Journal of Molecular Modeling

INSILICO DOCKING AND MOLECULAR DYNAMIC SIMULATION OF 3-

DEHYDROQUINATE SYNTHASE (DHQS) FROM MYCOBACTERIUM
TUBERCULOSIS
--Manuscript Draft--

Manuscript Number:

Full Title: INSILICO DOCKING AND MOLECULAR DYNAMIC SIMULATION OF 3-

DEHYDROQUINATE SYNTHASE (DHQS) FROM MYCOBACTERIUM
TUBERCULOSIS

Article Type: Original paper

Keywords: Docking, MD simulation, MTB, ADMET and 3-dehydroquinate synthase

Corresponding Author: Mustafa Alhaji Isa

University of Maiduguri
NIGERIA

Corresponding Author Secondary

Information:

Corresponding Author's Institution: University of Maiduguri

Corresponding Author's Secondary

Institution:

First Author: Mustafa Alhaji Isa

First Author Secondary Information:

Order of Authors: Mustafa Alhaji Isa

Order of Authors Secondary Information:

Funding Information:

Abstract: Tuberculosis (TB) is one of the major infectious diseases and responsible for the death
of 2 million people every year, especially where there is high poverty, lack of standard
living condition/basic amenities or adequate medical facilities. 3-dehydroquinate
synthase (DHQS) is the second enzymes in shikimate pathway, that catalysed the
conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate to 3-dehydroquinate, a
first cyclic compound formed in this pathway. This pathway serves as a prerequisite for
the synthesis of aromatic amino acids and mycobactin in Mycobacteria tuberculosis
(MTB), which is essential for the survival of the organism. In this study 400 compounds
were obtained from two public databases through virtual screening using PyRx tool
and subjected to molecular docking analysis using Autodock4.2. Eighteen (18)
compounds showed high binding affinity/less binding energy range from -13.23 to -
8.22kcal/mol were selected and subjected to absorption, distribution, metabolism,
excretion and toxicity (ADMET) analysis. These lead to the selection of 9 compounds
based on ADMET test which fulfilled all its criteria. Two (ZINC19334122=-9.65kcal/mol
and ZINC633887= -10.29kcal/mol) out of the 9 compounds, with minimum binding
energy were further selected for Molecular dynamic (MD) simulation analysis. This
revealed that both compounds formed a stable complex in the ligand binding sites
during 50ns MD simulation. Therefore, these compounds will serve as potential
candidates for MTB after in vivo and in vitro validation

Powered by Editorial Manager and ProduXion Manager from Aries Systems Corporation
Manuscript Click here to download Manuscript INSILICO DOCKING AND
MOLECULAR DYNAMIC SIMULATION OF 3.docx
Click here to view linked References

INSILICO DOCKING AND MOLECULAR DYNAMIC SIMULATION OF 3-

DEHYDROQUINATE SYNTHASE (DHQS) FROM MYCOBACTERIUM
TUBERCULOSIS
Mustafa Alhaji Isa, Rita Singh Majumdhar and Shazia Haider
Department of Biotechnology, School of Engineering and Technology, Sharda University,
India
Corresponding author email: mustafaisa@unimaid.edu.ng

Abstract

Tuberculosis (TB) is one of the major infectious diseases and responsible for the death of 2

million people every year, especially where there is high poverty, lack of standard living

condition/basic amenities or adequate medical facilities. 3-dehydroquinate synthase (DHQS)

is the second enzymes in shikimate pathway, that catalysed the conversion of 3-deoxy-D-

arabino-heptulosonate-7-phosphate to 3-dehydroquinate, a first cyclic compound formed in

this pathway. This pathway serves as a prerequisite for the synthesis of aromatic amino acids

and mycobactin in Mycobacteria tuberculosis (MTB), which is essential for the survival of

the organism. In this study 400 compounds were obtained from two public databases through

virtual screening using PyRx tool and subjected to molecular docking analysis using

Autodock4.2. Eighteen (18) compounds showed high binding affinity/less binding energy

range from -13.23 to -8.22kcal/mol were selected and subjected to absorption, distribution,

metabolism, excretion and toxicity (ADMET) analysis. These lead to the selection of 9

compounds based on ADMET test which fulfilled all its criteria. Two (ZINC19334122=-

9.65kcal/mol and ZINC633887= -10.29kcal/mol) out of the 9 compounds, with minimum

binding energy were further selected for Molecular dynamic (MD) simulation analysis. This

revealed that both compounds formed a stable complex in the ligand binding sites during

50ns MD simulation. Therefore, these compounds will serve as potential candidates for MTB

after in vivo and in vitro validation.

Key Words: Docking, MD simulation, MTB, ADMET and 3-dehydroquinate synthase

1
Introduction

Tuberculosis (TB) is one of the major infectious diseases cause public health threat. It is a

leading infectious disease caused by the oldest known human pathogens Mycobacterium

tuberculosis (MTB) [1]. The diseases responsible for the death of 2 million people every year

(one death in every 15 seconds) especially where there is high poverty, lack of standard living

condition/basic amenities or adequate medical facilities. TB affects more than 1/4th of the

world population, especially in low-resource nations. Despite the presence of numerous

antituberculosis drugs (isoniazid, rifampicin, ethambutol, pyrazinamide, streptomycin etc.)

and vaccine, yet the disease claims the life of many people across the globe, due to prolong

the time for effective treatment and the cost of the drugs, which limit its accessibility to the

less privilege individuals in most of the developing countries. This situation further

worsened, especially with the presence of TB-HIV co-infection, multidrug resistant (MDR-

TB), extensively drug-resistant (XDR) and total drug-resistant (TDR) tuberculosis [2]. This

justifies the need to develop a better method for developing TB drugs. However,

conventional method of drug discovery and development is generally time consuming and

laborious. It takes more than 10 years and requires about US $800 million to complete the

entire process. This generally involved synthesis of large compound libraries and screen for

bioactivity through high throughput virtual screenings to determine the one with best hit,

although, this process is not successful, due to a low hit rate of most of the molecules and

failure to fulfil the Adsorption, distribution, metabolism, excretion and toxicity (ADMET)

properties. Therefore, computer aided drug design through modeling and docking provide a

better alternative for drug discovery and development [3]. Also, with the availability of the

complete genome of MTB and the primary and tertiary structure of unique proteins, which

serve as prerequisite for the survival of the organisms, the virtual screen using computer

2
environment will help to reduce both cost and time consumption toward identifying lead

molecules which are pharmacologically active against MTB [4].

Shikimate pathway plays a vital role in the synthesis of nutritive compounds in bacteria,

fungi and plants, and due to its absence in human makes it an important target for drug

design. This pathway serves as a prerequisite for the synthesis of aromatic amino acids and

mycobactin in MTB, and its seven step process, which start from phosphoenol pyruvate and

erythrose-4-phosphate to chorismate, which is a precursor for the synthesis of phenylalanine,

tyrosine, and tryptophan biosynthesis [5]. 3-dehydroquinate synthase (DHQS) is the second

enzymes in shikimate pathway, that catalysed the conversion of 3-deoxy-D-arabino-

heptulosonate-7-phosphate to 3-dehydroquinate, a first cyclic compound formed in this

pathway. However, the enzymes require a catalytic amount of divalent cation and NAD+ for

normal activity. In bacterial enzymes, the most common active metal ions that activate

DHQS are Co2+ and Zn2+. DHQS catalyst the conversion through complex multi-step

process, which involve intramolecular oxidation reduction at carbon-5 of 3-deoxy-D-arabino-

heptulosonate-7-phosphate in which NAD+ cofactor tightly bind to it, this follow by

elimination of phosphate and the formation of alicyclic ring [6-7] This reaction plays

important role in assembling a carbocyclic ring of the 3-dehydroquinate, which subsequently

turn to benzene ring of various amino acids such as L-tyrosine, L-phenylalanine, L-

tryptophan, folic acid, coenzyme Q, and a wide range of secondary metabolites including

mycobactin in MTB. This makes this enzyme essential for the survival of the organism, since

its prerequisite for the biosynthesis of mycobactin which is a thick layer in the MTB cell wall

[8]. Also, the active site metal ions (Zn2+ and Co2+) bound to DHQS play important role in

substrate binding [8]. Therefore, DHQS serve as an attractive target for drug design because

its essential for the viability of the MTB. Thus, the aim of this study is to identify novel

inhibitor of DHQS through in silico docking and molecular dynamic simulation.

3
Materials and methods

Identification and preparation of the protein-ligand complexes

There are two crystal structures of DHQS in protein data bank (PDB); these are 3-

Dehydroquinate Synthase (aroB) from Mycobacterium tuberculosis in complex with NAD

(PDB ID: 3QBD, resolution 2.47) and another crystal structure without complex (PDB ID:

3QBE, resolution 2.07). In this study, we selected the 3D structure of DHQS (PDB ID:

3QBE) with low resolution of 2.07 from Protein Data Bank (PDB) [9]. The bound

molecules were removed from the protein, the protein structure was cleaned, missing atoms

were inserted to incomplete residues, missing loop were checked and modelled, alternate

conformations were removed, bonds order were determined, side chains were optimized and

fixed, improper chirality was determined, disulphide bonds were checked, steric clashed were

identified and fixed, protonation state were determined, protein optimization and energy were

performed using SwissPDViewer [10], Chiron energy minimization and refinement tool [11]

and MDWEB tool [12] with amber force field. The protein binding site was determined by

calculating the x, y and z coordinate of Zn2+ (which serve as a substrate binding) using PyRx

tool and Autodock4.2 [8].

Virtual Screening

To identify the natural compounds capable of binding to DHQS with less energy, virtual

screening was carried out against the commercial available ligands from zinc and PubChem

database. The compounds were screening against the DHQS using PyRx 8.0 tool to obtain the

ligands with best possible conformer against the target protein. The total of 12165 molecules

with good conformation were obtained and further screened on the basis of pharmacokinetic

properties (Molecular weight, Number of hydrogen bond donor (HBA), Number of hydrogen

bond acceptors (HBD) and Lipophilicity, Drug-likeness etc.) using DataWarrior tool.

4
Molecular Docking

Four hundred (400) ligands with best possible conformer and passed all the criteria for

pharmacokinetic properties were selected for molecular docking using AutoDock4.2

program, which is the extension suite for Python Molecular Viewer use for the preparation of

both protein and ligand to Autodock type, that served as a prerequisite for molecular docking

[13]. A Lamarckian genetic algorithm [14] was used for the automated docking of the protein

and the ligands. The merging of the charges of the non-polar hydrogens was assigned and

Gasteiger charges [15] were computed. For the protein, all non- amino acid residues such as

water were removed and the binding site used for a cubic docking box of x, y and z

coordinate, the grid was spaced at 0.375 and the grid map was set at 60 x 60 x 60.

ADMET analysis

The compounds with good binding energy were further screened for ADME (absorption,

distribution, metabolism and excretion) properties using AdmetSAR tool [16]. The toxicity of

the molecules was screened using DataWarrior tool and AdmetSAR tool.

Molecular Dynamic (MD) Simulation

The MD simulation of two ligands with good conformation and less binding energy were

determined using amber10 package of Molecular Dynamic [17]. The Protonate 3D was used

to insert hydrogens into the docked complex, while antechamber used to prepared ligand by

assigning all missing parameter. GAFF was used to assigned charges to the ligand and

ff12SB was used to assigned charges to the protein using tleap. Sodium ions were used to

neutralize a buffer solution in a truncated octahedral box of 10 TIP3P water molecules. The

whole system was minimized through restraint of 544kcal/mol/ and maximum minimization

cycles of 10000 steps. This followed by Steepest Descent method using 5000 steps and

another 5000 steps for the Conjugate Gradients method. Then, the system was heated to

100,000 steps (100ps) with an initial temperature of 0.0k and final temperature of 300K using

5
Langevin dynamics temperature regulation. For the first 90000 steps, the temperature was

increase from 0K to 300K and from 90001 to 100000, the temperature remains at 300K.

Langevin thermostat collision frequency was set at 1ps with no pressure control. The

production of MD simulation was performed at constant temperature of 300K and constant

pressure 1atm with time step of 2fs, using Berendsen barostat for constant pressure

simulation. A 50ns long MD simulation of protein-ligand complex was produced with enable

SHAKE to constrain all bonds involving hydrogen. The RMSD of the protein backbone

residues and ligands within the binding site of the simulated system were determined using

ptraj in AmberTool10 [18-20].

Results and Discussion

Virtual Screening and Molecular Docking

Virtual screening plays an important role in biological screening of lead compounds. It helps

to identify the lead molecules capable of binding to the protein macromolecules with less

energy so as to form stable complex. In this study, we used PyRx tool to screened molecules

from both Zinc and PubChem database of NCBI. We identified 12165 compounds with good

conformer capable of binding to DHQS with less energy. These molecules were further

filtered by restricting to pharmacokinetic properties (Molecular weight <= 500, number of

hydrogen bond acceptor <= 10, number of hydrogen bond donor <=5 and logP <=5) which

lead to further selection of 400 molecules, out of which 250 from Zinc database and 150

molecules from PubChem database (Table 1). These molecules were used for molecular

docking studies using Autodock4.2 tool to calculate the binding free energy of the complex.

Among the ligands used in this study, only eighteen (18) showed high binding affinity/less

binding energy range from -13.23 to -8.22kcal/mol (Table 2, Figure 1). From the docking

result PubChem72341 had minimum binding energy of -13.23kcal/mol, interacting with

DHQS by forming three hydrogen bondings through accepting electrons from polar amide of

6
Glu50 (distance=2.0), hydrogen of Gly70 (distance 2.3) and hydroxyl group of Thr131

(distance=1.9) (Figure 2o). ZINC633887 exerts a binding affinity of -10.29kcal/mol and

formed four hydrogen bondings with the polar amide of Gln45, (distance=3.00), hydrogen

atom of Gly107 (distance=3.21), hydroxyl group of Thr132 (distance=2.58) and carboxylic

group of Asp73 (distance=2.70) (Figure 2a). ZINC12455413 has shown binding affinity of -

10.27kcal/mol and formed three hydrogen bondings with carboxylic group of Asp73

(distance=2.72), carboxylic group of Glu75 (distance= 3.20) and methyl group of Ala108

(distance=2.75) (Figure 2b). Similarly, ZINC19334122 had a minimum binding energy of -

9.65kcal/mol and interact to formed two hydrogen bondings with carboxylic group of Glu 179

(distance=2.74) and hydroxyl group of Thr131 (distance=2.55) (Figure 2c).

ZINC08983432 showed binding affinity of -9.34kcal/mol and displayed to formed one

hydrogen bonding with carboxylic group of Glu70 (distance=2.79) (Figure 2d).

ZINC14986690 possessed binding energy of -8.84kcal/mol and interact to formed three

hydrogen bonding by accepting electrons from polar amide of Gln45 (distance=3.04),

carboxylic acid of Glu50 (distance 2.76) and hydroxyl group of Thr131 (distance=3.35)

(Figure 2e). ZINC14882944 has shown binding energy of -8.44kcal/mol and formed

hydrogen bondings by accepting electrons from hydrogen atom of Gly47, 107 (distance1=2.6,

distance2=3.07) and carboxylic group of Glu50 (distance=1.8) (Figure 2f). ZINC04113772

interact with polar residues and formed one hydrogen bonding by accepting electron from

carboxylic group of Asp73 (distance=2.58) and had a binding energy of -8.42kcal/mol

(Figure 2g). ZINC04113772 exhibited a binding affinity of -8.41kcal/mol by interacting with

basic side chain of Arg68, 92 (distance1= 2.58, distance2=3.18) and formed two hydrogen

bondings via accepting electron from amino group of the residue (Figure 2h). ZINC633895,

ZINC20136483, ZINC14743064, PubChem73393, PubChem441071 and PubChem265237

shown binding affinity of -8.33, -8.26, -8.25, -8.61, -8.46 and -8.24kcal/mol respectively by

7
interacting with polar residues of Glu70, Arg68, 92 and Thr131, 171, 174 (Figure 2j-l, 2p-r). The

residues in DHQS that involved in hydrophobic interaction with the aforementioned ligands

include Gly47, 105, 106, 107, 135, Gln45, Glu50, 53, 70, 75, 179, Thr51, 101, 131, 132, 171, 174, Leu45, 48, 134, 175,

Ala49, 52, 74, 108, Pro46, 72, 176, Ile69, 71, 85, Phe85, Val89, His44, 67, Tyr261 and Arg68, 92, 264 (Figure 2a-

r) (Table 2).

ADMET analysis

The molecular docking studies of 400 ligands against DHQS using AutoDock4.2 tool after

virtual screening with PyRx tool leads to identification of 18 compounds which could be

potential molecules for inhibition of DHQS. These compounds were further used for

ADMET analysis using AdmetSAR and DataWarrior tool (Table 3). The ADMET properties

such as absorption, Distribution, metabolism, excretion and toxicity (Human Intestinal

Absorption, Cytochrome P450 (CYP450 2D6) Inhibitor, Biodegradation, Ames test,

Carcinogens, Mutagenicity, tumorigenic, reproducibility and irritability) of the 18 compounds

were predicted (Table 3). Human Intestinal Absorption of all the compounds was positive

except ZINC04113772, where the rate of the absorption is less than 30%, although the

compound fitted the overall ADMET model. Similarly, the predicted CYP450 2D6 inhibitor

shown that, all the compounds were non-inhibitor of cytochrome except ZINC19334122,

ZINC14743064 and PubChem72341. ZINC19334122 and ZINC14743064 had AC50 greater

than 57M (>57M) based on the model calculation of Cheng et al. (2012), whereas

PubChem72341 had a PubChem activity score greater than 40 (>40), made it potent inhibitor

of CYP450 2D6. Considering the toxicity parameter (Mutagenicity, tumorigenic,

reproducibility and irritability) only 11 compounds (ZINC633887, ZINC19334122,

ZINC08983432, ZINC04113772, ZINC20779557, ZINC11881196, ZINC20136483,

ZINC18122756, ZINC12243261, PubChem73393, PubChem441071) out of the 18 were non-

toxic. However, two compounds (ZINC04113772 and ZINC19334122), were non-toxic, but

8
found to be human intestinal absorption negative and inhibitor of CYP450 2D6 respectively,

indicating lack of absorption and metabolism phase. Thus, 9 compounds (ZINC633887,

ZINC08983432, ZINC20779557, ZINC11881196, ZINC20136483, ZINC18122756,

ZINC12243261, PubChem73393 and PubChem441071) fulfilled all the ADMET features out

of the 18 ligands with the good binding energies (Table 3).

Molecular Dynamic Simulation Analysis

Based on Molecular docking analysis, 18 compounds with least docking scores were selected

and subjected to ADMET test, this leads to selection of 9 compounds (ZINC633887,

ZINC08983432, ZINC20779557, ZINC11881196, ZINC20136483, ZINC18122756,

ZINC12243261, PubChem73393 and PubChem441071) which fulfilled all the ADMET

criteria. Two (ZINC19334122=-9.65kcal/mol and ZINC633887= -10.29kcal/mol) out of the

9 compounds, with minimum binding energy were further selected for MD simulation

analysis. Out of the 2 compounds, one compound (ZINC633887) showed hydrogen bond

interaction with four amino acid residues (Thr-132, Gln-45, Gly-107 and Asp-73) in the

DHQS binding site (Figure 2a), while the second compound (ZINC19334122) formed two

hydrogen bonding with the Thr-131 and Glu-179 (Figure 2c). These compounds were further

analysing for MD simulation to determine the structural stability of the conformation of

bound ligands obtained from docking studies in the complex. The stability of the protein-

ligand complexes (DHQS- ZINC633887 and DHQS- ZINC19334122) were examined by

carefully observing the root mean square deviation (RMSD) during the MD simulation of

50ns (Figure 3). In order to determine the deviation of the ligand with respect to the binding

energy as well as motion of each amino acid residues within the complexes, root mean square

fluctuation (RMSF) were also analysed during the MD simulation of 50ns (Figure 4). Also

the equilibration of the protein-ligand complexes were determined by carefully examined the

radius of gyration (Figure 5). The RMSD of DHQS- ZINC633887 complex stayed at a steady

9
state between the ranges of 2.0 to 2.5 throughout the 50ns (Figure 3), which suggested

greater stability and lower flexibility of DHQS- ZINC633887 complex, which occur as a

result of interaction between the bound ligand and the flexible loop region, thus reduce the

flexibility of the complex. Similarly, DHQS- ZINC19334122 complex remain in a steady

state between the range of 2 and 3 for 8ns and further stable between the range of 3 and 4

throughout the 50ns, which also suggested that higher stability and lower flexibility, arise as a

result of interaction between the ZINC19334122 and the residues of the flexible region of

DHQS (Figure 3). Also for radius of gyration DHQS- ZINC633887 complex equilibrated at

the average of 21-21.5 throughout the 50ns, while DHQS- ZINC19334122 complex

equilibrated after 10ns at the average of 21-22 for the remaining 40ns. The RMSD shown in

the figure 3 corresponding to the value of protein-ligand complex (DHQS- ZINC633887 and

DHQS- ZINC19334122) of the two selected ligands in this study. Similarly, the RMSF

shown in figure 4 corresponding to the value of the selected complex (DHQS- ZINC633887

and DHQS- ZINC19334122), which represented the degree of motion of the initial position

of each residue in both protein and the ligands. Higher value of RMSF (Figure 4) was seen in

some the region of DHQS- ZINC19334122 complex, which clearly indicates the fluctuation

in the flexible loop region of the complex. This leads to a higher value of RMSD in some of

the region of the complex. Lower RMSF value was observed in some of the region of DHQS-

ZINC633887 complex, this indicates that both the binding site of the ligand as well as the

secondary structure element of the protein were close to the original position of their structure

(figure 4).

Conclusion

A total of 400 compounds were selected from two public databases (Zinc database and

PubChem) through virtual screening using PyRx tool against DHQS from Mycobacteria

tuberculosis. Eighteen (18) compounds showed high binding affinity were selected and

10
subjected to ADMET analysis. These lead to the selection of 9 compounds based on ADMET

test which fulfilled all its criteria. Two (ZINC19334122=-9.65kcal/mol and ZINC633887= -

10.29kcal/mol) out of the 9 compounds, with minimum binding energy were further selected

for Molecular dynamic (MD) simulation analysis. This revealed that both compounds formed

a stable complex in the ligand binding sites during 50ns MD simulation. Therefore, these

compounds will serve as potential candidates for MTB after in vivo and in vitro validation.

11
Table 1: Molecular Properties and Drug-likeness of the best selected ligands
S/No. Zinc / PubChem Molecular Number Number of MolLogP MolLogS (in MolPSA MolVol Number Drug-
Code weight of HBA HBD (<=5) Log(moles/L)) (A2) (A3) of stereo likeness
(<=500) (<=10) (<=5) centers
1. ZINC633887 449.07 6 2 3.15 -4.56 73.64 408.40 0 6.2836
2. ZINC12455413 493.25 5 1 4.66 -5.48 61.61 512.75 0 3.8083
3. ZINC19334122 489.35 4 0 3.74 -3.98 29.66 533.78 1 6.0735
4. ZINC08983432 493.31 3 0 1.99 -7.02 23.18 543.23 0 3.911
5. ZINC14986690 490.26 6 2 3.61 -6.47 76.77 511.91 1 -2.5862
6. ZINC14882944 494.28 4 3 4.87 -4.73 73.60 492.88 0 5.7604
7. ZINC04113772 488.29 6 2 3.33 -4.04 78.25 533.19 0 1.9135
8. ZINC20779557 497.30 3 2 2.38 -3.89 46.40 509.58 1 5.0092
9. ZINC11881196 496.28 4 1 4.60 -3.48 53.93 510.20 1 4.195
10. ZINC633895 449.07 6 2 3.03 -4.17 72.94 407.60 0 6.2836
11. ZINC20136483 478.27 3 1 3.08 -4.75 39.25 485.80 0 4.6073
12. ZINC14743064 495.27 5 0 3.51 -5.79 51.70 518.31 1 5.792
13. ZINC18122756 488.20 6 1 3.61 -3.523 66.95 515.86 0 11.116
14. ZINC12243261 492.35 4 1 4.32 -2.83 41.79 529.79 1 -0.15147
15. PubChem72341 475.28 5 3 4.11 -4.87 58.36 506.73 4 4.1737
16. PubChem73393 351.17 3 1 1.04 -2.34 40.62 385.00 6 0.15987
17. PubChem441071 334.17 3 0 1.77 -2.78 27.62 374.88 6 4.5843
18. PubChem265237 470.27 6 2 3.21 -4.07 75.66 564.08 11 1.6889

12
 Table 2: Docking result of DHQS with a ligands having a good binding affinities
S/No. Zinc/PubChem Docking Score/Minimum Interacting Residues Number of Residues involved in hydrophobic interaction
Code Free Energy of Binding Hydrogen
(kcal/mol) Bonding
1. Thr-132, Gln-45, Gly- 4 Glu179, Thr131, Leu175, Thr174, Leu48, Gly106, Glu75,
ZINC633887 -10.29 107 and Asp-73 Ala108, Ala74
2. Ala-108, Glu-75, Asp- 3 Gly107, Glu179, Thr101, Leu175, Thr132, Gln45, Pro176,
ZINC12455413 -10.27 73 Thr171, Thr51, Leu48, Thr174, Gly47, Ala74, Gly106
3. Thr-131 and Glu-179 2 Thr132, Leu48, Pro176, Gly47, Pro46, Asp73, Gln50, Thr174,
ZINC19334122 -9.65 Gln45, Gly106, Leu175, Gly105
4. ZINC08983432 -9.34 Glu-70 1 Phe85, Val82, Arg68, Ala49, Glu53, Ala52, His44, Ile71, Pro72
5. Gln-45, Glu-50 and 3 Gly107, Gly135, Ala108, Leu134, Thr132, Glu179, Glu75,
ZINC14986690 -8.84 Thr-131 Ala74, Leu48, Thr171, Gly47, Thr174, Leu175, Pro176
6. Gly-107 1 Gly106, Ala108, Leu175, Gln45, Ala74, Glu75, Ala108, Ala74,
ZINC14882944 -8.44 Pro46, Thr132, Glu179
7. Asp-73 1 Leu48, Leu175, Pro176, Gly47, Gln45, Thr174, Glu75, Ala108,
ZINC04113772 -8.42 Ala74, Pro46, Thr132, Glu179
8. Arg-68 and Arg-98 2 Glu70, Pro72, Pro81, Gly77, Asp79, Val82, Phe85, His44, Ile69,
ZINC20779557 -8.41 Val89
9. Glu-50, Gly-47 and 3 Ile69, Phe85, Glu70, Pro46, Ala49, His44, Val89
ZINC11881196 -8.36 Arg-68
10. Arg-68 and Glu-70 2 Ile71, Pro72, Arg92, Ala49, Glu50, Glu52, Glu53, His44, Ala52,
ZINC633895 -8.33 Val89, Ile69
11. Arg-92 1 Pro72, Pro46, Ile71, Glu70, His67, His44, Arg68, Val89, Ile69,
ZINC20136483 -8.26 Phe85
12. ZINC14743064 -8.25 Arg-68 and Glu-70 2 Pro72, Ile71, His67, Ile69, Phe85
13. Thr-131 and Gly-106 2 Tyr261, Arg264, Pro176, Glu179, Leu48, Thr171, Leu175,
Thr174, Gly105, Gln45, Ala109, Ala108, Gly107, Ala74, Glu75,
ZINC18122756 -8.23 Asp73
14. Thr-131 and Pro-46 2 Gly47, Glu50, Thr132, Thr174, Thr171, Gln45, Pro176, Glu179,
ZINC12243261 -8.22 Leu175, Asp73
15 PubChem72341 -13.23 Thr-131 1 Ala74, Glu75, Tyr261, Asp73, Gln45, Thr174, Gly47, Glu50,

13
 Leu48, Leu175, Thr132, Glu179, Gly106, Gly107
16 Thr-131 1 Gly106, Gln45, Glu179, Thr132, Gly105, Leu132, Thr171,
-8.61
PubChem73393 Pro176, Leu48, Asp73
17 PubChem44107 Thr-131 1 Gln45, Glu179, Pro176, Thr174, Leu175, Thr132, Thr171,
1 -8.46 Leu48, Gly106, Gly105, Asp73
18 PubChem26523 Thr-171 and Thr-174 2 Gly106, Glu50, Ala108, Asp73, Pro176, Thr51, Leu175, Leu48,
7 -8.24 Gly47, Thr132, Gln45, Gly107

Table 3: ADMET analysis of the 18 compounds with least binding energies

S/N BBB HIA CYP450 Biodegra AMES Test Carcinogens Mutagenic Tumorige Reproduci Irritant
o. Zinc/PubChem 2D6 dation nic bility
Database Inhibitor
1 BBB+ HIA+ Non- Not ready Non AMES Non- none none none none
inhibitor biodegrad toxic carcinogens
ZINC633887 able
2 BBB+ HIA+ Non- Not ready Non AMES Non- high high none none
inhibitor biodegrad toxic carcinogens
ZINC12455413 able
3 BBB+ HIA+ Inhibitor Not ready Non AMES Non- none none none none
biodegrad toxic carcinogens
ZINC19334122 able
4 BBB+ HIA+ Non- Not ready Non AMES Non- none none none none
inhibitor biodegrad toxic carcinogens
ZINC08983432 able
5 BBB- HIA+ Non- Not ready Non AMES Non- none Low none none
inhibitor biodegrad toxic carcinogens
ZINC14986690 able
6 BBB+ HIA+ Non- Not ready Non AMES Non- none none high none
inhibitor biodegrad toxic carcinogens
ZINC14882944 able

14
7 BBB+ HIA- Non- Not ready Non AMES Non- none none none none
inhibitor biodegrad toxic carcinogens
ZINC04113772 able
8 BBB+ HIA+ Non- Not ready Non AMES Non- none none none none
inhibitor biodegrad toxic carcinogens
ZINC20779557 able
9 BBB+ HIA+ Non- Not ready Non AMES Non- none none none none
inhibitor biodegrad toxic carcinogens
ZINC11881196 able
10 BBB+ HIA+ Non- Not ready Non AMES Non- none none none low
inhibitor biodegrad toxic carcinogens
ZINC633895 able
11 BBB+ HIA+ Non- Not ready Non AMES Non- none none none none
inhibitor biodegrad toxic carcinogens
ZINC20136483 able
12 BBB+ HIA+ Inhibitor Not ready Non AMES Non- high none none none
biodegrad toxic carcinogens
ZINC14743064 able
13 BBB+ HIA+ Non- Not ready Non AMES Non- none none none none
inhibitor biodegrad toxic carcinogens
ZINC18122756 able
14 BBB+ HIA+ Non- Not ready Non AMES Non- none none none none
inhibitor biodegrad toxic carcinogens
ZINC12243261 able
15 BBB+ HIA+ inhibitor Not ready Non AMES Non- none high none high
biodegrad toxic carcinogens
PubChem72341 able
16 BBB+ HIA+ Non- Not ready Non AMES Non- none none none none
inhibitor biodegrad toxic carcinogens
PubChem73393 able
17 HIA+ Non- Not ready none none none none
PubChem441071 inhibitor biodegrad

15
 able
18 BBB+ HIA+ Non- Not ready Non AMES Non- none none low none
inhibitor biodegrad toxic carcinogens
PubChem265237 able
BBB+ = Blood-Brain Barrier positive, BBB- = Blood-Brain Barrier negative, HIA+ = Human Intestinal Absorption positive and HIA- = Human
Intestinal Absorption negative

16
 PubChem265237
Minimum Free Energy of Binding (kcal/mol)

PubChem441071
PubChem73393
PubChem72341
Figure 1: Distribution different binding energies of the 18 best ligands

ZINC12243261
Zinc/PubChem Compounds

ZINC18122756
ZINC14743064
ZINC20136483
ZINC633895

17
ZINC11881196
ZINC20779557
ZINC04113772
ZINC14882944
ZINC14986690
ZINC08983432
ZINC19334122
ZINC12455413
ZINC633887

-2

-4

-6

-8

-10

-12

-14
0
18
19
Figure 2(a-r): Inteaction of 3-dehydroquinate synthase residues with the 18 selected ligands

20
Figure 3: The MD simulation (RMSD analysis) of DHQS- ZINC633887 and DHQS-
ZINC19334122 complex for 50ns

Figure 4: The MD simulation (RMSF analysis) of DHQS- ZINC633887 and DHQS-

ZINC19334122 complex for 50ns

21
Figure 5: The MD simulation (Radius of gyration analysis) of DHQS- ZINC633887 and
DHQS- ZINC19334122 complex for 50ns

Conflict Interest
We declare that we have no conflict of interest

Acknowledgment
The corresponding author of this paper is very much thankful to Prof. B. Jayaram (Coordinator),
Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of
Technology (IIT) Delhi and Mr Shashank Shekhar, Senior Project Scientist, Supercomputing
Facility for Bioinformatics & Computational Biology, Indian Institute of Technology (IIT) Delhi
for their tremendous support through providing facilities during the course of the research.

22
Reference

1. Mustyala KK, Malkhed V, Chittireddy VR, Vuruputuri U. Virtual screening studies to

identify novel inhibitors for Sigma F protein of Mycobacterium tuberculosis. The
International Journal of Mycobacteriology. 2015; 4(4):330.
2. Somvanshi P, Singh V, Seth PK. In silico prediction of epitopes in virulence proteins
of Mycobacterium tuberculosis H37Rv for diagnostic and subunit vaccine design. J
Proteomics Bioinform. 2008; 1:143-53.
3. Billones JB, Carrillo MC, Organo VG, Sy JB, Clavio NA, Macalino SJ, Emnacen IA,
Lee AP, Ko PK, Concepcion GP. in silico discovery and in vitro activity of inhibitors
against Mycobacterium tuberculosis 7, 8-diaminopelargonic acid synthase (Mtb
Bioa). Drug design, development and therapy. 2017; 11:563.
4. Billones JB, Carrillo MC, Organo VG, Macalino SJ, Sy JB, Emnacen IA, Clavio NA,
Concepcion GP. Toward antituberculosis drugs: in silico screening of synthetic
compounds against Mycobacterium tuberculosis l, d-transpeptidase 2. Drug design,
development and therapy. 2016;10:1147.
5. Tzin V, Galili G, Aharoni A, Shikimate Pathway and Aromatic Amino Acid
Biosynthesis. In: eLS. John Wiley & Sons, Ltd: Chichester. 2012. DOI:
10.1002/9780470015902.a0001315.pub2
6. Herrmann KM. The shikimate pathway: early steps in the biosynthesis of aromatic
compounds. The Plant Cell. 1995; 7(7): 907.
7. de Mendona JD, Ely F, Palma MS, Frazzon J, Basso LA, Santos DS. Functional
characterization by genetic complementation of aroB-encoded dehydroquinate
synthase from Mycobacterium tuberculosis H37Rv and its heterologous expression
and purification. Journal of bacteriology. 2007; 189(17): 6246-52.
8. Chandran SS, Frost JW. Aromatic inhibitors of dehydroquinate synthase: synthesis,
evaluation and implications for gallic acid biosynthesis. Bioorganic & medicinal
chemistry letters. 2001; 11(12): 1493-6.
9. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard
O, Shimanouchi T, Tasumi M. The protein data bank. The FEBS Journal. 1977; 80(2):
319-24.
10. Johansson MU, Zoete V, Michielin O, Guex N. Defining and searching for structural
motifs using DeepView/Swiss-PdbViewer. BMC bioinformatics. 2012; 13(1):173.
11. Ramachandran S, Kota P, Ding F, Dokholyan NV. Automated minimization of steric
clashes in protein structures. Proteins: Structure, Function, and Bioinformatics. 2011;
79(1): 261-70.
12. Porollo A, Meller J. POLYVIEW-MM: web-based platform for animation and
analysis of molecular simulations. Nucleic acids research. 2010; 38 (suppl_2):W662-
6.
13. Imran M, Alanazi GHA, Alam MdT, Design, molecular docking studies, in silico
drug likeliness prediction and synthesis of some Benzimidazole derivatives as
antihypertensive agents. IAJPS. 2017; 4 (04): 926-936.
14. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ.
Automated docking using a Lamarckian genetic algorithm and an empirical binding
free energy function. Journal of computational chemistry. 1998; 19(14): 1639-62.
15. Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativitya
rapid access to atomic charges. Tetrahedron. 1980; 36(22): 3219-28.

23
16. Cheng F, Li W, Zhou Y, Shen J, Wu Z, Liu G, Lee PW, Tang Y. admetSAR: a
comprehensive source and free tool for assessment of chemical ADMET properties.
2012; 3099-3105
17. Case DA, Berryman JT, Betz RM, Cerutti DS, Cheatham I. TE, TA Darden, RE
Duke, TJ Giese, H. Gohlke, AW Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus,
A. Kovalenko, TS Lee, S. LeGrand, P. Li, T. Luchko, R. Luo, B. Madej, KM Merz,
G. Monard, P. Needham, H. Nguyen, HT Nguyen, I. Omelyan, A. Onufriev, DR Roe,
A. Roitberg, R. Salomon-Ferrer, CL Simmerling, W. Smith, J. Swails, RC Walker, J.
Wang, RM Wolf, X. Wu, DM York, and PA Kollman. 2015.
18. Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham III T, Dans PD,
Jayaram B, Lankas F, Laughton C, Mitchell J. ABC: a systematic microsecond
molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic
acids research. 2014 ; 42(19):12272-83.
19. Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham III T, Dixit
S, Jayaram B, Lankas F, Laughton C, Maddocks JH. A systematic molecular
dynamics study of nearest-neighbor effects on base pair and base pair step
conformations and fluctuations in B-DNA. Nucleic acids research. 2009; 38(1): 299-
313.
20. Dixit SB, Beveridge DL, Case DA, Cheatham TE, Giudice E, Lankas F, Lavery R,
Maddocks JH, Osman R, Sklenar H, Thayer KM. Molecular dynamics simulations of
the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence
context effects on the dynamical structures of the 10 unique dinucleotide steps.
Biophysical journal. 2005; 89(6):3721-40.

24
25
26
27