A New Data Repository for Pharmacokinetic Natural Product-Drug Interactions: From Chemical Characterization to Clinical Studies

There are many gaps in scientific knowledge about the clinical significance of pharmacokinetic natural product–drug interactions (NPDIs) in which the natural product (NP) is the precipitant and a conventional drug is the object. The National Center for Complimentary and Integrative Health created the Center of Excellence for NPDI Research (NaPDI Center) (www.napdi.org) to provide leadership and guidance on the study of pharmacokinetic NPDIs. A key contribution of the Center is the first user-friendly online repository that stores and links pharmacokinetic NPDI data across chemical characterization, metabolomics analyses, and pharmacokinetic in vitro and clinical experiments (repo.napdi.org). The design is expected to help researchers more easily arrive at a complete understanding of pharmacokinetic NPDI research on a particular NP. The repository will also facilitate multidisciplinary collaborations, as the repository links all of the experimental data for a given NP across the study types. The current work describes the design of the repository, standard operating procedures used to enter data, and pharmacokinetic NPDI data that have been entered to date. To illustrate the usefulness of the NaPDI Center repository, more details on two high-priority NPs, cannabis and kratom, are provided as case studies. SIGNIFICANCE STATEMENT The data and knowledge resulting from natural product–drug interaction (NPDI) studies is distributed across a variety of information sources, rendering difficulties to find, access, and reuse. The Center of Excellence for NPDI Research addressed these difficulties by developing the first user-friendly online repository that stores data from in vitro and clinical pharmacokinetic NPDI experiments and links them with study data from chemical characterization and metabolomics analyses of natural products that are also stored in the repository.


Introduction
Natural products (NPs) include herbal and other botanical products (Paine and Roe, 2018). Pharmacokinetic interactions involving NPs and conventional [e.g., approved by the US Food and Drug Administration (FDA)] drugs could result in reduced treatment efficacy or adverse effects . Although up to 88% of older adults use herbal medicinal products concurrently with conventional drugs (Batanero-Hernán et al., 2017), there are many gaps in scientific knowledge about the clinical significance of pharmacokinetic NP-drug interactions (NPDIs) in which the NP is the precipitant and a conventional drug is the object. Although 6 of the 40 top-selling herbal medicinal products in 2017 were implicated in clinically significant pharmacokinetic NPDIs, there was minimal or no supporting clinical evidence for potential NPDIs involving nine products (Spanakis et al., 2019). Similarly, data were insufficient to conclude the clinical relevance of 11 of the 15 potential pharmacokinetic NPDIs involving antiretroviral drugs (Fasinu et al., 2015).
There are several unique challenges associated with pharmacokinetic NPDI research, including the large variability of phytoconstituents among marketed products, difficulty extrapolating results from animal and/or in vitro models to humans, variability in study design, and inadequate methods . Based on these knowledge gaps and challenges, the National Center for Complimentary and Integrative Health created the Center of Excellence for NPDI Research (NaPDI Center; www.napdi.org) to provide leadership and guidance on the study of pharmacokinetic NPDIs .
One objective of the NaPDI Center is to develop and apply a set of Recommended Approaches to determine the clinical relevance of pharmacokinetic NPDIs (Johnson et al., 2018;Kellogg et al., 2019). A key deliverable of the Center is the development of an online repository for data generated by the NaPDI Center (repo. napdi.org). The repository combines data currently distributed across a variety of information sources into a single user-friendly format complemented by an information portal. This portal, also developed by the NaPDI Center, disseminates the Recommended Approaches (Johnson et al., 2018;Kellogg et al., 2019) on the optimal conduct of pharmacokinetic NPDI studies (napdicenter.org). Combined, these new resources will help advance pharmacokinetic NPDI research by providing Recommended Approaches and novel pharmacokinetic NPDI data.
Pharmacokinetic NPDI data include chemical characterization of NPs, metabolomics analyses, and in vitro and clinical pharmacokinetic experimental results. This new repository stores data from all of these types of investigations. It provides a user-friendly interface that enables users with limited informatics skills to effectively explore relevant data (Li, 2015). As of March 2020, coverage of the repository is limited to four carefully selected high-priority NPs based on a systematic method for the purpose of demonstrating the Recommended Approaches (Johnson et al., 2018): cannabis (Cannabis sativa), goldenseal (Hydrastis canadensis), green tea (Camellia sinensis), and kratom (Mitragyna speciosa). A prior Recommended Approach (Johnson et al., 2018) reported the inclusion of licorice (Glycyrrhiza spp.). The Center later replaced licorice with kratom to 1) keep pace with public health needs in the face of an ever-changing NP market (Gaston et al., 2020) and 2) omit redundancy with the research efforts of a longstanding botanical center (https://pcrps.pharmacy.uic.edu/our-centers/uic-nih-center-for-botanicaldietary-supplements-research/).
The current work describes the design of the repository, standard operating procedures (SOPs) used to enter data, and pharmacokinetic NPDI data that have been entered to date. To illustrate the usefulness of the NaPDI Center repository, more details on two high-priority NPs, cannabis and kratom, are provided as case studies.

Construction and Content
Studies Conducted by NaPDI Center Investigators. To date, the repository has focused on original pharmacokinetic NPDI research conducted by NaPDI Center investigators, who are organized into three cores with complementary expertise (Fig. 1).
The Analytical Core is composed of NP chemists, analytical chemists, and clinical pharmacologists and serves multiple functions. This core chemically characterizes multiple commercially available products of a given NP, determines the contents of constituents in these products, and provides guidance on the proper selection of one or more commercially available products to be tested by the Pharmacology Core. The core also analyzes plasma and urine samples obtained from pharmacokinetic clinical studies for NP constituents and object drugs.
The Pharmacology Core is composed of clinical pharmacologists and medicinal chemists. This core designs and conducts rigorous experiments to evaluate the potential for NPs to precipitate pharmacokinetic interactions with certain object drugs. The core also characterizes the pharmacokinetics of select NP constituents in human subjects. The data obtained are used to develop physiologically based pharmacokinetic models that can be applied to other object drugs and patient populations of interest. Figure 2 shows the variety of different experiment types that the repository supports to store data from the NaPDI Center's interaction projects.
The Informatics Core ( Fig. 1) is composed of biomedical informaticists, computer scientists, and communication experts. This core compiles all data generated from NaPDI Center research activities into the data repository, which is accessible via the information portal. Prior to public release, NaPDI Center data are only accessible to researchers approved to access the site. Contributing researchers indicate when to make the data public. The data are made available according to a Recommended Approach for making pharmacokinetic NPDI research data findable, accessible, interoperable, and reusable (FAIR; https:// www.w3id.org/hclscg/npdi).
Data Types. A variety of data types are produced from pharmacokinetic NPDI studies (Supplemental Table 1). Initially, the specification and subsequent characterization of the NP source materials generated a diverse set of data, including chromatograms from conventional high-pressure liquid chromatography with UV detection and ultrahigh-pressure liquid chromatography-mass spectrometry methods, spectral data from nuclear magnetic resonance and circular dichroism, and bioactivity fractionation data. These data include instrument tracings that are often not retrievable in digitized form. Hence, the scanned image files are archived in the repository. Quantitative data on NP source materials, such as content of individual phytoconstituents and specific impurities or contaminants, are organized in tabular format.
The types of data generated from in vitro NPDI studies vary across the range of human-derived in vitro test systems, including enzymatic reactions involving recombinant enzymes, human tissue fractions (e.g., human liver microsomes), or cultured cells (e.g., hepatocytes), and drug transport experiments measuring uptake into membrane vesicles or efflux from transfected cells. Currently, the data repository tracks 82 measurements for quantitative data resulting from NPDI experiments. The full list is provided in Supplemental Table 1. Included in the list are, for example, percent inhibition, IC 50 , K m , and V max .
In addition, data generated from inhibition experiments involving drug metabolizing enzymes or transporters differ from those generated from induction experiments. Thus, the repository provides separate sets of data fields for each of these in vitro systems and mechanisms (Supplemental Table 1).
Pharmacokinetic data generated from clinical NPDI studies include human subject demographics, concentration-time data, and key pharmacokinetic endpoints (e.g., oral clearance, renal clearance, apparent volume of distribution, halflife, area under the plasma-concentration vs. time curve, maximum plasma concentration, and time to reach maximum concentration). Statistical analyses of primary and secondary pharmacokinetic endpoints generated additional data sets.
Data Findability, Accessibility, Interoperability, and Reusability. There is a growing recognition by both researchers and funding agencies that pharmacokinetic NPDI study data sets should be more FAIR (National Center for Complementary and Integrative Health, 2019). The NaPDI Center repository is designed to ensure that data satisfy these four foundational principles of good data management and stewardship. Table 1 summarizes the specific features of the repository that support FAIR pharmacokinetic NPDI data. Each feature is described in greater detail in a public and participative report that the NaPDI Center is developing in collaboration with the World Wide Web Consortium Semantic Web in Health Care and Life Sciences Community Group (https://www. w3id.org/hclscg/npdi).
Standard Operating Procedures for Data Entry. A major feature of the repository is that data are entered using validated SOPs. There are currently 11 SOPs, one for each experiment type listed in Figure 2. Data collection forms have been developed for both internal and external NPDI researchers, such as contract research organizations. These forms are based closely on the SOP documents. Both the SOPs and data entry forms are publicly available on GitHub (https:// github.com/dbmi-pitt/NaPDI-SOPs), and the SOP document for enzyme inhibition experiment type is provided as an example in Supplemental Data (Boyce et al., 2020).
Quality Control and Validation Processes. Given the variety of data types, close attention must be paid to enable accurate tracking and meticulous organization of the generated data. The structure, data organization, and concepts effectively used by the University of Washington's Drug Interaction Database (Hachad et al., 2010), now Drug Interaction Solutions (www.druginteractionsolutions.org), have been The NaPDI Center Data Repository applied to the NaPDI Center repository. These features have been validated over time with feedback from a large user base. To ensure the quality and consistency of the entry process, data are entered by experienced curators who are well versed in drug interactions using the aforementioned SOPs. All data entry undergoes review by a second reviewer prior to public release.
Current Status of the Repository. An overview of data entered into the NaPDI Center repository is provided for two of the high-priority NPs selected as case studies: cannabis (C. sativa) and kratom (M. speciosa). These NPs were chosen due to increasing use and public interest. Neither NP has been well studied with respect to NPDI potential. In the United States, a majority of states have legalized marijuana for recreational and/or medical purposes. Moreover, a growing number of products containing the nonpsychotropic phytocannabinoid cannabidiol are marketed every year. These products include the FDAapproved drug Epidiolex and numerous unapproved tinctures, oils, and extracts. Kratom, a member of the coffee family native to Southeast Asia, is touted for its analgesic and stimulant effects. Warnings about kratom toxicity have been raised by the US FDA and the Centers for Disease Control and Prevention (Food and Drug Administration, 2019; Gershman, 2019). Calls to US poison centers involving kratom exposures from 2011 to 2017 increased 52-fold, from 13 to 682, with more than one-third of the calls reported involving co-consumption with prescription or illicit drugs (Post et al., 2019).
Each case study begins with a summary of NaPDI Center research activities focusing on each NP as a precipitant of pharmacokinetic NPDIs. A description follows about how published evidence was added to the repository to both complement the data generated by the NaPDI Center and provide researchers with a more complete picture of the pharmacokinetic interaction potential for each NP.
NPDI Study Process. Four steps are crucial for conducting a rigorous research study on a given pharmacokinetic NPDI: NP selection; sourcing and chemical characterization of different commercial products of the selected NP; in vitro assessment of inhibition or induction of drug metabolizing enzymes and  Each "Study" record describes an activity that resulted in data from one or more related experiments. Each experiment record is assigned 1 of the 11 experiment types offered that provides the appropriate format for recording experimental conditions and results following instructions provided in the 11 SOPs. transporters by the NP; and, if necessary based on the prior data, a clinical study of potential pharmacokinetic NPDIs in human subjects (Fig. 3).
The upper half of Figure 3 shows the cannabis studies conducted by the NaPDI Center as of March 2020. Chemical characterization data for two products were obtained from the National Center for Natural Products Research at the University of Mississippi. One product was an extract enriched in delta-9-tetrahydrocannabinol (THC) and the other was an extract enriched in cannabidiol (CBD). Purified THC and CBD were tested as inhibitors of five major cytochrome P450 (P450) enzymes, namely, CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4/5. Results informed the design of an ongoing clinical cannabis-drug interaction study.
The lower half of Figure 3 shows the kratom studies conducted by the NaPDI Center as of March 2020. The Analytical Core conducted a metabolomics study involving 55 kratom products, informing the selection of one product for further in vitro and clinical studies. The selection criteria followed a published NaPDI Center Recommended Approach (Kellogg et al., 2019). The Analytical Core conducted chemical characterization of the selected product to quantify mitragynine, 7-hydroxymitragynine, and speciofoline (Fig. 3). Extracts prepared from three kratom products, including one that was eventually selected for the clinical study, were tested by the Pharmacology Core as inhibitors of three major P450s, specifically CYP2C9, CYP2D6, and CYP3A4/5. As with cannabis, the in vitro results informed the design of the ongoing clinical kratom-drug interaction study.
Literature Search Process. Additional data were identified from peerreviewed published reports in order for the data repository to provide greater research context for the NaPDI Center-conducted studies. Systematic literature searches were designed to retrieve studies on NP constituent pharmacokinetics and drug interactions involving either cannabis or kratom. The final search strategies are available in the Appendix. Queries were run in PubMed in July 2018 and again in February 2020.
The screening of titles and abstracts, and subsequently full text articles, was completed independently and in duplicate to identify experiments of the types shown in Figure 2. Mechanistic experiments of interest included assessing the NP as an inhibitor or inducer of P450s, UDP-glucuronosyltransferases (UGTs), and transporters. Clinical experiments of interest included pharmacokinetic NPDIs involving cannabis or kratom. Experiments involving only synthetic analogs, pharmacodynamics, or nonhuman animal studies and review articles were excluded. Full text articles available only in non-English languages were also excluded. Published reports cited in a recent review by the NaPDI Center (Cox et al., 2019) on cannabis pharmacology and pharmacokinetics (n = 6) were added to the screening results.
Data Entry of Published Literature and Pharmacokinetic NPDI Studies. Data from the included published reports were entered into the repository following the aforementioned SOPs (Boyce et al., 2020). When available, exact values from the text were entered. Otherwise, estimates were made from the study figures. Data extracted from each report were marked as "draft" during initial data entry and "pending" upon completion of data entry. After quality assurance by a second reviewer, the extracted data were made public. Data entry issues were tracked and addressed until quality assurance was complete for all studies.

Construction and Content
As of April 2020, the NaPDI Center repository contains data from 777 experiments (Table 2). Currently, the most common experiment types are in vitro enzyme inhibition (405), in vitro enzyme induction (99), in vitro transport inhibition (78), and clinical pharmacokinetic NPDIs (57). The remaining 138 experiments are of various other types supported by the repository. In line with FAIR recommendations, every experiment is assigned a unique and persistent identifier that also resolves to a downloadable copy of a data set. A clear description of each experiment's conditions is provided by the repository website. The repository publishes metadata about each experiment that is machine readable and confirmed to work with Google's Dataset Search  Fig. 3. Process and data undertaken by the NaPDI Center for the study of pharmacokinetic NPDIs precipitated by cannabis and kratom. *The Analytical Core did not source or characterize the cannabis study materials, whereas it conducted both investigations for kratom. The purified cannabis study materials were purchased from a commercial vendor.
The NaPDI Center Data Repository (https://datasetsearch.research.google.com/). To provide the most optimal experience to the researcher or editor wanting to search for data in the repository, an interactive and silent guided tour is provided on the home page (see the screen capture video in Supplemental Data).

Utility
This section reports the results of NaPDI Center repository data entry of the two high-priority NPs selected as case studies: cannabis (C. sativa) and kratom (M. speciosa).
Cannabinoids. Figure 4 provides an overview of reported NPDI data for cannabis from both NaPDI Center studies and peer-reviewed published reports. Links to the specific experiments are provided in Supplemental Table 2.
Kratom. Figure 5 provides an overview of pharmacokinetic NPDI data for kratom from both NaPDI Center studies and peer-reviewed published reports. Links to the specific experiments are provided in Supplemental Table 3.
The Analytical Core's metabolomics analysis of 51 kratom products highlighted differences in chemical compound profiles depending on the manufacturer, form, and geographic location where the plants grew. A principal components analysis of the data identified three principal components explaining 91% of the variability across the features included in the metabolomics analysis.
Chemical characterization of the methanolic kratom extract used in the ongoing NaPDI in vitro and clinical studies (made from a clinical product) identified mitragynine (22.7 mg/g of sample), 7-hydroxymitragynine (0.57 mg/g of sample), and speciofoline (0.41 mg/g of sample). The in vitro inhibition studies showed that both the methanolic kratom extract and mitragynine inhibited CYP2C9, CYP2D6, and CYP3A4/5 by differing extents (unpublished observations).

Discussion
Although rigorous pharmacokinetic NPDI research can mitigate adverse interactions, the data and knowledge resulting from these experiments are currently distributed across a variety of information sources, making them difficult to find, access, and reuse. The new Fig. 5. Overview of reported NPDI data for kratom from both NaPDI Center studies and peer-reviewed publications. The results shown in boxes "b" and "c" are for the product chosen from the metabolomics study (light blue highlight in box "a").

The NaPDI Center Data Repository
NaPDI Center repository is the first user-friendly online repository that stores and links pharmacokinetic NPDI data across chemical characterization, metabolomics analyses, and pharmacokinetic in vitro and clinical experiments. The design is expected to help researchers more easily arrive at a complete understanding of pharmacokinetic NPDI research on a particular NP. The repository will also facilitate multidisciplinary collaborations, as the repository links all of the experimental data for a given NP across the study types. For example, the repository links chemical characterization data with data from in vitro and clinical experiments and vice versa. This feature should help facilitate communication between multidisciplinary researchers working on different aspects of a particular pharmacokinetic NPDI.
The mission of the NaPDI Center is to provide leadership and guidance on the study of pharmacokinetic NPDIs. Currently, only data on the four high-priority NPs under study by the NaPDI Center have been entered in the repository. Future work hopes to expand the repository to include a larger selection of NPs and engage NPDI researchers external to the NaPDI Center. Toward that goal, pilot work is completed that includes data from experiments involving P450 inhibition by three licorice species (i.e., Glycyrrhiza glabra, G. uralensis, and G. inflata) (Li et al., 2017). The published report includes pharmacokinetic NPDI data specific to extracts of each licorice species and for individual constituents present in some or all licorice species. The repository links all of these data in a manner that allows researchers to explore P450 inhibition by licorice from a variety of perspectives (i.e., single or multiple licorice species and single or multiple licorice constituents). It is useful to emphasize that the NaPDI Center repository currently focuses on pharmacokinetic NPDI data. At the present time there are no plans to integrate pharmacodynamic NPDI data. Though it has not been the focus to date, the format for data in the NaPDI data repository allows for setting the NP as the object drug, and there are a handful of experiments in the repository of this kind that have been entered as test cases. The inclusion of this kind of data might become the focus in the future depending on feedback from the NPDI research community and other stakeholders.
Building upon this strong foundation, the NaPDI Center plans to create novel information visualizations to provide researchers a complete evidence-based overview of the potential of each NP to precipitate pharmacokinetic NPDIs. The Center also plans to permit other researchers to submit data using files or the repository's web-based application programming interface with the goal of supporting mediumto high-throughput assays that generate megabytes or gigabytes of data. Researchers external to the NaPDI Center can enter data by first requesting an account and then following the SOP documents during data entry. After a researcher's data entry is completed, a trained individual within the NaPDI Center will inspect the entered data before public release.
Finally, the NaPDI Center plans to implement automatic FAIR quality analytic reports that will run each time a data submitter marks a new study entry as "pending." Issues identified from the reports can then be addressed promptly by the data submitter. These functionalities, combined with the existing functionalities of the NaPDI Center repository, seek to facilitate pharmacokinetic NPDI research with the long-range goal of mitigating adverse interactions and improving public health.