Proprietary Compounds Research Articles

Discovery of 1-(4-phenoxypiperidin-1-yl)-2-arylaminoethanone stearoyl-CoA desaturase 1 inhibitors

A series of novel stearoyl-CoA desaturase 1 (SCD1) inhibitors were identified by scaffold design based on known SCD1 inhibitors. Large structural changes were made leading to multiple analogs with comparable or improved potency. This approach is valuable for generation of proprietary compounds without conducting a costly high-throughput screening.

What is the Objective of the Mass Balance Study? A Retrospective Analysis of Data in Animal and Human Excretion Studies Employing Radiolabeled Drugs

Mass balance excretion studies in laboratory animals and humans using radiolabeled compounds represent a standard part of the development process for new drugs. From these studies, the total fate of drug-related material is obtained: mass balance, routes of excretion, and, with additional analyses, metabolic pathways. However, rarely does the mass balance in radiolabeled excretion studies truly achieve 100% recovery. Many definitions of cutoff criteria for mass balance that identify acceptable versus unacceptable recovery have been presented as ad hoc statements without a strong rationale. To address this, a retrospective analysis was undertaken to explore the overall performance of mass balance studies in both laboratory animal species and humans using data for 27 proprietary compounds within Pfizer and extensive review of published studies. The review has examined variation in recovery and the question of whether low recovery was a cause for concern in terms of drug safety. Overall, mean recovery was greater in rats and dogs than in humans. When the circulating half-life of total radioactivity is greater than 50 h, the recovery tends to be lower. Excretion data from the literature were queried as to whether drugs linked with toxicities associated with sequestration in tissues or covalent binding exhibit low mass balance. This was not the case, unless the sequestration led to a long elimination half-life of drug-related material. In the vast majority of cases, sequestration or concentration of drug-related material in an organ or tissue was without deleterious effect and, in some cases, was related to the pharmacological mechanism of action. Overall, from these data, recovery of radiolabel would normally be equal to or greater than 90%, 85%, and 80% in rat, dog, and human, respectively. Since several technical limitations can underlie a lack of mass balance and since mass balance data are not sensitive indicators of the potential for toxicity arising via tissue sequestration, absolute recovery in humans should not be used as a major decision criteria as to whether a radiolabeled study has met its objectives. Instead, the study should be seen as an integral part of drug development answering four principal questions: 1) Is the proposed clearance mechanism sufficiently supported by the identities of the drug-related materials in excreta, so as to provide a complete understanding of clearance and potential contributors to interpatient variability and drug-drug interactions? 2) What are the drug-related entities present in circulation that are the active principals contributing to primary and secondary pharmacology? 3) Are there findings (low extraction recovery of radiolabel from plasma, metabolite structures indicative of chemically reactive intermediates) that suggest potential safety issues requiring further risk assessment? 4) Do questions 2 and 3 have appropriate preclinical support in terms of pharmacology, safety pharmacology, and toxicology? Only if one or more of these four questions remain unanswered should additional mass balance studies be considered.

Towards an Understanding of the Structurally Based Potential for Mechanically Activated Disordering of Small Molecule Organic Crystals

The potential for various small molecule organic crystals to undergo complete mechanically induced disordering is investigated. A model is proposed, which considers changes in free energy required for lattice incorporation of a critical dislocation density. Application requires knowledge of a few physical properties, namely the elastic shear modulus, Burgers vector magnitude, molar volume, melting temperature, and heat of fusion. The model was tested using seven compounds; acetaminophen, aspirin, γ-indomethacin, salicylamide, sucrose, and two proprietary drug compounds, PFZ1 and PFZ2. Crystalline solids were subjected to high shear, controlled temperature comminution for various durations, after which the samples were examined using powder X-ray diffraction (PXRD) and differential scanning calorimetry (DSC). The results verified that acetaminophen, aspirin, and salicylamide, which were suggested by the model to be resistant to complete mechanical disordering, remained fully crystalline, even after 5 h of milling. Sucrose and γ-indomethacin were both predicted to be susceptible to amorphization, which was confirmed by physical characterization. Single, 3-h grinding experiments were performed on two proprietary compounds, PFZ1 and PFZ2. The model indicated that each should be resistant to complete disordering, a trend held by PFZ1. Evidence of partial disordering of PFZ2 was unexpected and is discussed with respect to possible temperature effects.

Just-in-Time Purification: An Effective Solution for Cherry-Picking and Purifying Active Compounds from Large Legacy Libraries

Many companies possess a compound collection consisting of purified compounds and of unpurified products from combinatorial libraries. Using commercial and proprietary compounds as examples, this report provides clear examples of the significant impact purification can have on the activity observed for a compound and highlights the need to retest the purified compounds prior to creating structure-activity relationships. Crude mixtures made with commercial compounds led to an increase in the number of false positives in the SXR-GAL4 assay as compared with their pure and purified counterparts. An examination of proprietary compounds in an HIV assay resulted in the purification of 61 active crude synthetic mixtures. Of these 61 compounds, 32 were 5-fold less active and 2 were 5-fold more active after purification. This report details a semiautomated process developed and implemented for cherry-picking, tracking, and selectively purifying compounds found active in high-throughput screening campaigns.

Rapid in vivo oral screening in rats: Reliability, acceptance criteria, and filtering efficiency

The reliability and acceptance criteria of rapid oral exposure screening were evaluated by pharmacokinetic simulations and by comparing oral exposure of 100 proprietary compounds from 15 therapeutic programs obtained at different times by cassette accelerated rapid rat screen (CARRS) and conventional pharmacokinetic (full-PK) procedures. Once acceptance criteria were established, the filtering efficiency (discard rate) was assessed with a larger data set of 5289 compounds tested by CARRS only. These evaluations indicated that area under the concentration-time curve during the first 6 hours (AUC(6h)) captured >50% of AUC(infinity) for most (71%) of the compounds and AUC(6h) from CARRS is comparable to AUC(6h) from full-PK in categorizing oral exposure as low, moderate, or high; therefore, the truncated AUC(6h) derived from pooled plasma samples is suitable for oral exposure screening. The CARRS profiles did not provide reliable half-life estimates; however, compounds with substantial AUC beyond 6 hours can be identified when (C(6h)/Cmax x 100%) exceeds 80%. Of interest, both the observed data and the simulated data indicated that AUC(6h) can be estimated using a single time point plasma concentration at 3 hours. The relationship between the maximum bioavailability and AUC(infinity) over a range of clearance values was simulated. A threshold AUC (500 h*ng/mL) at the routine screening dose of 10 mg/kg was established below which a compound can be discarded. Examination of screening results for 5289 compounds evaluated over the last few years in our laboratory indicated that CARRS had a filtering efficiency of 50%, suggesting that this criterion provides a useful decision gate to avoid wasting the drug discovery resources on nonviable candidates.

Improved toxicogenomic screening for drug-induced phospholipidosis using a multiplexed quantitative gene expression ArrayPlate assay

We previously showed that a toxicogenomics analysis of drug-induced phospholipidosis enabled the identification of 12 specific gene markers and the establishment of an in vitro real-time PCR screening assay for the assessment of the phospholipidosis-inducing potential of compounds. The purpose of this study was to transfer our PCR-based assay into a 96-well microplate-based multiple mRNAs measuring assay (ArrayPlate™ assay) in order to increase throughput. Specifically, we determined the expression of the 12 marker genes using real-time PCR and ArrayPlate in human hepatoma HepG2 cells that were treated for 24 h with each of amiodarone and 80 proprietary compounds. The following three performance criteria were satisfied in the ArrayPlate analysis: 1. Sensitivity—the expression of mRNA for all target genes was detected at quantifiable levels. 2. Repeatability—signal intensities and fold change values of each marker gene were highly repeatable. 3. Correlation—fold change values and their average values, which were used as indices of phospholipidosis induction potential, showed apparent correlation between the ArrayPlate and real-time PCR assays. Thus, the in vitro screening assay for compound-induced phospholipidosis should be transferable from a PCR-based assay to the higher-throughput ArrayPlate-based method.

Measurement of drug–protein binding by immobilized human serum albumin-HPLC and comparison with ultrafiltration

An HPLC method employing CHIRAL-I (150 mm x 3 mm), 5 microm column from Chrom. Tech., immobilized with human serum albumin (HSA), was used to determine in vitro protein binding of several compounds. Experimentally obtained plasma protein data exhibited good correlation with the reported values. The method was compared with the conventional ultra filtration technique and both yielded similar results. Proprietary compounds that could not be analyzed by ultra filtration due to high non-specific binding to filter membrane were successfully analyzed by HSA-HPLC method. On the other hand, two proprietary compounds did not elute from HSA column due to strong binding, but were successfully analyzed by ultra filtration. This proves that both the techniques have their own merits and demerits and should be exploited judiciously as per the requirement. The plasma protein binding studies conducted on four gyrase inhibitors in rat and human plasma exhibited no interspecies difference via ultra filtration method. Further, it was also observed that the protein binding obtained for the four gyrase inhibitors by HSA-HPLC method was not only similar to that obtained by ultra filtration in human plasma but was also in accordance with ex vivo and in vitro protein binding obtained for rat plasma after ultra filtration because these compounds predominantly bind to HSA The binding of several compounds to alpha1-acid glycoprotein (AGP), another important plasma protein, was also examined using AGP immobilized column. However, the data could not be relied upon since some anti-bacterials and non-steroidal anti-inflammatory drugs (NSAIDS), which are known to predominantly bind to HSA, were also found to bind to AGP.

A Hybrid Mixture Discriminant Analysis−Random Forest Computational Model for the Prediction of Volume of Distribution of Drugs in Human

A computational approach is described that can predict the VD(ss) of new compounds in humans, with an accuracy of within 2-fold of the actual value. A dataset of VD values for 384 drugs in humans was used to train a hybrid mixture discriminant analysis-random forest (MDA-RF) model using 31 computed descriptors. Descriptors included terms describing lipophilicity, ionization, molecular volume, and various molecular fragments. For a test set of 23 proprietary compounds not used in model construction, the geometric mean fold-error (GMFE) was 1.78-fold (+/-11.4%). The model was also tested using a leave-class out approach wherein subsets of drugs based on therapeutic class were removed from the training set of 384, the model was recast, and the VD(ss) values for each of the subsets were predicted. GMFE values ranged from 1.46 to 2.94-fold, depending on the subset. Finally, for an additional set of 74 compounds, VD(ss) predictions made using the computational model were compared to predictions made using previously described methods dependent on animal pharmacokinetic data. Computational VD(ss) predictions were, on average, 2.13-fold different from the VD(ss) predictions from animal data. The computational model described can predict human VD(ss) with an accuracy comparable to predictions requiring substantially greater effort and can be applied in place of animal experimentation.

Short Hairpin RNA Loop Design for the Facilitation of Sequence Verification

cially available proprietary compounds, have been used in a trial-and-error fashion to relax the hairpin secondary structure of the single-stranded DNA plasmids during sequencing reactions. We sought to design a universal loop region that could facilitate the sequence verification of shRNA encoding plasmids. While several algorithms have been developed for the design of the stem portion of an shRNA molecule, such systematic studies have not been reported for the loop region. Given the wide variety of loop region sequences used by individual investigators and the ability of Dicer to efficiently process RNA duplexes lacking loop regions (9), we inferred that the actual nucleotide sequence of the loop is likely subject to minimal constraints. We therefore chose a loop sequence beginning with an “A” followed by the recognition site for the nonpalindromic restriction endonuclease BmgBI (5′-A[CACGTC]3′). Due to its nonpalindromic

Computational Models for Identifying Potential P-Glycoprotein Substrates and Inhibitors

Multidrug resistance mediated by ATP binding cassette (ABC) transporters such as P-glycoprotein (P-gp) represents a serious problem for the development of effective anticancer drugs. In addition, P-gp has been shown to reduce oral absorption, modulate hepatic, renal, or intestinal elimination, and restrict blood-brain barrier penetration of several drugs. Consequently, there is a great interest in anticipating whether drug candidates are P-gp substrates or inhibitors. In this respect, two different computational models have been developed. A method for discriminating P-gp substrates and nonsubstrates has been set up based on calculated molecular descriptors and multivariate analysis using a training set of 53 diverse drugs. These compounds were previously classified as P-gp substrates or nonsubstrates on the basis of the efflux ratio from Caco-2 permeability measurements. The program Volsurf was used to compute the compounds' molecular descriptors. The descriptors were correlated to the experimental classes using partial least squares discriminant analysis (PLSD). The model was able to predict correctly the behavior of 72% of an external set of 272 proprietary compounds. Thirty of the 53 previously mentioned drugs were also evaluated for P-gp inhibition using a calcein-AM (CAM) assay. On the basis of these additional P-gp functional data, a PLSD analysis using GRIND-pharmacophore-based descriptors was performed to model P-gp substrates having poor or no inhibitory activity versus inhibitors having no evidence of significant transport. The model was able to discriminate between 69 substrates and 56 inhibitors taken from the literature with an average accuracy of 82%. The model allowed also the identification of some key molecular features that differentiate a substrate from an inhibitor, which should be taken into consideration in the design of new candidate drugs. These two models can be implemented in a virtual screening funnel.

An assessment of the utility of the yeast GreenScreen assay in pharmaceutical screening

In this paper we describe an initial reproducibility study of 12 proprietary compounds followed by the assessment of 51 marketed pharmaceuticals and, lastly, a summary of the data so far from 2698 proprietary compounds from the Johnson & Johnson (J&J) compound library, in the yeast GreenScreen assay (GSA). In this assay, a reporter system in the yeast cells employs the DNA damage inducible promoter of the RAD54 gene, fused to the extremely stable green fluorescent protein (GFP). The assay proved to be very robust, the Excel templates provided by Gentronix with the assay interfaced well with in-house J&J systems with little adaptation, the assay was very rapid to perform and used very little compound. The results confirm previous work which suggests that the yeast GSA detects different classes of genotoxic compounds to the Ames assay and as a result can help screen out important genotoxic compounds at the pre-regulatory test phase that are missed by Ames-test-based screens alone. A combination of SAR evaluation of genotoxicity plus an Ames-test-based screen and the GSA provides a powerful pre-regulatory test battery to aid in the selection of successful drug candidates.

Ablation of Transparent Materials Using Excimer Lasers for Photonic Applications

For many years, the development of effective ablation or laser machining techniques for making micro-optical components has been the key factor in the birth of new photonic devices and systems. In this article, the ablation characteristics of two types of the most important transparent materials, transparent polymers and glasses, are studied. Simple shaped microcavities are first machined for studying the fundamental ablation parameters, including threshold fluence, effective absorption coefficient, and ablation rate. In studying polymer ablation, five standard grades and five proprietary polymeric compounds are selected. Ablation techniques using these transparent polymers for making arrayed ferrules and curved microlenses are presented. Applications of these ablated microstructures for optical fiber connectors, optical fiber coupling and alignment, and transparent chip encapsulants, are introduced and demonstrated with emphasis on the quality of the ablated profiles and dimensions to satisfy the required performance. In glass ablation, borosilicate glasses are considered and their associated ablation behaviors are studied. The procedures to ablate glass-based arrayed microstructures with flat and curved surfaces are described. The utilizations of these arrayed microstructures for optical waveguide, wave absorber, and beam guider, are specifically discussed. Finally, concluding remakes for future trends are presented.

Characterisation of sulphoxides by atmospheric pressure ionisation mass spectrometry

An observation that a series of proprietary compounds containing a methyl thiophenyl group all underwent metabolic S-oxidation, and that the product ion spectra of the resulting S-oxides showed methyl radical loss under low-energy atmospheric pressure ionisation tandem mass spectrometry (API-MS/MS) conditions, has led to an investigation of the fragmentation of commercially available sulphoxides. The phenyl methyl sulphoxides studied do lose methyl radicals under MS/MS conditions on triple quadrupole mass spectrometers. In addition, the phenyl sulphoxides, with simple substituents other than a methyl group, also showed a tendency to lose the substituent as a radical. It was concluded that radical loss from these simple sulphoxides was characteristic of S-oxidation of these molecules. Radical losses, such as those reported here, are used in-house to distinguish S-oxidation from N- and C-oxidation in metabolism studies.

Validation of a high‐throughput absorption, distribution, metabolism, and excretion (ADME) system and results for 60 literature compounds

A high-throughput analytical system for the support of absorption, distribution, metabolism, and excretion (ADME) was constructed in collaboration with Gubbs Inc. to commercialize corresponding software. We sought to quickly build and validate this system for microsomal clearance assessment using 60 commercially available non-proprietary compounds that are non-DEA-restricted in addition to 36 proprietary Millennium compounds that had already been assessed using a low-throughput infrastructure. The system was constructed such that a approximately 45 second total cycle time was achieved injection-to-injection. Software was successfully coded to enable the analyst to submit multiple batches, and modify multiple methods very quickly for use with Applied Biosystems Analyst 1.3. After acquisition the software was used to simultaneously integrate multiple injection chromatograms, regress the data, and calculate clearance such that all of the data could be easily and immediately reviewed by both bioanalytical and enzymology personnel. Unfortunately, despite an exhaustive search of the literature, we were unable to find a large number of non-proprietary compound data for validation, so we provide such a source of data here. Results are presented for the 60 literature compounds that were assessed. A good correlation was observed between literature results for 16 compounds that we were able to find and the results obtained using the system. The Millennium proprietary compounds that we assessed using both low- and high-throughput approaches also correlated well. We present here a system for the support of high-throughput in vitro ADME analysis and also present the results of 60 non-proprietary, non-DEA-scheduled compounds to facilitate the validation efforts of others. Finally, we present commercially available software to facilitate high-throughput ADME systems in the community.

Quantitative PCR assay for cytochromes P450 2B and 3A induction in rat precision-cut liver slices: Correlation study with induction in vivo

Introduction In drug development, new chemical entities that cause cytochrome P450 induction are considered to be undesirable since P450 induction is linked to tumor formation and may compromise the evaluation of drug safety when autoinduction results in poor drug exposure. Methods We evaluated the use of the precision-cut liver slice as a model for measuring induction of cytochrome P450 in rats. Quantitative real-time reverse-transcription polymerase chain reaction was used to analyze the induction of selected forms of cytochrome P450 at the mRNA level. Firstly, the system was validated against known inducers of CYP2B and 3A. Subsequently, 26 proprietary compounds were tested in rat liver slices and rats in vivo for CYP2B and 3A induction. Results Exposure of liver slices to the known CYP2B inducers phenobarbital, benzoyl-pyridine, cabarmazepine, metyrapone, RU486 and dexamethasone caused elevation of CYP2B1/2 expression 10- to 40-fold compared to the control values. The CYP3A inducers PCN, dexamethasone, nicardipine, nifedipine, clotrimazole and RU486 induced a 4- to 50-fold expression of CYP3A14. For 26 proprietary compounds, a correlation with an R 2 value of 0.74 was established between the induction of CYP2B expression in liver slices and that in rats in vivo. When liver slice results were used to predict the induction of CYP2B in rats in vivo, the success rate was 91%. The induction of CYP3A in rats in vivo was analyzed by Western blot, then quantified by densitometry. There was a good correlation between CYP3A induction in liver slices and induction in vivo as assessed by Western blot, with an 86% positive prediction rate. Discussion The use of liver slices in combination with TaqMan technology provides a good model for predicting CYP induction in the rat. This method is useful for identifying compounds with CYP2B and 3A induction liability in the early phase of drug discovery.

Development of CYP3A4 Inhibition Models: Comparisons of Machine-Learning Techniques and Molecular Descriptors

Computational models of cytochrome P450 3A4 inhibition were developed based on high-throughput screening data for 4470 proprietary compounds. Multiple models differentiating inhibitors (IC(50) <3 microM) and noninhibitors were generated using various machine-learning algorithms (recursive partitioning [RP], Bayesian classifier, logistic regression, k-nearest-neighbor, and support vector machine [SVM]) with structural fingerprints and topological indices. Nineteen models were evaluated by internal 10-fold cross-validation and also by an independent test set. Three most predictive models, Barnard Chemical Information (BCI)-fingerprint/SVM, MDL-keyset/SVM, and topological indices/RP, correctly classified 249, 248, and 236 compounds of 291 noninhibitors and 135, 137, and 147 compounds of 179 inhibitors in the validation set. Their overall accuracies were 82%, 82%, and 81%, respectively. Investigating applicability of the BCI/SVM model found a strong correlation between the predictive performance and the structural similarity to the training set. Using Tanimoto similarity index as a confidence measurement for the predictions, the limitation of the extrapolation was 0.7 in the case of the BCI/SVM model. Taking consensus of the 3 best models yielded a further improvement in predictive capability, kappa = 0.65 and accuracy = 83%. The consensus model could also be tuned to minimize either false positives or false negatives depending on the emphasis of the screening.

Effect of quorum sensing agents on the growth kinetics of Pseudomonas spp. of raw milk origin

Psychrotrophs, particularly strains of Pseudomonas fluorescens, dominate the microflora of refrigerated raw milk and secrete heat-stable extracellular enzymes (proteases and lipases) which survive pasteurisation and even UHT heat treatments and degrade the casein and fat components of raw milk causing a reduction in cheese yield, gelation of UHT milk and off flavours in many dairy products. These enzymes are usually produced in the late log/early stationary growth phases when the cell density is high. This fact indicated that induction of these enzymes may be a candidate for quorum sensing, a phenomenon by which bacteria can sense and respond to cell population size by means of chemical signals based on the homoserine lactone molecule. It is assumed that the production of these enzymes contributes to the selective advantage of psychrotrophs and hence have a significant effect on their growth kinetics. In the work reported here nine proprietary homoserine lactone compounds were screened, using water as a control, for their effect on the lag phase duration (LPD) and exponential growth rate (EGR) of three strains of Pseudomonas fluorescens isolated from refrigerated raw milk after 1, 3 and 5 days storage. Two compounds viz. N-benzoyloxycarbonyl-L-homoserine lactone and N-3-oxyhexanoyl-DL-homoserine lactone were found to significantly (P < 0.001) reduce the LPD and increase the EGR of the three strains. Further work with these compounds is warranted, monitoring growth in parallel with enzyme production, to determine the extent to which extracellular enzyme production is mediated by the quorum sensing phenomenon in this species.

Screening approach for chiral separation of pharmaceuticals: Part III. Supercritical fluid chromatography for analysis and purification in drug discovery

High-throughput and performance analysis and purification of enantiomers are important parts of drug discovery and provide high-quality compounds for pharmacological testing. We have previously reported two parts describing chiral chromatographic screens using normal-phase (NPLC) and reversed-phase (RPLC) liquid chromatography, in order to cope with increasing numbers of new compounds generated by chemistry programs. We present in this part the development and implementation of a third faster screen using supercritical fluid chromatography (SFC) to maximize chance in achieving rapid enantiomer resolution of large numbers of compounds in a minimum of time. The SFC screen utilizes a narrow combination of only four columns (Chirlapak AD and AS, and Chiralcel OD and OJ) and two solvent modifiers (methanol and isopropanol). A modifier and column-switching setup was employed to allow the entire screening process to be serially run in the order AD > OD > OJ > AS and methanol > isopropanol, so that the screening for a given molecule can be stopped when separation is achieved. The switching system was fully automated for unattended operation of multiple compounds. An optimization procedure was also defined, which can be performed if needed for unsuccessful separations in the screening step. The chiral SFC strategy proved its performance and robustness in resolution of hundreds proprietary chiral molecules generated by drug discovery programs, with a success rate exceeding 95%. In addition, the generic capability of the strategy was evaluated by applying the screen and optimization methodology to a test set comprising 40 marketed drugs differing from proprietary compounds in terms of chemical diversity, revealing a similar high success rate of 98%. Chiral separations developed at the analytical scale work easily and equally well at the semi-preparative level, as illustrated with an example. The SFC screen allows resolution of compounds that were partially separated by NPLC or not separated at all by RPLC, demonstrating the utility of implementing complementary chromatographic techniques. The SFC screen is currently an integral part of our analytical support to discovery chemical programs and is considered the first try for chiral separations of new compounds, because it offers a higher success rate, performance and throughput.

A novel liquid chromatography/tandem mass spectrometry based depletion method for measuring red blood cell partitioning of pharmaceutical compounds in drug discovery

A novel liquid chromatography/tandem mass spectrometry (LC/MS/MS)-based depletion method for measuring compound partitioning between human plasma and red blood cells (RBC) in a drug discovery environment is presented. Conventionally, RBC partitioning is determined by separate measurements of drug concentrations in equilibrating plasma and whole blood or RBC using separate standards prepared in their respective matrices, i.e., in plasma and whole blood or RBC lysates. The process is very tedious, labor-intensive, and difficult to automate. In addition, interferences from the heme and other highly abundant cellular composites make the measurement of the drug concentration in whole blood or RBC inevitably variable even with a highly specific LC/MS/MS method. Therefore, there is an imminent need to develop a straightforward and fast method to assess the partitioning of drug-like compounds in RBC. This work describes an LC/MS/MS-based depletion assay that measures the compound concentration in plasma that has been equilibrating with RBC. Compounds were spiked into fresh human whole blood and plasma respectively to a final concentration of 500 nM. Both the spiked whole blood and plasma control were incubated at 37 degrees C for up to 60 min. During the time course, aliquots of plasma and whole blood from both incubation mixtures were sampled at 10 and 60 min. The whole blood samples were centrifuged to yield the plasma. The plasma samples from both incubations were extracted using a protein precipitation method, and analyzed using LC/MS/MS under the multiple-reaction monitoring (MRM) mode. The RBC partitioning ratio was calculated using the analyte peak area responses of the plasma samples through an equation deduced in this work. The method was first tested using two commercial compounds, phenoprobamate and acetazolamide, to determine the optimal incubation conditions and the concentration dependency of the assay. The assay reproducibility was also assessed by three inter-day assays for phenoprobamate. This method was further evaluated using 20 commercial compounds of different classes with a wide range of RBC partitioning coefficients and the results were compared with those reported in the literature. Excellent correlation (R2=0.9396) was found between the measured and literature values. In addition, several proprietary compounds were assayed using both the new and traditional methods and the measured partitioning ratios from the two methods are equivalent. The experiments in this work demonstrate that the LC/MS/MS-based depletion method can provide direct and accurate measurement of RBC partitioning for compounds in drug discovery.

Valuation and design of pharmaceutical R&amp;D licensing deals

AbstractIn today's intensely competitive business environment, pharmaceutical companies are augmenting their product pipelines by both developing drugs on their own and in‐licensing proprietary compounds or drug discovery–related technologies from smaller biotechnology companies. In this work, the OptFolio model of pharmaceutical R&amp;D portfolio management is extended to evaluate partnership opportunities as real options and determine the optimal timing and investment policy for proposed alliances in the face of technological and market uncertainties and budgetary restrictions. Licensing deals are modeled within a decision tree as a series of continuation/abandonment options for the pharmaceutical company, deciding at each stage of R&amp;D whether to make a predetermined milestone payment to continue the alliance or terminate the alliance because of unfavorable market conditions and/or internal resource limitations. Results indicate that early stage alliances become more valuable as market uncertainty and the ability of pharmaceutical companies to enhance the value of the licensed drug increase because of the ability to control downside risk by the abandonment option. © 2004 American Institute of Chemical Engineers AIChE J, 51: 198–209, 2005