Population PBPK modeling using parametric and nonparametric methods of the Simcyp Simulator, and Bayesian samplers

Physiologically‐based pharmacokinetic (PBPK) models usually include a large number of parameters whose values are obtained using in vitro to in vivo extrapolation. However, such extrapolations can be uncertain and may benefit from inclusion of evidence from clinical observations via parametric inference. When clinical interindividual variability is high, or the data sparse, it is essential to use a population pharmacokinetics inferential framework to estimate unknown or uncertain parameters. Several approaches are available for that purpose, but their relative advantages for PBPK modeling are unclear. We compare the results obtained using a minimal PBPK model of a canonical theophylline dataset with quasi‐random parametric expectation maximization (QRPEM), nonparametric adaptive grid estimation (NPAG), Bayesian Metropolis‐Hastings (MH), and Hamiltonian Markov Chain Monte Carlo sampling. QRPEM and NPAG gave consistent population and individual parameter estimates, mostly agreeing with Bayesian estimates. MH simulations ran faster than the others methods, which together had similar performance.

Collaborating to Compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium

The cancer community understands the value of blood profiling measurements in assessing and monitoring cancer. We describe an effort among academic, government, biotechnology, diagnostic, and pharmaceutical companies called the Blood Profiling Atlas in Cancer (BloodPAC) Project. BloodPAC will aggregate, make freely available, and harmonize for further analyses, raw datasets, relevant associated clinical data (e.g., clinical diagnosis, treatment history, and outcomes), and sample preparation and handling protocols to accelerate the development of blood profiling assays.

Abstract PD8-05: Comparative analysis of the genomic landscape of breast cancers from women of African and European ancestry

Objectives: Paucity of data on populations of African Ancestry in clinical trials continues to limit our ability to design and implement innovative solutions to narrow the breast cancer survival gap amongst Africans, African Americans, and European Americans. We have developed a cross-continent research infrastructure to examine the spectrum of genomic alterations in breast tumors from West Africa and subsequently, to compare them to tumors from African American women and women of European Ancestry in The Cancer Genome Atlas (TCGA) database.

Methods: Consecutive women with breast cancer presenting for treatment at the University College Hospital, Ibadan and at Lagos State University Teaching Hospital, Lagos, Nigeria gave informed consent and were recruited to the West African Breast Cancer Study (WABCS) between 2013-2016. Tumor-normal pairs were subjected to exome and/or high-depth (90x) genome sequencing. High confidence somatic mutations (substitutions, insertions/deletions and structural variants) were obtained by using multiple variant callers. Furthermore, 1,089 exomic and 80 genomic breast tumor-normal pairs from TCGA were harmonized with WABCS samples, resulting in a cohort of 147 West Africans (147 exome; 40 genome), 154 African Americans (154 exome; 31 genome), and 776 Caucasians (776 exome; 43 genome).

Results: Across the exomes, genes commonly altered in breast cancer in TCGA are also altered in women of African ancestry, but the mutational spectrum is quite different, demonstrating overrepresentation of tumors with aggressive phenotypes. Overall, TP53 (65%), ERBB2 (27%), and GATA3 (17%) showed statistically significant higher alteration frequencies in West Africans and African Americans. In contrast, PIK3CA (24%) was less frequently mutated. Of note, GATA3 mutation was statistically significantly more frequent in Nigerians (39%) and African Americans (16.7%) compared to Caucasians (10.5%), in ER-positive cancers. Analysis on Structural Variants (SV), on the other hand, has shown that the genome-wide SV counts among three populations are comparable in ER-negative cancers, while Nigerians have significantly more SV counts compared to African Americans (P=0.0013) or European Americans (P=2.9x10-5) in ER-positive cancers. Similarly, genome-wide substitution patterns in ER+ and ER- cancers varied widely by race/ethnicity. In ER- cases, West Africans carried the highest proportion of canonical APOBEC-associated substitutions, particularly C>T transitions. Conversely, European Americans with ER+ disease showed a higher proportion of C>T than both West Africans (Welch t-test P = 0.044) and African Americans (Welch t-test P = 0.011). Mutation signature analyses highlighted multiple APOBEC signatures, with notable contribution differences across ancestry and ER status. A signature likely corresponding to DNA damage repair correlated with the proportion of genetic ancestry, being most prevalent in European Americans and least common in Nigerians, particularly in ER-negative cancers, with African Americans showing a degree of this signature's contribution in between the two populations (linear model adjusted for age, P=1.0x10-10).

Conclusions: Overall, our data suggests mutation spectra differences in across race/ethnicity and geography. Identification of molecular characteristics such as higher rates of HER2 enriched tumors and higher rates of GATA3 mutations in ER positive tumors are beginning to reveal the genomic basis of race-associated phenotypes and outcomes in breast cancer. Population differences in frequency and spectrum of mutations should now inform the design of innovative clinical trials that improve health equity and accelerate Precision Oncology care in diverse populations.

Citation Format: Olopade OI, Pitt JJ, Riester M, Odetunde A, Yoshimatsu T, Labrot E, Ademola A, Sanni A, Okedere B, Mahan S, Nwosu I, Leary R, Ajani M, Johnson RS, Sveen E, Zheng Y, Wang S, Fitzgerald DJ, Grundstad J, Tuteja J, Clayton W, Khramtsova G, Oludara M, Omodele F, Benson O, Adeoye A, Morhason-Bello O, Ogundiran T, Babalola C, Popoola A, Morrissey M, Chen L, Huo D, Falusi A, Winckler W, Obafunwa J, Papoutsakis D, Ojengbede O, White KP, Ibrahim N, Oluwasola O, Barretina J. Comparative analysis of the genomic landscape of breast cancers from women of African and European ancestry [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD8-05.

Abstract P6-03-17: Genomic landscape of breast cancers from women of African ancestry across the diaspora

Objectives: Of all ethnic/racial groups, age-standardized mortality rate from breast cancer is highest for African American women in the US for reasons that remain understudied. The paucity of genomic studies of breast tumors across the African Diaspora further restricts our understanding of the biology of breast cancer in underserved populations. To gain a better understanding of the genomic landscape of breast cancer in women of African Ancestry, we have developed a cross continent translational research infrastructure to examine the spectrum of genetic alterations in breast tumors from West Africa compared to the spectrum of alterations observed in tumors from African-American and other women who are predominantly white in The Cancer Genome Atlas (TCGA) dataset.

Methods: Peripheral blood and breast cancer biopsy tissues were collected from 214 patients enrolled in the West Africa Breast Cancer Study (WABCS) at the University of Ibadan/University College Hospital (UI/UCH) and at Lagos State University Teaching Hospital (LASUTH). Blood DNA as well as breast cancer tissue DNA and RNA were extracted at the Novartis Institutes for Biomedical Research (NIBR), UI/UCH, and LASUTH using a modified protocol of PAXgene Tissue DNA and RNA extraction method. Whole-exome (WES) and transcriptome (RNA-seq) sequencing were performed on the Illumina HiSeq2000 platform at NIBR. Single Nucleotide Variants (SNVs) and insertions/deletions (indels) were called using MuTect and Pindel, while Copy Number Alterations (CNAs) were called using an in-house implementation of the ABSOLUTE method. Observed mutations were compared against those reported in the TCGA dataset. ER, PR and HER2 status were determined by immunohistochemistry (IHC) at UI/UCH, LASUTH and UChicago.

Results: WES data for 95 tumors have been analyzed thus far. Genes commonly mutated in breast cancer in TCGA are also mutated in WABCS but the mutational spectrum is vastly different. TP53 (64%), MYC (31%), and GATA3 (26%), showed significantly higher alteration frequencies in WABCS and African Americans. In contrast, PIK3CA (20%), CDH1 (2%), and MAP3K1 (2%) were less frequently mutated in women of African ancestry. In addition to the high proportion with TP53 mutations, the proportion with HER2 positive subtype of 42.1% and triple-negative subtype of 37.9% suggest that tumors with the most aggressive features are overrepresented in breast cancer patients in West Africa.

Conclusions: In the first study of its kind, high throughput genomic analysis of the largest cohort of women of African ancestry has uncovered alterations in cancer genes, some of which may be amenable to treatment with targeted therapies. Furthermore, we provide evidence that population differences in frequency and spectrum of mutations should drive the design and deployment of precision medicine initiatives. Only then can we develop innovative interventions to reduce the unacceptably high rates of mortality from breast cancer in underserved and under resourced populations.

Citation Format: Olopade OI, Odetunde A, Riester M, Yoshimatsu T, Labrot E, Ademola A, Sanni A, Okedere B, Mahan S, Nwosu I, Leary R, Ajani M, Johnson RS, Sveen E, Zheng Y, Clayton W, Khramtsova G, Oludara M, Omodele F, Benson O, Adeoye A, Morhason-Bello O, Ogundiran T, Babalola C, Popoola A, Morrissey M, Huo D, Falusi A, Winckler W, Obafunwa J, Papoutsakis D, Ojengbede O, Ibrahim N, Oluwasola O, Barretina J. Genomic landscape of breast cancers from women of African ancestry across the diaspora. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-17.

Two general methods for population pharmacokinetic modeling: non-parametric adaptive grid and non-parametric Bayesian

Population pharmacokinetic (PK) modeling methods can be statistically classified as either parametric or nonparametric (NP). Each classification can be divided into maximum likelihood (ML) or Bayesian (B) approaches. In this paper we discuss the nonparametric case using both maximum likelihood and Bayesian approaches. We present two nonparametric methods for estimating the unknown joint population distribution of model parameter values in a pharmacokinetic/pharmacodynamic (PK/PD) dataset. The first method is the NP Adaptive Grid (NPAG). The second is the NP Bayesian (NPB) algorithm with a stick-breaking process to construct a Dirichlet prior. Our objective is to compare the performance of these two methods using a simulated PK/PD dataset. Our results showed excellent performance of NPAG and NPB in a realistically simulated PK study. This simulation allowed us to have benchmarks in the form of the true population parameters to compare with the estimates produced by the two methods, while incorporating challenges like unbalanced sample times and sample numbers as well as the ability to include the covariate of patient weight. We conclude that both NPML and NPB can be used in realistic PK/PD population analysis problems. The advantages of one versus the other are discussed in the paper. NPAG and NPB are implemented in R and freely available for download within the Pmetrics package from www.lapk.org.

4-N-pyridin-2-yl-benzamide nanotubes compatible with mouse stem cell and oral delivery in Drosophila

p-aminobenzoic acid (PABA), a structural moiety of many commercial drugs, is self-assembled with linker alkyl side chains to form tubular nanostructures. The tubes exhibited fluorescence either intrinsic or from fluorescent molecules embedded in the wall during self-assembly. Uptake and inter-cellular delivery of the conjugated nanotubes in human cancer cells and in mouse embryonic stem cells were demonstrated by fluorescence imaging and flow cytometry. Biocompatibility, cytotoxicity and clearance were monitored both ex vivo in mouse multipotent embryonic stem cells and in vivo in adult Drosophila. Accumulation of nanotubes had no adverse effects and abnormalities on stem cell morphology and proliferation rate. A distinct distribution of two separate nanotubes in various internal organs of Drosophila interprets that accumulation of nanomaterials might be interdependent on the side chain modifications and physiological settings of cell or tissue types. Unlike carbon nanomaterials, exposure of PABA nanotubes does not produce any hazards including locomotion defects and mortality of adult flies. Despite differential uptake and clearance from multiple live tissues, the use of self-assembled nanotubes can add new dimensions and scope to the development of dual-purpose oral carriers for the fulfilment of many biological promises.

Impact of Drug‐Exposure Intensity and Duration of Therapy on the Emergence ofStaphylococcus aureusResistance to a Quinolone Antimicrobial

We have shown previously in animal model and in vitro systems that antimicrobial therapy intensity has a profound influence on subpopulations of resistant organisms. Little attention has been paid to the effect of therapy duration on resistant subpopulations. We examined the influence of therapy intensity (area under the concentration/time curve for 24 h:minimum inhibitory concentration [AUC24:MIC] ratio) and therapy duration on resistance emergence using an in vitro model of Staphylococcus aureus infection. AUC24:MIC ratios of>or=100 were necessary to kill a substantial portion of the total population. Importantly, we demonstrated that therapy duration is a critical parameter. As the duration increased beyond 5 days, the intensity needed to suppress the antibiotic-resistant subpopulations increased, even when the initial bacterial kill was>4 log10 (cfu/mL). These findings were prospectively validated in an independent experiment in which exposures were calculated from the results of fitting a large mathematical model to all data simultaneously. All of the prospectively determined predictions were fulfilled in this validation experiment.

Parametric and Nonparametric Population Methods

BACKGROUND AND OBJECTIVES

This study examined parametric and nonparametric population modelling methods in three different analyses. The first analysis was of a real, although small, clinical dataset from 17 patients receiving intramuscular amikacin. The second analysis was of a Monte Carlo simulation study in which the populations ranged from 25 to 800 subjects, the model parameter distributions were Gaussian and all the simulated parameter values of the subjects were exactly known prior to the analysis. The third analysis was again of a Monte Carlo study in which the exactly known population sample consisted of a unimodal Gaussian distribution for the apparent volume of distribution (V(d)), but a bimodal distribution for the elimination rate constant (k(e)), simulating rapid and slow eliminators of a drug.

METHODS

For the clinical dataset, the parametric iterative two-stage Bayesian (IT2B) approach, with the first-order conditional estimation (FOCE) approximation calculation of the conditional likelihoods, was used together with the nonparametric expectation-maximisation (NPEM) and nonparametric adaptive grid (NPAG) approaches, both of which use exact computations of the likelihood. For the first Monte Carlo simulation study, these programs were also used. A one-compartment model with unimodal Gaussian parameters V(d) and k(e) was employed, with a simulated intravenous bolus dose and two simulated serum concentrations per subject. In addition, a newer parametric expectation-maximisation (PEM) program with a Faure low discrepancy computation of the conditional likelihoods, as well as nonlinear mixed-effects modelling software (NONMEM), both the first-order (FO) and the FOCE versions, were used. For the second Monte Carlo study, a one-compartment model with an intravenous bolus dose was again used, with five simulated serum samples obtained from early to late after dosing. A unimodal distribution for V(d) and a bimodal distribution for k(e) were chosen to simulate two subpopulations of 'fast' and 'slow' metabolisers of a drug. NPEM results were compared with that of a unimodal parametric joint density having the true population parameter means and covariance.

RESULTS

For the clinical dataset, the interindividual parameter percent coefficients of variation (CV%) were smallest with IT2B, suggesting less diversity in the population parameter distributions. However, the exact likelihood of the results was also smaller with IT2B, and was 14 logs greater with NPEM and NPAG, both of which found a greater and more likely diversity in the population studied. For the first Monte Carlo dataset, NPAG and PEM, both using accurate likelihood computations, showed statistical consistency. Consistency means that the more subjects studied, the closer the estimated parameter values approach the true values. NONMEM FOCE and NONMEM FO, as well as the IT2B FOCE methods, do not have this guarantee. Results obtained by IT2B FOCE, for example, often strayed visibly away from the true values as more subjects were studied. Furthermore, with respect to statistical efficiency (precision of parameter estimates), NPAG and PEM had good efficiency and precise parameter estimates, while precision suffered with NONMEM FOCE and IT2B FOCE, and severely so with NONMEM FO. For the second Monte Carlo dataset, NPEM closely approximated the true bimodal population joint density, while an exact parametric representation of an assumed joint unimodal density having the true population means, standard deviations and correlation gave a totally different picture.

CONCLUSIONS

The smaller population interindividual CV% estimates with IT2B on the clinical dataset are probably the result of assuming Gaussian parameter distributions and/or of using the FOCE approximation. NPEM and NPAG, having no constraints on the shape of the population parameter distributions, and which compute the likelihood exactly and estimate parameter values with greater precision, detected the more likely greater diversity in the parameter values in the population studied. In the first Monte Carlo study, NPAG and PEM had more precise parameter estimates than either IT2B FOCE or NONMEM FOCE, as well as much more precise estimates than NONMEM FO. In the second Monte Carlo study, NPEM easily detected the bimodal parameter distribution at this initial step without requiring any further information. Population modelling methods using exact or accurate computations have more precise parameter estimation, better stochastic convergence properties and are, very importantly, statistically consistent. Nonparametric methods are better than parametric methods at analysing populations having unanticipated non-Gaussian or multimodal parameter distributions.

Bacterial‐Population Responses to Drug‐Selective Pressure: Examination of Garenoxacin's Effect onPseudomonas aeruginosa

The emergence of resistance to antibiotics is a serious problem often related to suboptimal drug dosing; such suboptimal dosing results in the preferential killing of drug-susceptible microbial subpopulations, allowing amplification of drug-resistant microbial subpopulations. We determined the effect that fluctuating concentrations of quinolone drugs have on both the total population and the resistant subpopulation of Pseudomonas aeruginosa, by employing, over a 48-h period, human pharmacokinetics and multiple regimens in an in vitro-infection model. All data were simultaneously modeled by use of 3 parallel inhomogeneous differential equations. Model parameters were used to derive the minimal, or breakpoint, drug exposure necessary to suppress amplification of the resistant subpopulation. In a prospective-validation study, we found that a drug exposure near to but below the calculated breakpoint amplified the resistant subpopulation, whereas a drug exposure at the breakpoint suppressed it. This approach allows delineation of target drug exposures (area under the concentration/time curve for 24 h : minimal inhibitory concentration [AUC(24) : MIC] = 190) that will suppress amplification of the antibiotic-resistant subpopulation, thereby preserving the susceptibility of target pathogens.

Application of a mathematical model to prevent in vivo amplification of antibiotic-resistant bacterial populations during therapy

The worldwide increase in the prevalence of multi-antibiotic-resistant bacteria has threatened the physician's ability to provide appropriate therapy for infections. The relationship between antimicrobial drug concentration and infecting pathogen population reduction is of primary interest. Using data derived from mice infected with the bacterium Pseudomonas aeruginosa and treated with a fluoroquinolone antibiotic, a mathematical model was developed that described relationships between antimicrobial drug exposures and changes in drug-susceptible and -resistant bacterial subpopulations at an infection site. Dosing regimens and consequent drug exposures that amplify or suppress the emergence of resistant bacterial subpopulations were identified and prospectively validated. Resistant clones selected in vivo by suboptimal regimens were characterized. No mutations were identified in the quinolone resistance-determining regions of gyrA/B or parC/E. However, all resistant clones demonstrated efflux pump overexpression. At base line, MexAB-OprM, MexCD-OprJ, and MexEF-OprN were represented in the drug-resistant population. After 28 hours of therapy, MexCD-OprJ became the predominant pump expressed in the resistant clones. The likelihood of achieving resistance-suppression exposure in humans with a clinically prescribed antibiotic dose was determined. The methods developed in this study provide insight regarding how mathematical models can be used to identify rational dosing regimens that suppress the amplification of the resistant mutant population.

The use of ultrasound imaging to demonstrate reduced movement of the median nerve during wrist flexion in patients with non-specific arm pain

Following clinical screening, we examined movement of the median nerve at the wrist using high-resolution (10-22 MHz) ultrasound in 16 controls and 12 patients with non-specific arm pain (also referred to as repetitive strain injury). Imaging was performed just proximal to the carpal tunnel with the wrist in neutral, 30 degrees of extension and 30 degrees of flexion. In control subjects the position of the median nerve was 4.8 (SE=0.4) mm more radial with the wrist flexed than with the wrist extended. In the twelve arm pain patients the average change was only 1.2 (SE=0.5) mm. It appears that ultrasound imaging may be helpful in diagnosing non-specific arm pain, a condition for which there are no well-defined diagnostic tests at present. The reduced nerve movement seen with ultrasound imaging confirms previous work with magnetic resonance imaging.

The use of cross-correlation analysis between high-frequency ultrasound images to measure longitudinal median nerve movement

Impaired nerve movement can lead to nerve injury (e.g., carpal tunnel syndrome). A noninvasive method to measure nerve movement in longitudinal section would enable an extensive analysis of nerve entrapment syndromes. A method has been developed using cross-correlation between successive high-frequency ultrasound (US) images to measure longitudinal movement of nerve and muscle. Control "phantom" experiments demonstrated the accuracy and reliability of this method at velocities of 1-10 mm/s. Increasing the frame interval between the compared frames enabled the accurate calculation of slower velocities. The correlation algorithm successfully measured relative movement when the US transducer was moved 1-3 mm over the surface of the forearm. Median nerve movement was repeatedly measured in the forearm during 30 degrees passive wrist extension in three subjects (range 2.63-4.12 mm) and index finger extension in seven subjects (range 1.59-4.48 mm). Median nerve movement values were consistent with those from cadaver studies.

Medicare's outpatient code editor is key to APC payments

Since implementation of the outpatient prospective payment system (PPS) in August 2000, HCFA has used an inadequate communication process to inform providers about billing and coding requirements. Numerous program memorandums have been issued to communicate changes to the outpatient PPS and even to correct information that was provided in previous program memorandums. Providers need to monitor changes in outpatient PPS policy by reading the program memorandums posted on HCFA's Web site (www.hcfa.org) and through reviewing other informal communications posted to the HCFA Web site. In addition, the outpatient code editor (OCE) contains information about quarterly APC classification updates. In fact, the OCE is the only source of this information in many cases. Because the outpatient PPS differs from any other PPS implemented by HCFA, providers should ensure that they have all the current information they need to comply with the system's billing and coding requirements.

APCs: reimbursement implications

A transition to a new Medicare outpatient prospective payment system (PPS) will begin in July 2000, affecting many of the outpatient services provided by hospitals that participate in the Medicare program. The outpatient PPS will rely on ambulatory payment classifications (APCs) to classify outpatient services. Hospitals should anticipate that discounts and other factors will affect APC payments and take into account the impact that the new system will have on their revenue.

Reduced movement of median nerve in carpal tunnel during wrist flexion in patients with non-specific arm pain

Magnetic resonance scans on patients with non-specific arm pain (repetitive strain injury) show reduced median-nerve movement in the carpal tunnel, suggesting that this common condition may involve nerve entrapment.

Evidence for a role of the plasminogen activator--plasmin system in corneal ulceration

Plasminogen is present in the cornea andcan be activated to plasmin by plasminogen activator. Plasmin is able, in turn, to activate latent collagenase. This system could initiate and perpetuate the collagen degradation of corneal ulceration. This report details evidence for such a system in the cornea. Plasmin has been found to activate latent collagenase from organ cultures of ulcerating rabbit corneas and from fibroblast cultures derived from such corneas. As in the case of activation by trypsin, activation by plasmin results in the conversion of the 40,000 MW latent form to an active species of 23,000 MW. Explants of normal or alkali-burned, ulcerating corneas demonstrated plasminogen-dependent lysis of fibrin clots; frozen sections of such corneas demonstrated that lysis begins in the superficial stroma near the periphery of the cornea. Multiply freeze-thawed ulcerating corneas, but not normal corneas, showed initial lysis, not peripherally but at the ulcer region containing polymorphonuclear leukocytes. The fact that the peripheral lytic pattern existed in corneas that were obtained from eyes prefrozen in liquid nitrogen before excision of the corneas would suggest that plasminogen activator is normally contained in cells in vivo and is not made only in response to tissue injury. There was no correlation between the location of blood vessels or the presence of the corneal endothelium and the plasminogen-dependent lysis. Plasminogen activator from the ulcerating cornea and from fibroblasts was characterized by sodium dodecyl sulfate--gel electrophoresis of its cleavage products of plasminogen. The activator cleaves plasminogen into heavy- and light-chain fragments similar to those produced from plasminogen by urokinase. Plasminogen activator activity was quantitated by a new assay that restricts diffusion of the enzyme to one dimension into a narrow bore tube. The addition of plasminogen daily to cultures of ulcerating corneas resulted in earlier rises of plasminogen activator, collagenase, and collagen degradation fragments in the culture media. Although total plasminogen activator levels were not increased by the addition of plasminogen to culture, levels of both collagenase and solubilized collagen were approximately doubled. It is concluded that the plasminogen activator--plasmin system might play an important role in the destruction of stromal matrix in corneal ulceration.

Collagenase from corneal cell cultures and its modulation by phagocytosis

The uptake of latex by fibroblasts in confluent primary culture results in the secretion of collagenase at a linear rate for a prolonged period. Phagocytosis might therefore constitute an important level of collagenase regulation in corneal ulceration. The collagenase in cell cultures is present in a latent form (40,000 MW) like that obtained from organ cultures of ulcerating corneas and can be activated proteolytically. Production of the latent collagenase in cell culture depends upon the presence of serum and diminishes greatly when serum is removed from the medium. Collagenase activity can be demonstrated after the latent collagenase has been separated from serum antiproteases in the media. Alternatively, careful titration of the crude media with trypsin to saturate serum antiproteases, to release collagenase from the complex with alpha 2-macroglobulin, and to activate latent collagenase also results in measurable collagenase activity. The collagenase that is secreted cleaves fibrillar type I collagen and cleaves soluble type I collagen into the typical 3/4 and 1/4 length fragments, as demonstrated by SDS-gel electrophoresis and electron microscopy.

Diazomethyl ketone substrate derivatives as active-site-directed inhibitors of thiol proteases. Papain

The diazomethyl ketones of z-Phe-Phe inactivate papain by a stoichiometric reaction at the active-center thiol. Since the reagents are stable in mercaptoethanol, their reaction with papain is judged to be the result of complex formation characteristic of affinity-labeling reagents. The diazomethyl ketones react by a mechanism different from that of chloromethyl ketones, since the pH dependence of their inactivation of papain is different, the rate increasing with decreasing pH. This relationship has been observed in other cases, such as in the reaction of azaserine with glutamine amidotransferases [Buchanan, J. M. (1973), Adv. Enzmol. Relat. Areas Mol. Biol. 39, 91], and is interpreted as an indication of reaction with a thiol group in its protonated form.