Computational Assessment of Botrytis cinerea Lipase for Biofuel Production

The demand for ecofriendly green catalysts for biofuel synthesis is greatly increasing with the effects of fossil fuel depletion. Fungal lipases are abundantly used as biocatalysts for the synthesis of biofuel. The use of Botrytis cinerea lipase is an excellent approach for the conversion of agroindustrial residues into biofuel. In this study, phylogenetic analyses were carried out and the physicochemical properties of B. cinerea lipase were assessed. Furthermore, the protein structure of B. cinerea lipase was predicted and refined. Putative energy-rich phytolipid compounds were explored as a substrate for the synthesis of biofuel, owing to B. cinerea lipase catalysis. Approximately 161 plant-based fatty acids were docked with B. cinerea lipase in order to evaluate their binding affinities and interactions. Among the docked fatty acids, the top ten triglycerides having the lowest number of binding affinities with B. cinerea lipase were selected, and their interactions were assessed. The top three triglycerides having the greatest number of hydrogen bonds and hydrophobic interactions were selected for simulations of 20 ns. The docking and simulations revealed that docosahexaenoic acid, dicranin, and hexadeca-7,10,13-trienoic acid had stable bonding with the B. cinerea lipase. Therefore, B. cinerea lipase has the potential to be used for the transesterification of fatty acids into biofuels, whereas docosahexaenoic acid, dicranin, and hexadeca-7,10,13-trienoic acid can be used as substrates of B. cinerea lipase for biofuel synthesis.

Biochemical Characterization of 13-lipoxygenases of Arabidopsis thaliana

13-Lipoxygenases (13-LOX) catalyze the dioxygenation of various polyunsaturated fatty acids (PUFAs), of which α-linolenic acid (LeA) is converted to 13-S-hydroperoxyoctadeca-9, 11, 15-trienoic acid (13-HPOT), the precursor for the prostaglandin-like plant hormones cis-(+)-12-oxophytodienoic acid (12-OPDA) and methyl jasmonate (MJ). This study aimed for characterizing the four annotated A. thaliana 13-LOX enzymes (LOX2, LOX3, LOX4, and LOX6) focusing on synthesis of 12-OPDA and 4Z,7Z,10Z)-12-[[-(1S,5S)-4-oxo-5-(2Z)-pent-2-en-1yl] cyclopent-2-en-1yl] dodeca-4,7,10-trienoic acid (OCPD). In addition, we performed interaction studies of 13-LOXs with ions and molecules to advance our understanding of 13-LOX. Cell imaging indicated plastid targeting of fluorescent proteins fused to 13-LOXs-N-terminal extensions, supporting the prediction of 13-LOX localization to plastids. The apparent maximal velocity (Vmaxapp) values for LOX-catalyzed LeA oxidation were highest for LOX4 (128 nmol.s−1.mg protein−1), with a Km value of 5.8 µM. A. thaliana 13-LOXs, in cascade with 12-OPDA pathway enzymes, synthesized 12-OPDA and OCPD from LeA and docosahexaenoic acid, previously shown only for LOX6. The activities of the four isoforms were differently affected by physiologically relevant chemicals, such as Mg2+, Ca2+, Cu2+ and Cd2+, and by 12-OPDA and MJ. As demonstrated for LOX4, 12-OPDA inhibited enzymatic LeA hydroperoxidation, with half-maximal enzyme inhibition at 48 µM. Biochemical interactions, such as the sensitivity of LOX toward thiol-reactive agents belonging to cyclopentenone prostaglandins, are suggested to occur in human LOX homologs. Furthermore, we conclude that 13-LOXs are isoforms with rather specific functional and regulatory enzymatic features.

Uji Aktivitas Antidiabetes Senyawa Baru Daun Yakon (Smallanthus sonchifolius) sebagai Inhibitor Enzim DPP-4: Studi in Silico

Diabetes melitus merupakan gangguang kesehatan global yang menjadi perhatian penting untuk menemukan pencegahan dan terapi baru. Diabetes melitus dapat diobati menggunakan obat golongan inkreitin untuk menghambat kerja enzim DPP-4. Daun yakon (Smallanthus sonchifolius) merupakan tanaman herbal yang sering digunakan untuk mengobati berbagai penyakit dan diketahui memiliki turunan senyawa sekunder baru. Tujuan penelitian ini adalah mengetahui aktivitas senyawa baru daun yakon menginhibisi enzim DPP-4 berdasarkan energi dan ikatan kimia secara in silico. Senyawa baru daun yakon adalah turunan asam octadecatrienoic dan Benzyl glikosida. Senyawa tersebut diambil dari pubchem dan digambarkan kembali menggunakan chemdraw, sedangkan enzim DPP-4 (reseptor) didapat dari bank protein dunia dengan kode PDB ID: 3F8S. Penelitian ini dilakukan dengan metode In Silico dan perangkat lunak AutoDock Vina digunakan untuk proses penambatan. Hasil optimasi gridbox dengan melakukan penambatan ulang ligan kontrol diperoleh hasil RMSD sebesar 1.628 Å. Hasil penambatan molekuler dapat disimpulkan bahwa senyawa baru daun yakon berpotensi menghambat aktivitas enzim DPP-4 sebagai antidiabetes berdasarkan nilai energi bebas ΔG dan ikatan kimia. Interaksi yang terbentuk antara ligan dan reseptor tepat pada sisi aktif enzim DPP-4 yaitu Glu205, Glu206, Asn710, Tyr662, Arg125, Ser630, Phe357, Tyr666, Tyr547 dan Ser209. Interaksi yang terjadi antara ligan dan reseptor didominasi oleh ikatan hidrogen. Senyawa 13(R)-hydroxyoctadeca-(9E,11E,15Z)-trienoic acid (ligan 1), benzyl +alcohol 7-O-α-L-arabinopyranosyl-(1"→2')-β-D-glucopyranoside (ligan 2), 13(R)-Hydroxy-octadeca-(9Z,11E,15Z)-trienoic acid (ligan 3) memiliki nilai ΔG sebesar -6.2 kkal/mol, -7.7 kkal/mol dan -5.6 kkal/mol. Namun, Benzyl alcohol 7-O-α-L-arabinopyranosyl (1"→2')-β-D-glucopyranoside (ligan 2) lebih berpotensi menghambat enzim DPP-4 karena nilai energi bebas Gibbs (ΔG) dan ikatan kimia yang terbentuk lebih negatif dan stabil dibandingkan ligan 1 dan 3

Improvement Effect of Ficus vasculosa Ethanol Extract on D-galactose-Induced Mice Aging

This study was to investigate antioxidant activities of the ethanol extract from young edible leaves of Ficus vasculosa in vitro and in vivo . Ficus vasculosa ethanol extract (FVEE) showed significantly higher reducing power and α,α-diphenyl-β-picrylhydrazyl (DPPH) radical scavenge activity than vitamin C ( P < 0.05). FVEE also showed an activity to resist the D-galactose-induced aging in mice assessed by serum and tissue levels of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px). Total serum and tissue oxidative status, total antioxidantresponse, glutathione (GSH) and malondialdehyde (MDA) levels have been also measured. Pretreatment with FVEE at 200 mg/kg·body weight significantly increased enzyme activity of SOD and CAT in serum and hepatic tissue ( P < 0.05), as well as significantly increased enzyme activity of SOD in kidney ( P < 0.05). Furthermore, high concentration of FVEE pretreatment significantly increased the level of GSH in serum, hepatic tissue and kidney ( P < 0.05), meanwhile significantly decreased MDA production in hepatic tissue and kidney ( P < 0.05). In addition, the phytochemical investigation discovered six previously described compounds from FVEE, naringenin (1), vanillic acid (2), 9, 16-dioxo-10, 12, 14-octadeca-trienoic acid (3), 2, 6-dimethoxy-1, 4-benzoquinone (4), apigenin (5) and norartocarpetin (6), and all compounds were isolated from this plant for the first time. Among the various compounds found, the rare highly unsaturated fatty acid 9, 16-dioxo-10, 12, 14-octadeca-trienoic acid (3) has been identified, which had been isolated only once before from F. vasculosa. Evaluation of the antioxidant activity of isolated compounds showed naringenin (1) to be the most active. According to our research, FVEE present very high antioxidant activity in vitro due to the presence of several compounds known for their antioxidant activity such as flavonoid and phenolic acid. In vivo, the ethanol extract had improvement effects against D-galactose-induced aging by reducing oxidative stress.