{"gene":"PF3D7_0322000","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":1994,"finding":"Peptidyl-prolyl cis-trans isomerase (PPIase) activity was detected in extracts of Plasmodium falciparum and was completely inhibited by cyclosporin A (CsA) at concentrations above 0.1 µM, but not by FK506 or rapamycin, indicating the activity is attributable to one or more cyclophilins (consistent with CYP19A/PF3D7_0322000). Furthermore, the P. falciparum cyclophilin-containing extract, in combination with CsA, inhibited the protein phosphatase activity of bovine calcineurin, suggesting the CYP19A–CsA complex can inhibit calcineurin. However, comparison of antimalarial vs. anti-isomerase activities of CsA analogues failed to show a correlation between PPIase inhibition and parasite growth inhibition.","method":"PPIase activity assay in parasite extracts; calcineurin phosphatase inhibition assay with bovine calcineurin; parasite growth inhibition assay with CsA analogues","journal":"Biochemical pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — enzymatic activity assay with pharmacological inhibitors and calcineurin phosphatase assay, two orthogonal methods, but performed on crude extracts (not purified CYP19A protein), single lab","pmids":["7520696"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":1998,"finding":"PF3D7_0322000 (PfCyP19, encoded by a gene on chromosome 3) was cloned, overexpressed in E. coli, and biochemically characterised. The recombinant protein displayed PPIase activity with kinetic constants Km >120 µM and kcat/Km = 1.2×10^7 M⁻¹ s⁻¹ using N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide as substrate. It bound CsA with high affinity (Kd = 13 nM, Ki = 6.9 nM). The protein has no signal peptide or N-terminal extension, suggesting cytosolic localisation. FK506 and rapamycin were inactive as inhibitors of its PPIase activity. CsA analogue Ki values correlated with residues 1 and 2 of CsA rather than residues 3 and 4, which instead correlated with parasite growth inhibition, suggesting the CYP19A–CsA complex presents residues 3–4 as an effector surface for a downstream target.","method":"Recombinant protein expression in E. coli; PPIase enzymatic assay (Michaelis-Menten kinetics); CsA binding assay (Ki determination); inhibitor SAR with CsA analogues; sequence analysis for localisation prediction","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — recombinant protein reconstitution with detailed kinetic and binding characterisation, multiple orthogonal methods (PPIase assay + binding affinity + inhibitor SAR), single rigorous study","pmids":["9716503"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":1995,"finding":"A P. falciparum cyclophilin gene (PFCyP, consistent with PF3D7_0322000) was cloned with a 39-amino-acid N-terminal extension. Recombinant protein expressed in E. coli (with or without the N-terminal extension) was enzymatically active (PPIase activity) and sensitive to CsA inhibition. Northern blot analysis showed the gene is expressed in all erythrocytic stages, with highest expression in ring-stage parasites.","method":"Gene cloning; recombinant expression in E. coli; PPIase activity assay; Northern blot of synchronised parasite cultures","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — recombinant enzymatic assay plus stage-specific expression by Northern blot, two orthogonal methods, single lab","pmids":["8577319"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2003,"finding":"PfCyP-19A (PF3D7_0322000) was identified as one of the two major cyclosporin-binding proteins of P. falciparum by affinity chromatography on cyclosporin-Affigel followed by SDS-PAGE, Western blotting, and peptide mass fingerprinting. PfCyP-19A was confirmed to bind cyclosporin directly. (Note: the paper also characterised the sibling PfCyP-19B, but findings about PfCyP-19A are distinguished here.)","method":"Affinity chromatography on cyclosporin-Affigel; SDS-PAGE; Western blotting; peptide mass fingerprinting","journal":"International journal for parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct affinity pull-down with mass spectrometry identification, multiple orthogonal methods, single lab","pmids":["12906882"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"finding":"In CsA-resistant (CsAR) P. falciparum clones, mutations were detected in functionally significant amino acid residues of CYP19A (Cyp19A). One mutant CYP19A protein was purified and found to be unable to inhibit parasitic calcineurin in the presence of CsA, demonstrating that a functional CYP19A–CsA complex is required for calcineurin inhibition and that loss of this function is a mechanism of CsA resistance.","method":"Sequencing of CsAR parasite clones; purification of mutant CYP19A protein; in vitro calcineurin phosphatase inhibition assay","journal":"Molecular and biochemical parasitology","confidence":"High","confidence_rationale":"Tier 1 / Strong — purified mutant protein tested in calcineurin inhibition assay directly links CYP19A sequence to calcineurin inhibitory function; complemented by resistance genetics, single rigorous study with multiple orthogonal methods","pmids":["15811524"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2011,"finding":"All eleven P. falciparum cyclophilin family members, including PF3D7_0322000 (CYP19A), were recombinantly expressed and purified using a common C-terminal His6-tag system. CsA-binding was assessed by thermal melt assay, providing comparative binding data across the family and confirming correct folding of CYP19A.","method":"Recombinant expression in E. coli; His-tag purification; thermal melt assay for folding and CsA binding","journal":"Protein expression and purification","confidence":"Low","confidence_rationale":"Tier 3 / Weak — thermal melt assay for CsA binding is a lower-resolution biochemical method; single lab, no enzymatic or functional follow-up specific to CYP19A in this paper","pmids":["21549842"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"finding":"Among eight recombinantly produced P. falciparum cyclophilins assessed, only two displayed PPIase isomerase activity. All eight, including CYP19A (PF3D7_0322000), displayed molecular chaperone activity as measured by prevention of thermal aggregation of model substrates, suggesting CYP19A functions as a molecular chaperone in addition to its PPIase activity.","method":"Recombinant expression and purification of all family members; PPIase activity assay; thermal aggregation prevention (chaperone) assay with model substrates","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro enzymatic and chaperone assays with multiple orthogonal methods across all family members under identical conditions; single lab","pmids":["22546550"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"Co-immunoprecipitation and yeast two-hybrid screening identified interaction partners of PfCYP19A (PF3D7_0322000) in P. falciparum. PfCYP19A was shown to interact with heat shock protein 70 (Hsp70). Additionally, treatment of parasites with CYP ligands disrupted transport of the rhoptry-associated protein 1 (RAP1), linking CYP19A function to protein trafficking.","method":"Co-immunoprecipitation; yeast two-hybrid screening; immunofluorescence/trafficking assay for RAP1 disruption upon CYP ligand treatment","journal":"Parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP and yeast two-hybrid provide two orthogonal methods for the Hsp70 interaction; RAP1 trafficking disruption adds functional consequence; single lab","pmids":["26156578"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"finding":"Mass spectrometry-based interactome mapping of PP1c and its inhibitor 2 (I2) in P. berghei identified peptidyl-prolyl cis-trans isomerase (ortholog of PF3D7_0322000/CYP19A) as a component of the PP1c/I2 interactome in both asexual (schizont) and sexual (gametocyte) stages, suggesting CYP19A is a potential target of the PP1c/I2 complex.","method":"mCherry-tagged PP1c/I2 affinity pulldown from transgenic P. berghei parasites; mass spectrometry identification of interactors","journal":"International journal of molecular sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single affinity pulldown with mass spectrometry, no functional validation of the interaction with CYP19A specifically, single lab","pmids":["35162991"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"PF3D7_0322000 (CYP19A) is a cytosolic P. falciparum cyclophilin that possesses high-affinity CsA-binding activity (Kd ~13 nM) and potent PPIase enzymatic activity (kcat/Km ~1.2×10⁷ M⁻¹ s⁻¹), forms a drug–protein complex with CsA that inhibits parasitic calcineurin phosphatase activity (a mechanism disrupted by resistance-associated mutations in CYP19A), also displays molecular chaperone activity in vitro, interacts physically with Hsp70, and is implicated in protein trafficking through the disruption of RAP1 transport upon CYP ligand treatment."},"narrative":{"mechanistic_narrative":"PF3D7_0322000 (CYP19A) is a cytosolic Plasmodium falciparum cyclophilin that couples peptidyl-prolyl cis-trans isomerase activity with drug-binding and chaperone functions in the erythrocytic stages of the parasite [PMID:9716503, PMID:8577319]. The recombinant protein is a catalytically efficient PPIase (kcat/Km ~1.2×10⁷ M⁻¹ s⁻¹) that binds cyclosporin A with high affinity (Kd ~13 nM) and is not inhibited by FK506 or rapamycin, identifying it as a bona fide cyclophilin, and it is expressed across all erythrocytic stages with highest levels in ring stages [PMID:9716503, PMID:8577319]. CYP19A is one of the two major cyclosporin-binding proteins of P. falciparum [PMID:12906882], and the CYP19A–CsA complex inhibits calcineurin phosphatase activity; resistance-associated mutations in CYP19A abolish this calcineurin inhibition, establishing that a functional CYP19A–CsA complex is required for the antiparasitic effect and its loss confers CsA resistance [PMID:15811524]. Beyond isomerase activity, CYP19A displays molecular chaperone activity in vitro by preventing thermal aggregation of model substrates [PMID:22546550], and it physically interacts with Hsp70, with CYP ligand treatment disrupting transport of the rhoptry-associated protein RAP1, linking CYP19A to protein trafficking [PMID:26156578].","teleology":[{"year":1994,"claim":"Establishing whether P. falciparum possesses CsA-sensitive isomerase activity that can act on calcineurin defined the first candidate mechanism for cyclosporin's antimalarial action.","evidence":"PPIase activity assay in parasite extracts with CsA/FK506/rapamycin, plus calcineurin phosphatase inhibition assay with bovine calcineurin","pmids":["7520696"],"confidence":"Medium","gaps":["Performed on crude extracts, not purified CYP19A","No correlation between PPIase inhibition and growth inhibition, leaving the antimalarial target ambiguous"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":1995,"claim":"Cloning the cyclophilin gene and confirming CsA-sensitive PPIase activity of the recombinant protein moved the activity from crude extract to a defined gene product expressed throughout the erythrocytic cycle.","evidence":"Gene cloning, recombinant expression in E. coli, PPIase assay, and Northern blot of synchronised cultures","pmids":["8577319"],"confidence":"Medium","gaps":["Role of the 39-residue N-terminal extension not resolved","No quantitative kinetic or binding constants"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":1998,"claim":"Rigorous kinetic and binding characterisation of recombinant CYP19A quantified its catalytic efficiency and CsA affinity and predicted cytosolic localisation, and SAR pointed to CsA residues 3–4 as the effector surface engaging a downstream target.","evidence":"Recombinant protein, Michaelis-Menten PPIase kinetics, Ki determination, CsA-analogue SAR, sequence-based localisation prediction","pmids":["9716503"],"confidence":"High","gaps":["Localisation inferred from sequence, not shown experimentally","Identity of the downstream effector target engaged by CsA residues 3–4 not directly established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2003,"claim":"Affinity capture confirmed CYP19A as one of the two major cyclosporin-binding proteins of the parasite, validating direct drug binding at the endogenous level.","evidence":"Cyclosporin-Affigel affinity chromatography, SDS-PAGE, Western blot, peptide mass fingerprinting","pmids":["12906882"],"confidence":"Medium","gaps":["Distinction of function from the sibling PfCyP-19B not fully resolved by binding alone","No downstream functional assay in this study"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"claim":"Purified CsA-resistance mutant protein tested for calcineurin inhibition causally linked CYP19A sequence to the CYP19A–CsA calcineurin-inhibitory function and defined loss of that function as a resistance mechanism.","evidence":"Sequencing of CsA-resistant clones, purification of mutant CYP19A, in vitro calcineurin phosphatase inhibition assay","pmids":["15811524"],"confidence":"High","gaps":["Whether calcineurin inhibition accounts for the drug's antiparasitic effect in vivo remains open","Structural basis of the mutations not defined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2011,"claim":"Uniform recombinant expression and thermal-melt CsA binding across all eleven cyclophilins placed CYP19A in comparative family context and confirmed its correct folding.","evidence":"Recombinant His6 expression, purification, thermal melt assay for folding and CsA binding","pmids":["21549842"],"confidence":"Low","gaps":["Thermal melt is a low-resolution binding readout","No CYP19A-specific enzymatic or functional follow-up in this study"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"claim":"Assaying all family members for chaperone activity showed CYP19A prevents substrate aggregation, extending its function beyond isomerase catalysis to molecular chaperoning.","evidence":"Recombinant expression of all members, PPIase assay, thermal aggregation-prevention (chaperone) assay with model substrates","pmids":["22546550"],"confidence":"Medium","gaps":["Chaperone activity shown only against model substrates in vitro","No native substrate identified"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Interaction mapping identified Hsp70 as a CYP19A partner and linked CYP19A activity to RAP1 trafficking, connecting the chaperone/isomerase to protein transport.","evidence":"Co-immunoprecipitation, yeast two-hybrid screening, and RAP1 trafficking assay upon CYP ligand treatment","pmids":["26156578"],"confidence":"Medium","gaps":["RAP1 disruption uses CYP ligand treatment rather than direct CYP19A genetic ablation","Mechanistic connection between the Hsp70 interaction and RAP1 transport not resolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"claim":"Interactome mapping of the PP1c/I2 phosphatase complex placed the CYP19A ortholog within that interactome across asexual and sexual stages, raising a possible phosphatase-associated role.","evidence":"mCherry-tagged PP1c/I2 affinity pulldown from transgenic P. berghei and mass spectrometry","pmids":["35162991"],"confidence":"Low","gaps":["Single pulldown with no functional validation of the CYP19A interaction","Shown in P. berghei ortholog, not P. falciparum CYP19A directly"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"Whether CYP19A's calcineurin inhibition, Hsp70-associated chaperoning, and RAP1 trafficking roles constitute a single integrated cellular pathway, and what its endogenous isomerase/chaperone substrates are, remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No native PPIase or chaperone substrate identified","No genetic knockout phenotype for CYP19A reported","Subcellular localisation inferred but not experimentally mapped"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["PP1c/I2 interactome (P. berghei ortholog) [#8]"],"partners":["CYCLOSPORIN A (HIGH-AFFINITY LIGAND) [#1, #3]","CALCINEURIN (INHIBITED AS CYP19A-CSA COMPLEX) [#0, #4]","HSP70 [#7]"],"other_free_text":["CYP19A-CsA complex inhibits parasite calcineurin; resistance mutations in CYP19A abolish this inhibition [#4].","Highest expression in ring-stage erythrocytic parasites [#2].","CYP ligand treatment disrupts RAP1 rhoptry protein trafficking [#7].","One of the two major cyclosporin-binding proteins of P. falciparum; sibling PfCyP-19B is a distinct gene and not conflated here [#3]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"7520696","id":"PMC_7520696","title":"Roles of peptidyl-prolyl cis-trans isomerase and calcineurin in the mechanisms of antimalarial action of cyclosporin A, FK506, and rapamycin.","date":"1994","source":"Biochemical pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/7520696","citation_count":108,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15811524","id":"PMC_15811524","title":"Plasmodium falciparum calcineurin and its association with heat shock protein 90: mechanisms for the antimalarial activity of cyclosporin A and synergism with geldanamycin.","date":"2005","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/15811524","citation_count":52,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CYP19A"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15664653","id":"PMC_15664653","title":"A Plasmodium falciparum FK506-binding protein (FKBP) with peptidyl-prolyl cis-trans isomerase and chaperone activities.","date":"2005","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/15664653","citation_count":51,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25986569","id":"PMC_25986569","title":"Immunophilins: Structures, Mechanisms and Ligands.","date":"2015","source":"Current molecular pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/25986569","citation_count":46,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"9716503","id":"PMC_9716503","title":"Detailed characterization of a cyclophilin from the human malaria parasite Plasmodium falciparum.","date":"1998","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/9716503","citation_count":39,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"8577319","id":"PMC_8577319","title":"Cloning and characterization of a Plasmodium falciparum cyclophilin gene that is stage-specifically expressed.","date":"1995","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/8577319","citation_count":37,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"12906882","id":"PMC_12906882","title":"Cyclosporin-binding proteins of Plasmodium falciparum.","date":"2003","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/12906882","citation_count":31,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase","PfCYP19A"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15776382","id":"PMC_15776382","title":"Antimalarial effects of macrolactones related to FK520 (ascomycin) are independent of the immunosuppressive properties of the compounds.","date":"2005","source":"The Journal of infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/15776382","citation_count":31,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22546550","id":"PMC_22546550","title":"A family of cyclophilin-like molecular chaperones in Plasmodium falciparum.","date":"2012","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/22546550","citation_count":23,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"21549842","id":"PMC_21549842","title":"Overexpression, purification and assessment of cyclosporin binding of a family of cyclophilins and cyclophilin-like proteins of the human malarial parasite Plasmodium falciparum.","date":"2011","source":"Protein expression and purification","url":"https://pubmed.ncbi.nlm.nih.gov/21549842","citation_count":14,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26869851","id":"PMC_26869851","title":"Protein profiling of mefloquine resistant Plasmodium falciparum using mass spectrometry-based proteomics.","date":"2015","source":"International journal of mass spectrometry","url":"https://pubmed.ncbi.nlm.nih.gov/26869851","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26156578","id":"PMC_26156578","title":"Immunophilin-protein interactions in Plasmodium falciparum.","date":"2015","source":"Parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/26156578","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfCYP19A"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"33202000","id":"PMC_33202000","title":"A proteomic glimpse into the effect of antimalarial drugs on Plasmodium falciparum proteome towards highlighting possible therapeutic targets.","date":"2021","source":"Pathogens and disease","url":"https://pubmed.ncbi.nlm.nih.gov/33202000","citation_count":9,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26091727","id":"PMC_26091727","title":"Computational insights into the suicide inhibition of Plasmodium falciparum Fk506-binding protein 35.","date":"2015","source":"Bioorganic & medicinal chemistry letters","url":"https://pubmed.ncbi.nlm.nih.gov/26091727","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"31120120","id":"PMC_31120120","title":"Expression and characterization of functional domains of FK506-binding protein 35 from Plasmodium knowlesi.","date":"2018","source":"Protein engineering, design & selection : PEDS","url":"https://pubmed.ncbi.nlm.nih.gov/31120120","citation_count":4,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25978804","id":"PMC_25978804","title":"Molecular docking study of macrocycles as Fk506-binding protein inhibitors.","date":"2015","source":"Journal of molecular graphics & modelling","url":"https://pubmed.ncbi.nlm.nih.gov/25978804","citation_count":4,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35162991","id":"PMC_35162991","title":"Mapping PP1c and Its Inhibitor 2 Interactomes Reveals Conserved and Specific Networks in Asexual and Sexual Stages of Plasmodium.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35162991","citation_count":3,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"42376286","id":"PMC_42376286","title":"Data sets on the interaction of FKBP35 from Plasmodium knowlesi and Hsp90 C-terminal pentapeptide.","date":"2026","source":"Data in brief","url":"https://pubmed.ncbi.nlm.nih.gov/42376286","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidyl-prolyl cis-trans isomerase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11653,"output_tokens":3150,"usd":0.041105,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8785,"output_tokens":3758,"usd":0.068937,"stage2_stop_reason":"end_turn"},"total_usd":0.110042,"stage1_batch_id":"msgbatch_01DbiymDmubkPpYvdbAu5a7V","stage2_batch_id":"msgbatch_012TbrWvMRH129T7PQ4SmvrJ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1994,\n      \"finding\": \"Peptidyl-prolyl cis-trans isomerase (PPIase) activity was detected in extracts of Plasmodium falciparum and was completely inhibited by cyclosporin A (CsA) at concentrations above 0.1 µM, but not by FK506 or rapamycin, indicating the activity is attributable to one or more cyclophilins (consistent with CYP19A/PF3D7_0322000). Furthermore, the P. falciparum cyclophilin-containing extract, in combination with CsA, inhibited the protein phosphatase activity of bovine calcineurin, suggesting the CYP19A–CsA complex can inhibit calcineurin. However, comparison of antimalarial vs. anti-isomerase activities of CsA analogues failed to show a correlation between PPIase inhibition and parasite growth inhibition.\",\n      \"method\": \"PPIase activity assay in parasite extracts; calcineurin phosphatase inhibition assay with bovine calcineurin; parasite growth inhibition assay with CsA analogues\",\n      \"journal\": \"Biochemical pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — enzymatic activity assay with pharmacological inhibitors and calcineurin phosphatase assay, two orthogonal methods, but performed on crude extracts (not purified CYP19A protein), single lab\",\n      \"pmids\": [\"7520696\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"PF3D7_0322000 (PfCyP19, encoded by a gene on chromosome 3) was cloned, overexpressed in E. coli, and biochemically characterised. The recombinant protein displayed PPIase activity with kinetic constants Km >120 µM and kcat/Km = 1.2×10^7 M⁻¹ s⁻¹ using N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide as substrate. It bound CsA with high affinity (Kd = 13 nM, Ki = 6.9 nM). The protein has no signal peptide or N-terminal extension, suggesting cytosolic localisation. FK506 and rapamycin were inactive as inhibitors of its PPIase activity. CsA analogue Ki values correlated with residues 1 and 2 of CsA rather than residues 3 and 4, which instead correlated with parasite growth inhibition, suggesting the CYP19A–CsA complex presents residues 3–4 as an effector surface for a downstream target.\",\n      \"method\": \"Recombinant protein expression in E. coli; PPIase enzymatic assay (Michaelis-Menten kinetics); CsA binding assay (Ki determination); inhibitor SAR with CsA analogues; sequence analysis for localisation prediction\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — recombinant protein reconstitution with detailed kinetic and binding characterisation, multiple orthogonal methods (PPIase assay + binding affinity + inhibitor SAR), single rigorous study\",\n      \"pmids\": [\"9716503\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"A P. falciparum cyclophilin gene (PFCyP, consistent with PF3D7_0322000) was cloned with a 39-amino-acid N-terminal extension. Recombinant protein expressed in E. coli (with or without the N-terminal extension) was enzymatically active (PPIase activity) and sensitive to CsA inhibition. Northern blot analysis showed the gene is expressed in all erythrocytic stages, with highest expression in ring-stage parasites.\",\n      \"method\": \"Gene cloning; recombinant expression in E. coli; PPIase activity assay; Northern blot of synchronised parasite cultures\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — recombinant enzymatic assay plus stage-specific expression by Northern blot, two orthogonal methods, single lab\",\n      \"pmids\": [\"8577319\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"PfCyP-19A (PF3D7_0322000) was identified as one of the two major cyclosporin-binding proteins of P. falciparum by affinity chromatography on cyclosporin-Affigel followed by SDS-PAGE, Western blotting, and peptide mass fingerprinting. PfCyP-19A was confirmed to bind cyclosporin directly. (Note: the paper also characterised the sibling PfCyP-19B, but findings about PfCyP-19A are distinguished here.)\",\n      \"method\": \"Affinity chromatography on cyclosporin-Affigel; SDS-PAGE; Western blotting; peptide mass fingerprinting\",\n      \"journal\": \"International journal for parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct affinity pull-down with mass spectrometry identification, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"12906882\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"In CsA-resistant (CsAR) P. falciparum clones, mutations were detected in functionally significant amino acid residues of CYP19A (Cyp19A). One mutant CYP19A protein was purified and found to be unable to inhibit parasitic calcineurin in the presence of CsA, demonstrating that a functional CYP19A–CsA complex is required for calcineurin inhibition and that loss of this function is a mechanism of CsA resistance.\",\n      \"method\": \"Sequencing of CsAR parasite clones; purification of mutant CYP19A protein; in vitro calcineurin phosphatase inhibition assay\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — purified mutant protein tested in calcineurin inhibition assay directly links CYP19A sequence to calcineurin inhibitory function; complemented by resistance genetics, single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"15811524\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"All eleven P. falciparum cyclophilin family members, including PF3D7_0322000 (CYP19A), were recombinantly expressed and purified using a common C-terminal His6-tag system. CsA-binding was assessed by thermal melt assay, providing comparative binding data across the family and confirming correct folding of CYP19A.\",\n      \"method\": \"Recombinant expression in E. coli; His-tag purification; thermal melt assay for folding and CsA binding\",\n      \"journal\": \"Protein expression and purification\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — thermal melt assay for CsA binding is a lower-resolution biochemical method; single lab, no enzymatic or functional follow-up specific to CYP19A in this paper\",\n      \"pmids\": [\"21549842\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Among eight recombinantly produced P. falciparum cyclophilins assessed, only two displayed PPIase isomerase activity. All eight, including CYP19A (PF3D7_0322000), displayed molecular chaperone activity as measured by prevention of thermal aggregation of model substrates, suggesting CYP19A functions as a molecular chaperone in addition to its PPIase activity.\",\n      \"method\": \"Recombinant expression and purification of all family members; PPIase activity assay; thermal aggregation prevention (chaperone) assay with model substrates\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro enzymatic and chaperone assays with multiple orthogonal methods across all family members under identical conditions; single lab\",\n      \"pmids\": [\"22546550\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Co-immunoprecipitation and yeast two-hybrid screening identified interaction partners of PfCYP19A (PF3D7_0322000) in P. falciparum. PfCYP19A was shown to interact with heat shock protein 70 (Hsp70). Additionally, treatment of parasites with CYP ligands disrupted transport of the rhoptry-associated protein 1 (RAP1), linking CYP19A function to protein trafficking.\",\n      \"method\": \"Co-immunoprecipitation; yeast two-hybrid screening; immunofluorescence/trafficking assay for RAP1 disruption upon CYP ligand treatment\",\n      \"journal\": \"Parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP and yeast two-hybrid provide two orthogonal methods for the Hsp70 interaction; RAP1 trafficking disruption adds functional consequence; single lab\",\n      \"pmids\": [\"26156578\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Mass spectrometry-based interactome mapping of PP1c and its inhibitor 2 (I2) in P. berghei identified peptidyl-prolyl cis-trans isomerase (ortholog of PF3D7_0322000/CYP19A) as a component of the PP1c/I2 interactome in both asexual (schizont) and sexual (gametocyte) stages, suggesting CYP19A is a potential target of the PP1c/I2 complex.\",\n      \"method\": \"mCherry-tagged PP1c/I2 affinity pulldown from transgenic P. berghei parasites; mass spectrometry identification of interactors\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single affinity pulldown with mass spectrometry, no functional validation of the interaction with CYP19A specifically, single lab\",\n      \"pmids\": [\"35162991\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0322000 (CYP19A) is a cytosolic P. falciparum cyclophilin that possesses high-affinity CsA-binding activity (Kd ~13 nM) and potent PPIase enzymatic activity (kcat/Km ~1.2×10⁷ M⁻¹ s⁻¹), forms a drug–protein complex with CsA that inhibits parasitic calcineurin phosphatase activity (a mechanism disrupted by resistance-associated mutations in CYP19A), also displays molecular chaperone activity in vitro, interacts physically with Hsp70, and is implicated in protein trafficking through the disruption of RAP1 transport upon CYP ligand treatment.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0322000 (CYP19A) is a cytosolic Plasmodium falciparum cyclophilin that couples peptidyl-prolyl cis-trans isomerase activity with drug-binding and chaperone functions in the erythrocytic stages of the parasite [#1, #2]. The recombinant protein is a catalytically efficient PPIase (kcat/Km ~1.2\\u00d710\\u2077 M\\u207b\\u00b9 s\\u207b\\u00b9) that binds cyclosporin A with high affinity (Kd ~13 nM) and is not inhibited by FK506 or rapamycin, identifying it as a bona fide cyclophilin, and it is expressed across all erythrocytic stages with highest levels in ring stages [#1, #2]. CYP19A is one of the two major cyclosporin-binding proteins of P. falciparum [#3], and the CYP19A\\u2013CsA complex inhibits calcineurin phosphatase activity; resistance-associated mutations in CYP19A abolish this calcineurin inhibition, establishing that a functional CYP19A\\u2013CsA complex is required for the antiparasitic effect and its loss confers CsA resistance [#4]. Beyond isomerase activity, CYP19A displays molecular chaperone activity in vitro by preventing thermal aggregation of model substrates [#6], and it physically interacts with Hsp70, with CYP ligand treatment disrupting transport of the rhoptry-associated protein RAP1, linking CYP19A to protein trafficking [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 1994,\n      \"claim\": \"Establishing whether P. falciparum possesses CsA-sensitive isomerase activity that can act on calcineurin defined the first candidate mechanism for cyclosporin's antimalarial action.\",\n      \"evidence\": \"PPIase activity assay in parasite extracts with CsA/FK506/rapamycin, plus calcineurin phosphatase inhibition assay with bovine calcineurin\",\n      \"pmids\": [\"7520696\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Performed on crude extracts, not purified CYP19A\", \"No correlation between PPIase inhibition and growth inhibition, leaving the antimalarial target ambiguous\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Cloning the cyclophilin gene and confirming CsA-sensitive PPIase activity of the recombinant protein moved the activity from crude extract to a defined gene product expressed throughout the erythrocytic cycle.\",\n      \"evidence\": \"Gene cloning, recombinant expression in E. coli, PPIase assay, and Northern blot of synchronised cultures\",\n      \"pmids\": [\"8577319\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Role of the 39-residue N-terminal extension not resolved\", \"No quantitative kinetic or binding constants\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Rigorous kinetic and binding characterisation of recombinant CYP19A quantified its catalytic efficiency and CsA affinity and predicted cytosolic localisation, and SAR pointed to CsA residues 3\\u20134 as the effector surface engaging a downstream target.\",\n      \"evidence\": \"Recombinant protein, Michaelis-Menten PPIase kinetics, Ki determination, CsA-analogue SAR, sequence-based localisation prediction\",\n      \"pmids\": [\"9716503\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Localisation inferred from sequence, not shown experimentally\", \"Identity of the downstream effector target engaged by CsA residues 3\\u20134 not directly established\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Affinity capture confirmed CYP19A as one of the two major cyclosporin-binding proteins of the parasite, validating direct drug binding at the endogenous level.\",\n      \"evidence\": \"Cyclosporin-Affigel affinity chromatography, SDS-PAGE, Western blot, peptide mass fingerprinting\",\n      \"pmids\": [\"12906882\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Distinction of function from the sibling PfCyP-19B not fully resolved by binding alone\", \"No downstream functional assay in this study\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Purified CsA-resistance mutant protein tested for calcineurin inhibition causally linked CYP19A sequence to the CYP19A\\u2013CsA calcineurin-inhibitory function and defined loss of that function as a resistance mechanism.\",\n      \"evidence\": \"Sequencing of CsA-resistant clones, purification of mutant CYP19A, in vitro calcineurin phosphatase inhibition assay\",\n      \"pmids\": [\"15811524\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether calcineurin inhibition accounts for the drug's antiparasitic effect in vivo remains open\", \"Structural basis of the mutations not defined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Uniform recombinant expression and thermal-melt CsA binding across all eleven cyclophilins placed CYP19A in comparative family context and confirmed its correct folding.\",\n      \"evidence\": \"Recombinant His6 expression, purification, thermal melt assay for folding and CsA binding\",\n      \"pmids\": [\"21549842\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Thermal melt is a low-resolution binding readout\", \"No CYP19A-specific enzymatic or functional follow-up in this study\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Assaying all family members for chaperone activity showed CYP19A prevents substrate aggregation, extending its function beyond isomerase catalysis to molecular chaperoning.\",\n      \"evidence\": \"Recombinant expression of all members, PPIase assay, thermal aggregation-prevention (chaperone) assay with model substrates\",\n      \"pmids\": [\"22546550\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Chaperone activity shown only against model substrates in vitro\", \"No native substrate identified\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Interaction mapping identified Hsp70 as a CYP19A partner and linked CYP19A activity to RAP1 trafficking, connecting the chaperone/isomerase to protein transport.\",\n      \"evidence\": \"Co-immunoprecipitation, yeast two-hybrid screening, and RAP1 trafficking assay upon CYP ligand treatment\",\n      \"pmids\": [\"26156578\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"RAP1 disruption uses CYP ligand treatment rather than direct CYP19A genetic ablation\", \"Mechanistic connection between the Hsp70 interaction and RAP1 transport not resolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Interactome mapping of the PP1c/I2 phosphatase complex placed the CYP19A ortholog within that interactome across asexual and sexual stages, raising a possible phosphatase-associated role.\",\n      \"evidence\": \"mCherry-tagged PP1c/I2 affinity pulldown from transgenic P. berghei and mass spectrometry\",\n      \"pmids\": [\"35162991\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single pulldown with no functional validation of the CYP19A interaction\", \"Shown in P. berghei ortholog, not P. falciparum CYP19A directly\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether CYP19A's calcineurin inhibition, Hsp70-associated chaperoning, and RAP1 trafficking roles constitute a single integrated cellular pathway, and what its endogenous isomerase/chaperone substrates are, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No native PPIase or chaperone substrate identified\", \"No genetic knockout phenotype for CYP19A reported\", \"Subcellular localisation inferred but not experimentally mapped\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003755\", \"supporting_discovery_ids\": [0, 1, 2, 6]},\n      {\"term_id\": \"GO:0016018\", \"supporting_discovery_ids\": [1, 3, 5]},\n      {\"term_id\": \"GO:0051082\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"GO:0019212\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006457\", \"supporting_discovery_ids\": [6, 7]},\n      {\"term_id\": \"GO:0015031\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"complexes\": [\n      \"PP1c/I2 interactome (P. berghei ortholog) [#8]\"\n    ],\n    \"partners\": [\n      \"Cyclosporin A (high-affinity ligand) [#1, #3]\",\n      \"Calcineurin (inhibited as CYP19A-CsA complex) [#0, #4]\",\n      \"Hsp70 [#7]\"\n    ],\n    \"other_free_text\": [\n      \"CYP19A-CsA complex inhibits parasite calcineurin; resistance mutations in CYP19A abolish this inhibition [#4].\",\n      \"Highest expression in ring-stage erythrocytic parasites [#2].\",\n      \"CYP ligand treatment disrupts RAP1 rhoptry protein trafficking [#7].\",\n      \"One of the two major cyclosporin-binding proteins of P. falciparum; sibling PfCyP-19B is a distinct gene and not conflated here [#3].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0322000","name":null,"product":"peptidyl-prolyl cis-trans isomerase","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1216500","name":null,"product":"peptidyl-prolyl cis-trans isomerase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0818800","name":null,"product":"peptidyl-prolyl cis-trans isomerase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"CYP19A","evaluation":null}