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Background: Metal oxide nanomaterials are increasingly being exploited in cancer therapy thanks to their unique properties, which can enhance the efficacy of current cancer therapies. However, the nanotoxicity and mechanism of Ti0.8O2 nanosheets for specific site-targeting strategies in NSCLC have not yet been investigated.Methods: The effects of Ti0.8O2 nanosheets on cytotoxicity in NSCLC cells and normal cells were examined. The apoptosis characteristics, including condensed and fragmented nuclei, as assessed by positive staining with annexin V. The cellular uptake of the nanosheets and the induction of stress fiber were assessed via transmission electron microscopy (TEM) and scanning electron microscopy (SEM) analyses, respectively. We also evaluated the expression of protein in death mechanism to identify the molecular mechanisms behind the toxicity of these cells. We investigated the relationship between S-nitrosylation and the increase in p53 stability by molecular dynamics.Results: Ti0.8O2 nanosheets caused cytotoxicity in several lung cancer cells, but not in normal cells. The nanosheets could enter lung cancer cells and exert an apoptosis induction. Results for protein analysis further indicated the activation of p53, increased Bax, decreased Bcl-2 and Mcl-1, and activation of caspase-3. The nanosheets also exhibited a substantial apoptosis effect in drug-resistant metastatic primary lung cancer cells, and it was found that the potency of the nanosheets was dramatically higher than that of cisplatin and etoposide. In terms of their mechanism of action, we found that the mode of apoptosis induction was through the generation of cellular ONOO− mediated the S-nitrosylation of p53 at C182. Molecular dynamics analysis further showed that the S-nitrosylation of one C182 stabilized the p53 dimer. Consequently, this nitrosylation of the protein led to an upregulation of p53 through its stabilization.Conclusions: Taking all the evidence together, we provided information on the apoptosis induction effect of the nanosheets through a molecular mechanism involving reactive nitrogen species, which affects the protein stability; thus emphasizing the novel mechanism of action of nanomaterials for cancer therapy.

Clostridium difficile infection (CDI) is the most common hospital acquired diarrheal disease with its increasing incidence and mortality rate globally. DNA Gyrase B (GyrB) is a key component of DNA replication process across all bacterial genera; thus, this offers a potential target for the treatment of CDI. In the present study, several virtual screening approaches were employed to identify a novel C. difficile GyrB inhibitor. The 139 known metabolites were screened out from the 480 flavonoids in PhytoHub database. Molinspiration and PROTOX II servers were used to calculate the ADME properties and oral toxicity of the metabolites, whereas mutagenicity, tumorigenicity, irritant, and reproductive effect were predicted using DataWarrior program. The binding mode and the binding efficiency of the screened flavonoids against the GyrB were studied using FlexX docking program. From virtual screening of 139 metabolites, we found 25 flavonoids with no mutagenicity, tumorigenicity, irritant, and reproductive effect. Docking study suggested that flavonoids 1030 ((-)-epicatechin 3'-O-sulfate), 1032 ((-)-epicatechin 4'-O-sulfate), 1049 (3'-O-methyl-(-)-epicatechin 4-O-sulfate), 1051 (3'-O-methyl-(-)-epicatechin 7-O-sulfate), 1055 (4'-O-methyl-(-)-epicatechin 7-O-sulfate) and 1317 (quercetin sulfate) have significantly higher binding affinity than the known GyrB inhibitor novobiocin. The results from molecular dynamics simulation and free energy calculations based on solvated interaction energy suggested that (-)-epicatechin 3'-O-sulfate could be a potential drug candidate in the management of CDI.

The effect of microsolvation on excited-state proton transfer (ESPT) reaction of 3-hydroxyflavone (3HF) and its inclusion complex with γ-cyclodextrin (γ-CD) was studied using computational approaches. From molecular dynamics simulations, two possible inclusion complexes formed by the chromone ring (C-ring, Form I) and the phenyl ring (P-ring, Form II) of 3HF insertion to γ-CD were observed. Form II is likely more stable because of lower fluctuation of 3HF inside the hydrophobic cavity and lower water accessibility to the encapsulated 3HF. Next, the conformation analysis of these models in the ground (S0) and the first excited (S1) states was carried out by density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations, respectively, to reveal the photophysical properties of 3HF influenced by the γ-CD. The results show that the intermolecular hydrogen bonding (interHB) between 3HF and γ-CD, and intramolecular hydrogen bonding (intraHB) within 3HF are strengthened in the S1 state confirmed by the shorter interHB and intraHB distances and the red-shift of O–H vibrational modes involving in the ESPT process. The simulated absorption and emission spectra are in good agreement with the experimental data. Significantly, in the S1 state, the keto form of 3HF is stabilized by γ-CD, explaining the increased quantum yield of keto emission of 3HF when complexing with γ-CD in the experiment. In the other word, ESPT of 3HF is more favorable in the γ-CD hydrophobic cavity than in aqueous solution.

The coronavirus disease 2019 (COVID-19) pandemic causes many morbidity and mortality cases. Despite several developed vaccines and antiviral therapies, some patients experience severe conditions that need intensive care units (ICU); therefore, precision medicine is necessary to predict and treat these patients using novel biomarkers and targeted drugs. In this study, we proposed a multi-level biological network analysis framework to identify key genes via protein–protein interaction (PPI) network analysis as well as survival analysis based on differentially expressed genes (DEGs) in leukocyte transcriptomic profiles, discover novel biomarkers using microRNAs (miRNA) from regulatory network analysis, and provide candidate drugs targeting the key genes using drug–gene interaction network and structural analysis. The results show that upregulated DEGs were mainly enriched in cell division, cell cycle, and innate immune signaling pathways. Downregulated DEGs were primarily concentrated in the cellular response to stress, lysosome, glycosaminoglycan catabolic process, and mature B cell differentiation. Regulatory network analysis revealed that hsa-miR-6792-5p, hsa-let-7b-5p, hsa-miR-34a-5p, hsa-miR-92a-3p, and hsa-miR-146a-5p were predicted biomarkers. CDC25A, GUSB, MYBL2, and SDAD1 were identified as key genes in severe COVID-19. In addition, drug repurposing from drug–gene and drug–protein database searching and molecular docking showed that camptothecin and doxorubicin were candidate drugs interacting with the key genes. In conclusion, multi-level systems biology analysis plays an important role in precision medicine by finding novel biomarkers and targeted drugs based on key gene identification.

MotivationLung cancer is a chronic non-communicable disease and is the cancer with the world’s highest incidence in the 21stcentury. One of the leading mechanisms underlying the development of lung cancer in nonsmokers is an amplification of the epidermal growth factor receptor (EGFR) gene. However, laboratories employing conventional processes of drug discovery and development for such targets encounter several pain-points that are cost- and time-consuming. Moreover, high failure rates are caused by efficacy and safety problems during research and development. Therefore, it is imperative to develop improved methods for drug discovery. Herein, we developed a deep learning model with spatial graph embedding and molecular descriptors based on predicting pIC50potency estimates of small molecules and classifying hit compounds against the human epidermal growth factor receptor (LigEGFR). The model was generated with a large-scale cell line-based dataset containing broad lists of chemical features.ResultsLigEGFR outperformed baseline machine learning models for predicting pIC50. Our model was notable for higher performance in hit compound classification, compared to molecular docking and machine learning approaches. The proposed predictive model provides a powerful strategy that potentially helps researchers overcome major challenges in drug discovery and development processes, leading to a reduction of failure to discover novel hit compounds.AvailabilityWe provide an online prediction platform and the source code that are freely available athttps://ligegfr.vistec.ist, andhttps://github.com/scads-biochem/LigEGFR, respectively.Key pointsLigEGFR is a regression model for predicting pIC50that was developed for the human EGFR target. It can also be applied to hit compound classification (pIC50≥ 6) and has a higher performance than baseline machine learning algorithms and molecular docking approaches.Our spatial graph embedding and molecular descriptors based approach notably exhibited a high performance in predicting pIC50of small molecules against human EGFR.Non-hashed and hashed molecular descriptors were revealed to have the highest predictive performance by using in a convolutional layers and a fully connected layers, respectively.Our model used a large-scale and non-redundant dataset to enhance the diversity of the small molecules. The model showed robustness and reliability, which was evaluated by y-randomization and applicability domain analysis (ADAN), respectively.We developed a user-friendly online platform to predict pIC50of small molecules and classify the hit compounds for the drug discovery process of the EGFR target.

The impact of autophagy on cancer treatment and its corresponding responsiveness has galvanized the scientific community to develop novel inhibitors for cancer treatment. Importantly, the discovery of inhibitors that targets the early phase of autophagy was identified as a beneficial choice. Despite the number of research in recent years, screening of the DrugBank repository (9591 molecules) for the Vacuolar protein sorting 34 (VPS34) has not been reported earlier. Therefore, the present study was designed to identify potential VPS34 antagonists using integrated pharmacophore strategies. Primarily, an energy-based pharmacophore and receptor cavity-based analysis yielded five (DHRRR) and seven featured (AADDHRR) pharmacophore hypotheses respectively, which were utilized for the database screening process. The glide score, the binding free energy, pharmacokinetics and pharmacodynamics properties were examined to narrow down the screened compounds. This analysis yielded a hit molecule, DB03916 that exhibited a better docking score, higher binding affinity and better drug-like properties in contrast to the reference compound that suffers from a toxicity property. Importantly, the result was validated using a 50 ns molecular dynamics simulation study. Overall, we conclude that the identified hit molecule DB03916 is believed to serve as a prospective antagonist against VPS34 for cancer treatment.

Drug-resistant

Monoclonal antibodies (mAbs) are one of the fastest-growing areas of biopharmaceutical industry and have been widely used for a broad spectrum of diseases. Meanwhile, the immunogenicity of non-human derived antibodies can generate side effects by inducing the human immune response to produce human anti-mouse-immunoglobulin antibody (HAMA). In this work, we aim to reduce the immunogenicity of muMAb A.4.6.1 by substitute human sequences for murine sequences. Humanized antibodies are constructed by grafting, specificity determining residues (SDR), complementary determining regions (CDR), and chimeric region of muMAb A.4.6.1, onto variable domain of Trastuzumab (Herceptin). The interactions between grafted antibodies and their target, Vascular endothelial growth factor (VEGF), were theoretically investigated by molecular dynamics simulation in order to evaluate the antibodies-antigen binding behavior. The obtained protein-protein interactions and calculated binding free energy suggested that the SDR-VEGF complex presented a significantly greater binding affinity, number of contact and total number of H-bonds compared to CDR and chimeric mAbs, significantly. Moreover, the Camsol program predicted that the solubility of SDR mAb exhibits the greatest solubility. This result was supported by performing a western blot analysis of the grafted mAbs with soluble and insoluble fractions in order to evaluate their solubility, in which SDR was found to have a much lower amount of insoluble proteins. Consequently, the enhanced binding affinity and solubility of the designed SDR was achieved by the single S106D mutation using computational methods. With the aim of low immunogenicity, high solubility, and high affinity, this SDR humanized antibody was expected to have greater efficacy than murine or chimeric antibodies for future use in humans.

The emergence outbreak caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has received significant attention on the global risks. Due to itscrucial role in viral replication, the main protease 3CLpro is an important target for drug discovery and development to combat COVID-19. In this work, the structural and dynamic behaviors as well as binding efficiency of the four peptidomimetic inhibitors (N3, 11a, 13b, and 14b) recently co-crystalized with SARS-CoV-2 3CLpro were studied and compared using all-atom molecular dynamics (MD) simulations and solvated interaction energy-based binding free energy calculations. The per-residue decomposition free energy results suggested that the key residues involved in inhibitors binding were H41, M49, L141–C145, H163–E166, P168, and Q189–T190 in the domains I and II. The van der Waals interaction yielded the main energy contribution stabilizing all the focused inhibitors. Besides, their hydrogen bond formations with F140, G143, C145, H164, E166, and Q189 residues in the substrate-binding pocket were also essential for strengthening the molecular complexation. The predicted binding affinity of the four peptidomimetic inhibitors agreed with the reported experimental data, and the 13b showed the most efficient binding to SARS-CoV-2 3CLpro. From rational drug design strategies based on 13b, the polar moieties (e.g., benzamide) and the bulky N-terminal protecting groups (e.g., thiazole) should be introduced to P1’ and P4 sites in order to enhance H-bonds and hydrophobic interactions, respectively. We hope that the obtained structural and energetic information could be beneficial for developing novel SARS-CoV-2 3CLpro inhibitors with higher inhibitory potency to combat COVID-19., Graphical abstract Unlabelled Image, Highlights • The four recent peptidomimetic inhibitors were investigated using MD simulations and free energy calculations. • The key residues involved in inhibitors binding are H41, M49, L141–C145, H163–E166, P168, and Q189–T190. • The van der Waals interaction yielded the main energy contribution stabilizing all studied inhibitors. • The 13b is chosen as a template for structural modifications to gain more interactions with the surrounding amino acids.

MCR (mobile colistin resistance) enzymes catalyse phosphoethanolamine (PEA) addition to bacterial lipid A, threatening the "last-resort" antibiotic colistin. Molecular dynamics and density functional theory simulations indicate that monozinc MCR supports PEA transfer to the Thr285 acceptor, positioning MCR as a mono- rather than multinuclear member of the alkaline phosphatase superfamily.

Hepatitis B virus (HBV), a small enveloped DNA virus, attacks the human liver causing both acute and chronic diseases. Current therapeutic drugs use the nucleos(t)ide analogues (NAs) as a competitive inhibitor against HBV reverse transcriptase (HBV-RT), an essential enzyme pivotally involved in viral replication. Unfortunately, this treatment still causes the development of resistant variants of HBV against NAs. As HBV-RT is homologous to the human immunodeficiency virus reverse transcriptase (HIV-RT), it is reasonable to treat HBV-RT with anti-HIV drugs. In the present study, we aimed to investigate the structural dynamics and susceptibility of the known anti-HIV drugs (stavudine [d4T], didanosine [DDI], and zidovudine [ZDV]) against HBV-RT enzyme in comparison to the anti-HBV drug lamivudine (3TC) and deoxythymidine triphosphate (dTTP) substrate using several computational approaches. The ΔGbindresidue calculations revealed that seven polar residues (K32, R41, D83, S85, D205, N236, and K239) and three hydrophobic residues (A86, A87, and F88) of HBV-RT as well as the adjacent DNA strands play an important role in the ligand binding. In addition, the H-bond pattern of d4T is similar to that of 3TC, especially at the residues A86 and A87. Such interactions promote the favorable conformation of ligand in the HBV-RT binding pocket, while the several different conformations of ligand are found in the unbound state. The predicted binding free energy results based on QM/MM-GBSA and MM/GB(PB)SA methods suggested that the susceptibility towards HBV-RT of d4T and ZDV is higher than that of 3TC and dTTP. Altogether, this work sheds light on the potentiality of d4T and ZDV as a promising drug for HBV-infected patients harboring 3TC resistance. Communicated by Ramaswamy H. Sarma

Background: Neuraminidase (NA), a major glycoprotein found on the surface of the influenza virus, is an important target for the prophylaxis and treatment of influenza virus infections. Recently, several plant-derived polyphenols, especially caffeic acid analogs, have been reported to exert the inhibitory activity against NA. Objective: Herein, we aimed to investigate the anti-influenza NA activity of caffeic acid and its hydroxycinnamate analogues, rosmarinic acid and salvianolic acid A, in comparison to a known NA inhibitor, oseltamivir. Methods: In vitro MUNANA-based NA inhibitory assay was used to evaluate the inhibitory activity of the three interested hydroxycinnamic compounds towards the influenza NA enzyme. Subsequently, allatom molecular dynamics (MD) simulations and binding free energy calculations were employed to elucidate the structural insights into the protein-ligand complexations. Results: Rosmarinic acid showed the highest inhibitory activity against NA with the IC50 of 0.40 μM compared to caffeic acid (IC50 of 0.81 μM) and salvianolic acid A (IC50 of >1 μM). From 100-ns MD simulations, the binding affinity, hot-spot residues, and H-bond formations of rosmarinic acid/NA complex were higher than those of caffeic acid/NA model, in which their molecular complexations was driven mainly by electrostatic attractions and H-bond formations from several charged residues (R118, E119, D151, R152, E227, E277, and R371). Notably, the two hydroxyl groups on both phenyl and phenylacetic rings of rosmarinic acid play a crucial role in stabilizing NA through a strongly formed Hbond( s). Conclusion: Our findings shed light on the potentiality of rosmarinic acid as a lead compound for further development of a potential influenza NA inhibitor.

Drug target prediction is an important method for drug discovery and design, can disclose the potential inhibitory effect of active compounds, and is particularly relevant to many diseases that have the potential to kill, such as dengue, but lack any healing agent. An antiviral drug is urgently required for dengue treatment. Some potential antiviral agents are still in the process of drug discovery, but the development of more effective active molecules is in critical demand. Herein, we aimed to provide an efficient technique for target prediction using homopharma and network-based methods, which is reliable and expeditious to hunt for the possible human targets of three phenolic lipids (anarcardic acid, cardol, and cardanol) related to dengue viral (DENV) infection as a case study. Using several databases, the similarity search and network-based analyses were applied on the three phenolic lipids resulting in the identification of seven possible targets as follows. Based on protein annotation, three phenolic lipids may interrupt or disturb the human proteins, namely KAT5, GAPDH, ACTB, and HSP90AA1, whose biological functions have been previously reported to be involved with viruses in the family Flaviviridae. In addition, these phenolic lipids might inhibit the mechanism of the viral proteins: NS3, NS5, and E proteins. The DENV and human proteins obtained from this study could be potential targets for further molecular optimization on compounds with a phenolic lipid core structure in anti-dengue drug discovery. As such, this pipeline could be a valuable tool to identify possible targets of active compounds.

Human carbonic anhydrase isozyme II has been used as protein target for disorder treatment including glaucoma. Current clinically used sulfonamide-based CA inhibitors can induce side effects, and so alternatives are required. This study aimed to investigate a natural CA inhibitor from

&alpha, Mangostin (MGS) exhibits various pharmacological activities, including antioxidant, anticancer, antibacterial, and anti-inflammatory properties. However, its low water solubility is the major obstacle for its use in pharmaceutical applications. To increase the water solubility of MGS, complex formation with beta-cyclodextrins (&beta, CDs), particularly with the native &beta, CD and/or its derivative 2,6-dimethyl-&beta, CD (DM&beta, CD) is a promising technique. Although there have been several reports on the adsorption of &beta, CDs on the lipid bilayer, the release of the MGS/&beta, CDs inclusion complex through the biological membrane remains unclear. In this present study, the release the MGS from the two different &beta, CDs (&beta, CD and DM&beta, CD) across the lipid bilayer was investigated. Firstly, the adsorption of the free MGS, free &beta, CDs, and inclusion complex formation was studied by conventional molecular dynamics simulation. The MGS in complex with those two &beta, CDs was able to spontaneously release free MGS into the inner membrane. However, both MGS and DM&beta, CD molecules potentially permeated into the deeper region of the interior membrane, whereas &beta, CD only adsorbed at the outer membrane surface. The interaction between secondary rim of &beta, CD and the 1-palmitoeyl-2-oleoyl-glycero-3-phosphocholine (POPC) phosphate groups showed the highest number of hydrogen bonds (up to 14) corresponding to the favorable location of &beta, CD on the POPC membrane. Additionally, the findings suggested that electrostatic energy was the main driving force for &beta, CD adsorption on the POPC membrane, while van der Waals interactions played a predominant role in DM&beta, CD adsorption. The release profile of MGS from the &beta, CDs pocket across the lipid bilayer exhibited two energy minima along the reaction coordinate associated with the permeation of the MGS molecule into the deeper region of the POPC membrane.

Janus kinases (JAKs) are enzymes involved in signaling pathways that affect hematopoiesis and immune cell functions. JAK1, JAK2, and JAK3 play different roles in numerous diseases of the immune system and have also been considered as potential targets for cancer therapy. In the present study, the susceptibility of the oral JAK inhibitor tofacitinib against these three JAKs was elucidated using the 500-ns molecular dynamics (MD) simulations and free energy calculations based on MM-PB(GB)SA, QM/MM-GBSA (PM3 and SCC-DFTB), and SIE methods. The obtained results revealed that tofacitinib could interact with all JAKs at the ATP-binding site via electrostatic attraction, hydrogen bond formation, and in particular van der Waals interaction. The conserved glutamate and leucine residues (E957 and L959 of JAK1, E930 and L932 of JAK2, and E903 and L905 of JAK3) located in the hinge region stabilized tofacitinib binding through strongly formed hydrogen bonds. Complexation with the incoming tofacitinib led to a closed conformation of the ATP-binding site and a decreased protein fluctuation at the glycine loop of the JAK protein. The binding affinities of tofacitinib/JAKs were ranked in the order of JAK3 > JAK2 ∼ JAK1, which are in line with the reported experimental data.

Polyethylene vanillic (PEV), a bio-based material, has mechanical and thermal properties similar to polyethylene terephthalate (PET), the most common polymer used in industries. The present study aimed to investigate and compare their structural dynamics and physical data using a computational approach. The simple model of a single-chain polymer containing 100 repeating units was performed by all-atom molecular dynamics (MD) simulations with refined OPLS–AA force field parameters. As a result, the flexibility of the PEV structure was greater than that of PET. PET and PEV polymers had the predicted glass transition temperature Tg values of approximately 345 K and 353 K, respectively. PEV showed a slightly higher Tg than PET, consistent with current experimental evidence.

Outbreak of influenza virus is one of serious concerns for public health. Hemagglutinin (HA), a spike-shaped glycoprotein on the viral surface, plays an important role during the early stage of influenza infection. In the present work, a set of flavonoids were screened against 2009 H1N1 HA by computational chemistry techniques. Among 35 flavonoids, the docking results showed that the epicatechin gallate (ECG) and puerarin exhibited a good binding affinity towards 2009 H1N1 HA. These 2 compounds were then studied by all-atom molecular dynamics (MD) simulations. The predicted binding free energy of the H1-puerarin complex (–25.86 ± 2.92 kcal/mol) was slightly greater than that of H1-ECG (–22.81 ± 2.19 kcal/mol), suggesting that the puerarin and ECG could provide similar binding affinity towards 2009 H1 HA target. However, the stronger electrostatic energy contribution of ~10 kcal/mol was found in the puerarin binding to 2009 H1N1 HA. This molecular information of ligand-protein interaction could be helpful in further drug design and development for influenza treatment. HIGHLIGHTS The 35 flavonoid bioactive compounds were screened against 2009 H1N1 HA by molecular docking The epicatechin gallate (ECG) and puerarin exhibited a good binding affinity and were then studied by all-atom molecular dynamics (MD) simulations The predicted binding free energy revealed that the puerarin and ECG could provide similar binding affinity towards 2009 H1 HA target GRAPHICAL ABSTRACT

Emodin (ED), one prominent variant of naturally occurring anthraquinones traditionally used in Chinese medicine, exhibits a wide spectrum of pharmacological properties. However, the poor aqueous solubility of ED limits its significant usage in practical applications. β-cyclodextrin (βCD) and its derivatives have been extensively utilized to enhance the water solubility and stability of lipophilic guest molecules by acting as a molecular shield through host-guest encapsulation. In this work, the structural dynamics details of inclusion complexation of ED with βCD and its two derivatives: 2-hydroxypropyl-β-cyclodextrin (HPβCD) and sulfobutylether-β-cyclodextrin (SBEβCD), were studied using all-atom molecular dynamics (MD) simulations and molecular mechanics/generalized Born surface area (MM/GBSA)-based binding free energy (ΔGbind) calculations. The 500-ns MD simulations revealed that ED is able to form inclusion complexes with βCDs in two possible orientations: resorcinol ring insertion (R-form) and m-cresol ring insertion (C-form) mainly driven by van der Waals interaction. The ED/SBEβCD inclusion complex showed the highest number of atom contacts and the lowest solvent accessibility at the hydrophobic cavity, in line with the ΔGbind results ranked in the order of ED/SBEβCD (−6.18 ± 1.15 kcal/mol) > ED/HPβCD (−3.81 ± 0.65 kcal/mol) > ED/βCD (0.11 ± 0.51 kcal/mol). All findings suggested that βCD derivatives, especially SBEβCD, could be the appropriate host for ED in the potential development of ED into pharmaceutical applications.

This study reports UV–Visible spectra and electronic structures of indigo (IG) in aqueous solution using a combination of experimental and theoretical methods. In the visible region, the experimental absorption spectrum of the solution showed a broad peak with the longest wavelength of maximal absorption (λmax) value at 708 nm. For the theoretical method, a trans-IG monomer and a trans-IG bound with two water molecules (IG.2W) were optimized in the ground state using the B3LYP and B3LYP-D3 calculations with the 6-31 + G(d,p) basis set and the SCRF-CPCM model for taking solvent effect into account was also applied. Sequentially, the UV–Visible spectra and λmax of the optimized trans-IG and IG.2W models in the implicit water were simulated by the time-dependent density functional theory (TD-DFT) calculations. The TD-DFT methods including BLYP, B3LYP, PBE0, CAM-B3LYP, M06-2X, ωB97XD, LC-BLYP, and LC-ωPBE functionals without and with the D3 correction and the 6-31 + G(d,p) basis set were selected. The results pointed out that BLYP and BLYP-D3 were the best methods because they could reproduce the experimental λmax value of IG in aqueous solution. The predicted λmax values of IG.2W were almost equal to 708 nm (the experimental data), indicating that IG.2W could be responsible for optical properties of IG.

Genistein is an isoflavone with promising pharmaceutical applications. However, its low water solubility interferes with its potency, and therefore cyclodextrins (CDs) have been considered as possible drug delivery system (DDS). To investigate the complexation mechanism of genistein in cyclodextrin, we employed molecular dynamics (MD) simulations based on classical potentials and the density-functional tight-binding (DFTB) quantum chemical potential. Both classical and quantum chemical MD simulations predict that the phenol ring of genistein is preferentially complexed in the cavity of CD. The complexation process reduces the water-accessible solvation shell, and it is found that a hydrogen bond is formed between genistein and CD. The DFTB-based MD simulations reveal that spontaneous keto-enol tautomerization occurs even within a hundred picoseconds, which suggests that the encapsulated genistein is complexed in the ordinary enol form of the drug molecule. Analyses of the molecular charge distributions suggest that electrostatic interactions partially induce the complex formation, rather than extensive formation of hydrogen bonds.

Daidzein is an isoflavone of the group of phytoestrogens extracted from soybeans and other legumes. As its structure is relatively similar to that of the hormone estrogen, daidzein is able to bind with estrogen receptors leading to a reduced postmenopausal women symptom. A common problem of the compounds of this group is the rather low water solubility with the consequence of limited pharmaceutical applications. Inclusion complexation between daidzein and two β-CDs (β-CD and DM-β-CD) was investigated by theoretical and experimental techniques. Based on multiple MD simulations in combination with different binding-free energy calculations, the most preferential mode of daidzein binding to cyclodextrins is the insertion of the chromone ring fitting well into the hydrophobic cavity. All four methods of binding-free energy calculations (MM/PBSA, MM/GBSA, QM/PBSA, and QM/GBSA) predict the binding affinity of the daidzein/DM-β-CD complex significantly higher than the daidzein/β-CD. Following the same trend, the experimental results also indicated the enhancement of solubility and stability of the daidzein/DM-β-CD complex. Moreover, it was found that the complexation process was favorably enthalpy driven.

Cancer stem cells (CSCs) are unique populations of cells that can self-renew and generate different cancer cell lineages. Although CSCs are believed to be a promising target for novel therapies, the specific mechanisms by which these putative therapeutics could intervene are less clear. Nitric oxide (NO) is a biological mediator frequently up-regulated in tumors and has been linked to cancer aggressiveness. Here, we search for targets of NO that could explain its activity. We find that it directly affects the stability and function of octamer-binding transcription factor 4 (Oct4), known to drive the stemness of lung cancer cells. We demonstrated that NO promotes the CSC-regulatory activity of Oct4 through a mechanism that involves complex formation between Oct4 and the scaffolding protein caveolin-1 (Cav-1). In the absence of NO, Oct4 forms a molecular complex with Cav-1, which promotes the ubiquitin-mediated proteasomal degradation of Oct4. NO promotes Akt-dependent phosphorylation of Cav-1 at tyrosine 14, disrupting the Cav-1:Oct4 complex. Site-directed mutagenesis and computational modeling studies revealed that the hydroxyl moiety at tyrosine 14 of Cav-1 is crucial for its interaction with Oct4. Both removal of the hydroxyl via mutation to phenylalanine and phosphorylation lead to an increase in binding free energy (ΔG(bind)) between Oct4 and Cav-1, destabilizing the complex. Together, these results unveiled a novel mechanism of CSC regulation through NO-mediated stabilization of Oct4, a key stem cell transcription factor, and point to new opportunities to design CSC-related therapeutics.

This work systematically investigates a discrepancy in photocatalytic degradation pathway observed even when same kind of photocatalyst is used. This issue is particularly important for the degradation of toxic compound because the shifting in the pathway may result in intermediates having increased toxicity. Linuron, which is a toxic herbicide, is used as a model compound and zinc oxide (ZnO) is used as a catalyst. Two forms of ZnO having different exposing surfaces, i.e., conventional particles and nanorods are considered. It is experimentally shown and confirmed by molecular simulation that the adsorption and subsequent degradation are surface dependent. The adsorption capacity of linuron on polar surfaces of ZnO is much higher than that on non-polar surface. More importantly, alignments of linuron molecule adsorbing on different surfaces are different, leading to formation of different degradation intermediates. The degradation takes place on both aliphatic and aromatic sides when linuron adsorbs on polar surfaces whereas only the aliphatic part is attacked by hydroxyl radicals on the non-polar mixed terminated surface. The results in this work indicate that the exposing surface of the photocatalyst is the key factor in determining the degradation pathway and it should be considered in the catalyst design.

The structural dynamics and stability of inclusion complexes of mansonone E (ME) and H (MH) including their stereoisomers with various βCDs (methylated- and hydroxypropylated-βCDs) were investigated by classical molecular dynamics (MD) simulations and binding free energy calculations. The simulation results revealed that mansonones are able to form inclusion complexes with βCDs. The guest molecules are not completely inserted into the host cavity, their preferably positions are nearby the secondary rim with the oxane ring dipping into the hydrophobic inner cavity. The encapsulation process leads to a higher rigidity of the βCDs enhancing the intramolecular hydrogen bond formation ability and decreasing the chance of glucopyranose rotation. According to the MM-PBSA binding free energy calculation, all considered inclusion complexes are stable and the binding energies are mainly caused by van der Waals interactions. Moreover, the free energy calculations showed significant differences in the complexation energies for the stereoisomers, which could enable the separation of the isomers by analytical techniques for further pharmaceutical applications.

Atomistic molecular dynamics (MD) simulation of the inclusion complexes formation between scandenin, a phytochemical compound found in D. scandens, and five different types of cyclodextrin (CD); β-cyclodextrin (βCD), 2-hydroxypropyl βCD (2-HPβCD), 6-hydroxypropyl βCD (6-HPβCD), 2,6-dimethyl βCD (2,6-DMβCD), and 2,6-dihydroxypropyl βCD (2,6-DHPβCD) were carried out via two possible orientations of the guest molecule. The simulated results revealed that scandenin preferentially located within all the studied βCDs nanocavities by inserting its hydroxyphenyl ring and pyran terminal close to the narrow and wider rims (conf-A), respectively. In another feasible orientation (conf-B), the guest substance was deeply included into the lipophilic cavity of only 6-HPβCD and 2,6-DMβCD, but not in the other cyclodextrins. The favored inclusion formation of scandenin/2,6-DHPβCD occurred when the guest interpolated its hydroxyphenyl terminal into CD hydrophobic interior. Binding free energy calculation based on the MM-PBSA approach indicated that the modified βCDs (except for 2,6-DHPβCD) showed the stronger binding affinity to scandenin than did the parent host molecule. The results could help in selecting suitable βCD derivatives to enhance the stability of such guest molecules prior to in vitro testing.

α-Tocopherol is the most biologically active form of vitamin E (VE) exhibiting various biological activities such as strong antioxidant activity, antitumor properties and antiaging effects. However, the low water solubility of α-tocopherol has limited its prospective use in food, cosmetic and pharmaceutical industry. One of the promising strategies to tackle such issue is the use of a supramolecular complex with cyclodextrins (CDs). In this study, the encapsulation of α-tocopherol with six different initial un-complexed states into the large-ring CD containing 26 α-D-glucopyranose units (CD26) was studied by means of 400-ns molecular dynamics (MD) simulations to investigate their host–guest association process and the preferential binding efficiency upon complexation at low concentration of α-tocopherol. The MD results show that α-tocopherol spontaneously interacted with CD26 within 20 ns and formed a stable inclusion complex during 150–400 ns. From all six independent simulations, the inclusion complexes can be divided into two groups, which were fully and partly encapsulated inside the cavity of CD26. The α-tocopherol of the first group was covered by 13–14 subunits of CD26, while α-tocopherol in another group was attached by 6–10 subunits of CD26. In addition, α-tocopherol was surrounded by one- or two-turn helix of one half-ring of CD26, leaving the rest of cavities for forming complexation with a larger number of α-tocopherol molecules. Therefore, CD26 can be used as a solubility and stability enhancer for α-tocopherol through inclusion complexation.

2-Acetyl-1-pyrroline (2AP) is a key volatile compound contributing to a characteristic popcorn-like odor in several Asian aromatic rice varieties. Even though a demand for 2AP has been continuously increasing in global markets, its instability is a significant problem for commercial and food applications. Beta-cyclodextrin (βCD) has been extensively used to improve the stability, solubility, and sensorial properties of many hydrophobic and volatile compounds via an encapsulation process into its hydrophobic inner cavity. In this work, molecular complexation between 2AP and βCDs (hydroxypropyl (HP) and methyl (M) analogs) was theoretically and experimentally investigated using molecular dynamics (MD) simulation, molecular mechanics/generalized Born surface area-based free energy calculation, and gas chromatography–mass spectrometry (GC–MS). Triplicate 500 ns MD simulations revealed that, among six studied βCDs, only 6-HPβCD and 2,6-DMβCD derivatives could stably form inclusion complexes with 2AP, driven mainly by van der Waals interactions. The pyrroline ring of 2AP was preferentially embedded in the hydrophobic interior of 2,6-DMβCD, whereas the pyrroline and acetyl moieties of 2AP were freely rotated inside 6-HPβCD along the simulation times. The binding affinity, the compactness, and the number of atomic contacts of 2AP/2,6-DMβCD complex were higher than those of 2AP/6-HPβCD system, in good agreement with the highest remaining 2AP in the 2AP/2,6-DMβCD complex from GC–MS result. Altogether, the obtained theoretical and experimental data demonstrated the good potentiality of 2,6-DMβCD as suitable host molecule for 2AP encapsulation.

The water solubility of domperidone (DMP) could be improved by complexation with large ring cyclodextrins (LR-CDs). LR-CDs contain a relatively hydrophobic cavity that is capable of entrapping the molecules to form inclusion complexes. The complex formation capability of mixture LR-CDs having a degree of polymerization (DP) of 22–48, with DMP was investigated. The phase solubility profile of mixture LR-CD/DMP was classified as AN-type, resulting in increased DMP solubility in water by 3-fold. Various physicochemical techniques confirmed the mixture LR-CD/DMP complex formation. Single LR-CD with DP of 26, 27, 28, 29, 30, 33 and 34 (CD26 ~ CD34) were isolated from LR-CD mixtures using ODS column for HPLC separation. The CD33/DMP complex has demonstrated the most significant improvement compared to other single LR-CD complexes with a 2.7-fold increase in DMP solubility. The molecular dynamic result revealed that DMP formed stable complexes with CD33 by positioned fully encapsulated inside the cavity and covered by 13–14 subunits of CD33.

Several quinone-based metabolites of anticancer drugs and naturally occurring quinone-containing compounds have been characterized as potent inhibitors toward topoisomerase IIα (TopoIIα), an essential enzyme involved in maintaining genomic integrity during DNA replication and mitotic division. Mansonone G (MG), a naphthoquinone-containing compound extracted from the heartwood of Mansonia gagei , exhibits various biological activities including antitumor potential. In the present study, MG and its semi-synthetic derivatives were selected to study the preferential binding site and dynamics behavior as well as to predict the inhibitory activity against TopoIIα using molecular modeling approaches. The molecular docking results revealed that the entire series of MG preferentially target to the ATPase domain. Among all studied MGs, the ester derivative MG14 containing C-10 length exhibited the highest binding affinity against TopoIIα and greater than that of the ATP-competitive inhibitor salvicine as well as 1,4-benzoquinone. Interestingly, the MG14 binding could induce the closed form of the turn region (residues 147–151) inside ATP-binding pocket, implying that this event might be one of the crucial mechanisms underlying TopoIIα inhibition. The obtained theoretical information is useful as rational guide for further development of new anticancer agents containing naphthoquinone moiety against TopoIIα.

Enzyme I (EI) of bacterial phosphotransferase system is involved in the first step of the carbohydrate metabolism pathway. Due to its importance in bacterial survival and low similarity with human proteins, EI is an attractive drug target. With the aid of Computer Aided Drug Designing tools, we studied EI of Staphylococcus epidermidis, which recently adopted itself as a major etiological agent in discerning the cause of multi-drug resistant nosocomial infections of implanted medical devices. Due to a non-existent crystal structure, a high quality homology model of EI is predicted. Molecular docking analysis of potential inhibitors into the active site of the protein is performed and the best inhibitor is selected with according to the highest GoldScore (76.53). The protein-ligand complex was conducted through a 100 ns MD simulation. The trajectory analysis reveals that the N-terminal domain (EIN) and the P-His domain residues exhibited the greatest conformational changes while the active site shows minimum residual fluctuations and is considered as the most stable domain. The rigid body motions of EIN and P-His domain are recorded to be at their highest during the 35th and 83rd ns with highest RMSD values. Despite the highly flexible ‘personality’ of EI, the ligand remains tightly associated with the active site residues. The current lead compound holds potential as an effective drug against S. epidermidis which could be further tested in clinical settings. The dynamic nature of EI disclosed via MD simulation, can be further explored to understand the molecular kinetics of chemical reactions involved in the dedicated role of the protein would assist in better design of drugs in future.

The electronic properties of single-walled carbon nanotubes (SWCNTs) can be modified by deforming their structure under high pressure. The aim of this study was to use quantum calculations to investigate one such property, the energy band gap, in relation to molecular structures of armchair and zigzag SWCNTs of various sizes and shapes deformed by applied forces. To model the increase in pressure, the degree of flatness (η) of the SWCNTs was adjusted as the primary parameter. The calculations gave accurate C-C bond lengths of the SWCNTs in their distorted states; these distortions significantly affected the electronic properties, especially the energy band gap of the SWCNTs. These results may contribute to a more refined design of new nano-electronic devices.

The inclusion complexation of neral, a cis-isomer of citral found in lemon grass (Cymbopogon citratus Stapf), and four different types of cyclodextrin (β-cyclodextrin (βCD), 2,6-dimethyl-βCD (2,6DM...

Density functional theory (DFT) calculations have been carried out to investigate the ethylene insertion pathway using a Ziegler-Natta catalyst in the absence and presence of electron donor (ED) systems on the (1 1 0) MgCl 2 surface. The coadsorptions of four different EDs i.e. Si(OEt) m Cl n ( m + n = 4) were investigated. The presence of Si(OEt) 4 on the (1 1 0) MgCl 2 surface with the preferential bidentate mode was found to have the strongest adsorption energy (Δ E ads ). The potential energy surface (PES) map indicated that the reaction mechanism of the ethylene insertion into the Ti C bond on the (1 1 0) Mg 13 Cl 26 .TiCl 3 -CH 2 CH 3 surface is pseudo-concerted. As the differences in the intrinsic activation energies (Δ E a ) obtained from all systems are so small, this energy cannot be used to fully explain the significant changes in the rates of the ethylene insertion reaction observed when an ED is employed. Here, the apparent activation energy (ΔΔ E aa ) was calculated using the PBE functional and the 6-31G(d, p) basis set for C, H, O, Mg and Cl, and the LANL2DZ basis set with an ECP function for the Ti atom. All EDs presented in this work in the ethylene insertion reaction can significantly reduce the apparent energy barrier when compared to an absence of any ED system. The obtained ΔΔ E aa for the four ED complexes were found to decrease in the following order: SiOEtCl 3 > Si(OEt) 2 Cl 2 > Si(OEt) 3 Cl > Si(OEt) 4 . The obtained data lead to the conclusion that Si(OEt) 4 is the most suitable ED to increase the productivity of PE in the presence of alkoxysilane.

Avicequinone C (5a), a furanonaphthoquinone isolated from the Thai mangrove Avicennia marina has been shown previously to have interesting steroid 5α-reductase type 1 inhibitory activity. In this study, a series of avicequinone C analogues containing furanonaphthoquinone with different degrees of saturation and substituents at the furan ring were synthesized. The resulting synthetic avicequinone C and analogues (5a-f) along with some related compounds including 2,5-dihydroxy-1,4-benzoquinone (6) and natural naphthoquinones such as lawsone (7a) and lapachol (7b) were evaluated for their in vitro cell viability and steroid 5α-reductase type 1 inhibitory activities using the cultured cell line of human keratinocytes (HaCaT). This cell-based bioassay was performed based on a direct detection of the enzymatic product dihydrotestosterone (2) by using a non-radioactive high performance thin layer chromatography (HPTLC) method. Among the furanonaphthoquinones in this series, 5e having a propionic substituent at furan ring possessed approximately 22-fold more potent than the original isolated compound 5a. However, the compounds without furan motif such as 6, 7a and b could not inhibit the activity of steroid 5α-reductase. Molecular docking results of the in silico three-dimensional steroid 5α-reductase type 1-reduced nicotinamide adenine dinucleotide phosphate (NADPH) binary complex was performed via AutoDock Vina and it illustrated that the furanonaphthoquinone moiety and the substituent at furan ring might play a key role as pharmacophores for the steroid 5α-reductase inhibitory activity.

The human T1R2-T1R3 sweet taste receptor (STR) plays an important role in recognizing various low-molecular-weight sweet-tasting sugars and proteins, resulting in the release of intracellular heterotrimeric G protein that in turn leads to the sweet taste perception. Xylitol and sorbitol, which are naturally occurring sugar alcohols (polyols) found in many fruits and vegetables, exhibit the potential caries-reducing effect and are widely used for diabetic patients as low-calorie sweeteners. In the present study, computational tools were applied to investigate the structural details of binary complexes formed between these two polyols and the T1R2-T1R3 heterodimeric STR. Principal component analysis revealed that the Venus flytrap domain (VFD) of T1R2 monomer was adapted by the induced-fit mechanism to accommodate the focused polyols, in which α-helical residues 233-268 moved significantly closer to stabilize ligands. This finding likely suggested that these structural transformations might be the important mechanisms underlying polyols-STR recognitions. The calculated free energies also supported the VFD of T1R2 monomer as the preferential binding site for such polyols, rather than T1R3 region, in accord with the lower number of accessible water molecules in the T1R2 pocket. The E302 amino acid residue in T1R2 was found to be the important recognition residue for polyols binding through a strongly formed hydrogen bond. Additionally, the binding affinity of xylitol toward the T1R2 monomer was significantly higher than that of sorbitol, making it a sweeter tasting molecule.

Mansonone G (MG), a plant-derived compound isolated from the heartwood of Mansonia gagei, possesses a potent antitumor effect on several kinds of malignancy. However, its poor solubility limits the use for practical applications. Beta-cyclodextrin (&beta, CD), a cyclic oligosaccharide composed of seven (1&rarr, 4)-linked &alpha, D-glucopyranose units, is capable of encapsulating a variety of poorly soluble compounds into its hydrophobic interior. In this work, we aimed to enhance the water solubility and the anticancer activity of MG by complexation with &beta, CD and its derivatives (2,6-di-O-methyl-&beta, CD (DM&beta, CD) and hydroxypropyl-&beta, CD). The 90-ns molecular dynamics simulations and MM/GBSA-based binding free energy results suggested that DM&beta, CD was the most preferential host molecule for MG inclusion complexation. The inclusion complex formation between MG and &beta, CD(s) was confirmed by DSC and SEM techniques. Notably, the MG/&beta, CDs inclusion complexes exerted significantly higher cytotoxic effect (2&ndash, 7 fold) on A549 lung cancer cells than the uncomplexed MG.

The human T1R2-T1R3 sweet taste receptor (STR) plays an important role in recognizing various low-molecular-weight sweet-tasting sugars and proteins, resulting in the release of intracellular heterotrimeric G protein that in turn leads to the sweet taste perception. Xylitol and sorbitol, which are naturally occurring sugar alcohols (polyols) found in many fruits and vegetables, exhibit the potential caries-reducing effect and are widely used for diabetic patients as low-calorie sweeteners. In the present study, computational tools were applied to investigate the structural details of binary complexes formed between these two polyols and the T1R2-T1R3 heterodimeric STR. Principal component analysis revealed that the Venus flytrap domain (VFD) of T1R2 monomer was adapted by the induced-fit mechanism to accommodate the focused polyols, in which residues 233–268 moved significantly closer to stabilize ligands. This finding likely suggested that these structural transformations might be the important mechanisms underlying polyols-STR recognitions. The calculated free energies also supported the VFD of T1R2 monomer as the preferential binding site for such polyols, rather than T1R3 region, in accord with the lower number of accessible water molecules in the T1R2 pocket. The E302 amino acid residue in T1R2 was found to be the important recognition residue for polyols binding through a strongly formed hydrogen bond. Additionally, the binding affinity of xylitol toward the T1R2 monomer was significantly higher than that of sorbitol, making it a sweeter tasting molecule.

Zika virus (ZIKV) infection has become a global public health problem, associated with microcephaly in newborns and Guillain-Barre syndrome in adults. Currently, there are no commercially available anti-ZIKV drugs. The viral protease NS2B/NS3, which is involved in viral replication and maturation, is a potential drug target. Peptidomimetic aldehyde inhibitors bind covalently to the catalytic S135 of the NS3 protease. Here, we apply hybrid quantum mechanics/molecular mechanics (QM/MM) free-energy simulations at the PDDG-PM3/ff14SB level to investigate the inhibition mechanism of the ZIKV protease by a dipeptidyl aldehyde inhibitor (acyl-KR-aldehyde). The results show that proton transfer from the catalytic S135 to H51 occurs in concert with nucleophilic addition on the aldehyde warhead by S135. The anionic covalent complex between the dipeptidyl aldehyde and the ZIKV protease is analogous to the tetrahedral intermediate for substrate hydrolysis. Spontaneous protonation by H51 forms the hemiacetal. In addition, we use correlated ab initio QM/MM potential energy path calculations at levels up to LCCSD(T)/(aug)-cc-pVTZ to obtain accurate potential energy profiles of the reaction, which also support a concerted mechanism. These results provide detailed insight into the mechanism of ZIKV protease inhibition by a peptidyl aldehyde inhibitor, which will guide in the design of inhibitors.

Human cytosolic serine hydroxymethyltransferase (hcSHMT) is a promising target for anticancer chemotherapy and contains a flexible “flap motif” whose function is yet unknown. Here, using size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and ligand-binding and enzyme-kinetic analyses, we studied the functional roles of the flap motif by comparing WT hcSHMT with a flap-deleted variant (hcSHMT/Δflap). We found that deletion of the flap results in a mixture of apo-dimers and holo-tetramers, whereas the WT was mostly in the tetrameric form. MD simulations indicated that the flap stabilizes structural compactness and thereby enhances oligomerization. The hcSHMT/Δflap variant exhibited different catalytic properties in (6S)-tetrahydrofolate (THF)-dependent reactions compared with the WT but had similar activity in THF-independent aldol cleavage of β-hydroxyamino acid. hcSHMT/Δflap was less sensitive to THF inhibition than the WT (K(i) of 0.65 and 0.27 mm THF at pH 7.5, respectively), and the THF dissociation constant of the WT was also 3-fold lower than that of hcSHMT/Δflap, indicating that the flap is important for THF binding. hcSHMT/Δflap did not display the burst kinetics observed in the WT. These results indicate that, upon removal of the flap, product release is no longer the rate-limiting step, implying that the flap is important for controlling product release. The findings reported here improve our understanding of the functional roles of the flap motif in hcSHMT and provide fundamental insight into how a flexible loop can be involved in controlling the enzymatic reactions of hcSHMT and other enzymes.

Targeted cancer therapy has become a high potential cancer treatment. Epidermal growth factor receptor (EGFR), which plays an important role in cell signaling, enhanced cell survival and proliferation, has been suggested as molecular target for the development of novel cancer therapeutics. In this study, a series of chalcone derivatives was screened by in vitro cytotoxicity against the wild type (A431 and A549) and mutant EGFR (H1975 and H1650) cancer cell lines, and, subsequently, tested for EGFR-tyrosine kinase (TK) inhibition. From the experimental screening, all chalcones seemed to be more active against the A431 than the A549 cell line, with chalcones 1c, 2a, 3e, 4e, and 4t showing a more than 50% inhibitory activity against the EGFR-TK activity and a high cytotoxicity with IC50 values of &lt, 10 &micro, M against A431 cells. Moreover, these five chalcones showed more potent on H1975 (T790M/L858R mutation) than H1650 (exon 19 deletion E746-A750) cell lines. Only three chalcones (1c, 2a and 3e) had an inhibitory activity against EGFR-TK with a relative inhibition percentage that was close to the approved drug, erlotinib. Molecular dynamics studies on their complexes with EGFR-TK domain in aqueous solution affirmed that they were well-occupied within the ATP binding site and strongly interacted with seven hydrophobic residues, including the important hinge region residue M793. From the above information, as well as ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties, all three chalcones could serve as lead compounds for the development of EGFR-TK inhibitors.

Epidermal growth factor receptor (EGFR) is the key molecular target for non-small cell lung cancer (NSCLC) due to its major contribution to complex signaling cascades modulating the survival of cancer cells. Targeting EGFR-mediated signaling pathways has been proved as a potential strategy for NSCLC treatment. In the present study, mansonone G (MG), a naturally occurring quinone-containing compound, and its semi-synthetic ether derivatives were subjected to investigate the anticancer effects on human NSCLC cell lines expressing wild-type EGFR (A549) and mutant EGFR (H1975). In vitro cytotoxicity screening results demonstrated that butoxy MG (MG3) exhibits the potent cytotoxic effect on both A549 (IC50 of 8.54 &mu, M) and H1975 (IC50 of 4.21 &mu, M) NSCLC cell lines with low toxicity against PCS201-010 normal fibroblast cells (IC50 of 21.16 &mu, M). Western blotting and flow cytometric analyses revealed that MG3 induces a caspase-dependent apoptosis mechanism through: (i) inhibition of p-STAT3 and p-Akt without affecting upstream p-EGFR and (ii) activation of p-Erk. The 500-ns molecular dynamics simulations and the molecular mechanics combined with generalized Born surface area (MM/GBSA)-based binding free energy calculations suggested that MG3 could possibly interact with STAT3 SH2 domain and ATP-binding pocket of Akt. According to principal component analysis, the binding of MG3 toward STAT3 and Akt dramatically altered the conformation of proteins, especially the residues in the active site, stabilizing MG3 mainly through van der Waals interactions.

Secretory diarrhea is one of the most common causes of death world-wide especially in children under 5 years old. Isoliquiritigenin (ISLQ), a plant-derived chalcone, has previously been shown to exert anti-secretory action in vitro and in vivo by inhibiting CFTR Cl− channels. However, its CFTR inhibition potency is considerably low (IC50 > 10 μM) with unknown mechanism of action. This study aimed to identify novel chalcone derivatives with improved potency and explore their mechanism of action. Screening of 27 chalcone derivatives identified CHAL-025 as the most potent chalcone analog that reversibly inhibited CFTR-mediated Cl− secretion in T84 cells with an IC50 of ∼1.5 μM. As analyzed by electrophysiological and biochemical analyses, the mechanism of CFTR inhibition by CHAL-025 is through AMP-activated protein kinase (AMPK), a negative regulator of CFTR activity. Furthermore, Western blot analyses and molecular dynamics (MD) results suggest that CHAL-025 activates AMPK by binding at the allosteric site of an upstream kinase calcium/calmodulin-dependent protein kinase kinase β (CaMKKβ). Interestingly, CHAL-025 inhibited both cholera toxin (CT) and bile acid-induced Cl− secretion in T84 cells and prevented CT-induced intestinal fluid secretion in mice. Therefore, CHAL-025 represents a promising anti-diarrheal agent that inhibits CFTR Cl− channel activity via CaMKKβ-AMPK pathways. Keywords: Diarrhea, CFTR, Chalcone, AMPK, Chloride secretion

2-Hydroxypropyl-β-cyclodextrin (HPβCD) has unique properties to enhance the stability and the solubility of low water-soluble compounds by inclusion complexation. Understanding of the structural properties of HPβCD and its derivatives based on the number of 2-hydroxypropyl (HP) substituents at the a-D-glucopyranose subunits is rather important. In this work, replica exchange molecular dynamics simulations were performed to investigate the conformational changes of single- and double-sided HP-substitution called as 6-HPβCDs and 2,6-HPβCDs, respectively. The results show that glucose subunits in both 6-HPβCDs and 2,6-HPβCDs have lower chance to flip than in βCD. Also, HP groups are occasionally blocking the hydrophobic cavity of HPβCDs, thus hindering the drug inclusion. We found that HPβCDs with high number of HP-substitutions are more likely to be blocked, while HPβCDs with double-sided HP-substitution are even more probable to be blocked. Overall, 6-HPβCDs with three and four HP-substitutions are highlighted as the most suitable structures for guest encapsulation based on our conformational analyses such as structural distortion, radius of gyration, circularity and cavity self-closure of the HPβCDs.

Dengue infection is caused by a mosquito-borne virus, particularly in children, which may even cause death. No effective prevention or therapeutic agents to cure this disease are available up to now. The dengue viral envelope (E) protein was discovered to be a promising target for inhibition in several steps of viral infection. Structure-based virtual screening has become an important technique to identify first hits in a drug screening process, as it is possible to reduce the number of compounds to be assayed, allowing to save resources. In the present study, pharmacophore models were generated using the common hits approach (CHA), starting from trajectories obtained from molecular dynamics (MD) simulations of the E protein complexed with the active inhibitor, flavanone (FN5Y). Subsequently, compounds presented in various drug databases were screened using the LigandScout 4.2 program. The obtained hits were analyzed in more detail by molecular docking, followed by extensive MD simulations of the complexes. The highest-ranked compound from this procedure was then synthesized and tested on its inhibitory efficiency by experimental assays.

2-Hydroxypropyl-&beta, cyclodextrin (HP&beta, CD) has unique properties to enhance the stability and the solubility of low water-soluble compounds by inclusion complexation. An understanding of the structural properties of HP&beta, CD and its derivatives, based on the number of 2-hydroxypropyl (HP) substituents at the &alpha, d-glucopyranose subunits is rather important. In this work, replica exchange molecular dynamics simulations were performed to investigate the conformational changes of single- and double-sided HP-substitution, called 6-HP&beta, CDs and 2,6-HP&beta, CDs, respectively. The results show that the glucose subunits in both 6-HP&beta, CDs have a lower chance of flipping than in &beta, CD. Also, HP groups occasionally block the hydrophobic cavity of HP&beta, CDs, thus hindering drug inclusion. We found that HP&beta, CDs with a high number of HP-substitutions are more likely to be blocked, while HP&beta, CDs with double-sided HP-substitutions have an even higher probability of being blocked. Overall, 6-HP&beta, CDs with three and four HP-substitutions are highlighted as the most suitable structures for guest encapsulation, based on our conformational analyses, such as structural distortion, the radius of gyration, circularity, and cavity self-closure of the HP&beta, CDs.

Glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a binuclear metallohydrolase, which is capable of catalyzing the hydrolysis of mono-, di-, and tri-ester substrates, including some organophosphate pesticides and degradation products of nerve agents. The GpdQ has attracted recent attention as a promising enzyme for bioremediation. This enzyme utilizes two metal ions located in the α and β sites of the enzyme active site for catalysis and is found to bind to Fe(II) ion preferentially. In this study, we aimed to investigate the binding interactions of three organophosphate pesticides (i.e., profenofos, diazinon and chlorpyrifos) to the GpdQ using computational approaches. Firstly, each pesticide molecule was separately docked into the active site of the GpdQ using molecular docking. Then, 500-ns MD simulations were carried out on the systems without (apo enzyme) and with pesticides bound. The MD results showed that the Feβ binds well with the GpdQ active site in the presence of pesticide. It is also seen that the binding of the pesticide could stabilize the enzyme structure in the active conformation, allowing the substrate to be catalysed into less harmful products. Therefore, the ability of in silico analysis presented here could be informative for enhancing enzyme stability and activity in the future.

Influenza is a respiratory contagious disease infecting people all around the globe. The Center for Disease Control and Prevention had estimated that from 1 October 2018 to 4 May 2019, there have been about 40 million flu patients, in which about 50 thousand cases have died. Many subtypes of influenza have developed drug resistance due to high mutation rates. Neuraminidase (NA) is the glycoprotein on the virus particle surface. Its function is to cleave the glycosidic bond with the sialic acid, leading the new virus to be able to infect other uninfected cells. Therefore, it is a promising protein target for drug design and development. The E276D and R292K NA mutations in the H10N4 influenza virus have been reported to cause drug resistance. In this study, molecular dynamics simulations and free energy calculations were applied to study the source of oseltamivir resistance in E276D, R292K, and E276D/R292K NA strains. The obtained results suggested that all studied mutants reduced the number of contact atoms, interaction energies, H-bonds, per-residue interaction energies, and total binding free energies towards the oseltamivir binding, resulting in a lower susceptibility. Only the interactions at residues 118, 119, and 371 were maintained in stabilizing the oseltamivir. The opening at 150- and 430-loops in E276D and double mutations caused the drug unbinding from the active site, increasing water accessibility into the binding pocket of NA enzyme.