A 2.8 Å Structure of Zoliflodacin in a DNA Cleavage Complex with Staphylococcus aureus DNA Gyrase.

Since 2000, some thirteen quinolones and fluoroquinolones have been developed and have come to market. The quinolones, one of the most successful classes of antibacterial drugs, stabilize DNA cleavage complexes with DNA gyrase and topoisomerase IV (topo IV), the two bacterial type IIA topoisomerases. The dual targeting of gyrase and topo IV helps decrease the likelihood of resistance developing. Here, we report on a 2.8 Å X-ray crystal structure, which shows that zoliflodacin, a spiropyrimidinetrione antibiotic, binds in the same DNA cleavage site(s) as quinolones, sterically blocking DNA religation. The structure shows that zoliflodacin interacts with highly conserved residues on GyrB (and does not use the quinolone water-metal ion bridge to GyrA), suggesting it may be more difficult for bacteria to develop target mediated resistance. We show that zoliflodacin has an MIC of 4 µg/mL against Acinetobacter baumannii (A. baumannii), an improvement of four-fold over its progenitor QPT-1. The current phase III clinical trial of zoliflodacin for gonorrhea is due to be read out in 2023. Zoliflodacin, together with the unrelated novel bacterial topoisomerase inhibitor gepotidacin, is likely to become the first entirely novel chemical entities approved against Gram-negative bacteria in the 21st century. Zoliflodacin may also become the progenitor of a new safer class of antibacterial drugs against other problematic Gram-negative bacteria.

Direct measurement of X-ray-induced heating of microcrystals.

Temperature control is a key aspect of macromolecular crystallography, with the technique of cryocooling routinely being used to mitigate X-ray-induced damage. Beam-induced heating could cause the temperature of crystals to rise above the glass transition temperature, greatly increasing the rate of damage. X-ray-induced heating of ruby crystals of 20-40 µm in size has been quantified non-invasively by monitoring the emission wavelengths of X-ray-induced fluorescence during exposure to the X-ray beam. For the beam sizes and dose rates typically used in macromolecular crystallography, the temperature rises are of the order of 20 K. The temperature changes observed are compared with models in the literature and can be used as a validation tool for future models.

Exploiting Microbeams for Membrane Protein Structure Determination.

A reproducible, and sample independent means of predictably obtaining large, well-ordered crystals has proven elusive in macromolecular crystallography. In the structure determination pipeline, crystallisation often proves to be a rate-limiting step, and the process of obtaining even small or badly ordered crystals can prove time-consuming and laborious. This is particularly true in the field of membrane protein crystallography and this is reflected in the limited number of unique membrane protein structures deposited in the protein data bank (less than 650 by June 2016 - http://blanco.biomol.uci.edu/mpstruc ). Over recent years the requirement for, and time and cost associated with obtaining, large crystals has been partially alleviated through the development of beamline instrumentation allowing data collection, and structure solution, from ever-smaller crystals. Advances in several areas have led to a step change in what might be considered achievable during a synchrotron trip over the last decade. This chapter will briefly review the current status of the field, the tools available to ease data collection and processing, and give some examples of exploitation of these for membrane protein microfocus macromolecular crystallography.

In vacuo X-ray data collection from graphene-wrapped protein crystals.

The measurement of diffraction data from macromolecular crystal samples held in vacuo holds the promise of a very low X-ray background and zero absorption of incident and scattered beams, leading to better data and the potential for accessing very long X-ray wavelengths (>3 Å) for native sulfur phasing. Maintaining the hydration of protein crystals under vacuum is achieved by the use of liquid jets, as with serial data collection at free-electron lasers, or is side-stepped by cryocooling the samples, as implemented at new synchrotron beamlines. Graphene has been shown to protect crystals from dehydration by creating an extremely thin layer that is impermeable to any exchanges with the environment. Furthermore, owing to its hydrophobicity, most of the aqueous solution surrounding the crystal is excluded during sample preparation, thus eliminating most of the background caused by liquid. Here, it is shown that high-quality data can be recorded at room temperature from graphene-wrapped protein crystals in a rough vacuum. Furthermore, it was observed that graphene protects crystals exposed to different relative humidities and a chemically harsh environment.

Solid-state interconversions: unique 100 % reversible transformations between the ground and metastable states in single-crystals of a series of nickel(II) nitro complexes.

The solid-state, low-temperature linkage isomerism in a series of five square planar group 10 phosphino nitro complexes have been investigated by a combination of photocrystallographic experiments, Raman spectroscopy and computer modelling. The factors influencing the reversible solid-state interconversion between the nitro and nitrito structural isomers have also been investigated, providing insight into the dynamics of this process. The cis-[Ni(dcpe)(NO2)2] (1) and cis-[Ni(dppe)(NO2)2] (2) complexes show reversible 100 % interconversion between the η(1)-NO2 nitro isomer and the η(1)-ONO nitrito form when single-crystals are irradiated with 400 nm light at 100 K. Variable temperature photocrystallographic studies for these complexes established that the metastable nitrito isomer reverted to the ground-state nitro isomer at temperatures above 180 K. By comparison, the related trans complex [Ni(PCy3)2(NO2)2] (3) showed 82 % conversion under the same experimental conditions at 100 K. The level of conversion to the metastable nitrito isomers is further reduced when the nickel centre is replaced by palladium or platinum. Prolonged irradiation of the trans-[Pd(PCy3)2(NO2)2] (4) and trans-[Pt(PCy3)2(NO2)2] (5) with 400 nm light gives reversible conversions of 44 and 27 %, respectively, consistent with the slower kinetics associated with the heavier members of group 10. The mechanism of the interconversion has been investigated by theoretical calculations based on the model complex [Ni(dmpe)Cl(NO2)].

Crystals in the community and the classroom.

The growing pressure on school curricula has meant crystals and the science of crystallography have been cut from or made optional for many educational programs. This omission is a serious disservice to the history and understanding of modern sciences, given that crystallography underpins many of the greatest advancements in science over the past century, is a critical component of many modern research papers and patents, and has 29 Nobel Prizes awarded in the field. This contribution describes a simple activity to target classroom and public engagement with crystallography, using marshmallows or equivalent sweets/candy to represent atoms and cocktail sticks to represent bonds, together with examples of how crystals are studied and how they are useful. Though it has a simple basis, this activity can be extended in numerous ways to reflect the aims of the demonstrator, and a few of these are described.

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging.

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

Atomic structure of a nudivirus occlusion body protein determined from a 70-year-old crystal sample.

Infectious protein crystals are an essential part of the viral lifecycle for double-stranded DNA Baculoviridae and double-stranded RNA cypoviruses. These viral protein crystals, termed occlusion bodies or polyhedra, are dense protein assemblies that form a crystalline array, encasing newly formed virions. Here, using X-ray crystallography we determine the structure of a polyhedrin from Nudiviridae. This double-stranded DNA virus family is a sister-group to the baculoviruses, whose members were thought to lack occlusion bodies. The 70-year-old sample contains a well-ordered lattice formed by a predominantly α-helical building block that assembles into a dense, highly interconnected protein crystal. The lattice is maintained by extensive hydrophobic and electrostatic interactions, disulfide bonds, and domain switching. The resulting lattice is resistant to most environmental stresses. Comparison of this structure to baculovirus or cypovirus polyhedra shows a distinct protein structure, crystal space group, and unit cell dimensions, however, all polyhedra utilise common principles of occlusion body assembly.

Alkyne Derivatives of SARS-CoV-2 Main Protease Inhibitors Including Nirmatrelvir Inhibit by Reacting Covalently with the Nucleophilic Cysteine.

Nirmatrelvir (PF-07321332) is a nitrile-bearing small-molecule inhibitor that, in combination with ritonavir, is used to treat infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Nirmatrelvir interrupts the viral life cycle by inhibiting the SARS-CoV-2 main protease (Mpro), which is essential for processing viral polyproteins into functional nonstructural proteins. We report studies which reveal that derivatives of nirmatrelvir and other Mpro inhibitors with a nonactivated terminal alkyne group positioned similarly to the electrophilic nitrile of nirmatrelvir can efficiently inhibit isolated Mpro and SARS-CoV-2 replication in cells. Mass spectrometric and crystallographic evidence shows that the alkyne derivatives inhibit Mpro by apparent irreversible covalent reactions with the active site cysteine (Cys145), while the analogous nitriles react reversibly. The results highlight the potential for irreversible covalent inhibition of Mpro and other nucleophilic cysteine proteases by alkynes, which, in contrast to nitriles, can be functionalized at their terminal position to optimize inhibition and selectivity, as well as pharmacodynamic and pharmacokinetic properties.

A Sample Preparation Pipeline for Microcrystals at the VMXm Beamline.

The mounting of microcrystals (<10 µm) for single crystal cryo-crystallography presents a non-trivial challenge. Improvements in data quality have been seen for microcrystals with the development of beamline optics, beam stability and variable beam size focusing from submicron to microns, such as at the VMXm beamline at Diamond Light Source1. Further improvements in data quality will be gained through improvements in sample environment and sample preparation. Microcrystals inherently generate weaker diffraction, therefore improving the signal-to-noise is key to collecting quality X-ray diffraction data and will predominantly come from reductions in background noise. Major sources of X-ray background noise in a diffraction experiment are from their interaction with the air path before and after the sample, excess crystallization solution surrounding the sample, the presence of crystalline ice and scatter from any other beamline instrumentation or X-ray windows. The VMXm beamline comprises instrumentation and a sample preparation protocol to reduce all these sources of noise. Firstly, an in-vacuum sample environment at VMXm removes the air path between X-ray source and sample. Next, sample preparation protocols for macromolecular crystallography at VMXm utilize a number of processes and tools adapted from cryoTEM. These include copper grids with holey carbon support films, automated blotting and plunge cooling robotics making use of liquid ethane. These tools enable the preparation of hundreds of microcrystals on a single cryoTEM grid with minimal surrounding liquid on a low-noise support. They also minimize the formation of crystalline ice from any remaining liquid surrounding the crystals. We present the process for preparing and assessing the quality of soluble protein microcrystals using visible light and scanning electron microscopy before mounting the samples on the VMXm beamline for X-ray diffraction experiments. We will also provide examples of good quality samples as well as those which require further optimization and strategies to do so.

Scanning electron microscopy as a method for sample visualization in protein X-ray crystallography.

Developing methods to determine high-resolution structures from micrometre- or even submicrometre-sized protein crystals has become increasingly important in recent years. This applies to both large protein complexes and membrane proteins, where protein production and the subsequent growth of large homogeneous crystals is often challenging, and to samples which yield only micro- or nanocrystals such as amyloid or viral polyhedrin proteins. The versatile macromolecular crystallography microfocus (VMXm) beamline at Diamond Light Source specializes in X-ray diffraction measurements from micro- and nanocrystals. Because of the possibility of measuring data from crystalline samples that approach the resolution limit of visible-light microscopy, the beamline design includes a scanning electron microscope (SEM) to visualize, locate and accurately centre crystals for X-ray diffraction experiments. To ensure that scanning electron microscopy is an appropriate method for sample visualization, tests were carried out to assess the effect of SEM radiation on diffraction quality. Cytoplasmic polyhedrosis virus polyhedrin protein crystals cryocooled on electron-microscopy grids were exposed to SEM radiation before X-ray diffraction data were collected. After processing the data with DIALS, no statistically significant difference in data quality was found between datasets collected from crystals exposed and not exposed to SEM radiation. This study supports the use of an SEM as a tool for the visualization of protein crystals and as an integrated visualization tool on the VMXm beamline.

Dipyridyl ß-diketonate complexes and their use as metalloligands in the formation of mixed-metal coordination networks.

The iron(III) and aluminium(III) complexes of 1,3-di(4-pyridyl)propane-1,3-dionato (dppd) and 1,3-di(3-pyridyl)propane-1,3-dionato (dmppd), [Fe(dppd)(3)] 1, [Fe(dmppd)(3)] 2, [Al(dppd)(3)] 3 and [Al(dmppd)(3)] 4 have been prepared. These complexes adopt molecular structures in which the metal centres contain distorted octahedral geometries. In contrast, the copper(II) and zinc(II) complexes [Cu(dppd)(2)] 5 and [Zn(dmppd)(2)] 6 both form polymeric structures in which coordination of the pyridyl groups into the axial positions of neighbouring metal centres links discrete square-planar complexes into two-dimensional networks. The europium complex [Eu(dmppd)(2)(H(2)O)(4)]Cl·2EtOH·0.5H(2)O 7 forms a structure containing discrete cations that are linked into sheets through hydrogen bonds, whereas the lanthanum complex [La(dmppd)(3)(H(2)O)]·2H(2)O 8 adopts a one-dimensional network structure, connected into sheets by hydrogen bonds. The iron complexes 1 and 2 act as metalloligands in reactions with silver(I) salts, with the nature of the product depending on the counter-ions present. Thus, the reaction between 1 and AgBF(4) gave [AgFe(dppd)(3)]BF(4)·DMSO 9, in which the silver centres link the metalloligands into discrete nanotubes, whereas reactions with AgPF(6) and AgSbF(6) gave [AgFe(dppd)(3)]PF(6)·3.28DMSO 10 and [AgFe(dppd)(3)]SbF(6)·1.25DMSO 11, in which the metalloligands are linked into sheets. In all three cases, only four of the six pyridyl groups present on the metalloligands are coordinated. The reaction between 2 and AgNO(3) gave [Ag(2)Fe(dmppd)(3)(ONO(2))]NO(3)·MeCN·CH(2)Cl(2)12. Compound 12 adopts a layer structure in which all pyridyl groups are coordinated to silver centres and, in addition, a nitrate ion bridges between two silver centres. A similar structure is adopted by [Ag(2)Fe(dmppd)(3)(O(2)CCF(3))]CF(3)CO(2)·2MeCN·0.25CH(2)Cl(2)13, with a bridging trifluoroacetate ion playing the same role as the nitrate ion in 12.

Photoactivated linkage isomerism in single crystals of nickel, palladium and platinum di-nitro complexes--a photocrystallographic investigation.

Low temperature, single crystal photocrystallographic studies have been carried out on four square planar Group 10 complexes [Ni(PEt(3))(2)(NO(2))(2)] 1, [Pd(PPh(3))(2)(NO(2))(2)] 2, [Pd(AsPh(3))(2)(NO(2))(2)] 3 and [Pt(PPh(3))(2)(NO(2))(2)] 4, in which the two nitro groups adopt the trans configuration. Irradiation with UV light, at 100 K, of single crystals of complexes 1-3 photoisomerise from the η(1)-NO(2) nitro form to the η(1)-ONO nitrito form occurred. Complex 1 underwent 25% conversion to the nitrito form before crystal decomposition occurred. 2 and 3 underwent 46% and 39% conversion, respectively, to the nitrito form when a photostationary state was reached. While under the same experimental conditions 4 showed no isomerisation. The photocrystallographic results can be correlated with the results of DFT calculations and with the observed trends in the solution UV/visible absorption spectroscopy obtained for these complexes. The results suggest that while steric factors in the isomerization processes are important there may also be a kinetic effect relating to the lability of the metal involved.