Publications by authors named "Riccardo Martini"

10 Publications

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ATP modulates SLC7A5 (LAT1) synergistically with cholesterol.

Sci Rep 2020 10 7;10(1):16738. Epub 2020 Oct 7.

Department of DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via Bucci 4C, 87036, Arcavacata di Rende, Italy.

The plasma membrane transporter hLAT1 is responsible for providing cells with essential amino acids. hLAT1 is over-expressed in virtually all human cancers making the protein a hot-spot in the fields of cancer and pharmacology research. However, regulatory aspects of hLAT1 biology are still poorly understood. A remarkable stimulation of transport activity was observed in the presence of physiological levels of cholesterol together with a selective increase of the affinity for the substrate on the internal site, suggesting a stabilization of the inward open conformation of hLAT1. A synergistic effect by ATP was also observed only in the presence of cholesterol. The same phenomenon was detected with the native protein. Altogether, the biochemical assays suggested that cholesterol and ATP binding sites are close to each other. The computational analysis identified two neighboring regions, one hydrophobic and one hydrophilic, to which cholesterol and ATP were docked, respectively. The computational data predicted interaction of the ϒ-phosphate of ATP with Lys 204, which was confirmed by site-directed mutagenesis. The hLAT1-K204Q mutant showed an impaired function and response to ATP. Interestingly, this residue is conserved in several members of the SLC7 family.
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http://dx.doi.org/10.1038/s41598-020-73757-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7541457PMC
October 2020

Studies of structural determinants of substrate binding in the Creatine Transporter (CreaT, SLC6A8) using molecular models.

Sci Rep 2020 04 10;10(1):6241. Epub 2020 Apr 10.

University of Vienna, Department of Pharmaceutical Chemistry, Vienna, Austria.

Creatine is a crucial metabolite that plays a fundamental role in ATP homeostasis in tissues with high-energy demands. The creatine transporter (CreaT, SLC6A8) belongs to the solute carrier 6 (SLC6) transporters family, and more particularly to the GABA transporters (GATs) subfamily. Understanding the molecular determinants of specificity within the SLC6 transporters in general, and the GATs in particular is very challenging due to the high similarity of these proteins. In the study presented here, our efforts focused on finding key structural features involved in binding selectivity for CreaT using structure-based computational methods. Due to the lack of three-dimensional structures of SLC6A8, our approach was based on the realization of two reliable homology models of CreaT using the structures of two templates, i.e. the human serotonin transporter (hSERT) and the prokaryotic leucine transporter (LeuT). Our models reveal that an optimal complementarity between the shape of the binding site and the size of the ligands is necessary for transport. These findings provide a framework for a deeper understanding of substrate selectivity of the SLC6 family and other LeuT fold transporters.
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http://dx.doi.org/10.1038/s41598-020-63189-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148354PMC
April 2020

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

GRAIL: GRids of phArmacophore Interaction fieLds.

J Chem Theory Comput 2018 Sep 20;14(9):4958-4970. Epub 2018 Aug 20.

Inte:Ligand GmbH , Mariahilferstrasse 74B/11 , A-1070 Vienna , Austria.

In the absence of experimentally derived, three-dimensional structures of receptors in complex with active ligands, it is of high value to be able to gain knowledge about energetically favorable interaction sites solely from the structure of the receptor binding site. For de novo ligand design as well as for lead optimization, this information retrieved from the protein is inevitable. The herein presented method called GRAIL combines the advantages of traditional grid-based approaches for the identification of interaction sites and the power of the pharmacophore concept. A reduced pharmacophoric abstraction of the target system enables the computation of all relevant interaction grid maps in short amounts of time. This allows one to extend the utility of a grid-based method for the analysis of large amounts of coordinate sets obtained by long-time MD simulations. In this way it is possible to assess conformation dependent characteristics of key interactions over time. Furthermore, conformational changes of the protein can be taken into account easily and information thus obtained well-guides a rational ligand design process. A study employing MD trajectories of the oncology target heat shock protein 90 showcases how well our novel approach GRAIL performs for a set of different inhibitors bound to their target protein and how molecular features of the inhibitors are subject to optimization.
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http://dx.doi.org/10.1021/acs.jctc.8b00495DOI Listing
September 2018

Design and synthesis of a novel inhibitor of T. Viride chitinase through an in silico target fishing protocol.

Bioorg Med Chem Lett 2017 08 10;27(15):3332-3336. Epub 2017 Jun 10.

Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, PA 19122, USA; Lead Discovery Siena s.r.l, Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy. Electronic address:

In the last ten years, we identified and developed a new therapeutic class of antifungal agents, the macrocyclic amidinoureas. These compounds are active against several Candida species, including clinical isolates resistant to currently available antifungal drugs. The mode of action of these molecules is still unknown. In this work, we developed an in-silico target fishing procedure to identify a possible target for this class of compounds based on shape similarity, inverse docking procedure and consensus score rank-by-rank. Chitinase enzyme emerged as possible target. To confirm this hypothesis a novel macrocyclic derivative has been produced, specifically designed to increase the inhibition of the chitinase. Biological evaluation highlights a stronger enzymatic inhibition for the new derivative, while its antifungal activity drops probably because of pharmacokinetic issues. Collectively, our data suggest that chitinase represent at least one of the main target of macrocyclic amidinoureas.
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http://dx.doi.org/10.1016/j.bmcl.2017.06.016DOI Listing
August 2017

Natural Product Kuwanon-L Inhibits HIV-1 Replication through Multiple Target Binding.

Chembiochem 2017 02 18;18(4):374-377. Epub 2017 Jan 18.

Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy.

In recent years many advances have been made in the fight against HIV-1 infection. However, the lack of a vaccine, together with the increasing resistance to the highly active anti-retroviral therapy (HAART), make HIV-1 infection still a serious global emergency. Thus, new compounds with original modes of action are continuously required, and natural products have ever been a very interesting class of pharmacologically active molecules. Some of them have been used since ancient times against viral infections. Here we present a work in which we suggest that kuwanon-L, a natural product active as an HIV-1 integrase (IN) inhibitor, might exert its overall antiviral activity through binding to multiple viral targets. Specific enzymatic tests, together with a time-of-addition (TOA) experiment, support our hypothesis of binding both to IN and to reverse transcriptase (RT). Overall, this compound can be considered an attractive lead for the development of new classes of antiviral agents able to overcome the problem of resistance, due to its ability to exert its action by binding simultaneously to multiple viral targets.
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http://dx.doi.org/10.1002/cbic.201600592DOI Listing
February 2017

Biological Characterization and in Vivo Assessment of the Activity of a New Synthetic Macrocyclic Antifungal Compound.

J Med Chem 2016 04 19;59(8):3854-66. Epub 2016 Apr 19.

Department of Biotechnology Chemistry and Pharmacy, University of Siena , I-53100 Siena, Italy.

We recently identified a novel family of macrocyclic amidinoureas showing potent antifungal activity against Candida spp. In this study, we demonstrate the fungicidal effect of these compounds as well as their killing activity in a dose-dependent manner. Transcriptional analysis data indicate that our molecules induce a significant change in the transcriptome involving ATP binding cassette (ABC) transporter genes. Notably, experiments against Candida albicans mutants lacking those genes showed resistance to the compound, suggesting the involvement of ABC transporters in the uptake or intracellular accumulation of the molecule. To probe the mode of action, we performed fluorescence microscopy experiments on fungal cells treated with an ad-hoc synthesized fluorescent derivative. Fluorescence microscopy images confirm the ability of the compound to cross the membrane and show a consistent accumulation within the cytoplasm. Finally, we provide data supporting the in vivo efficacy in a systemic infection murine model setup with a drug-resistant strain of C. albicans.
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http://dx.doi.org/10.1021/acs.jmedchem.6b00018DOI Listing
April 2016

Kuwanon-L as a New Allosteric HIV-1 Integrase Inhibitor: Molecular Modeling and Biological Evaluation.

Chembiochem 2015 Nov 26;16(17):2507-12. Epub 2015 Oct 26.

Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy.

HIV-1 integrase (IN) active site inhibitors are the latest class of drugs approved for HIV treatment. The selection of IN strand-transfer drug-resistant HIV strains in patients supports the development of new agents that are active as allosteric IN inhibitors. Here, a docking-based virtual screening has been applied to a small library of natural ligands to identify new allosteric IN inhibitors that target the sucrose binding pocket. From theoretical studies, kuwanon-L emerged as the most promising binder and was thus selected for biological studies. Biochemical studies showed that kuwanon-L is able to inhibit the HIV-1 IN catalytic activity in the absence and in the presence of LEDGF/p75 protein, the IN dimerization, and the IN/LEDGF binding. Kuwanon-L also inhibited HIV-1 replication in cell cultures. Overall, docking and biochemical results suggest that kuwanon-L binds to an allosteric binding pocket and can be considered an attractive lead for the development of new allosteric IN antiviral agents.
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http://dx.doi.org/10.1002/cbic.201500385DOI Listing
November 2015

Investigation on the sucrose binding pocket of HIV-1 Integrase by molecular dynamics and synergy experiments.

Bioorg Med Chem Lett 2015 Aug 15;25(15):3013-6. Epub 2015 May 15.

Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via A. Moro, 53100 Siena, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Bldg., Suite 333, 1900 N 12th Street, Philadelphia, PA 19122, USA. Electronic address:

Enzymes whose catalytic activity depends on multimeric assembly are targets for inhibitors that perturb the interactions between the protein subunits such as the HIV-1 Integrase (IN). Sucrose has been recently crystallized in complex with IN revealing an allosteric binding pocket at the monomer-monomer interface. Herein, molecular dynamics were applied to theoretically test the effect of this small ligand on IN. As a result, such a compound increases the mutual free energy of binding between the two interacting monomers. Biological experiments confirmed the computational forecast.
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http://dx.doi.org/10.1016/j.bmcl.2015.05.011DOI Listing
August 2015

Successful treatment of persistent macular holes using "heavy silicone oil" as intraocular tamponade.

Retina 2006 Oct;26(8):905-8

Santa Chiara Hospital, Eye Surgery Clinic, Pisa, Italy.

Background: Silicone oil tamponade has been suggested in the treatment of persistent macular hole, but visual outcome is often poor. We describe two patients who underwent reoperation for persistent macular hole using "heavy silicone oil" (HSO) tamponade.

Methods: Two patients who underwent vitrectomy, removal of the posterior vitreous cortex, peeling of the internal limiting membrane, and long-acting gas tamponade had persistent macular hole 3 months after surgery. The patients underwent reoperation using an HSO (Oxane Hd, Bausch & Lomb) as internal tamponade. This tamponade did not require postoperative posturing and was removed after 3 months. Optical coherence tomography (OCT) was performed, and visual outcome was determined.

Results: OCT images showed that the HSO bubble conformed well with the retinal surface in the foveal region. Closure of the macular hole was achieved in both patients. Visual acuity increased from 20/100 to 20/40 in Patient 1 and from 20/600 to 20/100 in Patient 2.

Conclusion: HSO can be a useful tool in the treatment of persistent macular hole. OCT images showed that the tamponade was effective in the upright position in the foveal region. OCT allowed determination of the time of tamponade removal according to the anatomical stage of hole closure.
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http://dx.doi.org/10.1097/01.iae.0000250006.76155.3dDOI Listing
October 2006