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Instruments / Technical Area	Publication Details	Published
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength)	Multitarget, selective compound design yields potent inhibitors of a kinetoplastid pteridine reductase 1 Ina Pöhner , Antonio Quotadamo , Joanna Panecka-Hofman , Rosaria Luciani , Matteo Santucci , Pasquale Linciano , Giacomo Landi , Flavio Di Pisa , Lucia Dello Iacono , Cecilia Pozzi , Stefano Mangani , Sheraz Gul , Gesa Witt , Bernhard Ellinger , Maria Kuzikov , Nuno Santarem , Anabela Cordeiro-Da-Silva , Maria P. Costi , Alberto Venturelli , Rebecca C. Wade Journal Of Medicinal Chemistry 51 DOI: 10.1021/acs.jmedchem.2c00232 Open Access Show Abstract ▼ Abstract: The optimization of compounds with multiple targets is a difficult multidimensional problem in the drug discovery cycle. Here, we present a systematic, multidisciplinary approach to the development of selective antiparasitic compounds. Computational fragment-based design of novel pteridine derivatives along with iterations of crystallographic structure determination allowed for the derivation of a structure–activity relationship for multitarget inhibition. The approach yielded compounds showing apparent picomolar inhibition of T. brucei pteridine reductase 1 (PTR1), nanomolar inhibition of L. major PTR1, and selective submicromolar inhibition of parasite dihydrofolate reductase (DHFR) versus human DHFR. Moreover, by combining design for polypharmacology with a property-based on-parasite optimization, we found three compounds that exhibited micromolar EC50 values against T. brucei brucei while retaining their target inhibition. Our results provide a basis for the further development of pteridine-based compounds, and we expect our multitarget approach to be generally applicable to the design and optimization of anti-infective agents.	Jun 2022
	X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease Sebastian Gunther , Patrick Y. A. Reinke , Yaiza Fernández-García , Julia Lieske , Thomas J. Lane , Helen M. Ginn , Faisal H. M. Koua , Christiane Ehrt , Wiebke Ewert , Dominik Oberthuer , Oleksandr Yefanov , Susanne Meier , Kristina Lorenzen , Boris Krichel , Janine-Denise Kopicki , Luca Gelisio , Wolfgang Brehm , Ilona Dunkel , Brandon Seychell , Henry Gieseler , Brenna Norton-Baker , Beatriz Escudero-Pérez , Martin Domaracky , Sofiane Saouane , Alexandra Tolstikova , Thomas A. White , Anna Hänle , Michael Groessler , Holger Fleckenstein , Fabian Trost , Marina Galchenkova , Yaroslav Gevorkov , Chufeng Li , Salah Awel , Ariana Peck , Miriam Barthelmess , Frank Schluenzen , Paulraj Lourdu Xavier , Nadine Werner , Hina Andaleeb , Najeeb Ullah , Sven Falke , Vasundara Srinivasan , Bruno Alves França , Martin Schwinzer , Hévila Brognaro , Cromarte Rogers , Diogo Melo , Joanna J. Zaitseva-Doyle , Juraj Knoska , Gisel E. Peña-Murillo , Aida Rahmani Mashhour , Vincent Hennicke , Pontus Fischer , Johanna Hakanpää , Jan Meyer , Philip Gribbon , Bernhard Ellinger , Maria Kuzikov , Markus Wolf , Andrea R. Beccari , Gleb Bourenkov , David Von Stetten , Guillaume Pompidor , Isabel Bento , Saravanan Panneerselvam , Ivars Karpics , Thomas R. Schneider , Maria Marta Garcia-Alai , Stephan Niebling , Christian Günther , Christina Schmidt , Robin Schubert , Huijong Han , Juliane Boger , Diana C. F. Monteiro , Linlin Zhang , Xinyuanyuan Sun , Jonathan Pletzer-Zelgert , Jan Wollenhaupt , Christian G. Feiler , Manfred S. Weiss , Eike-Christian Schulz , Pedram Mehrabi , Katarina Karničar , Aleksandra Usenik , Jure Loboda , Henning Tidow , Ashwin Chari , Rolf Hilgenfeld , Charlotte Uetrecht , Russell Cox , Andrea Zaliani , Tobias Beck , Matthias Rarey , Stephan Günther , Dusan Turk , Winfried Hinrichs , Henry N. Chapman , Arwen R. Pearson , Christian Betzel , Alke Meents Science DOI: 10.1126/science.abf7945 Open Access Show Abstract ▼ Abstract: The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.	Apr 2021
I02-Macromolecular Crystallography	Structural insights into the development of cycloguanil derivatives as Trypanosoma brucei pteridine reductase 1 inhibitors Giacomo Landi , Pasquale Linciano , Chiara Borsari , Claudia P. Bertolacini , Carolina Borsoi Moraes , Anabela Cordeiro-Da-Silva , Sheraz Gul , Gesa Witt , Maria Kuzikov , Maria Paola Costi , Cecilia Pozzi , Stefano Mangani Acs Infectious Diseases DOI: 10.1021/acsinfecdis.8b00358 Diamond Proposal Number(s): [11690] Show Abstract ▼ Abstract: Cycloguanil is a known dihydrofolate reductase (DHFR) inhibitor, but there is no evidence of its activity on pteridine reductase (PTR), the main metabolic bypass to DHFR inhibition in trypanosomatid parasites. Here, we provide experimental evidence of cycloguanil as an inhibitor of Trypanosoma brucei PTR1 (TbPTR1). A small library of cycloguanil derivatives was develop, resulting in 1 and 2a having IC50 of 692 and 186 nM, respectively, towards TbPTR1. Structural analysis revealed that the increased potency of 1 and 2a is due to the combined contributions of hydrophobic interactions, H-bonds and halogen bonds. Moreover, in vitro cell growth inhibition tests indicated that 2a is also effective on T. brucei. The simultaneous inhibition of DHFR and PTR1 activity in T. brucei is a new promising strategy for the treatment of human African Trypanosomiasis. On this purpose, 1,6-dihydrotriazines represent new molecular tools to develop potent dual PTR and DHFR inhibitors.	Apr 2019
I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Enhancement of benzothiazoles as Pteridine Reductase-1 (PTR1) inhibitors for the treatment of Trypanosomatidic infections Pasquale Linciano , Cecilia Pozzi , Lucia Dello Iacono , Flavio Di Pisa , Giacomo Landi , Alessio Bonucci , Sheraz Gul , Maria Kuzikov , Bernhard Ellinger , Gesa Witt , Nuno Santarem , Catarina Baptista , Caio Franco , Carolina Borsoi Moraes , Wolfgang Müller , Ulrike Wittig , Rosaria Luciani , Antony Sesenna , Antonio Quotadamo , Stefania Ferrari , Ina Pöhner , Anabela Cordeiro-Da-Silva , Stefano Mangani , Luca Costantino , Maria Paola Costi Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.8b02021 Diamond Proposal Number(s): [11690, 15832] Show Abstract ▼ Abstract: 2-amino-benzo[d]thiazole has been identified as new core moiety for the development of improved PTR1 inhibitors and anti-Trypanosomatidic agents. Through a molecular docking approach and the crystal structure of 6-(methylsulfonyl)benzo[d]thiazol-2-amine ternary complex with TbPTR1, 42 new compounds were designed, synthesized and evaluated for their ability to inhibit T. brucei and L. major PTR1 enzymes and in-vitro activity against Trypanosoma brucei and amastigote stage of Leishmania infantum. We identified several 2-amino-benzo[d]thiazole derivatives with improved activity against the enzymes (TbPTR1 IC50 = 0.35 µM; LmPTR1 IC50 = 1.9 µM) and anti-parasitic activity against T. brucei in the low µM range. Ten compounds, with low/sub micromolar inhibitor activity against TbPTR1, were able to potentiate the antiparasitic activity of methotrexate (MTX) when evaluated in combination against T. brucei, with a Potentiating Index (PI) ranging between 1.2 and 2.7. The compound library was profile for an early ADME-Toxicity profile and the compounds showing the best in vitro/enzymatic inhibition properties were selected for progression. 2-amino-N-benzylbenzo[d]thiazole-6-carboxamide (4c), was finally identified as a novel potent and selective anti-trypanocydal agent (EC50 = 7.0 µM) with an overall safe early ADME-Toxicity profile. The pharmacokinetic studies of 4c in BALB/c mice using a hydroxypropyl-β-cyclodextrin formulation yielded good oral bioavailability, confirming its suitability for progression to in-vivo anti-parasitic studies.	Mar 2019
I04-Macromolecular Crystallography	Exploiting the 2-amino-1,3,4-thiadiazole scaffold to inhibit Trypanosoma brucei pteridine reductase in support of early-stage drug discovery Pasquale Linciano , Alice Dawson , Ina Pöhner , David M. Costa , Monica S. Sá , Anabela Cordeiro-Da-Silva , Rosaria Luciani , Sheraz Gul , Gesa Witt , Bernhard Ellinger , Maria Kuzikov , Philip Gribbon , Jeanette Reinshagen , Markus Wolf , Birte Behrens , Véronique Hannaert , Paul A. M. Michels , Erika Nerini , Cecilia Pozzi , Flavio Di Pisa , Giacomo Landi , Nuno Santarem , Stefania Ferrari , Puneet Saxena , Sandra Lazzari , Giuseppe Cannazza , Lucio H. Freitas-Junior , Carolina B. Moraes , Bruno S. Pascoalino , Laura M. Alcântara , Claudia P. Bertolacini , Vanessa Fontana , Ulrike Wittig , Wolfgang Müller , Rebecca C. Wade , William N. Hunter , Stefano Mangani , Luca Costantino , Maria P. Costi Acs Omega 2, 5666 - 5683 DOI: 10.1021/acsomega.7b00473 Diamond Proposal Number(s): [8574] Open Access Show Abstract ▼ Abstract: Pteridine reductase-1 (PTR1) is a promising drug target for the treatment of trypanosomiasis. We investigated the potential of a previously identified class of thiadiazole inhibitors of Leishmania major PTR1 for activity against Trypanosoma brucei (Tb). We solved crystal structures of several TbPTR1-inhibitor complexes to guide the structure-based design of new thiadiazole derivatives. Subsequent synthesis and enzyme- and cell-based assays confirm new, mid-micromolar inhibitors of TbPTR1 with low toxicity. In particular, compound 4m, a biphenyl-thiadiazole-2,5-diamine with IC50 = 16 μM, was able to potentiate the antitrypanosomal activity of the dihydrofolate reductase inhibitor methotrexate (MTX) with a 4.1-fold decrease of the EC50 value. In addition, the antiparasitic activity of the combination of 4m and MTX was reversed by addition of folic acid. By adopting an efficient hit discovery platform, we demonstrate, using the 2-amino-1,3,4-thiadiazole scaffold, how a promising tool for the development of anti-T. brucei agents can be obtained.	Sep 2017
I04-Macromolecular Crystallography	Chroman-4-one derivatives targeting pteridine reductase 1 and showing anti-parasitic activity Flavio Di Pisa , Giacomo Landi , Lucia Dello Iacono , Cecilia Pozzi , Chiara Borsari , Stefania Ferrari , Matteo Santucci , Nuno Santarem , Anabela Cordeiro-Da-Silva , Carolina Moraes , Laura Alcantara , Vanessa Fontana , Lucio Freitas-Junior , Sheraz Gul , Maria Kuzikov , Birte Behrens , Ina Pöhner , Rebecca Wade , Maria Costi , Stefano Mangani Molecules 22 DOI: 10.3390/molecules22030426 Diamond Proposal Number(s): [8574] Open Access Show Abstract ▼ Abstract: Flavonoids have previously been identified as antiparasitic agents and pteridine reductase 1 (PTR1) inhibitors. Herein, we focus our attention on the chroman-4-one scaffold. Three chroman-4-one analogues (1–3) of previously published chromen-4-one derivatives were synthesized and biologically evaluated against parasitic enzymes (Trypanosoma brucei PTR1–TbPTR1 and Leishmania major–LmPTR1) and parasites (Trypanosoma brucei and Leishmania infantum). A crystal structure of TbPTR1 in complex with compound 1 and the first crystal structures of LmPTR1-flavanone complexes (compounds 1 and 3) were solved. The inhibitory activity of the chroman-4-one and chromen-4-one derivatives was explained by comparison of observed and predicted binding modes of the compounds. Compound 1 showed activity both against the targeted enzymes and the parasites with a selectivity index greater than 7 and a low toxicity. Our results provide a basis for further scaffold optimization and structure-based drug design aimed at the identification of potent anti-trypanosomatidic compounds targeting multiple PTR1 variants.	Mar 2017
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Profiling of flavonol derivatives for the development of antitrypanosomatidic drugs Chiara Borsari , Rosaria Luciani , Cecilia Pozzi , Ina Poehner , Stefan Henrich , Matteo Trande , Anabela Cordeiro-Da-Silva , Nuno Santarem , Catarina Baptista , Annalisa Tait , Flavio Di Pisa , Lucia Dello Iacono , Giacomo Landi , Sheraz Gul , Markus Wolf , Maria Kuzikov , Bernhard Ellinger , Jeanette Reinshagen , Gesa Witt , Philip Gribbon , Manfred Kohler , Oliver Keminer , Birte Behrens , Luca Costantino , Paloma Tejera Nevado , Eugenia Bifeld , Julia Eick , Joachim Clos , Juan Torrado , María D. Jiménez-Antón , María J. Corral , José M Alunda , Federica Pellati , Rebecca C. Wade , Stefania Ferrari , Stefano Mangani , Maria Paola Costi Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.6b00698 Diamond Proposal Number(s): [11690] Open Access Show Abstract ▼ Abstract: Flavonoids represent a potential source of new antitrypanosomatidic leads. Starting from a library of natural products, we combined target-based screening on pteridine reductase 1 with phenotypic screening on Trypanosoma brucei for hit identification. Flavonols were identified as hits, and a library of 16 derivatives was synthesized. Twelve compounds showed EC50 values against T. brucei below 10 μM. Four X-ray crystal structures and docking studies explained the observed structure−activity relationships. Compound 2 (3,6-dihydroxy-2-(3-hydroxyphenyl)-4H-chromen-4-one) was selected for pharmacokinetic studies. Encapsulation of compound 2 in PLGA nanoparticles or cyclodextrins resulted in lower in vitro toxicity when compared to the free compound. Combination studies with methotrexate revealed that compound 13 (3-hydroxy-6-methoxy-2-(4- methoxyphenyl)-4H-chromen-4-one) has the highest synergistic effect at concentration of 1.3 μM, 11.7-fold dose reduction index and no toxicity toward host cells. Our results provide the basis for further chemical modifications aimed at identifying novel antitrypanosomatidic agents showing higher potency toward PTR1 and increased metabolic stability.	Aug 2016

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