Structure-activity relationships of organofluorine inhibitors of β-amyloid self-assembly

A broad group of structurally diverse small organofluorine compounds were synthesized and evaluated as inhibitors of β-amyloid (Aβ) self-assembly. The main goal was to generate a diverse library of compounds with the same functional group and to observe general structural features that characterize inhibitors of Aβ oligomer and fibril formation, ultimately identifying structures for further focused inhibitor design. The common structural motifs in these compounds are CF(3) -C-OH and CF(3) -C-NH groups that were proposed to be binding units in our previous studies. A broad range of potential small-molecule inhibitors were synthesized by combining various carbocyclic and heteroaromatic rings with an array of substituents, generating a total of 106 molecules. The compounds were tested by standard methods such as thioflavin-T fluorescence spectroscopy for monitoring fibril formation, biotinyl Aβ(1-42) single-site streptavidin-based assays for observing oligomer formation, and atomic force microscopy for morphological studies. These assays revealed a number of structures that show significant inhibition against either Aβ fibril or oligomer formation. A detailed analysis of the structure-activity relationship of anti-fibril and -oligomer properties is provided. These data present further experimental evidence for the distinct nature of fibril versus oligomer formation and indicate that the interaction of the Aβ peptide with chiral small molecules is not stereospecific in nature.     

pH effects on the conformational preferences of amyloid beta-peptide (1-40) in HFIP aqueous solution by NMR spectroscopy

The structure and aggregation state of amyloid beta-peptide (Abeta) in membrane-like environments are important determinants of pathological events in Alzheimer's disease. In fact, the neurotoxic nature of amyloid-forming peptides and proteins is associated with specific conformational transitions proximal to the membrane. Under certain conditions, the Abeta peptide undergoes a conformational change that brings the peptide in solution to a "competent state" for aggregation. Conversion can be obtained at medium pH (5.0-6.0), and in vivo this appears to take place in the endocytic pathway. The combined use of (1)H NMR spectroscopy and molecular dynamics-simulated annealing calculations in aqueous hexafluoroisopropanol simulating the membrane environment, at different pH conditions, enabled us to get some insights into the aggregation process of Abeta, confirming our previous hypotheses of a relationship between conformational flexibility and aggregation propensity. The conformational space of the peptide was explored by means of an innovative use of principal component analysis as applied to residue-by-residue root-mean-square deviations values from a reference structure. This procedure allowed us to identify the aggregation-prone regions of the peptide.     

Designed amyloid beta peptide fibril - a tool for high-throughput screening of fibril inhibitors

Amyloid beta peptide (Abeta) fibril formation is widely believed to be the causative event of Alzheimer's disease pathogenesis. Therapeutic approaches are therefore in development that target various sites in the production and aggregation of Abeta. Herein we present a high-throughput screening tool to generate novel hit compounds that block Abeta fibril formation. This tool is an application for our fibril model (Abeta(16-37)Y(20)K(22)K(24))(4), which is a covalent assembly of four Abeta fragments. With this tool, screening studies are complete within one hour, as opposed to days with native Abeta(1-40). A Z' factor of 0.84+/-0.03 was determined for fibril formation and inhibition, followed by the reporter molecule thioflavin T. Herein we also describe the analysis of a broad range of reported inhibitors and non-inhibitors of Abeta fibril formation to test the validity of the system.     

Benzofuran and Indole: Promising Scaffolds for Drug Development in Alzheimer's Disease

Alzheimer's disease (AD) is a progressive neurodegenerative disease with no clinically accepted treatment to cure or halt its progression. The Food and Drug Administration has approved drugs (e.g., rivastigmine, donepezil, galantamine, and memantine) that at best provide marginal benefits, thus emphasizing the urgent need to explore other molecular entities as future drug candidates for AD. Looking at the wide pharmaceutical applications of heterocyclic compounds and particularly those containing benzofuran and indole ring systems, these molecular frameworks have drawn special attention from medicinal chemists for further evaluation in numerous diseases. This article focuses on the history and recent advances of benzofuran‐ and indole‐based compounds as inhibitors of butyrylcholinesterase, acetylcholinesterase, γ‐secretase, β‐secretase, tau misfolding, and β‐amyloid aggregation.     

Equilibrium studies on enantioselective extraction of oxybutynin enantiomers by hydrophilic β‐cyclodextrin derivatives

The enantioselective extraction of hydrophobic oxybutynin (OBN) enantiomers by hydrophilic β‐cyclodextrin (β‐CD) derivatives was studied. The efficiency of extraction depends strongly on a number of process variables such as types of organic solvents and β‐CD derivatives, concentration of selector, pH, and temperature. The experimental data were described by a reactive extraction model with a homogeneous aqueous phase reaction of R,S‐OBN with β‐CD. Important parameters of this model were determined experimentally. The physical distribution coefficients for molecular and ionic OBN were 4.96 × 10^?3 and 9.52, respectively. The equilibrium constants of the complexation reactions were 1770 and 1340 L/mol for S‐ and R‐OBN, respectively. By modeling and experiment, an optimal extraction condition with pH of 5 and HP‐β‐CD concentration of 0.1 mol/L was obtained with enantioselectivity (α) of 1.26, which was close to the theoretical maximum of 1.32 and performance factor (pf_i) of 0.036. The model was verified experimentally with excellent results. © 2011 American Institute of Chemical Engineers AIChE J, 2011     

Cholesterol: A Key in the Pathogenesis of Alzheimer's Disease

Herein we highlight recent advances in our understanding of the role of cholesterol in Alzheimer′s disease (AD). It has been proposed that cholesterol could enhance the risk of AD, and the interaction between cholesterol and amyloid‐β peptide 42 (Aβ42) has been studied extensively, yet until recently, the specific interaction mechanisms between them and how this affects Aβ42 aggregation had not yet been fully explored and had remained ambiguous. Vendruscolo and co‐workers addressed these issues in their recent article entitled “Cholesterol catalyses Aβ42 aggregation through a heterogeneous nucleation pathway in the presence of lipid membranes” (Habchi et al., Nat. Chem. 2018 , 10, 673). In this article, the authors revealed the mechanism behind cholesterol‐catalyzed Aβ42 aggregation, providing the potential to address the molecular origins of AD, thereby opening a new avenue for effective AD therapy.     

Studies on the Interactions of Copper and Zinc Ions with ��-Amyloid Peptides by a Surface Plasmon Resonance Biosensor

The aggregation of β-amyloid peptide (Aβ) into fibrils plays an important role in the pathogenesis of Alzheimer’s disease (AD). Metal ions including copper and zinc are closely connected to the precipitation and toxicity of Aβ. In this study, a surface plasmon resonance (SPR) biosensor was constructed to investigate the interactions between Aβ and metal ions. Aβ peptide was immobilized on the SPR chip surface through a preformed alkanethiol self-assembled monolayer (SAM). Our observations indicate that the immobilized Aβ undergoes a conformational change upon exposure to the metal ions. A difference in metal binding affinity between Aβ_1–28 and Aβ_1–42 was also detected. The results suggest that SPR is an effective method to characterize the interactions between Aβ and metal ions.     

Design and Synthesis of Ranitidine Analogs as Multi-Target Directed Ligands for the Treatment of Alzheimer’s Disease

The aggregation of amyloid β (Aβ) peptides and deposition of amyloid plaques are implicated in the pathogenesis of Alzheimer’s disease (AD). Therefore, blocking Aβ aggregation with small molecules has been proposed as one therapeutic approach for AD. In the present study, a series of ranitidine analogs containing cyclic imide isosteres were synthesized and their inhibitory activities toward Aβ aggregation were evaluated using in vitro thioflavin T assays. The structure–activity relationship revealed that the 1,8-naphthalimide moiety provided profound inhibition of Aβ aggregation and structural modifications on the other parts of the parent molecule (compound 6) maintained similar efficacy. Some of these ranitidine analogs also possessed potent inhibitory activities of acetylcholinesterase (AChE), which is another therapeutic target in AD. These ranitidine analogs, by addressing both Aβ aggregation and AChE, offer insight into the key chemical features of a new type of multi-target directed ligands for the pharmaceutical treatment of AD.     

In silico theoretical molecular modeling for Alzheimer's disease: the nicotine-curcumin paradigm in neuroprotection and neurotherapy

The aggregation of the amyloid-β-peptide (AβP) into well-ordered fibrils has been considered as the key pathological marker of Alzheimer's disease. Molecular attributes related to the specific binding interactions, covalently and non-covalently, of a library of compounds targeting of conformational scaffolds were computed employing static lattice atomistic simulations and array constructions. A combinatorial approach using isobolographic analysis was stochastically modeled employing Artificial Neural Networks and a Design of Experiments approach, namely an orthogonal Face-Centered Central Composite Design for small molecules, such as curcumin and glycosylated nornicotine exhibiting concentration-dependent behavior on modulating AβP aggregation and oligomerization. This work provides a mathematical and in silico approach that constitutes a new frontier in providing neuroscientists with a template for in vitro and in vivo experimentation. In future this could potentially allow neuroscientists to adopt this in silico approach for the development of novel therapeutic interventions in the neuroprotection and neurotherapy of Alzheimer's disease. In addition, the neuroprotective entities identified in this study may also be valuable in this regard.     

Hereditary and Sporadic Forms of A��-Cerebrovascular Amyloidosis and Relevant Transgenic Mouse Models

Cerebral amyloid angiopathy (CAA) refers to the specific deposition of amyloid fibrils in the leptomeningeal and cerebral blood vessel walls, often causing secondary vascular degenerative changes. Although many kinds of peptides are known to be deposited as vascular amyloid, amyloid-β (Aβ)-CAA is the most common type associated with normal aging, sporadic CAA, Alzheimer’s disease (AD) and Down’s syndrome. Moreover, Aβ-CAA is also associated with rare hereditary cerebrovascular amyloidosis due to mutations within the Aβ domain of the amyloid precursor protein (APP) such as Dutch and Flemish APP mutations. Genetics and clinicopathological studies on these familial diseases as well as sporadic conditions have already shown that CAA not only causes haemorrhagic and ischemic strokes, but also leads to progressive dementia. Transgenic mouse models based on familial AD mutations have also successfully reproduced many of the features found in human disease, providing us with important insights into the pathogenesis of CAA. Importantly, such studies have pointed out that specific vastopic Aβ variants or an unaltered Aβ42/Aβ40 ratio favor vascular Aβ deposition over parenchymal plaques, but higher than critical levels of Aβ40 are also observed to be anti-amyloidogenic. These data would be important in the development of therapies targeting amyloid in vessels.     

Effects of Linkers and Substitutions on Multitarget Directed Ligands for Alzheimer’s Diseases: Emerging Paradigms and Strategies

Alzheimer’s disease (AD) is multifactorial, progressive and the most predominant cause of cognitive impairment and dementia worldwide. The current “one-drug, one-target” approach provides only symptomatic relief to the condition but is unable to cure the disease completely. The conventional single-target therapeutic approach might not always induce the desired effect due to the multifactorial nature of AD. Hence, multitarget strategies have been proposed to simultaneously knock out multiple targets involved in the development of AD. Herein, we provide an overview of the various strategies, followed by the multitarget-directed ligand (MTDL) development, rationale designs and efficient examples. Furthermore, the effects of the linkers and substitutional functional groups on MTDLs against various targets of AD and their modes of action are also discussed.     

Insight into the kinetic of amyloid beta (1-42) peptide self-aggregation: elucidation of inhibitors' mechanism of action

The initial transition of amyloid beta (1-42) (Abeta42) soluble monomers/small oligomers from unordered/alpha-helix to a beta-sheet-rich conformation represents a suitable target to design new potent inhibitors and to obtain effective therapeutics for Alzheimer's disease. Under optimized conditions, this reliable and reproducible CD kinetic study showed a three-step sigmoid profile that was characterized by a lag phase (prevailing unordered/alpha-helix conformation), an exponential growth phase (increasing beta-sheet secondary structure) and a plateau phase (prevailing beta-sheet secondary structure). This kinetic analysis brought insight into the inhibitors' mechanism of action. In fact, an increase in the duration of the lag phase can be related to the formation of an inhibitor-Abeta complex, in which the non-amyloidogenic conformation is stabilized. When the exponential rate is affected exclusively, such as in the case of Congo red and tetracycline, then the inhibitor affinity might be higher for the pleated beta-sheet structure. Finally, by adding the inhibitor at the end of the exponential phase, the soluble protofibrils can be disrupted and the Abeta amyloidogenic structure can revert into monomers/small oligomers. Congo red and tetracycline preferentially bind to amyloid in the beta-sheet conformation because both decreased the slope of the exponential growth, even if to a different extent, whereas no effect was observed for tacrine and galantamine. Some very preliminary indications can be derived about the structural requirements for binding to nonamyloidogenic or beta-sheet amyloid secondary structure for the development of potent antiaggregating agents. On these premises, memoquin, a multifunctional molecule that was designed to become a drug candidate for the treatment of Alzheimer's disease, was investigated under the reported circular dichroism assay and its anti-amyloidogenic mechanism of action was elucidated.     

Trends in the Molecular Pathogenesis and Clinical Therapeutics of Common Neurodegenerative Disorders

The term neurodegenerative disorders, encompasses a variety of underlying conditions, sporadic and/or familial and are characterized by the persistent loss of neuronal subtypes. These disorders can disrupt molecular pathways, synapses, neuronal subpopulations and local circuits in specific brain regions, as well as higher-order neural networks. Abnormal network activities may result in a vicious cycle, further impairing the integrity and functions of neurons and synapses, for example, through aberrant excitation or inhibition. The most common neurodegenerative disorders are Alzheimer’s disease, Parkinson’s disease, Amyotrophic Lateral Sclerosis and Huntington’s disease. The molecular features of these disorders have been extensively researched and various unique neurotherapeutic interventions have been developed. However, there is an enormous coercion to integrate the existing knowledge in order to intensify the reliability with which neurodegenerative disorders can be diagnosed and treated. The objective of this review article is therefore to assimilate these disorders’ in terms of their neuropathology, neurogenetics, etiology, trends in pharmacological treatment, clinical management, and the use of innovative neurotherapeutic interventions.     

The alkylation of naphthalene over three-dimensional large pore zeolites: The influence of zeolite structure and alkylating agent on the selectivity for dialkylnaphthalenes

In order to elucidate how zeolite structure and alkylating agent play roles in the shape-selective catalysis, the alkylation, i.e., isopropylation, sec-butylation, and tert-butylation, of naphthalene (NP) was examined over three-dimensional twelve-membered (12-MR) zeolites, Y (FAU), Beta (BEA), and CIT-1 (CON), and compared to that of H-mordenite (MOR). The β,β-selectivities (for β,β-dialkylnapthalene (β,β-DAN)) and the 2,6-selctivities (for 2,6-dialkylnaphthalene (2,6-DAN)) among DAN isomers varied with the types of zeolites and alkylating agents. FAU, BEA, and CON gave only low selectivities for 2,6-diisopropylnaphthalene (2,6-DIPN) in the isopropylation, and predominant isomers were bulky and thermodynamically unstable ,β-DIPN (1,3-, 1,6-, and 1,7-DIPN) and ,-DIPN (1,4- and 1,5-DIPN) at lower temperatures, and the formation of the less bulky and thermodynamically stable β,β-DIPN (2,6- and 2,7-DIPN) increased with increasing the temperature: they have quite different features from the shape-selective catalysis over MOR. These results suggest that FAU, BEA, and CON are not shape-selective in the isopropylation, and that the isopropylation is principally controlled kinetically at lower temperatures, and thermodynamically at higher temperatures.

The β,β-selectivities over FAU, BEA, and CON increased with increasing the bulkiness of alkylating agents, and were almost 100% in the tert-butylation. On the other hand, the 2,6-selectivities over these zeolites were much lower than those over MOR at a typically moderate temperature, 250 °C. These results mean that FAU, BEA, and CON have the shape-selective nature to give the less bulky isomers, β,β-DAN, in the sec-butylation and tert-butylation by using bulkier alkylating agents, particularly 2-methyl-2-propene: they can differentiate β,β-DAN from their isomers at the transition states by the steric restriction of zeolite channels. However, the channels of these zeolites are too large for differentiating 2,6- and 2,7-DAN even with 2-methyl-2-propene.     

Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field,Semi-Empirical,and Density Functional Theory Calculations

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.