Synthesis and X-ray crystallographic investigation of N-(a-D-arabi- nopyranosyl)alkanamides as N-glycoprotein linkage region analogs Amrita Srivastava a,⇑ , Babu Varghese b , Duraikkannu Loganathan a,  a Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India b Sophisticated Analytical Instrumentation Facility, Indian Institute of Technology Madras, Chennai 600036, India article info Article history: Received 14 June 2013 Received in revised form 28 July 2013 Accepted 29 July 2013 Available online 9 August 2013 Keywords: N-glycoprotein Linkage region Analogs C–HO interactions X-ray Molecular assembly abstract N-Glycoprotein linkage region constituents namely 2-deoxy-2-acetamido-b-D-glucopyranose (GlcNAc) and asparagine (Asn) are conserved among all eukaryotes. Earlier crystallographic studies on the linkage region conformation revealed that among all the models and analogs of the N-glycoprotein linkage region, XylbNHAc showed maximum deviation in the / N value as compared to the value reported for the model compound, GlcNAcbNHAc. In order to understand the effect of another pentopyranose, viz., arabinose, on the N-glycosidic torsion angles and molecular assembly, three arabinopyranosyl alkana- mides were synthesized and their X-ray crystal structures elucidated. A comparative analysis of the N-glycosidic torsion, / N of the three analogs revealed the greater rotational freedom around the C1–N1 bond as compared to the GlcNAc derivatives. Molecular assembly of propionamido and chloroacetamido derivatives is characterized by the presence of anti-parallel bilayers of the molecules. This unique molec- ular assembly is hitherto unknown in all other models and analogs of N-glycoprotein linkage region. This study reveals that N-glycosidic torsions are influenced by the glycan as well as molecular packing. Ó 2013 Elsevier Ltd. All rights reserved. 1. Introduction Glycan part of glycoproteins play vital roles in many biological processes. 1,2 As N-linked glycosylation influences the protein sta- bility and function, it is important to gain a complete understand- ing of how carbohydrates influence the peptide structure and function. To gain a better understanding for nature’s choice of Glc- NAcbAsn (Fig. 1) as linkage region constituents and inter- & intra- molecular carbohydrate–protein interactions, a detailed systemic structural study of linkage region conformation is needed. Due to conformational flexibility of carbohydrates, crystallization of gly- coproteins is still a daunting task. In this regard, using smaller models and analogs of the N-glycoprotein linkage region would be a valuable approach. A major focus of our laboratory is on the synthesis, X-ray crystallography, and ab initio calculations of the models and analogs of the N-glycoprotein linkage region. 3–15 A sys- tematic crystallographic investigation among several N-(b-glyco- pyranosyl)alkanamido derivatives, on the N-glycosidic torsion, / N (O5–C1–N1–C1 0 ) revealed variations up to 31.9° for XylbNHAc from the value observed for the model compound, GlcNAcbNHAc. 6 The / N value of the propionamido derivative of the xylose differs by 20° from that of the acetamido analog. In the case of fully acet- ylated XylbNHAc, / N value (90.2°) is found to be nearly same as observed for the model compound GlcNAcbNHAc. 11 Further stud- ies on the N-(b-D-glycopyranosyl)alkanamides and haloacetamides showed that the N-acetyl group at C2 controls the side chain tor- sion angle v 2 (N1–C1 0 –C2 0 –C3 0 ) at the linkage region and helps in establishing the extended aglycon conformation. 10 Influence of substituents at C2 & C5 and environmental factors mainly inter- and intramolecular interactions involving the hydrogen bonds and C–HO interactions on the energy preferences of the / N tor- sion angle was also examined. 11,12 The present work was initiated with the aim of understanding the conformational preferences of another common pentose, namely, arabinose. Arabinose is found a-linked to hydroxylysine in plant cell wall and attached in b fashion to hydroxyproline in the potato lectin. 16 We report herein the synthesis and X-ray crystallographic investigation of the three N-(a-D-arabinopyranosyl)alkanamides, namely, AraaNHAc, Ara- aNHCOEt, and AraaNHCOCH 2 Cl (Fig. 1). 2. Results and discussion 2.1. Synthesis of N-(a-D-arabinopyranosyl)alkanamides 2,3,4-Tri-O-acetyl-a-D-arabinopyranosyl azide (1) 17 was chosen as starting material. Azide (1) was reduced using Pd/C & hydrogen and acetylated with various acid anhydrides at 0 °C to give the fully acetylated arabinopyranosyl alkanamides (2–4) in good yield (Scheme 1). De-O-acetylation of the fully acetylated compounds 0008-6215/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.carres.2013.07.014 ⇑ Corresponding author. Tel.: +91 44 22575221; fax: +91 44 22574202. E-mail address: amrisriv9@gmail.com (A. Srivastava).   Deceased on February 9, 2013. Carbohydrate Research 380 (2013) 92–100 Contents lists available at ScienceDirect Carbohydrate Research journal homepage: www.elsevier.com/locate/carres