Search

The development of ligands for biological targets is critically dependent on the identification of sites on proteins that bind molecules with high affinity. A set of compounds, called FragLites, can identify such sites, along with the interactions required to gain affinity, by X-ray crystallography. We demonstrate the utility of FragLites in mapping the binding sites of bromodomain proteins BRD4 and ATAD2 and demonstrate that FragLite mapping is comparable to a full fragment screen in identifying ligand binding sites and key interactions. We extend the FragLite set with analogous compounds derived from amino acids (termed PepLites) that mimic the interactions of peptides. The output of the FragLite maps is shown to enable the development of ligands with leadlike potency. This work establishes the use of FragLite and PepLite screening at an early stage in ligand discovery allowing the rapid assessment of tractability of protein targets and informing downstream hit-finding.

Identifying ligand binding sites on proteins is a critical step in target-based drug discovery. Current approaches to this require resource-intensive screening of large libraries of lead-like or fragment molecules. Here, we describe an efficient and effective experimental approach to mapping interaction sites using a set of halogenated compounds expressing paired hydrogen-bonding motifs, termed FragLites. The FragLites identify productive drug-like interactions, which are identified sensitively and unambiguously by X-ray crystallography, exploiting the anomalous scattering of the halogen substituent. This mapping of protein interaction surfaces provides an assessment of druggability and can identify efficient start points for the de novo design of hit molecules incorporating the interacting motifs. The approach is illustrated by mapping cyclin-dependent kinase 2, which successfully identifies orthosteric and allosteric sites. The hits were rapidly elaborated to develop efficient lead-like molecules. Hence, the approach provides a new method of identifying ligand sites, assessing tractability and discovering new leads.

Peri-implantitis remains the major impediment to the long-term use of dental implants. With increasing concern over the growth in antibiotic resistance, there is considerable interest in the preparation of antimicrobial dental implant coatings that also induce osseointegration. One such potential coating material is fluorapatite (FA). The aim of this study was to relate the antibacterial effectiveness of FA coatings against pathogens implicated in peri-implantitis to the physicochemical properties of the coating. Ordered and disordered FA coatings were produced on the under and upper surfaces of stainless steel (SS) discs, respectively, using a hydrothermal method. Surface charge, surface roughness, wettability, and fluoride release were measured for each coating. Surface chemistry was assessed using X-ray photoelectron spectroscopy and FA crystallinity using X-ray diffraction. Antibacterial activity against periodontopathogens was assessed in vitro using viable counts, confocal microscopy, and scanning electron microscopy (SEM). SEM showed that the hydrothermal method produced FA coatings that were predominately aligned perpendicular to the SS substrate or disordered FA coatings consisting of randomly aligned rodlike crystals. Both FA coatings significantly reduced the growth of all examined bacterial strains in comparison to the control. The FA coatings, especially the disordered ones, presented significantly lower charge, greater roughness, and higher area when compared to the control, enhancing bacteria-material interactions and therefore bacterial deactivation by fluoride ions. The ordered FA layer reduced not only bacterial viability but adhesion too. The ordered FA crystals produced as a potential novel implant coating showed significant antibacterial activity against bacteria implicated in peri-implantitis, which could be explained by a detailed understanding of their physicochemical properties.

Biomimetic hydrogels based on natural polymers are a promising class of biomaterial, mimicking the natural extra-cellular matrix of biological tissues and providing cues for cell attachment, proliferation, and differentiation. With a view to providing an upstream method to guide subsequent experimental design, the aim of this study was to introduce a mathematical model that described the rheological properties of a hydrogel system based on covalently cross-linked collagen triple helices. In light of their organization, such gels exhibit limited collagen bundling that cannot be described by existing fibril network models. The model presented here treats collagen triple helices as discrete semiflexible polymers, permits full access to metrics for network microstructure, and should provide a comprehensive understanding of the parameter space associated with the development of such multifunctional materials. Triple helical hydrogel networks were experimentally obtained via the reaction of type I collagen with both aromatic and aliphatic diacids. The complex modulus G * was found from rheological testing in linear shear and quantitatively compared to model predictions. In silico data from the computational model successfully described the experimental trends in hydrogel storage modulus with either (i) the concentration of collagen triple helices during the cross-linking reaction or (ii) the type of cross-linking segment introduced in resulting hydrogel networks. This approach may pave the way to a step change in the rational design of biomimetic triple helical collagen systems with controlled multifunctionality.

The pharmaceutical industry is in a period of intense change. While this has many drivers, attrition through the development process continues to be an important pressure. The emerging definitions of "compound quality" that are based on retrospective analyses of developmental attrition have highlighted a new direction for medicinal chemistry and the paradigm of "quality at the point of design". The time has come for retrospective analyses to catalyze prospective action. Quality at the point of design places pressure on the quality of our predictive models. Empirical QSAR models when built with care provide true predictive control, but their accuracy and precision can be improved. Here we describe AstraZeneca's experience of automation in QSAR model building and validation, and how an informatics system can provide a step-change in predictive power to project design teams, if they choose to use it.

Bioisosteres have been defined as structurally different molecules or substructures that can form comparable intermolecular interactions, and therefore, fragments that bind to similar protein structures exhibit a degree of bioisosterism. We present KRIPO (Key Representation of Interaction in POckets): a new method for quantifying the similarities of binding site subpockets based on pharmacophore fingerprints. The binding site fingerprints have been optimized to improve their performance for both intra- and interprotein family comparisons. A range of attributes of the fingerprints was considered in the optimization, including the placement of pharmacophore features, whether or not the fingerprints are fuzzified, and the resolution and complexity of the pharmacophore fingerprints (2-, 3-, and 4-point fingerprints). Fuzzy 3-point pharmacophore fingerprints were found to represent the optimal balance between computational resource requirements and the identification of potential replacements. The complete PDB was converted into a database comprising almost 300,000 optimized fingerprints of local binding sites together with their associated ligand fragments. The value of the approach is demonstrated by application to two crystal structures from the Protein Data Bank: (1) a MAP kinase P38 structure in complex with a pyridinylimidazole inhibitor (1A9U) and (2) a complex of thrombin with melagatran (1K22). Potentially valuable bioisosteric replacements for all subpockets of the two studied protein are identified.

The reaction of NC-CN with a 1:1 mixture of S(4)(MF(6))(2) and S(8)(MF(6))(2) (M = As, Sb) (stoichiometrically equivalent to four "S(3)MF(6)" units) results in the quantitative formation of S(3)NCCNS(3)(MF(6))(2) [7(MF(6))(2)], which is the thermodynamic sink in this reaction. The Sb(2)F(11)(-) salt 7(Sb(2)F(11))(2) is prepared by the addition of an excess of SbF(5) to 7(AsF(6))(2). Crystal structure determinations for all three salts show that 7(2+) can be viewed as two R-CNS(3)(+) radical cations joined together by a C-C single bond. The two rings are coplanar and in a trans orientation due to electrostatic N(delta-)...S(delta+) interactions. The classically bonded alternative (quinoidal structure), in which the octet rule is obeyed, is not observed and is much higher in energy based on calculated estimates and a simple comparison of pi bond energies. Calculated molecular orbitals (MOs) support this, showing that the MO corresponding to the quinoidal structure lies higher in energy than the nearly degenerate singly occupied MOs of 7(2+). The vibrational spectra of 7(2+) in all salts were assigned based on a normal-coordinate analysis and theoretical vibrational frequencies calculated at the PBE0/6-31G* level. In the solid state, 7(2+) is a planar disjoint diradical with essentially degenerate open-shell singlet and triplet states. The disjoint nature of the diradical cation 7(2+) is established by magnetic susceptibility studies of the Sb(2)F(11)(-) salt doped in an isomorphous diamagnetic host material (CNSNS)(2)(Sb(2)F(11))(2) [10(Sb(2)F(11))(2)]. Intramolecular spin coupling is extremely weak corresponding to a singlet-triplet gap (DeltaE(ST) = 2J) of <+/-2 cm(-1). CASPT2[12,12]/6-311G* calculations support a triplet ground state with a small singlet-triplet gap. The single-crystal electron paramagnetic resonance (EPR) of 7(Sb(2)F(11))(2) doped in 10(Sb(2)F(11))(2) is in agreement with the triplet state arising from the weak coupling between the unpaired electrons residing in p(pi) orbitals in each of the rings. Variable-temperature susceptibility data for bulk samples of 7(A)(2) (A = SbF(6)(-), AsF(6)(-), Sb(2)F(11)(-)) are analyzed by employing both 1D chain and 2D sheet magnetic models. These studies reveal significant intermolecular exchange approximating that of a 1D chain for the SbF(6)(-) salt with |J| = 32 cm(-1). The exchange coupling is on the same order of magnitude as that for the AsF(6)(-) salt, although in this case it is likely that there are complex exchange pathways where no particular one is dominant. Intermolecular exchange in the Sb(2)F(11)(-) salt is an order of magnitude weaker. In solution, the EPR spectrum of 7(2+) shows a broad triplet resonance as well as a sharp resonance that is tentatively attributed to a rotomer of the 7(2+)/anion pair, which is likely the origin of the green species given on dissolution of the red 7(2+) salts in SO(2)/AsF(3)/MF(5). We account for the many similarities between O(2) and 7(2+), which are the only simple nonsterically hindered nonmetal diradicals to retain their paramagnetism in the solid state. 7(2+) is also the first isolable, essentially sulfur-based diradical as evidenced by calculated spin densities.

Binary kernel discrimination (BKD) uses a training set of compounds, for which structural and qualitative activity data are available, to produce a model that can then be applied to the structures of other compounds in order to predict their likely activity. Experiments with the MDL Drug Data Report database show that the optimal value of the smoothing parameter, and hence the predictive power of BKD, is crucially dependent on the number of false positives in the training set. It is also shown that the best results for BKD are achieved using one particular optimization method for the determination of the smoothing parameter that lies at the heart of the method and using the Jaccard/Tanimoto coefficient in the kernel function that is used to compute the similarity between a test set molecule and the members of the training set.

Cesium 5-cyano-1,2,3,4-tetrazolate, Cs[NCCNNNN] (Cs1), was prepared in 100% yield by a 3 + 2 cycloaddition reaction of CsN3 and (CN)2 in SO2. Cs1 forms monoclinic crystals (a = 8.297(2) A, b = 11.040(3) A, c = 6.983(2) A, beta = 120.31(2) degrees, space group C2/c, Z = 4, R1 = 0.048, wR2 = 0.120 for 1217 independent reflections). Cs1 is best described as a three-dimensional array of cations and anions connected by weak Cs(+)-N delta- contacts. The cations and anions each form a diamond-type lattice (tetrahedral arrangement of ions) with the counterions lying in hexagonal channels running parallel to the c-axis. The anions in the channels form stacks with the CN groups pointing in opposite directions in adjacent layers. The calculated (RB3PW91/6-311 + G*) geometry of 1 is in agreement with the X-ray crystal structure, and the calculated vibrational spectrum is in good agreement with the observed FT-IR and FT-Raman spectra. The lattice enthalpies and heats of formation of M1 (M = Cs, K) as well as the enthalpy of formation from MN3(s) and (CN)2(g) were estimated. The 13C and 14N NMR spectra of Cs1 are also reported. The ionization potential (450.7 kJ mol) and electron affinity (427.4 kJ/mol) of 1 were calculated. Attempts to oxidize 1 with AsF5 led to the formation of Cs1.xAsF5 (x approximately 2). The 7 pi dianion [NCCNNNN].2- is calculated to be a stable entity in the gas phase, but Cs(2)1 is estimated to be unstable with respect to dissociation to 2 CsCN and 3/2 N2 (delta Hdiss = -132.4 kJ/mol). The preparation of the potassium salt of 1 and the corresponding thermodynamic quantities are reported.