Exploring the Impact of C-Terminal Based Pentapeptides on the Disassembly of Aß42 Fibrils.

An effective therapeutic strategy to suppress Alzheimer's disease (AD) progression is to disrupt ß-sheet rich neurotoxic soluble amyloid-ß (Aß) aggregates. Previously, we identified new pentapeptides (RVVPI and RIAPA) with notably enhanced ability to block Aß42 aggregation as compared to Aß42 C-terminal derived peptide RIIGL using integrated computational protocol. In this work, the potential of RIIGL, RVVPI, and RIAPA for the structural destabilization of Aß42 protofibril was assessed by molecular dynamics (MD) simulations and in vitro studies. The binding free energy analysis depicts that charged residues influence Aß42 protofibril-pentapeptide interactions. Notably, RVVPI displays a more pronounced destabilization effect than other peptides due to higher conformational fluctuations, and disruption of salt bridge (K28-A42) interactions in Aß42 protofibril. RVVPI exhibited highest inhibitory activity (Inhibition= 66.2%, IC50= 5.57 ± 0.83 µM) against Aß42 aggregation consistent with computational results. Remarkably, RVVPI displayed ~4.5 fold lower IC50 value as compared to RIIGL. ThT and TEM studies highlighted the enhanced efficiency of RVVPI (62.4%) in the disassembly of pre-formed Aß42 fibrils than RIIGL and RIAPA. The combined in silico and in vitro studies identified a new peptide, RVVPI, as an efficient inhibitor of Aß42 fibrillation and disassembly of Aß42 aggregates.

Harnessing the Therapeutic Potential of Peptides for Synergistic Treatment of Alzheimer's Disease by Targeting Aß Aggregation, Metal-Mediated Aß Aggregation, Cholinesterase, Tau Degradation, and Oxidative Stress.

Alzheimer's disease (AD) is a progressive multifaceted neurodegenerative disease and remains a formidable global health challenge. The current medication for AD gives symptomatic relief and, thus, urges us to look for alternative disease-modifying therapies based on a multitarget directed approach. Looking at the remarkable progress made in peptide drug development in the last decade and the benefits associated with peptides, they offer valuable chemotypes [multitarget directed ligands (MTDLs)] as AD therapeutics. This review recapitulates the current developments made in harnessing peptides as MTDLs in combating AD by targeting multiple key pathways involved in the disease's progression. The peptides hold immense potential and represent a convincing avenue in the pursuit of novel AD therapeutics. While hurdles remain, ongoing research offers hope that peptides may eventually provide a multifaceted approach to combat AD.

Factor defining the effects of tetraalkylammonium chloride on stability, folding, and dynamics of horse cytochrome c.

This article describes the molecular mechanism by which tetraalkylammonium chloride ([R4N]Cl: R- = methyl (Me), ethyl (Et), propyl (Pr),butyl (Bu)) modulates the stability, folding, and dynamics of cytochrome c (Cyt c). Analysis of [R4N]Cl effects on thermal/chemical denaturations, millisecond refolding/unfolding kinetics, and slow CO-association kinetics of Cyt c without and with denaturant providing some significant results: (i) [R4N]Cl decreasing the unfolding free energy estimated by thermodynamic and kinetic analysis of thermal/chemical denaturation curves and kinetic chevrons (Log kobs-[GdmCl]) of Cyt c, respectively (ii) hydrophobicity of R-group of [R4N]Cl, preferential inclusion of [R4N]Cl at the protein surface, and destabilizing enthalpic attractive interactions of [Me4N]Cl and steric entropic interactions of [Et4N]Cl,[Pr4N]Cl and [Bu4N]Cl with protein contribute to [R4N]Cl-induced decrease thermodynamic stability of Cyt c (iii) [R4N]Cl exhibits an additive effect with denaturant to decrease thermodynamic stability and refolding rates of Cyt c (iv) low concentrations of [R4N]Cl (≤ 0.5 M) constrain the motional dynamics while the higher concentrations (>0.75 M [R4N]Cl) enhance the structural-fluctuations that denture protein (v) hydrophobicity of R-group of [R4N]Cl alters the [denaturant]-dependent conformational stability, refolding-unfolding kinetics, and CO-association kinetics of Cyt c. Furthermore, the MD simulations depicted that the addition of 1.0 M of [R4N]Cl increased the conformational fluctuations in Cyt c leading to decreased structural stability in the order [Me4N]Cl < [Et4N]Cl < [Pr4N]Cl < [Bu4N]Cl consistent with the experimental results.

Insights into the baicalein-induced destabilization of LS-shaped Aß42 protofibrils using computer simulations.

Amyloid-ß (Aß) peptides aggregate spontaneously into various aggregating species comprising oligomers, protofibrils, and mature fibrils in Alzheimer's disease (AD). Disrupting ß-sheet rich neurotoxic smaller soluble Aß42 oligomers formed at early stages is considered a potent strategy to interfere with AD pathology. Previous experiments have demonstrated the inhibition of the early stages of Aß aggregation by baicalein; however, the molecular mechanism behind inhibition remains largely unknown. Thus, in this work, molecular dynamics (MD) simulations have been employed to illuminate the molecular mechanism of baicalein-induced destabilization of preformed Aß42 protofibrils. Baicalein binds to chain A of the Aß42 protofibril through hydrogen bonds, π-π interactions, and hydrophobic contacts with the central hydrophobic core (CHC) residues of the Aß42 protofibril. The binding of baicalein to the CHC region of the Aß42 protofibril resulted in the elongation of the kink angle and disruption of K28-A42 salt bridges, which resulted in the distortion of the protofibril structure. Importantly, the ß-sheet content was notably reduced in Aß42 protofibrils upon incorporation of baicalein with a concomitant increase in the coil content, which is consistent with ThT fluorescence and AFM images depicting disaggregation of pre-existing Aß42 fibrils on the incorporation of baicalein. Remarkably, the interchain binding affinity in Aß42 protofibrils was notably reduced in the presence of baicalein leading to distortion in the overall structure, which agrees with the structural stability analyses and conformational snapshots. This work sheds light on the molecular mechanism of baicalein in disrupting the Aß42 protofibril structure, which will be beneficial to the design of therapeutic candidates against disrupting ß-sheet rich neurotoxic Aß42 oligomers in AD.

In silico design and identification of new peptides for mitigating hIAPP aggregation in type 2 diabetes.

The aberrant misfolding and self-aggregation of human islet amyloid polypeptide (hIAPP or amylin) into cytotoxic aggregates are implicated in the pathogenesis of type 2 diabetes (T2D). Among various inhibitors, short peptides derived from the amyloidogenic regions of hIAPP have been employed as hIAPP aggregation inhibitors due to their low immunogenicity, biocompatibility, and high chemical diversity. Recently, hIAPP fragment HSSNN18-22 was identified as an amyloidogenic sequence and displayed higher antiproliferative activity to RIN-5F cells. Various hIAPP aggregation inhibitors have been designed by chemical modifications of the highly amyloidogenic sequence (NFGAIL) of hIAPP. In this work, a library of pentapeptides based on fragment HSSNN18-22 was designed and assessed for their efficacy in blocking hIAPP aggregation using an integrated computational screening approach. The binding free energy calculations by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method identified HSSQN and HSSNQ that bind to hIAPP monomer with a binding affinity of -21.25 ± 4.90 and -19.73 ± 3.10 kcal/mol, respectively, which is notably higher as compared to HSSNN (-11.90 ± 4.12 kcal/mol). The sampling of the non aggregation-prone helical conformation was notably increased from 23.5 ± 3.0 in the hIAPP monomer to 38.1 ± 3.6, and 33.8 ± 3.0% on the incorporation of HSSQN, and HSSNQ, respectively, which indicate reduced aggregation propensity of hIAPP monomer. The pentapeptides, HSSQN and HSSNQ, identified as hIAPP aggregation inhibitors in this work can be further conjugated with various metal chelating peptides to yield more efficacious and clinically relevant multifunctional modulators for targeting various pathological hallmarks of T2D.

Multiepitope glycan based laser assisted fluorescent nanocomposite with dual functionality for sensing and ablation of Pseudomonas aeruginosa.

Pseudomonas aeruginosa (P. aeruginosa) infection is becoming a severe health hazard and needs early diagnosis with high specificity. However, the non-specific binding of a biosensor is a challenge to the current bacterial detection system. For the first time, we chemically synthesized a galactose tripod (GT) as a P. aeruginosa-specific ligand. We conjugated GT to a photothermally active fluorescent nanocomposite (Au@SiO2-TCPP). P. aeruginosa can be detected using Au@SiO2-TCPP-GT, and additionally ablated as well using synergistic photothermal and photodynamic therapy. Molecular dynamics and simulation studies suggested better binding of GT (binding energy = -6.6 kcal mol-1) with P. aeruginosa lectin than that of galactose monopod (GM) (binding energy = -5.9 kcal mol-1). Furthermore, a binding study was extended to target P. aeruginosa, which has a galactose-binding carbohydrate recognition domain receptor. The colorimetric assay confirmed a limit of detection (LOD) of 104 CFU mL-1. We also looked into the photosensitizing property of Au@SiO2-TCPP-GT, which is stimulated by laser light (630 nm) and causes photoablation of bacteria by the formation of singlet oxygen in the surrounding media. The cytocompatibility of Au@SiO2-TCPP-GT was confirmed using cytotoxicity assays on mammalian cell lines. Moreover, Au@SiO2-TCPP-GT also showed non-hemolytic activity. Considering the toxicity analysis and efficacy of the synthesized glycan nanocomposites, these can be utilized for the treatment of P. aeruginosa-infected wounds. Furthermore, the current glycan nanocomposites can be used for bacterial detection and ablation of P. aeruginosa in contaminated food and water samples as well.

Identification of new pentapeptides as potential inhibitors of amyloid-ß42 aggregation using virtual screening and molecular dynamics simulations.

Alzheimer's disease (AD) is a multifactorial neurodegenerative disease mainly characterized by extracellular accumulation of amyloid-ß (Aß) peptide. Previous studies reported pentapeptide RIIGL as an effective inhibitor of Aß aggregation and neurotoxicity induced by Aß aggregates. In this work, a library of 912 pentapeptides based on RIIGL has been designed and assessed for their efficacy to inhibit Aß42 aggregation using computational techniques. The top hit pentapeptides revealed by molecular docking were further assessed for their binding affinity with Aß42 monomer using MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) method. The MM-PBSA analysis identified RLAPV, RVVPI, and RIAPA, which bind to Aß42 monomer with a higher binding affinity -55.80, -46.32, and -44.26 kcal/mol, respectively, as compared to RIIGL (ΔGbinding = -41.29 kcal/mol). The residue-wise binding free energy predicted hydrophobic contacts between Aß42 monomer and pentapeptides. The secondary structure analysis of the conformational ensembles generated by molecular dynamics (MD) depicted remarkably enhanced sampling of helical and no ß-sheet conformations in Aß42 monomer on the incorporation of RVVPI and RIAPA. Notably, RVVPI and RIAPA destabilized the D23-K28 salt bridge in Aß42 monomer, which plays a crucial role in Aß42 oligomer stability and fibril formation. The MD simulations highlighted that the incorporation of proline and arginine in pentapeptides contributed to their strong binding with Aß42 monomer. Furthermore, RVVPI and RIAPA prevented conformational conversion of Aß42 monomer to aggregation-prone structures, which, in turn, resulted in a lower aggregation tendency of Aß42 monomer.

Unveiling How Hydroxytyrosol Destabilizes α-Syn Oligomers Using Molecular Simulations.

The etiology of Parkinson's disease (PD) is mainly linked to the α-synuclein (α-Syn) fibrillogenesis. Hydroxytyrosol (HT), also known as 3,4-dihydroxyphenylethanol, is a naturally occurring polyphenol, found in extra virgin olive oil, and has been shown to have cardioprotective, anticancer, antiobesity, and antidiabetic properties. HT has neuroprotective benefits in neurodegenerative diseases and lessens the severity of PD by reducing the aggregation of α-Syn and destabilizing the preformed toxic α-Syn oligomers. However, the molecular mechanism by which HT destabilizes α-Syn oligomers and alleviates the accompanying cytotoxicity remains unexplored. The impact of HT on the α-Syn oligomer structure and its potential binding mechanism was examined in this work by employing molecular dynamics (MD) simulations. The secondary structure analysis depicted that HT significantly reduces the ß-sheet and concomitantly increases the coil content of α-Syn trimer. Visualization of representative conformations from the clustering analysis depicted the hydrogen bond interactions of the hydroxyl groups in HT with the N-terminal and nonamyloid-ß component (NAC) region residues of α-Syn trimer, which, in turn, leads to the weakening of interchain interactions in α-Syn trimer and resulted in the disruption of the α-Syn oligomer. The binding free energy calculations depict that HT binds favorably to α-Syn trimer (ΔGbinding = -23.25 ± 7.86 kcal/mol) and a notable reduction in the interchain binding affinity of α-Syn trimer on the incorporation of HT, which, in turn, highlights its potential to disrupt α-Syn oligomers. The current research provided mechanistic insights into the destabilization of α-Syn trimer by HT, which, in turn, will provide new clues for developing therapeutics against PD.

Salmonella typhimurium detection and ablation using OmpD specific aptamer with non-magnetic and magnetic graphene oxide.

Foodborne diseases have increased in the last few years due to the increased consumption of packaged and contaminated food. Major foodborne bacteria cause diseases such as diarrhea, vomiting, and sometimes death. So, there is a need for early detection of foodborne bacteria as pre-existing detection techniques are time-taking and tedious. Aptamer has gained interest due to its high stability, specificity, and sensitivity. Here, aptamer has been developed against Salmonella Typhimurium through the Cell-Selex method, and to further find the reason for specificity and sensitivity, OmpD protein was isolated, and binding studies were done. Single molecular FRET experiment using aptamer and graphene oxide studies has also been done to understand the mechanism of FRET and subsequently used for target bacterial detection. Using this assay, Salmonella Typhimurium can be detected up to 10 CFU/mL. Further, Magnetic Graphene oxide was used to develop an assay to separate and ablate bacteria using 808 nm NIR where temperature increase was more than 60 °C within 30 s and has been shown by plating as well as a confocal live dead assay. Thus, using various techniques, bacteria can be detected and ablated using specific aptamer and Graphene oxide.

Triazole-Peptide Conjugate as a Modulator of Aß-Aggregation, Metal-Mediated Aß-Aggregation, and Cytotoxicity.

Amyloid-ß (Aß) aggregation plays a key role in the pathogenesis of Alzheimer's disease (AD). Along with this, the presence of redox-active metals like Cu2+ further enhances Aß aggregation, oxidative stress, and cellular toxicity. In this study, we have rationally designed, synthesized, and evaluated a series of triazole-peptide conjugates as potential promiscuous ligands capable of targeting different pathological factors of AD. In particular, peptidomimetic DS2 showed the best inhibitory activity against Aß aggregation with an IC50 value of 2.43 ± 0.05 µM. In addition, DS2 disaggregates preformed Aß42 fibrils, chelates metal ions, inhibits metal-mediated Aß aggregation, significantly controls reactive oxygen species production, and reduces oxidative stress. DS2 exhibited very low cytotoxicity and significantly ameliorated the Aß-induced toxicity in differentiated neuroblastoma cells, SH-SY5Y. In addition, alteration in the fibrillary architecture of Aß42 in the absence and presence of DS2 was validated by transmission electron microscopy (TEM) images. To shed light on the inhibitory mechanism of DS2 against Aß aggregation and disassembly of the protofibril structure, molecular dynamics (MD) simulations have been performed. DS2 binds preferentially with the central hydrophobic core (CHC) residues of Aß42 monomer and chains D-E of Aß42 protofibril. The dictionary of secondary structure of proteins analysis indicated a noteworthy increase in the helix content from 38.5 to 61% and, notably, a complete loss of ß-sheet content of Aß42 monomer when DS2 is added to it. DS2 suppressed Aß42 monomer aggregation by preserving helical conformations and was able to reduce the production of aggregation-prone ß-sheet structures, which are consistent with ThT, circular dichroism, and TEM assay that indicate a reduction in the formation of toxic Aß42 aggregated species on the addition of DS2. Moreover, DS2 destabilized the Aß42 protofibril structure by significantly reducing the binding affinity between chains D-E of protofibril, which highlighted the disruption of interchain interactions and subsequent deformation of the protofibril structure. The results of the present study demonstrate that triazole-peptide conjugates may be valuable chemotypes for the development of promising multifunctional AD therapeutic candidates.

Structural and molecular insights into tacrine-benzofuran hybrid induced inhibition of amyloid-ß peptide aggregation and BACE1 activity.

Amyloid-ß (Aß) aggregation and ß-amyloid precursor protein cleaving enzyme 1 (BACE1) are the potential therapeutic drug targets for Alzheimer's disease (AD). A recent study highlighted that tacrine-benzofuran hybrid C1 displayed anti-aggregation activity against Aß42 peptide and inhibit BACE1 activity. However, the inhibition mechanism of C1 against Aß42 aggregation and BACE1 activity remains unclear. Thus, molecular dynamics (MD) simulations of Aß42 monomer and BACE1 with and without C1 were performed to inspect the inhibitory mechanism of C1 against Aß42 aggregation and BACE1 activity. In addition, a ligand-based virtual screening followed by MD simulations was employed to explore potent new small-molecule dual inhibitors of Aß42 aggregation and BACE1 activity. MD simulations highlighted that C1 promotes the non aggregating helical conformation in Aß42 and destabilizes D23-K28 salt bridge that plays a vital role in the self-aggregation of Aß42. C1 displays a favourable binding free energy (-50.7 ± 7.3 kcal/mol) with Aß42 monomer and preferentially binds to the central hydrophobic core (CHC) residues. MD simulations highlighted that C1 strongly interacted with the BACE1 active site (Asp32 and Asp228) and active pockets. The scrutiny of interatomic distances among key residues of BACE1 highlighted the close flap (non-active) position in BACE1 on the incorporation of C1. The MD simulations explain the observed high inhibitory activity of C1 against Aß aggregation and BACE1 in the in vitro studies. The ligand-based virtual screening followed by MD simulations identified CHEMBL2019027 (C2) as a promising dual inhibitor of Aß42 aggregation and BACE1 activity.Communicated by Ramaswamy H. Sarma.

Unravelling the destabilization potential of ellagic acid on α-synuclein fibrils using molecular dynamics simulations.

The aberrant deposition of α-synuclein (α-Syn) protein into the intracellular neuronal aggregates termed Lewy bodies and Lewy neurites characterizes the devastating neurodegenerative condition known as Parkinson's disease (PD). The disruption of pre-existing disease-relevant α-Syn fibrils is recognized as a viable therapeutic approach for PD. Ellagic acid (EA), a natural polyphenolic compound, is experimentally proven as a potential candidate that prevents or reverses the α-Syn fibrillization process. However, the detailed inhibitory mechanism of EA against the destabilization of α-Syn fibril remains largely unclear. In this work, the influence of EA on α-Syn fibril and its putative binding mechanism were explored using molecular dynamics (MD) simulations. EA interacted primarily with the non-amyloid-ß component (NAC) of α-Syn fibril, disrupting its ß-sheet content and thereby increasing the coil content. The E46-K80 salt bridge, critical for the stability of Greek-key-like α-Syn fibril, was disrupted in the presence of EA. The binding free energy analysis using the MM-PBSA method demonstrates the favourable binding of EA to α-Syn fibril (ΔGbinding = -34.62 ± 11.33 kcal mol-1). Interestingly, the binding affinity between chains H and J of the α-Syn fibril was significantly reduced on the incorporation of EA, which highlights the disruptive ability of EA towards α-Syn fibril. The MD simulations provide mechanistic insights into the α-Syn fibril disruption by EA, which gives a valuable direction for the development of potential inhibitors of α-Syn fibrillization and its associated cytotoxicity.

Mechanistic insights into the mitigation of Aß aggregation and protofibril destabilization by a D-enantiomeric decapeptide rk10.

According to clinical studies, the development of Alzheimer's disease (AD) is linked to the abnormal aggregation of amyloid-ß (Aß) peptides into toxic soluble oligomers, protofibrils as well as mature fibrils. The most acceptable therapeutic strategy for the treatment of AD is to block the Aß aggregation. Sun and co-workers have reported a decapeptide, D-enantiomeric RTHLVFFARK-NH2 (rk10), which acts as a potent inhibitor of Aß aggregation and efficiently disaggregates pre-assembled Aß fibrils. However, the inhibitory mechanism of rk10 against Aß aggregation and disassembly of fibrils remains obscure. To investigate the inhibitory mechanism of rk10 against Aß aggregation and disassembly of fibrils, molecular dynamics (MD) simulations have been performed in the present study. The molecular docking analysis using AutoDock Vina predicted favourable binding of rk10 with the N-terminal and central hydrophobic core (CHC) residues of Aß42 monomer (-5.3 kcal mol-1), and with the residues of chain A of Aß42 protofibril structure (-6.9 kcal mol-1). The MD simulations depicted higher structural stability of Aß42 monomer in the presence of rk10. Notably, rk10 prevented the sampling of ß-sheet rich structures of Aß42 monomer by reducing the side-chain contacts between N-terminal and C-terminal residues of Aß42 monomer. The per-residue binding free energy analysis highlighted the significant contribution of Phe19 and Glu22 of Aß42 monomer in binding with rk10, which corroborate with the 1H NMR (nuclear magnetic resonance) spectra of Aß42 monomer + rk10 complex that depicted a change in the chemical shifts of amide protons of Phe19 and Glu22. Further, rk10 destabilized the Aß42 protofibril structure by lowering the number of interchain hydrogen bonds. The binding free energy analysis predicted lower binding affinity between Aß42 protofibril chains in the presence of rk10 as compared to Aß42 protofibril alone. The insights into the inhibitory mechanism of rk10 against Aß aggregation and disassembly of fibrils will be beneficial for the design and development of potent anti-amyloid inhibitors.

Near-Miss Incidents in Obstetric Patients Admitted to an Intensive Care Unit of a Tertiary Care Center in Eastern India: A Retrospective Cohort Study.

Aim: Obstetric patients presenting to the intensive care units (ICU) with or without underlying medical or surgical comorbidities can be a challenge to both the treating obstetrician and the intensivist. They occasionally present with near-miss events which if left untreated, can result in death. Objectives: To study the prevalence, indications of ICU admissions, near-miss events, and their effect on mortality in obstetric and puerperal patients. Material & methods: We conducted a retrospective analysis of the health records of all the obstetric and puerperal patients (pregnant and until 6 weeks postpartum) admitted to our tertiary care hospital from January 2019 to December 2020. Patient demographic characteristics, obstetric, surgical, and medical conditions, acute physiology, and chronic health evaluation (APACHE) II scores, organ failures, treatment, ICU and hospital length of stay, and mortality outcomes were studied. Results: A total of 22 obstetric patients were admitted to the ICU during the above study period. Mean age was 28.7 ± 6.24 years, mean gestation was 34.4 ± 6.61 weeks, mean APACHE II score was 12.68 ± 5.67, median ICU length of stay was 5 days, and median duration of hospital length of stay was 10 days. The antepartum risk factors such as severe preeclampsia (27%), antepartum bleeding (14%), and postpartum complications like postpartum haemorrhage (33%), sepsis with multiorgan failure (25%) are the commonest indications that resulted in ICU admission. Conclusion: Higher APACHE II scores at the time of ICU admission, prolonged ICU, and hospital length of stay may be associated with high maternal mortality.

Effect of imidazolium based ionic liquids on CO-association dynamics and thermodynamic stability of Ferrocytochrome c.

Analysis of kinetic and thermodynamic parameters measured for CO-association reaction of Ferrocytochrome c (Ferrocyt c) under variable concentrations of 1-butyl-3-methylimidazolium with varying anion ([Bmim]X) (X = Cl-, I-, Br-, HSO4-) at pH 7 revealed that the low concentration of [Bmim]X (≤0.5 M) constrains the CO-association dynamics of Ferrocyt c and typically follows the order: [Bmim]HSO4 > [Bmim]Cl > [Bmim]Br > [Bmim]I. At relatively higher concentrations (>0.5), the chaotropic action of [Bmim]+ dominates which consequently increases the thermal-fluctuations responsible to denature the protein and thus accelerates the speed of CO-association reaction. Analysis of thermal denaturation curves of Ferrocyt c measured at different concentrations of [Bmim]X revealed that the [Bmim]X decreases the thermodynamic stability of protein and typically follows the order: [Bmim]I > [Bmim]Br > [Bmim]Cl > [Bmim]CH3COO > [Bmim]HSO4, demonstrating that the effect of [Bmim]X on thermodynamic stability of protein is not in accordance to Hofmeister series effect of anions because instead of increasing the kosmotropic anion carrying [Bmim]X ([Bmim]CH3COO and [Bmim]HSO4) also decreases the thermodynamic stability of protein.

An α-helix mimetic oligopyridylamide, ADH-31, modulates Aß42 monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations.

Alzheimer's disease (AD), an epidemic growing worldwide due to no effective medical aid available in the market, is a neurological disorder. AD is known to be directly associated with the toxicity of amyloid-ß (Aß) aggregates. In search of potent inhibitors of Aß aggregation, Hamilton and co-workers reported an α-helix mimetic, ADH-31, which acts as a powerful antagonist of Aß42 aggregation. To identify the key interactions between protein-ligand complexes and to gain insights into the inhibitory mechanism of ADH-31 against Aß42 aggregation, molecular dynamics (MD) simulations were performed in the present study. The MD simulations highlighted that ADH-31 showed distinct binding capabilities with residues spanning from the N-terminal to the central hydrophobic core (CHC) region of Aß42 and restricted the conformational transition of the helix-rich structure of Aß42 into another form of secondary structures (coil/turn/ß-sheet). Hydrophobic contacts, hydrogen bonding and π-π interaction contribute to the strong binding between ADH-31 and Aß42 monomer. The Dictionary of Secondary Structure of Proteins (DSSP) analysis highlighted that the probability of helical content increases from 38.5% to 50.2% and the turn content reduces from 14.7% to 6.2% with almost complete loss of the ß-sheet structure (4.5% to 0%) in the Aß42 monomer + ADH-31 complex. The per-residue binding free energy analysis demonstrated that Arg5, Tyr10, His14, Gln15, Lys16, Val18, Phe19 and Lys28 residues of Aß42 are responsible for the favourable binding free energy in Aß42 monomer + ADH-31 complex, which is consistent with the 2D HSQC NMR of the Aß42 monomer that depicted a change in the chemical shift of residues spanning from Glu11 to Phe20 in the presence of ADH-31. The MD simulations highlighted the prevention of sampling of amyloidogenic ß-strand conformations in Aß42 trimer in the presence of ADH-31 as well as the ability of ADH-31 to destabilize Aß42 trimer and protofibril structures. The lower binding affinity between Aß42 trimer chains in the presence of ADH-31 highlights the destabilization of the Aß42 trimer structure. Overall, MD results highlighted that ADH-31 inhibited Aß42 aggregation by constraining Aß peptides into helical conformation and destabilized Aß42 trimer as well as protofibril structures. The present study provides a theoretical insight into the atomic level details of the inhibitory mechanism of ADH-31 against Aß42 aggregation as well as protofibril destabilization and could be implemented in the structure-based drug design of potent therapeutic agents for AD.

Targeting Human Islet Amyloid Polypeptide Aggregation and Toxicity in Type 2 Diabetes: An Overview of Peptide-Based Inhibitors.

Type 2 diabetes (T2D) is a chronic metabolic disease characterized by insulin resistance and a progressive loss of pancreatic islet ß-cell mass, which leads to insufficient secretion of insulin and hyperglycemia. Emerging evidence suggests that toxic oligomers and fibrils of human islet amyloid polypeptide (hIAPP) contribute to the death of ß-cells and lead to T2D pathogenesis. These observations have opened new avenues for the development of islet amyloid therapies for the treatment of T2D. The peptide-based inhibitors are of great value as therapeutic agents against hIAPP aggregation in T2D owing to their biocompatibility, feasibility of synthesis and modification, high specificity, low toxicity, proteolytic stability (modified peptides), and weak immunogenicity as well as the large size of involved interfaces during self-aggregation of hIAPP. An understanding of what has been done and achieved will provide key insights into T2D pathology and assist in the discovery of more potent drug candidates for the treatment of T2D. In this article, we review various peptide-based inhibitors of hIAPP aggregation, including those derived from the hIAPP sequence and those not based on the sequence, consisting of both natural as well as unnatural amino acids and their derivatives. The present review will be beneficial in advancing the field of peptide medicine for the treatment of T2D.

Impact of Mutations on the Conformational Transition from α-Helix to ß-Sheet Structures in Arctic-Type Aß40: Insights from Molecular Dynamics Simulations.

The amyloid-ß (Aß) protein aggregation into toxic oligomers and fibrils has been recognized as a key player in the pathogenesis of Alzheimer's disease. Recent experiments reported that a double alanine mutation (L17A/F19A) in the central hydrophobic core (CHC) region of [G22]Aß40 (familial Arctic mutation) diminished the self-assembly propensity of [G22]Aß40. However, the molecular mechanism behind the decreased aggregation tendency of [A17/A19/G22]Aß40 is not well understood. Herein, we carried out molecular dynamics simulations to elucidate the structure and dynamics of [G22]Aß40 and [A17/A19/G22]Aß40. The results for the secondary structure analysis reveal a significantly increased amount of the helical content in the CHC and C-terminal region of [A17/A19/G22]Aß40 as compared to [G22]Aß40. The bending free-energy analysis of D23-K28 salt bridge suggests that the double alanine mutation in the CHC region of [G22]Aß40 has the potential to reduce the fibril formation rate by 0.57 times of [G22]Aß40. Unlike [G22]Aß40, [A17/A19/G22]Aß40 largely sampled helical conformation, as determined by the minimum energy conformations extracted from the free-energy landscape. The present study provided atomic level details into the experimentally observed diminished aggregation tendency of [A17/A19/G22]Aß40 as compared to [G22]Aß40.

How Does the Mono-Triazole Derivative Modulate Aß42 Aggregation and Disrupt a Protofibril Structure: Insights from Molecular Dynamics Simulations.

Clinical studies have identified that abnormal self-assembly of amyloid-ß (Aß) peptide into toxic fibrillar aggregates is associated with the pathology of Alzheimer's disease (AD). The most acceptable therapeutic approach to stop the progression of AD is to inhibit the formation of ß-sheet-rich structures. Recently, we designed and evaluated a series of novel mono-triazole derivatives 4(a-x), where compound 4v was identified as the most potent inhibitor of Aß42 aggregation and disaggregates preformed Aß42 fibrils significantly. Moreover, 4v strongly averts the Cu2+-induced Aß42 aggregation and disaggregates the preformed Cu2+-induced Aß42 fibrils, halts the generation of reactive oxygen species, and shows neuroprotective effects in SH-SY5Y cells. However, the underlying molecular mechanism of inhibition of Aß42 aggregation by 4v and disaggregation of preformed Aß42 fibrils remains obscure. In this work, molecular dynamics (MD) simulations have been performed to explore the conformational ensemble of the Aß42 monomer and a pentameric protofibril structure of Aß42 in the presence of 4v. The MD simulations highlighted that 4v binds preferentially at the central hydrophobic core region of the Aß42 monomer and chains D and E of the Aß42 protofibril. The dictionary of secondary structure of proteins analysis indicated that 4v retards the conformational conversion of the helix-rich structure of the Aß42 monomer into the aggregation-prone ß-sheet conformation. The binding free energy calculated by the molecular mechanics Poisson-Boltzmann surface area method revealed an energetically favorable process with ΔG binding = -44.9 ± 3.3 kcal/mol for the Aß42 monomer-4v complex. The free energy landscape analysis highlighted that the Aß42 monomer-4v complex sampled conformations with significantly higher helical contents (35 and 49%) as compared to the Aß42 monomer alone (17%). Compound 4v displayed hydrogen bonding with Gly37 (chain E) and π-π interactions with Phe19 (chain D) of the Aß42 protofibril. Further, the per-residue binding free energy analysis also highlighted that Phe19 (chain D) and Gly37 (chain E) of the Aß42 protofibril showed the maximum contribution in the binding free energy. The decreased binding affinity and residue-residue contacts between chains D and E of the Aß42 protofibril in the presence of 4v indicate destabilization of the Aß42 protofibril structure. Overall, the structural information obtained through MD simulations indicated that 4v stabilizes the native helical conformation of the Aß42 monomer and persuades a destabilization in the protofibril structure of Aß42. The results of the study will be useful in the rational design of potent inhibitors against amyloid aggregation.

Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy.

A new coronavirus (CoV) caused a pandemic named COVID-19, which has become a global health care emergency in the present time. The virus is referred to as SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) and has a genome similar (∼82%) to that of the previously known SARS-CoV (SARS coronavirus). An attractive therapeutic target for CoVs is the main protease (Mpro) or 3-chymotrypsin-like cysteine protease (3CLpro), as this enzyme plays a key role in polyprotein processing and is active in a dimeric form. Further, Mpro is highly conserved among various CoVs, and a mutation in Mpro is often lethal to the virus. Thus, drugs targeting the Mpro enzyme significantly reduce the risk of mutation-mediated drug resistance and display broad-spectrum antiviral activity. The combinatorial design of peptide-based inhibitors targeting the dimerization of SARS-CoV Mpro represents a potential therapeutic strategy. In this regard, we have compiled the literature reports highlighting the effect of mutations and N-terminal deletion of residues of SARS-CoV Mpro on its dimerization and, thus, catalytic activity. We believe that the present review will stimulate research in this less explored yet quite significant area. The effect of the COVID-19 epidemic and the possibility of future CoV outbreaks strongly emphasize the urgent need for the design and development of potent antiviral agents against CoV infections.