Interactions of a multifunctional di-triazole derivative with Alzheimer's Aß42 monomer and Aß42 protofibril: a systematic molecular dynamics study.

Amyloid aggregation modulators offer a promising treatment strategy for Alzheimer's disease (AD). We have recently reported a novel di-triazole based compound 6n as a multi-target-directed ligand (MTDL) against AD. 6n effectively inhibits Aß42 aggregation, metal-induced Aß42 aggregation, reactive oxygen species (ROS) generation, and rescues SH-SY5Y cells from Aß42 induced neurotoxicity. However, the underlying inhibitory mechanism remains uncovered. In this regard, molecular dynamics (MD) simulations were performed to understand the effect of 6n on the structure and stability of monomeric Aß42 and a pentameric protofibril structure of Aß42. Compound 6n binds preferably to the central hydrophobic core (CHC) and C-terminal regions of the Aß42 monomer as well as the protofibril structure. The secondary structure analysis suggests that 6n prevents the aggregation of the Aß42 monomer and disaggregates Aß42 protofibrils by sustaining the helical content in the Aß42 monomer and converting the ß-sheet into random coil conformation in the Aß42 protofibril structure. A significant decrease in the average number of hydrogen bonds, binding affinity, and residue-residue contacts between chains D-E of the Aß42 protofibril in the presence of 6n indicates destabilization of the Aß42 protofibril structure. The MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) analysis highlighted favourable binding free energy (ΔGbinding) for the Aß42 monomer-6n and Aß42 protofibril-6n complex. Overall, MD results highlighted that 6n stabilizes the native α-helix conformation of the Aß42 monomer and induces a sizable destabilization in the Aß42 protofibril structure. This work provides theoretical insights into the inhibitory mechanism of 6n against amyloid aggregation and will be beneficial as a molecular guide for structure-based drug design against AD.

Computational design and evaluation of ß-sheet breaker peptides for destabilizing Alzheimer's amyloid-ß42 protofibrils.

The ß-sheet breaker (BSB) peptides interfere with amyloid fibril assembly and used as therapeutic agents in the treatment of Alzheimer's disease (AD). In this regard, a simple yet effective in silico screening methodology was applied in the present study to evaluate a potential 867 pentapeptide library based on known BSB peptide, LPFFD, for destabilizing Aß42 protofibrils. The molecular docking based virtual screening was used to filter out pentapeptides having binding affinities stronger than LPFFD. In the next step, binding free energies of the top 10 pentapeptides were evaluated using the MM-PBSA method. The residue-wise binding free energy analysis reveals that two pentapeptides, PVFFE, and PPFYE, bind to the surface of Aß42 protofibril and another pentapeptide, PPFFE, bind in the core region of Aß42 protofibril. By employing molecular dynamics simulation as a post filter for the top-hit peptides from MM-PBSA, the pentapeptides, PPFFE, PVFFE, and PPFYE, have been identified as potential BSB peptides for destabilizing Aß42 protofibril structure. The conformational microstate analysis, a significant decrease in the ß-sheet content of Aß42 protofibril, a loss in the total number of hydrogen bonds in Aß42 protofibril, Asp23-Lys28 salt bridge destabilization and analysis of the free energy surfaces highlight Aß42 protofibril structure destabilization in presence of pentapeptides. Among three top-hit pentapeptides, PPFFE displayed the most potent Aß42 protofibril destabilization effect that shifted the energy minima toward lowest value of ß-sheet content as well as lowest number of hydrogen bonds in Aß42 protofibril. The in silico screening workflow presented in the study highlight an alternative tool for designing novel peptides with enhanced BSB ability as potential therapeutic agents for AD.

Molecular insights into the effect L17A/F19A double mutation on the structure and dynamics of Aß40 : A molecular dynamics simulation study.

The aggregation of amyloid-ß (Aß) peptide has been associated with the pathogenesis of Alzheimer disease. The recent studies highlighted that L17A/F19A double mutation increases the structural stability of Aß40 and diminish Aß40 aggregation. However, the underlying effect of L17A/F19A double mutation on the Aß40 structure and dynamics remain elusive. In this regard, the influence of L17A/F19A double mutation on the structure and dynamics of Aß40 was investigated using all-atom molecular dynamics (MD) simulation. MD simulation reveals that mechanism behind modulation of Aß40 aggregation is associated with a decrease in the ß-sheet content and dynamics of the salt bridge D23-K28. The secondary structure analysis highlight more abundant α-helix content in the central hydrophobic core and C-terminal region of Aß40 upon L17A/F19A double mutation that is consistent with circular dichroism (CD) results. The free-energy landscape reveal that coil conformation is the most dominant conformation in Aß40 whereas the helical conformation is the most-populated and energetically favorable conformation in Aß40 (L17A/F19A). MD simulation, in accord with the experiment, highlight that L17A/F19A double mutation diminish Aß40 aggregation as the population of the fibril-prone state substantially decreased. The present study, in conjunction with experiment, highlight that L17 and F19 are the critical residues involved in the conformational change that triggers a neurotoxic cascade of Aß40 . Overall, MD simulation provides key structural and physical insights into the reduced Aß40 aggregation upon L17A/F19A double mutation and an atomic picture of the L17A/F19A-mediated conformational changes in Aß40 .

Assessing the effect of D59P mutation in the DE loop region in amyloid aggregation propensity of ß2-microglobulin: A molecular dynamics simulation study.

Dialysis-related amyloidosis (DRA) is a severe condition characterized by the accumulation of amyloidogenic ß2-microglobulin (ß2m) protein around skeletal joints and bones. The recent studies highlighted a critical role of the DE loop region for ß2m stability and amyloid aggregation propensity. Despite significant efforts, the molecular mechanism of enhanced aggregation due to D59P mutation in the DE loop region remain elusive. In the present study, explicit-solvent molecular dynamics (MD) simulations were performed to examine the key changes in the structural and dynamic properties of wild type (wt) ß2m upon D59P mutation. MD simulations reveal a decrease in the average number of hydrogen bonds in the loop regions on D59P mutation that enhances conformational flexibility, which lead to higher aggregation propensity of D59P as compare to wt ß2m. The principal component analysis (PCA) highlight that D59P covers a larger region of phase space and display a higher trace value than wt ß2m, which suggest an overall enhancement in the conformational flexibility. D59P display two minimum energy basins in the free energy landscape (FEL) that are associated with thermodynamically less stable conformational states as compare to single minimum energy basin in wt ß2m. The present study provides theoretical insights into the molecular mechanism behind the higher aggregation propensity of D59P as compare to wt ß2m.

Molecular insights into Aß42 protofibril destabilization with a fluorinated compound D744: A molecular dynamics simulation study.

The aggregation of amyloid ß-peptide (Aß42 ) into toxic oligomers, fibrils, has been identified as a key process in Alzheimer's disease (AD) progression. The role of halogen-substituted compounds have been highlighted in the disassembly of Aß protofibril. However, the underlying inhibitory mechanism of Aß42 protofibril destabilization remains elusive. In this regard, a combined molecular docking and molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a fluorinated compound, D744, which has been reported previously for potential in vitro and in vivo inhibitory activity against Aß42 aggregation and reduction in the Aß-induced cytotoxicity. The molecular docking analysis highlights that D744 binds and interacts with chain A of the protofibril structure with hydrophobic contacts and orthogonal multipolar interaction. MD simulations reveal destabilization of the protofibril structure in the presence of D744 due to the decrease in ß-sheet content and a concomitant increase of coil and bend structures, increase in the interchain D23-K28 salt bridge distance, decrease in the number of backbone hydrogen bonds, increase in the average distance between Cα atoms, and decrease in the binding affinity between chains A and B of the protofibril structure. The binding free-energy analysis between D744 and the protofibril structure with Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) reveal that residues Leu17, Val18, Phe19, Phe20, Ala21, Glu22, Asp23, Leu34, Val36, Gly37, and Gly38 of chain A of the protofibril structure contribute maximum towards binding free energy (ΔGbinding  = -44.87 kcal/mol). The insights into the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aß42 will be beneficial for the current and future AD therapeutic studies.

In silico-guided identification of potential inhibitors against ß2m aggregation in dialysis-related amyloidosis.

In dialysis-related amyloidosis (DRA), misfolding of ß2-microglobulin (ß2m) leads to amyloid fibril deposition mainly in the skeletal joints seriously affecting their functionality. The identification and characterization of small-molecules that bind ß2m and possibly inhibit its aggregation remain unexplored. In the present study, a ligand-based virtual screening approach and molecular dynamics (MD) simulations were employed to explore potent small-molecule inhibitors against ß2m aggregation. The compounds were screened from various small-molecule databases by applying ligand-based virtual screening with rifamycin SV (RSV) as a reference compound. The molecular docking analysis was performed to filter out lead compounds with a higher binding affinity than RSV from a library of ∼800 compounds. Three compounds, ChEBI68321 (C1), ChEMBL360190 (C2) and ZINC3091144 (C3), displaying excellent binding free energies of -51.29, -36.51 and -34.36 kcal/mol, respectively, with ß2m were subjected to MD simulations to get insights into the binding locations, key interactions and structural stability of the ß2m-ligand complexes. The hydrogen bond analysis highlight higher structural stability and reduced flexibility of the loop regions of ß2m in presence of C1, C2 and C3. The integrated computational approach employed in the present study identify promising lead compounds against ß2m aggregation in DRA. Abbreviationsß2mß2-microglobulin3Dthree dimensionalADAlzheimer's diseaseADTAutoDock ToolsDRADialysis-related amyloidosisDSSPdictionary of secondary structure of proteinsFELfree energy landscapeGROMACSGROningen MAchine for Chemical SimulationsLGALamarckian Genetic AlgorithmLINCSLINear Constraint SolverMCmain chainMDmolecular dynamicsMHC-Imajor histocompatibility complex class IMM-PBSAmolecular mechanics Poisson-Boltzmann surface areaPMEnanometer (nm); particle mesh ewaldPCAprincipal component analysisPDBprotein data bankRgradius-of-gyrationRSVrifamycin SVRMSDroot-mean-square deviationRMSFroot-mean-square fluctuationSCside chainSPCsimple point chargeSASASolvent accessible surface areaVMDvisual molecular dynamicsCommunicated by Ramaswamy H. Sarma.

Impact of K16A and K28A mutation on the structure and dynamics of amyloid-ß42 peptide in Alzheimer's disease: key insights from molecular dynamics simulations.

The aggregation of amyloid-ß42 (Aß42) peptide into toxic oligomers and fibrils is a key step in the Alzheimer disease pathogenesis. The recent studies highlighted that lysine residues (K16 and K28) play a critical role in the Aß42 self-assembly and are the target of entities like molecular tweezer, CLR01. The studies reveal that lysine to alanine mutation significantly affect Aß oligomerization, toxicity and aggregation process. However, the molecular mechanism behind reduced Aß toxicity on K16A and K28A mutation remain elusive. In this regard, molecular dynamics (MD) simulations were performed in the present study to get insights into the effect of K16A and K28A mutation in Aß42 self-assembly. The MD simulations highlighted that K16A and K28A mutation in the aggregation-prone region, i.e., central hydrophobic core (KLVFF, 16-20) and bend region (D23-K28), cause major structural changes in the Aß42 monomer. The secondary structure analysis highlight that modulation of aggregation in K16A and K28A is linked to the increase in the overall helix content and a concomitant decrease in the ß-sheet content of Aß42 monomer. The short-range tertiary contacts between central hydrophobic core and C-terminal region were relatively reduced in K16A and K28A as compare to wild type (wt) Aß42. The mechanistic insights from the study will be beneficial for the design and development of novel inhibitors that will bind and block the interactions, mediated by lysine residues specifically, critical for the Aß42 self-assembly in Alzheimer disease. [Formula: see text] The molecular mechanism behind modulation of amyloid-ß42 (Aß42) self-assembly on K16A and K28A mutation has been investigated using molecular dynamics (MD) simulations. MD simulations reveal that reduced aggregation in K16A and K28A is linked to the increase in the overall helix content and a concomitant decrease in the ß-sheet content, particularly at the C-terminal region, of Aß42.Communicated by Ramaswamy H. Sarma.

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.

Insights into the inhibitory mechanism of a resveratrol and clioquinol hybrid against Aß42 aggregation and protofibril destabilization: A molecular dynamics simulation study.

Amyloid-ß (Aß) peptide instinctively aggregate and form plaques in the brain of Alzheimer's disease (AD) patients. At present, there is no cure or treatment for AD, and significant effort has, therefore, been made to discover potent drugs against AD. Previous studies reported that a resveratrol and clioquinol hybrid compound [(E)-5-(4-hydroxystyryl)quinolone-8-ol], C1, strongly inhibit Aß42 aggregation and disassemble preformed fibrils. However, the atomic level details of the inhibitory mechanism of C1 against Aß42 aggregation and protrofibril disassembly remains elusive. In this regard, molecular docking and molecular dynamics (MD) simulation of Aß42 monomer, Aß42 monomer-C1 complex, Aß42 protofibril, and Aß42 protofibril-C1 complex were performed in the present study. MD simulations highlighted that C1 bind in the central hydrophobic core (CHC) region, i.e., KLVFF (16-20) of Aß42 monomer, which plays a critical role in Aß42 aggregation. C1 promote the formation of native helical conformation in the Aß42 monomer and decrease the probability of D23-K28 salt bridge interaction that is critical in the formation of aggregation-prone ß-sheet conformation. Further, C1 destabilize Aß42 protofibril structure by increasing the interchain distance between chains A-B, disrupting the salt-bridge interaction between D23-K28, and decreasing the number of backbone hydrogen bonds between chains A-B of the Aß42 protofibril structure. The insights into the underlying inhibitory mechanism of small molecules that display potential in vitro anti-aggregation activity against Aß42 will be beneficial for the rational design of more potent drug molecules against AD. Communicated by Ramaswamy H. Sarma.

Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-ß42 monomer: insights from molecular dynamics simulations.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-ß42 (Aß42) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aß42 aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aß42. MD simulations reveal that C1 stabilizes native α-helix conformation of Aß42 by interacting with key residues in the central helix region (13-26) with hydrogen bonds and π-π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16-20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM-PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (-43.1 kcal/mol) between C1 and Aß42 monomer. Overall, MD simulations reveal that C1 inhibits Aß42 aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone ß-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aß42.

Molecular insights into the inhibitory mechanism of rifamycin SV against ß2-microglobulin aggregation: A molecular dynamics simulation study.

Dialysis-related amyloidosis (DRA) is a severe condition characterized by the accumulation of amyloidogenic ß2-microglobulin (ß2m) protein around skeletal joints and bones. The small molecules that modulate ß2m aggregation have been identified in vitro, however, the underlying inhibitory mechanism remain elusive. In the present study, molecular docking and molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of an antibiotic, rifamycin SV (C1) reported for its in vitro anti-aggregation activity against ß2m. The molecular docking analysis highlight that C1 display hydrophobic contacts with residues in the aggregation prone region of ß2m. MD simulations reveal enhanced structural stability of ß2m in the presence of C1. C1 inhibit the conformational transition of the C-terminal region of ß2m from a ß-sheet to random coil conformation, which is reported for the initiation of fibrillogenesis of ß2m. The results of the present study provide insight into the key interactions and underlying inhibitory mechanism of a small molecule against ß2m aggregation that will help in the design and development of more potent, novel inhibitors of ß2m aggregation.

Rationally Designed Peptides and Peptidomimetics as Inhibitors of Amyloid-ß (Aß) Aggregation: Potential Therapeutics of Alzheimer's Disease.

Alzheimer's disease (AD) is a progressive neurodegenerative disease with no clinically accepted treatment to cure or halt its progression. The worldwide effort to develop peptide-based inhibitors of amyloid-ß (Aß) aggregation can be considered an unplanned combinatorial experiment. An understanding of what has been done and achieved may advance our understanding of AD pathology and the discovery of effective therapeutic agents. We review here the history of such peptide-based inhibitors, including those based on the Aß sequence and those not derived from that sequence, containing both natural and unnatural amino acid building blocks. Peptide-based aggregation inhibitors hold significant promise for future AD therapy owing to their high selectivity, effectiveness, low toxicity, good tolerance, low accumulation in tissues, high chemical and biological diversity, possibility of rational design, and highly developed methods for analyzing their mode of action, proteolytic stability (modified peptides), and blood-brain barrier (BBB) permeability.