Publications by authors named "Melanie Grandits"

12 Publications

  • Page 1 of 1

The RESOLUTE consortium: unlocking SLC transporters for drug discovery.

Authors:
Giulio Superti-Furga Daniel Lackner Tabea Wiedmer Alvaro Ingles-Prieto Barbara Barbosa Enrico Girardi Ulrich Goldmann Bettina Gürtl Kristaps Klavins Christoph Klimek Sabrina Lindinger Eva Liñeiro-Retes André C Müller Svenja Onstein Gregor Redinger Daniela Reil Vitaly Sedlyarov Gernot Wolf Matthew Crawford Robert Everley David Hepworth Shenping Liu Stephen Noell Mary Piotrowski Robert Stanton Hui Zhang Salvatore Corallino Andrea Faedo Maria Insidioso Giovanna Maresca Loredana Redaelli Francesca Sassone Lia Scarabottolo Michela Stucchi Paola Tarroni Sara Tremolada Helena Batoulis Andreas Becker Eckhard Bender Yung-Ning Chang Alexander Ehrmann Anke Müller-Fahrnow Vera Pütter Diana Zindel Bradford Hamilton Martin Lenter Diana Santacruz Coralie Viollet Charles Whitehurst Kai Johnsson Philipp Leippe Birgit Baumgarten Lena Chang Yvonne Ibig Martin Pfeifer Jürgen Reinhardt Julian Schönbett Paul Selzer Klaus Seuwen Charles Bettembourg Bruno Biton Jörg Czech Hélène de Foucauld Michel Didier Thomas Licher Vincent Mikol Antje Pommereau Frédéric Puech Veeranagouda Yaligara Aled Edwards Brandon J Bongers Laura H Heitman Ad P IJzerman Huub J Sijben Gerard J P van Westen Justine Grixti Douglas B Kell Farah Mughal Neil Swainston Marina Wright-Muelas Tina Bohstedt Nicola Burgess-Brown Liz Carpenter Katharina Dürr Jesper Hansen Andreea Scacioc Giulia Banci Claire Colas Daniela Digles Gerhard Ecker Barbara Füzi Viktoria Gamsjäger Melanie Grandits Riccardo Martini Florentina Troger Patrick Altermatt Cédric Doucerain Franz Dürrenberger Vania Manolova Anna-Lena Steck Hanna Sundström Maria Wilhelm Claire M Steppan

Nat Rev Drug Discov 2020 07;19(7):429-430

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http://dx.doi.org/10.1038/d41573-020-00056-6DOI Listing
July 2020

Vienna LiverTox Workspace-A Set of Machine Learning Models for Prediction of Interactions Profiles of Small Molecules With Transporters Relevant for Regulatory Agencies.

Front Chem 2019 10;7:899. Epub 2020 Jan 10.

Pharmacoinformatics Research Group, Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria.

Transporters expressed in the liver play a major role in drug pharmacokinetics and are a key component of the physiological bile flow. Inhibition of these transporters may lead to drug-drug interactions or even drug-induced liver injury. Therefore, predicting the interaction profile of small molecules with transporters expressed in the liver may help medicinal chemists and toxicologists to prioritize compounds in an early phase of the drug development process. Based on a comprehensive analysis of the data available in the public domain, we developed a set of classification models which allow to predict-for a small molecule-the inhibition of and transport by a set of liver transporters considered to be relevant by FDA, EMA, and the Japanese regulatory agency. The models were validated by cross-validation and external test sets and comprise cross validated balanced accuracies in the range of 0.64-0.88. Finally, models were implemented as an easy to use web-service which is freely available at https://livertox.univie.ac.at.
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http://dx.doi.org/10.3389/fchem.2019.00899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966498PMC
January 2020

Engineering the interactions between a plant-produced HIV antibody and human Fc receptors.

Plant Biotechnol J 2020 02 10;18(2):402-414. Epub 2019 Aug 10.

Hotung Molecular Immunology Unit, Institute for Infection and Immunity, St George's University of London, London, UK.

Plants can provide a cost-effective and scalable technology for production of therapeutic monoclonal antibodies, with the potential for precise engineering of glycosylation. Glycan structures in the antibody Fc region influence binding properties to Fc receptors, which opens opportunities for modulation of antibody effector functions. To test the impact of glycosylation in detail, on binding to human Fc receptors, different glycovariants of VRC01, a broadly neutralizing HIV monoclonal antibody, were generated in Nicotiana benthamiana and characterized. These include glycovariants lacking plant characteristic α1,3-fucose and β1,2-xylose residues and glycans extended with terminal β1,4-galactose. Surface plasmon resonance-based assays were established for kinetic/affinity evaluation of antibody-FcγR interactions, and revealed that antibodies with typical plant glycosylation have a limited capacity to engage FcγRI, FcγRIIa, FcγRIIb and FcγRIIIa; however, the binding characteristics can be restored and even improved with targeted glycoengineering. All plant-made glycovariants had a slightly reduced affinity to the neonatal Fc receptor (FcRn) compared with HEK cell-derived antibody. However, this was independent of plant glycosylation, but related to the oxidation status of two methionine residues in the Fc region. This points towards a need for process optimization to control oxidation levels and improve the quality of plant-produced antibodies.
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http://dx.doi.org/10.1111/pbi.13207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6953194PMC
February 2020

Interspecies comparison of putative ligand binding sites of human, rat and mouse P-glycoprotein.

Eur J Pharm Sci 2018 Sep 22;122:134-143. Epub 2018 Jun 22.

University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria. Electronic address:

Prior to the clinical phases of testing, safety, efficacy and pharmacokinetic profiles of lead compounds are evaluated in animal studies. These tests are primarily performed in rodents, such as mouse and rats. In order to reduce the number of animal experiments, computational models that predict the outcome of these studies and thus aid in prioritization of preclinical candidates are heavily needed. However, although computational models for human off-target interactions with decent quality are available, they cannot easily be transferred to rodents due to lack of respective data. In this study, we assess the transferability of human P-glycoprotein activity data for development of in silico models to predict in vivo effects in rats and mouse using a structure-based approach. P-glycoprotein (P-gp) is an ATP-dependent efflux transporter that transports xenobiotic compounds such as toxins and drugs out of cells and has a broad substrate and inhibitor specificity. Being mostly expressed at barriers, it influences the bioavailability of drugs and thus contributes also to toxicity. Comparison of the binding site interaction profiles of human, rat and mouse P-gp derived from docking studies with a set of common inhibitors suggests that the inhibitors share potentially similar binding modes. These findings encourage the use of in vitro human P-gp data for predicting in vivo effects in rodents and thus contributes to the 3Rs (Replace, Reduce and Refine) of animal experiments.
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http://dx.doi.org/10.1016/j.ejps.2018.06.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6422297PMC
September 2018

Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors.

J Med Chem 2018 05 10;61(10):4397-4411. Epub 2018 May 10.

Department of Pharmaceutical Chemistry , University of Vienna , UZA 2, Althanstrasse 14 , 1090 Vienna , Austria.

Residence time and more recently the association rate constant k are increasingly acknowledged as important parameters for in vivo efficacy and safety of drugs. However, their broader consideration in drug development is limited by a lack of knowledge of how to optimize these parameters. In this study on a set of 176 heat shock protein 90 inhibitors, structure-kinetic relationships, X-ray crystallography, and molecular dynamics simulations were combined to retrieve a concrete scheme of how to rationally slow down on-rates. We discovered that an increased ligand desolvation barrier by introducing polar substituents resulted in a significant k decrease. The slowdown was accomplished by introducing polar moieties to those parts of the ligand that point toward a hydrophobic cavity. We validated this scheme by increasing polarity of three Hsp90 inhibitors and observed a 9-, 13-, and 45-fold slowdown of on-rates and a 9-fold prolongation in residence time. This prolongation was driven by transition state destabilization rather than ground state stabilization.
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http://dx.doi.org/10.1021/acs.jmedchem.8b00080DOI Listing
May 2018

Structure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP.

J Comput Aided Mol Des 2017 Jun 19;31(6):507-521. Epub 2017 May 19.

Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.

The bile salt export pump (BSEP) actively transports conjugated monovalent bile acids from the hepatocytes into the bile. This facilitates the formation of micelles and promotes digestion and absorption of dietary fat. Inhibition of BSEP leads to decreased bile flow and accumulation of cytotoxic bile salts in the liver. A number of compounds have been identified to interact with BSEP, which results in drug-induced cholestasis or liver injury. Therefore, in silico approaches for flagging compounds as potential BSEP inhibitors would be of high value in the early stage of the drug discovery pipeline. Up to now, due to the lack of a high-resolution X-ray structure of BSEP, in silico based identification of BSEP inhibitors focused on ligand-based approaches. In this study, we provide a homology model for BSEP, developed using the corrected mouse P-glycoprotein structure (PDB ID: 4M1M). Subsequently, the model was used for docking-based classification of a set of 1212 compounds (405 BSEP inhibitors, 807 non-inhibitors). Using the scoring function ChemScore, a prediction accuracy of 81% on the training set and 73% on two external test sets could be obtained. In addition, the applicability domain of the models was assessed based on Euclidean distance. Further, analysis of the protein-ligand interaction fingerprints revealed certain functional group-amino acid residue interactions that could play a key role for ligand binding. Though ligand-based models, due to their high speed and accuracy, remain the method of choice for classification of BSEP inhibitors, structure-assisted docking models demonstrate reasonably good prediction accuracies while additionally providing information about putative protein-ligand interactions.
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http://dx.doi.org/10.1007/s10822-017-0021-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5487762PMC
June 2017

Selectivity of cytosolic phospholipase A2 type IV toward arachidonyl phospholipids.

J Mol Recognit 2015 Jul 23;28(7):447-57. Epub 2015 Feb 23.

Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.

Cytosolic phospholipase A2 (cPLA2 ) is an interesting protein involved in inflammatory processes and various diseases. Its catalytic mechanism as well as its substrate specificity for arachidonyl phospholipids is not typical for other phospolipases. Furthermore, a lid structure, which ensures a hydrophilic surface of the protein without any substrate bound and the movement of this flexible loop to make the hydrophobic active site accessible, is of high interest. Therefore, the focus of this work was to determine the binding mode of cPLA2 with various substrates, such as arachidonic acid, a synthetic inhibitor, a saturated phospholipid, and most importantly an arachidonyl phospholipid. To understand the selectivity of the protein toward the arachidonyl phospholipid and the interaction in a protein-ligand complex, molecular dynamics simulations were performed using the GROMOS suite of simulation programs. The simulations provide insight into the protein and showed that selective binding of arachidonyl phospholipids is because of the shape of the sn-2 tail. The amino acids Asn555 and Ala578 are involved in the strongest interactions observed in the protein-ligand complexes.
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http://dx.doi.org/10.1002/jmr.2462DOI Listing
July 2015

Molecular dynamics simulations of the auxin-binding protein 1 in complex with indole-3-acetic acid and naphthalen-1-acetic acid.

Proteins 2014 Oct 17;82(10):2744-55. Epub 2014 Jul 17.

Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190, Vienna, Austria.

Auxin-binding protein 1 (ABP1) is suggested to be an auxin receptor which plays an important role in several processes in green plants. Maize ABP1 was simulated with the natural auxin indole-3-acetic acid (IAA) and the synthetic analog naphthalen-1-acetic acid (NAA), to elucidate the role of the KDEL sequence and the helix at the C-terminus. The KDEL sequence weakens the intermolecular interactions between the monomers but stabilizes the C-terminal helix. Conformational changes at the C-terminus occur within the KDEL sequence and are influenced by the binding of the simulated ligands. This observation helps to explain experimental findings on ABP1 interactions with antibodies that are modulated by the presence of auxin, and supports the hypothesis that ABP1 acts as an auxin receptor. Stable hydrogen bonds between the monomers are formed between Glu40 and Glu62, Arg10 and Thr97, Lys39, and Glu62 in all simulations. The amino acids Ile22, Leu25, Trp44, Pro55, Ile130, and Phe149 are located in the binding pocket and are involved in hydrophobic interactions with the ring system of the ligand. Trp151 is stably involved in a face to end interaction with the ligand. The calculated free energy of binding using the linear interaction energy approach showed a higher binding affinity for NAA as compared to IAA. Our simulations confirm the asymmetric behavior of the two monomers, the stronger interaction of NAA than IAA and offers insight into the possible mechanism of ABP1 as an auxin receptor.
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http://dx.doi.org/10.1002/prot.24639DOI Listing
October 2014

Expression and glycoengineering of functionally active heteromultimeric IgM in plants.

Proc Natl Acad Sci U S A 2014 Apr 31;111(17):6263-8. Epub 2014 Mar 31.

Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.

IgM antibodies are an important player of the human's innate defense mechanisms and increasingly have gained interest as therapeutics. Although the expression of IgM antibodies in mammalian cell culture is established, this approach remains costly and alternative methods have not been developed yet. Plants have a proven record for the production of therapeutically relevant recombinant proteins. However, whether they are able to express proteins like IgM antibodies, which range among the most complex human proteins, remains unknown so far. Here we report the in planta generation of the functionally active monoclonal antitumor IgM PAT-SM6 (SM6). SM6 efficiently accumulates in plant leaves and assembles correctly into heterooligomers (pentamers and hexamers). Detailed glycosylation analysis exhibited complex and oligomannosidic N-glycans in a site-specific manner on human-serum IgM and on plant- and human-cell-line-produced SM6. Moreover, extensive in planta glycoengineering allowed the generation of SM6 decorated with sialylated human-type oligosaccharides, comparable to plasma-derived IgM. A glycosylated model of pentameric IgM exhibits different accessibility of the glycosylation sites, explaining site-specific glycosylation. Biochemical and biophysical properties and importantly biological activities of plant-derived SM6 glycoforms are comparable to the human-cell-derived counterparts. The in planta generation of one of the most complex human proteins opens new pathways toward the production of difficult-to-express proteins for pharmaceutical applications. Moreover, the generation of IgMs with a controlled glycosylation pattern allows the study of the so far unknown contribution of sugar moieties to the function of IgMs.
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http://dx.doi.org/10.1073/pnas.1320544111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035941PMC
April 2014

Azido derivatives of cellobiose: oxidation at C1 with cellobiose dehydrogenase from Sclerotium rolfsii.

Carbohydr Res 2013 Dec 16;382:86-94. Epub 2013 Sep 16.

Department of Pharmacy, Faculty of Medicine, University of Prishtina, QKUK, Prishtina 10000, Republic of Kosovo, Serbia.

We report the chemo-enzymatic synthesis of three cellobiono-1,5-lactone azido derivatives, designed as building blocks for biomedical polymer scaffolds. The synthesis is based on regioselective protection of cellobiose or 1,6-O-anhydro-β-d-cellobiose before azidation and subsequent deprotection. The oxidation to the corresponding cellobiono-1,5-lactones was investigated with 6'-azido-6'-deoxycellobiose (6'N3Clb, 5), 6-azido-6-deoxycellobiose (6N3Clb, 11) and 2-azido-2-deoxycellobiose (2N3Clb, 15) under the catalysis of cellobiose dehydrogenase (CDH) from the plant-pathogenic fungus Sclerotium rolfsii. Substrate binding characteristics and kinetics of CDH for the three cellobiose azido derivatives were studied employing computational docking, steady-state and presteady-state techniques. The process of enzymatic oxidation of the cellobiose azido intermediates was optimized by using the available kinetic information. Whereas the conversion of 15 by CDH is very slow, the conversion of 5 and 11 by a regenerated, bi-enzymatic process (CDH/redox mediator/laccase/O2) is fast, quantitative and produces azido derivatives of cellobiono-1,5-lactone in an environmentally friendly, oxygen-driven process.
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http://dx.doi.org/10.1016/j.carres.2013.09.004DOI Listing
December 2013

Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations.

J Mol Catal B Enzym 2013 Aug;92(100):34-43

Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria.

Ram2 from is a rhamnosidase from the glycoside hydrolase family 78. It shows remarkable selectivity for rutinose rather than para-nitrophenyl-alpha-l-rhamnopyranoside (p-NPR). Molecular dynamics simulations were performed using a homology model of this enzyme, in complex with both substrates. Free energy calculations lead to predicted binding affinities of -34.4 and -30.6 kJ mol respectively, agreeing well with an experimentally estimated relative free energy of 5.4 kJ mol. Further, the most relevant binding poses could be determined. While p-NPR preferably orients its rhamnose moiety toward the active site, rutinose interacts most strongly with its glucose moiety. A detailed hydrogen bond analysis confirms previously implicated residues in the active site (Asp217, Asp222, Trp226, Asp229 and Glu488) and quantifies the importance of individual residues for the binding. The most important amino acids are Asp229 and Phe339 which are involved in many interactions during the simulations. While Phe339 was observed in more simulations, Asp229 was involved in more persistent interactions (forming an average of at least 2 hydrogen bonds during the simulation). These analyses directly suggest mutations that could be used in a further experimental characterization of the enzyme. This study shows once more the strength of computer simulations to rationalize and guide experiments at an atomic level.
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http://dx.doi.org/10.1016/j.molcatb.2013.03.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663046PMC
August 2013

A systematic framework for molecular dynamics simulations of protein post-translational modifications.

PLoS Comput Biol 2013 18;9(7):e1003154. Epub 2013 Jul 18.

Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter, Vienna, Austria.

By directly affecting structure, dynamics and interaction networks of their targets, post-translational modifications (PTMs) of proteins play a key role in different cellular processes ranging from enzymatic activation to regulation of signal transduction to cell-cycle control. Despite the great importance of understanding how PTMs affect proteins at the atomistic level, a systematic framework for treating post-translationally modified amino acids by molecular dynamics (MD) simulations, a premier high-resolution computational biology tool, has never been developed. Here, we report and validate force field parameters (GROMOS 45a3 and 54a7) required to run and analyze MD simulations of more than 250 different types of enzymatic and non-enzymatic PTMs. The newly developed GROMOS 54a7 parameters in particular exhibit near chemical accuracy in matching experimentally measured hydration free energies (RMSE=4.2 kJ/mol over the validation set). Using this tool, we quantitatively show that the majority of PTMs greatly alter the hydrophobicity and other physico-chemical properties of target amino acids, with the extent of change in many cases being comparable to the complete range spanned by native amino acids.
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http://dx.doi.org/10.1371/journal.pcbi.1003154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715417PMC
February 2014