Integrating molecular dynamics simulation and molecular mechanics/generalized Born surface area calculation into pharmacophore modeling: a case study on the proviral integration site for Moloney murine leukemia virus (Pim)-1 kinase inhibitors

Two birds with one stone: The detection of nerve agents and AChE activity with an ICT-ESIPT-based fluorescence sensor

Nerve agents are among the world's deadliest poisons, and the target enzyme is acetylcholinesterase (AChE). To better diagnosis nerve agent poisonings, a reliable diagnostic method for both nerve agents and AChE is desirable. Herein, we synthesized a series of fluorescent sensors for both real nerve agents and acetylcholinesterase activity detection. Among these sensors, HBQ-AE exhibited a fast response rate (within 10 s for nerve agent and 8 min for AChE), good sensitivity (the limit of detection is 6 nM and 0.2 U/mL) and a high off/on contrast. To the best of our knowledge, HBQ-AE is the first fluorescence sensor for nerve agents and AChE activity detection. The fluorescent change of HBQ-AE from nonfluorescence to blue fluorescence (nerve agent) or orange fluorescence (AChE) by excitation at 365 nm can be easily observed with the naked eye. HBQ-AE was successfully applied to image nerve agents and AChE activity in living cells. Moreover, HBQ-AE is the vital member to construct a test paper that can be employed to detect and diagnose chemical warfare agents.

Computational investigation on the effect of Oleuropein aglycone on the α-synuclein aggregation

Parkinson's disease (PD) is considered to be the second most common progressive neurodegenerative brain disorder after Alzheimer's disease, which is caused by misfolding and aggregation of Alpha-synuclein (α-synuclein). It is characterized by distinct aggregated fibrillary form of α-synuclein known as the Lewy bodies and Lewy neurites. The most promising approach to combat PD is to prevent the misfolding and subsequent aggregation of α-synuclein. Recently, Oleuropein aglycone (OleA) has been reported to stabilize the monomeric structure of α-synuclein, subsequently favoring the growth of nontoxic aggregates. Therefore, understanding the conformational dynamics of α-synuclein monomer in the presence of OleA is significant. Here, we have investigated the effect of OleA on the conformational dynamics and the aggregation propensity of α-synuclein using molecular dynamics simulation. From molecular dynamics trajectory analysis, we noticed that when OleA is bound to α-synuclein, the intramolecular distance between non-amyloid-β component domain and C-terminal domain of α-synuclein was increased, whereas long-range hydrophobic interactions between the two region were reduced. Oleuropein aglycone was found to interact with the N-terminal domain of α-synuclein, making this region unavailable for interaction with membranes and lipids for the formation of cellular toxic aggregates. From the binding-free energy analysis, we found binding affinity between α-synuclein and OleA to be indeed high (ΔG_bind = -12.56 kcal mol^-1 from MM-PBSA and ΔG_bind = -27.41 kcal mol^-1from MM-GBSA). Our findings in this study thus substantiate the effect of OleA on the structure and stabilization of α-synuclein monomer that subsequently favors the growth of stable and nontoxic aggregates.Communicated by Ramaswamy H. Sarma.

Effect of CTerm of human albumin on the aggregation propensity of Aβ1-42 peptide: a potential of mean force study

Alzheimer's disease (AD) is the most common progressive neurodegenerative brain disorder. It is characterized by the presence of extracellular aggregated fibrillary form of amyloid beta (Aβ) peptide and intraneuronal neurofibrillary tangles caused by the hyperphosphorylation of tau protein. Monomeric form of Aβ peptide in α-conformation is not toxic but it can undergo self-aggregation to form β-conformation which is neurotoxic. The most promising approach to combat AD is to prevent the self-aggregation of Aβ peptide. Recently, it has been reported that C-terminal (CTerm) of human albumin (HA) binds to the Aβ_1-42 peptide and impairs the Aβ_1-42 aggregation and promotes disassembly of Aβ_1-42 aggregates. In this work, using potential of mean force (PMF) and binding free energy (BFE) calculations, we have demonstrated the effect of CTerm of HA on the dimerization of Aβ_1-42 peptide. From the PMF profile, we noticed Aβ_1-42-CTerm Heterodimer (10.99 kcal mol - 1) complex to have higher disassociation energy than Aβ_1-42-Aβ_1-42 homodimer (2.23 kcal mol - 1) complex. And also from the BFE calculations, we found that the binding affinity between Aβ_1-42 peptide and CTerm (ΔG_bind = -32.27 kcal mol - 1 from MM-GBSA and ΔG_bind = -2.83 kcal mol - 1 from MM-PBSA (molecular mechanics-Poisson - Boltzmann surface area)) to be stronger than the Aβ_1-42 peptide and another Aβ_1-42 peptide (ΔG_bind = -16.20 kcal mol - 1 from MM-GBSA and ΔG_bind = -1.95 kcal mol - 1 from MM-PBSA). In this study, our findings from PMF and BFE analysis of the two complexes provide salient structural, binding and unbinding features and thermodynamics that support the ability of CTerm of HA in affecting the dimerization of Aβ_1-42. Communicated by Ramaswamy H. Sarma.