An analysis of hydrophobic interactions of thymidylate synthase with methotrexate: Free energy calculations involving mutant and native structures bound to methotrexate

Since the human body for many reasons can adapt and become resistant to drugs, it is important to develop and validate computer aided drug design (CADD) methods that could help predict binding affinity changes that can result from these resistant enzymes. The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between inhibitors and protein variants. In this paper, we describe the role played by hydrophobic residues lining the active site region, particularly ⁷⁹ Ile and ¹⁷⁶ Phe, in the binding of methotrexate to the Escherichia coli (E. coli) thymidylate synthase (TS) enzyme, using the thermodynamic cycle perturbation (TCP) approach. The computed binding free energy differences on the binding of methotrexate to the native and some mutant E. coli TS structures have been compared with experimental results. Computationally, four different ‘mutations’ have been simulated on the TS enzyme with methotrexate (MTX): ⁷⁹ Ile →  ⁷⁹ Val; ⁷⁹ Ile → ⁷⁹ Ala; ⁷⁹ Ile → ⁷⁹ Leu; and ¹⁷⁶ Phe →  ¹⁷⁶ Ile. The calculated results indicate that in each of these cases, the native residues ( ⁷⁹ Ile and ¹⁷⁶ Phe) interact more favorably with methotrexate than the mutant residues and these results are corroborated by experimental measurements. Binding preference to wild type residues can be rationalized in terms of their better hydrophobic contacts with the phenyl ring of methotrexate.     

Opioid Peptides: Synthesis and Biological Activity of New Endomorphin Analogues

Summary Syntheses are described of new endomorphin 1 and 2 peptoid–peptide hybrids in which Tyr¹ and either one or both Phe³ and Phe⁴ have been replaced by N-substituted-glycine. The preparation is also described of two glycosylated Hyp²-endomorphin 2 analogues in which either 2,3,4,6-tetra-O-acetyl glucose or glucose are β-O-glycosidically linked to the hydroxyproline residue. The Hyp²-endomorphin sequences have also been elongate by adding a C-terminal β-alanine residue and several linear dimers have been prepared by coupling either the native peptides or the modified analogues. The cyclo endomorphin 2 has also been synthesized. Preliminary pharmacological experiments on isolated organ preparations showed that the agonist activities of both endomorphin 1 and 2 are not significantly affected by the Pro/Hyp substitution. Phe⁴/Nphe substitution in the endomorphin 1 reduced the potency on guinea pig ileum (GPI) by about 100 times and abolished the agonist activity on mouse vas deferens (MVD) preparation. The decrease of the agonist activity induced by modification of one phenylalanine residue only, either Phe³ or Phe⁴, is lower on endomorphin 2. Either modification of both Phe³ and Phe⁴ or glycosylation of the Hyp²-endomorphin 2 cancelled any agonist activity on both preparations. The linear peptide dimers [endomorphin 1]₂, [endomorphin 2]₂, [Hyp²-endomorphin 1]₂, [Hyp²-endomorphin 2]₂, [Hyp²-endomorphin 1-Hyp²-endomorphin 2]₂ or [Hyp²-endomorphin 2-Hyp²-endomorphin 1]₂, are 7–19 times less potent than endomorphin 1 on GPI and significantly less active than endomorphins 1 and 2 on MVD. The other afforded modifications significantly affected or abolished the agonist activity of the resulting endomorphin analogues on both GPI and MVD preparations.The α-amino acid residues are of the L-configuration. Standard abbreviations for amino acid derivatives and peptides are according to the suggestions of the IUPAC-IUB Commission on Biochemical Nomenclature (1984) Eur. J. Biochem., 138, 9–37. Abbreviations listed in the guide published in (2003) J. Peptide Sci., 9, 1–8 are used without explanation.     

Synthesis and Hybridization Properties of Oligonucleotides Containing (2 S ,3 R )-9-(2,3,4-Trihydroxybutyl)Adenine

The synthesis and properties of oligonucleotides (ONs) containing 9-(2,3,4-trihydroxybutyl)adenine, A ^C2 and A ^C3, are described. The ON containing A ^C2 involves the 3′ → 4′ and 3′ → 5′ phosphodiester linkages in the strand, whereas that containing A ^C3 possesses the 3′ → 4′ and 2′ → 5′ phosphodiester linkages. It was found that incorporation of the analogs, A ^C2 or A ^C3, into ONs significantly reduces the thermal and thermodynamic stabilities of the ON/DNA duplexes, but does not largely decrease the thermal and thermodynamic stabilities of the ON/RNA duplexes as compared with the case of the ON/DNA duplexes. It was revealed that the base recognition ability of A ^C2 is greater than that of A ^C3 in the ON/RNA duplexes.     

Evaluation of novel <Superscript>99m</Superscript>Tc(I)-labeled homobivalent α-melanocyte-stimulating hormone analogs for melanocortin-1 receptor targeting

Abstract  

Aiming to apply the multivalency concept to melanoma imaging, we have assessed the in vivo melanocortin type 1 receptor (MC1R)-targeting properties of ^99mTc(I)-labeled homobivalent peptide conjugates which contain copies of the α-melanocyte-stimulating hormone (α-MSH) analog [Ac-Nle⁴, Asp⁵, d-Phe⁷, Lys¹¹]α-MSH_4–11 separated by linkers of different length (L ² nine atoms and L ³ 14 atoms). The MC1R-binding affinity of L ² and L ³ is significantly higher than that of the monovalent conjugate L ¹ . Metallation of these conjugates yielded the complexes fac-[M(CO)₃(k³-L)]⁺ (M is ^99mTc/Re; 1/1a, L is L ¹ ; 2/2a, L is L ² ; 3/3a, L is L ³ ), with IC₅₀ values in the subnanomolar and nanomolar range. The MC1R-mediated internalization of 2 and 3 is higher than that of 1 in B16F1 melanoma cells. Biodistribution studies in melanoma-bearing mice have shown low nonspecific accumulation with a tumor uptake that correlates with IC₅₀ values. However, no correlation between tumor uptake and valency was found. Nevertheless, 2 displayed the highest tumor retention, and the best tumor to nontarget organ ratios.     

Structure-activity study of phosphoramido acid esters as acetylcholinesterasf inhibitors

Phosphoramido acid esters (CH₃)₂NP(O)X(p-OC₆H₄-CH₃) (containing P-Cl (1), P-O (2), P-F (3), P-CN (5), and P-N (4,6) bonds, X for 2, 4 and 6 is OCH₃, (C₂H₅)₂N and morpholin) have been synthesized to investigate the structure-activity study of AChE enzyme inhibition, through the parameters logP, δ³¹P and IC₅₀. After their characterization by ³¹P, ³¹P{¹H}, ¹³C, ¹H NMR, IR and mass spectroscopy, the parameters logP and δ³¹P (³¹P chemical shift in NMR) were used to evaluated the lipophilicity and electronical properties. The ability of compounds to inhibit human AChE was predicted by PASS software (version 1.193), and experimentally evaluated by a modified Ellman's assay.     

Synthesis,characterization and nucleic acid binding studies of mononuclear copper(II) complexes derived from azo containing O,O donor ligands

Abstract

Azo linked salicyldehyde and a new 2-hydroxy acetophenone based ligands (HL¹ and HL²) with their copper(II) complexes [Cu(L¹)₂] (1) and [Cu(L²)₂] (2) were synthesized and characterized by spectroscopic methods such as ¹H, 13C NMR, UV–Vis spectroscopy and elemental analyses. Calculation based on Density Functional Theory (DFT), have been performed to obtain optimized structures. Binding studies of these copper (II) complexes with calf thymus DNA (ct-DNA) and torula yeast RNA (t-RNA) were analyzed by absorption spectra, emission spectra and Viscosity studies and Molecular Docking techniques. The absorption spectral study indicated that the copper(II) complexes of 1 and 2 had intrinsic binding constants with DNA or RNA in the range of 7.6?±?0.2?×?10³?M^?1 or 6.5?±?0.3?×?10³M^?1 and 5.7?±?0.4?×?10⁴ M^?1 or 1.8?±?0.5?×?10³ M^?1 respectively. The synthesized compounds and nucleic acids were simulated by molecular docking to explore more details mode of interaction of the complexes and their orientations in the active site of the receptor.     

Community Structure,Geochemical Characteristics and Mineralogy of a Hypersaline Microbial Mat,Cabo Rojo,PR

Seasonal variations in precipitation changed the community composition and microbial activity in a hypersaline, tropical microbial mat, in Cabo Rojo, PR. Using a combination of dissection, light, and transmission electron microscopy, terminal restriction fragment length polymorphism (T-RFLP), in situ microelectrode studies, and ³⁵ S isotope incubations, we documented the major differences between wet and dry seasons. During the wet season (precipitation 177 mm), cyanobacterial (green layer) and anoxyphototrophic (pink layer) communities, as well as the black FeS layer were well-developed, and T-RFLP patterns indicated a diverse community. The rate of oxygenic photosynthesis was 49 μ M min ^{? 1} . Aerobic respiration was 29 μ M min ^{? 1} , and sulfate reduction was 264 nmol cm ^{? 3} h ^{? 1} . During the dry season (precipitation 51 mm), cyanobacteria and anoxyphototrophs were less diverse and abundant, and T-RFLP patterns were less complex. The O ₂ production rate was reduced to 9 μ M min ^{? 1} , as was O ₂ consumption (7 μ M min ^{? 1} ) and sulfate reduction (26 nmol cm ^{? 3} h ^{? 1} ). Aragonite, calcite, halite, and quartz were the predominant minerals. Seasonal differences were found in the green and pink layers for both halite and quartz. Gypsum was not observed, likely due to a sample handling artifact. The fluctuations in community composition and metabolic activity, principally reflected in fluctuations in binding and trapping potential of the uppermost mat community, might be responsible for the observed differences in mineralogy.     

Synthesis and biological evaluation of tricarbonyl Re(I) and Tc(I) complexes anchored by poly(azolyl)borates: application on the design of radiopharmaceuticals for the targeting of 5-HT<Subscript>1A</Subscript> receptors

The building blocks fac-[^99mTc{κ³-HB(tim^Me)₃}(CO)₃] and fac-[^99mTc{κ³-R(μ-H)B(tim^Me)₂}(CO)₃] [R is H (4a), Ph (5a); tim^Me is 2-mercapto-1-methylimidazolyl] were obtained almost quantitatively by reacting fac-[^99mTc(CO)₃(H₂O)₃]⁺ with the corresponding scorpionate. These compounds cross the intact blood–brain barrier in mice, with significant retention in the case of 4a and 5a. Using 4a as the lead structure, we have synthesized the functionalized complexes fac-[M{κ³-H(μ-H)B(tim^Bu-pip)₂}(CO)₃] [M is Re (8), ^99mTc (8a); tim^Bu-pip is methyl[4-((2-methoxyphenyl)-1-piperazinyl)butyl](2-mercapto-1-methylimidazol-5-yl)methanamide] and fac-[M{κ ³-H(μ-H)B(tim^Me)(tim^Bu-pip)}(CO)₃] [M is Re (9), ^99mTc (9a)] and evaluated their potential as radioactive probes for the targeting of brain 5-HT_1A serotonergic receptors. The Re complexes exhibit excellent affinity [IC₅₀=0.172 ± 0.003 nM (8); IC₅₀=0.65 ± 0.01 nM (9)] for the 5-HT_1A receptor. The radioactive congeners (^99mTc) have shown an initial brain uptake of 1.38 ± 0.46%ID g⁻¹ (8a) and 0.43 ± 0.12%ID g⁻¹ (9a), but suffer from a relatively fast washout.     

A Novel Zeolite Coating for Protection of Concrete Sewers from Biological Sulfuric Acid Attack

Microbial growth inhibition and resistance to biological deterioration of concrete specimens coated with silver-loaded zeolite was evaluated by measuring the time course of bacterial growth, biological sulfur oxidation, and sulfate production using Acidithiobacillus thiooxidans as a corrosive agent. Live bacterial cells declined from an initial inoculum concentration of 1.1 × 10₄ cell ml_-1 to zero in 10 days, during which only 0.5–1% of the initial sulfur concentration of 10 g l_-1 was biologically oxidized, corresponding to sulfate production rates of 35–42 mg SO ₄ ^{2 ?} g ^{? 1} S ^{? 1} . Leaching coefficients of calcium and silicon in the specimens coated with silver-loaded zeolite of 1.6 × 10 ^{? 4} to 4.6 × 10 ^{? 2} cm ² d ^{? 1} respectively, were only 0.8% and 1% of the uncoated specimens.     

MOLECULAR AND PHARMACOLOGICAL CHARACTERISATION OF THE MSH-R ALLELES IN SWISS CATTLE BREEDS

ABSTRACT

The coat colour in mammals is determined by the relative amounts of eumelanin (black/brown) and phaeomelanin (red/yellow), produced in melanocytes, which are controlled by melanocyte stimulating hormone receptor (MSH-R). Melanocyte stimulating hormone receptor is activated by α-melanocyte-stimulating hormone (α-MSH). Stimulated MSH-R activates adenylyl cyclase (AC), thereby increasing the amount of cyclic AMP in the cell, which activates the enzyme tyrosinase resulting in eumelanin synthesis. In this study the complete coding sequences of five alleles of the MSH-R gene found in Holstein, Red Holstein, Simmental, and Brown Swiss cattle were cloned into a mammalian expression vector and transfected into human embryonic kidney (HEK) 293 cells. The expressed receptors were analyzed for their ability to increase intracellular cAMP in response to stimulation by α-MSH. The recessive red allele (e) found in Red Holstein and Simmental and the dominant black allele (E^D) found in Holstein were unresponsive to a wide range of α-MSH concentrations. Two alleles from Brown Swiss (E^d1, E^d2) and one allele found in the Simmental breed (e^f) responded to stimulation by α-MSH in a dose-dependent manner. When compared to E^d1 and E^d2, the cells transfected with the e^f MSH-R allele, however, reached the corresponding intracellular cAMP concentrations at a 10-fold higher concentration of α-MSH. In conjunction with the mode of inheritance of coat colour, the results indicate that the e MSH-R allele is a non-functional receptor, E^D is constitutively activated receptor, and E^d1 and E^d2 are hormonally activated receptors. The delay in e^f MSH-R response may explain the similarity between the e and e^f phenotypes.     

Synthesis,characterization and inhibitory potency of two oxono and thiono analogues of phosphoramidate compounds on acetylcholinesterase

Two novel structurally related phosphoramidate compounds, 1 and 2, with likely β-diketone system were synthesized and characterized by ¹H, ¹³C, ³¹P NMR, IR spectroscopy and elemental analysis. Compound 2 exhibited a ³¹P NMR signal which was significantly shielded (8 ppm) relative to compound 1. Determination of human erythrocyte acetylcholinesterase (hAChE) inhibitory activity was carried out according to Ellman's modified kinetic method and the IC₅₀ values of compounds 1 and 2 were 1.567 and 2.986 mM, respectively. The k_i values of 1 and 2 were 1.39 to 2.65 min^{? 1} respectively. A comparison of the bimolecular rate constant (k_i) and IC₅₀ values for the irreversible inhibitors 1 and 2 revealed that the oxono analogue has greater affinity for hAChE than the thiono compound. Furthermore effects of two conventional oximes paralidoxime (A) and obidoxime (B) on reactivation of the inhibited hAChE were studied but low reactivity was shown by both the oximes.     

Structure-activity relationship on DNA binding and anticancer activities of a family of mixed-ligand oxidovanadium(V) hydrazone complexes

The title family of mixed-ligand oxidovanadium(V) hydrazone complexes are [V^VO(HL¹)(hq)] (1) and [V^VO(HL²)(hq)] (2), where (HL¹)^2? and (HL²)^2? are the dinegative form of 2-hydroxybenzoylhydrazone of acetylacetone (H₃L¹) and benzoylacetone (H₃L²), respectively, and hq^? is the mononegative form of 8-hydroxyquinoline (Hhq). Complexes were used to determine their binding constant with CT DNA using various spectroscopic techniques namely, electronic absorption, fluorescence and circular dichroism spectroscopy. The binding constant values suggest the intercalative mode of binding with the CT DNA and follow the order: 2 > 1. The bulky size as well as electron withdrawing property of the phenyl group (which is present in the β-diketone part of the hydrazone moiety in complex 2 in place of a CH₃ group in complex 1) is responsible for the higher activity of 2 than 1. Complexes were screened for cytotoxic activity on cervical cancer cells and were found to be potentially active (IC₅₀ value for 1 and 2 is 33 and 29 μM, respectively), even better than the widely used cis-platin (IC₅₀ = 63.5 μM) and carboplatin (IC₅₀ = > 200 μM) which is evident from the respective IC₅₀ value. Nuclear staining experiment suggests that these complexes kill the SiHa cancer cells through apoptotic mode. The molecular docking study also suggested the intercalative mode of binding of these complexes with CT DNA and HPV 18 DNA.     

Synthesis and Characterization of C8 Analogs of c-di-GMP

We have synthesized five analogs of c-di-GMP with different substituents at the guanine C8 position, to study their effects on the metal-dependent polymorphism we had previously demonstrated for the parent compound. Of these, only the K⁺ salt of c-di-Br-GMP, 2, forms higher order complexes, predominantly two different syn octamolecular ones. Its Na⁺ salt, as well as both the K⁺ and Na⁺ salts of c-di-thio-GMP, 3, c-di-methylthio-GMP, 4, c-di-phenyl-GMP, 5, and c-di-acetylphenyl-GMP, 6, all form primarily a syn bimolecular structure.     

Antioxidant activity of 5-alkoxymethyl-6-chromanols

Abstract

The 5-alkoxymethyl-2,2,7,8-tetramethyl-6-chromanols (II) are excellent antioxidants against autoxidising safflower oil (ASO), although not as good as 2,2,5,7,8-pentamethyl-6-chromanol (I), the model compound of -tocopherol. The aim of this work was to determine whether the rate of reaction of (II) with the radicals diphenylpicrylhydrazyl (DPP^·) and galvinoxyl (ArO^·) was directly proportional to their antioxidant activity against ASO. Compounds (II) reacted faster with DPP^·. than with ArO^·. but, in each case, slower than compound (I). The rates of reaction of I and II with both radicals followed the order I > II (R = H) > II (R = CH₃) > II (R = other alkyls) and were directly proportional to their antioxidant activity against ASO.     

Selective Metalation of 6-Methylpurines: Synthesis of 6-Fluoromethylpurines and Related Nucleosides

Abstract

A selective metalation at the 6-CH3 over C-8 of 6-methylpurine derivative 6 was observed with softer counter cation (Na⁺ or K⁺) of the base, while the harder Li⁺ showed no selectivity. In the presence of N-fluorobenzenesulfonamide (NFSI), this property was utilized for the synthesis of 6-fluoromethylpurine derivatives 4 and 5 as potential toxins for suicide gene therapy.     

Calcium-dependent trapping of mitochondria near plasma membrane in stimulated astrocytes

Growing evidence suggests that astrocytes are the active partners of neurons in many brain functions. Astrocytic mitochondria are highly motile organelles which regulate the temporal and spatial patterns of Ca ²⁺ dynamics, in addition to being a major source of ATP and reactive oxygen species. Previous studies have shown that mitochondria translocate to endoplasmic reticulum during Ca ²⁺ release from internal stores, but whether a similar spatial interaction between mitochondria and plasma membrane occurs is not known. Using total internal reflection fluorescence (TIRF) microscopy we show that a fraction of mitochondria became trapped near the plasma membrane of cultured hippocampal astrocytes during exposure to the transmitters glutamate or ATP, resulting in net translocation of the mitochondria to the plasma membrane. This translocation was dependent on the intracellular Ca ²⁺ rise because it was blocked by pre-incubation with BAPTA AM and mimicked by application of the Ca ²⁺ ionophore ionomycin. Transmembrane Ca ²⁺ influx induced by raising external Ca ²⁺ also caused mitochondrial trapping, which occurred more rapidly than that produced by glutamate or ATP. In astrocytes treated with the microtubule-disrupting agent nocodazole, intracellular Ca ²⁺ rises failed to induce trapping of mitochondria near plasma membrane, suggesting a role for microtubules in this phenomenon. Our data reveal the Ca ²⁺ -dependent trapping of mitochondria near the plasma membrane as a novel form of mitochondrial regulation, which is likely to control the perimembrane Ca ²⁺ dynamics and regulate signaling by mitochondria-derived reactive oxygen species. Electronic Supplementary Materials Supplementary Materials is available in the online version of this article at     

The Chemical Synthesis of E. coli tRNALys Anticodon Loop Fragment and Its Analogues

Abstract

E. coli tRNA^Lys anticodon loop fragment (Umnm⁵sUUUt⁶A) 1 and its analogues 2–6 were synthesized by the classical phosphotriester approach in solution. The preparation of suitably protected derivatives of N⁶-threonylcarbamoyladenosine 18 is also described.     

Plant regeneration from protoplasts ofCapsicum annuum L. cv. California Wonder

Plant regeneration from mesophyll protoplasts of pepper,Capsicum annuum L. cv. California Wonder has been demonstrated via shoot organogenesis. Protoplasts isolated from fully expanded leaves of 3-week-old axenic shoots when cultured in TM medium supplemented with 1 mg l ⁻¹ NAA, 1 mg l ⁻¹ 2,4-D, 0 5 mg l ⁻¹ BAP (CM 1) resulted in divisions with a frequency ranging from 20–25 %. Antioxidant ascorbic acid and polyvinylpyrrolidone (PVP) in the medium and incubation in the dark helped overcome browning of protoplasts. Microcalli and macrocalli were formed in TM medium containing 2 mg l ⁻¹ NAA and 0.5 mg l ⁻¹ BAP (CM II) and MS gelled medium containing 2 mg 1 ⁻¹ NAA and 0 5 mg 1 ⁻¹ BAP (CM III), respectively. Regeneration of plantlets was possible via caulogenesis. Microshoots, 2–5 percallus appeared on MS gelled medium enriched with 0.5 mg l ⁻¹ IAA, 2mg l ⁻¹ GA and l0mg l ⁻¹ BAP (CM IVc). Rooting of microshoots was obtained on half strength gelled medium containing 1 mg l ⁻¹ NAA and 0.5mg l ⁻¹ BAP. Protoplasts isolated from cotyledons failed to divide and degenerated eventually.     

Methanogenesis and Methanogen Diversity in Three Peatland Types of the Discontinuous Permafrost Zone,Boreal Western Continental Canada

Because recent patterns of permafrost collapse in boreal peatlands appear to enhance emissions of CH ₄ to the atmosphere, we examined methanogenesis and methanogen diversity in peat soil from peatlands with and without permafrost in two peatland complexes situated in continental western Canada. Peat soil from the active layer of permafrost bogs had very low rates of CH ₄ production (ca. 10 nmol g ^?1 day ^?1 ), and we were unable to PCR-amplify 16s rRNA gene sequences using Archaea-specific primers in four peat samples. Surface peat soil from continental bogs with no permafrost supported moderate rates of CH ₄ production (20–600 nmol g ^?1 day ^?1 ), with maximum rates in soil located close to the mean water table level. Additions of ethanol stimulated CH ₄ production rates, suggesting metabolic substrate limitations. Peat from internal lawns, which have experienced surface permafrost degradation in the past 150 years, had very rapid rates of CH₄ production (up to 800 nmol g ^?1 day ^?1 ) occurring within the soil profile. Concomitant rates of anaerobic CO ₂ production were greater in continental bogs (ca. 6 μmol g ^?1 day ^?1 ) than in internal lawns (ca. 4 μ mol g ^?1 day ^?1 ) or in permafrost bogs (2.8 μ mol g ^?1 day ^?1 ). Analysis of the 16s rRNA gene for Archaea in the continental bog indicated mostly sequences associate with Methanobacteriales and RC-I with a Methanosarcinaceae sequence in the deepest peat soil. In the internal lawn, Methanosarcinaceae were most common in peat soil with a Methanosaetaceae sequence in the deepest peat soil. This study showed that patterns of discontinuous permafrost and ongoing permafrost degradation in boreal regions create patchy soil environments for methanogens and rates of methanogenesis.     

Transglycosylation Reactions of 6-Thioguanine Acyclonucleosides

Abstract

9-(2-Acetoxyethoxy)methyl-N²-acetyl-6-thioguanine (2) undergoes two different transglycosylation reactions: i) the 7 ? 9 isomerization, which gives the respective 7-regioisomer (3) as the major product, ii) the 9 ? S⁶ glycosyl migration, which leads to a 9,S⁶-disubstituted product (4). S⁶-Methylation completely stopped the reversibility of transglycosylation.