“…Several compounds in the list, such as vitamin C, retinol, retinoic acid, resveratrol, LR2412/JAD, c-xyloside (Proxylane TM ) were reported to affect skin ageing parameters. 43–51 Rapamycin, metformin, resveratrol, C8-SA, acetyl salicylic acid, salicylic acid have also been described as longevity compounds in model organisms. 42,50,52–61 Fig.…”
Designing alternative approaches to efficiently screen chemicals on the efficacy landscape is a challenging yet indispensable task in the current compound profiling methods. Particularly, increasing regulatory restrictions underscore the need to develop advanced computational pipelines for efficacy assessment of chemical compounds as alternative means to reduce and/or replace in vivo experiments. Here, we present an innovative computational pipeline for large-scale assessment of chemical compounds by analysing and clustering chemical compounds on the basis of multiple dimensions—structural similarity, binding profiles and their network effects across pathways and molecular interaction maps—to generate testable hypotheses on the pharmacological landscapes as well as identify potential mechanisms of efficacy on phenomenological processes. Further, we elucidate the application of the pipeline on a screen of anti-ageing-related compounds to cluster the candidates based on their structure, docking profile and network effects on fundamental metabolic/molecular pathways associated with the cell vitality, highlighting emergent insights on compounds activities based on the multi-dimensional deep screen pipeline.
“…Several compounds in the list, such as vitamin C, retinol, retinoic acid, resveratrol, LR2412/JAD, c-xyloside (Proxylane TM ) were reported to affect skin ageing parameters. 43–51 Rapamycin, metformin, resveratrol, C8-SA, acetyl salicylic acid, salicylic acid have also been described as longevity compounds in model organisms. 42,50,52–61 Fig.…”
Designing alternative approaches to efficiently screen chemicals on the efficacy landscape is a challenging yet indispensable task in the current compound profiling methods. Particularly, increasing regulatory restrictions underscore the need to develop advanced computational pipelines for efficacy assessment of chemical compounds as alternative means to reduce and/or replace in vivo experiments. Here, we present an innovative computational pipeline for large-scale assessment of chemical compounds by analysing and clustering chemical compounds on the basis of multiple dimensions—structural similarity, binding profiles and their network effects across pathways and molecular interaction maps—to generate testable hypotheses on the pharmacological landscapes as well as identify potential mechanisms of efficacy on phenomenological processes. Further, we elucidate the application of the pipeline on a screen of anti-ageing-related compounds to cluster the candidates based on their structure, docking profile and network effects on fundamental metabolic/molecular pathways associated with the cell vitality, highlighting emergent insights on compounds activities based on the multi-dimensional deep screen pipeline.
“…Heparin and HS-derived oligosaccharides were prepared as previously described (30,31) by partial heparinase I (Grampian enzymes, Orkney, UK) depolymerization of porcine mucosal heparin and exhaustive digestion of porcine mucosal HS with heparinase III (Grampian enzymes). Disaccharide analysis of SAGAG heparin tetrasaccharides was achieved by reverse-phase ion-pair high-performance liquid chromatography (RPIP-HPLC) as described before (32). Treatment of heparin by the 6-O-endosulfatase HSulf-2 was performed as described previously (33), for details on the disaccharide composition, see (34).…”
“…GAG disaccharide analysis was performed as previously described [28]. CS in 50 mM Tris-HCl pH 7.5, 50 mM NaCl, 2 mM CaCl2 was digested with 500 mU of chondroitinase ABC for 24 h at 37°C.…”
Semaphorin 3A (Sema3A) is a secreted protein that signals to cells through binding to neuropilin and plexin receptors and provides neurons with guidance cues key for axon pathfinding, and also controls cell migration in several other biological systems. Sema3A interacts with glycosaminoglycans (GAGs), an interaction that could localize the protein within tissues and involves the C-terminal domain of the protein. This domain comprises several furin cleavage sites that are processed during secretion and in previous works have hampered recombinant production of full-length wild type Sema3A, and the biochemical analysis of Sema3A interaction with GAGs. In this work, we have developed a strategy to purify the full-length protein in high yield and identified two sequences in the C-terminal domain, KRDRKQRRQR and KKGRNRR, which confer to the protein sub nM affinity for chondroitin sulfate and heparan sulfate polysaccharides. Using chemically defined oligosaccharides and solid phase binding assays, we report that Sema3A recognizes a (GlcA-GalNAc4S6S)2 motif but not a (GlcA2S-GalNAc6S)2 motif and is thus highly specific for type E chondroitin sulfate. Functionally, we found that Sema3A rigidified CS-E films that mimic the GAG presentation within extracellular matrices (ECMs), suggesting that Sema3A may have a previously unidentified function to cross-link and thus stabilize GAG-rich ECMs. Finally, we demonstrated that the full-length Sema3A is more potent at inhibiting neurite outgrowth than the truncated or mutant forms that were previously purified and that the GAG binding sites are required to achieve full activity. The results suggest that Sema3A can rigidify and cross-link GAG matrices, implicating Sema3A could function as an extracellular matrix organizer in addition to binding to and signaling through its cognate cell surface receptors.
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