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Flexible wearable electronic skin (e-skin) has great potential in health monitoring, human–computer interaction, and other fields. However, traditional devices are often unable to maintain high sensitivity while achieving a wide detection range. In this work, inspired by biomimicry, we proposed a design based on mimosa flowers and developed a composite pressure sensing device (reduced graphene oxide (rGO)/NiMoO4@CMF). The strain layer of the sensor undergoes hydrothermal growth, allowing nickel molybdate (NiMoO4) to grow in situ on the surface of the carbon melamine foam (CMF). This enhances the substrate morphology, and rGO is then applied to increase the electrical conductivity. The devices prepared by this method have sensitivities of 19.3, 12.5, and 8.1 kPa–1 in the ranges of 0–12, 12–29, and 29–40 kPa, respectively. In addition, the sensor demonstrates a low detection limit (10 Pa), a fast response (160 ms), and a cycle retention rate of 86% after 5000 cycles. Based on these characteristics, the flexible sensor can detect strong human body movements in real time, such as finger bending, elbow movement, and knee bending. The study shows that this pressure sensor has broad application prospects in health monitoring. [ABSTRACT FROM AUTHOR]

Microtubule targeting agents (MTAs) are used as clinically effective chemotherapies for cancer treatment but might be limited by the acquired or intrinsic resistance of cancer cells to apoptosis. The vulnerability of therapy-resistant cancers to ferroptosis provides an alternative way to overcome drug resistance. In this study, on the basis of the MTAs obtained in our previous studies, a series of MTAs were synthesized, and detailed structure-activity relationships were obtained through extensive molecular dynamics studies. Among them, a diphenylethene derivative, compound 33 , displayed the most potent activity in vitro and in vivo, with IC 50 values of 10-50 nM toward six cancer cell lines and a 78.6% tumor growth inhibition in vivo. Interestingly, although it acted as the MTA, compound 33 triggered cell death mainly through cell ferroptosis rather than apoptosis, which might provide an alternative way to eradicate apoptosis-related drug resistance.

Blockade of the human ether-à-go-go-related gene (hERG) channel by small molecules induces the prolongation of the QT interval which leads to fatal cardiotoxicity and accounts for the withdrawal or severe restrictions on the use of many approved drugs. In this study, we develop a deep learning approach, termed deephERG, for prediction of hERG blockers of small molecules in drug discovery and postmarketing surveillance. In total, we assemble 7,889 compounds with well-defined experimental data on the hERG and with diverse chemical structures. We find that deephERG models built by a multitask deep neural network (DNN) algorithm outperform those built by single-task DNN, naı̈ve Bayes (NB), support vector machine (SVM), random forest (RF), and graph convolutional neural network (GCNN). Specifically, the area under the receiver operating characteristic curve (AUC) value for the best model of deephERG is 0.967 on the validation set. Furthermore, based on 1,824 U.S. Food and Drug Administration (FDA) approved drugs, 29.6% drugs are computationally identified to have potential hERG inhibitory activities by deephERG, highlighting the importance of hERG risk assessment in early drug discovery. Finally, we showcase several novel predicted hERG blockers on approved antineoplastic agents, which are validated by clinical case reports, experimental evidence, and the literature. In summary, this study presents a powerful deep learning-based tool for risk assessment of hERG-mediated cardiotoxicities in drug discovery and postmarketing surveillance.

The development of novel isoform/class-selective inhibitors is still of great biological and medical significance to conquer the continuously reported side effects for the histone deacetylase (HDAC) drugs. The first potent HDAC allosteric inhibitor was discovered last year, and this allosteric inhibitor design is thought to be a promising strategy to overcome the current challenges in HDAC inhibitor design. However, the detailed allosteric mechanism and its remote regulatory effects on the catalytic/inhibitor activity of HDAC are still unclear. In this work, on the basis of microsecond-time-scale all-atom molecular dynamics (MD) simulations and picosecond-time-scale density functional theory/molecular mechanics MD simulations on HDAC8, we propose that the allostery is achieved by the intrinsic conformational flexibility of the binding rail (constituted by a highly conserved X-D residue dyad), which steers the loop-loop motion and creates the diverse shapes of the allosteric sites in different HDAC isoforms. Additionally, the rotatability of the binding rail is an inherent structural feature that regulates the hydrophobicity of the linker binding channel and thus further affects the HDAC enzyme inhibitory/catalytic activity by utilizing the promiscuity of X-D dyad. Since the plastic X residue is different among class I HDACs, these new findings provide a deeper understanding of the allostery, which is guidable for the design of new allosteric inhibitors toward the allosteric site and structure modifications on the conventional inhibitors binding into the active pocket by exploiting the intrinsic dynamic features of the conserved X-D dyad.

The Ca 2 (UO 2 )(CO 3 ) 3 complex has been shown to be the dominant species of uranyl in different aqueous environments, and thermodynamic data of the complexation have been measured accurately recently. However, a detailed understanding of the binding processes with explicit consideration of the water molecules in the presence of common salt ions such as Na + and Cl - has been lacking. Here we use classical molecular dynamics combined with umbrella sampling to map the complete binding processes and their free-energy profiles leading to formation of the Ca 2 (UO 2 )(CO 3 ) 3 complex from UO 2 2+ , CO 3 2- , and Ca 2+ in an aqueous NaCl solution to simulate the seawater conditions. We find that the presence of Na + ions affects the binding between UO 2 2+ and CO 3 2- as well as between [(UO 2 )(CO 3 ) 3 ] 4- and Ca 2+ by changing the coordination mode of carbonate to UO 2 2+ . The free energies of binding from our simulations are in good agreement with the experimental data for both pure water and the NaCl solution. Our work shows that free-energy simulations based on classical molecular dynamics simulations can be a useful tool to examine the atomistic process of the ligand binding to form the Ca 2 (UO 2 )(CO 3 ) 3 complex under different aqueous environments and that the presence of common ions can impact the complexation chemistry of uranyl.

Uranium from the sea provides a long-time supply guarantee of nuclear fuels for centuries to come, and the neutral Ca2UO2(CO3)3 complex has been shown to be the dominant species of uranium in seawater. However, the solvation and structure of the Ca2UO2(CO3)3 complex in seawater have been unclear. Herein we simulate the Ca2UO2(CO3)3 complex in a model seawater solution via classical molecular dynamics. We find that Na(+) and Cl(-) ions interact very differently with the neutral Ca2UO2(CO3)3 complex in seawater. Especially, one Na(+) ion is closely associated with the Ca2UO2(CO3)3 complex, thereby effectively making the complex have a +1 charge, while Cl(-) ions are much farther away. Hence, this work reveals the important role of Na(+) ions in affecting the solvation of the Ca2UO2(CO3)3 complex in seawater, which has implications in designing ligands to attract the Ca2UO2(CO3)3 complex to the sorbent.

Bromodomains (BRDs) are protein modules that selectively recognize histones as a "reader" by binding to an acetylated lysine substrate. The human BRD4 has emerged as a promising drug target for a number of disease pathways, and several potent BRD inhibitors have been discovered experimentally recently. However, the detailed inhibition mechanism especially for the inhibitor binding kinetics is not clear. Herein, by employing classical molecular dynamics (MD) and state-of-the-art density functional QM/MM MD simulations, the dynamic characteristics of ZA-loop in BRD4 are revealed. And then the correlation between binding pocket size and ZA-loop motion is elucidated. Moreover, our simulations found that the compound (-)-JQ1 could be accommodated reasonably in thermodynamics whereas it is infeasible in binding kinetics against BRD4. Its racemate (+)-JQ1 proved to be both thermodynamically reasonable and kinetically achievable against BRD4, which could explain the previous experimental results that (+)-JQ1 shows a high inhibitory effect toward BRD4 (IC50 is 77 nM) while (-)-JQ1 is inactive (>10 μM). Furthermore, the L92/L94/Y97 in the ZA-loop and Asn140 in the BC-loop are identified to be critical residues in (+)-JQ1 binding/releasing kinetics. All these findings shed light on further selective inhibitor design toward BRD family, by exploiting the non-negligible ligand binding kinetics features and flexible ZA-loop motions of BRD, instead of only the static ligand-protein binding affinity.

Development of isoform-selective histone deacetylase (HDAC) inhibitors is of great biological and medical interest. Among 11 zinc-dependent HDAC isoforms, it is particularly challenging to achieve isoform inhibition selectivity between HDAC1 and HDAC2 due to their very high structural similarities. In this work, by developing and applying a novel de novo reaction-mechanism-based inhibitor design strategy to exploit the reactivity difference, we have discovered the first HDAC2-selective inhibitor, β-hydroxymethyl chalcone. Our bioassay experiments show that this new compound has a unique time-dependent selective inhibition on HDAC2, leading to about 20-fold isoform-selectivity against HDAC1. Furthermore, our ab initio QM/MM molecular dynamics simulations, a state-of-the-art approach to study reactions in biological systems, have elucidated how the β-hydroxymethyl chalcone can achieve the distinct time-dependent inhibition toward HDAC2.

Terpenes (isoprenoids) represent the most functionally and structurally diverse group of natural products. Terpenes are assembled from two building blocks, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP or DPP), by prenyltransferases (PTSs). Geranyl pyrophosphate synthase (GPPS) is the enzyme that assembles DPP and IPP in the first step of chain elongation during isoprenoid biosynthesis. The mechanism by which GPPS assembles the terpene precursor remains unknown; elucidating this mechanism will help in development of new technology to generate novel natural product-like scaffolds. With classic and QM/MM MD simulations, an "open-closed" conformation change of the catalytic pocket was observed in the GPPS active site at its large subunit (LSU), and a critical salt bridge between Asp91(in loop 1) and Lys239(in loop 2) was identified. The salt bridge is responsible for opening or closing the catalytic pocket. Meanwhile, the small subunit (SSU) regulates the size and shape of the hydrophobic pocket to flexibly host substrates with different shapes and sizes (DPP/GPP/FPP, C5/C10/C15). Further QM/MM MD simulations were carried out to explore the binding modes for the different substrates catalyzed by GPPS. Our simulations suggest that the key residues (Asp91, Lys239, and Gln156) are good candidates for site-directed mutagenesis and may help in protein engineering.

Human oxidosqualene cyclase (OSC) is one key enzyme in the biosynthesis of cholesterol. It can catalyze the linear-chain 2,3-oxidosqualene to form lanosterol, the tetracyclic (6-6-6-5 members for A-B-C-D rings) cholesterol precursor. It also has been treated as a novel antihyperlipidemia target. In addition, the structural diversity of cyclic terpenes in plants originates from the cyclization of 2,3-oxidosqualene. The enzyme catalytic mechanism is considered to be one of the most complicated ones in nature, and there are a lot of controversies about the mechanism in the past half a century. Herein, state-of-the-art ab initio QM/MM MD simulations are employed to investigate the detailed cyclization mechanism of C-ring and D-ring formation. Our study reveals that the C and D rings are formed near-synchronously from a stable "6-6-5" ring intermediate. Interestingly, the transition state of this concerted reaction presents a "6-6-6" structure motif, while this unstable "6-6-6" structure in our simulations is thought to be a stable intermediate state in most previous hypothetical mechanisms. Furthermore, as the tailed side chain of 2,3-oxidosqualene shows a β conformation while it is α conformation in lanosterol, finally, it is observed that the rotatable "tail" chain prefers to transfer β conformation to α conformation at the "6-6-5" intermediate state.