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Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5938_Библиотеки_им_академика_М_И_Перельмана
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70 3 DrugBank Online: A How-to Guide
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attributes and connections. Navigating to, and practical use of, these datasets will be
covered in Section 3.3.
3.2.2.1 Drug Cards: An Overview and Navigation Guide
The heart of DrugBank data is the drug entry, which in this context is synonymous
with active ingredient. At the time of authoring this chapter, there were 15,234 such
entries in the DrugBank database, each with a unique identier prexed by the
letters “DB” (referred to within this chapter as a “DBID”). One such example is
DB00316, corresponding to acetaminophen, one of the most commonly used analgesics worldwide. These entries contain a variety of information, described below,
but also act as key hubs linking various other datasets within DrugBank.
Each drug entry has an associated drug card, analogous to gene or protein cards
in other biomedical databases, which summarizes information linked to the drug
(Figure 3.2a). Drug cards are divided into sections, which are navigated via a side
bar (Figure 3.2a). The majority of these sections contain further divisions into elds.
In these cases, clicking on the section name in the side bar will move the user to
the beginning of the section and will also expand the elds under that section in
the side bar (Figure 3.2b); eld names can be selected to move to the corresponding
eld. Each section represents a single unifying concept associated with a drug. These
sections are summarized in Table 3.1 and several are described in detail below.
3.2.2.2 Identification
The Identication section is the rst information a user will see when navigating to
a drug card. As the name implies, this section is primarily concerned with providing
an overview of the drug and the various ways in which it may be referred to. The
Summary eld provides a one- or two-sentence overview appropriate for a clinician
or scientist while the Background eld provides a more in-depth explanation of the
drug, including its primary use and approval information; both elds are authored
in-house.
Below the Background eld, there are several important identiers associated
with the drug, such as the chemical structure, formula, and external identiers
in other databases. The Type eld categorizes the drug based on its chemical
properties and source, and its value will be either “Small Molecule” or “Biotech.”
Similarly, the Groups eld summarizes the approval status of the drug, either
“Approved,” “Investigational,” “Experimental,” “Illicit,” “Vet Approved,” “Nutraceutical,” or “Withdrawn.” Investigational drugs are those that have not yet
been approved but are currently in clinical trials, whereas experimental drugs have
not yet reached clinical trials. The remaining eld values are less common but
correspond to drugs that are approved for veterinary use, those that are primarily
based on natural products (nutraceutical), and those for which approved indications
do not exist (illicit/withdrawn). As approved drugs may also be investigated for
other indications, it is possible for a drug to have multiple values in this eld.
The last notable eld is Synonyms, which provide alternative names for the drug
in question. One obvious application of these is to assist in regional localization by
language, but drugs will often have several English synonyms as well. As an example,
(a)
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3.2 DrugBank 71
(b)
Figure 3.2 Overview of DrugBank drug cards. This figure shows an example drug card for
DB00316 (acetaminophen). (a) The view a user would see after navigating to the drug card.
Note the side navigation bar containing the drug card sections (also see Table 3.1). The
search widget at the top of this side bar allows users to search for specific sections or fields.
(b) An example of clicking on one of the section names (in this case, Categories). Note that
the view is centered on the first field within the section (ATC Codes) and that the four fields
available within Categories are shown in the side bar; these may be selected directly.
acetaminophen is usually referred to as paracetamol in the United Kingdom and
Europe. Searching any of these synonyms within DrugBank will retrieve the same
entry.
3.2.2.3 Pharmacology
The Pharmacology section contains a combination of unstructured text and links
to related structured data surrounding a drug’s pharmacodynamic and pharmacokinetic properties. The pharmacodynamic properties include the drug indication(s)
along with linked structured entries of the conditions for which the drug is indicated (under Associated Conditions). If the drug is used in specic therapies or
72 3 DrugBank Online: A How-to Guide
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Table 3.1 Summary of relevant sections within a DrugBank drug card.
Section title Description
Identication An overview of the drug: what it is, what it is used for, and its
Pharmacology Information related to a drug’s pharmacodynamic and
Interactions A summary of potential drug–drug and drug–food interactions.
Products Information related to prescription, generic, mixture, and other
Categories Relevant ATC codes related to the drug, DrugBank categories
Chemical Identiers Identiers for the drug, including UNII, CAS number, InChI,
References Journal, textbook, and link references used throughout the drug
Clinical Trials Clinical trials involving the drug.
Pharmacoeconomics Information related to the sale of the drug, including
Properties Chemical and pharmacokinetic properties of a drug, including
Spectra Relevant spectral information related to the drug.
Targets Structured entries representing direct drug–target interactions
Enzymes Structured entries representing direct interactions between the
Carriers Structured entries representing direct interactions between the
Transporters Structured entries representing direct interactions between the
approval history. Brand names and synonyms are provided,
where available.
pharmacokinetic properties.
products containing the drug.
containing the drug, and structure-based chemical
classication of the drug.
InChI key, IUPAC name, and SMILES.
card. Links to relevant external resources and a specic
reference for the drug’s synthesis.
manufacturers, packaging, product routes/forms, prices, and
patents.
both experimental and predicted properties.
(may be absent).
drug and enzymes (may be absent).
drug and blood proteins (may be absent).
drug and transmembrane transport proteins (may be absent).
procedures, these will also be linked in Associated Therapies. The Pharmacody-
namics eld includes information on the high-level view of the drug’s mechanism
of action (MoA) together with other notable eects the drug may have on the body.
Lastly, the MoA eld provides a detailed view of the drug–biomolecule (usually protein) interactions that result in the observed therapeutic eect. Those targets (see
Section 3.2.2.6) relevant to the MoA are summarized below with links to the full
entries.
The included pharmacokinetic properties are largely focused on Absorption,
Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties, which
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are further summarized elsewhere (see Section 3.2.2.5). Of special interest is the
Metabolism eld, which provides both a detailed description of the metabolic
pathways as well as a graphical depiction of the possible routes from starting
compounds to excreted metabolites (Figure 3.3). The nal two elds in this section,
Pathways and Pharmacogenomic Eects/ADRs, provide links to structured
entries describing known pathways the drug is involved in and known genetic
associations related to drug action or safety, respectively.
3.2.2.4 Categories
The Categories section is primarily concerned with the ways in which the drug can
be classied. All relevant ATC codes [12] are provided; each listed code is a hyperlink that, when clicked, will navigate to a representation of the ATC code hierarchy
focused on the code in question.
The Drug Categories eld contains a tabular list of associated DrugBank categories, each of which has a unique identier prexed with “DBCAT.” These categories are a union of external sources, including ATC [12], MeSH [13], and EPC
[14], with our own proprietary in-house curation. Navigating to the individual category page yields more detailed information for each, including a description, a list
of drugs categorized into the category, and targets (see Section 3.2.2.6) for each of
these drugs. In this way, it is possible to easily discern, which targets represent possible drug targets for a given category of drugs.
The Chemical Taxonomy eld provides a classication on the basis of chemical
structure, powered by the ClassyFire tool [15]. In keeping with the output of ClassyFire
itself, the rst four levels of taxonomy, “Kingdom,” “Super Class,” “Class,” and
“Sub Class,” are provided, together with the direct parent and alternative parents.
These categories are hyperlinked to the relevant entry within the ClassyFire website
[15] and a description of each is provided as hover text. Links to the classication
in other taxonomies/ontologies are provided, when available. In addition, a full list
of the extracted substituents, including functional groups, is provided under the
Substituents eld, which may be useful in grouping or comparing chemicals (see
Section 3.3.2.2).
3.2.2.5 Properties
The Properties section compiles experimental and predicted properties. The State
and the Experimental Properties elds are curated based on Material Safety
Data Sheets (MSDS) and other relevant literature. A number of chemical properties are predicted using ALOGPS [16] or ChemAxon (https://chemaxon.com/;
Figure 3.4a), and a selection of ADMET properties are predicted using admetSAR
[17] (Figure 3.4b).
3.2.2.6 Targets, Enzymes, Carriers, and Transporters
Four (possibly absent) sections of a drug card include the associated targets,
enzymes, carriers, and transporters. The Targets section contains entries for each
biomolecule that the drug is known to directly bind; the type of biomolecule
is denoted by the Kind eld, which may hold a value of “protein,” “protein
74 3 DrugBank Online: A How-to Guide
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(a)
(b)
Figure 3.3 The drug card metabolism section. This figure shows the available information
within the Metabolism field of a DrugBank drug card. (a) An exemplar Metabolism entry
(DB00806, pentoxifylline) is shown. Note the detailed description of the reactions and the
acknowledgment of uncertainty for some steps within the scientific literature. The graphic
at the bottom of the panel shows the known pathways by which the starting drug may be
transformed into terminal metabolites. (b) An enhanced view of the graphic shown in (a),
demonstrating its interactive nature by placing the cursor over “M2, pentoxifylline external
diol.” The currently selected metabolite and its direct parent are highlighted in pink, while
other ancestors are highlighted in grey, including the starting drug.
(a)
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3.2 DrugBank 75
(b)
Figure 3.4 Predicted properties available within drug cards. This figure shows the
predicted properties, both chemical (a) and pharmacokinetic (b) available for DrugBank
entries through the drug card (acetaminophen shown here). Each chemical property has a
hyperlink to its specific source (either ALOGPS or ChemAxon) while all pharmacokinetic
properties are predicted by admetSAR. See the main text for more information.
group,” “nucleotide,” “small molecule,” or “group.” Proteins are the most common
kind of target and include information pulled from UniProt [18]. More detailed
information can be obtained by clicking on the hyperlinked UniProt ID. Protein
groups are a collection of proteins; target entries of this kind have an additional
table, “components,” that lists the constituent proteins. Protein groups are used
in cases where the drug targets a protein complex, where experimental evidence
cannot adequately discern between specic members of a protein family, or where
the presumed target is deduced on the basis of phenotype rather than detailed
molecular studies. Nucleotides, small molecules, and groups have dierent sets of
included information, but will not be discussed in detail here.
76 3 DrugBank Online: A How-to Guide
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Each target will be associated with an organism. This is usually humans but, in
other cases such as anti-infectives, may correspond to a dierent organism. The
Pharmacological Action eld will hold one of three possible values: “yes,” “no,”
or “unknown.” A value of “yes” indicates that this drug–biomolecule interaction is
known to contribute to the drug’s therapeutic eect while “no” indicates the opposite; a value of “unknown” indicates that there is insucient evidence to either
demonstrate or rule out a therapeutic eect. If the value is “yes,” the target will also
be mentioned in the MoA eld under the Pharmacology section (see Section 3.2.2.3).
The Actions eld contains one or more entries capturing the eect of the drug on
the biomolecule. This can be as simple as “binder,” but is often more specic. A list
of common possible actions is given in Table 3.2.
The Enzymes section captures information for enzymes known to participate
in the drug’s metabolism. If an enzyme is the target of a drug action (e.g. suicide
inhibitors), it will be listed in the Targets section instead. Similar to protein
Table 3.2 List of common actions within DrugBank.
Action Description
Agonist The drug promotes the activity of the target (usually a
Antagonist The drug reduces the activity of the target (usually a
Partial Agonist As above, but the drug does not fully promote the activity.
Activator The drug activates the target, increasing its ability to induce
Inhibitor The drug inhibits the target, preventing it from carrying out
Inducer The drug induces the target, either directly or by increasing
Binder The drug binds to the target.
Ligand The drug forms a complex with the target.
Cofactor The drug serves as a cofactor for the target.
Potentiator The drug does not directly activate the target but alters its
Antibody The drug is an antibody (or derivative) that specically
Modulator The drug alters the activity of the target.
Positive Allosteric
Modulator
Product of The drug is a product of the target (usually an enzyme).
Regulator The drug regulates the target.
receptor).
receptor).
a given eect or promote a specic process.
its normal function.
its transcription or translation (usually relevant with
enzymes).
activation threshold for another molecule.
binds the target.
The drug increases the activity of the target by binding to a
site removed from the main active site.
This table lists the most frequent (used at least 50 times) actions between drugs and biomolecules
within DrugBank and a description of their meaning.
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targets, enzyme entries contain additional information associated with the relevant
UniProt entry. The Pharmacological Action eld for an enzyme is usually either
“no” or “unknown,” but maybe “yes” in some cases, such as if an enzyme is
known to activate a prodrug. Common actions include “substrate,” “inducer,”
and “inhibitor.” Induction and inhibition of common metabolic enzymes, or the
identication of the drug as a substrate of such enzymes, including those of the
CYP superfamily, are usually mirrored with corresponding DBCAT category entries
(see Section 3.2.2.4).
Carriers and Transporters are additional sections that relate to blood protein binding and cross-membrane transport of the drug, respectively. Both sections will similarly relate to UniProt entries. The Pharmacological Action eld for carriers and
transporters is usually either “no” or “unknown.” Rare exceptions may be found
though, such as when induction/inhibition of a transporter is the intended mechanistic action of the drug, or when a drug requires a transporter to reach its intended
therapeutic target.
3.2.2.7 References
An important trait for all data within DrugBank is the presence of associated references. These references may correspond to published literature indexed in PubMed,
other published literature such as textbooks, or links to online resources. The Syn-
thesis Reference eld provides either a patent or other literature reference that
describes in detail how to synthesize the drug. The General References eld contains references that are cited throughout the drug card. Each in-text reference callout is formatted to match this section and is available as hover text on the callout
itself. Also included in this section are external links to related page entries and any
related protein structures in the PDB [19, 20].
3.3 Protocols
3.3.1 General Workflows
Described below are several general protocols for utilizing DrugBank Online. Readers will be shown how to conduct both a basic and advanced search of DrugBank
and how to browse drugs via DrugBank’s drug categories. These protocols and their
accompanying descriptions are intended to provide users with a practical guide for
a handful of DrugBank Online’s numerous functionalities, with a focus on features
useful in the realm of drug discovery.
3.3.1.1 Using DrugBank Online’s Search Functionality
The landing page of DrugBank Online has search functionality allowing users to
search across more than 15,000 drugs and 500,000 drug products. Entering the name
of a drug, or a branded drug product, will pull up the relevant drug card and all
of its associated data (described in Section 3.2.2). Searching via unique chemical
identiers (e.g. CAS or UNII) is also supported. Additionally, users can search via
78 3 DrugBank Online: A How-to Guide
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(a)
(b)
(c)
Figure 3.5 Using DrugBank Online’s basic search functionality.Thisfigureshows a
screenshot of the landing page search bar (a) and the smaller search bar accessible below
the upper navigation bar (b). Searches that return a single match will jump the user directly
to the relevant page, while searches with multiple results (c) will display in list format.
keywords – for example, “tricyclic” or “glycopeptide” – to nd any drugs relevant
to those terms. The search bar also allows users to search through DrugBank’s drug
targets, pathways, and indications (Figure 3.5).
In this rst protocol, we will perform a simple search for a drug molecule. Tobegin,
navigate to the DrugBank Online search bar found centered in the landing page near
the bottom of the window (Figure 3.5a) or in the top right of the window beneath
the navigation bar (Figure 3.5b). Next:
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1. Enter a drug, drug product, or keyword for which to search. Ensure the lter is
set appropriately (in this case to “Drugs”) and click the magnifying glass or press
“Enter” to run the search.
a. As discussed above, DrugBank Online’s search function also supports searches
using unique chemical identiers, e.g. CAS numbers, DBIDs, or UNIIs.
2. Searches returning an exact match will direct the user immediately to the relevant
drug card (Section 3.2.2.1). If an exact match is not found, or if the user is searching via keyword, any relevant results will be displayed in list format (Figure 3.5c).
a. Each result will display the name of the drug, an excerpt from its Background
data (see Section 3.2.2.2), and a list of drug card sections within which the
search term was matched.
b. Thislist can be further ltered by market availability and/or Group (discussed
in Section 3.2.2.2) using the buttons at the top of the page.
3. Individual drug cards can be viewed by clicking the name of the desired drug
from the list of search results.
a. See Section 3.2.2 of this document for detailed information regarding the con-
tent of each section of the drug card.
4. The search bar additionally allows users to search through DrugBank’s targets,
pathways, and indications data.
a. Targets, as described in Section 3.2.2.6, are proteins or other biomolecules
with which a drug may interact to exert its pharmacologic eect(s). After
selecting the “Target” lter under the search bar, users can enter the name
of a protein (e.g. “Angiotensin-converting enzyme (ACE)”) to return a list of
targets matching that name. Each result will display the name of the matched
target and the specic sections of the target’s data to which the search term
was matched. Clicking the hyperlinked name of the target will direct the user
to a page containing more detailed information about the target in question,
including the Kind of the target (e.g. “protein”), the organism in which it is
present, its UniProt ID, and a list of drugs with which it is known to interact.
b. Pathways are visual representations of physiologic or pharmacologic pro-
cesses. DrugBank Online allows users to search through the Small Molecule
Pathway Database (SMPDB) [21, 22], which contains more than 48,000
pathways comprising drug-specic pathways illustrating the metabolism and
MoA of a given drug, as well as various biological processes involved in disease
pathogenesis, signaling, and metabolism. After selecting the “Pathways” lter
under the search bar, users can search for relevant pathways by entering the
name of a drug, disease, or other physiological phenomena. For example,
searching for the term “Insulin” returns a pathway illustrating endogenous
insulin signaling, and also returns several results illustrating mechanistic
pathways for drugs aecting insulin secretion and production. Each search
result displays a truncated description of the pathwayalong with a list of drugs
and enzymes relevant to that pathway. Clicking the hyperlinked pathway
name will open a new window wherein the pathway and its description can
be viewed in full.
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