Challenges of docking in large, flexible and promiscuous binding sites

After decades of work, the correct determination of the binding mode of a small molecule into a target protein is still a challenging problem, whose difficulty depends on: (i) the sizes of the binding site and the ligand; (ii) the flexibility of both interacting partners, and (iii) the differential solvation of bound and unbound partners. We have evaluated the performance of standard rigid(receptor)/flexible(ligand) docking approaches with respect to last-generation fully flexible docking methods to obtain reasonable poses in a very challenging case: soluble Epoxide Hydrolase (sEH), a flexible protein showing different binding sites. We found that full description of the flexibility of both protein and ligand and accurate description of solvation leads to significant improvement in the ability of docking to reproduce well known binding modes, and at the same time capture the intrinsic binding promiscuity of the protein.Peer ReviewedPostprint (author's final draft

Pushing the Limits of Computational Structure-Based Drug Design with a Cryo-EM Structure: The Ca2+ Channel α2δ-1 Subunit as a Test Case

Cryo-electron microscopy (cryo-EM) is emerging as a real alternative for structural elucidation. In spite of this, very few cryo-EM structures have been described so far as successful platforms for in silico drug design. Gabapentin and pregabalin are some of the most successful drugs in the treatment of epilepsy and neuropathic pain. Although both are in clinical use and are known to exert their effects by binding to the regulatory α2δ subunit of voltage gated calcium channels, their binding modes have never been characterized. We describe here the successful use of an exhaustive protein–ligand sampling algorithm on the α2δ-1 subunit of the recently published cryo-EM structure, with the goal of characterizing the ligand entry path and binding mode for gabapentin, pregabalin, and several other amino acidic α2δ-1 ligands. Our studies indicate that (i) all simulated drugs explore the same path for accessing the occluded binding site on the interior of the α2δ-1 subunit; (ii) they all roughly occupy the same pocket; (iii) the plasticity of the binding site allows the accommodation of a variety of amino acidic modulators, driven by the flexible “capping loop” delineated by residues Tyr426-Val435 and the floppy nature of Arg217; (iv) the predicted binding modes are in line with previously available mutagenesis data, confirming Arg217 as key for binding, with Asp428 and Asp467 highlighted as additional anchoring points for all amino acidic drugs. The study is one of the first proofs that latest-generation cryo-EM structures combined with exhaustive computational methods can be exploited in early drug discovery.The authors would like to thank Modesto Orozco for fruitful discussions and feedback on the manuscript. Suggestions by the reviewers are also gratefully acknowledged. Nostrum is supported by Fundacion Marcelino Botin (Mind the Gap) and CDTI (Neotec grant −EXP 00094141/SNEO-20161127). M.K. and R.S. would like to thank BSC and IRB for technical support. V.G. is supported by the CTQ2016-79138-R grant.Peer ReviewedPostprint (author's final draft

Effects of polysaccharide-based edible coatings enriched with dietary fiber on quality attributes of fresh-cut apples

Little information is available regarding the incorporation of dietary fiber into edible films and coatings. In this work, apple fiber and inulin were incorporated into polysaccharide-based (alginate, pectine and gellan gum) edible coating formulations and their effects on the quality attributes of fresh-cut apples were evaluated. Antioxidant properties, color, firmness, sensory quality and microbial growth of fresh-cut apple were studied during 16 days of storage at 4 A degrees C. Results show that dietary fiber extracts incorporated to gellan gum, pectin and alginate-based coatings together with calcium chloride and ascorbic acid successfully maintained the firmness and color of coated fresh-cut apples in comparison with uncoated control samples, which presented severe texture softening and browning. The firmness of apple pieces coated with polysaccharide-based coating formulations incorporating apple fiber doubled, and sometimes tripled, that of uncoated samples. Any of the assayed coatings exhibited a positive effect on the sensory properties of fresh-cut apples. The incorporation of apple fiber, together with the use of ascorbic acid, contributed to keep the antioxidant potential of the fruit at least during the first week of storage. Furthermore, gellan gum coatings had a marked effect in reducing mesophilic and psychrophilic counts on fresh-cut apples throughout storage regardless the addition of dietary fibers. The results achieved demonstrate the feasibility of the addition of dietary fiber to edible coating formulations for increasing the nutritional value of fresh-cut apples without compromising their fresh-like quality attributes.This work was supported by Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT, Argentina) and by Spanish Ministry of Economy and Competitiveness, through the project AGL2010-21572. An ICREA Academia Award is also acknowledged