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Duay SS, Yap RCY, Gaitano AL, Santos JAA, Macalino SJY. Roles of Virtual Screening and Molecular Dynamics Simulations in Discovering and Understanding Antimalarial Drugs. Int J Mol Sci 2023; 24:ijms24119289. [PMID: 37298256 DOI: 10.3390/ijms24119289] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Malaria continues to be a global health threat, with approximately 247 million cases worldwide. Despite therapeutic interventions being available, patient compliance is a problem due to the length of treatment. Moreover, drug-resistant strains have emerged over the years, necessitating urgent identification of novel and more potent treatments. Given that traditional drug discovery often requires a great deal of time and resources, most drug discovery efforts now use computational methods. In silico techniques such as quantitative structure-activity relationship (QSAR), docking, and molecular dynamics (MD) can be used to study protein-ligand interactions and determine the potency and safety profile of a set of candidate compounds to help prioritize those tested using assays and animal models. This paper provides an overview of antimalarial drug discovery and the application of computational methods in identifying candidate inhibitors and elucidating their potential mechanisms of action. We conclude with the continued challenges and future perspectives in the field of antimalarial drug discovery.
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Affiliation(s)
- Searle S Duay
- Department of Chemistry, De La Salle University, Manila 0922, Philippines
| | - Rianne Casey Y Yap
- Department of Chemistry, De La Salle University, Manila 0922, Philippines
| | - Arturo L Gaitano
- Chemistry Department, Adamson University, Manila 1000, Philippines
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Antoszczak M, Müller S, Cañeque T, Colombeau L, Dusetti N, Santofimia-Castaño P, Gaillet C, Puisieux A, Iovanna JL, Rodriguez R. Iron-Sensitive Prodrugs That Trigger Active Ferroptosis in Drug-Tolerant Pancreatic Cancer Cells. J Am Chem Soc 2022; 144:11536-11545. [PMID: 35696539 DOI: 10.1021/jacs.2c03973] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Persister cancer cells represent rare populations of cells resistant to therapy. Cancer cells can exploit epithelial-mesenchymal plasticity to adopt a drug-tolerant state that does not depend on genetic alterations. Small molecules that can interfere with cell plasticity or kill cells in a cell state-dependent manner are highly sought after. Salinomycin has been shown to kill cancer cells in the mesenchymal state by sequestering iron in lysosomes, taking advantage of the iron addiction of this cell state. Here, we report the chemo- and stereoselective synthesis of a series of structurally complex small molecule chimeras of salinomycin derivatives and the iron-reactive dihydroartemisinin. We show that these chimeras accumulate in lysosomes and can react with iron to release bioactive species, thereby inducing ferroptosis in drug-tolerant pancreatic cancer cells and biopsy-derived organoids of pancreatic ductal adenocarcinoma. This work paves the way toward the development of new cancer medicines acting through active ferroptosis.
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Affiliation(s)
- Michał Antoszczak
- Department of Chemical Biology, Institut Curie, CNRS UMR 3666, INSERM U1143, PSL Université, 26 rue d'Ulm, 75005 Paris, France
| | - Sebastian Müller
- Department of Chemical Biology, Institut Curie, CNRS UMR 3666, INSERM U1143, PSL Université, 26 rue d'Ulm, 75005 Paris, France
| | - Tatiana Cañeque
- Department of Chemical Biology, Institut Curie, CNRS UMR 3666, INSERM U1143, PSL Université, 26 rue d'Ulm, 75005 Paris, France
| | - Ludovic Colombeau
- Department of Chemical Biology, Institut Curie, CNRS UMR 3666, INSERM U1143, PSL Université, 26 rue d'Ulm, 75005 Paris, France
| | - Nelson Dusetti
- CRCM, CNRS UMR 7258, INSERM U1068, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
| | - Patricia Santofimia-Castaño
- CRCM, CNRS UMR 7258, INSERM U1068, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
| | - Christine Gaillet
- Department of Chemical Biology, Institut Curie, CNRS UMR 3666, INSERM U1143, PSL Université, 26 rue d'Ulm, 75005 Paris, France
| | - Alain Puisieux
- Department of Chemical Biology, Institut Curie, CNRS UMR 3666, INSERM U1143, PSL Université, 26 rue d'Ulm, 75005 Paris, France
| | - Juan Lucio Iovanna
- CRCM, CNRS UMR 7258, INSERM U1068, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
| | - Raphaël Rodriguez
- Department of Chemical Biology, Institut Curie, CNRS UMR 3666, INSERM U1143, PSL Université, 26 rue d'Ulm, 75005 Paris, France
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Sharma S, Ali ME. Nonreductive homolytic scission of endoperoxide bond for activation of artemisinin: A parallel mechanism to Heterolytic cleavage. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shikha Sharma
- Institute of Nano Science and Technology Knowledge City India
| | - Md. Ehesan Ali
- Institute of Nano Science and Technology Knowledge City India
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Zhu G, Ma L, Zhang K, Zhou Z, Song H, Yi W. Cascade Reductive Rearrangement for the Stereoselective Synthesis of Multifunctional Piperidinones: A Combined Experimental and Computational Study. ChemistrySelect 2020. [DOI: 10.1002/slct.201904106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Guoxun Zhu
- School of Chemical Engineering and TechnologySun Yat-sen University 135 Xin Gang West Road Guangzhou 510275 P.R. China
| | - Lei Ma
- Key Laboratory of Molecular Target and Clinical Pharmacology & the State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University Guangzhou, Guangdong 511436 P. R. China
| | - Kaixin Zhang
- School of Chemical Engineering and TechnologySun Yat-sen University 135 Xin Gang West Road Guangzhou 510275 P.R. China
| | - Zhi Zhou
- Key Laboratory of Molecular Target and Clinical Pharmacology & the State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University Guangzhou, Guangdong 511436 P. R. China
| | - Huacan Song
- School of Chemical Engineering and TechnologySun Yat-sen University 135 Xin Gang West Road Guangzhou 510275 P.R. China
| | - Wei Yi
- School of Chemical Engineering and TechnologySun Yat-sen University 135 Xin Gang West Road Guangzhou 510275 P.R. China
- Key Laboratory of Molecular Target and Clinical Pharmacology & the State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University Guangzhou, Guangdong 511436 P. R. China
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Saleh G, Soave R, Lo Presti L, Destro R. Progress in the Understanding of the Key Pharmacophoric Features of the Antimalarial Drug Dihydroartemisinin: An Experimental and Theoretical Charge Density Study. Chemistry 2013; 19:3490-503. [DOI: 10.1002/chem.201202486] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 11/29/2012] [Indexed: 12/12/2022]
Affiliation(s)
- Gabriele Saleh
- Università degli Studi di Milano, Dipartimento di Chimica, Via Golgi 19, I‐20133 Milano (Italy), Fax: (+39) 02‐50314300
- Center for Materials Crystallography, Århus University, Langelandsgade 140, 8000 Århus (Denmark)
| | - Raffaella Soave
- Istituto di Scienze e Tecnologie Molecolari del CNR (CNR‐ISTM), Via Golgi 19 I‐20133 Milano (Italy), Fax: (+39) 02‐50314300
| | - Leonardo Lo Presti
- Università degli Studi di Milano, Dipartimento di Chimica, Via Golgi 19, I‐20133 Milano (Italy), Fax: (+39) 02‐50314300
- Center for Materials Crystallography, Århus University, Langelandsgade 140, 8000 Århus (Denmark)
- Istituto di Scienze e Tecnologie Molecolari del CNR (CNR‐ISTM), Via Golgi 19 I‐20133 Milano (Italy), Fax: (+39) 02‐50314300
| | - Riccardo Destro
- Università degli Studi di Milano, Dipartimento di Chimica, Via Golgi 19, I‐20133 Milano (Italy), Fax: (+39) 02‐50314300
- Istituto di Scienze e Tecnologie Molecolari del CNR (CNR‐ISTM), Via Golgi 19 I‐20133 Milano (Italy), Fax: (+39) 02‐50314300
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Hsu YG, Wan YS, Lin WY, Hsieh WL. Cationic Polymerization of cis-2,3-Tetramethylene-1,4,6-trioxaspiro[4,4]nonane Photosensitized by Anthracene. Macromolecules 2010. [DOI: 10.1021/ma101628n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ying-Gev Hsu
- Department of Polymer Science and Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan, ROC
| | - Yen-Shen Wan
- Department of Polymer Science and Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan, ROC
| | - Wei-Yang Lin
- Department of Polymer Science and Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan, ROC
| | - Wei-Lun Hsieh
- Department of Polymer Science and Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan, ROC
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7
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Lacaze-Dufaure C, Najjar F, André-Barrès C. First Computational Evidence of a Competitive Stepwise and Concerted Mechanism for the Reduction of Antimalarial Endoperoxides. J Phys Chem B 2010; 114:9848-53. [DOI: 10.1021/jp100718p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Corinne Lacaze-Dufaure
- Centre Interuniversitaire de Recherche et d’Ingénierie des Matériaux, CNRS UMR 5085, ENSIACET, 4 allée Emile Monso, BP 44362, 31432 Toulouse cedex 04, France, Laboratoire de Synthèse et Physicochimie de Molécules d’Intérêt Biologique, CNRS UMR 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France, and Faculty of Sciences-2, Lebanese University, Jdaidet el-Maten, B.P. 90656, Lebanon
| | - Fadia Najjar
- Centre Interuniversitaire de Recherche et d’Ingénierie des Matériaux, CNRS UMR 5085, ENSIACET, 4 allée Emile Monso, BP 44362, 31432 Toulouse cedex 04, France, Laboratoire de Synthèse et Physicochimie de Molécules d’Intérêt Biologique, CNRS UMR 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France, and Faculty of Sciences-2, Lebanese University, Jdaidet el-Maten, B.P. 90656, Lebanon
| | - Christiane André-Barrès
- Centre Interuniversitaire de Recherche et d’Ingénierie des Matériaux, CNRS UMR 5085, ENSIACET, 4 allée Emile Monso, BP 44362, 31432 Toulouse cedex 04, France, Laboratoire de Synthèse et Physicochimie de Molécules d’Intérêt Biologique, CNRS UMR 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France, and Faculty of Sciences-2, Lebanese University, Jdaidet el-Maten, B.P. 90656, Lebanon
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Moles P, Oliva M, Sánchez-González A, Safont VS. A topological study of the decomposition of 6,7,8-trioxabicyclo[3.2.2]nonane induced by Fe(II): modeling the artemisinin reaction with heme. J Phys Chem B 2010; 114:1163-73. [PMID: 20028005 DOI: 10.1021/jp910207z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a theoretical study on the electronic and topological aspects of the reaction of dihydrated Fe(OH)(2) with 6,7,8-trioxabicyclo[3.2.2]nonane, as a model for the reaction of heme with artemisinin. A comparison is made with the reaction of dihydrated ferrous hydroxide with O(2), as a model for the heme interaction with oxygen. We found that dihydrated Fe(OH)(2) reacts more efficiently with the artemisinin model than with O(2). This result suggests that artemisinin instead of molecular oxygen would interact with heme, disrupting its detoxification process by avoiding the initial heme to hemin oxidation, and killing in this way the malaria parasite. The ELF and AIM theories provide support for such a conclusion, which further clarifies our understanding on how artemisinin acts as an antimalarial agent.
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Affiliation(s)
- Pamela Moles
- Departament de Química Física i Analítica, Universitat Jaume I, Avda. Sos Baynat s/n, 12071 Castelló, Spain
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Moles P, Oliva M, Safont VS. A theoretical study on the decomposition mechanism of artemisinin. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.07.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Araújo JQ, Carneiro JWDM, de Araujo MT, Leite FHA, Taranto AG. Interaction between artemisinin and heme. A Density Functional Theory study of structures and interaction energies. Bioorg Med Chem 2008; 16:5021-9. [PMID: 18375130 DOI: 10.1016/j.bmc.2008.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 03/11/2008] [Accepted: 03/13/2008] [Indexed: 11/18/2022]
Abstract
Malaria is an infectious disease caused by the unicellular parasite Plasmodium sp. Currently, the malaria parasite is becoming resistant to the traditional pharmacological alternatives, which are ineffective. Artemisinin is the most recent advance in the chemotherapy of malaria. Since it has been proven that artemisinin may act on intracellular heme, we have undertaken a systematic study of several interactions and arrangements between artemisinin and heme. Density Functional Theory calculations were employed to calculate interaction energies, electronic states, and geometrical arrangements for the complex between the heme group and artemisinin. The results show that the interaction between the heme group and artemisinin at long distances occurs through a complex where the iron atom of the heme group retains its electronic features, leading to a quintet state as the most stable one. However, for interaction at short distances, due to artemisinin reduction by the heme group, the most stable complex has a septet spin state. These results suggest that a thermodynamically favorable interaction between artemisinin and heme may happen.
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Affiliation(s)
- Jocley Queiroz Araújo
- Programa de Pós-Graduação em Química Orgânica, Universidade Federal Fluminense, Outeiro de São João Batista, s/n, 24020-150, Niterói, RJ, Brazil
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Nosoongnoen W, Pratuangdejkul J, Sathirakul K, Jacob A, Conti M, Loric S, Launay JM, Manivet P. Elucidation of the natural artemisinin decomposition route upon iron interaction: a fine electronic redistribution promotes reactivity. Phys Chem Chem Phys 2008; 10:5083-93. [DOI: 10.1039/b804516j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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De novo identification and stability of the artemisinin pharmacophore: Studies of the reductive decomposition of deoxyartemisinins and deoxyarteethers and the implications for the mode of antimalarial action. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Pereira MSC, Kiralj R, Ferreira MMC. Theoretical Study of Radical and Neutral Intermediates of Artemisinin Decomposition. J Chem Inf Model 2007; 48:85-98. [DOI: 10.1021/ci700011f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mírian S. C. Pereira
- Laboratório de Quimiometria Teórica e Aplicada, Instituto de Química, Universidade Estadual de Campinas, 13081-970 Campinas, SP, Brazil
| | - Rudolf Kiralj
- Laboratório de Quimiometria Teórica e Aplicada, Instituto de Química, Universidade Estadual de Campinas, 13081-970 Campinas, SP, Brazil
| | - Márcia M. C. Ferreira
- Laboratório de Quimiometria Teórica e Aplicada, Instituto de Química, Universidade Estadual de Campinas, 13081-970 Campinas, SP, Brazil
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Drew MGB, Metcalfe J, Dascombe MJ, Ismail FMD. Reactions of Artemisinin and Arteether with Acid: Implications for Stability and Mode of Antimalarial Action. J Med Chem 2006; 49:6065-73. [PMID: 17004720 DOI: 10.1021/jm060673d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The currently accepted mechanism of trioxane antimalarial action involves generation of free radicals within or near susceptible sites probably arising from the production of distonic radical anions. An alternative mechanistic proposal involving the ionic scission of the peroxide group and consequent generation of a carbocation at C-4 has been suggested to account for antimalarial activity. We have investigated this latter mechanism using DFT (B3LYP/6-31+G* level) and established the preferred Lewis acid protonation sites (artemisinin O5a>>O4a approximately O3a>O2a>O1a; arteether O4a>or=O3a>O5b>>O2a>O1a; Figure 3) and the consequent decomposition pathways and hydrolysis sites. In neither molecule is protonation likely to occur on the peroxide bond O1-O2 and therefore lead to scission. Therefore, the alternative radical pathway remains the likeliest explanation for antimalarial action.
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Affiliation(s)
- Michael G B Drew
- Department of Chemistry, University of Reading, Reading RG6 6AD, UK
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Abstract
A theoretical study on artemisinin decomposition mechanisms is reported. The calculations have been done at the HF/3-21G and B3LYP/6-31G(d,p) theoretical levels, by using 6,7,8-trioxybicyclo[3.2.2]nonane as the molecular model for artemisinin, and a hydrogen atom, modeling the single electron transfer from heme or Fe(II) in the highly acidic parasite's food vacuole, as inductor of the initial peroxide bond cleavage. All relevant stationary points have been characterized, and the appearance of the final products can be explained in a satisfactory way. Several intermediates and radicals have been found as relatively stable species, thus giving support to the current hypothesis that some of these species can be responsible for the antimalarial action of artemisinin and its derivatives.
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Affiliation(s)
- Pamela Moles
- Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
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