Structural Studies on New, Non-reducing Oligosaccharides Produced by<i>Rhizobium meliloti</i>J7017

Hisamatsu, Makoto; Yamada, Tetsuya; Akaki, Morio; Nashinoki, Hiroshi; Takai, Yoshio; Amemura, Akinori

doi:10.1080/00021369.1985.10866904

Cited by 3 publications

(2 citation statements)

References 2 publications

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“…In the same series of Supernatural product database, the second top-ranked molecule is SN00334894. SN00334894 is a glycan produced by Rhizobium meliloti J7017 (Hisamatsu et al, 1985). This molecule revealed less docking scores when compared with the previously discussed top-ranked molecule and significant docking score when compared with the co-crystal ligand.…”

Section: Molecular Docking Studiesmentioning

confidence: 88%

Pharmacophore based virtual screening, molecular docking, molecular dynamics and MM-GBSA approach for identification of prospective SARS-CoV-2 inhibitor from natural product databases

Kumar

Faheem

Sekhar

et al. 2020

Journal of Biomolecular Structure and Dynamics

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COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily appeared in Wuhan, China, in December 2019. At present, no proper therapy and vaccinations are available for the disease, and it is increasing day by day with a high mortality rate. Pharmacophore based virtual screening of the selected natural product databases followed by Glide molecular docking and dynamics studies against SARS-CoV-2 main protease was investigated to identify potential ligands that may act as inhibitors. The molecules SN00293542 and SN00382835 revealed the highest docking score of 214.57 and 212.42 kcal/mol, respectively, when compared with the co-crystal ligands of PDB-6Y2F (O6K) and 6W63 (X77) of the SARS-CoV-2 M pro. To further validate the interactions of top scored molecules SN00293542 and SN00382835, molecular dynamics study of 100 ns was carried out. This indicated that the protein-ligand complex was stable throughout the simulation period, and minimal backbone fluctuations have ensued in the system. Post-MM-GBSA analysis of molecular dynamics data showed free binding energy-71.7004 1/2 7.98, 256.811/2 7.54 kcal/mol, respectively. The computational study identified several ligands that may act as potential inhibitors of SARS-CoV-2 M pro. The top-ranked molecules SN00293542, and SN00382835 occupied the active site of the target, the main protease like that of the co-crystal ligand. These molecules may emerge as a promising ligands against SARS-CoV-2 and thus needs further detailed investigations.

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Section: Molecular Docking Studiesmentioning

confidence: 88%

Pharmacophore based virtual screening, molecular docking, molecular dynamics and MM-GBSA approach for identification of prospective SARS-CoV-2 inhibitor from natural product databases

Kumar

Faheem

Sekhar

et al. 2020

Journal of Biomolecular Structure and Dynamics

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“…Kojibiose is the only kojidextrin found in mammals, where it is part of the lipid-linked oligosaccharide precursor for protein glycosylation . Kojitriose occurs in bacterial teichoic acids 5 and in native dextrans, and kojitetraose and -pentaose constitute part of the glucans secreted by Rhizobium meliloti J 7017 was identified as an extracellular saccharide of a slow-growing strain of Rhizobium japonicum strain 561, and an antigenic polysaccharide isolated from Mycobacterium tuberculosis strains H37 and A33, termed polysaccharide II, is said to be poly-α-(1→2)- d -glucan .…”

Section: Introductionmentioning

confidence: 99%

Synthesis of Kojidextrins and Their Protein Conjugates. Incidence of Steric Mismatch in Oligosaccharide Synthesis

1997

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Kojidextrins are biologically important oligosaccharides that are involved in many physiological processes including protein glycosylation and bacterial growth. As part of our project to explore the role kojidextrins may play in bacterial pathogenesis, here we report synthetic routes to kojibiose (54), -triose (58), -tetraose (64), and -pentaose (69) equipped with alpha-linked (hydrazinocarbonyl)pentyl aglycon, using linear and convergent strategies. In the search for a rapid convergent strategy for the construction of extended kojidextrins, four kojibiose donors (1-4) were synthesized that contain acyl- and ether-type protecting groups in various ratios. These were tested to probe the influence of diverse protecting group assemblies on their glycosyl donor ability. Attempted condensation of these donors with kojitriose and -tetraose acceptors failed to give the desired products apparently because of steric mismatch between the donor and the acceptor moieties. A one-pot procedure was developed for the covalent attachment of the synthetic saccharides through their hydrazido group to human serum albumin (HSA) using Tietze's squarate method to give neoglycoproteins containing up to 28 saccharide units per HSA.

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Osmotically induced oligo- and polysaccharide synthesis by Rhizobium meliloti SU-47

Breedveld¹,

Zevenhuizen²,

Zehnder³

1990

Journal of General Microbiology

106

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In standard liquid medium containing 5 g mamitoll-' and 1 g glutamic acid 1-l, Rhizobium mefifoti SU-47 cells accumulated 350 mg cyclic 1,2-Q-glucans (g protein)-'. The cyclic glucans were 36 % glycerol-1-phosphatesubstituted and 64% were uncharged. In the same medium with 10 g mamitoll-' , repeating units of succinoglycan (1110 mg 1-l) were found as extracellular carbohydrates, and only low amounts of the succinoglycan polymer (up to 300 mg 1-l) were excreted. By raising the osmotic pressure of the medium by the addition of NaCl or other ionic and non-ionic osmolytes, succinoglycan production could be stimulated: up to 2.4 g 1-1 at 0.2 M-NaCI was produced at the expense of the repeating units. Above 0.2 M-NaCl growth was slowed down, and succinoglycan excretion diminished. At 1 M-NaCl growth stopped completely. In standard medium containing 0.6 M-NaCl the amount of cellular cyclic l,2-Q-glucans was lowered to 150 mg (g protein)-l out of which the glycerol-1-phosphatesubstituted glucan fraction was reduced to 15%. Instead, high amounts of oligosaccharides were synthesized as osmoprotectants, with trehalose as the major component [up to 200 mg (g protein)-']. Glycogen synthesis was completely suppressed at this salt concentration, while p l y Q-hydroxybutyric acid synthesis was unaffected.

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Structural Studies on New, Non-reducing Oligosaccharides Produced byRhizobium melilotiJ7017

Cited by 3 publications

References 2 publications

Pharmacophore based virtual screening, molecular docking, molecular dynamics and MM-GBSA approach for identification of prospective SARS-CoV-2 inhibitor from natural product databases

Pharmacophore based virtual screening, molecular docking, molecular dynamics and MM-GBSA approach for identification of prospective SARS-CoV-2 inhibitor from natural product databases

Synthesis of Kojidextrins and Their Protein Conjugates. Incidence of Steric Mismatch in Oligosaccharide Synthesis

Osmotically induced oligo- and polysaccharide synthesis by Rhizobium meliloti SU-47

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