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Soft corals belonging to the family Nephtheidae have been appreciated as marine sources of diverse metabolites with promising anticancer potential. In view of that, the current work investigates the anti-proliferative potential of the crude extract, different fractions, and green synthesized silver nanoparticles (AgNPs) of the Red Sea soft coral, Nephthea sp. against a panel of tumor cell lines. The metabolic pool of the soft coral under study was also explored via an LC-HR-ESI-MS metabolomics approach, followed by molecular docking analysis of the characterized metabolites against the target proteins, EGFR, VEGFR, and HER2 (erbB2) that are known to be involved in cancer cell proliferation, growth, and survival. Overall, the n-butanol fraction of Nephthea sp. exhibited the highest inhibitory activities against MCF7 (breast cancer) and A549 (lung cancer) cell lines, with interesting IC50 values of 2.30 ± 0.07 and 3.12 ± 0.10 μg ml−1, respectively, whereas the maximum growth inhibition of HL60 (leukemia) cells was recorded by the total extract (IC50 = 2.78 ± 0.09 μg ml−1). More interestingly, the anti-proliferative potential of the total soft coral extract was evidently improved when packaged in the form of biogenic AgNPs, particularly against A549 and MCF7 tumor cells, showing IC50 values of 0.72 ± 0.06 and 9.32 ± 0.57 μg ml−1, respectively. On the other hand, metabolic profiling of Nephthea sp. resulted in the annotation of structurally diverse terpenoids, some of which displayed considerable binding affinities and molecular interactions with the studied target proteins, suggesting their possible contribution to the anti-proliferative properties of Nephthea sp. via inhibition of tyrosine kinases, especially the EGFR type. Taken together, the present findings highlighted the relevance of Nephthea sp. to future anticancer drug discovery and provided a base for further work on the green synthesis of a range of bioactive NPs from marine soft corals.

The current study aimed to investigate the anti-epileptic potential of the ethanol extract and its different fractions from the Lamiaceous plant, Ocimum menthiifolium. The results revealed that the aqueous fraction with the latest onset of myoclonic convulsions (1095 ± 45**** s) was the most biologically active one. This was followed by LC-HR-MS-coupled metabolic profiling which led to dereplication of 8 compounds from that fraction. A molecular docking study was performed on the dereplicated compounds to discover the main responsible ones for the activity. The results highlighted Apigenin-7,4'-di-O-glucoside as the top scoring ligand with a possible mechanism of action involving the modulation of the voltage-gated sodium channel.

Ocimum forskolei (Habak), Lamiaceae, is an endemic species from Yemen and KSA; where our present study was aimed at investigating the Metabolic profiling coupled with LC HR-MS analysis of the dichloromethane fraction from the aerial parts of that plant with a special emphasis on ursolic acid as the major predominating compound from this fraction. Histopathological evaluation of ursolic acid in different doses against indomethacin-induced ulcers in rats revealed a highly significant and dose dependent protection. With the dose level of 50 mg/kg b.w., Ursolic acid gave an ulcer index of 1.33 ± 0.33 and 97.8% inhibition, compared to cimetidine as a standard with 3.0 ± 0.58 and 95.2%. To rationalize this activity, docking on various macromolecular targets was performed, followed by molecular dynamics on the most promising target; the M3 receptor. A high binding energy of -344 kJ/mol is predicted between Ursolic acid and the protein indicating the stability of the predicted pose.

Purpose: Olanzapine (OLZ) is an atypical antipsychotic agent that is characterized by low brain porousness. The present work aimed to develop radiolabeled olanzapine (OLZ) without colloidal impurities and evaluate its biodistribution following intravenous (I.V.) and intranasal (I.N.) administration as a potential agent for brain diagnosis. Materials and methods: OLZ was radiolabeled with technetium-99m by using sodium dithionite as the reducing agent. Biodistribution of 99mTc-OLZ complex in mice following I.V. and I.N. administrations was examined. Furthermore, a molecular docking study was performed.Results: Sodium dithionite labeling procedure resulted in highest radiochemical yield (96.30 ± 0.09%) and in vitro stability in serum up to 8 h. Biodistribution study of 99mTc-OLZ complex showed high brain uptake following I.N. (6.2 ± 0.12% ID/g) and I.V. (5.5 ± 0.09% ID/g) at 0.5 and 1 h post administration (P.I.), respectively. Docking into two brain targets predicts higher affinity of 99mTc-OLZ than free OLZ. Additionally, docking to P-glycoproteins shows less affinity for the radiolabelled OLZ and hence it is expected to be associated with better brain exposure than free OLZ.Conclusion: These chemical and preliminary biological merits strongly suggest that the 99mTc-OLZ complex with new reducing agent could be used as a potential diagnostic agent for brain.

The present investigation was oriented to the discovery of chemical compounds from the Red Sea sponge Amphimedon sp., as a source of active agents against Trypanosoma brucei, the causal agent of human sleeping sickness. Dereplication analysis of the active fraction from Amphimedon sp. using liquid chromatography coupled with high-resolution mass spectrometry revealed the chemical richness of this sponge with diverse alkaloidal classes such as purine, manzamine, bis-piperidine, and pyridine. Activity-guided fractionation of the total extract showed the antitrypanosomal activity concentrated in the ethyl acetate fraction (IC50 = 3.8 μg/ml). In silico modelling was carried out on the dereplicated compounds to provide an insight into their antitrypanosomal mechanism of action with docking study on eight trypanosomal proteins. Molecular dynamics was run for the complex of zamamidine D and ornithine decarboxylase, which illustrated that zamamidine D has the highest affinity to the ornithine decarboxylase enzyme. These results highlight the valuable chemical profile of Amphimedon sp., as a lead source for antitrypanosomal natural products.

Novel pyrazolyl 2-hydroxychalcone derivatives 3a–e and pyrazolylpyrazoline derivatives 4a–e and 5a–j derived from the naturally existing furochromone (Khellin) were synthesized and evaluated for th...

The novel strain of human coronavirus, emerged in December 2019, which has been designated as SARS-CoV-2, causes a severe acute respiratory syndrome. Since then, it has arisen as a serious threat to the world public health. Since no approved vaccines or drugs has been found to efficiently stop the virulent spread of the virus, progressive inquiries targeting these viruses are urgently needed, especially those from plant sources. Metabolic profiling using LC-HR-ESI-MS of the butanol extract of Ocimum menthiifolium (Lamiaceae) aerial parts yielded 10 compounds including flavonoids, iridoids and phenolics. As it has been previously reported that some flavonoids can be used as anti-SARS drugs by targeting SARS-CoV-1 3CLpro, we chose to examine 14 flavonoids (detected by metabolomics and other compounds isolated via several chromatographic techniques). We investigated their potential binding interactions with the 4 main SARS-CoV-2 targets: Mpro, nsp16/nsp10 complex, ACE2-PD and RBD-S-protein via molecular docking. Docking results indicated that the nsp16/nsp10 complex has the best binding affinities where the strongest binding was detected with apigenin-7-O-rutinoside, prunin and acaciin with −9.4, −9.3 and −9.3 kcal/mol binding energy, respectively, compared to the control (SAM) with −8.2 kcal/mol. Furthermore, the stability of these complexes was studied using molecular dynamics of 150 ns, which were then compared to their complexes in the other three targets. MM-PBSA calculations suggested the high stability of acaciin-nsp16 complex with binding energy of −110 kJ/mol. This study sheds light on the structure-based design of natural flavonoids as anti-SARS-CoV-2 drugs targeting the nsp16/10 complex. Communicated by Ramaswamy H. Sarma

The novel strain of human coronavirus, emerged in December 2019, which has been designated as SARS-CoV-2, causes a severe acute respiratory syndrome. Since then, it has arisen as a serious threat to the world public health. Since no approved vaccines or drugs has been found to efficiently stop the virulent spread of the virus, progressive inquiries targeting these viruses are urgently needed, especially those from plant sources. Metabolic profiling using LC-HR-ESI-MS of the butanol extract of Ocimum menthiifolium (Lamiaceae) aerial parts yielded 10 compounds including flavonoids, iridoids and phenolics. As it has been previously reported that some flavonoids can be used as anti-SARS drugs by targeting SARS-CoV-1 3CLpro, we chose to examine 14 flavonoids (detected by metabolomics and other compounds isolated via several chromatographic techniques). We investigated their potential binding interactions with the 4 main SARS-CoV-2 targets: Mpro, nsp16/nsp10 complex, ACE2-PD and RBD-S-protein via molecular docking. Docking results indicated that the nsp16/nsp10 complex has the best binding affinities where the strongest binding was detected with apigenin-7-O-rutinoside, prunin and acaciin with −9.4, −9.3 and −9.3 kcal/mol binding energy, respectively, compared to the control (SAM) with −8.2 kcal/mol. Furthermore, the stability of these complexes was studied using molecular dynamics of 150 ns, which were then compared to their complexes in the other three targets. MM-PBSA calculations suggested the high stability of acaciin-nsp16 complex with binding energy of −110 kJ/mol. This study sheds light on the structure-based design of natural flavonoids as anti-SARS-CoV-2 drugs targeting the nsp16/10 complex. Communicated by Ramaswamy H. Sarma

The current study aimed to investigate the anti-epileptic potential of the ethanol extract and its different fractions from the

The present study aimed to detect the bioactive metabolites from

Many classes of organic reactions exhibit a remarkable increase in reaction rates when they occur at the water–organic interface. Although this observed ‘on-water’ catalysis has been extensively studied, the suggested mechanisms still do not explain some of the experimental findings. The mechanism proposed by Jung and Marcus (JACS 129, 5492 (2007)) involves stabilising the transition-state (TS) complex via H-bonds to ‘dangling’ interfacial water molecules. Although the reactants also experience H-bonding to interfacial water molecules in the reactant configuration, it has been argued that the H-bonds are enhanced, in terms of number and strength, in the TS. Therefore, the observed decrease in activation energy has been attributed to this preferential enhancement of H-bonds which leads to a more pronounced TS stabilisation. We employ energy decomposition analysis using the method of absolutely localised molecular orbitals to study this proposition. We find that H-bonds to interfacial water molecules are equivalent in the TS and reactant configurations. Nevertheless, these H-bonds result in significantly enhanced charge-transfer between the reactants in the TS complex, which rationalises the decrease in activation energy.

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Repurposing of approved pharmaceutical drugs for COVID-19 treatment represents an attractive approach to quickly identify promising drug candidates. SARS-CoV-2 main protease (Mpro) is responsible for the maturation of viral functional proteins making it a key antiviral target. Based on the recently revealed crystal structures of SARS-CoV-2 Mpro, we herein describe a multi-stage virtual screening protocol including pharmacophore screening, molecular docking and protein-ligand interaction fingerprints (PLIF) post-docking filtration for efficient enrichment of potent SARS-CoV-2 Mpro inhibitors. Potential hits, along with a cocrystallized control were further studied via molecular dynamics. A 150-ns production trajectory was followed by RMSD, free energy calculation, and H-bond analysis for each compound. The applied virtual screening protocol led to identification of five FDA-approved drugs with promising binding modes to key subsites of the substrate-binding pocket of SARS-CoV-2 Mpro. The identified compounds belong to different pharmaceutical classes, including several protease inhibitors, antineoplastic agents and a natural flavonoid. The drug candidates discovered in this study present a potential extension of the recently reported SARS-CoV-2 Mpro inhibitors that have been identified using other virtual screening protocols and may be repurposed for COVID-19 treatment.

The present study aimed to detect the bioactive metabolites from Ocimum forskolei aerial parts which are responsible for the local anaesthetic activity of the ethyl acetate fraction. Following a bioassay-guided fractionation, twelve compounds were dereplicated from the ethyl acetate fraction which was the most potent one with a mean onset of action (1.43 ± 0.07****) min compared to tetracaine as a positive control (1.37 ± 0.07****) min. These compounds, along with seven other compounds (isolated by diverse chromatographic techniques) were subjected to a molecular docking study to declare the top scoring compounds predicted to be responsible for such activity. The results highlighted Rabdosiin and Apigenin-7-O-rutinoside as the main bioactive leaders of the local anaesthesia via forming multiple H- bonding with the sodium ion channels leading to their blockade and loss of pain sensation, which strongly supports the use of O. forskolei as a local anaesthetic agent.

Non-invasive molecular imaging techniques are accruing more interest in the last decades. Several radiolabelling elements have been FDA-approved and are currently used to characterize tumors. In this study, the DNA intercalating agent doxorubicin was radiolabelled with 125I. Several parameters for the radiolabelling reaction were investigated and optimized. A maximum yield of 94 ± 0.3% was reached after reacting 20 μg of doxorubicin with 200 μg Chloramine-T at pH 5 for 30 min. The in vivo stability of 125I-doxorubicin is validated by the low propensity for thyroid uptake in mice. The preclinical T/NT ratio was approximately 6.4 at 30 min. Docking and molecular dynamics confirmed that the radiolabelling of doxorubicin did not affect (or slightly improved its binding to DNA). Overall, 125I-doxorubicin was demonstrated to be a promising non-invasive probe for solid tumor imaging.

The present study aimed to detect the bioactive metabolites from

The present study aimed to detect the bioactive metabolites from Ocimum forskolei aerial parts which are responsible for the antiulcer activity of the total ethanol extract (TEE) as well as different fractions (petroleum ether, dichloromethane, ethyl acetate and aqueous). Six flavonoids were isolated from the dichloromethane fraction which was the most potent; with an ulcer index value of 2.67 ± 2.18*** and % inhibition of ulcer of 97.7%; following a bioassay-guided fractionation. The isolated flavonoids were subjected to molecular docking analysis in an attempt to explain their significant antiulcer potential, and the results revealed that salvitin followed by sideritiflavone were the main active ones acting against M3 and H-2 receptors, respectively. Moreover, a molecular dynamics simulation illustrated the formation of two persistent H-bonds between salvitin and the two amino acids of the active site (Asn507 and Asp147) formed in 42 and 65% of the frames, respectively.

Microbial resistance, oxidative stress, and inflammatory conditions are among the leading causes of death worldwide. In the current work, silver nanoparticles (AgNPs) were biosynthesized using the aqueous extracts of parsley, corn silk (CS), gum Arabic (GA) or combination of the three extracts. The formed nanoparticles were characterized using three techniques including transmission electron microscopy (TEM), UV-visible spectrophotometer and Fourier-transform infrared spectroscopy (FTIR). The antioxidant, anti-inflammatory, and antimicrobial activities were tested for the formed nanoparticles, the aqueous extracts of each of the three plants and their combination. Oxidative stress was induced by alloxan which promoted the development of diabetes mellitus in rats. Inflammation was induced by injecting carrageenan in rats’ paws. Pathogenic microorganisms causing serious urinary tract infection (UTI) were selected for the antimicrobial assay. All aqueous extracts and the biosynthesized AgNPs showed variable degrees of antioxidant, anti-inflammatory and antimicrobial activities, however, the AgNPs biosynthesized by the combination of the three aqueous extracts was the most effective one. LC/MS was done to identify the compounds present in the crude extracts that may be responsible for the observed biological activities. LC/MS resulted in the identification of 13 compounds. Docking experiments on COX-1 (cyclooxygenase-1) and COX-2 (cyclooxygenase-2) were performed to determine the compounds responsible for the anti-inflammatory activity of the extracts. The results showed that silver nanoparticles synthesized by the combination of the three aqueous extracts are considered promising candidates for the development of antioxidant, anti-inflammatory and antimicrobial agents.

New pyrazole derivatives 2–5 were synthesized and evaluated for their COX-1 and COX-2 inhibitory activity in vitro. All compounds showed good inhibitory activity at a nanomolar level and most compounds exhibited selectivity towards COX-2 inhibition. Compounds 2a, 3b, 4a, 5b and 5e exhibited IC50 towards COX-2 enzyme of 19.87, 39.43, 61.24, 38.73 and 39.14 nM, respectively. Furthermore, compounds 3b, 4a, 5b and 5e exhibited a selectivity index of 22.21, 14.35, 17.47 and 13.10, respectively. The most active compounds were further subjected to in vivo anti-inflammatory assay. The tested compounds showed better or comparable activity to celecoxib as positive control. In order to explore their binding mode and selectivity behaviour, molecular docking in the active site of COX-2 was carried out for these derivatives. Analysis of the docked poses of the compounds showed that they adopt similar conformations to the highly selective COX-2 inhibitor, SC-558. The docking pose of compound 3b was confirmed by molecular dynamics. All the tested compounds exhibited potent inhibitory effect on the production of PGE2, in addition to their inhibition of COX-2 enzyme.

Novel heterocyclic oxadiazoles viz. 2-subsituted-5-(4-pyridyl)-1,3,4-oxadiazoles, 2-subsituted-5-(3-pyridyl)-1,3,4-oxadiazoles and 2-subsituted-5-(phenyl or 4-chlorophenyl-1,3,4-oxadiazoles) were designed and synthesized as potential anticancer agents. In this investigation, all compounds were evaluated for their COX-1 and COX-2 inhibitory activity in vitro as new therapeutic approaches assumed cytotoxic effect associated with selective COX-2 inhibition. Results showed that most of the derivatives demonstrated inhibition towards both isoforms of COX comparable to the standard reference drugs indomethacin, diclofenac sodium and celecoxib. Then, nine selected compounds (IIId, VIb, VIIc, IX, XI, XIIa, XIVa, XVIb and XVIIIb) were subjected to cytotoxic screening against UO-31 renal cancer cell line using MTT assay. Compounds IIId, IX and XIIa displayed promising behavior by showing good anticancer activity. Moreover, kinase inhibitory assay against the tyrosine kinase EGFR was performed for the three compounds showing the highest cytotoxic activity. The tested compounds were potent against EGFR with the highest activity being observed for compound IX showing nearly double the potency of the reference drug Erlotinib. Moreover, molecular docking and molecular dynamics were performed for IIId, IX and XIIa against EGFR, in an attempt to elucidate a model for their binding at the molecular level, simulate and understand the possible binding interactions underlying the association between these small molecules and the kinase enzyme ATP binding pocket essential amino acids. Finally, in silico pharmacokinetic profile predication was investigated for IIId, IX and XIIIa using SWISS/ADME to identify the most promising small-molecule cytotoxic agent on the basis of displaying the best drug-like properties. Results indicated that compound IX has a potential to serve as a lead compound for developing novel anticancer therapeutic agents.

Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool characterized by deep tissue penetration and little damage. However, two-photon spectroscopy has lower sensitivity than one-photon microscopy alternatives and hence a protein with a large two-photon absorption cross-section is needed. We use time-dependent density functional theory (TD-DFT) at the B3LYP/6-31+G(d,p) level of theory to screen twenty-two possible chromophores that can be formed upon replacing the amino-acid Tyr66 that forms the green fluorescent protein (GFP) chromophore with a non-canonical amino acid. A proposed chromophore with a nitro substituent was found to have a large two-photon absorption cross-section (29 GM) compared to other fluorescent protein chromophores as determined at the same level of theory. Classical molecular dynamics are then performed on a nitro-modified fluorescent protein to test its stability and study the effect of the conformational flexibility of the chromophore on its two-photon absorption cross-section. The theoretical results show that the large cross-section is primarily due to the difference between the permanent dipole moments of the excited and ground states of the nitro-modified chromophore. This large difference is maintained through the various conformations assumed by the chromophore in the protein cavity. The nitro-derived protein appears to be very promising as a two-photon absorption probe.

The tetrameric red fluorescent protein from Discosoma sp. coral (DsRed) has previously been engineered to produce dimeric and monomeric fluorescent variants with excitation and emission profiles that span the visible spectrum. The brightest of the effectively monomeric DsRed variants is tdTomato-a tandem fusion of a dimeric DsRed variant. Here we describe the engineering of brighter red (RRvT), green (GGvT), and green-red heterodimeric (GRvT) tdTomato variants. GRvT exhibited 99 % intramolecular FRET efficiency, resulting in long Stokes shift red fluorescence. These new variants could prove useful for multicolor live-cell imaging applications.

Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool known for deep tissue penetration and little cellular damage. Being less sensitive than the one-photon microscopy alternatives, a protein with a large two-photon absorption (TPA) cross-section is needed. Here, we use time-dependent density functional theory (TD-DFT) at the B3LYP and CAM-B3LYP/6-31+G(d,p) levels of theory to screen twenty-two possible chromophores that can be formed upon replacing the amino-acid Tyr66 that forms the red fluorescent protein (RFP) chromophore with a non-canonical amino acid. The two-level model for TPA was used to assess the properties (i.e., transition dipole moment, permanent dipole moment difference, and the angle between them) leading to the TPA cross-sections determined via response theory. Computing TPA cross-sections with B3LYP and CAM-B3LYP yields similar overall trends. Results using both functionals agree that the RFP-derived model of the Gold Fluorescent Protein chromophore (Model 20) has the largest intrinsic TPA cross-section at the optimized geometry. TPA was further computed for selected chromophores following conformational changes: variation of both the dihedral angle of the acylimine moiety and the tilt and twist angles between the rings of the chromophore. The TPA cross-section assumed an oscillatory trend with the rotation of the acylimine dihedral, and the TPA is maximized in the planar conformation for almost all models. Model 21 (a hydroxyquinoline derivative) is shown to be comparable to Model 20 in terms of TPA cross-section. The conformational study on Model 21 shows that the acylimine angle has a much stronger effect on the TPA than its tilt and twist angles. Having an intrinsic TPA ability that is more than 7 times that of the native RFP chromophore, Models 20 and 21 appear to be very promising for future experimental investigation.

Two-photon spectroscopy of fluorescent proteins is a powerful bioimaging tool. Considerable effort has been made to measure absolute two-photon absorption (TPA) for the available fluorescent proteins. Being a technically involved procedure, there is significant variation in the published experimental measurements even for the same protein. In this work, we present a time-dependent density functional theory (TDDFT) study on isolated chromophores comparing the ability of four functionals (PBE0, B3LYP, CAM-B3LYP, and LC-BLYP) combined with the 6-31+G(d,p) basis set to reproduce averaged experimental TPA energies and cross sections. The TDDFT energies and TPA cross sections are also compared to corresponding CC2/6-31+G(d,p) results for excitation to S1 for the five smallest chromophores. In general, the computed TPA energies are less functional dependent than the TPA cross sections. The variation between functionals is more pronounced when higher-energy transitions are studied. Changes to the conformation of a chromophore are shown to change the TPA cross-section considerably. This adds to the difficulty of comparing an isolated chromophore to the one embedded in the protein environment. All functionals considered give moderate agreement with the corresponding CC2 results; in general, the TPA cross sections determined by TDDFT are 1.5-10 times smaller than the corresponding CC2 values for excitation to S1. LC-BLYP and CAM-B3LYP give erroneously large TPA cross sections in the higher-energy regions. On the other hand, B3LYP and PBE0 yield values that are of the same order of magnitude and in some cases very close to the averaged experimental data. Thus, based on the results reported here, B3LYP and PBE0 are the preferred functionals for screening chromphores for TPA. However, at best, TDDFT can be used to semiquantitatively scan chromophores for potential TPA probes and highlight spectroscopic peaks that could be present in the mature protein.