Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Olive-Derived Triterpenes Suppress SARS COV-2 Main Protease: A Promising Scaffold for Future Therapeutics

SARS CoV-2 pandemic is still considered a global health disaster, and newly emerged variants keep growing. A number of promising vaccines have been recently developed as a protective measure; however, cost-effective treatments are also of great importance to support this critical situation. Previously, betulinic acid has shown promising antiviral activity against SARS CoV via targeting its main protease. Herein, we investigated the inhibitory potential of this compound together with three other triterpene congeners (i.e., ursolic acid, maslinic acid, and betulin) derived from olive leaves against the viral main protease (M^pro) of the currently widespread SARS CoV-2. Interestingly, betulinic, ursolic, and maslinic acids showed significant inhibitory activity (IC₅₀ = 3.22–14.55 µM), while betulin was far less active (IC₅₀ = 89.67 µM). A comprehensive in-silico analysis (i.e., ensemble docking, molecular dynamic simulation, and binding-free energy calculation) was then performed to describe the binding mode of these compounds with the enzyme catalytic active site and determine the main essential structural features required for their inhibitory activity. Results presented in this communication indicated that this class of compounds could be considered as a promising lead scaffold for developing cost-effective anti-SARS CoV-2 therapeutics.     

初始微观结构缺陷和断裂的温度依赖及相关性

纳米线(NW)结构内的微观结构缺陷对NW的机械性能存在一定的影响。NW断裂位置的预测关系着纳米器件应用的寿命,进而引起了人们的广泛关注。在本工作中,基于统计分析,分别研究了单晶铜纳米线(Cu NW)拉伸过程中出现的断裂位置以及在应力屈服点处产生的初始微观结构缺陷(初始缺陷)的位置对温度的依赖性,进一步探究了两者之间的联系。利用分子动力学(MD)模拟了单晶Cu NW在20~300 K的温度范围内的拉伸状态,共包含6个体系,各温度体系包含300个独立的样本。基于机器学习,采用density-based spatial clustering of applications with noise (DBSCAN)算法,将hexagonal close-packed (hcp)原子划分为各个初始缺陷以进一步确定其位置。统计结果显示,当温度低于50 K时,初始缺陷的位置集中在NW的两端。随着模拟温度的上升,MD模拟结果展现了单晶Cu NW的拉伸过程中的杨氏模量、平均屈服应力、平均势能等机械性能对温度的依赖性。温度的升高进一步促使了更多初始缺陷的产生,并使得初始缺陷的位置由统计分布的两端向中间平均化。与初始缺陷相比,各温度下的断裂位置集中在两端。统计结果表明,模拟的温度范围对NW的断裂位置无明显影响,但对初始缺陷的产生具有明显影响。当温度低于100 K时,初始缺陷的位置分布与断裂位置分布呈现了一致性。由于两者具有不同的温度依赖,其差异随着温度的上升逐渐显现。对不同温度下的微观结构形变行为观察发现,断裂失效明显受到NW两端的表面效应和阻挡效应的影响。最终的断裂位置受塑性形变中后期的影响,与应力屈服区产生的初始缺陷无直接联系。     

Combinatorial Screening of Water/Proton Permeation of Self-Assembled Pillar[5]arene Artificial Water Channel Libraries

Artificial water channels (AWCs) that selectively transport water and reject ions through bilayer membranes have potential to act as synthetic Aquaporins (AQPs). AWCs can have a similar osmotic permeability, better stability, with simpler manufacture on a larger-scale and have higher functional density and surface permeability when inserted into the membrane. Here, we report the screening of combinatorial libraries of symmetrical and unsymmetrical rim-functionalized PAs A – D that are able to transport ca. 10⁷–10⁸ water molecules/s/channel, which is within 1 order of magnitude of AQPs’ and show total ion and proton rejection. Among the four channels, C and D are 3–4 times more water permeable than A and B when inserted in bilayer membranes. The binary combinations of A – D with different molar ratios could be expressed as an independent (linear ABA ), a recessive (inhibition AB , AC , DB , ACA ), or a dominant (amplification, DBD ) behavior of the water net permeation events.     

Nanometer‐Scale Water‐ and Proton‐Diffusion Heterogeneities across Water Channels in Polymer Electrolyte Membranes

Nafion, the most widely used polymer for electrolyte membranes (PEMs) in fuel cells, consists of a fluorocarbon backbone and acidic groups that, upon hydration, swell to form percolated channels through which water and ions diffuse. Although the effects of the channel structures and the acidic groups on water/ion transport have been studied before, the surface chemistry or the spatially heterogeneous diffusivity across water channels has never been shown to directly influence water/ion transport. By the use of molecular spin probes that are selectively partitioned into heterogeneous regions of the PEM and Overhauser dynamic nuclear polarization relaxometry, this study reveals that both water and proton diffusivity are significantly faster near the fluorocarbon and the acidic groups lining the water channels than within the water channels. The concept that surface chemistry at the (sub)nanometer scale dictates water and proton diffusivity invokes a new design principle for PEMs.     

Intermolecular Dynamic Kinetic Resolution Cooperatively Catalyzed by an N‐Heterocyclic Carbene and a Lewis Acid

The ubiquitous structure of δ‐lactones makes the development of new methods for their enantioselective and stereoselective synthesis an important ongoing challenge. The intermolecular dynamic kinetic resolution (DKR) of β‐halo‐α‐ketoesters cooperatively catalyzed by an N‐heterocyclic carbene and a Lewis acid generates two contiguous stereocenters with remarkable diastereoselectivity through an oxidation/lactonization sequence.     

A Combined Experimental and Theoretical Study on the Stereodynamics of Monoaza[5]helicenes: Solvent‐Induced Increase of the Enantiomerization Barrier in 1‐Aza‐[5]helicene

Helicenes and heterohelicenes are attractive compounds with great potential in materials sciences to be used in optoelectronics as ligand backbones in enantioselective catalysis and as chiral sensors. The properties of these materials are related to the stereodynamics of these helical chiral compounds. However, little is known about features controlling stereodynamics in helicenes; in particular, for heterohelicenes the position of the heteroatom could be relevant in this respect. Herein the complete stereodynamic characterization of monoaza[5]helicenes is shown by enantioselective dynamic HPLC and DFT calculations. At variance with previous theoretical calculations, 1‐aza[5]helicene shows a surprisingly high enantiomerization barrier, which is triggered by specific solvent interactions.