|Year : 2015 | Volume
| Issue : 2 | Page : 85-89
Role of quassinoids as potential antimalarial agents: An in silico approach
Department of Biochemistry, Cachet Labs, Yousufguda, Hyderabad, Telangana, India
|Date of Web Publication||14-Dec-2015|
Department of Biochemistry, Cachet Labs, Yousufguda, Hyderabad, Telangana
Source of Support: None, Conflict of Interest: None
Background: Malaria is an infection caused by mosquitoes in human beings which can be dangerous if untreated. A well known plant product, quassinoids are known to have antimalarial activity. These bioactive phytochemicals belong to the triterpene family. Quassinoids are used in the present study to act against malarial dihydrofolate reductase (Pf-DHFR), a potential antimalarial target. Nevertheless, viṣama jvara (~malaria) has been treated with the bark of Cinchona since a long time.
Aim: The aim of the present experiment is to perform the protein-ligand docking for Pf- DHFR and Quassinoids and study their binding affinities.
Setting and Design: The software used for the present study is the discovery studio (Accelrys 2.1), Protein Data Bank (PDB), and Chemsketch.
Materials and Methods: The protein for the present study was imported from protein data bank with the PDB Id, 4dpd and was prepared for docking. The ligands used for the study are the quassinoids. They were drawn using chemsketch and the 3D structures were generated. The docking was done subsequently.
Statistical Analysis Used: Molecular modeling technique was used for the protein-ligand docking analysis.
Results: The docking results showed that the Quassinoids Model_1 showed the highest dock score of 40.728.
Conclusion: The present study proves the promising potential of quassinoids as novel drugs against malaria. The dock results conclude that the quassinoids can be adopted as an alternative drug against malaria.
Keywords: 4dpd, malaria, P. falciparum, protein-ligand docking, quassinoids
|How to cite this article:|
Rampogu S. Role of quassinoids as potential antimalarial agents: An in silico approach. Ancient Sci Life 2015;35:85-9
| Introduction|| |
Quassinoids are the naturally available plant agents which exhibit a host of biological activities ,,,, seen mostly in Simaroubaceae species. These bioactive phytochemical agents belong to the triterpene  chemical family. The main active groups of quassinoids are ailanthionone, glaucorubinone and holacanthone besides benzoquinone, canthin, dehydroglaucarubinone, glaucarubine, simarolide, sitosole and melianone.
The picrasane skeleton, a pentacyclic derivative of the Quassinoids have shown a remarkable antitumor activity. Quassinoids also are known for their potent antimalarial, antimicrobial  and antiprotozoal  activities. The antimalarial activity of the quassinoids was evaluated earlier by the folate/anlifolates the drugs which prevent folic acid production and is essential for the folate dependent enzymes. Whereas, quassinoids are the plant extracts belonging to the simaroubceae family with 150 different compounds. These plant extracts are known widely for their anti-leukemic activity besides showing a host of other medicinal properties.
The enzyme malarial dihydrofolate reductase (Pf-DHFR) (E.C.18.104.22.168) is the target for antifolate antimalarial drugs such as pyrimethamine and cycloguanil. Dihydrofolate reductase is a bi-functional enzyme and is critical for folate metabolism. It involves in de novo dTMP biosynthesis, containing two polypeptide chains, A and B with 608 amino acid residues existing along with the heteromeric compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.) [Figure 1]. But their efficacy has been compromised by mutations at various sites on the enzymes.
The present experiment aims to create the analogues for quassinoids exploiting their antimalarial property and studying the binding affinity of these analogues against malarial DHFR, a validated target for malaria.
Malaria and its treatment in Ayurveda
Malarial parasites are probably assumed to be from Africa and exist even before the earliest known history. In Ayurveda malaria like symptoms are called as viṣama jvara. It is one of the known infectious diseases which recurs if untreated or ignored and could turn out to be epidemic and fatal. During the times of Atharva Veda (1500 BC) certain types of malarial fevers were prevelant which were associated with trembling, rigor, headache, debility etc. These are the common symptoms seen in association with malaria.
According to Ayurveda, the pathology of the disease is studied under pañcalakṣaṇa nidāna which helps  in the efficient diagnosis of the disease. The pañcalakṣaṇas are nidāna, pūrvarūpa, rūpa, samprāīpti and upaśaya.
Once the disease and its manifestation is vivid, the treatment can be performed  by removal of the cause or alternating the internal environment known as parivarjana and prakṛti vighāta respectively.
The bark of the cinchona tree was first used for treating malaria by native Peruvian Indians. Herbs and medicinal plants were the medicines of choice for treating malaria. Reported cases exist the use of quassinoids in treating against malaria.,,, Some of the plants used in treating malaria are: Cinchona spp., quasinoids, Cassia accidental, Caesalpinia crista, Morinda lucida, Picrasma nitida, Brucea javanica, Artemisia annua, Plumbago benesis, Azadirachta indica.
| Materials and Methods|| |
The quassinoids act as ligands for the present study and were drawn using chemsketch (ACD Labs 12.0). Removal of duplicates was done and bonds were then added to it.
Chemistry at HARvard Macromolecular Mechanics (CHARM m) force field was used to minimize the energy and thereafter the 3D structures were generated.
Further, 20 ligands were designed by substituting the groups at R1 position and Y position. This was followed by the ligand optimization [Figure 2].
Substituents of "Y"
If the "Y" group is substituted with substituents with R8 and R9[Table 1].
The protein for the present study was imported from PDB (Protein Data Bank). The X-ray crystal structure with high resolution of 2.5 A o malarial DHFR (Dihydrofolate reductase) PDB ID: 4dpd was imported into the discovery studio (Accelrys 2.1).
Protein preparation was carried out by correcting the missing residues and removing the complexes bound to receptor molecules and the water molecules between the ligands and protein.
The structure is then refined using appropriate charges and parameters and an energy minimization was carried out using steepest descent gradient until the convergence gradient was satisfied, implying that the protein has reached its least energy level.
The active site pockets of the protein malarial DHFR were identified using eraser algorithm and a sphere was created around the active site. As the protein 4dpd is known as an antifolates protein, the present investigation aims at identifying the active site of the protein. The active site of the protein was predicted by using the CAST p  software which reveals the packet information. It was identified that the pocket ID 142 exhibited the highest area and volume of 4940.3 and 16623 respectively [Figure 3].
This study was conducted to investigate the interaction of the ligand molecules in the active region of the protein and to predict the binding modes and affinities between the ligand and the protein molecule. The active site of the protein is first identified and it is defined as the binding site.
The binding sites are defined based on the ligand present in the PDB file which is followed by site sphere definition.
For accurate docking of ligands into protein active sites, the docking method used in this study is ligand fit. Dock scores are used to estimate the ligand binding energies.
Ligand – protein docking
Protein – ligand docking is a molecular modeling technique that aims at predicting the position and orientation of the ligand when it binds to the proteins. This method is mostly employed in designing new drugs.
The CHARMm-based docking program, which is called DOCK algorithm, offers a full ligand flexibility (including bonds, angles, dihedrals). This was employed to find the potential binding mode between both the protein and the ligand. In the present experiment the quassinoid-analogues were docked with the malarial DHFR.
| Results and Discussion|| |
The ligands in the present investigation, quassinoids interacted with the protein to generate 57 poses [Table 2]. Out of the 20 ligands selected, only 3 quassinoids showed binding affinity with the protein. The highest dock score was found with Quassinoid_Model_1 showing 40.728, succeeded by quassinoid_model_4, with a dock score of 38.809 and Quassinoid_model_2 with 38.553 dock score respectively [Table 3]. The dock results seem to explain that substituting groups on "Y," R8 and R9 with "H" atom, shows the maximum binding affinity proving it to be a potential anti-malarial agent. The amino acids, which interact with the H of Quassinoid sSER 111, ILE112, ILE164, PHE 58, TRY 170 [Figure 4] and [Figure 5].
|Figure 4: The H-bond interactions of quassinoid 1 with active site residues of quassinoid 1 with DHFR from Plasmodium falciparum|
Click here to view
Because the quassinoid_model_1 showed the highest dock score, it can hence be considered as the best protein-ligand pose among 57 poses generated.
Interaction of quassinoids with active site residues
The amino acids, which interact with the H of Quassinoid_1 are SER 111, ILE112, ILE164, PHE 58, TRY 170.
| Conclusion|| |
Malaria is a mosquito borne disease which is caused by Plasmodium which in severe cases causes death. The present experiment is a novel approach with the objective of designing the drugs for malaria using the medicinal plants. Quassinoids are the plants with many medicinal values. Quassinoids were docked with the protein 4dpd, a target antimalarial drug. It is evident that the "Y" substitutents play an essential role in increasing the efficacy of the drug. When the R8 and R9 positions of the "Y" group are replaced with "H" group, respectively, it leads to an increase in drug efficacy, followed by NO2 and CH3 group substituents. Further, pharmacological studies are needed to better assess their efficacy. The results seem promising and this proves that the Quassinoids can be used as new drugs for Malaria.
Financial support and sponsorship
Conflicts of interest
There are no conflicts of interest.
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[Figure 1], [Figure 2], [Figure 3], [Figure 4], [Figure 5]
[Table 1], [Table 2], [Table 3]
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