I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[13775]
Open Access
Abstract: Integrase strand transfer inhibitors (INSTIs) block the integration step of the retroviral lifecycle and are first-line drugs used for the treatment of HIV-1/AIDS. INSTIs have a polycyclic core with heteroatom triads, chelate the metal ions at the active site, and have a halobenzyl group that interacts with viral DNA attached to the core by a flexible linker. The most broadly effective INSTIs inhibit both wild-type (WT) integrase (IN) and a variety of well-known mutants. However, because there are mutations that reduce the potency of all of the available INSTIs, new and better compounds are needed. Models based on recent structures of HIV-1 and red-capped mangabey SIV INs suggest modifications in the INSTI structures that could enhance interactions with the 3′-terminal adenosine of the viral DNA, which could improve performance against INSTI resistant mutants. We designed and tested a series of INSTIs having modifications to their naphthyridine scaffold. One of the new compounds retained good potency against an expanded panel of HIV-1 IN mutants that we tested. Our results suggest the possibility of designing inhibitors that combine the best features of the existing compounds, which could provide additional efficacy against known HIV-1 IN mutants.
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Mar 2021
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Corentine M. C.
Laurin
,
Joseph P.
Bluck
,
Anthony K. N.
Chan
,
Michelle
Keller
,
Andrew
Boczek
,
Amy R.
Scorah
,
K. F. Larissa
See
,
Laura E.
Jennings
,
David S.
Hewings
,
Fern
Woodhouse
,
Jessica K.
Reynolds
,
Matthias
Schiedel
,
Philip G.
Humphreys
,
Philip C.
Biggin
,
Stuart J.
Conway
Abstract: The Trypanosoma cruzi (T. cruzi) parasite is the cause of Chagas disease, a neglected disease endemic in South America. The life cycle of the T. cruzi parasite is complex and includes transitions between distinct life stages. This change in phenotype (without a change in genotype) could be controlled by epigenetic regulation, and might involve the bromodomain-containing factors 1–5 (TcBDF1–5). However, little is known about the function of the TcBDF1–5. Here we describe a fragment-based approach to identify ligands for T. cruzi bromodomain-containing factor 3 (TcBDF3). We expressed a soluble construct of TcBDF3 in E. coli, and used this to develop a range of biophysical assays for this protein. Fragment screening identified 12 compounds that bind to the TcBDF3 bromodomain. On the basis of this screen, we developed functional ligands containing a fluorescence or 19F reporter group, and a photo-crosslinking probe for TcBDF3. These tool compounds will be invaluable in future studies on the function of TcBDF3 and will provide insight into the biology of T. cruzi.
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Nov 2020
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Open Access
Abstract: Trypanosoma cruzi is the etiologic agent of Chagas disease, which affects over seven million people, especially in developing countries. Undesirable side effects are frequently associated with current therapies, which are typically ineffective in the treatment of all stages of the disease. Here, we report the first synthesis of the neolignan dehydrodieugenol B, a natural product recently shown to exhibit activity against T. cruzi. Using this strategy, a series of synthetic analogues were prepared to explore structure–activity relationships. The in vitro antiparasitic activities of these analogues revealed a wide tolerance of modifications and substituent deletions, with maintained or improved bioactivities against the amastigote forms of the parasite (50% inhibitory concentration (IC50) of 4–63 μM) and no mammalian toxicity (50% cytotoxic concentration (CC50) of >200 μM). Five of these analogues meet the Drugs for Neglected Disease Initiative (DNDi) “hit criteria” for Chagas disease. This work has enabled the identification of key structural features of the natural product and sites where scaffold modification is tolerated.
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Oct 2020
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I04-Macromolecular Crystallography
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David T.
Davies
,
Simon
Leiris
,
Nicolas
Sprynski
,
Jérôme
Castandet
,
Clarisse
Lozano
,
Justine
Bousquet
,
Magdalena
Zalacain
,
Srinivas
Vasa
,
Praveen K.
Dasari
,
Ramesh
Pattipati
,
Naresh
Vempala
,
Swetha
Gujjewar
,
Syamkumar
Godi
,
Raju
Jallala
,
Rajashekar Reddy
Sathyap
,
Narasimha A.
Darshanoju
,
Vengala R.
Ravu
,
Ramakrishna R.
Juventhala
,
Narender
Pottabathini
,
Somesh
Sharma
,
Srinivasu
Pothukanuri
,
Kirsty
Holden
,
Peter
Warn
,
Francesca
Marcoccia
,
Manuela
Benvenuti
,
Cecilia
Pozzi
,
Stefano
Mangani
,
Jean-denis
Docquier
,
Marc
Lemonnier
,
Martin
Everett
Diamond Proposal Number(s):
[21741]
Abstract: The clinical effectiveness of the important β-lactam class of antibiotics is under threat by the emergence of resistance, mostly due to the production of acquired serine- (SBL) and metallo-β-lactamase (MBL) enzymes. To address this resistance issue, multiple β-lactam/β-lactamase inhibitor combinations have been successfully introduced into the clinic over the past several decades. However, all of those combinations contain SBL inhibitors and, as yet, there are no MBL inhibitors in clinical use. Consequently, there exists an unaddressed yet growing healthcare problem due to the rise in recent years of highly resistant strains which produce New Delhi metallo (NDM)-type metallo-carbapenemases. Previously, we reported the characterization of an advanced MBL inhibitor lead compound, ANT431. Herein, we discuss the completion of a lead optimization campaign culminating in the discovery of the preclinical candidate ANT2681, a potent NDM inhibitor with strong potential for clinical development.
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Aug 2020
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I03-Macromolecular Crystallography
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João A.
Ribeiro
,
Alexander
Hammer
,
Gerardo A.
Libreros-zúñiga
,
Sair M.
Chavez-pacheco
,
Petros
Tyrakis
,
Gabriel S.
De Oliveira
,
Timothy
Kirkman
,
Jamal
El Bakali
,
Silvana A.
Rocco
,
Mauricio L.
Sforça
,
Roberto
Parise-filho
,
Anthony G.
Coyne
,
Tom L.
Blundell
,
Chris
Abell
,
Marcio V. B.
Dias
Abstract: Dihydrofolate reductase (DHFR), a key enzyme involved in folate metabolism, is a widely explored target in the treatment of cancer, immune diseases, bacteria, and protozoa infections. Although several antifolates have proved successful in the treatment of infectious diseases, they have been underexplored to combat tuberculosis, despite the essentiality of M. tuberculosis DHFR (MtDHFR). Herein, we describe an integrated fragment-based drug discovery approach to target MtDHFR that has identified hits with scaffolds not yet explored in any previous drug design campaign for this enzyme. The application of a SAR by catalog strategy of an in house library for one of the identified fragments has led to a series of molecules that bind to MtDHFR with low micromolar affinities. Crystal structures of MtDHFR in complex with compounds of this series demonstrated a novel binding mode that considerably differs from other DHFR antifolates, thus opening perspectives for the development of relevant MtDHFR inhibitors.
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Jul 2020
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I03-Macromolecular Crystallography
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Leah S.
Torrie
,
David A.
Robinson
,
Michael G.
Thomas
,
Judith V.
Hobrath
,
Sharon M
Shepherd
,
John M.
Post
,
Eun-jung
Ko
,
Rafael Augusto
Alves Ferreira
,
Claire J.
Mackenzie
,
Karolina
Wrobel
,
Darren
Edwards
,
Ian H.
Gilbert
,
David W.
Gray
,
Alan H.
Fairlamb
,
Manu
De Rycker
Diamond Proposal Number(s):
[14980]
Abstract: Methionyl-tRNA synthetase (MetRS) is a chemically validated drug target in the kinetoplastid parasites Trypanosoma brucei and Leishmania donovani. To date, all kinetoplastid MetRS inhibitors described bind in a similar way to an expanded methionine pocket and an adjacent, auxiliary pocket. In the current study we have identified a structurally novel class of inhibitors containing a 4,6-diamino substituted pyrazolopyrimidine core (‘MetRS02’ series). Crystallographic studies revealed that ‘MetRS02’ compounds bind to an allosteric pocket in L. major MetRS not previously described and enzymatic studies demonstrated a non-competitive mode of inhibition. Homology modelling of the Trypanosoma cruzi MetRS enzyme revealed key differences in the allosteric pocket between the T. cruzi and Leishmania enzymes. These provide a likely explanation for the lower ‘MetRS02’ potencies that we observed for the T. cruzi enzyme compared to the Leishmania enzyme. The identification of a new series of MetRS inhibitors and the discovery of a new binding site in kinetoplastid MetRS enzymes provides a novel strategy in the search for new therapeutics for kinetoplastid diseases.
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Apr 2020
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I04-Macromolecular Crystallography
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Fraser
Cunningham
,
Jorge
Esquivias
,
Raquel
Fernández-menéndez
,
Arancha
Pérez
,
Ana
Guardia
,
Jaime
Escribano
,
Cristina
Rivero
,
Mythily
Vimal
,
Mónica
Cacho
,
Paco
De Dios-antón
,
María Santos
Martínez-martínez
,
Elena
Jiménez
,
Leticia
Huertas Valentín
,
María José
Rebollo-lópez
,
Eva María
López-román
,
Verónica
Sousa-morcuende
,
Joaquín
Rullas
,
Margaret
Neu
,
Chun-wa
Chung
,
Robert H.
Bates
Diamond Proposal Number(s):
[5799]
Abstract: In the course of optimizing a novel indazole sulfonamide series that inhibits β-ketoacyl-ACP synthase (KasA) of Mycobacterium tuberculosis, a mutagenic aniline metabolite was identified. Further lead optimization efforts were therefore dedicated to eliminating this critical liability by removing the embedded aniline moiety or modifying its steric or electronic environment. While the narrow SAR space against the target ultimately rendered this goal unsuccessful, key structural knowledge around the binding site of this underexplored target for TB was generated to inform future discovery efforts.
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Mar 2020
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I04-Macromolecular Crystallography
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Abstract: β-Lactamases comprise the most important known mode of resistance to β-lactam antibiotics. Boronic acids/boronate esters show promise as a new class of β-lactamase inhibitors with the potential to inhibit both the metallo- and serine-β-lactamases. We report studies employing representative β-lactamases concerning a bicyclic boronate ester with a thioether rather than the more typical β-lactam antibiotic ‘C-6/C-7’ acylamino side chain as present in the penicillin/cephalosporin antibiotics. The results, including a crystal structure of the clinically relevant VIM-2 metallo β-lactamase in complex with the inhibitor, reveal the potential of boronate inhibitors without the canonical acylamino side chain for inhibition of a broader range of serine- and metallo- β-lactamases compared to previous bicyclic boronates, including the metallo-β-lactamase L1. They imply further SAR studies will expand the already broad scope of -lactamase inhibition by bicyclic boronates.
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Dec 2019
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I02-Macromolecular Crystallography
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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
Diamond Proposal Number(s):
[11690]
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.
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Apr 2019
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I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Simon
Leiris
,
Alicia
Coelho
,
Jérôme
Castandet
,
Maëlle
Bayet
,
Clarisse
Lozano
,
Juliette
Bougnon
,
Justine
Bousquet
,
Martin John
Everett
,
Marc
Lemonnier
,
Nicolas
Sprynski
,
Magdalena
Zalacain
,
Thomas David
Pallin
,
Michael
Cramp
,
Neil
Jennings
,
Gilles
Raphy
,
Mark William
Jones
,
Ramesh
Pattipati
,
Battu
Shankar
,
Relangi
Sivasubrahmanyam
,
Ashok Kumar
Soodhagani
,
Ramakrishna Reddy
Juventhala
,
Narender
Pottabathini
,
Srinivasu
Pothukanuri
,
Manuela
Benvenuti
,
Cecilia
Pozzi
,
Stefano
Mangani
,
Filomena
De Luca
,
Giulia
Cerboni
,
Jean-denis
Docquier
,
David
Davies
Diamond Proposal Number(s):
[8574, 15832]
Abstract: The clinical effectiveness of carbapenem antibiotics such as meropenem is becoming increasingly compromised by the spread of both metallo β-lactamase (MBL) and serine β-lactamase (SBL) enzymes on mobile genetic elements, stimulating research to find new β-lactamase inhibitors to be used in conjunction with carbapenems and other β-lactam antibiotics. Herein we describe our initial exploration of a novel chemical series of metallo β-lactamase inhibitors, from concept through to efficacy in a survival model using an advanced tool compound (ANT431) in conjunction with meropenem.
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Nov 2018
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