Mass spectrometry and n-in-one analytics in early drug discovery: Combinatorial chemistry libraries, lipophilicity and absorption screening

This thesis describes current and past n-in-one methods and presents three early experimental studies using mass spectrometry and the triple quadrupole instrument on the application of n-in-one in drug discovery. N-in-one strategy pools and mix samples in drug discovery prior to measurement or analysis. This allows the most promising compounds to be rapidly identified and then analysed. Nowadays properties of drugs are characterised earlier and in parallel with pharmacological efficacy. Studies presented here use in vitro methods as caco-2 cells and immobilized artificial membrane chromatography for drug absorption and lipophilicity measurements. The high sensitivity and selectivity of liquid chromatography mass spectrometry are especially important for new analytical methods using n-in-one. In the first study, the fragmentation patterns of ten nitrophenoxy benzoate compounds, serial homology, were characterised and the presence of the compounds was determined in a combinatorial library. The influence of one or two nitro substituents and the alkyl chain length of methyl to pentyl on collision-induced fragmentation was studied, and interesting structurefragmentation relationships were detected. Two nitro group compounds increased fragmentation compared to one nitro group, whereas less fragmentation was noted in molecules with a longer alkyl chain. The most abundant product ions were nitrophenoxy ions, which were also tested in the precursor ion screening of the combinatorial library. In the second study, the immobilized artificial membrane chromatographic method was transferred from ultraviolet detection to mass spectrometric analysis and a new method was developed. Mass spectra were scanned and the chromatographic retention of compounds was analysed using extract ion chromatograms. When changing detectors and buffers and including n-in-one in the method, the results showed good correlation. Finally, the results demonstrated that mass spectrometric detection with gradient elution can provide a rapid and convenient n-in-one method for ranking the lipophilic properties of several structurally diverse compounds simultaneously. In the final study, a new method was developed for caco-2 samples. Compounds were separated by liquid chromatography and quantified by selected reaction monitoring using mass spectrometry. This method was used for caco-2 samples, where absorption of ten chemically and physiologically different compounds was screened using both single and nin- one approaches. These three studies used mass spectrometry for compound identification, method transfer and quantitation in the area of mixture analysis. Different mass spectrometric scanning modes for the triple quadrupole instrument were used in each method. Early drug discovery with n-in-one is area where mass spectrometric analysis, its possibilities and proper use, is especially important.

BER analysis of space-time block codes from generalized complex orthogonal designs for M-PSK

In this paper, we present an analysis for the bit error rate (BER) performance of space-time block codes (STBC) from generalized complex orthogonal designs for M-PSK modulation. In STBCs from complex orthogonal designs (COD), the norms of the column vectors are the same (e.g., Alamouti code). However, in generalized COD (GCOD), the norms of the column vectors may not necessarily be the same (e.g., the rate-3/5 and rate-7/11 codes by Su and Xia in [1]). STBCs from GCOD are of interest because of the high rates that they can achieve (in [2], it has been shown that the maximum achievable rate for STBCs from GCOD is bounded by 4/5). While the BER performance of STBCs: from COD (e.g., Alamouti code) can be simply obtained from existing analytical expressions for receive diversity with the same diversity order by appropriately scaling the SNR, this can not be done for STBCs from GCOD (because of the unequal norms of the column vectors). Our contribution in this paper is that we derive analytical expressions for the BER performance of any STBC from GCOD. Our BER analysis for the GCOD captures the performance of STBCs from COD as special cases. We validate our results with two STBCs from GCOD reported by Su and Xia in [1], for 5 and 6 transmit antennas (G(5) and G(6) in [1]) with rates 7/11 and 3/5, respectively.

On the maximal rate of (n+1) x n and (n+2) x n complex orthogonal designs

For p x n complex orthogonal designs in k variables, where p is the number of channels uses and n is the number of transmit antennas, the maximal rate L of the design is asymptotically half as n increases. But, for such maximal rate codes, the decoding delay p increases exponentially. To control the delay, if we put the restriction that p = n, i.e., consider only the square designs, then, the rate decreases exponentially as n increases. This necessitates the study of the maximal rate of the designs with restrictions of the form p = n+1, p = n+2, p = n+3 etc. In this paper, we study the maximal rate of complex orthogonal designs with the restrictions p = n+1 and p = n+2. We derive upper and lower bounds for the maximal rate for p = n+1 and p = n+2. Also for the case of p = n+1, we show that if the orthogonal design admit only the variables, their negatives and multiples of these by root-1 and zeros as the entries of the matrix (other complex linear combinations are not allowed), then the maximal rate always equals the lower bound.

A Novel Construction of Complex Orthogonal Designs with Maximal Rate and Low-PAPR

Space-time block codes based on orthogonal designs are used for wireless communications with multiple transmit antennas which can achieve full transmit diversity and have low decoding complexity. However, the rate of the square real/complex orthogonal designs tends to zero with increase in number of antennas, while it is possible to have a rate-1 real orthogonal design (ROD) for any number of antennas.In case of complex orthogonal designs (CODs), rate-1 codes exist only for 1 and 2 antennas. In general, For a transmit antennas, the maximal rate of a COD is 1/2 + l/n or 1/2 + 1/n+1 for n even or odd respectively. In this paper, we present a simple construction for maximal-rate CODs for any number of antennas from square CODs which resembles the construction of rate-1 RODs from square RODs. These designs are shown to be amenable for construction of a class of generalized CODs (called Coordinate-Interleaved Scaled CODs) with low peak-to-average power ratio (PAPR) having the same parameters as the maximal-rate codes. Simulation results indicate that these codes perform better than the existing maximal rate codes under peak power constraint while performing the same under average power constraint.

On the Nash-Williams′ Lemma in Graph Reconstruction Theory

A generalization of Nash-Williams′ lemma is proved for the Structure of m-uniform null (m − k)-designs. It is then applied to various graph reconstruction problems. A short combinatorial proof of the edge reconstructibility of digraphs having regular underlying undirected graphs (e.g., tournaments) is given. A type of Nash-Williams′ lemma is conjectured for the vertex reconstruction problem.

Combinatorial manifolds with complementarity

A simplicial complex is said to satisfy complementarity if exactly one of each complementary pair of nonempty vertex-sets constitutes a face of the complex.

Training-Symbol Embedded, High-Rate Complex Orthogonal Designs for Relay Networks

Distributed Space-Time Block Codes (DSTBCs) from Complex Orthogonal Designs (CODs) (both square and non-square CODs other than the Alamouti design) are known to lose their single-symbol ML decodable (SSD) property when used in two-hop wireless relay networks using the amplify and forward protocol. For such a network, a new class of high rate, training-symbol embedded (TSE) SSD DSTBCs are proposed from TSE-CODs. The constructed codes include the training symbols within the structure of the code which is shown to be the key point to obtain high rate along with the SSD property. TSE-CODs are shown to offer full-diversity for arbitrary complex constellations. Non-square TSE-CODs are shown to provide better rates (in symbols per channel use) compared to the known SSD DSTBCs for relay networks when the number of relays is less than 10. Importantly, the proposed DSTBCs do not contain zeros in their codewords and as a result, antennas of the relay nodes do not undergo a sequence of switch on and off transitions within every codeword use. Hence, the proposed DSTBCs eliminate the antenna switching problem.

Symmetrizing a Hessenberg matrix: Designs for VLSI parallel processor arrays

A symmetrizer of a nonsymmetric matrix A is the symmetric matrix X that satisfies the equation XA = A(t)X, where t indicates the transpose. A symmetrizer is useful in converting a nonsymmetric eigenvalue problem into a symmetric one which is relatively easy to solve and finds applications in stability problems in control theory and in the study of general matrices. Three designs based on VLSI parallel processor arrays are presented to compute a symmetrizer of a lower Hessenberg matrix. Their scope is discussed. The first one is the Leiserson systolic design while the remaining two, viz., the double pipe design and the fitted diagonal design are the derived versions of the first design with improved performance.

Combinatorial logic synthesis using technology directed decomposition

The aim of logic synthesis is to produce circuits which satisfy the given boolean function while meeting timing constraints and requiring the minimum silicon area. Logic synthesis involves two steps namely logic decomposition and technology mapping. Existing methods treat the two as separate operation. The traditional approach is to minimize the number of literals without considering the target technology during the decomposition phase. The decomposed expressions are then mapped on to the target technology to optimize the area, Timing optimization is carried out subsequently, A new approach which treats logic decomposition and technology maping as a single operation is presented. The logic decomposition is based on the parameters of the target technology. The area and timing optimization is carried out during logic decomposition phase itself. Results using MCNC circuits are presented to show that this method produces circuits which are 38% faster while requiring 14% increase in area.

An iterative auction mechanism for combinatorial exchanges

Combinatorial exchanges are double sided marketplaces with multiple sellers and multiple buyers trading with the help of combinatorial bids. The allocation and other associated problems in such exchanges are known to be among the hardest to solve among all economic mechanisms. In this paper, we develop computationally efficient iterative auction mechanisms for solving combinatorial exchanges. Our mechanisms satisfy Individual-rationality (IR) and budget-nonnegativity (BN) properties. We also show that our method is bounded and convergent. Our numerical experiments show that our algorithm produces good quality solutions and is computationally efficient.

Tatonnement Mechanisms for Combinatorial Exchanges

Combinatorial exchanges are double sided marketplaces with multiple sellers and multiple buyers trading with the help of combinatorial bids. The allocation and other associated problems in such exchanges are known to be among the hardest to solve among all economic mechanisms. It has been shown that the problems of surplus maximization or volume maximization in combinatorial exchanges are inapproximable even with free disposal. In this paper, the surplus maximization problem is formulated as an integer linear programming problem and we propose a Lagrangian relaxation based heuristic to find a near optimal solution. We develop computationally efficient tâtonnement mechanisms for clearing combinatorial exchanges where the Lagrangian multipliers can be interpreted as the prices of the items set by the exchange in each iteration. Our mechanisms satisfy Individual-rationality and Budget-nonnegativity properties. The computational experiments performed on representative data sets show that the proposed heuristic produces a feasible solution with negligible optimality gap.

A lower bound for the hitting set size for combinatorial rectangles and an application

We prove a lower bound of Omega(1/epsilon (m + log(d - a)) where a = [log(m) (1/4epsilon)] for the hitting set size for combinatorial rectangles of volume at least epsilon in [m](d) space, for epsilon is an element of [m(-(d-2)), 2/9] and d > 2. (C) 2002 Elsevier Science B.V. All rights reserved.