Steric and electronic influences on the torsional energy landscape of retinal

We have performed quantum mechanical calculations for retinal model compounds to establish the rotational energy barriers for the C5-, C9-, and C13-methyl groups known to play an essential role in rhodopsin activation. Intraretinal steric interactions as well as electronic effects lower the rotational barriers of both the C9- and C13-methyl groups, consistent with experimental ²H NMR data. Each retinal methyl group has a unique rotational behavior which must be treated individually. These results are highly relevant for the parameterization of molecular mechanics force fields which form the basis of molecular dynamics simulations of retinal proteins such as rhodopsin.     

The uncoupling activity of substituted anthracene derivatives on isolated mitochondria from Phaseolus aureus

Unsubstituted anthraquinones and anthrones have a low uncoupling activity on isolated mitochondria. The presence of phenolic groups is a prerequisite for a marked effect. The number of phenolic groups is of minor importance but their substitution pattern is important. The methylene group of the anthrones increases the activity.     

Quantitative analysis of uncoupling activity of substituted phenols with a physicochemical substituent and molecular parameters

The uncoupling potency of a series of substituted phenols with rat-liver mitochondria was analyzed quantitatively with physicochemical substituent and molecular parameters such as log P, P being the partition coefficient in a phosphatidylcholine liposome/water system, log KA, KA being the acid dissociation constant, and the Taft-Kutter-Hansch steric constant, Es, for ortho-substituents. The potency evaluated from the concentration in the medium required for a defined response was analyzed, showing that the incorporation of compounds in terms of log P, a certain balance between neutral and ionized forms expressible by a parabolic function of log KA and the steric shielding effect of the ortho-substituents on the negatively charged center of ionized form are highly significant factors governing the variations in potency. The potency was also quantitatively separated into the intrinsic potency as the protonophore inside the inner mitochondrial membrane and the incorporation factor in terms of log P. Some phenols found as outliers from the correlations and some others distorting the quality of the correlations were shown to have inhibitory effects on the respiratory chain by specific and non-specific modes of action, respectively, besides uncoupling activity.     

Steric and electronic effects of the alkyl group on the activation parameters of the water substitution reaction of some cobaloximes

The activation parameters for the water substitution reactions of some organocobaloximes with thiourea in aqueous solution at I = 1 M (NaNO₃) are reported and discussed. Scatter in an isokinetic plot indicates that more than one interaction mechanism is at play. The ΔH* values are shown to be influenced by the electron withdrawing power and by the steric bulk of alkyl group. The influence of these factors on ΔS* cannot be rationalized.     

Quantitative analyses of the uncoupling activity of substituted phenols with mitochondria from flight muscles of house flies

Uncoupling activity with flight-muscle mitochondria from house flies was measured for a series of weakly acidic uncouplers (substituted phenols) and compared with the protonophoric potency across lecithin liposomal membranes. The activity was linearly related to the protonophoric potency when such factors as the stability of anionic species in the membrane phase and the difference in the pH conditions of the extramembranous aqueous phase were taken into account. Relationships of the flight-muscle activity with activities measured previously with rat-liver mitochondria and spinach chloroplasts were linear. Our findings were further evidence for the shuttle-type mechanism of the uncoupling action of weakly acidic uncouplers.     

Separation of electronic and hydrophobic effects for the papain hydrolysis of substituted N-benzoylglycine esters

The role of hydrophobic and electronic effects on the kinetic constants kcat and Km for the papain hydrolysis of a series of 22 substituted N-benzoylglycine pyridyl esters was investigated. The series studied comprises a wide variety of substituents on the N-benzoyl ring, with about a 300,000-fold range in their hydrophobicities, and 2.1-fold range in their electronic Hammet constants (sigma). It was found that the variation in the log kcat and log 1/Km constants could be explained by the following quantitative-structure activity relationships (QSAR): log 1/Km = 0.40 pi 4 + 4.40 and log 1/kcat = 0.45 sigma + 0.18. The substituent constant, pi 4, is the hydrophobic parameter for the 4-N-benzoyl substituents. QSAR analysis of two smaller sets of glycine phenyl and methyl esters produced similar results. A clear separation of the substituent effects indicates that in the case of these particular esters, acylation appears to be the rate limiting catalytic step.     

The electronic structure and radiorprotective activity of a series of substituted iminodihydrofurans]

Compounds that increase the survival rate of lethally exposed hybrid (CBA x C57B1/6)F1 mice have been revealed within the series of iminodihydrofurans. The quantum-chemical estimates, made by the MNDO method, show that substances which are capable of donor-acceptance interaction with DNA nucleotides and have the energy of donor orbitals, comparable with the electron structure of nucleotides, possess radioprotective efficacy.     

Inhibitory effects of cis- and trans-isomers of 3,5-dihydroxystilbene on the activity of mushroom tyrosinase

The effects of cis- and trans-isomers of 3,5-dihydroxystilbene on the activity of mushroom tyrosinase have been studied. The results show that both cis- and trans-isomers of 3,5-dihydroxystilbene can inhibit the diphenolase activity of the enzyme and the inhibition type was reversible. The IC(50) values were estimated as 0.405+/-0.013 and 0.705+/-0.017 mM, respectively. Kinetic analysis showed that the inhibition of cis-3,5-dihydroxystilbene and trans-3,5-dihydroxystilbene on the diphenolase activity of the enzyme belonged to competitive type, and the inhibition constants (K(I)) were determined to be 0.232+/-0.015 and 0.395+/-0.020 mM, respectively. In this investigation, the inhibitory effects of cis-3,5-dihydroxystilbene and trans-3,5-dihydroxystilbene on the diphenolase activity of mushroom tyrosinase were compared. The inhibitory capacity of cis-isomer was stronger than that of corresponding trans-isomer. Nevertheless, the trans-3,5-dihydroxystilbene was used more frequently than its corresponding cis-form compound. This research may offer some references for designing and synthesizing some novel and effective tyrosinase inhibitors. Furthermore, it may improve the use of stilbenes on the field of food preservation and depigmentation.     

Quantitative relationship between protonophoric and uncoupling activities of substituted phenols

The protonophoric activity through liposomal membranes was measured and compared with the uncoupling activity with the oxidative phosphorylation of rat-liver mitochondria for 19 substituted phenols. Quantitative analyses of the protonophoric activity of the phenols in terms of physicochemical molecular parameters showed that the activity was mostly decided by two factors: the partition coefficient between the liposome and aqueous buffer phases and the acid dissociation constant. Correlation was excellent between protonophoric and uncoupling activities when the difference in the effect of acidity of phenols between liposomal and mitochondrial membranes was taken into account. The results were further evidence for the shuttle-type of mechanism of weakly acidic uncouplers based on the Mitchell chemiosmotic hypothesis.     

Steric and counterion effects on the structure of dipicolylamine nickel complexes

Four nickel complexes each containing an R-2,2′-dipicolylamine ligand species (RDPA; R = benzyl, isopropyl, or tert-butyl) were synthesized and structurally characterized. In the absence of an interfering coordinating counterion, BzDPA and iPrDPA form 1:2 nickel:ligand complexes, with two facial ligands completing an pseudooctahedral nickel(II) coordination environment. In contrast, the sterically hindered tBuDPA ligand instead forms 1:1 metal:ligand complexes, even in the absence of associating counterions. Two novel tBuDPA nickel complexes with different counterions are described: nickel(II) chloride gives rise to an unusual 2Ni-3Cl dimer complex, while nickel(II) nitrate affords a 1:1 nickel:ligand complex which crystallizes with both fac and mer conformations in the same unit cell.     

Steric effects on activation energy for the electrochemical oxidation of organocobaloximes

Heterogeneous electron transfer rate constants were determined as a function of electrode potential for one-electron oxidation in acetonitrile (AN) at O °C of a series of organocobaloximes [R-Co(DH)₂L] bearing widely different organic groups. Reaction entropies were determined by voltammetric half-wave potential (E^r_{$\text{1}\text{2}$}) measurements in a non-isothermal cell. The electron transfer coefficients and reorganization parameters were calculated following the Marcus theory. The reaction free energies relative to a reference couple ΔG° are linearly correlated with the polar Taft constant of the organic substituent R.The steric effects on ΔG° are shown by the correlation of E^r_{$\text{sol1}\text{2}$} with the CoC bond distance.Assuming constancy of double layer effects along the series in the given solution composition, the trends of the apparent rate constants k_app were considered in order to evaluate the effects of the nature of the organic ligand on the activation energy ΔG³ of the electron transfer. The steric effects on ΔG³ are pointed out i.a. by consideration of the relationship between ΔG³ and ΔG°.     

Steric effects on the direct mutagenicity of N-acyloxy-N-alkoxyamides-probes for drug-DNA interactions

N-Acyloxy-N-alkoxyamides (see structure 1, below) are direct-acting mutagens for which a QSAR has been established that predicts with accuracy their activity in the bacterial reverse-mutation assay (Ames test) in Salmonella typhimurium TA100. Steric bulk next to oxygen on the alkoxyl side-chain in structure 4 has no impact on activity, but branching at the position adjacent (alpha) to the ester-carbonyl of the leaving group in structure 5 strongly inhibits mutagenicity. Both results reflect the manner in which these molecules interact with DNA. The alkoxyl group has greater flexibility, which minimises steric effects within the major groove. Bulk adjacent to the carbonyl of the ester group must impose conformational constraints that impede reaction at the N7 position of guanine. A new, expanded QSAR shows a clear dependence of activity on logP, although with a smaller coefficient relative to indirect-acting mutagens.     

Steric interactions and the activity of fentanyl analogs at the mu-opioid receptor

Fentanyl is a highly potent and clinically widely used narcotic analgesic. The synthesis of its analogs remains a challenge in the attempt to develop highly selective mu-opioid receptor agonists with specific pharmacological properties. In this paper, the use of flexible molecular docking in a study of the formation of complexes between a series of active fentanyl analogs and the mu-opioid receptor is described. The optimal position and orientation of fourteen fentanyl analogs in the binding pocket of the mu-receptor were determined. The major receptor amino acids and the ligand functional groups participating in the complex formation were identified. Stereochemical effects on the potency and binding are explained. The proposed model of ligand-receptor binding is in agreement with point mutation experiments explaining the role of the amino acids: Asp147, Tyr148, Asn230, His297, Trp318, His319, Cys321, and Tyr326 in the complex formation. In addition, the following amino acids were identified as being important for ligand binding or receptor activation: Ile322, Gly325, Val300, Met203, Leu200, Val143, and Ile144.     

Photophysics of 3,5-diphenoxy substituted BODIPY dyes in solution.

We have prepared two fluorescent dyes derived from 8-(4-tolyl)-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene with phenoxy and (o-bromo)phenoxy substituents at the 3,5-positions by a novel nucleophilic substitution reaction of the corresponding 3,5-dichloroBODIPY analogue. UV-vis absorption, steady-state and time-resolved fluorimetry have been used to investigate their solvent-dependent photophysical properties. The two BODIPY derivatives show narrow absorption and emission bands and display small Stokes shifts. The substituents at the 3,5-positions (phenoxy in 1 and o-bromophenoxy in 2) have a minor effect on the fluorescence quantum yields (0.16-0.40 for 1, 0.17-0.44 for 2) and lifetimes (1.09-2.51 ns for 1, 1.11-2.78 ns for 2). For both compounds, the fluorescence rate constant equals (1.5 +/- 0.1) x 10(8) s(-1).     

Steric effects on interaction of tea catechins with lipid bilayers

Interaction of tea catechins with lipid bilayers has been investigated with liposome systems. Tea catechins are classified into cis-type and trans-type from the configuration of the two hydrogens at the 2 and 3 positions on the C-ring. The amount of trans-type catechins incorporated into liposomes was less than that of the respective cis-type catechins. Furthermore, the order of the partition coefficients of catechins in an n-octanol/PBS system is the same as that of the amount incorporated into liposomes. These results indicate that in addition to the number of hydroxyl groups on the B-ring and the presence of the galloyl moiety, the stereochemical structure of the C-ring also governs the hydrophobicity and the affinity for lipid bilayers. Trans-type catechins with the galloyl moiety were located on the surface of the lipid bilayer, as well as cis-type catechins with the galloyl moiety, and perturbed the membrane structure. These different stereochemical structures should influence the affinity for lipid bilayers, the alteration of membrane structures, and the difference in the order of the biological activities.     

Effect of oxidative phosphorylation inhibitors and uncoupling agents on cAMP activity

Uncouplers of oxidative phosphorylation increased the speed of substrate oxidation and ATP hydrolysis and raised cAMP induced neuron membrane current. Different inhibitors decreased it. Both effects support the hypothesis that a signal of intracellular injected cAMP spreads to the neuron membrane as a mechanical signal. This signal propagated to the membrane along microtubules which according to this hypothesis serve as a sound generator with metabolic heat pumping.