Het(aryl)isatin to het(aryl)aminoindoline scaffold hopping: A route to selective inhibitors of matrix metalloproteinases

Matrix metalloproteinases (MMPs) are a large family of zinc-dependent endoproteases known to exert multiple regulatory roles in tumor progression. A variety of chemical classes have been explored for targeting individual MMP isoforms. In the present study, we further developed our isatin based scaffold BB0223107 capable of binding to and inactivating MMP-2 in a zinc-independent manner (Agamennone et al., 2016). Forty four new compounds were synthesized based on the modified BB0223107. All compounds were tested in enzyme inhibition assays against MMP-2, ?8 and ?13. SAR studies demonstrated that 5-het(aryl)-3-aminoindolin-2-ones (37–39) were active toward MMP-2 and MMP-13. The most potent compounds 33 and 37 displayed an IC₅₀ of 3 µM against MMP-13 and showed a negligible activity toward MMP-8; almost all new compounds were inactive toward MMP-8. Replacement of the isatin ring with a biaryl system (compound 33) did not decrease the potency against MMP-13 but reduced the selectivity. Structure-based computational studies were carried out to rationalize the inhibitory activity data. The analysis of binding geometries confirmed that all fragments occupied the S1′ site in the three enzymes while no ligand was able to bind the catalytic zinc ion. To the best of our knowledge, this is the first example of 3-aminoindolin-2-one-based MMP inhibitors that, based on the computer modeling study, do not coordinate the zinc ion. Thus, the het(aryl)-3-aminoindolin-2-one derivatives emerge as a drug-like and promising chemotype that, along with the hetaryl variations, represents an alternative and thrifty tool for chemical space exploration aimed at MMP inhibitor design.     

Formal proofs of operator identities by a single formal computation

A formal computation proving a new operator identity from known ones is, in principle, restricted by domains and codomains of linear operators involved, since not any two operators can be added or composed. Algebraically, identities can be modelled by noncommutative polynomials and such a formal computation proves that the polynomial corresponding to the new identity lies in the ideal generated by the polynomials corresponding to the known identities. In order to prove an operator identity, however, just proving membership of the polynomial in the ideal is not enough, since the ring of noncommutative polynomials ignores domains and codomains. We show that it suffices to additionally verify compatibility of this polynomial and of the generators of the ideal with the labelled quiver that encodes which polynomials can be realized as linear operators. Then, for every consistent representation of such a quiver in a linear category, there exists a computation in the category that proves the corresponding instance of the identity. Moreover, by assigning the same label to several edges of the quiver, the algebraic framework developed allows to model different versions of an operator by the same indeterminate in the noncommutative polynomials.     

矩阵方程A^TXB=C的正定和半正定解

给出了矩阵方程Ａ＾ＴＸＢ＝Ｃ在正定和半正定矩阵类中有解的充要条件及解的一般表达式。     

Method of lines with boundary elements for 1‐D transient diffusion‐reaction problems

Time‐dependent differential equations can be solved using the concept of method of lines (MOL) together with the boundary element (BE) representation for the spatial linear part of the equation. The BE method alleviates the need for spatial discretization and casts the problem in an integral format. Hence errors associated with the numerical approximation of the spatial derivatives are totally eliminated. An element level local cubic approximation is used for the variable at each time step to facilitate the time marching and the nonlinear terms are represented in a semi‐implicit manner by a local linearization at each time step. The accuracy of the method has been illustrated on a number of test problems of engineering significance. © 2005 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2006     

Interlaboratory comparisons and improvements of methods for acid number determination in used motor oils

The results of two interlaboratory comparisons of acid number determinations in used motor oils are discussed. It is shown that the comparability of the measurement results is not as good as that required by known standards for petroleum products. The problem is motor oil contaminants which accumulated during use, and which are the source of a matrix effect in the acid number determination. The standard methods’ drawbacks are analyzed and some improvements are proposed. Repeatability and accuracy of the improved methods are evaluated. Received: 11 December 2001 Accepted: 15 February 2002     

Finite Element Solution of Conical Diffraction Problems

This paper is devoted to the numerical study of diffraction by periodic structures of plane waves under oblique incidence. For this situation Maxwell's equations can be reduced to a system of two Helmholtz equations in R ² coupled via quasiperiodic transmission conditions on the piecewise smooth interfaces between different materials. The numerical analysis is based on a strongly elliptic variational formulation of the differential problem in a bounded periodic cell involving nonlocal boundary operators. We obtain existence and uniqueness results for discrete solutions and provide the corresponding error analysis.     

Hypernormal form theory: foundations and algorithms

Hypernormal forms (unique normal forms, simplest normal forms) are investigated both from the standpoint of foundational theory and algorithms suitable for use with computer algebra. The Baider theory of the Campbell-Hausdorff group is refined, by a study of its subgroups, to determine the smallest substages into which the hypernormalization process can be divided. This leads to a linear algebra algorithm to compute the generators needed for each substage with the least amount of work. A concrete interpretation of Jan Sanders’ spectral sequence for hypernormal forms is presented. Examples are given, and a proof is given for a little-known theorem of Belitskii expressing the hypernormal form space (in the inner product style) as the kernel of a higher-order differential operator.     

Cochran's statistical theorem for outer inverses of matrices and matrix quadratic forms

We extend the matrix version of Cochran's statistical theorem to outer inverses of a matrix. As applications, we investigate the Wishartness and independence of matrix quadratic forms for Kronecker product covariance structures.     

Direct numerical simulation of settling of a large solid particle during bioconvection

Settling of a large solid particle in bioconvection flow caused by gyrotactic microorganisms is investigated. The particle is released from the top of the bioconvection chamber; its settling pattern depends on whether it is released in the centre of the bioconvection plume or at its periphery. The Chimera method is utilized; a subgrid is generated around a moving particle. The method suggested by Liu and Wang (Comput. Fluid 2004; 33 :223–255) is further developed to account for the presence of a moving boundary in the streamfunction‐vorticity formulation using the finite‐difference method. A number of cases for different release positions of the particle are computed. It is demonstrated that bioconvection can either accelerate or decelerate settling of the particle depending on the initial position of the particle relative to the plume centre. It is also shown that the particle impacts bioconvection plume by changing its shape and location in the chamber. Copyright © 2005 John Wiley & Sons, Ltd.     

The Gram Matrix of a PT-Symmetric Quantum System

The eigenstates of a diagonalizable PT-symmetric Hamiltonian satisfy unconventional completeness and orthonormality relations. These relations reflect the properties of a pair of bi-orthonormal bases associated with non-hermitean diagonalizable operators. In a similar vein, such a dual pair of bases is shown to possess, in the presence of PT symmetry, a Gram matrix of a particular structure: its inverse is obtained by simply swapping the signs of some its matrix elements.