Dataset Information

Anti-methanogenic effect of rhubarb (Rheum spp.) - An in silico docking studies on methyl-coenzyme M reductase (MCR).

ABSTRACT: The present study explored anti-methanogenic properties of rhubarb compounds using in silico analysis on methyl-coenzyme M reductase (MCR) for identifying its anti-methanogen mechanism. To identify pharmacokinetics of 35 compounds from rhubarb, molecular docking and ADME analysis were performed against MCR using AutoDockVina, FAFDrugs3 and PROTOX programs. Docking results successfully indicated three possible candidate compounds 9,10-anthracenedione, 1,8-dihydroxy-3-methyl (-6.92?kcal/mol); phthalic acid isobutyl octadecyl ester (-5.26?kcal/mol); and diisooctyl phthalate (-5.61?kcal/mol) showed minimum binding energy (kcal/mol) with the target protein MCR which catalyze the biosynthesis of rumen methane. In conclusion, the identified compounds showed the most docking fitness score against the target methyl-coenzyme M reductase and the decrease in ruminal methane emission by rhubarb might be a result of these compounds by inhibition of methanogenesis.

SUBMITTER: Arokiyaraj S

PROVIDER: S-EPMC6864367 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Anti-methanogenic effect of rhubarb (Rheum spp.) - An in silico docking studies on methyl-coenzyme M reductase (MCR).

Arokiyaraj Selvaraj S Stalin Antony A Shin Hakdong H

Saudi journal of biological sciences 20190613 7

The present study explored anti-methanogenic properties of rhubarb compounds using in silico analysis on methyl-coenzyme M reductase (MCR) for identifying its anti-methanogen mechanism. To identify pharmacokinetics of 35 compounds from rhubarb, molecular docking and ADME analysis were performed against MCR using AutoDockVina, FAFDrugs3 and PROTOX programs. Docking results successfully indicated three possible candidate compounds 9,10-anthracenedione, 1,8-dihydroxy-3-methyl (-6.92 kcal/mol ...[more]

PMID: 31762609

Similar Datasets

Project description:Methyl-coenzyme M reductase (MCR) catalyzes the final and rate-limiting step in methane biogenesis: the reduction of methyl-coenzyme M (methyl-SCoM) by coenzyme B (CoBSH) to methane and a heterodisulfide (CoBS-SCoM). Crystallographic studies show that the active site is deeply buried within the enzyme and contains a highly reduced nickel-tetrapyrrole, coenzyme F(430). Methyl-SCoM must enter the active site prior to CoBSH, as species derived from methyl-SCoM are always observed bound to the F(430) nickel in the deepest part of the 30 A long substrate channel that leads from the protein surface to the active site. The seven-carbon mercaptoalkanoyl chain of CoBSH binds within a 16 A predominantly hydrophobic part of the channel close to F(430), with the CoBSH thiolate lying closest to the nickel at a distance of 8.8 A. It has previously been suggested that binding of CoBSH initiates catalysis by inducing a conformational change that moves methyl-SCoM closer to the nickel promoting cleavage of the C-S bond of methyl-SCoM. In order to better understand the structural role of CoBSH early in the MCR mechanism, we have determined crystal structures of MCR in complex with four different CoBSH analogues: pentanoyl, hexanoyl, octanoyl, and nonanoyl derivatives of CoBSH (CoB(5)SH, CoB(6)SH, CoB(8)SH, and CoB(9)SH, respectively). The data presented here reveal that the shorter CoB(5)SH mercaptoalkanoyl chain overlays with that of CoBSH but terminates two units short of the CoBSH thiolate position. In contrast, the mercaptoalkanoyl chain of CoB(6)SH adopts a different conformation, such that its thiolate is coincident with the position of the CoBSH thiolate. This is consistent with the observation that CoB(6)SH is a slow substrate. A labile water in the substrate channel was found to be a sensitive indicator for the presence of CoBSH and HSCoM. The longer CoB(8)SH and CoB(9)SH analogues can be accommodated in the active site through exclusion of this water. These analogues react with Ni(III)-methyl, a proposed MCR catalytic intermediate of methanogenesis. The CoB(8)SH thiolate is 2.6 A closer to the nickel than that of CoBSH, but the additional carbon of CoB(9)SH only decreases the nickel thiolate distance a further 0.3 A. Although the analogues do not induce any structural changes in the substrate channel, the thiolates appear to preferentially bind at two distinct positions in the channel, one being the previously observed CoBSH thiolate position and the other being at a hydrophobic annulus of residues that lines the channel proximal to the nickel.

Project description:In an era of anthropocene, threatened and endemic species with small population sizes and habitat specialists experience a greater global conservation concern in view of being at higher risk of extinction. Predicting and plotting appropriate potential habitats for such species is a rational method for monitoring and restoring their dwindling populations in expected territories. Ecological niche modelling (ENM) coalesces species existence sites with environmental raster layers to construct models that describe possible distributions of plant species. The present study is aimed to study the potential distribution and cultivation hotspots for reintroducing the high value, vulnerable medicinal herb (Rheum webbianum) in the Union territories of Jammu and Kashmir and Ladakh using population attributes and ecological niche modelling approach. Sixty-three populations inventoried from twenty-eight areas display a significant change in the phytosociological attributes on account of various anthropogenic threats. The current potential habitats coincide with actual distribution records and the mean value of Area Under Curve (AUC) was 0.98 and the line of predicted omission was almost adjacent to omission in training samples, thus validating a robustness of the model. The potential habitat suitability map based on the current climatic conditions predicted a total of 103760 km2 as suitable area for the growth of Rheum webbianum. Under the future climatic conditions, there is a significant reduction in the habitat suitability ranging from -78531.34 Km2 (RCP 4.5 for 2050) to -77325.81 (RCP 8.5 for 2070). Furthermore, there is a slight increase in the suitable habitats under future climatic conditions, ranging from +21.99 Km2 under RCP 8.5 (2050) to +3.14 Km2 under RCP 4.5 (2070). The Jackknife tests indicated Precipitation of Driest Month (BIO14) as the most contributing climatic variable in governing the distribution of R. webbianum. Therefore, scientifically sound management strategies are urgently needed to save whatever populations are left in-situ to protect this species from getting extinct. Present results can be used by conservationists for mitigating the biodiversity decline and exploring undocumented populations of R. webbianum on one hand and by policymakers in implementing the policy of conservation of species with specific habitat requirements by launching species recovery programmes in future on the other.

Dataset Information

Anti-methanogenic effect of rhubarb (Rheum spp.) - An in silico docking studies on methyl-coenzyme M reductase (MCR).

Publications

Anti-methanogenic effect of rhubarb (<i>Rheum</i> spp.) - An <i>in silico</i> docking studies on methyl-coenzyme M reductase (MCR).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure