Synthesis of calcineurin-resistant derivatives of FK506 and selection of compensatory receptors

We used olefin metathesis to synthesize C40 derivatives of FK506 and measured their ability, when complexed to FKBP12, to inhibit calcineurin's phosphatase activity. We identified modular dimerization domains (CABs) containing segments of the calcineurin A and B polypeptides. These CABs respond to FK506 both when overexpressed in mammalian cells and in yeast or mammalian three-hybrid assays. Using chemical genetic selection, we identified compensatory mutant CABs that respond to a calcineurin-resistant FK506 derivative at concentrations well below the response threshold for CABs containing only wild-type calcineurin sequence. These reagents provide a small molecule-protein combination orthogonal to existing dimerizer systems and may be used with existing systems to increase the complexity of induced-proximity experiments. This new use of the "bump-hole" strategy protects target cells from complications arising from the inhibition of endogenous calcineurin.     

Drug Discovery Based on the Structure of FKBPs： Design, Synthesis and Evaluation of L-1, 4-Thiazane-3-carboxylic Acid Derivatives as Neuroimmunophilin Ligands

Based on the structure of FK506, FKBP12 and calcineurin complex and the interactive characteristics of small molecular ligands with FKBPs, a series of L-1,4-thiazane-3-carboxylic acid derivatives as neuroimmunophilin ligands was designed and synthesized. The results of evaluation show that compound N308 has a great promise as a candidate of neuroprotective and neuroregenerative agent.     

Structure-based design of a highly selective catalytic site-directed inhibitor of Ser/Thr protein phosphatase 2B (calcineurin)

Protein serine/threonine phosphatases (PP1, PP2A and PP2B) play important roles in intracellular signal transductions. The immunosuppressant drugs FK506 and cyclosporin A (CsA) bind to immunophilins, and these complexes selectively inhibit PP2B (calcineurin), leading to the suppression of T-cell proliferation. Both FK506 and CsA must, however, form complexes with immunophilins to exert their inhibitory action on PP2B. Thus, it is of interest to find a direct and selective inhibitor of PP2B that does not involve the immunophilins as a biological tool for studies of PP2B and also as a candidate therapeutic agent. We selected the simple natural product cantharidin, a known PP2A-selective inhibitor, as a lead compound for this project. Primary SAR indicated that norcantharidin (7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic anhydride) inhibits not only PP1 and PP2A but also PP2B, and a binding model of norcantharidin carboxylate to the PP2B catalytic site was computationally constructed. Based on this binding model, we designed and synthesized several cantharidin derivatives. Among these compounds, 1,5-dibenzoyloxymethyl-substituted norcantharidin was found to inhibit PP2B without inhibiting PP1 or PP2A. To our knowledge, this is the first highly selective catalytic site-directed inhibitor of PP2B.     

Biosynthesis of the allylmalonyl-CoA extender unit for the FK506 polyketide synthase proceeds through a dedicated polyketide synthase and facilitates the mutasynthesis of analogues

The allyl moiety of the immunosuppressive agent FK506 is structurally unique among polyketides and critical for its potent biological activity. Here, we detail the biosynthetic pathway to allylmalonyl-coenzyme A (CoA), from which the FK506 allyl group is derived, based on a comprehensive chemical, biochemical, and genetic interrogation of three FK506 gene clusters. A discrete polyketide synthase (PKS) with noncanonical domain architecture presumably in coordination with the fatty acid synthase pathway of the host catalyzes a multistep enzymatic reaction to allylmalonyl-CoA via trans-2-pentenyl-acyl carrier protein. Characterization of this discrete pathway facilitated the engineered biosynthesis of novel allyl group-modified FK506 analogues, 36-fluoro-FK520 and 36-methyl-FK506, the latter of which exhibits improved neurite outgrowth activity. This unique feature of FK506 biosynthesis, in which a dedicated PKS provides an atypical extender unit for the main modular PKS, illuminates a new strategy for the combinatorial biosynthesis of designer macrolide scaffolds as well as FK506 analogues.     

A genome-wide overexpression screen in yeast for small-molecule target identification

We describe a multicopy gene suppression screen of drug sensitivity in Saccharomyces cerevisiae that facilitates the identification of cellular targets of small molecules. An array of yeast transformants harboring a multicopy yeast genomic library was screened for resistance to growth inhibitors. Comparison of array growth patterns for several such inhibitors allowed the differentiation of general and molecule-specific genetic suppressors. Specific resistance to phenylaminopyrimidine (1), an inhibitor identified from a kinase-directed library, was associated with the overexpression of Pkc1 and a subset of downstream kinases. Components of two other pathways (pheromone response/filamentous growth and Pho85 kinase) that genetically interact with the PKC1 MAPK signaling cascade were also identified. Consistent with the suppression screen, inhibitor 1 bound to Pkc1 in yeast cell lysate and inhibited its activity in vitro. These results demonstrate the utility of this approach for the rapid deconvolution of small-molecule targets.     

Study of the effect of Wuzhi tablet (Schisandra sphenanthera extract) on tacrolimus tissue distribution in rat by liquid chromatography tandem mass spectrometry method

A liquid chromatography/tandem mass spectrometry (LC‐MS/MS) method was developed and validated for determining tacrolimus (FK506) in rat tissues to study the effect of Schisandra sphenanthera extract on FK506 tissue distribution. After a liquid–liquid extraction with ethyl acetate, FK506 and ascomycin (IS) were subjected to LC‐MS/MS analysis using positive electrospray ionization under multiple reactions monitoring mode. Chromatographic separation of FK506 and ascomycin was achieved on a Hypersil BDS C₁₈ column with a mobile phase consisting of methanol‐water (containing 2 mM ammonium acetate, 95 : 5, v/v). The intra‐ and inter‐batch precision of the method were less than 8.8 and 9.8%, respectively. The intra‐ and inter‐batch accuracies ranged from 97.5 to 104.0%. The lowest limit of quantification for FK506 was 0.5 ng/mL. The method was applied to a FK506 tissue distribution study with or without a dose of Wuzhi (WZ) tablet. Most of the FK506 tissue concentrations were slightly increased after a concomitant WZ tablet dose, but the whole blood concentration of FK506 was dramatically increased 3‐fold after a concomitant WZ tablet dose. These results indicated that the LC‐MS/MS method was rapid and sensitive enough to quantify FK506 in different rat tissues, and strict drug monitoring is recommended when co‐administering WZ tablet in clinical use. Copyright © 2009 John Wiley & Sons, Ltd.     

Involvement of some large immunophilins and their ligands in the protection and regeneration of neurons: a hypothetical mode of action

The powerful immunosuppressive drugs such as FK506 and its derivatives induce some regeneration and protection of neurons from ischaemic brain injury and some other neurological disorders. The drugs form complexes with diverse FKBPs but apparently the FKBP52/FK506 complex was shown to be involved in the protection and regeneration of neurons. We used several different sequence attributes in searching diverse genomic databases for similar motifs as those present in the FKBPs. A Fortran library of algorithms (Par_Seq) has been designed and used in searching for the similarity of sequence motifs extracted from the multiple sequence alignments of diverse groups of proteins (query motifs) and the target motifs which are encoded in various genomes. The following sequence attributes were used in the establishment of the degree of convergence between: (A) amino acid (AA) sequence similarity (ID) of the query/target motifs and (B) their: (1) AA composition (AAC); (2) hydrophobicity (HI); (3) Jensen-Shannon entropy; and (4) AA propensity to form a particular secondary structure. The sequence hallmark of two different groups of peptidylprolyl cis/trans isomerases (PPIases), namely tetratricopetide repeat (TPR) motifs, which are present in the heat-shock cyclophilins and in the large FK506-binding proteins (FKBPs) were used to search various genomic databases. The Par_Seq algorithm has revealed that the TPR motifs have similar sequence attributes as a number of hydrophobic sequence segments of functionally unrelated membrane proteins, including some of the TMs from diverse G protein-coupled receptors (GPCRs). It is proposed that binding of the FKBP52/FK506 complex to the membranes via the TPR motifs and its interaction with some membrane proteins could be in part responsible for some neuro-regeneration and neuro-protection of the brain during some ischaemia-induced stresses.     

Detection of noncovalent FKBP-FK506 and FKBP-Rapamycin complexes by capillary electrophoresis-mass spectrometry and capillary electrophoresis-tandem mass spectrometry

The well known biospecific noncovalent receptor-ligand association complexes between the immunophilin FKBP and the immunosuppressive drugs FK506 and Rapamycin (RM) were investigated by on-line capillary electrophoresis-mass spectrometry (CE-MS) under selected ion monitoring (SIM) conditions and by CE-MS with tandem mass spectrometry (CE-MS/MS) under selected reaction monitoring (SRM) conditions. Solutions of hFKBP (33.3 µM) were dissolved in 50 mM ammonium acetate at pH 7.5. Samples that contained 100 µM of FK506 or RM also were prepared under the same solution conditions. By using these aqueous pH neutral conditions, samples were analyzed by SIM CE-MS and SRM CE-MS and the target complexes were separated by CE with mass spectrometer detection of the individual complexes between FKBP and FK506 [hFKBP + FK506 + 7HJ⁷⁺ as well as FKBP and RM [hFKBP + RM + 7HJ⁷⁺. In an experiment where a mixture of FK506 and RM was analyzed in the presence of FKBP, a nine-to-one ratio of ion current abundances between the RM and FK506 complexes was observed as reported in the literature from other studies. These results suggest that CE-MS and CE-MS/MS may be yet another analytical method for studying noncovalent interactions of biologically important macromolecules under physiological conditions.     

Evidence for the Preservation of Native Inter- and Intra-Molecular Hydrogen Bonds in the Desolvated FK-Binding Protein·FK506 Complex Produced by Electrospray Ionization

It is now well established that electrospray ionization (ESI) is capable of introducing noncovalent protein assemblies into a desolvated environment, thereby allowing their analysis by mass spectrometry. The degree to which native interactions from the solution phase are preserved in this environment is less clear. Site-directed mutagenesis of FK506-binding protein (FKBP) has been employed to probe specific intra- and inter-molecular interactions within the complex between FKBP and its ligand FK506. Collisional activation of wild-type and mutant-FKBP?FK506 ions, generated by ESI, demonstrated that removal of native protein-ligand interactions formed between residues Asp37, Tyr82, and FK506 significantly destabilized the complex. Mutation of Arg42 to Ala42, or Tyr26 to Phe26 also resulted in lower energy dissociation of the FKBP·FK506 complex. Although these residues do not form direct H-bonds to FK506, they interact with Asp37, ensuring its correct orientation to associate with the ligand. Comparison with solution-based affinity measurements of these mutants has been discussed, including the stabilization afforded by ordered water molecules. Ion mobility spectrometry (IMS) has been employed to provide gas-phase structural information on the unfolding of the complexes. The [M + 6H](6+) complexes of the wild-type and mutants have been shown to resist unfolding and retain compact conformations. However, removal of the basic Arg42 residue was found to induce significant structural weakening of the [M + 7H](7+) complex when raised to dissociation-level energies. Overall, destabilization of the FKBP·FK506 complex, resulting from targeted removal of specific H-bonds, provides evidence for the preservation of these interactions in the desolvated wild-type complex.     

Stevastelins,a novel group of immunosuppressants,inhibit dual-specificity protein phosphatases

Background: Since the molecular target of the immunosuppressive reagents FK506 and cyclosporin A was revealed to be protein phosphatase PP2B (calcineurin), many researchers have been screening the protein phosphatase inhibitors from microbial metabolites to develop new immunosuppressive reagents. We isolated stevastelin B, which is composed of valine, threonine, serine and 3,5-dihydroxy-2,4-dimethyl stearic acid, and stevastelin A, which is a sulphonylated derivative of stevastelin B. To understand the action mechanism of stevastelins A and B, we synthesized a series of stevastelin derivatives and investigated their structure-activity relationships.Results: A series of stevastelin derivatives have been systematically synthesized. Stevastelin B inhibited gene expression that is dependent on interleukin-2 (IL-2) or IL-6 promoters in situ, but it had no inhibitory activity against any protein phosphatases in vitro. In contrast, stevastelin A, which is a sulphonylated derivative of stevastelin B, inhibited the phosphatase activity of a dual-specificity phosphatase, VH1-related human protein (VHR), in vitro, but it had no inhibitory activity against gene expression or cell-cycle progression in situ.Conclusions: Stevastelin B is a novel immunosuppressant. It inhibited IL-2 or IL-6 dependent gene expression but did not inhibit the phosphatase activity of calcineurin. The structure-activity relationships show that the acidic functional group on the threonine residue and the stearic acid moiety in the stevastelin molecule are important for inhibitory effects on the dephosphorylation activity of VHR in vitro. Stevastelin B might be sulphonylated or phosphorylated after incorporation into the target cell, and then it interacts with protein tyrosine phosphatases and regulates cell-cycle progression.     

Structural Investigations of 13-O-Demethyl-FK506 and Its Isomers Generated by in vitro Metabolism of FK506 Using Human-Liver Microsomes

FK506 is currently under investigation as immunosuppressant after organ transplantation and in immune diseases. The structure of a demethylated metabolite 1 of FK506 isolated after in vitro metabolism by human-liver microsomes was established using two-dimensional homo- and heteronuclear NMR experiments. The demethylation position was found to be at O? C(13) using HMBC spectra. In contrast to FK506, 7 different isomers could be differentiated in COSY, HMBC, and HMQC spectra. The intensity of their signals was 50:18:11:9:6:6 (one isomer could not be quantified). This isomerization may be explained by epimerization at C(10) or alternative formations of the hemiketal ring between C(10) and C(13) or C(9) and C(13), in addition to cis/trans-isomerism about the amide bond (see Scheme). The structural variation is possible by participation of the OH group at C(13) formed after demethylation and could be derived from HMBC spectra. Chemical exchange evidenced by ROESY spectra proved the rotational isomerism. NMR investigation of the structure of 13-O-demethyl-FK 506 ( 1 ) revealed at least seven isomers.     

3-磷酸甘油醛脱氢酶与酵母线粒体基因组维持蛋白Mgm101的相互作用

采用酵母双杂交方法, 以Mgm101p为诱饵, 筛选酵母cDNA文库. 分离鉴定15个与Mgm101p相互作用的蛋白因子, 其中5个阳性克隆均为GPD1编码的3-磷酸甘油醛脱氢酶(GAPDH). 克隆了GPD1在 S. cerevisiae的同系物ScTDH2基因, 进行绿色荧光蛋白GFP标记、 亚细胞组分分离和蛋白质印迹分析, 结果表明, GAPDH除了在细胞质为糖酵解酶的主要作用外, 可能为多功能蛋白, 在酵母线粒体中与Mgm101p相互作用参与线粒体DNA维持的生物过程.     

Conformational sensitivity analysis of FKBP–FK506/rapamycin complexes

Sensitivity analysis techniques are applied to the FKBP–FK506 and FKBP–rapamycin complexes to quantify the conformational relationships between FKBP and its ligands. Crystal structures of the two FKBP complexes are energy minimized in the Amber force field using a continuum solvent model, and derived Green's function sensitivity coefficients are developed to describe the relationship between the ?, ψ, and χ₁ torsional angles of the FKBP residues and the bound ligand macrocycle torsional angles. Sensitivity analysis is applied to the entire FKBP structure and reveals that the local conformation of the residues of the 80s and 50s loops and of the active site are sensitive to the ligand conformation. The analysis also reveals that the torsional angles controlling the orientation of the amide and keto carbonyls of FK506 are sensitive to the aromatic side chains in the FKBP carbonyl binding pocket. © 1994 by John Wiley & Sons, Inc.     

Small molecule microarray screening methodology based on surface plasmon resonance imaging

In order to increase the scope and utility of small molecule microarrays (SMMs) we have combined SMMs and SPRi to screen small molecule antagonists against protein targets. Several small molecules, including immunosuppressive drugs (rapamycin and FK506) and reported inhibitors (FOBISIN and Blapsin) of 14-3-3ζ proteins have been used to validate this technology. Furthermore, a small library of isatin derivatives have been synthesized and screened on developed platform against 14-3-3ζ protein. Three molecules, derived from the endogenous intermediate isatin termed, FZIB-35, FZIB-36 and FZIB-38 were identified as novel inhibitors which shows significant interaction with 14-3-3ζ. A mutation in the binding groove of 14-3-3ζ, (K49E), almost abolishes the binding of these compounds to 14-3-3ζ protein. To exclude the probability of false positives, two more purified proteins (PtpA and BirA) were also tested. Furthermore, in order to confirm the binding pocket specificity, competition assay against R18 peptide was also carried out on presented platform. We show that SMMs in combination with SPRi are a powerful method to identify lead compounds in high throughput manner without the need to develop an activity based assay.     

Down syndrome critical region 1 enhances the proteolytic cleavage of calcineurin

Down syndrome critical region 1 (DSCR1), an oxidative stress-response gene, interacts with calcineurin and represses its phosphatase activity. Recently it was shown that hydrogen peroxide inactivates calcineurin by proteolytic cleavage. Based on these facts, we investigated whether oxidative stress affects DSCR1-mediated inactivation of calcineurin. We determined that overexpression of DSCR1 leads to increased proteolytic cleavage of calcineurin. Convertsely, knockdown of DSCR1 abolished calcineurin cleavage upon treatment with hydrogen peroxide. The PXIIXT motif in the COOH-terminus of DSCR1 is responsible for both binding and cleavage of calcineurin. The knockdown of overexpressed DSCR1 in DS fibroblast cells also abrogated calcineurin proteolysis by hydrogen peroxide. These results suggest that DSCR1 has the ability to inactivate calcineurin by inducing proteolytic cleavage of calcineurin upon oxidative stress.     

Chemical genetic control of protein levels: selective in vivo targeted degradation

Genetic loss of function analysis is a powerful method for the study of protein function. However, some cell biological questions are difficult to address using traditional genetic strategies often due to the lack of appropriate genetic model systems. Here, we present a general strategy for the design and syntheses of molecules capable of inducing the degradation of selected proteins in vivo via the ubiquitin-proteasome pathway. Western blot and fluorometric analyses indicated the loss of two different targets: green fluorescent protein (GFP) fused with FK506 binding protein (FKBP12) and GFP fused with the androgen receptor (AR), after treatment with PROteolysis TArgeting Chimeric moleculeS (PROTACS) incorporating a FKBP12 ligand and dihydrotestosterone, respectively. These are the first in vivo examples of direct small molecule-induced recruitment of target proteins to the proteasome for degradation upon addition to cultured cells. Moreover, PROTAC-mediated protein degradation offers a general strategy to create "chemical knockouts," thus opening new possibilities for the control of protein function.     

Screening,isolation and selection of a potent lipase producing microorganism and its use in the kinetic resolution of drug intermediates

Lipases are ubiquitous enzymes that belong to family of serine hydolases with a wide variety of industrial applications. This study reports isolation, screening and identification of enantioselctive lipase producing microorganism for kinetic resolution of racemic alcohols. For this, we collected soil samples from different oil rich environments and we performed primary screening that was by carried out by using MSM-tributryin clear zone assay. The selected samples from first screen were subjected to secondary screening to distinguish lipase producing strains from esterase producing strains using p-nitrophenyl palmitate lipase assay. In tertiary screening, 16 lipase producing strains that were identified in secondary screening were employed for resolution of 5 different (RS)-alcohols. Out of all 16 lipase producing strains, only one strain selectively converted 3 racemic alcohols. Based on morphological, biochemical and physiological characteristics, and 16S rRNA gene sequencing, the strain was identified as Pseudomonas beteli. The strain was found to be S-selective and there been no reports on use of Pseudomonas beteli lipase for kinetic resolution of alcohols. The lipase activity was further increased by media optimization and by improving growth conditions, and production of lipase in shake flask study as well as in laboratory scale fermenter. The optimum time for enzyme production by Pseudomonas beteli was 96 ​h whereas cell mass growth was highest at 72 ​h. Optimum temperature and pH were 30 ​°C and 6, respectively. Beef extract (5 ​g/L), peptone (5 ​g/L), sodium chloride (5 ​g/L), yeast extract (1 ​g/L) and glucose (5 ​g/L) were found as optimum nutrition sources for the cell mass growth and lipase production by Pseudomonas sp. Overall, 3.4 times higher enzyme activity and 2.75 times higher cell mass growth were achieved in bioreactor in comparison to the shake flask study. Lipase having high titer was employed successfully for the kinetic resolution of several drug intermediates.     

Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides

The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for the sp(3) carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low-energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.     

Brasenia-inspired hydrogel with sustained and sequential release of BMP and WNT activators for improved bone regeneration

Although bone morphogenetic protein (BMP) and WNT signaling play pivotal roles in bone development, homeostasis, and regeneration, the applications of proteins to stimulate corresponding signaling pathways showed limited outcomes in the repair and regeneration of bone defects that might be attributed to the reciprocal interventions of these pathways. In order to satisfy the combinational and sequential activation of BMP and WNT pathways, inspired by the heterogeneous hydrogel-liked structures of Brasenia, heterogeneous alginate/chitosan hydrogels were fabricated and spatially loaded with FK506 and BIO to achieve sustained and sequential release of the activators. Alkaline phosphatase staining, alizarin red staining and qRT-PCR results suggested that FK506 and BIO enhanced osteoblastic differentiation in vitro when used separately. Besides, by mixing and matching the activators and the hydrogel layers, a superior releasing mode that a combination of early FK506 release and following BIO release was identified via both in vitro and in vivo explorations for most efficient bone regeneration. These results suggested that drug-loaded heterogeneous hydrogels possess great potentials in treating bone loss defects for future clinical practice.