Design and Synthesis, In Silico Analysis of Condensed Pyrimidine derivatives as Potent Antimicrobial Agents

 

S. A. Khedkar1, J. S. Patil2, P. M. Sabale3

1Department of Pharmaceutical Chemistry, JNT University, Kakinada, Andhra Pradesh, India.

2Shivajirao Jondhale College of Pharmacy, Asangaon, Maharashtra, India.

3Rashtrasant Tukadoji Maharaj University, Nagpur, Maharashtra, India.

*Corresponding Author E-mail: samratkhedkar@yahoo.in

 

ABSTRACT:

A series of 24 condensed pyrimidine derivatives was synthesized via multistep reactions using microwave radiation and have opted to explore the possible inhibition mechanism via virtual analysis by using V life MDS. The synthesized compounds were characterized by spectroscopic analysis. All the synthesized compounds were found to show good in-silico binding analysis which indicated their potential to explore as good antimicrobial agents. All the synthesized derivatives were screened in-vitro for their antibacterial activity against two gram positive and gram negative bacteria. Among the compounds tested, SAKB2, SAKB7, SAKB8, SAKB9 SAKB10, SAKB11, SAKB12 and SAKB13derivatives exhibited potent antimicrobial activity.

 

KEYWORDS: Pyrimidine, Heterocyclic, Synthesis, In silico, Antimicrobial, Molecular docking.

 

 


INTRODUCTION:

Microbial infections are one of the major reasons of the mortality and morality in the mankind. Microorganism like bacteria, virus and fungi are posing the significant problem to the healthcare systems. The discovery of the antibiotics and chemotherapeutic agents has significantly controlled this problem but due to continuous increase in the multidrug-resistant microbial strains infectivity of this microorganism is increased significantly. The resistance of these microbes towards antibiotics is one of the major reasons behind the increase in the infectivity. The irrational or continuous use of the agents like antibiotics and other chemotherapeutic agents leads to the strains which are totally resistance towards all the agents in the dosage regime which might leads to the critical situation. Development of the strains like methacilin resistant S. Aureus (MRSA), MDRTB, XDRTB, TDRTB pushing medicinal chemist for development of the new chemotherapeutic against all these resistant strains.

 

Development of the antibacterial agents is an interesting job which is mainly focused on the development of the agents which targets the replication of the bacteria. The replication cycle of the bacteria can be inhibited via inhibiting the critical enzymes which are important for the bacterial growth like DNA gyrase and Topoisomerase. DNA gyrase and topoisomerase are well known antimicrobial targets which are targeted by the one of the most widely utilized antimicrobial class fluroquinolones. Pyrimidine is one of most researched heterocyclic nucleus due to its wide spread presences in the nature and its importance in the overall development. Pyrimidine derivatives are often showed biological activities like antimicrobial, analgesic, anti-inflammatory, antidiabetic, antioxidant, antitumor, antibacterial. Keeping the biological significance in mind here we are reporting development of condensed pyrimidine derivatives using microwave assisted synthesis and their virtual and in vitro biological analysis as potent antimicrobial agents.

 

EXPERIMENTAL:

Design of condensed pyrimidine derivatives:

The optimized Condensed pyrimidine derivatives were designed on the basis of modification of the pyrimidine nucleus. The designed set of inhibitors has then scrutinized via computational analysis and the molecules which are shown promising results in the computational analysis are selected for the further analysis.

 

Docking analysis:28

Molecular docking analysis was performed on the selected protein target Crystal Structure of E. coli 24kDa domain in complex with Clorobiocin (PDB ID 1KZN) was downloaded from the free protein databank www.rcsb.org. The docking analysis was performed using V life MDS. Biopredicta Module of the V life MDS was utilized for the docking analysis. The prepared protein structures were further utilized for docking simulation.

 

Synthesis of heterocyclic amine derivatives:

A mixture of thiosemicarbazide (0.01mol) and aryl carboxylic acid (0.01mol) was refluxed for 6–8 h using methanol: water (60:40) as solvent in the presence of conc. H2SO4 (10 drops). The mixture was then poured on crushed ice to get the amines.

 

Synthesis of condensed pyrimidine derivatives:

Equimolar quantities of the quinazoline derivatives and corresponding amines/heterocyclic amines are taken in to the round bottom flask and mixed well. 20ml of isopropyl alcohol is added into the reaction mixture and heated for 10 min in microwave. Reaction mixture is poured in to ice and separated product washed with water. All synthesized derivatives are shown in table no1.

 

Table no 1: Table showing synthesized lead derivatives

 

 

Molecule Code

R1

R2

SAKB1

 

 

 

SAKB2

 

 

SAKB3

 

 

SAKB4

 

 

 

SAKB5

-H

 

SAKB6

 

 

SAKB7

 

 

SAKB8

 

 

SAKB9

 

 

SAKB10

 

 

SAKB11

 

 

SAKB12

 

 

SAKB13

 

 

SAKB14

 

 

SAKB15

 

 

SAKB16

 

 

SAKB17

 

 

SAKB18

 

 

SAKB19

-H

 

SAKB20

-H

 

SAKB21

-H

 

SAKB22

-H

 

SAKB23

-H

 

SAKB24

-H

 

 

N-(4-methylphenyl)-2-phenylquinazolin-4-amine (SAK18): Crystaline solid, point:.3499 (NH),334(C-H) 1H NMR (δ ppm) 2.48 (3H, s, CH3), 7.2-7.5 (12 H m, ArH), 9.96 (1 H NH).

 

N-(4-bromo-phenyl)-2-phenylquinazolin-4-amine (SAKB10): Crystaline solid, point:.3400 (NH),2982(C-H) 1H NMR (δ ppm) 7.2-8.6 (13 H, m, ArH ), 8.61 (1 H NH )

 

N-(4-fluro-phenyl)-2-phenylquinazolin-4-amine (SAKB15): Crystaline solid, point:.3315.14 (NH),2900(C-H) 1H NMR (δ ppm) 7.2-8.2 (13H, m, ArH), 8.58 (1 H NH)

 

N-(4-chlorophenyl)quinazolin-4-amine (SAKB19): Crystaline solid, point:.3100 (NH),2800(C-H) 1H NMR (δ ppm) 6.9-8.4(13H, m, ArH ), 8.9(1 H NH)

 

Antimicrobial activity:

The inoculums of the microorganism were prepared from the bacterial cultures. 15ml of nutrient agar (Hi media) medium was poured in clean sterilized Petri plates and allowed to cool and solidify. 100 µl of broth of bacterial strain was pipette out and spread over the medium evenly with a spreading rod till it dried properly. Wells of 6mm in diameter were bored using a sterile cork borer. Solutions of all the extracts (1, 5 and 10mg/ml) in DMSO were prepared. 100µl of plant extracts solutions was added to the wells. The petri plates incubated at 370C for 24 h. streptomycin (1mg/ml) was prepared as a positive control DMSO was taken as negative control. Antibacterial activity was evaluated by measuring the diameters of the zone of inhibitions (ZI) all the determination were performed in triplicates.

 

RESULTS AND DISCUSSION:

Docking Analysis:

Grip based docking simulation are performed and all targeted molecules were found to be binding with selected target with good binding affinity and showing key interactions like hydrogen bond, Charge, Aromatic, hydrophobic and Vander wall interactions. All the molecules are having significant binding interaction with the targeted protein SAKB2 showed hydrogen bonding interaction with ARG76 and SAKB7 interacted via hydrogen bonding with ARG76, SAKB10 interacted with ARG76 with formation of hydrogen bond and, SAKB11 with ARG76, SAKB12 with ARG76 and ARG136 with formation of two hydrogen bond and, SAKB13 via formation of hydrogen bond with ASN46 anddARG76. Docking interactions are shown in figure no 1- 4.

 

 

Figure no 1: Docking Interactions of SAKB2

 

Figure no 2: Docking Interactions of SAKB7

 

Figure no 3: Docking Interactions of SAKB10

 

Figure no 4: Docking Interactions of SAKB11

 

Biological activity:

Anti-bacterial activity of the molecules was determined using disk plate method using Ciprofloxacin as standard. Anti-bacterial activity of the molecules was given in following table no 2 and figures no.5

 

Table No 2: Table showing antimicrobial activity of the synthesized derivatives.

Molecule Code

Zone of Inhibition

B. Substilus

P. aeruginosa

E. coli

S. Aureus

SAKB1

03

04

05

02

SAKB2

14

15

12

11

SAKB3

02

02

01

01

SAKB4

05

06

04

03

SAKB5

04

05

06

04

SAKB6

04

01

01

02

SAKB7

13

10

14

12

SAKB8

17

16

14

12

SAKB9

11

10

13

16

SAKB10

14

12

14

15

SAKB11

12

14

11

15

SAKB12

14

12

14

15

SAKB13

15

14

15

16

SAKB14

04

05

06

07

SAKB15

14

12

11

10

SAKB16

04

05

07

08

SAKB17

11

10

14

12

SAKB18

04

05

01

03

SAKB19

12

14

15

16

SAKB20

15

20

09

17

SAKB21

14

15

14

12

SAKB22

03

02

01

02

SAKB23

05

02

04

03

SAKB24

01

02

02

04

Ciprofloxacin

26

21

28

27

 

Figure No 5: Figure Showing Antimicrobial Activity of synthesized derivatives.

 

CONCLUSION:

N,2-diphenylquinazolin-4-amine derivatives was synthesized using 4-chloro quinazoline derivatives and various aromatic amines. All the reaction was monitored using TLC and products are confirmed using analytical methods. Antibacterial activity of the all the derivatives was analysed using well diffusion method using Ciprofloxacin as a standard against B. Substilus, P.aeruginosa, E. coli and S. Aureus. All synthesized derivatives showed good activity against all the microorganisms. Among the compounds tested, SAKB2, SAKB7, SAKB8, SAKB9 SAKB10, SAKB11, SAKB12 and SAKB13 derivatives exhibited potent antimicrobial activity. The antibacterial activity revelled that the presence of the nitro, chloro, bromo substituted compounds are active than other derivatives. Our prediction is that by introducing these potent moieties into other new ring systems such as pyrazolopyrimidines and pyridopyrimidines may show even better antimicrobial activities.

 

ACKNOWLEDGEMENT:

Authors are thankful to Vlife Sciences for providing facility for research work.

 

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Received on 04.05.2021           Modified on 29.06.2021

Accepted on 02.08.2021         © RJPT All right reserved

Research J. Pharm. and Tech. 2022; 15(6):2422-2426.

DOI: 10.52711/0974-360X.2022.00403