Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery

Fragment-based drug design (FBDD) starts with finding fragment-sized compounds that are highly ligand efficient and can serve as a core moiety for developing high-affinity leads. Although the core-bound structure of a protein facilitates the construction of leads, effective design is far from straightforward. We show that protein mapping, a computational method developed to find binding hot spots and implemented as the FTMap server, provides information that complements the fragment screening results and can drive the evolution of core fragments into larger leads with a minimal loss or, in some cases, even a gain in ligand efficiency. The method places small molecular probes, the size of organic solvents, on a dense grid around the protein and identifies the hot spots as consensus clusters formed by clusters of several probes. The hot spots are ranked based on the number of probe clusters, which predicts the binding propensity of the subsites and hence their importance for drug design. Accordingly, with a single exception the main hot spot identified by FTMap binds the core compound found by fragment screening. The most useful information is provided by the neighboring secondary hot spots, indicating the regions where the core can be extended to increase its affinity. To quantify this information, we calculate the density of probes from mapping, which describes the binding propensity at each point, and show that the change in the correlation between a ligand position and the probe density upon extending or repositioning the core moiety predicts the expected change in ligand efficiency.     

Structural transitions induced by shear flow and temperature variation in a nonionic surfactant/water system

In this study, we investigate structural transitions of tetraethylene glycol monohexadecyl ether (C(16)E(4)) in D(2)O as a function of shear flow and temperature. Via a combination of rheology, rheo-small-angle neutron scattering and rheo-small-angle light scattering, we probe the structural evolution of the system with respect to shear and temperature. Multi-lamellar vesicles, planar lamellae, and a sponge phase were found to compete as a function of shear rate and temperature, with the sponge phase involving the formation of a new transient lamellar phase with a larger spacing, coexisting with the preceding lamellar phase within a narrow temperature-time range. The shear flow behavior of C(16)E(4) is also found to deviate from other nonionic surfactants with shorter alkyl chains (C(10)E(3) and C(12)E(4)), resembling to the C(16)E(7) case, of longer chain.     

Application of the maximum likelihood principle to separate exponential terms in T2 relaxation of nuclear magnetic resonance

The method of maximum likelihood has been implemented for the estimation of multiple exponential components of T2 decay curves in spin echo NMR measurements on biologic tissues. Each Each component contributes an exponential term described by two parameters (initial amplitude and T2) to the T2 decay curve. The maximum likelihood method estimates the parameters and their standard errors for all terms simultaneously, avoiding the subjectivity inherent in methods such as graphical peeling. In the model used, it was assumed that water protons are compartmentalized and that the measured spin echo signals from the protons undergoing relaxation obey the Poisson distribution. A system of non-linear equations was derived and solved iteratively for the values of the exponential parameters which maximize the likelihood of obtaining the observed data under these assumptions. The approach was implemented for bi- and tri-exponential models on a MicroVAX II computer (Digital Equipment Corporation, Maynard, MA). Simulations of bi- and tri-exponential data, with and without system noise, were analyzed to assess the accuracy and reproducibility of the method. A subset of the simulations was repeated with non-linear least squares techniques and was compared to the results obtained with maximum likelihood. Rabbit muscle and gerbil brain samples were measured and analyzed with the maximum likelihood method. The simulations showed that within specific limits on relative sizes and relaxation rates of components, these parameters can be estimated with errors less than 5%. The comparison to non-linear least squares analysis showed that the maximum likelihood method is generally superior in estimating the parameters in difficult cases. The results from tissue measurements demonstrate that the method is effective even in cases where graphical peeling would clearly not yield reliable results.     

Solubility characteristics ofβ-cyclodextrin inclusion complexes

Some inclusion complexes of-cyclodextrin (cyclomaltoheptaose) have been investigated, particularly with respect to their solubility. The mathematical characterization of the equilibrated host-guest system containing both solid and solution phases is discussed (first of all those, which contain 1:1 or 1:1 + 2:1 species) and demonstrated by different examples.     

The chemistry of 2H-3,1-benzoxazine-2,4-(1H)dione (isatoic anhydride) 3. One step synthesis of 2,3-dihydro-4,1,6-benzoxadiazonine-5,7-(1H,6H)diones

Reactions of N-haloalkylisatoic anhydrides with amines to produce piperidinobenzamides ( 2 ), pyrrolidinobenzamides ( 4 and 5 ), and 2,3-dihydro-6-methyl-4,1,6-benzoxadiazonine-5,7-(1H,6H)diones ( 10 ) are described. Spectral data are also discussed.     

Capillary electrophoretic separation of mono- and dimaltosyl-β-cyclodextrins and determination of the stability constants of their benzoate complexes

Summary Capillary zone electrophoresis method has been developed for the separation (and determination) of monoand dimaltosyl-β-cyclodextrins using indirect UV absorbance detection. The separation is based on inclusion complex formation with benzoate ion which is used as background electrolyte and absorbance provider simultaneously. Good resolution of cyclodextrin mixtures can be achieved optimizing the pH and the benzoic acid concentration in the background electrolyte. Capillary zone electrophoresis method has also been developed for the determination of formation constants of inclusion complexes.     

Finite-state and reduced-parameter representations of protein backbone conformations

This article studies the representation of protein backbone conformations using a finite number of values for the backbone dihedral angles. We develop a combinatorial search algorithm that guarantees finding the global minima of functions over the configuration space of discrete protein conformations, and use this procedure to fit finite-state models to the backbones of globular proteins. It is demonstrated that a finite-state representation with a reasonably small number of states yields either a small root-mean-square error or a small dihedral angle deviation from the native structure, but not both at the same time. The problem can be resolved by introducing limited local optimization in each step of the combinatorial search. In addition, it is shown that acceptable approximation is achieved using a single dihedral angle as an independent variable in local optimization. Results for 11 proteins demonstrate the advantages and shortcomings of both the finite-state and reduced-parameter approximations of protein backbone conformations. © 1994 by John Wiley & Sons, Inc.