Comparison of Tetrahedral Order, Liquid State Anomalies, and Hydration Behavior of mTIP3P and TIP4P Water Models

Identification of novel xanthine oxidase inhibitory peptides from Takifugu obscurus: Peptidomic analysis, molecular docking, and dynamics simulation

Hyperuricemia, caused by abnormal purine metabolism, is commonly treated with xanthine oxidase (XOD) inhibitors, uricosuric, and dietary adjustments. Recently, marine-derived bioactive peptides have gained attention as potential functional food ingredients due to their therapeutic potential. Takifugu obscurus, an economically significant offshore fish rich in crude proteins was explored in this study as a source of XOD inhibitory peptides. Enzyme hydrolysis combined with computer simulation identified TOH-A > 1 kDa and TOH-P > 1 kDa hydrolysates with high XOD inhibition rates, which were further selected for peptidomics characterization. After screening, seven peptides were synthesized, four of which (W11, DD7, WY7, and GA9) had inhibitory activity, with W11 showing the lowest IC50. The combination of molecular docking positions with molecular dynamics simulations explains that W11, DD7, and WY7 have the potential to be used to alleviate hyperuricemia. This study provides new insights into the structural mechanism and screening strategy of novel bioactive peptides in the future.

Hydrolyzing collagen by extracellular protease Hap of Aeromonas salmonicida: Turning chicken by-products into bioactive resources

Collagen-rich meat processing by-products have potential utilization value. Extracellular protease Hap from meat-borne Aeromonas salmonicida has been identified as an ideal protease for hydrolyzing collagen. Here, to explore the possible application of Hap for giving chicken by-products a high added value, the hydrolysis ability and mechanism were investigated. With a Vmax of 31.9 μg/mL/min and a Km of 1.18 mg/mL, Hap demonstrated obvious substrate specificity to pepsin-solubilized collagen (PSC) derived from chicken by-products, and significantly affected the tertiary structure and microstructure of PSC. Hap was found to preferentially cleave the peptide bond between Gly-X by peptide release kinetics, attacking from two ends to the middle region for α1 chain. Sixteen peptides are anticipated to be non-toxic with twenty potential biological activities at the end of hydrolysis. These observations will enrich the collagen hydrolysis mechanism of protease secreted by meat-borne bacteria and provide new insights into the utilization of meat by-products.

Luteolin ameliorates chronic stress-induced depressive-like behaviors in mice by promoting the Arginase-1+ microglial phenotype via a PPARγ-dependent mechanism

Accumulating evidence shows that neuroinflammation substantially contributes to the pathology of depression, a severe psychiatric disease with an increasing prevalence worldwide. Although modulating microglial phenotypes is recognized as a promising therapeutic strategy, effective treatments are still lacking. Previous studies have shown that luteolin (LUT) has anti-inflammatory effects and confers benefits on chronic stress-induced depression. In this study, we investigated the molecular mechanisms by which LUT regulates the functional phenotypes of microglia in mice with depressive-like behaviors. Mice were exposed to chronic restraint stress (CRS) for 7 weeks, and were administered LUT (10, 30, 40 mg· kg-1 ·day-1, i.g.) in the last 4 weeks. We showed that LUT administration significantly ameliorated depressive-like behaviors and decreased hippocampal inflammation. LUT administration induced pro-inflammatory microglia to undergo anti-inflammatory arginase (Arg)-1+ phenotypic polarization, which was associated with its antidepressant effects. Furthermore, we showed that LUT concentration-dependently increased the expression of PPARγ in LPS + ATP-treated microglia and the hippocampus of CRS-exposed mice, promoting the subsequent inhibition of the NLRP3 inflammasome. Molecular dynamics (MD) simulation and microscale thermophoresis (MST) analysis confirmed a direct interaction between LUT and peroxisome proliferator-activated receptor gamma (PPARγ). By using the PPARγ antagonist GW9662, we demonstrated that LUT-driven protection, both in vivo and in vitro, resulted from targeting PPARγ. First, LUT-induced Arg-1+ microglia were no longer detected when PPARγ was blocked. Next, LUT-mediated inhibition of the NLRP3 inflammasome and downregulation of pro-inflammatory cytokine production were reversed by the inhibition of PPARγ. Finally, the protective effects of LUT, which attenuated the microglial engulfment of synapses and prevented apparent synapse loss in the hippocampus of CRS-exposed mice, were eliminated by blocking PPARγ. In conclusion, this study showed that LUT ameliorates CRS-induced depressive-like behaviors by promoting the Arg-1+ microglial phenotype through a PPARγ-dependent mechanism, thereby alleviating microglial pro-inflammatory responses and reversing microglial phagocytosis-mediated synapse loss.

Discovery of Novel and Highly Potent Dual PD-L1/Histone Deacetylase 6 Inhibitors with Favorable Pharmacokinetics for Cancer Immunotherapy

A series of novel PD-L1/HDAC6 dual inhibitors were designed and synthesized, and compound HP29 was identified as the most potent candidate, which demonstrated excellent and selective HDAC6 inhibitory activity (IC50 = 78 nM, SI > 1282), and high anti-PD-1/PD-L1 activity (IC50 = 26.8 nM). Further studies showed that HP29 could bind with high affinity to PD-L1 and HDAC6 protein. Furthermore, HP29 possessed favorable in vivo pharmacokinetic properties, such as decent oral bioavailability (F = 15.3%). Moreover, HP29 exhibited significant in vivo antitumor efficacy in a melanoma tumor model with a greater tumor growth inhibition (TGI) (65.5%) than that of NP19 (43.2%), ACY-1215 (45.6%), and the combination group (53.9%). Mechanistically, the percentages of tumor-infiltrating lymphocytes (TILs) in the HP29-treated tumor tissues were significantly higher than the combination group or PD-L1 inhibitor monotherapy group, suggesting potential synergistic antitumor immune effects. Collectively, HP29 represents a novel PD-L1/HDAC6 dual inhibitor deserving further investigation as a potential cancer immunomodulating agent.

CADD-based discovery of novel oligomeric modulators of PKM2 with antitumor activity in aggressive human glioblastoma models

Pyruvate kinase isoform M2 (PKM2) is a multifunctional enzyme capable of transitioning between monomeric, dimeric, and tetrameric states, with its oligomeric equilibrium playing a pivotal role in tumour progression and survival. The unique exon ten at the dimer-dimer interface represents an attractive target for isoform-specific modulation, offering opportunities for disrupting this equilibrium and altering tumour cell dynamics. This study identifies a novel druggable pocket at the PKM2 dimer interface through conformational analysis. This pocket was exploited in a virtual screening of a large small-molecule library, identifying two promising candidates, C599 and C998. Both compounds exhibited dose-dependent antiproliferative effects in glioblastoma cell lines and induced apoptosis, as evidenced by caspase 3/7 activation. These effects were directly linked to their inhibition of PKM2 enzymatic activity, validating the proposed mechanism of action in their rational design. ADMET studies further highlighted their strong potential as lead PKM2 inhibitors for GBM treatment. Molecular dynamics (MD) simulations and post-MD analyses, including Dynamic Cross-Correlation Maps (DCCM), Probability Density Function (PDF), and Free Energy Landscape (FEL), confirmed the stability of the protein-ligand interactions and highlighted critical residues at the dimer-dimer interface. The Steered MD simulations demonstrated the high affinity of the compounds for PKM2, as evidenced by the requirement of high rupture forces to induce an unbinding event. These results highlight the potential of the compounds as oligomeric modulators of PKM2. These findings position C599 and C998 as promising lead compounds for antitumor applications. Future studies will focus on optimising these candidates and assessing their efficacy in vivo glioblastoma models, reassuring the thoroughness of our research and the potential for further advancements.

Computational Elucidation of a Monobody Targeting the Phosphatase Domain of SHP2

Src homology 2 (SH2) domain-containing phosphatase 2 (SHP2) is a key regulator in cellular signaling pathways because its dysregulation has been implicated in various pathological conditions, including cancers and developmental disorders. Despite its importance, the molecular basis of SHP2's regulatory mechanism remains poorly understood, hindering the development of effective targeted therapies. In this study, we utilized the high-specificity monobody Mb11 to investigate its interaction with the SHP2 phosphatase domain (PTP) using multiple replica molecular dynamics simulations. Our analyses elucidate the precise mechanisms through which Mb11 achieves selective recognition and stabilization of the SHP2-PTP domain, identifying key residues and interaction networks essential for its high binding specificity and regulatory dynamics. Furthermore, the study highlights the pivotal role of residue C459 in preserving the structural integrity and functional coherence of the complex, acting as a central node within the interaction network and underpinning its stability and efficiency. These findings have significantly advanced the understanding of the mechanisms underlying SHP2's involvement in disease-related signaling and pathology while simultaneously paving the way for the rational design of targeted inhibitors, offering significant implications for therapeutic strategies in SHP2-associated diseases and contributing to the broader scope of precision medicine.

Rational design of thiazolidine-4-one-gallic acid hybrid derivatives as selective partial PPARγ modulators: an in-silico approach for type 2 diabetes treatment

Type 2 diabetes mellitus is a bipolar metabolic disorder characterized by abnormalities in insulin production from β-cells and insulin resistance. Thiazolidinediones are potent anti-diabetic agents that act through the modulation of the peroxisome proliferator-activated receptor γ (PPARγ), a nuclear receptor. However, their full agonistic activity leads to severe side effects by stabilizing Helix12 through strong hydrogen bonding with the TYR473 residue. Partial and selective PPARγ modulators (GW0072, GQ16, VSP-51, MRL-20, MBX-213, INT131) have demonstrated superior results compared to full agonists without causing adverse effects, as reported in existing data. To address this uncertainty and advance therapeutic options, we identified and designed a novel class of compounds (A1-A23) based on a hybrid structure combining phenolic and Thiazolidine-4-one's moieties. Our rational drug design strategy incorporated structural-activity relationship principle, and validated the docking studies through calculated the root mean square deviation. Additionally, we conducted molecular docking, binding energy, molecular dynamics simulations, and post-molecular dynamics calculations to evaluate the dynamics behavior between the ligands and protein. The selected ligands demonstrated highly favorable docking scores and binding energies, comparable to the co-crystal (rosiglitazone) such as A12 (-13.9 kcal/mol and -86.2 kcal/mol), A1 (-11.1 kcal/mol and -79.5 kcal/mol), A13 (-11.3 kcal/mol and -91.4 kcal/mol), and the co-crystal itself (-9.8 kcal/mol and -76 kcal/mol), respectively. Finally, the MD revealed that, the selected ligands were equally contributed for stabilization of Helix12 and β-sheets. It was concluded, the designed ligands (A12, A1, and A13) exhibited weaker hydrogen-bond interactions with specific residue TYR473 which partially modulated the PPARγ protein.Communicated by Ramaswamy H. Sarma.

Discovery of Novel Coumarin Pleuromutilin Derivatives as Potent Anti-MRSA Agents

Treating methicillin-resistant Staphylococcus aureus (MRSA) infection remains one of the most difficult challenges in clinical practice, primarily due to the resistance of MRSA to multiple antibiotics. Therefore, there is an urgent need to develop novel antibiotics with high efficacy and low cross-resistance rates. In this study, a series of novel pleuromutilin derivatives with coumarin structures were synthesized and subsequently assessed for their biological activities. Most of these derivatives showed potent antimicrobial activity against drug-resistant Gram-positive bacterial strains. Compound 14b displayed particularly rapid bactericidal effects, slow resistance development, and low cytotoxicity. Moreover, it decreased bacterial loads in the lung, liver, kidney, spleen, and heart and exhibited better antibacterial efficacy (ED50 = 11.16 mg/kg) than tiamulin (ED50 = 28.93 mg/kg) in a mouse model of systemic MRSA infection. Both in vitro and in vivo analyses suggest that compound 14b is a promising agent for the treatment of MRSA infections.

Identification of novel PD-1/PD-L1 small molecule inhibitors: virtual screening, synthesis and in vitro characterisation

The PD-1/PD-L1 pathway is considered as one of the most promising immune checkpoints in tumour immunotherapy. However, researchers are faced with the inherent limitations of antibodies, driving them to pursue PD-L1 small molecule inhibitors. Virtual screening followed by experimental validation is a proven approach to discover active compounds. In this study, we employed multistage virtual screening methods to screen multiple compound databases to predict new PD-1/PD-L1 ligands. 35 compounds were proposed by combined analysis of fitness scores, interaction pattern and MM-GBSA binding affinities. Enzymatic assay confirmed that 10 out of 35 ligands were potential PD-L1 inhibitors, with inhibitory rate higher than 50% at the concentration of 30 µM. Among them, ZDS20 was identified as the most effective inhibitor with low micromolar activity (IC50 = 3.27 μM). Altogether, ZDS20 carrying novel scaffold was identified and could serve as a lead for the development of new classes of PD-L1 inhibitors.

Drug repurposing to tackle parainfluenza 3 based on multi-similarities and network proximity analysis

Given that there is currently no clinically approved drug or vaccine for parainfluenza 3 (PIV3), we applied a drug repurposing method based on disease similarity and chemical similarity to screen 2,585 clinically approved chemical drugs using PIV3 potential drugs BCX-2798 and zanamivir as our controls. Twelve candidate drugs were obtained after being screened with good disease similarity and chemical similarity (S > 0.50, T > 0.56). When docking them with the PIV3 target protein, hemagglutinin-neuraminidase (HN), only oseltamivir was docked with a better score than BCX-2798, which indicates that oseltamivir has an inhibitory effect on PIV3. After the distance (Z d c ) between the drug target of 14 drugs and the PIV3 disease target was measured by the network proximity method based on the PIV3 disease module, it was found that theZ d c values of amikacin, oseltamivir, ribavirin, and streptomycin were less than those of the control. Thus, oseltamivir is the best potential drug because it met all the above screening requirements. Additionally, to explore whether oseltamivir binds to HN stably, molecular dynamics simulation of the binding of oseltamivir to HN was carried out, and the results showed that the RMSD value of the complex tended to be stable within 100 ns, and the binding free energy of the complex was low (-10.60 kcal/mol). It was proved that oseltamivir screened by our drug repurposing method had the potential feasibility of treating PIV3.

Effects of Curcumin on Radiation/Chemotherapy-Induced Oral Mucositis: Combined Meta-Analysis, Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation

The study aims to investigate the effects of curcumin on radiation/chemotherapy-induced oral mucositis (R/CIOM) and preliminarily explore its mechanism. Randomized controlled trials were identified from the PubMed, Embase, Web of Science, Cochrane Library, Medline, and Google Scholar databases. RevMan 5.4 was used for statistical analysis to calculate the combined risk ratios (RRs). The mechanism was analyzed through network pharmacology, molecular docking, and a molecular dynamics simulation. The targets of curcumin were collected in HERB, PharmMapper, Targetnet, Swiss Target Prediction, and SuperPred. OMIM, GeneCards, and Disgenet were used to collect relevant targets for R/CIOM. Cytoscape software 3.8.0 was used to construct the component-target-pathway network. Protein-Protein Interaction (PPI) networks were constructed using the STRING database. GO and KEGG enrichment analyses were performed by Metascape. AutoDock Vina 4.2 software was used for molecular docking. The molecular dynamics simulation was performed by Gromacs v2022.03. It is found that 12 studies involving 565 patients were included. Meta-analyses showed that curcumin reduced the incidence of severe R/CIOM (RR 0.42 [0.24, 0.75]) and the mean severity of R/CIOM (MD -0.93 [-1.34, -0.52]). Eleven core target genes were identified in the treatment of R/CIOM with curcumin. The results of molecular docking and the molecular dynamics simulation showed that curcumin had strong binding energy and stability with target proteins including MAPK3, SRC, and TNF. Overall, these findings suggest curcumin can effectively improve severe R/CIOM, perhaps by affecting MAPK3, SRC, and TNF.

Simultaneously degradation of various phthalate esters by Rhodococcus sp. AH-ZY2: Strain, omics and enzymatic study

Phthalate esters (PAEs) are widely used as plasticizers and cause serious complex pollution problem in environment. Thus, strains with efficient ability to simultaneously degrade various PAEs are required. In this study, a newly isolated strain Rhodococcus sp. AH-ZY2 can degrade 500 mg/L Di-n-octyl phthalate completely within 16 h and other 500 mg/L PAEs almost completely within 48 h at 37 °C, 180 rpm, and 2 % (v/v) inoculum size of cultures with a OD600 of 0.8. OD600 = 0.8, 2 % (v/v). Twenty genes in its genome were annotated as potential esterase and four of them (3963, 4547, 5294 and 5359) were heterogeneously expressed and characterized. Esterase 3963 and 4547 is a type I PAEs esterase that hydrolyzes PAEs to phthalate monoesters. Esterase 5294 is a type II PAEs esterase that hydrolyzes phthalate monoesters to phthalate acid (PA). Esterase 5359 is a type III PAEs esterase that simultaneously degrades various PAEs to PA. Molecular docking results of 5359 suggested that the size and indiscriminate binding feature of spacious substrate binding pocket may contribute to its substrate versatility. AH-ZY2 is a potential strain for efficient remediation of PAEs complex pollution in environment. It is first to report an esterase that can efficiently degrade mixed various PAEs.

Insights into the Interaction Mechanisms of Peptide and Non-Peptide Inhibitors with MDM2 Using Gaussian-Accelerated Molecular Dynamics Simulations and Deep Learning

Inhibiting MDM2-p53 interaction is considered an efficient mode of cancer treatment. In our current study, Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and binding free energy calculations were combined together to probe the binding mechanism of non-peptide inhibitors K23 and 0Y7 and peptide ones PDI6W and PDI to MDM2. The GaMD trajectory-based DL approach successfully identified significant functional domains, predominantly located at the helixes α2 and α2', as well as the β-strands and loops between α2 and α2'. The post-processing analysis of the GaMD simulations indicated that inhibitor binding highly influences the structural flexibility and collective motions of MDM2. Calculations of molecular mechanics-generalized Born surface area (MM-GBSA) and solvated interaction energy (SIE) not only suggest that the ranking of the calculated binding free energies is in agreement with that of the experimental results, but also verify that van der Walls interactions are the primary forces responsible for inhibitor-MDM2 binding. Our findings also indicate that peptide inhibitors yield more interaction contacts with MDM2 compared to non-peptide inhibitors. Principal component analysis (PCA) and free energy landscape (FEL) analysis indicated that the piperidinone inhibitor 0Y7 shows the most pronounced impact on the free energy profiles of MDM2, with the piperidinone inhibitor demonstrating higher fluctuation amplitudes along primary eigenvectors. The hot spots of MDM2 revealed by residue-based free energy estimation provide target sites for drug design toward MDM2. This study is expected to provide useful theoretical aid for the development of selective inhibitors of MDM2 family members.

Exploration on the potential efficacy and mechanism of methyl salicylate glycosides in the treatment of schizophrenia based on bioinformatics, molecular docking and dynamics simulation

The etiological and therapeutic complexities of schizophrenia (SCZ) persist, prompting exploration of anti-inflammatory therapy as a potential treatment approach. Methyl salicylate glycosides (MSGs), possessing a structural parent nucleus akin to aspirin, are being investigated for their therapeutic potential in schizophrenia. Utilizing bioinformation mining, network pharmacology, molecular docking and dynamics simulation, the potential value and mechanism of MSGs (including MSTG-A, MSTG-B, and Gaultherin) in the treatment of SCZ, as well as the underlying pathogenesis of the disorder, were examined. 581 differentially expressed genes related to SCZ were identified in patients and healthy individuals, with 349 up-regulated genes and 232 down-regulated genes. 29 core targets were characterized by protein-protein interaction (PPI) network, with the top 10 core targets being BDNF, VEGFA, PVALB, KCNA1, GRIN2A, ATP2B2, KCNA2, APOE, PPARGC1A and SCN1A. The pathogenesis of SCZ primarily involves cAMP signaling, neurodegenerative diseases and other pathways, as well as regulation of ion transmembrane transport. Molecular docking analysis revealed that the three candidates exhibited binding activity with certain targets with binding affinities ranging from -4.7 to -109.2 kcal/mol. MSTG-A, MSTG-B and Gaultherin show promise for use in the treatment of SCZ, potentially through their ability to modulate the expression of multiple genes involved in synaptic structure and function, ion transport, energy metabolism. Molecular dynamics simulation revealed good binding abilities between MSTG-A, MSTG-B, Gaultherin and ATP2B2. It suggests new avenues for further investigation in this area.

Antidiabetic potency and molecular insights of natural products bearing indole moiety: A systematic bioinformatics investigation targeting AKT1

Diabetic mellitus (DM) is a chronic disorder, and type 2 DM (T2DM) is the most prevalent among all categories (nearly 90%) across the globe every year. With the availability of potential drugs, the prevalence rate has remained uncontrollable, while natural resources showed a promising potency, and exploring such potential candidates at the preclinical stage is essential. An extensive literature search selected 89 marine and plant-derived indole derivatives with anti-inflammatory, antioxidant, lipid-lowering, etc., activities. However, as we know, drugs have not been able to convert from 'lead' to 'mainstream' due to inadequate drug-ability profiles, as our systematic investigation proved and selected herdmanine_A (HERD_A) and penerpene_D (PENE_D) as the most potential antidiabetic candidates from the library of indole derivatives. Based on our previous network pharmacology study, we selected three new target enzymes: Acetyl-CoA carboxylase 2 (ACACB; PDB ID: 3JRX), cyclin-dependent kinase 4 (CDK4; PDB ID: 3G33), and alpha serine/threonine-protein kinase 1 (AKT1; PDB ID: 3O96) to assess the antidiabetic potency of selected indole derivatives through binding energy or docking score. To conduct molecular docking studies with these enzymes, we used the PyRx-AutoDock platform. Furthermore, molecular dynamic simulation at 100 ns, physicochemical analysis, pharmacokinetics, toxicity assessment, and drug-likeness evaluation suggested that HERD_A and penerpene PENE_D were the most potent inhibitors against AKT1 compared to koenimbine (most potential based on the recorded IC50 value) and murrayakonine_A (most potential based on the docking score). In summary, HERD_A and/or PENE_D have the potential to be used as alternative therapeutic agent for the treatment of diabetes after some pharmacological investigation.

Mechanism of Mutation-Induced Effects on the Catalytic Function of TEV Protease: A Molecular Dynamics Study

Tobacco etch virus protease (TEVp) is wildly exploited for various biotechnological applications. These applications take advantage of TEVp's ability to cleave specific substrate sequences to study protein function and interactions. A major limitation of this enzyme is its relatively slow catalytic rate. In this study, MD simulations were conducted on TEV enzymes and known highly active mutants (eTEV and uTEV3) to explore the relationship between mutation, conformation, and catalytic function. The results suggest that mutations distant from the active site can influence the substrate-binding pocket through interaction networks. MD analysis of eTEV demonstrates that, by stabilizing the orientation of the substrate at the catalytic site, mutations that appropriately enlarge the substrate-binding pocket will be beneficial for Kcat, enhancing the catalytic efficiency of the enzyme. On the contrary, mutations in uTEV3 reduced the flexibility of the active pocket and increased the hydrogen bonding between the substrate and enzyme, resulting in higher affinity. At the same time, the MD simulation demonstrates that mutations outside of the active site residues could affect the dynamic movement of the binding pocket by altering residue networks and communication pathways, thereby having a profound impact on reactivity. These findings not only provide a molecular mechanistic explanation for the excellent mutants, but also serve as a guiding framework for rational computational design.

Structure-guided design of a trivalent nanobody cluster targeting SARS-CoV-2 spike protein

Nanobodies are natural anti-SARS-CoV-2 drug candidates. Engineering multivalent nanobodies is an effective way to improve the functional binding affinity of natural nanobodies by simultaneously targeting multiple sites on viral proteins. However, multivalent nanobodies have usually been engineered by trial and error, and rational designs are still lacking. Here, we describe a structure-guided design of a self-assembled trivalent nanobody cluster targeting the SARS-CoV-2 spike protein. Using the nanobody Nb6 as a monovalent binder, we first selected a human-derived trimerization scaffold evaluated by molecular dynamics simulations, then selected an optimal linker according to the minimum distance between Nb6 and the trimerization scaffold, and finally successfully engineered a trivalent nanobody cluster called Tribody. Compared with the low-affinity monovalent counterpart (Nb6), Tribody showed much higher target binding affinity (KD < 1 pM) and thus had a 900-fold increase in antiviral neutralization against SARS-CoV-2 pseudovirus. We determined the cryo-EM structure of the Tribody-spike complex and confirmed that all three Nb6 binders of Tribody collectively bind to the three receptor-binding domains (RBDs) of the spike and lock them in a 3-RBD-down conformation, fully consistent with our structure-guided design. This study demonstrates that synthetic nanobody clusters with human-derived self-assembled scaffolds are potential protein drugs against SARS-CoV-2 coronaviruses.

Elastic network models and molecular dynamic simulations reveal the molecular basis of allosteric regulation in ubiquitin-specific protease 7 (USP7)

Ubiquitin-specific protease 7 (USP7) is one of the most abundant deubiquitinases and plays an important role in various malignant tumors. However, the molecular mechanisms underlying USP7's structures, dynamics, and biological significance are yet to be investigated. In this study, we constructed the full-length models of USP7 in both the extended and compact state, and applied elastic network models (ENM), molecular dynamics (MD) simulations, perturbation response scanning (PRS) analysis, residue interaction networks as well as allosteric pocket prediction to investigate allosteric dynamics in USP7. Our analysis of intrinsic and conformational dynamics revealed that the structural transition between the two states is characterized by global clamp motions, during which the catalytic domain (CD) and UBL4-5 domain exhibit strong negative correlations. The PRS analysis, combined with the analysis of disease mutations and post-translational modifications (PTMs) further highlighted the allosteric potential of the two domains. The residue interaction network based on MD simulations captured an allosteric communication path which starts at CD domain and ends at UBL4-5 domain. Moreover, we identified a pocket at the TRAF-CD interface as a high-potential allosteric site for USP7. Overall, our studies not only provide molecular insights into the conformational changes of USP7, but also aid in the design of allosteric modulators that target USP7.

Association of a single amino acid replacement with dorsal pigmentation in a lizard from the Qinghai-Tibetan Plateau

Reptiles can evolve adaptive colors in different environments, but relatively little is known about the genetic mechanisms. Here, we identified the MC1R gene and its association with intraspecific color variation in the lizard Phrynocephalus erythrurus. Analysis of the MC1R sequence in 143 individuals from dark South Qiangtang Plateau (SQP) and light North Qiangtang plateau (NQP) populations, revealed two amino acid sites that showed significant differences in frequency between two areas. One SNP, corresponding to Glu183Lys residue, was found to be a highly significant outlier and differentially fixed for SQP and NQP populations. This residue is located in an extracellular area in the second small extracellular loop within the secondary structure of MC1R, which represents an "attachment pocket" part of the 3D structure. Cytological expression of MC1R alleles with the Glu183Lys replacement showed a 39 % increase in intracellular agonist-induced cyclic AMP levels and a 23.18 % greater cell surface expression of MC1R protein in the SQP relative to the NQP allele. Further in silico 3D modeling and in vitro binding experiments indicated a higher MC1R-α-MSH binding for the SQP allele, and elevated melanin synthesis. We provide an overview of how a single amino acid replacement leads to fundamental changes in MC1R function, and hence shapes variation in dorsal pigmentation in lizards from different environments.

Relationships between Molecular Structural Order Parameters and Equilibrium Water Dynamics in Aqueous Mixtures

Water's unique thermophysical properties and how it mediates aqueous interactions between solutes have long been interpreted in terms of its collective molecular structure. The seminal work of Errington and Debenedetti [Nature 2001, 409, 318-321] revealed a striking hierarchy of relationships among the thermodynamic, dynamic, and structural properties of water, motivating many efforts to understand (1) what measures of water structure are connected to different experimentally accessible macroscopic responses and (2) how many such structural metrics are adequate to describe the collective structural behavior of water. Diffusivity constitutes a particularly interesting experimentally accessible equilibrium property to investigate such relationships because advanced NMR techniques allow the measurement of bulk and local water dynamics in nanometer proximity to molecules and interfaces, suggesting the enticing possibility of measuring local diffusivities that report on water structure. Here, we apply statistical learning methods to discover persistent structure-dynamic correlations across a variety of simulated aqueous mixtures, from alcohol-water to polypeptoid-water systems. We investigate a variety of molecular water structure metrics and find that an unsupervised statistical learning algorithm (namely, sequential feature selection) identifies only two or three independent structural metrics that are sufficient to predict water self-diffusivity accurately. Surprisingly, the translational diffusivity of water across all mixed systems studied here is strongly correlated with a measure of tetrahedral order given by water's triplet angle distribution. We also identify a separate small number of structural metrics that well predict an important thermodynamic property, the excess chemical potential of an idealized methane-sized hydrophobe in water. Ultimately, we offer a Bayesian method of inferring water structure by using only structure-dynamics linear regression models with experimental Overhauser dynamic nuclear polarization (ODNP) measurements of water self-diffusivity. This study thus quantifies the relationships among several distinct structural order parameters in water and, through statistical learning, reveals the potential to leverage molecular structure to predict fundamental thermophysical properties. In turn, these findings suggest a framework for solving the inverse problem of inferring water's molecular structure using experimental measurements such as ODNP studies that probe local water properties.

Identifying novel selective PPO inhibitors through structure-based virtual screening and bio-evaluation

Protoporphyrinogen oxidase (PPO) is a key enzyme in chlorophyll and heme biosynthesis, and the development of its inhibitors is of great importance both in the pharmaceutical and pesticide industries. However, the currently developed PPO inhibitors have insignificant bio-selectivity and have a serious impact on non-target organisms. In this study, a docking-based virtual screening approach combined with bio-activity testing was used to obtain novel selective inhibitors of PPO. The results of the bio-activity test showed that thirteen compounds showed 10-fold selectivity over human PPO. And the best selective compound, ZINC70338, has a K _i value of 2.21 μM for Nicotiana tabacum PPO and >113-fold selectivity for human PPO. The selectivity mechanism of ZINC70338 in different species of PPO was then analyzed by molecular dynamics simulations to provide a design basis and theoretical guidance for the design of novel selective inhibitors.

Structure, energetics and dynamics in crowded amino acid solutions: a molecular dynamics study

A comprehensive understanding of crowding effects on biomolecular processes necessitates investigating the bulk thermodynamic and kinetic properties of the solutions with an accurate molecular representation of the crowded milieu. Recent studies have reparameterized the non-bonded dispersion interaction of solutes to precisely model intermolecular interactions, which would circumvent artificial aggregation as shown by the original force-fields. However, the performance of this reparameterization is yet to be assessed for concentrated crowded solutions in terms of investigating the hydration shell structure, energetics and dynamics. In this study, we perform molecular dynamics simulations of crowded aqueous solutions of five zwitterionic neutral amino acids (Gly, Ala, Thr, Pro, and Ser), mimicking the molecular crowding environment, using a modified AMBER ff99SB-ILDN force-field. We systematically examine and show that the reproducibility of the osmotic coefficients, density, viscosity and self-diffusivity of amino acids improves using the modified force-field in crowded concentrations. The modified force-field also improves the structuring of the solute solvation shells, solute interaction energy and convergence of tails of radial distribution functions, indicating reduction in the artificial aggregation. Our results also indicate that the hydrogen bonding network of water weakens and water molecules anomalously diffuse at small time scales in the crowded solutions. These results underscore the significance of examining the solution properties and anomalous hydration behaviour of water in crowded solutions, which have implications in shaping the structure and dynamics of biomolecules. The findings also illustrate the improvement in predicting bulk solution properties using the modified force-field, thereby providing an approach towards accurate modeling of crowded molecular solutions.

The effect of electric field on the structural order of water molecules around chitosan between nano gold plates determined by molecular dynamics simulations

In this paper, we classified the types of water in the vicinity of the chitosan polymer and gold plate by applying an electric field of magnitude 1 V Å^-1 in various directions at varying temperatures by using molecular dynamics simulation. The three types of water were categorized by analyzing the data through the tetrahedral order method with four water regions separated in the distance from 1 to 6 Å around polymers. The interaction between water molecules and functional groups, such as hydroxyl, ether, and ester, leads to the formation of intermediate and nonfreezing water. Under an electric field, this formation appeared more clearly due to the transformation of liquid water to crystal cubic ice with two structural formations depending on gold plates at a temperature of 300 K. The enhancement of the tetrahedral order of water in cubic ice is related to the existence of a four-fold H-bonded structure and lower ones in the XES experiment.

IL-2 Flexible Loops Might Play a Role in IL-2 Interaction with the High-Affinity IL-2 Receptor: A Molecular Dynamics (MD) Study

The clinical use of high-dose IL-2 in cancer immunotherapy faces several drawbacks such as toxicity and unfavorable pharmacokinetic profile. These drawbacks can be avoided by inhibiting IL-2 interaction with the CD25 subunit, which is a component of the high-affinity IL-2 receptor (IL-2Rαβγ). Several studies showed mutations of potential IL-2 residues such as R38, F42, Y45, and Y72 would produce IL-2 that is CD25-independent. In essence, structural comparison between wild-type (WT) IL-2 and CD25-independent IL-2 can be very insightful to assess the role of IL-2 flexibility and conformation in the IL-2 receptor interactions. Here, we investigated the flexibility loops and conformation of IL-2m (F24A, Y45A, and L72G), which is known to be CD25-independent, and IL-2m2 (F42Y and L72R) mutants along with WT IL-2 using MD simulations. Despite residue mutations, both IL-2m and IL-2m2 showed comparable conformational compactness and better stability than WT IL-2. Interestingly, IL-2m and IL-2m2 mutants showed rigid BC and CD loops in comparison to WT IL-2 . Also, the AB loop conformation of IL-2m was a bent structure compared to the WT IL-2 and IL-2m2. Principal component analysis (PCA) and free-energy landscape results suggested IL-2m and IL-2m2 have stable conformations compared to the WT IL-2. Therefore, these mutation sites of IL-2 produced stable and rigid loops that might prevent IL-2 from binding to the CD25 subunit. Our results can help to assess IL-2 flexibility loops to design new CD25-independent IL-2 mutants without compromising the IL-2 structure.

Discovery of novel IDH1-R132C inhibitors through structure-based virtual screening

Isocitrate dehydrogenase (IDH) belongs to a family of enzymes involved in glycometabolism. It is found in many living organisms and is one of the most mutated metabolic enzymes. In the current study, we identified novel IDH1-R132C inhibitors using docking-based virtual screening and cellular inhibition assays. A total of 100 molecules with high docking scores were obtained from docking-based virtual screening. The cellular inhibition assay demonstrated five compounds at a concentration of 10 μM could inhibit cancer cells harboring the IDH1-R132C mutation proliferation by > 50%. The compound (T001-0657) showed the most potent effect against cancer cells harboring the IDH1-R132C mutation with a half-maximal inhibitory concentration (IC₅₀) value of 1.311 μM. It also showed a cytotoxic effect against cancer cells with wild-type IDH1 and normal cells with IC₅₀ values of 49.041 μM and >50 μM, respectively. Molecular dynamics simulations were performed to investigate the stability of the kinase structure binding of allosteric inhibitor compound A and the identified compound T001-0657 binds to IDH1-R132C. Root-mean-square deviation, root-mean-square fluctuation, and binding free energy calculations showed that both compounds bind tightly to IDH1-R132C. In conclusion, the compound identified in this study had high selectivity for cancer cells harboring IDH1-R132C mutation and could be considered a promising hit compound for further development of IDH1-R132C inhibitors.

Binding of the M. tuberculosis EccC ATPase double hexameric ring to the EsxAB virulence factor is enhanced by ATP

The EccC enzyme of M. tuberculosis ESX-1 secretion system is involved in EsxAB virulence factor secretion and offers an attractive target for antivirulence inhibitors development against M. tuberculosis.  The EccCb1 polypeptide of the EccC enzyme contains two Ftsk/SpoIIIE type ATPase domains (D2 and D3) and binds to EsxAB factor at C-terminal region of the D3 domain. In current study, we have determined a low-resolution structure of EccCb1, and its mechanism involved in ATPase activity and EsxAB factor binding. Small-angle X-ray scattering data yielded a double hexameric ring structure of EccCb1 in solution and was further confirmed by SEC-MALS and dynamic light scattering. ATPase activity of wild-type, D2, and D3 mutants showed that D2-K90A and D3-K382A mutations led to a complete loss of enzyme activity. The full-length EccCb1 showed ~ 3.7-fold lower catalytic efficiency than D2 domain and ~1.7 fold lower than D3 domain.  The EsxAB factor binds EccCb1 with Kd ~ 11.3±0.6 nM and its affinity is enhanced ~2 fold in presence of ATP+Mg2+. These data indicate the involvement of ATPase activity in EsxAB factor translocation.  Molecular dynamics simulation on wild-type, ATP+Mg2+ and EsxAB+ATP+Mg2+ bound EccCb1 double-ring structure showed enhanced stability of enzyme upon ATP+Mg2+ and EsxAB binding. Overall, our study showed a low-resolution structure of EccCb1, and the mechanism involved in ATPase activity and EsxAB factor recognition, which can be targeted for the development of anti-virulence drugs against M. tuberculosis.

Identification of PRMT5 inhibitors with novel scaffold structures through virtual screening and biological evaluations

Protein arginine methyltransferase 5 (PRMT5), an important member in PRMT family, has been validated as a promising anticancer target. In this study, through the combination of virtual screening and biological experiments, we have identified two PRMT5 inhibitors with novel scaffold structures. Among them, compound Y2431 showed moderate activity with IC50 value of 10.09 μM and displayed good selectivity against other methyltransferases. The molecular docking analysis and molecular dynamics (MD) simulations suggested that the compound occupied the substrate-arginine binding site. Furthermore, Y2431 exhibited anti-proliferative activity to leukemia cells by inducing cell cycle arrest. Overall, the hit compound could provide a novel scaffold for further optimization of small-molecule PRMT5 inhibitors.

Temperature induced change of TMAO effects on hydrophobic hydration

The effect of trimethylamine-N-oxide (TMAO) on hydrophobic solvation and hydrophobic interactions of methane has been studied with Molecular Dynamics simulations in the temperature range between 280 and 370 K at 1 bar ambient pressure. We observe a temperature transition in the effect of TMAO on the aqueous solubility of methane. At low temperature (280 K), methane is preferentially hydrated, causing TMAO to reduce its solubility in water, while above 320 K, methane preferentially interacts with TMAO, causing TMAO to promote its solubility in water. Based on a statistical-mechanical analysis of the excess chemical potential of methane, we find that the reversible work of creating a repulsive methane cavity opposes the solubility of methane in TMAO/water solution more than in pure water. Below 320 K, this solvent-excluded volume effect overcompensates the contribution of methane–TMAO van der Waals interactions, which promote the solvation of methane and are observed at all temperatures. These van der Waals interactions with the methyl groups of TMAO tip the balance above 320 K where the effect of TMAO on solvent-excluded volume is smaller. We furthermore find that the effective attraction between dissolved methane solutes increases with the increasing TMAO concentration. This observation correlates with a reduction in the methane solubility below 320 K but with an increase in methane solubility at higher temperatures.

Metallo-beta-lactamase CphA evolving into more efficient hydrolases through gene mutation is a novel pathway for the resistance of super bacteria

The evolution of metallo-beta-lactamase CphA in discontinuous gradient concentration of imipenem was investigated in this work. The results suggested that single-base mutations K218R, K249T, K249M, Q253H, and a frameshift mutation M1 were observed. Compared with wild type, the minimum inhibitory concentration (MICs) of K249T, K249M, and M1 increased by at least 128 times and that of K218R increased by 64 times. And the catalytic efficiency increased by 312% and 653%, respectively. It is speculated from the details of the structural changes revealed by molecular dynamics simulations that the carbon skeleton migration caused by the outward motion of the loop 3 in the mutant may have significantly increased the cavity volume of the binding pocket, which is more conducive to the entry and expulsion of imipenem and its hydrolytic product. And the conformational change of the TDRAGGN (71-77) is located at the bottom of the binding pocket from order α-helix to disorder random coil enabled the binding pocket to be more conducive to accommodate and hold the imipenem respectively. All these indicated that during the repeated drug resistance, the wild-type achieved gene mutations and conformational change and evolved to the mutant enzymes with a more delicate structure and stronger hydrolysis ability. KEY POINTS: • The mutation and evolution of CphA under the selective pressure of imipenem. • The CphA evolved to the mutants with stronger hydrolysis capacity. • A novel pathway for the resistance of super bacteria.

Structural order of water molecules around polyrotaxane including PEG, α-cyclodextrin, and α-lipoic acid linker on gold surface by molecular dynamics simulations

In materials science, water plays an important part, especially at the molecular level. It shows various properties when sorbed onto surfaces of polymers. The structure of the molecular water ensemble in the vicinity of the polymers is under discussion. In this study, we used molecular dynamics methods to analyze the structure of water in the vicinity of the polymer polyrotaxane (PR), composed of α-cyclodextrins (α-CDs), a poly(ethylene glycol) (PEG) axial chain, and α-lipoic acid linkers, at various temperatures. The distribution of water around the functional groups, hydrogen bond network, and tetrahedral order were analyzed to classify the various types of water around the polymer. We found that the tetrahedral order of water had a strained relationship from the XES experiment. Four water regions were separated from each other in the vicinity of 1 to 5 Å around PR. The intermediate and non-freezing water were formed due to the interaction between water molecules and the functional groups, such as hydroxyl, ether, and ester.

Structural and ATPase activity analysis of nucleotide binding domain of Rv3870 enzyme of M. tuberculosis ESX-1 system

The EccC enzyme of ESX-1 system contains (i) a membrane bound Rv3870 with single ATPase domain and (ii) a cytoplasmic Rv3871 with two ATPase domains and involved in secretion of ESAT6/CFP10 factor out of the cell. In current study, we have structurally and biochemically characterized the ATPase domain (442-747 residues) of Rv3870 enzyme. The ΔRv3870 eluted as oligomer (~813 kDa) from Superdex 200 (16/60) column, as identified based on molecular mass standard and dynamics light scattering. The SAXS analysis yielded a tetrameric ring envelope of ΔRv3870, quite consistent to dynamic light scattering data. The ΔRv3870 exhibited ATPase activity having kinetic parameters, K_m ~ 100 ± 40 μM, k_cat ~ 1.81 ± 0.27 min^-1 and V_max ~ 54.41 μM/min/mg. ATPase activity using nine ΔRv3870 mutants showed 70-91% decrease in catalytic efficiency of the enzyme. ΔRv3870 binds Rv3871 with K_D ~ 484.0 ± 10.3 nM and its catalytic efficiency is enhanced ~6.7-fold in presence of Rv3871. CD data revealed the high T_M ~ 82.2 ± 0.5 °C for ΔRv3870 and enhanced in presence of ATP + Mg²⁺, as observed in dynamics simulation on ΔRv3870 hexameric models. Overall, our structural and biochemical studies on ΔRv3870 have explained the mechanism, which will contribute in development of antivirulence inhibitors against M. tuberculosis.

Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions

DNA methyltransferases (DNMTs) including DNMT1 are a conserved family of cytosine methylases that play crucial roles in epigenetic regulation. The versatile functions of DNMT1 rely on allosteric networks between its different interacting partners, emerging as novel therapeutic targets. In this work, based on the modeling structures of DNMT1-ubiquitylated H3 (H3Ub)/ubiquitin specific peptidase 7 (USP7) complexes, we have used a combination of elastic network models, molecular dynamics simulations, structural residue perturbation, network modeling, and pocket pathway analysis to examine their molecular mechanisms of allosteric regulation. The comparative intrinsic and conformational dynamics analysis of three DNMT1 systems has highlighted the pivotal role of the RFTS domain as the dynamics hub in both intra- and inter-molecular interactions. The site perturbation and network modeling approaches have revealed the different and more complex allosteric interaction landscape in both DNMT1 complexes, involving the events caused by mutational hotspots and post-translation modification sites through protein-protein interactions (PPIs). Furthermore, communication pathway analysis and pocket detection have provided new mechanistic insights into molecular mechanisms underlying quaternary structures of DNMT1 complexes, suggesting potential targeting pockets for PPI-based allosteric drug design.

Identification of imidazo[4,5-c]pyridin-2-one derivatives as novel Src family kinase inhibitors against glioblastoma

Glioblastoma multiforme (GBM) is the most common and malignant primary brain tumour in the central nervous system (CNS). As the ideal targets for GBM treatment, Src family kinases (SFKs) have attracted much attention. Herein, a new series of imidazo[4,5-c]pyridin-2-one derivatives were designed and synthesised as SFK inhibitors. Compounds 1d, 1e, 1q, 1s exhibited potential Src and Fyn kinase inhibition in the submicromolar range, of which were next tested for their antiproliferative potency on four GBM cell lines. Compound 1s showed effective activity against U87, U251, T98G, and U87-EGFRvIII GBM cell lines, comparable to that of lead compound PP2. Molecular dynamics (MDs) simulation revealed the possible binding patterns of the most active compound 1s in ATP binding site of SFKs. ADME prediction suggested that 1s accord with the criteria of CNS drugs. These results led us to identify a novel SFK inhibitor as candidate for GBM treatment.

Microscopic structural features of water in aqueous-reline mixtures of varying compositions

Reline, a mixture of urea and choline chloride in a 2 : 1 molar ratio, is one of the most frequently used deep eutectic solvents. Pure reline and its aqueous solution have large scale industrial use. Owing to the presence of active hydrogen bond formation sites, urea and choline cations can disrupt the hydrogen-bonded network in water. However, a quantitative understanding of the microscopic structural features of water in the presence of reline is still lacking. We carry out extensive all-atom molecular dynamics simulations to elucidate the effect of the gradual addition of co-solvents on the microscopic arrangements of water molecules. We consider four aqueous solutions of reline, between 26.3 and 91.4 wt%. A disruption of the local hydrogen-bonded structure in water is observed upon inclusion of urea and choline chloride. The extent of deviation of the water structure from tetrahedrality is quantified using the tetrahedral order parameter (q_tet). Our analyses show a monotonic increase in the structural disorder as the co-solvents are added. Increase in the q_tet values are observed when highly electro-negative hetero-atoms like nitrogen, oxygen of urea and choline cations are counted as partners of the central water molecules. Further insights are drawn from the characterization of the hydrogen-bonded network in water and we observe the gradual rupturing of water-water hydrogen bonds and their subsequent replacement by the water-urea hydrogen bonds. A negligible contribution from the hydrogen bonds between water and bulky choline cations has also been found. Considering all the constituents as the hydrogen bond partners we calculate the possibility of a successful hydrogen bond formation with a central water molecule. This gives a clear picture of the underlying mechanism of water replacement by urea.

Pressure, Peptides, and a Piezolyte: Structural Analysis of the Effects of Pressure and Trimethylamine-N-oxide on the Peptide Solvation Shell

The osmolyte trimethylamine-N-oxide (TMAO) is able to increase the thermodynamic stability of folded proteins, counteracting pressure denaturation. Herein, we report experimental solubility data on penta-alanine (pAla) in aqueous TMAO solutions (at pH = 7 and pH = 13) together with molecular simulation data for pAla, penta-serine (pSer), and an elastin-like peptide (ELP) sequence (VPGVG) under varying pH and pressure conditions. The effect of the peptide end groups on TMAO-peptide interactions is investigated by comparing the solvation of zwitterionic and negatively charged pentamers with the solvation of pentamers with charge-neutral C- and N-termini and linear, virtually infinite, peptide chains stretched across the periodic boundaries of the simulation cell. The experiments and simulations consistently show that TMAO is net-depleted from the pAla-water interface, but local accumulation of TMAO is observed just outside the first hydration shell of the peptide. While the same observations are also made in the simulations of the zwitterionic pentamers (Ala, Ser, and ELP) and virtually infinite peptide chains (Ala and ELP), weak preferential binding of TMAO is instead observed for pAla with neutral end groups at a 1 M TMAO concentration and for an ELP pentamer with capped neutral end groups at a 0.55 M TMAO concentration studied in previous work (Y.-T. Liao et al. Proc. Natl. Acad. Sci. USA, 2017, 114, 2479-2484). The above observations made at 1 bar ambient pressure remain qualitatively unchanged at 500 bar and 2 kbar. Local accumulation of TMAO correlates with a reduction in the total number of peptide-solvent hydrogen bonds, independent of the peptide's primary sequence and the applied pressure. By weakening water hydrogen bonds with the protein backbone, TMAO indirectly contributes to stabilizing internal hydrogen bonds in proteins, thus providing a protein stabilization mechanism beyond net depletion.

Water Structure and Properties at Hydrophilic and Hydrophobic Surfaces

The properties of water on both molecular and macroscopic surfaces critically influence a wide range of physical behaviors, with applications spanning from membrane science to catalysis to protein engineering. Yet, our current understanding of water interfacing molecular and material surfaces is incomplete, in part because measurement of water structure and molecular-scale properties challenges even the most advanced experimental characterization techniques and computational approaches. This review highlights progress in the ongoing development of tools working to answer fundamental questions on the principles that govern the interactions between water and surfaces. One outstanding and critical question is what universal molecular signatures capture the hydrophobicity of different surfaces in an operationally meaningful way, since traditional macroscopic hydrophobicity measures like contact angles fail to capture even basic properties of molecular or extended surfaces with any heterogeneity at the nanometer length scale. Resolving this grand challenge will require close interactions between state-of-the-art experiments, simulations, and theory, spanning research groups and using agreed-upon model systems, to synthesize an integrated knowledge of solvation water structure, dynamics, and thermodynamics.

Conformational Landscapes of HER2 Exon 20 Insertions Explain Their Sensitivity to Kinase Inhibitors in Lung Adenocarcinoma

INTRODUCTION

HER2 exon 20 insertion (ex20ins) is one of the most intractable problems in lung cancer. Most ex20ins are resistant to available EGFR or pan-HER tyrosine kinase inhibitors (TKIs), with the exception of a few mutants. However, the mechanism for TKI response and resistance of HER2 ex20ins remains poorly understood.

METHODS

Next-generation sequencing-based genomic profiling data of 4139 patients with lung cancer were interrogated for HER2 ex20ins. Structural modeling and molecular dynamics simulations of common HER2 ex20ins were carried out to provide insights into the mechanism of activation and response heterogeneity of ex20ins. Molecular docking was performed to predict affinity to TKIs. Therapeutic decisions for patients were made on the basis of the results of genomic profiling.

RESULTS

From 155 HER2-mutant lung cancer cases, Y772_A775dup and G778_P780dup were identified in 74 (47.7%) and 18 (11.6%) cases, respectively. Molecular dynamics simulations revealed that HER2 ex20ins led to ligand-independent kinase activation by changing the conformational landscape of HER2 kinase and restricting kinase conformation in the active state. G778_P780dup had a three-amino acid extension in the αC-β4 loop and retained the HER2-characteristic G776 and G778. Compared with Y772_A775dup, it had less restriction on kinase conformational sampling and higher affinity to afatinib, dacomitinib, pyrotinib, and poziotinib. Treating lung adenocarcinomas carrying G778_P780dup with these inhibitors led to sustained tumor responses in six of the 10 patients.

CONCLUSIONS

The kinase conformational landscape dictated by the length of the αC-β4 loop and residues at HER2 776 and 778 position explains TKI sensitivity in ex20ins. This finding could guide therapeutic decisions with currently available therapies and future drug development strategies.

Termination of Biological Function at Low Temperatures: Glass or Structural Transition?

Energy of life is produced by electron transfer in energy chains of respiration or photosynthesis. A small input of free energy available to biology puts significant restrictions on how much free energy can be lost in each electron-transfer reaction. We advocate the view that breaking ergodicity, leading to violation of the fluctuation-dissipation theorem (FDT), is how proteins achieve high reaction rates without sacrificing the reaction free energy. Here we show that a significant level of nonergodicity, represented by a large extent of the configurational temperature over the kinetic temperature, is maintained in the entire physiological range for the cytochrome c electron transfer protein. The protein returns to the state consistent with the FDT below the crossover temperature close to the temperature of the protein glass transition. This crossover leads to a sharp increase in the activation barrier of electron transfer and is displayed by a kink in the Arrhenius plot for the reaction rate constant.

Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds

Water molecules at interfaces of materials exhibit enigmatic properties. A variety of spectroscopic studies have observed a high-frequency motion in these water molecules, represented by a blueshift, at both hydrophobic and hydrophilic interfaces. However, the molecular mechanism behind this blueshift has remained unclear. Using Raman spectroscopy and ab initio molecular dynamics simulations, we reveal the molecular mechanism of the blueshift of water molecules around six monosaccharide isomers. In the first hydration shell, we found weak hydrogen-bonded water molecules that cannot have a stable tetrahedral water network. In the water molecules, the vibrational state of the OH bond oriented toward the bulk solvent strongly contributes to the observed blueshift. Our work suggests that the blueshift in various solutions originates from the vibrational motions of these observed water molecules.

The sensitivity of folding free energy landscapes of trpzips to mutations in the hydrophobic core

The sensitivity of the stability of folded states and free energy landscapes to the differences in the hydrophobic content of the core residues has been studied for the set of 16-residue trpzips, namely, Trpzip4, Trpzip5 and Trpzip6.

Comparison of hydration behavior and conformational preferences of the Trp-cage mini-protein in different rigid-body water models

Trp-cage unfolds at different temperatures in different water models revealing the sensitivity of conformational order metrics to the choice of water models.

Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models

Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.

Triplet correlation functions in liquid water

Triplet correlations have been shown to play a crucial role in the transformation of simple liquids to anomalous tetrahedral fluids [M. Singh, D. Dhabal, A. H. Nguyen, V. Molinero, and C. Chakravarty, Phys. Rev. Lett. 112, 147801 (2014)]. Here we examine triplet correlation functions for water, arguably the most important tetrahedral liquid, under ambient conditions, using configurational ensembles derived from molecular dynamics (MD) simulations and reverse Monte Carlo (RMC) datasets fitted to experimental scattering data. Four different RMC data sets with widely varying hydrogen-bond topologies fitted to neutron and x-ray scattering data are considered [K. T. Wikfeldt, M. Leetmaa, M. P. Ljungberg, A. Nilsson, and L. G. M. Pettersson, J. Phys. Chem. B 113, 6246 (2009)]. Molecular dynamics simulations are performed for two rigid-body effective pair potentials (SPC/E and TIP4P/2005) and the monatomic water (mW) model. Triplet correlation functions are compared with other structural measures for tetrahedrality, such as the O-O-O angular distribution function and the local tetrahedral order distributions. In contrast to the pair correlation functions, which are identical for all the RMC ensembles, the O-O-O triplet correlation function can discriminate between ensembles with different degrees of tetrahedral network formation with the maximally symmetric, tetrahedral SYM dataset displaying distinct signatures of tetrahedrality similar to those obtained from atomistic simulations of the SPC/E model. Triplet correlations from the RMC datasets conform closely to the Kirkwood superposition approximation, while those from MD simulations show deviations within the first two neighbour shells. The possibilities for experimental estimation of triplet correlations of water and other tetrahedral liquids are discussed.