Pseudopeptide Amyloid Aggregation Inhibitors: In Silico, Single Molecule and Cell Viability Studies.

Neurodegeneration in Alzheimer's disease (AD) is defined by pathology featuring amyloid-ß (Aß) deposition in the brain. Aß monomers themselves are generally considered to be nontoxic, but misfold into ß-sheets and aggregate to form neurotoxic oligomers. One suggested strategy to treat AD is to prevent the formation of toxic oligomers. The SG inhibitors are a class of pseudopeptides designed and optimized using molecular dynamics (MD) simulations for affinity to Aß and experimentally validated for their ability to inhibit amyloid-amyloid binding using single molecule force spectroscopy (SMFS). In this work, we provide a review of our previous MD and SMFS studies of these inhibitors and present new cell viability studies that demonstrate their neuroprotective effects against Aß(1-42) oligomers using mouse hippocampal-derived HT22 cells. Two of the tested SG inhibitors, predicted to bind Aß in anti-parallel orientation, demonstrated neuroprotection against Aß(1-42). A third inhibitor, predicted to bind parallel to Aß, was not neuroprotective. Myristoylation of SG inhibitors, intended to enhance delivery across the blood-brain barrier (BBB), resulted in cytotoxicity. This is the first use of HT22 cells for the study of peptide aggregation inhibitors. Overall, this work will inform the future development of peptide aggregation inhibitors against Aß toxicity.

Exploring Amyloid-ß Dimer Structure Using Molecular Dynamics Simulations.

A major hallmark of Alzheimer's disease (AD) is the aggregation of amyloid-ß peptides in the brains of people afflicted by the disease. The exact pathway to this catastrophic event is unknown. In this work, a total of 9.5 µs molecular dynamics simulations have been performed to investigate the structure and dynamics of the smallest form of toxic Aß oligomers, i.e., the Aß dimers. This study suggests that specific hydrophobic regions are vital in the aggregation process. Different possible structures for Aß dimers are reported along with their relative binding affinity. These data may be used to design better Aß-aggregation inhibitors. The diversity of the dimer structures suggests several aggregation pathways.

New Orbital Symmetry-Allowed Route for Cycloreversion of Silacyclobutane and Its Methyl Derivatives.

The [2+2] cycloreversion of silacyclobutane (SCB) and its two methyl-substituted derivatives, 1-methyl-1-silacyclobutane (MSCB) and 1,1-dimethyl-1-silacyclobutane (DMSCB), were studied using ab initio quantum chemistry calculations. The second-order Møller-Plesset (MP2) perturbation theory, complete active space self-consistent field (CASSCF), and coupled clusters methods were used to explore both the concerted and the stepwise cycloreversions of the three molecules. In addition to the orbital symmetry-forbidden supra-supra [2s+2s] transition state, a new orbital symmetry-allowed supra-antara [2s+2a] transition state was discovered for the concerted route for all three molecules. Both methyl substitution and temperature play a role in the kinetic competition between the [2s+2s] and [2s+2a] routes. At 0 and 298 K, the concerted [2s+2a] cycloreversion is kinetically more favorable than the [2s+2s] cycloreversion for SCB, but the opposite is true for MSCB and DMSCB. With increasing temperatures to above 600 and 1800 K, the [2s+2a] cycloreversion becomes more favorable for MSCB and DMSCB, respectively. The methyl substitutions on Si atoms also affect the stability of the diradical intermediate formed by Si-C bond rupture, leading to a less stable diradical with increasing methyl groups.

d-Amino Acid Pseudopeptides as Potential Amyloid-Beta Aggregation Inhibitors.

A causative factor for neurotoxicity associated with Alzheimer's disease is the aggregation of the amyloid-ß (Aß) peptide into soluble oligomers. Two all d-amino acid pseudo-peptides, SGB1 and SGD1, were designed to stop the aggregation. Molecular dynamics (MD) simulations have been carried out to study the interaction of the pseudo-peptides with both Aß13⁻23 (the core recognition site of Aß) and full-length Aß1⁻42. Umbrella sampling MD calculations have been used to estimate the free energy of binding, ∆G, of these peptides to Aß13⁻23. The highest ∆Gbinding is found for SGB1. Each of the pseudo-peptides was also docked to Aß1⁻42 and subjected up to seven microseconds of all atom molecular dynamics simulations. The resulting structures lend insight into how the dynamics of Aß1⁻42 are altered by complexation with the pseudo-peptides and confirmed that SGB1 may be a better candidate for developing into a drug to prevent Alzheimer's disease.

NMR and computational studies of the configurational properties of spirodioxyselenuranes. Are dynamic exchange processes or temperature-dependent chemical shifts involved?

Spirodioxyselenurane 4a and several substituted analogs revealed unexpected (1)H NMR behavior. The diastereotopic methylene hydrogens of 4a appeared as an AB quartet at low temperature that coalesced to a singlet upon warming to 267 K, suggesting a dynamic exchange process with a relatively low activation energy. However, DFT computational investigations indicated high activation energies for exchange via inversion through the selenium center and for various pseudorotation processes. Moreover, the NMR behavior was unaffected by the presence of water or acid catalysts, thereby ruling out reversible Se-O or benzylic C-O cleavage as possible stereomutation pathways. Remarkably, when 4a was heated beyond 342 K, the singlet was transformed into a new AB quartet. Further computations indicated that a temperature dependence of the chemical shifts of the diastereotopic protons results in convergence upon heating, followed by crossover and divergence at still higher temperatures. The NMR behavior is therefore not due to dynamic exchange processes, but rather to temperature dependence of the chemical shifts of the diastereotopic hydrogens, which are coincidentally equivalent at intermediate temperatures. These results suggest the general need for caution in ascribing the coalescence of variable-temperature NMR signals of diastereotopic protons to dynamic exchange processes that could instead be due to temperature-dependent chemical shifts and highlight the importance of corroborating postulated exchange processes through additional computations or experiments wherever possible.

Structures and stabilities of Fe2+/3+ complexes relevant to Alzheimer's disease: an ab initio study.

Iron is one of the most abundant metals found in senile plaques of post mortem patients with Alzheimer's disease. However, the interaction mode between iron ions and ß-amyloid peptide as well as their precise affinity is unknown. In this study we apply ab initio computational methodology to calculate binding energies of Fe(2+/3+) with the His13-His14 sequence of Aß, as well as other important ligands such as His6 and Tyr10. Calculations were carried out at the "MP2/6-311+G(2df,2p)"//B3LYP/6-31+G(d) level of theory and solvent effects included by the IEFPCM procedure. Several reaction paths for the binding of imidazole, phenol, and the His13-His14 fragment (modeled by N-(2-(1H-imidazol-4-yl)ethyl)-3-(1H-imidazol-4-yl)propanamide) were sequentially explored. The results show that the most stable complexes containing His13-His14 and phenolate of Tyr10 are the pentacoordinated [Fe(2+)(O-HisHis)(PhO(-))(H(2)O)](+) and [Fe(3+)(N-HisHis)(PhO(-))(H(2)O)](+) compounds and that simultaneous coordination of tyrosine and His13-His14 to Fe(2+/3+) is thermodynamically favorable in water at physiological pH. Computed Raman spectra confirm the conclusion obtained by Miura et al. ( Biochemistry 2000 , 39 , 7024 ) that tyrosine is coordinated to Fe(3+) but do not exclude coordination of imidazoles. Finally, calculations of standard reduction potentials indicate that phenol coordination reduces the redox activity of the iron/Aß complexes.

The chemistry of Alzheimer's disease.

The chemistry of Alzheimer's disease is largely centred on the amyloid beta-peptide, its formation, structure, and interactions with metals, membranes, proteins and other species. This critical review summarizes the current state of knowledge (252 references).

Mechanism of hydrogen peroxide production by copper-bound amyloid beta peptide: a theoretical study.

The amyloid beta peptide (Abeta) of Alzheimer's disease evolves hydrogen peroxide in vitro in the presence of Cu(II), external reducing agents, and molecular oxygen, without producing detectable amounts of the one-electron reduced intermediate, superoxide, O(2)(-*). The mechanism of this process was examined by ab initio computational chemistry techniques in systems that model the binding of Cu(II) to the His13His14 fragment of Abeta. The catalytic cycle begins with the reduction of the most stable Cu(II) complex to the most stable Cu(I) complex. This Cu(I) complex forms a Cu(II)-like adduct with (3)O(2) that cannot dissociate in water to yield O(2)(-*). However, it can be reduced by proton-coupled electron transfer to an adduct between HOO(-) and the Cu(II)-like complex, which in turn can be protonated. The protonated complex decomposes to yield H(2)O(2) by an associative-dissociative mechanism, thus completing the cycle.

Can copper binding to the prion protein generate a misfolded form of the protein?

The native prion protein (PrP) has a two domain structure, with a globular folded alpha-helical C-terminal domain and a flexible extended N-terminal region. The latter can selectively bind Cu(2+) via four His residues in the octarepeat (OR) region, as well as two sites (His96 and His111) outside this region. In the disease state, the folded C-terminal domain of PrP undergoes a conformational change, forming amorphous aggregates high in beta-sheet content. Cu(2+) bound to the ORs can be redox active and has been shown to induce cleavage within the OR region, a process requiring conserved Trp residues. Using computational modeling, we have observed that electron transfer from Trp residues to copper can be favorable. These models also reveal that an indole-based radical cation or Cu(+) can initiate reactions leading to protein backbone cleavage. We have also demonstrated, by molecular dynamics simulations, that Cu(2+) binding to the His96 and His111 residues in the remaining PrP N-terminal fragment can induce localized beta-sheet structure, allowing us to suggest a potential mechanism for the initiation of beta-sheet misfolding in the C-terminal domain by Cu(2+).

Pseudopeptide Designed to Inhibit Oligomerization and Redox Chemistry in Alzheimer?s Disease.

Aggregation of amyloid beta peptide (A?) and inflammatory processes associated with the generation of superoxide, hydrogen peroxide, and hydroxyl radicals are responsible for neurotoxicity in Alzheimer?s disease. The latter are a result of the redox activity of copper-bound A? complexes with molecular oxygen. A ligand (PI1), previously designed to compete with A? for copper, and a pseudopeptide (SGC1) with a property of breaking the self-aggregation of A?, are attached to each other to form a new pseudopeptide (TGC1) in this study. Using a combination of density functional theory and molecular dynamics simulations, we show that TGC1 should have the ability to inhibit self-aggregation of A?, prevent the binding of copper to A?, and quench the redox activity of the copper. This trifunctional ligand is a good candidate for development into an anti-Alzheimer drug.

A DFT study on the formation of a phosphohistidine intermediate in prostatic acid phosphatase.

Histidine phosphatases are a class of enzymes that are characterized by the presence of a conserved RHGXRXP motif. This motif contains a catalytic histidine that is being phosphorylated in the course of a dephosphorylation reaction catalyzed by these enzymes. Prostatic acid phosphatase (PAP) is one such enzyme. The dephosphorylation of phosphotyrosine by PAP is a two-step process. The first step involves the transfer of a phosphate group from the substrate to the histidine (His12). The present study reports on the details of the first step of this reaction, which was investigated using a series of quantum chemistry calculations. A number of quantum models were constructed containing various residues that were thought to play a role in the mechanism. In all these models, the transition state displayed an associative character. The transition state is stabilized by three active site arginines (Arg11, Arg15, and Arg79), two of which belong to the aforementioned conserved motif. The work also demonstrated that His12 could act as a nucleophile. The enzyme is further characterized by a His257-Asp258 motif. The role of Asp258 has been elusive. In this work, we propose that Asp258 acts as a proton donor which becomes protonated when the substrate enters the binding pocket. Evidence is also obtained that the transfer of a proton from Asp258 to the leaving group is possibly mediated by a water molecule in the active site. The work also underlines the importance of His257 in lowering the energy barrier for the nucleophilic attack.

Ab initio and QM/MM study of electron addition on the disulfide bond in thioredoxin.

Thioredoxin controls the intracellular redox potential through a disulfide/dithiol couple. Under conditions of oxidative stress, this protein functions via one-electron exchange, in which formation of the disulfide radical anion occurs. Combined quantum mechanical (QM) and molecular mechanical (MM) calculations using two- and three-level ONIOM schemes were performed on the thioredoxin (Trx) protein of Chlamydomonas reinhardtii in its oxidized-disulfide and one-electron-reduced forms. In both cases, the active site disulfide moiety was described at the MP2(fc)/6-31+G(d) level, and larger regions of varying sizes around the active site were described at the B3LYP/6-31+G(d) level. The remainder of the 112 residues and 33 water molecules of the crystal structure (PDB entry 1EP7) were described by the AMBER force field. Adiabatic electron affinities were calculated for the disulfide bond in all systems. Separate QM or QM/QM calculations were performed on the QM regions to establish the role of the remainder of the protein on the active site properties. The radical anion species becomes more stable as the number of amide groups in the vicinity increases. One-electron reduction potentials were calculated for the small molecule models, and approximated for the protein for which the values are similar to the experimental one (approximately 0 V). This high reduction potential is due to interaction with the charged end of Lys40, as indicated by mutation in silico to norleucine. The inclusion of the protonated Asp30 side chain and a water molecule in the QM region leads to an increase in the electron affinity. Proton transfer from the Asp30 side chain to the Cys39 sulfur in the radical anion species is strongly disfavored. The radical anion is more stable than the protonated form, which is consistent with experimental results.

ß- N-Methylamino-l-alanine (BMAA) Not Involved in Alzheimer's Disease.

ß- N-Methylamino-l-alanine (BMAA) is a neurotoxic agent implicated in ALS as well as Parkinson's and Alzheimer's diseases. It is produced by blue-green algae and could find its way via fish and seafood into the human food supply. Isolation from biological samples yields the compound in monomeric and protein-bound form. It has been suggested that the protein-bound fraction may result from genetic misincorporation into proteins in place of serine. Concomitant misfolding of the mutated proteins may be responsible for the neurological diseases. Recent reports that contradict the misincorporation theory leave unresolved the nature of the protein-bound form of BMAA. We have found from quantum mechanical calculations on model systems that it is possible to bind BMAA with high affinity in a noncovalent fashion to proteins. Because of our interest in Alzheimer's disease, molecular dynamics simulations were applied to search for such binding between BMAA and the ß-amyloid peptide and to discover whether replacement of either of its two serine residues could affect its aggregation into neurotoxic oligomers. No stable noncovalently bound complex was found, and it was concluded that incorporation of BMAA in place of serine would not alter the conformational dynamics of the ß-amyloid peptide.

Molecular dynamics study of the beta amyloid peptide of Alzheimer's disease and its divalent copper complexes.

The Abeta1-42 monomer structure was assessed with a 790 ns molecular dynamics (MD) simulation, and the results were compared with the NMR experiment on Abeta10-35 and Abeta1-40. Previous theoretical work in a model of the His13-His14 region of Abeta defined the possible Cu(II) binding geometries at this site (Raffa et al. J. Biol. Inorg. Chem. 2005, 10, 887-902). MD simulations totalling almost 2 micros were also carried out on Cu(II)/Abeta1-42 systems, using the ab initio structures as templates for the copper binding site. This work finds that the copper-free Abeta1-42 system may stabilize after approximately 350 ns into a collapsed coil conformation, and we find good agreement with some, but not all, of the structural features determined experimentally for the Abeta10-35 and Abeta1-40 peptides. The results of the Cu(II)/Abeta1-42 systems are compared to the Cu(II)-free Abeta1-42 simulation.

Copper(I) Chelators for Alzheimer's Disease.

A component of the neurotoxicity of the beta amyloid peptide (Aß) of Alzheimer's disease is its ability to generate superoxide, hydrogen peroxide, and hydroxyl radicals by reaction of its reduced copper complex Aß/Cu+ with molecular oxygen. The objective of the present work was to devise compounds, L, that could remove Cu+ from Aß/Cu+, with the property that L/Cu+ itself would not be capable of reducing O2 or hydrogen peroxide. We show by density functional calculations that several pincer-type compounds with two imidazole rings and a sulfur or nitrogen have the desired combination of Cu+ binding affinity and Cu2+ reduction potential.

Computational modelling of the redistribution of copper isotopes by proteins in the liver.

Changes in the stable isotope composition of copper in blood serum as a result of biological processes in the liver were quantified as coupled equilibrium fractionation processes. The model used calculated reduced partition function ratios corresponding to interactions involving individual proteins using Density Functional Theory. This quantified the effect that each process had on the redistribution of copper isotopes in the liver. It was not possible to calculate the reduced partition function of CTR1 as a high resolution crystal structure of its copper binding domains are unavailable at the time of writing, and an optimization process was used to estimate the reduced partition function of CTR1 and constrain the possible isotopic fractionation associated with interactions involving CTR1 independent of direct DFT calculations and assumptions of its structure. The exchange of copper between ceruloplasmin and ATP7B has the most significant impact on the copper isotopic composition of blood serum. The model calculation for the isotopic composition of ceruloplasmin and albumin are δ65Cu = (-0.54 ± 0.10)‰ and δ65Cu = (0.08 ± 0.25)‰ respectively, assuming that serum is 90% ceruloplasmin and 10% albumin using a measured δ65Cu of serum of (0.52 ± 0.08)‰. The model also predicts that the isotopic composition of the tri-nuclear binding motif of ceruloplasmin may be relatively depleted in the lighter isotope of Cu compared to the other copper binding sites by as much as -1.08 ± 0.45‰.

Alzheimer's disease and the 'ABSENT' hypothesis: mechanism for amyloid beta endothelial and neuronal toxicity.

Alzheimer's disease [AD] is the most common cause of dementia among people age 65 and older. One of the biggest stumbling blocks in developing effective drug therapy for Alzheimer's disease has been the lack of a comprehensive hypothesis that explains the mechanism behind all of the histopathological changes seen in patients suffering from Alzheimer's disease. An overview of the currently popular 'amyloid' and 'vascular' hypotheses for AD demonstrates that neither hypothesis by itself can explain all the known histopathological and biochemical lesions seen in Alzheimer's disease. The paper presents a hypothesis that tries to explain the mechanism behind almost all the histopathological changes, and varying clinical manifestations seen in both diagnosed AD and Vascular Dementia [VaD]. The new hypothesis is based on the known dual toxicity of beta amyloid to both vascular and neuronal tissues, their synergy and the resultant net effect on the onset and progression of AD. The new hypothesis therefore will be known as the Amyloid Beta Synergistic Endothelial and Neuronal Toxicity [ABSENT] hypothesis. The ABSENT hypothesis will try to show the common chemical mechanism behind almost all of the pathological changes seen in AD. According to the ABSENT hypothesis, beta amyloid itself generates all the free radicals that cause both vascular dysfunction and the neuronal damage seen in AD. The chemical mechanism proposed is based on evidence from physical chemistry experiments, calculations as well as in vitro/in vivo experiments. The ABSENT hypothesis does not favor one mode of beta amyloid-induced brain damage over the other, rather it considers the net effects of the neuronal stress/damage caused by both the cerebrovascular dysfunction and direct neurotoxicity caused by beta amyloid. The hypothesis states that each patient has a different balance of predisposing factors that modulate the extent of neurotoxicity and cerebrovascular dysfunction caused by beta amyloid and thereby explains the wide range and mixed nature of damage and dysfunction seen in the studies done on patients diagnosed with AD, VaD or 'mixed dementias'. According to the hypothesis, beta amyloid peptides are necessary if not sufficient to cause AD, VaD and mixed senile dementias. The hypothesis, therefore, proposes the term Beta Amyloid Dementias [BAD] to describe the conditions currently covered by the diagnoses of 'AD', 'VaD' and 'Mixed [senile] Dementias'. Finally, the ABSENT hypothesis tries to put forth a direct chemical mechanism behind the apparent synergy and increased association between old age, pre- and coexisting vascular disease, diabetes and AD.

The radical model of Alzheimer's disease: specific recognition of Gly29 and Gly33 by Met35 in a beta-sheet model of Abeta: an ONIOM study.

The Radical Model of Alzheimer's Disease (AD) is presented in some detail. The model provides a unified picture for the role of the amyloid beta peptide (Abeta), Met35, copper ions, oxygen, beta sheet secondary structure, and the generation of hydrogen peroxide, in mediating oxidative stress in AD. It predicts a role for glycyl radicals as long-lived species which can transport the damage into cell membranes and initiate lipid peroxidation. Previous work has established the thermodynamic and kinetic viability of most of the steps. In the present work, QM/MM and Amber calculations reveal that self assembly of antiparallel beta-sheet which brings Met35 into the required close proximity to a glycine residue is more likely if the residue is Gly29 or Gly33, than any of the other four glycine residues of Abeta.

Why Do Catalytic Quantities of Lewis Acid Generally Yield More Product than 1.1 Equiv in the Intramolecular Diels-Alder Reaction with a Furan Diene? 2.(1) AM1 Calculations and Mathematical Simulation of the Equilibria.

The results presented here provide additional support for our hypothesis based on the relative basicity of the reaction controlling functional group to rationalize experimental observations on intramolecular Diels-Alder reactions with a furan diene (IMDAF) regarding the quantity (0.1 or 1.1 equiv) of Lewis acid required to facilitate the reaction most effectively. Heats of formation, DeltaH(f), and heats of reaction, DeltaH(R), have been obtained using AM1 calculations for 26 IMDAF reactions. These DeltaH(R) are generally exothermic (indicating that these IMDAF reactions are favorable) and can be qualitatively correlated with experimental yields of adduct, thereby providing a means of predicting the feasibility of the IMDAF promoted by 0.1 equiv of Lewis acid. The equilibria involved in the Lewis acid-promoted IMDAF reaction have been qualitatively interpreted using reaction coordinate diagrams and quantitatively investigated by generating a mathematical simulation of the reaction scheme. This demonstrates that the experimental behavior of the IMDAF reaction is well represented by the relative basicity hypothesis and that the LA concentration-dependent behavior should also be observed for other Lewis acid-promoted organic reactions.

Chiroptical Properties of the Ketene and Diazo Chromophores. 1. Conformation and Optical Activity of 1-Alken-1-ones and 1-Diazoalkanes vs Aldehydes.

Ab initio methods have been employed to study the conformational behavior and chiroptical properties of acyclic, structurally related aldehydes, ketenes, and diazoalkanes of the type MeCHRCH=XY. The study involved aldehydes 1, 4, and 7 (XY = O, R = H, Me, Et, correspondingly), ketenes (1-alken-1-ones) 2, 5, and 8 (XY = CO, R = H, Me, Et), and 1-diazoalkanes 3, 6, and 9 (XY = NN, R = H, Me, Et). Geometries were optimized at the B3LYP/6-31G level, stationary points were characterized by vibrational frequency analysis, and final energies of 7-9 were obtained at the B3LYP/6-311+G//B3LYP/6-31G level. The chiroptical properties were calculated by the CIS/6-31+G method. It was found that rotational barriers of the functional group (CHXY) about the CC bond are lowered in the following order: aldehydes (1.5-2.1 kcal mol(-1)) > ketenes (1.3-1.6) > diazoalkanes (0.5-0.7). A conformer with the C=X bond eclipsed by an alpha-hydrogen is the global minimum of the ketenes and diazoalkanes, unlike the aldehydes where eclipsing by an alpha-alkyl group is preferred over a hydrogen. In all three classes of compounds, the optical rotational strength of the n-pi transition is greatest for conformers with the dihedral angle, CCCX, in the range 80-100 degrees. Within this range, the signs of the n-pi rotational strengths for the ketenes and diazoalkanes are opposite to ones for the aldehydes. As a whole, the torsional dependencies of the n-pi rotational strength of the ketene and diazo chromophores can be explained within the framework of a model of "through-bond" perturbation. CD spectra of (S)-alpha-methyl-substituted butanal (7), 1-penten-1-one (8), and 1-diazobutane (9) were obtained experimentally. The calculated chiroptical properties of equilibrium mixtures of conformers of compounds 7-9 are in agreement with experimental data.