J Sci Educ Technol (2008) 17:366–372
DOI 10.1007/s10956-008-9106-6
New Simulation Methods to Facilitate Achieving a Mechanistic
Understanding of Basic Pharmacology Principles
in the Classroom
Anita Grover Æ Tai Ning Lam Æ C. Anthony Hunt
Published online: 3 April 2008

Springer Science+Business Media, LLC 2008
Abstract We present a simulation tool to aid the study of
basic pharmacology principles. By taking advantage of the
properties of agent-based modeling, the tool facilitates
taking a mechanistic approach to learning basic concepts,
in contrast to the traditional empirical methods. Pharma-
codynamics is a particular aspect of pharmacology that can
benefit from use of such a tool: students are often taught a
list of concepts and a separate list of parameters for
mathematical equations. The link between the two can be
elusive. While wet-lab experimentation is the proven
approach to developing this link, in silico simulation can
provide a means of acquiring important insight and
understanding within a time frame and at a cost that cannot
be achieved otherwise. We suggest that simulations and
their representation of laboratory experiments in the
classroom can become a key component in student
achievement by helping to develop a student’s positive
attitude towards science and his or her creativity in scien-
tific inquiry. We present results of two simulation
experiments that validate against data taken from current
literature. We follow with a classroom example demon-
strating how this tool can be seamlessly integrated within
the traditional pharmacology learning experience.
Keywords Education
Pharmacology
Systems biology

In silico
Model
Simulation
Mechanism
A. Grover
T. N. Lam
C. A. Hunt (&)
The Biosystems Group, Department of Bioengineering
and Therapeutic Sciences, The University of California,
513 Parnassus Ave., S-926, San Francisco,
CA 94143-0912, USA
e-mail: a.hunt@ucsf.edu
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Motivation
The field of pharmacodynamics encompasses the study of
the time–course of a drug effect at target site within a
living system. There are numerous, intertwining concepts
associated with the field: it is often hard for the new student
to comprehend how these concepts emerge from biological
experiments, and how these concepts relate to the com-
ponent interactions within biology to create the dose–
response and time–course curves scattered throughout
textbooks and the pharmacology literature.
Achieving a mechanistic understanding is expected to
provide insights into the biology and experimental methods
that is often not achieved when following the traditional
data-based, empirical teaching approach. For example,
students in an introductory pharmacology course are often
taught the Emax model of the concentration–response
relationship. The model uses the Hill function [a common
form is E = EmaxCa/(EC50 + Ca)] to describe idealized
experimental data. The equation is used to predict the
effect of a drug, E, given its concentration, C, the maxi-
mum effect (Emax), concentration at half the maximum
effect (EC50), several assumptions about the experimental
system, and an elusive parameter a known as the steepness
factor or Hill coefficient. Although aspects of the mecha-
nism are typically discussed and sketched, student
experience with the actual experimental details and data to
which of these parameters are expected to map is rare.
Often, students are expected to understand only how to use
this equation for its basic predictive properties.
Providing a comprehensive wet-lab experience to gen-
erate an appreciation for science and experimental methods
and to thereby provide a foundation for mechanistic under-
standing is problematic at the student level. There are
several delimiting and demotivating considerations.
J Sci Educ Technol (2008) 17:366–372
Providing such experiences would require that a time-
intensive and costly laboratory component accompany the
introductory pharmacology course. Even when the living
components of experiments behave reliably, the significant
variability associated with conducting wet-lab experiments
and accumulating sufficient data within a limited time frame
can complicate the experience and its interpretation for the
novice.
The method of mechanism based in silico simulation
used here is one of several methods referred to collectively
as executable biology (Fisher and Henzinger 2007). The
method emerges as a potential solution to the above
problem. In particular, simulation of the type described
below offers an alternative that can be both cost and time
effective. It provides a world in which experiments always
‘‘work,’’ although outcomes can differ from expectations.
Through the visualizations afforded by the simulation, a
student can observe mechanisms in operation and thereby
develop and understanding of what effect changing bio-
logically rooted characteristics might have on the
accumulated data and empirically derived parameters.
The development of such pharmacodynamic simulations
has at its basis two significant motivations.
• Towards the understanding of how the interplay of
various drug and biological system characteristics can
affect dose–response and time–course relationships.
• Reciprocally, towards the understanding of how various
observed phenomena can be understood mechanisti-
cally through manipulation of key drug and biological
system characteristics.
Simulation
The simulation was created using the agent-based model-
ing framework Net-Logo (Wilensky 1999). In this context,
an agent-based model (ABM) is an analogue of a referent,
wet-lab system created from software components. It is
created using a set of entities, called ‘‘agents’’; an inter-
active version is available (Grover and Tang 2008). During
a simulation, the agents interact with each other and their
environment according to rules (principles of operation)
defined by the programmer and, to some degree, by the
user. Those principles of operation are expected to have
biological counterparts, although they may not be fully
understood. In the analogue described below, there are two
types of agents: one maps to drug molecules and the other
maps to target macromolecules or sites in the referent
system. For simplicity, all other aspects of the referent
biological system are conflated and pushed into an inactive
background (but not forgotten). To distinguish clearly in
silico components and processes from corresponding
367
biological components and processes, we hereafter use
SMALL CAPS when referring to the former. The analogue
system, or ‘‘world,’’ is visualized with stationary TARGETS
and mobile DRUGS that move through the system. That
movement can map to perfusion of drug through a bio-
logical system in vitro. When a DRUG and TARGET contact
each other, they can bind to produce a measurable EFFECT.
The EFFECT, along with the numbers of TARGET and DRUG,
are plotted against TIME in the Time–Course graph; the
EFFECT and the TARGET are plotted against the number of
DRUGS in the Dose–Response graph.
At the start of a simulation, the TARGETS are distributed
randomly through the WORLD. In most cases, DRUGS are
distributed randomly within the top of the WORLD. DRUGS
PERFUSE down the world using a random walk that is biased
in the x-direction. They are ELIMINATED at the bottom
(exceptions are bolus time-course simulations,
detailed in Table 1). The input of drug can follow one of
four patterns, detailed as simulationTypes in Table 1.
The events occurring in the analogue system during sim-
ulations can be imagined as representing flow of drug
through a single cell, where the blood supply is at the top of
the cell. In such a referent, drug would interact with
receptors within the cell on its way through. However, as
described in the examples below, the same analogue can
represent a number of other in vitro systems equally well.
TIME in an agent-based simulation progresses in discrete
steps. Each time step is a simulation cycle. During a sim-
ulation cycle, each active agent is given an opportunity to
update itself (e.g., apply its rules). During each time step,
DRUG has an opportunity to move (or not) into and adjacent
space. We define an experiment as a simulation in which
all DRUGS comprising a dose have an opportunity to move
through the WORLD.
The user has the option of changing a number of variables
associated with the system. The screen shot in Fig. 1 shows
various user interfaces and the location of the sliders used to
change variable values. The variables are described in Table 1.
Reproducibility
The first test of the analogue was to document the repro-
ducibility of the results. We ran seven experiments using
the same parameter values. We plotted the mean and range
of the number of TARGETS remaining at the end of each time
step in Fig. 2 along with the DRUG input profile. The results
attest to the reliability of the simulations.
Validation 1
Delacher et al. studied the time–course relationship of
bacteria to ciprofloxacin, an antibiotic drug. At the
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Table 1 User controlled variables

a. start&Start/Stop The Start/Stop switch must be turned to On to run the simulation. Click start to begin. To stop
the simulation at any time while it is running, turn the Start/Stop switch to Off.
b. simType: The drop-down menu offers four choices for the manner in which DRUG will be delivered to the WORLD:
c. dose-response To create a standard dose-response curve: at each turn, more DRUG will enter the world in a linear
fashion until the maxDrugMols have been delivered.

d. bolus time-course To understand how a bolus dose of DRUG will affect TARGET, the maxDrugMols amount of drugs will
circulate through the WORLD until simLength time is reached. In this case, DRUGS are initially
distributed and move randomly through the WORLD (not necessarily towards the bottom) at each step.

e. steady-state Towards a situation where the effect site is different from the administration site, where concentration
is slow to rise but reaches a plateau at the maxDrugMols amount. At each turn, an amount of DRUG
will enter the WORLD according to a standard hill function, until a plateau has been significantly
established.

f. hysteresis Towards another situation where the effect site is different from the administration site, where the
concentration rises and falls to produce a hysteresis type dose-response curve. At each turn, an
amount of DRUG will enter the world according to a two-exponential function, until the DRUG amount
has fallen to 0.

g. simLength (applies only to bolus Slider to specify the amount of time steps the simulation will run in the bolus time-course
time-course) simType.
h. initialTargetMols The amount of TARGET molecules created at the start of simulation; the amount of TARGET molecules will
change depending on targetRegulation and growthRate.
i. maxDrugMols The maximum number of DRUGS to enter the WORLD in the experiment.
j. bindingAffinity The probability a DRUG and TARGET at the same location in the WORLD will bind.
k. dissociation The probability a DRUG bound to a TARGET will dissociate from the TARGET.

l. efficacy The probability the bound DRUG-TARGET will create an EFFECT.

m. timeDelay Number of steps in delay between when the DRUG binds to the TARGET and the EFFECT can be seen.
n. targetRegulation Probability the DRUG binding to the TARGET will:
targetRegulation \ 0: kill the TARGET. targetRegulation [ 0: cause the TARGET to
replicate, creating a new TARGET adjacent to the bound TARGET.
o. growthRate (per 100 turns) Regardless of DRUG binding, how the numbers of TARGETS change overtime.
p. Visualization Slider Slide to adjust the speed of the animation.
q. Visualization ON/OFF Turn the visualization screen ON or OFF. Turning the screen off may allow the simulation to run faster.

concentrations studied ciprofloxacin is bactericidal: it kills
bacteria. The group first studied human interstitial con-
centration data to determine the pharmacokinetic time
profile of drug at the active site. They successfully descri-
bed that profile using a two-exponential hysteresis model
(we had provided the same model as an input option).
Delacher et al. then performed an in vitro experiment using
cultured bacteria. They added drug to the culture according
to the hysteresis input model and measured the remaining
number of viable bacteria using a colony count method. The
extracted data is graphed in Fig. 3a.
To simulate the preceding in vitro experiments, we
applied the two-exponential hysteresis input option. The
TARGET agents now represent one or more bacteria, and the
DRUG agents represent ciprofloxacin. We defined effect in
this analogue as an observed DRUG–TARGET pair. We obtained
an acceptable match by assuming bacteria would die within
one time step following contact by at least one DRUG.

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Fig. 1 Screen shot of the

simulation program

350.00
a 10
300.00

Bacteria (cfu/ml* 10^8)

250.00 8
Agents

200.00
6
150.00
4
100.00

50.00 2
0.00
0 10 20 30 40 50 0
0 50 100 150 200 250
Time Time (min)

Fig. 2 Reproducibility: the upper graph shows the mean and range b
(error bars) of number of targets remaining for seven experiments at
the end of each time step. The lower graph shows corresponding drug
input values

We achieved that by having targetRegulation

= –100. The results are graphed in Fig. 3b.
The dramatic initial decrease in bacterial numbers with a
slight terminal fall off is evident in both plots. Because the
TARGETS die upon binding with the DRUG, there are never any
active DRUG–TARGET complexes, as evidenced by the
effect line consistently at 0 through the run. This plot also
shows the input of DRUG according to the hysteresis input type
described above. The quantitative numbers of TARGETS, DRUG,
and TIME will not necessarily be equivalent between the wet-
lab and simulation experiments, in the same manner that
results between in vitro and in vivo representations of a Fig. 3 (a) Data extracted from the literature Delacher et al. (2000).
system might not be quantitatively equal. The simulation Bacterial death in time in the presence of antibiotic; (b) Simulation
results of data extracted from (Delacher et al. 2000). The dashed
aims to develop an understanding of how the plot in the
overlay follows the shape of the extracted data in Fig. 3a, serving as
literature might develop, and the associated visualizations of validation of the simulation
this simulation run quickly provide this understanding.
gefitinib-treated human tumor cells: those that, following
transduction, expressed the transporter gene for breast
Validation 2 cancer resistance protein (BCRP), and control cells that
were not transduced. The BCRP transporter is believed to
The anticancer drug gefitinib inhibits cancer cell growth. pump various anticancer drug molecules, including gefiti-
Sugimoto et al. studied growth inhibition of two types of nib, out of cells, thus limiting their effectiveness. To test

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Fig. 4 (a) Inhibition of BCRP- a

Cell Numbers (% of Control)

100
transduction of human cancer
cells on the growth-inhibitory 80
effect of gefitinib. The data
were extracted from Sugimoto 60
et al. (2005). The values are
40
percent of untreated control cell
numbers after 5 days of growth 20
in increasing concentrations of
gefitinib. Squares: cells were 0
BCRP-transduced; circles: cells 0 20 40 60 80 100 120 140
were not BCRP-transduced; (b) Drug Concentration (nM)
measurements taken during b
simulated experiments mimic
data extracted from Sugimoto
et al. Left: results from a
simulated experiment used
agents representing non-
transduced cells. Right: results
from a simulated experiment
used agents representing BCRP-
transduced cells. The
differences in the final percent
targets remaining are similar to
those extracted from the data,
which serves as validation
evidence

this theory for both cell types, the authors measured cell
growth in the presence of different gefitinib concentrations.
They observed that growth over a 5-day period of the cells
transduced with the BCRP gene approached that of
untreated controls (not shown). That result confirmed that
BCRP-transduction enabled cells to become resistant to the
drug. From the extracted data shown in Fig. 4a, it is clear
that gefitinib is more efficacious against the non-transduced
cells than it is against the transduced cells.
To mimic the data in Fig. 4a, using simulation, we note
that the resistance conferred by BCRP-transduction
increased the likelihood that the tumor cells growth after
5 days would be normal when cells are treated with gefi-
tinib. In the simulation TARGET agents represent control
numbers of tumor cells after 5 days of growth. DRUG agents
represent gefitinib. We conducted two simulations in the
dose-response mode. Only the targetRegula-
tion parameter was changed. A non-transduced cell fails
to grow once it has contacted and bound the drug agent, so
targetRegulation is set at –100. To demonstrate
resistance in transduced cells, we set this parameter to
larger values. The simulation results shown are for tar-
getRegulation = -20.
The bottom line in each plot shows the number of TARGETS
that fail to grow despite contacting and binding the DRUG. The
number is consistently 0 when targetRegulation =
-100. However, when targetRegulation = -20,
some TARGETS grow normally, even after treatment with the
DRUG. Note again that the scales on the simulation are not
intended to match quantitatively the scales used in the wet-
lab experiments. The key is that changing the response of
targets to the drug had two consequences: it changed the
maximum effect over this dose range (Emax) and it changed
the rate (effectively the EC50) at which an effect occurred.
The result was that the observed simulated effect mirrored
that from the wet-lab experiments.
Classroom Example
The previous two examples have been concerned with
understanding observed wet-lab experimental data. Recip-
rocally, simulation can be used to design, evaluate, and
build insight into experiments outside of the wet-lab.
For example, the student is asked to determine if drug A
or drug B is more potent in activating a key target molecule
in an essential regulatory system. Effect is caused by drug
binding to targets.
1. Drug A binds tightly—essentially irreversibly—to the
target receptors, but its intrinsic efficacy is qualita-
tively low.
2. Drug B has a slight probability of dissociating from the
receptor after binding, and its intrinsic efficacy is twice
that of drug A. Once the drug dissociates, the target is
fully active: it is the same as if it had never been
bound.

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Fig. 5 Simulation results from a b
a hypothetical experiment
comparing the dose–effect
relationship of two hypothetical
drugs, A (left) and B (right).
Horizontal dotted lines:
maximum effect (Emax); vertical
dotted lines: dose at which half
maximal effect is achieved
(EC50)
The student’s task, in empirical pharmacological terms, is
to determine which drug has a lower EC50, the concentra-
tion at which half the maximum effect is reached?
We choose the dose-response simulation setting to
solve this problem, and choose 40 initial TARGETS with a
maximum DRUG input of 200. In the first case, efficacy is
set to 50 and dissociation is set to 0. In the second,
efficacy is set to 100 and dissociation is set to 3.
The results are shown in Fig. 5.
The dramatic variability observed during the single
simulations in Fig. 5 are typical of what one could
encounter during wet-lab experiments. Nevertheless, the
significantly lower Emax and higher EC50 are evident in
the graph on the right even though the dissociation
probability was small. These results are not entirely
intuitive. Working with simulations helps one develop an
intuition for, and an understanding of how the system
responds to two different drug interventions. Such exer-
cises can give the student important mechanistic insight
into the origin of the elusive mathematical parameters of
empirical, inductive models such as the Hill function
introduced previously.
Discussion
The three above examples combine to document the
effectiveness of the simulation method in achieving the
goals previously set forth.
• Towards the understanding of how the interplay of
various drug and biological system characteristics can
affect dose–response and time–course relationships.
• Reciprocally, towards the understanding of how various
observed phenomena can be understood mechanisti-
cally through manipulation of key drug and biological
system characteristics.
371
Inclusion of traditional, hands-on, wet-lab experimentation
experiences within life science curricula is becoming
increasingly rare. That is because doing so is becoming
more costly and time-consuming. We suggest that ABM
simulations of the type described here can help fill the void.
The importance of providing laboratory experiences, as
part of life science coursework, is well documented. Most
notably, laboratory experiences have a positive effect on
secondary students’ attitudes towards science, and there is
a highly significant correlation between attitude and
achievement (Freedman 1997). A comprehensive review
of thoughts on the importance of laboratory experience
(Hofstein and Lunetta 2003) details a number of related
concepts. First, experimentation plays a critical role in
developing a student’s sense of inquiry, or his or her ability
to study systems in diverse and novel ways. This is
furthered when the laboratory activities are well integrated
with the non-laboratory portions of the class, and even
more so when the level of ‘‘open-endedness’’ of the
activity, or how well the activity promotes an open-ended
approach to research, is high. Hofstein and Lunetta also
allude to a number of studies focusing on the use of
technology in the classroom—in particular, how computer
visualization provides unique benefits, and the technology
can afford a more complete understanding than other
teaching methods. These concepts are markedly repre-
sented in the above two goals.
Building an intuitive understanding of the concepts
associated with pharmacology and pharmacodynamics is
important within many life science fields. However, it can
be hard for a student to develop, and can truly only be done
through experiences such as those traditionally provided by
laboratory activities. We posit that improved, more realistic
simulation methods of the type demonstrated could facili-
tate developing this understanding within students at all
levels. The approach described above affords this
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372
possibility by using simulation systems in which obser-
vable and measurable behaviors are a consequence of
actual mechanisms: interacting components. These mech-
anisms, although in silico, can be sufficiently realistic so
that they behave during experiments analogously to how
biological systems behave.
In the traditional approach, the scientist offers an
abstract, inductive, mathematical model to explain sys-
temic observations. Model parameters are used to describe
properties of the data believed to have been caused by the
underlying, but abstracted away, mechanisms. The simu-
lation approach described here builds a mechanism of
interacting components. So doing allows one to observe the
emergence of the characteristics seen at the empirical level.
The two validation experiments demonstrate that it is
relatively straightforward to construct abstract in silico
systems that can exhibit behaviors that mimic those
observed in wet-lab experiments. The classroom example
demonstrates that interesting informative examples can be
created to learn how particular phenomena can arise. We
suggest that such exercises can be easily integrated with
and used to supplement the traditional pharmacological
classroom practices.
Acknowledgments This research was funded in part by the CDH
Research Foundation (R21-CDH-00101). The software described
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J Sci Educ Technol (2008) 17:366–372
along with supporting documentation may be obtained without charge
from the corresponding author.
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