B*15:01-neoepitope structural complexes showed that compared to the nonamer, the self-peptide tended to move outward to the solvent, whereas the decamer moved deep to the HLA-B*15:01 groove. These different dynamic observations of the ALK neoepitopes can explain the distinct binding affinities of self-peptide, nonamer, and decamer to the HLA-B*15:01. The results may be useful for the design of more selective ALK neoepitopes.
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Affiliation(s)
- Wenchao Tian
- Pediatric Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, China
| | - Xianxian Liu
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, China
| | - Lulu Wang
- Department of Critical Care Medicine, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, China
| | - Bufeng Zheng
- Pediatric Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, China
| | - Kun Jiang
- Pediatric Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, China
| | - Guoyong Fu
- Pediatric Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, China
| | - Wenyu Feng
- Pediatric Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, China.
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