Biomedical subjects

David T Stanton

Publications and source records attributed to David T Stanton.

11 recordsLinked to original sources

PubMed2006

Comparison of LC/MS and SFC/MS for screening of a large and diverse library of pharmaceutically relevant compounds.

The search for greater speed of analysis has fueled many innovations in high-performance liquid chromatography (HPLC), such as the use of higher pressures and smaller stationary-phase particles, and the development of monolithic columns. Alternatively, one might alter the chromatographic mobile phase. The low viscosity and high diffusivity of the mobile phase in supercritical fluid chromatography (SFC) allows higher flow rates and lower pressure drops than is possible in traditional HPLC. In addition, SFC requires less organic, or aqueous-organic, solvent than LC (important in preparative-scale chromatography) and provides an alternative, normal-phase retention mechanism. But fluids that are commonly used as the main mobile-phase component in SFC, such as CO2, are relatively nonpolar. As a result, SFC is commonly believed to only be applicable to nonpolar and relatively low-polarity compounds. Here we build upon recent work with SFC of polar and ionic compounds and peptides, and we compare the LC/MS and SFC/MS of a diverse library of druglike compounds. A total of 75.0% of the library compounds were eluted and detected by SFC/MS, while 79.4% were eluted and detected by LC/MS. Some samples provided strong peaks that appeared to be related to the purported compound contained in the sample. When these were added to the "hits", the numbers rose to 86.7 and 89.9%, respectively. A total of 3.7% of the samples were observed by SFC/MS, but not by LC/MS, and 8.1% of the samples were observed by LC/MS, but not by SFC/MS. The only compound class that appeared to be consistently detected in LC/MS, but not in SFC/MS under our conditions, consisted of compounds containing a phosphate, a phosphonate, or a bisphosphonate. The SFC/MS method was at least as durable, reliable, and user-friendly as the LC/MS method. The APCI source required less cleaning during the SFC/MS separations than it did during LC/MS.

Chromatography, High Pressure Liquid↗

PubMed2006

Identification of latent variables in a semantic odor profile database using principal component analysis.

Many classifications of odors have been proposed, but none of them have yet gained wide acceptance. Odor sensation is usually described by means of odor character descriptors. If these semantic profiles are obtained for a large diversity of compounds, the resulting database can be considered representative of odor perception space. Few of these comprehensive databases are publicly available, being a valuable source of information for fragrance research. Their statistical analysis has revealed that the underlying structure of odor space is high dimensional and not governed by a few primary odors. In a new effort to study the underlying sensory dimensions of the multivariate olfactory perception space, we have applied principal component analysis to a database of 881 perfume materials with semantic profiles comprising 82 odor descriptors. The relationships identified between the descriptors are consistent with those reported in similar studies and have allowed their classification into 17 odor classes.

Cluster Analysis↗

PubMed2004

Elution and preliminary structure-retention modeling of polar and ionic substances in supercritical fluid chromatography using volatile ammonium salts as mobile phase additives.

Supercritical fluid chromatography has primarily been applied to relatively nonpolar analytes, even when polar organic solvents are used as modifiers. Here, we show that low levels of volatile ammonium salts as mobile-phase additives allow the elution of polar and even ionic organic materials such as sulfonate salts, carboxylate salts, polyamines, and quaternary ammonium salts. Also, volatile ammonium salts are compatible with mass spectrometric detection, in contrast to other common additives. We have performed preliminary structure-activity-relationship modeling for retention in the CO2/methanol/NH4OAc/Deltabond Cyano system. We have developed a three-descriptor model, where one descriptor, the "relative negative charged surface" explains over 61% of the variance in the retention values. We suggest that two mechanisms have the greatest influence on retention in this system. One is related to the presence of a volatile ammonium salt, the other is related to the ability of a molecule to "hide" its atom with the greatest partial negative charge.

Journal Article↗

PubMed2003

Development and use of a high-throughput bacterial DNA gyrase assay to identify mammalian topoisomerase II inhibitors with whole-cell anticancer activity.

A high-throughput screen (HTS) was developed and used to identify inhibitors of bacterial DNA gyrase. Among the validated hits were 53 compounds that also inhibited mammalian topoisomerase II with IC(50) values of <12.5 micro g/mL for 51 of them. Using computational methods, these compounds were subjected to cluster analysis to categorize them according to their chemical and structural properties. Nine compounds from different clusters were tested for their whole-cell inhibitory activity against 3 cancer cell lines-NCI-H460 (lung), MCF7 (breast), and SF-268 (CNS)-at a concentration of 100 micro M. Five compounds inhibited cell growth by >50% for all 3 cell lines tested. These compounds were tested further against a panel of 53 to 57 cell lines representing leukemia, melanoma, colon, CNS, ovarian, renal, prostate, breast, and non-small cell lung cancers. In this assay, PGE-7143417 was found to be the most potent compound, which inhibited the growth of all the cell lines by 50% at a concentration range of 0.31 to 2.58 micro M, with an average of 1.21 micro M. An additional 17 compounds were also tested separately against a panel of 10 cell lines representing melanoma, colon, lung, mammary, ovarian, prostate, and renal cancers. In this assay, 4 compounds-PGE-3782569, PGE-7411516, PGE-2908955, and PGE-3521917-were found to have activity with concentrations for 50% cell growth inhibition in the 0.59 to 3.33, 22.5 to 59.1, 7.1 to >100, and 24.7 to >100 micro M range.

Animals↗

PubMed2003

The effect of room-temperature storage on the stability of compounds in DMSO.

The stability of approximately 7200 compounds stored as 20-mM DMSO solutions under ambient conditions was monitored for 1 year. Compound integrity was measured by flow injection analysis using positive and negative electrospray ionization mass spectrometry. Each sample was assessed at the beginning of the study, after 12 months of storage, and at a randomized time point between the initial and final time points of the study. The relationship between length of storage and the probability of observing the compound was described by a repeated-measures logistic regression model. The probability of observing the compound was 92% after 3 months of storage at room temperature, 83% after 6 months, and 52% after 1 year in DMSO. An acceptable limit for compound loss and corresponding maximum storage time for samples in DMSO can be determined based on these results.

Dimethyl Sulfoxide↗

PubMed2003

The effect of freeze/thaw cycles on the stability of compounds in DMSO.

A diverse set of 320 compounds from the Procter & Gamble Pharmaceuticals organic compound repository was prepared as 20-mM DMSO solutions and stored at 4 degrees C under argon in pressurized canisters to simulate a low-humidity environment. The plates were subjected to 25 freeze/thaw cycles while being exposed to ambient atmospheric conditions after each thaw to simulate the time and manner by which compound plates are exposed to the atmosphere during typical liquid-handling and high-throughput screening processes. High-performance liquid chromatography-mass spectrometry with evaporative light-scattering detection was used to quantitate the amount of compound remaining after every 5th freeze/thaw cycle. Control plates were stored either at room temperature under argon or at 4 degrees C under argon without freeze/thaw cycling and were evaluated at the midpoint and the endpoint of the study. The study was conducted over a short time period (i.e., 7 weeks) to minimize the effect of compound degradation over time due to the exposure of the compounds to DMSO. The results from this study will be used to determine the maximum number of freeze/thaw cycles that can be achieved while maintaining acceptable compound integrity.

Argon↗

PubMed2002

Profiling of drugs for membrane activity using liposomes as an in vitro model system.

The increasing size of chemical libraries being analyzed by high-throughput screening results in a growing number of active compounds that need to be assessed before moving forward in the drug development process. As a consequence, more rapid and highly sensitive strategies are required to accelerate the process of drug discovery without increasing the cost. Due to the fact that significant numbers of compounds from combinatorial libraries are hydrophobic in nature, approaches are needed to evaluate the potentialfor these compounds to interfere with the functions of biological membranes. The liposome system was used to detect agents that act as follows: (i) ionophores able to induce specific ion permeability, e.g., valinomycin for K+ and protonophoric uncouplers for H+; (ii) ion antiporters which exchange H+ for other ions, e.g., nigericin; (iii) agents that form low specificity ion channels in the membrane, e.g., gramicidin; and (iv) detergents and other membrane-disrupting agents. We propose using this liposome assay during the drug development process to identify compounds that have membrane activity and, as a consequence, produce a biological effect by altering the physico-chemical properties of the cell membrane rather than interacting with a protein target. Screening of a representative set of biologically-active compounds (198) indicated that the majority of systemic antimicrobial drugs, but not topical drugs, lack membrane activity in this model system.

Animals↗

PubMedDate not supplied

On the physical interpretation of QSAR models.

Multidimensional quantitative structure-activity models (QSAR) developed using molecular structure descriptors and regression analysis techniques have found wide utility and acceptance. However, it is often difficult to extract a physical interpretation of such models because of the types of descriptors involved and the multidimensional nature of the model. The work described here illustrates a method of model interpretation that employs partial least squares (PLS) analysis. Structure-activity relationship information is derived from the positions of specific sets of structures in the PLS score plots and the weights for each variable in the PLS components. Using these data, information regarding major structure-activity trends, trend exceptions, and unique or outlying observations is easily obtained. Examples of this methodology are illustrated using QSAR equations developed for the inhibition of quinolone-resistant bacterial DNA gyrase and human topoisomerase-II inhibition by a series of quinolone antibacterial agents.

Bacterial Proteins↗

PubMedDate not supplied

Development of a quantitative structure-activity relationship model for inhibition of gram-positive bacterial cell growth by biarylamides.

A set of compounds consisting of a new and diverse collection of biarylamides was examined using quantitative structure-activity relationship techniques for the purpose of developing a model to describe inhibition of gram-positive bacterial growth (minimum inhibition concentration). The model was sought in order to obtain insight for designing new molecules. A detailed analysis of the underlying structure-activity relationship helped provide insight concerning which structural features of the molecules modulated the activity of the compounds against gram-positive organisms.

Amides↗

PubMedDate not supplied

Development and use of hydrophobic surface area (HSA) descriptors for computer-assisted quantitative structure-activity and structure-property relationship studies.

A new series of 25 whole-molecule molecular structure descriptors are proposed. The new descriptors are termed Hydrophobic Surface Area, or HSA descriptors, and are designed to capture information regarding the structural features responsible for hydrophobic and hydrophilic intermolecular interactions. The utility of the HSAs in capturing this type of information is demonstrated using two properties that have a known hydrophobic component. The first study involves the modeling of the inhibition of Gram-positive bacteria cell growth of a series of biarylamides. The second application involves the study of the blood-brain barrier penetration of a diverse series of drug molecules. In both cases, the HSAs are shown to effectively capture information related to the hydrophobic components of these two properties. Additional evaluation of the new class of descriptors shows them to be unique in their ability to measure hydrophobic features among a diverse set of conventional structural descriptors. The HSAs are evaluated regarding their sensitivity to conformational changes and are found to be similar in that regard to other widely used molecular descriptors.

Amides↗

PubMedDate not supplied

Interpreting computational neural network quantitative structure-activity relationship models: a detailed interpretation of the weights and biases.

In this work, we present a methodology to interpret the weights and biases of a computational neural network (CNN) quantitative structure-activity relationship model. The methodology allows one to understand how an input descriptor is correlated to the predicted output by the network. The method consists of two parts. First, the nonlinear transform for a given neuron is linearized. This allows us to determine how a given neuron affects the downstream output. Next, a ranking scheme for neurons in a layer is developed. This allows us to develop interpretations of a CNN model similar in manner to the partial least squares (PLS) interpretation method for linear models described by Stanton. The method is tested on three datasets covering both physical and biological properties. The results of this interpretation method correspond well to PLS interpretations for linear models using the same descriptors as the CNN models, and they are consistent with the generally accepted physical interpretations for these properties.

Algorithms↗