Course Name : Medicinal Chemistry I Lab

Course Code : PHR306

Submitted by :
Md.Rafiullah Abir
Id: 19146087
Lab Section: 03

Submitted to :
Easin Uddin Syed
Lecturer, Department of Pharmacy
BRAC University
 Date of Submission: August 22, 2021
Table of Contents

Experiment Name of the Experiment Date Page

Number Number

1 Drawing complex molecules structure with Ketcher 12/08/21 3-4

2 Prediction of organic reaction outcomes using IBM 15/08/21 5-6

RXN

3 Obtaining protein-related information using the 17/08/21 7 - 13

UniProt platform

4 Synthesis of Acetaminophen 18/08/21 14 - 16

5 Synthesis of Aspirin 19/08/21 17 - 20

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Experiment 1 :

Name of the experiment:Drawing complex molecules structure with Ketcher

Results:

Figure: Here in the Ketcher board the first molecule is the structure of Paracetamol and the
second molecule is the structure of Aspirin.

Discussion:
1. Write why it is important to draw molecules in two dimensions.
Ans: Drawing a 3D structure of a molecule on a plane surface or paper is not possible all
that time. In order to gain the concept or design of the specific molecule, it is drawn in
two dimensions. That's why it is important to draw molecules in two dimensions.

2. What other software is available to draw molecules in 2D and 3D?

Ans: The other softwares are:
● Chemsketch
● ChemDoodle
● Avogadro
● Hypercube
● Rasmol
● Chemaxon

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 3. Write about the pharmaceutical uses of these drugs and propose a method of
synthesis for each (Draw the synthesis scheme).

Ans: Pharmaceutical uses of Aspirin and Paracetamol,

● Aspirin is used as a pain reliever and fever reducer.
● Aspirin relieves pain in mild arthritis but has no effect on the underlying inflammation
and swelling of the joint.
● Paracetamol is prescribed for the treatment of migraine, neuralgia, toothache, sore
throat and period pains.
● Paracetamol relieves pain in mild arthritis.

Paracetamol can be synthesized using 4-acetamidophenol,

Aspirin can be synthesized using Salicylic acid,

Conclusion: The experiment examined the method and importance of utilizing computer
software to build 2D structures for aspirin and paracetamol, as well as their medicinal
applications and synthesis procedures.

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Experiment 2 :

Name of the experiment:Prediction of organic reaction outcomes using IBM RXN

Results:

Figure: The product of this reaction is Warfarin, a blood thinner agent which delivers
anticoagulant function.

Discussion:
1. Write why it is important to predict the reaction outcomes and why it is important
to predict the reaction outcomes using artificial intelligence (AI).

Ans. Reacting two different compounds finally results in many products, but it makes us
lose the reactants we used. So it's not a cost effective way to react to reactants without
knowing the final product.This method of blindly reacting two reactants might result in a
different compound having unwanted properties as well due to the interference of
environmental conditions. It is important to predict the reaction outcomes, because it will
allow us to use the needed reactants to get our desired product in a more efficient way.
Then using artificial intelligence is a more developed and morden way to predict the
reaction outcome as it can help us to know whether we can get our desired product from
the reactants we are using without actually performing the reaction itself. Using Artificial

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 Intelligence(AI) can save us from wasting valuable time, costly resources and can
provide us a better understanding about the reaction prior to performing it in real time
which will eventually give us better control over the whole reaction procedure.
2. What other software is available to predict reaction outcomes?

Ans. The other software available to predict reaction outcomes are listed below,

● Chembio 3D
● ChemReaX
● ChemDb
● Chemistry world
● Reactor by ChemAxon
● ChemDraw Professional

Conclusion: The experiment investigated retrosynthetic routes as well as the method and
advantages of predicting responses using computer software and artificial intelligence.

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Experiment 3 :

Name of the Experiment: Obtaining protein-related information using the UniProt

platform

Results:

Protein a:

a. Name of protein: Prostaglandin G/ H synthase 1

b. Organism: Homo sapiens (Human)

c. Structure:

d. Structure (description):Human COX-1 Crystal structure

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e. Sites (mention key sites):

Key sites Positions Description

Active site 206 Proton acceptor

Active site 384 For cyclooxygenase activity

Metal binding 387 Iron (heme axial ligand)

Site 529 Aspirin-acetylated serine

f. Drug interacting with protein:

Drug Action Value Parameter

Paracetamol Inhibition 3.9

k
p i

Bromfenac Inhibition 8.1

plC50

Diclofenac Inhibition 7.9

plC50

Aspirin Inhibition 3.3

plC50

Naproxen Inhibition 5.5

plC50

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 Protein b:

a. Name of protein: Prostaglandin G/H synthase 2

b. Organism:Homo sapiens (human)
c. Structure:

d. Structure (description):The Crystal Structure of Salicylate Bound to Human Cyclooxygenase-

2

e. Sites (mention key sites):

Key sites Positions Description

Active site 193 Proton acceptor

Active site 371 For cyclooxygenase activity

Metal binding 374 Iron (heme axial ligand)

Site 516 Aspirin-acetylated serine

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f. Drug interacting with protein:

Drug Action Value Parameter

Meloxicam Inhibition 6.3

plC50

Rofecoxib Inhibition 6.1-6.5

plC50

Ibuprofen Inhibition 5.9

plC50

Aspirin Inhibition 5.6

plC50

Naproxen Inhibition 5.6

plC50

Protein c:

a. Name of protein:Cholinesterase
b. Organism:Homo sapiens (human)
c. Structure:

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d. Structure (description):CryoEM reconstruction of full-length, fully-glycosylated human
butyrylcholinesterase

e. Sites (mention key sites):

Key sites Positions Description

Binding site 110 Tacrine

Active site 226 Acyl-ester intermediate

Active site 353 Charge relay system

Active site 466 Charge relay system

Binding site 466 Tacrine; via carbonyl oxygen

f. Drug interacting with protein:

Drug Action Value Parameter

Tacrine Inhibition 7.2

k
p i

Bambuterol Inhibition 8.5

plC50

Physostigmine Inhibition 7.6 -7.8

plC50

Rivastigmine Inhibition 7.4

plC50

Pyridostigmine Inhibition 6.1

plC50

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Discussion:
• Discuss the physiological role of the proteins.
Ans.1- Prostaglandin G/H synthase is important in the inflammatory response. It is an important
step in the formation of prostaglandins in gastric epithelial cells, such as prostaglandin E2
(PGE2), which is important for cytoprotection. It plays a role in platelet thromboxane A2
(TXA2) generation, which enhances platelet activation and aggregation, as well as vascular
constriction and vascular smooth muscle contraction.

• Discuss the implications of the proteins as drug targets.

Ans: Drug molecules connect to protein receptors, triggering a series of biochemical and
physiologic reactions. One of the most often used pharmacological targets is protein. The
substance functions as an inhibitor when it binds to the proteins Prostaglandin G/H synthase 1,
Prostaglandin G/H synthase 2, and Cholinesterase. How much an inhibitor impacts a drug's
metabolism is determined by factors like the inhibitor's capacity to bind to the enzyme and the
dosage.

• Discuss the forces involved when drugs interact with the binding sites of proteins.
Ans: The forces involved when the drug interact with the binding sites of proteins are given
below:
● Hydrogen bonds: The attractive force between a hydrogen bond that is covalently connected
to an electronegative atom (O, N, or F)leads to the formation of these bonds.
● Hydrophobic bonds: When non-polar bonds of molecules that aren't soluble in water create
aggregation in the presence of water, then these bond forms.

● Ionic bonds: These bonds are formed between the molecules of opposite charges. Drugs are
often getting ionized and the active sites of receptors do contain charged groups to help from
these bonds.
● Van Der Waals forces: In non-polar compounds, the temporary dipoles of one molecule will
generate the opposing dipoles in the other approaching molecules when the atoms of the drug
and protein target approach each other. This is how these forces happen.

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● The covalent bonds: When two atoms share a pair of electrons, these bonds are formed. This
interaction between the drug and the target results in a biological effect that is irreversible.

Conclusion: The experiment looked into the varied protein structure, drug binding
characteristics, and physiological roles of proteins in humans, as well as how various medicines
attach to these proteins to create antagonistic or agonistic effects.

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Experiment 4 :

Name of the Experiment: Synthesis of Acetaminophen

Procedure:
1. Firstly, 5.5gm of para-aminophenol was weighted in a balance and poured in a conical
flask.
2. Then, 6ml of acetic anhydride was added into the same conical flask.
3. Then the mixture was heated.
4. Lastly, for the final product the conical flask was shaken for 2 minutes.

Results:

• If 3.5 g of crude acetaminophen was produced by the method described above, what is the %
yield?
Ans.
Para aminophenol molecular mass= 109.13g/mol
In reaction 5.5g para aminophenol is used
Paracetamol molecular mass = 151.163g/mol
Actual paracetamol gained from reaction is = 3.5g
From the reaction we get the molar ratio = 1:1
Then 5.50g para-aminophenol have = 5.50/109.13= 0.05 mol
So according to the ratio the theoretical mole number of paracetamols will be same = 0.05 mol
Then theoretical molar mass will be = 151.163*0.05
= 7.6g
Then % yield will be = (3.5/7.6) *100 = 46%

● Physicochemical properties:
★ Molecular Weight - 151.16
★ Density - 1.263 g/cm3
★ Melting point - 169 °C
● Physical state: solid

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 ● Solubility: poorly water soluble, soluble in alcohol and organic solvents
● Incompatibility: N-acetyl-p-benzoquinone imine (NAPQI)
● Uses: to treat pains and fever
● Dose: Oral: Immediate-release: 325 mg to 1 g orally every 4 to 6 hours
Minimum Dosing Interval: every 4 hours
Maximum Single Dose: 1000 mg
Maximum Dose: 4 g per 24 hours
● Dosage form: solid and liquid
● Toxicity and Adverse effect: loss of appetite. nausea. vomiting. pain in the abdomen or
belly. Adults should not take more than 3,000 mg of single-ingredient acetaminophen a
day. Should take less if the patient is over 65 years old. Taking more, especially 7,000 mg
or more, can lead to severe overdose problems.

Discussion:
• Discuss the mechanism of action of paracetamol.
Ans. Acetaminophen enhances the pain threshold by inhibiting two cyclooxygenase isoforms,
COX-1 and COX-2, both of which are involved in prostaglandin (PG) production. Prostaglandins
are responsible for the sense of pain. As opposed to the recognized COX-1 and COX-2 enzymes,
acetaminophen specifically inhibits a variant form of the enzyme. This enzyme is known as
COX-3. Antipyretic effects are likely due to acetaminophen affecting heat-regulating brain
regions, resulting in peripheral vasodilatation, sweating, and a decrease in body temperature.

• Discuss the reaction mechanism using an appropriate diagram.

Ans.

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The lone pair of electrons on the amine of 4-aminophenol attacks the C-O bond of acetic
anhydride causing it to break. Nitrogen has a positive charge but regains electrons by losing a
proton. The negative charge on the oxygen comes back in to reform the C-O bond. This causes
the outer C-O bond to break. The result is an amine bond formation and a carboxylic acid by
product.

• Give reasons why the crude product in most reactions is not pure.
Ans.
1. For pure products, crude products are crystallized further. In general, the products are
produced by combining two or more components. In the final solution, certain reactants
are still present since they were used in greater quantities throughout the synthesis.
Because of this, the end products won't have a pure finish.
2. Some processes, such as condensation, produce alcohol as well as the main components.
To achieve a pure product, it is necessary to remove any side products.

• Write an equation for its preparation of phenacetin starting from 4-ethoxyaniline.

Ans. 4-ethoxyaniline + acetic anhydride -------- > phenacetin + acetic acid

Conclusion: in this experiment, we learned about the synthesis of acetaminophen, which is the
most commonly used NSAID. The mechanism of this drug and also the disadvantages of using
the crude drug product.

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Experiment 5:
Name of the Experiment: Synthesis of Aspirin

Procedure:
1. Firstly, 5gm of salicylic acid was weighted in a balance and poured in a conical flask.
2. Then, 7ml of acetic anhydride was added in the same conical flask.
3. 3 drops of sulfuric acid were also added into the conical flask.
4. After that the mixture was heated until it became clear.
5. Then 75ml of cold water was added in the flask and the mixture was shaken.
6. Lastly, to get the final product, the mixture was filtered.

Results:
• If 7.5 g of crude aspirin was produced by the method described above, what is the %
yield? (Please assume that the quantity of starting materials to be as shown in the video).

Ans.
Salicylic acid molecular mass= 138.121 g/mol
In reaction 5g Salicylic acid is used
Aspirin molecular mass = 180.158 g/mol
Actual Aspirin gained from reaction is = 7.5g
From the reaction, we get the molar ratio = 1:1
Now,
138.121g/mol Salicylic acid is equivalent to 1 mol Salicylic acid
5g salicylic acid is equivalent to = 5/138.121 mol
=0.0362 mol
So according to the ratio the theoretical mole number of Aspirin will be same = 0.0362 mol
Then theoretical molar mass will be = 180.158*0.0362 g
= 6.522 g
Then % yield will be = (7.5/ 6.522) *100 = 114.995%

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Physicochemical properties: molar mass is 180.16 g/mol.
★ The melting point is 136 ℃.
★ The boiling point is 140 ℃.
★ weakly acidic in nature.
▪ Physical state: white crystalline solid
▪ Solubility: soluble in water
▪ Incompatibility: iron salts, carbonates and alkali hydroxides
▪ Uses: to reduce fever and relieve mild to moderate pain from
▪ Dose: Adults: 325-650 mg orally/rectally once every 4-6 hours as needed
▪ Dosage form: solid
▪ Toxicity and Adverse effect: The acutely toxic dose of aspirin is generally considered greater
than 150 mg per kg of body mass. A potentially lethal dose is greater than 500 mg/kg.
➢ conditions of excess stomach acid secretion.
➢ irritation of the stomach or intestines.
➢ nausea.
➢ vomiting.
➢ heartburn.
➢ stomach cramps.

Discussion:
• Discuss the mechanism of action of aspirin.
Ans. Acetylsalicylic acid inhibits prostaglandin synthesis throughout the body by targeting
cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2). Acetylsalicylic acid's acetyl group
binds to a serine residue of the cyclooxygenase-1 (COX-1) enzyme, resulting in permanent
inactivation. This inhibits the synthesis of prostaglandins, which cause pain. This mechanism
also prevents the conversion of arachidonic acid to thromboxane A2 (TXA2), a powerful inducer
of platelet aggregation.

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• Discuss the reaction mechanism using an appropriate diagram.
Ans.

Salicylic acid is chemically synthesized into aspirin, which is then acetylated with acetic
anhydride. Aspirin is made by converting salicylic acid to acetic anhydride by a nucleophilic
mechanism. Esterification is the chemical process that produces acetic acid as a by-product. The
acid catalyst reacts with one of the doubly linked oxygens in acetic anhydride at first. This
allows the nucleophile to attack the carbon atom (salicylic acid). The catalyst then reacts with
more double-bonded oxygen, yielding acetic acid as a by-product. Acetyl salicylic acid 1,
commonly known as aspirin, is the end product.

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• Typically, during the final filtration step the aspirin crystals are rinsed several times with
small portions of cold water. Why is the aspirin washed with cold water?
Ans. Because water helps to hydrolyse excess acetic anhydride and to complete the precipitation
of aspirin. Aspirin is very less soluble in cold water. During this synthesis process by adding cold
water we are not trying to chill the aspirin content we are trying to prevent it from dissolving too
much in the solution so that we can get a better yield.
Because aspirin is less soluble in cold water. In fact, aspirin is not very soluble in water at all,
which is why you are supposed to take it with lots of water. You are not "chilling the aspirin",
you are preventing it from dissolving too much so that you have a better yield of your product.

• Aspirin that has been stored for a long time may give a vinegar-like odor and give a
purple color with FeCl3. What reaction would cause this to happen?
Ans. Moisture within the container would result in the formation of acetic acid. Aspirin interacts
with water molecules, protonation of an oxygen in the acetic group and causing it to separate
from the molecule, resulting in acetic acid, which is the major cause of the vinegar odor. Acetic
acid, which has a phenol group that interacts with FeCl3 to produce a purplish color.

Conclusion: To conclude, we can say that Aspirin is a very important drug for pain relief and
also works as blood thinner. The synthesis and the yield calculation will help us to make the drug
in desired quantity. In addition to that, we learned the mechanism of drug action also the result of
storing aspirin for a longer period of time and the reaction behind it,

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