Computational investigation of the binding characteristics of β-amyloid fibrils

Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies

Intrinsically disordered proteins (IDPs) are a novel class of proteins that have established a significant importance and attention within a very short period of time. These proteins are essentially characterized by their inherent structural disorder, encoded mainly by their amino acid sequences. The profound abundance of IDPs and intrinsically disordered regions (IDRs) in the biological world delineates their deep-rooted functionality. IDPs and IDRs convey such extensive functionality through their unique dynamic nature, which enables them to carry out huge number of multifaceted biomolecular interactions and make them "interaction hub" of the cellular systems. Additionally, with such widespread functions, their misfunctioning is also intimately associated with multiple diseases. Thus, understanding the dynamic heterogeneity of various IDPs along with their interactions with respective binding partners is an important field with immense potentials in biomolecular research. In this context, molecular docking-based computational approaches have proven to be remarkable in case of ordered proteins. Molecular docking methods essentially model the biomolecular interactions in both structural and energetic terms and use this information to characterize the putative interactions between the two participant molecules. However, direct applications of the conventional docking methods to study IDPs are largely limited by their structural heterogeneity and demands for unique IDP-centric strategies. Thus, in this chapter, we have presented an overview of current methodologies for successful docking operations involving IDPs and IDRs. These specialized methods majorly include the ensemble-based and fragment-based approaches with their own benefits and limitations. More recently, artificial intelligence and machine learning-assisted approaches are also used to significantly reduce the complexity and computational burden associated with various docking applications. Thus, this chapter aims to provide a comprehensive summary of major challenges and recent advancements of molecular docking approaches in the IDP field for their better utilization and greater applicability.Asp (D).

Structural modelling and in silico pharmacology of β-carboline alkaloids as potent 5-HT1A receptor antagonists and reuptake inhibitors

Serotonin (5-HT) antagonists and reuptake inhibitors (SARIs) are atypical antidepressants for managing major depressive disorder. They are oftentimes applied as adjuvants for ameliorating aftereffects of SSRI antidepressants including insomnia and sexual dysfunction. The few available candidates of this class including lorpiprazole and trazodone also display some daunting side effects, making a continuous search for improved alternatives essential. Natural β-carboline alkaloids (NβCs) are interestingly renowned with broad pharmacological spectrum against several neuropsychiatric disorders including depression. However, their potentials as SARIs remain underexplored. In this study, 982 NβCs retrieved from the Ambinter-Greenpharma (Amb) database were virtually screened for potent SARI alternatives using computational and biocheminformatics approaches: homology modelling of 5-HT1A receptor, Glide HTVS, SP and XP molecular docking, molecular dynamics (MD) simulation, ADMET and mutagenicity predictions. The homology receptor was validated as a good representative of human 5HT1A receptor using the RCSB structure validation and quality protocols. From the virtual screening against the 5-HT1A receptor, Amb ligands, Amb18709727 and Amb37857532 showed higher binding affinities by XP scores of -8.725 and -7.976 kcal/mol, and MMGBSA of -87.972 and -107.585 kcal/mol respectively compared to lorpiprazole, a reference SARI with XP score and MMGBSA of -6.512 and -62.788 kcal/mol respectively. They maintained ideal contacts with pharmacologically essential amino acid residues implicated in SARI mechanisms and expressed higher stability and compactness than lorpiprazole throughout the trajectories of 100 ns MD simulation. They also displayed interesting ADME, druggability, low toxicity and mutagenicity profiles, ideal for CNS drug prospects, thus, recommended as putative SARI candidates for further study.

Bio-Evaluation of 99mTc-Labeled Homodimeric Chalcone Derivative as Amyloid-β-Targeting Probe

Chalcone derivatives have been successfully utilized for a range of biological applications and can cross the blood–brain barrier easily. β-amyloid-specific bis-chalcone derivative, 6,9-bis(carboxymethyl)-14-(4-[(E)-3-(4-(dimethylamino)phenyl)acryloyl]phenoxy)-3-(2-[(2-(4-[(E)-3-(4-(dimethylamino)phenyl)acryloyl]phenoxy)ethyl)amino]-2-oxoethyl)-11-oxo-3,6,9,12-tetraazatetradecanoic acid, DT(Ch)₂, was analyzed using molecular modeling to explain the binding modes of the ligand with amyloid fibril and monomer followed by ^99mTc-complexation in 95% yield and 98.7% efficiency. High-binding specificity of the radiocomplex was established following in vitro evaluation against 100-fold excess of DT(Ch)₂. ^99mTc–DT(Ch)₂ exhibited <3% trans-complexation in human serum after 24 h, indicating high stability. A fast clearance rate in pharmacokinetics studies displayed a biphasic pattern with t_1/2(F) = 30 min ± 0.09 and t_1/2(S) = 4 h 20 min ± 0.06. In vivo single-photon emission computed tomography (SPECT) imaging in rabbits reiterated the pharmacokinetics data with initially high brain uptake followed by rapid washout. Biodistribution studies confirmed the initial brain uptake as 1.16 ± 0.02% ID/g after 2 min and the brain_2min/brain_30min ratio was 3.74. Radioactivity distribution in the brain was >40% in the cingulate cortex followed by >25% in the hippocampus, a distribution pattern aligned to Alzheimer’s affected brain regions. Radiocomplex also displayed rapid plasma clearance followed by hepatobolic and renal modes of excretion.

Exploiting the glycan receptor-binding site of PltB subunit in salmonella typhi toxin for novel inhibitors: An in-silico approach

Salmonella typhi (S. typhi), a gram-negative bacterium responsible for gastroenteritis - typhoid - has continually evolved into drug-resistant strains with the most recent being the haplotype H58 strain. The haplotype H58 strain has spread across the globe causing outbreaks in countries such as Pakistan, Zimbabwe, and several underdeveloped regions located in parts of Asia, Central and Southern Africa. Treatment by conventional antibiotics is gradually failing as recorded in the affected countries, including Nigeria and Barcelona - Spain. Therefore, the research presented herein aims to identify novel compounds targeting the typhoid toxin of S. typhi which is responsible for several virulence factors associated with typhoid. In-silico methods that include virtual screening, molecular dynamics (MD) and computation of binding free energies were utilized. Our research identified furan derivatives as top-scoring lead compounds from a database of more than 1,5 million compounds curated from the ZINC20 database. Post docking analysis and trajectory analysis post-MD simulations showed that π - π interactions are vital to holding the ligand within the receptor pocket whereas hydrophobic and Van der Waals interactions are crucial for the overall bonding. Through docking, MD simulations and free energy computations, we hypothesize that ZINC000114543311, ZINC000794380763 and ZINC000158992484 (docking scores of -9.06, -8.20 and -8.12 in conjunction with ΔG values of -64.691, -63.670 and -59.024 kcal/mol, respectively) bear a great potential to pave the way to fighting antibiotic resistance for typhoid in both humans and animals. The compounds presented here can also be used as lead materials for designing other compounds targeting the Salmonella typhi toxin.

Kinetic and thermodynamic insights into the interaction of Aβ1-42 with astaxanthin and aggregation behavior of Aβ1-42: Surface plasmon resonance, microscopic, and molecular docking studies

Amyloid-β 1-42 (Aβ1-42) aggregation is considered as an important process in the pathology of Alzheimer's disease (AD). Astaxanthin (ATX), a xanthophyll carotenoid, has a broad range of biological activities such as neuroprotective one. The present study aimed to elucidate the interaction of ATX with Aβ1-42, as well as its effect on Aβ1-42 aggregates under different conditions. Based on the surface plasmon resonance (SPR) results, ATX possessed a high affinity towards Aβ1-42 and the binding process was spontaneous, endothermic, and entropy-driven. Additionally, the binding affinity of ATX to Aβ1-42 was glucose and insulin concentration-dependent. Hydrophobic interactions may play an important role in the interaction between ATX and Aβ1-42. The results of SPR, thioflavin T (ThT), and transmission electron microscopy (TEM) analyses represented the dependency of the anti-amyloid activity of ATX on glucose, insulin, and ATX concentrations. Further, molecular docking results indicated the presence of some same binding sites on Aβ1-42 for ATX and glucose, as well as ATX and insulin, which suggests the possible competition between the molecules for Aβ1-42 binding. Furthermore, the MTT results confirmed that ATX effect on the viability of Aβ1-42-treated PC12 cells was dependent on glucose, insulin, and ATX concentrations. In general, the results provided further insights into the interaction between Aβ1-42 and ATX, as well as the effect of ATX on Aβ1-42 aggregates under various conditions.

Enhancing the binding of the β-sheet breaker peptide LPFFD to the amyloid-β fibrils by aromatic modifications: A molecular dynamics simulation study

Alzheimer's is a fatal neurodegenerative disease for which there is no cure at present. The disease is characterized by the presence of plaques in the brains of a patient, which are composed mainly of aggregates of the amyloid-β peptide in the form of β-sheet fibrils. Here, we investigated the possibility of exploiting the superior binding ability of aromatic amino acids to a particular model of the amyloid-β fibrils. which is a difficult target for drug design. The β-sheet breaker peptide LPFFD was modified with aromatic amino acids and its binding to these fibrils was studied. We found that the orientation and the electrostatic complementarity of the modified peptide with respect to the fibrils played a crucial role in determining whether its binding was improved by the aromatic amino acids. The modified LPFFD peptides were able to bind to those fibril residues. which are important in the aggregation of amyloid-β peptides and thus can potentially inhibit the further aggregation of the amyloid-beta peptides by blocking their interactions. We found that the tryptophan modified LPFFD peptides had the best binding affinities. In most cases, the aromatic amino acids in the N-terminus of the modified peptides made more contacts with the fibrils than those in the C-terminus. We also found that increasing the aromatic content did not significantly improve the binding of the LPFFD peptide to the fibrils. Our study can serve as a basis for the design of novel peptide-based drugs for Alzheimer's disease in which aromatic interactions play an important role.

Molecular dynamics simulations reveal the destabilization mechanism of Alzheimer's disease-related tau R3-R4 Protofilament by norepinephrine

Aggregation of Tau protein into neurofibrillary tangles is associated with the pathogenesis of Alzheimer's disease (AD) which has no cure yet. Clearing neurofibrillary tangles is one of major therapeutic strategies. Experimental studies reported that norepinephrine (NE) has the ability to disrupt Tau filament and cause Tau degradation. However, the underlying mechanism remains elusive. Herein, we performed molecular dynamic simulations to investigate the influence of NE on the C-shaped Tau R3-R4 protofilament. Our simulations show that NE compound destabilizes Tau protofilament by mostly disrupting β6/β8 and altering the β2-β3 and β6-β7 angles. NE binds mainly with aromatic residues Y310/P312/H374/F378 through ππ stacking and charged residues E338/E342/D348/D358/E372 via hydrogen-bonding interactions. Our results, together with the findings that exercise can markedly increase NE level, suggest that exercise might be a potent therapy against AD. This study reveals the disruptive mechanism of Tau protofilament by NE molecules, which may provide new clues for AD drug candidate design.

A new naphthalene derivative with anti-amyloidogenic activity as potential therapeutic agent for Alzheimer's disease

The aggregation of β-amyloid peptides is associated to neurodegeneration in Alzheimer's disease (AD) patients. Consequently, the inhibition of both oligomerization and fibrillation of β-amyloid peptides is considered a plausible therapeutic approach for AD. Herein, the synthesis of new naphthalene derivatives and their evaluation as anti-β-amyloidogenic agents are presented. Molecular dynamic simulations predicted the formation of thermodynamically stable complexes between the compounds, the Aβ_1-42 peptide and fibrils. In human microglia cells, these compounds inhibited the aggregation of Aβ_1-42 peptide. The lead compound 8 showed a high affinity to amyloid plaques in mice brain ex vivo assays and an adequate log P_oct/PBS value. Compound 8 also improved the cognitive function and decreased hippocampal β-amyloid burden in the brain of 3xTg-AD female mice. Altogether, our results suggest that 8 could be a novel therapeutic agent for AD.