I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Maria-Agustina
Rossi
,
Veronica
Martinez
,
Philip
Hinchliffe
,
Maria F.
Mojica
,
Valerie
Castillo
,
Diego M.
Moreno
,
Ryan
Smith
,
Brad
Spellberg
,
George L.
Drusano
,
Claudia
Banchio
,
Robert A.
Bonomo
,
James
Spencer
,
Alejandro J.
Vila
,
Graciela
Mahler
Diamond Proposal Number(s):
[17212]
Open Access
Abstract: Infections caused by multidrug resistant (MDR) bacteria are a major public health threat. Carbapenems are among the most potent antimicrobial agents that are commercially available to treat MDR bacteria. Bacterial production of carbapenem-hydrolysing metallo-β-lactamases (MBLs) challenges their safety and efficacy, with subclass B1 MBLs hydrolysing almost all β-lactam antibiotics. MBL inhibitors would fulfil an urgent clinical need by prolonging the lifetime of these life-saving drugs. Here we report the synthesis and activity of a series of 2-mercaptomethyl-thiazolidines (MMTZs), designed to replicate MBL interactions with reaction intermediates or hydrolysis products. MMTZs are potent competitive inhibitors of B1 MBLs in vitro (e.g., Ki = 0.44 μM vs. NDM-1). Crystal structures of MMTZ complexes reveal similar binding patterns to the most clinically important B1 MBLs (NDM-1, VIM-2 and IMP-1), contrasting with previously studied thiol-based MBL inhibitors, such as bisthiazolidines (BTZs) or captopril stereoisomers, which exhibit lower, more variable potencies and multiple binding modes. MMTZ binding involves thiol coordination to the Zn(II) site and extensive hydrophobic interactions, burying the inhibitor more deeply within the active site than D/L-captopril. Unexpectedly, MMTZ binding features a thioether–π interaction with a conserved active-site aromatic residue, consistent with their equipotent inhibition and similar binding to multiple MBLs. MMTZs penetrate multiple Enterobacterales, inhibit NDM-1 in situ, and restore carbapenem potency against clinical isolates expressing B1 MBLs. Based on their inhibitory profile and lack of eukaryotic cell toxicity, MMTZs represent a promising scaffold for MBL inhibitor development. These results also suggest sulphur–π interactions can be exploited for general ligand design in medicinal chemistry.
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Jan 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Open Access
Abstract: 2-Oxoglutarate (2OG) oxygenases are validated agrochemical and human drug targets. The potential for modulating their activity with 2OG derivatives has not been explored, possibly due to concerns regarding selectivity. We report proof-of-principle studies demonstrating selective enhancement or inhibition of 2OG oxygenase activity by 2-oxo acids. The human 2OG oxygenases studied, factor inhibiting hypoxia-inducible transcription factor HIF-α (FIH) and aspartate/asparagine-β-hydroxylase (AspH), catalyze C3 hydroxylations of Asp/Asn-residues. Of 35 tested 2OG derivatives, 10 enhance and 17 inhibit FIH activity. Comparison with results for AspH reveals that 2OG derivatives selectively enhance or inhibit FIH or AspH. Comparison of FIH structures complexed with 2OG derivatives to those for AspH provides insight into the basis of the observed selectivity. 2-Oxo acid derivatives have potential as drugs, for use in biomimetic catalysis, and in functional studies. The results suggest that the in vivo activity of 2OG oxygenases may be regulated by natural 2-oxo acids other than 2OG.
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Nov 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Yves
Nkizinkiko
,
Jenny
Desantis
,
Jarkko
Koivunen
,
Teemu
Haikarainen
,
Sudarshan
Murthy
,
Luca
Sancineto
,
Serena
Massari
,
Federica
Ianni
,
Ezeogo
Obaji
,
Maria I.
Loza
,
Taina
Pihlajaniemi
,
Jose
Brea
,
Oriana
Tabarrini
,
Lari
Lehtiö
Diamond Proposal Number(s):
[14794]
Open Access
Abstract: Tankyrases (TNKSs) are enzymes specialized in catalyzing poly-ADP-ribosylation of target proteins. Several studies have validated TNKSs as anti-cancer drug targets due to their regulatory role in Wnt/β-catenin pathway. Recently a lot of effort has been put into developing more potent and selective TNKS inhibitors and optimizing them towards anti-cancer agents. We noticed that some 2-phenylquinazolinones (2-PQs) reported as CDK9 inhibitors were similar to previously published TNKS inhibitors. In this study, we profiled this series of 2-PQs against TNKS and selected kinases that are involved in the Wnt/β-catenin pathway. We found that they were much more potent TNKS inhibitors than they were CDK9/kinase inhibitors. We evaluated the compound selectivity to tankyrases over the ARTD enzyme family and solved co-crystal structures of the compounds with TNKS2. Comparative structure-based studies of the catalytic domain of TNKS2 with selected CDK9 inhibitors and docking studies of the inhibitors with two kinases (CDK9 and Akt) revealed important structural features, which could explain the selectivity of the compounds towards either tankyrases or kinases. We also discovered a compound, which was able to inhibit tankyrases, CDK9 and Akt kinases with equal µM potency.
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Jan 2018
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[11235]
Open Access
Abstract: The tumor suppressor p53 has the most frequently mutated gene in human cancers. Many of p53’s oncogenic mutants are just destabilized and rapidly aggregate, and are targets for stabilization by drugs. We found certain 2-sulfonylpyrimidines, including one named PK11007, to be mild thiol alkylators with anticancer activity in several cell lines, especially those with mutationally compromised p53. PK11007 acted by two routes: p53 dependent and p53 independent. PK11007 stabilized p53 in vitro via selective alkylation of two surface-exposed cysteines without compromising its DNA binding activity. Unstable p53 was reactivated by PK11007 in some cancer cell lines, leading to up-regulation of p53 target genes such as p21 and PUMA. More generally, there was cell death that was independent of p53 but dependent on glutathione depletion and associated with highly elevated levels of reactive oxygen species and induction of endoplasmic reticulum (ER) stress, as also found for the anticancer agent PRIMA-1MET(APR-246). PK11007 may be a lead for anticancer drugs that target cells with nonfunctional p53 or impaired reactive oxygen species (ROS) detoxification in a wide variety of mutant p53 cells.
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Sep 2016
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I04-Macromolecular Crystallography
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Dongsheng
Zhu
,
Huocong
Huang
,
Daniel
Pinkas
,
Jinfeng
Luo
,
Debolina
Ganguly
,
Alice E.
Fox
,
Emily
Arner
,
Qiuping
Xiang
,
Zheng-Chao
Tu
,
Alex N.
Bullock
,
Rolf A
Brekken
,
Ke
Ding
,
Xiaoyun
Lu
Diamond Proposal Number(s):
[15433]
Open Access
Abstract: Pancreatic cancer is a leading cause of cancer-related death. A series of 2-amino-2, 3-dihydro-1H-indene-5-carboxamide derivatives were designed and synthesized as novel selective DDR1 inhibitors to exhibit promising in vitro and in vivo anti-pancreatic cancer activity. One of the representative compounds, 7f, binds with DDR1 with a Kd value of 5.9 nM and suppresses the kinase activity with an IC50 value of 14.9 nM, but is significantly less potent for majority of a panel of 403 wild-type kinases. The compound potently inhibited collagen-induced epithelial-mesenchymal transition (EMT) and dose-dependently suppressed colony formation of pancreatic cancer cells. Furthermore, 7f also demonstrated reasonable pharmacokinetic profiles and displayed promising in vivo therapeutic efficacy in an orthotopic mouse model of pancreatic cancer. Compound 7f may serve as a new lead compound for future drug discovery.
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Jul 2019
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Philip
Hinchliffe
,
Diego M.
Moreno
,
Maria-Agustina
Rossi
,
Maria F.
Mojica
,
Veronica
Martinez
,
Valentina
Villamil
,
Brad
Spellberg
,
George L.
Drusano
,
Claudia
Banchio
,
Graciela
Mahler
,
Robert A.
Bonomo
,
Alejandro J.
Vila
,
James
Spencer
Diamond Proposal Number(s):
[12342, 17212]
Abstract: Metallo-β-lactamase (MBL) production in Gram-negative bacteria is an important contributor to β-lactam antibiotic resistance. Combining β-lactams with β-lactamase inhibitors (BLIs) is a validated route to overcoming resistance, but MBL inhibitors are not available in the clinic. On the basis of zinc utilization and sequence, MBLs are divided into three subclasses, B1, B2, and B3, whose differing active-site architectures hinder development of BLIs capable of “cross-class” MBL inhibition. We previously described 2-mercaptomethyl thiazolidines (MMTZs) as B1 MBL inhibitors (e.g., NDM-1) and here show that inhibition extends to the clinically relevant B2 (Sfh-I) and B3 (L1) enzymes. MMTZs inhibit purified MBLs in vitro (e.g., Sfh-I, Ki 0.16 μM) and potentiate β-lactam activity against producer strains. X-ray crystallography reveals that inhibition involves direct interaction of the MMTZ thiol with the mono- or dizinc centers of Sfh-I/L1, respectively. This is further enhanced by sulfur-π interactions with a conserved active site tryptophan. Computational studies reveal that the stereochemistry at chiral centers is critical, showing less potent MMTZ stereoisomers (up to 800-fold) as unable to replicate sulfur-π interactions in Sfh-I, largely through steric constraints in a compact active site. Furthermore, in silico replacement of the thiazolidine sulfur with oxygen (forming an oxazolidine) resulted in less favorable aromatic interactions with B2 MBLs, though the effect is less than that previously observed for the subclass B1 enzyme NDM-1. In the B3 enzyme L1, these effects are offset by additional MMTZ interactions with the protein main chain. MMTZs can therefore inhibit all MBL classes by maintaining conserved binding modes through different routes.
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Aug 2021
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Krios I-Titan Krios I at Diamond
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Pu
Qian
,
Alastair T.
Gardiner
,
Ivana
Šímová
,
Katerina
Naydenova
,
Tristan I.
Croll
,
Philip J.
Jackson
,
Nupur
Nupur
,
Miroslav
Kloz
,
Petra
Čubáková
,
Marek
Kuzma
,
Yonghui
Zeng
,
Pablo
Castro-Hartmann
,
Bart
Van Knippenberg
,
Kenneth N.
Goldie
,
David
Kaftan
,
Pavel
Hrouzek
,
Jan
Hájek
,
Jon
Agirre
,
C. Alistair
Siebert
,
David
Bína
,
Kasim
Sader
,
Henning
Stahlberg
,
Roman
Sobotka
,
Christopher J.
Russo
,
Tomáš
Polívka
,
C. Neil
Hunter
,
Michal
Koblížek
Diamond Proposal Number(s):
[29785]
Open Access
Abstract: Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo-microscopy structure of the Gemmatimonas phototrophica photosystem at 2.4 Å reveals a unique, double-ring complex. Two unique membrane-extrinsic polypeptides, RC-S and RC-U, hold the central type 2 reaction center (RC) within an inner 16-subunit light-harvesting 1 (LH1) ring, which is encircled by an outer 24-subunit antenna ring (LHh) that adds light-gathering capacity. Femtosecond kinetics reveal the flow of energy within the RC-dLH complex, from the outer LHh ring to LH1 and then to the RC. This structural and functional study shows that G. phototrophica has independently evolved its own compact, robust, and highly effective architecture for harvesting and trapping solar energy.
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Feb 2022
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Nuria
Tapia-Ruiz
,
A. Robert
Armstrong
,
Hande
Alptekin
,
Marco A.
Amores
,
Heather
Au
,
Jerry
Barker
,
Rebecca
Boston
,
William R
Brant
,
Jake M.
Brittain
,
Yue
Chen
,
Manish
Chhowalla
,
Yong-Seok
Choi
,
Sara I. R.
Costa
,
Maria
Crespo Ribadeneyra
,
Serena A
Cussen
,
Edmund J.
Cussen
,
William I. F.
David
,
Aamod V
Desai
,
Stewart A. M.
Dickson
,
Emmanuel I.
Eweka
,
Juan D.
Forero-Saboya
,
Clare
Grey
,
John M.
Griffin
,
Peter
Gross
,
Xiao
Hua
,
John T. S.
Irvine
,
Patrik
Johansson
,
Martin O.
Jones
,
Martin
Karlsmo
,
Emma
Kendrick
,
Eunjeong
Kim
,
Oleg V
Kolosov
,
Zhuangnan
Li
,
Stijn F L
Mertens
,
Ronnie
Mogensen
,
Laure
Monconduit
,
Russell E
Morris
,
Andrew J.
Naylor
,
Shahin
Nikman
,
Christopher A
O’keefe
,
Darren M. C.
Ould
,
Robert G.
Palgrave
,
Philippe
Poizot
,
Alexandre
Ponrouch
,
Stéven
Renault
,
Emily M.
Reynolds
,
Ashish
Rudola
,
Ruth
Sayers
,
David O.
Scanlon
,
S.
Sen
,
Valerie R.
Seymour
,
Begoña
Silván
,
Moulay Tahar
Sougrati
,
Lorenzo
Stievano
,
Grant S.
Stone
,
Chris I.
Thomas
,
Maria-Magdalena
Titirici
,
Jincheng
Tong
,
Thomas J.
Wood
,
Dominic S
Wright
,
Reza
Younesi
Open Access
Abstract: Increasing concerns regarding the sustainability of lithium sources, due to their limited availability and consequent expected price increase, have raised awareness of the importance of developing alternative energy-storage candidates that can sustain the ever-growing energy demand. Furthermore, limitations on the availability of the transition metals used in the manufacturing of cathode materials, together with questionable mining practices, are driving development towards more sustainable elements. Given the uniformly high abundance and cost-effectiveness of sodium, as well as its very suitable redox potential (close to that of lithium), sodium-ion battery technology offers tremendous potential to be a counterpart to lithium-ion batteries (LIBs) in different application scenarios, such as stationary energy storage and low-cost vehicles. This potential is reflected by the major investments that are being made by industry in a wide variety of markets and in diverse material combinations. Despite the associated advantages of being a drop-in replacement for LIBs, there are remarkable differences in the physicochemical properties between sodium and lithium that give rise to different behaviours, for example, different coordination preferences in compounds, desolvation energies, or solubility of the solid–electrolyte interphase inorganic salt components. This demands a more detailed study of the underlying physical and chemical processes occurring in sodium-ion batteries and allows great scope for groundbreaking advances in the field, from lab-scale to scale-up. This roadmap provides an extensive review by experts in academia and industry of the current state of the art in 2021 and the different research directions and strategies currently underway to improve the performance of sodium-ion batteries. The aim is to provide an opinion with respect to the current challenges and opportunities, from the fundamental properties to the practical applications of this technology.
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Jul 2021
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Theoretical Physics
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Abstract: A historical overview of magnetic x-ray dichroism is presented. I describe the first theoretical and experimental results that have led to the development of this powerful technique for element-specific magnetometry. The theoretical progress of the sum rules is also described, starting with the spinorbit sum rule for the isotropic spectrum which led on to the spin and orbital moment sum rules for x-ray magnetic circular dichroism. The latter has been particularly useful to understand the magnetic anisotropy in thin films and multilayers. Further developments of circular dichroism in (resonant) photoemission and Auger, as well as x-ray detected optical activity, also are summarized. Currently, magnetic x-ray dichroism finds a wide application in x-ray spectroscopy and imaging for the study of magnetic materials and it is considered to be one of the most important discoveries in the field of magnetism in the last few decennia. It is hard to imagine modern research into magnetism without the aid of polarized x-rays.
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Nov 2013
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[10344]
Abstract: The hexapodal ligand hexakis(isonicotinoyl)cyclotricatechylene (L1) belonging to the cyclotriveratrylene family of host-molecules has been synthesised and used in the assembly of a series of coordination polymer materials with Re(I), Co(II), Cu(II), Ni(II) and Ag(I) salts. Single crystal structures of the coordination polymers [Re3(L1)2Br3(CO)3] 1, and an isomorphic [M3L2] series where M = Co, Cu or Ni, reveal 2D framework structures with a simplified topology of 36 or hxl. These are composed of M6(L1)2 metallo-cages linked together in a pair-wise fashion through each metal centre. Compound 1 is a rare example of a rhenium coordination polymer and was investigated for guest uptake from solution, complexing I2. The mixed-ligand species [Cu2(L1)(CF3CO2)3(isonicotinate)] forms a (3,4,5)-connected 2D coordination polymer, while [Ag2(L1)(DMF)2]·2BF4·2(H2O)·6(DMF) features a 2D network of (3,6)-connectivity and with kagome dual (kgd) topology.
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Jun 2018
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