Benjamin D. Bax

Type IIA topoisomerase inhibition by a new class of antibacterial agents

Despite the success of genomics in identifying new essential bacterial genes, there is a lack of sustainable leads in antibacterial drug discovery to address increasing multidrug resistance. Type IIA topoisomerases cleave and religate DNA to regulate DNA topology and are a major class of antibacterial and anticancer drug targets, yet there is no well developed structural basis for understanding drug action. Here we report the 2.1 Å crystal structure of a potent, new class, broad-spectrum antibacterial agent in complex with Staphylococcus aureus DNA gyrase and DNA, showing a new mode of inhibition that circumvents fluoroquinolone resistance in this clinically important drug target. The inhibitor ‘bridges’ the DNA and a transient non-catalytic pocket on the two-fold axis at the GyrA dimer interface, and is close to the active sites and fluoroquinolone binding sites. In the inhibitor complex the active site seems poised to cleave the DNA, with a single metal ion observed between the TOPRIM (topoisomerase/primase) domain and the scissile phosphate. This work provides new insights into the mechanism of topoisomerase action and a platform for structure-based drug design of a new class of antibacterial agents against a clinically proven, but conformationally flexible, enzyme class.

The X-ray structure of human serum ceruloplasmin at 3.1 Å: nature of the copper centres

Abstract The X-ray structure of human serum ceruloplasmin has been solved at a resolution of 3.1 Å. The structure reveals that the molecule is comprised of six plastocyanin-type domains arranged in a triangular array. There are six copper atoms; three form a trinuclear cluster sited at the interface of domains 1 and 6, and there are three mononuclear sites in domains 2, 4 and 6. Each of the mononuclear coppers is coordinated to a cysteine and two histidine residues, and those in domains 4 and 6 also coordinate to a methionine residue; in domain 2, the methionine is replaced by a leucine residue which may form van der Waals type contacts with the copper. The trinuclear centre and the mononuclear copper in domain 6 form a cluster essentially the same as that found in ascorbate oxidase, strongly suggesting an oxidase role for ceruloplasmin in the plasma.

Structural basis of quinolone inhibition of type IIA topoisomerases and target-mediated resistance.

Quinolone antibacterials have been used to treat bacterial infections for over 40 years. A crystal structure of moxifloxacin in complex with Acinetobacter baumannii topoisomerase IV now shows the wedge-shaped quinolone stacking between base pairs at the DNA cleavage site and binding conserved residues in the DNA cleavage domain through chelation of a noncatalytic magnesium ion. This provides a molecular basis for the quinolone inhibition mechanism, resistance mutations and invariant quinolone antibacterial structural features.

Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation

PAD4 has been strongly implicated in the pathogenesis of autoimmune, cardiovascular and oncological diseases, through clinical genetics and gene disruption in mice. Novel, selective PAD4 inhibitors binding to a calcium-deficient form of the PAD4 enzyme have, for the first time, validated the critical enzymatic role of human and mouse PAD4 in both histone citrullination and neutrophil extracellular trap formation. The therapeutic potential of PAD4 inhibitors can now be explored.

Phosducin induces a structural change in transducin βγ

Background: Phosducin binds tightly to the βγ subunits (Gtβγ) of the heterotrimeric G protein transducin, preventing Gtβγ reassociation with Gtα–GDP and thereby inhibiting the G-protein cycle. Phosducin-like proteins appear to be widely distributed and may play important roles in regulating many heterotrimeric G-protein signaling pathways. Results: The 2.8 a crystal structure of a complex of bovine retinal phosducin with Gtβγ shows how the two domains of phosducin cover one side and the top of the seven-bladed β propeller of Gtβγ. The binding of phosducin induces a distinct structural change in the β propeller of Gtβγ, such that a small cavity opens up between blades 6 and 7. Electron density in this cavity has been assigned to the farnesyl moiety of the γ subunit. Conclusions:βγ subunits of heterotrimeric G proteins can exist in two distinct conformations. In the R (relaxed) state, corresponding to the structure of the free βγ or the structure of βγ in the αβγ heterotrimer, the hydrophobic farnesyl moiety of the γ subunit is exposed, thereby mediating membrane association. In the T (tense) state, as observed in the phosducin–Gtβγ structure, the farnesyl moiety of the γ subunit is effectively buried in the cavity formed between blades 6 and 7 of the β subunit. Binding of phosducin to Gtβγ induces the formation of this cavity, resulting in a switch from the R to the T conformation. This sequesters βγ from the membrane to the cytosol and turns off the signal-transduction cascade. Regulation of this membrane association/dissociation switch of Gtβγ by phosducin may be a general mechanism for attenuation of G protein coupled signal transduction cascades.

GSK-3 inhibition by adenoviral FRAT1 overexpression is neuroprotective and induces Tau dephosphorylation and β-catenin stabilisation without elevation of glycogen synthase activity

Glycogen synthase kinase 3 (GSK‐3) has previously been shown to play an important role in the regulation of apoptosis. However, the nature of GSK‐3 effector pathways that are relevant to neuroprotection remains poorly defined. Here, we have compared neuroprotection resulting from modulation of GSK‐3 activity in PC12 cells using either selective small molecule ATP‐competitive GSK‐3 inhibitors (SB‐216763 and SB‐415286), or adenovirus overexpressing requently earranged in dvanced ‐cell lymphomas 1 (FRAT1), a protein proposed as a negative regulator of GSK‐3 activity towards Axin and β‐catenin. Our data demonstrate that cellular overexpression of FRAT1 is sufficient to confer neuroprotection and correlates with inhibition of GSK‐3 activity towards Tau and β‐catenin, but not modulation of glycogen synthase (GS) activity. By comparison, treatment with SB‐216763 and SB‐415286 proved more potent in terms of neuroprotection, and correlated with inhibition of GSK‐3 activity towards GS in addition to Tau and β‐catenin.

Integration of Lead Optimization with Crystallography for a Membrane-Bound Ion Channel Target: Discovery of a New Class of Ampa Receptor Positive Allosteric Modulators.

A novel series of AMPAR positive modulators is described that were identified by high throughput screening. The molecules of the series have been optimized from a high quality starting point hit to afford excellent developability, tolerability, and efficacy profiles, leading to identification of a clinical candidate. Unusually for an ion channel target, this optimization was integrated with regular generation of ligand-bound crystal structures and uncovered a novel chemotype with a unique and highly conserved mode of interaction via a trifluoromethyl group.

Challenges for and current status of research into positive modulators of AMPA receptors

AMPA receptors consist of a family of hetero‐oligomeric (tetrameric) receptors arising from four genes, each of which encodes a distinct receptor subunit (GluA1‐4). Recombinant homo‐tetrameric AMPA receptors, comprising four identical subunits, are functionally active and have been used in in vitro assays. However, the many different subunit permutations make possible the functional and anatomical diversity of AMPA receptors throughout the CNS. Furthermore, AMPA receptor subunit stoichiometry influences the biophysical and functional properties of the receptor. A number of chemically diverse positive modulators of AMPA receptor have been identified which potentiate AMPA receptor‐mediated activity in vitro as well as improving cognitive performance in rodents and non‐human primates with several being taken further in the clinic. This review article summarizes the current status in the research on positive allosteric modulation of AMPA receptors and outlines the challenges involved in identifying a chemically distinct series of AMPA receptor positive modulators, addressing the challenges created by the heterogeneity of the AMPA receptor populations and the development of structure‐activity relationships driven by homomeric, recombinant systems on high‐throughput platforms. We also review the role of X‐ray crystallography in the selection and prioritization of targets for lead optimization for AMPA receptor positive modulators.

X-ray diffraction and structure of crystallins

The 3-dimensional organisation of crystallin polypeptides into globular proteins and their interactions into higher order structures are important factors governing optical functions related to refraction, accommodation and transparency. Single crystal X-ray diffraction studies have revealed the tertiary and quaternary structural organisation of β-, γ- and δ-crystallins. Regions of the lens with high refractive index contain high levels of monomeric y-crystallins while the accommodating, hydrated avian lens has largely replaced γ-crystallins with δ-crystallin. The βγ-crystallins form a superfamily of proteins of high symmetry and great diversity in which the basic building block is a 10 kD pseudo-symmetrical 2-Greek key domain. A γ-crystallin comprises two of these β-sheet domains, joined by a linker, and a short C-terminal extension. In β-crystallins the linker has an extended conformation resulting in dimer formation by a mechanism known as domain swapping. Crystallographic analysis of engineered single domains of γ-crystallins, analogous to the ancestral domain, has indicated the importance of the short C-terminal extension in directing domain pairing. γ-crystallins have numerous cysteine residues, some are conserved in the core of the protein molecule and some are variable on the protein surface. The structure of γB-crystallin has been determined at very high resolution using cryo-crystallography allowing the visualisation of the complete protein-protein and protein-water structure at the surface. β-crystallins are seen as tetramers in the crystal structures but their long sequence extensions are harder to visualise in the electron density of the hydrated crystal lattice structure. In one tight packing lattice of βB2 crystallin the N-terminal extension is seen to mediate protein-protein interactions between tetramers to form a 42 helix. The X-ray structure of the taxon-restricted avian δ-crystallin shows that the 50 kD subunit contains 22 helices that form three α-helical domains which dimerise followed by a dimer-dimer interaction to form a tetramer with a 20-helix bundle at the centre. Analysis of the spatial disposition of the sequence conserved regions showed the location of the active site cleft of the superfamily of enzymes related to δ-crystallin and argininosuccinate lyase. A different crystal structure of δ-crystallin solved under more physiological conditions revealed that tetramers assembled as higher order supramolecular helices and that the N-terminal extension may be involved. Combining the observations of higher order helical structures in both the oligomeric β-crystallin and δ-crystallin crystal lattices, we have proposed a highly speculative model for crystallin assembly in the lens fibre cells.

Close packing of an oligomeric eye lens β-crystallin induces loss of symmetry and ordering of sequence extensions

beta-Crystallins are oligomeric eye lens proteins that are related to monomeric gamma-crystallins. The main sequence difference between the two families is the presence of sequence extensions in the beta-crystallins. A major question concerns the role that these extensions play in mediating interactions at the high protein concentrations found in the lens. The predominant beta-crystallin polypeptide, beta B2, can be crystallized in two different space groups, I222 and C222. The I222 crystal structure revealed that the protein packed as a tetramer with perfect 222 symmetry but that the extensions were disordered. The X-ray structure of the C222 lattice of beta B2 has now been refined at 3.3 A, the structure analysed and compared with the I222 lattice. The protein is also a tetramer with 222 symmetry in the C222 lattice but differs in that parts of the N-terminal extensions have been visualized. In the asymmetric unit of the C222 lattice there are four subunits, each comprising a single polypeptide chain, in which certain flexible loops in the N-terminal domains and the N-terminal extensions have various conformations. The tetramers in the C222 lattice are more tightly packed than in the I222 form. Analysis of the tetramer contacts shows that the sites of interaction break the 222 symmetry of the tetramers. The N-terminal extensions play a major role in directing interactions between tetramers. One of the N-terminal extensions interacts with a hydrophobic patch on the N-terminal domain of another tetramer. These crystallographic observations obtained over a physiological concentration range indicate how, in beta-crystallin oligomers, the N-terminal extensions of beta B2 can switch from interacting with water to interacting with protein depending on their relative concentrations. This could be useful in maintaining a gradient of refractive index.