Critical Assessment of Self-Consistency Checks in the All-Atom Molecular Dynamics Simulation of Intrinsically Disordered Proteins.

All atom simulations can be used to quantify conformational properties of Intrinsically Disordered Proteins (IDP). However, simulations must satisfy convergence checks to ensure observables computed from simulation are reliable and reproducible. While absolute convergence is purely a theoretical concept requiring infinitely long simulation, a more practical, yet rigorous, approach is to impose Self Consistency Checks (SCCs) to gain confidence in the simulated data. Currently there is no study of SCCs in IDPs, unlike their folded counterparts. In this paper, we introduce different criteria for self-consistency checks for IDPs. Next, we impose these SCCs to critically assess the performance of different simulation protocols using the N terminal domain of HIV Integrase and the linker region of SARS-CoV-2 Nucleoprotein as two model IDPs. All simulation protocols begin with all-atom implicit solvent Monte Carlo (MC) simulation and subsequent clustering of MC generated conformations to create the representative structures of the IDPs. These representative structures serve as the initial structure for subsequent molecular dynamics (MD) runs with explicit solvent. We conclude that generating multiple short (∼3 µs) MD simulation trajectories─all starting from the most representative MC generated conformation─and merging them is the protocol of choice due to (i) its ability to satisfy multiple SCCs, (ii) consistently reproducing experimental data, and (iii) the efficiency of running independent trajectories in parallel by harnessing multiple cores available in modern GPU clusters. Running one long trajectory (greater than 20 µs) can also satisfy the first two criteria but is less desirable due to prohibitive computation time. These findings help resolve the challenge of identifying a usable starting configuration, provide an objective measure of SCC, and establish rigorous criteria to determine the minimum length (for one long simulation) or number of trajectories needed in all-atom simulation of IDPs.

Maackia amurensis Rupr. et Maxim.: Supercritical CO2 Extraction and Mass Spectrometric Characterization of Chemical Constituents.

Three types of extraction were used to obtain biologically active substances from the heartwood of M. amurensis: supercritical CO2 extraction, maceration with EtOH, and maceration with MeOH. The supercritical extraction method proved to be the most effective type of extraction, giving the highest yield of biologically active substances. Several experimental conditions were investigated in the pressure range of 50-400 bar, with 2% of ethanol as co-solvent in the liquid phase at a temperature in the range of 31-70 °C. The most effective extraction conditions are: pressure of 100 bar and a temperature of 55 °C for M. amurensis heartwood. The heartwood of M. amurensis contains various polyphenolic compounds and compounds of other chemical groups with valuable biological activity. Tandem mass spectrometry (HPLC-ESI-ion trap) was applied to detect target analytes. High-accuracy mass spectrometric data were recorded on an ion trap equipped with an ESI source in the modes of negative and positive ions. The four-stage ion separation mode was implemented. Sixty-six different biologically active components have been identified in M. amurensis extracts. Twenty-two polyphenols were identified for the first time in the genus Maackia.

Comparative Study of Novel Methods for Olive Leaf Phenolic Compound Extraction Using NADES as Solvents.

Natural deep eutectic solvents (NADES) composed of choline chloride with maltose (CMA), glycerol (CGL), citric (CCA) and lactic acid (CLA) combined with microwave (MAE), ultrasound (UAE), homogenate (HAE) and high hydrostatic pressure (HHPAE)-assisted extraction methods were applied to recover and compare olive leaf phenolic compounds. The resultant extracts were evaluated for their total phenol content (TPC), phenolic profile and antioxidant activity and compared with those of water and ethanol:water 70% v/v extracts. HAE was proven to be the most efficient method for the recovery of olive leaf phenolic compounds. The highest TPC (55.12 ± 1.08 mg GAE/g d.w.) was found in CCA extracts after HAE at 60 °C and 12,000 rpm, and the maximum antioxidant activity (3.32 ± 0.39 g d.w./g DPPH) was found in CGL extracts after UAE at 60 °C for 30 min. The TPCs of ethanol extracts were found to be higher than those of NADES extracts in most cases. The predominant phenolic compounds in the extracts were oleuropein, hydrohytyrosol and rutin.

Electronic Structures and Reactivities of COVID-19 Drugs: A DFT Study.

These days, the world is facing the threat of pandemic Coronavirus Disease 2019 (COVID-19). Although a vaccine has been found to combat the pandemic, it is essential to find drugs for an effective treatment method against this disease as soon as possible. In this study, electronic and thermodynamic properties, molecular electrostatic potential (MEP) analysis, and frontier molecular orbitals (FMOs) of nine different covid drugs were studied with Density Functional Theory (DFT). In addition, the relationship between the electronic structures of these drugs and their biological effectiveness was examined. All parameters were computed at the B3LYP/6-311++g(d,p) level. The Solvent effect was evaluated using conductor-like polarizable continuum model (CPCM) as the solvation model. It was observed that electrophilic indexes were important to understand the efficiencies of these drugs in COVID-19 disease. Paxlovid, hydroxyquinone, and nitazoxanide were found as the most thermodynamically stable molecules. Thermodynamic parameters also demonstrated that these drugs were more stable in the aqueous media. Global descriptors and the reactivity of these drugs were found to be related. Nitazoxanide molecule exhibited the highest dipole moment. The high dipole moments of drugs can cause hydrophilic interactions that increase their effectiveness in an aqueous solution.

Experimental and Theoretical Study of Fluorescent Properties of Morin.

Morin (M) is one of the most widely distributed flavonoids with several beneficial effects on human health, and has the potential of being used as a possible treatment for COVID-19. To achieve a better understanding of the process of M dissolution, the fluorescent (FL) emission from M solutions prepared with different polar and nonpolar solvents (methanol, DMSO, and chloroform) was measured and compared with the FL emission from M powder and M crystals. In the FL spectra of the solutions with high M concentration, as well as in the spectra of M in solid state, two features, at 615 nm and 670 nm, were observed. As the solution concentration decreases, the maxima of FL spectra of the M solutions in all considered solvents shift to the blue side of the spectrum until reaching the value of 520 nm. To explain the experimental results, the TDDFT-M06-2X/6-31++G(d,p) method was used to determine the possible electronic transitions in the M molecule. The computations show that the FL emission in the spectral range of detection of our setup (405-800 nm) is related to the excited state intramolecular proton transfer (ESIPT). Comparison of the experimental data with the computations strongly suggests that in low-concentrated solutions, the FL emission is mostly due to electronic transitions in the keto OH3 form, whereas in aggregated states, the dominate contribution to the FL emission spectra is due to the transitions in keto OH5 form. Moreover, the time evolution of the M solutions FL spectra was observed, measured and explained for the first time.

A simple and efficient derivatization strategy combined with switchable solvent liquid-liquid microextraction hydroxychloroquine methyl acetate-d3 -based quadruple isotope dilution gas chromatography mass spectrometry for the determination of hydroxychloroquine sulfate in biological fluids.

RATIONALE: A derivatization switchable solvent liquid-liquid microextraction quadruple isotope dilution gas chromatography mass spectrometry (D-SS-LLME-ID4 -GC/MS) method is presented for the determination of hydroxychloroquine sulfate in human biofluids. METHODS: While mixing type/period and concentration of NaOH were optimized via a univariate optimization approach, a multivariate optimization approach was used to determine optimum values for relatively more important parameters such as volumes of derivatization agent (acetic anhydride), NaOH and switchable solvent. RESULTS: Under the optimum experimental conditions, limit of detection and limit of quantification were calculated as 0.03 and 0.09 mg/kg (mass based), respectively. An isotopically labelled material (hydroxychloroquine methyl acetate-d3 ) was firstly synthesized to be used in ID4 experiments which give highly accurate and precise recovery results. After the application of D-SS-LLME-ID4 , superior percent recovery results were recorded as 99.9 ± 1.6-101.3 ± 1.2 for human serum, 99.9 ± 1.7-99.8 ± 1.8 for urine and 99.6 ± 1.5-101.0 ± 1.1 for saliva samples. CONCLUSIONS: The developed D-SS-LLME-ID4 -GC/MS method compensates the complicated matrix effects of human biofluids and provides highly accurate quantification of an analyte with precise results.

Optimizing Procedures of Ultrasound-Assisted Extraction of Waste Orange Peels by Response Surface Methodology.

The simultaneous effects of three continuous factors: solvent concentration (50-100%), treated times (25-85 min), treated temperatures (25-55 °C), and two categorical factors: type of solvents (methanol or ethanol) and ultrasonic frequency (28 kHz or 40 kHz) on ultrasonic-assisted extraction yield from waste orange peels were evaluated and optimized by response surface methodology. Fourier Transform Infrared (FTIR) spectroscopy with a wavelength of 500 cm-1 to 4000 cm-1 was employed to rapidly identify the orange extracts. The significant polynomial regression models on crude extraction, sediments after evaporation, and precipitation yield were established (p < 0.05). Results revealed that solvent concentration affected crude extraction and precipitation yield linearly (p < 0.01). The optimal and practical ultrasound-assisted extraction conditions for increasing the precipitation yield were using 61.42% methanol with 85 min at 55 °C under 40 kHz ultrasonic frequency. The spectra of extracts showed a similar fingerprint of hesperidin.

Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges.

We systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many instances expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable benefit-cost ratio. Some interesting features of Autodock4 predictions are revealed, yielding valuable hints on the overall reliability of docking screening campaigns in drug discovery projects.

Paper-based aptamer-antibody biosensor for gluten detection in a deep eutectic solvent (DES).

Paper has been widely employed as cheap material for the development of a great number of sensors such as pregnancy tests, strips to measure blood sugar, and COVID-19 rapid tests. The need for new low-cost analytical devices is growing, and consequently the use of these platforms will be extended to different assays, both for the final consumer and within laboratories. This work describes a paper-based electrochemical sensing platform that uses a paper disc conveniently modified with recognition molecules and a screen-printed carbon electrode (SPCE) to achieve the detection of gluten in a deep eutectic solvent (DES). This is the first method coupling a paper biosensor based on aptamers and antibodies with the DES ethaline. Ethaline proved to be an excellent extraction medium allowing the determination of very low gluten concentrations. The biosensor is appropriate for the determination of gluten with a limit of detection (LOD) of 0.2 mg L-1 of sample; it can detect gluten extracted in DES with a dynamic range between 0.2 and 20 mg L-1 and an intra-assay coefficient of 10.69%. This approach can be of great interest for highly gluten-sensitive people, who suffer from ingestion of gluten quantities well below the legal limit, which is 20 parts per million in foods labeled gluten-free and for which highly sensitive devices are essential.

ARGOS: An adaptive refinement goal-oriented solver for the linearized Poisson-Boltzmann equation.

An adaptive finite element solver for the numerical calculation of the electrostatic coupling between molecules in a solvent environment is developed and tested. At the heart of the solver is a goal-oriented a posteriori error estimate for the electrostatic coupling, derived and implemented in the present work, that gives rise to an orders of magnitude improved precision and a shorter computational time as compared to standard finite difference solvers. The accuracy of the new solver ARGOS is evaluated by numerical experiments on a series of problems with analytically known solutions. In addition, the solver is used to calculate electrostatic couplings between two chromophores, linked to polyproline helices of different lengths and between the spike protein of SARS-CoV-2 and the ACE2 receptor. All the calculations are repeated by using the well-known finite difference solvers MEAD and APBS, revealing the advantages of the present finite element solver.

Development and Validation of a Method for Quantification of Favipiravir as COVID-19 Management in Spiked Human Plasma.

In the current work, a simple, economical, accurate, and precise HPLC method with UV detection was developed to quantify Favipiravir (FVIR) in spiked human plasma using acyclovir (ACVR) as an internal standard in the COVID-19 pandemic time. Both FVIR and ACVR were well separated and resolved on the C18 column using the mobile phase blend of methanol:acetonitrile:20 mM phosphate buffer (pH 3.1) in an isocratic mode flow rate of 1 mL/min with a proportion of 30:10:60 %, v/v/v. The detector wavelength was set at 242 nm. Maximum recovery of FVIR and ACVR from plasma was obtained with dichloromethane (DCM) as extracting solvent. The calibration curve was found to be linear in the range of 3.1-60.0 µg/mL with regression coefficient (r2) = 0.9976. However, with acceptable r2, the calibration data's heteroscedasticity was observed, which was further reduced using weighted linear regression with weighting factor 1/x. Finally, the method was validated concerning sensitivity, accuracy (Inter and Intraday's % RE and RSD were 0.28, 0.65 and 1.00, 0.12 respectively), precision, recovery (89.99%, 89.09%, and 90.81% for LQC, MQC, and HQC, respectively), stability (% RSD for 30-day were 3.04 and 1.71 for LQC and HQC, respectively at -20 °C), and carry-over US-FDA guidance for Bioanalytical Method Validation for researchers in the COVID-19 pandemic crisis. Furthermore, there was no significant difference for selectivity when evaluated at LLOQ concentration of 3 µg/mL of FVIR and relative to the blank.

Simultaneous Determination of Paracetamol, Propyphenazone and Caffeine in Presence of Paracetamol Impurities Using Dual-Mode Gradient HPLC and TLC Densitometry Methods.

Two chromatographic methods were validated for the determination of the widely prescribed analgesic and antipyretic drug combination of paracetamol (PC) (recently integrated into the supportive treatment of COVID-19), propyphenazone (PZ) and caffeine (CF) in the presence of two PC impurities, namely 4-aminophenol and 4-nitrophenol. A "dual-mode" gradient high-performance liquid chromatography method was developed, where the separation was achieved via "dual-mode" gradient by changing both the ternary mobile phase composition (acetonitrile: methanol: water) and the flow rate. This enables a good resolution within a relatively shorter analysis time. The analysis was realized using Zorbax Eclipse XDB column C18, 5 µm (250 × 4.6 mm) and the UV detector was set at 220 nm. The other method is a thin-layer chromatography densitometry method, where the separation was achieved using a mobile phase composed of chloroform: toluene: ethyl acetate: methanol: acetic acid (6: 6: 1: 2: 0.1, by volume). Densitometric detection was performed at 220 nm on silica gel 60 F254 plates. The developed methods were fully validated as per the ICH guidelines and proved to be accurate, robust, specific and suitable for application as purity indicating methods for routine analysis of PC in pure form or in pharmaceuticals with PZ and CF in quality control laboratories.