X-ray Crystallography Research Articles

Structures of LIG1 uncover the mechanism of sugar discrimination against 5′-RNA-DNA junctions during ribonucleotide excision repair

Ribonucleotides in DNA cause several types of genome instability and can be removed by ribonucleotide excision repair (RER) that is finalized by DNA ligase 1 (LIG1). However, the mechanism by which LIG1 discriminates the RER intermediate containing a 5'-RNA–DNA lesion generated by RNase H2-mediated cleavage of ribonucleotides remains unknown. Here, we determine X-ray structures of LIG1/5'-rG:C at the initial step of ligation where AMP is bound to the active site of the ligase, and uncover a large conformational change downstream the nick resulting in a shift at Arg(R)871 residue in the Adenylation domain of the ligase. Furthermore, we demonstrate a diminished ligation of the nick DNA substrate with a 5'-ribonucleotide in comparison to an efficient end joining of the nick substrate with a 3'-ribonucleotide by LIG1. Finally, our results demonstrate that mutations at the active site residues of the ligase and LIG1 disease-associated variants significantly impact the ligation efficiency of RNA–DNA heteroduplexes harboring “wrong” sugar at 3'- or 5'-end of nick. Collectively, our findings provide a novel atomic insight into proficient sugar discrimination by LIG1 during processing of the most abundant form of DNA damage in cells, genomic ribonucleotides, during initial step of the RER pathway.

Novel lignans from Syringa pinnatifolia and protective effect against H2O2-induced oxidative injury through regulating the expression of Nrf2/HO-1 in H9c2 cells

Phytochemical analysis of the peeled stems of Syringa pinnatifolia Hemsl. led to the discovery of 13 undescribed lignans, namely helanols A and B (1 and 2) and alashanenols W–G1 (3–13), as well as four known analogues, of which helanols A and B were lignans with novel skeleton of α-β′ linkage. The structures were unambiguously established by extensive spectroscopic analyses, NMR calculations, ECD calculations, and single crystal X-ray crystallography. Five lignans (1, 2, 5, 11 and 13) exhibited a moderate protective effect against H2O2-induced oxidative injuries in H9c2 cells with the protective rates of 11.3–20.6 % at the concentration of 0.3–20 μM, while the positive control quercetin showed protective rates of 58.7 % at 10 μM. Further mechanism investigation suggested that 1 and 2 exerted the protective effect by regulating the expression of Nrf2/HO-1.

Syntheses, structures and magnetisms of dimethyl phosphate-bridged dinuclear lanthanide complexes with pentadentate macrocyclic ligand

A series of air-stable dinuclear complexes, [HNEt3]2[Ln2(L)2((CH3O)2PO2)4](BPh4)4 (L = 2,14-dimethyl-3,6,10,13,19-pentaazabicyclo[13.3.1]nonadeca1(19), 2,13,15,17-pentene, Ln = Dy, 1-Dy; Tb, 2-Tb; Gd, 3-Gd), has been synthesized and characterized using single-crystal X-ray crystallography and magnetic measurements. The crystal structures disclose that two dimethyl phosphate anions act as bridging ligands, linking two Ln(III) ions. Each Ln(III) ion is eight-coordinated by five nitrogen atoms from a pentadentate Schiff based ligand L and three oxygen atoms from three dimethyl phosphates, forming a triangular dodecahedral coordination geometry. Direct-current magnetic susceptibility measurements indicate an extremely weak antiferromagnetic exchange between Gd(III) ions in 3-Gd. Complex 1-Dy exhibits slow magnetic relaxation with an effective energy barrier (Ueff) of 13 K under an applied field of 1000 Oe, whereas 2-Tb does not exhibit single-molecule magnet behavior. This work presents a novel strategy for constructing polynuclear single-molecular magnets by using a pentadetate macrocycle as magnetic building blocks integrated with replaceable axial ligands.

De novo design of miniprotein antagonists of cytokine storm inducers

Cytokine release syndrome (CRS), commonly known as cytokine storm, is an acute systemic inflammatory response that is a significant global health threat. Interleukin-6 (IL-6) and interleukin-1 (IL-1) are key pro-inflammatory cytokines involved in CRS and are hence critical therapeutic targets. Current antagonists, such as tocilizumab and anakinra, target IL-6R/IL-1R but have limitations due to their long half-life and systemic anti-inflammatory effects, making them less suitable for acute or localized treatments. Here we present the de novo design of small protein antagonists that prevent IL-1 and IL-6 from interacting with their receptors to activate signaling. The designed proteins bind to the IL-6R, GP130 (an IL-6 co-receptor), and IL-1R1 receptor subunits with binding affinities in the picomolar to low-nanomolar range. X-ray crystallography studies reveal that the structures of these antagonists closely match their computational design models. In a human cardiac organoid disease model, the IL-1R antagonists demonstrated protective effects against inflammation and cardiac damage induced by IL-1β. These minibinders show promise for administration via subcutaneous injection or intranasal/inhaled routes to mitigate acute cytokine storm effects.

Synthesis of cadmium(II) complexes with polyamines: Crystal structure, theoretical calculation, photocatalytic, DNA interaction and biological studies

Three cadmium(II) complexes of N-(2-aminoethyl)-1, 2-ethanediamine (DETA) (1), N-(3-aminopropyl)-1, 3-propanediamine (DPTA) (2) and N,N'-(ethane-1,2-diyl)bis(propane-1,3-diamine) (DPETA) (3) have been synthesized and characterized by single crystal X-ray crystallography, UV–visible spectroscopy, IR and conductivity measurements. Complexes 1 and 3 show octahedral geometry while complex 2 show five coordinated square pyramidal geometry. Two molecules of DETA ligand are coordinated to the Cd(II) ion in complex 1. But one molecule each of DPTA and DPETA ligands and two bromide ions are coordinated to the Cd(II) ions to form square pyramidal (2) and octahedral structure (3). DFT results show that complex 3 is the most favoured complex thermodynamically while complex 1 is the least. The complexes exhibit good photocatalytic activity with reference to the intensity of organic dye methylene blue. The complexes were investigated for DNA interaction by absorption and fluorescence spectroscopy suggesting both hypochromism (internal contact or intercalative interaction) and hyperchromism (external contact or electrostatic binding). The cadmium (II) complexes show growth inhibitory activity against four pathogenic bacteria, two gram +ve, viz., Staphyloccus aureus, Bacillus subtilis and two gram –ve, viz., Escherichia coli, Salmonella typhi. Albumin denaturation assay and Heat Induced Haemolysis were studied for the complexes for anti-inflammatory activity.

Integrating molecular dynamics simulation with small- and wide-angle X-ray scattering to unravel the flexibility, antigen-blocking, and protease-restoring functions in a hindrance-based pro-antibody.

Spatial hindrance-based pro-antibodies (pro-Abs) are engineered antibodies to reduce monoclonal antibodies' (mAbs) on-target toxicity using universal designed blocking segments that mask mAb antigen-binding sites through spatial hindrance. By linking through protease substrates and linkers, these blocking segments can be removed site-specifically. Although many types of blocking segments have been developed, such as coiled-coil and hinge-based Ab locks, the molecular structure of the pro-Ab, particularly the region showing how the blocking fragment blocks the mAb, has not been elucidated by X-ray crystallography or cryo-EM. To achieve maximal effect, a pro-Ab must have high antigen-blocking and protease-restoring efficiencies, but the unclear structure limits its further optimization. Here, we utilized molecular dynamics (MD) simulations to study the dynamic structures of a hinge-based Ab lock pro-Ab, pro-Nivolumab, and validated the simulated structures with small- and wide-angle X-ray scattering (SWAXS). The MD results were closely consistent with SWAXS data (χ2 best-fit = 1.845, χ2 allMD = 3.080). The further analysis shows a pronounced flexibility of the Ab lock (root-mean-square deviation = 10.90 Å), yet it still masks the important antigen-binding residues by 57.3%-88.4%, explaining its 250-folded antigen-blocking efficiency. The introduced protease accessible surface area method affirmed better protease efficiency for light chain (33.03 Å2) over heavy chain (5.06 Å2), which aligns with the experiments. Overall, we developed MD-SWAXS validation method to study the dynamics of flexible blocking segments and introduced methodologies to estimate their antigen-blocking and protease-restoring efficiencies, which would potentially be advancing the clinical applications of any spatial hindrance-based pro-Ab.

Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ.

The adenosine triphosphate (ATP)-binding cassette (ABC) importer GlnPQ from Lactococcus lactis has two sequential covalently linked substrate-binding domains (SBDs), which capture the substrates and deliver them to the translocon. The two SBDs differ in their ligand specificities, binding affinities and the distance to the transmembrane domain; interestingly, both SBDs can bind their ligands simultaneously without affecting each other. In this work, we studied the binding of ligands to both SBDs using X-ray crystallography and molecular dynamics simulations. We report three high-resolution structures of SBD1, namely, the wild-type SBD1 with bound asparagine or arginine, and E184D SBD1 with glutamine bound. Molecular dynamics (MD) simulations provide a detailed insight into the dynamics associated with open-closed transitions of the SBDs.

Dioxygenase Chemistry in Nucleophilic Aldehyde Deformylations Utilizing Dicopper O2-Derived Peroxide Complexes.

The chemistry of copper-dioxygen complexes is relevant to copper enzymes in biology as well as in (ligand)Cu-O2 (or Cu2-O2) species utilized in oxidative transformations. For overall energy considerations, as applicable in chemical synthesis, it is beneficial to have an appropriate atom economy; both O-atoms of O2(g) are transferred to the product(s). However, examples of such dioxygenase-type chemistry are extremely rare or not well documented. Herein, we report on nucleophilic oxidative aldehyde deformylation reactivity by the peroxo-dicopper(II) species [Cu2II(BPMPO-)(O22-)]1+ {BPMPO-H = 2,6-bis{[(bis(2-pyridylmethyl)amino]methyl}-4-methylphenol)} and [Cu2II(XYLO-)(O22-)]1+ (XYLO- = a BPMPO- analogue possessing bis(2-{2-pyridyl}ethyl)amine chelating arms). Their dicopper(I) precursors are dioxygenase catalysts. The O2(g)-derived peroxo-dicopper(II) intermediates react rapidly with aldehydes like 2-phenylpropionaldehyde (2-PPA) and cyclohexanecarboxaldehyde (CCA) in 2-methyltetrahydrofuran at -90 °C. Warming to room temperature (RT) followed by workup results in good yields of formate (HC(O)O-) along with ketones (acetophenone or cyclohexanone). Mechanistic investigation shows that [Cu2II(BPMPO-)(O22-)]1+ species initially reacts reversibly with the aldehydes to form detectable dicopper(II) peroxyhemiacetal intermediates, for which optical titrations provide the Keq (at -90 °C) of 73.6 × 102 M-1 (2-PPA) and 10.4 × 102 M-1 (CCA). In the reaction of [Cu2II(XYLO-)(O22-)]1+ with 2-PPA, product complexes characterized by single-crystal X-ray crystallography are the anticipated dicopper(I) complex, [Cu2I(XYLO-)]1+ plus a mixed-valent Cu(I)Cu(II)-formate species. Formate was further identified and confirmed by 1H NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS) analysis. Using 18O2(g)-isotope labeling the reaction produced a high yield of 18-O incorporated acetophenone as well as formate. The overall results signify that true dioxygenase reactions have occurred, supported by a thorough mechanistic investigation.

Alkene Isomerisation Catalysed by a Superbasic Sodium Amide.

Typically catalysed by transition metals, alkene isomerisation is a powerful methodology for preparation of internal olefins. In contrast, the use of more earth abundant main group reagents is limited to activated substrates, requiring high temperatures and excess stoichiometric amounts. Opening a new avenue for progressing this field, here we report applications of bulky sodium amide NaTMP (TMP=2,2,6,6-tetramethylpiperidide) when partnered with tridentate Lewis donor PMDETA (N,N,N',N'',N''-pentamethyldiethylenetriamine) in catalytic alkene isomerisation of terminal olefins under mild reaction conditions. An array of distinct olefins could successfully be isomerised, including unactivated olefins, allylamines, and allylethers, showing the high activity of this partnership. In-depth mechanistic insights provided by X-ray crystallography, real-time nuclear magnetic resonance (NMR) monitoring, and density functional theory (DFT) calculations have unveiled the crucial role of in situ-generated TMP(H) in facilitating efficient isomerisation, and the choice of alkali-metal. Additionally, theoretical studies shed light on the observed E/Z selectivity, particularly accounting for the selective formation of Z-vinyl ethers. The versatility of our method is further demonstrated through the isomerisation of unactivated cycloalkenes, which undergo hydrogen isotope exchange to produce deuterated compounds.

CheckMyMetal (CMM): validating metal-binding sites in X-ray and cryo-EM data.

Identifying and characterizing metal-binding sites (MBS) within macromolecular structures is imperative for elucidating their biological functions. CheckMyMetal (CMM) is a web based tool that facilitates the interactive validation of MBS in structures determined through X-ray crystallography and cryo-electron microscopy (cryo-EM). Recent updates to CMM have significantly enhanced its capability to efficiently handle large datasets generated from cryo-EM structural analyses. In this study, we address various challenges inherent in validating MBS within both X-ray and cryo-EM structures. Specifically, we examine the difficulties associated with accurately identifying metals and modeling their coordination environments by considering the ongoing reproducibility challenges in structural biology and the critical importance of well annotated, high-quality experimental data. CMM employs a sophisticated framework of rules rooted in the valence bond theory for MBS validation. We explore how CMM validation parameters correlate with the resolution of experimentally derived structures of macromolecules and their complexes. Additionally, we showcase the practical utility of CMM by analyzing a representative cryo-EM structure. Through a comprehensive examination of experimental data, we demonstrate the capability of CMM to advance MBS characterization and identify potential instances of metal misassignment.

Study of Chalcogen Aspirin Derivatives with Carbonic Anhydrase Inhibitory Properties for Treating Inflammatory Pain.

Carbonic anhydrase (CA) inhibitors represent intriguing tools for treating pain. This study aims at studying the pharmacological profile of chalcogen bioisosteres of aspirin, as inhibitors of CA isoforms (hCA I, II, IV, VII, IX, and XII). Our results show that selenoaspirin (5) displayed markedly superior inhibitory potency across all tested isoforms compared to thioaspirin (7) and aspirin, with a strong selectivity against the isoform CA IX. X-ray crystallography confirmed that both compounds bind effectively within the active site of hCA II, revealing unique structural characteristics compared to those of aspirin. In a preclinical model of inflammatory pain, compound 7 exhibited a longer lasting antihyperalgesic effect than aspirin, though with a lower potency. Conversely, compound 5 exhibited both lower potency and efficacy than aspirin in reducing pain, which entailed both adverse effects. Nevertheless, the therapeutic potential of chalcogen-based aspirin derivatives as novel CA inhibitors deserves to be further explored for clinical applications.

Torsional Twist of the SARS-CoV and SARS-CoV-2 SUD-N and SUD-M domains.

Coronavirus non-structural protein 3 (nsp3) forms hexameric crowns of pores in the double membrane vacuole that houses the replication-transcription complex. Nsp3 in SARS-like viruses has three unique domains absent in other coronavirus nsp3 proteins. Two of these, SUD-N (Macrodomain 2) and SUD-M (Macrodomain 3), form two lobes connected by a peptide linker and an interdomain disulfide bridge. We resolve the first complete x-ray structure of SARS-CoV SUD-N/M as well as a mutant variant of SARS-CoV-2 SUD-N/M modified to restore cysteines for interdomain disulfide bond naturally lost by evolution. Comparative analysis of all structures revealed SUD-N and SUD-M are not rigidly associated, but rather, have significant rotational flexibility. Phylogenetic analysis supports that the disulfide bond cysteines are also absent in pangolin-SARS and closely related viruses, consistent with pangolins being the presumed intermediate host in the emergence of SARS-CoV-2. The absence of these cysteines does not impact viral replication or protein translation.

Symmetry-Breaking and Symmetry-Retaining Morphological Evolution of the Single Crystals of Cyclodextrin Metal-Organic Frameworks.

The morphological symmetry-retaining and symmetry-breaking of single crystals of the γ-cyclodextrin metal-organic framework have been achieved via introducing lower symmetric β-cyclodextrins and α-cyclodextrins, respectively. β-cyclodextrins led to a morphological evolution with retained symmetry from cubic to rhombic dodecahedra, while α-cyclodextrins resulted in the original cubic crystal missing a vertex angle presenting symmetry-breaking behavior. The crystal structures of rhombic dodecahedra and angle-deficient crystals were confirmed through X-ray crystallography, and the mechanisms underlying the morphological transformation evolution were further analyzed. Our work not only provides a rare case realizing two different paths of morphological evolution in one system, but also encourages future efforts towards the evolution of artificial crystal systems in a natural way.

A thiopyridine-bound mirror-image copper center in an artificial non-heme metalloenzyme

Artificial metalloenzymes, in which a metal complex and protein matrix are combined, have been synthesized to catalyze stereoselective reactions using the chiral environment provided by the protein cavity. Artificial metalloenzymes can be engineered by the chemical modification and mutagenesis of the protein matrix. We developed artificial non-heme metalloenzymes using a cupin superfamily protein (TM1459) with a 4-His tetrad-metal-binding motif. The Cu-bound H52A/C106D mutant with 3-His triad showed a S-enantioselective Michael addition of nitromethane to α,β-unsaturated ketone, 2-aza-chalcone 1. In this study, we demonstrated a chemical modification near the copper-binding site of this mutant to reverse its enantioselectivity. For chemical modification, the amino acid on the Si-face of the binding state of 1 to the copper center was replaced with Cys, followed by reaction with 4,4′-dithiopyridine (4-PDS) to form S-(pyridin-4-ylthio)cysteine (Cys-4py). Cu-bound I49C-4py/H52A/C106D showed reversal of the enantioselectivity from S-form to R-form (ee = 71%, (R)). The effect of steric hindrance of the amino acids at position 49 on enantioselectivity was investigated using I49X/H52A/C106D mutants (X = A, C, I, F, and W). Additionally, chemical modification with 2,2′-dithiopyridine (2-PDS) produced I49-2py/H52A/C106D, which showed lower R-enantioselectivity than I49-4py/H52A/C106D. Among the mutants, the 4py-modification on the Si-face was the most effective in reversing the enantioselectivity. By tuning the Re-face side, the H54A mutation introduced into the I49C-4py/H52A/C106D increased the R-enantioselectivity (ee = 88%, (R)). X-ray crystallography revealed a coordinated structure with ligation of thiopyridine in Cu-bound I49C-4py/H52A/H54A/C106D.

Synthesis of MeBICAAC Supported Si(III) Radicals and a Silylone via Reduction Route From MeBICAAC-Si(IV) Precursors.

Past one decade has witnessed a tremendous growth in the field of carbene stabilized low-valent silicon compounds unravelling very exciting properties of these molecules. Herein, we have employed a bicyclic (alkyl)(amino)carbene, (MeBICAAC) to explore the low-valent chemistry of silicon. The reduction of bicyclic (alkyl)(amino)carbene-SiCl4 complex, [(MeBICAAC)SiCl4] (1) with KC8 afforded low-valent Si complexes, including Si(III) radical [(MeBICAAC)SiCl3] (2) and a complex with silicon center in a formal zero-valent state, [(MeBICAAC)2Si] (3). Similarly, the reduction of in-situ generated MeBICAAC adduct of Me2SiCl2 with one equivalent of KC8 led to the formation of [(MeBICAAC)SiMe2Cl] (4) complex having an unpaired electron. These complexes have been characterized by IR, UV-Vis., NMR, HRMS, EPR and their solid-state structures were also elucidated by single crystal X-ray crystallography. Further, DFT calculations revealed the lower energy singlet state for complexes 1, 3 and doublet state for complexes 2, 4.

Functionalization of a porous copper(ii) metal-organic framework and its capacity for loading and delivery of ibuprofen.

A porous copper(ii) metal-organic framework (MOF) of 4,4',4''-tri-tert-butyl-2,2':6',2''-terpyridine(N3ttb) and 5-nitroisophthalic acid (npd) formulated as [Cu(npd)(N3ttb)]·(DMF)(H2O) 1 (DMF = dimethylformamide) was synthesized and characterized by elemental analyses, spectroscopic techniques, single crystal X-ray crystallography, and scanning electron microscopy. Single crystal X-ray crystallographic analysis of the copper(ii) metal-organic framework reveals a monoclinic crystal system with space group P21/c. The copper(ii) ion is in a five-coordinate geometry consisting of three meridional nitrogen atoms of 4,4',4''-tri-tert-butyl-2,2':6',2''-terpyridine and two oxygen atoms of 5-nitroisophthalic acid to form a square pyramidal structure. The compound was functionalized with ethylenediamine (ED) to form [Cu(npd)(N3ttb)]-ED 2 that was characterized by FT-IR, PXRD, SEM-EDX and BET and the drug loading capacity was investigated and compared with that of as-synthesized MOFs. The amount of ibuprofen loaded was 916.44 mg g-1 (15.27%) & 1530.20 mg g-1 (25.50%) over 1 and 2, respectively. The results indicate that the functionalized MOFs 2 have a higher loading capacity for ibuprofen than 1 by 613.76 mg g-1 (10.23%), which could be ascribed to the acid-base interactions in the functionalized molecules. The results show that [Cu(npd)(N3ttb)]-ED 2 is a better drug transporter than [Cu(npd)(N3ttb)]·(DMF)(H2O) 1 due to the presence of an amine functional group that interacts with the acid group on the ibuprofen through non-covalent bonds interactions.

Exo-6b2-Methyl-Substituted Pentabenzocorannulene: Synthesis, Structural Analysis, and Properties.

exo-6b2-Methyl-substituted pentabenzocorannulene (exo-PBC-Me) was synthesized by the palladium-catalyzed cyclization of 1,2,3-triaryl-1H-cyclopenta[l]phenanthrene. Its bowl-shaped geometry with an sp3 carbon atom in the backbone and a methyl group located at the convex (exo) face was verified by X-ray crystallography. According to DFT calculations, the observed conformer is energetically more favorable than the endo one by 39.9 kcal/mol. Compared to the nitrogen-doped analogs with intact π-conjugated backbones (see the main text), exo-PBC-Me displayed a deeper bowl depth (avg. 1.93 Å), redshifted and broader absorption (250-620 nm) and emission (from 585 to more than 850 nm) bands and a smaller optical HOMO-LUMO gap (2.01 eV). exo-PBC-Me formed polar crystals where all bowl-in-bowl stacking with close π ⋅ ⋅ ⋅ π contacts is arranged unidirectionally, providing the potential for applications as organic semiconductors and pyroelectric materials. This unusual structural feature, molecular packing, and properties are most likely associated with the assistance of the methyl group and the sp3 carbon atom in the backbone.

A Fragment-Based Competitive 19F LB-NMR Platform For Hotspot-Directed Ligand Profiling.

Ligand binding hotspots are regions of protein surfaces that form particularly favourable interactions with small molecule pharmacophores. Targeting interactions with these hotspots maximises the efficiency of ligand binding. Existing methods are capable of identifying hotspots but often lack assays to quantify ligand binding and direct elaboration at these sites. Herein, we describe a fragment-based competitive 19F Ligand Based NMR (LB-NMR) screening platform that enables routine, quantitative ligand profiling focused at ligand-binding hotspots. As a proof of concept, the method was applied to 4'-phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium abscessus (Mabs). X-ray crystallographic characterisation of the hits from a 960-member fragment screen identified three ligand-binding hotspots across the PPAT active site. From the fragment hits a collection of 19F reporter candidates were designed and synthesised. By rigorous prioritisation and use of optimisation workflows, a single 19F reporter molecule was generated for each hotspot. Profiling the binding of a set of structurally characterised ligands by competitive 19F LB-NMR with this suite of 19F reporters recapitulated the binding affinity and site ID assignments made by ITC and X-ray crystallography. This quantitative mapping of ligand binding events at hotspot level resolution establishes the utility of the fragment-based competitive 19F LB-NMR screening platform for hotspot-directed ligand profiling.

The striking influence of solubility on the nuclearity of cobalt NCN pincer complexes

The synthesis and characterization of two Co(II) complexes stabilized by NCN pincer ligands are described. The paramagnetic Co(II) complex [Co(κ3NCN-NCNCH2-iPr)Br] is obtained via a transmetalation protocol from CoBr2 and NC(C–Br)NCH2-iPr in THF. Surprisingly, the dinuclear complex [Co2(κ3NCN-μ2-NCNCH2-iPr)(μ-Cl)(Cl)2] was synthesized following the same synthetic protocol but using an ultrasonicated CoCl2 suspension instead of CoBr2 in the same solvent. Both complexes are paramagnetic species exhibiting solution magnetic moments of 1.9(1) and 5.8(3) μB, respectively. This corresponds to low-spin and high-spin d7 configurations featuring one and three unpaired electrons at the metal centers. X-ray structures of both complexes are presented.Graphical abstract

Molecular basis for JAK2 inhibition with type II compounds.

176 Background: Upon prolonged exposure, the therapeutic efficiency of current clinical JAK2 inhibitors (type I inhibitors) can be attenuated, leading to drug resistance both in vitro and in vivo through non-genetic mechanisms. In contrast, type II inhibitors stabilize the inactive conformation of the kinase domain preventing the heterodimerization-mediated JAK2 activation. This confers efficacy to type I inhibitor persistent cells, improved efficacy against myeloproliferative neoplasms and other cancers such as B-cell acute lymphoblastic leukemia. Despite the advantages of type II JAK inhibitors, the discovery of type II inhibitor resistance mutation, L884P, in the kinase domain has hampered the further development of JAK2-targeted type II therapeutics. Methods: Here we use combination of protein-inhibitor binding assays, cell-based assays, X-ray crystallography, and computational tools to elucidate the resistance mechanism of JAK2-L884P mutation, to facilitate the development of type II inhibitors with activity against both wild-type and L884P mutated JAK2. Results: We have determined an atomic resolution crystal structure of JAK2-L884P mutant, revealing that mutation induces local changes in the structure but not in the ATP pocket. Furthermore, we have identified several type II compounds inhibiting. Interestingly, they show no major differences in potency in vitro against wild-type of L884P mutated JAK2. Selected compounds profiled in cell lines carrying wild-type or L884P-mutated JAK2, show differences in their cell viability, indicating that a resistance arises via allosteric effects. Conclusions: L884P mutation impacts the inhibitory potency of type II inhibitors via allosteric mechanism.Crystallographic analysis of our type II shortlisted compounds revealed that they differ in their binding modes and suggests that L884P-insensitive drugs can be developed. Preliminary cell-based experiments results confirm these findings. We will now focus on validating these observations with biomolecular simulations to clarify the molecular basis for the inhibitor resistance via L884P mutation. Our studies will facilitate the development of novel type II drugs against JAK2 in myeloproliferative neoplasms.