Determination of total phenolic and flavonoid content of Ghontoghe (Kleinhovia hospita L.) leaves: in vitro antioxidant study

The Ghontohge plant (Kleinhovia hospita L.) has been used as a traditional medicine to treat scurvy, lice, eye pain, jaundice and hepatitis, cholesterol, diabetes, hypertension and treat pneumonia. Therefore, it is possible that plants can be used as antioxidants and redox signalling sourced from natural materials. The purpose of this study was to investigate the antioxidant potential and evaluate the total phenolic and flavonoid content of Ghontoghe leaves and investigate the most potent fraction as an antioxidant from the extract and fractions of Ghontoghe leaves. Ghontoghe leaf powder was extracted using the maceration method. Antioxidant activity was evaluated using 2,2-diphenyl-1-picryhidrazyl (DPPH) and 2,2-Azinobis 3-ethyl benzothiazoline 6-sulfonic acid radicals (ABTS). The total phenolic content was determined using the Folin-Ciocalteau method. Meanwhile, the total flavonoid content was determined using the aluminium chloride complex colourimetric method. The ethyl acetate fraction showed the strongest antioxidant activity on both DPPH radicals and ABTS radicals with IC50 values of 6.253±0.008 g/mL and 6.486±0.023 g/mL, respectively. The ethyl acetate fraction also showed high phenolic and flavonoid content with values of 26.92±0.10 mg GAE/g sample and 95±0.69 mg QE/g sample, respectively. The ethyl acetate fraction has the potential to be used as a source of natural antioxidants and has the potential to be used as a functional food.

Unraveling the binding mechanism of the active form of Remdesivir to RdRp of SARS-CoV-2 and designing new potential analogues: Insights from molecular dynamics simulations

The binding of the active form of Remdesivir (RTP) to RNA-dependent RNA Polymerase (RdRp) of SARS-CoV-2 was studied using molecular dynamics simulation. The RTP maintained the interactions observed in the experimental cryo-EM structure. Next, we designed new analogues of RTP, which not only binds to the RNA primer strand in a similar pose as that of RTP, but also binds more strongly than RTP does as predicted by MM-PBSA binding energy. This suggest that these analogues might be able to covalently link to the primer strand as RTP, but their 3' modification would terminate the primer strand growth.

Novel inhibitors to ADP ribose phosphatase of SARS-CoV-2 identified by structure-based high throughput virtual screening and molecular dynamics simulations

The outbreak of a new coronavirus (SARS-CoV-2) was first identified in Wuhan, People's Republic of China, in 2019, which has led to a severe, life-threatening form of pneumonia (COVID-19). Research scientists all around the world have been trying to find small molecule drugs to treat COVID-19. In the present study, a conserved macrodomain, ADP Ribose phosphatase (ADRP), of a critical non-structural protein (Nsp3) in all coronaviruses was probed using large-scale Molecular Dynamics (MD) simulations to identify novel inhibitors. In our virtual screening workflow, the recently-solved X-ray complex structure, 6W6Y, with a substrate-mimics was used to screen 17 million ZINC15 compounds using drug property filters and Glide docking scores. The top twenty output compounds each underwent 200 ns MD simulations (i.e. 20 × 200 ns) to validate their individual stability as potential inhibitors. Eight out of the twenty compounds showed stable binding modes in the MD simulations, as well as favorable drug properties from our predctions. Therefore, our computational data suggest that the resulting top eight out of twenty compounds could potentially be novel inhibitors to ADRP of SARS-CoV-2.

GC-MS, LC-MS/MS, Docking and Molecular Dynamics Approaches to Identify Potential SARS-CoV-2 3-Chymotrypsin-Like Protease Inhibitors from Zingiber officinale Roscoe

This study aims to identify and isolate the secondary metabolites of Zingiber officinale using GC-MS, preparative TLC, and LC-MS/MS methods, to evaluate the inhibitory potency on SARS-CoV-2 3 chymotrypsin-like protease enzyme, as well as to study the molecular interaction and stability by using docking and molecular dynamics simulations. GC-MS analysis suggested for the isolation of terpenoids compounds as major compounds on methanol extract of pseudostems and rhizomes. Isolation and LC-MS/MS analysis identified 5-hydro-7, 8, 2'-trimethoxyflavanone (9), (E)-hexadecyl-ferulate (1), isocyperol (2), N-isobutyl-(2E,4E)-octadecadienamide (3), and nootkatone (4) from the rhizome extract, as well as from the leaves extract with the absence of 9. Three known steroid compounds, i.e., spinasterone (7), spinasterol (8), and 24-methylcholesta-7-en-3β-on (6), were further identified from the pseudostem extract. Molecular docking showed that steroids compounds 7, 8, and 6 have lower predictive binding energies (MMGBSA) than other metabolites with binding energy of -87.91, -78.11, and -68.80 kcal/mole, respectively. Further characterization on the single isolated compound by NMR showed that 6 was identified and possessed 75% inhibitory activity on SARS-CoV-2 3CL protease enzyme that was slightly different with the positive control GC376 (77%). MD simulations showed the complex stability with compound 6 during 100 ns simulation time.

Determination of antiradical activity and phenolic and flavonoid contents of extracts and fractions of jackfruit (Artocarpus heterophyllus Lamk) seeds

Jackfruit (Artocarpus heterophyllus Lamk) is a plant from the Moraceae family that is widespread in Indonesia. Empirically, jackfruit can be used to cure hypertension, diabetes, cancer, asthma, dermatosis, coughs, wounds, acne, and diarrhea. The bioactive compounds in jackfruit include phenolics and flavonoids, which function as natural antioxidants. This research investigated the antiradical activity of jackfruit seed extracts and fractions using DPPH (2-2-diphenyl-1-picrylhydrazyl) and examined the total phenolic and flavonoid contents which may be developed as functional medicines and foods. The jackfruit seed powder was extracted using the maceration method. Radical scavenging activities were measured using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) method. Total phenolic contents were determined using the Folin-Ciocalteu method. Meanwhile, the contents of flavonoids were determined using the aluminum chloride complex colorimetric method. The IC50 value of ethyl acetate fraction, methanol extract, n -hexane fraction, and water fraction was 5.435±0.064 µg/mL, 5.639±0.302 µg/mL, 7.201±0.475 µg/mL, and 9.134±0.2911 µg/mL, respectively. The phenolic and flavonoid contents of ethyl acetate fraction, methanol extract, n-hexane fraction, and water fraction were 49.597±1.589, 47.949±1.966, 41.214±4.354 and 35.504±0.913 g GAE/100 g of sample, respectively for phenolic, and 70.199±0.458, 65.228±0.615, 59.907±0.719, and 54.234±0.351 g of quercetin equivalent/100 g of sample, respectively of flavonoids, with a correlation value (R2 ) to antiradical power of 0.4582 for phenolic and 0.5281 for flavonoids. The ethyl acetate fraction of jackfruit seeds can be further developed as an anti -radicals and functional food.

Mechanistic insight on the remdesivir binding to RNA-Dependent RNA polymerase (RdRp) of SARS-cov-2

The RNA-dependent RNA polymerase (RdRp) is a key enzyme which regulates the viral replication of SARS-CoV-2. Remdesivir (RDV) is clinically used drug which targets RdRp, however its mechanism of action remains elusive. This study aims to find out the binding dynamics of active Remdesivir-triphosphate (RDV-TP) to RdRp by means of molecular dynamics (MD) simulation. We built a homology model of RdRp along with RNA and manganese ion using RdRp hepatitis C virus and recent SARS-CoV-2 structures. We determined that the model was stable during the 500 ns MD simulations. We then employed the model to study the binding of RDV-TP to RdRp during three independent 500 ns MD simulations. It was revealed that the interactions of protein and template-primer RNA were dominated by salt bridge interactions with phosphate groups of RNA, while interactions with base pairs of template-primer RNA were minimal. The binding of RDV-TP showed that the position of phosphate groups was at the entry of the NTP channel and it was stabilized by the interactions with K551, R553, and K621, while the adenosine group on RDV-TP was pairing with U2 of the template strand. The manganese ion was located close to D618, D760, and D761, and helps in stabilization of the phosphate groups of RDV-TP. Further we identified three hits from the natural product database that pose similar to RDV-TP while having lower binding energies than that of RDV-TP, and that SN00359915 had binding free energy about three times lower than that of RDV-TP.

Recoil Directionality Experiment

Directional sensitivity to nuclear recoils could provide a smoking gun for a possible discovery of dark matter in the form of WIMPs. A hint of directional dependence of the response of a dual-phase liquid argon Time Projection Chamber was found in the SCENE experiment. Given the potential importance of such a capability in the frame work of dark matter searches, a new dedicated experiment, ReD (Recoil Directionality), was designed in the framework of the DarkSide Collaboration, in order to scrutinize this hint. This contribution will describe the performance of the detectors achieved during the first test-beam, the current status of ReD and the perspectives for physics measurements during the forthcoming beam-time.

Pharmacophore-based virtual screening for identifying β5 subunit inhibitor of 20S proteasome

Proteasomal system plays an important role in maintaining cell homeostatis. Overexpression of proteasomes leads to several major diseases, such as cancer and autoimmune disorder. The β5 subunit of proteasome is a crucial active site in proteolysis, and targeting proteasome β5 subunit is essential for proteasome inhibition. In the present study, a pharmacophore-based virtual screening and molecular docking were employed to identify ligands as inhibitors of β5 subunit of proteasome. The pharmacophore features were built with one hydrogen bond donor, two hydrogen bond acceptors, and one hydrophobic feature using native ligand of proteasome (HU10), which was then used to screen ZINC database using ZINCPharmer. The retrieved virtual hits were subjected to molecular docking analysis using iDock. The best six hits were subjected to molecular dynamics (MD) simulation and each complex was stable during 40 ns MD simulation as indicated by root-mean-square-deviation (RMSD) and root-mean-square-fluctuation (RMSF) values. The current study identifies 5 best hits having better binding potentials than HU10 as predicted by molecular mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method, i.e. Lig1540/ZINC33356240, Lig1546/ZINC33356235, Lig1522/ZINC20854878, Lig980/ZINC12391945, and Lig1119/ZINC19865241, which can be used in the development of new proteasome inhibitors.

Hubungan Kuantitatif Struktur-Aktivitas (HKSA) dan Penambatan Molekul Senyawa Turunan Benzamida sebagai Inhibitor Alosterik Mitogen Enhanced Kinase (MEK)

Jalur sinyal protein kinase Ras-Raf-MEK-ERK adalah salah satu target penting dalam penemuan obat antikanker. Senyawa turunan benzamida diketahui berpotensi sebagai inhibitor alosterik Mitogen Enhanced Kinase (MEK). Pada penelitian ini dilakukan studi hubungan kuantitatif stuktur dan aktivitas (HKSA) dan penambatan molekul pada 30 senyawa turunan benzamida sebagai inhibitor alosterik MEK untuk mendapatkan senyawa baru turunan benzamida yang lebih poten sebagai inhibitor alosterik MEK. Perhitungan 13 deskriptor molekul yang mewakili parameter sterik, hidrofobik dan elektronik dilakukan dengan perangkat lunak MOE 2009.10, sedangkan analisis regresi multi linear dengan SPSS 19.0 digunakan untuk mencari hubungan antara variabel bebas (deksriptor molekul) dengan variabel terikat (aktivitas penghambatan senyawa pada MEK). Model HKSA terbaik yang diperoleh adalah pIC50 = 14.229 – 0.00001(AM1_E) + 0.043(ASA_H) + 33.609(Glob) – 0.648(Log S) – 0.047(Vol) dengan kriteria statistik R=0.965; R2=0.931; Fhitung/ Ftabel= 17.693, dan q2 = 0.8897. Desain senyawa baru dilakukan menggunakan model HKSA tervalidasi dan diperoleh 2 senyawa baru turunan benzamida, C1, dan C2, yang memiliki aktivitas lebih baik dari senyawa induk. Studi penambatan molekul menunjukkan bahwa kedua senyawa baru tersebut mampu berinteraksi pada sisi alosterik protein MEK melalui ikatan hidrogen dan ikatan van der Waals dengan residu-residu asam amino krusial protein MEK. Penelitian ini mengindikasikan bahwa kedua senyawa baru yang didesain dapat ditindaklanjuti pada studi penemuan obat yang menargetkan MEK pada sisi alosterik.DOI:http://dx.doi.org/10.15408/jkv.v4i1.7454

Effect of irrigation at critical stages on the phenology of flowering and fruiting of the cactus Opuntia spp

This paper briefly reports some effects of irrigations at two critical periods on the phenology of three varieties of cactus pear cultivated in Agadir area: the spineless varieties 'Aissa' and 'Moussa' and the thorny one 'Achefri'. In the first year experiments (2010-2011) treatments of irrigation used were: (T1) 0 mm, (T2) 30 mm during flowering and 30 mm during fruit enlargement and (T3) 30 mm only during fruit enlargement. In the 2nd year experiments, irrigation treatments were: (T1) 0 mm, (T2) 60 mm during flowering and 60 mm during fruit enlargement and (T3) 60 mm only during fruit enlargement. Treatments of irrigation were applied between mid-April and mid-June in the 1st year experiments and in February and May in the 2nd year experiments. Results of the first year experiments showed that the emission of buds was higher in the thorny variety than in the spineless ones (more than 6 emitted buds/cladode vs less than 4.5 in the spineless varieties). In the second year, irrigation increased the emission of buds in the three varieties (more than 7 emitted buds/cladode for each T2 and T3 of all varieties vs not more than 5 for T1) and the duration of the flowering phase of these varieties. However, irrigation did not modify the proportions of fruits reaching commercial maturity during the early or the late period of maturation.

Molecular modeling of cationic porphyrin-anthraquinone hybrids as DNA topoisomerase IIβ inhibitors

Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIβ inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIβ employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIβ complex using Amber 14. We found that the binding of porphyrin hybrids occured through intercalation and groove binding mode in addition interaction with the amino acid residues constituting the active cavity of Topo IIβ. Each porphyrin-Topo IIβ complex was stabilized during 20-ns dynamics simulations. The MM-PBSA free energy calculation shows that the binding affinities of porphyrin hybrids were modified with the number of meso substituent. Interestingly, the affinity of all porphyrin hybrids to Topo IIβ was stronger than that of native ligand (EVP), indicating the potential of the designed porphyrin to be considered in experimental research.

In silico study of porphyrin-anthraquinone hybrids as CDK2 inhibitor

Cyclin-Dependent Kinases (CDKs) are known to play crucial roles in controlling cell cycle progression of eukaryotic cell and inhibition of their activity has long been considered as potential strategy in anti-cancer drug research. In the present work, a series of porphyrin-anthraquinone hybrids bearing meso-substituents, i.e. either pyridine or pyrazole rings were designed and computationally evaluated for their Cyclin Dependent Kinase-2 (CDK2) inhibitory activity using molecular docking, molecular dynamics simulation, and binding free energy calculation. The molecular docking simulation revealed that all six porphyrin hybrids were able to bind to ATP-binding site of CDK2 and interacted with key residues constituted the active cavity of CDK2, while molecular dynamics simulation indicated that all porphyrins bound to CDK2 were stable for 6ns. The binding free energies predicted by MM-PBSA method showed that most compounds exhibited higher affinity than that of native ligand (4-anilinoquinazoline, DTQ) and the affinity of mono-H₂PyP-AQ was about three times better than that of DTQ, indicating its potential to be advanced as a new CDK2 inhibitor.

Molecular docking and dynamics simulations on the interaction of cationic porphyrin-anthraquinone hybrids with DNA G-quadruplexes

A series of cationic porphyrin-anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the meso-positions have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamics simulations. Three types of DNA G-quadruplexes were utilized, which comprise parallel, antiparallel, and mixed hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to the antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in the antiparallel due to the presence of diagonal and lateral loops that crowd the G-quartet. The binding to the antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of the total binding free energies that were calculated using the MMPBSA method. Free energy analysis shows that the favorable contribution came from the electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from the van der Waals energy, which primarily contributed through end stacking interaction.

The binding modes of cationic porphyrin-anthraquinone hybrids to DNA duplexes: in silico study

Cationic porphyrin-anthraquinone hybrids bearing peripheral substituents, either pyridine, imidazole, or pyrazole rings have been investigated for their binding mode to DNA duplexes. The four kinds of DNA duplexes were used, which represent intercalation and groove binding modes. AutoDock 4.2 was used to dock nine hybrid compounds to four DNA duplexes, while monitoring of conformational changes of four best hybrid-DNA complexes during 2 ns was performed by Amber9 molecular dynamics package. The binding energy calculation of best four complexes was then carried out using MMPBSA method. The hybrid compounds interacted to DNA duplexes through intercalation and groove binding modes. The minor groove binding of DNA was energetically preferred by cationic porphyrin hybrids due to favorable electrostatic and van der Waals interactions. Both electrostatic and van der Waals contributions were able to distinguish the binding mode of porphyrin hybrid to DNA duplexes.