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Designing and In-Silico Analysis of Some New 4-Aminoquinoline analogues as Potential New Antimalarial Agent

Soumendranath Bhakat; Department of Pharmaceutical Sciences; Birla Institute of Technology, Mesra-835215, INDIA

Email: /

Abstract

In this study some new chloroquine analogues have been designed and computational study was carried out on those molecules to predict their antimalarial property. Different ADME parameters, drug likeness score, toxicity parameters and other properties have been calculated using different in-silico methods and based on that the best molecule has been sort out. It is has been evident from this study that changing the position and nature of substitution and chain length of chloroquine or 4-aminoquinoline can ultimately leads to molecules which predict to have better antimalarial activity than chloroquine. This study will be hope for developing new cheap chloroquine analogues which might be active against chloroquine resistant Plasmodium strains.

Key words: Malaria; Plasmodium; Chloroquine; SAR (Structure Activity Relationship); Docking

Introduction

Malaria is the most deadly protozoal disease in the world which affects around 500 million individuals throughout the tropical and subtropical region with mortality with about 800,000deaths worldwide each year [1]. 4-aminoquinoline derivatives often widely used as for the treatment of malaria. Chloroquine is one of the most cost effective 4-aminoquinoline analogues used because of its good safety profile [2]. However due to emergence of chloroquine resistant Plasmodium falciparum and Plasmodium vivax strains chloroquine is no longer used as first line treatment for malaria [3-5]. Now-a-days artemisinin based combination therapy is become the first line drug for choice in the treatment of malaria but recent emergence of artemisinin resistant Plasmodium falciparum strain leads to a new challenge towards the drug designers to design some new potent antimalarial drugs[6-7].

Despite the emergence of chloroquine resistant strain drug designers continuously designing new chloroquine analogues and some new 4-aminoquinoline analogues with the vision that change in carbon number in side chain or change in substitution will make the chloroquine analogues effective against the resistant and normal strain of Plasmodium [8-13]

In present work we have designed some new chloroquine analogues and validate their antimalarial activity by in-silico methods.

Materials & Methods

Designing of the ligands:

The ligands have been designed taking 4-amino quinoline as core structure as 4 aminoquinoline is the basic core of chloroquine. The core structure for structural modification is depicted below in Fig. 1.

Fig.1.Core structure for structural modification

The designed ligands which have the basic structure that of core are depicted below with their code

Code: Molecule A

Code: Molecule B

Code: Molecule C

Code: Molecule D

Code: Molecule E

The modifications at different positions of the core structure (Fig.1) is listed below

Table 1: List of ligands with modifications

Ligand Code / R1 / R2 / R3 / R4
Molecule A / -Cl / NH(CH2)4N(CH2CH2CH3)2 / -H / -H
Molecule B / -Cl / NHCH(CH3)(CH2)3N(CH2CH2CH3)2 / -H / -H
Molecule C / -F / NH(CH2)4N(CH2CH2CH3)2
Molecule D / -F / NHCH(CH3)(CH2)3N(CH2CH2CH3)2 / -H / -H
Molecule E / -H / CH2CH(CH3)CH(NH2)(CH2)2N(Et)2 / -F / -OH

Drug Likeness and Property Prediction:

Drug likeness score, Lipinski Rule of 5[14] violation and other molecular properties of all the ligands have been predicted using MolSoft Drug likeness prediction tool ( and activity of all the molecules have been predicted using PASS online server ( and it is observed that all molecules show greater probability of active(Pa) than probability of inactive(Pi) as antimalarial agent.

ADME and Toxicity Prediction:

The ADME/T properties of a drug, together with its pharmacological properties are conventionally viewed as part of drug development. The ligands identified were subjected to predict the pharmacokinetic properties using pre-ADMET online server. Structures with unfavorable absorption, distribution, metabolism and elimination have been identified as the major cause of failure of candidate molecules in drug development. So there is an early prediction of ADME properties, with the objective of increasing the success rate of compounds reaching further stages of the development [17-21].

Target Choosing and Molecular Docking:

The automated molecular docking of designed analogues was performed using Glide software [22a, b, c, d, e, f] included in Schrödinger suite 9.0.02. The ligands were drawn and energy minimized in Ligprep module [23]. The crystal structure of Plasmodiumfalciparum l-lactate dehydrogenase (PfLDH) complexed with NADH and oxamate was downloaded from protein data bank (Pdb id 1LDG) [24] as target for docking with designed ligands taking chloroquine as prototype. The protein was energy minimized in MacroModel module [25] using 100 iterations and OPLS2005 force fields. The energy minimized protein structure was prepared using protein preparation module of Schrödinger suite 9.0.02. The centre of co-crystallized NADH was considered as centre of receptor grid as it covers all reported interacting amino acid residues. The grid size of 26Å was used to accommodate designed ligand in active site of 1LDG. Molecular docking was performed with standard precision, OPLS 2001 force field, scaling factor of 0.80 with partial cut-off of 0.25 and Coulomb-vdW cut-off of 50 kcal/mol were used. The best-docked structure for each ligand was selected using a glide docking energy score that predicted the binding and the internal strain energy which has major of electrostatic and van der Waals energies.

Results & Discussion

The drug-likeness and the molecular properties of the designed ligands (Molecule A,Molecule B,Molecule C, Molecule D,Molecule E) are analyzed using Molsoft program and the designed ligands presented better drug-likeness values than the chloroquine prototype. In this study we also verified whether the designed ligands are satisfying the Lipinski rule of five, which indicates if a chemical compound could be an orally active drug in humans. Our results showed that all the designed ligands have fulfilled this rule which can be seen in Table II.

Table II: Drug Likeness and Molecular Property Prediction using MolSoft Drug-Likeness and molecular property prediction tool

Ligand Code / Number of HBA / Number of HBD / MolLogS
in Log(moles/L) / MolPSA(A2) / Number of stereo centers / Molecular weight / Lipski Rule of 5 violation / Drug likeness score
Molecule A / 2 / 1 / -5.71 / 24.58 / 0 / 333.20 / None / 1.38
Molecule B / 2 / 1 / -5.89 / 24.04 / 1 / 347.21 / Do / 1.25
Molecule C / 2 / 1 / -5.13 / 24.58 / 0 / 317.23 / Do / 1.23
Molecule D / 2 / 1 / -5.31 / 24.04 / 1 / 331.24 / Do / 1.20
Molecule E / 4 / 3 / -3.74 / 52.50 / 2 / 333.22 / Do / 1.56

All the molecules show greater drug likeness score than that of chloroquine prototype (drug likeness score of chloroquine: 1.17).

The antimalarial property was predicted using PASS server and Pa (Probability of active) of all the designed ligands have been greater than that of Pi (Probability of inactive) which confirms all molecules antimalarial effect (Table III).

Table III: Probability of Activeness as Antimalarial agent showed in PASS Server

Ligand Code / Pa / Pi
Molecule A / 0,709 / 0,003
Molecule B / 0,743 / 0,003
Molecule C / 0,580 / 0,004
Molecule D / 0,705 / 0,003
Molecule E / 0,288 / 0,039

Predicted ADME and toxicity parameter of all the designed molecules with the comparison with chloroquine has been shown in the Table IV.

Table IV. Predicted ADME and Toxicity parameters of all designed molecules with Chloroquine

Sl. no / Name of the Ligand / Human intestinal absorption (HIA, %)* / in vitro Caco-2 cell permeability (nm/sec)* / In-vitro plasma protein binding (%)* / Ames Test / Carcinogenicity (Mouse) / Carcinogenicity (Rat)
1 / Molecule A / 98.072007 / 57.1311 / 98.152304 / Mutagen / Positive / Positive
2 / Molecule B / 98.081039 / 56.9683 / 98.468311 / Mutagen / Negative / Positive
3 / Molecule C / 97.927642 / 54.1152 / 88.734003 / Mutagen / Positive / Negative
4 / Molecule D / 97.960833 / 52.5262 / 89.442646 / Mutagen / Negative / Negative
5 / Molecule E / 94.321810 / 30.981 / 40.206612 / Non-mutagen / Negative / Negative
6 / Chloroquine / 98.056241 / 56.6153 / 92.534271 / Mutagen / Negative / Positive

*%human intestinal absorption: 70-100 % well absorbed, 20-70% moderately absorbed, 0-20 poorly absorbed, in vitro Caco-2 cell permeability(nm/sec) low permeability(<4),medium permeability(4-70),high permeability(>70)%plasma protein binding: >90 strongly bound, <90% weakly bound.

According to Table IV we predict that Molecule E will be the best drug of choice among our designed molecules because not only its %HIA is quite high but its % plasma protein binding is quite lower than all other molecules which make it more effective as the less bound a drug is, the more efficiently it can traverse cell membranes or diffuse [26].

In the molecular docking study all the designed molecules show more negative docking score (kcal/mol) (Table V) than that of prototype chloroquine when molecules docked with PfLDH (Pdb id 1LDG). Among all the designed molecules Molecule B and Molecule C shows hydrogen bond interaction with Asp53, Ala98, Ser245 of PfLDH(Pdb id: 1LDG) which matches with chloroquine but these ligands shows better docking score (More negative docking score better it is) than that of chloroquine prototype. But Molecule E shows hydrogen bond interaction with Asp53, Asp53, Tyr85, Ala98, Glu122 of PfLDH and its docking score is better than that of prototype chloroquine which makes Molecule E the best molecule as it shows more H bond interaction with the target than all other ligands and prototype.

Table V: Docking Score and H Bond interaction table of all ligands using GLIDE

Sr. no. / Compound / Docking score (kcal/mol) / H-bond
1. / Chloroquine / -4.872 / Asp53, Ala98, Ser245
2. / Molecule A / -5.146 / Asp53, Ala98
3. / Molecule B / -5.647 / Asp53, Ala98, Ser245
4. / Molecule C / -5.258 / Asp53, Ala98, Ser245
5. / Molecule D / -5.285 / Ala98
6. / Molecule E / -5.052 / Asp53, Asp53, Tyr85, Ala98, Glu122

Figure 2. Docking of Prototype Chloroquine with PfLDH (Pdb id 1LDG)

Figure 3. Docking of Molecule A with PfLDH (PDB id: 1LDG)

Figure 4. Docking of Molecule B with PfLDH (PDB id: 1LDG)

Figure 5. Docking of Molecule C with PfLDH (PDB id: 1LDG)

Figure 6. Docking of Molecule D with PfLDH (PDB id: 1LDG)

Figure 7. Docking of Molecule E with PfLDH (PDB id: 1LDG)

It is clear from Table V that Molecule B and C interacts with the same amino acid residues (Asp53, Ala98, Ser245) that of chloroquine but having more negative docking energy that of chloroquine also this two molecules have almost same ADME and toxicity profile(as predicted) that of chloroquine which makes Molecule B and C potential new antimalarial agent. And molecule E interacts with Asp53, Asp53, Tyr85, Ala98, Glu122 and its ADME and toxicity profile is better than prototype and all other designed molecules. Not only it is predicted to be non-mutagenic and non-carcinogenic but also its % plasma protein binding is quite less which makes it a better molecule as potential new antimalarial agent.

Conclusion

In this study we predict that certain changes in substitution or in side chain of chloroquine along with site of substitution make the new ligand better antimalarial agent than chloroquine which we predict can act effectively on resistant strains of Plasmodium. As per this in-silico study Molecule E has found to be best chloroquine analogue with Molecule B&C which can be possibly act as new antimalarial agent on Plasmodium sp. resistant strains.

We are currently working on the synthesis of these molecules and further development of new analogues of 4-amino chloroquine.

Acknowledgement

I am very much thankful to Prajwal Nandekar of Department of Pharmacoinformatics; National Institute of Pharmaceutical Education and Research (NIPER); Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062 for helping me by performing molecular docking.

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