Therapeutic Drugs:

A History of Discovery, A Future of

Design

Zach Jarou
PSL 480
Fall 2007
Michigan State University
Introduction

By their most basic definition, drugs are exogenous chemical

compounds that modify the way the body and mind work by acting

upon biological targets. Throughout history and today, many different

groups of people have used drugs for many different purposes,

including medical, recreational and spiritual.

My interest in this topic is due to the culmination of several

different factors. I have always been fascinated by the idea that our

physical and mental states could be reduced to a network of

complicated, self-regulating chemical reactions within our bodies. As a

child, I had no idea about the complexities of this system could

function, but my experiences here at Michigan State have done

wonders in explaining the details; to take a reference from Dr. Steve

Heidemann of the Physiology Department, each of the trillion cells that

make up our bodies are nothing more than miniature Rube Goldberg

machines.

By understanding the functions of different biochemical

pathways present in each cell and the mechanisms by which they are

regulated, researchers are able to attribute failures in these pathways

to certain disease states. To date, researchers have been very

successful in synthesizing various chemical compounds that can be

administered to patients to correct deficiencies in these systems.

Unfortunately, most of this research has been targeted towards

diseases that more commonly afflict people in Western cultures due to

their ability to pay for such products. Worldwide, there are still many

devastating diseases for which no cures exist either because the

prevalence is considered too small to warrant the costly research

required or their inabilities to pay for treatment if one was created.

During my time at MSU, I have been lucky to have numerous

opportunities to get involved with and be mentored by several talented

faculty members. Dr. Donna Koslowsky, of the Microbiology and

Molecular Genetics department, served as my Cell and Molecular

Biology professor in the spring of 2007 and from my achievements in

the course, encouraged me to apply for the National Science

Foundation’s Undergraduate Research Fellowship in Mathematical and

Biological Sciences. I was subsequently accepted and began working in

Dr. Maria Zavodszky’s computational biology lab. Our lab is focused on

correctly predicting the orientation that ligands, or other small

molecules, take when they dock into the active or regulatory sites of

their target proteins.

The final reason for my interest would be my interest in pursing a

career in the pharmaceutical industry, which is one of the largest and

most profitable in the world.

The History of Drug Discovery

Throughout history, drugs have played important roles in the

lives of the human race. As early as 10 million years ago, the

accidental discovery of plants with healing powers probably occurred

by our earliest nomadic ancestors. It was not until the formation of

agricultural communities, 20,000 years ago, that individuals began to

specialize in role of healing; ambitious leaders emerged from these

communities and their authority often came from their ability to heal

the sick. These early medicine men created a variety of medicines

containing mainly botanical specimens but also could contain animal

parts, which deepened their mysterious powers. Guided only by vague

symptoms and no knowledge of anatomy or physiology, once a certain

treatment was found to have an effect, it was often used for a variety

of ailments. As time went on, valid explanations were sought for

particular treatments; the first of these pharmacopoeias was compiled

in 2735 BC by the Chinese scholar-emperor Shen Nung (Burger 1995).

In the 4th century BC, Hippocrates of Greece, the “Father of

Medicine,” became interested in using inorganic salts, rather than

botanicals, as medications. His authority lasted through the Middle

Ages and while his famous oath may have survived better than his

preferences for inorganic salts, they are still used today under certain

circumstances (Burger 1995).

The next revolution in medicinal thought occurred in 2nd century

AD Rome, when Galen prepared medicine by soaking or boiling plants.

His insistence of carefully identifying the type and age of plants was
one of the earliest examples of controlling drug purity. His teaching had

a lasting impact, as the herb gardens of medieval monasteries

contained the necessities for his prescriptions (Burger 1995).

Today, more than 200 major pharmaceutical firms, comprising a

$602 billion industry as of 2006 and expected to reach $1.3 trillion by

2020, perform the majority of drug discovery. These large multinational

corporations are often vertically integrated to discover, develop,

manufacture, market, sell and distribute new drugs to treat human

ailments. Annually, the FDA approves about only 25 truly novel drugs,

along with several reformulations. As of 2003, each new drug costs

about $1.7 billion to develop; to encourage drug companies to pursue

this research, patents are granted to protect the drug discovering

company’s exclusivity rights for 20 years to ensure that they are able

to recoup their huge investments before other firms are able to

introduce lower priced generic substitutes (DiMasi 2003).

From Mythology to Molecular Biology

While these early pharmacists may have been somewhat

successful in accurately prescribing the proper medication to treat a

patient’s ailment, they were practically clueless about the mechanism

of its action to restore health. The supernatural explanations for

healing held by the earliest shamans and vitalistic separation of the

organic life processes from the inorganic matter first suggested by

Aristotle have been replaced. Improved understanding of individual

organ function and Pastuer’s 16th century germ theory of disease

reduced the allusion to mystical forces, but it was not until 1828 when

Wohler synthesized urea from inorganic components that vitalism was

rejected by the majority of scientists.

In 1674, Anton Van Leeuwenhoek became the first person to

view a living cell using microscopy and by the mid-1800s the classical

cell theory was introduced. But, the question still plaguing the minds of

many biologists was how tiny structures visible under their

microscopes were linked to the molecules being characterized by

physiological chemists.

The attempt to explain the phenomena of life starting on the

molecular level first began with the convergence of several disciplines

in the early 20th century to form a new field known as molecular

biology. The results of these early experiments can best be

summarized by Crick’s “Central Dogma” which states that genetic

information coded in DNA is carried out of the nucleus by RNA to a

ribosome where the code corresponds to amino acids required to

create a specific proteins, which are the “molecular machines” of the

cell.

Mechanisms of Drug Action

Recognizing the hierarchical organization of the human body is

important to understanding the mechanisms by which drugs work.

Each of our bodies is comprised of nearly 1.5 trillion cells, which are

specialized into nearly 200 different types to form different tissues

found in the various organs of our bodies. These organs perform

individual functions within larger, interconnected organ systems that

support the continued survival of the organism. Thus, changes at the

cellular level are reflected upwards through the chain.

In order to cause a change in cellular physiology, a drug must

interact with a biological target, such as a receptor, enzyme, or other

protein. Receptors come in many different varieties based on their

location within the cell and their mechanism of action. Because the

size and chemical nature of ligands determines their ability to move

through the selectively permeable membrane of the cell,

transmembrane receptors are located within the plasma membrane

and serve to conduct the signals of hydrophilic ligands into the cell,

while lipophilic signals are able to pass directly through the membrane

to interact with intracellular receptors. There are two main classes of

transmembrane receptors, including those that are metabotropic,

which activated second messenger systems within the cell via a series

of intracellular events, and ionotropic receptors, which directly open

channels that allows the flow of ions down their respective

concentration gradients. Intracellular receptors often act as

transcription factors, which bind to specific DNA sequences to regulate

the activity of RNA polymerase. Drugs that bind to receptors can either

be agonists, which activate the activity of the receptor, or antagonists,

which bind to but do not activate the receptor, limiting the ability of

agonists to bind.

The other major class of biological targets, enzymes, are proteins

that act to catalyze chemical reactions within the cell. Enzymes are

extremely selective for their substrates and the products of one

enzyme typically become the substrates for others to form metabolic

pathways. Enzymes catalysis occurs in a region referred to as the

active site, where the activation every of the reaction is lowered

through the formation of multiple non-covalent interactions with the

ligand. It is important to note that enzymes only increase the rate of

the reaction, but do not alter its equilibrium. Other than the active site,

enzymes may also have binding sites that allosterically or otherwise

regulate the activity of the enzyme; this is important to efficiently

allocate energy and required compounds within the cell. The majority

of drugs used on enzyme targets work through reversible inhibition,

which can competitively compete with biological substrate to bind into

the active site or uncompetitively binding to an allosteric regulatory

site. A few inhibitors are irreversible and react with the enzyme to form

a covalent linkage between the pair.

Modern/Future Drug Discovery/Design Methods

 In recent history, drugs have traditionally been discovered using

a variety of different methods, including identifying and isolating active

ingredients from traditional remedies, serendipity or by trial-and-error

testing on animals. As scientists’ understanding of biological systems

has advanced, accompanied by advances in automation and

computational technologies, the methods used to identify potentially

therapeutic drug compounds has, and continues to, increase in

complexity. High-throughput screening combined with combinatorial

chemistry and in silico methods are greatly increasing the rates at

which novel drugs can be brought to market.

Traditional methods based on bioprospecting have been highly

successful by both using traditional and indigenous biomedical

knowledge, and also by searching for previously unknown compounds

in organisms. A 2007 estimates that between 1981 and 2006, up to

63% new chemical entities were derived from plants or other natural

sources. Overall, this figure reaches as high as 75% including

compounds such as morphine from opium and digoxin from digitalis

(Newman 2007). Many notable drugs have also been discovered by

accident, including penicillin, LSD and viagara. It is also interesting to

note that research carried out at Michigan State led to the accidental

discovery of the anti-cancer drug cis-platin.

In the late 20th century, the use of synthetic compounds became

increasingly favored as drug candidates. High-throughput screening is

a drug discovery method involving the usage robotic automation to

rapidly observe the effect that millions of compounds on a particular

biological target. Currently, there are HTS robots that can test up to

100,000 compounds per day. It is very unlikely that any of the

compounds screened will act as a perfect drug, but there will instead

be many compounds that cause differing degrees of response. By

examining the similarities between these compounds, scientists are

able to determine which the spatial arrangement of chemical

interactions that are necessary between the target and ligand to alter

its activity, known as a pharmacophore (Hann 2004).

In order to increase the interaction specificity, the

pharmacophore serves then as a lead compound whose structure is

modified in various ways to create several new molecules with

activities that must be determined by another round of high-

throughput screening. A process known as combinatorial chemistry can

also automate the generation of these compounds. This process can

continually be repeated for several iterations and in a brute-force

manner in which the exploration of chemical space function can be

thought as the equivalent of picking a lock.

Although experimental high-throughput screening may

eventually generate good lead compounds, the process is very time

and money intensive and is in essence based on nothing more than

sophisticated trial and error. Newer computational techniques merging

biological and computer sciences have developed a technique known

as virtual or in silico high-throughput screening; rather than

discovering drugs, they can be rationally designed based on the

structure of the desired target obtained from x-ray crystallography. By

assigning discrete coordinates to each atom of the protein, it can be 3-

dimensionally visualized on a computer. During the overall process,

several possible docked conformations are generated for each ligand-

protein complex that must be subsequently to indicate their correlation

to which most likely to occur in vivo. As with any type of computation

there is a trade-off between time and accuracy, therefore research is

currently being done to investigate which chemical models and scoring

criteria are most efficient in generating good drug leads.

From my research in the Zavodszky Lab, I have had the

opportunity to work with a docking program known as SLIDE that was

developed at MSU by Dr. Leslie Kuhn’s Protein Structural Analysis &

Design Lab. SLIDE, which is an acronym for “Screen for Ligands by

Induced-fit Docking, Efficiently,” operates on a fairly simple chemical

model. First, the space containing the active site is permeated with a

grid, to which specific favorable interaction types can be made with

the protein are assigned. Then, the ligand, which is also represented by

several interaction centers, first binds a rigid base fragment by

matching triplets of these points onto complementary points of the

protein; the flexible side-chains are then added in a way that avoid
steric clashes between the two. Finally, each complex is scored by the

predicted free energy as a result of their hydrophobic and hydrogen

bond interactions.

Although x-ray crystallography has been successfully used to

characterize many targets, the structures of several proteins still

remain unknown. Protein folding, a process to predict structure given

an amino acid sequence, is another area of research that if elucidated

could have important implications to virtual screening. Since the

completion of the human genome project, scientists have been

scrambling to annotate the sequence into the individual genes

responsible for coding particular proteins. Aside from possibly filling in

the gaps left by x-ray crystallography, consideration of a patient’s

individual genetic make up could allow for the development of

increasingly sophisticated medications based upon a especially as the

prices for personal genome sequencing continues to significantly

decrease (Smith 2003).

Program: MMKIN (Michaelis-Menten Kinetics)

As previously described, the mechanism of some drugs is to alter

Vmax [S]
V0 =
K M + [S]
the rate at which enzymes are able to perform catalysis. In situations
where the concentration of non-allosteric enzyme is much lower than
its substrate, the kinetics can be modeled by the Michaelis-Menten
equation:

Where Vmax is equal to the maximum rate of catalysis that can

occur due to saturation of the enzyme, therefore increased substrates
will have no free active sites to interact with and KM is equal to the
substrate concentration related to the rate ½ Vmax. Competitive
inhibitors block the substrate at the active site and thus can be
overcome by increasing the substrate concentration. Noncompetitive
inhibitors act upon the enzyme-substrate complex and thus the rate
will never reach Vmax. The HP50g program I have designed will calculate
the initial rate, V0, for the enzyme and substrate alone, as well as
under both types of inhibition.

MMKIN Flow Diagram

 MMKIN Program Listing

BEGIN PURGE

<< 2 FIX 1CF 2 CF TN CLLCD "Again?

"Km?" ":M:" I 'KM' STO TN 1. Yes

2. No
"Vmax?" ":rxns/sec:" I 'VM' STO
TN -key 1 or 2-" DUP 1. DISP 0.
WAIT 'C' STO
"[S]?" ":M:" I 'CS' STO TN
IF C 92.1 SAME
CLLCD "Inhibition? THEN MMKIN
ELSE CLEAR
1. None END
2. Competitive >>
3. Non-competitive”
DUP 1. DISP 0. WAIT 'C' STO I

IF C 92.1 SAME << INPUT OBJ>>

THEN ‘(VM*CS)/(KM+CS)’ 
NUM ‘ANS’ STO TN
ELSE
IF C 93.1 SAME << 800. 2.E-1 BEEP>>
THEN 1 SF INHIB
ELSE INHIB
IF C 94.1 SAME
THEN 2 SF INHIB "[I]?" ":M:" I 'CI' STO TN
END
END "Ki?" ":M:" I 'KI' STO TN
END TN
IF 1 FS?
CLLCD THEN
"Initial Velocity, Vo =" 2 DISP ‘(VM*CS)/((1+(CI/KI))*KM+CS)’
ANS 3 DISP NUM ‘ANS’ STO
“rxns/sec” 4 DISP ELSE
‘(VM*CS)/(KM+(1+(CI/KI))*CS)’
3 WAIT { KM VM CS CI KI ANS } NUM ‘ANS’ STO

References
Burger, A. (1995). A Brief History of Drugs in Understanding

Medications: What the Label Doesn't Tell You. American Chemical

Society Publication.

DiMasi, J. et al. (2003). The price of innovation: new estimates of drug

development costs. Journal of Health Economics, 22(2): 151-185.

Hann, M. and Oprea, T. (2004). Pursuing the leadlikeness concept in

pharmaceutical research. Current Opinion in Chemical Biology. 8,

255-263.

Newman, D. and Cragg, G. (2007). Natural products as drug over the

past 25 years. Journal of Natural Products, 70(3): 461-477.

Smith. C. (2003). Drug target validation: Hitting the target. Nature,

422: 341-7.