Combination Of Docking Research Articles

From nature’s pharmacy: harnessing bioactive phytoconstituents as fibroblast growth factor receptor 3 inhibitors for anti-cancer therapeutics

Fibroblast growth factor receptor 3 (FGFR3) is a key protein involved in regulating cell growth and development. Aberrant activation of FGFR3 has been linked to several diseases, including cancer and skeletal disorders. Therefore, identifying potential inhibitors of FGFR3 is of great interest in developing targeted therapies. In this study, we employed a combined docking and molecular dynamics simulation (MDS) approach to investigate the inhibitory potential of plant-based compounds against FGFR3. Here, we utilized structure-based virtual screening to identify potential phytoconstituents from the IMPPAT library with the ability to inhibit FGFR3 activity. The initial screening process involved molecular docking to assess the binding potential of the compounds towards FGFR3. Afterward, we employed various filters to determine physicochemical properties, ADMET, and PASS evaluation to identify potential hits against FGFR3. This process discovered two phytoconstituents, Cycloartobiloxanthone and Desoxylimonin, as promising candidates against FGFR3. These compounds exhibited favorable binding affinity, efficiency, and specific interaction towards the FGFR3 binding pocket. They preferred binding to the active site of FGFR3 and possessed desirable drug-like properties. To gain a deeper understanding of their interaction mechanism, conformational dynamics, and stability, we conducted all-atom MDS lasting 200 nanoseconds (ns) on the FGFR3-Cycloartobiloxanthone and FGFR3-Desoxylimonin complexes. The MDS consistently demonstrated the formation of stable protein-ligand complexes between FGFR3 and Cycloartobiloxanthone/Desoxylimonin throughout the trajectory. Based on these results, it can be inferred that Cycloartobiloxanthone and Desoxylimonin can potentially serve as valuable scaffolds in developing drugs targeting FGFR3 for cancer therapeutic after required validation.

Exploration of Specific Fluoroquinolone Interaction with SARS-CoV-2 Main Protease (Mpro) to Battle COVID-19: DFT, Molecular Docking, ADME and Cardiotoxicity Studies.

Herein, the pharmacokinetic profiles, binding interactions, and molecular properties of fluoroquinolone derivatives as prospective antiviral drugs are examined using a combination of docking, ADME, and DFT simulations. The effectiveness of the ligands is compared with the clinically tested and FDA-authorized medicine remdesivir. The findings demonstrated encouraging binding energies, indicating possible inhibitory effectiveness against SARS-CoV-2 Mpro. The fluoroquinolone derivatives also exhibit promising ADME characteristics, although compounds 5, 6, 9, 12-20 possess poor values, suggesting that oral administration may be possible. The potential of the selected compounds as SARS-CoV-2 Mpro inhibitors is thoroughly understood because of the integrated analysis of DFT, with compound 11 demonstrating the highest energy gap of 0.2604 eV of, docking with viral targets with docking scores of -7.9 to -5.9 kcal/mol, with compound 18 demonstrating the highest docking score, which is at the 13th position in energy difference in the DFT data. Their favorable electrical properties, robust binding interactions with viral targets, and attractive pharmacokinetic profiles boost their potential as prospective study subjects. These substances have the potential to be transformed into cutting-edge antiviral therapies that specifically target SARS-CoV-2 Mpro and related coronaviruses.

Inclusion complex of trans-p-coumaroyl-secologanoside (comselogoside) with β-cyclodextrin. Part I. structural characterization and study of solubilization and stabilization.

Comselogoside (COM) is a secoiridoid, derivative of p-coumaric acid with a wide range of potential beneficial properties, although its poor aqueous solubility and low stability limit its study and application. The formation of an inclusion complex with β-cyclodextrin (β-CD) could improve the solubility and photostability of COM. The complexation of COM with β-CD in an aqueous solution has been studied for the first time, using the freeze-drying method with high encapsulation yield and efficiency. The formation of the inclusion complex was confirmed by electrospray ionization (ESI) mass and 1H NMR spectroscopy. Phase solubility studies provided an AN-type diagram with an increase in aqueous solubility by 100% and the formation of a high stoichiometric order complex COM: β-CD. The 1H NMR analysis with different COM/β-CD molar ratio established the formation of the 2:1 stoichiometric complex by Job ҆ s plot. In addition, the complexation of COM with β-CD improved the stability of COM against irradiation with UV light at 254 nm. Finally, combined docking and DFT calculations have been performed to study the formation and interactions of the COM: β-CD complexes. The computational results show excellent agreement with experimental observations.

Discovering potential WRN inhibitors from natural product database through computational methods

Microsatellite instability (MSI) is a relatively common feature associated with multiple cancers, and Werner syndrome (WRN) ATP-dependent helicase has been recognized as a novel target for treating MSI cancers, such as colorectal cancer. A small-molecule inhibitor targeting WRN would be a promising strategy for treating colorectal cancer with high MSI expression. In this study, we employed a computer-assisted drug discovery strategy to screen over 30,000 natural product molecules. By using a combination of docking, ligand efficiency, Molecular Mechanics/Generalized Born Surface Area (MM/GBSA), and thermodynamic integration (TI) calculations, we identified MOL008980, MOL010740, MOL011832, T4743, TN1166, and TNP-002173 as potential WRN inhibitors. Subsequent molecular dynamics simulation revealed that these screened natural products possessed better binding dynamic characteristics than ATP substrate and were capable of inhibiting the dynamic process of WRN, making them potential strong ATP competitive inhibitors. In conclusion, our computational approach revealed potential WRN inhibitors from a natural product database, providing a theoretical basis for future research.

Exploring MTH1 inhibitory potential of Thymoquinone and Baicalin for therapeutic targeting of breast cancer

Cancers frequently have increased ROS levels due to disrupted redox balance, leading to oxidative DNA and protein damage, mutations, and apoptosis. The MTH1 protein plays a crucial role by sanitizing the oxidized dNTP pools. Hence, cancer cells rely on MTH1 to prevent the integration of oxidized dNTPs into DNA, preventing DNA damage and allowing cancer cell proliferation. We have discovered Thymoquinone (TQ) and Baicalin (BC) as inhibitors of MTH1 using combined docking and MD simulation approaches complemented by experimental validations via assessing binding affinity and enzyme inhibition. Docking and MD simulations studies revealed an efficient binding of TQ and BC to the active site pocket of the MTH1, and the resultant complexes are appreciably stable. Fluorescence measurements estimated a strong binding affinity of TQ and BC with Ka 3.4 ×106 and 1.0 ×105, respectively. Treating breast cancer cells with TQ and BC significantly inhibited the growth and proliferation (IC50 values 28.3 µM and 34.8 µM) and induced apoptosis. TQ and BC increased the ROS production in MCF7 cells, imposing substantial oxidative stress on cancer cells and leading to cell death. Finally, TQ and BC are proven strong MTH1 inhibitors, offering promising prospects for anti-cancer therapy.

Qihuang Zhuyu formula alleviates coronary microthrombosis by inhibiting PI3K/Akt/αIIbβ3-mediated platelet activation

BackgroundCoronary microembolism (CME) is commonly seen in the peri-procedural period of Percutaneous Coronary Intervention (PCI), where local platelet activation and endothelial cell inflammation crosstalk may lead to micro thrombus erosion and rupture, with serious consequences. Qihuang Zhuyu Formula (QHZYF) is a Chinese herbal compound with high efficacy against coronary artery disease, but its antiplatelet mechanism is unclear. Hypothesis/PurposeThis study aimed to elucidate the effects and mechanisms of QHZYF on sodium laurate-induced CME using network pharmacology and in vitro and in vivo experiments. MethodsWe employed high-performance liquid chromatography mass spectrometry to identify the main components of QHZYF. Network pharmacology analysis, molecular docking and surface plasmon resonance (SPR) were utilized to predict the primary active components, potential therapeutic targets, and intervention pathways mediating the effects of QHZYF on platelet activation. Next, we pretreated a sodium laurate-induced minimally invasive CME rat model with QHZYF. In vivo experiments were performed to examine cardiac function in rats, to locate coronary arteries on heart sections to observe internal microthrombi, to extract rat Platelet-rich plasma (PRP) for adhesion assays and CD62p and PAC-1 (ITGB3/ITGA2B) flow assays, and to measure platelet-associated protein expression in PRP. In vitro clot retraction and Co-culture of HUVECs with PRP were performed and the gene pathway was validated through flow cytometry and immunofluorescence. ResultsCombining UPLC-Q-TOF/MS technology and database mining, 78 compounds were finally screened as the putative and representative compounds of QHZYF, with 75 crossover genes associated with CME. QHZYF prevents CME mainly by regulating key pathways of the inflammation and platelets, including Lipid and atherosclerosis, Fluid shear stress, platelet activation, and PI3K-Akt signaling pathways. Five molecules including Calyson, Oroxin A, Protosappanin A,Kaempferol and Geniposide were screened and subjected to molecular docking and SPR validation in combination with Lipinski rules (Rule of 5, Ro5). In vivo experiments showed that QHZYF not only improved myocardial injury but also inhibited formation of coronary microthrombi. QHZYF inhibited platelet activation by downregulating expression of CD62p receptor and platelet membrane protein αIIbβ3 and reduced the release of von Willebrand Factor (vWF), Ca2+ particles and inflammatory factor IL-6. Further analysis revealed that QHZYF inhibited the activation of integrin αIIbβ3, via modulating the PI3K/Akt pathways. In in vitro experiments, QHZYF independently inhibited platelet clot retraction. Upon LPS induction, the activation of platelet membrane protein ITGB3 was inhibited via the PI3K/Akt pathway, revealing an important mechanism for attenuating coronary microthrombosis. We performed mechanistic validation using PI3K inhibitor LY294002 and Akt inhibitor MK-2206 to show that QHZYF inhibited platelet membrane protein activation and inflammation to improved coronary microvessel embolism by regulating PI3K/Akt/αIIbβ3 pathways, mainly by inhibiting PI3K and Akt phosphorylation. ConclusionQHZYF interferes with coronary microthrombosis through inhibition of platelet adhesion, activation and inflammatory crosstalk, thus has potential in clinical anti-platelet applications. Calyson, Oroxin A, Protosappanin A, Kaempferol and Geniposide may be the major active ingredient groups of QHZYF that alleviate coronary microthrombosis.

Investigating potential of cholic acid, syringic acid, and mangiferin as cancer therapeutics through sphingosine kinase 1 inhibition

The signaling of sphingosine kinase 1 (SphK1) and sphingosine-1-phosphate (S1P) regulates various diseases, including multiple sclerosis, atherosclerosis, rheumatoid arthritis, inflammation-related ailments, diabetes, and cancer. SphK1 is considered an attractive potential drug target and is extensively explored in cancer and other inflammatory diseases. In this study, we have investigated the inhibitory potential and binding affinity of SphK1 with cholic acid (CA), syringic acid (SA), and mangiferin (MF) using a combination of docking and molecular dynamics (MD) simulation studies followed by experimental measurements of binding affinity and enzyme inhibition assays. We observed these compounds bind to SphK1 with a significantly high affinity and eventually inhibit its kinase activity with IC50 values of 28.23 μM, 33.35 μM, and 57.2 μM for CA, SA, and MF, respectively. Further, the docking and 100 ns MD simulation studies showed that CA, SA, and MF bind with the active site residues of SphK1 with favorable energy and strong non-covalent interactions that might be accountable for inhibiting its kinase activity. Our finding indicates that CA, SA, and MF may be implicated in designing novel anti-cancer therapeutics with an improved affinity and lesser side effects by targeting SphK1.

Reactive natural deep eutectic solvents increase selectivity and efficiency of lipase catalyzed esterification of carbohydrate polyols

A novel approach for the enzymatic esterification of carbohydrate polyols with fatty acids was investigated, with reactive natural deep eutectic solvents (R-NADES) as reaction medium and source of reagents. Three binary hydrophilic R-NADES consisting of choline chloride (ChCl) as hydrogen bond acceptor (HBA) and sugar alcohols (D-sorbitol, xylitol, D-arabitol) as hydrogen bond donors (HBD), were prepared and characterized. The carbohydrate polyol-based R-NADES were durable viscous fluids between 40 and 80⁰C, the common temperature range for an enzymatic reaction. The commercially accessible lipase B from Candida antarctica immobilized on acrylic resins (LAR) showed significant esterification activity and exceptional thermal stability in all three tested R-NADES and successfully catalyzed the synthesis of polyol esters. Box Behnken factorial design with three levels-three variables was used for optimizing the reaction conditions. The preparative esterification of D-arabitol with lauric acid (LA) at predicted optimal values for enzyme load, (i.e., 800 U/gram D-arabitol), temperature (70 °C) and LA/D-arabitol molar ratio of 1), attained 80 mol% LA conversion after 24 h reaction time. Structural analysis based on mass, infrared and nuclear magnetic resonance spectroscopy demonstrated that the reaction product is solely the diester 1,5-dilauryl-D-arabitol (1,5-DLDA). The 1,5-DLDA product, with an NMR-purity above 99.9%, was isolated in 95% yield. Under similar conditions, 1,5-dilauryl-xylitol (1,5-DLX) and 1,6-dilauryl-D-sorbitol (1,6-DLDS) were obtained, at a LA conversion of 56 mol% and 62 mol%, respectively. A combination of docking and molecular dynamics simulations allowed to rationalize the structural stability of the lipase B from Candida antarctica (CalB) active site in R-NADES, as well as the selectivity of the catalyzed esterification.

Molecular Dynamics as a Tool for Virtual Ligand Screening.

Rational drug design is essential for new drugs to emerge, especially when the structure of a target protein or nucleic acid is known. To that purpose, high-throughput virtual ligand screening campaigns aim at discovering computationally new binding molecules or fragments to modulate particular biomolecular interactions or biological activities, related to a disease process. The structure-based virtual ligand screening process primarily relies on docking methods which allow predicting the binding of a molecule to a biological target structure with a correct conformation and the best possible affinity. The docking method itself is not sufficient as it suffers from several and crucial limitations (lack of full protein flexibility information, no solvation and ion effects, poor scoring functions, and unreliable molecular affinity estimation).At the interface of computer techniques and drug discovery, molecular dynamics (MD) allows introducing protein flexibility before or after a docking protocol, refining the structure of protein-drug complexes in the presence of water, ions, and even in membrane-like environments, describing more precisely the temporal evolution of the biological complex and ranking these complexes with more accurate binding energy calculations. In this chapter, we describe the up-to-date MD, which plays the role of supporting tools in the virtual ligand screening (VS) process.Without a doubt, using docking in combination with MD is an attractive approach in structure-based drug discovery protocols nowadays. It has proved its efficiency through many examples in the literature and is a powerful method to significantly reduce the amount of required wet experimentations (Tarcsay et al, J Chem Inf Model 53:2990-2999, 2013; Barakat et al, PLoS One 7:e51329, 2012; De Vivo et al, J Med Chem 59:4035-4061, 2016; Durrant, McCammon, BMC Biol 9:71-79, 2011; Galeazzi, Curr Comput Aided Drug Des 5:225-240, 2009; Hospital et al, Adv Appl Bioinforma Chem 8:37-47, 2015; Jiang et al, Molecules 20:12769-12786, 2015; Kundu et al, J Mol Graph Model 61:160-174, 2015; Mirza et al, J Mol Graph Model 66:99-107, 2016; Moroy et al, Future Med Chem 7:2317-2331, 2015; Naresh et al, J Mol Graph Model 61:272-280, 2015; Nichols et al, J Chem Inf Model 51:1439-1446, 2011; Nichols et al, Methods Mol Biol 819:93-103, 2012; Okimoto et al, PLoS Comput Biol 5:e1000528, 2009; Rodriguez-Bussey et al, Biopolymers 105:35-42, 2016; Sliwoski et al, Pharmacol Rev 66:334-395, 2014).

Repurposing of antiparasitic drugs against the NS2B-NS3 protease of the Zika virus

To date, no approved drugs are available to treat the Zika virus (ZIKV) infection. Therefore, it is necessary to urgently identify potential drugs against the ZIKV infection. Here, the repurposing of 30 antiparasitic drugs against the NS2B-NS3 protease of the ZIKV has been carried out by using combined docking and molecular dynamics- (MD) simulations. Based on the docking results, 5 drugs, such as Amodiaquine, Primaquine, Paromomycin, Dichlorophene, and Ivermectin were screened for further analysis by MD simulations and free energy calculations. Among these drugs, Amodiaquine and Dichlorophen are found to produce the most stable complexes and possess relative binding free energies of about −44.3 ± 3.7 kcal/mol and −41.1 ± 5.3 kcal/mol respectively. Therefore, they would act as potent small-molecule inhibitors of the ZIKV protease.However, evaluations of biological and safety activities of these drugs against the ZIKV protease are required before their clinical use. Communicated by Ramaswamy H. Sarma

Exploring potential Plasmodium kinase inhibitors: a combined docking, MD and QSAR studies

Malaria is a disease caused mostly by Plasmodium falciparum, affects millions of people each year. The kinases are validated targets for malaria infection. In this study, we investigate for real and hypothetical compounds that can inhibit cyclic guanosine monophosphate (CGMP)-dependent protein kinase using molecular docking via combined similarity analysis, molecular dynamics simulations, quantitative structure activity relationship (QSAR). Using Tanimoto similarity scores, ∼8.4 million compounds were screened. Compounds that have at least 70% similarity are used in further analysis. These compounds are assessed by means of docking, MMBPSA, MMGBSA and ANI_LIE. Based on consensus of different free energy methods and docking we revealed two potential inhibitors that can be useful for treatment of malaria. Apart from screening of real compounds, we have also selected the 10 most plausible hypothetical compounds by performing QSAR. By QSAR proposed pharmacophores, we generated over 247 hypothetical compounds and among them 19 molecules with lower QSAR predicted IC50 values and high docking scores were selected for further analysis. We selected the top 10 inhibitor candidates and performed MD simulations for free energy calculations like the protocol applied for real compounds. According to the free energy calculations, we suggest 2 real (C34H29F5N8O4S and C30H27F2N7O2S2, PubChem IDs: 140564801 and 89035196, respectively) and 2 hypothetical (C23H27FN6O2S, MOL3 and C23H25FN6O2S, MOL4) compounds that can be effective inhibitors against the protein kinase of Plasmodium falciparum. Communicated by Ramaswamy H. Sarma

Integrated Approach Including Docking, MD Simulations, and Network Analysis Highlights the Action Mechanism of the Cardiac hERG Activator RPR260243.

hERG is a voltage-gated potassium channel involved in the heart contraction whose defections are associated with the cardiac arrhythmia Long QT Syndrome type 2. The activator RPR260243 (RPR) represents a possible candidate to pharmacologically treat LQTS2 because it enhances the opening of the channel. However, the molecular detail of its action mechanism remains quite elusive. Here, we address the problem using a combination of docking, molecular dynamics simulations, and network analysis. We show that the drug preferably binds at the interface between the voltage sensor and the pore, enhancing the canonical activation path and determining a whole-structure rearrangement of the channel that slightly impairs inactivation.

Structure-based identification of potential inhibitors of ribosomal protein S6 kinase 1, targeting cancer therapy: a combined docking and molecular dynamics simulations approach

Ribosomal protein S6 kinase 1 (S6K1), commonly known as P70-S6 kinase 1 (p70S6), is a key protein kinase involved in cellular signaling pathways that regulate cell growth, proliferation, and metabolism. Its significant role is reported in the PIK3/mTOR signaling pathway and is associated with various complex diseases, including diabetes, obesity, and different types of cancer. Due to its involvement in various physiological and pathological conditions, S6K1 is considered as an attractive target for drug design and discovery. One way to target S6K1 is by developing small molecule inhibitors that specifically bind to its ATP-binding site, preventing its activation and thus inhibiting downstream signaling pathways necessary for cell growth and survival. In this study, we have conducted a multitier virtual screening of a pool of natural compounds to identify potential S6K1 inhibitors. We performed molecular docking on IMPPAT 2.0 library and selected top hits based on their binding affinity, ligand efficiency, and specificity towards S6K1. The selected hits were further assessed based on different filters of drug-likeliness where two compounds (Hecogenin and Glabrene) were identified as potential leads for S6K1 inhibition. Both compounds showed appreciable affinity, ligand efficiency and specificity towards S6K1 binding pocket, drug-like properties, and stable protein-ligand complexes in molecular dynamics (MD) simulations. Finally, our study has suggested that Hecogenin and Glabrene can be potential S6K1 inhibitors which are presumably implicated in the therapeutic management of associated diseases such as diabetes, obesity, and varying types of cancer. Communicated by Ramaswamy H. Sarma

Colchicine as potential inhibitor targeting MMP-9, NOX2 and TGF-β1 in myocardial infarction: a combination of docking and molecular dynamic simulation study

The global data revealed that myocardial infarction (MI) in coronary heart disease has been the leading cause of mortality worldwide in both developing and developed countries. The remodeling process after MI is essential to be the leading cause of heart failure due to cardiac remodeling. The evidence showed the increment of MMP-9, NOX2 and TGF-β1 expressions are biomarkers that influence cardiac remodeling. Lately, colchicine is widely used in the treatment of cardiovascular diseases. The effects of colchicine on NOX2, MMP-9 and TGF-β1 in the molecular models are still not yet discussed. We proposed a molecular docking and molecular dynamics simulation study to show the interaction between colchicine, NOX2, MMP-9 and TGF-β1. Colchicine has a good binding affinity with MMP-9, NOX2 and TGF-β1 based on the value, which are −8.3 Kcal/mol, −6.7 Kcal/mol and −6.5 Kcal/mol, respectively. Colchicine also binds to some catalytic residues in MMP-9, NOX2 and TGF-β1 that are responsible for inhibitor effects. The RMSD values between colchicine and MMP-9, NOX2 and TGF-β1 are 2.4 Å, 2 Å and 2.1 Å, respectively. The RMSF values of ligand and receptors complex showed relatively similar fluctuations. The SASA analysis showed that colchicine could create a more stable interaction with MMP-9. PCA analysis revealed that colchicine is capable of creating a solid and stable interaction with MMP-9 mainly, also NOX2 and TGF-β1. In conclusion, docking and molecular dynamics analysis showed evidence of colchicine roles in the inhibition of MMP-9, NOX2 and TGF-β1 in order to inhibit the remodeling process after MI. Communicated by Ramaswamy H. Sarma

Structural basis of Nrf2 activation by flavonolignans from silymarin

Several properties of silymarin (SM) extract have been attributed to their three major flavonolignans (silybin, silychristin, and silydianin) and their 2,3-dehydro derivatives (2,3-dehydrosilybin, 2,3-dehydrosilychristin, and 2,3-dehydrosilydianin). Experimental findings have suggested that the antioxidative and protective activities of these compounds could be due to their ability to activate nuclear factor erythroid 2-related factor 2 (Nrf2). The mechanism by which SM compounds exert their effect has been suggested to be by disrupting the complex between Nrf2 and Kelch-like ECH-associated protein 1 (Keap1). However, information about the structural and energetic basis of the inhibitory mechanism of SM compounds on the Nrf2-Keap1 pathway is lacking. We evaluated the binding properties of SM compounds because experimental findings have pointed to them as potential activators of Nrf2. Our study combined docking and molecular dynamics (MD) simulations with the Poisson–Boltzmann and generalized Born and surface area (MMPBSA and MMGBSA) methods and quantum mechanics-molecular mechanics (QMMM) calculations to investigate Keap1–ligand interactions. Our results predicted that silybinA and 2,3-dehydrosilybin bind to Keap1, forming interactions with the same pockets as those observed for the cocrystallized Keap1-Cpd16 complex but with more favorable binding free energies. These findings indicate that both natural compounds are potential activators of Nrf2.

Site-selective covalent immobilization of PPARγ using a label-free strategy for chromatographic study

The development of site-selective covalent protein immobilization strategies is crucial for many protein-based bioanalytical assays. Herein, we proposed a label-free, site-selective, covalent immobilization strategy for the functionalization of PPARγ on GW9662 modified macroporous silica gels. The gels were characterized by X-ray photoelectron spectroscopy (XPS) and scanning electron microscope (SEM). Molecular docking in combination with competitive study, adsorption energy distribution (AED) calculation, and frontal analysis were used to investigate the binding of ligands with GW9662 occupied PPARγ. Docking results indicated that rosiglitazone, pioglitazone, and gensenoside Rh1 could cooperatively bind to the receptor with GW9662. Competitive studies revealed that the three ligands bond with PPARγ through the same site in the presence of GW9662. AED calculation showed one type of binding site for the three ligands on the receptor. Due to the presence of GW9662, the affinities of the three ligands ((2.35 ± 0.05) × 105 M−1 for rosiglitazone, (1.27 ± 0.02) × 105 M−1 for pioglitazone, and (3.18 ± 0.13) × 105 M−1 for gensenoside Rh1) with PPARγ were one or two orders of magnitude smaller than the literature reported values. The good performance of the immobilized PPARγ provided an opportunity for application in receptor-ligand interactions and cooperative partner screening. Our strategy is, therefore, a promising way to realize the label-free, covalent immobilization of functional proteins.

Analysis of P-Glycoprotein Transport Cycle Reveals a New Way to Identify Efflux Inhibitors.

P-glycoprotein (P-gp) is found to be of considerable interest for the design of drugs capable of treating chemoresistant tumors. This transporter is an interesting target for which an efficient approach has not yet been developed in terms of computer simulation. In this work, we use a combination of docking, molecular dynamics, and metadynamics to fully explore the states that occur during the capture of a ligand and subsequent efflux by P-gp. The proposed approach allowed us to substantiate a number of experimentally established facts, as well as to develop a new criterion for identifying potential P-gp inhibitors.

Activity dependent inhibition of TRPC1/4/5 channels by duloxetine involves voltage sensor-like domain.

Transient receptor potential canonical 5 (TRPC5) is a polymodal, calcium-permeable, nonselective ion channel that is expressed in the brain and 75 % of human sensory neurons. Its pharmacological or genetic inhibition leads to the relief of neuropathic and inflammatory pain. The clinically approved drug duloxetine is superior to other serotonin and norepinephrine reuptake inhibitors at managing painful neuropathies, but it is not known why. Here we ask whether the TRPC5 receptor is modulated by duloxetine and may contribute to its analgesic effect. Electrophysiological measurements of heterologously expressed human TRPC5 in HEK293T cells were performed to evaluate the effect of duloxetine. The interaction site was identified by molecular docking and molecular dynamics simulations in combination with point mutagenesis. We found that duloxetine inhibits TRPC5 in a concentration-dependent manner with a high potency (IC50 = 0.54±0.03µM). Our data suggest that duloxetine binds into a voltage sensor-like domain. For the interaction, Glu418 exhibited particular importance due to putative hydrogen bond formation. Duloxetine effectively inhibits TRPC5 currents induced by cooling, voltage, direct agonists and by the stimulation of the PLC pathway. The finding that this TRPC5 inhibitor is widely used and well tolerated provides a scaffold for new pain treatment strategies.

Authenticity and traceability of goat milk: Molecular mechanism of β-carotene biotransformation and accessibility

The efficiently extraction and accurately quantify of β-carotene and its metabolites are crucial for authenticity and traceability in goat milk. Nevertheless, its reliability can be largely improved. In this study, meticulously designed native ESI-MS, fluorescence spectroscopy and molecular docking in combination with cold-induced acetonitrile aqueous two-phase separation system weaken the interaction between β-lactoglobulin and β-carotene metabolites and realized the efficiently extraction. Furthermore, established non-targeted quantitative metabolomics with optimal ion source and variable data-independent acquisition minimized the matrix effects and potential ion suppression. Validated atmospheric pressure chemical ionization-ultra high performance liquid chromatography-Orbitrap method showed that β-carotene as distinctive biomarker in cow milk, and retinol, retinaldehyde, retinoic acid and abscisic acid in goat milk. Collectively, the proposed method is a powerful tool to detect cow adulteration risks in goat milk samples and provides valuable information for availability on authenticity of goat milk.

In Silico Exploration of Novel Tubulin Inhibitors: A Combination of Docking and Molecular Dynamics Simulations, Pharmacophore Modeling, and Virtual Screening.

Microtubules play a critical role in mitosis and cell division and are regarded as an excellent target for anticancer therapy. Although microtubule-targeting agents have been widely used in the clinical treatment of different human cancers, their clinical application in cancer therapy is limited by both intrinsic and acquired drug resistance and adverse toxicities. In a previous work, we synthesized compound 9IV-c, ((E)-2-(3,4-dimethoxystyryl)-6,7,8-trimethoxy-N-(3,4,5-trimethoxyphenyl)quinoline-4-amine) that showed potent activity against multiple human tumor cell lines, by targeting spindle formation and/or the microtubule network. Accordingly, in this study, to identify potent tubulin inhibitors, at first, molecular docking and molecular dynamics studies of compound 9IV-c were performed into the colchicine binding site of tubulin; then, a pharmacophore model of the 9IV-c-tubulin complex was generated. The pharmacophore model was then validated by Güner–Henry (GH) scoring methods and receiver operating characteristic (ROC) analysis. The IBScreen database was searched by using this pharmacophore model as a screening query. Finally, five retrieved compounds were selected for molecular docking studies. These efforts identified two compounds (b and c) as potent tubulin inhibitors. Investigation of pharmacokinetic properties of these compounds (b and c) and compound 9IV-c displayed that ligand b has better drug characteristics compared to the other two ligands.