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1.
The design of novel organic compounds containing no strongly basic amidine or guanidine functional groups typical of serine protease inhibitors was performed to develop an oral anticoagulant drug. A three-dimensional computational model for thrombin active site was constructed and optimized for docking of small-molecule organic compounds and calculating the energies of inhibitor-enzyme interactions. Novel racemic derivatives of 1-[2-(4-chlorophenylthio)acetyl]-5-phenylpyrrolidine-2,4-dicarboxylic acids were synthesized for which Cl-π interactions between the inhibitors and the S1 pocket of thrombin active site are predicted by modeling. The compounds synthesized deactivate thrombin in vitro and the inhibition properties show good correlations with the results of calculations.  相似文献   

2.
Structure‐activity relationships for new members of a class of nonpeptidic, low‐molecular‐weight inhibitors of thrombin, a key serine protease in the blood coagulation cascade, are described. These compounds, which originate from X‐ray‐structure‐based design, feature a conformationally rigid, bi‐ or tricyclic core from which side chains diverge into the four major binding pockets (distal D, proximal P, recognition or specificity S1, and oxyanion hole O) at the thrombin active site (Fig. 1). Phenylamidinium is the side chain of choice for the S1 pocket, while the most active inhibitors orient an i‐Pr group into the P‐pocket (Table 1). The key step in the synthesis of the inhibitors is the construction of the central bi‐ or tricyclic scaffold by 1,3‐dipolar cycloaddition of an in situ prepared azomethine ylide and an N‐substituted maleimide (Schemes 1–3, and 8–10). One series of compounds was designed to explore the binding features of the large hydrophobic D pocket. This pocket provides space for lipophilic residues as bulky as benzhydryl groups. A new strategy was developed, allowing introduction of these sterically demanding substituents very late in the synthesis (Schemes 5 and 6). Benzhydryl derivative (±)‐ 2 was found to be the most selective member (Ki (trypsin)/Ki (thrombin)=1200) of this class of nonpeptidic thrombin inhibitors, while the ‘dipiperonyl' analog (±)‐ 3 (Ki=9 nM , 7.60‐fold selectivity) displays the highest potency of all compounds prepared so far (Table 1). A second series of inhibitors features side chains designed to orient into the oxyanion hole and to undergo H‐bonding with the backbone NH groups lining the catalytic site of the enzyme. Unfortunately, neither activity nor selectivity could be substantially improved by introduction of these substituents (Table 2). Presumably, the high degree of pre‐organization and the rigidity of the tightly bound scaffolds prevents the new substituents from assuming a position that would allow favorable interactions in the oxyanion hole. However, the oxyanion hole and the S1′ pocket next to it were found to be capable of accommodating quite large groups, which leaves much room for further exploration.  相似文献   

3.
A novel class of nonpeptidic, active, and selective thrombin inhibitors has resulted from X‐ray‐structure‐based design and subsequent improvement of the initial lead molecules. These inhibitors possess a bi‐ or tricyclic central core structure with attached side chains to reach the three binding pockets (selectivity S1 pocket, distal D pocket, and proximal P pocket) present in the active site of the enzyme. The key step in the preparation of these compounds is the 1,3‐dipolar cycloaddition between an azomethine ylide, prepared in situ by the decarboxylative method from an aromatic aldehyde and an α‐amino acid, with an N‐substituted maleimide (e.g., see Schemes 1 and 2). All potent inhibitors contain an amidinium residue in the side chain for incorporation into the S1 pocket, which was introduced in the last step of the synthesis by a Pinner reaction. The compounds were tested in biological assays for activity against thrombin and the related serine protease trypsin. The first‐generation lead compounds (±)‐ 11 and (±)‐ 19 (Scheme 1) with a bicyclic central scaffold showed Ki values for thrombin inhibition of 18 μM and 0.67 μM , respectively. Conformationally more restricted second‐generation analogs (Scheme 2) were more active ((±)‐ 22i : Ki=90 nM (Table 1)); yet the selectivity for thrombin over trypsin remained weak. In the third‐generation compounds, a small lipophilic side chain for incorporation into the hydrophobic P pocket was introduced (Schemes 7 and 8). Since this pocket is present in thrombin but not in trypsin, an increase in binding affinity was accompanied by an increase in selectivity for thrombin over trypsin. The most selective inhibitor (Ki=13 nM , 760‐fold selectivity for thrombin over trypsin; Table 2) was (±)‐ 1 with an i‐Pr group for incorporation into the P pocket. Optical resolution of (±)‐ 1 (Scheme 9) provided (+)‐ 1 with a Ki value of 7 nM and a 740‐fold selectivity, whereas (−)‐ 1 was 800‐fold less active (Ki=5.6 μM , 21‐fold selectivity). The absolute configuration of the stronger‐binding enantiomer was assigned based on the X‐ray crystal structure of the complex formed between thrombin and this inhibitor. Compound (+)‐ 1 mimics the natural thrombin substrate, fibrinogen, which binds to the enzyme with the Ph group of a phenylalanine (piperonyl in (+)‐ 1 ) in the distal D pocket, with the i‐Pr group of a valine (i‐Pr in (+)‐ 1 ) in the proximal P pocket, and with a guanidinium side chain of an arginine residue (phenylamidinium group in (+)‐ 1 ) in the selectivity S1 pocket of thrombin. A series of analogs of (±)‐ 1 with the phenylamidinium group replaced by aromatic and aliphatic rings bearing OH or NH2 groups (Schemes 10 – 14) were not effectively bound by thrombin. A number of X‐ray crystal‐structure analyses of free inhibitors confirmed the high degree of preorganization of these compounds in the unbound state. Since all inhibitors prefer similar modes of association with thrombin, detailed information on the strength of individual intermolecular bonding interactions and their incremental contribution to the overall free energy of complexation was generated in correlative binding and X‐ray studies. The present study demonstrates that defined mutations in highly preorganized inhibitors provide an attractive alternative to site‐directed mutagenesis in exploring molecular‐recognition phenomena at enzyme active sites.  相似文献   

4.
BACKGROUND: The 20S proteasome is a multicatalytic protease complex that exhibits trypsin-like, chymotrypsin-like and post-glutamyl-peptide hydrolytic activities associated with the active sites of the beta2, beta5 and beta1 subunits, respectively. Modulation of these activities using inhibitors is essential for a better understanding of the proteasome's mechanism of action. Although there are highly selective inhibitors of the proteasome's chymotryptic activity, inhibitors of similar specificity have not yet been identified for the other activities. RESULTS: The X-ray structure of the yeast proteasome reveals that the sidechain of Cys118 of the beta3 subunit protrudes into the S3 subsite of the beta2 active site. The location of this residue was exploited for the rational design of bidentated inhibitors containing a maleinimide moiety at the P3 position for covalent linkage to the thiol group and a carboxy-terminal aldehyde group for hemiacetal formation with the Thr1 hydroxyl group of the active site. Structure-based modelling was used to determine the optimal spacing of the maleinimide group from the P2-P1 dipeptide aldehydes and the specificity of the S1 subsite was exploited to limit the inhibitory activity to the beta2 active site. X-ray crystallographic analysis of a yeast proteasome-inhibitor adduct confirmed the expected irreversible binding of the inhibitor to the P3 subsite. CONCLUSIONS: Maleoyl-beta-alanyl-valyl-arginal is a new type of inhibitor that is highly selective for the trypsin-like activity of eukaryotic proteasomes. Despite the reactivity of the maleinimide group towards thiols, and therefore the limited use of this inhibitor for in vitro studies, it might represent an interesting new biochemical tool.  相似文献   

5.
The regiochemistry of nucleophilic substitution of 4-phenylsulfonyl tetrafluoropyridine with unequal bidentate nucleophiles was investigated. The first nucleophilic substitution occurs at the 2-position of the pyridine ring by nitrogen nucleophile site (secondary or primary amine) followed by intermolecular ring closure at the geometrically accessible 3-position of the pyridine ring (by S, O and N nucleophiles). From this investigation, difluorinated tetrahydropyrido[3,4-b][1,4]oxazine, thiazine and pyrazine scaffolds were synthesized very readily by a one-pot annelation reaction of 4-phenylsulfonyl tetrafluoropyridine with appropriate unequal bidentate nucleophiles.  相似文献   

6.
A new series of 4‐hetroaryl substituted quinazolines were designed and synthesized by the reaction of pentafluoro(chloro)pyridine and 2‐substituted quinazolinone. The aromatic nucleophilic substitution of pentafluoro(chloro)pyridine with quinazolinone occurs at the 4‐position of pyridine ring by the oxygen site (O‐centered nucleophile) of quinazolinone. The structures of all the compounds were confirmed by IR, 1H NMR, 19F NMR, and 13C NMR spectroscopy as well as elemental analysis.  相似文献   

7.
[structure: see text] A series of squaric acid-peptide conjugates were synthesized and evaluated as inhibitors of MMP-1. The cyclobut-3-enedione core was substituted at the 3-position with several functional groups, such as -N(alkyl)OH, -NHOH, and -OH, that are designed to bind to the zinc atom in the active site of the metalloprotease. The 4-position of the cyclobut-3-enedione was derivatized with mono- or dipeptides that are designed to bind in the S1' and S2' subsites of the enzyme, and position the metal chelating group appropriately in the active site for binding to zinc. Positional scanning revealed that -N(Me)OH provided the highest level of inhibition among the chelating groups that were tested, and Leu-Tle-NHMe was the preferred amino acid sequence. A combination of these groups yielded an inhibitor with an IC50 value of 95 microM. For one inhibitor, conversion of one of the carbonyl groups on the cyclobut-3-enedione core to a thiocarbonyl group resulted in a 18-fold increase in potency, and yielded a compound with an IC50 value of 15 microM.  相似文献   

8.
A series of carboxylate-substituted trinudear molybdenum dus-ter compounds formulated as Mo3S4(DTP)3(RCO2)(L), where RffiH, CH3, C2H5, CH2Cl, CCl3, R^1C6H4(R^1 is the group on the benzene ring of aromatic carboxylate ), L=pyridine,CH3CN, DMF, have been synthesized by the ligand substitu-tion reaction. The dissociation of the loosely-coordinated ligand L from the cluster core was studied by ^31p NMR. The dissocia-tion process of L is related to the solvent, temperature, and acidity of carboxylate groups, so as to affect the solution struc-ture and reactive properties of the duster. The long-distance in-teraction between ligands RCO2 and L is transported by Mo3S4 core.  相似文献   

9.
The current study deciphers the combined ligand- and structure-based computational insights to profile structural determinants for the selectivity of representative diverse classes of FXa-selective and thrombin-selective as well as dual FXa-thrombin high affinity inhibitors. The thrombin-exclusive insertion 60-loop (D-pocket) was observed to be one of the most notable recognition sites for the known thrombin-selective inhibitors. Based on the topological comparison of four common active-site pockets (S1-S4) of FXa and thrombin, the greater structural disparity was observed in the S4-pocket, which was more symmetrical (U-shaped) in FXa as compared to thrombin mainly due to the presence of L99 and I174 residues in latter in place of Y99 and F174 respectively in former protease. The S2 pocket forming partial roof at the entry of 12 ? deep S1-pocket, with two extended β-sheets running antiparallel to each other by undergoing U-turn (~180?), has two conserved glycine residues forming H-bonds with the bound ligand for governing ligand binding affinity. The docking, scoring, and binding pose comparison of the representative high-affinity and selective inhibitors into the active sites of FXa and thrombin revealed critical residues (S214, Y99, W60D) mediating selectivity through direct- and long-range electrostatic interactions. Interestingly, most of the thrombin-selective inhibitors attained S-shaped conformation in thrombin, while FXa-selective inhibitors attained L-shaped conformations in FXa. The role of residue at 99th position of FXa and thrombin toward governing protease selectivity was further substantiated using molecular dynamics simulations on the wild-type and mutated Y99L FXa bound to thrombin-selective inhibitor 2. Furthermore, predictive CoMFA (FXa q2 = 0.814; thrombin q2 = 0.667) and CoMSIA (FXa q2 = 0.807; thrombin q2 = 0.624) models were developed and validated (FXa r2(test) = 0.823; thrombin r(2)(test) = 0.816) to feature molecular determinants of ligand binding affinity using the docking-based conformational alignments (DBCA) of 141 (88(train)+53(test)) and 39 (27(train)+11(test)) nonamidine class of potent FXa (0.004 ≤ K(i) (nM) ≤ 4700) and thrombin (0.001 ≤ K(i) (nM) ≤ 940) inhibitors, respectively. Interestingly, the ligand-based insights well corroborated with the structure-based insights in terms of the role of steric, electrostatic, and hydrophobic parameters for governing the selectivity for the two proteases. The new computational insights presented in this study are expected to be valuable for understanding and designing potent and selective antithrombotic agents.  相似文献   

10.
M. Mallet  G. Quéguiner 《Tetrahedron》1979,35(13):1625-1631
The reaction of n-butyllithium with 2-bromo-3-chloro pyridine as a function of temperature, the amount of n-butyllithium used and the order of introduction of the reagents, gives, besides bromine-lithium exchange, an unexpected métallation of the pyridine ring and bromine migration from the 3 to 4 position. A novel mechanism to explain this and the similar behavior of 3-bromo-2-fluoro pyridine with n-butyllithium is proposed.  相似文献   

11.
Functionality map analysis of the active site cleft of human thrombin   总被引:1,自引:0,他引:1  
Summary The Multiple Copy Simultaneous Search methodology has been used to construct functionality maps for an extended region of human thrombin, including the active site. This method allows the determination of energetically favorable positions and orientations for functional groups defined by the user on the three-dimensional surface of a protein. The positions of 10 functional group sites are compared with those of corresponding groups of four thrombin-inhibitor complexes. Many, but not all features, of known thrombin inhibitors are reproduced by the method. The results indicate that certain aspects of the binding modes of these inhibitors are not optimal. In addition, suggestions are made for improving binding by interaction with functional group sites on the thrombin surface that are not used by the thrombin inhibitors. Abbreviations: MCSS, multiple copy simultaneous search; PPACK, d-phenylalanyl-l-propyl-l-arginine chloromethane; NAPAP, N -(2-naphthylsulfonylglycyl)-d-para-amidinophenylalanylpiperidine; argatroban, (2R,4R)-4-methyl-1-[N -(3-methyl-1,2,3,4-tetrahydro-8-quinolinylsulfonyl)-l-arginyl]-2-piperidine carboxylic acid; rms, root mean square. The thrombin residues are numbered according to the chymotrypsin-based numbering by Bode et al. [8]. P1, P2, P3, etc., denote the peptide inhibitor residues on the amino-terminal side of the scissile peptide bond, and S1, S2, S3, etc., the corresponding subsites of thrombin  相似文献   

12.
A series of 2-, 3- and 4-substituted pyridines was metabolised using the mutant soil bacterium Pseudomonas putida UV4 which contains a toluene dioxygenase (TDO) enzyme. The regioselectivity of the biotransformation in each case was determined by the position of the substituent. 4-Alkylpyridines were hydroxylated exclusively on the ring to give the corresponding 4-substituted 3-hydroxypyridines, while 3-alkylpyridines were hydroxylated stereoselectively on C-1 of the alkyl group with no evidence of ring hydroxylation. 2-Alkylpyridines gave both ring and side-chain hydroxylation products. Choro- and bromo-substituted pyridines, and pyridine itself, while being poor substrates for P. putida UV4, were converted to some extent to the corresponding 3-hydroxypyridines. These unoptimised biotransformations are rare examples of the direct enzyme-catalysed oxidation of pyridine rings and provide a novel synthetic method for the preparation of substituted pyridinols. Evidence for the involvement of the same TDO enzyme in both ring and side-chain hydroxylation pathways was obtained using a recombinant strain of Escherichia coli (pKST11) containing a cloned gene for TDO. The observed stereoselectivity of the side-chain hydroxylation process in P. putida UV4 was complicated by the action of an alcohol dehydrogenase enzyme in the organism which slowly leads to epimerisation of the initial (R)-alcohol bioproducts by dehydrogenation to the corresponding ketones followed by stereoselective reduction to the (S)-alcohols.  相似文献   

13.
Two pyridine-modified NAD'analogs, 3–(3-azido benzo-yl) pyridine adenine dinucleotide 1 and N -(3-azido-5-car-boxyl) phenyl nicotinamide adenine dinucleotide 2 have been prepared and evaluated for photoaffinity labeling experiments. The syntheses were accomplished via a mammalian NADase-catalyzed base exchange reaction. The new NAD+ analogs retained the carbonyl or carhox-amido functional group at the 3 position of the pyridine ring. The analog 1 is the first pyridine-modified azido derivative of NAD+ that has shown coenzyme activity in a stereospecific hydride transfer reaction catalyzed by a dehydrogenase. Both NAD+ analogs have shown potential for the study of active sites of NAD+-utilizing enzymes.  相似文献   

14.
BACKGROUND: Urokinase-type plasminogen activator (uPA) is a protease associated with tumor metastasis and invasion. Inhibitors of uPA may have potential as drugs for prostate, breast and other cancers. Therapeutically useful inhibitors must be selective for uPA and not appreciably inhibit the related, and structurally and functionally similar enzyme, tissue-type plasminogen activator (tPA), involved in the vital blood-clotting cascade. RESULTS: We produced mutagenically deglycosylated low molecular weight uPA and determined the crystal structure of its complex with 4-iodobenzo[b]thiophene 2-carboxamidine (K(i) = 0.21 +/- 0.02 microM). To probe the structural determinants of the affinity and selectivity of this inhibitor for uPA we also determined the structures of its trypsin and thrombin complexes, of apo-trypsin, apo-thrombin and apo-factor Xa, and of uPA, trypsin and thrombin bound by compounds that are less effective uPA inhibitors, benzo[b]thiophene-2-carboxamidine, thieno[2,3-b]-pyridine-2-carboxamidine and benzamidine. The K(i) values of each inhibitor toward uPA, tPA, trypsin, tryptase, thrombin and factor Xa were determined and compared. One selectivity determinant of the benzo[b]thiophene-2-carboxamidines for uPA involves a hydrogen bond at the S1 site to Ogamma(Ser190) that is absent in the Ala190 proteases, tPA, thrombin and factor Xa. Other subtle differences in the architecture of the S1 site also influence inhibitor affinity and enzyme-bound structure. CONCLUSIONS: Subtle structural differences in the S1 site of uPA compared with that of related proteases, which result in part from the presence of a serine residue at position 190, account for the selectivity of small thiophene-2-carboxamidines for uPA, and afford a framework for structure-based design of small, potent, selective uPA inhibitors.  相似文献   

15.
A series of ten glycosyltransferase inhibitors has been designed and synthesized by using pyridine as a pyrophosphate surrogate. The series was prepared by conjugation of carbohydrate, pyridine, and nucleoside building blocks by using a combination of glycosylation, the Staudinger–Vilarrasa amide‐bond formation, and azide–alkyne click chemistry. The compounds were evaluated as inhibitors of five metal‐dependent galactosyltransferases. Crystallographic analyses of three inhibitors complexed in the active site of one of the enzymes confirmed that the pyridine moiety chelates the Mn2+ ion causing a slight displacement (2 Å) from its original position. The carbohydrate head group occupies a different position than in the natural uridine diphosphate (UDP)–Gal substrate with little interaction with the enzyme.  相似文献   

16.
3,3'-Bis(pyridin-[n]-ylethynyl)biphenyl (n = 3, 4) and the corresponding 2,2'-bipyridines assemble with (dppp)Pt(II) triflate into metallo-supramolecular polygons. Depending on the position of the terminal pyridine N atoms, the assembly reaction leads to different equilibrium products. With the slow ligand exchange on Pt(II) complexes, the equilibrium is reached on a many-hour time-scale. During the assembly process, larger polygons form under kinetic control. This was confirmed by time-dependent (1)H and (31)P NMR spectroscopy in line with complementary ESI mass spectrometric experiments. The constitutional difference in the pyridine N-atom position is reflected in the tandem mass spectra of the complex ions. In addition, a highly specific fragmentation process of mass-selected M(3)L(3) ions was observed, which proceeds through a ring contraction yielding smaller M(2)L(2) ions.  相似文献   

17.
A series of novel C2‐symmetric chiral pyridine β‐amino alcohol ligands have been synthesized from 2,6‐pyridine dicarboxaldehyde, m‐phthalaldehyde and chiral β‐amino alcohols through a two‐step reaction. All their structures were characterized by 1H NMR, 13C NMR and IR. Their enantioselective induction behaviors were examined under different conditions such as the structure of the ligands, reaction temperature, solvent, reaction time and catalytic amount. The results show that the corresponding chiral secondary alcohols can be obtained with high yields and moderate to good enantiomeric excess. The best result, up to 89% ee, was obtained when the ligand 3c (2S,2′R)‐2,2′‐((pyridine‐2,6‐diylbis(methylene))bisazanediyl))bis(4‐methyl‐1,1‐diphenylpentan‐1‐ol) was used in toluene at room temperature. The ligand 3g (2S,2′R)‐2,2′‐((1,3‐phenylenebis(methylene))bis(azanediyl))bis(4‐methyl‐1,1‐diphenylpentan‐1‐ol) was prepared in which the pyridine ring was replaced by the benzene ring compared to 3c in order to illustrate the unique role of the N atom in the pyridine ring in the inductive reaction. The results indicate that the coordination of the N atom of the pyridine ring is essential in the asymmetric induction reaction. Copyright © 2014 John Wiley & Sons, Ltd.  相似文献   

18.
A series of 1,3,5-trisubstituted 1,2,4-triazoles was designed and synthesized as potential inhibitors of steroidogenic CYP enzymes. The 1,2,4-triazole is part of the core structure fixing the geometry of the substances. A pyridine moiety was introduced as heme-binder. The target compounds were synthesized in two to four steps using silver carbonate mediated ring closure and Suzuki cross coupling reaction as key synthetic transformations. Biological testing of the synthesized compounds for the inhibition of the most important steroidogenic CYPs revealed compounds 29a and 30 as moderate inhibitors of aldosterone synthase (CYP11B2).  相似文献   

19.
In order to develop orally active CCR5 antagonists, we investigated 1-benzoxepine derivatives containing new polar substituents, such as phosphonate, phosphine oxide or pyridine N-oxide moieties, as replacements for the previously reported quaternary ammonium moiety. Among these compounds, the 2-(alpha-hydroxybenzyl)pyridine N-oxide 5e exhibited moderate CCR5 antagonistic activity and had an acceptable pharmacokinetic profile in rats. Subsequent chemical modification was performed and compound (S)-5f possessing the (S)-configuration hydroxy group was found to be more active than the (R)-isomer. Replacement of the 1-benzoxepine ring with a 4-methylphenyl group by a 1-benzazepine ring with a 4-[2-(butoxy)ethoxy]phenyl group enhanced the activity in the binding assay. In addition, introduction of a 3-trifluoromethyl group on the phenyl group of the anilide moiety led to greatly increased activity in the HIV-1 envelope-mediated membrane fusion assay. In particular, compound (S)-5s showed the most potent CCR5 antagonistic activity (IC(50)=7.2 nM) and inhibitory effect (IC(50)=5.4 nM) in the fusion assay, together with good pharmacokinetic properties in rats.  相似文献   

20.
Regioselective reaction of 2-bromomethyl-1,3-thiaselenole with pyridine and its derivatives is followed by rearrangement with ring expansion and the formation of a bond between a nitrogen atom and a carbon in the position 2. A set of derivatives of 2,3-dihydro-1,4-thiaselenine was obtained, substituted in the position 2 by a pyridinium residue functionalized by pharmacophoric groups.  相似文献   

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