Identification of the furanose ring conformations and the factors driving their adoption

Walczak, Dominik; Sikorski, Artur; Grzywacz, Daria; Nowacki, Andrzej; Liberek, Beata

doi:10.1016/j.carres.2023.108780

Cited by 8 publications

(5 citation statements)

References 54 publications

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“…In compound 5e, the furanose ring (O1-C2-C3-C4-C5, numbering of atoms in crystallographic descriptions consistent with the numbering of atoms in Figure 4) adopts a conformation close to the 4 T 0 (twisted on C5-O1 bond-Figure 4) [36,37] with ring-puckering parameters [38,39] . Comparison of previously determined structures of muscarine iodide and chloride differ from each other and differ from the structure of compound 5e.…”

Section: Crystal Structure and Analysis Of Intermolecular Interactionsmentioning

confidence: 84%

Oxolane Ammonium Salts (Muscarine-Like)—Synthesis and Microbiological Activity

Bogdanowicz,

Madaj,

Szweda

et al. 2024

IJMS

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Commercially available 2-deoxy-D-ribose was used to synthesize the appropriate oxolane derivative—(2R,3S)-2-(hydroxymethyl)oxolan-3-ol—by reduction and dehydration/cyclization in an acidic aqueous solution. Its monotosyl derivative, as a result of the quaternization reaction, allowed us to obtain eight new muscarine-type derivatives containing a quaternary nitrogen atom and a hydroxyl group linked to the oxolane ring. Their structure was fully confirmed by the results of NMR, MS and IR analyses. The crystal structure of the pyridinium derivative showed a high similarity of the conformation of the oxolane ring to previously published crystal structures of muscarine. Two reference strains of Gram-negative bacteria (Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853), two reference strains of Gram-positive staphylococci (Staphylococcus aureus ATCC 25923 and Staphylococcus aureus ATCC 29213) and four reference strains of pathogenic yeasts of the genus Candida spp. (Candida albicans SC5314, Candida glabrata DSM 11226, Candida krusei DSM 6128 and Candida parapsilosis DSM 5784) were selected for the evaluation of the antimicrobial potential of the synthesized compounds. The derivative containing the longest (decyl) chain attached to the quaternary nitrogen atom turned out to be the most active.

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Section: Crystal Structure and Analysis Of Intermolecular Interactionsmentioning

confidence: 84%

Oxolane Ammonium Salts (Muscarine-Like)—Synthesis and Microbiological Activity

Bogdanowicz,

Madaj,

Szweda

et al. 2024

IJMS

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“…On the other hand, two of the ring atoms of chain B for l -KDF (C3 and C4) were located outside the plane defined by the three other atoms (C2-C5-O5), one above this plane (C3) and the other (C4) below it. These features corresponded to the envelope and twist conformations of furanose, respectively (referred to as species E and T ) 25 .…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of l-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a α-furanosyl hemiketal of substrates

Akagashi,

Watanabe,

Kwiatkowski

et al. 2024

Sci Rep

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Abstractl-2-Keto-3-deoxyfuconate 4-dehydrogenase (l-KDFDH) catalyzes the NAD+-dependent oxidization of l-2-keto-3-deoxyfuconate (l-KDF) to l-2,4-diketo-3-deoxyfuconate (l-2,4-DKDF) in the non-phosphorylating l-fucose pathway from bacteria, and its substrate was previously considered to be the acyclic α-keto form of l-KDF. On the other hand, BDH2, a mammalian homolog with l-KDFDH, functions as a dehydrogenase for cis-4-hydroxy-l-proline (C4LHyp) with the cyclic structure. We found that l-KDFDH and BDH2 utilize C4LHyp and l-KDF, respectively. Therefore, to elucidate unique substrate specificity at the atomic level, we herein investigated for the first time the crystal structures of l-KDFDH from Herbaspirillum huttiense in the ligand-free, l-KDF and l-2,4-DKDF, d-KDP (d-2-keto-3-deoxypentonate; additional substrate), or l-2,4-DKDF and NADH bound forms. In complexed structures, l-KDF, l-2,4-DKDF, and d-KDP commonly bound as a α-furanosyl hemiketal. Furthermore, l-KDFDH showed no activity for l-KDF and d-KDP analogs without the C5 hydroxyl group, which form only the acyclic α-keto form. The C1 carboxyl and α-anomeric C2 hydroxyl groups and O5 oxygen atom of the substrate (and product) were specifically recognized by Arg148, Arg192, and Arg214. The side chain of Trp252 was important for hydrophobically recognizing the C6 methyl group of l-KDF. This is the first example showing the physiological role of the hemiketal of 2-keto-3-deoxysugar acid.

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“…Focusing on the ribose units, besides the detected anomeric mixture, the interconversion among ring conformations was further studied through J H−H coupling analysis. 49 For the βfuranose ribose, the 3 T 2 conformation is always more populated in solution for both the internal ribose residues and the reducing one, while for the α-furanose ribose, no preference for a specific ring shape was detected (Figure S7). Fittingly, the major 3 T 2 conformation is in full agreement with the X-ray-based bound conformation to the mAb.…”

Section: ■ Discussionmentioning

confidence: 97%

“…However, once bound to the CA4 antibody, they adopt a well-defined conformation, in which the ribitol chain is perfectly accommodated into the antibody-binding pocket and the ribose ring displays a precise ring shape. Focusing on the ribose units, besides the detected anomeric mixture, the interconversion among ring conformations was further studied through J H–H coupling analysis . For the β-furanose ribose, the 3 T 2 conformation is always more populated in solution for both the internal ribose residues and the reducing one, while for the α-furanose ribose, no preference for a specific ring shape was detected (Figure S7).…”

Section: Discussionmentioning

confidence: 99%

A Multidisciplinary Structural Approach to the Identification of the Haemophilus influenzae Type b Capsular Polysaccharide Protective Epitope

Nonne,

Iacono,

Bertuzzi

et al. 2024

ACS Cent. Sci.

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Glycoconjugate vaccines so far licensed are generally composed of a native or size-reduced capsular polysaccharide conjugated to carrier proteins. Detailed information on the structural requirements necessary for CPS recognition is becoming the key to accelerating the development of next-generation improved glycoconjugate vaccines. Structural glycobiology studies using oligosaccharides (OS) complexed with functional monoclonal antibodies represent a powerful tool for gaining information on CPS immunological determinants at the atomic level. Herein, the minimal structural epitope of Haemophilus influenzae type b (Hib) CPS recognized by a functional human monoclonal antibody (hmAb) is reported. Short and well-defined Hib oligosaccharides originating from the depolymerization of the native CPS have been used to elucidate saccharide−mAb interactions by using a multidisciplinary approach combining surface plasmon resonance (SPR), saturation transfer differencenanomagnetic resonance (STD-NMR), and X-ray crystallography. Our study demonstrates that the minimal structural epitope of Hib is comprised within two repeating units (RUs) where ribose and ribitol are directly engaged in the hmAb interaction, and the binding pocket fully accommodates two RUs without any additional involvement of a third one. Understanding saccharide antigen structural characteristics can provide the basis for the design of innovative glycoconjugate vaccines based on alternative technologies, such as synthetic or enzymatic approaches.

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Identification of the furanose ring conformations and the factors driving their adoption

Cited by 8 publications

References 54 publications

Oxolane Ammonium Salts (Muscarine-Like)—Synthesis and Microbiological Activity

Oxolane Ammonium Salts (Muscarine-Like)—Synthesis and Microbiological Activity

Crystal structure of l-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a α-furanosyl hemiketal of substrates

A Multidisciplinary Structural Approach to the Identification of the Haemophilus influenzae Type b Capsular Polysaccharide Protective Epitope

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