QSAR studies

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Assignment

Structure Activity Relationship of a

Novel Anti malarial Agent

Submitted for the partial fulfilment of course

Advanced Medicinal Chemistry

PHA G621

Submitted by

L Naga Rajiv

2014H147206P

Under the supervision of

Dr. Hemant R Jadhav

Associate Professor

Department of Pharmacy

BITS Pilani


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Contents

1.0 Introduction ......................................................................................................................... 1

2.0 SAR studies on a novel antimalarial agent .......................................................................... 3

3.0 Conclusion ......................................................................................................................... 13

4.0 Acknowledgements ............................................................................................................ 13

5.0 References .......................................................................................................................... 14


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1.0Introduction

Discovery of new drugs initially was largely based on trial and error basis. Medicinal chemistsused to synthesize random molecules and evaluate them. Serendipity also contributed a lot to

drug discovery. But as Medicinal chemistry evolved, along with other sciences like biological

sciences, computer science, Physics etc., drug design and discovery became more and more

based on some rational. However, the time, energy and other resources which are involved in

drug design is still high. Application of Computer science in drug design greatly reduced this

effort. The probability that a molecule being designed will actually be launched in the market

was previously very low, but the in-silico methods have surely contributed in increasing this

probability.

There are several in-silico methods which have been practiced and applied till date, like 2D

QSAR, 3D QSAR, Docking, prediction of ADME properties etc. However, one of the first

applications is QSAR, where mathematical models were developed to predict the activity of a

compound of similar structure. Even before QSAR models were developed, medicinal chemists

studied the Structure Activity Relationships (SAR). As the name suggests, in SAR, the

structure of a molecule is related to its activity. That is, the influence of specific moieties in amolecule on its activity is studied, so that this knowledge can be applied to design and

synthesize molecules of improved activity but of the same series.

SAR is based on the principle similar structures-similar effects. QSAR also has the same

principle, but it uses parameters called descriptors to describe the potency. To do an SAR study,

it just needs the structures of a series of compounds and their activity. However, QSAR study

needs some knowledge of statistics. QSAR models correlate in vivo biological activity to

physicochemical properties of compounds while SARs attempt to explain chemical moieties

or structural features that contribute to or are detrimental to the biological activity.


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SAR involves making certain changes to the lead molecule like changing the number of

methylene groups, increasing or decreasing the degree of unsaturation, introducing or removing

ring systems, halogens etc. These changes in turn effect the activity of the molecule which is

studied. For example, increasing the number of methylene groups increases the lipophilicity

which in turns increases activity. Increasing the degree of unsaturation will increase rigidity.

Substituting a methyl group with naphthyl can create steric hindrance at the site of action. Such

changes and the effect on activity are studied in SAR.

This work presents in brief the SAR studies done by a group of researchers in Germany. The

aim was this work was to optimize a lead which was found to be active against multi-drug

resistant Plasmodium falciparum strains. The work was published in 6 parts, all of which have

been summarized step-by-step in this report.


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2.0SAR studies on a novel antimalarial agent

Malaria is one of the most threatening tropical diseases causing between 1.5 and 2.7 million

fatal cases annually. It is more prominent in children and women, particularly in Africa. Thisis largely due to the emergence of resistance of Plasmodium falciparum strains. The researchers

therefore found an urgent need for new agents active against multi-drug resistant plasmodium

strains.

The researchers chose a library of 61 compounds of different structural classes from various

literature studies. They were assayed for their inhibitory activity against Plasmodium

falciparum. They found that 47 of the compounds showed activity at 100m. But only 7 of

them retained activity at 10 M. The inhibitory activity of the 61 compounds were found as

shown in Table 1.

Compunds were evaluated for their inhibitory activity against intraerythrocytic forms of

Plasmmodium falcioarum strains Dd2 and 3D7 using a semi-automated microdilution assay.

The growth of the parasite was monitored thorugh incorporation of tritium labelled

hypoxanthine. All values were estimated to be correct within 30%. This procedure was

adopted for all the assays used in this study.

Of the 61 compounds, the compound labelled 7p showed best activity and was chosen as the

lead.

Other than its activity, another reason why this compound was chosen as lead because it allows

a variety modifications. The first step after lead identification was to find the exact inhibitory

concentration of compound 7p.


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Next some dramatic modifications were done with compound 7p, as illustrated above. Each of

the three derivatives lack one of the substituents on the central benzene core. It was found that

all the three modifications resulted in marked decrease of activity, which means that all the

three substituents are necessary for activity. As all three substituents are necessary for activity,

all three are open for modifications to possible improve activity.

In the first set of modifications, the acylamino substituent at 5 position was replaced with some

substituted cinnamic acid derivatives and tested for activity. It was found that 4-phenyl and 4-

benzyloxy derivatives (11a and 11c) showed improved activity, while others didnt. The exact

values of inhibitory concentration of 11a and 11c were found out to be 5 times lower than that

of 7p. This improvement upon structural modifications demonstrates the potential for further

development.

At this stage, the researchers were concerned if the activity is due to cytotoxicity. So,

compounds 7p and 11a were assayed against cell lines for their potential cytotoxic effects. It

was found out that 7p was indeed cytotoxic whereas the 5-fold better compound 11a didnt

show any cytotoxicity till 300 times the concentration in which it showed activity! This made

the researchers to work on cinnamic acid derivatives.


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So considering the cytotoxic effects, the researchers chose to work on cinnamic acid derivatives

as one of the substituents on the central benzene core, although it was showed slightly reduces

activity. In the second series of modifications, they chose to study the effect of substituents in

the para position of cinnamic acid derivative. So the lead for this series is as shown below.

R:H corresponds to compound 11a. 18 substituents were tried on the para position and labelled

3a-r. The activity was assayed as described earlier. The values are as under:


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SAR: Substituting the proton in para position with electron withdrawing groups like NO2,

CF3, -Cl, -Br etc. did not improve the activity. But substituting with methyl and methoxy

groups improved the activity. So, the researchers focused on 4-alkyl and 4-alkoxy derivatives.

The 4-alkyl series showed no improvement in activity compared to 4-methyl. But the alkoxy

series showed improvement, with the peak activity shown by propoxy substitution. Further

lengthening of the alkoxy chain decreased activity.

Substitution of 3-phenylpropionyl moiety of the lead structure with 4-propoxycinnamic acid

residue resulted in better activity.

In the next set of modifications, published as part 3 of their work, the researchers replaced the

tolylacetyl residue at the 2-amino group by several acyl substituents. 11 substituents were

synthesized, labelled 6a-l, and assayed for antimalarial activity as described earlier. The initial


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compound of this series 3q is same as 6e. It has a tolyl group attached to the acetyl moiety and

an IC50 value of 340nM.

The modifications started with removal of methyl group in toluene. The activity decreased

significantly to 9000nM. Introduction of bulky groups also improve the activity. But a benzyl


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group in place of phenyl improved the activity. This shows that the methyl group is necessary

for better activity. Next, ortho substitution was tried in place of para and again the activity

decreased, suggesting that only para substitution will lead to better activity. A series

electronegative substitutions were tried. Strangely it was observed that these electronegative

groups (-Cl, -Br) had similar activity as that ofCH3 substitution although it is electropositive.

In fact, -CF3 in para position improved the activity 3-fold (120nM).

The conclusion of this part was that acyl substituent does play an important role in anti-malarial

activity.

i. A methylene attached to carbonyl carbon is necessary for activity.

ii. Substitution of the benzyl group should be at para position only.

iii.

The substituent must of the size comparable to methyl.

iv.

CF3 substitution at para position gives best activity

In the next series of experiments, published as Part 4 by the researchers, the authors replaced

the 4-propoxy phenyl residue of the cinnamoyl moiety by biaryl structure consisting of a

terminal aryl residue and a central 2-furyl ring.

The 4-propoxy phenyl residue had an IC50 value of 340nM. The modifications done and the

found activities are shown in the following table.

The phenylfurylacrolyl derivative inhibited with an IC50 value of 415nM. This is comparable

to that of the lead (340nM). Thus, there is a scope of some substituents leading to a much better

activity profile.


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Introduction of bulky group in place of phenyl resulted in a drastic decrease of activity. This

suggests steric hinderance. However, introduction of methyl group in para position improved

the activity 3-fold (120nM). Increasing the carbon chain length to 2 and introduction of double

bond improved the activity further. However, further increase in length decreased the activity.

Alkoxy substitutions and halogens in para position also, did not show activity better than their

alkyl counterparts. Strangely, para nitro substitution showed better activity (75nM) than the

alkyl substituents, although it is polar. Repositioning of the substitution to ortho or meta

positions decreased the activity.

The conclusions of this part are:

i. The aryl group cannot be too bulky

ii.

Substitution must be at para position only.

iii.

Non-polar moieties in para position show better activity than polar moieties, with the

exception of nitro substitution, which turned out to be the best.

In part 5 of their work, the researchers repeated their work done in part 3, but by applying the

conclusions of part 4 of their work. As found in part 3, the conclusion were:

i.

A methylene attached to carbonyl carbon is necessary for activity.

ii.

Substitution of the benzyl group should be at para position only.iii. The substituent must of the size comparable to methyl.

iv. CF3 substitution at para position gives best activity

The advantage ofCF3 group is that it lacks the metabolic instability that might be associated

with the methyl group.


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In the last series of experiments, the researchers repeated their work published in part 5, but

with some different substitutions. However the values were compared with the compound

which gave the best activity in part 5, i.e., the one with nitro group in para substitution.


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The trifluoromethyl and the acetyl group were identified as equipotent replacements of the

terminal nitro group in this type of anti-malarial agents. Furthermore, incorporation of amethylsulfonyl moiety led to an inhibitor twice as active as the lead structure 1. In addition,

this inhibitor lacks the nitro group of lead structure 1 potentially associated with an

unfavourable toxicological profile.


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3.0Conclusion

The researchers optimized the lead structure obtained by assay of 63 compunds and proposed

the following structure.

The SAR of this compound is as follows:

i. Both the amides and benzoyl moieties are required as substituents to the central

benzene core.

ii.

At the 5thposition, a CH2=CH2 is required to connect the biaryl moiety. Saturating

this bond will decrease the activity.

iii. The substitution of terminal phenyl ring of the biaryl moiety has to be in para position

only. Ortho and meta substitutions greatly decrease the activity.

iv. The para substitution has to be electron donating, with the exceptions ofNO2 and

SO2CH3.

v. The benzoyl substitution at position 1 is best unsubstituted.

vi. At position 2, benzyl is required to be attached to amide bond. Phenyl in place of

benzyl will result in loss of activity.

vii.

Substitution of this phenyl ring must be in para position only.

viii.

The size of the para substitution must be of size comparable to methyl.

4.0Acknowledgements

The author thanks Prof. Martin Schlitzer, Department of Pharmacy, University of Marburg,

Germany for providing the series of articles which they published. This work is based on the 6

publications provided by him.


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