Krios I-Titan Krios I at Diamond
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Yu
Zhang
,
Lijie
Zhong
,
Yun
Song
,
Mingcheng
Guo
,
Keli
Ren
,
Tingting
Yang
,
Yixin
Huang
,
Ilia
Sirotkin
,
Gangshun
Yi
,
Fang
Jiao
,
Peijun
Zhang
,
Robert J. C.
Gilbert
,
Tao
Ni
,
Xiulian
Yu
Diamond Proposal Number(s):
[21004, 29812]
Open Access
Abstract: Malaria-causing Plasmodium parasites must pass through several host cell types to complete their life cycle. This cell traversal is facilitated by perforin-like proteins (PLPs), among which PLP2 is essential for erythrocyte rupture by gametocytes. However, the mechanism by which PLP2 forms pores is not yet understood. Here, we combine cryo-electron microscopy and tomography to reveal the structural basis of Plasmodium vivax PLP2-mediated membrane attack. PvPLP2 assembles on lipid bilayers into heterogeneous arc- and ring-shaped pores with variable stoichiometries. Among them, we determine the structure of a 17-subunit pore complex in which the pore-forming MACPF domains form the central β-barrel, while the peripheral Apicomplexan PLP C-terminal β-pleated sheet (APCβ) domains anchor the complex to the membrane surface. A disulfide-stabilized mutant captures an intermediate pre-pore complex prior to membrane insertion, delineating the structural transitions that underpin β-barrel deployment. Functionally, PvPLP2 acts preferentially on the inner leaflet of the erythrocyte membrane, a specificity driven by its affinity for negatively charged lipids. Together, these findings establish the pore-formation pathway for a key Plasmodium virulence factor and provide a structural framework for rational design of transmission-blocking agents that prevent gametocyte egress.
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Jul 2026
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I03-Macromolecular Crystallography
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Barbara
Forte
,
Fiona
Bellany
,
Peter S.
Campbell
,
Giulia
Chemi
,
Alice
Dawson
,
Mark
Anderson
,
Yaw
Aniweh
,
Anna Y.
Burkhard
,
Anna Caroline Campos
Aguiar
,
Alisje
Churchyard
,
Caitlin A.
Cooper
,
Amália
Dos Santos Ferreira
,
Mufuliat Toyin
Famodimu
,
Francis G.
Fang
,
Xiao
Hu
,
Tonnie
Huijs
,
Delphine
Baud
,
Chimed
Jansen
,
María Belén
Jiménez Díaz
,
Roger
Bonnert
,
Susan
Boyd
,
Benigno
Crespo-Fernández
,
Branko
Mitasev
,
Simone
Montagna
,
Sachel
Mok
,
Dinakaran
Murugesan
,
Sunil K.
Narwal
,
Neil R.
Norcross
,
John
Okombo
,
Heekuk
Park
,
Caroline
Peet
,
Dhelio B.
Pereira
,
John M.
Post
,
Janette
Reader
,
Jennifer
Riley
,
David A.
Robinson
,
Raku
Shinkyo
,
Frederick R. C.
Simeons
,
Laura
Simpson
,
Alasdair
Smith
,
Dennis
Smith
,
Josefine
Striepen
,
Carolina B. G.
Teles
,
Rianne
Van Der Laak
,
Anne-Catrin
Uhlemann
,
Amélie
Vantaux
,
Caroline
Wilson
,
Benoît
Witkowski
,
Gavin
Wood
,
Tomas
Yeo
,
Fabio
Zuccotto
,
Iñigo
Angulo-Barturen
,
Jake
Baum
,
Judith M.
Bolscher
,
Rafael Victorio Carvalho
Guido
,
Lyn-Marié
Birkholtz
,
Michael J.
Delves
,
Laurent
Dembele
,
David A.
Fidock
,
Francisco Javier
Gamo
,
Dennis E.
Kyle
,
Steven P.
Maher
,
Jean
Popovici
,
Chris
Walpole
,
Fabian
Gusovsky
,
Paul A.
Willis
,
Kevin D.
Read
,
Ian H.
Gilbert
,
Beatriz
Baragaña
Diamond Proposal Number(s):
[10071, 26793]
Open Access
Abstract: A fused dihydropyrrolidino-pyrimidine hit with low lipophilicity and excellent ligand efficiency was identified in a biochemical screen of the Global Health Chemical Diversity Library (GHCDL) against Plasmodium lysyl-tRNA synthetase (KRS). Structure-guided lead optimization delivered analogues with potent parasite growth inhibition, excellent biochemical and cellular selectivity (>1000-fold), and oral efficacy in the malaria NOD-scid-IL2Rγnull (SCID) mouse model. Structural information and computational methods were deployed to identify a potent and selective basic KRS inhibitor (30) with an extended half-life to reduce the dose regimen to a single-dose cure. Compound 30 displayed a long half-life across preclinical species, favorable safety, and activity across Plasmodium species as well as against drug-resistant and sensitive P. falciparum strains and field isolates. Unfortunately, 30 lacked oral bioavailability, which could not be mitigated with a prodrug approach. Nevertheless, learnings from this series will assist future KRS programs in delivering a clinical candidate with this novel mode of action.
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Jun 2026
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[38313]
Open Access
Abstract: Malaria remains a major global health concern. The development of point-of-care diagnostic aptasensors could improve malaria detection, patient management, and eradication efforts. We selected and validated single-stranded DNA aptamers against Plasmodium falciparum lactate dehydrogenase (Pf-LDH) using Systematic Evolution of Ligands by Exponential Enrichment (SELEX). The five most abundant aptamers were validated with an enzyme-linked oligonucleotide assay (ELONA). The aptamer binding affinities to Pf-LDH varied between 0.35-3.08 nM. Truncation of aptamers enhanced binding affinities in most cases, with all truncated aptamers showing comparable or improved dissociation constants (Kd) relative to full-length aptamers, except Pf-LDH5t, which lost binding. Selectivity analysis against LDH from P. ovale, P. vivax, and P. malariae showed that Pf-LDH1 and Pf-LDH1t specifically recognized Pf-LDH (Kd = 2.74 ± 0.28 nM and 1.13 ± 0.26 nM, respectively), while Pf-LDH2, Pf-LDH3, Pf-LDH4, and their truncated forms, as well as Pf-LDH5, recognized both Pf-LDH and P. ovale LDH (Po-LDH). Crystallography of Pf-LDH4t revealed a binding site overlapping that of the previously characterized aptamer 2008 but involving distinct molecular interactions. These findings demonstrate the structural versatility of Plasmodium LDH specific aptamers and provide a novel Pf- and Po-LDH co-specific aptamer panel with strong potential for next-generation aptamer-based malaria diagnostics.
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Jun 2026
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[31353]
Open Access
Abstract: Effective vaccines against malaria are urgently required. All components of the PfPCRCR complex are essential for erythrocyte invasion by Plasmodium falciparum and are potential vaccine immunogens against blood-stage malaria. Of these, PfRH5 has progressed furthest in clinical development, while PfCyRPA also induces parasite growth-inhibitory antibodies. Here, we used direct nanoparticle coupling and structure-guided design to generate improved PfCyRPA-based immunogens. PfCyRPA is a six-bladed β-propeller. Blades 1 and 2 are exposed in the PfPCRCR complex and contain the epitopes of the most potent known growth-inhibitory antibodies. We therefore performed structure-guided design to generate a correctly folded, thermostable epitope mimic, PfCyRPA-EM, containing blades 1 and 2. In a pre-clinical model, PfCyRPA-EM elicited antibodies that inhibited parasite growth at lower concentrations than those elicited by PfCyRPA. In addition, the higher thermostability of PfCyRPA-EM and its improved expression as an I53-50 nanoparticle fusion make it well-suited for clinical development, alone or with other immunogens.
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Mar 2026
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Open Access
Abstract: Among the biophysical techniques used in fragment-based drug discovery (FBDD) campaigns, crystallography is the most sensitive, allowing for the identification of low-affinity ligands and the characterization of protein–ligand complexes at atomic resolution. Although powerful, the proper application of this technique depends on obtaining crystals capable of diffracting X-rays at high resolution. Additionally, in crystallographic compound screening, the crystals must be resistant to multiple organic solvents used in chemical libraries, such as DMSO. In this protocol, we describe recombinant protein production suitable for crystallization and procedures for X-ray crystallographic screening of a library of 768 fragments. As a case study, we used the Schistosoma mansoni thioredoxin glutathione reductase (SmTGR), a redox enzyme with a key role in controlling oxidative stress in parasites of the Schistosoma genus, which causes schistosomiasis. As a validated pharmacological target, SmTGR is used in the development of new schistosomicidal drugs. The experimental pipeline includes SmTGR expression, purification, and crystallization, crystal soaking, diffraction data collection, and refinement. The 768 fragments from the Diamond-SGC Poised Library (DSPL) were individually soaked onto the crystals, and diffraction data were collected and processed at the I04-1 beamline of the Diamond Light Source synchrotron. Diffraction data were subsequently analyzed using PanDDA to identify fragment-binding events and to enable reliable detection of low-occupancy ligands within the protein crystal structures. In addition to the core experimental steps, this protocol incorporates systematic approaches to overcome limitations frequently encountered in crystallographic screening campaigns, including assessment of crystal solvent tolerance, acceleration of crystal mounting through the use of auxiliary devices, acoustic dispensing–based soaking of hundreds of fragments for low material consumption and high throughput, automated data collection, and efficient data analysis pipeline for the detection of weakly bound ligand. This protocol can be broadly applied to screen diverse compound sets against multiple targets amenable to crystallization.
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Mar 2026
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I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[23269]
Open Access
Abstract: The malarial parasite, Plasmodium falciparum (Pf), utilizes aminopeptidases in the breakdown of hemoglobin-derived oligopeptides to release amino acids for protein synthesis during growth and asexual reproduction of erythrocytic stages of the parasite. However, a N-terminal peptide bond that involves proline is difficult to hydrolyze. Aminopeptidase P (APP) is capable of cleaving peptide bonds with proline in the second position. Inhibition of PfAPP is therefore an attractive strategy for developing therapeutics for the treatment of malaria by limiting the supply of amino acids at the erythrocytic stage. We employed the structure-activity relationship of an existing APP inhibitor, apstatin, to design a more potent PfAPP inhibitor by introducing a hydroxamic acid metal-binding group in place of the amino-alcohol of apstatin, and an aromatic P4′ moiety. A hydroxamic tetrapeptide with phenylalanine at P4′ (6d) greatly increased the inhibitory potency (apstatin Ki, 16 μM; 6d, Ki 685 nM). Replacing the P3′ proline of 6d with a 2-substituted piperidine (6e) further improved the potency (Ki, 24 nM). Crystal structure analysis of PfAPP in complex with 6d and 6e showed binding at the active site with coordination of the hydroxamic acid metal binding group to the di-metal center, and several protein-inhibitor interactions involving domains II and III. A comparison of PfAPP-6e with human APP1 indicated that the P4′ phenylalanine drives inhibitor potency and selectivity towards PfAPP, by forming an interaction with Tyr617 of the adjacent monomer within the dimer. The details presented here should be useful for the future design of potent and selective PfAPP inhibitors.
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Mar 2026
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B21-High Throughput SAXS
Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[24557, 39224]
Open Access
Abstract: Histone variants define distinct chromatin states by modulating the biophysical properties of nucleosomes. Variants play a particularly important role in the parasitic protist Trypanosoma brucei, which has unusual chromatin and lacks a canonical repressive heterochromatin system. Instead, T. brucei utilizes specialized divergent histone variants H3.V and H4.V. However, the biochemical basis of their repressive functions is unknown. Here, we determined the structure of the H3.V-H4.V nucleosome core particle and biochemically characterized variant-containing nucleosomes and nucleosome arrays, probing their unique properties. We discovered that surprisingly for repressive-state nucleosomes, H3.V promotes pronounced DNA splaying, largely via its N-terminal tail region, while retaining overall stability that is comparable to canonical nucleosomes. In contrast, H4.V exhibits near-identical binding to DNA but mediates a slight increase in histone octamer stability. The surface of the H3.V-H4.V nucleosome is altered and provides a differential platform for chromatin-binding proteins, linking the variants to parasite pathogenicity.
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Feb 2026
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VMXi-Versatile Macromolecular Crystallography in situ
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Diamond Proposal Number(s):
[28534, 34263]
Open Access
Abstract: Schistosoma mansoni cathepsin D1 (SmCD1) has been shown to be an essential enzyme for helminth metabolism due to its role in haemoglobin degradation: a key amino-acid source for the developing parasite. Therefore, the enzyme is a potential target for the development of antischistosomal inhibitors. SmCD1 has significant sequence identity to cathepsin D-like proteases found in other schistosome species and homology to mammalian aspartic proteases. Here, we report the first crystal structures of a helminth cathepsin D, SmCD1, and have identified a single-domain antibody (nanobody) that specifically binds to SmCD1 with nanomolar affinity but does not recognize human cathepsin D. We have mapped the epitope of the nanobody by determining the crystal structure of the enzyme–nanobody complex, revealing the conformation of SmCD1 in the propeptide-bound state.
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Feb 2026
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[23459]
Open Access
Abstract: Intestinal amoebiasis is caused by Entamoeba histolytica, one of the deadliest human-infective parasites. Central to its pathogenicity is its binding to mucosal carbohydrates, which precedes tissue damage by trogocytosis. Carbohydrate binding is mediated by a single adhesin, the galactose/N-acetylgalactosamine (Gal/GalNAc) lectin, which is the leading vaccine candidate for amoebiasis. We present the structure of the native heterodimeric lectin, revealing an ordered core containing the light chain and the N-terminal region of the heavy chain. Structures obtained in the presence of ligand show that the Gal/GalNAc binding site is in the light chain, which adopts a β-trefoil fold found in other lectins. An elongated arm emerges from the heavy chain, which adopts multiple positions and may be modulated by sugar binding. This study reveals the molecular basis for sugar binding by the Entamoeba histolytica Gal/GalNAc lectin, a prerequisite for parasite invasion and development of intestinal disease.
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Feb 2026
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[38168]
Open Access
Abstract: Cyclophilins (Cyps) are ubiquitous cytosolic proteins with peptidyl-prolyl cis-trans isomerase (PPIase) activity and the ability to bind the immunosuppressant cyclosporin A (CsA). The genome of Toxoplasma gondii, the parasite responsible for toxoplasmosis, encodes multiple putative Cyps, whose specific functions remain largely unexplored.
Here, we characterize TgCyp21, a predicted Cyp from T. gondii. TgCyp21 displays PPIase activity and is inhibited by CsA in vitro. Importantly, its activity decreases markedly under oxidizing conditions but is partially restored by reducing agents, including dithiothreitol (DTT) and the parasite endogenous thioredoxin (TgTrx). TgCyp21 contains four cysteines, with Cys87 and Cys141 predicted to be spatially close based on structural modeling. Substitution of both residues significantly reduced PPIase activity, with Cys87 emerging as the main contributor to this loss. Structural modeling further indicates that Cys87 and Cys141 are suitably oriented to interact with the conserved active-site cysteines of TgTrx. This interaction is supported experimentally by mixed disulfide trapping, which identifies a stable disulfide-linked intermediate between TgCyp21 and TgTrx, consistent with a thiol-disulfide exchange mechanism. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy further confirm the formation of the complex.
Taken together, our data indicate that TgCyp21 behaves in vitro as a redox-responsive Cyp and a substrate for Trx, suggesting a potential involvement in Trx-mediated redox processes in T. gondii.
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Nov 2025
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