Non-canonical amino acid bioincorporation into antimicrobial peptides and its challenges.

The rise of antimicrobial resistance and multi-drug resistant pathogens has necessitated explorations for novel antibiotic agents as the discovery of conventional antibiotics is becoming economically less viable and technically more challenging for biopharma. Antimicrobial peptides (AMPs) have emerged as a promising alternative because of their particular mode of action, broad spectrum and difficulty that microbes have in becoming resistant to them. The AMPs bacitracin, gramicidin, polymyxins and daptomycin are currently used clinically. However, their susceptibility to proteolytic degradation, toxicity profile, and complexities in large-scale manufacture have hindered their development. To improve their proteolytic stability, methods such as integrating non-canonical amino acids (ncAAs) into their peptide sequence have been adopted, which also improves their potency and spectrum of action. The benefits of ncAA incorporation have been made possible by solid-phase peptide synthesis. However, this method is not always suitable for commercial production of AMPs because of poor yield, scale-up difficulties, and its non-'green' nature. Bioincorporation of ncAA as a method of integration is an emerging field geared towards tackling the challenges of solid-phase synthesis as a green, cheaper, and scalable alternative for commercialisation of AMPs. This review focusses on the bioincorporation of ncAAs; some challenges associated with the methods are outlined, and notes are given on how to overcome these challenges. The review focusses particularly on addressing two key challenges: AMP cytotoxicity towards microbial cell factories and the uptake of ncAAs that are unfavourable to them. Overcoming these challenges will draw us closer to a greater yield and an environmentally friendly and sustainable approach to make AMPs more druggable.

Cheminformatics-Based Identification of Potential Novel Anti-SARS-CoV-2 Natural Compounds of African Origin.

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome virus 2 (SARS-CoV-2) has impacted negatively on public health and socioeconomic status, globally. Although, there are currently no specific drugs approved, several existing drugs are being repurposed, but their successful outcomes are not guaranteed. Therefore, the search for novel therapeutics remains a priority. We screened for inhibitors of the SARS-CoV-2 main protease and the receptor-binding domain of the spike protein from an integrated library of African natural products, compounds generated from machine learning studies and antiviral drugs using AutoDock Vina. The binding mechanisms between the compounds and the proteins were characterized using LigPlot+ and molecular dynamics simulations techniques. The biological activities of the hit compounds were also predicted using a Bayesian-based approach. Six potential bioactive molecules NANPDB2245, NANPDB2403, fusidic acid, ZINC000095486008, ZINC0000556656943 and ZINC001645993538 were identified, all of which had plausible binding mechanisms with both viral receptors. Molecular dynamics simulations, including molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) computations revealed stable protein-ligand complexes with all the compounds having acceptable free binding energies <-15 kJ/mol with each receptor. NANPDB2245, NANPDB2403 and ZINC000095486008 were predicted as antivirals; ZINC000095486008 as a membrane permeability inhibitor; NANPDB2403 as a cell adhesion inhibitor and RNA-directed RNA polymerase inhibitor; and NANPDB2245 as a membrane integrity antagonist. Therefore, they have the potential to inhibit viral entry and replication. These drug-like molecules were predicted to possess attractive pharmacological profiles with negligible toxicity. Novel critical residues identified for both targets could aid in a better understanding of the binding mechanisms and design of fragment-based de novo inhibitors. The compounds are proposed as worthy of further in vitro assaying and as scaffolds for the development of novel SARS-CoV-2 therapeutic molecules.

Molecular Informatics Studies of the Iron-Dependent Regulator (ideR) Reveal Potential Novel Anti-Mycobacterium ulcerans Natural Product-Derived Compounds.

Buruli ulcer is a neglected tropical disease caused by the bacterium Mycobacterium ulcerans. Its virulence is attributed to the dermo-necrotic polyketide toxin mycolactone, whose synthesis is regressed when its iron acquisition system regulated by the iron-dependent regulator (ideR) is deactivated. Interfering with the activation mechanism of ideR to inhibit the toxin's synthesis could serve as a possible cure for Buruli ulcer. The three-dimensional structure of the ideR for Mycobacterium ulcerans was generated using homology modeling. A library of 832 African natural products (AfroDB), as well as five known anti-mycobacterial compounds were docked against the metal binding site of the ideR. The area under the curve (AUC) values greater than 0.7 were obtained for the computed Receiver Operating Characteristics (ROC) curves, validating the docking protocol. The identified top hits were pharmacologically profiled using Absorption, Distribution, Metabolism, Elimination and Toxicity (ADMET) predictions and their binding mechanisms were characterized. Four compounds with ZINC IDs ZINC000018185774, ZINC000095485921, ZINC000014417338 and ZINC000005357841 emerged as leads with binding energies of -7.7 kcal/mol, -7.6 kcal/mol, -8.0 kcal/mol and -7.4 kcal/mol, respectively. Induced Fit Docking (IFD) was also performed to account for the protein's flexibility upon ligand binding and to estimate the best plausible conformation of the complexes. Results obtained from the IFD were consistent with that of the molecular docking with the lead compounds forming interactions with known essential residues and some novel critical residues Thr14, Arg33 and Asp17. A hundred nanoseconds molecular dynamic simulations of the unbound ideR and its complexes with the respective lead compounds revealed changes in the ideR's conformations induced by ZINC000018185774. Comparison of the lead compounds to reported potent inhibitors by docking them against the DNA-binding domain of the protein also showed the lead compounds to have very close binding affinities to those of the potent inhibitors. Interestingly, structurally similar compounds to ZINC000018185774 and ZINC000014417338, as well as analogues of ZINC000095485921, including quercetin are reported to possess anti-mycobacterial activity. Also, ZINC000005357841 was predicted to possess anti-inflammatory and anti-oxidative activities, which are relevant in Buruli ulcer and iron acquisition mechanisms, respectively. The leads are molecular templates which may serve as essential scaffolds for the design of future anti-mycobacterium ulcerans agents.

Investigating the Influence of Temperature on the Kaolinite-Base Synthesis of Zeolite and Urease Immobilization for the Potential Fabrication of Electrochemical Urea Biosensors.

Temperature-dependent zeolite synthesis has revealed a unique surface morphology, surface area and pore size which influence the immobilization of urease on gold electrode supports for biosensor fabrication. XRD characterization has identified zeolite X (Na) at all crystallization temperatures tested. However, N2 adsorption and desorption results showed a pore size and pore volume of zeolite X (Na) 60 °C, zeolite X (Na) 70 °C and zeolite X (Na) 90 °C to range from 1.92 nm to 2.45 nm and 0.012 cm³/g to 0.061 cm³/g, respectively, with no significant differences. The specific surface area of zeolite X (Na) at 60, 70 and 90 °C was 64 m²/g, 67 m²/g and 113 m²/g, respectively. The pore size, specific surface area and pore volumes of zeolite X (Na) 80 °C and zeolite X (Na) 100 °C were dramatically increased to 4.21 nm, 295 m²/g, 0.762 cm³/g and 4.92 nm, 389 m²/g, 0.837 cm³/g, in that order. The analytical performance of adsorbed urease on zeolite X (Na) surface was also investigated using cyclic voltammetry measurements, and the results showed distinct cathodic and anodic peaks by zeolite X (Na) 80 °C and zeolite X (Na) 100 °C. These zeolites' molar conductance was measured as a function of urea concentration and gave an average polynomial regression fit of 0.948. The findings in this study suggest that certain physicochemical properties, such as crystallization temperature and pH, are critical parameters for improving the morphological properties of zeolites synthesized from natural sources for various biomedical applications.

Distance measurements and conformational analysis of sn-2-arachidonoylglycerol-membrane sample by ²H-³¹P REDOR NMR.

The purpose of these studies is to determine the intermolecular distances that define the location, orientation, and conformation of 2-AG in palmitoyl-oleoyl-phosphatidylcholine (POPC) lipid bilayers using rotational-echo double-resonance (REDOR) NMR. All five protons on the glycerol backbone of 2-AG were replaced with ²H and the distance between the deuterons and naturally occurring ³¹P on the POPC lipid headgroup determined with REDOR. To determine the distance from each deuteron to the phosphorus, the POPC headgroup was arranged in a hexagonal array. The 2-AG intercalates between the lipid molecules and the ²H labels, resulting in an average distance of z directly above or below the center of the parallelogram of the four phosphorus atoms P1, P2, P3, and P4. For different z values, the ²H-³¹P inter-nuclear distances were 7.6-9.1 Å (²H-³¹P1 and ²H-³¹P31) and 4.4-6.7 Å (²H-³¹P2 and ²H-³¹P4). Each result involved the calculations and summation of 893,101 terms. Based on the curve-fitting parameters, the calculations with z = 0 fits the data the best, which means these methylene ²H atoms are at the same level as the phosphate group of the POPC lipid bilayer. Molecular dynamic simulation data suggested that the ²H atoms at the glycerol backbone of 2-AG are involved in an extended H-bonding network with the phosphorus atoms after 10-ns simulation.

Curcumin loaded Ag-TiO2-halloysite nanotubes platform for combined chemo-photodynamic therapy treatment of cancer cells.

The use of naturally occurring anticancer materials in combination with doped metal oxide has emerged as one of the most promising ways for improving anticancer treatment efficacy. In this study, the anticancer potential of curcumin-loaded Ag-TiO2-halloysite nanotubes (curcumin-loaded Ag-TiO2-HNTs) was examined. Ag-TiO2-HNTs with different wt% of Ag-TiO2 were synthesized and characterized using XRD, TGA, FT-IR, UV-Vis spectroscopy, and SEM-EDX. The XRD results revealed the presence of crystalline TiO2. However, the presence of Ag was detected through the SEM-EDX analysis. Cyclic voltammetry measurements suggested the enhancement of the release of ROS from TiO2 upon deposition with Ag. FT-IR and TGA analysis confirmed the successful loading of curcumin inside the nanotubes of the halloysite. In vitro drug released studies revealed the release of approximately 80-99% curcumin within 48 hours. Kinetic model studies revealed that the release of curcumin from HNT and Ag-TiO2-HNT followed the first-order and Higuchi models, respectively. The light irradiated curcumin-loaded Ag-TiO2-HNTs samples exhibited considerable anticancer potential as compared to the free curcumin, irradiated Ag-TiO2 NPs samples, and unirradiated curcumin loaded Ag-TiO2-HNTs samples. The obtained results revealed that combined chemo- and photodynamic therapy using curcumin-loaded Ag-TiO2-HNTs nanomaterial has the potential as an effective anticancer treatment method.

Computer-aided identification of potential inhibitors against Necator americanus glutathione S-transferase 3.

Hookworm infection is caused by the blood-feeding hookworm gastrointestinal nematodes. Its harmful effects include anemia and retarded growth and are common in the tropics. A current control method involves the mass drug administration of synthetic drugs, mainly albendazole and mebendazole. There are however concerns of low efficacy and drug resistance due to their repeated and excessive use. Although, Necator americanus glutathione S-transferase 3 (Na-GST-3) is a notable target, using natural product libraries for computational elucidation of promising leads is underexploited. This study sought to use pharmacoinformatics techniques to identify compounds of natural origins with the potential to be further optimized as promising inhibitors. A compendium of 3182 African natural products together with five known helminth GST inhibitors including Cibacron blue was screened against the active sites of the Na-GST-3 structure (PDB ID: 3W8S). The hit compounds were profiled to ascertain the mechanisms of binding, anthelmintic bioactivity, physicochemical and pharmacokinetic properties. The AutoDock Vina docking protocol was validated by obtaining 0.731 as the area under the curve calculated via the receiver operating characteristics curve. Four compounds comprising ZINC85999636, ZINC35418176, ZINC14825190, and Dammarane Triterpene13 were identified as potential lead compounds with binding energies less than -9.0 kcal/mol. Furthermore, the selected compounds formed key intermolecular interactions with critical residues Tyr95, Gly13 and Ala14. Notably, ZINC85999636, ZINC14825190, and dammarane triterpene13 were predicted as anthelmintics, whilst all the four molecules shared structural similarities with known inhibitors. Molecular modelling showed that the compounds had reasonably good binding free energies. More so, they had high binding affinities when screened against other variants of the Na-GST, namely Na-GST-1 and Na-GST-2. Ligand quality assessment using ligand efficiency dependent lipophilicity, ligand efficiency, ligand efficiency scale and fit quality scale showed the molecules are worthy candidates for further optimization. The inhibitory potentials of the molecules warrant in vitro studies to evaluate their effect on the heme regulation mechanisms.

The Influence of Pineapple Leaf Fiber Orientation and Volume Fraction on Methyl Methacrylate-Based Polymer Matrix for Prosthetic Socket Application.

This work reports on the use of low-cost pineapple leaf fiber (PALF) as an alternative reinforcing material to the established, commonly used material for prosthetic socket fabrication which is carbon-fiber-reinforced composite (CFRC) due to the high strength and stiffness of carbon fiber. However, the low range of loads exerted on a typical prosthetic socket (PS) in practice suggests that the use of CFRC may not be appropriate because of the high material stiffness which can be detrimental to socket-limb load transfer. Additionally, the high cost of carbon fiber avails opportunities to look for an alternative material as a reinforcement for composite PS development. PALF/Methyl Methacrylate-based (MMA) composites with 0°, 45° and 90° fiber orientations were made with 5-50 v/v fiber volume fractions. The PALF/MMA composites were subjected to a three-point flexural test to determine the effect of fiber volume fraction and fiber orientation on the flexural properties of the composite. The results showed that 40% v/v PALF/MMA composite with 0° fiber orientation recorded the highest flexural strength (50 MPa) and stiffness (1692 MPa). Considering the average load range exerted on PS, the flexural performance of the novel composite characterized in this work could be suitable for socket-limb load transfer for PS fabrication.

Chitosan-Coated Halloysite Nanotubes As Vehicle for Controlled Drug Delivery to MCF-7 Cancer Cells In Vitro.

The aim of the work is to improve the release properties of curcumin onto human breast cancer cell lines using coated halloysite nanotubes (HNTs) with chitosan as a polycation. A loading efficiency of 70.2% (w/w) was attained for loading 4.9 mg of the drug into 0.204 g bed volume of HNTs using the vacuum suction method. Results acquired from Brunauer-Emmett-Teller (BET), Fourier-transform infrared (FTIR) spectroscopy, transmission electron microscopy (TEM), scanning electron spectroscopy (SEM), zeta potential, and thermogravimetric analysis (TGA) indicated the presence of the drug and the biopolymer in and around the nanotubes. The release properties of drug-loaded HNTs (DLHNTs) and chitosan-coated drug-loaded HNTs (DLHNTs-CH) were evaluated. The release percentages of DLHNTs and DLHNTs-CH after 6 h were 50.7 and 37%, respectively. Based on the correlation coefficients obtained by fitting the release nature of curcumin from the two samples, the Korsmeyer-Peppas model was found to be the best-fitted model. In vitro cell viability studies were carried out on the human breast cancer cell line MCF-7, using the MTT and trypan blue exclusion assays. Prior to the Trypan blue assay, the IC50 of curcumin was determined to be ~30 µM. After 24 h of incubation, the recorded cell viability values were 94, 68, 57, and 51% for HNTs, DLHNTs-CH, DLHNTs, and curcumin, respectively. In comparison to the release studies, it could be deducted that sustained lethal doses of curcumin were released from the DLHNTs-CH within the same time. It is concluded from this work that the "burst release" of naked drugs could be slowly administered using chitosan-coated HNTs as potential drug carriers.

Solid-state NMR and molecular dynamics characterization of cannabinoid receptor-1 (CB1) helix 7 conformational plasticity in model membranes.

Little direct information is available regarding the influence of membrane environment on transmembrane (TM) G-protein-coupled receptor (GPCR) conformation and dynamics. The human CB1 cannabinoid receptor (hCB1) is a prominent GPCR pharmacotherapeutic target in which helix 7 appears critical to ligand recognition. We have chemically synthesized a hCB1 peptide corresponding to a segment of TM helix 7 and the entire contiguous helix 8 domain (fourth cytoplasmic loop) and reconstituted it in defined phospholipid-bilayer model membranes. Using an NMR-based strategy combined with molecular dynamics simulations, we provide the first direct experimental description of the orientation of hCB1 helix 7 in phospholipid membranes of varying thickness and the mechanism by which helix-7 conformation adjusts to avoid hydrophobic mismatch. Solid-state (15)N NMR data show that hCB1 helices 7 and 8 reconstituted into phospholipid bilayers are oriented in a TM and in-plane (i.e., parallel to the phospholipid membrane surface) fashion, respectively. TM helix orientation is influenced by the thickness of the hydrophobic membrane bilayer as well as the interaction of helix 8 with phospholipid polar headgroups. Molecular dynamics simulations show that a decrease in phospholipid chain-length induces a kink at P394 in TM helix 7 to avoid hydrophobic mismatch. Thus, the NP(X)nY motif found in hCB1 and highly conserved throughout the GPCR superfamily is important for flexing helix 7 to accommodate bilayer thickness. Dynamic modulation of hCB1-receptor TM helix conformation by its membrane environment may have general relevance to GPCR structure and function.

Dynamic conformational responses of a human cannabinoid receptor-1 helix domain to its membrane environment.

The influence of membrane environment on human cannabinoid 1 (hCB(1)) receptor transmembrane helix (TMH) conformational dynamics was investigated by solid-state NMR and site-directed spin labeling/EPR with a synthetic peptide, hCB(1)(T377-E416), corresponding to the receptor's C-terminal component, i.e., TMH7 and its intracellular alpha-helical extension (H8) (TMH7/H8). Solid-state NMR experiments with mechanically aligned hCB(1)(T377-E416) specifically (2)H- or (15)N-labeled at Ala380 and reconstituted in membrane-mimetic dimyristoylphosphocholine (DMPC) or 1-palmitoyl-2-oleoyl-sn-glycerophosphocholine (POPC) bilayers demonstrate that the conformation of the TMH7/H8 peptide is more heterogeneous in the thinner DMPC bilayer than in the thicker POPC bilayer. As revealed by EPR studies on hCB(1)(T377-E416) spin-labeled at Cys382 and reconstituted into the phospholipid bilayers, the spin label partitions actively between hydrophobic and hydrophilic environments. In the DMPC bilayer, the hydrophobic component dominates, regardless of temperature. Mobility parameters (DeltaH(0)(-1)) are 0.3 and 0.73 G for the peptide in the DMPC or POPC bilayer environment, respectively. Interspin distances of doubly labeled hCB(1)(T377-E416) peptide reconstituted into a TFE/H(2)O mixture or a POPC or DMPC bilayer were estimated to be 10.6 +/- 0.5, 16.8 +/- 1, and 11.6 +/- 0.8 A, respectively. The extent of coupling (>or=50%) between spin labels located at i and i + 4 in a TFE/H(2)O mixture or a POPC bilayer is indicative of an alpha-helical TMH conformation, whereas the much lower coupling (14%) when the peptide is in a DMPC bilayer suggests a high degree of peptide conformational heterogeneity. These data demonstrate that hCB(1)(T377-E416) backbone dynamics as well as spin-label rotameric freedom are sensitive to and altered by the peptide's phospholipid bilayer environment, which exerts a dynamic influence on the conformation of a TMH critical to signal transmission by the hCB(1) receptor.

Structural biology of human cannabinoid receptor-2 helix 6 in membrane-mimetic environments.

We detail the structure and dynamics of a synthetic peptide corresponding to transmembrane helix 6 (TMH6) of human cannabinoid receptor-2 (hCB2) in biomembrane-mimetic environments. The peptide's NMR structural biology is characterized by two alpha-helical domains bridged by a flexible, nonhelical hinge region containing a highly-conserved CWFP motif with an environmentally sensitive, Pro-based conformational switch. Buried within the peptide's flexible region, W(258) may hydrogen-bond with L(255) to help stabilize the Pro-kinked hCB2 TMH6 structure and position C(257) advantageously for interaction with agonist ligands. These characteristics of hCB2 TMH6 are potential structural features of ligand-induced hCB2 activation in vivo.

NMR solution structure of human cannabinoid receptor-1 helix 7/8 peptide: candidate electrostatic interactions and microdomain formation.

We report the NMR solution structure of a synthetic 40-mer (T(377)-E(416)) that encompasses human cannabinoid receptor-1 (hCB1) transmembrane helix 7 (TMH7) and helix 8 (H8) [hCB1(TMH7/H8)] in 30% trifluoroethanol/H(2)O. Structural features include, from the peptide's amino terminus, a hydrophobic alpha-helix (TMH7); a loop-like, 11 residue segment featuring a pronounced Pro-kink within the conserved NPxxY motif; a short amphipathic alpha-helix (H8) orthogonal to TMH7 with cationic and hydrophobic amino-acid clusters; and an unstructured C-terminal end. The hCB1(TMH7/H8) NMR solution structure suggests multiple electrostatic amino-acid interactions, including an intrahelical H8 salt bridge and a hydrogen-bond network involving the peptide's loop-like region. Potential cation-pi and cation-phenolic OH interactions between Y(397) in the TMH7 NPxxY motif and R(405) in H8 are identified as candidate structural forces promoting interhelical microdomain formation. This microdomain may function as a flexible molecular hinge during ligand-induced hCB1 conformer transitions.

Electrochemical Response of Saccharomyces cerevisiae Corresponds to Cell Viability upon Exposure to Dioclea reflexa Seed Extracts and Antifungal Drugs.

Dioclea reflexa bioactive compounds have been shown to contain antioxidant properties. The extracts from the same plant are used in traditional medical practices to treat various diseases with impressive outcomes. In this study, ionic mobility in Saccharomyces cerevisiae cells in the presence of D. reflexa seed extracts was monitored using electrochemical detection methods to link cell death to ionic imbalance. Cells treated with ethanol, methanol, and water extracts were studied using cyclic voltammetry and cell counting to correlate electrochemical behavior and cell viability, respectively. The results were compared with cells treated with pore-forming Amphotericin b (Amp b), as well as Fluconazole (Flu) and the antimicrobial drug Rifampicin (Rif). The D. reflexa seed water extract (SWE) revealed higher anodic peak current with 58% cell death. Seed methanol extract (SME) and seed ethanol extract (SEE) recorded 31% and 22% cell death, respectively. Among the three control drugs, Flu revealed the highest cell death of about 64%, whereas Amp b and Rif exhibited cell deaths of 35% and 16%, respectively, after 8 h of cell growth. It was observed that similar to SWE, there was an increase in the anodic peak current in the presence of different concentrations of Amp b, which also correlated with enhanced cell death. It was concluded from this observation that Amp b and SWE might follow similar mechanisms to inhibit cell growth. Thus, the individual bioactive compounds from the water extracts of D. reflexa seeds could further be purified and tested to validate their potential therapeutic application. The strategy to link electrochemical behavior to biochemical responses could be a simple, fast, and robust screening technique for new drug targets and to understand the mechanism of action of such drugs against disease models.

Pharmacoinformatics-based identification of potential bioactive compounds against Ebola virus protein VP24.

BACKGROUND: The impact of Ebola virus disease (EVD) is devastating with concomitant high fatalities. Currently, various drugs and vaccines are at different stages of development, corroborating the need to identify new therapeutic molecules. The VP24 protein of the Ebola virus (EBOV) plays a key role in the pathology and replication of the EVD. The VP24 protein interferes with the host immune response to viral infections and promotes nucleocapsid formation, thus making it a viable drug target. This study sought to identify putative lead compounds from the African flora with potential to inhibit the activity of the EBOV VP24 protein using pharmacoinformatics and molecular docking. METHODS: An integrated library of 7675 natural products originating from Africa obtained from the AfroDB and NANPDB databases, as well as known inhibitors were screened against VP24 (PDB ID: 4M0Q) utilising AutoDock Vina after energy minimization using GROMACS. The top 19 compounds were physicochemically and pharmacologically profiled using ADMET Predictor™, SwissADME and DataWarrior. The mechanisms of binding between the molecules and EBOV VP24 were characterised using LigPlot+. The performance of the molecular docking was evaluated by generating a receiver operating characteristic (ROC) by screening known inhibitors and decoys against EBOV VP24. The prediction of activity spectra for substances (PASS) and machine learning-based Open Bayesian models were used to predict the anti-viral and anti-Ebola activity of the molecules, respectively. RESULTS: Four natural products, namely, ZINC000095486070, ZINC000003594643, ZINC000095486008 and sarcophine were found to be potential EBOV VP24-inhibitiory molecules. The molecular docking results showed that ZINC000095486070 had high binding affinity of -9.7 kcal/mol with EBOV VP24, which was greater than those of the known VP24-inhibitors used as standards in the study including Ouabain, Nilotinib, Clomiphene, Torimefene, Miglustat and BCX4430. The area under the curve of the generated ROC for evaluating the performance of the molecular docking was 0.77, which was considered acceptable. The predicted promising molecules were also validated using induced-fit docking with the receptor using Schrödinger and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The molecules had better binding mechanisms and were pharmacologically profiled to have plausible efficacies, negligible toxicity as well as suitable for designing anti-Ebola scaffolds. ZINC000095486008 and sarcophine (NANPDB135) were predicted to possess anti-viral activity, while ZINC000095486070 and ZINC000003594643 to be anti-Ebola compounds. CONCLUSION: The identified compounds are potential inhibitors worthy of further development as EBOV biotherapeutic agents. The scaffolds of the compounds could also serve as building blocks for designing novel Ebola inhibitors.

Structural divergence among cannabinoids influences membrane dynamics: a 2H solid-state NMR analysis.

Cannabinoids are compounds that can modulate neuronal functions and immune responses via their activity at the CB(1) receptor. We used (2)H NMR order parameters and relaxation rate determination to delineate the behavior of magnetically aligned phospholipid bilayers in the presence of several structurally distinct cannabinoid ligands. THC (Delta(9)-Tetrahydrocannabinol) and WIN-55,212-2 were found to lower the phase transition temperature of the DMPC and to destabilize their acyl chains leading to a lower average S(CD) ( approximately 0.13), while methanandamide and CP-55,940 exhibited unusual properties within the lipid bilayer resulting in a greater average S(CD) ( approximately 0.14) at the top of the phospholipid upper chain. The CB(1) antagonist AM281 had average S(CD) values that were higher than the pure DMPC lipids, indicating a stabilization of the lipid bilayer. R(1Z) versus |S(CD)|(2) plots indicated that the membrane fluidity is increased in the presence of THC and WIN-55,212-2. The interaction of CP-55,940 with a variety of zwitterionic and charged membranes was also assessed. The unusual effect of CP-55,940 was present only in bicelles composed of DMPC. These studies strongly suggest that cannabinoid action on the membrane depends upon membrane composition as well as the structure of the cannabinoid ligands.

Chitosan Composites Synthesized Using Acetic Acid and Tetraethylorthosilicate Respond Differently to Methylene Blue Adsorption.

The sol-gel and cross-linking processes have been used by researchers to synthesize silica-based nanostructures and optimize their size and morphology by changing either the material or the synthesis conditions. However, the influence of the silica nanostructures on the overall physicochemical and mechanistic properties of organic biopolymers such as chitosan has received limited attention. The present study used a one-step synthetic method to obtain chitosan composites to monitor the uptake and release of a basic cationic dye (methylene blue) at two different pH values. Firstly, the composites were synthesized and characterized by Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Diffraction (XRD) to ascertain their chemical identity. Adsorption studies were conducted suing methylene blue and these studies revealed that Acetic Acid-Chitosan (AA-CHI), Tetraethylorthosilicate-Chitosan (TEOS-CHI), Acetic Acid-Tetraethylorthosilicate-Chitosan (AA-TEOS-CHI), and Acetic Acid-Chitosan-Tetraethylorthosilicate (AA-CHI-TEOS) had comparatively lower percentage adsorbances in acidic media after 40 h, with AA-CHI adsorbing most of the methylene blue dye. In contrast, these materials recorded higher percentage adsorbances of methylene blue in the basic media. The release profiles of these composites were fitted with an exponential model. The R-squared values obtained indicated that the AA-CHI at pH ~ 2.6 and AA-TEOS-CHI at pH ~ 7.2 of methylene blue had steady and consistent release profiles. The release mechanisms were analyzed using Korsmeyer-Peppas and Hixson-Crowell models. It was deduced that the release profiles of the majority of the synthesized chitosan beads were influenced by the conformational or surface area changes of the methylene blue. This was justified by the higher correlation coefficient or Pearson's R values (R ≥ 0.5) computed from the Hixson-Crowell model. The results from this study showed that two of the novel materials comprising acetic acid-chitosan and a combination of equimolar ratios of acetic acid-TEOS-chitosan could be useful pH-sensitive probes for various biomedical applications, whereas the other materials involving the two-step synthesis could be found useful in environmental remediation of toxic materials.

Investigating the Conformation of S100ß Protein Under Physiological Parameters Using Computational Modeling: A Clue for Rational Drug Design.

BACKGROUND: Physiochemical factors such as temperature, pH and cofactors are well known parameters that confer conformational changes in a protein structure. With S100ß protein being a metal binding brain-specific receptor for both extracellular and intracellular functions, a change in conformation due to the above-mentioned factors, can compromise their cellular functions and therefore result in several pathological conditions such as Alzheimer's disease, Ischemic stroke, as well as Myocardial Infarction. OBJECTIVE: The studies conducted sought to elucidate the effect of these physiological factors on the conformational dynamics of S100ß protein using computational modeling approaches. METHOD: Temperature-dependent and protein-cofactor complexes molecular dynamics simulations were conducted by varying the temperature from 100 to 400K using GROMACS 5.0.3. Additionally, the conformational dynamics of the protein was studied by varying the pH at 5.0, 7.4 and 9.0 using Ambertools17. This was done by preparing the protein molecule, solvating and minimizing its energy level as well as heating it to the required temperature, equilibrating and simulating under desired conditions (NVT and NPT ensembles). RESULTS: The results show that the protein misfolds as a function of increasing temperature with alpha helical content at 100K and 400K being 57.8% and 43.3%, respectively. However, the binding sites of the protein was not appreciably affected by temperature variations. The protein displayed high conformational instability in acidic medium (pH ~5.0). The binding sites of Ca2+, Mg2+ and Zn2+ were identified and each exhibited different groupings of the secondary structural elements (binding motifs). The secondary structure analysis revealed different conformational changes with the characteristic appearance of two beta hairpins in the presence of Zn2+and Mg2+. CONCLUSION: High temperatures, different cofactors and acidic pH confer conformational changes to the S100ß structure and these results may inform the design of novel drugs against the protein.

The structural properties of the transmembrane segment of the integral membrane protein phospholamban utilizing (13)C CPMAS, (2)H, and REDOR solid-state NMR spectroscopy.

Solid-state NMR spectroscopic techniques were used to investigate the secondary structure of the transmembrane peptide phospholamban (TM-PLB), a sarcoplasmic Ca(2+) regulator. (13)C cross-polarization magic angle spinning spectra of (13)C carbonyl-labeled Leu39 of TM-PLB exhibited two peaks in a pure 1-palmitoyl-2-oleoyl-phosphocholine (POPC) bilayer, each due to a different structural conformation of phospholamban as characterized by the corresponding (13)C chemical shift. The addition of a negatively charged phospholipid (1-palmitoyl-2-oleoylphosphatidylglycerol (POPG)) to the POPC bilayer stabilized TM-PLB to an alpha-helical conformation as monitored by an enhancement of the alpha-helical carbonyl (13)C resonance in the corresponding NMR spectrum. (13)C-(15)N REDOR solid-state NMR spectroscopic experiments revealed the distance between the (13)C carbonyl carbon of Leu39 and the (15)N amide nitrogen of Leu42 to be 4.2+/-0.2A indicating an alpha-helical conformation of TM-PLB with a slight deviation from an ideal 3.6 amino acid per turn helix. Finally, the quadrupolar splittings of three (2)H labeled leucines (Leu28, Leu39, and Leu51) incorporated in mechanically aligned DOPE/DOPC bilayers yielded an 11 degrees +/-5 degrees tilt of TM-PLB with respect to the bilayer normal. In addition to elucidating valuable TM-PLB secondary structure information, the solid-state NMR spectroscopic data indicates that the type of phospholipids and the water content play a crucial role in the secondary structure and folding of TM-PLB in a phospholipid bilayer.

Expression, Purification, and Monitoring of Conformational Changes of hCB2 TMH67H8 in Different Membrane-Mimetic Lipid Mixtures Using Circular Dichroism and NMR Techniques.

This work was intended to develop self-assembly lipids for incorporating G-protein coupled receptors (GPCRs) in order to improve the success rate for nuclear magnetic resonance spectroscopy (NMR) structural elucidation. We hereby report the expression and purification of uniformly 15N-labeled human cannabinoid receptor-2 domain in insect cell media. The domain was refolded by screening several membrane mimetic environments. Different q ratios of isotropic bicelles were screened for solubilizing transmembrane helix 6, 7 and 8 (TMH67H8). As the concentration of dimyristoylphosphocholine (DMPC) was increased such that the q ratio was between 0.16 and 0.42, there was less crowding in the cross peaks with increasing q ratio. In bicelles of q = 0.42, the maximum number of cross peaks were obtained and the cross peaks were uniformly dispersed. The receptor domain in bicelles beyond q = 0.42 resulted in peak crowding. These studies demonstrate that GPCRs folding especially in bicelles is protein-specific and requires the right mix of the longer chain and shorter chain lipids to provide the right environment for proper folding. These findings will allow further development of novel membrane mimetics to provide greater diversity of lipid mixtures than those currently being employed for GPCR stability and folding, which are critical for both X-ray and NMR studies of GPCRs.