Basic Principle of

Pharmacology:
Molecular Drug Binding
(BBC-2 K 25 K 26)

Dept. Pharmacology & Therapeutic

School of Medicine
Universitas Sumatera Utara
 Molecular Drug Binding
K-25
• Menjelaskan konformasi dan kimia reseptor dan ligand
• Menjelaskan efek pada membrane akibat interaksi obat-
reseptor
• Menjelaskan jenis-jenis reseptor utama obat :
– Transmembrane ion channels
– Tranmembrane G Protein-coupled receptors
– Transmembrane receptors with enzymatic cytosolic domains
– Intracellular receptors
K-26
• Menjelaskan obat yang bekerja tdk melalui ikatan
reseptor-obat
• Menjelaskan regulasi seluler interaksi obat reseptor
• Menjelaskan determinan molekuler dan seluler terhadap
selektivitas obat
 Extra Signal Transduction Intra
cellular M
cellular
Ligand

E
M
B Function
R of Cell
A
Ligand

N
E
Directly Cellular Biochemistry
• Ion Conductant
Receptor • Protein phosphorylation
• DNA Transcription
Indirectly
 Stages of cell signaling
1. Reception
– chemical message (signal molecule) binds to a
protein (receptor) on the cell surface
2. Transduction
– binding of the signal molecule alters the receptor
protein
– signal usually starts a cascade of reactions known as
signal transduction pathway
– there is usually amplification and modulation of signal
3. Response
– transduction pathway finally leads to response
– responses can vary from turning on a gene, activating
an enzyme, rearranging the cytoskeleton…
Paul Ehrlich: Corpora non agunt fixata
(= a drug will not act, unless it is bound)
to what ?  to “ receptor”
Signaling molecule

Receptor of target cell

Signal
transduction
Intracellular molecule

biological effect
 Proteins and peptides:

Effect by Hormones, cytokines

membrane Amino acid derivatives:
receptors
Catecholamines
Extracellular Fatty acid derivatives:
molecules
Prostaglandins

Effect by
Signal intracellular Steroid hormones,
molecules receptors Thyroxine, VD3

Intracellular
cAMP, cGMP, IP3, DG, Ca2+
molecules
 Receptors in RT System
Sensory Afferents
• Chemoreceptors are activated by hypoxemia, acute
hypercapnia, and acidemia. Stimulation of these
receptors, that lead to an increase in ventilation, produce
a sensation of air hunger.
• Mechanoreceptors in the lungs, when stimulated by
bronchospasm, lead to a sensation of chest tightness.
• J-receptors, sensitive to interstitial edema, and
pulmonary vascular receptors, activated by acute
changes in pulmonary artery pressure, appear to
contribute to air hunger.
– Hyperinflation is associated with the sensation of an inability to get a
deep breath or of an unsatisfying breath.
• Metaboreceptors, located in skeletal muscle, are
believed to be activated by changes in the local
biochemical milieu of the tissue active during exercise
and, when stimulated, contribute to the breathing
discomfort.
Metabo- and chemo-receptor
Membrane effects on drug-
receptor interactions
Membrane effects on drug-receptor interactions
 Transmembrane Signaling Mechanisms

1. A lipid-soluble chemical signal crosses the plasma membrane and acts on an

intracellular receptor which maybe an enzyme or a regulator of gene transcription
2. The signal binds to the extracellular domain of a transmembrane protein, thereby
activating an enzymatic activity of its cytoplasmic domain
3. The signal binds to the extracellular domain of a transmembrane receptor bound
to a protein thyrosine kinase, which it activates
4. The signal binds to and directly regulates the opening of an ion channel
5. The signal binds to a cell-surface receptor linked to an effector enzyme by a G
protein. (A,C, substrates; B,D, products; R,receptor; G, G protein; E, effector
(enzyme or ion channel); Y, tyrosine; P, phosphate.)
 Major types of drug receptor
1. Transmembrane ion channels
2. Transmembrane G Protein-coupled
receptors
3. Transmembrane receptors with enzymatic
cytosolic domains
4. Intracellular receptors
 Major types of drug receptor
SITE OF DRUG SITE OF
RECEPTOR
TYPE RECEPTOR RESULTANT
INTERACTION ACTION
Transmembrane Extracellular,
intrachannel, or Cytoplasm
ion channel
intracellular
Transmembrane
linked to intracellular
Extracellular or Cytoplasm
G protein intramembrane
Transmembrane
with enzymatic Extracellular Cytoplasm
cytosolic domain
Intracelluar Cytoplasm or Cytoplasm or
nucleus nucleus
 Major types of drug receptor

Four major types of interactions between drug and receptors

• Drugs can bind to ion channels spanning the plasma membrane  alteration in
the channel’s conductance.
• Heptahelical receptor spanning the plasma membrane are functionally coupled to
intracellular G-proteins. Drugs can influence the actions of these receptors by
binding to the extracellular surface or transmembrane region of the receptor.
• Drugs can bind to the extracellular domain of a transmembrane receptor and
cause a change in signaling within the cell by activating or inhibiting an enzymatic
intracellular domain of the same receptor molecule.
• Drugs can diffuse through the plasma membrane and bind to cytoplasmic or
nuclear receptor  often pathway used by lipophilic drugs (e.g., drugs that bind
to steroid hormone receptors).
Transmembrane ion channels
 Transmembrane ion channels
• The functions of ion channels are diverse
• but fundamental roles are in :
– neurotransmission,
– cardiac conduction, and
– muscle contraction
 Three types of
Transmembrane Ion Channels
CHANNEL MECHANISM OF FUNCTION
TYPE ACTIVATION
Binding of ligand to Altered ion
Ligand-gated channel conductance
Change in
Voltage-gated Altered ion
transmembrane
conductance
voltage gradient
Binding of ligand to Second
Second transmembrane receptor messenger
messenger with G protein-coupled
regulates ion
regulated cytosolic domain,
leading to second conductance of
messenger generation channel
The plasma membrane acetylcholine (Ach) receptor
is composed of 5 subunits
(2  subunit,  subunit,  subunit, and  subunit).

The  subunit has been removed to show an

Internal schematic view of the receptor,
demonstrating that it forms a
transmembrane channel. In the absence of
Ach  receptor gate is closed, and cations
(most importantly, Na+ are unable to traverse
the channel)

When Ach is bound to both  subunits, the

channel opens, and Na+ can pass down its
concentration gradient into the cell
Channel Gating Mechanisms
AChR: Proposed gating mechanism
(Unwin, 1995)

Closed Open
 Transmembrane ion channels
• State-dependent binding  important in the
mechanism of action some local anesthetic, anti-
arrhythmic and benzodiazepine derivatives that act
by altering the conductance of ion channels :
– local anesthetics  blocks the conductance of Na+ ions
through voltage-gated Na+ channels in neurons that
transmit pain information from the periphery to CNS 
preventing action potential propagation, and hence, pain
perception (nociception)
– benzodiazepines  inhibit neurotransmission in the CNS
by potentiating the ability of the neurotransmitter GABA to
increase the conductance of Cl ions across neuronal
membrane  driving the membrane potential further
away from its threshold for activation.
i_03_m_par_benzodiazepines[1].swf
 Channel Families
• Voltage-gated
• Extracellular ligand-gated
• Intracellular ligand-gated
• Inward rectifier
• Intercellular
• Other
 Outside Cell

Na+

Cl- Ca2+

K+

Inside Cell
 Voltage-gated
• sodium:
– I, II, III, µ1, H1, PN3
• potassium:
– KA, Kv (1-5), Kv(r), Kv(s),KSR, BKCa, IKCa, SKCa,
KM, KACh
• calcium:
– L, N, P, Q, T
• chloride:
– ClC-0 - ClC-8
 Extracellular ligand-gated
• nicotinic ACh (muscle): α embryonic, α
adult
• nicotinic ACh (neuronal): α (2-10), α (2-4)
• glutamate: NMDA, kainate, AMPA
• P2X (ATP)
• 5-HT3
• GABAA: (1-6), (1-4), (1-4), , , (1-
3)
• Glycine
 Intracellular ligand-gated
• leukotriene C4-gated • Ca2+-gated Cl–
Ca2+ • cAMP cation
• ryanodine receptor • cGMP cation
Ca2+ • cAMP chloride
• IP3-gated Ca2+ • ATP Cl–
• IP4-gated Ca2+ • volume-regulated Cl–
• Ca2+-gated K+ • arachidonic acid-
• Ca2+-gated non- activated K+
selective cation • Na+-gated K+
 Cellular Mechanisms of
Seizure Generation
 Excitation (too much)
• Ionic-inward Na+, Ca++ currents
• Neurotransmitter: glutamate,
aspartate

 Inhibition (too little)

• Ionic-inward Cl; outward K+ currents
• Neurotransmitter: GABA
Transmembrane Ion Channels
G PROTEIN and Second Messenger
Endogenous ligands and associated second messengers

Ligand Second messenger

Adrenocorticotropic hormone cAMP
Acethylcholine (reseptor muskarinik) Ca2+, phosphoinositide
Angiotensin Ca2+, phosphoinositide
Catecholamine (adrenoseptor –α1) Ca2+, phosphoinositide
Catecholamine (adrenoseptor – β) cAMP
Chorionic gonadotropin cAMP
Follicle – stimulating hormone cAMP
Glucagon cAMP
Histamine (reseptor H2) cAMP
Luteinizing hormone cAMP
Melacocyte-stimulating hormone cAMP
Parathyroid hormone cAMP
Platelet-activating factor Ca2+, phosphoinositide
Prostacylin, prostaglanding E2 cAMP
Serotonin (reseptor 5-HT4) cAMP
Serotonin (reseptor 5-HT1c dan 5-HT2) Ca2+, phosphoinositide
Thyrotropin cAMP
Tyrotropin-releasing hormone Ca2+
Vasopressin (reseptor V1) Ca2+
Vasopressin (reseptor V2) cAMP
Transmembrane G Protein-
coupled receptors
 Transmembrane G Protein-
coupled receptors
 The most abundant class of receptors in the human
body
 Exposed at the extracellular surface of the cell
membrane, traverse the membrane, and posses
intracellular regions that activate a unique class of
signaling molecules called G-protein
G-protein
 G-protein coupled signaling mechanisms are
involved in many processes  vision, olfaction, and
neurotransmission
 G-protein coupled receptors have seven
transmembrane regions within a single polypeptide
chain
G Protein Coupled Receptors
C

Cytoplasmic Domain

Trans-
membrane 1 2 3 4 5 6 7
Domain

Extracellular Domain

• Largest family of cell surface receptors

• >8000 sequences known

• 60% of all known drugs target GPCR

 Receptor mediated activation of a G protein and the
Resultant Effector interaction

a) In the resting state, the  and  subunits of G protein are associated with one another, and
GDP is boud to  subunit.
b) Binding of an extracellular ligand (agonist) to a G protein-coupled receptor  exchange of
GTP for GDP on the  subunit.
c) The  subunit dissociates from the  subunit, which diffuses to interact with effector
proteins. Interaction of the GTP-associated  subunit with an effector activates the effector.
o In some cases , the  subunit can also activate effector proteins.
o Depending on the receptor subtype and the spesific G isoform, G can also inhibit the activity of an effector
molecule.
o The  subunit posseses intrinsic GTPase activity, which leads to hydrolysis of GTP to GDP. This leads to reassociation
of the  subunit with the  subunit and the cycle can begin again.
Transmembrane G Protein-
coupled receptors
Activation of Adenylyl cyclase (AC) and Phospholipase C
(PLC) by G proteins

G consist of Gs and Gq

A. When stimulated by Gs  adenylyl
cyclase converts ATP to cAMP. cAMP
activates protein kinase A (PKA), which
phosphorylates a number of spesific
cytosolic proteins.
B. When stimulated by Gq  phospholipase
C (PLC) cleaves the membrane
phospholipid phosphatidylinositol-4,5-
bisphosphate (PIP2) into diacylglycerol
(DAG) and inositol-1,4,5-triphosphate
(IP3).
• DAG diffuses in the membrane to activate
PKC, which then phosphorylates specific
cellular proteins.
• IP3 stimulates release of Ca2+ from
endoplasmic reticulum into the cytosol.
Ca2+ release also stimulates protein
phosphorylation events that lead to
changes in protein activation.
 The major G proteins and
examples of their actions

G Protein Actions
G-stimulatory (Gs) Activates Ca2+ channels,
activates adenylyl cyclase
G-inhibitory (Gi) Activates K+ channels,
inhibits adenylyl cyclase
Go Inhibits Ca2+ channels
Gq Activates phospholiphase C
G12/13 Diverse ion transporter
interaction
 G-protein linked receptors
coupled to ion channels
• Acetylcholine (muscarinic) • Histamine
• Adenosine & adenine • 5-Hydroxytryptamine (1,2)
nucleotides • Leukotriene
• Adrenaline & noradrenaline • Melatonin
• Angiotensin • Neuropeptide Y
• Bombesin • Neurotensin
• Bradykinin • Glutamate (quisqualate)
• Calcitonin • Odorant peptides
• Cannabinoid • Opioid peptides
• Chemokine • Platelet-activating factor
• Cholecystokinin & gastrin • Prostanoid
• Dopamine • Protease-activated
• Endothelin • Tachykinins
• Galinin • Taste receptors
• GABA (GABAB) • VIP
• Vasopressin and oxytocin
Transmembrane receptors with
enzymatic cytosolic domains
Transmembrane receptors with enzymatic
cytosolic domains
• Transmembrane receptors that transduce an extracellular
ligand binding interaction into an intracellular action through
the activation of a linked enzymatic domain
• Play roles in a diverse set of physiologic processes:
– Cell metabolism
– Cell growth, and
– Cell differentiation
• Has five major classes based on their cytoplasmic mechanism
of action. All of these receptors are single-membrane
spanning proteins, in contrast to the seven-membrane
spanning motif present in G protein-coupled receptors.
• Phosphorilation is a ubiquitous mechanism of protein
signaling
Five transmembrane receptors with enzymatic
cytosolic domains
A. After ligand-induced activation, these receptor
dimerize and transphosphorylate tyrosine
residues in the receptor and, often, on target
cytosolic proteins. Examples of receptor
tyrosine kinases include the insulin receptor
and the BCR-Abl protein
B. Some receptor can act as tyrosine
phosphatases. This receptors dephosphorylate
tyrosine residues either on other
transmembrane receptors or on cytosolic
proteins. Many cells of the immune system have
receptor tyrosine phosphatases.
C. Some tyrosine kinase-associated receptors lack
a defenitive enzymatic domain, but binding of
ligand to the receptor triggers activation of
receptor associated protein kinase termed non
receptor tyrosine kinase) that then
phosphorylate tyrosine residues on certain
cytosolic proteins.
Five transmembrane receptors with enzymatic
cytosolic domains
D. Receptor serine/threonine kinases
phosphorylate serine and threonine
residues on cetain target cytosolic
proteins. Member of the TGF-
superfamily are in this category.
E. Receptorr guanylyl cyclases contain
a cytosolic domain that catalyzes
the formation of cGMP from GTP.
The receptor for B-type natriuretic
peptide is one of the receptor
guanylyl cyclases that has been well
characterized.
Intracellular receptors
 Intracellular receptors
• The transcription regulatory factors are
important cytosolic receptors that are
targeted by lipophilic drugs.
• Steroid hormons are important class of
lipophilic drugs that can diffuse readily
through the plasma membrane and achieve
their action by binding to transcription factors
in the cytoplasm or nucleus
 Lipophilic molecule binding to an intracellular
transcription factor

A. Small lipophilic can diffuse through the plasma membrane and bind to intracellular transcription factors. Ex.
Steroid hormone binding to a cytosolic hormone receptor is shown, although some receptor of this class
maybe located in the nucleus before ligand binding.
B. Ligand binding triggers a conformational change in the receptor (and often, as shown here, dissociation of a
chaperone repressor protein) that leads to transport of the ligand receptor complex into the nucleus. In the
nucleus, the ligand receptor complex typically dimerizes. In the examples shown, the active form of the
receptor is a homodimer (two identical receptors binding to one another), but heterodimers such as the
thyroid hormone receptor and the retinoid X receptor) may also form.
C. The dimerized ligand receptor complex binds to DNA, and may than recruit coactivators or copressors (not
shown). These complexes alter the rate of gene transcription, leading to a change either up or down) in
cellular protein expession
 Impact of drug binding on receptor
conformation
A .Some drugs:
= act by preventing the endogenous ligands to
interact with their receptor  no change in
conformation of the receptor.
B . Other drugs result in a change in the
conformation of the receptor altering the shape
of the receptor
 Action-Effect Sequence
I. Drug action:
= initial interaction of the drug with its
receptor, resulting in:
a. conformational change in the receptor 
(agonist)
b. prevention of conformational change 
(antagonist)

II.Drug effect:
= the ultimate change in biologic function
brought about as a consequence of drug
action,thru‘ a series of intermediate steps
------ transducer
 CELLULAR REGULATION OF
DRUG – RECEPTOR INTERACTIONS
• Drug  Foreign Body To Our Cells 
Homeostasis
Number of receptors
• Up regulation  Beta blocker
• Down regulation  TCA
•  Opiate tolerance
Tachyphylaxis
• Reduced effect produced after repeated
administration.
• Occurs faster than tolerance.
 CELLULAR REGULATION OF
DRUG – RECEPTOR INTERACTIONS
Desensitization
Homologous  decrease response of a single
class of receptor
Heterologous  multiple class.
Inactivation
Loss of ability of a receptor to respond to
stimulation by a drug.
Refractory
After a receptor is stimulated, a period of time is
required before the next drug-receptor
interaction can produce an effect.
 MOLECULAR AND CELLULAR
DETERMINANTS OF DRUG SELECTIVITY
Drug – receptor interactions
SPECIFICITY:
 tissue, systems, organ where receptors are
distributed
Adrenergic
Cholinergic
SELECTIVITY :
 drug interacts preferentially on particular
receptor types or subtypes.
- Propranolol : non-selective antagonist of 1 and 2
adrenergic.
- Atenolol : 1 – selective, 2 less.
- Terbutaline : agonist of 
 Drugs that do not fit
the drug-receptor model
Ex.
1. Osmotic diuretics;
= many of diuretics act on ion-channels,-
thru” receptor binding
= SUGAR MANNITOL act by changing the
osmolarity in the nephron directly ,
because mannitol is secreted into the
lumen  water is drawn into the lumen 
volume urine increased
 Drugs that do not fit
the drug-receptor model
Ex.
2. Antacids; NaHCO3 and Mg(OH)2
= act nonspecifically by;
Stomach
- absorbing,or
acid
- chemically neutralizing
3. Chelating agents;
= bind the heavy metals like Fe++,As
4. Cholestyramine; binds the bile acid in
GI-tract
Phospholipid

+ Phospho + Bradykinin
lipase A2

Arachidonic Acid

+ COX +
Prostaglandin
+ Nociceptor

Hyperalgesia
 BK
Actions of Bradikinin on Sensory Neurons
B 2R

Desensitize?
cGMP PLC PLA2
mediated by B2 Receptors

Guanylate
cyclase DAG
Lipase
NO IP3 DAG AA
NOS

Calmodulin
[Ca2+] PKC
Activation PGs

Calcium Open ion

influx channels

Depolarize
Bevan, 2001
 Mechanisms of Pain: Peripheral Sensitization

AA=arachidonic acid; PGE2=prostaglandin E2; NGF=nerve growth factor; BK=bradykinin; PKA=protein

kinase A; PKC=protein kinase C; EP=prostaglandin E receptor; COX-2=cyclooxygenase-2; TRPV-
1=transient receptor potential V-1; TrkA=tyrosine kinase A; Nav 1.8/1.9=sodium channel 1.8/1.9 72
 Crosstalk among chemokine receptors,
bradykinin, and transient receptor
potential channels (TRP).

The increased trafficking of the calcium channel subunit alpha2delta-1 to presynaptic

terminals in neuropathic pain is inhibited by the alpha2delta ligand pregabalin.
CS Bauer, et al. J Neurosci (2009) 29: 4076-88.
 Cellular Regulation of Drug Rec’r Interaction

MECHANISM DEFINITION
Tachyphylaxis Repeated adm. Of the same dose of a drug results in a reduced
effect of the drug over time
Desensitization ↓ ability of a rec’r to respond tostimulation by a drug or ligand
1.Homologous 1. ↓ response of a single class of rec’r
2. Heterologous 2. ↓ response of a multiple classes of rec’r
Inactivation Loss of ability of a rec’r to respond to stimulation by a drug or
ligand
Refractory After a rec’r is stimulated, a period of time is required before
the next drug-rec’r interaction can produce an effect
Down Regulation Repeated or persistent drug-rec’r interaction results in removal
of the rec’r from sites where subsequent drug-rec’r interactions
could take place.
Molecular and Cellular Determinants of Drug Selectivity

Selectivity of drug action

1. The cell type specificity of rec’r subtype

2. The cell-type specificity of rec’r-effector coupling
• The more restricted the cell-type distribution of the
rec’r targeted by a particular drug, the more selective
the drug is likely to be

• The more rec’r-effector coupling mechanisms differ

among the various cell types that express a particular
molecular target for a drug, the more selective the
drug is likely to be.
 Content
• Introduction of pharmacology
• Chemistry and physical properties of molecule of drugs
• Drug size & shape
• Conformation and chemistry of receptors and ligands
• Drug receptor binding :
1. van der Waals
2. Hydrogen
3. Ionic
4. Covalent
• Drugs that do not fit the drug-receptor model
• Impact of drug binding on receptor conformation
• Membrane effects on drug- receptor interactions
• Major types of drug receptor ;
1.Transmembrane ion channels
2.Tranmembrane G Protein-coupled receptors
3.Transmembrane receptors with enzymatic cytosolic domains
4.Intracellular receptors
• Processing of signals resulting from drug-receptor interactions
• Cellular regulation of drug-receptor interactions
• Molecular and cellular determinants of drug selectivity
Trans-membrane Transport
 Typical Ion Channels with Known Structure:

K+ channel (KCSA) Acetylcholine receptor M2

transmembrane segment

Types of ion channels:

 Simple pores (GA, GAP junctions)
 Substrate gated channels (Nicotinic receptor)
 Voltage-gated channels (K-channels)
 Pumps (ATP-synthase, K+,Na+-ATPase)
 Molecular modeling in drug discovery
I. Two case studies for sequence to structure mapping:
– Small changes in protein sequence cause dramatic
difference in drug binding: COX inhibitors
– Large changes in protein sequence still maintain similar
structure: G protein coupled receptors

II. Protein Structure Prediction

III. Ligand Docking to Protein Structures

 Case study COX
A Wonder Drug: What is the most commonly-taken drug today?
It is an effective painkiller.
It reduces fever and inflammation when the body gets overzealous in its
defenses against infection and damage.
It slows blood clotting, reducing the chance of stroke and heart attack in
susceptible individuals.
It may be an effective addition to the fight against cancer.

Aspirin has been used professionally for a century, and

traditionally since ancient times. A similar compound
found in willow bark, salicylic acid, has a long history of
use in herbal treatment. But only in the last few decades
have we understood how aspirin works, and how it might
be improved

http://www.rcsb.org/pdb/molecules/pdb17_1.html
 Prostaglandins
As you might expect from a drug with such diverse actions, aspirin blocks a central
process in the body: Aspirin blocks the production of prostaglandins, key hormones
that are used to carry local messages.
Unlike most hormones, which are produced in specialized glands and then delivered
throughout the body by the blood, prostaglandins are created by cells and then act
only in the surrounding area before they are broken down.
Prostaglandins control many of these neighborhood processes, including the
constriction of muscle cells around blood vessels, aggregation of platelets during
blood clotting, and constriction of the uterus during labor.
Prostaglandins also deliver and strengthen pain signals and induce inflammation.
When aspirin blocks production of prostaglandins, the normal messages are not
delivered, so we don't feel the pain and don't launch an inflammation response.
These many different processes are all controlled by different prostaglandins, but all
created from a common precursor molecule.

http://www.rcsb.org/pdb/molecules/pdb17_1.html
 What does COX do?
COX = Cyclooxygenase (PDB entry 1prh) performs the first step in the
creation of prostaglandins from a common fatty acid: It adds two
oxygen molecules to arachidonic acid, beginning a set of reactions.

http://www.rcsb.org/pdb/molecules/pdb17_1.html
 Structure-based drug design
• Compare the structures of COX-1 and COX-2
• Identify differences that could be exploited
• Need to know the mechanism of COX
inhibition
Mechanism of COX inhibition?
Ser530 is not a catalytic
residue.

But it is located in the

tunnel that allows entry of
arachidonic acid to the
active site.

Aspirin sterically blocks the

binding of arachidonic acid in
the cyclooxygenase active
site.
Hydrophilic Side Pocket
HIS90

ARG513

Hydrophilic
side pocket
Structural Differences Cox1/2
 Molecular modeling in drug discovery
I. Two case studies for sequence to structure mapping:
– Small changes in protein sequence cause dramatic
difference in drug binding: COX inhibitors
– Large changes in protein sequence still maintain similar
structure: G protein coupled receptors

II. Protein Structure Prediction

III. Ligand Docking to Protein Structures

CELL SIGNALING
 Cell signaling mediates:
 reaction to signals from environment
 communication between cells
 teamwork of cells in multicell organism

Signaling pathway includes:

Signal cells - produce specific type of signal molecules
Signal molecules
hydrophilic - large, do not diffuse through the membrane
(proteins)
hydrophobic - small, less numbered, difuse through the
membrane (steroids, NO, gases)
Receptores - located on target cell, can distinguish signal
molecule and specifically react to it (one type of receptor
to one type of signal)
Target cells - transfer the extracellular signal to intracellular
and thus control the cell behavior
 Stages of cell signaling

1. Reception
 chemical message (signal molecule) binds to a protein
(receptor) on the cell surface

2. Transduction
 binding of the signal molecule alters the receptor protein
 signal usually starts a cascade of reactions known as
signal transduction pathway
 there is usually amplification and modulation of signal

3. Response
 transduction pathway finally leads to response
 responses can vary from turning on a gene, activating an
enzyme, rearranging the cytoskeleton…
 TYPES OF EXTRACELLULAR SIGNALS
PHYSICAL SIGNALS
 light, heat, gravitation, pressure, magnetic field
 electric events mediated by transport of ions through
plasmatic membrane
CHEMICAL SIGNALS
1. HORMONS
 derived from amino acids (adrenalin)
 peptides and proteins (insulin, oxytocin)
 steroid hormons (testosteron, oestrogene, progesterone)
 tissue hormons (pepsin, trypsin)
2. NEUROTRANSMITTERS
 (acetylcholin, adrenalin, noradrenalin, dopamin)
3. NEUROHORMONS
 (D-serine, carnosin..)
4. CYTOKINS
- proteins produced by cell as a signals for proliferation,
differentiation or survival of cells
 interleukins – produced by lymfocytes
 interferons – induction of resistence against viruses
 tumor necrotizing factors – inhibition of cell division
 grow factors – stimulation of proliferation and differentiation
 FORMS OF EXTRACELLULAR SIGNALING
A) ENDOCRINE
e.g. cells of thyroid produce  tyrosin (hormone)  increase
the metabolism
B) AUTOCRINE
e.g. chemical messenger is produced and accepted by one cell
ENDOCRINE AUTOCRINE
C) PARACRINE
e.g. mastocyts produce  histamin (local mediator)  cells
enlarge, increase their permeability  inflammation

*Animation of endocrine, autocrine and paracrine signaling:

http://www.sinauer.com/cooper5e/animation1501.html
D) CONTACT-DEPENDENT
e.g. embryonic cells produce  membrane-bound signal
molecule  prevent neighbouring cells in same specialization

(C)
E) NEURONAL
e.g. neurons produce chemical signal  acetylcholin
(neurotransmitter)  electrical excitation (change in membrane
potential = action potential)  signal is transmited rapidly and
over long distances in body
MEMBRANE POTENTIAL (-70 mV inside)
outside +++++++++++++ Na+ Animation of action potencial and
synaptic transmisssion:
inside ----------------------- K- http://bcs.whfreeman.com/thelifewi
re/content/chp44/4402002.html

 membrane is highly impermeable to Na+

------------------------------------------------------------------------------------
ACTION POTENTIAL (0 to +20 mV inside)
 nerve signal  channels open, Na+ diffuse inside  local
change in membrane potential  membrane depolarization
(inside less negative) spreads forward

direction of action potential

K+
outside ++ ---+++++++++
inside --- ++ ---------------
Na+

 then Na+ channels switch off  membrane returns to its

original membrane potential (prevents signal from going backwards)
 TYPES OF RECEPTORS
1. receptors connected with ion channels
 signal = flow of ions across the membrane  change of
membrane potential (electric event)  nerve impuls
 in membrane of nerve and muscle cells

2. receptors connected with G-proteins

(the largest family of receptors)
G-protein
 one polypeptid chain
 three subunits , , 
 7x goes through the membrane
 is activated by GTP from GDP
Other informations:
http://users.rcn.com/jki
mball.ma.ultranet/Biolo
gyPages/C/CellSignali
ng.html
 ACTIVATION OF KINASE A
signal

receptor connected with G-protein

activation
ADENYLYL CYCLASE
increase of concentration

ATP cAMP (second messenger)

KINASE A (cAMP dependent protein kinase)

quick answer (s. to min.) slow answer (min. to hours)

- phosphorylation (activation) of - phosphorylation (activation) of proteins that
proteins that are present in the cell regulate gene expression (transcription)
Animation of kinase A
activation:
*http://bcs.whfreeman.com/thelifewire
/content/chp15/15020.html

http://www.celanphy.science.ru.nl/Bru
ce%20web/Flash%20Movies.htm

Animation of signal
transducion and amplification:
http://www.sinauer.com/coope
r/4e/animations15.html
http://www.wiley.com/college/b
oyer/0470003790/animations/s
ignal_transduction/signal_tran
sduction.htm
 ACTIVATION OF KINASE C
signal

receptor connected with G-protein

activation
DAG - diacylglycerol
IP3 - inositol triphosphate

PHOSPHOLIPASE C

ER
LIPIDS DAG + IP3

Ca2+

KINASE C (Ca2+ dependent protein kinase)

quick answer slaw answer

Diacylglycerol - remains in the membrane, has 2 signaling roles:
1) to activate protein kinase C (Ca2+dependent)
2) can be cleaved to release arachidonic acid = messenger that participate
in pain and inflammatory responses (anti-inflammatory drugs such as aspirin,
ibuprofen and cortisone inhibit their synthesis)
 ACTIVATION OF KINASE CAM
signal

receptor connected with G-protein

activation
Calmodulin – binds 4 ions of Ca2+

PHOSPHOLIPASE C
ER

LIPIDS DAG + IP3 Ca2+

CALMODULIN

KINASE CAM (Ca2+- calmodulin dependent protein kinase)

quick answer slow answer

3. receptors connected with enzymes
ACTIVATION OF PROTEIN KINASE III
signal (grow factors)

tyrosine kinase (receptor connected with enzyme)

tyrosine 1. 2.

adaptor protein
PHOSPHOLIPASE C
Ras protein
PROTEIN KINASE I

PROTEIN KINASE II
KINASE C
PROTEIN KINASE III

quick answer slow answer quick answer slow answer

Tyrosine-Kinase receptors
 part of the receptor on the cytoplasmic side serves as an
enzyme which catalyzes the transfer of phosphate
groups from ATP to the amino acid Tyrosine on a
substrate protein
Animation:
*http://www.learner.org/courses/bi
ology/archive/animations/hires/a_
cancer1_h.html
 PROTEIN KINASES = KINASES
ACTIVATION OF PROTEINS
= PHOSPHORYLATION
(ATP is used as a donor of phosphate group)

In human, there is about 2 % of genes

for protein kinases, in cell can be about
1000 protein kinase at the same moment
 Animations:
Cell signaling-text:
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellSignaling.ht
ml
Endocrine, autocrine and paracrine signaling - animation:
http://www.sinauer.com/cooper/4e/animations15.html
Signal transducion and amplification - animation:
http://www.sinauer.com/cooper/4e/animations15.html
Kinase A activation - animation:
http://bcs.whfreeman.com/thelifewire/content/chp15/15020.html
http://www.celanphy.science.ru.nl/Bruce%20web/Flash%20Movies.htm
Action potencial and synaptic transmisssion - animation:
http://bcs.whfreeman.com/thelifewire/content/chp44/4402002.html