ANTIPROTOZOAL

DRUGS
BY
Dr. SANJEEV K. SAHU

1
 Protozoal Infection
Protozoal diseases are less easily treated than bacterial
infections:
Unicellular protozoal cells have metabolic processes closer to
human cells than bacteria.
 Many of antiprotozoal drugs cause serious toxic effects and most of
them are not safe in pregnancy.

Protozoal diseases
Malaria
Amebiasis
 Leishmaniasis (Kala-azar)
 Trypanosomiasis
 Trichomoniasis
 Giardiasis
WHO IS A PARASITE?

 Parasites are usually

much smaller than their
hosts, they also do not
kill before they eat.
 INTRODUCTION TO AMOEBA
 Entamoeba histolytica
 Amoebic dysentery
 Naegleria
 primary amoebic
meningoencephalitis
 Acanthamoeba
 contact lens contaminant

• Protozoa with no truly defined shape

• Move and acquire food through the use of pseudopodia
• Found in water sources throughout the world
• Few cause disease

Figure 12.18a
3
CLASSIFICATION OF ANTIPROTOZOAL DRUGS
PRINCIPAL PROTOZOAL INFECTIONS AND COMMON DRUG TREATMENTS

8
 6 CYCLE OF ENTAMOEBA HISTOLYTICA

7
 Classification of Antiamoebics
I. Tissue or Systemic Amoebicides
A. Intestinal as well as extra intestinal amoebicide
i) Nitroimidazole derivatives: Metronidazole,
Ornidazole, Secnidazole, Tinidazole
ii) Alkaloid: Emetine and Dehydroemetine

B. Extra intestinal/hepatic amoebicide:

Chloroquine
II. Luminal Amoebicide
a. Amide Derivatives: Diloxanide Furoate
b. 8-Hyroxyquinolines: Iodoquinol, clioquinol
c. Antibiotic : Tetracycline, Pramomycin
III. Mixed amebicides : both systemic and luminal
 Metronidazole, Tinidazole
 Chemical Classification
1. Nitroimidazole derivatives: Metronidazole, Tinidazole , Ornidazole ,
Secnidazole

2. Dichloroacetamides: Diloxanide Furoate, Etofamide, Clefamide, Teclozan

3. Emetines: Emetine, Dehydroemetine

4. Halogenated 8 Hydroxyquinolines: Clioquinol Iodoquinol

5. 4-amino quinoline derivatives: Chloroquine

6. Antibiotics: Paromomycin, Tetracycline

7. Nitrothiazolidines: Nitazoxanide
 Nitro imidazole derivatives

Metronidazole Tinidazole

Ornidazole Secnidazole
Releases toxic superoxide or hydroxyl radical in the parasites forming reduced cytotoxic
compounds that bind to proteins and DNA --- resulting in cell death.
Alkaloid

Dehydroemetine
Emetine
 Diloxanide furoate
Diloxanide destroys the trophozoites of E. histolytica that eventually
form into cysts

Iodoquinol Clioquinol

It acts by chelation of ferrous ions essential for metabolism

 Giardiasis
Giardiasis is a parasitic disease caused by Giardia
duodenalis (also known as G. lamblia and G. intestinalis).

The drugs used in Giardiasis are:

 Metronidazole
 Mepracrine
 Quiniodochlor
 Furazolidone
 Giardiasis
Furazolidone has not been definitively determined but appears to
include:
 Inhibition of oxidative reactions,
 Including the decarboxylation of pyruvate to acetyl coenzyme
A,
 Thereby reducing the available energy for vital cellular
functions.
 Leishmaniasis
Leishmaniasis is a disease caused by parasites of the
Leishmania type. Also known as Kala azar, black fever,
sandfly disease.
The drugs used in Leishmaniasis are:
 Sodium stibogluconate
 Pentamidine
 Miltefosine
 Paromomycin Sulfate
 Allopurinol and Amphotericin B
 Leishmaniasis
 Sodium stibogluconate
Decrease in parasite DNA, RNA
protein and purine nucleoside
triphosphate levels

 Pentamidine

It appears to interact directly with the pathogen genome by binding to AT-rich regions of duplex
DNA and the minor groove of DNA, thereby interfering with DNA replication.
 Trypanosomiasis
This is the name of several diseases in vertebrates caused by
parasitic protozoa of the genus Trypanosoma.
In humans this includes:
 African trypanosomiasis: caused by Trypanosoma brucei and also
known as sleeping sickness. It is transmitted by the tsetse fly.
 American trypanosomiasis : caused by Trypanosoma cruzii and
called as Chagas disease
It is transmitted by biting of insect
known as Triatominase (kissing buggs)
 Trypanosomiasis
The drugs used in Trypanosomiasis are:
 Eflornithine
 Nifurtimox
 Benznidazole
 Melarsoprol
 Suramin sodium Benznidazole

Melarsoprol
 Toxoplasmosis
Toxoplasmosis is a parasitic disease caused by Toxoplasma
gondii.

Atovaquone is used for it treatment.

 Piperazine Derivatives

Pioperazine citrate
Diethylcarbamazine citrate

Their mode of action is generally by paralysing parasites, which allows the host body
to easily remove or expel the invading organism. The neuromuscular effects are
thought to be caused by blocking acetylcholine at the myoneural junction.
 Heterocyclic Derivatives

Oxaminquine Prazinquantel

Mode of action:

Oxamniquine is a semisynthetic tetrahydroquinoline and possibly acts by DNA

binding, resulting in contraction and paralysis of the worms and eventual
detachment from terminal venules in the mesentry, and death.
 Benzimidazole Derivatives

Mebendazole Thiabendazole Albendazole

Mode of action:
 Natural Derivatives

 Member of the macrocylic lactone class of endectocides

 Bind selectively and with high affinity to GABA or glutamate-gated

chloride ion channels induce the tonic paralysis and expel worms from

GIT.
 Vinyl Pyrimidine Derivatives

Pyrantel

 Member of the macrocylic lactone class of endectocides

 Bind selectively and with high affinity to GABA or glutamate-gated

chloride ion channels induce the tonic paralysis and expel worms from

GIT.
Amide Derivatives

Niclosamide
Synthesis of Niclosamide
SULFONAMIDES

Dr. Sanjeev Kumar Sahu

 INTRODUCTION OF SULFONAMIDES
 Sulfonamides are synthetic chemotherapeutic agents. They were in
common use as antimicrobial drugs prior to the advent of antibiotics.

 In 1935, Domagk, a German scientist demonstrated the antibacterial

therapeutic property of Prontosil-an azo dye possessing p-amino-benzene
sulfonamide group. He was awarded Nobel Prize of Medicine in 1939 for his
outstanding contribution. The antibacterial activity of the drug was due to
its sulfanilamide component.

 Recently their use in combination with trimethoprim or orimethoprim is

favoured on account of synergistic action and prevention of emergence of
resistant bacteria.
CHEMISTRY
Chemically sulfa drugs are amphoteric. They
behave as weak organic acid with pKa 4.79 to 8.56.
Though they are weakly soluble in water, their
solubility is increased at alkaline pH. Sodium salts
are however easily soluble in water. The
sulfacetamide is neutral in pH and is used to
combat eye infections. The basic structure of
sulfanilamide and PABA is given in Fig
CONTINUE…..
 The nitrogen of amino group at para position is
designated as N4 while nitrogen of So2 NH2 is
designated as N1. Systemic sulfa drugs are
evolved by substitution at N1 position whereas
gut active sulfa drugs are produced by
substituting N4 posi-tion.

 By substitution at N1 and N4 po-sitions about

5000 compounds are synthesized. Among them
30 are of clinical significance. Sulfanilamide and
its derivatives are popularly known as
sulfonamide or sulfa drug
SOME SULFONAMIDES
CLASSIFICATION OF SULFONAMIDES
Sulphonamides employed for treatment of systemic
infection. Depending upon duration , they can be
further subdivided into

1. Short acting sulfonamides:

2. Intermediate acting sulfonamides:

3. Long acting sulfonamides:

4. Ultra/Extra long acting sulfonamides:

5. Poorly absorbed sulfonamides:

6. Tropically used sulfonamides:

SHORT ACTING SULFONAMIDES (4-8 HOURS):

1. Sulfadiazine

2. Sulphadimidine

3. Sulfafurazole

4. Sulfamethiazole

5. Sulfafisomidine

6. Sulfathiazole

7. Sulfaisoxazole
INTERMEDIATE ACTING SULFONAMIDES (8-12
HOURS):

1. Sulfamethoxazole

2. Sulfaphenazole

LONG ACTING SULFONAMIDES (24-36 HOURS):

1. Sulfadimethoxine

ULTRA LONG ACTING SULFONAMIDES (7 DAYS):

1. Sulfadoxine

2. Sulfalene
POORLY ABSORBED SULFONAMIDES:

1. Sulfaguanidine

2. Succinyl sulfathiazole

3. Phthalyl sulfathiazole

4. Sulfasalazine

TOPICALLY USED SULFONAMIDES:

1. Silver Sulfadiazine

2. Sulfacetamide

3. Mafenide
0

A)SHORT TO INTERMEDIATE ACTING

SULPHONAMIDES.

CH3
N
H2N SO2N H2N SO2N
H N H
O N

Sulphamethoxazole Sulphadiazine

H3C
CH3 H2N SO2N
H N
H 2N SO2N N
H N
O
Sulfafisoxazole
Sulphaphenazole
0

B. LONG ACTING
SULPHONAMIDES
CH3

H2N SO2N OMe H2N SO2N N

H H
N N N
CH3
Sulphadimethoxine
Sulphamethoxypyridazine

C. Extra long acting sulphonamides

Sulfadoxine
2. TOPICALLY USED SULPHONAMIDES
N
+
H 2N S O 2N COCH3 H 2N S O 2N Ag
H
N
Sulphacetamide
O S ilve r S u l p h a d i a z i n e
O
S O CH3
N
H
H2N O

Mafenide acetate

3. Poorly absorbed sulphonamides

NH O S
H2N SO 2 N N SO 2 N
H H 2C H H
NH 2 N
C OH
H2
Sulphaguanidine O
Succinyl Sulphathiazole
O O S
HO N SO 2 N
H H
N

Phthalyl Sulphathiazole 10
0

MECHANISM OF ACTION
• Competitive inhibitor to dihydropteroate synthase
enzyme due to resemblance with para-amino benzoic
acid.

• Sulfonamides therefore are reversible inhibitors of

folic acid synthesis and bacteriostatic not
bactericidal.

• Inhibit bacterial growth without affecting normal

cells
0

M ECHANIS M OF ACTION
C ONTINUE ----------

 The active form of sulphonamide is the ionized form.

Maximum activity is observed bretween the pka value
6.6-7.4.

 Sulphonamides competes for binding site on plasma

albumin with causes increased action of drugs like

Aspirin, Phenylbutazone, methotrexate etc.

11
 SULPHUR ATOM SHOULD BE
The free aromatic amino group should DIRECTLY LINKED TO THE
reside para to the sulphonamide group BENZENE RING

1 4
RHN SO2NHR'

Substituents at these positions results

in devoid of antibacterial activity
Substitution at this position activity varies with the nature of
substituents.
1) Electron donating substituents to SO2 leads to increase in
antibacterial activity.
2) Heterocyclic substituents leads to highly potent derivatives.
3) Substitution of free Sulphonic acid (-SO3H) group for
sulphonamide function destroys activity.
4)Replacement by a sulfinic acid group (-SO2H) an acetylation
of N1 positio retains activity.

Structure activity relationship of sulphonamide 12

SYNTHESIS OF SULPHADIAZINE,

4-ASC
CONTINUE….
SYNTHESIS OF SULPHAMETHOXAZOLE
CONTINUE….
SYNTHESIS OF SULFACETAMIDE
B.Pharmacy
Subject-Medicinal Chemistry III
Sub Code-BP601T

Anthelmintics
Baljeet Kaur
Asst Professor
Pharmaceutical Chemistry
 Introduction
• Anti –against and helminths –worms
• May be
 Vermicide –Drugs that kill worms
 Vermifuge –expel infesting helminths
 Peristaltic movement of Intestine
 Cathartic and purgative action

 Ideal anthelmintics:
 Orally effective
 Effective in single dose
 Inexpensive
 Wide safety of margin with highest toxicity to worms, but lesser toxic to the
host
Objective of the course:
Understand the importance of drug design
and different techniques of drug design
Learning Outcomes:
Students will learn about the structures and
MOA of antifungal,antiprotozoal agents and
anthelmintics.
Students will learn about SAR of above
mentioned agents.
 Common Helminths
• Roundworm: Ascaris lumbricoides
• Hookworm: Ancylostoma duodenale and Necater
americanus
• Threadworm: Enterobius vermicularis and
Strongyloides stercoralis
• Whipworm: Trichuris trichiuria and Trichinella spiralis
• Filaria: W. Bancrofti, Brugia malayi
• Tapeworms: T. saginata, T. solium, H.nana
• Hydatid disease: E granulosus and Emultilocuralis
• Guniea worm: Dracunculus medinensis
 Available Drugs
1) Mebendazole
2) Albendazole
3) Pyrantel pamoate
4) Piperazine
5) Levamisole and tetramisole
6) Diethyl carbamazine citrate(DEC)
7) Ivermectin
8) Niclosamide
9) Praziquantel
Mebendazole
• Synthetic benzimidazole derivative
• Action:
o 100% cure rate for round worm, hookworm, enterobius (less for
Strongyloides) and trichuris (not for tissue Trichinella spiralis)
o 75% effective for tape worms but not for H. nana
o Hadatid cyst: prolonged treatment
o Hatching of nematode eggs and larva inhibited and Ascaris eggs are
killed

• MOA:
o Slow in action, takes 2-3 days to develop
o Blocks glucose uptake in the parasite and depletion of glycogen store
o Site of action: microtubular protein “ß-tubulin” –inhibitspolymerization
o Intracellular mictotubules are grdually lost
 Mebendazole – contd.
• Pharmacokinetics: Minimal absorption, 75-90% ispassed
unabsorbed in the faeces. Excreted mainly in urine as
inactive metabolite

• Adverse effects:
o No adverse effects with short term therapy, mild GIT disturbanes-
nausea, diarrhoea and abdominal pain
o Allergic reactions, granulocytopenia, loss of hair and elevation of liver enzymes
o Enzyme inducers and inhibitors
o Pregnancy -????

• Uses: Available as 100 mg chewable tablet and

100mg/ml suspension
o Common indications: 100 mg twice daily for 3 days
o Enterobius 100 mg single dose +repeat after2-3 weeks
o Trichinella spiralis – 200 mg twice daily for 4 days Albendazole
o Hydatid cyst: 200-400 mg twice daily for 3-4 weeks
preferred
 Albendazole
• Congener of Mebendazole
• Action: comparable efficacy with mebendazole for
round worm, hook worm and enterobius
o Less effective against trichuris
o But, more effective against strongyloides
o Trichinella effectiveness is almostsame
o More effective in tape worm (including H. nana) and hydatid larvae and ova
of ascaris and hook worm
o Weak microfilarial action and cutaneous larva migrans
• Pharmacokinetics: Moderate and inconsistentoral
absorption
o Fatty meals enhance absorption
o Fraction absorbed is converted to “sulfoxide” metabolite – active
o Its active and penetrates brain with t1/2 of 8-9 Hrs –BASISof TISSUE
Anthelmintic action
o For intesinal worm given in empty stomach and for tissue action – with fatty
meals
 Albendazole – contd.
• Uses and dosage: Available as 400 mg tablet and
200 mg/5ml susp.
o Normal dosing: Single dose of 400 mg (200 mg below 2 years)
o Tape worm: 400 mg for 3days
o Cutaneous larva migrans: treatment of choice - 400 mg for 3 days
o Neurocysticercosis: treatment of choice – 400 mg twice daily for 1-2
weeks
o Hydatid disease: 400 mg BD for 4 weeks, repeat after 2 weeks upto 3
courses. Treatment of choice before and after urgery
o Filariasis: with DEC or Ivermectin –in lymphatic filariasis
o Used in mass programmes –yearly dose for microfilaraemia transmission
o Contraindicated in pregnancy
• Drug of choice for the treatment of filariasis, loiasis and
tropical eosinophillia
• Pharmacokinetics:
o It is synthetic piprazine derivative
o Rapidly absorbed from gut
o It has a half life of 2-3 hours which increases in alkaline urine to 10 hours
o It is excreted in urineunchanged
o Dosage is reduced in urinary alkalosis and renal impairment
• MOA: 2mechanisms
o Alteration of Mf membrane – to be readily phagocytosed by tissue monocytes
o Since piperazine derivative – hyperpolarization and muscular weakness
• Uses: 50 mg, 100 mg tabs and susp available
o Filariasis: 2 mg/kg tds X 7 days –improved
• Intermittent microfilaria is problem (100 mg/kg for 3 weeks) – more than 1 course
of therapy in a gap of 3-4 weeks
• Elephantiasis not affected
o Tropical eosinophilia (2-4 mg/kg tds for 2-3 weeks)
• ADRs: Nausea, vomiting, loss of appetite etc.
o Febrile condition – rash, pruritus, enlargement of lymph nodes – withdraw the drug
and start antihistamines and corticosteroids
o Can be minimized by starting low dose
 Ivermectin
• Obtained from Streptomyces avermitilis
• Action:
o Drug of choice for Onchocercosis volvulus and Strongyloides and equal to DEC in Filaria
o Also efective against cutaneous larva migrans and ascariasis – also scabies and head lice

• MOA:
o Acts via special type of glutamate gated Cl- channel found only in invertebrates
o Such channels are absent in man, flukes and tape worms – not effective
o Potentiation of GABA activity – paralysis of muscles of worms
• Pharmacokinetics: absorbed well orally, widely distributed but not
in CNS, long half-life –48 to 60Hrs

• Uses: 3/6 mg tablets

o Filaria: single dose 0.2 mg per kg with 400 mg Albendazole annually for 5-6 years
o Strongyloides: 0.2 mg/kg single dose
o Replaced DEC in O. volvulous by WHO

• ADRs: Pruritus, giddiness, nausea, abdominal pain and sudden

ECG changes
 Niclosamide
• Against tape worms – saginata, solium, latum and
nana
• MOA: Inhibition of oxidative phosphorylation in
mitochondria and interference of anaerobic
generation of ATP
o Injured worms are digested or expelled (purgation)
o But, problem with T. solium –dangerous visceral cysticercosis

• Regimen: available as 0.5 gm tabs.

1. 2 gm stat – repeat after 1 Hr and saline purgation
2. 2 gm daily for 5 days in H. nana infestation

• ADRs: well tolerated, no systemic toxicity and can

be givenin pregnancy
• Novel anthelmintic with wide range of action
• Action: Mainly on Schisosomiasis and other
Trematodes, cestodes but notnematodes
• MOA:
o Rapidly taken up by worms
o Leakage of intracellular Ca++ causing paralysis
o Worms lose grip on intestinal wall including tissues and veins
o Acts against all stages of worms including larvae
o Other MOA – vacuolization of membrane and release of contents of tap
worms
• Pharmacokinetics: Rapidly absorbed and enhanced by
food
o High first pass metabolism
o Crosses BBB and attains therapeutic conc. In CSF
o Phenytoin, carbamazepine and steroids induce metabolism – failure of therapy
 Praziquantel – contd.
• ADRs: Bitter in taste, produce nausea and vomiting
and abdominal pain
o Headache, dizziness and sedation
o Urticaria, rash, fever etc- destroyred flukes

• Uses: available as 500 mg/600 mg tabs

o First line of drug in all tape worms except Neurocysticercosis (10-25 mg/kg
per day single dose)
o Neurocysticercosis (50-100mg/kg/day for 2 weeks)
o First line of drug in all schistosome infestations and flikes except Fasciola
hepatica (50-75mg/kg/day)
THANK
YOU
B.Pharmacy
Subject-Medicinal Chemistry III
Sub Code-BP601T

Module 4
Anti protozoal Agents

Baljeet Kaur
Asst Professor
Pharmaceutical Chemistry
16
 Protozoal Infection
Protozoal diseases are less easily treated than bacterial
infections:
Unicellular protozoal cells have metabolic processes closer to
human cells than bacteria.
Many of antiprotozoal drugs cause serious toxic effects and most of
them are not safe I n pregnancy.
 Protozoal diseases, such as:
 Malaria
 Amebiasis
 Leishmaniasis
 Trypanosomiasis
 Trichomoniasis
 Giardiasis 17
 Amoeba
• Dientamoeba fragilis-causes Dientamoebiasis
• Entamoeba dispar
• Entamoeba hartmanni
• Entamoeba coli
• Entamoeba moshkovskii
• Endolimax nana
• Iodamoeba butschii

18
 Amoebiasis
• Amoebiasis is caused by E. histolytica, a protozoa
parasite
• Approximately 48 million individuals suffer from
amoebiasis throughout the world.
• At least 40 thousand deaths are attributable to
amoebiasis
• Ranks third among parasitic causes of deaths,
behind only malaria and schistosomiasis

19
20
 Clinical Classification Antiamoebic
Drugs
Mixed amebicides : both systemic and luminal
 Metronidazole
 Tinidazole
Luminal amebicides
– treatment of the asymptomatic colonization state.
 Iodoquinol,
 Paromomycin
 diloxanide furoate
systemic amebicides
– These drugs are useful for treating liver abscesses and intestinal wall
infections caused by amebas
 Chloroquine
 Emetine
 Dehydroemetine
21
 Another Classification of Antiamoebics
I. Tissue Amoebicide
A. Intestinal as well as extra intestinal amoebicide
i) Nitroimidazole derivatigves: Metronidazole,
Ornidazole, Secnidazole, Tinidazole
ii) Alkaloid: Emetine and Dehydroemetine
B. Extra intestinal/hepatic amoebicide
Chloroquine
II. Luminal Amoebicide
a. Amide Derivatives: Diloxanide Furoate
b. 8-Hyroxyquinolines: Iodoquinol, clioquinol
c. Antibiotic : Tetracycline, Pramomycin
22
 Chemical Classification
1. Nitroimidazole derivatives: Metronidazole, Tinidazole , Ornidazole ,
Secnidazole

2. Dichloroacetamides: Diloxanide Furoate, Etofamide, Clefamide, Teclozan

3. Emetines: Emetine, Dehydroemetine

4. Halogenated 8 Hydroxyquinolines: Clioquinol Iodoquinol

5. 4-amino quinoline derivatives: Chloroquine

6. Antibiotics: Paromomycin, Tetracycline

7. Nitrothiazolidines: Nitazoxanide

23
Life cycle of Entameaba histolytica and the sites of action of
amebicidal drugs

24
1. Nitroimidazole derivatives:
Metronidazole, Tinidazole , Ornidazole ,
Secnidazole

25
Nitroimidazoles
 Metronidazole
 MOA: Releases in the parasites toxic superoxide
or hydroxyl radical forming reduced cytotoxic
compounds that bind to proteins and DNA,
resulting in cell death.
 Metronidazole is Drug of choice (DOC) for
amebic infection and for infections caused by:
 Giardia lamblia
 Trichomonas vaginalis
 Anaerobic cocci, gram+ve bacilli and “C.difficile” that
cause Pseudomemberanous colitis

26
 Metronidazole (cont.)
 It kills the trophozoites and less effective
against the cyst
 Most effective against the invasive amebae
 Less effective against the luminal amebae

SO
• it is usually administered with a luminal amebicide,
such as iodoquinol or paromomycin

27
28
Metabolism of Metronidazole

29
30
 Tinidazole

• Tinidazole is an anti-parasitic drug used gainst protozoan infections. It is

widely known throughout Europe and the developing world as a
treatment for a variety of amoebic and parasitic infections. It was
developed in 1972 and is a prominent member of he nitroimidazole use
of tinidazole for infections from amoebae, giardia, and trichomonas, just
like metronidazole.

• Tinidazole may be a therapeutic alternative in the setting of

metronidazole tolerance. Tinidazole may also be used to treat a variety of
other bacterial infections (e.g., as part of combination therapy for
Helicobacter pylori eradication protocols).

• Elimination half-life is 13.2 ± 1.4 hours. Plasma half-life is 12 to 14 hours

• Drinking alcohol while taking tinidazole causes an unpleasant disulfiram-
like reaction, which includes nausea, vomiting, headache, increased blood
pressure, flushing, and shortness of breath.
31
 Ornidazole

• Ornidazole is a antibiotic used to treat some protozoan

infections. It has also been investigated for use in Crohn's
disease after bowel resection.
• After passive absorption into bacterium cell, the nitro
group of ornidazole is reduced to an amine group by
ferrodoxin-type redox systems. The formation of redox
intermediate intracellular metabolites is believed to be the
key component responsible for killing microorganisms. The
drug is active against anaerobic bacteria including
Peptostreptococcus, Clostridium, Bacteroides fragilis,
Prevotella, Porphyromonas gingivalis, and
Fusobacterium as well
as protozoa including Entamoeba histolytica, Trichomonas
vaginalis, and Giardia lamblia
32
MOA of Ornidazole

33
2. Dichloroacetamides: Diloxanide Furoate,
Etofamide, Teclozan

34
 Luminal Amebicides
Iodoquinol *Paromomycin *diloxanide furoate
• They have a direct amebicidal effect to the
trophozoites and cyst forms.
• Used in: asymptomatic cyst carriers and in intestinal
amebiasis.
• Amebae feed on intestinal Flora so tetracycline is
added to luminal amebicides to decrease major food
source.
• Side effects
• iodoquinol include rash, diarrhea, and dose-related
peripheral neuropathy, including a rare optic neuritis.

35
Diloxanide
furoate
• Diloxanide is a medication used to treat amoeba
infections. It is a second line treatment after
paromomycin when no symptoms are present in places
where infections are not common. For people who are
symptomatic, it is used after treatment with
metronidazole or tinidazole. It is taken by mouth.
• Diloxanide generally has mild side effects. Side effects
may include flatulence, vomiting, and itchiness. During
pregnancy it is recommended that it be taken after the
first trimester. It is a luminal amebicide meaning that it
only works on infections within the intestines.

36
• Dloxanide furoate works only in the digestive
tract and is a lumenal amebicide. It is considered
second line treatment for infection with
amoebas when no symptoms are present but the
person is passing cysts, in places where
infections are not common. Paromomycin is
considered the first line treatment for these
cases.
• For people who are symptomatic, it is used after
treatment with ambecides that can penetrate
tissue, like metronidazole or tinidazole.
Diloxanide is considered second-line, while
paromomycin is considered first line for this use
as well.

37
 MOA of Diloxanide
• Diloxanide furoate destroys trophozoites of E.
histolytica and prevents amoebic cyst formation. The
exact mechanism of diloxanide is unknown.
• Diloxanide is structurally related to chloramphenicol
and may act in a similar fashion by blocking protein
synthesis.
• The prodrug, diloxanide furoate, is metabolized in the
gastrointestinal tract to release the active drug,
diloxanide.
• 90% of each dose is excreted in the urine and the other
10% is excreted in the feces
• Diloxanide 500 mg tid x 10d

38
3. Halogenated 8 Hydroxyquinolines:
Clioquinol & Iodoquinol

39
Iodoquinol

• Iodoquinol is an amebocide used against Entamoeba

histolytica, and it is active against both cyst and
trophozoites that are localized in the lumen of the
intestine. It is considered the drug of choice for
treating asymptomatic or moderate forms of
amebiasis. The mechanism of action is unknown.
Iodoquinol is used for diseases caused by moderate
intestinal amebiasis.

• Iodoquinol 650 mg tid x 21d

40
Pentamidine

• Positively charged aromatic diamine

• Accidentally discovered in 1937
• Broad spectrum agent with activity against
many protozoa and fungi
Mechanism of action
• Exact mechanism not known
• Multiple effects on a single parasite and different
mechanisms in different parasites
• Transporter systems (energy dependent high
affinity uptake – P2 purine transporter best
characterized)
• Reacts with negatively charged intracellular organelles
and leads to;
 Ribosomal aggregation
 Inhibition of DNA and protein synthesis
 Enzyme inhibition
 Loss of kinetoplast (topoisomerase II inhibition)
Enflornithine

α-D,L difluromethylornithine
Mechanism of action
• Irreversible inhibitor ornithine decarboxylase by
covalent binding (rate limiting step in polyamine
biosynthesis)
• Polyamines (Putrescine, Spermidine and Spermine) are
needed for cell division and normal cell differentiation
• In trypanosomes, spermidine is additionally
needed for trypanothione synthesis
• Can also inhibit human enzymes
• T. brucei rhodesiense less sensitive than T. brucei
gambiense (effective dose is 10-20 times more)
Synthesis of Metronidazole

45
46
SulphonamideS

4
7
 Description
• One of the oldest antibacterial agents used to
combat infection

• Used for coccal infection in 1935

• They are bacteriostatic because it inhibits
bacterial synthesis of folic acid

• Clinical usefulness has decreased because of the

effectiveness of other antibiotics and penicillin

4
8
 ✓ Presence of free amino group

Antibacterial action
✓ Prontosil red Prodrug
✓ In vitro Inactive
✓ In vivo Active

N N NH 2 NH 2 NH 2
H 2N
H 2N Metablic cleavage
+
SO 2 NH 2 SO 2 NH 2 NH 2

Prontosil Red Sulphonamide

3
 ➢ Chemical modification of the sulphonamide structure
has given rise to several important group of drugs.

➢Gloucoma – Acetazolamide

➢Diuretic – Thiazides

➢Anti-mycobacterial – Sulphones

➢Oral hypoglycemic – Sulphonyl ureas

1) Sodium salt-- water soluble
2)Substitution on these group gives
different molecules having different
pharmacokinetic properties
Substitution gives
prodrug
NH2SO2 NH2
5
0
 Mechanism of action
• Competitive inhibitor to dihydropteroate synthase
enzyme due to resemblance with para-amino benzoic
acid.

• Sulfonamides therefore are reversible inhibitors of

folic acid synthesis and bacteriostatic not
bactericidal.

• Inhibit bacterial growth without affecting normal

cells
5
1
MechanisM of action

5
2
 Antibacterial activity
• Gram-positive and gram negative.

• Nocardia, chlamydia trachomatis, some protozoa.

Classification
A. Sulphonamides employed for treatment of
systemic infection. Depending upon duration , they
can be further subdivided into

5
3
a) Short to intermediate acting sulphonamides.

CH3
N
H 2N SO2N H 2N SO2N
H N H
O N

Sulphamethoxazole Sulphadiazine

H 3C
CH3 H 2N SO2N
H N
H 2N SO 2N N
H N
O
Slpfisoxazole
Sulphaphenazole

5
4
B. Long acting sulphonamides
CH3

H2N SO2N OMe H2N SO2N N

H H
N N N
CH3
Sulphamethoxypyridazine Sulphadimethoxine

C. Extra long acting sulphonamides

N
HO N N SO2N
H H2N SON
2
N H
N
HOOC
MeO
Sulphasalazine
Sulphadiazine

5
5
2. Poorly absorbed sulphonamides
N
+
H 2N S O 2N COCH3 H 2N S O 2N Ag
H
N
S u l p h ac et a m i d e
O Silver S u l p h ad i az i n e
O
S O CH3
N
H
H2N O

M af en i d e ac et at e

3. Topically used sulphonamides

NH O S
H2N SO2N N SO2N
H H 2C H H
NH 2 N
C OH
H2
Sulphaguanidine O
Succinyl Sulphathiazole
O O S
HO N SO2N
H H
N

Phthalyl Sulphathiazole 10
 Structure activity
relationShip
➢ General
1.Sulphonamide skeleton is the minimum structural
requirement for antibacterial activity.

2.The active form of sulphonamide is the ionized form.

Maximum activity is observed bretween the pka value
6.6-7.4.

3. Sulphonamides competes for binding site on plasma

albumin with causes increased action of drugs like
Aspirin, Phenylbutazone, methotrexate etc. 11
 The free aromatic amino group should Sulphur atom should be directly
reside para to the sulphonamide group linked to the benzene ring

1 4
RHN SO2NHR'

Substituents at these positions results

in devoid of antibacterial activity
Substitution at this position activity varies with the nature of
substituents.
1) Electron donating substituents to SO2 leads to increase in
antibacterial activity.
2) Heterocyclic substituents leads to highly potent derivatives.
3) Substitution of free Sulphonic acid (-SO3H) group for
sulphonamide function destroys activity.
4)Replacement by a sulfinic acid group (-SO2H) an acetylation
of N1 positio retains activity.

Structure activity relationship of sulphonamide 12

 Therapeutic uses
• Urinary tract infections

• Upper respiratory tract infections

• Nocardiosis

• Sulfasalazine in IBD.

• Sulfacetamide in bacterial conjunctivitis & trachoma

• Silver sulfadiazine for prevention of infection of
burn wounds .

59
 Adverse effects

• Hypersensitivity reactions

• Crystalluria,hematuria,renal obstruction.

• Allergic nephritis

• Haemolytic anaemia, aplastic anaemia, thrombocytopenia.

• Kernicterus in new born

60
Trimethoprim - Sulfamethoxazole combination
(Co-trimoxazole)
NH2 CH3
N
CH3
H2N C CH3
H2N SON H2
2
H N N
O
CH3
Sulphamethoxazole Trimethoprim

61
 Mechanism of action:

• Sequential blocking of purine synthesis

(synergism).

• Trimethoprim inhibits dihydrofolate reductase

enzyme so inhibits tetrahydrofolic acid synthesis

• The combination is bactericidal

62
63
 Clinical uses
• Acute or Complicated or recurrent urinary tract
infections especially in females

• Upper respiratory tract infections

• Pneumocystis jiroveci pneumonia

• Toxoplasmosis

• Shigellosis

• Nocardiosis

64
 Clinical uses continues…………..
• Typhoid fever

• Salmonella infections

• Prostatitis

• Community –acquried bacterial pneumonia

65
 Adverse effects
• Megaloblastic anemia, leukopenia & granulocytopenia
(can be prevented by administration of folic acid )

• All side effects associated with sulfonamides

66
 LEARNING MATERIAL
COURSE: B.PHARMACY, 6th Sem, Medicinal Chemistry, BP -601T

Module 05 Introduction to Drug Design.

Combinatorial chemistry

Ms. Baljeet Kaur

Assistant Professor
Department of Pharmaceutical Chemistry
ASBASJSM College of Pharmacy, Bela (Ropar)
Objectives:
1. Understand the importance of Drug Design and
different technique for drug designing.
2.Know the importance of SAR ofdrugs.

Learning Outcomes:
1.Student will learn about the different techniques of
drug designing.
2. Student will learn about the Relation of drug and its
Activity.
Quantitative Structure Activity
Relationships (QSAR)
 CONTENTS

 INTRODUCTION
 HYDROPHOBICITY OF MOLECULE
 HYDROPHOBICITY OF SUBSTITUENTS
 ELECTRONIC EFFECT
 STERIC EFFECT
 HANSCH EQUATION
 C R AIG PLOT
 REFERENCES
 INTRODUCTION

Drug designing....

Principles of drug designing

Improving the binding of drugs

Increasing the selectivity
Reduce side effects
Easy synthesisable
Arrangement functional groups and identification of a
pharmacophore
Drug designing...

Based on lead molecule

Traditional
Lead compound
 Analogue molecules designing new molecule
Eg; salicylic acid and aspirin

Based on target structure

 By identifying the structure of drug target

Designing by denovo drug designing

Based on both leading compound and drug target

• Combination of both methods

QSAR

QSAR approach attempts to identify and quantify the

physicochemical properties of a drug and to see whether any of
these properties has an effect on the drug’s biological activity by
using a mathematical equation

PHYSICOCHEMICAL PROPERTIES

 Hydrophobicity of the molecule

 Hydrophobicity of substituents
 Electronic properties of substituents
 Steric properties of substituents
 A range of compounds is synthesized in order to vary one
physicochemical property and to test it affects the bioactivity.

 A graph is then drawn to plot the biological activity on the

y axis versus the physicochemical feature on the x axis.

 It is necessary to draw the best possible line through the

data points on the graph. This done by procedure known as
linear regression analysis by the least square method.
 If we draw a line through a set of data points will be
scattered on either side of the line. The best line will be the
one closest to the data points.

 To measure how close the data points are , vertical lines

are drawn from each point.

Log (1/C)

. . .
.
.. . . .
0.78 3.82 Log P
HYDROPHOBICITY

Hydrophobic character of a drug is crucial to how easily it

crosses the cell membrane and may also important in receptor
interactions.

Hydrophobicity of a drug is measured experimentally by

testing the drugs relative distribution in octanol water mixture.
This relative distribution is known as partition coefficient.

Partition Coefficient P = conc. Drug in in octanol]

[Conc.of drug in water]
 Activity of drugs is often related to P

Biological activity log(1/c) = K1 log P + K2

Eg: binding of a drug to serum albumin determined by

hydrophobicity and study of 42 compounds.
(straight line - limited range of log P)

Log (1/C)

. . .
log(1/c) = 0.075 log P + 230
(n= 42, r= 0.960 s= 0.159)
.
.. . . .
0.78 3.82 Log P
 If the partition coefficient is the only
factor influencing biological activity, the
parabolic curve can expressed by the
equation

Log (1/C)
log(1/c) = -K1 (log P)2 + K2 log P + k3

Few drugs where activity is related to

log P factor alone.
Log P o Log P
 QSAR equations are only applicable to
compounds in the same structural class
(e.g. ethers)

 However, log Po is similar for

anaesthetics of different structural
classes
THE SUBSTITUENT HYDROPHOBICITY CONSTANT (π)

Partition coefficient can be calculated by knowing the

contribution that various substituents, is known as substituent
hydrophobicity constant(π)

 A measure of a substituent’s hydrophobicity relative to hydrogen

 Partition coefficient is measured experimently for a standard

compound such as benzene with or without a substituent (X).

 The hydrophobicity constant (π x) for sustituent X.

The equation is
x= logPx-logPH
 A possitive  value shows that the substituent is more
hydrophobic than hydrogen

A negative value indicates that the substituent is less

hydrophobic.
The  value is charecteristic for sustituent.

Example:

Cl = 0.71 CONH2 = -1.49

 THE SUBSTITUENT HYDROPHOBICITY CONSTANT (π)

Cl
Log P(theory) = log P(benzene) +   
2
O
     
NH2  
meta c h l o r o b e n z a m i d e     

 A QSAR equation may include both P and π.

 P measures the importance of a molecule’s overall hydrophobicity
(relevant to absorption, binding etc)

π identifies specific regions of the molecule which might interact

with hydrophobic regions in the binding site
ELECTRONIC EFFECT

The electronic effect of various sustituents will clearly have

an effect on drug ionisation and polarity.

Have an effect on how easily a drug can pass through the cell
membrane or how strongly it can interact with a binding site.

Hammet substituent constant(σ) this is a measure of electron

with-drawing or electron-donating ability of a substituents on an
aromatic ring.
 o for aromatic substituents is measured by comparing the
dissociation constants of substituted benzoic acids with
benzoic acid

+
COO +
- H
COOH

[PhCO -2]
K H = Dissociationconstant = [PhCO 2H]
 X= electron withdrawing group (e.g. NO2,)

X = electron
withdrawing X X
group CO2H CO2 + H

Charge is stabilised by X
Equilibrium shifts to right
KX > KH

 X = log
K X = logK
X - logK H
KH
Positive value
X= electron donating group (e.g. CH3)

X X +
COOH COO
-
+ H

Charge destabilised
Equilibrium shifts to left
KX < KH

 X = log K X = logK X - logK H

KH

Negative value
 EXAMPLES:  p (NO2)    m (NO2)  

meta-Substitution
O

N
O

e-withdrawing (inductive effect only)

DRUG

para-Substitution

O O O O O O O O
N N N N

e-withdrawing
(inductive +
resonance effects)
DRUG DRUG DRUG DRUG
o value depends on inductive and resonance effects

o value depends on whether the substituent is meta or para

ortho values are invalid due to steric factors

Electronic Factors R & F

 R - Quantifies a substituent’s resonance effects

 F - Quantifies a substituent’s inductive effects

The constants σ,R and F can only be used for aromatic substituents
Aliphatic electronic substituents

 Obtained experimentally by measuring the rates of hydrolyses

of aliphatic esters
 Purely inductive effects
 given by σI
 Hydrolysis rates measured under basic and acidic conditions
O O
Hydrolysis
C C + HOMe
X CH2 OMe X CH2 OH

X= electron donating Rate I = -ve

X= electron withdrawing Rate I = +ve

Basic conditions: Rate affected by steric + electronic factors

Gives σI after correction for steric effect
Acidic conditions: Rate affected by steric factors only (see Es)
STERIC FACTORS

The bulk, size and shape of a drug will influence how easily it can
approach and interact with binding site.

A bulky substituents may act like a shield and hinder the ideal
interaction between a drug and its binding site.

Bulky substituent may help to orient a drug properly for

maximum binding and increase activity.
Taft’s Steric Factor (Es)

 Measured by comparing the rates of hydrolysis of substituted

aliphatic esters against a standard ester under acidic conditions
Es = log kx - log ko

kx represents the rate of

hydrolysis of a substituted ester
ko represents the rate of hydrolysis of the parent ester

 Limited to substituents which interact sterically with the

tetrahedral transition state for the reaction
 Not by resonance or hydrogen bonding

Disadvantages

ES value measures intramolecular steric effect but drugs interact

with target binding site in intermolecular process (i.e. a drug
Molar Refractivity (MR)
this is a measure of a substituent’s volume

(n 2 - 1) mol. wt.
MR = x
(n 2 - 2) density

Correction factor Defines volume

for polarisation
(n=index of
refraction)

This is perticularly significant if the substituent has π

electrons or lone pair of electrons
Verloop Steric Parameter

- calculated by software (STERIMOL)

- gives dimensions of a substituent from the standard
bond angle ,van der Waals radii, bond length and possible
conformations for the substituents
- can be used for any substituent
Example - Carboxylic acid

B4 B3

O B
3

B2
C
B1
O H O C O
B
4

L
 HANSCH EQUATION

 A QSAR equation relating various physicochemical

properties to the biological activity of a series of compounds

 Usually includes log P, electronic and steric factors

 Start with simple equations and elaborate as more structures

are synthesised

 Typical equation for a wide range of log P is parabolic


Log  1 C   - k1(logP)2 + k 2 logP + k 3  + k 4 Es + k 5
Craig Plot
Craig plot shows values for 2 different physicochemical
properties for various substituents

. . + 1.0

. .
CF 3 SO 2

. .. .. CN
.75

.50
NO 2

SF 5

.
SO 2 NH 2 CH 3S O 2
CF 3

..
CH 3 CO

.
CONH 2

. .25
OCF 3

. . -.8 -.4
CO 2 H

.4
Cl Br I

.
-2.0 -1.6 -1.2 .8 1.2 1.6 2.0

.
F

-
. .CH 3CONH +
. OCH 3
-.25 Me Et
t-B utyl

.
OH

. NH 2
-.50

NMe 2
-.75

-1.0

-
 Allows an easy identification of suitable substituents for
a QSAR analysis which includes both relevant
properties

 Choose a substituent from each quadrant to ensure

orthogonality

 Choose substituents with a range of values for each

property
REFERENCES

1. An introduction to medicinal chemistry by Graham L Patric

3rd edition pagee no:271-298

2. Foye : Principles of medicinal chemistry

3. Burgers medicinal chemistry

 Introduction:
•Combinatorial Chemistry is a new method developed by academics
and researchers to reduce the time and cost of producing effective,
marketable and competitive new drugs.

•Scientists use Combinatorial Chemistry to create large numbers of

molecules that can be detected efficiently.

•This technique has captured the attention of many areas such as

Pharmaceutical chemistry, Biotechnology and Agro chemistry.
Definition:
•Combinatorial chemistry is a technique by which large numbers of
different but structurally similar molecules are produced rapidly and
submitted for pharmacological assay.

•This technique uses the same reaction conditions with the same
reaction vessels to produce a large range of analogues.

•Technique invented in the late 1980s and early 1990s to enable

tasks to be applied to many molecules simultaneously
 Application:
Applications of combinatorial chemistry are very wide
Scientists use combinatorial chemistry to create large
populations of molecules that can be screened efficiently.
B y producing larger, more diverse compoundlibraries,
companies increase the probability that they will find
novel compounds of significant therapeutic and
commercial value.
• Provides a stimulus for robot-controlled and
immobilization strategies that allow high-thrughput and
multiple parallel approaches to drug discovery
Advantages:
Fast
Combinatorial approach can give rise to million of compound in
same time as it will take to produce one compound by
traditional method of synthesis .
Economical
A negative result of mixture saves the effort
of synthesis, purification & identification of each compound
Easy
Isolation purification & identification of active molecule from
combinatorial library is relatively easy.
Drug Discovery
Mixed Combinatorial synthesis produces chemical pool.
Probability of finding a molecule in a random screening
process is proportional to the number of molecules subjected
to the screening process
Drug Optimization
Parallel synthesis produces analogues with slight differences
which is required for lead optimization
Disadvantages:
Efficiency is highly affected by compound's size,
solubility and function group.

Compounds produced tend to be Achiral of Racemic

 Combinatorial Chemistry within drug design (
Impact at lead discovery

• traditionally lead drugs were found from

• natural products
•synthetic custom crafted organic molecules made in
small numbers
• analogues of known actives (analogue me-toos)

•High Throughput screening (HTS) requires large numbers of

compounds to fuel the discovery process

•As an alternative to traditional synthesis many compounds rapidly

constructed was needed
 Tools:
1. Solid Phase Techniques
2.1. Advantages
2.2. Requirements
2.3. Examples of Solid Supports (2 slides)
2.4. Anchor or linker
1. Merrifield resin for peptide synthesis (chloromethyl
group)
2. Wang resin (2 slides)
3. Rink resin (2 slides)
4. Dihydropyran resin (2 slides)
2. Parallel Synthesis
3.1. Houghton’s Tea Bag Procedure
3.2. Automated parallel synthesis (2 slides)
3.3. Automated parallel synthesis of all 27 tripeptides from 3 amino
acids (2 slides)
3. Mixed Combinatorial Synthesis
4. Solution phase synthesis
1. SOLID PHASE TECHNIQUES
• Reactants are bound to a polymeric surface and modified whilst still
attached. Final product is released at the end of the synthesis

Advantages
• Specific reactants can be bound to specific beads
• Beads can be mixed and reacted in the same reaction vessel
• Products formed are distinctive for each bead and physically distinct
• Excess reagents can be used to drive reactions to completion
• Excess reagents and by products are easily removed
• Reaction intermediates are attached to bead and do not need to be isolated
and purified
• Individual beads can be separated to isolate individual products
• Polymeric support can be regenerated and re-used after cleaving the
product
• Automation is possible
 1. SOLID PHASE TECHNIQUES

Requirements
• A resin bead or a functionalised surface to act as a solid support
• An anchor or linker
• A bond linking the substrate to the linker. The bond must be
stable to the reaction conditions used in the synthesis
• A means of cleaving the product from the linker at the end
• Protecting groups for functional groups not involved in the
synthesis
 1. SOLID PHASE TECHNIQUES

Examples of Solid Supports

• Partially cross-linked polystyrene beads hydrophobic in nature
causes problems in peptide synthesis due to peptide folding

• Sheppard’s polyamide resin - more polar

• Tentagel resin - similar environment to ether or THF

• Beads, pins and functionalised glass surfaces

1. SOLID PHASE TECHNIQUES

• Beads must be able to swell in the solvent used, and remain

stable
• Most reactions occur in the bead interior

Swelling Starting material,

Resin bead reagents and solvent
Linkers
1. SOLID PHASE TECHNIQUES
Anchor or linker
• A molecular moiety which is covalently attached to the solid
support, and which contains a reactive functional group
• Allows attachment of the first reactant
• The link must be stable to the reaction conditions in the synthesis
but easily cleaved to release the final compound
• Different linkers are available depending on the functional group to
be attached and the desired functional group on the product
• Resins are named to define the linker e.g.
Merrifield, Wang, Rink
Solid phase synthesis: protecting groups
A few protecting groups used in solid phase synthesis.

For amines.
➢ Boc ( t-butoxycarbonyl )
➢ Fmoc (9-fluorenylmetoxy carbonyl)
Tmsec (2 [ trimethylsilyl ] ethoxycarbonyl)

For carboxylic acids.

➢ Tert Bu ester(t-butyl ester)

➢ Fm ester(9-fluronyl methyl ester)

➢ Tmse ester(2 [trimethylsilyl] ethyl)

17
17
ield resin for peptide synthesis (c hloromethyl group)
= resin bead

Cl HO2C NHBoc O Deprotection

+ O
R H
NHBoc

Linker R H

HO2C NHBoc

O O
R2 H
O O O
NH2 coupling NH NHBoc
R H R H H
R2

O HF
O
Release from OH
aa1aa2aa3 aan NH2
solid support
HO2C aa1aa2aa3 aan NH2

Peptide
5. Identification of structures from mixed
combinatorial synthesis
5.1 Recursive Deconvolution:
• Method of identifying the active component in a mixture
• Quicker than separately synthesising all possible components
• Need to retain samples before each mix and split stage

Example:
Consider all 27 tripeptides synthesised by the mix and split strategy
from glycine, alanine and valine
 Gly
Gly

Ala
Ala

Val
Val

Mix and Split

Gly Val Gly Val Gly Val

Ala Ala Ala

Gly Ala Val

Gly Gly Gly Ala Gly Val

Ala Gly Ala Ala Ala Val

Val Gly Val Val

Val Ala

All possible di peptides in three vessels

Retain a sample from each vessel
 Gly Gly Gly Gly Gly Gly Gly Gly
Ala Gly
Ala Gly Ala Gly Ala Gly
Val Gly Val Gly Val Gly Val Gly

Gly Ala Gly Ala Gly Ala Gly Ala

Ala Ala
Ala Ala Ala Ala Ala Ala
Val Ala Val Ala Val Ala Val Ala

Gly Val Gly Val Gly Val Gly Val

Ala Val
Ala Val Ala Val Ala Val
Val Val Val Val Val Val Val Val

Mix and Gly Ala Val

Split
Gly Gly Gly Gly Gly Ala Gly Gly Val
Ala Gly Gly Ala Gly Ala Ala Gly Val
Val Gly Gly Val Gly Ala Val Gly Val

Gly Ala Gly Gly Ala Ala Gly Ala Val

Ala Ala Gly Ala Ala Ala Ala Ala Val

Val Ala Gly Val Ala Ala Val Ala Val

Gly Val Gly Gly Val Ala Gly Val Val

Ala Val Gly Ala Val Ala Ala Val Val

Val Val Gly Val Val Ala Val Val Val

All possible tripeptides in three vessels

 5. Identification of structures from mixed
RceocumrbsiivneatDoerciaolnsvyonluthtieosnis
Gly Gly Gly Gly Gly Ala Gly Gly Val
Ala Gly Gly Ala Gly Ala Ala Gly Val
Val Gly Gly Val Gly Ala Val Gly Val

Gly Ala Gly Gly Ala Ala Gly Ala Val

Ala Ala Gly Ala Ala Ala Ala Ala Val

Val Ala Gly Val Ala Ala Val Ala Val

Gly Val Gly Gly Val Ala Gly Val Val

Ala Val Gly Ala Val Ala Ala Val Val
Val Val Gly Val Val Ala Val Val Val

Mixture Mixture Mixture

Inactive Inactive Active

• 9 Possible tripeptides in active mixture

• All end in valine
• Add valine to the three retained dipeptide mixtures
 5. Identification of structures from mixed
c o m b i n at o r i
a l s y n t
h e
Re cu r siv e D ec onv o lu ti on s i
s
Gly Gly Gly Ala Gly Val

Ala Gly Ala Ala Ala Val

Val Gly Val Val

Val Ala

Val Val Val

Gly Gly Val Gly Ala Val Gly Val Val

Ala Gly Val Ala Ala Val Ala Val Val

Val Gly Val Val Val Val

Val Ala Val

Active

• Active component narrowed down to one of three possible

tripeptides
• Synthesise each tripeptide and test
5. Identification of structures from mixed
combinatorial synthesis
5.2 Tagging:
SCAL = Safety CAtch Linker H
N

H 2N H

O NH2 HN
MeOS O

NH H
O Tryptophan
SOMe
HN
O

Lysine
NH2
NH2
5.2 Tagging
Example NH2
NH2 NH2 aa1
RCHBrCO2H amino acid(aa 1) R'NH2
NH2 NH R HN

Step 1 Tag 1 NH R
Step 2
O Br
O Br

NH2 NH2
NH2 aa2 aa2

aa1 aa1 aa1

HN HN HN
amino acid(aa 2) R"COCl
NH R NH R NH R
Tag 2 Step 3
O NHR' O NHR' O NR'COR"

aa3 NH2
aa2

amino acid(aa 3) aa1

HN
Tag 3 NH R

O NR'COR"
6. Identification of struc tures LIGHT from
combinatorial synthesis LIGHT

6.2 Photolithography - example

NHX NHX NHX NHX NHX

NHX NHX NHX NHX NHX NHX

MASK 1
Mask
NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX

NHX NHX NHX

NHX NHX NHX

NHX NHX NH2 NH2 NH2 NHX NHX

Deprotection CO2H
NHX NH2 NH2 NHX NHX NHX NHX NHX NHX NHX

coupling
NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX
6. Identification of structures from
combinatorial synthesis
6.2 Photolithography - example Y
Y Y Y

repeat

O O Me
Y fluorescent tag

O2N OMe
Target receptor
amino acids X= Nitroveratryloxycarbonyl
7. Planning a Combinatorial Synthesis
7.1 Aims
• To generate a large number of compounds
• To generate a diverse range of compounds
• Increase chances of finding a lead compound to fit a binding site
• Synthesis based on producing a molecular core or scaffold with
functionality attached
Centroid
or scaffold

Substituent
'arms' Binding groups
7. Planning a Combinatorial Syntheses
7.1 Aims
Target molecules should obey Lipinski’s ‘Rule of Five’ for oral
activity

• a molecular weight less than 500

• a calculated log P value less than +5
• no more than 5 H-bond donating groups
• no more than 10 H-bond accepting groups
7. Planning a Combinatorial Syntheses
7.2 Scaffolds
• ‘Spider’ scaffolds preferable for exploring conformational space
• Allows variation of functional groups around whole molecule to
increase chances of finding suitable binding interactions
Binding
regions

Screen compound
library
RECEPTOR
BINDING
SITE

Molecular weight of scaffold should be low to allow variation of

functionality, without getting products with a MWt > 500
7. Planning a Combinatorial Syntheses
2. Scaffolds
Tadpole scaffolds
- variation restricted to a specific region round the molecule
- less chance of favourable interactions with a binding site

'Spider' Scaffold with 'Tadpole' scaffold with

'dispersed' substituents 'restricted' substituents

Privileged scaffolds
- scaffolds which are common in medicinal chemistry and
which are associated with a diverse range of activities
- benzodiazepines, hydantoins, benzenesulphonamide etc
7. Planning a Combinatorial Syntheses
7.2 Scaffolds - examples
R"
R O Me O
N R4
O R2 R3 R HO2C
N R1 4
R' R2
O
N
N N N
X Ar R1 R2 O R5 R3
R3 R

Benzodiazepines Hydantoins -Lactams Pyridines

R3 R4

O
R5
• Good scaffolds
•
C N
R1 O C N
R6
Spider like
O
• Low molecular weight
R2 • Variety of synthetic routes available
Dipeptides
7. Planning a Combinatorial Syntheses
7.2 Scaffolds - poor examples
OR5
Spider like and small molecular weight - good
R4O O
OR1
points
R3O
OR2 But multiple OH groups
Glucose Difficult to vary R1-R5 independently
Me

Me
M.Wt. relatively high
Restricts no. of functional groups to keep MWt.<
R1CO 500
R2
Relatively few positions where substituents
Steroid easily added
O
R3
Tadpole like scaffold
H 2N
R2 Restricted region of
N

R
variability
Indole
VIRTUAL SCREENING IN
DRUG DISCOVERY
 dsdht.wikispaces.com

Challenge in Drug Discovery

Chemical Space Biological Space

> 1020 104 to 105

Computational
Screening,
Experimental Screening

“Available” Validated
Compounds Targets
 Choosing the right molecule
• Goal: to find a lead compound that can be optimized to give a drug candidate

− Optimization: using chemical synthesis to modify the lead molecule in order to

improve its chances of being a successful drug.

• The challenge: chemical space is vast

− Estimates vary

• Reymond et al. suggest there are ~1 billion compounds with up to 13 heavy atoms

• There are ~65 million known compounds (example UniChem, PubChem)

• A typical pharmaceutical compound collection contains ~1-5 million compounds

• High throughput screening allows large (up to 1 million) numbers of compounds to be tested

− But very small proportion of “available” compounds

− Large scale screening is expensive

− Not all targets are suitable for HTS

Screening Schema in DrugDiscovery
Target Disease
The basic goal of the virtual screening is the reduc4on of
the enormous virtual chemical space, to a manageable
number of the compounds that would inhibit a target
protein responsible for disease and also have highest
chance to lead to a drug candidate.
Metabolic Pathways

Virtual Target Protein 3D Structure

Library

Screening Database
Virtual
Screening

Leads
HTS

Comb
Library Lead
Optimization
 Virtual Screening
Depending upon structural and Bioactvity
data available :
3D
Structure
• One or more actives molecule known
perform similarity searching.
unknown Known
• Several active known try to identify a
common 3D pharmacophore and
Structure then do 3D database search.
Ligand
Based Based • Reasonable number of active and
inactive known train a machine
learning model.
Actives Known Actives and Inactive Known
• 3D structure of protein known use
protein ligand docking.

Similarity Pharmacophore Machine

Mapping Learning Docking
Searching
Hybrid Virtual Screening
Mostly, people in pharmaceutical industry does not follow a specific route they follow a hybrid of methods
as discussed in previous slide.

Starting Cleaning Molecules

database
LUDI, Ligand Scout,
Filter : Rule of 5 , Remove isotopes, salts and
Phase, DrugScore
ADME, TOX mixtures
Structure based
Shape Pharmacophore Protonation and
Similarity normalization
ROCS, FlexS
Remove duplicates and
invalid structures
Prepared
database
Pharmacophore Filtering Molecules
based Screening
Ligand Scout, Phase, Ligand fit User defined or other
filter
Docking based
Screening Remove problematic
moieties using PAINS,
Dock, Gold, Glide, ICM Frequent Hitters etc.

PhyChem property
Post Process descriptor calculation
and filtration
Cscore, MM/PBSA, Solvation Corrections
Apply protonation at
Potential Lead compounds pH 7.4
 Drug Like Properties
Drug-like properties are an integral element of drug discovery projects.
Properties of interest to discovery scientists include the following:

• Structural properties
Hydrogen Bonding, Polar Surface area , Lipophilicity, Shape , Molecular
Weight, Reactivity, pka

• Physicochemical Properties
Solubility, Permeability, Chemical Stability

• Biochemical Properties
Metabolism(Phase 1 and 2) , Protein and tissue binding, transport

• Pharmacokinetics(PK) and toxicity

Clearance, Half-life, Bioavailability, Drug-Drug Interaction,LD50
 Leadlike & Druglike
• Leadlike
- Molecular weight (MW) = 200–350 (optimization might add 100–200)
- clogP <1.0–3.0 (optimization might increase by 1–2 log units)
- Single charge present (secondary or tertiary amine preferred)
-Importantly, exclude chemically reactive functional groups ,‘promiscuous
inhibitors’, ‘frequent hitters’ and warheads
- Non-substrate peptides are suitable.

• Druglike
-Importantly, exclude chemically reactive functional groups ,‘promiscuous
inhibitors’, ‘frequent hitters’ and warheads
- MW < 500
- cloP < 5
- H-bond donors < 5
- Sum of N and O (H-bond acceptors) < 10
- Polar surface area < 140 A2
- Number of rotatable bonds <= 10
 Filtering molecules using structuralproperties
Basic Washing –
• Removing Salts & Unwanted Elements
Filter out cationic atoms: Ca2+, Na+, etc.
Filter out metals:
Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd
Often the salt “filter” = keeping the largest molecule in the sdf entry.
• ALLOWED_ELEMENTS H, C, N, O, F, P, S, Cl, Br, I
• Check proper Atom Types by adding hydrogen and checks if O, N, C valences are
correct.
• Check formal charge
Filter out Reactives (false positives for proteins)
 Filter out: Synthesis Intermediates, Chelators
‘warhead’ agents - functional groups which shows high reactivity to proteins due
which there is high attrition rate in drug development.
PAINS Filter
• PAINS = “Pan-Assay Interference Compounds”
• Problematic scaffolds – has cost their Institute time and $$
 dsdht.wikispaces.com

Rules-of-Thumb for Hit Selection & Lead Optimization

Muchmore, SW et al. “Cheminformatic Tools for Medicinal Chemists” J. Med. Chem. (2010) 53, 4830 – 4841
Similarity Searching
What is it ??
Chemical, pharmacological or biological properties of two compounds
match.
The more the common features, the higher the similarity between two
molecules.

Chemical

The two structures on top are chemically similar to each other. This is reflected in their
common sub-graph, or scaffold: they share 14 atoms

Pharmacophore

The two structures above are less similar chemically (topologically) yet have the same
pharmacological activity, namely they both are Angiotensin-Converting Enzyme (ACE)
inhibitors
What is required for a similarity search ?
• A Database SQL or NoSQL ( Postgres, MySQL,
MongoDB) or flat file of descriptors eg: ChemFP
• Chemical Cartridge to generate fingerprints(descriptors)
for molecules ( RDKit, openbabel)
• Similarity function to calculate similarity( Jaccard, Dice,
Tversky) this can be written in c,c++ or python as a
function inside SQL databases.
 2D fingerprints: molecules
represented as binary vectors

• Each bit in the bit string (binary vector) represents one molecular fragment. Typical length is ~1000 bits

• The bit string for a molecule records the presence (“1”) or absence (“0”) of each fragment in the molecule

• Originally developed for speeding up substructure search

− for a query substructure to be present in a database molecule each bit set to “1”
in the query must also be set to “1” in the database structure

• Similarity is based on determining the number of bits that are common to two structures
Calculate molecular similarity
Sequences/vectors of bits, or numeric values that can be compared by
distance functions, similarity metrics .

E= Euclidean distance T = Tanimoto index /Jaccard

n B(x & y)
 x  yi 
T (x, y)
E(x, y) 
2
i B(x)  B( y)  B(x &y)
i1
 3D based similarity
• Shape-based
ROCS (Rapid Overlay of Chemical Structures)
Silicos-it.com (Shape it)

• Computationally more expensive than 2D methods

• Requires consideration of conformational flexibility

− Rigid search - based on a single conformer

− Flexible search

• Conformation explored at search time

• Ensemble of conformers generated prior to search time with each

conformer of each molecule considered in turn

• How many conformers are required

Multiple actives known: pharmacophore
searching
• IUPAC Definition: “An ensemble of steric and electronic features that is necessary to
ensure the optimal supramolecular interactions with a specific biological target and to
trigger (or block) its biological response“

H Aromatic HBA R HBD

• In drug design, the term 'pharmacophore‘ refers to a set of features that is common to a
series of active molecules
• Hydrogen-bond donors and acceptors, positively and negatively charged groups, and
hydrophobic regions are typical features

We will refer to such features as 'pharmacophoric groups'

Workflow of pharmacophore modeling
Tools to perform pharmacophore
searching
1) Catalyst (Accelrys)
2) Phase (Schrodinger)
3) LigandScout (Inte:Ligand)
4) PharmaGist
5) Pharmer
6) SHAFTS
 Many Actives and inactives known : Machine learning
methods
• SAR Modeling
• Use knowledge of known active and known inactive compounds to build a predictive
model

• Quantitative-Structure Activity Relationships (QSARs)

− Long established (Hansch analysis, Free-Wilson analysis)

− Generally restricted to small, homogeneous datasets eg lead optimization.

• Structure-Activity Relationships (SARs)

− “Activity” data is usually treated qualitatively

− Can be used with data consisting of diverse structural classes and multiple binding
modes
− Some resistance to noisy data (HTS data)
− Resulting models used to prioritize compounds for lead finding (not to identify
candidates or drugs)
Protein Ligand Docking

Computational method which mimics the binding of a ligand to a protein.

It predicts ..
a) the pose of the molecule in the binding site
b) The binding affinity or score representing the strength of binding
Pose and Binding Site
• Binding Site (or “active site”)

- the part of the protein where the ligand binds .

- generally a cavity on the protein surface.
- can be identified by looking at the crystal structure of the protein bund with
a known inhibitor.

• Pose ( “binding mode”)

- the geometry of the ligand in the binding site
- Geometry- location , orientation and conformation of the molecule
Protein Ligand Docking
• How does a ligand (small molecule) bind into the active site of a
protein?

• Docking algorithms are based on two key components

− search algorithm
• to generate “poses” (conformation, position and orientation) of
the ligand within the active site
− scoring function
• to identify the most likely pose for an individual ligand
• to assign a priority order to a set of diverse ligands
docked to the same protein – estimate binding affinity
DOCK (Kuntz et al.1982)
• Rigid docking based on shape
• A negative image of the cavity is constructed
by filling it with spheres
• Spheres are of varying size
• Each touches the surface at two points
• The centres of the spheres become
potential locations for ligand atoms.
 DOCK
• Ligand atoms are matched to sphere centers
so that distances between atoms equals
distances between sphere centers.

• The matches are used to position the ligand

within the active site.

• If there are no steric clashes the ligand is scored.

• Many different mappings (poses) are possible

• Each pose is scored based on goodness of fit

• Highest scoring pose is presented to the user

 Energetics of protein-ligand binding
a) Ligand-receptor binding is driven by
• electrostatics (including hydrogen bonding interactions)
• dispersion or van der Waals forces
• hydrophobic interactions
• desolvation: surfaces buried between the protein and the ligand
have to be desolvated
• Conformational changes to protein and ligand
• ligand must be properly orientated and translated to interact and
form a complex
• loss of entropy of the ligand due to being fixed in one conformation.
b) Free energy of binding

ΔGbind = ΔGsolvent + ΔGconf + ΔGint + ΔGrot + ΔGt/r + ΔGvib