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biomolecules Review Peptidylprolyl Isomerases as In Vivo Carriers for Drugs That Target Various Intracellular Entities Andrzej Galat Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université Paris-Saclay, F-91191 Gif/Yvette, France; [email protected]; Fax: +33-169089137 Academic Editor: John A. Carver Received: 24 August 2017; Accepted: 26 September 2017; Published: 29 September 2017 Abstract: Analyses of sequences and structures of the cyclosporine A (CsA)-binding proteins (cyclophilins) and the immunosuppressive macrolide FK506-binding proteins (FKBPs) have revealed that they exhibit peculiar spatial distributions of charges, their overall hydrophobicity indexes vary within a considerable level whereas their points isoelectric (pIs) are contained from 4 to 11. These two families of peptidylprolyl cis/trans isomerases (PPIases) have several distinct functional attributes such as: (1) high affinity binding to some pharmacologically-useful hydrophobic macrocyclic drugs; (2) diversified binding epitopes to proteins that may induce transient manifolds with altered flexibility and functional fitness; and (3) electrostatic interactions between positively charged segments of PPIases and negatively charged intracellular entities that support their spatial integration. These three attributes enhance binding of PPIase/pharmacophore complexes to diverse intracellular entities, some of which perturb signalization pathways causing immunosuppression and other system-altering phenomena in humans. Keywords: PPIase; FKBP; cyclophilin; rapamycin; FK506 1. Introduction About forty years ago, two different types of macrocyclic molecules were isolated and shown to possess immunosuppressive activities, such as the cyclic peptide containing non-standard amino acid residues (AAs) cyclosporine A (CsA) and its homologues [1], and two polyketides having L-pipecolic acid ring, namely immunosuppressive macrolide FK506 [2] and rapamycin [3,4]. Rapamycin and its different natural and synthetic derivatives such as everolimus, temsirolimus (CCI-779) or zotarolimus (ABT-578) have been used as anticancer drugs [5–7]. Some natural homologues of CsA, FK506 and rapamycin are devoid of immunosuppressive activity [7,8]. All those compounds have been found in soil samples coming from three different regions of Earth, namely CsA and its derivatives were purified from the ascomycete fungus Tolypocladium inflatum found in a soil sample from Norway [1], FK506 (tacrolimus) was isolated from a bacterial culture of Streptomyces tsukubaensis found in a soil sample from Japan [2] whereas rapamycin (sirolimus) was recuperated from a filament-forming bacterium, Streptomyces hygroscopicus found in a soil sample of Rapa Nui (Easter Island) [3,4], respectively. Several other natural polyketides have some structural similarity to FK506, namely meridamycin from Streptomyces hydroscopicus that was found in a soil sample from Venezuela [9], nocardiopsins isolated from a marine sediment sample found off the cost of Brisbane [10], or antascomicins purified from Micromonospora species found in a Chinese soil sample [11]. Even if they bind to 12 kDa FK506-binding protein (FKBP12), curiously these molecules are not immunosuppressive but instead they antagonize the actions caused by FK506 [11]. Moreover, non-immunosuppressive meridamycin [9] has neuroprotective activity [12,13]. The macrolide sanglifehrin-A and its natural homologues bind to cyclophilin A (CyPA) and perturb some immune responses [14], but its mode of Biomolecules 2017, 7, 72; doi:10.3390/biom7040072 www.mdpi.com/journal/biomolecules Biomolecules 2017, 7, 72 2 of 21 Biomolecules 2017, 7, 72 2 of 21 action is different from that of the CsA-driven immunosuppression [15]. These different effects are depicted in Figure1. Figure 1. 1. SchemeScheme depicting depicting two polyketides two polyketides (FK506 and (FK506 rapamycin) and rapamycin) and cyclic peptide and cyclic cyclosporine peptide Acyclosporine (CsA) with A (CsA)a brief with asummary brief summary of their of theirintracellular intracellular targets targets whose whose blocking blocking by immunophilin/(immunosuppressive drug) drug) complex complex causes causes diverse diverse clinically clinically useful useful effects. effects. Pioneer works leading to isolation and characterization of several natural isoforms of peptidylprolyl ciscis/trans/trans isomeraseisomerase (PPIases) (PPIases) [16] such [16] as such CyPA as [17], CyPA CyPB, [17], CyPD, CyPB, CyP40 CyPD, (reviewed CyP40 (reviewedin [8]), and in FKBP12a [8]), and [18], FKBP12a FKBP13, [18 ],FKBP25 FKBP13, and FKBP25 FKBP52 and (reviewed FKBP52 in (reviewed [7]) revealed in [7 ])that revealed these immunophilinsthat these immunophilins have sizeable have expression sizeable levels expression in diverse levels organs in diverse (reviewed organs in [1 (reviewed9]). The principal in [19]). Theintracellular principal binders intracellular of CsA bindersare: (1) CyPA of CsA (cytoplasm) are: (1) CyPA[17]; (2) (cytoplasm) cyclophilin [ 17B ];(CyPB, (2) cyclophilin endoplasmic B (CyPB,reticulum endoplasmic (ER)) [20], reticulum and (3) cyclophilin (ER)) [20], andD (CyPD, (3) cyclophilin mitochondrial D (CyPD, membrane) mitochondrial (reviewed membrane) in [8]) (reviewedwhereas abundantly in [8]) whereas expressed abundantly heat‐shock expressed protein heat-shock‐associated protein-associated CyP40 binds weakly CyP40 bindsto CsA weakly [21]. FKBP12ato CsA [21 (cytoplasm)]. FKBP12a (cytoplasm)[18], FKBP25 [18 (cytoplasm,], FKBP25 (cytoplasm,diverse organelles diverse organellesand nucleus) and ],[22 nucleus) FKBP13 [22], (ERFKBP13‐protein), (ER-protein), or tetratricopeptide or tetratricopeptide domain (TPR) domain‐containing (TPR)-containing FKBP51 and FKBP51 FKBP52 and (reviewed FKBP52 (reviewed in [7,19]) bindin [7 ,to19 ])FK506 bind or to rapamycin FK506 or rapamycin and their structural and their analogues structural [23]. analogues It has been [23]. shown It has beenthat either shown of that the followingeither of the two following complexes, two namely complexes, CyPA/CsA namely or CyPA/CsAFKBP12a/FK506 or FKBP12a/FK506 hinders the access hinders to phosphatase the access activityto phosphatase site of calcineurin activity site heterodimer of calcineurin [24]. heterodimerIn consequence, [24]. the In phosphoryla consequence,ted the pool phosphorylated of the nuclear poolfactor of of the activated nuclear factorT cells of transcription activated T cells factor transcription (NF‐ATc) remains factor (NF-ATc) in the cytoplasm remains in (see the cytoplasm Figure 2) (see[25,26]. Figure FKBP12/rapamycin2)[ 25,26]. FKBP12/rapamycin binds to serine‐threonine binds to serine-threonine kinase mTOR and kinase it hinders mTOR the and access it hinders to its kinasethe access activity to its site kinase [27,28], activity which site causes [27,28 anergy], which of causesT cells. anergy These ofhypotheses T cells. Theseimply hypothesesthat under physiologicalimply that under conditions physiological the intracellular conditions contents the intracellular of calcineurin contents heterodimer of calcineurin and mTOR heterodimer in T cells areand mTORsmall, inthus T cells their are small, enzymatic thus their activities enzymatic could activities be could effectively be effectively blocked blocked by by the immunophilin/(iimmunophilin/(immunosuppressivemmunosuppressive drug) drug) complexes. complexes. Biomolecules 2017, 7, 72 3 of 21 Biomolecules 2017, 7, 72 3 of 21 FigureFigure 2. 2. SchemeScheme of of the the X‐ray X-ray structure structure of a of complex a complex between between human human cyclophilin cyclophilin (hCyPA) (hCyPA) (green (greenribbon) ribbon) bound bound to cyclosporine to cyclosporine A (CsA) A (violet (CsA) spheres) (violet and spheres) the calcineurin and the calcineurin heterodimer, heterodimer, calcineurin calcineurinA (CnA), yellow A (CnA), ribbon), yellow calcineurin ribbon), calcineurin B (CnB) (red B (CnB) ribbon) (red with ribbon) four with Ca+2 four ions Ca shown+2 ions as shown green asspheres. green spheres. The cyclophilin The cyclophilin A (CyPA)/CsA A (CyPA)/CsA complex hinders complex access hinders to phosphatase access to phosphatase activity site activity (shown siteas (shownbound asphosphate bound phosphate ion in ionlight in lightred spheres) red spheres) (1mf8.pdb (1mf8.pdb [29]). [29 ]).Similar Similar action action causescauses thethe FK506/FKBP12aFK506/FKBP12a complexcomplex ifif itit is is bound bound to to CnA–CnB CnA–CnB (data (data not not shown). shown). Different Different phosphorylated phosphorylated componentscomponents of of transcription transcription machinery machinery rest rest immobilized immobilized in in the the cytoplasm, cytoplasm, namely namely cytoplasmic cytoplasmic form form ofof transcription transcription factor factor NF-ATc. NF‐ATc. On theOn leftthe panel left panel is shown is shown the X-ray the structure X‐ray structure (1s9k.pdb) (1s9k.pdb) of a complex of a betweencomplex human between interleukin-2 human interleukin (IL-2) ARRE1‐2 (IL promoter‐2) ARRE1 element promoter (blue/red element ribbon) (blue/red and the ribbon) fragments and ofthe thefragments activator of protein the activator (AP-1) transcription protein (AP complex,‐1) transcription namely nuclearcomplex, form namely of NF-ATn nuclear (cyan), form cFos of NF (violet)‐ATn and(cyan), cJun cFos (orange) (violet) [30 ].and cJun (orange) [30]. RecentRecent analyses analyses of of a human a human interactome interactome have have shown shown that the that expression the expression