{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:09:03Z","timestamp":1785409743615,"version":"3.56.0"},"reference-count":52,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T00:00:00Z","timestamp":1785369600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Gates Foundation","doi-asserted-by":"publisher","award":["INV-060657"],"award-info":[{"award-number":["INV-060657"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["gatesopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Gates Open Res"],"abstract":"<ns5:p>\n                    <ns5:italic>Plasmodium falciparum<\/ns5:italic>\n                    , the deadliest malaria parasite, continues to burden health systems across sub-Saharan Africa, where artemether-lumefantrine remains a frontline treatment. Partial artemisinin resistance is emerging, increasing selection pressure on lumefantrine (LM), yet the molecular basis of reduced LM susceptibility remains poorly defined. While LM has been described as refractory to resistance, its efficacy could be compromised if resistance arises. To explore candidate determinants of LM response and guided by a Gly332Ser substitution previously identified in Ferredoxin NADP\n                    <ns5:sup>+<\/ns5:sup>\n                    reductase from LM-selected\n                    <ns5:italic>Plasmodium berghei<\/ns5:italic>\n                    , we investigated the homologous G340S variant in\n                    <ns5:italic>Plasmodium falciparum<\/ns5:italic>\n                    ferredoxin NADP\n                    <ns5:sup>+<\/ns5:sup>\n                    reductase (\n                    <ns5:italic>PfFNR<\/ns5:italic>\n                    ), a central enzyme of the apicoplast redox system. To predict the structural and functional impact of the G340S substitution, this study integrated sequence conservation analysis, AlphaFold 3 structural modelling, structural superimposition, molecular dynamics simulation, NADPH and NADP\n                    <ns5:sup>+<\/ns5:sup>\n                    docking, HADDOCK docking with\n                    <ns5:italic>P. falciparum<\/ns5:italic>\n                    ferredoxin (\n                    <ns5:italic>PfFd<\/ns5:italic>\n                    ), and comparative docking of lumefantrine, primaquine, artemisinin and dihydroartemisinin. Gly340 was conserved across the Plasmodium FNR orthologs examined and mapped to a constrained loop adjacent to the NADP\n                    <ns5:sup>+<\/ns5:sup>\n                    binding region. Structural superimposition showed that G340S preserved the global\n                    <ns5:italic>PfFNR<\/ns5:italic>\n                    fold but introduced localized changes near residue 340. Exploratory single-trajectory molecular dynamics suggests that G340S may alter PfFNR conformational sampling, with increased RMSD, radius of gyration, solvent-accessible surface area and residue-level flexibility. Cofactor docking predicted a modest mutation-associated shift, strongest for NADPH, whereas NADP\n                    <ns5:sup>+<\/ns5:sup>\n                    docking remained largely stable. HADDOCK analysis indicated altered\n                    <ns5:italic>PfFNR-PfFd<\/ns5:italic>\n                    docking preferences, and antimalarial docking showed ligand-dependent effects, greatest for artemisinin and dihydroartemisinin, with minimal lumefantrine change. Together, these data support G340S as a redox-associated candidate variant that may reshape cofactor and partner-interface, but not as a validated lumefantrine-resistance marker until confirmed by biochemical, genetic and parasite-based assays. The findings define testable mechanisms for future functional assays of\n                    <ns5:italic>PfFNR<\/ns5:italic>\n                    in antimalarial response phenotypes.\n                  <\/ns5:p>","DOI":"10.12688\/gatesopenres.16393.1","type":"journal-article","created":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:49:07Z","timestamp":1785408547000},"page":"43","update-policy":"https:\/\/doi.org\/10.12688\/gatesopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Structural and Functional Impact of the G340S Mutation in Plasmodium falciparum Ferredoxin NADP\u207a Reductase: In silico Analysis and Molecular Docking"],"prefix":"10.12688","volume":"10","author":[{"given":"Daniel","family":"Kiboi","sequence":"first","affiliation":[{"name":"62000, Nairobi 00200 Jomo Kenyatta University of Agriculture and Technology"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brenda","family":"Muriithi","sequence":"additional","affiliation":[{"name":"62000, Nairobi 00200 Jomo Kenyatta University of Agriculture and Technology"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2026,7,30]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.17944198","article-title":"GROMACS 2026.0 Manual.","author":"M Abraham","year":"2026","journal-title":"Zenodo."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"19-25","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers.","volume":"1-2","author":"M Abraham","year":"2015","journal-title":"SoftwareX."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"493-500","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3.","volume":"630","author":"J Abramson","year":"2024","journal-title":"Nature."},{"key":"ref4","first-page":"868-881","article-title":"The ferredoxin redox system \u2013 an essential electron distributing hub in the apicoplast of Apicomplexa.","volume":"38","author":"O Akuh","year":"2022","journal-title":"Trends Parasitol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"3825-3836","DOI":"10.1111\/j.1742-4658.2009.07100.x","article-title":"The ferredoxin-NADP+ reductase\/ferredoxin electron transfer system of Plasmodium falciparum.","volume":"276","author":"E Balconi","year":"2009","journal-title":"Febs j."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"1163-1171","DOI":"10.1056\/NEJMoa2101746","article-title":"Evidence of Artemisinin-Resistant Malaria in Africa.","volume":"385","author":"B Balikagala","year":"2021","journal-title":"N Engl J Med."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"3819-3826","DOI":"10.1021\/bi300078p","article-title":"A single tyrosine hydroxyl group almost entirely controls the NADPH specificity of Plasmodium falciparum ferredoxin-NADP+ reductase.","volume":"51","author":"S Baroni","year":"2012","journal-title":"Biochemistry."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"4858-4865","DOI":"10.1128\/AAC.01748-10","article-title":"Genomewide scan reveals amplification of mdr1 as a common denominator of resistance to mefloquine, lumefantrine, and artemisinin in Plasmodium chabaudi malaria parasites.","volume":"55","author":"S Borges","year":"2011","journal-title":"Antimicrob Agents Chemother."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"1996-2012","DOI":"10.1021\/acsinfecdis.1c00054","article-title":"Plasmodium falciparum Ferredoxin-NADP(+) Reductase-Catalyzed Redox Cycling of Plasmodione Generates Both Predicted Key Drug Metabolites: Implication for Antimalarial Drug Development.","volume":"7","author":"B Cichocki","year":"2021","journal-title":"ACS Infect Dis."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1422-1423","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics.","volume":"25","author":"P Cock","year":"2009","journal-title":"Bioinformatics."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"9525-9533","DOI":"10.1021\/bi9013209","article-title":"Plasmodium falciparum ferredoxin-NADP+ reductase His286 plays a dual role in NADP(H) binding and catalysis.","volume":"48","author":"D Crobu","year":"2009","journal-title":"Biochemistry."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"e13289","DOI":"10.1111\/cmi.13289","article-title":"Molecular approaches to Malaria 2020.","volume":"23","author":"T Koning-Ward","year":"2021","journal-title":"Cell Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"1731-1737","DOI":"10.1021\/ja026939x","article-title":"HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.","volume":"125","author":"C Dominguez","year":"2003","journal-title":"J Am Chem Soc."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"455-467","DOI":"10.1056\/NEJMoa0808859","article-title":"Artemisinin resistance in Plasmodium falciparum malaria.","volume":"361","author":"A Dondorp","year":"2009","journal-title":"N Engl J Med."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"864-874","DOI":"10.1038\/nrmicro2239","article-title":"Artemisinin-based combination therapies: a vital tool in efforts to eliminate malaria.","volume":"7","author":"R Eastman","year":"2009","journal-title":"Nat Rev Microbiol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"3891-3898","DOI":"10.1021\/acs.jcim.1c00203","article-title":"AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings.","volume":"61","author":"J Eberhardt","year":"2021","journal-title":"J Chem Inf Model."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"167-177","DOI":"10.1517\/14728222.2013.739158","article-title":"Targeting apicoplasts in malaria parasites.","volume":"17","author":"C Goodman","year":"2013","journal-title":"Expert Opin Ther Targets."},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1093\/jtm\/taad159","article-title":"Out of Africa: Increasing reports of artemether-lumefantrine treatment failures of uncomplicated Plasmodium falciparum infection.","volume":"30","author":"E Halsey","year":"2023","journal-title":"J Travel Med."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"357-362","DOI":"10.1038\/s41586-020-2649-2","article-title":"Array programming with NumPy.","volume":"585","author":"C Harris","year":"2020","journal-title":"Nature."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"3219-3241","DOI":"10.1038\/s41596-024-01011-0","article-title":"The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.","volume":"19","author":"R Honorato","year":"2024","journal-title":"Nat Protoc."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"27-40","DOI":"10.1111\/j.1365-2958.2007.05753.x","article-title":"Gene encoding a deubiquitinating enzyme is mutated in artesunate- and chloroquine-resistant rodent malaria parasites.","volume":"65","author":"P Hunt","year":"2007","journal-title":"Mol Microbiol."},{"key":"ref23","article-title":"Genome analysis of lumefantrine-resistant Plasmodium berghei reveals a new protein associated with multidrug resistance [Poster No: 67].","author":"D Kiboi","year":"February 23\u201327, 2020","journal-title":"Molecular Approaches to Malaria (MAM) Conference."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"23-32","DOI":"10.1016\/j.exppara.2014.10.008","article-title":"Piperaquine and Lumefantrine resistance in Plasmodium berghei ANKA associated with increased expression of Ca2+\/H+ antiporter and glutathione associated enzymes.","volume":"147","author":"D Kiboi","year":"2014","journal-title":"Exp Parasitol."},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.17010754","article-title":"Extended data: Structural and Functional Impact of the G340S Mutation in Plasmodium falciparum Ferredoxin NADP+ Reductase: In silico Analysis and Molecular Docking.","author":"D Kiboi","year":"2025"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.20217529","article-title":"Extended data 2: Structural and Functional Impact of the G340S Mutation in Plasmodium falciparum Ferredoxin NADP+ Reductase: In silico Analysis and Molecular Docking.","author":"D Kiboi","year":"2026"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"196-202","DOI":"10.1016\/j.exppara.2009.03.010","article-title":"Plasmodium berghei ANKA: selection of resistance to piperaquine and lumefantrine in a mouse model.","volume":"122","author":"D Kiboi","year":"2009","journal-title":"Exp Parasitol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"2126-2136","DOI":"10.1002\/2211-5463.12752","article-title":"NADP(H) allosterically regulates the interaction between ferredoxin and ferredoxin-NADP(+) reductase.","volume":"9","author":"Y Kimata-Ariga","year":"2019","journal-title":"FEBS Open Bio."},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.3390\/antiox11020273","article-title":"Effect of Artemisinin on the Redox System of NADPH\/FNR\/Ferredoxin from Malaria Parasites.","volume":"11","author":"Y Kimata-Ariga","year":"2022","journal-title":"Antioxidants (Basel)."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"715-720","DOI":"10.1093\/jb\/mvm184","article-title":"Molecular interaction of ferredoxin and ferredoxin-NADP+ reductase from human malaria parasite.","volume":"142","author":"Y Kimata-Ariga","year":"2007","journal-title":"J Biochem."},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21093234","article-title":"Reactions of Plasmodium falciparum Ferredoxin:NADP(+) Oxidoreductase with Redox Cycling Xenobiotics: A Mechanistic Study.","volume":"21","author":"M Lesanavi\u010dius","year":"2020","journal-title":"Int J Mol Sci."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"2946-2955","DOI":"10.1093\/jac\/dkac244","article-title":"Plasmodium falciparum merozoite invasion ligands, linked antimalarial resistance loci and ex vivo responses to antimalarials in The Gambia.","volume":"77","author":"H Mbye","year":"2022","journal-title":"J Antimicrob Chemother."},{"key":"ref34","first-page":"e4792","article-title":"UCSF ChimeraX: Tools for structure building and analysis.","volume":"32","author":"E Meng","year":"2023","journal-title":"Protein Science."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1186\/1471-2105-7-339","article-title":"Tools for integrated sequence-structure analysis with UCSF Chimera.","volume":"7","author":"E Meng","year":"2006","journal-title":"BMC Bioinformatics."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"501-513","DOI":"10.1016\/j.jmb.2007.01.005","article-title":"Ferredoxin-NADP+ reductase from Plasmodium falciparum undergoes NADP+-dependent dimerization and inactivation: functional and crystallographic analysis.","volume":"367","author":"M Milani","year":"2007","journal-title":"J Mol Biol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"226-234","DOI":"10.1038\/ng.3189","article-title":"Genetic architecture of artemisinin-resistant Plasmodium falciparum.","volume":"47","author":"O Miotto","year":"2015","journal-title":"Nat Genet."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"D412-D419","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: The protein families database in 2021.","volume":"49","author":"J Mistry","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"1005-1009","DOI":"10.4269\/ajtmh.2010.10-0339","article-title":"Association between the pfmdr1 gene and in vitro artemether and lumefantrine sensitivity in Thai isolates of Plasmodium falciparum.","volume":"83","author":"M Mungthin","year":"2010","journal-title":"Am J Trop Med Hyg."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1758-2946-3-33","article-title":"Open Babel: An open chemical toolbox.","volume":"3","author":"N O\u2019Boyle","year":"2011","journal-title":"J Cheminform."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"D290-D301","DOI":"10.1093\/nar\/gkr1065","article-title":"The Pfam protein families database.","volume":"40","author":"M Punta","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"203-216","DOI":"10.1038\/nrmicro843","article-title":"Tropical infectious diseases: metabolic maps and functions of the Plasmodium falciparum apicoplast.","volume":"2","author":"S Ralph","year":"2004","journal-title":"Nat Rev Microbiol."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"e591-e600","DOI":"10.1016\/S1473-3099(24)00141-5","article-title":"The emergence of artemisinin partial resistance in Africa: how do we respond?","volume":"24","author":"P Rosenthal","year":"2024","journal-title":"Lancet Infect Dis."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"161-228","DOI":"10.1016\/S1937-6448(10)81005-6","volume":"281","author":"F Seeber","year":"2010","journal-title":"International Review of Cell and Molecular Biology."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"MSB201175","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.","volume":"7","author":"F Sievers","year":"2011","journal-title":"Mol Syst Biol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"D344-D347","DOI":"10.1093\/nar\/gks1067","article-title":"New and continuing developments at PROSITE.","volume":"41","author":"C Sigrist","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"1014-1017","DOI":"10.1086\/427997","article-title":"In vivo selection of Plasmodium falciparum pfmdr1 86N coding alleles by artemether-lumefantrine (Coartem).","volume":"191","author":"C Sisowath","year":"2005","journal-title":"J Infect Dis."},{"key":"ref48","first-page":"e0302321-e0303021","article-title":"Roles of Ferredoxin-Dependent Proteins in the Apicoplast of Plasmodium falciparum Parasites.","volume":"13","author":"R Swift","year":"2022","journal-title":"mBio."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"455-461","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.","volume":"31","author":"O Trott","year":"2010","journal-title":"J Comput Chem."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"6353","DOI":"10.1038\/s41467-022-33873-x","article-title":"Decreased susceptibility of Plasmodium falciparum to both dihydroartemisinin and lumefantrine in northern Uganda.","volume":"13","author":"P Tumwebaze","year":"2022","journal-title":"Nat Commun."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"720-725","DOI":"10.1016\/j.jmb.2015.09.014","article-title":"The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.","volume":"428","author":"G Zundert","year":"2016","journal-title":"J Mol Biol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"1403-1414","DOI":"10.1038\/s41564-017-0007-4","article-title":"Hexahydroquinolines are antimalarial candidates with potent blood-stage and transmission-blocking activity.","volume":"2","author":"M Vanaerschot","year":"2017","journal-title":"Nat Microbiol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"6848-6854","DOI":"10.1016\/S0021-9258(19)50504-X","article-title":"Hydroxylated metabolites of the antimalarial drug primaquine. Oxidation and redox cycling.","volume":"267","author":"J V\u00e1squez-Vivar","year":"1992","journal-title":"J Biol Chem."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"102193","DOI":"10.1016\/j.mib.2022.102193","article-title":"Plasmodium falciparum resistance to artemisinin-based combination therapies.","volume":"69","author":"K Ward","year":"2022","journal-title":"Curr Opin Microbiol."}],"container-title":["Gates Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/gatesopenresearch.org\/articles\/10-43\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/gatesopenresearch.org\/articles\/10-43\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/gatesopenresearch.org\/articles\/10-43\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:49:13Z","timestamp":1785408553000},"score":1,"resource":{"primary":{"URL":"https:\/\/gatesopenresearch.org\/articles\/10-43\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,30]]},"references-count":52,"URL":"https:\/\/doi.org\/10.12688\/gatesopenres.16393.1","relation":{"has-preprint":[{"id-type":"doi","id":"10.12688\/verixiv.2019.3","asserted-by":"subject"}]},"ISSN":["2572-4754"],"issn-type":[{"value":"2572-4754","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,30]]},"assertion":[{"value":"Awaiting Peer Review","URL":"https:\/\/gatesopenresearch.org\/articles\/10-43\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"This research received financial assistance from the Gates Foundation under the study 2022 GC | Ferredoxin-NADP+ reductase and link to drug resistance in Plasmodium falciparum, INV-060657 awarded to D.K.  The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. DK is an African Postdoctoral Training Initiative (APTI) fellow. APTI is implemented by the African Academy of Sciences with support from the Gates Foundation and in Partnership with the US National Institutes of Health, where the grantees receive mentorship during their first and second years of the fellowship. The contents of this document are the sole responsibility of the author(s) and can under no circumstances be regarded as reflecting the position of the Gates Foundation, the African Academy of Sciences, and the US National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":0,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}