UNIVERSITY OF ZIMBABWE

QSAR MODELING OF A NOVEL SELECTIVE

SEROTONIN REUPTAKE INHIBITOR

NAME: TENDEKAYI CRAIG MAZAIWANA

FIELD: COMPUTATIONAL CHEMISTRY

SUPERVISOR: DR. R. MASUKA

DEPARTMENT: CHEMISTRY DEPARTMENT

A DISSERTATION SUBMITTED IN PARTIAL FULFILMENT OF THE

REQUIREMENTS FOR:

BACHELOR OF SCIENCE HONOURS DEGREE IN CHEMISTRY

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DECLARATION
I, Tendekayi Craig Mazaiwana, do hereby declare that I am the author of this dissertation titled,
“QSAR Modeling of a novel selective serotonin reuptake inhibitor”, done under the guidance of
Dr. R. Masuka. The results are from my own research except where mentioned in the references.
This research work has not been submitted for an award in any degree in this or any other tertiary
institution.

Date: ………...……………………………………
Name: MAZAIWANA CRAIG TENDEKAYI...
Signature………………………………………….

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ACKNOWLEDGEMENTS
I would like to take this opportunity to thank my supervisor Dr. Masuka for continuously guiding
me throughout this project. I faced various challenges and continued to work as hard as I could.
The research experience was a new experience for me because it gave me the chance to learn as well.
I discovered my potential to work as hard as I can and to do research. I believe that this will forever
shape my professional lifestyle and open doors to more development. My gratitude to the chemistry
department and staff members will truly be for my future success. My learning experience during this
project was wonderful and gave me the chance to explore the possibilities of computational
chemistry. I would also like to thank Mr. Wakandigara for teaching me how to use the computational
software that I used for this project.

Many thanks go to my parents, family and friends for their continuous support.
Finally, I would like to thank the Lord for giving me the strength to persevere.

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LIST OF ABBREVIATIONS
CNS - Central Nervous System
CADD - Computer Aided Drug Design
PDB - Protein Data Bank
HB - Hydrogen Bond
Mol_MW - Molecular Weight
SBDD - Structure Based Drug Design
LBDD - Ligand Based Drug Design
QSAR - Quantitative Structure Activity Relationship
SBVS - Structure based virtual screening
LBVS - Ligand based virtual screening
ADME - Absorption, Distribution, Metabolism and Excretion
hSERT - Human serotonin transporter
5HT - 5-hydroxytryptamine
SSRIs – Selective serotonin reuptake inhibitors
TYR – Tyrosine
ASP – Asparagine
ALA – Alanine
PHE – Phenylalanine
GLU – Glutamine

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ABSTRACT
Major Depressive Disorder (MDD) is a disorder that is recognized world wide. Scientists have
created antidepressants that have different mechanisms of actions to treat this disorder. The
mechanism of action that selective serotonin reuptake inhibitors use makes them effective. There
are 6 commercially available selective serotonin reuptake inhibitors (SSRIs) around the world.
These antidepressants are known to have many side effects. In Zimbabwe there are a variety of
reasons why people become depressed and this depression is normally observed among women.
The state of the economy, infertility, lack of cash savings, job losses and chronic illness for more
than a month are a few of the reasons. Designing a drug that can be used to treat major
depressive disorder in Zimbabwe is important.

The aim of this project was to design a new selective serotonin reuptake inhibiting drug that has
few or no side effects and that can treat mental disorders such as depression. Computational
analysis was used to accomplish this. In order to achieve this, the Maestro Schrodinger software
was used. Protein preparation was done using the Protein Preparation Wizard. Derivatives were
suggested using visual inspections of the binding between fluvoxamine and the serotonin
transporter. The other derivatives were suggested using Fieldbased QSAR. Ligand preparation
was done using LigPrep. Docking calculations were carried out using Glide Docking. QikProp
calculations were carried out using QikProp. Sites of metabolism tests were carried out using the
Site of Metabolism software.

The suggested derivatives were analysed to see if they are effective. The most promising of the 6
derivatives was derivative 3. It has a variety of properties that make it the molecule that would
most likely be effective.

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 Table of Contents

DECLARATION ....................................................................................................................................................... 2
ACKNOWLEDGEMENTS ....................................................................................................................................... 3
LIST OF ABBREVIATIONS ..................................................................................................................................... 4
ABSTRACT.............................................................................................................................................................. 5
LIST OF TABLES ............................................................................................................................................. 6
CHAPTER 1 .............................................................................................................................................................. 12
1. INTRODUCTION .................................................................................................................................................. 12
Background ............................................................................................................................................................ 12
1.1 Antidepressant drugs ..................................................................................................................................... 13
1.2 Computer Aided Drug Design ....................................................................................................................... 15
1.2.1 Structure Activity Relationships ................................................................................................................. 16
1.2.2 Ligand docking .......................................................................................................................................... 16
1.2.3 Force Field Scoring Functions .................................................................................................................... 17
1.2.4 Protein-ligand interaction diagrams ............................................................................................................ 17
1.2.5 Scoring ...................................................................................................................................................... 17
1.2.6 Virtual screening ........................................................................................................................................ 18
1.3 Problem Statement ............................................................................................................................................ 18
1.4 Knowledge gap ................................................................................................................................................. 18
1.5 Aim .................................................................................................................................................................. 18
1.6 Objectives ......................................................................................................................................................... 18
1.7 Research question ........................................................................................................................................... 18
1.8 Literature Review ........................................................................................................................................... 18
CHAPTER 2 ............................................................................................................................................................ 22
2. EXPERIMENTAL ............................................................................................................................................... 22
2.1 Introduction .................................................................................................................................................... 22
2.2 Research methodology .................................................................................................................................... 22
2.2.1 Protein preparation ................................................................................................................................... 22
2.2.2 Determination of derivatives by QSAR..................................................................................................... 22
2.2.3 Ligand preparation ................................................................................................................................... 28
2.2.4 Docking studies ........................................................................................................................................ 28

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 2.2.5 Metabolism calculations ........................................................................................................................... 28
2.2.6 Toxicity tests ............................................................................................................................................ 29
2.3 Material and procedures .................................................................................................................................. 29
2.3.1 Materials .................................................................................................................................................. 29
2.3.1.1 Hardware .............................................................................................................................................. 29
2.3.1.2 Software ................................................................................................................................................ 29
2.3.2 Procedures ................................................................................................................................................... 30
2.3.2.1 Protein preparation ................................................................................................................................ 30
2.3.2.2 Ligand preparation ................................................................................................................................ 31
2.3.2.3 Pharmacophore Hypothesis ................................................................................................................... 32
2.3.2.4 3D Field-Based QASR .......................................................................................................................... 33
2.3.2.5 Ligand-Based Virtual Screening ............................................................................................................ 34
2.3.2.6 Receptor grid generation........................................................................................................................ 35
2.3.2.7 Docking ................................................................................................................................................ 36
2.3.2.8 Prediction of the Site of metabolism using cytochrome P450 enzymes ................................................... 36
2.3.2.9 Toxicity tests ......................................................................................................................................... 38
CHAPTER 3 ............................................................................................................................................................ 38
3. RESULTS ........................................................................................................................................................ 38
3.1 Protein preparation .......................................................................................................................................... 38
3.2 Pharmacophore hypothesis .............................................................................................................................. 39
3.3 Determination of derivatives by QSAR ........................................................................................................... 41
3.4 Ligand-based virtual screening ........................................................................................................................ 44
3.5 Docking results ............................................................................................................................................... 45
3.5.1 Fluvoxamine and hSERT docking results ................................................................................................. 45
3.5.2 Docking results for the suggested derivatives............................................................................................ 46
3.3 P450 Metabolism tests .................................................................................................................................... 52
3.4 Toxicity tests using Qikprop ........................................................................................................................... 55
CHAPTER 4 ............................................................................................................................................................ 56
4. DISCUSSION ...................................................................................................................................................... 56
4.1 Ramachandran plot ......................................................................................................................................... 56
4.2 Docking results ............................................................................................................................................... 57
4.2.1 The target protein hSERT docked with fluvoxamine ................................................................................. 57
4.2.2 Docking with derivatives .......................................................................................................................... 57

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 4.3 Metabolism tests ............................................................................................................................................. 59
4.4 Toxicity Tests ................................................................................................................................................. 60
CHAPTER 5 ............................................................................................................................................................ 62
5. CONCLUSION .................................................................................................................................................... 62
CHAPTER 6 ............................................................................................................................................................ 63
6. RECOMMENDATIONS ...................................................................................................................................... 63
REFERENCES......................................................................................................................................................... 64

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 List of Figures
Figure 1: A presynaptic and postsynaptic cell with action of the reuptake transporter .................................. 14
Figure 2: A presynaptic and postsynaptic neuron with norepinephrine being transporter ............................. 15
Figure 3: Fluoxetine (orange) and paroxetine (grey) bonded to the central site of the serotonin
transporter ................................................................................................................................................... 20
Figure 4: Fluvoxamine bonded at a site of the serotonin transporter ............................................................ 21
Figure 5: Structure of Fluvoxamine ............................................................................................................... 23
Figure 6: Derivative .................................................................................................................................... 23
Figure 7: Derivative 2 ................................................................................................................................. 24
Figure 8: Derivative 3................................................................................................................................. 24
Figure 9: QSAR dialogue box with the ligand names and the activities ......................................................... 25
Figure 10: Scatter plot for the predicted activity vs activity .......................................................................... 26
Figure 11: Derivative 4 structure suggested by field-based QSAR ................................................................ 27
Figure12: Derivative 5 from field-based QSAR ............................................................................................ 27
Figure 13: Derivative 6 from field-based QSAR .......................................................................................... 28
Figure 14: Protein preparation dialogue box showing some of the options selected ..................................... 31
Figure 15: LigPrep dialogue box showing the selected parameters .............................................................. 32
Figure 16: Develop pharmacophore model dialogue box ............................................................................. 33
Figure 17: Ligand-based virtual dialogue box with sub tasks....................................................................... 34
Figure 18: Phase ligand screening panel .................................................................................................... 35
Figure 19: The receptor grid generation dialogue box ................................................................................. 36
Figure 20: p450 site of metabolism panel .................................................................................................... 37
Figure 21: start P450 Job panel.................................................................................................................. 37
Figure 22: The QikProp dialogue box ......................................................................................................... 38
Figure 23: Ramachandran plot for prepared hSERT(6AWP)........................................................................ 39
Figure 24: HHPR hypothesis with different features displayed .................................................................... 40
Figure 25: 5 SSRIs wuth hypothesis features displayed................................................................................. 40
Figure 26: The 3D Field-based QSAR panel with results ............................................................................. 41
Figure 27: Scatter plot with the test set of the model .................................................................................... 42
Figure 28: Scatter plot with the training set of the model ............................................................................. 42
Figure 29: Hits obtained for each pharmacophore hypothesis in the project table ....................................... 45
Figure 30: hSERT binding site docked with fluvoxamine ............................................................................. 46
Figure 31: Derivative 1 and binding site protein-ligand interaction diagram............................................... 47
Figure 32: Derivative 2 and binding site protein-ligand interaction diagram............................................... 48
Figure 33: Derivative 3 and binding site protein-ligand interaction diagram............................................... 49
Figure 34: Derivative 4 and binding site protein-ligand interaction diagram............................................... 49
Figure 35: Derivative 5 and binding site protein-ligand interaction diagram............................................... 50
Figure 36: Derivative 6 and binding site protein-ligand interaction diagram............................................... 51
Figure 37: Reactive sites for derivative 1 .................................................................................................... 52
Figure 38: Reactive sites for derivative 2 .................................................................................................... 53

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Figure 39: Reactive sites for derivative 3 .................................................................................................... 53
Figure 40: Reactive sites for derivative 4 .................................................................................................... 54
Figure 41: Reactive sites for derivative 5 .................................................................................................... 54
Figure 42: Reactive sites for derivative 6 .................................................................................................... 55

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 List of Tables
Table 1: QSAR statistics for 50% random training set................................................................................. 44
Table 2: QSAR statistics for 20% random training set................................................................................. 44
Table 3: Fluvoxamine and derivatives bonding interactions with the target protein ..................................... 52
Table 4: Ligand characterization using QikProp......................................................................................... 55

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 CHAPTER 1
1 INTRODUCTION
Background
Depression may be defined in terms of a state of feeling sad. It can also be defined as a
psychoneurotic disorder that can be characterized by mental and functional activity, difficulty in
thinking, sadness, reduction in activity, perturbations in appetite, loss of concentration, sleeping,
and feelings of dejection, hopelessness, and generation of suicidal tendencies. (D’Agostino,
2015)

Antidepressants are those drugs which help in the reduction in symptoms of depressive disorders
by altering chemical imbalances of neurotransmitters in the brain. The change in mood and
behavior is due to chemical imbalance. Neurotransmitters are the communication link between
neurons in the brain. In nerve cells, there are neurotransmitters that are found in vesicles. The
neurotransmitters such as serotonin, dopamine and noradrenaline or norepinephrine are released
by the pre-synaptic end of one nerve and received by the post-synaptic end. This is called
reuptake. Reuptake of the neurotransmitters can also take place at the pre-synaptic end. The
antidepressants inhibit the reuptake of neurotransmitters through selective receptors thereby
increasing the concentration of a specific neurotransmitter around the nerves in the brain.

Selective serotonin reuptake inhibitors have many side effects which are nausea, anxiety,
insomnia, dry mouth, headache, somnolence, dizziness, agitation, anorexia, diarrhoea,
constipation, tremor, sweating and sexual dysfunction. (Khushboo, 2017)

In Zimbabwe, people complain about headaches and fatigue as the most common form of
depression. After inquiring, many of the patients freely confessed their emotional symptoms.
Many individuals that are depressed said that their symptoms are due to “thinking too much”
(kufungisisa), which occurs because of many problems in society.

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There was a study that was done among adults. A third of the people that were attending
traditional healers and a quarter of people that were attending primary care had depression. 40%
of them were still ill after 12 months and the occurrence of new cases was 16%. The regularity of
depressive and anxiety disorders in one month was 15.7% in a random sample of women from
the community. 16% was the percentage of the random sample with postnatal depression. In
other developing countries the high rates of depression were observed in women. After
community surveys were done it was revealed that the prevalence rates were more than 50%.
Depression was associated with infertility, lack of cash savings, job losses and chronicity of
illness for more than a month. In the community sample of women, harsh life events were the
main cause of depression. Significant events were marital or other relationship crises, deaths, and
events directly associated with infertility or unwanted pregnancy. (Patel, 2001)

1.1 Antidepressant drugs

There are 13 different classes of antidepressants that are as follows:
1. Tricyclic antidepressants (TCAs) - both norepinephrine (NE) and serotonin (5HT)
reuptake can be blocked by it. It has been reported that TCAs block histaminic, alpha1
adrenergic and muscarinic receptors.
2. Monoamine Oxidase Inhibitors (MAOIs) - The enzymatic conversion of 5HT and NE
into their metabolites will be inhibited by these. MAOIs are usually prescribed for drug-
resistant or atypical depression. These compounds contain a certain level of toxicity that
can lead to lethal cardiac arrhythmias and seizures.
3. Selective serotonin-reuptake inhibitors (SSRIs) - may block the reuptake of 5HT and
increase synaptic 5HT transmission. The SSRIs have very little or insignificant effect on
the reuptake of other neurotransmitters. It has been observed that SSRIs does not display
any activity at the muscarinic and histaminergic receptors.
4. Serotonin/norepinephrine/dopamine reuptake inhibitor (SNRI) - At low doses, it
essentially acts as an SSRI and a NE reuptake inhibition at medium to high doses. It also
causes DA reuptake inhibition at very high doses.
5. Serotonin receptors antagonist with serotonin reuptake inhibition (SARI)
6. Serotonin 5-HT1A autoreceptor partial agonist with serotonin reuptake inhibition (SPARI)

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 7. Norepinephrine-dopamine reuptake inhibitor (NDRI) – The only type of antidepressant
that selectively acts on the noradrenergic and dopaminergic systems but not on the
serotonin system. It may exert positive effect in overcoming the attention deficit disorder
and in the treatment of smoking cessation.
8. Selective NRIs - a noradrenaline (norepinephrine) reuptake inhibitor which is exclusively
unrelated to TCA or SSRIs. The particular properties are its high affinity for the
noradrenaline transporter, and low affinity for other neuro receptors including serotonin,
dopamine, histamine, muscarinergic and alpha adrenergic sites.
9. Noradrenergic α2-receptor antagonist with specific serotonergic receptors-2 and-3
antagonism (NASSA) - noradrenergic and specific serotonergic antidepressant. it has
some side effects such as weight gain and sedation.
10. Norepinephrine reuptake inhibitor with serotonin receptors antagonism (NRISA)
11. Serotonin-norepinephrine reuptake inhibitor and serotonin receptors antagonism
antidepressant with potent antipsychotic D2 receptor blockade/antagonism (SNRISA with
potent antipsychotic D2 receptor blockade/antagonism)
12. Atypical antipsychotics that exhibit weak D2 receptor antagonism with potently strong 5-
HT2A receptor blockade
13. NMDA-glutamatergic ionoceptor antagonist/inverse agonist/partial agonist that exhibit a
direct action on the excitatory glutamatergic neurotransmission system. (Fasipe,2018)

Figure 1: A presynaptic and postsynaptic cell with action of the reuptake transporter.
(PsychEducation Org, 2019)

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Figure 2: A presynaptic and postsynaptic neuron with norepinephrine being transported. (Foley
et. al, 2006)

These drugs have been allowed to be used for treating panic disorders (PD), obsessive-
compulsive disorders (OCD), pre-menstrual dysphoric disorder (PMDD), social phobia, post
traumatic stress disorders (PTSD) and anorexia. (Nenecetti, 2011)

1.2 Computer Aided Drug Design

Drug design is the process involving research and development of new medication. A drug is
usually a small organic molecule which leads to the activation or inhibition of the role of a
biomolecule. Computer aided drug design is done with the aid of a computer. It is an effective
technique for the acceleration of the process of drug discovery and development.
Computer aided drug design reduces the cost of research and development time of drugs.
There are a number of drug discovery approaches which can be used using computer.(Ou-Yang
et al., 2012)

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Computer aided drug design is done to increase the levels of the drug discovery and development
course. Computer drug design provides hope for the development of better drug design tools.
Two main types of approaches for computer aided drug design are available.
These are structure based drug design (this approach is direct) and ligand based drug design (this
approach is indirect)
In Structure based drug design SBDD, the interactions for all the tested compounds are
calculated after the docking process. The structure of the protein is also known.
Target Identification & validation
ꜜ
Analysis of the structure for the potential binding sites
ꜜ
Lead Identification& Molecular Docking
ꜜ
Lead Validation &Optimization
ꜜ
Clinical Trials
(Das, 2017)
Ligand based drug design
In LBDD, the 3D structure of the target protein is not known but the information of ligands
which bind to the chosen target site is known. A pharmacophore model can be developed from
these ligands. (Das, 2017)

1.2.1 Structure Activity Relationships

This is used to describe the relationship in computational chemistry quantitatively. This is also
used to predict and characterize chemical toxicity levels. SAR is used to come up with drugs
which have the desired chemical properties. Field Based Quantitative Structure
Activity Relationship (QSAR) is used by most researchers to adjust and upgrade lead
compounds. Scatter plots for the known and predicted activities can be created in order to assess
the model. (Liu and Wang, 2018)

1.2.2 Ligand docking

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For docking to occur a receptor or lock and a ligand or key are involved, when they bind they
form a complex. The two behave in a lock and key manner. To predict the main binding mode
and bioaffinity of a ligand with a protein of known structure docking is done. Several possible
binding modes are generated and these are ranked using the scoring functions in the software
used. Binding energies, stability of complexes and the free energy can be suggested from the
information obtained from docking. Scoring functions are used for docking. These 8 are
mathematical functions which are used to predict the binding affinity between the receptor and
the lock.

1.2.3 Force Field Scoring Functions

Classic molecular mechanics are used for energy calculations. Parameters derived from
experimental results and ab initio calculations are used. The sum of the Van der Waals and
electrostatic interactions is used to estimate the binding force energy of the protein ligand
complexes. (Talevi, 2018)
More time is required for drug modification in the laboratory and also it involves the use of
expensive equipment and reagents. Clinical trials are an important requirement.
Computational chemistry can be used for the modification of drugs. This involves docking of
ligands and proteins of interest. A number of drugs can be modified using computational
chemistry.

1.2.4 Protein-ligand interaction diagrams

Proteins are large molecules responsible for most of the work done by cells. These include
catalysing metabolic reactions, responding to stimuli and they are responsible for the structure of
cells. For a drug to perform its duty it should be able to bind to the protein. The binding occurs
according to the lock and key mechanism. If the drug does not fit into the proteins active site
then the drug will cease to perform its role. Protein-ligand interactions for all ligand protein
processes are important. These interactions are a result of molecular mechanics (Chowdhry and
Harding, 2001)

1.2.5 Scoring
Scoring is the process whereby a particular pose is assessed by calculating the number of
favourable intermolecular conformational interactions and these include Hbonds and

17
hydrophobic interactions. Docking scores are predicted values of free energy of the proteinligand
or binding affinity. (Friesner, R et al., 2006)

1.2.6 Virtual screening

This is an alternative for high throughput screening which increases the probability of finding the
most appropriate drug. The suggested derivatives pass through a filtering process. There are two
types of virtual screening, which are structure based virtual screening (SBVS) and
ligand based virtual screening (LBVS). SBVS method rely on the structure of target protein
active site and LBVS method is based on approximation of calculated similarity between the
known active and the compounds come from databases. The filtering tools include the drug and
lead like properties, toxicity and the type of pose (bad or good) after docking. (OuYang et al.,
2012)

1.3 Problem Statement

People in Zimbabwe also experience depression because of the state of the economy and the
degree of difficulty in finding jobs that pay enough money for living expenses. In Zimbabwe the
effects of cyclone idai were that of a natural disaster. Many lives were lost and many other
people suffered from injuries. People that survived could be suffering from depression because
of losing their homes, businesses and family members.

1.4 Knowledge gap

There is a need to substitute the existing antidepressants with its derivatives that are effective but
with less or no side effects.

1.4 Aim
Designing a new selective serotonin reuptake inhibiting drug that has few or no side effects and
that can treat mental disorders such as depression.

1.6 Objectives
 Perform docking calculations with existing SSRIs.
 Build a pharmacophore model and a QSAR model.

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  Perform virtual screening of the CHEMBL database with the QSAR model.
 Identify hits from the compounds obtained.
 Perform docking calculations using the derivatives.
 Screen the derivatives for toxicity.

1.7 Research question

Can a new antidepressant that also treats different disorders be discovered?

1.9 Literature Review

Molecular modeling is important for all drug discovery programs to obtain new molecular
entities (NMEs). Molecular modeling involves a variety of tools, each tool being used in
particular elements of the drug discovery process. For the problem at hand, tools like
comparative protein modeling, docking and quantitative structure-activity relationships (QSAR)
are ideal. Thus, comparative protein modeling has been used to build the 3D structure of the
serotonin transporter (SERT) with the leucine transporter (LeuT) as a template. (Coutinho, 2011)

The serotonin transporter (SERT) regulates extracellular levels of serotonin (5-

hydroxytryptamine, 5HT) in the brain by transporting 5HT into neurons and glial cells. The
human SERT (hSERT) is the primary target for drugs used in the treatment of emotional
disorders, including depression. hSERT belongs to the solute carrier 6 family that includes a
bacterial leucine transporter (LeuT), for which a high-resolution crystal structure has become
available. LeuT has proved to be an excellent model for human transporters and has advanced
the understanding of solute carrier 6 transporter structure-function relationships. (Andersen,
2009)

Rationalizing activity trends can be achieved through molecular docking of paroxetine,

fluoxetine or other antidepressant molecules being performed in the homology models of the
serotonin transporter (SERT), dopamine transporter (DAT) and norepinephrine transporter
19
(NET) made using a leucine template (LeuT). Compounds can be docked in the central binding
pocket of SERT, DAT, and NET, corresponding to the substrate-binding pocket of leucine in the
LeuTAa crystal structure. Paroxetine specifically engages an ionic interaction between the
protonated N of piperidine and Asp98. The piperonilic part interacts with Asn177 and with the
non-conserved Thr439, following the proposed binding mode of 5-HT, which permits the same
ionic interaction with Asp98 and a hydrogen bond between the hydroxyl group of 5-HT and
Thr439. The fluorophenyl moiety of paroxetine is stabilized through a stacking with Phe341 and
placed in a pocket defined by Tyr95, Ala169, Ile172, Val343, apart from Phe341. Fluoxetine has
a similar binding mode, but the CF3 cannot interact with the same strength of the piperonilic
moiety of paroxetine with Asn177 and Thr439. (Nencetti, 2011)

Figure 3: fluoxetine (orange) and paroxetine (grey) bonded to the central site of the serotonin
transporter. (Nencetti, 2011)

The docking performed in SERT, DAT and NET shows the importance of the SERT Thr439
substitution with DAT Ala423 and NET Ser420 in directing the orientation of the ligands in the
binding site and the importance of the Tyr95/Phe76/Phe72, Ala169/Ser149/Ala145,

20
Ile172/Val152/Val148, Thr497/Ala480/Ala477 replacements in SERT/DAT/NET in determining
a different stabilization of compounds in the three transporters. The Asn177 and/or Thr439
contribution in the polar interaction with the ligands seems to be determinant for an effective
binding in SERT. The lack of these interactions in DAT and NET precludes any significant
activity of the ligands.

The amine group of fluvoxamine occupies subsite A, interacting with Asp98 and Try95 residues
crucial for drug binding. In subsite B, Ser439 is within 3.9 Å of the halide atoms of fluvoxamine.

Figure 4: fluvoxamine bonded at a site of the serotonin transporter. (Coleman, 2018)

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CHAPTER 2
2. EXPERIMENTAL
2.1 Introduction
This chapter provides information on the instruments used during the course of the study and
detail on how the experiments were carried out.

2.2 Research methodology

2.2.1 Protein preparation
The target protein, with a PDB code 6AWP was extracted from the protein data bank in a Co-
crystallised form. Using the Protein Preparation Wizard which is part of the Maestro software
protein preparation of the primary protein was carried out. The protein has a fluvoxamine ligand
at the binding site. After protein preparation, receptor grid generation was carried out. This was
done at the ligand binding site. The grid generation is responsible for the setting up of the grids
required for docking and includes options to stimulate some protein flexibility.

2.2.2 Determination of derivatives by QSAR

Possible derivatives were suggested using fluvoxamine as the lead compound. Inspection of the
protein-ligand interactions was done using the ligand protein-interaction diagram. The main lead
compound group responsible for protein-ligand interaction was considered. Overally the
derivatives were suggested on the basis of the results obtained from the visual inspections of a
pharmacophore model that was developed using 5 commercially available selective serotonin re-
uptake inhibitors.

22
Figure 5: Structure of fluvoxamine

Figure 6: Derivative 1

23
Figure 7: Derivative 2

Figure 8: Derivative 3

24
The other 3 derivatives were suggested using field based QSAR. This builds and applies a QSAR
model for a set of ligands based on forcefield and gaussian fields.

Figure 9: QSAR dialogue box with the ligand names and the activities.
A QSAR set was created and this contained test and training sets. Predicted activity and
prediction errors were calculated. After that a scatter plot was created for 30 of the selected
values.

25
Figure 10: Scatter plot for the predicted activity vs activity
The ligands with the highest predicted activity from the plotted graph were selected.

26
Figure 11: Derivative 4, structure suggested by fiel-based QSAR.

Figure 12: Derivative 5 from field based QSAR

27
Figure 13: Derivative 6 from field based QSAR

2.2.3 Ligand preparation

Ligand preparation was done for the suggested derivatives from QSAR. This was done using
LigPrep which is also part of the Maestro Schrodinger software.

2.2.4 Docking studies

Using the receptor grid generated binding site and the prepared ligands docking was carried out.
Fluvoxamine and four other commercially available SSRIs were docked with the prepared
primary protein. The suggested derivatives were also docked with the prepared primary protein.
Maestro Glide Docking was used for the docking processes. The results were captured. The data
obtained was analysed using the interactive forces such as the hydrogen bond energies. The
docking process was repeated 5 times for each interaction.

2.2.5 Metabolism calculations

Prediction of metabolism was done using Site of Metabolism software. This method involves
induced fit docking with cytochrome P450, which is a supper family of enzymes. The

28
cytochrome P450 enzymes facilitate the metabolism of drugs. Fluvoxamine and the derivatives
were tested for the sites of metabolism. The results were used to conclude on the metabolism of
the derivatives.

2.2.6 Toxicity tests

Using the QikProp software toxicity tests were carried out for fluvoxamine and the suggested
derivatives. The data obtained was analysed and compared. This data was used to conclude on
the toxicity of the derivatives.

2.3 Material and procedures

2.3.1 Materials
2.3.1.1 Hardware
 Personal Samsung laptop
 Manufacturer – Samsung
 Processor : Intel(R) Celeron(R) CPU B800
 System type: 64bit Operating system, x64 based processor (Windows 10)

2.3.1.2 Software
The maestro Schrodinger suite 11.2 model was used.
 Protein preparation was done using the Protein Preparation Wizard.
 Ligand preparation was done using LigPrep
 Pharmacophore hypothesis generated using Phase
 QSAR model created using 3D Field-Based QSAR
 Virtual screening done using Ligand-Based Virtual screening
 Docking tests were done using Glide Docking
 QikProp calculations were done using QikProp
 Sites of metabolism tests were calculated using the Site of Metabolism software

29
2.3.2 Procedures
Procedures from the Maestro user manuals were used.

2.3.2.1 Protein preparation

A cocrystallised structure of the ts3 human serotonin transporter complexed with fluvoxamine at
the binding site was downloaded. The PDB code 6AWP was obtained from the protein data bank
in the PDB format.
The cocrystallised protein was imported to the work space from the downloaded documents
folder. The options selected under import and process were assign bond orders, add hydrogens,
the creation of zero order bonds to metals, the creation of disulphide bonds, filling in the missing
side chains using prime, filling in the missing loops using prime and the deletion of waters. The
protein was the preprocessed. The minimise hydrogens of altered species option was selected and
protein was optimised. Lastly waters were removed and the protein was minimised. To release
strains from the protein structure it was refined. Finally, the Ramachandran plot was analysed.
(Protein preparation wizard, 2012)

30
Figure 14: Protein preparation dialogue box showing some of the options selected.

2.3.2.2 Ligand preparation

The lead compound ligand and the derivatives were drawn using the 2D sketcher and saved. The
sketch was then saved again in 3D format on the 3D workspace. To perform the LigPrep process,
LigPrep panel was opened from the application menu in the main window. The ligand was
imported to the workspace.

31
Figure 15: LigPrep dialogue box showing the selected parameters

Other parameters were left in the default format. The job name was entered and the job was
submitted by clicking run. The results were then obtained. The process was also repeated with
the derivatives. Some LigPrep settings were left in the default form that is the force field OPLS3
and at most 32 structures were generated per ligand. (LigPrep, 2009).

2.3.2.3 Pharmacophore Hypothesis

A pharmacophore model was created using the Develop pharmacophore model window. There
are 5 commercially available SSRIs that were included and pre-aligned as actives. These drug
molecules are called fluoxetine, fluvoxamine, paroxetine, sertaline and citalopram. The
Hypothesis settings have a ‘features’ tab that had the number of features in hypothesis set as 4 to
5. The features could be acceptor (A), donor (D), hydrophobic (H), positive ionic (P), negative
ionic (N) and aromatic ring (R).

32
Figure 16: Develop pharmacophore model dialogue box with the options selected.

2.3.2.4 3D Field-Based QASR

Derivatives were suggested on the basis of the inspection of the protein-ligand interaction
diagrams. They were also suggested using the field based QSAR. This applies a QSAR model
for a set of ligands, based on force field and gaussian fields.

Choose Tasks → QSAR → FieldBased QSAR.

The ligands were added by clicking the ‘add from file’ option. The Field based QSAR panel had
30 ligands selected which had already been prepared using the LigPrep task. The 30 ligands were
obtained from CHEMBL drug database which had all the ligands that inhibit the serotonin
transporter. The IC50 values for each drug were also provided and these were the values used for
the activity of each molecule. The 30 molecules had 18 actives and 12 inactives. Control click

33
was selected and the values in the column changed to test all the selected rows. Models were
built with the maximum number of PLS factors set to 1. The random training set percentage was
first set to 50% and a model was built. The random training set was then set to 20 % and a model
was built. The rest of the settings were left as default settings. Ok was then selected. The models
were then examined so that the models to be used could be determined. A scatter plot was used
to examine the process. A scatter plot of predicted activity vs activity was constructed by
clicking the scatter plot option and the main outliers were examined.

2.3.2.5 Ligand-Based Virtual Screening

Ligand-based virtual screening was the task used before suggesting derivatives. This is a task
that uses a pharmacophore hypothesis obtained from the ‘develop pharmacophore model’ task.

Choose Tasks → Ligand-Based virtual screening → ligand screening

Figure 17: Ligand-Based Virtual Screening dialogue box with sub tasks.

The ligand screening task was chosen and the appropriate options were selected in the dialogue
box. The CHEMBL database of ligands that inhibit the hSERT was screened using hypotheses
that were developed.

34
Figure 18: Phase Ligand Screening panel

2.3.2.6 Receptor grid generation

Using glide, receptor grid generation was carried out.

35
Figure 19: The receptor grid generation dialogue box.

The prepared fluvoxamine and the prepared hSERT were imported to the workspace and docking
calculations were processed. No docking constraints were set.

2.3.2.7 Docking
Using Glide, the ligand fluvoxamine was docked with the primary protein. Default settings were
used for the ligand, the program was not to dock or score ligands with more than 500 atoms and
100 rotatable bonds and Van Der Waals scaling factor of 0.80 and partial charge cutoff of was
0.15. Extra Precision (XP) was used. Ligand flexibility option was selected and also the
sampling of nitrogen inversions and ring conformations. Epik states penalties were added to the
docking score. At most 5 poses were to be generated and post docking minimizations were
allowed. The force field OPLS3 was used. Docking was done with all six derivatives. (Glide
docking, 2015)

2.3.2.8 Prediction of the Site of metabolism using cytochrome

P450 enzymes

36
Using the 2D sketcher the ligand molecule was drawn. It was the converted to a 3D structure.
The cytochrome P450 analysis was carried out. Calculations were set up from the P450 Site of
Metabolism Perform
Calculation panel, which was opened by choosing Tasks → ADME and Molecular Properties →
Structure Based P450 Site of Metabolism → Perform Calculation.

The ligands were taken from the workspace proper preparation of the ligands was done before
running the calculation.

Figure 20: p450 site of metabolism panel

3A4 isoform was used and the intrinsic reactivity was calculated. After selecting the start option,
the Start P450 Job dialog box opened, in which the name of the job was entered, the host was
chosen.

Figure 21: start P450 Job panel

37
The number of processors used for the Prime and the Glide stages of docking calculations were
set to 1. After the job was finished the results were examined. The results were imported to the
workspace by clicking import results (P450 site of metabolism, 2012).

2.3.2.9 Toxicity tests

The biochemical properties of the ligand and the derivatives such as absorption, distribution,
metabolism, excretion as well as the toxicity were predicted. QikProp predicts physically
significant descriptors and pharmaceutically appropriate properties of organic molecules. In
addition to predicting molecular properties, QikProp provides ranges for comparison purposes,
of a particular molecule’s properties with those of 95% of the known drugs
(QikProp, 2015).

Figure 22: The QikProp dialogue box

CHAPTER 3
3 RESULTS
3.1 Protein preparation

38
The protein obtained from the PDB was in the cocrystallised form. Cocrystallised protein refers
to a protein which is attached to a ligand. The results indicated in Figure 23 show the
Ramachandran plot for the prepared hSERT protein.

Figure 23: Ramachandran plot for prepared hSERT (6AWP)

3.2 Pharmacophore Hypothesis

From the 5 active ligands that were used to develop a pharmacophore hypothesis, 3 different
types of hypotheses were produced. The 3 were HHPR_1 (Hydrophobic, Hydrophobic, Positive
ionic, Aromatic Ring), AHHR_1 (Acceptor, Hydrophobic, Hydrophobic, Aromatic Ring) and
AHHR_2 (Acceptor, Hydrophobic, Hydrophobic, Aromatic Ring). The most fitting hypothesis
was HHPR.

39
Figure 24: HHPR hypothesis with different features displayed.

Figure 25: 5 SSRIs with hypothesis features displayed.

40
3.3 Determination of derivatives by QSAR
The Field-Based QSAR panel was opened and a QSAR model was built. There were QSAR
statistics that were obtained. Field Fractions were also obtained and the results were analysed.

Figure 26: The Field-Based QSAR panel with results

Scatter plots for the training set and test set were opened separately. The plots are for the model
that used 50% of the ligands as the training set and 50% of the ligands as the test set.

41
Figure 27: Scatter plot with the test set of the model.

42
Figure 28: Scatter plot with the training set of the model

After looking at the overall statistics, the predictions for both the training set and the test set were
looked at using the scatter plots. In the scatter plot dialogue box the number of partial least
squares (PLS) factors was set to 1. The training set was selected and a 45 degree line was also
selected. Nearly all the points were close to the line so the training set fit was generally good.
The same options were selected to view the scatter plot of the test set. The test set box was
selected instead of the training set box and other settings were the same as for the first scatter
plot. Nearly all the points were also close to the line so the test set fit was quite good.

The outlying points on the plot for ligands with largest error were picked and then placed on the
workspace. These outlying ligands were superimposed to check for similarity with ligands that
have a much smaller error. The outlying ligands of the scatter plot that appeared similar to
ligands that were seen near the 45 degree line were compared and displayed separately. The
differences between the two were seen more easily. Bonds of the ligands with the largest error in
the test set were modified and then their activities were predicted. The model showed no

43
difference resulting from the rotations of bonds and modifications which meant that the
orientations of certain rings were not relevant to the activity.

Table 1: QSAR statistics for 50% random training set.

# Factors SD R2 R2 Scramble Stability RMSE Pearson-r
1 19.5003 0.8285 0.7925 0.0265 59.38 -0.4193

Table 2: QSAR statistics for 20% random training set.

# Factors SD R2 R2 Scramble Stability RMSE Pearson-r
1 1.6980 0.9470 0.9208 0.202 54.47 -0.1663

3.4 Ligand-Based Virtual Screening

The QSAR models generated from the molecules along with the pharmacophore models were
used to suggest derivatives. LBVS method is based on approximation of calculated similarity
between the known active and the compounds come from databases. The filtering tools include
the drug and lead like properties, toxicity and the type of pose (bad or good) after docking.

The Phase ligand screening task was used. The ligands that were screened with the hypotheses
from the development of a hypothesis model were obtained from the CHEMBL database. The
database provided ligands that act as SSRIs. These were the ligands also used for the 3D Field-
Based QSAR. The hypothesis was added and the hypothesis settings were also considered. The
output tab in the hypothesis settings had the hits per molecule set as 1. The total number of hits
to be returned was set as 1000. The other settings were left as default and the job was run

44
Figure 29: Hits obtained for each pharamacophore hypothesis in project table.

3.5 Docking results

3.5.1 Fluvoxamine and hSERT docking results
Figure 30 shows the redocking results for the target protein 6AWP and
fluvoxamine for binding site.

45
Figure 30: hSERT binding site docked with fluvoxamine

3.5.2 Docking results for the suggested derivatives

Figure 31 to Figure 36 show the docking results for the target protein SERT and the six
suggested derivatives. Docking with each derivative was done at the site that was generated by
the receptor grid generation.

46
Figure 31: Derivative 1 and binding site protein-ligand interaction diagram

47
Figure 32: Derivative 2 and binding site protein-ligand interaction diagram

48
Figure 33: Derivative 3 and binding site protein-ligand interaction diagram

49
Figure 34: Derivative 4 and binding site protein-ligand interaction diagram

Figure 35: Derivative 5 and binding site protein-ligand interaction diagram

50
Figure 36: Derivative 6 and binding site protein-ligand interaction diagram

The docking results selected for the analysis of the interaction between ligands and the proteins
are:
 Total hydrogen bonding
 Total van der Waals forces

The bonding interactions for between hSERT and all the derivatives are as shown in Table 3

51
Table 3: Fluvoxamine and derivatives bonding interactions with the target protein
Ligand Total HBond Total evdw
Fluvoxamine -1.522 -34.648
Derivative 1 -0.900 -40.114
Derivative 2 -1.078 -34.442
Derivative 3 -1.600 -21.283
Derivative 4 -1.416 -33.650
Derivative 5 -1.657 -19.894
Derivative 6 -0.900 -34.789

3.6 P450 Metabolism tests

The following diagrams (Figure 37- 42) show the combined metabolism (reactive) scores for all
the suggested derivatives.

Figure 37: Reactive sites for derivative 1

52
Figure 38: Reactive sites for derivative 2

Figure 39: Reactive sites for derivative 3

53
Figure 40: Reactive sites for derivative 4

Figure 41: Reactive sites for derivative 5

54
Figure 42: Reactive sites for derivative 6

3.7 Toxicity tests using QikProp

Fluvoxamine and the suggested derivatives were characterized using QikProp.
Table 4: Ligand characterization using QikProp
Ligand # of polarizability dipole Mol_MW Donor CNS
stars HB
Fluvoxamine 0 28.867 4.867 318.338 2 1
Derivative 1 1 38.352 1.232 384.333 2 1
Derivative 2 0 33.284 2.982 302.391 2 1
Derivative 3 0 34.332 4.073 513.109 3.5 0
Derivative 4 2 29.180 5.227 314.214 3 1
Derivative 5 0 25.429 5.105 290.346 4 2
Derivative 6 1 30.960 3.738 310.240 2 2

55
CHAPTER 4
4 DISCUSSION
4.1 Ramachandran plot
Figure 23 shows the Ramachandran plot for the prepared hSERT. The plot generally shows the
positions of the amino acid residues within the protein structure. It is used to visualise the
energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in
a protein structure.
The Ramachandran plot has three sections that are:
 The red region which is the favoured region.
 The yellow region which is the allowed region.
 The white region which is the disallowed region.

The plot shows that most of the points are within the favoured red region. Many points are within
the yellow allowed region and 17 triangles which represent glycine are in the disallowed white
region.
Usually the plot should not have more than 1 amino acid that appears in the white disallowed
region for a well-prepared protein. Glycine is represented by the triangles, squares represent
proline and the circles represent all the other amino acids.
In Figure 23 a lot of the glycine amino acid residues are in the disallowed region. This deviation
from the usual could have been due to the facts that glycine residues have a very short side chain
compared to the other amino acids. As a result, glycine residues can be very flexible and their
torsion angles are not restricted to the “allowed regions” and are in fact all over the
Ramachandran plot. The flexibility is also why glycine is found in the loop regions of the protein
structure where the polypeptide chain has to make sharp turns. Therefore, the structure of the
protein tends to go back to its initial orientation after protein preparation because that is how it is
in nature. For the docking process to be successful the protein should be well prepared. Protein

56
preparation allows for the removal of loops and waters from the protein to insure docking
efficiency.

4.2 Docking results

4.2.1 The target protein hSERT docked with fluvoxamine
The primary protein hSERT was obtained in the co-crystallised form from the PDB.
In Figure 24 it is shown that there is an interaction between fluvoxamine and the target protein.
Purple arrows show the presence of hydrogen bonding between the protein and the drug and
there is a red arrow which shows a pi-cation interaction between the aromatic ring of TYR 95
and the amine of the drug at the binding site. At the binding site a blue line is present
surrounding the fluorine atoms. This shows the presence polar interactions. The green line
present is an indication of a pi-pi stacking interaction.

4.2.2 Docking with derivatives

I. Figure 31 shows the docking interactions between the binding site and derivative 1. There is
hydrogen bonding between the derivative and the binding site. The hydrogen bonding is taking
place between ASP 98, ALA 96, TYR95 the positively charged amine of the ligand. An
interaction of a pi-cation nature is also present at this binding site. There is a pi-pi stacking
interaction between an aromatic ring of the ligand and an aromatic ring of PHE 335. A blue line
surrounding the complex in binding site A shows polar interactions.

II. Derivative 2 is compatible with the binding site and docking was successfully done. There is
H-bonding between the amide of the ligand and the ASP98 residue. There is also a pi-cation
interaction between the methyl group of the amide and the TYR95 residue. A blue line is present
surrounding the fluorine atom of the derivative which means that there is a polar interaction.

III. In the protein-ligand interaction diagrams for derivative 3 docked to the target protein, There
is hydrogen bonding between the ASP98, ALA 96 and TYR 95 residues and the protonated
amine of the derivative. There is a pi-pi stacking interaction between the aromatic ring of the
ligand and an aromatic ring of the PHE 335 residue. An amine that is bonded to an aromatic ring

57
of the ligand forms a hydrogen bond with GLU 493. A small part of the ligand experiences polar
interactions where the line is blue.

IV. In the protein-ligand interaction diagram for derivative 4. The binding site has H-bonding
between the amine of the ligand and the ASP 98 and TYR 95 residues of the protein. Hydrogen
bonding is also present between the ligand and PHE 335. A pi-cation interaction is present
between an aromatic ring of the TYR 95 residue and the protonated amine of the ligand.

V. As for the protein-ligand interaction diagram of derivative 5, Hydrogen bonding is present

between a protonated amine of the ligand and ASP 98 of the protein. Another hydrogen bond is
also formed between TYR 95 and a different amine of the ligand.

VI. For derivative 6, there is hydrogen bonding between the protonated amine of the ligand and
the residues ALA 96 and ASP 98. There is a pi-pi stacking interaction between the aromatic ring
of the ligand and an aromatic ring of the TYR 95 residue. Fewer polar interactions are
experienced.

 Van Der Waals interactions

Data in Table 3 shows that for the binding site derivative 1 has the largest Van der Waals energy
which is indicated by a large negative value of -40.114 followed by derivative 6 which has a
value of -34.789, then fluvoxamine which has a value of -34.648. Derivative 2 which has a value
of -34.442, derivative 4 which has a value of -33.650, derivative 3 which has a value of -21.283
and lastly derivative 5 which has the lowest Van der Waals energy which is -19.894.

The major interactions used in ranking are the Van der Waals interactions. Ligands with the
highest Van der Waals bond more to the viral protein and therefore are considered as a better
substitute with respect to Van der Waals. The best derivatives considering Table 3 are, derivative
1 followed by derivative 6 then derivative 2.
However, since the mechanism is not known it is not clear if the Van der Waals forces are the
necessary requirement for activity of the ligand. It means that the derivatives with smaller values
of interaction cannot be simply ruled out as yet.

58
  H-bonds
The data in Table 3 shows that for binding site fluvoxamine has a H-bond energy value of -
1.522, derivative 1 has a value of -0.900, derivative 2 has a value of -1.078, derivative 3 has a
value of -1.600, derivative 4 has a value of -1.416, derivative 5 has a value of -1.657 and
derivative 6 has a value of -0.900.
Of all the suggested derivatives, derivative 5 has the largest bond energy value of -1.657,
derivative 1 has -0.900 and so does derivative 6 which makes them the lowest H-bond energy
values.

Of all the suggested derivatives, derivative 5 has the highest H-bond value of -1.657 and
derivatives 1 and 6 have the lowest H-bond value of -0.900. The hydrogen bond energy for
derivative 3 is -1.600 which is higher than that of fluvoxamine meaning it to could be used for
inhibition.
The derivative with the highest H-bond value is considered to be the best as this will bind more
strongly to the target protein active site and therefore prevent the transportation of serotonin. If
H-bonding is critical for activity, then derivative 5 would be the most effective ligand.

4.3 Metabolism tests

Combined Scores
Cytochrome P450 enzymes are required for the elimination of foreign compounds like drugs and
toxins from the body. This is important for the effective elimination of the compounds by the
kidneys and the liver. Combined scores showed the overall sites of metabolism of the
fluvoxamine molecule and the derivatives designed.
Different sizes and colours are used to show differences in the levels of reactivity. The circles
show both the overall metabolism and the intrinsic reactivity. In this study green circles can be
observed in the results. The different radius is directly proportional to the metabolism score. The
ability of a drug to be metabolised easily shows that it is less toxic. If the drug is not easily
metabolised it stays within the system and therefore is said to be toxic.

59
Derivative 2, 4 and 6 have more green circles and these are larger in radius compared to the other
derivatives. This shows that they can be easily metabolised.
Derivative 1 and derivative 5 only have 3 sites of metabolism. This shows that they are not easily
metabolised and hence can be very toxic.
Derivative 3 has 2 sites of metabolism compared to derivative 4 and 5.

4.4 Toxicity Tests

QikProp was used to test for the toxicity of the derivatives and the results are shown in Table 4.

I. Number of stars
Derivative 4 has the highest number of stars which is 2. Derivatives 1 and 6 have 1 star and
the remaining derivatives 2, 3 and 5 have 0 stars. The number of stars is directly linked to
the toxicity of a compound. An increase in the number of stars shows an increase in toxicity.
The allowed number of stars is in the range 0-5. The results in Table 4 show that all the
derivatives have their number of stars within the allowed range. Derivatives 2, 3 and 5 are the
least toxic of all the derivatives.

II. Polarizability
Fluvoxamine has a polarizability value of 28.867. Comparing the values of all the suggested
derivatives in Table 4, derivative 1 has the highest value which is 38.352 and derivative 5 has
the lowest value which is 25.429. Polarizability is a measure of the response of a molecule to
an electric field. The higher the polarizability value the higher the degree of interaction with
its target and the higher the absorptivity. The recommended range is between 13-70. The
polarizability values for all the derivatives are within the recommended range. Derivative 1 is
the most easily polarizable one because of the high value of 38.352.

III. Dipole
Fluvoxamine has a dipole value of 4.867. Derivative 4 has the highest dipole value which is
5.227. Derivative 1 has the lowest dipole value which is 1.232. A larger dipole moment
shows that a compound has good reactivity properties. The recommended range for dipole is
between 1.0-12.5. Molecules that have 0 dipole moment are non-polar whilst molecules with
60
dipole values within the range are polar. All the dipole values for the suggested derivatives
are within the recommended range. Derivative 1 has a very low dipole moment compared to
the other derivatives. This is a sign of lower reactivity. Derivative 4 has the largest dipole
value, followed by derivative 5. This shows the ability of the two having good interactions
with the target protein.

IV. Molecular weight

This refers to the molecular weight of the molecule. Fluvoxamine has a molecular weight of
318.338. Analysis of the derivatives shows that derivative 3 has the largest molecular weight
of 513.109 whilst derivative 5 has the lowest molecular weight of 290.346 this might be due
to the reduced number of rings in the structure compared to the other molecules. The
recommended range is between 130-725. From the results obtained all the values are within
the range. Smaller drugs are more effective therefore derivative 5 would be suitable for use
as a drug when considering molecular weight.
V. Donor HB
Fluvoxamine has 2 donor HB. Derivative 5 has the largest amount of donor HB which is 5.
Derivative 2 and 3 both have the lowest number of donor HB which is 1.
The donor hydrogen bond is the number of H-bonds that would be donated by the solute to
water. The recommended range is between 0-6. The larger the value the better, as this allows
for the easy transportation of the drug.

VI. CNS
It is the predicted central nervous system activity. The scale used is +2 active and -2 inactive.
The CNS is related to cases of addiction to drugs. Fluvoxamine, Derivative 1, Derivative 2
and Derivative 4 have a CNS value of 1 which means they are active but not as much as
Derivative 5 and 6. Derivatives 5 and 6 have a CNS value of 2 therefore they are the most
active. Derivative 3 has a CNS value of 0 which means it is the least active.

61
CHAPTER 5
5. CONCLUSION
The Quantitative structure activity relationship is an important way to analyse molecules.
Possible derivatives can be discovered using this method. Examining the scaffold of the
molecules with that bind strongly to the target protein is an essential part of the determinating
process. Computational modeling was used to design derivatives that target the serotonin
transporter.
Fluvoxamine is a good drug that binds strongly but it causes undesirables side effects that
include nausea, dry mouth, dizziness, agitation, anorexia, diarrhoea, constipation, sweating,
tremor and sexual dysfunction.

The results obtained are promising. From the analysis of the results obtained from the project,
derivative 3 could be the most effective drug derivative.
Derivative 3 can be used as a drug that targets the serotonin transporter with respect to
 Total hydrogen bonding energy value for derivative 3 means it forms stronger bonds
compared to fluvoxamine.
 The QikProp toxicity values for derivative 3 are within the recommended range and are
high enough for efficiency.
 Derivative 3 also had a low number of stars, that is 0.
 The polarizability value is higher than that of the fluvoxamine which is a positive
attribute.
 The CNS value is 0 which means it is the least addictive derivative.
 The donor HB result reveals that it would be easier to transport this drug in the body
compared to other derivatives.

Derivative 5 is the second best derivative as it also has advantages including the number of stars
being 0, polarizability, dipole, molecular weight and a CNS value all being within the
recommended range. This derivative has the highest hydrogen bonding strength. The dipole
value is higher than that of fluvoxamine which is a good thing. This derivative is the smallest

62
molecule if one looks at the molecular weight meaning it could be an effective drug. The
metabolism test shows that the drug would be fairly easy to metabolise. This drug would be the
easiest to transport in the body when considering the donor HB value.

Derivative 2 is the next promising derivative after the other two mentioned above considering all
the results obtained which are within the acceptable range. These results include the number of
stars (0), dipole, polarizability, CNS and donor HB. The polarizability is higher than that of
fluvoxamine and the molecular weight is smaller than that of fluvoxamine too. This derivative
has 7 sites of metabolism therefore it is the easiest to metabolise.

Derivative 4 has very good results however the number of stars is higher than the rest meaning it
is the most toxic. This derivative and the other derivatives can be further modified to make them
more suitable.
Therefore, the derivatives that are most promising are 3, 5 and 2.

CHAPTER 6
6. RECOMMENDATIONS

It is recommended that derivatives 2, 3 and 5 be synthesised and tested for efficacy. If the results
are negative then these 3 can also be used as lead compounds for further modification, by
computer modeling.
Further studies can be done on the binding mechanism involving other receptors that are the
target for other types of antidepressants. If the derivatives bind strongly to the other receptors
that are targeted when treating other mental disorders then this will make the drugs even more
beneficial.

63
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