Sagar alone qsar studies of saponin analogues for anticancer activity
GUIDED BY- Dr. S. L. DEORE.
Govt. College Of Pharmacy,
PRESENTED BY – Mr. SAGAR S. ALONE.
(Pharmacognosy & Phytochemistry)
Review of Literature
Aim & Objective
Need & Scope
Plan of Work
Result & Discussion
2Government College Of Pharmacy, Amravati.2August 2013
QSAR is the mathematical relationship between the chemical
structure (Describe as Descriptors) and Biological activity.
Physicochemical properties or descriptors are expressed by
One can form a mathematical relationship, or quantitative
structure-activity relationship between the two.
The mathematical equation can then be used to predict the
biological response of other chemical structures or analogues.
Biological Activity = ƒ (Physicochemical properties and /or
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4) Drug metabolism and
5) Inhibitor constant
8) Blood brain barrier
11) Receptor binding
1) Boiling point
3) Dielectric constant
4) Diffusion coefficient
5) Dissociation constant
6) Melting point
Government College Of Pharmacy, Amravati. 42August 2013
Carcinogens can be present in food ,water, air, in
chemicals and sunlight that people are exposed to.
In 1996 there were 10 million new cancer cases
worldwide and six million deaths attributed to cancer.
In 2020 there are predicted to be 20 million new cases
and 12 million deaths.
A globalization of unhealthy lifestyles, particularly
cigarette smoking and the adoption of many features of
the modern Western diet (high fat, low fibre content)
will increase cancer incidence.
5Government College Of Pharmacy, Amravati.2August 2013
Soap-like foaming when shaken in aqueous solutions .
Two kinds of saponins are recognized – The steroidal and The pentacyclic
triterpenoid types .
More than half of terrestrial plants may contain saponins.
Diversified pharmacological effects (haemolytic, cytotoxic, antitumor, anti-
inflammatory, molluscicidal .
Saponins have been shown to induce both cycle arrest and apoptosis within
cancerous cells .
Isolation of saponins from plant extracts is often a long and fastidious process
involving many purification steps and usually only small amounts of products
are obtained in a pure and homogeneous form .
Therefore, chemical synthesis or semisynthesis of saponin analogue appear to be
a rational way to gain access to adequate amounts of saponins in order to
promote further pharmaceutical studies .
6Government College Of Pharmacy, Amravati.2August 2013
Quantifying the relationship between structure and
Biological Activity data provides an understanding of the
effect of structure on activity.
Potential to make predictions leading to the synthesis of
Help to understand interactions between functional
groups in the molecules of greatest activity, with those of
7Government College Of Pharmacy, Amravati.2August 2013
Modern drug design & drug discovery.
Prediction of biological activity.
Study of different physicochemical properties affecting
Prediction of Chemical toxicity.
To study Mechanism of action.
Prediction of molecular properties.
ADME properties prediction.
8Government College Of Pharmacy, Amravati.2August 2013
Siddiqi Mohammad Imran,CDRI Lucknow have been reported which included following
aspects of molecular modeling containing, a technique for the investigation of molecular
structures and Activities/properties using computational chemistry & biology and graphical
visualization techniques in order to provide a plausible 3-D representation .
Bang Seong-Cheol, et al, (2005) have been reported antitumor Activity of Pulsatilla koreana
Saponins and Their Structure–Activity Relationship he mentioned Seventeen saponins
isolated from the root of Pulsatilla koreana were examined for their in vitro cytotoxic
activity against the human solid cancer cell lines .
Yan L. L et al. (2009) have been reported invitro and in vivo anticancer activity of steroid
saponins of Paris Polyphylla Var. Yunnanensis, to confirm the anticancer activity of steroid
saponins isolated from the rhizome of Paris polyphylla var. yunnanensis and evaluate the
structure-activity relationships of these steroid saponins in vitro and in vivo .
Malik Adeel et al. (2006) have been reported Databases and QSAR for Cancer Research in
this review, he take a survey of bioinformatics databases and quantitative structure-activity
relationship studies reported in published literature .
9Government College Of Pharmacy, Amravati.2August 2013
Gauthier Charles et al. (2009) have been investigated recent Progress in the Synthesis of
Naturally Occurring Triterpenoid Saponins and describe recently reported semi- and total
syntheses of naturally occurring triterpenoid saponins .
Matthew J. et al, (2009) have been reported Structural analogues of diosgenyl saponins
synthesis and anticancer activity and he studied Saponins display various biological
activities including anti-tumor activity .
Chanin Nantasenamat et al (2009) have been reported a practical overview of quantitative
structure-activity relationship in this review article author describes history and
development of QSAR model and study QSAR modeling pertains to the construction of
predictive models of biological activities as a function of structural and molecular
information of a compound library .
Dholwani K. K et al (2008) have been reported on plant derived natural product and their
analogue with antitumor activity” and describes traditional medicine including Chinese
herbal formulation can serve as a potential new drugs and initial research focus on the
isolation of bioactive lead compounds .
Tsubuki Masayoshi et al. (2008) has been reported a new synthesis of potent antitumor
saponin OSW-1 Via Witting rearrangement and he work on OSW-1 and its analogues .
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GovernmentCollege Of Pharmacy,Amravati. 11
From the literature  I have selected 17 saponin analogues for QSAR studies
GovernmentCollege Of Pharmacy,Amravati. 122August 2013
To review saponin analogues having anticancer
To select training and test set of saponin analogues.
To perform 2D QSAR of selected sets.
To relate different descriptor parameters to saponin
To find out specific descriptors affecting anticancer
To elaborate the role of structural changes in saponin
analogues for Anticancer activity.
Finally to predict the structural changes which tends to
increses anticancer activity.
13Government College Of Pharmacy, Amravati.2August 2013
Medical oncology is an important frontier which has gained attention from various research
The mortality rate of cancer patients is usually high (65%).
Primarily there are three treatment methods for cancer: 
Invasive methods - Surgical removal of cancer tissue.
Irradiation methods - Use of high energy radiation.
Chemotherapy - Administration of drugs.
To control cancer from mankind we should discover or make new compound by using QSAR
before going work into actual wet laboratory.
QSAR techniques will continue to make a valuable contribution to the computer-assisted
analysis of structure-bioactivity relationships.
Hence taking into consideration the part of present research which we are performing to do
QSAR study of different saponin analogues having anticancer activity by using Modern
computational technology (QSAR).
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1) Literature survey.
2) Selection of saponin analogues for anticancer activity.
3) Study of descriptors.
4) Design and making structure of saponin analogues.
5) QSAR studies.
6) Result and Discussion.
15Government College Of Pharmacy, Amravati.2August 2013
17 saponins molecules isolated from the Pulsatilla koreana as anticancer agent are
taken from literature for QSAR analysis. Pulsatilla koreana belongs to the family
Ranunculaceae and is an endemic species in Korea containing 17 saponins in which
eight lupane-type (1, 3, 5, 7, 9, 11, 13, 15) and nine oleanane-type (2, 4, 6, 8, 10, 12, 14,
16, 17), isolated from P. koreana roots. Molecule sketching- sketched by using 2D draw
application of VLife MDS (Molecular Design Suite).
2D to 3D- by using VLife MDS (Molecular Design Suite) TM 3.5 software supplied by
VLife Sciences Technologies Pvt. Ltd., Pune, India.
Batch optimization & energy minimization - Batch optimization by taking 100000 cycle
Statistical method- Multiple linear regression (MLR)
QSAR models were generated by a training set of 11 molecules for each model and a
test set of 6 molecules
Training set of molecules (3,4,6,7,11,12,13,14,15,16,17)
Test set of molecules (1,2,5,8,9,10)
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2D Physicochemical descriptors including Individual, Chi chain, Path count, Chiv,
Element count and Kappa categories and Alignment independent including topological
structure descriptors were calculated for QSAR analysis using Vlife MDS software.
Multiple linear regression method is used to generate QSAR equation.
For validating the quality of the models, Selection of molecules in the training set and
test is a key and important feature of any QSAR model.
Therefore, the care was taken in such a way that biological activities of all compounds
in test lie within the maximum and minimum value range of biological activities of
training set of compounds.
The Uni-Column Statistics of test and training sets further reflected the correct selection
of test and training sets. A Uni-Column statistics for training set and test set were
generated to check correctness of selection criteria for trainings and test set molecules.
MLR is a statistical method for creating linear relationship between a dependent
variable Y (ED50) and independent variable X (2D descriptors).
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Uni-column statistics of the training and test sets for QSAR models
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Cell line Training/Test
Average Max Min Std. Dev Sum
A-549 Training set 94.1109 300.000 4.2400 114.9137 1035.2200
Test set 131.5417 300.000 2.5600 138.64.97 789.2500
SK-OV-3 Training set 88.6536 300.0000 3.9500 112.7344 975.1900
Test set 127.3850 300.0000 2.3100 139.3976 764.3100
SK-MEL-2 Training set 94.0000 300.0000 3.0400 116.5289 1034.0000
Test set 136.1183 300.0000 1.5700 139.8473 816.7100
HCT-15 Training set 96.4845 300.0000 5.5000 114.9111 1061.3300
Test set 138.8817 300.0000 8.3600 138.1815 833.2900
Multiple linear Regression equation takes the form
Y = b1 x1 + b2 x2 + b3 x3 + c
Where- Y is dependent variable, ‘b’s are regression coefficients for corresponding ‘x’s
(independent variable), ‘c’ is a regression constant or intercept [6, 7].
Statistics of the Models for 4 different cancer cell lines
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Statistics A-549 SK-OV-3 SK-MEL-2 HCT-15
N 11 11 11 11
Degree of freedom 8 8 8 8
r2 0.9281 0.9554 0.9160 0.9203
q2 0.8691 0.9187 0.8285 0.8357
F test 51.6079 85.7357 43.6084 46.1887
r2 se 34.4579 26.6109 37.7639 36.2697
q2 se 46.4909 35.9315 53.9485 52.0702
pred_r2 0.9538 0.9686 0.8950 0.8899
pred_r2se 31.0692 25.8051 47.7110 48.3659
N - Number of molecules, K - Number of descriptors in a model,
DOF - Degree of freedom (higher is better),
r2 - Coefficient of determination (> 0.7),
q2 - Cross-validated r (>0.5),
pred_r2 - r for external test set (>0.5),
F-test - F-test for statistical significance of the model (higher is better, for same set of descriptors and compounds),
r2_Se, q2_se, pred_r2_se = error for r2, q2, pred_r2 respectively.
Here generate four QSAR Equation which is a Mathematical relationship between
Physicochemical properties (Descriptors) & Biological activity
ED50= + 55.3309( 6.5096) T_2_C_7 + 23.9224( 8.9012) 6ChainCount - 616.7280
ED50= + 53.2371( 0.5713) T_2_C_7 + 553.1007( 130.2520) chi6chain -612.2515
ED50 = + 53.9707( 7.2274) T_2_C_7 + 7.3979( 2.5587) T_O_O_5 - 493.8088
ED50 = + 53.2728( 6.9414) T_2_C_7 + 7.3583( 2.4574) T_O_O_5 - 484.2732
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9 PK09 135.28 104.038 114.32 93.2087 165.54 112.479 171.29 114.68
10 PK10 2.56 17.2984 2.31 14.9598 1.57 4.53761 8.36 8.13401
11 PK11 43.64 80.1154 38.90 68.1195 39.67 90.2853 49.04 92.6047
12 PK12 13.49 -6.624 13.71 -10.1294 14.12 -17.6561 14.17 -13.9409
13 PK13 155.32 104.038 124.12 93.2087 145.68 127.275 138.73 129.396
14 PK14 4.24 17.2984 3.95 14.9598 3.47 19.3334 5.50 22.8506
15 PK15 41.35 80.1154 38.91 68.1195 40.02 75.4896 40.86 77.8882
16 PK16 9.58 -6.624 11.39 -10.1294 10.37 -32.4518 12.74 -28.6574
17 PK17 10.73 41.2208 10.66 40.049 9.81 48.925 14.09 52.2837
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From the following data we can conclude that first 4 analogues has no anticancer
activity because all 4 has sugar ester group attached to C-28.
But all analogues from 5 to 17 has free carboxylic acid group at C-28 position and
showing anticancer activity.
Graphical representation & comparison of Actual vs. Predicted activity for
training and test set of 4 cancer cell lines
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GovernmentCollege Of Pharmacy,Amravati. 242August 2013
Fitness plot of 4 model for 4 different cancer cell lines
Government College Of Pharmacy, Amravati. 25
Contribution plot of 4 model for 4 different cancer cell lines showing
which descriptors are responsible for anticancer activity
Government College Of Pharmacy, Amravati.
SK-MEL-2 HCT 15
I have evaluated a series of Pulsatilla koreana saponin analogues by doing 2D QSAR with the help of
different descriptors in order to determine the better structural characteristics and to study different
descriptors responsible for anticancer activity.
From the QSAR studies it was found that the Alignment Independent category is most responsible for all 4
types of cancer cell lines which includes
T_2_C_7: This is the count of No. of double bounded atoms (i.e. - Any double bonded atoms, T-2)
separated from carbon atom by 7 bonds in a molecule.
T_O_O_5: This is the count of No. of oxygen atoms (Single double or triple bounded) separated from
other other oxygen by 5 bond distance in a molecule.
6chain count: These descriptors signify total numbers of six membered rings in a compound.
Chi6chain: These descriptors signify a retention index for six membered rings.
It was found that all descriptors have positive correlation with the anticancer activity.
Hence increase in all descriptor values will help to increase the anticancer activity of Pulsatilla koreana
saponins analogues for anticancer activity.
Hence, the model proposed in this work is useful and can be employed to design new saponin derivative of
Pulsatilla koreana as most active anticancer agent.
GovernmentCollege Of Pharmacy,Amravati. 272August 2013
To determine the better structural characteristics
and to study different descriptors (3D
Descriptors) responsible for anticancer activity
(3D QSAR Study).
To identify all other cancer cell lines to which
Pulsatilla koreana saponin analogues exhibits its
To design new saponin derivative of Pulsatilla
koreana as most active anticancer agent.
GovernmentCollege Of Pharmacy,Amravati. 282August 2013
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THANK YOU 31GovernmentCollege Of Pharmacy,Amravati.2August 2013