pubs.acs.

org/jchemeduc Article

Development of a Web-Based Laboratory Class to Reduce the

Challenges in Teaching Fragment-Based Drug Design
Xing-Xing Shi,# Jing-Yi Li,# Qiong Chen,# Xiao-Lei Zhu, Ge-Fei Hao,* and Guang-Fu Yang*
Cite This: https://dx.doi.org/10.1021/acs.jchemed.9b00198 Read Online

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ABSTRACT: Fragment-based drug design (FBDD) is a promis-

ing methodology to find quality drug leads. It is important in the
Downloaded via UNIV OF TEXAS AT AUSTIN on January 10, 2020 at 10:49:53 (UTC).

curriculum of a drug design course due to its impact on drug

discovery. However, teaching FBDD and its use by students
remain challenging in most cases. A web-based laboratory class to
teach FBDD in the form of our copyrighted workshops is
described. The students’ feedback and a quantitative evaluation of
the results show that the web-based laboratory class is popular with
students and facilitates students’ learning of FBDD for design of
possible drug-like molecules.

KEYWORDS: Graduate Education/Research, Chemoinformatics, Internet/Web-Based Learning, Medicinal Chemistry,

Laboratory Computing/Interfacing

■ INTRODUCTION
Drug design contributes greatly to human health and quality of
life.1 Hence, a course on drug design is typically included in a
well-rounded curriculum in pharmacy, chemistry, biology, and
other related fields.2,3 Technologies of drug discovery are
constantly changing.4 In recent years, fragment-based drug
design (FBDD) has rapidly developed as a promising method-
ology to find quality leads for subsequent optimization into drug
candidates.5,6 In addition, dozens of drug candidates derived
from application of FBDD have successfully and rapidly reached
the clinic.7 Thus, FBDD has accelerated the identification of
some clinical candidates, such as vemurafenib.8 On average, it
takes at least about 10 years to complete the process from project
initiation to the market for a new drug, but for vemurafenib, the
process took only 6 years. Another high-profile example is the
identification of venetoclax.9 FBDD was used to successfully
identify venetoclax hits, while high-throughput screening failed.
Therefore, as an important strategy for drug discovery, the
concepts and basic principles of FBDD have been included in
the teaching of drug design and in some instructional
books.10−12
Extensive efforts have been directed to the development of
strategies for teaching drug design. Over the past few decades,
the use of computer technology in laboratory and lecture
courses has increased. Several studies have suggested that
manipulating computer-based tools for teaching drug design
may enhance student understanding of the concepts. In 2012,
Sutch et al.13 used free software to teach structure-based drug
design and to increase students’ awareness for considering
© XXXX American Chemical Society and
Division of Chemical Education, Inc.
A J. Chem. Educ. XXXX, XXX, XXX−XXX
biopharmaceutical properties in the process. Daina et al.14
introduced a web-based educational tool, Drug Design Work-
shop, which provided the general public with an opportunity to
design potential drugs. Rodrigues et al.15 described the use of a
series of computer laboratories to improve students’ under-
standing of a drug discovery pipeline. Hayes16 detailed a
visualization and basic molecular modeling laboratory for
undergraduates that received a positive response from the
participants. In 2019, Tantillo et al.17 described a pharmaceut-
ical chemistry course in which a series of computational
laboratory experiments was designed to teach students
principles of rational drug design and to increase their
appreciation for the roles of chemists in the drug discovery
development process. However, integration of the teaching of
FBDD into computational resources has been less explored.
Meanwhile, teaching FBDD experimentally is challenging, due
to its strict requirements for biochemical detection instruments
and raw materials.
In this context, an educational strategy of teaching FBDD
using computer-based tools appears to be appealing. Previously,
we have independently designed two, freely available, web-based
resources, Auto Core Fragment in silico Screening (ACFIS)18,19
and Pesticide And Drug Fragments (PADFrag).20,21 Both are
Received: March 11, 2019
Revised: November 24, 2019
https://dx.doi.org/10.1021/acs.jchemed.9b00198
Journal of Chemical Education pubs.acs.org/jchemeduc Article

Figure 1. Some important concepts in FBDD. aΔG is defined as the binding free energy. bN(het) is defined as the count of non-hydrogen atoms.

specialized tools for designing drugs through FBDD. With the
combined use of ACFIS and PADFrag, academic institutions
may provide an opportunity for students to experience the
FBDD process. This process allows students to learn the key
concepts and the workflow of FBDD.
Chemistry degree programs. In the past, lecturing was the
primary method to teach FBDD in the course. However, to
supplement the lecture component of the course, ACFIS and
PADFrag were incorporated into the instruction of FBDD in a
90 min class. The class consists of a lecture, a computational

■ BACKGROUND
Instructional Context
The Drug Design course (2 credits) is taught in the second
semester for first-year masters students in the Agronomy and the
B https://dx.doi.org/10.1021/acs.jchemed.9b00198
laboratory experiment, and classroom discussion.
The FBDD class is scheduled in a computer laboratory in the
middle of the Drug Design course. Approximately 30−40 first-
year graduate students specializing in organic chemistry or
pesticide science attend each FBDD class. Because it is a first-
year master’s course, the age range of participants is generally
J. Chem. Educ. XXXX, XXX, XXX−XXX
Journal of Chemical Education
between 21 and 25. Each student is assigned a computer and
works individually.
Pedagogical Objectives
The first objective is to explain the following key concepts:
fragment library, fragment binding subpocket, pharmacophore,
ligand efficiency, fragment growing, scaffold hopping, bioisoster-
ism, and virtual screening. The web-based tools present the
basics of FBDD and allow the demonstration of concrete
examples of abstract ideas.
The second objective is to introduce the necessary steps and
processes of FBDD using ACFIS and PADFrag. Students learn
how FBDD is applied to real-world problems through the
simulation of an FBDD workflow.
The third objective is to convey the need to simultaneously
consider the ligand efficiency and pharmacokinetics properties
of drug-like molecules. This requires the application of
knowledge in various disciplines, including biology, physics,
chemistry, and computer science. Students are expected to
comprehend the necessity of reading the academic literature and
learning the experimental skills to evaluate the properties, if they
plan to pursue a future career in the field of drug development.
The last objective is to illustrate the advantages, practicability,
and the significance of FBDD by designing a possible fragment-
derived drug.
■
IMPORTANT CONCEPTS OF FRAGMENT-BASED
DRUG DESIGN
Drug design is an inventive and comprehensive process. The
effective implementation of FBDD involves the joint use of
multiple strategies, such as virtual screening, bioisosteric
replacement, and scaffold hopping. Some important concepts
(shown in Figure 1) are fundamental to learning FBDD and
must be explained to students.
Fragment and Fragment Library
A “fragment” is the most basic concept in FBDD. Fragments are
generally defined as low-weight, small organic molecules having
fewer than 20 non-hydrogen (or “heavy”) atoms. Compared to
larger drug-like molecules, fragments are more likely to bind to
more sites on different proteins and have better pharmaceutical
properties, such as solubility. A “fragment library” is a database
containing fragments with proper physicochemical properties. A
set of rules has been proposed for constructing fragment
libraries, among which the following “rule of three (Ro3)”22 is
the most widely employed: a molecular weight below 300 Da,
fewer than three hydrogen bond donors or acceptors, fewer than
three rotatable bonds, and a c log P equal to or less than 3. In fact,
many other factors, such as the diversity, complexity, aqueous
solubility, and lipophilicity of fragments, need to be considered
for constructing a good fragment library. For instance, Over et
al.23 deconstructed more than 180,000 natural products to arrive
at a fragment library with diverse chemical space.
Fragment Binding Subpocket
The concept of a “subpocket” may be envisioned as
“subdividing” the binding cavity of a target protein. The
fragment binding subpocket refers to the smaller structural
domains of an active pocket, in which fragments bind to the
target protein through interactions such as steric, electrostatic,
van der Waals, or hydrogen bonds. It is crucial for students to
realize that a pair of proteins may differ significantly in their
whole active sites but may share resemblance at the subpocket
level.24 This resemblance accounts for why two cavities with
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pubs.acs.org/jchemeduc Article
overall low sequence similarity can bind to identical fragments.
For example, cyclooxygenase-2 and the carbonic anhydrase
family are different proteins, but both have trifluoromethyl- and
sulfonamide binding subpockets. They can bind to the
fragments with the same functional groups in the same relative
orientations.25
Pharmacophore Structure or Core Fragment
In medicinal chemistry, a pharmacophore is an abstract
description of a molecular feature that is required for a ligand
to be recognized by a target protein. A core fragment refers to a
specific fragment that has a highly conserved binding pose and
an effective affinity contribution to the binding. Within the scope
of FBDD, a “core fragment” is equivalent to a “pharmacophore
structure”. An example is the trioxane pharmacophore of
artemisinins, in which the endoperoxide bridge structure is the
core fragment and is vital for antimalarial activity.26
Ligand Efficiency
Ligand efficiency (LE), defined as the binding free energy
divided by the number of heavy atoms in a ligand, characterizes
the average contribution of each heavy atom to the activity. The
LE metric is used to prioritize fragments. Fragments having an
LE greater than 0.3 kcal mol −1 atom−1 are generally
preferred.27,28 Reducing the number of useless atoms in
molecules may maintain high biological activity. For example,
saquinavir (LE = 0.25), the first HIV-1 protease inhibitor, is
much larger and less potent than darunavir (LE = 0.40), a
subsequent HIV-1 protease inhibitor, as a result of continuous
efforts to attain desirable physical properties and affinity.29
Fragment Growing
Fragment growing is one of the major strategies to accelerate the
development of lead compounds from core fragments. The
process starts from a core fragment placed at the binding site.
Other suitable fragments are linked to the core fragment in turn
to improve binding affinity. The newly assembled compound
conserves the binding mode of the initial fragments. Because
every subtle change in the binding mode at each step can be
monitored, fragment growing is an attractive strategy. An
example is the significant improvement in the compounds
against β-secretase.30 The initial core fragment, 2-aminoquino-
line, which had a potency of 900 μM, was optimized to the final
drug-like molecule, which had an IC50 value of 11 nM.
Scaffold Hopping
Scaffold hopping is widely applied to discover novel compounds
containing topologically different scaffolds but similar bio-
activities from known parent compounds. The concept of
scaffold hopping is based on the perspective that key interactions
between ligands and residues at binding sites may be replicated.
The replication of the interaction might be achieved by
replacement with an alternative scaffold that has identical
binding points and is capable of exhibiting a similar interaction
at the binding positions.31 Bemis and Murcko’s definition32 of a
scaffold (the BM scaffold) is generally used in medicinal
chemistry. A BM scaffold usually consists of ring systems and
linker moieties between rings, which are extracted by removing
all other substituents from the original compound. Heterocyclic
ring replacement, ring closure reaction, and ring opening
reaction are three common methods to achieve scaffold
hopping. Scaffold hopping is often used not only to improve
absorption, distribution, metabolism, excretion, and toxicity
(ADMET) properties, but also to overcome patent limitations
for current leads. One of the early examples of successful scaffold
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Journal of Chemical Education
Figure 2. Five steps of virtual drug design experiments based on the FBDD method.
hopping is the discovery of zopiclone, zolpidem, and zaleplon
starting from the benzodiazepine scaffold.33
Bioisosterism
Bioisosterism replacement is a new way to access diverse
chemical space. The concept of bioisosterism is based on the
idea that atoms, groups, or whole molecules with similar shape,
volume, electron distribution, and/or physicochemical proper-
ties may produce broadly similar biological effects.6 When two
or more functional groups or molecules have similar
physicochemical properties and share a wide range of similar
biological activities, they may be referred to as bioisosteres. The
similarity of bioisosteres can be defined only by specific
biological targets. A pair of bioisosteres in the context of a
protein target is not necessarily bioisosteres for other targets. A
successful example of bioisosterism is the replacement of a
phenol group by an arylsulfonamide, resulting in a new
compound (PhNHSO2CH3) 4-fold more potent than the
parent prototype (PhOH) as an antagonist of gonadotropin
hormone receptors.34
Virtual Fragment Screening
Virtual fragment screening is a computational technique for
filtering fragments with desired biological activities from
fragment libraries, by docking fragments to particular targets
and calculating the binding affinity between the targets and the
fragments. Because of the reduction in time, cost, and expertise
compared to experimental fragment screening, virtual fragment
screening is becoming an important tool in drug discovery
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research. For example, Tubeleviciute-Aydin et al.35 acquired 40
candidates from 57,700 molecules in just 1 day, by docking small
fragments to the putative site of the Caspase-6 structure,
alleviating the workload of in vitro biological activity assays.
■
INTEGRATED DESIGN OF THE WORKSHOPS AND
THE FBDD EXPERIMENT
The computational laboratory experiment is designed to
correspond to the FBDD workflow. The process of FBDD
generally involves five steps (Figure 2). Integrated with our web-
based workshops, the laboratory class is designed by progressive
principle. In the class, students perform each step in ACFIS and
PADFrag.
PADFrag: Fragment Library Design
Construction of a good fragment library is at the heart of any
FBDD project. We produced an integrated web interface
(Figure 3A) in PADFrag, named “Search Fragment”, for
students to design a fragment library of interest and study the
concepts of fragments and fragment libraries. In this step,
students set a physicochemical threshold for the fragment
library. Additionally, this step provides an opportunity to
illustrate to students that many important physicochemical
properties related to ADMET, such as the molecular weight,
number of hydrogen bond acceptors or donors, and solubility,
are essential to consider when designing a fragment library.
Information about eligible fragments, including the name,
structural formula, frequency of occurrences in commercial
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Figure 3. Screenshots of some PADFrag and ACFIS pages. (A, B) Screenshots of the input page and results page of the “Search fragments” module in
PADFrag. (C) Screenshots of the input page of the “CORE_GEN” module in ACFIS. (D) Screenshots of the input page of the “CAND_GEN”
module in ACFIS. (E) Screenshots of the result page of the “CORE_GEN” module in ACFIS. (F) Screenshots of the result page of the “CAND_GEN”
module in ACFIS.

drugs, and physicochemical properties, is displayed on a teacher to state that small molecules derived from commercial
dedicated output page (Figure 3B). All fragments in the drugs and pesticides are more likely to present “drug-like”
PADFrag database are generated from FDA-approved drugs or properties. It is more convenient to maintain, assemble, and
agricultural chemicals, which provides a good basis for the screen a library of a few thousand fragments than a library of
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Table 1. Class Organization and Learning Outcomes

Activity (Time, Min)
Professor’s Lecture
Overview of the FBDD strategy
(10)
Related concepts to FBDD (10)
Discovery stories of two FBDD-
derived drugs (10)
The Virtual Experiment of Strobilurin Fungicides
Fragment library design (10)
Core fragment generation (10)
Fragment growing (10)
Activity evaluation for new hits
(10)
New candidate selection (10)
Discussion
Questions and discussion (10)
Expected Outcomes: Students...
1. Are familiar with the FBDD strategy.
2. Know the advantages, unique features, and workflow of FBDD.
3. Understand that FBDD is a promising and important methodology to discover drugs.
1. Know the following concepts: fragment, fragment library, fragment binding subpocket, LE, fragment growing, pharmacophore,
scaffold hopping, bioisosterism, and virtual fragment screening.
1. Understand that the FBDD strategy is more than a theory and that it has been successfully applied to achieve new drug discovery.
1. Understand how to design a good fragment library.
2. Further understand fragment and fragment library concepts.
1. Understand generally where the core fragments are extracted.
2. Know the significance of LE in selecting core fragments.
3. Further understand the concepts of the core fragment, fragment binding subpocket, and LE.
4. Are able to use ACFIS to finish the core fragment generation job.
1. Understand that fragment growing is the most common strategy for assembling fragments as novel molecules.
2. Know the contribution of virtual screening to reducing drug development costs.
3. Further understand the concepts of fragment growing, virtual fragment screening, scaffold hopping, and bioisosterism.
4. Are able to use ACFIS to finish the fragment growing job.
1. Understand the relationship between binding affinity, biological activity, and binding free energy.
2. Know the common binding free energy calculation methods, especially MM-PBSA and GM-PBSA.
3. Know how to view the ACFIS result page and compare the activities of new molecules.
1. Understand that both affinity and pharmacokinetics (ADMET properties) need to be considered in drug design.
2. Know some key physicochemical properties that affect pharmacokinetics, including pKa, solubility, log P, and log D.
3. Know how to view physicochemical properties of new ligands in ACFIS.
1. Actively ask questions about FBDD and the workshops, as well as participate in discussions.

millions of larger molecules, which is an advantage of FBDD and
deserves to be emphasized to students.
ACFIS: Core Fragment Generation
Core fragments vary by biological targets. Analysis of the
structures and intermolecular interactions of known protein−
ligand complexes is conductive to core fragment discovery. To
acquire proper core fragments, students are invited to enter the
ACFIS server homepage and click the “CORE_GEN” box. This
opens the input page for the core generation module for users to
upload a protein−ligand complex file and the necessary
parameter files (Figure 3C). Once the “Upload file” button is
clicked, the ligand molecule is deconstructed into fragments, and
the binding free energy of each protein−fragment structure is
calculated in the background. The CORE_GEN results are
presented via an output page (Figure 3E). The information
about the results includes the structure, binding free energy, and
LE value of each protein−fragment complex. This kind of
information provides a good basis for learning what LE is and
why LE, to some extent, is a major quality criterion for core
fragments. The complex structure of fragment and protein
subpockets can be visualized by clicking the corresponding 2D
structure image. The structure is shown as an interactive 3D
session in the web browser. This step is also an excellent
occasion to explain why commercial drugs are often effective and
valuable starting points for extracting core fragments, because
biologically validated products are rich in stereocenters and
uniquely populate areas of chemical space.23
ACFIS: Fragment Growing
Hands-on application of fragment growing processes may help
students to comprehend the ability to create novel molecules by
F https://dx.doi.org/10.1021/acs.jchemed.9b00198
assembling fragments and the importance of virtual fragment
screening. We developed a module called “CAND_GEN” in the
ACFIS server that is dedicated to generating new molecules
through fragment growing. In this module, students are invited
to upload a protein-core structure in pdb format and choose a
specific fragment library (Figure 3D). Each fragment in the
fragment library undergoes virtual fragment screening first, and
then the proper fragments are separately connected to the core
fragment in the workshop. As a result, a series of newly generated
compounds is shown on the web page (Figure 3F). The
structures of new compounds vary widely. On the results page,
students can click the 2D structure image of a new compound to
enter a 3D session. Students are required to observe the 3D
structures of top ligand−protein complexes and analyze the
molecular interactions. After their observations, students might
more easily understand the definition of scaffold hopping.
ACFIS: Activity Evaluation for New Hits
A high affinity between the drug-like molecule and the target is
generally desirable, since it contributes to a more effective drug
with fewer side effects. The binding free energy between a
protein receptor and a ligand is an important thermodynamic
quantity and is usually used to predict the binding affinity. In this
step, the importance of binding energy calculations in drug
design is a key piece of knowledge that needs to be explained to
students. In most cases, high activity is accompanied by low
binding free energy. For convenience, we added an intelligent
energy calculation protocol to the CAND_GEN module when
designing ACFIS. The binding free energy of all newly obtained
ligand−protein complexes is automatically estimated by using
the molecular mechanics Poisson−Boltzmann surface area
(MM-PBSA) or the molecular mechanics generalized Born
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Table 2. Comparison of Students’ Feedback Results on the Web-Based Resources and Virtual Experimenta
Response Results by Category, a%, N = 40
Questions for Students: Do You... 1 2 3 4 5 4+5
1. Like this kind of virtual experimental teaching method based on web-based resources? 0.8 4.7 9.4 41.4 43.7 85.1
2. Think the virtual experimental teaching method based on web-based resources assists you in comprehending the 1.6 0.8 8.6 44.5 44.5 89.0
concepts or key points in FBDD?
3. Think the web-based teaching captures your interest in learning FBDD? 0.8 5.5 3.9 42.2 47.6 89.8
4. Think the virtual experiment offers you motivation to learn and understand FBDD? 0.8 8.6 7.0 34.4 49.2 83.6
5. Think the web-based virtual experiments are easy to perform? 1.6 7.8 14.8 38.3 37.5 75.8
6. Think virtual experiment aids in decreasing the difficulty in learning FBDD, compared with nonexperimental 1.6 2.3 10.9 49.2 35.9 85.1
teaching?
7. Think the web-based resources are professional and clear in their information delivery? 1.6 3.1 5.5 50.0 39.8 89.8
8. Think it is necessary to conduct virtual experiments by using web-based resources in FBDD course? 0.8 5.5 7.8 40.6 45.3 85.9
9. Want more inclusion of web-based resource like these in other courses in the future? 0.8 1.6 7.0 33.6 57.0 90.6
a
The response categories, translated by the authors into English, are 1, “Strongly Dislike/Strongly Disagree/Strongly Don’t Want”; 2, “Dislike/
Disagree/Don’t Want”; 3, “Undecided”; 4, “Like/Agree/Want”; and 5, “Strongly Like/Strongly Agree/Strongly Want”.

surface area (MM-GBSA). This allows a brief introduction of
these two calculation methods in this step. The CAND_GEN
results page (Figure 3F) gives the calculated energy value, which
is a rough reference for evaluating bioactivity for new hits.
ACFIS: Selection of New Candidates
On the input page of the CAND_CORE module (Figure D) in
ACFIS, students choose the MM-PBSA or MM-GBSA to sort
the hit candidates and set the number of reported hit candidates.
In this step, students try to select candidates for new drugs on
the basis of their current knowledge. This participation process
is helpful for students to understand the multiple objectives and
iterative nature of FBDD. In the selection process of new
candidates, the affinity between the ligand and target should be
considered, as well as the pharmacokinetics (ADMET proper-
ties) that are closely related to physicochemical properties. For
this educational purpose, we linked an external molecular
property prediction server, Molinspiration, 36 on the
CAND_GRN result page (Figure 3F). Students click the ligand
name to enter the server and obtain the predicted
physicochemical properties. Comprehensive guidance regarding
binding free energy and physicochemical properties is more
conducive to selecting reasonable candidates.
venetoclax. The slides for this lecture link the Web sites of our
web-based workshops, PADFrag and ACFIS, allowing the
introduction of the two web-based resources, with focus on
describing their functionality.
In the next 50 min, students are guided by the professor in
carrying out the virtual design experiment of strobilurin
fungicides (all the detailed operations are shown in the
Supporting Information, pp S3−S6). During this period, the
relevant concepts to FBDD are briefly reviewed, and the FBDD
workflow experiment is introduced in detail. At the beginning of
the experiment, students view the property profiles and chemical
space layouts of the fragments in PADFrag. Subsequently,
students construct a smaller fragment library by searching for
fragments in accordance with the threshold conditions in
PADFrag. Then, students begin using the ACFIS server and
must prepare the ACFIS input files. Students are required to
download the structure file of azoxystrobin bound to the
cytochrome bc1 complex (PDB code: 3L71) from the RCSB
Protein Databank.38 To avoid computation errors, it is
recommended that students use PYMOL39 visualization
software to delete the irrelevant molecules, i.e., cofactors,
ligands other than azoxystrobin, and chains that do not interact

■
CLASS DESCRIPTION
The web-based laboratory FBDD class consists of three parts: a
professor’s lecture, a student experiment under the professor’s
instruction, and a classroom discussion between students or
between students and the professor. The classroom activities,
time allocation, and corresponding expected learning outcomes
are described in Table 1.
To illustrate the workshop procedures and the FBDD process,
an example of designing strobilurin fungicides is used in the
class. The practicability of the virtual design of strobilurin
fungicides using our workshops has been verified by previous
experimental research.37 Strobilurin fungicides are widely used
in agricultural production. Their receptor protein is the
cytochrome bc1 complex. Azoxystrobin is a well-known
representative commercial strobilurin fungicide. The complex
structure of the cytochrome bc1 complex bound with
azoxystrobin provides the basis for the fragment-based design
of novel strobilurin fungicide leads.
In the first 30 min of the class, the professor in charge of the
course gives a lecture to introduce and provide an overview of
the FBDD strategy, the key concepts mentioned above, and the
discovery stories of the FBDD-derived drugs, vemurafenib and
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with azoxystrobin, before uploading the structure file in
CORE_GEN module. In the CORE_GEN module of the
ACFIS workshop, students upload the processed structure and
type “AZO”, the abbreviation of azoxystrobin, to submit a core
fragment generation calculation job. The calculation might be
time-consuming. Therefore, to reduce unnecessary waiting time,
students enter the “Job Status and Results” interface and click on
the corresponding ID for a completed job that teaching staff
submit in advance. The result of the job is a summary table
containing information on the structure, properties, binding
energy, and LE of 15 newly generated fragments. Students select
the fragment with the highest LE as the core fragment and then
proceed directly to the fragment growing step by clicking on the
“RUN CAND_GEN” icon in the “CORE_GEN Results”
interface. In this step, the default choice is to screen 290
fragments, run a 5 ps MD simulation, output 40 hit candidates,
and sort candidates based on the MM-PBSA energy. Similarly, to
avoid wasting time in class, the professor suggests that students
directly view the fragment growing results by clicking on the
corresponding ID in the “Job Status and Results” interface. On
the results page of the “CAND_GEN” module, students click
the “Molinspiration” icons to check the predicted properties of
the top five ligands, which have higher binding free energies to
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the target protein and are more likely to have bioactivity. Finally,
by comprehensively considering the activity and physicochem-
ical properties, students select an ideal new drug candidate.
In the last 10 min, the professor organizes a discussion on the
FBDD method and the web-based tools designed for FBDD.
Students are free to leave their seats and communicate with each
other. Additionally, students are allowed to ask questions
directly to the professor, and the professor answers them
immediately. Students are required to record key data and their
discussions in lab reports (the report template is shown in the
Supporting Information, p S7). The professor assigns homework
requiring students to independently design lead candidates for
other protein targets in the workshops after reviewing the
literature.
■ DISCUSSION
An anonymous online questionnaire on students’ perceptions of
the integrated teaching of FBDD was sent to each student after
the class was delivered. A total of 135 first-year master students
attended the class, and 128 valid questionnaires were collected,
for 95% recovery rate. Overall, the students’ anonymous
feedback was satisfactory. The core aim of the class as
implemented is to reduce students’ difficulty in understanding
FBDD through the integrated use of web-based workshops. All
statistical results of the questionnaires are available in Table 2.
For question 2, 89% of students acknowledged the role of web-
based resources in assisting FBDD learning. For question 6, 85%
of students thought the virtual FBDD experiment contributed to
reducing difficulty with learning. These two results indicate the
preliminary achievement of the core aim of the class. For
questions 3 and 4, 90% of students and 84% of students,
respectively, agreed that web-based workshops captured
students’ interest and offered them motivation to learn FBDD.
For question 8, 86% of students thought that it is necessary to
conduct virtual experiments. These three results confirm the
importance of the integrated web-based resources teaching
approach. Questions 5 and 7 were related to the performance of
the web-based workshops. A total of 76% of students were
satisfied with the ease of operation of the workshops, and 90% of
students thought the messages in the workshops were clear.
Thus, we may conclude that our web-based workshops, ACFIS
and PADFrag, are generally applicable as auxiliary teaching tools
for FBDD teaching at the graduate level. Notably, for question 9,
91% of students wanted more inclusion of web-based resources
in in other courses, reflecting the trend toward computer-based
teaching methods. Overall, on the basis of students’ feedback, it
appears that the use of our workshops in FBDD teaching is
popular with students and makes the teaching of FBDD easier to
implement
The professor’s observation indicated that the students were
attentive and actively participated in class discussions. An FBDD
quiz (the questions and answers are shown in the Supporting
Information, pp S9 and S13) was conducted in the next FBDD
class that was delivered. A class of 40 students who took the
FBDD quiz received an average grade of 82.58/100, compared
with their average score of less than 75.00/100 before using the
two web-based tools, indicating that the students’ performance
improved. The quiz questions were designed on the basis of the
pedagogical objectives, and they are helpful for teachers to assess
students’ learning outcomes. The performance of students
participating in the web-based lab class meets our expectations
and suggests the overall achievement of our pedagogical
objectives. According to statistical results of the quiz (shown
H https://dx.doi.org/10.1021/acs.jchemed.9b00198
pubs.acs.org/jchemeduc Article
in the Supporting Information, p S14), 32 of the 40 students
were able to describe the steps of FBDD accurately or roughly,
indicating that approximately 80% of the graduate students after
this class have acquired the basic framework of conducting drug
design research using the FBDD method in the class.
In the step for activity evaluation for new hits, the teaching
focus is to emphasize that the evaluation of binding affinity
between receptors and ligands is a core problem of structure-
based drug design, because many drugs express bioactivity
through interaction with receptors. The accurate prediction of
protein−ligand binding free energy is one of the most common
areas of computer applications in drug development. In our
virtual experiment, the MM-PBSA energies are chosen by
default in ACFIS to sort new candidates. The concept40 of
energy term decomposition in the MM-PBSA is an entry point
for the professor to describe binding energy. The MM-PBSA
approach combines three energetic terms to account for the
change in the free energy on binding. The first term corresponds
to a change in the potential energy in the vacuum, including
bonded terms, as well as nonbonded terms such as van der Waals
and electrostatic interactions. The second term accounts for the
desolvation of the different species, i.e., the polar and nonpolar
solvation energies. The third term accounts for the configura-
tional entropy associated with complex formation in the gas
phase. This basic idea is beneficial to students’ comprehension of
the binding process. The professor’s introduction to the binding
energy calculation methods may be appropriately extended
according to the availability of class time. In addition to the MM-
PBSA and MM-GBSA, it is also appropriate to mention some
classical methods, such as free energy perturbation (FEP) and
thermodynamic integration (TI), and other MD sampling-based
methods, such as linear interaction energy (LIE), if time is
sufficient.
The workshops are easy to use for teaching not only at the
graduate level but also at the upper-division undergraduate level,
and even at the senior high school level, since they are web-based
and do not require materials other than computers and the
Internet. Upper-division undergraduates in related majors, such
as chemistry, biology, and pharmacy, can learn the FBDD
strategy through the virtual experiment because they have
completed basic courses. The lab is also suitable for the
popularization of drug design among senior high school
students. Originally, the ACFIS and PADFrag workshops were
designed for scientific research. Therefore, they can be applied
not only in schools but also during scientific exhibitions.
In response to the first question of the questionnaire, students
gave an overall appraisal of 4.23/5 (on a scale of 1 (strongly
dislike) to 5 (strongly like)) of the virtual experimental teaching
method. A small number of students (less than 6%) did not like
the teaching approach. By asking for students’ suggestions on
the teaching approach, we deduced that their dislike might be
attributed to the long duration of the calculations. Hence, these
tools need to be further optimized for teaching. To improve the
performance of the workshops, we can increase the number of
processor cores and CPUs of our machines. In addition, other
feasible optimization methods include building a powerful
computing cluster and installing a batch queuing system in the
cluster that distributes jobs in parallel. We would like to improve
the computational efficiency so that students can submit
calculation jobs at the start of a lab session and the results will
be available before the end of the lab session. If we can achieve
this goal, students will be able to design drug-like molecules that
J. Chem. Educ. XXXX, XXX, XXX−XXX
Journal of Chemical Education
they are interested in, rather than just experiencing the design
process of strobilurin fungicides in the class.
■
ASSOCIATED CONTENT
*
sı Supporting Information
The Supporting Information is available at https://pubs.ac-
s.org/doi/10.1021/acs.jchemed.9b00198.
Detailed operation of strobilurin fungicides design
example, an experimental report template, the FBDD
quiz questions, the FBDD quiz reference answers, and the
statistics results for the grades of the FBDD quiz (PDF,
DOCX)
■
AUTHOR INFORMATION
Corresponding Authors
Ge-Fei Hao − Central China Normal University, Wuhan,
P. R. China, and Guizhou University, Guiyang, P. R.
China; orcid.org/0000-0003-4090-8411;
Email: gfhao@gzu.edu.cn
Guang-Fu Yang − Central China Normal University,
Wuhan, P. R. China, and Collaborative Innovation Center
of Chemical Science and Engineering, Tianjin, P. R. China;
orcid.org/0000-0003-4384-2593; Email: gfyang@
mail.ccnu.edu.cn
Other Authors
Xing-Xing Shi − Central China Normal University,
Wuhan, P. R. China
Jing-Yi Li − Central China Normal University, Wuhan, P.
R. China
Qiong Chen − Central China Normal University, Wuhan,
P. R. China
Xiao-Lei Zhu − Central China Normal University, Wuhan,
P. R. China
Complete contact information is available at:
https://pubs.acs.org/10.1021/acs.jchemed.9b00198
Author Contributions
#
X.-X.S., J.-Y.L, and Q.C. are co-first-authors.
Notes
The authors declare no competing financial interest.
■
ACKNOWLEDGMENTS
The authors thank Ching-Yuan Hu (University of Hawaii at
Manoa) for giving a suggestion on the title. This research was
supported in part by the National Key R&D Program
(2017YFD0200501) and the National Natural Science
Foundation of China (21772059, 91853127, and 31960548).
■
REFERENCES
(1) Bunker, J. P. The role of medical care in contributing to health
improvements within societies. Int. J. Epidemiol. 2001, 30 (6), 1260−
1263.
(2) Dube, D. H. Design of a drug discovery course for non-science
majors. Biochem. Mol. Biol. Educ. 2018, 46 (4), 327−335.
(3) Philip, A.; Stephens, M.; Mitchell, S. L.; Watkins, E. B. Design and
Implementation of a Laboratory-Based Drug Design and Synthesis
Advanced Pharmacy Practice Experience. Am. J. Pharm. Educ. 2015, 79
(3), 43.
I https://dx.doi.org/10.1021/acs.jchemed.9b00198
pubs.acs.org/jchemeduc Article
(4) Erlanson, D. A.; Fesik, S. W.; Hubbard, R. E.; Jahnke, W.; Jhoti, H.
Twenty years on: the impact of fragments on drug discovery. Nat. Rev.
Drug Discovery 2016, 15 (9), 605−619.
(5) Jhoti, H.; Cleasby, A.; Verdonk, M.; Williams, G. Fragment-based
screening using X-ray crystallography and NMR spectroscopy. Curr.
Opin. Chem. Biol. 2007, 11 (5), 485−493.
(6) Lolli, M.; Narramore, S.; Fishwick, C. W. G.; Pors, K. Refining the
chemical toolbox to be fit for educational and practical purpose for drug
discovery in the 21st Century. Drug Discovery Today 2015, 20 (8),
1018−1026.
(7) Erlanson, D. A.; Davis, B. J.; Jahnke, W. Fragment-Based Drug
Discovery: Advancing Fragments in the Absence of Crystal Structures.
Cell Chem. Biol. 2019, 26 (1), 9−15.
(8) Bollag, G.; Tsai, J.; Zhang, J. Z.; Zhang, C.; Ibrahim, P.; Nolop, K.;
Hirth, P. Vemurafenib: the first drug approved for BRAF-mutant
cancer. Nat. Rev. Drug Discovery 2012, 11 (11), 873−886.
(9) Souers, A. J.; Leverson, J. D.; Boghaert, E. R.; Ackler, S. L.; Catron,
N. D.; Chen, J.; Dayton, B. D.; Ding, H.; Enschede, S. H.; Fairbrother,
W. J.; Huang, D. C. S.; Hymowitz, S. G.; Jin, S.; Khaw, S. L.; Kovar, P. J.;
Lam, L. T.; Lee, J.; Maecker, H. L.; Marsh, K. C.; Mason, K. D.; Mitten,
M. J.; Nimmer, P. M.; Oleksijew, A.; Park, C. H.; Park, C. M.; Phillips,
D. C.; Roberts, A. W.; Sampath, D.; Seymour, J. F.; Smith, M. L.;
Sullivan, G. M.; Tahir, S. K.; Tse, C.; Wendt, M. D.; Xiao, Y.; Xue, J. C.;
Zhang, H. C.; Humerickhouse, R. A.; Rosenberg, S. H.; Elmore, S. W.
ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor
activity while sparing platelets. Nat. Med. 2013, 19 (2), 202−208.
(10) Erlanson, D. A. Introduction to Fragment-Based Drug Discovery.
In Fragment-Based Drug Discovery and X-Ray Crystallography; Davies, T.
G., Hyvonen, M., Eds.; Springer-Verlag Berlin: Berlin, 2012; Vol. 317,
pp 1−32. DOI: 10.1007/128_2011_180
(11) Hubbard, R. E.; Murray, J. B. Experiences in Fragment-Based
Lead Discovery. In Fragment-Based Drug Design: Tools, Practical
Approaches, and Examples; Kuo, L. C., Ed.; Elsevier Academic Press
Inc.: San Diego, 2011; Vol. 493, pp 509−531. DOI: 10.1016/b978-0-
12-381274-2.00020-0
(12) Lamoree, B.; Hubbard, R. E. Current perspectives in fragment-
based lead discovery (FBLD). In Structure-Based Drug Design: Insights
from Academia and Industry; VanMontfort, R. L. M., Workman, P., Eds.;
Portland Press Ltd.: London, 2017; Vol. 61, pp 453−464.
DOI: 10.1042/ebc20170028
(13) Sutch, B. T.; Romero, R. M.; Neamati, N.; Haworth, I. S.
Integrated Teaching of Structure-Based Drug Design and Biopharma-
ceutics: A Computer-Based Approach. J. Chem. Educ. 2012, 89 (1), 45−
51.
(14) Daina, A.; Blatter, M. C.; Gerritsen, V. B.; Palagi, P. M.; Marek,
D.; Xenarios, I.; Schwede, T.; Michielin, O.; Zoete, V. Drug Design
Workshop: A Web-Based Educational Tool To Introduce Computer-
Aided Drug Design to the General Public. J. Chem. Educ. 2017, 94 (3),
335−344.
(15) Rodrigues, R. P.; Andrade, S. F.; Mantoani, S. P.; Eifler-Lima, V.
L.; Silva, V. B.; Kawano, D. F. Using Free Computational Resources To
Illustrate the Drug Design Process in an Undergraduate Medicinal
Chemistry Course. J. Chem. Educ. 2015, 92 (5), 827−835.
(16) Hayes, J. M. An Integrated Visualization and Basic Molecular
Modeling Laboratory for First-Year Undergraduate Medicinal Chem-
istry. J. Chem. Educ. 2014, 91 (6), 919−923.
(17) Tantillo, D. J.; Siegel, J. B.; Saunders, C. M.; Palazzo, T. A.;
Painter, P. P.; O’Brien, T. E.; Nuñez, N. N.; Nouri, D. H.; Lodewyk, M.
W.; Hudson, B. M.; Hare, S. R.; Davis, R. L. Computer-Aided Drug
Design for Undergraduates. J. Chem. Educ. 2019, 96 (5), 920−925.
(18) Auto Core Fragment in Silico Screening, ACFIS. http://
chemyang.ccnu.edu.cn/ccb/server/ACFIS/ (accessed Nov 23, 2019).
(19) Hao, G. F.; Jiang, W.; Ye, Y. N.; Wu, F. X.; Zhu, X. L.; Guo, F. B.;
Yang, G. F. ACFIS: a web server for fragment-based drug discovery.
Nucleic Acids Res. 2016, 44 (W1), W550−W556.
(20) Pesticide And Drug Fragments, PADFrag. http://chemyang.
ccnu.edu.cn/ccb/database/PADFrag/ (accessed Nov 23, 2019).
(21) Yang, J. F.; Wang, F.; Jiang, W.; Zhou, G. Y.; Li, C. Z.; Zhu, X. L.;
Hao, G. F.; Yang, G. F. PADFrag: A Database Built for the Exploration
J. Chem. Educ. XXXX, XXX, XXX−XXX
Journal of Chemical Education pubs.acs.org/jchemeduc Article

of Bioactive Fragment Space for Drug Discovery. J. Chem. Inf. Model.

2018, 58 (9), 1725−1730.
(22) Congreve, M.; Carr, R.; Murray, C.; Jhoti, H. A ‘rule of three’ for
fragment-based lead discovery? Drug Discovery Today 2003, 8 (19),
876−877.
(23) Over, B.; Wetzel, S.; Grutter, C.; Nakai, Y.; Renner, S.; Rauh, D.;
Waldmann, H. Natural-product-derived fragments for fragment-based
ligand discovery. Nat. Chem. 2013, 5 (1), 21−28.
(24) Kalliokoski, T.; Olsson, T. S. G.; Vulpetti, A. Subpocket Analysis
Method for Fragment-Based Drug Discovery. J. Chem. Inf. Model. 2013,
53 (1), 131−141.
(25) Weber, A.; Casini, A.; Heine, A.; Kuhn, D.; Supuran, C. T.;
Scozzafava, A.; Klebe, G. Unexpected nanomolar inhibition of carbonic
anhydrase by COX-2-selective celecoxib: New pharmacological
opportunities due to related binding site recognition. J. Med. Chem.
2004, 47 (3), 550−557.
(26) Cui, L. W.; Su, X. Z. Discovery, mechanisms of action and
combination therapy of artemisinin. Expert Rev. Anti-Infect. Ther. 2009,
7 (8), 999−1013.
(27) Hopkins, A. L.; Keseru, G. M.; Leeson, P. D.; Rees, D. C.;
Reynolds, C. H. The role of ligand efficiency metrics in drug discovery.
Nat. Rev. Drug Discovery 2014, 13 (2), 105−121.
(28) Hopkins, A. L.; Groom, C. R.; Alex, A. Ligand efficiency: a useful
metric for lead selection. Drug Discovery Today 2004, 9 (10), 430−431.
(29) Reynolds, C. H. Ligand efficiency metrics: why all the fuss?
Future Med. Chem. 2015, 7 (11), 1363−1365.
(30) Cheng, Y.; Judd, T. C.; Bartberger, M. D.; Brown, J.; Chen, K.;
Fremeau, R. T.; Hickman, D.; Hitchcock, S. A.; Jordan, B.; Li, V.;
Lopez, P.; Louie, S. W.; Luo, Y.; Michelsen, K.; Nixey, T.; Powers, T. S.;
Rattan, C.; Sickmier, E. A.; St. Jean, D. J.; Wahl, R. C.; Wen, P. H.;
Wood, S. From Fragment Screening to In Vivo Efficacy: Optimization
of a Series of 2-Aminoquinolines as Potent Inhibitors of Beta-Site
Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1). J. Med. Chem.
2011, 54 (16), 5836−5857.
(31) Hu, Y.; Stumpfe, D.; Bajorath, J. Recent Advances in Scaffold
Hopping. J. Med. Chem. 2017, 60 (4), 1238−1246.
(32) Bemis, G. W.; Murcko, M. A. The properties of known drugs. 1.
Molecular frameworks. J. Med. Chem. 1996, 39 (15), 2887−2893.
(33) Teuber, L.; Watjens, F.; Jensen, L. H. Ligands for the
benzodiazepine binding sitea survey. Curr. Pharm. Des. 1999, 5
(5), 317−343.
(34) Lima, L. M. A.; Barreiro, E. J. Bioisosterism: A useful strategy for
molecular modification and drug design. Curr. Med. Chem. 2005, 12
(1), 23−49.
(35) Tubeleviciute-Aydin, A.; Beautrait, A.; Lynham, J.; Sharma, G.;
Gorelik, A.; Deny, L. J.; Soya, N.; Lukacs, G. L.; Nagar, B.; Marinier, A.;
LeBlanc, A. C. Identification of Allosteric Inhibitors against Active
Caspase-6. Sci. Rep. 2019, 9, 5504.
(36) Molinspiration website. http://www.molinspiration.com/ (ac-
cessed Nov23, 2019).
(37) Hao, G. F.; Wang, F.; Li, H.; Zhu, X. L.; Yang, W. C.; Huang, L.
S.; Wu, J. W.; Berry, E. A.; Yang, G. F. Computational Discovery of
Picomolar Q(o) Site Inhibitors of Cytochrome bc(1) Complex. J. Am.
Chem. Soc. 2012, 134 (27), 11168−11176.
(38) RCSB Protein Data Bank website. http://www.rcsb.org/
(accessed Nov23, 2019).
(39) PyMOL website. http://pymol.org/ (accessed Nov23, 2019).
(40) Miller, B. R.; McGee, T. D.; Swails, J. M.; Homeyer, N.; Gohlke,
H.; Roitberg, A. E. MMPBSA.py: An Efficient Program for End-State
Free Energy Calculations. J. Chem. Theory Comput. 2012, 8 (9), 3314−
3321.

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