A compression strategy for particle mesh Ewald theory

SARS-CoV-2 Evolution: Immune Dynamics, Omicron Specificity, and Predictive Modeling in Vaccinated Populations

Host immunity is central to the virus's spread dynamics, which is significantly influenced by vaccination and prior infection experiences. In this work, we analyzed the co-evolution of SARS-CoV-2 mutation, angiotensin-converting enzyme 2 (ACE2) receptor binding, and neutralizing antibody (NAb) responses across various variants in 822 human and mice vaccinated with different non-Omicron and Omicron vaccines is analyzed. The link between vaccine efficacy and vaccine type, dosing, and post-vaccination duration is revealed. The classification of immune protection against non-Omicron and Omicron variants is co-evolved with genetic mutations and vaccination. Additionally, a model, the Prevalence Score (P-Score) is introduced, which surpasses previous algorithm-based models in predicting the potential prevalence of new variants in vaccinated populations. The hybrid vaccination combining the wild-type (WT) inactivated vaccine with the Omicron BA.4/5 mRNA vaccine may provide broad protection against both non-Omicron variants and Omicron variants, albeit with EG.5.1 still posing a risk. In conclusion, these findings enhance understanding of population immunity variations and provide valuable insights for future vaccine development and public health strategies.

Molecular Dynamics Simulation Investigation of Freezing Point Depression in NaClO4 Electrolyte Solution by CaCl2

The development of inorganic antifreeze electrolytes is of paramount importance for the application of sodium-ion batteries under low-temperature conditions. However, there is little reported about their molecular mechanism for lowering the freezing point of electrolytes. Therefore, this study explores the mechanism by which CaCl2 lowers the freezing point of the NaClO4 electrolyte. Hexagonal ice (ice Ih) was used as the ice seed, and CaCl2 was selected as the antifreeze agent. The coexistence system of ice and solution was constructed to simulate the freezing process. It was found that there is ion rejection at the ice layer, with ions predominantly distributed in the solution. Over time, ions form an ion adsorption layer at the ice-solution interface. The radial distribution function (RDF) and spatial distribution function (SDF) of Na+, ClO4-, Ca2+, and Cl- revealed that ions form the first solvation shells with water molecules. The interaction energy between ions and water molecules is greater than that between ice nuclei and water. Therefore, ions are better able to maintain the stability of their solvation shells and inhibit the growth of ice Ih through a mechanism of competition for water molecules. Furthermore, the dissolution free energy of Na+ and Ca2+ in the aqueous phase was studied. The results indicated that Ca2+ has a stronger affinity for water molecules than Na+, making it more competitive in competing for water with ice Ih. Therefore, CaCl2 in NaClO4 solution can reduce the freezing point. This work provides a molecular-level understanding of how CaCl2 reduces the freezing point of NaClO4 solution, which is beneficial for designing strategies for low-temperature electrolytes.

Discovery of an 8-oxoguanine regulator PCBP1 inhibitor by virtual screening and its synergistic effects with ROS-modulating agents in pancreatic cancer

Introduction: Drugs that target reactive oxygen species (ROS) metabolism have progressed the treatment of pancreatic cancer treatment, yet their efficacy remains poor because of the adaptation of cancer cells to high concentration of ROS. Cells cope with ROS by recognizing 8-oxoguanine residues and processing severely oxidized RNA, which make it feasible to improve the efficacy of ROS-modulating drugs in pancreatic cancer by targeting 8-oxoguanine regulators. Methods: Poly(rC)-binding protein 1 (PCBP1) was identified as a potential oncogene in pancreatic cancer through datasets of The Cancer Genome Atlas (TCGA) project and Gene Expression Omnibus (GEO). High-throughput virtual screening was used to screen out potential inhibitors for PCBP1. Computational molecular dynamics simulations was used to verify the stable interaction between the two compounds and PCBP1 and their structure-activity relationships. In vitro experiments were performed for functional validation of silychristin. Results: In this study, we identified PCBP1 as a potential oncogene in pancreatic cancer. By applying high-throughput virtual screening, we identified Compound 102 and Compound 934 (silychristin) as potential PCBP1 inhibitors. Computational molecular dynamics simulations and virtual alanine mutagenesis verified the structure-activity correlation between PCBP1 and the two identified compounds. These two compounds interfere with the PCBP1-RNA interaction and impair the ability of PCBP1 to process RNA, leading to intracellular R loop accumulation. Compound 934 synergized with ROS agent hydrogen peroxide to strongly improve induced cell death in pancreatic cancer cells. Discussion: Our results provide valuable insights into the development of drugs that target PCBP1 and identified promising synergistic agents for ROS-modulating drugs in pancreatic cancer.

Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability

Designing effective monoclonal antibody (mAb) therapeutics faces a multi-parameter optimization challenge known as "developability", which reflects an antibody's ability to progress through development stages based on its physicochemical properties. While natural antibodies may provide valuable guidance for mAb selection, we lack a comprehensive understanding of natural developability parameter (DP) plasticity (redundancy, predictability, sensitivity) and how the DP landscapes of human-engineered and natural antibodies relate to one another. These gaps hinder fundamental developability profile cartography. To chart natural and engineered DP landscapes, we computed 40 sequence- and 46 structure-based DPs of over two million native and human-engineered single-chain antibody sequences. We find lower redundancy among structure-based compared to sequence-based DPs. Sequence DP sensitivity to single amino acid substitutions varied by antibody region and DP, and structure DP values varied across the conformational ensemble of antibody structures. We show that sequence DPs are more predictable than structure-based ones across different machine-learning tasks and embeddings, indicating a constrained sequence-based design space. Human-engineered antibodies localize within the developability and sequence landscapes of natural antibodies, suggesting that human-engineered antibodies explore mere subspaces of the natural one. Our work quantifies the plasticity of antibody developability, providing a fundamental resource for multi-parameter therapeutic mAb design.

Entropy of Liquid Water as Predicted by the Two-Phase Thermodynamic Model and Data-Driven Many-Body Potentials

We investigate the entropy of liquid water at ambient conditions using the two-phase thermodynamic (2PT) model, applied to both common pairwise-additive water models and the MB-pol and MB-pol(2023) data-driven many-body potentials. Our simulations demonstrate that the 2PT model yields entropy values in semiquantitative agreement with experimental data when using MB-pol and MB-pol(2023). Additionally, our analyses indicate that the entropy values predicted by pairwise-additive water models may benefit from error compensation between the inherent approximations of the 2PT model and the known limitations of these water models in describing many-body interactions. Despite its approximate nature, the simplicity of the 2PT model makes it a valuable tool for estimating relative entropy changes of liquid water across various environments, especially when combined with water models that provide a consistently robust representation of the structural, thermodynamic, and dynamical properties of liquid water.

Leveraging shape screening and molecular dynamics simulations to optimize PARP1-Specific chemo/radio-potentiators for antitumor drug design

PARP1 plays a pivotal role in DNA repair within the base excision pathway, making it a promising therapeutic target for cancers involving BRCA mutations. Current study is focused on the discovery of PARP inhibitors with enhanced selectivity for PARP1. Concurrent inhibition of PARP1 with PARP2 and PARP3 affects cellular functions, potentially causing DNA damage accumulation and disrupting immune responses. In step 1, a virtual library of 593 million compounds has been screened using a shape-based screening approach to narrow down the promising scaffolds. In step 2, hierarchical docking approach embedded in Schrödinger suite was employed to select compounds with good dock score, drug-likeness and MMGBSA score. Analysis supplemented with decomposition energy, molecular dynamics (MD) simulations and hydrogen bond frequency analysis, pinpointed that active site residues; H862, G863, R878, M890, Y896 and F897 are crucial for specific binding of ZINC001258189808 and ZINC000092332196 with PARP1 as compared to PARP2 and PARP3. The binding of ZINC000656130962, ZINC000762230673, ZINC001332491123, and ZINC000579446675 also revealed interaction involving two additional active site residues of PARP1, namely N767 and E988. Weaker or no interaction was observed for these residues with PARP2 and PARP3. This approach advances our understanding of PARP-1 specific inhibitors and their mechanisms of action, facilitating the development of targeted therapeutics.

Dental biomaterials redefined: molecular docking and dynamics-driven dental resin composite optimization

BACKGROUND

Dental resin-based composites are widely recognized for their aesthetic appeal and adhesive properties, which make them integral to modern restorative dentistry. Despite their advantages, adhesion and biomechanical performance challenges persist, necessitating innovative strategies for improvement. This study addressed the challenges associated with adhesion and biomechanical properties in dental resin-based composites by employing molecular docking and dynamics simulation.

METHODS

Molecular docking assesses the binding energies and provides valuable insights into the interactions between monomers, fillers, and coupling agents. This investigation prioritizes SiO2 and TRIS, considering their consistent influence. Molecular dynamics simulations, executed with the Forcite module and COMPASS II force field, extend the analysis to the mechanical properties of dental composite complexes. The simulations encompassed energy minimization, controlled NVT and NPT ensemble simulations, and equilibration stages. Notably, the molecular dynamics simulations spanned a duration of 50 ns.

RESULTS

SiO2 and TRIS consistently emerged as influential components, showcasing their versatility in promoting solid interactions. A correlation matrix underscores the significant roles of van der Waals and desolvation energies in determining the overall binding energy. Molecular dynamics simulations provide in-depth insights into the mechanical properties of dental composite complexes. HEMA-SiO2-TRIS excelled in stiffness, BisGMA-SiO2-TRIS prevailed in terms of flexural strength, and EBPADMA-SiO2-TRIS offered a balanced combination of mechanical properties.

CONCLUSION

These findings provide valuable insights into optimizing dental composites tailored to diverse clinical requirements. While EBPADMA-SiO2-TRIS demonstrates distinct strengths, this study emphasizes the need for further research. Future investigations should validate the computational findings experimentally and assess the material's response to dynamic environmental factors.

Ensemble-Based Virtual Screening Led to the Discovery of Novel Lead Molecules as Potential NMBAs

Neuromuscular blocking agents (NMBAs) are routinely used during anesthesia to relax skeletal muscle. Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels; NMBAs can induce muscle paralysis by preventing the neurotransmitter acetylcholine (ACh) from binding to nAChRs situated on the postsynaptic membranes. Despite widespread efforts, it is still a great challenge to find new NMBAs since the introduction of cisatracurium in 1995. In this work, an effective ensemble-based virtual screening method, including molecular property filters, 3D pharmacophore model, and molecular docking, was applied to discover potential NMBAs from the ZINC15 database. The results showed that screened hit compounds had better docking scores than the reference compound d-tubocurarine. In order to further investigate the binding modes between the hit compounds and nAChRs at simulated physiological conditions, the molecular dynamics simulation was performed. Deep analysis of the simulation results revealed that ZINC257459695 can stably bind to nAChRs' active sites and interact with the key residue Asp165. The binding free energies were also calculated for the obtained hits using the MM/GBSA method. In silico ADMET calculations were performed to assess the pharmacokinetic properties of hit compounds in the human body. Overall, the identified ZINC257459695 may be a promising lead compound for developing new NMBAs as an adjunct to general anesthesia, necessitating further investigations.

Evaluation of Adenanthera pavonina-derived compounds against diabetes mellitus: insight into the phytochemical analysis and in silico assays

Adenanthera pavonina is a medicinal plant with numerous potential secondary metabolites showing a significant level of antidiabetic activity. The objective of the current study was to identify potential phytochemicals from the methanolic leaf extract of Adenanthera pavonina as therapeutic agents against diabetes mellitus using GC-MS and in silico methods. The GC-MS analysis of the leaf extract revealed a total of 17 phytochemicals. Molecular docking was performed using these phytochemicals, targeting the mutated insulin receptor tyrosine kinase (5hhw), which inhibits glucose uptake by cells. Diazoprogesterone (-9.2 kcal/mol), 2,4,4,7a-Tetramethyl-1-(3-oxobutyl)octahydro-1H-indene-2-carboxylic acid (-6.9 kcal/mol), and 2-Naphthalenemethanol, decahydro-.alpha.,.alpha.,4a-trimethyl-8-methylene-, [2R-(2.alpha.,4a.alpha.,8a.beta.)] (-6.6 kcal/mol) exhibited better binding with the target protein. The ADMET analysis was performed for the top three compounds with the best docking scores, which showed positive results with no observed toxicity in the AMES test. Furthermore, the molecular dynamics study confirmed the favorable binding of Diazoprogesterone, 2,4,4,7a-Tetramethyl-1-(3-oxobutyl)octahydro-1H-indene-2-carboxylic acid and 2-Naphthalenemethanol, decahydro-.alpha.,.alpha.,4a-trimethyl-8-methylene-, [2R-(2.alpha.,4a.alpha.,8a.beta.)] with the receptor throughout the 100 ns simulation period.

Comparative analysis of structural dynamics and allosteric mechanisms of RecA/Rad51 family proteins: Integrated atomistic MD simulation and network-based analysis

Homologous recombination plays a key role in double-strand break repair, stalled replication fork repair, and meiosis. The RecA/Rad51 family recombinases catalyze the DNA strand invasion reaction that occurs during homologous recombination. However, the high sequence differences between homologous groups have hindered the thoroughly studies of this ancient protein family. The dynamic mechanisms of the family, particularly at the residual level, remain poorly understood. In this work, five representative RecA/Rad51 recombinase family members from all major kingdoms of living organisms: prokaryotes, eukaryotes, archaea, and viruses, were selected to explore the molecular mechanisms behind their conserved biological significance. A variety of techniques, including all-atom molecular dynamics simulation, perturbation response scanning, and protein structure network analysis, were used to examine the flexibility and correlation of protein domains, distribution of sensors and effectors and conserved hub residues. Furthermore, the potential communication routes between the ATP-binding region and the DNA-binding region of each recombinase were identified. Our results demonstrate the conserved molecular dynamics of these recombinases in the early stage of homologous recombination, including cooperative motions between regions, conserved sensing and effecting functional residue distribution, and conserved hub residues. Meanwhile, the unique ATP-DNA communication routes of each recombinase was also revealed. These results provide new insights into the mechanism of RecA/Rad51 family proteins, and provide new theoretical guidance for the development of allosteric inhibitors and the application of RecA/Rad51 family proteins.

Molecular Insights into the Influence of Ions on the Water Structure. I. Alkali Metal Ions in Solution

In this study, we explore the impact of alkali metal ions (Li+, Na+, K+, Rb+, and Cs+) on the hydration structure of water using molecular dynamics simulations carried out with MB-nrg potential energy functions (PEFs). Our analyses include radial distribution functions, coordination numbers, dipole moments, and infrared spectra of water molecules, calculated as a function of solvation shells. The results collectively indicate a highly local influence of all of the alkali metal ions on the hydrogen-bond network established by the surrounding water molecules, with the smallest and most densely charged Li+ ion exerting the most pronounced effect. Remarkably, the MB-nrg PEFs demonstrate excellent agreement with available experimental data for the position and size of the first solvation shells, underscoring their potential as predictive models for realistic simulations of ionic aqueous solutions across various thermodynamic conditions and environments.

Unsolved problem of long-range interactions: dipolar spin-ice study

Long-range interactions derive various strange phenomena. As illustrated by cutoff simulations of water, increasing cutoff length does not improve the simulation result necessarily; on the contrary, it makes the result worse. In the extreme situation, the structure of water transforms into a layer structure. In this study, to explore the underlying mechanism of this phenomenon, we performed Monte Carlo simulations on dipolar spins arranged on a pyrochlore spin-ice lattice. Like the water case, the present dipolar spin system also showed cutoff-induced dipole ordering and layer formation. The width of the layers depended on the cutoff length; and longer cutoff length led to a broader layer. These features are certainly consistent with the previous water case. This indicates that layer formation is the general behavior of dipolar systems whose interactions are truncated within a finite distance. The result is important for future exploration of the relationship between long-range interactions and resulting structures. In addition, it emphasizes the necessity of rigorous treatment of long-range interactions because increasing the cutoff length prevents convergence and provides an entirely different result from the rigorous Ewald calculation.

van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD

Molecular dynamics simulations can be used in combination with experimental techniques to uncover the intricacies of biomolecular structure, dynamics, and the resulting interactions. However, many noncanonical nucleic acid structures have proven to be challenging to replicate in accurate agreement with experimental data, often attributed to known force field deficiencies. A common force field criticism is the handling of van der Waals (vdW) parameters, which have not been updated since the regular use of Ewald's methods became routine. This work dives into the effects of minute vdW radii shifts on RNA tetranucleotide, B-DNA, and Z-DNA model systems described by commonly used Amber force fields. Using multidimensional replica exchange molecular dynamics (M-REMD), the GACC RNA tetranucleotide demonstrated changes in the structural distribution between the NMR minor and anomalous structure populations based on the O2' vdW radii scanning. However, no significant change in the NMR Major conformation population was observed. There were minimal changes in the B-DNA structure but there were more substantial improvements in Z-DNA structural descriptions, specifically with the Tumuc1 force field. This occurred with both LJbb vdW radii adjustments and incorporation of the CUFIX nonbonded parameter modifications. Though the limited vdW modifications tested did not provide a universal fix to the challenge of simulating the various known nucleic acid structures, they do provide direction and a greater understanding for future force field development efforts.

Discovery of 4-aminophenylacetamide derivatives as intestine-specific farnesoid X receptor antagonists for the potential treatment of nonalcoholic steatohepatitis

Farnesoid X receptor (FXR) plays a key role in bile acid homeostasis, inflammation, fibrosis, lipid and glucose metabolism and is emerging as a promising therapeutic target for nonalcoholic steatohepatitis (NASH). Emerging evidence suggested that intestine-specific FXR antagonists exhibited remarkable metabolic improvements and slowed NASH progression. In this study, we discovered several potent FXR antagonists using a multistage ligand- and structure-based virtual screening approach. Notably, compound V023-9340, which possesses a 4-aminophenylacetamide scaffold, emerged as the most potent FXR antagonist with an IC50 value of 4.27 μM. In vivo, V023-9340 demonstrated selective accumulation in the intestine, substantially ameliorating high-fat diet (HFD)-induced NASH in mice by mitigating hepatic steatosis and inflammation. Mechanistic studies revealed that V023-9340 strongly inhibited intestinal FXR while concurrently feedback-activated hepatic FXR. Further structure-activity relationship optimization employing V023-9340 has resulted in the synthesis of a more efficacious compound V02-8 with an IC50 value of 0.89 μM, which exhibited a 4.8-fold increase in FXR antagonistic activity compared to V023-9340. In summary, 4-aminophenylacetamide derivative V023-9340 represented a novel intestine-specific FXR antagonist and showed improved effects against HFD-induced NASH in mice, which may serve as a promising lead in discovering potential therapeutic drugs for NASH treatment.

Elucidating the Competitive Adsorption of H2O and CO2 in CALF-20: New Insights for Enhanced Carbon Capture Metal-Organic Frameworks

In light of the pressing need for efficient carbon capture solutions, our study investigates the simultaneous adsorption of water (H2O) and carbon dioxide (CO2) as a function of relative humidity in CALF-20, a highly scalable and stable metal-organic framework (MOF). Advanced computer simulations reveal that due to their similar interactions with the framework, H2O and CO2 molecules compete for the same binding sites, occupying similar void regions within the CALF-20 pores. This competition results in distinct thermodynamic and dynamical behaviors of H2O and CO2 molecules, depending on whether one or both guest species are present. Notably, the presence of CO2 molecules forces the H2O molecules to form more connected hydrogen-bond networks within smaller regions, slowing water reorientation dynamics and decreasing water entropy. Conversely, the presence of water speeds up the reorientation of CO2 molecules, decreases the CO2 entropy, and increases the propensity for CO2 to be adsorbed within the framework due to stronger water-mediated interactions. Due to the competition for the same void spaces, both H2O and CO2 molecules exhibit slower diffusion when molecules of the other guest species are present. These findings offer valuable strategies and insights into enhancing the differential affinity of H2O and CO2 for MOFs specifically designed for carbon capture applications.

Inhibitory selectivity to the AKR1B10 and aldose reductase (AR): insight from molecular dynamics simulations and free energy calculations

AKR1B10 is over-expressed in many cancer types and is related to chemotherapy resistance, which makes AKR1B10 a potential anti-cancer target. The high similarity of the protein structure between AKR1B10 and AR makes it difficult to develop highly selective inhibitors against AKR1B10. Understanding the interaction between AKR1B10 and inhibitors is very important for designing selective inhibitors of AKR1B10. In this study, Fidarestat, Zopolrestat, MK184 and MK204 bound to AKR1B10 and AR were used to investigate the selectivity mechanism. The results of MM/PBSA calculations show that van der Waals and electrostatic interaction provide the main contributions of the binding free energy. The hydrogen bonding between residues Y49 and H111 and inhibitors plays a pivotal role in contributing to the high inhibitory activity of AKR1B10 inhibitors. The π-π stacking interaction between residue W112 and inhibitor also plays a key role in the stability of inhibitors and AKR1B10, but W112 should keep its natural conformation to stabilize the inhibitor-AKR1B10 complex. Highly selective AKR1B10 inhibitors should have a bulky moiety like a phenyl group, which can change its binding with ABP in binding with AR and cannot change its binding with AKR1B10. The free energy decomposition shows that residues W21, V48, Y49, K78, W80, H111, R298 and V302 are beneficial to the stability of the inhibitor-AKR1B10. Our work will provide an important in silico basis for researchers to develop highly selective inhibitors of AKR1B10.

MBX: A many-body energy and force calculator for data-driven many-body simulations

Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be employed either as a stand-alone package or as an energy/force engine that can be integrated with generic software for molecular dynamics and Monte Carlo simulations. MBX is parallelized internally using Open Multi-Processing and can utilize Message Passing Interface when available in interfaced molecular simulation software. MBX enables classical and quantum molecular simulations with MB-nrg PEFs, as well as hybrid simulations that combine conventional force fields and MB-nrg PEFs, for diverse systems ranging from small gas-phase clusters to aqueous solutions and molecular fluids to biomolecular systems and metal-organic frameworks.

ANKH: A Generalized O(N) Interpolated Ewald Strategy for Molecular Dynamics Simulations

To evaluate electrostatics interactions, molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM) approaches. However, the FFTs low scalability remains a strong bottleneck for large-scale PME simulations on supercomputers. On the opposite, FFT-free FMM techniques are able to deal efficiently with such systems but they fail to reach PME performances for small- to medium-size systems, limiting their real-life applicability. We propose ANKH, a strategy grounded on interpolated Ewald summations and designed to remain efficient/scalable for any size of systems. The method is generalized for distributed point multipoles, and so for induced dipoles, which makes it suitable for high performance simulations using new generation polarizable force fields toward exascale computing.

Computational Insights into the Dynamic Structural Features and Binding Characteristics of Recombinase UvsX Compared with RecA

RecA family recombinases are the core enzymes in the process of homologous recombination, and their normal operation ensures the stability of the genome and the healthy development of organisms. The UvsX protein from bacteriophage T4 is a member of the RecA family recombinases and plays a central role in T4 phage DNA repair and replication, which provides an important model for the biochemistry and genetics of DNA metabolism. UvsX shares a high degree of structural similarity and function with RecA, which is the most deeply studied member of the RecA family. However, the detailed molecular mechanism of UvsX has not been resolved. In this study, a comprehensive all-atom molecular dynamics simulation of the UvsX protein dimer complex was carried out in order to investigate the conformational and binding properties of UvsX in combination with ATP and DNA, and the simulation of RecA was synchronized with the property comparison learning for UvsX. This study confirmed the highly conserved molecular structure characteristics and catalytic centers of RecA and UvsX, and also discovered differences in regional conformation, volatility and the ability to bind DNA between the two proteins at different temperatures, which would be helpful for the subsequent understanding and application of related recombinases.

Charge transfer as a mechanism for chlorophyll fluorescence concentration quenching

Highly concentrated solutions of chlorophyll display rapid fluorescence quenching. The same devastating energy loss is not seen in photosynthetic light-harvesting antenna complexes, despite the need for chromophores to be in close proximity to facilitate energy transfer. A promising, though unconfirmed mechanism for the observed quenching is energy transfer from an excited chlorophyll monomer to a closely associated chlorophyll pair that subsequently undergoes rapid nonradiative decay to the ground state via a short-lived intermediate charge-transfer state. In this work, we make use of newly emerging fast methods in quantum chemistry to assess the feasibility of this proposed mechanism. We calculate rate constants for the initial charge separation, based on Marcus free-energy surfaces extracted from molecular dynamics simulations of solvated chlorophyll pairs, demonstrating that this pathway will compete with fluorescence (i.e., drive quenching) at experimentally measured quenching concentrations. We show that the rate of charge separation is highly sensitive to interchlorophyll distance and the relative orientations of chromophores within a quenching pair. We discuss possible solvent effects on the rate of charge separation (and consequently the degree of quenching), using the light-harvesting complex II (LH2) protein from rps. acidophila as a specific example of how this process might be controlled in a protein environment. Crucially, we reveal that the LH2 antenna protein prevents quenching, even at the high chlorophyll concentrations required for efficient energy transfer, by restricting the range of orientations that neighboring chlorophyll pairs can adopt.

Molecular docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors

Pin1 (protein interacting with never-in-mitosis akinase-1) is a member of the PPIase (peptidylprolyl cis-trans isomerase) family. It can interact with a variety of carcinogenic or tumor suppressive phosphorylated proteins. The interaction results in the conformational changes of target proteins, and ultimately regulates the activity of these proteins. These activity changes play a key role in tumorigenesis. Pin1 is an attractive target for cancer therapy due to its over-expression and/or activation in various types of cancer and the disorder of Proline directed phosphorylation. In this study, molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR) and molecular dynamics (MD) simulations were performed to investigate the structure-activity relationship and binding mechanism of 45 thiazole-class Pin1 inhibitors. Molecular docking studies predict the binding mode and the interactions between the ligand and the receptor protein. The results of the 3 D-QSAR model show that electrostatic field, hydrophobic field and hydrogen bond play important roles in the binding process of inhibitors to protein. Molecular dynamics simulation results reveal that the complex of the ligand and the receptor protein are stable at 300 K. The binding free energy calculation and energy decomposition results show that His59, Cys113, Ser114, Ser115, Leu122, Met130, Gln131, Phe134, Ser154 and His157 may be the key to the inhibitor binding to Pin1 protein. This study provides an important theoretical basis for further development of the new Pin1 inhibitor design. These results can provide more useful information for our further drug design. Communicated by Ramaswamy H. Sarma.

A molecular simulation study of hepatitis B virus core protein and the nuclear protein allosteric modulators of phthalazinone derivatives

Hepatitis B virus, causing hepatitis, cirrhosis, liver failure, and liver cancer, poses a serious threat to human health, and the currently approved drugs still cannot eliminate the virus completely. HBV core protein allosteric modulators (CpAMs) with a phthalazinone structure which targets the HBV core (HBc) protein have been seen as a new kind of drug because of their excellent antiviral effects. This study explores the structure-activity relationship and binding mechanism of phthalazinone molecules through three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, molecular dynamics, and binding free energy calculation and decomposition studies. In addition, CoMFA and CoMSIA models revealed that the steric field, the hydrophobic field, and the hydrogen bond acceptor field may play important roles in the binding process. The molecular docking and dynamics disclosed the most likely binding pose of phthalazinone derivatives with the HBc protein. The binding free energy calculation and decomposition analysis indicated that the van der Waals force was the driving force and that ValE124, ThrD109, ThrE128, LeuD140, IleD105, PheD110, ThrD33, and TrpD102 were the key residues. This study provides an important theoretical basis for the design and optimization of phthalazinone compounds.

Formation of lysozyme-caseinate heteroprotein complexes for encapsulation of lysozyme by spray-drying: Effect of mass ratio and temperature

The formation of heteroprotein complexes obtained by the interactions between sodium caseinate (CAS) and lysozyme (LYS) at pH 7 was investigated by using turbidimetric analysis, particle size distribution, and zeta potential at different CAS/LYS ratios. Moreover, isothermal titration calorimetry (ITC) was used to determine the type and magnitude of the energies involved in the CAS/LYS complexation process and evaluated the thermodynamic behavior of their complexation. Results revealed that the structure of CAS/LYS complexes drastically changed when CAS/LYS ratio increased to 1.0 and the structuring stages were characterized by exothermic signals and were controlled by favorable enthalpy changes due to electrostatic interactions between both proteins. In addition, the interaction between two proteins was temperature-dependent and mainly entropy-driven, which was verified by molecular dynamics (MD) simulations, and the hydrophobic interactions and hydrogen bonding were shown to play an important role in CAS/LYS interactions. Furthermore, CAS/LYS complexes showed minimum LYS enzymatic activity at CAS/LYS ratio 1.0. Though spray-drying of CAS/LYS complexes with ratio 1.0, the LYS activity in reconstituted solution was recovered >80 % of initial activity after calcium chloride addition. The present study provides useful information about CAS/LYS complexation and binding processes, which could facilitate their application in antimicrobial edible food packaging.

Antibacterial and Anti-Inflammatory Effects of Apolipoprotein E

Apolipoprotein E (APOE) is a lipid-transport protein that functions as a key mediator of lipid transport and cholesterol metabolism. Recent studies have shown that peptides derived from human APOE display anti-inflammatory and antimicrobial effects. Here, we applied in vitro assays and fluorescent microscopy to investigate the anti-bacterial effects of full-length APOE. The interaction of APOE with endotoxins from Escherichia coli was explored using surface plasmon resonance, binding assays, transmission electron microscopy and all-atom molecular dynamics (MD) simulations. We also studied the immunomodulatory activity of APOE using in vitro cell assays and an in vivo mouse model in combination with advanced imaging techniques. We observed that APOE exhibits anti-bacterial activity against several Gram-negative bacterial strains of Pseudomonas aeruginosa and Escherichia coli. In addition, we showed that APOE exhibits a significant binding affinity for lipopolysaccharide (LPS) and lipid A as well as heparin. MD simulations identified the low-density lipoprotein receptor (LDLR) binding region in helix 4 of APOE as a primary binding site for these molecules via electrostatic interactions. Together, our data suggest that APOE may have an important role in controlling inflammation during Gram-negative bacterial infection.

Identification of an AXL kinase inhibitor in triple-negative breast cancer by structure-based virtual screening and bioactivity test

Breast cancer is a malignant tumor that occurs in the glandular epithelium of the breast, and more than 15% of the patients are triple-negative breast cancer (TNBC). Therefore, finding new targets and targeted therapeutic drugs for TNBC is urgent. Overexpression of the AXL is associated with motility and invasiveness of the TNBC cells, which is a potential target for breast cancer therapy. A compound Y041-5921 (IC₅₀  = 6.069 μm for AXL kinase and IC₅₀  = 4.1 μm for MDA-MB-231 cell line) was identified through structure-based virtual screening and bioassay test for the first time. The compound Y041-5921 could significantly inhibit the proliferation and invasion of the TNBC cells and the toxicity of Y041-5921 to normal immortalized breast epithelial cells was far lower than that of commonly used clinical chemotherapy drugs. Besides, it also had well inhibitory effect on the proliferation of many other malignant tumor cell lines (the IC₅₀  value are 10.0 m, 7.1 m, 10.3 m, 11.4 m and 5.8 m for U251 cell, COLO cell, PC-9 cell, CAKI-1 cell and MG63 cell, respectively). The interaction mechanism between Y041-5921 and AXL was studied by molecular dynamics (MD) simulations and binding free energy calculation, and the key residues whose energy contribution mainly comes from non-polar solvation interaction (such as Ala565, Lys567, Met598, Leu620, Pro621, Met623, Lys624, Arg676, Asn677 and Met679) were identified. The small molecule inhibitors Y041-5921 targeting AXL reported in this work will lay a foundation and provide a theoretical basis for the development of the TNBC.