Biomedical subjects

C L Waller

Publications and source records attributed to C L Waller.

At least 19 recordsLinked to original sources

PubMed1998

Percutaneous absorption and disposition of [14C]chlordecone in young and adult female rats.

The objective of this study was to evaluate the effect of age and dosage on percutaneous absorption and disposition of [14C]chlordecone (Kepone) and to describe results using a physiological based pharmacokinetic (PBPK) model. Female Fischer 344 rats 33 and 82 days old were used as the young and adult animal models, respectively, and were studied over a 10-fold dose range. [14C]Chlordecone (0.286 micromol/cm2) was applied to dorsal skin (2. 3% BSA) and radioactivity was quantified in selected tissues and excreta up to 120 h. Absorption and disposition were also determined at three dose levels up to 2.68 micromol/cm2; fraction absorbed decreased as dose increased. In vitro percutaneous absorption was measured by static and flow-through methods; these yielded similar penetration rates, which were lower than those obtained in vivo. In vivo percutaneous absorption over 120 h was 14.4+/-0.99 and 14.2+/-1. 5% dose in young and adults, respectively. Organ and tissue content increased over time (carcass>liver>kidney), indicating prolonged absorption. Statistical differences between young and old were found for liver, skin, and urine, but not for absorption. Excretion occurred primarily in feces, but also in urine. A biophysically based percutaneous model was fitted to both young and adult in vivo absorption data. This was embedded in a whole body PBPK model which, upon optimization with SAAM II, estimated apparent tissue partition coefficients, urinary and fecal excretion rates, and parameters characterizing hepatic nonlinear uptake of bound chlordecone. The model reasonably predicted tissue chlordecone content at higher doses, when decreased absorption was accounted for.

Age Factors↗

PubMed1996

Three-dimensional quantitative structure--activity relationships for androgen receptor ligands.

Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm, was used to examine androgen receptor-binding affinities of a series of structurally diverse natural, synthetic, and environmental chemicals of interest. The CoMFA/3D-QSAR model successfully illustrates that the overall steric and electrostatic properties of structurally diverse ligands for the androgen receptor are necessary and sufficient to describe the binding affinity. The practical utility of models of this type is demonstrated using parent compounds in the training set and known as well as putative biological metabolites as test set molecules. The ability of the model to accurately predict binding affinity of test set molecules suggests that structure-based 3D-QSAR models may be used to supplement the process of hazard identification. The application of 3D-QSAR models within a toxicological framework is, at present, limited by the quantity and quality of biological data for relevant biomarkers of toxicity.

Hazardous Substances↗

PubMed1996

Increased [3H]phorbol ester binding in rat cerebellar granule cells and inhibition of 45Ca2+ sequestration in rat cerebellum by polychlorinated diphenyl ether congeners and analogs: structure-activity relationships.

Our previous reports indicate that ortho-substituted non-coplanar polychlorinated biphenyl (PCB) congeners perturbed neuronal Ca2+-homeostasis in vitro, altered agonist-stimulated inositol phosphate accumulation, and caused protein kinase C (PKC) translocation. The structure-activity relationship (SAR) with 24 PCB congeners was consistent with a chlorination pattern that favored non-coplanarity while those with chlorination that favored coplanarity were less active. To test the hypothesis that coplanarity (or lack thereof) is a significant factor in the activity of PCBs, studies with related classes of chemicals such as the polychlorinated diphenyl ethers (PCDEs), in which coplanarity is more difficult to achieve regardless of degree and pattern of chlorination, were initiated. The selected PCDEs and their analogs are predicted to be active, since they are non-coplanar in nature. The effects of these chemicals were studied using the same measures for which PCBs had differential effects based on structural configuration. These measures include PKC translocation as determined by [3H]-phorbol ester ([3H]PDBu) binding in cerebellar granule cells and 45Ca2+ sequestration as determined by 45Ca2+ uptake by microsomes and mitochondria isolated from adult rat cerebellum. All the PCDE congeners studied, increased [3H]PDBu binding in a concentration-dependent manner. The order of potency was 2,4,4'-trichlorodiphenyl ether > 4,4'-dichlorodiphenyl ether > diphenyl ether, 3,3',4,4'-tetrachlorodiphenyl ether and, 2,2',4,4',5- and 2,3',4,4',5-pentachlorodiphenyl ethers. The structurally related diphenyl ether nitrofen and diphenyl ethanes o,p'-1,1,1-trichloro-2,2-bis[p-chlorophenyl]ethane (DDT) and p,p'-DDT increased [3H]PDBu binding to a similar extent (28-35% stimulation at 100 microM). All PCDE congeners and their analogs inhibited 45Ca2+ sequestration by microsomes and mitochondria. Of all the chemicals, unchlorinated diphenyl ether was the least active. These results are in agreement with previous SAR findings in which non-coplanar PCBs are active and support our hypothesis that the extent of coplanarity determined by a pattern of chlorination on certain aromatic hydrocarbons can weaken their potency in vitro, although the extent of chlorination is also important.

Animals↗

PubMed1996

A pharmacokinetic model of anaerobic in vitro carbon tetrachloride metabolism.

Carbon tetrachloride (CCl4) is a potent hepatotoxic agent whose toxicity is mediated through cytochome P450-dependent metabolism. Results from anaerobic in vitro experiments with hepatic microsomes isolated from male F-344 rats indicate that chlorofom (CHCl3) formation from CCl4 is nonlinear with dose. Dose is traditionally expressed as the amount of CCl4 added to the vial. In this study, a pharmacokinetic model has been developed to calculate the concentration of CCl4 in the microsomal suspension. Hepatic microsomes prepared from fed and fasted animals were incubated with CCl4 under anaerobic conditions and formation of CHCl3 over a 5-min incubation period was monitored by headspace gas chromatography. Dose-response curves, based on total amount of CCl4 added to the microsomes, revealed a nonlinear, biphasic appearance of CHCl3, with fasting slightly increasing CHCl3 production in microsomes prepared from fasted rats. Microsomes were also pretreated with the CYP2E1 inhibitor, diallyl sulfone (DAS), before addition of CCl4. In uninhibited microsomes, there appeared to be a high-affinity saturable phase of metabolism occurring at lower concentrations followed by a linear phase at higher CCl4 concentrations. Following DAS pretreatment, the saturable portion of the dose-response curve was inhibited more than the linear phase with the biphasic CHCl3 production becoming more linear. DAS inhibition eliminated the effect of fasting on CHCl3 formation. The best fit kinetic constants for the saturable phase resulted in an estimate of V(max) of 0.017 mg/h/mg protein (V(maxc) = 7.61 mg/h/kg) and Km of 2.3 mg/l (15 microM). The linear phase rate constant (kf) was determined to be 0.046 h-1) (kfc = 0.03 h-1). In conclusion, a pharmacokinetic model has been developed for anaerobic in vitro metabolism of CCl4 to CHCl3 that estimates metabolic rates based on CHCl3 formation and actual CCl4 concentration in the microsomal suspension.

Allyl Compounds↗

PubMed1996

Ligand-based identification of environmental estrogens.

Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm, was used to examine the estrogen receptor (ER) binding affinities of a series of structurally diverse natural, synthetic, and environmental chemicals of interest. The CoMFA/3D-QSAR model is statistically robust and internally consistent, and successfully illustrates that the overall steric and electrostatic properties of structurally diverse ligands for the estrogen receptor are both necessary and sufficient to describe the binding affinity. The ability of the model to accurately predict the ER binding affinity of an external test set of molecules suggests that structure-based 3D-QSAR models may be used to supplement the process of endocrine disruptor identification through prioritization of novel compounds for bioassay. The general application of this 3D-QSAR model within a toxicological framework is, at present, limited only by the quantity and quality of biological data for relevant biomarkers of toxicity and hormonal responsiveness.

Animals↗

PubMed1996

Modeling the cytochrome P450-mediated metabolism of chlorinated volatile organic compounds.

Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm, has been used to analyze the metabolic rates, as intrinsic clearance, of a series of chlorinated volatile organic compounds (VOCs). A comparison between 3D-QSAR and conventional Hansch-type QSAR is provided. To develop predictive 3D-QSARs for metabolism, the standard CoMFA model based on steric and electrostatic potential fields must be supplemented with hydropathic and molecular orbital information also in the form of three-dimensional fields. A mechanistic interpretation of chlorinated VOC metabolism by cytochrome P450 isozymes is provided as a rationalization for the inclusion of multiple fields in the CoMFA 3D-QSAR model. Models of this type have practical utility in the development of generalized physiologically-based pharmacokinetic models, as well as the rational, structure-based, design and/or selection of compounds for use in the in vivo and in vitro metabolic studies.

Cytochrome P-450 Enzyme System↗

PubMed1995

Three-dimensional quantitative structure-activity relationships of dioxins and dioxin-like compounds: model validation and Ah receptor characterization.

In the present study we have utilized comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship paradigm, to explore the physico-chemical requirements for binding to the Ah (dioxin) receptor. Recent developments by Gillner et al. [(1993) Mol. Pharmacol. 44, 336-345] prompted us to review and revise our previous CoMFA/QSAR model [Waller, C. L., and McKinney, J. D. (1992) J. Med. Chem. 36, 3660-3666] to include a structurally-diverse training set of Ah receptor ligands ranging in size from naphthalene to indolo[3,2-b]carbazole nuclei. An exhaustive validation process utilizing external test sets and hierarchical cluster analysis routines was employed during model construction and is discussed herein. The limitations of the approach presented herein are discussed with respect to predictive ability of the CoMFA/QSAR models, which is demonstrated to be dependent on a balance between structural diversity and redundancy in the molecules comprising the training set. The results of our modified CoMFA/QSAR model are consistent with and unify all previously established structure-activity relationships established for less structurally-diverse training sets of Ah receptor ligands. As a result of the more complete nature of the series of molecules under examination in the present study, the CoMFA/QSAR steric and electrostatic field contour plots as well as the essential and excluded volume plots provide for a more detailed characterization of the molecular binding domain of the Ah receptor. The implications of the CoMFA/QSAR model presented herein are explored with respect to quantitative hazard identification of potential toxicants.

Binding Sites↗

PubMed1994

Three-dimensional quantitative structure-activity relationship of human immunodeficiency virus (I) protease inhibitors. 2. Predictive power using limited exploration of alternate binding modes.

NewPred, a semiautomated procedure to evaluate alternate binding modes and assist three dimensional quantitative structure-activity relationship (3D-QSAR) studies in predictive power evaluation is exemplified with a series of 30 human immunodeficiency virus 1 protease (HIV PR) inhibitors. Five comparative molecular field analysis (CoMFA) models (Waller, C. L.; et al. J. Med. Chem. 1993, 36, 4152-4160) based on 59 HIV-PR inhibitors were tested. The test set included 18 compounds (set A) having a different transition state isostere (TSI), hydroxyethylurea (Getman, D. P.; et al. J. Med. Chem. 1993, 36, 288-291), to investigate the binding mode in P1' and P2'. Twelve dihyroxyethylenes (set B) (Thaisrivongs, S.; et al. J. Med. Chem. 1993, 36, 941-952) were used to investigate binding in P2 and P3 as well as in P2' and P3'. Six other compounds with known or inferred binding structure (set C) were part of the test set, but not investigated with NewPred. Each compound was aligned in accordance to predefined alignment rules for the training set prior to the inclusion in the test set (except for set C). Using NewPred, geometrically different conformers for each compound were generated and individually relaxed in the HIV-PR binding site. Energy comparisons allowed selection of lowest energy structures to be included in the test set. Only in vacuo minimized conformers derived from low-energy complexes were used to determine the predictive power of the five models (predictive r2 varied from 0.1 to 0.7 when two chemical and statistical outliers were excluded). Our models correctly predict the poor inhibitor activity of 1(S)-amino-2(R)-hydroxyindan-containing peptides (set B), which is explained and interpreted from a 3D-QSAR perspective. The use of a new, flexibility-based, semiautomated method to explore alternate binding models for 3D-QSAR models is demonstrated.

Amino Acid Sequence↗

PubMed1994

Effects of [(N-alkyl-1,3-dihydro-1-oxoisoindolin-5-yl)oxy]alkanoic acids on chloride transport in primary astroglial cultures.

It has been demonstrated that agents which inhibit chloride influx and, therefore, lower intracellular chloride levels in the astrocyte, a major cell type in the cerebral gray matter, inhibit astrocytic swelling in vitro and in vivo. Herein, we report additional examples of a series of [(N-alkyl-1,3-dihydro-1-oxoisoindolin-5-yl)oxy]alkanoic acids and their effects upon ion transport in primary rat astrocyte cultures. The 4-chloro-substituted 1-oxoisoindolines demonstrated superior astrocytic chloride influx inhibitory activity as compared to the 6-chloro and non-chlorinated analogs. The four-carbon acid side chain derivatives were more active than the three- and two-carbon analogs. The pharmacological profile of these compounds was examined with respect to inhibition of the Cl(-)-Cl-/Cl(-)-HCO3- anion exchanger and Na(+)-K(+)-2Cl- cotransport mechanisms in glia, and the compounds were found to exhibit a similar profile to that of furosemide by inhibiting both transporters.

Animals↗

PubMed1994

Conformational analysis, molecular modeling, and quantitative structure-activity relationship studies of agents for the inhibition of astrocytic chloride transport.

Molecular modeling studies were carried out on a series of 1-oxoisoindolines which are pharmacologically active as inhibitors of astrocytic chloride transport. Conformational analysis revealed that the halogen substituent exerted a pronounced steric directing effect on the acid side chain. The 4-substituted analogs apparently provided for the best spatial arrangement of pharamacophoric elements of the molecules. Conventional quantitative structure-activity relationship (QSAR) studies using lipophilic and dipole moment characteristics of the molecules as physical descriptor variables in the regression equation yielded a statistically significant model. Comparative molecular field analysis (CoMFA) was utilized as a three-dimensional QSAR technique to explore changes in the steric and electrostatic fields of the molecules that can account for differences in biological activity values. A highly predictive model was attained which supported the results from the qualitative and conventional quantitative structure-activity relationship analyses. These modeling techniques represent the evolutionary process by which structure-activity methods were employed to aid in the development of novel more potent inhibitors of astrocytic chloride transport.

Astrocytes↗

PubMed1994

Polychlorinated biphenyls as hormonally active structural analogues.

Among the environmental chemicals that may be able to disrupt the endocrine systems of animals and humans, the polychlorinated biphenyls (PCBs) are a chemical class of considerable concern. One possible mechanism by which PCBs may interfere with endocrine function is their ability to mimic natural hormones. These actions reflect a close relationship between the physicochemical properties encoded in the PCB molecular structure and the responses they evoke in biological systems. These physicochemical properties determine the molecular reactivities of PCBs and are responsible for their recognition at biological acceptors and receptors, as well as for triggering molecular mechanisms that lead to tissue response. "Coplanarity" of PCB phenyl rings and "laterality" of chlorine atoms are important structural features determining specific binding behavior with proteins and certain toxic responses in biological systems. We compare qualitative structure-activity relationships for PCBs with the limited information on the related non-coplanar chlorinated diphenyl ethers, providing further insights into the nature of the molecular recognition processes and support for the structural relationship of PCBs to thyroid hormones. Steroidlike activity requires conformational restriction and possibly hydroxylation. We offer some simple molecular recognition models to account for the importance of these different structural features in the structure-activity relationships that permit one to express PCB reactivities in terms of dioxin, thyroxine, and estradiol equivalents. The available data support the involvement of PCBs as mimics of thyroid and other steroidal hormones. The potential for reproductive and developmental toxicity associated with human exposure to PCBs is of particular concern.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1994

3D-QSAR of human immunodeficiency virus (I) protease inhibitors. III. Interpretation of CoMFA results.

Comparative Molecular Field Analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm (Cramer, R.D.; et al. (1988), J. Am. Chem. Soc., 110, 5959-5967), correlates variations in the (experimental) biological activity with 3D variance in the steric and electrostatic field of modeled compounds. Of general interest to the drug design area is the interpretation of CoMFA results, in order to gain maximum benefit from an established 3D-QSAR model. CoMFA studies report results using the standard deviation (stdev) times(*) coefficient (beta) field and its contributions to make SAR statements. This field is the scalar product of the absolute stdev of the CoMFA field at a lattice point and the QSAR equation coefficient (beta) at the same point. Negative beta values yield detrimental contributions, while positive beta values are considered beneficial. The QSAR equation is based on actual field values, therefore both positive and negative field values can have beneficial effect to the target property (Y), depending on the sign of beta. The results of a CoMFA model on 59 HIV-1 protease (HIV-PR) inhibitors (Waller, C.L.; et al. (1993), J. Med. Chem., 36, 4152-4160) were compared with the HIV-PR crystal structure to analyze the correspondence between CoMFA fields and ligand binding regions in the enzyme. Local steric and electrostatic interactions were analyzed in terms of various field values and beta coefficients. While redundant for some regions, other field contours besides stdev* beta bring additional information. Using this method, we observed a unique region with negative beta values for the electrostatic field (based on a -1 charged probe) located opposite of the scissile bond, between P1 and P1', where steric stdev* beta values are positive. Four hydrophobic residues in the HIV-PR crystal delimit the region, which is suggested as a new potential hydrophobic binding site for the inhibitors. The same region was confirmed using the stdev* beta contours of a HINT (Kellogg, G.; et al. (1991), J. Comput.-Aided Mol. Design, 5, 545-552) calculation on the same model. The steric, electrostatic and lipophilic fields of the CoMFA and HINT models are presented in various forms, and the information extracted is detailed.

Binding Sites↗

PubMed1993

Three-dimensional QSAR of human immunodeficiency virus (I) protease inhibitors. 1. A CoMFA study employing experimentally-determined alignment rules.

Comparative molecular field analysis (CoMFA), a three-dimensional, quantitative structure-activity relationship (QSAR) paradigm, was used to examine the correlations between the calculated physicochemical properties and the in vitro activities of a series of human immunodeficiency virus (HIV-1) protease inhibitors. The training set consisted of 59 molecules from five structurally-diverse transition-state isostere classes: hydroxyethylamine, statine, norstatine, keto amide, and dihydroxyethylene. The availability of X-ray crystallographic data for at least one representative from each class bound to the protease provided information regarding not only the active conformation of each ligand but also, via superimposition of protease backbones, the relative positions of each ligand with respect to one another in the active site of the enzyme. Once aligned, these molecules served as templates on which additional congeners were field-fit minimized. Additional alignment rules were derived from minimizations of the ligands in the active site of the semirigid protease. The predictive ability of each resultant model was evaluated using a test set comprised of molecules containing a novel transition-state isostere: hydroxyethylurea. Crystallographic studies (Getman, D.P.; et al. J. Med. Chem. 1993, 36, 288-291) indicated an unexpected binding mode for this series of compounds which precluded the use of the field-fit minimization alignment technique. The test set molecules were, therefore, subjected to a limited systematic search in conjunction with active-site minimization. The conformer of each molecule expressing the lowest interaction energy with the active site was included in the test set. Field-fit minimization of neutral molecules to crystal ligands and active-site minimizations of protonated ligands yielded predictive correlations for HIV-1 protease inhibitors. The use of crystallographic data in the determination of alignment rules and field-fit minimization as a molecular alignment tool in the absence of direct experimental data regarding binding modes is strongly supported by these results.

Amides↗

PubMed1993

Three-dimensional quantitative structure-activity relationship of angiotesin-converting enzyme and thermolysin inhibitors. II. A comparison of CoMFA models incorporating molecular orbital fields and desolvation free energies based on active-analog and complementary-receptor-field alignment rules.

The utility of comparative molecular field analysis (CoMFA), a three-dimensional Quantitative Structure-Activity Relationship (3-D QSAR) paradigm, as a tool to aid in the development of predictive models has been previously addressed (Depriest, S.D. et al., J. Am. Chem. Soc. 1993, in press). Although predictive correlations were obtained for angiotensin-converting and thermolysin inhibitors, certain inadequacies of the CoMFA technique were noted. Primarily, CoMFA steric and electrostatic fields alone do not fully characterize the zinc-ligand interaction. Previously, this was partially rectified by the inclusion of indicator variables into the QSAR table to designate the class of zinc-binding ligand. Recent advances in molecular modeling technology have allowed us to further address this limitation of the preceding study. Using molecular orbital fields derived from semiempirical calculations as additional descriptors in the QSAR table, predictive correlations were produced based on CoMFA and molecular orbital fields alone--indicator variables no longer being necessary. Arbitrary information concerning the alignment of molecules under study within the active-site introduces ambiguities into the CoMFA study. Crystallographic information detailing the binding mode of several thermolysin enzyme inhibitors has previously been used as a guide for the alignment of additional, noncrystallized, inhibitors. However, this process was complicated by the lack of parameters for zinc in the molecular mechanical force field. Therefore, zinc-ligand interactions were ignored during the standard minimization procedure. The use of field-fit minimization using complementary receptor fields as templates is presented as a possible solution to the problem. Predictive correlations were obtained from analyses based on this method of molecular alignment. The availability of crystallographic data for thermolysin enzyme-inhibitor complexes allowed for an alternate definition of the CoMFA region. Herein, promising results from analyses using actual receptor active-site atom probe atoms are presented.

Angiotensin-Converting Enzyme Inhibitors↗

PubMed1992

Comparative molecular field analysis of polyhalogenated dibenzo-p-dioxins, dibenzofurans, and biphenyls.

Comparative molecular field analysis (CoMFA) was performed on polyhalogenated dibenzo-p-dioxins, dibenzofurans, and biphenyls for Ah (dioxin) receptor binding and associated enzyme inducing activities determined by others using in vitro assays. Since various members of all three classes of compounds have been shown to produce qualitatively similar toxicities, a separate CoMFA was performed on each class of compounds and combinations of the different classes for each bioactivity which included combining all three classes of molecules in one CoMFA study. For the Ah receptor binding, the CoMFA-derived QSARs for all three classes of compounds and combinations thereof showed strong crossvalidated correlations indicating that they are highly predictive. For enzyme induction, the CoMFA-derived QSARs were highly predictive for the dibenzofurans but were only partially successful for the dioxins. For the biphenyls, the results were clearly unpredictive. The overall results of these CoMFA studies which include both steric and electrostatic considerations are compared and contrasted to other SAR models that have met with some success in making qualitative predictions about the potential for receptor binding and associated toxicity in these classes of compounds. The CoMFA-derived QSAR for the dioxin series of molecules in most cases significantly overestimates the enzyme inducing ability of the ortho-substituted biphenyls. This weak inducing activity of the o-biphenyls is, however, consistent with their relatively low dioxin-like toxicity as measured in other biological systems. Fundamentally different mechanisms may be operating in the expression of dioxin-like toxic responses for the o-biphenyls, and their direct, dioxin-like toxic equivalency perhaps needs to be reconsidered in this light.

Aryl Hydrocarbon Hydroxylases↗

PubMedDate not supplied

Progress in predicting human ADME parameters in silico.

Understanding the development of a scientific approach is a valuable exercise in gauging the potential directions the process could take in the future. The relatively short history of applying computational methods to absorption, distribution, metabolism and excretion (ADME) can be split into defined periods. The first began in the 1960s and continued through the 1970s with the work of Corwin Hansch et al. Their models utilized small sets of in vivo ADME data. The second era from the 1980s through 1990s witnessed the widespread incorporation of in vitro approaches as surrogates of in vivo ADME studies. These approaches fostered the initiation and increase in interpretable computational ADME models available in the literature. The third era is the present were there are many literature data sets derived from in vitro data for absorption, drug-drug interactions (DDI), drug transporters and efflux pumps [P-glycoprotein (P-gp), MRP], intrinsic clearance and brain penetration, which can theoretically be used to predict the situation in vivo in humans. Combinatorial synthesis, high throughput screening and computational approaches have emerged as a result of continual pressure on pharmaceutical companies to accelerate drug discovery while decreasing drug development costs. The goal has become to reduce the drop-out rate of drug candidates in the latter, most expensive stages of drug development. This is accomplished by increasing the failure rate of candidate compounds in the preclinical stages and increasing the speed of nomination of likely clinical candidates. The industry now understands the reasons for clinical failure other than efficacy are mainly related to pharmacokinetics and toxicity. The late 1990s saw significant company investment in ADME and drug safety departments to assess properties such as metabolic stability, cytochrome P-450 inhibition, absorption and genotoxicity earlier in the drug discovery paradigm. The next logical step in this process is the evaluation of higher throughput data to determine if computational (in silico) models can be constructed and validated from it. Such models would allow an exponential increase in the number of compounds screened virtually for ADME parameters. A number of researchers have started to utilize in silico, in vitro and in vivo approaches in parallel to address intestinal permeability and cytochrome P-450-mediated DDI. This review will assess how computational approaches for ADME parameters have evolved and how they are likely to progress.

Catalysis↗

PubMedDate not supplied

Polarizability fields for use in three-dimensional quantitative structure-activity relationship (3D-QSAR).

Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) technique, has proven to be a valuable tool in the field of rational drug design. In its native form, CoMFA utilizes a pseudoreceptor, in the form of a regularly spaced lattice of probe atoms, to characterize the steric and electrostatic properties of a series of mutually superimposed molecules. Statistical analyses are performed in an attempt to correlate changes in these shape and charge related fields to observed differences in biological activities at a given target. Graphical analyses of the resulting "negative receptor images" have been demonstrated to provide insight into the physicochemical requirements of novel ligands. Several groups have previously demonstrated the benefits of additional or alternative fields for these types of analyses. In this report, a novel molecular potential field derived from atomistic contributions to molecular polarizability is presented. Comparison studies will be presented using literature data sets and CoMFA models derived from steric, electrostatic, and polarizability fields. The overall conclusion is that molecular polarizability fields derived from semiempirically determined atomic polarizabilities are highly predictive and graphically descriptive supplements to, and perhaps surrogates for, the standard CoMFA steric and electrostatic fields.

Computer Simulation↗

PubMedDate not supplied

Rational combinatorial library design. 3. Simulated annealing guided evaluation (SAGE) of molecular diversity: a novel computational tool for universal library design and database mining.

We have developed a novel method for molecular diversity sampling called SAGE (simulated annealing guided evaluation of molecular diversity). Compounds in chemical databases or virtual combinatorial libraries are conventionally represented as points in multidimensional descriptor space. The SAGE algorithm selects a desired number of optimally diverse points (compounds) from a database. The diversity of a subset of points is measured by a specially designed diversity function, and the most diverse subset is selected using Simulated Annealing (SA) as the optimization tool. Application of SAGE to two simulated data sets of randomly distributed points in two-dimensional space afforded diverse and representative selection as judged by visual inspection. SAGE was also applied, in comparison with random sampling, to two other simulated data sets with points distributed among many clusters. We found that SAGE sampling covered significantly more clusters than the random sampling. By defining a fraction of data points as active, we also compared SAGE with random sampling in terms of hit rates. We showed that when the percentage of active points was low, the hit rates obtained by SAGE were always higher than those obtained by random sampling. When the percentage of active points was high, the performance of SAGE, in terms of individual hit rates, depended upon the data structure. However, in all cases, SAGE performed better than random sampling when cluster hit rates were used as the criterion.

Algorithms↗