Harvesting free energy landscapes in biological systems

A sophisticated mechanistic investigation of biological processes is the starting point for the calculation of accurate free energy figures, which enable comparison with experimental results. Applied to drug discovery, the use of molecular methods can guide the formulation and optimisation of novel drugs, specifically targeting molecular processes as they are learned from simulations. This is illustrated here based on two examples, the study of secondary DNA structures (G4s) as target for small gold-based molecules, and the investigation of the mechanisms of glycerol permeation via the membrane channel aquaglyceroporin-3 (AQP3). Both approaches leverage the enhanced sampling efficiency of accelerated molecular dynamics

Unveiling the Mechanisms of Aquaglyceroporin‐3 Water and Glycerol Permeation by Metadynamics

Water and glycerol permeation via human AQP3 are described exploiting advanced metadynamics approaches, which enabled to both explore the free energies involved in pore permeation, as well as to achieve a description of the mechanisms with an atomistic level of detail. Moreover, thanks to this technique, a basic water transport mechanism, single‐filed and bidirectional in nature was retrieved, on which glycerol molecules are inserted during channel permeation. Therein, activation energies result from static and dynamic effects involving hydrogen bonds within the water filament and among substrate molecules and pore internal residues

Discovery of novel human Aquaporin-1 Blockers

Human aquaporin-1 (hAQP1) is a water channel found in many tissues and potentially involved in several human pathologies. Selective inhibitors of hAQP1 are discussed as novel treatment opportunities for glaucoma, brain edema, inflammatory pain, and certain types of cancer. However, only very few potent and chemically attractive blockers have been reported to date. In this study we present three novel hAQP1 blockers that have been identified by virtual screening and inhibit water flux through hAQP1 in Xenopus laevis oocyte swelling assays at low micromolar concentrations. The newly discovered compounds display no chemical similarity to hitherto known hAQP1 blockers and bind at the extracellular entrance of the channel, close to the ar/R selectivity filter. Futhermore, mutagenesis studies showed that Lys36, which is not conserved among the hAQP family, is crucially involved in binding and renders the discovered compounds suitable as leads for the development of selective hAQP1 inhibitors. © 2012 American Chemical SocietyPeer Reviewe

Conditions promoting effective very high gravity sugarcane juice fermentation

Abstract Background: Applying very high gravity (VHG) fermentation conditions to the sugarcane juice (SCJ) bioethanol industry would improve its environmental and economic sustainability without the need for major infrastructure changes or investments. It could enable a decrease in the consumption of biological and natural resources (cane/ land, water and energy) while maintaining acceptable production parameters. The present study attempts to demonstrate and characterise an efective industrially relevant SCJ-VHG fermentation process. Results: An industry-like SCJ-VHG bioethanol production process with 30 and 35 °Bx broth was employed to investigate the efects of both the yeast strain used and nitrogen source supplementation on process yield, process productivity, biomass viability, glycerol concentration and retention-associated gene expression. Process performance was shown to be variably afected by the diferent process conditions investigated. Highest process efciency, with a 17% (w/v) ethanol yield and only 0.2% (w/v) sugar remaining unfermented, was observed with the Saccharomyces cerevisiae industrial strain CAT-1 in 30 °Bx broth with urea supplementation. In addition, efcient retention of glycerol by the yeast strain was identifed as a requisite for better fermentation and was consistent with a higher expression of glycerol permease STL1 and channel FPS1. Urea was shown to promote the deregulation of STL1 expression, overcoming glucose repression. The consistency between Fps1-mediated ethanol secretion and ethanol in the extracellular media reinforces previous suggestions that ethanol might exit the cell through the Fps1 channel. Conclusions: This work brings solid evidence in favour of the utilisation of VHG conditions in SCJ fermentations, bringing it a step closer to industrial application. SCJ concentrated up to 30 °Bx maintains industrially relevant ethanol production yield and productivity, provided the broth is supplemented with a suitable nitrogen source and an appropriate industrial bioethanol-producing yeast strain is used. In addition, the work contributes to a better understanding of the VHG-SCJ process and the variable efects of process parameters on process efciency and yeast strain response. Keywords: Biofuel, Bioethanol, Sugarcane, Saccharomyces cerevisiae, CAT-1, Very high gravity, Process optimisation, Process sustainabilityB. Monteiro was supported by the Ph.D. Grant 2011/12185-0 from the Fundação de Amparo à Pesquisa do Estado de São Paulo-FAPESP. P. Ferraz and M. Barroca are supported by the Doctoral Programme in Applied and Environmental Microbiology (DP-AEM) and the FCT by Ph.D. Grants PD/ BD/113814/2015 and PD/BD/113810/2015, respectively. T. Collins thanks the FCT for support through the Investigador FCT Programme (IF/01635/2014). T. Collins and C. Lucas are supported by the strategic programme UID/ BIA/04050/2013 (POCI-01-0145-FEDER-007569) funded by national funds through the FCT I.P. and the ERDF through COMPETE2020-Programa Operacional Competitividade e Internacionalização (POCI). P. Ferraz, T. Collins and C. Lucas were further funded by the project EcoAgriFood (NORTE-01- 0145-FEDER-000009), supported by the Norte Portugal Regional Operational Programme (NORTE 2020) under the PORTUGAL 2020 Partnership Agreement through the European Regional Development Fund (ERDF).info:eu-repo/semantics/publishedVersio