Virtual Screening on Marine Natural Products for Discovering TMPRSS2 Inhibitors.

Although SARS-CoV-2 entry to cells strictly depends on angiotensin-converting enzyme 2 (ACE2), the virus also needs transmembrane serine protease 2 (TMPRSS2) for its spike protein priming. It has been shown that the entrance of SARS-CoV-2 through ACE2 can be blocked by cellular TMPRSS2 blockers. The main aim of this study was to find potential inhibitor(s) of TMPRSS2 through virtual screening against a homology model of TMPRSS2 using the library of marine natural products (MNPs). The homology modeling technique for generating a three-dimensional structure of TMPRSS2 was applied. Molecular docking, MM-GBSA and absorption, distribution, metabolism, excretion (ADME) evaluations were performed to investigate the inhibitory activity of marine natural products (MNPs) against TMPRSS2 and their pharmacokinetic properties. Camostat and nafamostat mesylate were used as the standard inhibitory molecules. Seven MNPs were able to inhibit TMPRSS2 better than the standard compounds. MNP 10 with CAS number 107503-09-3, called Watasenia ß-D- Preluciferyl glucopyrasoiuronic acid, was found to be the best inhibitor of TMPRSS2 with acceptable pharmacokinetic properties. Herein, for the first time, a new marine natural product was introduced with potent inhibitory effects against TMPRSS2. MNP 10 exhibited favorable drug-like pharmacokinetic properties and it promises a novel TMPRSS2 blocker to combat SARS-CoV-2.

Chemical compositions and experimental and computational modeling activity of sea cucumber Holothuria parva ethanolic extract against herpes simplex virus type 1.

Sea cucumber has antiviral activities against various viruses including herpes simplex virus type 1 (HSV-1). The purpose of the current study was to determine the chemical profile and inhibitory effects of tegument ethanolic extract of Holothuria parva on HSV-1 infection and to elucidate the mechanism of antiviral action of this marine invertebrate. Cytotoxic activity of the extract on Vero cell line was determined using the methyl thiazolyl tetrazolium (MTT) method. The different components in H. parva were determined by GC-MS analysis. To assess the antiviral activity of the extract, MTT and 50% tissue culture infective dose (TCID50) were applied. Finally, computational molecular docking was performed to screen the potential binding ability of extract contents with HSV-1 surface glycoproteins and host cell surface receptors. Using MTT assay, the non-cytotoxic concentration of the extract was measured 46.5 µg/mL. Octadecanoic acid 2-hydroxy-1-(hydroxymethyl) ethyl ester and 2',6'-acetoxylidide were two major constituents in the H. parva extract. Pre-treatment of HSV-1 with the ethanolic extract of H. parva led to a 2.1 log10 TCID50 reduction in virus titers when compared to the control group (P = 0.002). The log10 TCID50 reductions relative to the control group for co-penetration and post-penetration assays were 1.5 (P = 0.009) and 0.7 (P = 0.09), respectively. The tegument ethanolic extract of H. parva has significant antiviral properties against HSV-1. Docking analysis demonstrated that compounds of the extract [lidocaine and 2-hydroxy-1-(hydroxymethyl) ethyl ester octadecanoic acid] may cover similarly both virus and host cells binding domains leading to interference in virus attachment to cell receptors.

Density Functional Theory Studies on the Antioxidant Mechanism and Electronic Properties of Some Bioactive Marine Meroterpenoids: Sargahydroquionic Acid and Sargachromanol.

Certain meroterpenoids isolated from brown alga of the genus Sargassum are known to be antioxidant agents. Herein, density functional theory has been performed to analyze the preferred antioxidant mechanism of the two reactive antioxidant compounds derived from the Sargassum genus, that is, Sargahydroquinoic acid and Sargachromanol and some of their derivatives. Their global reactivity descriptors have been calculated to reveal their reactivity as an antioxidant. Molecule 1 is the most reactive antioxidant according to calculated descriptors. The results of molecule 1 are comparable to that of Trolox, suggesting their similar activity. The calculated descriptors are closely matched with experimental pieces of evidence. It has been found that hydrogen atom transfer (HAT) is more favored in gas media. Also, the effect of solvent polarity on the antioxidant activity has been explored for molecule 1. The results disclose that the polarity of the solvent increases the contribution of two other mechanisms, that is, single-electron transfer, followed by proton transfer and sequential proton loss electron transfer.

Acetylcholinesterase inhibitory activity of a neurosteroidal alkaloid from the upside-down jellyfish Cassiopea andromeda venom

Abstract Natural compounds from marine organisms have been rarely studied for their acetylcholinesterase inhibitory activities. The aim of this study was to isolate novel compounds with antiAChE activity from the venom of upside-down jellyfish Cassiopea andromeda Forskål, 1775. The compounds of the fractionated venom on gel filtration chromatography were identified by analyzing gas chromatography-mass spectroscopy data. The structure of the isolated compound that showed the most potent antiAChE activity in a docking study was elucidated by different spectral data, including 1H NMR and 13C NMR. Three compounds, including a neurosteroidal alkaloid androtoxin B, were identified from two venom fractions. This neurosteroidal alkaloid showed strong acetylcholinesterase inhibitory activity (IC50 2.24 ± 0.1 µM) compared with the reference standard, galantamine. The results obtained by a docking study demonstrated that Androtoxin B had close contact with two of the three amino acid residues of the catalytic triad of acetylcholinesterase gorge and was accommodated within a peripheral hydrophobic pocket composed of numerous aromatic site chains. In conclusion, the isolated neurosteroidal alkaloid from Cassiopea andromeda was a potent antiAChE agent with strong binding to both the catalytic and peripheral sites of acetylcholinesterase that correlated well with the experimental data. Further studies are required to determine whether androtoxin B could be a potential treatment for Alzheimer's disease.

Molecular Dynamics and Docking Investigations of Several Zoanthamine-Type Marine Alkaloids as Matrix Metaloproteinase-1 Inhibitors.

Zoanthamine-type alkaloids display a wide spectrum of biological effects. This study aimed to examine the inhibitory effects of norzoanthamine and its ten homologues of zoanthamine class on human fibroblast collagenase by modeling a three-dimensional structure of the ligands at collagenase using energy minimization, docking, molecular dynamics simulation and MM-PB/GBSA binding free energy calculations. The results showed that zoanthamide, zooxathellamine and enol-iminium form of norzoanthamine, with lower binding free energies than other compounds, are potent inhibitors of collagenase. However, the enol-iminium form of norzoanthamine showed a more inhibitory activity against collagenase than its keto form. This suggests that it can be used for treatment of many diseases such as osteoporosis, autoimmune diseases, and cancer. Zinc-binding residues such as His 118, His 122 and His 128 for hydrogen bonds and Leu 81, Tyr 110, Val 115, Leu 126, Pro 138, Ser 139 for hydrophobic interactions should be considered for designing an inhibitor for collagenase. Our theoretical results and MM/GBSA binding free energy calculations are consistent with experimental studies.

Development of a new colorimetric assay for detection of bisphenol-A in aqueous media using green synthesized silver chloride nanoparticles: experimental and theoretical study.

In the present study, a cost-effective, green and simple synthesis method was applied for preparation of stable silver chloride nanoparticles (AgCl-NPs). The method was done by forming AgCl-NPs from Ag+ ions using aqueous extract of brown algae (Sargassum boveanum) obtained from the Persian Gulf Sea. This extract served as capping agent during the formation of AgCl-NPs. Creation of AgCl-NPs was confirmed by UV-visible spectroscopy, powder X-ray diffraction, energy-dispersive X-ray spectroscopy, and high-resolution transmission electron microscopy, while the morphology and size analyses were characterized using high-resolution transmission electron microscopy and dynamic light scattering. After optimization of some experimental conditions, particularly pH, a simple and facile system was developed for the naked-eye detection of bisphenol-A. Moreover, a theoretical study of AgCl interaction with bisphenol-A was performed at the density functional level of theory in both gas and solvent phases. Theoretical results showed that electrostatic and van der Waal interactions play important roles in complexation of bisphenol-A with AgCl-NPs, which can lead to aggregation of the as-prepared AgCl-NPs and results in color change from specific yellow to dark purple, where a new aggregation band induced at 542 nm appears. The absorbance at 542 nm was found to be linearly dependent on the bisphenol-A concentration in the range of 1 × 10-6-1 × 10-4 M, with limit of detection of 45 nM. In conclusion, obtained results from the present study can open up an innovative application of the green synthesis of AgCl-NPs using brown algae extract as colorimetric sensors.

Variable selection in multivariate calibration based on clustering of variable concept.

Recently we have proposed a new variable selection algorithm, based on clustering of variable concept (CLoVA) in classification problem. With the same idea, this new concept has been applied to a regression problem and then the obtained results have been compared with conventional variable selection strategies for PLS. The basic idea behind the clustering of variable is that, the instrument channels are clustered into different clusters via clustering algorithms. Then, the spectral data of each cluster are subjected to PLS regression. Different real data sets (Cargill corn, Biscuit dough, ACE QSAR, Soy, and Tablet) have been used to evaluate the influence of the clustering of variables on the prediction performances of PLS. Almost in the all cases, the statistical parameter especially in prediction error shows the superiority of CLoVA-PLS respect to other variable selection strategies. Finally the synergy clustering of variable (sCLoVA-PLS), which is used the combination of cluster, has been proposed as an efficient and modification of CLoVA algorithm. The obtained statistical parameter indicates that variable clustering can split useful part from redundant ones, and then based on informative cluster; stable model can be reached.

Chlamydia pneumoniae and Helicobacter pylori IgG seropositivities are not predictors of osteoporosis-associated bone loss: a prospective cohort study.

The potential link between infection with Chlamydia pneumoniae or Helicobacter pylori and osteoporosis has not been investigated in population-based longitudinal studies. A total of 250 healthy postmenopausal women who participated in a prospective cohort study were evaluated for IgG antibodies directed against C. pneumoniae and H. p ylori, osteoprotegerin (OPG), the receptor activator of nuclear factor kappa B ligand (RANKL), CrossLaps, and osteocalcin. Bone mineral density (BMD) was measured at the femoral neck and lumbar spine at baseline and at follow-up 5.8 years later. There were no significant differences in age-adjusted bone turnover markers, OPG, RANKL, the RANKL/OPG ratio, and BMD between the C. p neumoniae and H. p ylori IgG seropositive and seronegative subjects (P > 0.05). Neither C. p neumoniae nor H. p ylori IgG seropositivity was associated with age-and body mass index-adjusted BMD at the femoral neck and lumbar spine or bone loss at the 5.8-year follow-up. In logistic regression analysis, neither C. p neumoniae nor H. p ylori IgG seropositivities predicted incident lumbar or spine osteoporosis 5.8 years later. In conclusion, neither C. p neumoniae nor H. p ylori IgG seropositivity was associated with bone turnover markers, the RANKL/OPG ratio, BMD, or bone loss in postmenopausal women. In addition, chronic infection with C. p neumoniae or H. p ylori did not predict incident osteoporosis among this group of women.

Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods.

We have used combined quantum mechanical and molecular mechanical free-energy perturbation methods in combination with explicit solvent simulations to study the reaction mechanism of the multicopper oxidases, in particular, the regeneration of the reduced state from the native intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states of the copper ions and the protonation states of water- and O2-derived ligands, we have studied redox potentials, acidity constants, isomerization reactions, as well as water- and O2 binding reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with atomic detail. We also show that the two copper sites in the protein communicate so that redox potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change in the oxidation state of the other site.

Marine natural products as acetylcholinesterase inhibitor: comparative quantum mechanics and molecular docking study.

Alzheimer's disease (AD) is the most common form of dementia which affects the elderly population throughout the world. The inhibition of acetylcholinesterase (AChE) has appeared as one of the most promising strategies for the AD treatment. In this study, the density functional theory and molecular docking studies have been carried out on seven halogenated sesquiterpenes derived from the Persian Gulf sea hare, Aplysia dactylomela, to reveal their electronic, structural and chemical properties. Moreover, influences of these properties on their AChE-inhibition properties have been investigated theoretically. The results indicate that these compounds have several interactions with important residues of AChE active sites. Three of the investigated molecules correlate better to well-known AD drugs such as huperzine A, galanthamine and donepezil which represent possible AChE inhibitors against Alzheimer disease. In conclusion, the information obtained from this theoretical study may aid in the discovery of new potential AChE inhibitors with marine origin.

Association of pathogen burden and hypertension: the Persian Gulf Healthy Heart Study.

BACKGROUND: Chronic infection with cytomegalovirus (CMV), Chlamydia pneumoniae, herpes simplex virus 1 (HSV-1), and Helicobacter pylori may contribute to essential hypertension. However, the evidence now available does not clarify whether the aggregate number of pathogens (pathogen burden) may be associated with hypertension. METHODS: Sera from 1,754 men and women aged ≥25 years were analyzed for immunoglobulin G antibodies to C. pneumoniae, HSV-1, H. pylori, and CMV using enzyme-linked immunosorbent assay. The aggregate number of seropositives to the studied viral and bacterial agents was defined as pathogen burden. Hypertension was defined according to World Health Organization criteria. RESULTS: A total of 459 (26.3%) of the subjects had hypertension. In the hypertensive group, 4.2% had 0 or 1 pathogens present, 20.6% had 2, 43.2% had 3, and 32.1% had 4; in the normotensive group, 7.9% had 0 or 1, 28.4% had 2, 42.7% had 3, and 21.0% had 4. Of the 4 studied pathogens, H. pylori seropositivity showed a significant independent association with hypertension (odds ratio (OR) =1.37; 95% confidence interval (CI) =1.05-1.79; P = 0.02). In multiple logistic regression analyses, the pathogen burden did not show a significant independent association with hypertension. Coinfection with H. pylori and C. pneumoniae was significantly associated with hypertension compared with double seronegativity after adjustment for age, sex, chronic low-grade inflammation, and cardiovascular risk factors (OR = 1.68; 95% CI = 1.14-2.47; P = 0.008]. CONCLUSIONS: The pathogen burden was not associated with hypertension. However, coinfection with C. pneumoniae and H. pylori showed a significant association with essential hypertension, independent of cardiovascular risk factors and chronic low-grade inflammation.

Omentin-1, visfatin and adiponectin levels in relation to bone mineral density in Iranian postmenopausal women.

The bone and fat interface is implicated in the pathogenesis of postmenopausal osteoporosis. The association between circulating omentin-1 levels and bone mineral density (BMD) in postmenopausal women has never been assessed. A total of 382 healthy postmenopausal women were randomly selected. Omentin-1, visfatin, adiponectin, the receptor activator of nuclear factor-κB ligand (RANKL), osteoprotegerin, high sensitivity C-reactive protein, degradation products of C-terminal telopeptides of type I collagen, and osteocalcin were measured by highly specific enzyme-linked immunosorbent assay methods. BMD was determined for the lumbar spine (L2-L4) and the proximal femur using dual-energy X-ray absorptiometry. In multivariable-adjusted linear regression, serum omentin-1 levels were inversely correlated with BMD at the lumbar spine (ß=-0.11, p=0.020). In multiple regression analyses, serum visfatin and adiponectin levels were not significantly correlated with BMD at different skeletal sites after controlling for age, body mass index, and bone-related markers. However, the highest quartile of adiponectin compared to the lowest quartile, after adjusting for potential confounders, revealed an inverse association with BMD in the lumbar spine (ß=-0.19, p=0.010). In conclusion, circulating omentin-1 levels had an inverse correlation with BMD at the lumbar spine in Iranian postmenopausal women. To further understand the role of omentin-1 in bone and mineral metabolism, large-scale longitudinal studies focusing on BMD and osteoporotic fractures are warranted.

Reduced serum osteocalcin concentrations are associated with type 2 diabetes mellitus and the metabolic syndrome components in postmenopausal women: the crosstalk between bone and energy metabolism.

Although it has been shown that osteocalcin functions as a hormone in the regulation of glucose metabolism and fat mass, no population-based study to date has addressed serum osteocalcin levels in relation to energy metabolism concurrent with bone metabolism in postmenopausal women. In a population-based study, cardiovascular risk factors, high-sensitivity C-reactive protein (hs-CRP), osteoprotegerin, receptor activator of nuclear factor-κB ligand, osteocalcin, CrossLaps, alkaline phosphatase, and bone mineral density (BMD) at the lumbar spine (L2-L4) and the proximal femur were measured in 382 Iranian postmenopausal women. In multiple logistic regression analysis, lower osteocalcin and CrossLaps levels were associated with a higher odds ratio (OR) of having type 2 diabetes mellitus when adjustments were made for age, hs-CRP, cardiovascular risk factors, BMD, and markers of bone metabolism [OR 5.17, CI (2.66-10.04), p < 0.0001 and OR 2.51, CI (1.37-4.61), p = 0.003, respectively]. However, lower alkaline phosphatase levels were associated with a lower OR of having type 2 diabetes mellitus [OR 0.28, CI (0.15-0.52), p < 0.0001] in regression analysis. No significant difference was found between serum osteocalcin levels of those with and without metabolic syndrome. Among the metabolic syndrome components, low osteocalcin levels had significant associations with elevated blood glucose [OR 1.89, CI (1.16-3.07), p = 0.010] and elevated waist circumference [OR 2.53, CI (1.13-5.67), p = 0.024] in multivariate analyses. In conclusion, serum osteocalcin was independently associated with glucose intolerance and abdominal obesity as the components of metabolic syndrome and type 2 diabetes mellitus in postmenopausal women. Since CrossLaps and alkaline phosphatase levels were independently associated with the presence of type 2 diabetes mellitus, the unique contribution of osteocalcin in glucose metabolism could not be concluded.

Reorganization energy for internal electron transfer in multicopper oxidases.

We have calculated the reorganization energy for the intramolecular electron transfer between the reduced type 1 copper site and the peroxy intermediate of the trinuclear cluster in the multicopper oxidase CueO. The calculations are performed at the combined quantum mechanics and molecular mechanics (QM/MM) level, based on molecular dynamics simulations with tailored potentials for the two copper sites. We obtain a reorganization energy of 91-133 kJ/mol, depending on the theoretical treatment. The two Cu sites contribute by 12 and 22 kJ/mol to this energy, whereas the solvent contribution is 34 kJ/mol. The rest comes from the protein, involving small contributions from many residues. We have also estimated the energy difference between the two electron-transfer states and show that the reduction of the peroxy intermediate is exergonic by 43-87 kJ/mol, depending on the theoretical method. Both the solvent and the protein contribute to this energy difference, especially charged residues close to the two Cu sites. We compare these estimates with energies obtained from QM/MM optimizations and QM calculations in a vacuum and discuss differences between the results obtained at various levels of theory.