On scaffold hopping: Challenges in the discovery of sulfated small molecules as mimetics of glycosaminoglycans

Abstract

The design of sulfated, small, non-saccharide molecules as modulators of proteins is still in its infancy as standard drug discovery tools such as library of diverse sulfated molecules and in silico docking and scoring protocol have not been firmly established. Databases, such as ZINC, contain too few sulfate-containing non-saccharide molecules, which severely limits the identification of new hits. Lack of a generally applicable protocol for scaffold hopping limits the development of sulfated small molecules as synthetic mimetics of the highly sulfated glycosaminoglycans. We explored a sequential ligand-based (LBVS) and structure-based virtual screening (SBVS) approach starting from our initial discovery of monosulfated benzofurans to discover alternative scaffolds as allosteric modulators of thrombin, a key coagulation enzyme. Screening the ZINC database containing nearly 1 million non-sulfated small molecules using a pharmacophore developed from the parent sulfated benzofurans followed by a genetic algorithm-based dual-filter docking and scoring screening identified a group of 10 promising hits, of which three top-scoring hits were synthesized. Each was found to selectively inhibit human alpha-thrombin suggesting the possibility of this approach for scaffold hopping. Michaelis-Menten kinetics showed allosteric inhibition mechanism for the best molecule and human plasma studies confirmed good anticoagulation potential as expected. Our simple sequential LBVS and SBVS approach is likely to be useful as a general strategy for identification of sulfated small molecules hits as modulators of glycosaminoglycan–protein interactions.

Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins

“…Nevertheless, the relative lack of experimental structural data for these systems, combined with a growing awareness of their biological significance, has led to a number of innovative approaches to GAG docking. Recent examples include advances in the prediction of GAG binding sites [38,39], improvement in pose prediction via inclusion of specific bound waters [40], co-complex generation via threading and superimposition [41], mimetic discovery [42], as well as combining spectroscopic data with GAG modelling [43,44]. Very recently, an online utility for the automatic generation of 3D structures for GAGs has appeared (www.glycam.org/gag, [25]) that should find application in GAG modelling.…”

Synthesis and biological evaluation of some dibenzofuran-piperazine derivatives

“…Aglafolin (Figure 1) is another benzofuran including molecule, isolated from the stems of Aglaia elliptifolia, was notified with effective inhibitor activity of platelet aggregation induced by PAF both in vitro and in vivo 22 . Recently, in a series of study Sidhu et al [23][24][25][26][27] and Thalji et al 28 have also declared different benzofuran-bearing compounds with significant antiplatelet activity. Moreover, benzofuran ring analog dibenzofuran-bearing compounds have been reported to exhibit a great variety of biological some effects, including thrombosis 29,30 and anticholinesterase activity [31][32][33] distinct from the mentioned above.…”

Allosteric inhibitors of thrombin

“…Recently, a class of inhibitors was reported by Sidhu et al which selectively inhibits the coagulation activity of thrombin by binding to exosite II. [4][5][6][7][8][9] These were benzofuran-based scaffold derived from β-5 linkage present in naturally occurring lignin polymer. The focused libraries of benzofuran-based monomers and dimers were synthesized and determined to inhibit thrombin in low micromolar range.…”

“…This proposed binding model can be effectively used to design new inhibitors with improved inhibition potency. 7 Designing allosteric inhibitors for thrombin opens the new avenue to discover newer generation of inhibitors with fewer side effects. This mode of inhibition is advantageous due to partial inhibition of thrombin activity and ease of designing the antidote.…”