3,5-Bis(Phenylmethylene)-1-(N-arylmaleamoyl)-4-piperidones: A Novel Group of Cytotoxic Agents

A series of novel 3,5-bis(phenylmethylene)-1-(N-arylmaleamoyl)-4-piperidones 3 have been synthesized which displayed potent cytotoxicity towards human Molt 4/C8 and CEM T-lymphocytes as well as murine P388 and L1210 leukemic cells. In contrast, the related N-arylmaleamic acids 4 possessed little or no cytotoxicity in these four screens. Molecular modeling revealed certain interplanar and bond angles and interatomic distances which were perceived to contribute to the observed bioactivity as well as providing suggestions for future structural modifications of the piperidones 3. Evaluation of representative compounds in series 3 and 4 on the activity of human N-myristoyltransferase revealed that, at the maximum concentration utilized, namely 250?μM, only weak inhibiting properties were displayed by some of the compounds in series 4. Various members of series 3 and 4 were well tolerated in mice.     

β-Lactams: A New Class of Conformationally-Rigid Inhibitors of γ-Aminobutyric Acid Aminotransferase

Abstract

A structural similarity of several monobactams (2–4), 3-aminonocardicinic acid (6), 6-aminopenicillanic acid (7), 7-aminocephalosporanic acid (8), and 7-aminodesacetoxycephalosporanic acids (9, 10) to γ-aminobutyric acid (GABA) and to known inhibitors and substrates of GABA aminotransferase is described. Because of this, the above-mentioned compounds were tested as competitive inhibitors and as inactivators of pig brain GABA aminotransferase. All of the compounds were competitive inhibitors of GABA aminotransferase. On the basis of the inhibitory potency of these conformationally-rigid GABA analogues it is hypothesized that GABA is bound at the active site with its amino and carboxylate groups in a syn orientation. None of the compounds inactivates GABA aminotransferase. These β-lactam analogues represent the first examples of a new class of inhibitors of GABA aminotransferase.     

Formation Mechanism of the Free Radical Product and Its Precursor by the Reaction of Dehydro-L-ascorbic Acid with Amino Acid

During the formation of radical A (2) and its precursor (tris(2-deoxy-2-L-ascorbyl)amine, 1) by the reaction of dehydroascorbic acid (DHA) with amino acid, ascorbic acid (AsA) and the reduced red pigment (3) were newly identified, in addition to scorbamic acid (SCA) and the red pigment (4), as intermediate products. The addition of AsA to the DHA-amino acid reaction, as well as to the DHA-SCA reaction, greatly increased the formation of 3 and 1. The reaction of AsA with 4 gave rapidly 3, followed by the gradual production of 1. From these results, a reaction pathway is proposed that 3 formed by the reduction of 4 with AsA is a key intermediate and its condensation with DHA followed by reduction with AsA might produce 2 and 1.     

Structure of Pna-Nucleic Acid Complexes

Abstract

The solution structure of the PNA-DNA hybrid H-GCTATGTC-NH₂d(GACATAGC), determined by NMR methods, shows a new conformation which has elements of both A- and B-form DNA. Comparison with other PNA-nucleic acid complexes points to common structural features, but also demonstrates the ability of PNA to conform to nucleic acid partners of different conformations.     

Design,synthesis and pharmacological evaluation of novel azole derivatives of aryl acetic acid as anti-inflammatory and analgesic agents

A series of substituted azole derivatives (3a–e, 4a–e and 5a–e) were synthesised by the cyclisation of N¹(diphenylethanoyl)-N⁴-substituted phenyl thiosemicarbazides under various reaction conditions. These compounds were tested in vivo for their anti-inflammatory activity. The compounds which showed activity comparable to the standard drug ibuprofen, were screened for their analgesic, ulcerogenic and lipid peroxidation activities. The compounds 5-(diphenylmethyl)-N-(4-fluorophenyl)-1,3,4-oxadiazol-2-amine (3b) and 5-(diphenylmethyl)-N-(3-chloro-4-fluorophenyl)-1,3,4-oxadiazol-2-amine (3c) emerged as the most active compounds of the series, and were moderately more potent than the standard drug, ibuprofen. (This abstract was published in Inflammation Research, Supplement 2, Volume 56, page A101, 2008.)     

Synthesis and Binding Properties of a Homopyrimidine 2′,5′-Linked Xylose Nucleic Acid (2′,5′-XNA)

Abstract

The synthesis and hybridization properties of pyrimidine 2′,5′-RNA and 2′,5′-Xylose Nucleic Acid (2′,5′-XNA) are described.     

Universal Labeling Chemistry for Nucleic Acid Detection on DNA-Arrays

Abstract

We show here a new and efficient aqueous chemistry for labeling of any class of nucleic acids for their detection on DNA chip. The labels contain a diazo function as reactive moiety and biotin as detectable unit. The highly selective reaction of diazo group on the phosphate does not disrupt base pairing recognition and hybridization specificity.     

Cytotoxicity of boron containing dipeptide analogs

Summary This work is an extension of our previous work (Hall et al., 1993) on the synthesis and cytotoxic activity of boronated peptides. The aim of this work was to carry out structural modifications of the amine terminal in compounds1 and2, to increase water solubility, and its effect on the cytotoxicity to tumor cell lines. Surprisingly, only compounds4,7 and8 were more water soluble than the parent compounds. With the exception of compound4, the new derivatives were generally less effective than the parent compounds (1 and2). There was no apparent correlation between structure and activity. Cytotoxic effect was more pronounced in single cell suspended cells. The growth of solid tumor cell lines was not significantly reduced. The most active derivative, (methanamine)dihydro[[[1-(phenylmethyl)-2-methylamino-2-oxoethyl]amino]carboxy]boron (4), inhibited DNA, RNA, and protein synthesis in Tmolt₃ cells. Enzymatic activities, e.g., DNA polymerase, m-RNA polymerase, PRPP amidotransferase, carbamyl phosphate synthetase, TMP-kinase, TDP-kinase, dihydrofolate reductase, and ribonucleoside reductase were reduced after 60 min incubation with4. d(TTP) and d(CTP) pool levels were also reduced by 60 min incubation with4.     

Synthesis of 2′,3′-Dideoxy-2′-fluoro-3′-thioarabinothymidine and Its 3′-Phosphoramidite Derivative

Abstract

An efficient method for the synthesis of 5′-O-monomethoxytrityl-2′,3′-dideoxy-2′-fluoro-3′-thioarabinothymidine [^5′-MMTaraF-T_3′SH, (5)] and its 3′-phosphoramidite derivative (6) suitable for automated incorporation into oligonucleotides, is demonstrated. A key step in the synthesis involves reaction of 5′-O-MMT-2,3′-O-anhydrothymidine (4) (Eleuteri, A.; Reese, C.B.; Song, Q., J. Chem. Soc. Perkin Trans. 1 1996, 2237 pp.) with sodium thioacetate to give ^5′-MMTaraF-T_3′SAc (5) (Elzagheid, M.I.; Mattila, K.; Oivanen, M.; Jones, B.C.N.M.; Cosstick, Lönnberg, H. Eur. J. Org. Chem. 2000, 1987–1991). This nucleoside was then converted to its corresponding phosphoramidite derivative, 6, as described previously ((a) Sun, S.; Yoshida, A.; Piccirilli, J.A. RNA, 1997, 3, 1352–1363; (b) Matulic-Adamic, J.; Beigelman, L. Helvetica Chemica Acta 1999, 82, 2141–2150; (c) Fettes, K.J.; O’Neil, I.; Roberts, S.M.; Cosstick, R. Nucleosides, Nucleotides and Nucl. Acids 2001, 20, 1351–1354).     

An Investigation of the Structural Diversities of Lithiated HMPA Complexes of o-Mercaptopyridine and Trithiocyanuric Acid: Syntheses, Crystal structures and Model Molecular Orbital Calculations

Reaction of o-mercaptopyridine (o-MPH) and trithiocyanuric acid (TTCyH₃) with one equivalent of BuⁿLi in the presence of HMPA yields the mono-lithiated salts MPLi.HMPA (1) and TTCyH₂Li.2HMPA (2) respectively, which have been characterised by NMR spectroscopy and X-ray crystallography. Reaction of three equivalents of BuⁿLi with anhydrous TTCyH₃ in THF yields the tri-lithiated species TTCyLi₃.4THF (3). In all three compounds the lithium centres have N,S-bridged coordination modes. Whereas 1 is dimeric in the solid state, 2 has an unusual monomeric structure and 3, which is a very rare example of a structurally characterised tri-lithiated compound, has an unprecedented polymeric structure incorporating (NCSLi) _n (n = 1, 2) rings. The structural diversities displayed by 1 and 2 have been probed, and thereby in part rationalised, by ab initio (6-31G*/RHF, 6-31G**/RHF and 6-31G*/MP2 levels) MO calculations on both their thio-keto and thiol isomers and on their uncomplexed and complexed lithiated derivatives. In particular, the optimised structures predict and reproduce the N,S-bridging coordination modes found for lithium and explain why structure 1 is dimeric whereas 2 is monomeric.Electronic Supplementary Material available.     

Citric Acid Fermentation

Abstract

Dielectrophoresis is the motion of particles caused by electrical polarization effects in inhomogeneous (nonuniform) electric fields. Unlike electrophoresis, the particles do not require a net electrical charge for motion to occur and AC rather than DC fields are employed to exploit the dielectric properties of the particles. Factors controlling the effective dielectric properties of cells and microorganisms include electrical double layers associated with surface charges, the conductivity and permittivity of their membranes and any cell walls, and their morphologies and structural architectures. In recent years, several laboratories have developed separation and manipulation techniques for cells and microorganisms based on dielectrophoresis, using both static and traveling AC fields. In this article, the basic physical factors influencing the dielectrophoretic behavior of particles are outlined, and ways in which these can be employed to achieve selective separation of cells and microorganisms are described.     

Inhibition of Zinc Metallopeptidases by Flavonoids and Related Phenolic Compounds: Structure-Activity Relationships

Abstract

Flavonoids and other benzopyrone substances, having an appropriate hydroxylation profile, may inhibit the metalloenzymes leucine aminopeptidase (LAP), aminopeptidase M (AP-M), and carboxypeptidase A (CP-A). A structural feature that evidently favours the interaction between flavonoids and the three metalloenzymes is the 2,3-double bond conjugating the A and B rings and conferring a planar structure. This can be considered virtually indispensable for inhibition of the three metallopeptidases, though the hydroxylation profile required differed for each of the enzymes, and the interaction mechanism and behaviour also differed. The inhibitory effect of flavonoids on LAP was reversible, and to be effective the flavonoid had to have conjugated A and B rings and or tho-dihydroxylation on at least one of the aromatic rings. This same requirement was essential for inhibition by coumarins and was attributed to a catechol-like mechanism of interaction. The inhibitory effects on AP-M were due to inactivation of the enzyme, irreversibly altered by flavonoids with a 2,3-double bond and a minimum of one hydroxyl substituent on each of the aromatic rings. With CP-A, conjugation of the A and B rings enhanced the inhibitory effect of flavonoids, though it was not strictly required. The interaction between the polyphenolic substances tested and the two zinc aminopeptidases was not reversed by adding zinc to the reaction medium, indicating that the inhibition is not due to the coordination of the phenolic hydroxyl groups with the catalytical zinc of active site, though the presence of zinc affected the interaction behaviour differently according to each substance's hydroxylation profile.     

Protein Architecture Chronology Deduced From Structures of Amino Acid Synthases

Abstract

Inferring the protein architecture chronology is one of central topics in origin of life study and has been given much attention. Based on an amino acid evolutionary model that late amino acids were bio-synthesized prior to early counterparts, we addressed the issue by examining the structures of amino acid synthases. Despite the limited structural information on amino acid synthases, our deduction revealed that α/β was the oldest protein class, which is in good agreement with the prior fold-usage-based conclusion.     

哈氏弧菌脂酰-ACP合成酶的体外功能

【目的】系统鉴定哈氏弧菌脂酰-ACP合成酶(Acyl-ACP synthetase,Aas S)以不同链长游离脂肪酸和非脂肪链羧酸作为底物的体外催化反应。【方法】利用非变性蛋白质凝胶电泳和紫外分光光度计法从定性和定量两个方面分析了Aas S的体外催化功能与活性。【结果】Aas S能够催化不同链长直链的自由脂肪酸合成脂酰-ACP,其中以C6–C12作为底物时活性最高;以羟基脂肪酸作为底物的情况下,Aas S催化C8–C14的羟基脂肪酸有较高的活性。非脂肪链羧酸类作为底物的反应中,20种蛋白质氨基酸、苯甲酸和水杨酸均可以作为Aas S的底物,合成相应的脂酰-ACP。【结论】本研究系统地证明了哈氏弧菌脂酰-ACP合成酶(Aas S)对不同底物的不同催化活性,为生物体内氨基酸代谢和菌黄素合成代谢的研究提供了可行性的分析依据。     

Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa

The peptidases in clan MH are known as cocatalytic zinc peptidases that have two zinc ions in the active site, but their metal preference has not been rigorously investigated. In this study, the molecular basis for metal preference is provided from the structural and biochemical analyses. Kinetic studies of Pseudomonas aeruginosa aspartyl aminopeptidase (PaAP) which belongs to peptidase family M18 in clan MH revealed that its peptidase activity is dependent on Co²⁺ rather than Zn²⁺: the k_cat (s⁻¹) values of PaAP were 0.006, 5.10 and 0.43 in no-metal, Co²⁺, and Zn²⁺ conditions, respectively. Consistently, addition of low concentrations of Co²⁺ to PaAP previously saturated with Zn²⁺ greatly enhanced the enzymatic activity, suggesting that Co²⁺ may be the physiologically relevant cocatalytic metal ion of PaAP. The crystal structures of PaAP complexes with Co²⁺ or Zn²⁺ commonly showed two metal ions in the active site coordinated with three conserved residues and a bicarbonate ion in a tetragonal geometry. However, Co²⁺- and Zn²⁺-bound structures showed no noticeable alterations relevant to differential effects of metal species, except the relative orientation of Glu-265, a general base in the active site. The characterization of mutant PaAP revealed that the first metal binding site is primarily responsible for metal preference. Similar to PaAP, Streptococcus pneumonia glutamyl aminopeptidase (SpGP), belonging to aminopeptidase family M42 in clan MH, also showed requirement for Co²⁺ for maximum activity. These results proposed that clan MH peptidases might be a cocatalytic cobalt peptidase rather than a zinc-dependent peptidase.     

An Alternative Biotechnological Tool for Magnesite Enrichment: Lactic Acid Bacteria Isolated from Soil

Abstract

Calcium carbonate (CaCO₃) is found in different polymorph structures such as aragonite, vaterite, and calcite. The most common and stable form of CaCO₃, calcite, which is abundant in sedimentary rocks as magnesite ore. Magnesite has application areas in many industrial fields including paper, pharmaceutical and refractory materials. Magnesite is theoretically formulated MgCO₃, but contains many impurities (silicium, iron, and also calcite), that limits its usability and applicability. In this research, we aimed to investigate the decalcification possibility of the raw magnesite material through application of Enterococcus feacelis (EF) with CaCO₃ dissolution ability. The exact mechanism of CaCO₃ dissolution was investigated by carbonic anhydrase enzyme assay and HPLC analysis of organic acids produced by EF. Consequently, EF reduced the amount of CaCO₃ from 2.94% to 0.49% which means a reduction (≈83.33%) in the rate of CaCO₃ percentage. As a result of the experiments, it was observed that different organic acids produced by bacteria reacted with CaCO₃ and removed the lime of magnesite ore. The bacteria used in the study did not show any pathogenic properties in rats, thus, it can be used safely for the industrial applications.     

Structure of (dG)n · (dC)n Under Superhelical Stress and Acid pH

Abstract

We have recently shown that a (GA)_n · (TC)_n tract undergoes a sharp structural transition under superhelical stress (V.I. Lyamichev, S.M. Mirkin and M.D. Frank-Kamenetskii, J. Biomol. Struct. Dyn. 2, 327 (1985)). Unlike the well studied transitions to the cruciform and to the Z form, this novel transition was strongly pH-dependent. We have found the (dG)_n · (dC)_n insert to undergo a pH-dependent structural transition similar to that of the (GA)_n · (TC)_n tract. These new data meet our earlier expectations and disagree with the data of D.E. Pulleyblank, D.B. Haniford and A.R. Morgan, Cell 42, 271 (1985). We conclude that a novel DNA structure (the H-form) is typical of homopurine-homopyrimidine mirror repeats (the H palindromes) under superhelical stress and/or acid pH. In the H-form the homopyrimidine strand forms a hairpin while half of the homopurine strand interacts with the hairpin forming a triplex, the other half of the homopurine strand being unstructured (V.I. Lyamichev, S.M. Mirkin and M.D. Frank-Kamenetskii, J. Biomol. Struct. Dyn. 2, 3,667 (1986)).     

Molecular Docking and Interaction Studies of Identified Abscisic Acid Receptors in Oryza sativa: An In-Silico Perspective on Comprehending Stress Tolerance Mechanisms

BackgroundAbiotic stresses affect plants in several ways and as such, phytohormones such as abscisic acid (ABA) play an important role in conferring tolerance towards these stresses. Hence, to comprehend the role of ABA and its interaction with receptors of the plants, a thorough investigation is essential.AimThe current study aimed to identify the ABA receptors in Oryza sativa, to find the receptor that binds best with ABA and to examine the mutations present to help predict better binding of the receptors with ABA.MethodsProtein sequences of twelve PYL (Pyrabactin resistance 1) and seven PP2C (type 2C protein phosphatase) receptors were retrieved from the Rice Annotation Project database and their 3D structures were predicted using RaptorX. Protein-ligand molecular docking studies between PYL and ABA were performed using AutoDock 1.5.6, followed by 100ns molecular dynamic simulation studies using Desmond to determine the acceptable conformational changes after docking via root mean square deviation RMSD plot analysis. Protein-protein docking was then carried out in three sets: PYL-PP2Cs, PYL-ABA-PP2C and PYL(mut)-ABA-PP2C to scrutinize changes in structural conformations and binding energies between complexes. The amino acids of interest were mapped at their respective genomic coordinates using SNP-seek database to ascertain if there were any naturally occurring single nucleotide polymorphisms (SNPs) responsible for triggering rice PYLs mutations.ResultsInitial protein-ligand docking studies revealed good binding between the complexes, wherein PYL6-ABA complex showed the best energy of -8.15 kcal/mol. The 100ns simulation studies revealed changes in the RMSD values after docking, indicating acceptable conformational changes. Furthermore, mutagenesis study performed at specific PYL-ABA interacting residues followed by downstream PYL(mut)-ABA-PP2C protein-protein docking results after induction of mutations demonstrated binding energy of -8.17 kcal/mol for PP2C79-PYL11-ABA complex. No naturally occurring SNPs that were responsible for triggering rice PYL mutations were identified when specific amino acid coordinates were mapped at respective genomic coordinates.ConclusionThus, the present study provides valuable insights on the interactions of ABA receptors in rice and induced mutations in PYL11 that can enhance the downstream interaction with PP2C.     

Structural and reactivity studies on the ternary system guanine/methionine/trans-[PtCl2(NH3)L] (L=NH3, quinoline): implications for the mechanism of action of nonclassical trans-platinum antitumor complexes

 The present model study explores the chemistry of methionine complexes and ternary methionine-guanine adducts formed by trans-[PtCl₂(NH₃)₂] (1) and antitumor trans-[PtCl₂(NH₃)quinoline] (2) using 1D (¹H, ¹⁹⁵Pt) and 2D NMR spectroscopy. Compound 2 was substitution inert in reactions with N-acetyl-lmethionine [AcMet(H)]. Reactions of trans-[PtCl(NO₃)(NH₃)quinoline] (5) ("monoactivated" 2) with AcMetH in water and acetone at various stoichiometries point to Pt(II)-S binding that requires prior activation of the Pt-Cl bond by labile oxygen donors. Trans-[PtCl{AcMet(H)-S}(NH₃)quinoline](NO₃) (6) and trans-[Pt{AcMet(H)-S}₂(NH₃)quinoline](NO₃)₂ (7) were isolated from these mixtures. At high [Cl^–], AcMet(H) is displaced from 7, giving 6. Frozen stereodynamics in 6 at the thioether-S and slow rotation about the Pt-N_quinoline bond result in four spectroscopically distinguishable diastereomers. ¹H NMR spectra of 7 show faster exchange dynamics due to mutual trans-labilization of the sulfur donors. Substitution of chloride in trans-[PtCl(9-EtGua)(NH₃)L]NO₃ (L=NH₃, 3; L=quinoline, 4; 9-EtGua=9-ethylguanine, which mimics the first DNA binding step of 1 and 2) by methionine-sulfur proceeded ca. 2.5 times slower for the quinoline compound. Both reactions, in turn, proved to be ca. 4 times faster than binding of a second nucleobase under analogous conditions. From the resulting mixtures the ternary adducts trans-[Pt(AcMet-S)(9-EtGua-N7)(NH₃)L](NO₃, Cl) (L=NH₃, 8; L=quinoline, 9) were isolated. A species analogous to 9 formed in a rapid reaction between 6 and 5′-guanosine monophosphate (5′-GMP). From NMR data an AMBER-based solution structure of the resulting adduct, trans-[Pt(AcMet-S)(5′-GMP-N7)(NH₃)quinoline] (10), was derived. The unusual reactivity along the N7-Pt-S axis in 8–10 resulted in partial release of both 9-EtGua and AcMet at high [Cl^–]. Possible consequences of the kinetic and structural effects (e.g., trans effect of sulfur, steric demand of quinoline) observed in these systems with respect to the (trans)formation of potential biological cross-links are discussed. Received: 25 May 1998 / Accepted: 6 August 1998     

Amide derivatives with pyrazole carboxylic acids of 5-amino-1,3,4-thiadiazole 2-sulfonamide as new carbonic anhydrase inhibitors: Synthesis and investigation of inhibitory effects

Pyrazole carboxylic acid amides of 5-amino-1,3,4-thiadiazole-2-sulfonamide were synthesized from 4-benzoyl-1,5-diphenyl-1H-pyrazole-3-carbonyl chloride and 4-benzoyl-1-(3-nitrophenyl)-5-phenyl-1H-pyrazole-3-carbonyl chloride. Carbonic anhydrase isoenzymes (hCA-I and hCA-II) were purified from human erythrocyte cells by the affinity chromatography method. The inhibitory effects of 5-amino-1,3,4-thiadiazole-2-sulfonamide 1, acetazolamide 2 and new synthesized amides on these isozymes have been studied in vitro. The I₅₀ concentrations (the concentration of inhibitor producing a 50% inhibition of CA activity) against hydratase activity ranged from 1.2 to 2.2 nM for hCA-I and from 0.4 to 2 nM for hCA-II. The I₅₀ values against esterase activity ranged from 1.4 to 8 nM for hCA-I and from 1.3 to 6 nM for hCA-II. The K_i values were observed between 8.2·10^{? 5} to 6.2·10^{? 4} M for hCA-I and between 2.9·10^{? 4} to 8.2·10^{? 4} M for hCA-II. The comparison of new synthesized amides to 5-amino-1,3,4-thiadiazole-2-sulfonamide 1, acetazolamide 2 indicated that the new synthesized compounds (18–23) inhibit CA activity more potently than the parent compounds.