I24-Microfocus Macromolecular Crystallography
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Alexandra
Borodovsky
,
Christine M
Barbon
,
Yanjun
Wang
,
Minwei
Ye
,
Laura
Prickett
,
Dinesh
Chandra
,
Joseph
Shaw
,
Nanhua
Deng
,
Kris
Sachsenmeier
,
James D.
Clarke
,
Bolan
Linghu
,
Giles A
Brown
,
James
Brown
,
Miles
Congreve
,
Robert K. Y.
Cheng
,
Andrew
Dore
,
Edward
Hurrell
,
Wenlin
Shao
,
Richard
Woessner
,
Corinne
Reimer
,
Lisa
Drew
,
Stephen
Fawell
,
Alwin G
Schuller
,
Deanna A
Mele
Open Access
Abstract: Background: Accumulation of extracellular adenosine within the microenvironment is a strategy exploited by tumors to escape detection by the immune system. Adenosine signaling through the adenosine 2A receptor (A2AR) on immune cells elicits a range of immunosuppressive effects which promote tumor growth and limit the efficacy of immune checkpoint inhibitors. Preclinical data with A2AR inhibitors have demonstrated tumor regressions in mouse models by rescuing T cell function; however, the mechanism and role on other immune cells has not been fully elucidated.
Methods: We report here the development of a small molecule A2AR inhibitor including characterization of binding and inhibition of A2AR function with varying amounts of a stable version of adenosine. Functional activity was tested in both mouse and human T cells and dendritic cells (DCs) in in vitro assays to understand the intrinsic role on each cell type. The role of adenosine and A2AR inhibition was tested in DC differentiation assays as well as co-culture assays to access the cross-priming function of DCs. Syngeneic models were used to assess tumor growth alone and in combination with alphaprogrammed death-ligand 1 (αPD-L1). Immunophenotyping by flow cytometry was performed to examine global immune cell changes upon A2AR inhibition.
Results: We provide the first report of AZD4635, a novel small molecule A2AR antagonist which inhibits downstream signaling and increases T cell function as well as a novel mechanism of enhancing antigen presentation by CD103+ DCs. The role of antigen presentation by DCs, particularly CD103+ DCs, is critical to drive antitumor immunity providing rational to combine a priming agent AZD4635 with check point blockade. We find adenosine impairs the maturation and antigen presentation function of CD103+ DCs. We show in multiple syngeneic mouse tumor models that treatment of AZD4635 alone and in combination with αPD-L1 led to decreased tumor volume correlating with enhanced CD103+ function and T cell response. We extend these studies into human DCs to show that adenosine promotes a tolerogenic phenotype that can be reversed with AZD4635 restoring antigen-specific T cell activation. Our results support the novel role of adenosine signaling as an intrinsic negative regulator of CD103+ DCs maturation and priming. We show that potent inhibition of A2AR with AZD4635 reduces tumor burden and enhances antitumor immunity. This unique mechanism of action in CD103+ DCs may contribute to clinical responses as AZD4635 is being evaluated in clinical trials with IMFINZI (durvalumab, αPD-L1) in patients with solid malignancies.
Conclusion: We provide evidence implicating suppression of adaptive and innate immunity by adenosine as a mechanism for immune evasion by tumors. Inhibition of adenosine signaling through selective small molecule inhibition of A2AR using AZD4635 restores T cell function via an internal mechanism as well as tumor antigen cross-presentation by CD103+ DCs resulting in antitumor immunity.
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Jul 2020
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I24-Microfocus Macromolecular Crystallography
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Willem
Jespers
,
Gregory
Verdon
,
Jhonny
Azuaje
,
Maria
Majellaro
,
Henrik
Keränen
,
Xerardo
García‐mera
,
Miles
Congreve
,
Francesca
Deflorian
,
Chris
De Graaf
,
Andrei
Zhukov
,
Andrew S.
Dore
,
Jonathan S.
Mason
,
Johan
Åqvist
,
Robert M.
Cooke
,
Eddy
Sotelo
,
Hugo
Gutiérrez‐de‐terán
Diamond Proposal Number(s):
[17185]
Open Access
Abstract: We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X‐ray crystallography to reveal the binding mode of an antagonist series to the A2A adenosine receptor (AR). Eight A2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A2AAR were experimentally determined and investigated through a cycle of ligand‐FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X‐ray crystallography of the A2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A2AAR, an emerging target in immuno‐oncology.
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Jul 2020
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I24-Microfocus Macromolecular Crystallography
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Mathieu
Rappas
,
Ammar
Ali
,
Kirstie A.
Bennett
,
Jason D.
Brown
,
Sarah J.
Bucknell
,
Miles
Congreve
,
Robert M.
Cooke
,
Gabriella
Cseke
,
Chris
De Graaf
,
Andrew S.
Dore
,
James C.
Errey
,
Ali
Jazayeri
,
Fiona H.
Marshall
,
Jonathan S.
Mason
,
Richard
Mould
,
Jayesh C.
Patel
,
Benjamin G.
Tehan
,
Malcolm
Weir
,
John A.
Christopher
Diamond Proposal Number(s):
[5788, 20025, 12425, 5999, 5788, 17185, 20025]
Abstract: The orexin system, which consists of the two G protein-coupled receptors OX1 and OX2, activated by the neuropeptides OX-A and OX-B, is firmly established as a key regulator of behavioural arousal, sleep and wakefulness, and has been an area of intense research effort over the past two decades. X-ray structures of the receptors in complex with ten new antagonist ligands from diverse chemotypes are presented, which complement the existing structural information for the system and highlight the critical importance of lipophilic hotspots and water molecules for these peptidergic GPCR targets. Learnings from the structural information regarding the utility of pharmacophore models and how selectivity between OX1 and OX2 can be achieved are discussed.
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Dec 2019
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[8547]
Abstract: G protein-coupled receptors (GPCRs) in the G protein-coupled active state have higher affinity for agonists compared to when they are in the inactive state, but the molecular basis for this is unclear. We have determined four active-state structures of the β1-adrenoceptor (β1AR) bound to conformation-specific nanobodies in the presence of agonists of varying efficacy. Comparison with inactive-state structures of β1AR bound to the identical ligands showed a 24-42% reduction in the volume of the orthosteric binding site. Potential hydrogen bonds were also shorter, and there was up to a 30% increase in the number of atomic contacts between the receptor and ligand. This explains the increase in agonist affinity of GPCRs in the active state for a wide range of structurally distinct agonists.
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May 2019
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I24-Microfocus Macromolecular Crystallography
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John A.
Christopher
,
Zoltán
Orgován
,
Miles
Congreve
,
Andrew S.
Dore
,
James C.
Errey
,
Fiona H.
Marshall
,
Jonathan S.
Mason
,
Krzysztof
Okrasa
,
Prakash
Rucktooa
,
Maria J.
Serrano-Vega
,
György G.
Ferenczy
,
Gyorgy M.
Keseru
Abstract: Two interesting new X-ray structures of negative allosteric modulator (NAM) ligands for the mGlu5 receptor, M-MPEP (3) and fenobam (4), are reported. The new structures show how the binding of the ligands induces different receptor water channel conformations to previously published structures. The structure of fenobam, where a urea replaces the acetylenic linker in M-MPEP and mavoglurant, reveals a binding mode where the ligand is rotated by 180º compared to a previously proposed docking model. The need for multiple ligand structures for accurate GPCR structure-based drug design is demonstrated by the different growing vectors identified for the head groups of M-MPEP and mavoglurant and by the unexpected water mediated receptor interactions of a new chemotype represented by fenobam. The implications of the new structures for ligand design are discussed, with extensive analysis of the energetics of the water networks of both pseudo-apo and bound structures providing a new design strategy for allosteric modulators.
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Feb 2018
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I24-Microfocus Macromolecular Crystallography
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Open Access
Abstract: Here we report an efficient method to generate multiple co-structures of the A2A G protein-coupled receptor (GPCR) with small-molecules from a single preparation of a thermostabilised receptor crystallised in Lipidic Cubic Phase (LCP). Receptor crystallisation is achieved following purification using a low affinity “carrier” ligand (theophylline) and crystals are then soaked in solutions containing the desired (higher affinity) compounds. Complete datasets to high resolution can then be collected from single crystals and seven structures are reported here of which three are novel. The method significantly improves structural throughput for ligand screening using stabilised GPCRs, thereby actively driving Structure-Based Drug Discovery (SBDD).
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Jan 2018
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I24-Microfocus Macromolecular Crystallography
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Abstract: The complement system is a crucial component of the host response to infection and tissue damage. Activation of the complement cascade generates anaphylatoxins including C5a and C3a. C5a exerts a pro-inflammatory effect via the G-protein-coupled receptor C5a anaphylatoxin chemotactic receptor 1 (C5aR1, also known as CD88) that is expressed on cells of myeloid origin1,2. Inhibitors of the complement system have long been of interest as potential drugs for the treatment of diseases such as sepsis, rheumatoid arthritis, Crohn’s disease and ischaemia-reperfusion injuries1. More recently, a role of C5a in neurodegenerative conditions such as Alzheimer’s disease has been identified3. Peptide antagonists based on the C5a ligand have progressed to phase 2 trials in psoriasis and rheumatoid arthritis; however, these compounds exhibited problems with off-target activity, production costs, potential immunogenicity and poor oral bioavailability. Several small-molecule competitive antagonists for C5aR1, such as W-540115 and NDT95137276, have been identified by C5a radioligand-binding assays4. NDT9513727 is a non-peptide inverse agonist of C5aR1, and is highly selective for the primate and gerbil receptors over those of other species. Here, to study the mechanism of action of C5a antagonists, we determine the structure of a thermostabilized C5aR1 (known as C5aR1 StaR) in complex with NDT9513727. We found that the small molecule bound between transmembrane helices 3, 4 and 5, outside the helical bundle. One key interaction between the small molecule and residue Trp2135.49 seems to determine the species selectivity of the compound. The structure demonstrates that NDT9513727 exerts its inverse-agonist activity through an extra-helical mode of action.
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Jan 2018
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I24-Microfocus Macromolecular Crystallography
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Abstract: The structural analysis of class B G protein-coupled receptors (GPCR), cell surface proteins responding to peptide hormones, has until recently been restricted to the extracellular domain (ECD). Corticotropin-releasing factor receptor type 1 (CRF1R) is a class B receptor mediating stress response and also considered a drug target for depression and anxiety. Here we report the crystal structure of the transmembrane domain of human CRF1R in complex with the small-molecule antagonist CP-376395 in a hexagonal setting with translational non-crystallographic symmetry. Molecular dynamics and metadynamics simulations on this novel structure and the existing TMD structure for CRF1R provides insight as to how the small molecule ligand gains access to the induced-fit allosteric binding site with implications for the observed selectivity against CRF2R. Furthermore, molecular dynamics simulations performed using a full-length receptor model point to key interactions between the ECD and extracellular loop 3 of the TMD providing insight into the full inactive state of multidomain class B GPCRs.
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Oct 2017
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[12425]
Abstract: The adenosine A1 and A2A receptors belong to the purinergic family of G protein-coupled receptors, and regulate diverse functions of the cardiovascular, respiratory, renal, inflammation, and CNS. Xanthines such as caffeine and theophylline are weak, non-selective antagonists of adenosine receptors. Here we report the structure of a thermostabilized human A1 receptor at 3.3 Å resolution with PSB36, an A1-selective xanthine-based antagonist. This is compared with structures of the A2A receptor with PSB36 (2.8 Å resolution), caffeine (2.1 Å), and theophylline (2.0 Å) to highlight features of ligand recognition which are common across xanthines. The structures of A1R and A2AR were analyzed to identify the differences that are important selectivity determinants for xanthine ligands, and the role of T2707.35 in A1R (M2707.35 in A2AR) in conferring selectivity was confirmed by mutagenesis. The structural differences confirmed to lead to selectivity can be utilized in the design of new subtype-selective A1R or A2AR antagonists.
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Jul 2017
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I24-Microfocus Macromolecular Crystallography
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Ali
Jazayeri
,
Mathieu
Rappas
,
Alastair J. H.
Brown
,
James
Kean
,
James C.
Errey
,
Nathan J.
Robertson
,
Cédric
Fiez-Vandal
,
Stephen P.
Andrews
,
Miles
Congreve
,
Andrea
Bortolato
,
Jonathan S.
Mason
,
Asma H.
Baig
,
Iryna
Teobald
,
Andrew S.
Dore
,
Malcolm
Weir
,
Robert M.
Cooke
,
Fiona H.
Marshall
Diamond Proposal Number(s):
[12425]
Abstract: Glucagon-like peptide 1 (GLP-1) regulates glucose homeostasis through the control of insulin release from the pancreas. GLP-1 peptide agonists are efficacious drugs for the treatment of diabetes. To gain insight into the molecular mechanism of action of GLP-1 peptides, here we report the crystal structure of the full-length GLP-1 receptor bound to a truncated peptide agonist. The peptide agonist retains an α-helical conformation as it sits deep within the receptor-binding pocket. The arrangement of the transmembrane helices reveals hallmarks of an active conformation similar to that observed in class A receptors. Guided by this structural information, we design peptide agonists with potent in vivo activity in a mouse model of diabetes.
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May 2017
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