Molecular Biology of

Pharmacology
Indwiani Astuti
Dept. of Pharmacology &
Toxicology Fac. Of Medicine
Gadjah Mada University

Structure of DNA

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 The flow of the expression of genetic

information in cells is almost
exclusively one way: DNA RNA
Protein
the central dogma of molecular
biology.

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A gene codes for a protein

DNA

CCTGAGCCAACTATTGATGAA

transcription

mRNA

CCUGAGCCAACUAUUGAUGAA

translation

Protein

PEPTIDE
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Introduction
Pharmacology: knowledge of how drugs interact
with body constituents to produce therapeutic
effects
The spectrum from the molecular to the whole
body
The elucidation of molecular mechanisms of drug
response, the development of new drugs, & the
formulation of clinical guidelines for safe &
effective use of drugs in therapy or prevention of
disease & in relief symptoms.

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 Pharmacological responses by molecular

interaction of drugs with cells, tissues, or other
body constituents
The key word is molecular
What specific biological molecules must be
present ?
How do drugs & biological molecules interact to
produce changes ?
How are these changes converted into
observable responses ?

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Control of cell growth complicated, considering the

alternate pathways now identified

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I. Describing the concept of

membrane & receptors
For most drugs the site of action is at a
specific biological molecule: Receptor
Drug organ or tissue selectivity for the
biological molecule (Cardiac & pulmonary
tissue)
Concept of receptors as sites of drug
action

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 A molecular drug-initiated response

(biological target) -> together
The interaction must result in
selective binding of the drug
molecule to the biological target
before the response can take place.
(molecular level recognition)

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OUT

IN

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 Drugs binding: Langley late 1800 - early 1900 &

Ehrlich 1920
1930 Clark & Gaddum: drug-receptor interactions
1960 receptor proteins isolated & purified
1970 amino acid sequence of receptor subunit
determined
1980 primary amino acid sequence of many
receptor determined from cDNA
1990 three-dimentional structure
- improved drug design

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 Drugs are receptor modulators and

do not confer new properties on cells
or tissues
Receptors must have properties of
recognition and tranduction
Receptors can be upregulated or
downregulated

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Antibiotics

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Peptidoglycan synthesis
Cytoplasm

Cell Membrane

Cell wall

undecaprenol
sugar
amino
acid

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Cycloserine
1.
2.
3.

alanine (ala) analog

inhibits conversion of L-ala to D-ala
inhibits formation of D-ala-D-ala

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Cycloserine
Analog of alanine

Cytoplasm

X X

sugar
amino
acid

X
X

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Bacitracin
Inhibits dephosphorylation

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Bacitracin
Cell membrane
undecaprenol

P
P

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Vancomycin
binds to D-ala-D-ala
inhibits cross-linking

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Vancomycin
Cell wall

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Beta lactam antibiotics

penicillins
cephalosporins
monobactams

inhibit penicillin binding proteins

stop cross-linking
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Beta lactams
Cell wall

Penicillin binding
protein
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Cross-linking of peptidoglycan

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STRUCTURE OF PENICILLIN
O
C

S
NH

CH
O

CH
N

CH3
C
CH

CH3
COOH

Site of penicillinase action.

Breakage of the lactam ring.
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II. Explaining the cell signaling

Important of ligand-receptor binding:
transmembrane signal transmission
The mechanisms:
Direct receptor control of ion channels (ligand gated
or voltage gated)
Receptor-controlled generation of second
messengers (G protein/cAMP or Gprotein/phosphoinositide systems)
Receptor internalization & recycling polypeptide
redistribution
Receptor-initiated phosphorylation involving tyrosine
kinase activity

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Classical Receptors & Ligand

binding
Receptors = proteins in a cellular or subcellular
membrane facilitate communication between the
two sides of the membrane
Membranes of cells consist: phospholipid bilayers
Phospholipid molecules have two distinct region
(amphipathic). One region nonpolar (tails of the fatty
acyl chain). The other very polar (phosphate, choline,
& ethanolamine)
Transmembrane regions of receptors formed by
alpha helices (19 to 24 sequential amino acids
nonpolar side groups)

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G-protein-based second messenger

receptors
A family of membrane-associated
proteins that serve a key role in receptor
modification of adenylate cyclase activity
Guanosine groups= G
G-proteins exist in 2 states: inactive
states GDP bound to the protein, & active
form GTP bound to protein interact
with adenylate cyclase

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Receptor with intrinsic Tyrosine

Kinase Activity
Large group of receptors for growth
factors (insulin, EGF, PDGF,
hepatocyte GF etc)
Extracellular domain contains
regions bind GF, Intracellular domain
contains a kinase activity capable of
phosphorylating proteins on tyrosine
residues
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Membrane Receptors
G-Protein Coupledreceptor biogenic
amines, peptides,
glycoproteins
Activate adenylate
cyclase
Inhibit adenylate
cyclase
Activate
phospholipase C
Regulate ion channels

Tyrosine kinasesreceptors for peptide GFs

Guanylate Cyclasesreceptors for atrial
natriuretic peptide, E.Coli
heat-stable enterotoxin
Serine/Threonine
kinases-receptors for
activin, inhibin, TGF beta,
Mullerian inhibiting
substance

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Membrane receptor
Growth Hormon
Prolactin &
Cytokine receptorsreceptors that
assosiate with
tyrosine kinases,
reseptors for
cytokines, growth
hormone prolactin

The steroid
receptor
superfamilytranscriptional
regulators,
receptors for
steroid, sterols, T3,
retinoic acid &
vitamin D

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III. Explaining the biology molecular

of drugs action
For examples:
Hormone
GF (Herseptin=Her)
Tyrosine kinase sensitive

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Second messenger involved in Hormone-Receptor

Signaling Pathways
Second messenger

Pathway

cAMP

G-protein-coupled rec.
cAMP dependent protein kinase

cGMP

cGMP dependent protein kinase

Diacylglycerol

C-C-kinase

Inositol triphosphate

Ca++ realease from

endoplasmic reticulum & cell
entry

Calcium ions

Ca++ calmodulin-dependent
protein kinase

Nitric oxide

Guanylate cyclase
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G-Protein
Hormone

Coupled Receptors
Action

Glucagon

Stimulate Adenyl cyclase (AC)

Somatostatin

Inhibit AC, activate K+ channels

Antidiuretic hormone

Stimulate AC & Phospholipase C (PLC)

Oxytoxin

Stimulate Adenyl cyclase

Adrenocorticotrophic hormone

Stimulate Adenyl cyclase

Thyroid Stimulating Hormone

Stimulate Adenyl cyclase

Leutenizing hormone

Stimulate Adenyl cyclase

Follicle stimulating hormone

Stimulate Adenyl cyclase

Growth hormone-releasing

Stimulate Adenyl cyclase & PLC

Corticothrophin-releasing hormone

Stimulate Adenyl cyclase

Thyrothrophin releasing hormone

Stimulate Adenyl cyclase & PLC

Luteinizing releasing hormone

Stimulate PLC

Parathormone

Stimulate Adenyl cyclase

Calcitonin

Stimulate Adenyl cyclase

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Proximal Elements in Tyrosine Kinase Signaling

Pathways
IRS-1: major substrate of insulin & IGF-1
receptor kinase
grb-2: adapter protein that functions in the
activation of ras by insulin, PDGF & EGF
P13-kinase: activated by insulin & PDGF as
a concequence of binding to
autophosphorylated PDGF receptor &
tyrosine phosphorylated IRS-1
Phospholipase Cy: activated by EGF &
PDGF not insulin
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Herceptin (c-erb2)

Product oncogen (EGFR)

Receptor Growth factors family
Indication: Solid tumor with Her-2 +
Breast Cancer

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Monoclonal Ab
GF/Ligand
EGFR

EGFR

Membrane

Membrane

Tirosine kinase

Tirosine kinase

Proliferation
Invasion
Angiogenesis

Inhibition
apoptosis
Metastasis

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GF/Ligand
EGFR
Membrane

EGFR-TK
Tirosine kinase

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Tyrosine kinase sensitive

CML expression of gene bcr-abl +
(Chr. Ph)
Imatinib (ST1571)

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Artificial bone, cartilage, & skin with no

immune rejection
Vitoss (Orthovita): nanoparticels
bone growth (orthopaed)
Navavax-estrasorb (cream):
nanoparticels Skin burns
Nucrest-Silcrest : nanocrystaline
Skin burns
Nanodot (Nasa): cells repairs
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Improved, direct chemotherapy and

radiotherapy
Drug delivery
Maximizing bioavailability both over a
period of time and at specific places in
the body
Deliver drug directly to the site without
interacting with the rest of the body
Smart drugs

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Nanotechnology for Drug Delivery

Molecule encapsulated within
nanoscale cavities inside polymer :
time-released drugs
Grind solid drugs into fine powders :
to increase surface area and reactivity
& to increase solubility
Encapsulate polar drug in a nonpolar
coating : easily pass through the cell
membrane
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 Coat DNA with cholesterol to easily pass through

the oily cell membrane
Liposome structures to deliver soluble protein
(cytokine) such as interferon to cancer cells
Magnetic nanopoarticles : local bioavailability
control by external magnetic field
Triggered response : inactive drug
moleculewakes up on encountering a particular
signal
Antacid enclosed in a coating of polymer that
dissolves only in highly acidic conditions

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Therapeutic use of CTLA-4 chimeras to block T-cell

activation

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Blocking of Co-Stimulatory Signals Can Prevent Graft

Rejection

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Modulation of T cell responses to tumors with CTLA-4

blockade
CTLA-4-mediated
inhibition may
restrict T cell
activation during
both the initiation
& the progression
of an anti-tumor
response. So
blockade to the
CTLA-4 inhibitory
signals during T
cell-APC interaction
might result in
enhanced antitumor responses.
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Simultaneous induction of Tr1 cells & of TH1 cells ensures a

balance of the inflammatory response so that infection is
terminated with minimal collateral damage to host tissue

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DRUG PRODUCTION

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DNA molecule therapy

A from of gene therapy
taking advantages of
DNAs selfbinding
property
Drug DNA combines with
the disease-causing DNA
to prevent its replicating
again and thus be
removed as a threat
DNA molecule
engineering is one of the
most active area of
bionanoscience

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Strategies for killing cancer cells:

Cancer drugs target:

DNA replication
Transcription
Translation

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BLOCK EGFR
Tyrosine kinase
inhibitors

Signal cascades are useful:

1. At each step of the cascade, the signal is amplified
2. The information that arrived at the plasma membrane in the form of a
signal is communicated to the nucleus
3. The multitude of steps enables a signal to have different effects in
different cells (because they have different target proteins)
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AminoAcid

SLC

DNAcodons

Isoleucine

ATT,ATC,ATA

Leucine

CTT,CTC,CTA,CTG,TTA,TTG

Valine

GTT,GTC,GTA,GTG

Phenylalanine

TTT,TTC

Methionine

ATG

Cysteine

TGT,TGC

Alanine

GCT,GCC,GCA,GCG

Glycine

GGT,GGC,GGA,GGG

Proline

CCT,CCC,CCA,CCG

Threonine

ACT,ACC,ACA,ACG

Serine

TCT,TCC,TCA,TCG,AGT,AGC

Tyrosine

TAT,TAC

Tryptophan

TGG

Glutamine

CAA,CAG

Asparagine

AAT,AAC

Histidine

CAT,CAC

Glutamicacid

GAA,GAG

Asparticacid

GAT,GAC

Lysine

AAA,AAG

Arginine

CGT,CGC,CGA,CGG,AGA,AGG

Stopcodons

Stop

TAA,TAG,TGA

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