Impact of GSK199 and GSK106 binding on protein arginine deiminase IV stability and flexibility: a computational approach

Protein arginine deiminase IV (PAD4) is a potential target for diseases including rheumatoid arthritis and cancers. Currently, GSK199 is a potent, selective yet reversible PAD4 inhibitor. Its derivative, GSK106, on the other hand, was reported as an inactive compound when tested against PAD4 assay. Although they had similar skeleton, their impact towards PAD4 structural and flexibility is unknown. In order to fill the research gap, the impact of GSK199 and GSK106 binding towards PAD4 stability and flexibility is investigated via a combination of computational methods. Molecular docking indicates that GSK199 and GSK106 are capable to bind at PAD4 pocket by using its back door with − 10.6 kcal/mol and − 9.6 kcal/mol, respectively. The simulations of both complexes were stable throughout 100 ns. The structure of PAD4 exhibited a tighter packing in the presence of GSK106 compared to GSK199. The RMSF analysis demonstrates significant changes between the PAD4-GSK199 and PAD4-GSK106 simulations in the regions containing residues 136, 160, 220, 438, and 606. The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis shows a marked difference in binding free energies, with − 11.339 kcal/mol for the PAD4-GSK199 complex and 1.063 kcal/mol for the PAD4-GSK106 complex. The hydrogen bond analysis revealed that the GSK199 and GSK106 binding to PAD4 are assisted by six hydrogen bonds and three hydrogen bonds, respectively. The visualisation of the MD simulations revealed that GSK199 remained in the PAD4 pocket, whereas GSK106 shifted away from the catalytic site. Meanwhile, molecular dockings of benzoyl arginine amide (BAEE) substrate have shown that BAEE is able to bind to PAD4 catalytic site when GSK106 was present but not when GSK199 occupied the site. Overall, combination of computational approaches successfully described the behaviour of binding pocket of PAD4 structure in the presence of the active and inactive compounds

Cytotoxic xanthones isolated from calophyllum depressinervosum and calophyllum buxifolium with antioxidant and cytotoxic activities

The stem bark of Calophyllum depressinervosum and Calophyllum buxifolium were extracted and examined for their antioxidant activities, together with cytotoxicity towards human cancer cells. The methanol extract of C. depressinervosum exhibited good DPPH and NO scavenging effects. The strongest BCB inhibition and FIC effects were shown by dichloromethane and ethyl acetate extracts of both species. Overall, DPPH, FRAP and FIC assays showed strong correlation with TPC. For cytotoxicity, hexane extract of C. depressinervosum possessed the strongest anti-proliferative activities towards SNU-1 cells while the hexane extract of C. buxifolium showed the strongest activity towards LS-174T and K562 cells with the IC values ranging from 7 to 17 μg/mL. The purification of plant extracts afforded eight xanthones, ananixanthone (1), caloxanthone B (2), caloxanthone I (3), caloxanthone J (4) xanthochymone B (5), thwaitesixanthone (6), 1,3,5,6-tetrahydroxyxanthone (7) and dombakinaxanthone (8). All the xanthones, except 1 were reported for the first time from both Calophyllum species. The xanthones were examined for their cytotoxic effect against K562 leukemic cells. Compounds 1 and 2 showed strong cytotoxicity with the IC values of 2.96 and 1.23 μg/mL, respectively. The molecular binding interaction of 2 was further investigated by performing molecular docking study with promising protein receptor Src kinase

In-silico identification of potential Protein Arginine Deiminase IV (PAD4) inhibitors

Protein Arginine Deiminase IV (PAD4) is a promising target for treating rheumatoid arthritis. Here, an in-silico screening was performed using PAD4 crystal structure against National Cancer Institute Diversity Set III compounds. Results obtained from the docking studies showed that the compounds have high affinity towards the protein. Visual inspections of the top compounds indicated that they preferred to bind at the front door of the catalytic pocket instead of the back door. The current results from this screening could provide a basis for the development of new PAD4 inhibitors

LC-MS-based metabolomics and molecular docking to characterize α-glucosidase inhibitors from Psychotria Malayana Jack leaves extract

The plant Psychotria malayana Jack belongs to the Rubiaceae family and is locally referred to as "meroyan sakat/salung" in Malaysia. Diabetes has traditionally been treated with P. malayana Jack. Despite its potential, scientific evidence for this plant is still lacking. Thus, the current study sought to investigate α�glucosidase inhibitors in P. malayana leaf extracts using a metabolomics approach, as well as to illuminate ligand-protein interactions using in-silico techniques (molecular docking). The plant leaves were extracted in five different ratios with methanol and water (100, 75, 50, 25 and 0% v/v; water–methanol). After testing for α-glucosidase inhibition activity, each extract was analyzed using liquid chromatography tandem to mass spectrometry. Additionally, the data were subjected to multivariate data analysis by developing an orthogonal partial least squares method in order to establish a correlation between the chemical profile and the bioactivity. The loading plots demonstrated that the m/z signals correspond to the activity of α-glucosidase inhibitors, allowing five putative bioactive compounds to be identified, namely 1-monopalmitin (1), 5′-hydroxymethyl-1′-(1, 2, 3, 9-tetrahydro-pyrrolo (2, 1-b) quinazolin-1-yl)-heptan-1′-one (2), α-terpinyl-β-glucoside (3), machaeridiol-A (4), and 4-hydroxyphenylpyruvic acid (5). The discovered inhibitors were docked against the crystal structure of Saccharomyces cerevisiae isomaltase (Protein Data Bank code: 3A4A) using the Auto Dock Vina software. Nine hydrogen bonds were detected in the docked complex, involving several residues, namely ASP352, ARG213, ARG442, GLU277, GLN279, HIE280, HIE351, ASH215, and GLU411. Compound 1, 2, 3, 4, and 5 showed binding affinity values of −6.1, −8.3, −7.6, −10.0, and −6.5 kcal/mol, respectively, indicating the moderate to the good binding affinity of the compounds towards the active site of the enzyme when compared to that of a known α-glucosidase inhibitor, quercetin (−8.4 kcal/mol). The five identified compounds showing potential binding affinity towards the α-glucosidase enzyme in in-silico study could be the bioactive compounds associated with this plant's traditional use

Identification of α-glucosidase inhibitorsfrom Clinacanthus nutans leaf extract using liquid chromatography-mass spectrometry-based metabolomics and protein-ligand interaction with molecular docking

The present study used in vitro and in silico techniques, as well as the metabolomics approach to characterise α-glucosidase inhibitors from different fractions of Clinacanthus nutans. C. nutans is a medicinal plant belonging to the Acanthaceae family, and is traditionally used to treat diabetes in Malaysia. n-Hexane, n-hexane: ethyl acetate (1:1, v/v), ethyl acetate, ethyl acetate: methanol (1:1, v/v), and methanol fractions were obtained via partitioning of the 80% methanolic crude extract. The in vitro α-glucosidase inhibitory activity was analyzed using all the fractions collected, followed by profiling of the metabolites using liquid chromatography combined with mass spectrometry. The partial least square (PLS) statistical model was developed using the SIMCA P+14.0 software and the following four inhibitors were obtained: (1) 4,6,8-Megastigmatrien-3-one; (2) N-Isobutyl-2-nonen-6,8-diynamide; (3) 1′,2′-bis(acetyloxy)-3′,4′-didehydro-2′-hydro-β, ψ-carotene; and (4) 22-acetate-3-hydroxy-21-(6-methyl-2,4-octadienoate)-olean-12-en-28-oic acid. The in silico study performed via molecular docking with the crystal structure of yeast isomaltase (PDB code: 3A4A) involved a hydrogen bond and some hydrophobic interactions between the inhibitors and protein. The residues that interacted include ASN259, HID295, LYS156, ARG335, and GLY209 with a hydrogen bond, while TRP15, TYR158, VAL232, HIE280, ALA292, PRO312, LEU313, VAL313, PHE314, ARG315, TYR316, VAL319, and TRP343 with other forms of bonding

Rapid investigation of Αlpha-Glucosidase inhibitory activity of Psychotria Malayana Jack leaf using infrared fingerprinting

Background: Psychotria malayana Jack is the plant belongs to Rubiaceae family and known in Malaysia as “meroyan sakat/salung”. The analytical approach used in the quality control of Psychotria malayana leaves has not been developed yet. Objectives: Therefore, this research was aimed to evaluate the α-glucosidase inhibitory activity of Psychotria malayana Jack leave extracts in correlation to its Fourier transform infrared spectroscopy (FT-IR) fingerprint, utilizing orthogonal partial least square. Methodology: The dried extracts prepared by sonication of different solvents ratios of methanol-water (0, 25, 50, 75, and 100% v/v), were evaluated for the α-glucosidase inhibitory activity and analyzed via infrared spectroscopy. Multivariate data analysis was done through correlating the bioactivity and infrared spectra of every extract using orthogonal partial least square (OPLS) method. Results: The 100% methanol extract of the leave is more effective against α-glucosidase activity. The loading plot from multivariate data analysis identified several functional groups which actively induced α- -glucosidase inhibitory activity. Discussion and Conclusion: The results of the present study developed the FT-IR spectrum profile for the medicinally important plant Psychotria malayana Jack that further confirms its medicinal values. Therefore, Psychotria malayana Jack leaves extract is medicinally potent that assist to develop this plant as an alternative anti-diabetic natural plant-based medicine

Cytotoxic xanthones isolated from Calophyllum depressinervosum and Calophyllum buxifolium with antioxidant and cytotoxic activities

The stem bark of Calophyllum depressinervosum and Calophyllum buxifolium were extracted and examined for their antioxidant activities, together with cytotoxicity towards human cancer cells. The methanol extract of C. depressinervosum exhibited good DPPH and NO scavenging effects. The strongest BCB inhibition and FIC effects were shown by dichloromethane and ethyl acetate extracts of both species. Overall, DPPH, FRAP and FIC assays showed strong correlation with TPC. For cytotoxicity, hexane extract of C. depressinervosum possessed the strongest anti-proliferative activities towards SNU-1 cells while the hexane extract of C. buxifolium showed the strongest activity towards LS-174T and K562 cells with the IC50 values ranging from 7 to 17 μg/mL. The purification of plant extracts afforded eight xanthones, ananixanthone (1), caloxanthone B (2), caloxanthone I (3), caloxanthone J (4) xanthochymone B (5), thwaitesixanthone (6), 1,3,5,6-tetrahydroxyxanthone (7) and dombakinaxanthone (8). All the xanthones, except 1 were reported for the first time from both Calophyllum species. The xanthones were examined for their cytotoxic effect against K562 leukemic cells. Compounds 1 and 2 showed strong cytotoxicity with the IC50 values of 2.96 and 1.23 μg/mL, respectively. The molecular binding interaction of 2 was further investigated by performing molecular docking study with promising protein receptor Src kinase

Antidiabetic and antioxidants activities of Clinacanthus nutans (Burm F.) Lindau leaves extracts

Clinacanthus nutans (C. nutans) is a local plant belongs to the family Acanthaceae. It is consumed as ‘jamu’ (healthy drink) in Indonesia and as ‘ulam’ in Malaysia. This plant has been claimed for its ability to prevent many diseases including diabetes. However, its scientific proof on this claim is still lacking. Thus, this study was designed to evaluate the antidiabetic potential and antioxidant capacity of C. nutans leaves extracts using in vitro bioassay tests. The 80% methanolic crude extract of this plant was further partitioned using different polarity solvents viz., hexane, hexane: ethyl acetate (1:1, v/v), ethyl acetate, ethyl acetate: methanol (1:1, v/v) and methanol. All the sub-fractions were analysed for antioxidant effect via 2, 2-diphenyl-2-picrylhydrazil (DPPH) scavenging activity, ferric reducing power (FRAP) and xanthine oxidase (XO) assays followed by antidiabetic evaluation via α-glucosidase and dipeptidyl peptidase-IV (DPP-IV) inhibitory assays and glucose uptake experiment. The ethyl acetate fraction showed a good antioxidant potential while hexane exhibit high α-glucosidase and DPP-IV enzyme inhibition. The hexane fraction also improved glucose uptake in a dose-dependent manner. The study provides an informative data on the potential of C. nutans to be developed as a functional food in preventing diabetes

Rapid analysis of alpha-glucosidase inhibitory activity of Psychotria Malayana jack leaf applying infrared fingerprinting

Psychotria malayana Jack is the plant belongs to Rubiaceae family and known in Malaysia as “meroyan sakat/salung”. Despite its potential use as an antidiabetic agent, a rapid analytical approach for the quality control of this plant has not been developed. Thus, the objective of this study was to establish a validated analytical method for the prediction for the alpha-glucosidase inhibitory activity of the leaves of P. malayana through implementation of Fourier Transformation Infrared Spectroscopy-fingerprinting utilizing a multivariate statistical calculation, orthogonal partial least square. The dried extracts prepared with different solvents ratios of methanol-water (0, 25, 50, 75, and 100% v/v), were evaluated for the bio-activity and analyzed via infrared spectroscopy. Orthogonal partial least square was accomplished through correlating the bioactivity and infrared spectra of every extract. The 100% methanol extract possessed the highest inhibitory activity against the alpha-glucosidase (IC50 2.83 ± 0.32 μg/mL). The loading plot from the statistical calculation revealed several functional groups, including hydroxyl (O-H), alkenyl (C=C), methylene (C-H), carbonyl (C=O), and secondary amine (N-H) groups, which actively induced the α-glucosidase inhibitory activity. The established validated model can be utilized in predicting the inhibitory activity of new set of P. malayana Jack leaves and can also be used as an assessment tool in the quality control of this plant

In Vitro neurotoxicity and myotoxicity of Malaysian Naja sumatrana and Naja kaouthia venoms: Neutralization by monovalent and Neuro Polyvalent Antivenoms from Thailand

Naja sumatrana and Naja kaouthia are medically important elapids species found in Southeast Asia. Snake bite envenoming caused by these species may lead to morbidity or mortality if not treated with the appropriate antivenom. In this study, the in vitro neurotoxic and myotoxic effects N. sumatrana and N. kaouthia venoms from Malaysian specimens were assessed and compared. In addition, the neutralizing capability of Cobra Antivenom (CAV), King Cobra Antivenom (KCAV) and Neuro Polyvalent Antivenom (NPAV) from Thailand were compared. Both venoms produced concentration-dependent neurotoxic and myotoxic effects in the chick biventer cervicis nerve-muscle preparation. Based on the time to cause 90% inhibition of twitches (i.e. t90) N. kaouthia venom displayed more potent neurotoxic and myotoxic effects than N. sumatrana venom. All three of the antivenoms significantly attenuated venom-induced twitch reduction of indirectly stimulated tissues when added prior to venom. When added after N. sumatrana venom, at the t90 time point, CAV and NPAV partially restored the twitch height but has no significant effect on the reduction in twitch height caused by N. kaouthia venom. The addition of KCAV, at the t90 time point, did not reverse the attenuation of indirectly stimulated twitches caused by either venom. In addition, none of the antivenoms, when added prior to venom, prevented attenuation of directly stimulated twitches. Differences in the capability of antivenoms, especially NPAV and CAV, to reverse neurotoxicity and myotoxicity indicate that there is a need to isolate and characterize neurotoxins and myotoxins from Malaysian N. kaouthia and N. sumatrana venoms to improve neutralization capability of the antivenoms