Description of the Variability Data in VARIDT

Drug transporters (DTs) are acknowledged as important determinants governing drug absorption, excretion, and, in many cases, extent of drug entry into target organs (Annu Rev Pharmacol Toxicol. 2012, 52: 249-73). The variability of DTs has thus attracted considerable attentions and broad interests (Nat Rev Drug Discov. 2015, 14: 29-44; Clin Pharmacol Ther. 2019, doi: 10.1002/cpt.1373; Ann Oncol. 2013, 24: 1513-25). There are three aspects of variability: (1) epigenetic regulations and genetic polymorphisms of DTs playing key role in drug resistance (Sci Transl Med. 2016, 8: 348ra97) and clinical treatment optimization (Adv Drug Deliv Rev. 2017, 116: 21-36); (2) species-, tissue-, and disease-specific abundances of DT proteins essential for bridging preclinical study with clinical trial (Mol Pharm. 2015, 12: 4259-69), balancing efficacy and safety (Sci Transl Med. 2016, 8: 352ra109), and predicting disease-drug interaction (Clin Pharmacol Ther. 2018, 104: 900-15), respectively; (3) exogenous factors modulating activity of DTs and leading to the altered disposition of natural substrates and the transported drugs (Adv Drug Deliv Rev. 2015, 86: 17-26; Clin Pharmacol Ther. 2016, 100: 259-67). These variability data are vital for the clinical studies, and the accumulation of such data can lay the foundation for big data-driven precision medicine.

Moreover, due to the extreme complexity of drug dispositions in living organisms, the interplays among different aspects of DT variability have recently emerged to be a new promising research direction of high-impact studies (Drug Resist Updat. 2017, 32: 23-46; Cancer Lett. 2016, 370: 153-64). Particularly, one of the common mechanisms of the cancer multidrug resistance (MDR) is the overexpression of the particular DTs in cancer cells (Cancer Lett. 2016, 370: 153-64), and the developments of exogenous chemical to inhibit the efflux of these DTs are successfully proposed to reverse caner MDR (Drug Resist Updat. 2017, 32: 23-46; Cancer Lett. 2016, 370: 153-64). These and other potential studies require the collectively analyses of multiple data among different aspects of DT variability. However, no database has been available so far to provide the comprehensive information of all aspects of DT variability.

Therefore, the Variability of Drug Transporter Database (VARIDT) was introduced. First, a comprehensive literature review on all drugs approved by U.S. FDA and >1,000 drugs in clinical trial or preclinical research was conducted. Different from the small amount of DTs (~20) well characterized in previous work (Nat Rev Drug Discov. 2010, 9: 215-36), 177 DTs were confirmed for the first time in VARIDT to transport approved drug(s) and 146 DTs were to transport the drug(s) in clinical/preclinical test. Second, for these hundreds of newly confirmed DTs, the VARIDT not only comprehensively provided all three aspect of their variability data but also allowed the mutual connection (interplay) between any two aspects. All in all, the VARIDT is UNIQUE in (1) covering the largest number of DTs confirmed by their corresponding drugs among available knowledge bases, (2) providing for the first time the comprehensive sets of DT variability data, and (3) allowing the interplay analysis among different aspects of DT variability. All diseases in VARIDT were standardized using the latest revision of International Classification of Diseases (ICD-11) to serve comprehensive health management, and the vast majority (~80%) of the confirmed DTs in VARIDT had the data from multiple aspects of variability, which allowed interplays among these aspects. All data are FULLY DOWNLOADABLE .

Description of the Structural Variability in VARIDT

DT variability is reported to be critical for balancing drug efficacy with safety (Sci Transl Med. 2016, 8: 352ra109), reversing drug resistance (Sci Transl Med. 2016, 8: 348ra97), and predicting drug-drug interaction (Adv Drug Deliv Rev. 2015, 86: 17-26; Br J Pharmacol. 2019, 176: 4558-4573; Chin Med. 2020, 15: 71). Recently, there are increasing demands on the three-dimensional structural variability data of DT, which are expected to provide key information for the studies on precision medicine and rational drug use (Nature. 2019, 576: 315-320). Such data include: (a) the mutation-induced spatial variations in folded state that are critical for the understanding of drug sensitivity and selectivity (Proc Natl Acad Sci U S A. 2019, 116: 8960-8965), (b) the difference among the DT structures of human and model organisms that are key for bridging preclinical study with clinical trials (Science. 2019, 363: 753-756), (c) the outward-facing and inward-facing conformations that are essential for elucidating the dynamics and underlying steps of transporting cycle (Proc Natl Acad Sci U S A. 2019, 116: 12275-12284), and (d) the xenobiotics-driven alterations in 3D complexes of DT that are crucial for revealing the mechanism underlying drug-drug interaction (Elife. 2020, 9: e56427; Oxid Med Cell Longev. 2021, 15: 7467156; Chin J Nat Med. 2019, 17: 490-497). These structure variability data would be indispensable for explaining drug sensitivity and selectivity, bridging preclinical research with clinical trial, revealing the mechanism underlying drug-drug interaction, and so on.

Therefore, the structural variability data of DTs were collected and described in VARIDT. First, the experimental structures of all DTs reported in VARIDT were systematically discovered from PubMed and Protein Data Bank. Furthermore, due to the lack of DTs’ structures and their structural variability data, homology modeling is applied as a well-established protocol to construct protein structure (Nat Methods. 2015, 12: 747-750). Four types of DTs’ structural variability data were provided in VARIDT, which included both the experimentally resolved structures and the variability of DT structures generated by homology modeling: (a) 145 mutation-induced structures originating from 42 DTs were collected, (b) 1,622 inter-species structures from 17 species (human, rat, mouse, dog, zebrafish, rabbit, bovine, pig, chicken, sheep, fruit fly, frog, orangutan, monkey, guinea pig, horse, hamster) covering 292 DTs were described, (c) 118 outward/inward-facing conformations belonging to 59 DTs were provided, and (d) 822 xenobiotics-regulated structures of 506 xenobiotics in complex with 57 DTs were collected and described. A total of 292 DTs with at least one type of structure variability data were provided in the latest version of VARIDT, which were closely related to the transportation of 751 drugs (including 508 approved & 243 clinical/preclinical drugs) for the treatment of 259 disease classes (such as coronavirus infections, lung cancer, diabetes mellitus, depression, parkinsonism, hypertension, and asthma) as defined by the latest WHO International Classification of Diseases (Lancet. 2019, 393: 2275). All structure variability data can be viewed, assessed, and downloaded from VARIDT, which is freely assessable without login requirement.

Identify Entries by Whole Database Search

Users can identify entries by searching transporter protein name, transporter gene name, transporter family name, drug name, disease/disease class name of the transported drug, International Classification of Diseases (ICD) code, and so on among the entire textual component of VARIDT. Query can be submitted by entering keywords into the main searching frame. Users can specify part/full drug name, DT name or any other related information in the text field. Moreover, user can search by put drug, DT or other information together into text field (separated by space or tab) for narrowing output results. To facilitate a more customized input query, the wild characters of "*" and "?" are fully supported in VARIDT. For example:

1. If search: "ABCG2", finds only ERD entry with DT name "ABCG2"

2. If search: "Oxaliplatin", finds three ERD entries of three DTs transporting "Oxaliplatin"

3. If search: "Influenza", finds six ERD entries of six DTs transporting "Influenza" drugs

4. If search: "Multidrug and toxin extrusion protein?", finds ERD entry of the DT "Multidrug and toxin extrusion protein 1". Here, "?" represents any one character

5. If search: "Multidrug and toxin *", finds the same entry as above. Here "*" represents a string of any length. In this case, it represents "extrusion protein 1"

For example, if you want to know the detail information of organic anion transporter 1 (SLC22A6), you can search it's transporter information by searching "organic anion transporter 1 (SLC22A6)" in the "Search for Drug Transporter Entries:" field of the home page.

Identify Entries by Transporter Name/Transporter Family/Drug Name/Xenobiotic Name/Exogenous Factor Name/Disease Class/Model Organism Name

Users can identify entries among the entire textual component of VARIDT by selecting a DT name, DT family name, drug name, xenobiotic name, exogenous factor name, model organism name or ICD-11 defined disease class name from the corresponding drop-down lists.

(a) The drop-down list of DT name (gene name: DT protein name) contains DTs that are confirmed by at least one drug transported by these DTs; (b) The drop-down list of DT family name (family full name (abbreviation)) contains protein families that are occupied by all DTs in this section; (c) The drop-down list of drug name contains drugs that have been approved or in clinical/preclinical studies; (d) The drop-down list of DT xenobiotic name contains xenobiotics that driven DT structural alterations in 3D complexes, (e) The drop-down list of exogenous factor name contains a various of distinct exogenous factors; (f) The drop-down list of model organism name contains 16 species (rat, mouse, dog, zebrafish, rabbit, bovine, pig, chicken, sheep, fruit fly, frog, orangutan, monkey, guinea pig, horse, hamster); (g) The drop-down list of ICD-11 defined disease class (ICD-11 code: disease class name) contains distinct disease classes. To accelerate the ERD identification process, these drop-down lists are alphabetically sorted (A-Z). Contrary to the field of "Search for the Epigenetic Regulations of Drug Transporter (ERD)", these drop-down lists search the keyword by the EXACT matching instead of the fuzzy one.

For example, searching "OAT1: Organic anion transporter 1" in the "Search Drug Transporter by Transporter Name:" drop-down list.

Drug Transporter (DT)

DT is known as the key determinant of drug absorption, distribution, clearance, and elimination (Annu Rev Pharmacol Toxicol. 2012, 52: 249-73). This section provides various general information, variability data (general variability data and structural variability data), and molecular transporting profile (drugs, endogenous, and affinity data) of DTs.

For example, searching "P-glycoprotein 1" in the " Search for Drug Transporter Entries:" field of the home page.

The search result lists transporter with transporter information. In this page, the Transporter Info button links to the Drug Transporter (DT) Information page and the Drug Info button links to the Representative Drug/Compound Information.

In the Drug Transporter (DT) Information page, "General Information of DT" section displays a various of general information of OAT1, such as namds, DT family, structural model, function, Diseases, endogenous substrates, and so on.

The “Variability Data of This DT” section contains general and structural variability data. Three aspects of general variability data of OAT1 along with the hyperlink to (a) Epigenetic Regulations of DT (ERD), (b) Genetic Polymorphisms of DT (GPD), (c) Disease-specific Protein Abundances of DT (DPAD), (d) Species/Tissue-specific Protein Abundances of DT (S/TPAD), and (e) Exogenous Factors (drugs, dietary constituents, natural products, etc.) Modulating DT Activity (EFMDA). The structural variability data of OAT1 contain (a) Mutation-induced Structural Variation (MSV), (b) Inter-species Structural Differences (ISD), (c) Outward/inward-facing Conformation (OIC), and (d) Xenobiotics-regulated Structural Variability (XSV).

The “Molecular Transporting Profile of This DT” shows the related drugs, endogenous, and affinity data. The brief information (drug name, indication and highest status) of drugs which are transported by OAT1 is displayed by a list and the drugs are classified by its highest status.

The Drug Info button links to the drug information in more detail, including names, 3D and 2D structures, therapeutic class, etc.

In this page, the "Drug-DT Affinity Assessed by Cell Line" section displays the drugs with drug-DT affinity data, which is constructed by drug name, cell line and Km value.

Structural Variability (2022 Update)

There are increasing demands on the three-dimensional structural variability data of DT, which are expected to provide key information for the studies on precision medicine and rational drug use (Nature. 2019, 576: 315-320). A major update of VARIDT was conducted, which systematically described all four aspects of DT structural variability: (a) the mutation-induced spatial variations in folded state, (b) the difference among the DT structures of human and model organisms, (c) the outward-facing and inward-facing conformations of the transporting cycle, and (d) the xenobiotics-driven alterations in 3D complex.

Mutation-induced Spatial Variation (MSV)

Mutation-induced spatial variations in the folded state of DT are critical for the understanding of drug sensitivity and selectivity (Proc Natl Acad Sci U S A. 2019, 116: 8960-8965). In this section, 145 mutation-induced structures originating from 42 DTs are described.

For example, selecting "Monocarboxylate transporter 1" in the "Search for Mutation-induced Spatial Variations (MSV)" drop-down list.

The MSV Info button links to the Detail Information of Mutation-induced Spatial Variation page, and more mutation information is provided.

The “General Information of Drug Transporter (DT)” and “Mutation-induced Spatial Variation (MSV) of This DT” sections are displayed in this page. The mutation model (can be download), variation type, alleles, and the information of minor allele frequency are provided.

For the structural model, the modelling method, templet, model performance (two different perspectives: Ramachandran plot and QMEANBrane score) and other information are described in detail.

At the bottom of this page, experimental structures related to this DT with mutations are also been shown.

Moreover, the Transporter Info and GPD Info buttons link to Drug Transporter (DT) Information page and Detail Information of Genetic Polymorphisms page, respectively. More information of genetic polymorphisms related to this MSV can be obtained.

Inter-species Structural Differences

The differences among DT structures of human and model organisms were essential for bridging preclinical study with clinical trial (Science. 2019, 363: 753-756). A total of 1,622 inter-species structures from 17 species (human, rat, mouse, dog, zebrafish, rabbit, bovine, pig, chicken, sheep, fruit fly, frog, orangutan, monkey, guinea pig, horse, hamster) covering 292 DTs are described in this section.

For example, searching “urea transporter 1 or UT1” in the “Search for Inter-species Structural Difference (ISD):” filed.

The search result lists of the transporter with transporter information, and ISD Info button links to the Detail Information of Inter-species Structural Difference.

In the Detail Information of Inter-species Structural Difference page, the “General Information of Drug Transporter (DT)” section displays the general information of UT1, and the detailed information of 3D structure can be accessed by clicking Structure Info button.

Data on multiple aspects of DT structural model in Homo sapiens are described, including the structure, template, performance of modelling, and the experimental structures of this DT.

By scrolling down the Detail Information of Inter-species Structural Difference page, the “Inter-species Structural Differences (ISD)” can also provide UT1 structural information of other species.

Outward/inward-facing Conformation

The outward- and inward-facing conformations of DTs were reported as essential for elucidating the underlying steps of a transporting cycle (Proc Natl Acad Sci U S A. 2019, 116: 12275-12284). In this section, a total of 118 conformations belonging to 59 DTs are provided.

Taking ATP-Binding Cassette as an example, searching “ATP-binding cassette (ABC)” in the “Search for OIC by Transporter Families:” field.

All the transporters belonging to the ATP-Binding Cassette (ABC) Superfamily with outward/inward-facing conformation information are provided. Searching for the OIC Info button to obtain more information.

The general information (gene name, transporter name, and gene ID), detail information of inward/outward-facing conformation (structures, modeling methods, templates, and model performance) and other information are provided.

Xenobiotics-driven Alterations in 3D Complexes

The xenobiotics-driven alterations were essential for revealing mechanisms underlying drug-drug interactions (Elife. 2020, 9: e56427). A total of 822 xenobiotics-regulated structures of 506 xenobiotics in complex with 57 DTs are collected and described in this section.

The users can obtain the detail information of xenobiotics-driven alterations in 3D complexes by searching the transporter name (taking SERT as an example) in the “Search for Xenobiotics-driven Alterations in 3D Complexes (XSV):” field.

The XSV Info button links to the Detail Information of Xenobiotics-driven Alterations in 3D Complexes page.

All of the xenobiotics-binding complexes of this DT are provided in this page. Furthermore, more drug information and exogenous factor modulated information can be obtained from the Drug Info and EFMD Info buttons.

Variability of DT

The variability of DT has attracted considerable attentions and broad interests (Nat Rev Drug Discov. 2015, 14: 29-44; Ann Oncol. 2013, 24: 1513-25). This section describes three aspects of DT variability: (a) genetic polymorphism, and epigenetic regulation of DT; (b) species/tissue/disease-specific DT abundance; and (c) exogenous factors modulating DT activity or altering the disposition of transported drug.

Genetic/Epigenetic Variability

Epigenetic regulation and genetic polymorphism of DT that are key in drug resistance and clinical treatment optimization (Sci Transl Med. 2016, 8: 348ra397; Adv Drug Deliv Rev. 2017, 116: 21–36). A total of 23947 DNA methylations, 7317 noncoding RNA/histone regulations, and 1278 genetic polymorphisms are provided.

Searching "ABCG2" in the "Search for Drug Transporter Entries:" field, the ERD Info button links to the Detail Information of Epigenetic Regulations page. In the “Epigenetic Regulations of DT (ERD)” section, the epigenetic regulations information including three aspects “methylation”, “histone acetylation” and “microRNA” are provided.

Moreover, the detail information of each epigenetic regulation (methylation, histone acetylation and microRNA) is displayed by a list.

Protein Abundance Variability

Protein abundance of DT was always a critical issue in various aspects of drug development, such as clinical pharmacokinetics, adverse reaction assessments and drug-drug interactions (Nat Rev Drug Discov. 2015, 14: 543–560). Differential abundance profiles of 257 DTs in 21 781 patients/healthy individuals, expression of 245 DTs in 67 tissues of human/model organism are shown in this section.

Taking ATP-binding cassette sub-family A member 1 as an example, searching the “ABCA1: ATP-binding cassette sub-family A member 1” in the “Search for DPAD by Transporter Names:” field.

The Detail Information of Disease-specific Protein Abundances page can be accessed by clicking the DPAD Info button. Multiple aspects of data are presented by a list.

Exogenous Modulation

The activity or expression of DTs could be inhibited or induced by exogenous factors, which, in turn, affected the pharmacokinetics, efficacy and safety of drugs or the tissue level of drugs/substrates that were transported by the corresponding DTs (Nat Rev Drug Discov. 2010, 9: 215–236). A total of 1225 exogenous factors altering the activity of 148 DTs are collected in this section.

For example, searching the “Ketoconazole” in the “Search for Drug Transporter(s) Modulated by Exogenous Factor (DTMEF):” filed. The result displays several related DTs.

The Information of Exogenous Factor Modulation page can be accessed by clicking the DTMEF Info button. This page provides various detail information of the exogenous factors (drugs have been approved or in in clinical/preclinical studies, natural product, dietary constituent, environmental toxicant, pharmaceutical excipient, etc.), related drug/substrate, modulation type and activity.

Download

Download the Full Data of VARIDT from a Variety of Customized Links. VARIDT provides functions for downloading all VARIDR data from various customized links.

(1) full 3D variability data of DT (mutation-induced spatial variations of DTs, inter species structural differences, outward/inward-facing conformations, xenobiotics-driven alterations in 3D complexes)

(2) full DT variability data (epigenetic regulation data of DTs, genetic polymorphism data of DTs, disease-specific protein abundances of DTs, species-specific protein abundances of DTs, tissue-specific protein abundances of DTs and exogenous factors altering DT activity)

(3) full sequence/structure/function data/ cross-matching data (sequence and structure data of DTs, transporter-drug affinity data based on cell line experiment, functional family data for each DT, 2D structure data for the drugs transported by DTs, 3D structure data for the drugs transported by DTs, SMILES and InChI for the drugs transported by DTs and therapeutic classes and physicochemical properties for the drugs, cross-matching ID between the DTs and a variety of public databases, synonyms of DTs and their corresponding drugs, DTs to disease mapping with ICD identifiers and Drug to disease mapping with ICD-11 identifiers)

All data can be readily downloaded by simply clicking the corresponding 'Click to Save' button.

If you find any error in data or bug in web service, please kindly report it to Dr. Yin and Dr. Li.