Molecular Modeling and Docking Study of 2,5-Disubstituted ... · design of antifungal agents in silico study. Eight derivatives of 5-aryl/alkyl-substituted-1,3,4-thidiazole were selected

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IJCPS Vol. 7, Special Issue ISSN:2319-6602 RICES - Jan 2018 International Journal of Chemical and Physical Sciences

Molecular Modeling and Docking Study of 2,5-Disubstituted-1,3,4-Thidiazole Derivatives and their Docking Interactions with Lanosterol 14 Α-Demethylase

S. S. KADAM - 180 -

Molecular Modeling and Docking Study of 2,5-Disubstituted-1,3,4-Thidiazole Derivatives and

their Docking Interactions with Lanosterol 14 Α-Demethylase

S. S. KADAM

Dept. Of Chemistry, Hon B.J. A., C. & S. College, Ale, Tal.Junnar, Dist- Pune, MH, India Corresponding author: [email protected]

___________________________________________________________________________ Abstract

Fungus is common primitive microorganism cause severe fungal infections on skin and lungs in human which is too much for the immune system to handle. These are common throughout much of the natural world. Diabetic and cancer patients are more prone to fungal infections. If they are treated in earlier stage it doesn't cause severe danger. Due to proliferation of immuno-suppressive diseases such as HIV/AIDS the chances of fungal infections have been increases. Researchers trying to find the treatment of such infective diseases by targeting the 14 α-demethylase enzyme in fungi; destroying the fungal cell's ability to produce ergosterol causes a disruption of the plasma membrane, thereby resulting in cellular leakage and ultimately the death of the pathogen. (Drug Bank). In this research article especial emphasis on the antifungal activity of 1,3,4-thidiazole and their derivatives. Lanosterol 14α-demethylase is an attractive selected drug target in the design of antifungal agents in silico study. Eight derivatives of 5-aryl/alkyl-substituted-1,3,4-thidiazole were selected for rational docking study especially antifungal activity. It has showed the high binding affinity to lanosterol 14α-demethylase (-4 and -8.5 kcal/mol) for compounds TDB1 and emerged as the most potent antifungal agent among all compounds with a half maximal inhibitory concentration (IC50) is 422.3 nanomolar.The best docked derivative TDB1 and remaining all derivatives showed acceptable pharmacological significance produced by computational molecular modelling and docking methods. Key words: 14 α-demethylase enzyme, in silico, 1,3,4-thidiazole, antifungal agent, pharmacological significance, etc.

Introduction

A fungal infection can grow everywhere in air, in soil, on plants and in water too. These infections are difficult to treat because fungus can't easily kill. To treat fungal infections antimycotic medication is used to treat mycoses such as athlete's foot, ringworm, candidiasis (thrush), serious systemic infections such as cryptococcal meningitis, and others.Fungal lanosterol 14-α demethylase (CYP51) is the key enzyme in the ergosterol biosynthesis pathway and a major antifungal drug target [1,2]. In 1,3,4-thidiazole ring substituent is introduced into 2 or 5 position enhanced the reactivity and various derivatives of this core ring synthesized and evaluated their antimicrobial properties in vitro and in silico.[3] The structure of the molecule has displayed divergent in biological activity [4-5]. The binding interaction with targeted proteins through hydrogen bond donor or acceptor interaction has more potent [6-10]. Computational study of the synthesized molecule is the best method to evaluate their pharmacolgical significance as compare to in vitro and in vivo study. Structure based drug designing

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(SBDD) are useful to design and synthesis drugs are typically small molecules that bind on or inside the protein, thus inhibit the protein's function directly or hinder its interaction with other proteins. Virtual screening is the primary method; synthesis and biological evaluation were carried out in pursuit of designing some potential novel antimicrobial compounds carrying 1,3,4–1,3,4-Thiadiazoles rings as core nucleus. Chemistry

The synthesis of selected route was rarely observed; use of substituted / unsubstituted nitriles and thiosemicarbazide as a starting material. MCR's i.e. one pot synthesis, minimum time and ease to recovery of desired product in good yield. This is explained in general synthetic scheme and details synthetic procedure and characterization data of synthesized derivatives will be available in supplementary material and published research paper [11-12] (supplementary data). TDA / TDB as a code of 5-phenyl-1,3,4-thidiazole-2-amine, and 2,3 diphenyl-1,3,4-thidiazole-2-amine respectively.

Table 1: Analytical data:

Entry R R’ Mol.Formula Mol.Wt Appearence % Yield M.P 0c

TDA Phenyl -H C8H7N3S 177 White solid 35 225 TDA1 Phenyl Morpholine C13H14N4O2S 290 White solid 15 285 TDA2 Phenyl Cyclopentyl C14H16N4OS 288 White solid 17 287 TDA3 Phenyl Glycine C11H10N4O3S 278 White solid 20 185

IDB 2,3-difluro Phenyl

-H C8H5N3F2 211 White solid 30 220

TDB1 2,3-difluro phenyl

Morpholine C13H12F2N4O2S 326 White solid 15 285


Cyclopentyl C14H14F2N4OS 324 White solid 10 290


Glycine C11H8F2N4O3S 314 White solid 20 185

Methodology Computational methods Software and program Schrodinger’s maestro visualization program v9.6 [13] is utilized to visualize the receptors, ligand structures, hydrogen bonding network, to calculate length of the bonds and to render images. Chemdraw was used to draw the ligand compounds. Autodock 4.0 [14] is the primary docking program used in this work for the semi-flexible docking studies. Preparation of the ligands and protein receptors in pdbqt file and determination of the grid box size were carried out using Auto-Dock Tools version 1.5.6. Molinspiration, Orissis property explorer program was used to study the ADMET properties of the compounds. Preparation of protein receptor and Ligand.The crystal structure of the Lanosterol 14 α-demethylase (PDB ID: 4LXJ) for anti-fungal activity was obtained from the Protein Data Bank (PDB) [15].

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Table 2: Reaction conditions used for the synthesis of desired derivatives by nucleophilic substitution reaction:

Sr.no. Starting Material

D1 and D2 Substituted

R part

Reagents, and reaction conditions

Desired products

1

DIPEA, 1,2-DCE, 60 οC, 4 h

2


3


4


5


6


The crystal structure contained many missing atoms which were supplemented by the repair

commands module of AutoDock. Before docking, the protein crystal structure was cleaned by removing the water molecules. H-atoms were added to these target proteins for correct ionization and tautomeric states of amino acid residues. The modified structure so obtained was used for the semi-flexible dockings. The ligand molecules were drawn using chemsketch software. The energy of the ligand molecule and receptors were minimized in Steepest Descent and Conjugate Gradient methods using Accelrys

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Discovery Studio (Version 4.0, Accelrys Software Inc.) [16] Minimization methods were carried out with CHARMM force field [17]. Semi-flexible docking Autodock Version 4.0 is used to predict binding pose with associated energy along with the IC50 value prediction of the compounds with drug target the Lanosterol 14 α-demethylase (PDB ID: 4LXJ). Protocol followed for carrying out the docking studies using Autodock version 4.0 in order to predict binding pose and IC50 values along with associated binding energies is of default parameters similar to the protocol followed elsewhere [18-20].In order to understand the plausible experimental antifungal activity of the present studied derivatives, we have carried out the half maximal inhibitory concentration (IC50) value predictions. IC50 value is a useful parameter to quantitatively measure the effectiveness of compound to inhibit a given biological process by half and is universally used to symbolize the inhibitory effect of compounds. Results and discussion Docking of the compounds with Lanosterol 14 α-demethylase drug target active site: In order to predict the anti-fungal activity of the 5-aryl/alkyl-substituted-1,3,4-thidiazole synthesized compounds, we have selected drug targets based on their biological importance and wide range of reporting in the literature especially Lanosterol 14 α-demethylase (PDB ID: 4LXJ) was the for anti-fungal activity. The docking studies for the present synthesized six derivatives of 5-aryl/alkyl-substituted-1,3,4-thidiazole with Lanosterol 14 α-demethylase (PDB ID: 4LXJ)domain protein targeting its active binding site in order to know the binding energy involved in this complex formation and to know the molecular interactions responsible for this target specific inhibition. Docking results are tabulated in Table 3. We have performed the docking studies for the present synthesized six derivatives of 5-aryl/alkyl-substituted-1,3,4-thidiazole with Lanosterol 14 α-demethylase (PDB ID: 4LXJ) domain protein targeting its active binding site in order to know the binding energy involved in this complex formation and to know the molecular interactions responsible for this target specific inhibition. Docking results are tabulated in Table 1. All the eight compounds studied in this present work have shown to be successfully docking inside the active site of Lanosterol 14 α-demethylase domain with a binding energy in a range of -4.00 to -8.05 Kcal/mol. Table 3: Docking results of Compounds targeting Lanosterol 14 α-demethylase (PDB ID:

4LXJ) for anti-fungal activity:

S.No code Binding Energy in Kcal/mol Predicted IC50 value

1 TDA -4.0 1.28 micro molar 2 TDA1 -8.4 422.3 nanomolar 3 TDA2 -8.5 391.8 nanomolar 4 TDA3 -6.4 812.6 nanomolar 5 TDB -4.8 1.12 micromolar 6 TDB1 -8.4 422.3 nanomolar 7 TDB2 -8.6 383.4 nanomolar 8 TDB3 -6.5 782.5 nanomolar

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Table 4: ADME parameters of the synthesized derivatives: Sr No

synthesized derivative

Molecular Formula

Mol. wt.

Log P

H-bond donors

H-Bond acceptors

Rotatable bonds

TPSA

1 TDA C8H7N3S 177.2 1.6 1 3 1 80.0

2 TDA1

C14H16N4OS 288.3 2.9 2 5 3 95.1

3

TDA2 C13H14N4O2S 290.3 1.9 1 6 2 95.5

4 TDA3

C11H10N4O3S 278.2 0.8 3 7 4 132.4

5 TDB C8H5N3F2S 213.2 1.8 1 3 1 80.0

6 TDB1

C14H14N4OF2

S 324.3 3.1 2 5 3 95.1

7

TDB2 C13H12N4O2F2

S 326.3 2.1 1 6 2 95.5

8 N N

S NH

FFO

HN

O

OH

TDB3 C12H12N4O3F2 S

310.3 1.3 3 7 4 132.4

For Lanosterol 14 α-demethylase drug target, compound TDA-D-2 has been identified as the best target specific binding compound based on the binding energies. From the visualization of the docked pose it was revealed that TYR72, LEU95, TYR126, LEU129, PRO238, HIS381, SER382, PHE384 and MET509 residues were observed to be key role players towards stabilizing this protein-ligand complex (Figure 1). In silico evaluation for the best compound based on docking and drug likeliness results with the help of values such as binding energies, IC50 values and ADME parameters of the investigated derivatives and parent molecule it was found that compound TDB1 (1-cyclopentyl-3-(5-(2,3-difluorophenyl)-1,3,4-thiadiazol-2-yl)urea) has the promising antifungal activity has showed drug like properties based on its ΔG binding energy and IC50 value. Based on Pharmacological properties, all the eight compounds showed good pharmacological attributes. These compounds were found to comply with Lipinski’s rule, Veber’s rule and oral bioavailability parameters. Whereas, compound TDB1showed good pharmacological attributes, since it satisfied the Lipinski’s Rule. The parameters of according to this rules are, the molecular weight must be < 500 Da, Log P < 5, the number of hydrogen donors must be < 5, the number of acceptor hydrogens must be < 10, and the refractivity molar range must be between 40–130. [21-25]

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Conclusion In silico studies provides a rationalization to the ability of present studied novel derivatives of 5-

aryl/alkyl-substituted-1,3,4-thidiazole as a valuable small ligand molecule with strong binding affinity towards Lanosterol 14 α-demethylase (PDB ID: 4LXJ) for anti-fungal activity involving large value of negative binding energy by forming various interactions with the residues, all or some of which fall under catalytic active site important residues consolidating their complex’s thermodynamic stability. Moreover, predicted IC50 values further substantiated our hypothesis that these compounds have the potential to inhibit Lanosterol 14 α-demethylase domain. The knowledge gained through this present study could be of high value for computational screening of target specific Lanosterol 14 α-demethylase domain domain inhibitors by understanding the molecular interaction basis between ligand and receptor. On the other hand, promising ADME drug like profile for the synthesized derivatives 5-aryl/alkyl-substituted-1,3,4-thidiazole required the need of further evaluating this compounds ability to inhibit antifungal activity. The present investigated 1,3,4-thidiazole scaffold of derivatives offers the possibility of expedient additional modifications that could give rise to lead structures with enhanced inhibitory activity and selectivity towards the drug receptor target like Lanosterol 14 α-demethylase domain. Acknowledgements

My sincere thanks to Syed Hussain Basha Innovative Informatica Technologies, Hyderabad, for assisting in producing the data required for this research work. References [1] Daum G, Lees ND, Bard M, Dickson R. Yeast. 1998. 14(16):1471-1510. [2] Kelly, S.L.; Lamb, D.C.; Cannieux, M.; Greetham, D.; Jackson, C.J.; Marczylo, T.;

Ugochukwu, C.; Kelly, D.E. Biochem. Soc. Trans. 2001, 29, 122–128. [3] Cresnar, B.; Petric, S. BBA Proteins Proteomics 2011, 1814, 29–35. [4] Sushama S. Kadam, G. M. Nazeruddin Int. J. Curr. Res. Chem. Pharma. Sci. 2015 2(12),

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[15] Bernstein FC et al. Arch Biochem Biophys. 1977 112: 535 [PMID: 626512] [16] http://accelrys.com/products/discovery-studio/visualization-download.php. [17] Vanommeslaeghe K et al. J Comput Chem. 2010 31: 671 [PMID: 19575467] [18] Reddy SV et al. J Biomol Struct Dyn. 2015 11: 1 [PMID: 25671592] [19] SH Basha et al. European Journal of Biotechnology and Bioscience. 2014 2: 30 [20] SH Basha et al. scientific reports. 2012 566: 2 [21] Morris GM et al. Journal of Computational Chemistry. 1998 19: 1639 [22] Sander T et al. J Chem Inf Model. 2009 49: 232 [PMID: 19434825] [23] Sander et al. J Chem Inf Model. 2015 55: 460 [PMID: 25558886] [24] BT Burlingham et al. Journal of chemical education 2003 2: 214 [25] Lipinski CA, Drug Discov Today Technol. 2004 1: 337 [PMID: 24981612] [26] Miles et al. Drug Discov Today. 2003 8: 876 [PMID: 14554012]

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Molecular Modeling and Docking Study of 2,5-Disubstituted ... · design of antifungal agents in silico study. Eight derivatives of 5-aryl/alkyl-substituted-1,3,4-thidiazole were selected