Interaction of cyclophilin and cyclosporins monitored by affinity capillary electrophoresis.

The affinity capillary electrophoretic separation of the complex of the enzyme cyclophilin (Cyp) with the immunosuppressive drug cyclosporin A (CsA) from uncomplexed Cyp and CsA in phosphate buffer (pH 8) under non-denaturing conditions by equilibrium-mixture analysis is reported. Using a new approach combining mobility-shift analysis and electrophoretically mediated microanalysis the binding constant of rhCyp18 to CsA and derivatives was estimated.     

Potent HIV-1 protease inhibitors incorporating meso-bicyclic urethanes as P2-ligands: structure-based design, synthesis, biological evaluation and protein-ligand X-ray studies

Recently, we designed a series of novel HIV-1 protease inhibitors incorporating a stereochemically defined bicyclic fused cyclopentyl (Cp-THF) urethane as the high affinity P2-ligand. Inhibitor with this P2-ligand has shown very impressive potency against multi-drug-resistant clinical isolates. Based upon the -bound HIV-1 protease X-ray structure, we have now designed and synthesized a number of meso-bicyclic ligands which can conceivably interact similarly to the Cp-THF ligand. The design of meso-ligands is quite attractive as they do not contain any stereocenters. Inhibitors incorporating urethanes of bicyclic-1,3-dioxolane and bicyclic-1,4-dioxane have shown potent enzyme inhibitory and antiviral activities. Inhibitor (K(i) = 0.11 nM; IC(50) = 3.8 nM) displayed very potent antiviral activity in this series. While inhibitor showed comparable enzyme inhibitory activity (K(i) = 0.18 nM) its antiviral activity (IC(50) = 170 nM) was significantly weaker than inhibitor . Inhibitor maintained an antiviral potency against a series of multi-drug resistant clinical isolates comparable to amprenavir. A protein-ligand X-ray structure of -bound HIV-1 protease revealed a number of key hydrogen bonding interactions at the S2-subsite. We have created an active model of inhibitor based upon this X-ray structure.     

Solution structures of cyclosporin a and its complex with dysprosium(III) in SDS micelles: NMR and molecular dynamics studies

Cyclosporin A (CsA) is a cyclic naturally occurring peptide used to prevent graft rejection in organ transplantations. Its immunosuppressive activity is due to the formation of a complex with cyclophilin A (Cyp), in which the cis 9MeLeu-10MeLeu amide bond of CsA assumes a trans conformation. The mechanism of the conformational inversion has not been delineated, but it has been postulated that metal ions binding induces a conformational change that enables CsA to bind Cyp. In this work, we solved the structures of CsA in sodium dodecyl sulfate (SDS) micelles (which enhance its solubility and mimic the hydrophobic environment clinically used for drug delivery) and its complex with Dy(III) ion, whose coordination chemistry is frequently used to reproduce the effect of Ca(II). The paramagnetic properties of Dy(III) allowed us to build up a structure using proton relaxation enhancements, which remains stable in a MD simulation in the micelle environment.     

Application of a green fluorescent fusion protein to study protein-protein interactions by electrophoretic methods

A screening procedure for protein-protein interactions in cellular extracts using a green fluorescent protein (GFP) and affinity capillary electrophoresis (ACE) was established. GFP was fused as a fluorescent indicator to the C-terminus of a cyclophilin (rDmCyp20) from Drosophila melanogaster. Cyclophilins (Cyps) belong to the ubiquitously distributed enzyme family of peptidyl-prolyl cis/trans isomerases (PPlases) and are well known as cellular targets of the immunosuppressive drug cyclosporin A (CsA). The PPlase activity of the GFP fused rDmCyp20 as well as the high affinity to CsA remain intact. Using native gel electrophoresis and ACE mobility-shift assays, it was demonstrated that the known moderate affinity of Cyp20 to the capsid protein p24 of HIV-1 was detectable in the case of rDmCyp20 fused to the fluorescent tag. For the p24 / rDmCyp20-GFP binding an ACE method was established which allowed to determine a dissociation constant of Kd = 20+/-1.5 x 10(-6) M. This result was verified by size-exclusion chromatography and is in good agreement with published data for the nonfused protein. Moreover the fusion protein was utilized to screen rDmCyp20-protein interactions by capillary electrophoresis in biological matrices. A putative ligand of rDmCyp20 in crude extracts of embryonic D. melanogaster was discovered by mobility-shift assays using native gel electrophoresis with fluorescence imaging and ACE with laser-induced fluorescence detection. The approach seems applicable to a wide range of proteins and offers new opportunities to screen for moderate protein-protein interactions in biological samples.     

Formation and Loading of a (2S)-2-Ethylmalonamyl Starter Unit in the Assembly Line of Polyketide-Nonribosomal Peptide Hybrid Sanglifehrin A

Sanglifehrin A (SFA) is a spirolactam-conjugated, 22-membered macrolide with remarkable immunosuppressive and antiviral activities. This macrolide is a result of a hybrid polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) assembly line that utilizes (2S)-2-ethylmalonamyl as a starter unit. Here, we report that the formation and loading of this starter unit in the SFA assembly line involve two unusual enzymatic reactions that occur on a discrete acyl carrier protein (ACP), SfaO. An amide synthetase, SfaP, catalyzes the amidation of (2S)-2-ethylmalonyl in a SfaO-dependent manner. Then, a β-ketoacyl-ACP synthase III-like protein, SfaN, transfers resultant (2S)-2-ethylmalonamyl from SfaO onto the loading ACP domain of the hybrid PKS-NRPS assembly line to prime SFA biosynthesis. Both SfaP and SfaN display promiscuous activities. This study furthers the appreciation of assembly line chemistry, as a new paradigm for unusual building block formation and incorporation is provided.     

Thermodynamics of buried water clusters at a protein-ligand binding interface

The structure of the complex of cyclophilin A (CypA) with cyclosporin A (CsA, 1) shows a cluster of four water molecules buried at the binding interface, which is rearranged when CsA is replaced by (5-hydroxynorvaline)-2-cyclosporin (2). The thermodynamic contributions of each bound water molecule in the two complexes are explored with the inhomogeneous fluid solvation theory and molecular dynamics simulations. Water (WTR) 133 in complex 1 contributes little to the binding affinity, while WTR6 and 7 in complex 2 play an essential role in mediating protein-ligand binding with a hydrogen bond network. The calculations reveal that the rearrangement of the water molecules contributes favorably to the binding affinity, even though one of them is displaced going from ligand 1 to 2. Another favorable contribution comes from the larger protein-ligand interactions of ligand 2. However, these favorable contributions are not sufficient to overcome the unfavorable desolvation free energy change and the conformational entropy of the hydroxylpropyl group of ligand 2 in the complex, leading to a lower binding affinity of ligand 2. These physical insights may be useful in the development of improved scoring functions for binding affinity prediction.     

Crystal structure of (5,14-methyl-7,12-dimethyl-1,4,8,11-tetraazadiiminecyclotetradecylene-N,N',N',N')nickel(II) bis(diisopropyldithiophosphate) complex.

The macrocyclic tetradentate Ni(II) compound was obtained in a reaction and determined by X-ray diffraction. The crystal structure shows that the molecule is centrosymmetric, and Ni atom located in a square planar coordination environment. The two [(iPrO)2PS2]- anions are outside the macrocycle complex to balance. The Ni-N bond lengths are in the range of 1.906(2) to 1.950(2)A.     

Crystal structure of (1,10-phenanthroline-N,N')(1,4,7,10-tetraazacyclododecane-N,N',N",N"')nickel(II) diperchlorate.

The crystal structure of the title compound, [Ni(C8H20N4)(C12H8N2)](ClO4)2, has been determined by X-ray diffraction. The Ni(II) ion is six coordinated with four nitrogen atoms of the tetradentate macrocyclic ligand and two nitrogen atoms of the bidentate ligand in a distorted octahedron geometry. The folded tetradentate macrocyclic ligand adopts a configuration having four five-membered chelate rings in distorted eclipsed conformations. The four hydrogen atoms of the amine groups of the macrocyclic ligand are on the same side towards the bidentate ligand.     

Palmerolide A, a cytotoxic macrolide from the antarctic tunicate Synoicum adareanum

Palmerolide A, a 20-membered macrocyclic polyketide bearing carbamate and vinyl amide functionality, was isolated from the tunicate Synoicum adareanum collected from the vicinity of Palmer Station on the Antarctic Peninsula. Palmerolide A displays potent and selective cytotoxicity toward melanoma (UACC-66 LC50 = 0.018 muM) and appears to operate via inhibition (IC50 = 2 nM) of V-ATPase.     

含噁二唑大环冠醚的合成、 结构及金属离子识别性能

合成了含有1,3,4-噁二唑基团的大环冠醚: 2,3,11,12-二苯并-4,7,10,16-四氧-14,15-二氮杂双环[11.2.1]-十六烷-13,15-二烯(2)、 2,3,14,15-二苯并-4,7,10,13,19-五氧-17,18-二氮杂双环[14.2.1]-十九烷-16,18-二烯(3)和2,3,17,18-二苯并-4,7,10,13,16,22-六氧-20,21-二氮杂双环[17.2.1]-二十二烷-19,21-二烯(4), 并培养得到其单晶; 通过核磁共振波谱、 高分辨质谱及X射线单晶衍射对其结构进行了表征. 结果表明, 冠醚2属正交晶系, Pna2₁空间群; 冠醚3属于单斜晶系, C2/c空间群; 冠醚4属正交晶系, Pbca空间群. 在3个主体化合物中均存在分子间氢键和π-π相互作用将分子连接成三维空间结构. 采用荧光光谱测定了开链冠醚2,5-二[2-(2-甲氧乙氧基)苯基]-1,3,4-噁二唑(1)和不同环空腔大小的噁二唑冠醚(2~4)对金属离子Li ⁺, Na ⁺, K ⁺, Rb ⁺, Mg ²⁺和Ca ²⁺的键合行为. 研究结果表明, 开链冠醚1和冠醚4对碱土金属Mg ²⁺和Ca ²⁺表现出荧光猝灭行为, 且对Ca ²⁺表现出良好的键合能力和选择性; 而冠醚2对Na ⁺和K ⁺表现出良好的键合能力, 但其Na ⁺/K ⁺的选择性较差.     

Synthesis and Crystal Structure of a Novel (2:2) Macrocyclic Thiocarbohydrazone

Thiocarbohydrazoneshavebeentestedasantindcrobialandantitumouragentsandwidelyusedinanalyticalchemistry'-'.Ontheotherhand,thechemistryofmacrocycliccompoundshasattTactedcontinuousinterestformanyyears.Thiocarbohydrazide,HZN'N'HC(S)NHN'Hz,anditsSchiffbasecomplexesconstitUteintersstingligandsystemsbecauseoftheavailbilityofseveralpotentialdonorsites,inwhichthioketo-thioenoltautomerismispossible.Significantly,theyareabletoformbothmono-andbinuclearcomplexesbydifferentmethods3-6.Withtheaimofdesign…     

大环多胺配体BDBPH的设计合成及其晶体结构

用Pb(SN)₂作模板,2,6-二甲酰基对甲苯酚与二亚乙基三胺通过[2+2]缩合反应,经NaBH₄还原、脱Pb²⁺、酸化等操作,得晶体BDBPH·6HBr·4H₂O.晶体属单斜晶系,P2_1/c空间群,晶体学参数:a=1.4441(5)nm,b=1.1482(4)nm,c=1.2090(6)nm,α=90°,β=96.92°,γ=90°,V=1.9900nm³大环分子采取椅式构型,6个Br-和4个H₂O分子对称分布于大环两侧.该大环配体结构新颖,可用于多种金属配合物的研究,对进一步了解金属酶活性中心的结构及其催化作用机理具有重要价值.     

Potent "clicked" MMP2 inhibitors: synthesis, molecular modeling and biological exploration

A new series of MMP2 inhibitors is described, following a fragment-based drug design approach. One fragment containing an azide group and a well known hydroxamate Zinc Binding Group in a α-sulfone, α-tetrahydropyrane scaffold, has been synthesized. Water-LOGSY, STD and competition-STD experiments indicate that this fragment binds to the active site of the enzyme. A click chemistry reaction was used to connect the azide to lipophilic alkynes selected to interact selectively with the S1' subunit of MMP2, as shown by docking and molecular dynamic experiments of the designed compounds. The most potent compounds 18 and 19 displayed an IC(50) of 1.4 and 0.3 nM against MMP2 respectively, and showed negligible activity towards MMP1 and MMP7, two metalloproteinases which have a shallow S1' subsite. Compound 18 also showed a promising selectivity profile against some antitarget metalloproteinases, such as MMP8, and considerably less activity against MMP14 (IC(50) = 65 nM), and MMP9 (IC(50) = 98 nM), other MMPs characterized by having a deep S1' pocket and, therefore, more similar to MMP2.     

Neomycin-capped aromatic platforms: quadruplex DNA recognition and telomerase inhibition

A series of aminoglycoside-capped macrocyclic structures has been prepared using intramolecular bis-tethering of neomycin on three aromatic platforms (phenanthroline, acridine, quinacridine). Based on NMR and calculations studies, it was found that the cyclic compounds adopt a highly flexible structure without conformational restriction of the aminoglycoside moiety. FRET-melting stabilization measurements showed that the series displays moderate to high affinity for the G4-conformation of human telomeric repeats, this effect being correlated with the size of the aromatic moiety. In addition, a FRET competition assay evidenced the poor binding ability of all macrocycles for duplex DNA and a clear binding preference for loop-containing intramolecular G4 structures compared to tetramolecular parallel G4 DNA. Finally, TRAP experiments demonstrated that the best G4-binder (quinacridine ) is also a potent and selective telomerase inhibitor with an IC(50) in the submicromolar range (200 nM).     

Bisubstrate inhibitors for the enzyme catechol-O-methyltransferase (COMT): influence of inhibitor preorganisation and linker length between the two substrate moieties on binding affinity

Inhibition of the enzyme catechol-O-methyltransferase (COMT) is an important approach in the treatment of Parkinson's disease. A series of new potent bisubstrate inhibitors for COMT, resulting from X-ray structure-based design and featuring adenosine and catechol moieties have been synthesised. Biological results show a large dependence of binding affinity on inhibitor preorganisation and the length of the linker between nucleoside and catechol moieties. The most potent bisubstrate inhibitor for COMT has an IC50 value of 9 nM. It exhibits competitive kinetics for the SAM and mixed inhibition kinetics for the catechol binding site. Its bisubstrate binding mode was confirmed by X-ray structure analysis of the ternary complex formed by the inhibitor, COMT and a Mg2+ ion.     

Total Synthesis and Stereochemical Revision of Iriomoteolide‐2a

Total syntheses of the proposed and correct structures of iriomoteolide‐2a, a cytotoxic marine macrolide natural product with an unusual 23‐membered macrolactone skeleton, have been accomplished for the first time. The synthesis of the correct structure involves an asymmetric epoxidation/diepoxide cyclization cascade for the construction of the bis(tetrahydrofuran) moiety, a Suzuki–Miyaura coupling for the fragment assembly, and a ring‐closing metathesis for the closure of the macrocyclic backbone. In addition, the original stereochemical assignment of iriomoteolide‐2a was revised.     

Synthesis of the macrocyclic core of leiodermatolide

The macrocyclic core (2) of the marine macrolide leiodermatolide (1) has been synthesized in 19 steps through a convergent strategy exploiting boron aldol methodology to install the requisite stereochemistry and a selective Stille coupling reaction for controlled fragment assembly, followed by a Yamaguchi macrolactonization and carbamate introduction at the C9-OH.     

Macrolide Analogues of the Novel Immunosuppressant Sanglifehrin: New Application of the Ring-Closing Metathesis Reaction

Macrocycles containing a conjugated 1,3-diene moiety have been synthesized for the first time in good yields by the ring-closing metathesis reaction [Eq. (1)]. The new compounds represent cyclophilin-binding, simplified analogues of the macrocyclic core of sanglifehrin A, an immunosuppressant which binds with high affinity to cyclophilin.     

Is there a scaffolding domain within the structure of the immunosuppressive agent cyclosporin a (CsA)? Studies of the cyclophilin binding domain of CsA

The synthesis of a peptide that approximates the critical binding/immunosuppressive domain within CsA but which is lacking any form of molecular scaffolding is described. The analysis of the conformation and cyclophilin binding properties of this synthetic analogue provides further evidence for the existence of a scaffolding domain within the natural product.     

Surrogate AutoShim: predocking into a universal ensemble kinase receptor for three dimensional activity prediction, very quickly, without a crystal structure

"Ensemble surrogate AutoShim" is a kinase specific extension of the AutoShim docking method that solves the three traditional limitations of conventional docking: (1) it gives good correlations with affinity, (2) does not require a target protein structure, and (3) for a preprocessed company archive of 1.5 million compounds, is as fast as traditional 2D QSAR. It does require several hundred experimental IC 50 values for each new target. Original AutoShim adds pharmacophore "shims" to a crystal structure binding site. An iterative partial least squares (PLS) procedure selects the best pose, while adjusting the shim weights to reproduce IC 50 data. Surrogate AutoShim adjusts shims in one crystal structure to reproduce IC 50 data for a different kinase target. Ensemble surrogate AutoShim uses 16 structurally diverse kinase crystal structures as a "universal ensemble kinase receptor", suitable for any kinase target. The 1.5 million member Novartis screening collection has been predocked into the shimmed ensemble, so new kinase models can be built, and the entire corporate archive virtually screened, in hours rather than weeks. A kinase-biased set of 10,000 compounds, that samples the entire corporate archive, has been designed for lead discovery by iterative kinase screening.