Studying the Inhibition Activity of Rutin on Xenobiotic Inducible Lambda-Class Glutathione Transferases (GSTLs) along with its 2d- and 3d Pharmacophore Pattern


K. Soujanya*, C. Chandra Shekar

Department of Chemistry, CMR College of Engineering & Technology, Hyderabad.

*Corresponding Author E-mail:



Drug design, commonly known as rational drug design, is the novel process to develop new medications based on existing knowledge of the required biological target. The term drug design can be misleading by taking its literal meaning. It is a design of a small molecule that will bind tightly to its target. This present work on the anti-oxidant activity of rutin by inhibiting the normal functioning of lambda-class GSTLs of specific xenobiotic inducible GSTLs, TaGSTL1 has been observed that it firmly bind the rutin. The pharmacophore pattern and 2D- and 3D- descriptors of rutin were derived and analyzed to determine the structural features that govern the anti-oxidant activity. The Physico-chemical parameters of rutin were also studied and presented in this article.


KEYWORDS: Xenobiotic, Rutin, Pharmacophore, Physico-chemical properties, Bio-flavonoids.




The drug is commonly a small organic molecule that activates or inhibits the function of a biomolecule such as a protein, which results in a therapeutic benefit to the patient1-2. In the most basic sense, drug design involves the design of small molecules that are complementary in shape and charge to the biomolecular target with which they interact and bind it. Drug design, in general, relies on computer modeling techniques regarded as computer-aided drug design3-6. Lastly, drug design that depends on the knowledge of the three-dimensional structure of the biomolecular target is known as structure-based drug design.


Computer modeling techniques for the prediction of binding affinity are successful to a greater extent. Still, properties like bioavailability, metabolic half-life, lack of side effects, etc., must be optimized before a ligand can become a safe and efficient drug. These other features were found to be difficult to optimize using current drug design techniques7-10.


A drug target is a molecule which involves in a metabolic pathway unique to the pathology of a microbial pathogen11-12. There are many approaches that attempt to attenuate the functioning of the pathway in the diseased state by causing a crucial molecule to stop functioning. Drugs can be designed which binds to the active region and inhibit the key molecule. There is another approach to enhance the normal pathway by promoting specific molecules that may have been affected in the diseased state. The design of Drug molecules is such a way that they must not affect off-target or anti-target molecules13. Many times there can be interactions between off-target molecules that leads to undesirable effects. Sequence homology, a method frequently used to identify such risks14-16. There are two types of drug design; the first is ligand-based drug design, the second, structure-based drug design.


Ligand-based drug design (or indirect drug design) depends on molecules that bind to the biological target of interest17. The molecules are used to derive a pharmacophore model that defines the minimum necessary structural characteristics a molecule must possess to bind the target. Alternatively, QSAR studies derive a correlation between the calculated properties of molecules and their experimentally determined biological activities of new analogs. The structure-based drug design18-20 on the other hand, plays a pivotal role in the design of novel drugs for several diseases. Recent advances in the large-scale determination of protein structures are improving the drug discovery process by starting with the protein structure and using it to design and identify new ligands. Literature survey reveals21-24 that rutin and many other bio-flavonoids exhibit anti-oxidant activity by inhibiting the normal functioning of lambda-class glutathione transferases(GSTLs), for particular xenobiotic inducible GSTLs, TaGSTL1 has found that tightly bind rutin, taxifolin, etc. The 3D- structure of the target enzyme TaGSTL1 is yet to be determined; therefore, pharmacophore patterns and 2D- and 3D- descriptors of rutin were derived and analyzed to determine the structural features that govern the anti-oxidant activity.



Molecular structures  were drawn using Chem Sketch 12 freeware and then energy optimization by MMFF94 force field using TINKER.  PyMol 1.7 and Avogadro 1 were used to calculate the molecular surface potential, to determine the intra molecular H-bonds. All the software's  used with default settings, operating in Linux Ubuntu 12.0425-26. The default settings of different parameters were shown in the table below.


Table 1: default settings of different parameters





Maximum number of iterations



Minimum RMS gradient



Steric energy limit

250 kJ/Mol


Total charge



Spin multiplicity



Spin Pairing







The final structures using the MMFF94 force field optimized structure of ASR (Rutin) is as shown in figure -1. From the figure, it is clear that the glycosidic moiety is almost perpendicular to flavones and catechol moieties; the same is true for catechol moiety. This could be a possible reason for high stability of rutin27. Another possible explanation is the presence of diverse intra-molecular H- bonds.



(a) Front view of Rutin


(b) Side view (90o) of Rutin


Fig .1:MMFF94 force field optimized structure of ASR (Rutin)


The molecular surface face potential for Rutin is depicted in figure -2 which indicates that majority Rutin is either H-bonding or Mild polar in nature. It is the flavone that imparts hydrophobic nature to it.


(a) Front view of molecular surface potential


(b) Side view (90o)

Fig-2: Molecular surface potential

(Blue-H-bonding, Red- Mild Polar and White- hydrophobic region)


Generally, the approach in the connectivity method is different from the traditional biological method based on the assumed mechanism and Physico-chemical properties as regression variables. It seeks to extract the structural information from a data set and relate it directly to the set of activities. From this angle, it is seen that the physical significance of molecular connectivity is coterminous for molecular structure. So the zero and first-order connectivity indices were calculated for the rutin. TPSA gives the transport properties of drug moieties in the intestines and BBB. Rutin with a TPSA of 269.43, which suggests that it likely acts as hydrophilic in nature.


Lipophilicity is an imperative parameter used by medicinal chemists in drug discovery on a routine basis. It plays a pivotal role in governing kinetic and dynamic aspects of drug action. It can be defined as the ratio of the concentrations of a neutral compound in organic and aqueous phases of a two-compartment system under equilibrium conditions28-30. which  mostly calculated as log P. Moriguchi developed one of the earliest yet successful methods, MLOGP, which uses the model variables include: the sum of lipophilic and hydrophilic atoms, N/O atom proximity effect, number of unsaturated bonds, number of polar aromatic substitutes, presence of ring-type structures, number of nitrogen groups, presence of intramolecular hydrogen bonds, amphoteric properties31. The MLogp of Rutin was -3.148 which is negative. The calculated physio-chemical properties of Rutin have been tabulated in table-2


Table -2: In silico calculated physico-chemical properties of Rutin

S. No

Physico-Chemical Properties

Corresponding value


Molecular Weight (MW)



X0(Zero order connectivity index)



X1 (First order connectivity index)



Number of H-Donating groups



Number of H-accepting groups



Number of H-Bonds



Polar surface area (due to N and O) PSA(NO)



Total polar surface area TPSA (Tot)



MLOGP (MoriguchiLipophilicity)



In the absence of information about the 3D- structure of the target enzyme, pharmacophoric pattern and QSAR are considered  voluble techniques to identify the structural features that steer the activity. In the present work, pharmacophore modeling was performed to achieve these goals. The pharmacophoric pattern of Rutin has been depicted in figures 3(a) and (b). From the pharmacophoric pattern, it is evident that the flavonoid moiety (shown by the green ball) controls the hydrophobic nature of Rutin32. It is approximately at a distance of 12.76 and 6.13A0 from sugar and catechol moieties, respectively. The angle between the corner of the sugar moiety, flavonoid part, and catechol moiety is 66.50



Fig 3(a):2D- representation of Pharmacophore pattern of Rutin



a) With distances


((b) With angles


Fig 3(b) 3D- representation of pharmacophoric pattern for Rutin (Green colored in Angstrom unit)


Another way to understand the pharmacophoric pattern is to calculate the charge on each atom of the molecule.  The charges were calculated using the MMFF94 method, depicted in figure 4 (for the sake of simplicity, Hydrogen has been eliminated). Charge on each atom using MMFF94 method (900 view)


(a) Front view


(b) 90o view


Fig 4: Charge on each atom using MMFF94 method



By using  free software like Chemsketch 12 and other free wares the molecules were designed and insilico studies were conducted. The study shows that rutin has strong anti-oxidant binding activity by inhibiting the normal functioning of lambda-class glutathione transferases (GSTLs), of particular xenobiotic inducible GSTLs, TaGSTL1. The 3D- structure of the target enzyme TaGSTL1 is not determined as of now; therefore, pharmacophore patterns and 2D- and 3D- descriptors of rutin were derived and analyzed. This is done in order to detect the key structural features that govern the anti-oxidant activity. From the MMFF94 force field optimized structure of ASR (Rutin) , it is clear that the glycosidic moiety is almost perpendicular to flavones and this is the most probable reason for the high stability of rutin.  It has a TPSA of 269.43, which suggests that it likely acts as hydrophilic in nature. Taking this study as the base 3D- structure of the target enzyme TaGSTL1 can be determined and further in silico studies can be conducted.



Authors declare none.



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Received on 22.11.2021            Modified on 13.04.2022

Accepted on 23.07.2022           © RJPT All right reserved

Research J. Pharm. and Tech 2023; 16(4):1940-1944.

DOI: 10.52711/0974-360X.2023.00318