Donepezil structure-based hybrids as potential multifunctional anti-Alzheimer’s drug candidates

A new series of multifunctional hybrids, based on the structure of the donepezil (DNP) drug, have been developed and evaluated as potential anti Alzheimer’s disease (AD) agents. The rationale of this study was the conjugation of a benzylpiperidine/benzylpiperazine moiety with derivatives of bioactive heterocyclics (benzimidazole or benzofuran), to mimic the main structure of DNP and to endow the hybrids with additional relevant properties such as inhibition of amyloid beta (Aβ) peptide aggregation, antioxidant activity and metal chelation. Overall, they showed good activity for AChE inhibition (IC₅₀=4.0–30.0 μΜ) and moderate ability for inhibition of Aβ_1–42 self-mediated aggregation. The hybrids containing chelating groups showed improvement in the inhibition of Cu-induced Aβ₄₂ aggregation and the antioxidant capacity. Moreover, neuroprotective effects of these compounds were evidenced in neuroblastoma cells after Aβ_1–42 induced toxicity. Structure–activity relationship allowed the identification of some promising compounds and the main determinant structural features for the targeted properties.     

Fast and reliable prediction of domain–peptide binding affinity using coarse-grained structure models

Domain–peptide recognition and interaction are fundamentally important for eukaryotic signaling and regulatory networks. It is thus essential to quantitatively infer the binding stability and specificity of such interaction based upon large-scale but low-accurate complex structure models which could be readily obtained from sophisticated molecular modeling procedure. In the present study, a new method is described for the fast and reliable prediction of domain–peptide binding affinity with coarse-grained structure models. This method is designed to tolerate strong random noises involved in domain–peptide complex structures and uses statistical modeling approach to eliminate systematic bias associated with a group of investigated samples. As a paradigm, this method was employed to model and predict the binding behavior of various peptides to four evolutionarily unrelated peptide-recognition domains (PRDs), i.e. human amph SH3, human nherf PDZ, yeast syh GYF and yeast bmh 14-3-3, and moreover, we explored the molecular mechanism and biological implication underlying the binding of cognate and noncognate peptide ligands to their domain receptors. It is expected that the newly proposed method could be further used to perform genome-wide inference of domain–peptide binding at three-dimensional structure level.     

TGF-β binding in human Wharton’s jelly

Our previous study reported that TGF-β may be isolated from human Wharton’s jelly (WJ) in a form of soluble, high molecular complex(es). We decided to study the effect of extracellular matrix degradation and reduction of disulphide bridges reduction on the release of TGF-β from WJ. The WJ prepared from the umbilical cords of newborns delivered at term by healthy mothers was homogenised and treated with hyaluronidase, collagenase, heparinase, chondroitinase and β-mercaptoethanol, the resulting extracts were then submitted to TGF-β immunoassay and SDS/PAGE followed by Western immunoblotting. The effect of metalloproteinase activation on TGF-β was also studied. Pre-treatment of WJ homogenates with hyaluronidase or collagenase markedly increased the extractability of TGF-β, but did not dissociate the complexes. In contrast, the action of β-mercaptoethanol resulted in the release of free TGF-β; but activation of metalloproteinases resulted in the disappearance of this factor. We conclude that TGF-β1 is bound through disulphide bonds to an extracellular matrix component of WJ. The large amount of collagen fibrils and hyaluronate molecules which surround the cells scattered in WJ may prevent the access of extracting solution to TGF-β causing a low extractability of this factor. Although hyaluronate and collagen do not bind TGF-β directly, they may present a barrier that prevents the diffusion of TGF-β in WJ and results in its concentration around the cells thereby facilitating its interaction with membrane receptors and subsequent stimulation of cell division and synthesis of extracellular matrix components.     

New approaches for the treatment of Alzheimer’s disease

Alzheimer’s disease (AD) is the most prevalent chronic neurodegenerative disease. Current approved therapies are symptomatic treatments having some effect on cognitive function. Therapies that target β-amyloid (Aβ) have been the focus of efforts to develop a disease modification treatment for AD but these approaches have failed to show any clinical benefit so far. Beyond the ‘Aβ hypothesis’, there are a number of newer approaches to treat AD with neuroinflammation emerging as a very active area of research based on risk gene analysis. This short review will summarize approved drug therapies, recent clinical trials and new approaches for the treatment of AD.     

Current approaches to the treatment of Parkinson’s Disease

Parkinson’s Disease (PD) is the second most common neurodegenerative disorder. Clinical approaches to manage PD include symptomatic therapies, serving to compensate for the effects of dopaminergic neuronal deficits, as well as more recently a move toward disease modification, with the goal of slowing or stopping disease progression. This perspective surveys the approved therapies for PD treatment as well as provides a view of the ongoing clinical approaches aimed at improving outcomes for PD patients.     

A β-tryptase inhibitor with a tropanylamide scaffold to improve in vitro stability and to lower hERG channel binding affinity

Tropanylamide was investigated as a possible scaffold for β-tryptase inhibitors with a basic benzylamine P1 group and a substituted thiophene P4 group. Comparing to piperidinylamide, the tropanylamide scaffold is much more rigid, which presents less opportunity for the inhibitor to bind with off-target proteins, such as cytochrome P450, SSAO, and hERG potassium channel. The proposed binding mode was further confirmed by an in-house X-ray structure through co-crystallization.     

Computational study of coagulation factor VIIa’s affinity for phospholipid membranes

The interaction between the γ-carboxyglutamic acid-rich domain of coagulation factor VIIa (FVIIa), a vitamin-K-dependent enzyme, and phospholipid membranes plays a major role in initiation of blood coagulation. However, despite a high sequence and structural similarity to the Gla domain of other vitamin-K-dependent enzymes with a high membrane affinity, its affinity for negatively charged phospholipids is poor. A few amino acid differences are responsible for this observation. Based on the X-ray structure of lysophosphatidylserine (lysoPS) bound to the Gla domain of bovine prothrombin (Prth), models of the Gla domain of wildtype FVIIa and mutated FVIIa Gla domains in complex with lysoPS were built. Molecular dynamics (MD) and steered molecular dynamics (SMD) simulations on the complexes were applied to investigate the significant difference in the binding affinity. The MD simulation approach provides a structural and dynamic support to the role of P10Q and K32E mutations in the improvement of the membrane contact. Hence, rotation of the Gly11 main chain generated during the MD simulation results in a hydrogen bond with Q10 side chain as well as the appearance of a hydrogen bond between E32 and Q10 forcing the loop harbouring Arg9 and Arg15 to shrink and thereby enhances the accessibility of the phospholipids to the calcium ions. Furthermore, the application of the SMD simulation method to dissociate C6-lysoPS from a series of Gla domain models exhibits a ranking of the rupture force that can be useful in the interpretation of the PS interaction with Gla domains. Finally, adiabatic mapping of Gla6 residue in FVIIa with or without insertion of Tyr4 confirms the critical role of the insertion on the conformation of the side chain Gla6 in FVIIa and the corresponding Gla7 in Prth.     

Docking studies on kinesin spindle protein inhibitors: an important cooperative ‘minor binding pocket’ which increases the binding affinity significantly

Fifteen KSP inhibitors were docked into the receptor and the binding mode was analyzed for the first time. It was considered that in addition to the main binding pocket all the inhibitors merged in, there exists a cooperative minor binding pocket, which could be explored for significantly increased binding affinity. In addition, a good linear relationship between the biological activities and the lowest binding free energies has also been found. This may help in predicting the binding affinity of newly designed KSP inhibitors. Figure Two binding pockets considered after the analysis. Seven docked ligands (compound 1–7) were overlapped at the binding site. All inhibitors tested interacted with the main pocket, while CK0106023, interacted also with the cooperative minor pocket mainly surrounded by Arg221 and Ala218. Coloring of the binding site surface are different ends of each amino acid residue: blue represents amino group while red means carboxyl     

Copper binding to the Alzheimer’s disease amyloid precursor protein

Alzheimer’s disease is the fourth biggest killer in developed countries. Amyloid precursor protein (APP) plays a central role in the development of the disease, through the generation of a peptide called Aβ by proteolysis of the precursor protein. APP can function as a metalloprotein and modulate copper transport via its extracellular copper binding domain (CuBD). Copper binding to this domain has been shown to reduce Aβ levels and hence a molecular understanding of the interaction between metal and protein could lead to the development of novel therapeutics to treat the disease. We have recently determined the three-dimensional structures of apo and copper bound forms of CuBD. The structures provide a mechanism by which CuBD could readily transfer copper ions to other proteins. Importantly, the lack of significant conformational changes to CuBD on copper binding suggests a model in which copper binding affects the dimerisation state of APP leading to reduction in Aβ production. We thus predict that disruption of APP dimers may be a novel therapeutic approach to treat Alzheimer’s disease. Australian Society for Biophysics Special Issue: Metals and Membranes in Neuroscience.     

Antipyretic activity of Caesalpinia digyna (Rottl.) leaves extract along with phytoconstituent’s binding affinity to COX-1, COX-2, and mPGES-1 receptors: In vivo and in silico approaches

Caesalpinia digyna (Rottl.) (Family: Fabaceae) is well known for its numerous medicinal values against several human disorders including fever, senile pruritis, diarrhea, tuberculosis, tonic disorder, diabetes, etc. The current study is intended to investigate the in vivo antipyretic activity of the methanol extract of C. digyna leaves (MECD) and its carbon-tetrachloride (CTCD) and butanol fraction (BTCD). Besides, in silico molecular docking and ADME/T profiling of the selective identified bioactive compounds of C. digyna has been also studied to validate the experimental outcomes and establish a better insight into the possible receptor-ligand interaction affinity. In vivo antipyretic activity of MECD, CTCD and BTCD were evaluated by employing yeast induced pyrexia technique in mice model and in silico analysis of the identified compounds of C. digyna has been implemented using PyRx autodock vina, Discovery Studio 2020, UCSF Chimera software and ADME/T online tools. MECD and BTCD unveiled significant antipyretic activity in dose dependent manner whereas, CTCD failed to exhibit significant antipyretic activity. Comparing to other test sample, MECD (400 mg/kg; b.w) (p < 0.001) displayed maximum inhibition of pyrexia. In molecular docking approach, docking score between −6.60 to −10.20 kcal/mol have been revealed. Besides, in ADME/T analysis, no compound violated the lipiniski’s 5 rules and displayed any toxicity. Biological and computational approaches ascertain the ethno-botanical use of C. digyna as a good agent against pyrexia and the compounds of C. digyna are primarily proved as safe. Hereafter, further analysis is suggested to validate this research.     

SH3 domain ligand binding: What’s the consensus and where’s the specificity?

An increasing number of SH3 domain-ligand interactions continue to be described that involve the conserved peptide-binding surface of SH3, but structurally deviate substantially from canonical docking of consensus motif-containing SH3 ligands. Indeed, it appears that that the relative frequency and importance of these types of interactions may have been underestimated. Instead of atypical, we propose referring to such peptides as type I or II (depending on the binding orientation) non-consensus ligands. Here we discuss the structural basis of non-consensus SH3 ligand binding and the dominant role of the SH3 domain specificity zone in selective target recognition, and review some of the best-characterized examples of such interactions.     

Molecular dynamics and quantum chemistry-based approaches to identify isoform selective HDAC2 inhibitor – a novel target to prevent Alzheimer’s disease

Histone deacetylase 2 (HDAC2) is an emerging target of Alzheimer’s disease. Four featured pharmacophore model (ADRR) with one H-bond acceptor (A), one H-bond donor (D), and two aromatic rings (R) was generated using experimentally reported compounds, ((E-5[3-benzenesulfonamido) phenyl]-N-hydroxypent-2-en-4-ynamide)) and (N’-hydroxy-N-phenyloctanediamide) with IC₅₀ values of 0.16?±?0.11?nM and 62?±?0.15?nM, respectively. Quantum Polarized Ligand Docking and Binding Free Energy calculation was performed for the top three identified leads RH01652, JFD02573, and HTS00800 from HitFinder database. RH01652 (methyl 2-[({5-[(benzoylamino) methyl]-2-thienyl} sulfonyl) amino]-3-(1H-indol-3-yl) propanoate) with docking score (?12.62?kcal/mol) and binding free energy (?75.27?kcal/mol), shows good binding affinity. RH01652 interacts with Gly154, His183, Glu208, and Phe210 with four H-bonds and stabilized by π–π interactions with His146, Tyr209, and Phe210. DFT studies at B3LYP level with 6-31G* basis set for the lead RH01652 reveals low band gap/ΔE (E_HOMO–E_LUMO) of ?0.16?eV, which illustrates good reactivity of the lead. MD simulation studies (40?ns) was performed to confirm the stability of lead binding. Comparative molecular docking studies of the lead RH01652 with class I HDACs (HDAC1, HDAC2, HDAC3, and HDAC8) shows higher binding affinity towards HDAC2. Thus, lead RH01652 could serve as template to design novel and potent inhibitor of HDAC2.     

Autophagic dysfunction in Alzheimer’s disease: Cellular and molecular mechanistic approaches to halt Alzheimer’s pathogenesis

Autophagy is a preserved cytoplasmic self-degradation process and endorses recycling of intracellular constituents into bioenergetics for the controlling of cellular homeostasis. Functional autophagy process is essential in eliminating cytoplasmic waste components and helps in the recycling of some of its constituents. Studies have revealed that neurodegenerative disorders may be caused by mutations in autophagy-related genes and alterations of autophagic flux. Alzheimer’s disease (AD) is an irrevocable deleterious neurodegenerative disorder characterized by the formation of senile plaques and neurofibrillary tangles (NFTs) in the hippocampus and cortex. In the central nervous system of healthy people, there is no accretion of amyloid β (Aβ) peptides due to the balance between generation and degradation of Aβ. However, for AD patients, the generation of Aβ peptides is higher than lysis that causes accretion of Aβ. Likewise, the maturation of autophagolysosomes and inhibition of their retrograde transport creates favorable conditions for Aβ accumulation. Furthermore, increasing mammalian target of rapamycin (mTOR) signaling raises tau levels as well as phosphorylation. Alteration of mTOR activity occurs in the early stage of AD. In addition, copious evidence links autophagic/lysosomal dysfunction in AD. Compromised mitophagy is also accountable for dysfunctional mitochondria that raises Alzheimer’s pathology. Therefore, autophagic dysfunction might lead to the deposit of atypical proteins in the AD brain and manipulation of autophagy could be considered as an emerging therapeutic target. This review highlights the critical linkage of autophagy in the pathogenesis of AD, and avows a new insight to search for therapeutic target for blocking Alzheimer’s pathogenesis.     

Inactivation of nitrate reductase involves NR-protein phosphorylation and subsequent ‘binding’ of an inhibitor protein

The function of two proteins (P67 and P100) required for the MgATP-dependent inactivation of nitrate reductase (NR) from spinach leaves (Spinacia oleracea L.) was studied. When NR was incubated with -[³²P]ATP and P67, NR-protein was phosphorylated, but without a change in NR activity. Protein P100 by itself was neither able to phosphorylate nor to inactivate NR, and when added together with P67 it did not change the extent of NR phosphorylation. However, when NR was first phosphorylated with MgATP and P67, subsequent addition of P100 after removal of unreacted ATP caused an immediate NR inactivation. In presence of both P67 and P100 the time-course of ATP-dependent NR phosphorylation paralleled the time course of inactivation. The extent of NR phosphorylation and of NR inactivation (in the presence of P67 plus P100) was similarly affected by metabolites or high salt concentrations. Magnesium (Mg²⁺) played a dual role in the inactivation process: the phosphorylation of NR by P67 was strictly Mg²⁺-dependent. Further, phospho-NR (+P100) was inactive only in the presence of Mg²⁺, but active in the presence of excess EDTA. Dephospho-NR appeared to be Mg²⁺-insensitive. The observations suggest that phosphorylation of NR by P67 is obligatory, but not sufficient for inactivation. In addition to protein phosphorylation, inactivation requires binding of an inhibitor protein (P100) to phospho-NR.Abbreviations G6P glucose-6-phosphate - NR NADH-nitrate reductase - NRA nitrate reductase activity The skilled technical assistance of Elke Brendle-Behnisch is gratefully acknowledged. We also wish to thank Dr. C. MacKintosh, University of Dundee, UK, who supplied us with an immuno-affinity column for NR purification. This work was supported by the Deutsche Forschungsgemeinschaft (SFB 251).     

Investigations of Takeout proteins’ ligand binding and release mechanism using molecular dynamics simulation

Takeout (To) proteins exist in a diverse range of insect species. They are involved in many important processes of insect physiology and behaviors. As the ligand carriers, To proteins can transport the small molecule to the target tissues. However, ligand release mechanism of To proteins is unclear so far. In this contribution, the process and pathway of the ligand binding and release are revealed by conventional molecular dynamics simulation, steered molecular dynamics simulation and umbrella sampling methods. Our results show that the α4-side of the protein is the unique gate for the ligand binding and release. The structural analysis confirms that the internal cavity of the protein has high rigidity, which is in accordance with the recent experimental results. By using the potential of mean force calculations in combination with residue cross correlation calculation, we concluded that the binding between the ligand and To proteins is a process of conformational selection. Furthermore, the conformational changes of To proteins and the hydrophobic interactions both are the key factors for ligand binding and release.     

Heart fatty acid binding protein and Aβ-associated Alzheimer’s neurodegeneration

Background

Epidemiological and molecular findings suggest a relationship between Alzheimer’s disease (AD) and dyslipidemia, although the nature of this association is not well understood.

Results

Using linear mixed effects models, we investigated the relationship between CSF levels of heart fatty acid binding protein (HFABP), a lipid binding protein involved with fatty acid metabolism and lipid transport, amyloid-β (Aβ), phospho-tau, and longitudinal MRI-based measures of brain atrophy among 295 non-demented and demented older individuals. Across all participants, we found a significant association of CSF HFABP with longitudinal atrophy of the entorhinal cortex and other AD-vulnerable neuroanatomic regions. However, we found that the relationship between CSF HABP and brain atrophy was significant only among those with low CSF Aβ_1–42 and occurred irrespective of phospho-tau_181p status.

Conclusions

Our findings indicate that Aβ-associated volume loss occurs in the presence of elevated HFABP irrespective of phospho-tau. This implicates a potentially important role for fatty acid binding proteins in Alzheimer’s disease neurodegeneration.