{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T21:19:08Z","timestamp":1771535948859,"version":"3.50.1"},"reference-count":60,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,4,4]],"date-time":"2022-04-04T00:00:00Z","timestamp":1649030400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:p><jats:italic>Plasmodium falciparum<\/jats:italic> is one of the plasmodium species responsible for the majority of life-threatening malaria cases. The current antimalarial therapies are becoming less effective due to growing drug resistance, leading to the urgent requirement for alternative and more effective antimalarial drugs or vaccines. To facilitate the novel drug discovery or vaccine development efforts, recent advances in sequencing technologies provide valuable information about the whole genome of the parasite, yet a lot more needs to be deciphered due to its incomplete proteome annotation. Surprisingly, out of the 5,389 proteins currently annotated in the <jats:italic>Plasmodium falciparum<\/jats:italic> 3D7 strain, 1,626 proteins (\u223c30% data) are annotated as hypothetical proteins. In parasite genomic studies, the challenge to annotate hypothetical proteins is often ignored, which may obscure the crucial information related to the pathogenicity of the parasite. In this study, we attempt to characterize hypothetical proteins of the parasite to identify novel drug targets using a computational pipeline. The study reveals that out of the overall pool of the hypothetical proteins, 266 proteins have conserved functional signatures. Furthermore, the pathway analysis of these proteins revealed that 23 proteins have an essential role in various biochemical, signalling and metabolic pathways. Additionally, all the proteins (266) were subjected to computational structure analysis. We could successfully model 11 proteins. We validated and checked the structural stability of the models by performing molecular dynamics simulation. Interestingly, eight proteins show stable conformations, and seven proteins are specific for <jats:italic>Plasmodium falciparum<\/jats:italic>, based on homology analysis<jats:italic>.<\/jats:italic> Lastly, mapping the seven shortlisted hypothetical proteins on the <jats:italic>Plasmodium falciparum<\/jats:italic> protein-protein interaction network revealed 3,299 nodes and 2,750,692 edges. Our study revealed interesting functional details of seven hypothetical proteins of the parasite, which help learn more about the less-studied molecules and their interactions, providing valuable clues to unravel the role of these proteins via future experimental validation.<\/jats:p>","DOI":"10.3389\/fgene.2022.821516","type":"journal-article","created":{"date-parts":[[2022,4,4]],"date-time":"2022-04-04T06:53:32Z","timestamp":1649055212000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":12,"title":["In-Silico Functional Annotation of Plasmodium falciparum Hypothetical Proteins to Identify Novel Drug Targets"],"prefix":"10.3389","volume":"13","author":[{"given":"Gagandeep","family":"Singh","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dinesh","family":"Gupta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,4,4]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a New Generation of Protein Database Search Programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"B2","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1093\/nar\/gkg081","article-title":"PlasmoDB: The Plasmodium Genome Resource. A Database Integrating Experimental and Computational Data","volume":"31","author":"Bahl","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"B3","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-e","article-title":"GROMACS: a Message-Passing Parallel Molecular Dynamics Implementation","volume":"91","author":"Berendsen","year":"1995","journal-title":"Comp. Phys. Commun."},{"key":"B4","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1002\/elps.1150150171","article-title":"Reference Points for Comparisons of Two-Dimensional Maps of Proteins from Different Human Cell Types Defined in a pH Scale where Isoelectric Points Correlate with Polypeptide Compositions","volume":"15","author":"Bjellqvist","year":"1994","journal-title":"Electrophoresis"},{"key":"B5","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1021\/jm9911027","article-title":"Antimalarial Activity of Compounds Interfering with Plasmodium Falciparum Phospholipid Metabolism: Comparison between Mono- and Bisquaternary Ammonium Salts","volume":"43","author":"Calas","year":"2000","journal-title":"J. Med. Chem."},{"key":"B6","doi-asserted-by":"publisher","first-page":"9962","DOI":"10.1074\/jbc.M109.087098","article-title":"Crystal Structure of Get4-Get5 Complex and its Interactions with Sgt2, Get3, and Ydj1","volume":"285","author":"Chang","year":"2010","journal-title":"J. Biol. Chem."},{"key":"B7","doi-asserted-by":"publisher","first-page":"12127","DOI":"10.1073\/pnas.1006036107","article-title":"Structural Characterization of the Get4\/Get5 Complex and its Interaction with Get3","volume":"107","author":"Chartron","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1002\/pro.5560020916","article-title":"Verification of Protein Structures: Patterns of Nonbonded Atomic Interactions","volume":"2","author":"Colovos","year":"1993","journal-title":"Protein Sci."},{"key":"B9","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1111\/mmi.12397","article-title":"Mitochondrial Translation Factors ofTrypanosoma Brucei:elongation Factor-Tu Has a Unique Subdomain that Is Essential for its Function","volume":"90","author":"Cristodero","year":"2013","journal-title":"Mol. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"1917","DOI":"10.1007\/s00894-011-1212-3","article-title":"Structure-based Functional Inference of Hypothetical Proteins from Mycoplasma Hyopneumoniae","volume":"18","author":"da Fons\u00eaca","year":"2012","journal-title":"J. Mol. Model."},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bav012","article-title":"Improving the Consistency of Domain Annotation within the Conserved Domain Database","volume":"2015","author":"Derbyshire","year":"2015","journal-title":"Database"},{"key":"B12","doi-asserted-by":"publisher","first-page":"e0151323","DOI":"10.1371\/journal.pone.0151323","article-title":"An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian mulberry","volume":"11","author":"Dhanyalakshmi","year":"2016","journal-title":"PLoS One"},{"key":"B13","doi-asserted-by":"publisher","first-page":"953","DOI":"10.1038\/nprot.2007.131","article-title":"Locating Proteins in the Cell Using TargetP, SignalP and Related Tools","volume":"2","author":"Emanuelsson","year":"2007","journal-title":"Nat. Protoc."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1242\/dev.042564","article-title":"Smed-SmB, a Member of the LSm Protein Superfamily, Is Essential for Chromatoid Body Organization and Planarian Stem Cell Proliferation","volume":"137","author":"Fernand\u00e9z-Taboada","year":"2010","journal-title":"Development"},{"key":"B15","doi-asserted-by":"publisher","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","article-title":"Pfam: the Protein Families Database","volume":"42","author":"Finn","year":"2014","journal-title":"Nucl. Acids Res."},{"key":"B16","doi-asserted-by":"publisher","first-page":"5452","DOI":"10.1093\/nar\/gkh885","article-title":"'Conserved Hypothetical' Proteins: Prioritization of Targets for Experimental Study","volume":"32","author":"Galperin","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"B17","doi-asserted-by":"publisher","first-page":"17510","DOI":"10.1021\/acsomega.1c01988","article-title":"Atomic Resolution Homology Models and Molecular Dynamics Simulations of Plasmodium Falciparum Tubulins","volume":"6","author":"Hema","year":"2021","journal-title":"ACS Omega"},{"key":"B18","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1038\/381272a0","article-title":"Errors in Protein Structures","volume":"381","author":"Hooft","year":"1996","journal-title":"Nature"},{"key":"B19","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.molbiopara.2008.11.010","article-title":"Control of Gene Expression in Plasmodium Falciparum - Ten Years on","volume":"164","author":"Horrocks","year":"2009","journal-title":"Mol. Biochem. Parasitol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"119","DOI":"10.3389\/fgene.2015.00119","article-title":"Annotation and Curation of Uncharacterized Proteins- Challenges","volume":"6","author":"Ijaq","year":"2015","journal-title":"Front. Genet."},{"key":"B21","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1002\/prot.10613","article-title":"A Hierarchical Approach to All-Atom Protein Loop Prediction","volume":"55","author":"Jacobson","year":"2004","journal-title":"Proteins"},{"key":"B22","doi-asserted-by":"publisher","first-page":"1805","DOI":"10.1093\/bioinformatics\/bts251","article-title":"DAVID-WS: A Stateful Web Service to Facilitate Gene\/protein List Analysis","volume":"28","author":"Jiao","year":"2012","journal-title":"Bioinformatics"},{"key":"B23","doi-asserted-by":"publisher","first-page":"166910","DOI":"10.1016\/j.jmb.2021.166910","article-title":"Structure Basis for Shaping the Nse4 Protein by the Nse1 and Nse3 Dimer within the Smc5\/6 Complex","volume":"433","author":"Jo","year":"2021","journal-title":"J. Mol. Biol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: Genome-Scale Protein Function Classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"B26","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1016\/j.celrep.2015.03.011","article-title":"Genetic Investigation of Tricarboxylic Acid Metabolism during the Plasmodium Falciparum Life Cycle","volume":"11","author":"Ke","year":"2015","journal-title":"Cel Rep."},{"key":"B28","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1038\/419490a","article-title":"The Plasmodium Genome Database","volume":"419","author":"Kissinger","year":"2002","journal-title":"Nature"},{"key":"B29","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete genomes11Edited by F. Cohen","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"e1009442","DOI":"10.1371\/journal.ppat.1009442","article-title":"Some Conditions Apply: Systems for Studying Plasmodium Falciparum Protein Function","volume":"17","author":"Kudyba","year":"2021","journal-title":"Plos Pathog."},{"key":"B32","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1111\/j.1365-3024.2011.01340.x","article-title":"Genomics and Integrated Systems Biology in Plasmodium Falciparum: A Path to Malaria Control and Eradication","volume":"34","author":"Le Roch","year":"2012","journal-title":"Parasite Immunol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"D257","DOI":"10.1093\/nar\/gku949","article-title":"SMART: Recent Updates, New Developments and Status in 2015","volume":"43","author":"Letunic","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B34","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1038\/356083a0","article-title":"Assessment of Protein Models with Three-Dimensional Profiles","volume":"356","author":"L\u00fcthy","year":"1992","journal-title":"Nature"},{"key":"B35","doi-asserted-by":"publisher","first-page":"D394","DOI":"10.1093\/nar\/gkaa1106","article-title":"PANTHER Version 16: A Revised Family Classification, Tree-Based Classification Tool, Enhancer Regions and Extensive API","volume":"49","author":"Mi","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B36","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1016\/j.ejcb.2018.06.003","article-title":"A Comprehensive Review of Signal Peptides: Structure, Roles, and Applications","volume":"97","author":"Owji","year":"2018","journal-title":"Eur. J. Cel Biol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"216","DOI":"10.6026\/97320630010216","article-title":"Analysis of P-Loop and its Flanking Region Subsequence of Diverse NTPases Reveals Evolutionary Selected Residues","volume":"10","author":"Pathak","year":"2014","journal-title":"Bioinformation"},{"key":"B38","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1006\/jmbi.1996.0628","article-title":"Deviations from Standard Atomic Volumes as a Quality Measure for Protein crystal Structures","volume":"264","author":"Pontius","year":"1996","journal-title":"J. Mol. Biol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.molbiopara.2007.01.002","article-title":"Characterization and Localization of Plasmodium Falciparum Homolog of Prokaryotic ClpQ\/HslV Protease","volume":"152","author":"Ramasamy","year":"2007","journal-title":"Mol. Biochem. Parasitol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/s0168-9525(00)02024-2","article-title":"EMBOSS: the European Molecular Biology Open Software Suite","volume":"16","author":"Rice","year":"2000","journal-title":"Trends Genet."},{"key":"B41","doi-asserted-by":"publisher","first-page":"4289","DOI":"10.1073\/pnas.93.9.4289","article-title":"The SNAP45 Subunit of the Small Nuclear RNA (snRNA) Activating Protein Complex Is Required for RNA Polymerase II and III snRNA Gene Transcription and Interacts with the TATA Box Binding Protein","volume":"93","author":"Sadowski","year":"1996","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B42","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1093\/bfgp\/elx024","article-title":"Analysis of Protein Targets in Pathogen-Host Interaction in Infectious Diseases: A Case Study on Plasmodium Falciparum and Homo sapiens Interaction Network","volume":"17","author":"Saha","year":"2018","journal-title":"Brief. Funct. Genomics."},{"key":"B43","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1080\/07391102.2020.1711807","article-title":"In-silico Profiling and Structural Insights into the Impact of nSNPs in the P. Falciparum Acetyl-CoA Transporter Gene to Understand the Mechanism of Drug Resistance in Malaria","volume":"39","author":"Sardar","year":"2021","journal-title":"J. Biomol. Struct. Dyn."},{"key":"B44","doi-asserted-by":"publisher","first-page":"2255","DOI":"10.1093\/molbev\/msn175","article-title":"Evolutionary Diversification of the Sm Family of RNA-Associated Proteins","volume":"25","author":"Scofield","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"B45","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"B46","doi-asserted-by":"publisher","first-page":"D161","DOI":"10.1093\/nar\/gkp885","article-title":"PROSITE, a Protein Domain Database for Functional Characterization and Annotation","volume":"38","author":"Sigrist","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"B47","doi-asserted-by":"publisher","first-page":"FSO169","DOI":"10.4155\/fsoa-2016-0066","article-title":"In Silico functional Elucidation of Uncharacterized Proteins of Chlamydia Abortus Strain LLG","volume":"3","author":"Singh","year":"2017","journal-title":"Future Sci. OA"},{"key":"B48","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1007\/s13562-019-00492-5","article-title":"Functional Annotation and Characterization of Hypothetical Protein Involved in Blister Blight Tolerance in tea (Camellia Sinensis (L) O. Kuntze)","volume":"28","author":"Singh","year":"2019","journal-title":"J. Plant Biochem. Biotechnol."},{"key":"B49","doi-asserted-by":"publisher","first-page":"906","DOI":"10.1080\/07391102.2017.1302361","article-title":"Functional Elucidation of Hypothetical Proteins for Their Indispensable Roles toward Drug Designing Targets from Helicobacter pylori Strain HPAG1","volume":"36","author":"Singh","year":"2018","journal-title":"J. Biomol. Struct. Dyn."},{"key":"B50","doi-asserted-by":"publisher","first-page":"101000","DOI":"10.1016\/j.bbrep.2021.101000","article-title":"Plasmodium Falciparum DDX17 Is an RNA Helicase Crucial for Parasite Development","volume":"26","author":"Sourabh","year":"2021","journal-title":"Biochem. Biophys. Rep."},{"key":"B51","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.ijbiomac.2018.12.123","article-title":"Role of DHH Superfamily Proteins in Nucleic Acids Metabolism and Stress Tolerance in Prokaryotes and Eukaryotes","volume":"127","author":"Srivastav","year":"2019","journal-title":"Int. J. Biol. Macromolecules"},{"key":"B52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-021-21269-2","article-title":"Genotyping Cognate Plasmodium Falciparum in Humans and Mosquitoes to Estimate Onward Transmission of Asymptomatic Infections","volume":"12","author":"Sumner","year":"2021","journal-title":"Nat. Commun."},{"key":"B53","doi-asserted-by":"publisher","first-page":"D605","DOI":"10.1093\/nar\/gkaa1074","article-title":"The STRING Database in 2021: Customizable Protein-Protein Networks, and Functional Characterization of User-Uploaded Gene\/measurement Sets","volume":"49","author":"Szklarczyk","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B54","doi-asserted-by":"publisher","first-page":"1197","DOI":"10.1128\/mcb.00767-07","article-title":"Identification of the Proteins, Including MAGEG1, that Make up the Human SMC5-6 Protein Complex","volume":"28","author":"Taylor","year":"2008","journal-title":"Mol. Cel. Biol."},{"key":"B55","doi-asserted-by":"publisher","first-page":"W401","DOI":"10.1093\/nar\/gkv485","article-title":"The TOPCONS Web Server for Consensus Prediction of Membrane Protein Topology and Signal Peptides","volume":"43","author":"Tsirigos","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B56","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1093\/bioinformatics\/17.9.849","article-title":"The HMMTOP Transmembrane Topology Prediction Server","volume":"17","author":"Tusnady","year":"2001","journal-title":"Bioinformatics"},{"key":"B57","doi-asserted-by":"publisher","first-page":"1602","DOI":"10.1038\/s41591-020-1005-2","article-title":"Emergence and Clonal Expansion of In Vitro Artemisinin-Resistant Plasmodium Falciparum Kelch13 R561H Mutant Parasites in Rwanda","volume":"26","author":"Uwimana","year":"2020","journal-title":"Nat. Med."},{"key":"B60","doi-asserted-by":"publisher","first-page":"6032","DOI":"10.1074\/jbc.M110888200","article-title":"Mechanism of Elongation Factor (EF)-Ts-catalyzed Nucleotide Exchange in EF-Tu","volume":"277","author":"Wieden","year":"2002","journal-title":"J. Biol. Chem."},{"key":"B61","doi-asserted-by":"publisher","first-page":"D308","DOI":"10.1093\/nar\/gkl910","article-title":"The SUPERFAMILY Database in 2007: Families and Functions","volume":"35","author":"Wilson","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"B62","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1002\/prot.21018","article-title":"Prediction of Protein Subcellular Localization","volume":"64","author":"Yu","year":"2006","journal-title":"Proteins"},{"key":"B63","doi-asserted-by":"publisher","first-page":"e99368","DOI":"10.1371\/journal.pone.0099368","article-title":"CELLO2GO: A Web Server for Protein subCELlular lOcalization Prediction with Functional Gene Ontology Annotation","volume":"9","author":"Yu","year":"2014","journal-title":"PLoS One"},{"key":"B64","doi-asserted-by":"publisher","first-page":"1790","DOI":"10.1007\/s00018-006-6126-3","article-title":"Proteomic Analysis of Low-Abundant Integral Plasma Membrane Proteins Based on Gels","volume":"63","author":"Zhang","year":"2006","journal-title":"Cell. Mol. Life Sci."}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2022.821516\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,4]],"date-time":"2022-04-04T06:53:36Z","timestamp":1649055216000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2022.821516\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4,4]]},"references-count":60,"alternative-id":["10.3389\/fgene.2022.821516"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2022.821516","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,4,4]]},"article-number":"821516"}}