Docking Analysis of Potent Inhibitors of β-Ketoacyl-Acyl Carrier Protein Synthase III as Potential Antimicrobial Agents

 

C. Buvana¹, M. Sukumar², Sijamol¹, Udhyakumri¹, Hannath¹

¹Dept. of. Pharmaceutical Chemistry, Grace College of Pharmacy, Palakkad-678004.

²Dept. of. Pharmaceutical Chemistry, Sri Ramakrishna Institute of Paramedical Sciences -Coimbatore

*Corresponding Author E-mail: Boviblue@gmail.com

 

According to data of the World Health Organization, Tuberculosis (TB) caused by Mycobacterium tuberculosis, is considered to be the most chronic communicable disease in the World especially in Asia and Africa. This situation was made worse by the emergence of multi drug resistant TB (MDR-TB) and the increasing number of HIV-positive TB cases. Worldwide, TB accounts for approximately one-fourth of HIV-related deaths and is the leading cause of death in HIV-infected adults in developing countries, thus an urgent need exists for the development of new antimycobacterial agents with a unique mechanism of action. Mycobacterium tuberculosis FabH, an essential enzyme in the mycolic acid biosynthetic pathway, is an attractive target for novel anti-tubercolosis agents. A series of pyrazolone linked with isonicotinic acid hydrazide were computationally designed and energy minimized. The molecular properties were calculated from suitable computational tools. These ligands were investigated for drug like properties by calculating Lipinski’s rule of five using molinspiration. All of the derivatives showed a zero violations of the rule of 5 which indicates good bioavailability. The positive bioactivity score of the derivative were also in agreement with their probability of drug likeness. These compounds were docked into the active site of FabH, (PDB code-1HZP) using Argus lab docking software which showed good binding energy  for the enzyme, when compared with the binding energies of standard drug isoniazid -6.17kcal/mol.) Among all the designed ligands, the ligand II and V  showed more binding energy values (-8.68 and -8.86Kcal/mol) . In future we planned to synthesise these ligand and to screen for their anti TB activity.

 

 

INTRODUCTION: ^(1-7)

Tuberculosis now-a-days is one of the major reasons of death all across the world. The responsible microbe for this dreaded disease is none but a bacterium, Mycobacterium tuberculosis, which has an unusual cell wall composition for its survival. The cell wall component has mycolic acid which is synthesized due to the Fatty acid synthase-II enzyme (FAS-II). This prevents binding of broad range of drug molecule due to presence of a precursor of mycolic acid, the Meromycolic acid. This facilitates the bacterium with Pathogenicity, survival and multi drug resistant functionality. Every year huge population is being chomped by tuberculosis at a rate of about 2-3 million annually (Sullivan et al.). thus an urgent need exists for the development of new antimycobacterial agents with a unique mechanism of action.

 

The mycobacterial cell wall, which is composed of mycolic acids (α-alkyl-β-hydroxy long chain fatty acids) is known to be important for the growth, survival, and pathogenicity of mycobacteria. Mycobacteria contain both type I (FAS I) and type II (FAS II) fatty acid biosynthetic pathways. FAS is a single multifunctional polypeptide that catalyzes all the reactions in the elongation pathway. On the other hand, FAS II system is catalyzed by a series of small, soluble proteins that are each encoded by a discrete gene existing as separate proteins. Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthase III (mtFabH) is a key condensing enzyme responsible for initiation of FAS II fatty acid biosynthetic pathway, and has emerged as an attractive new target for novel anti-tuberculosis agents in recent years.(8)

 

Pyrazolone  derivatives are known to possess antitubercular, antifungal, anti-neoplastic activities

 

Construction of our compounds containing both the pyrazolone and isonicotinic acid derivative systems (9) towards the development of novel antimycobacterial agents. Based on we  planned to link pyrazolone and isonicotinic acid derivative systems to produce better anti tubercular agents and to evaluate the interactions with the target(β-ketoacyl-acyl carrier protein synthase III ) by using ARGUS LAB docking software.

 

MATERIALS AND METHODS:

STEP I:

CALCULATION OF MOLECULAR: PHYSICOCHEMICAL PROPERTIES: ^(10-11)

The physiochemical properties involve determination of drug-like property of the designed compounds. It is based on Lipinski^,s rule of five and can be determined by using molinspiration cheminformatics software. All the designed  compounds showed zero violation of  Lipinski^’s rule of five, which indicates good bioactivity and bioavailability.

 

The Rule:

        Lipinski's Rule of Five states that in general, an orally active drug has not more than one violation of the following criteria.

Ø    Not more than 5 hydrogen bond donors (nitrogen or oxygen atoms with one or more hydrogen atoms).

Ø    Not more than 10 hydrogen bond acceptors (nitrogen or oxygen atoms)

Ø    A molecular weight under 500 g/ mol.

Ø    A partition coefficient log P less than 5.

Ø      Not more than 15 rotatable bonds.

 

STEPII:

MOLECULAR DOCKING: ^(12-13)

Preparation of protein molecule

The experimental structure of β-ketoacyl-acyl carrier protein synthase III (mtFabH) (PDB ID: HZP)  as shown in Figure 1 was retrieved from the RCSB protein data bank as a PDB file. The protein molecules were prepared mainly by using the software Swiss PDB viewer. Active site residues within a range of 4.0 A0 were selected and saved in PDB format.

 

Preparation of ligand:

The ligands were drawn using ACD/ Chemsketch (12.0) (Alex, 2009) and saved in mol 2 format. The saved ligand compounds were later imported and minimized in Argus Lab after adding hydrogen bonds. The molecules thus obtained were saved in PDB format.

 

 

Table no: 1 PHYSICO-CHEMICAL PROPERTIES:

COMP	Log P	TPSA	MW	No of hydrogen bond acceptor	No of hydrogen bond donor	Violation	No of rotatable bond	Molar volume
INH I	1.182	103.76	385.81	8	2	0	5	321.98
INH II	0.463	149.58	396.36	10	2	0	6	331.77
INH III	0.561	112.995	381.39	9	2	0	6	333.99
INH IV	0.157	133.22	397.39	10	3	0	6	342.00
INH V	0.439	‘149.58	396.36	10	2	0	6	337.77

 

Table no: 2 BIOLOGICAL ACTIVITES:

COMP	GPCR	ION CHANNEL	KINASE INHIBITOR	NUCLEAR RECEPTOR LIGAND	PROTEASE INHIBITOR	ENZYME INHIBITOR
INH I	-0.20	-0.52	-0.20	-0.68	-0.43	-0.29
INH II	-0.33	-0.53	-0.30	-0.71	-0.49	-0.34
INH III	-0.23	-0.56	-0.21	-0.65	-0.43	-0.29
INH IV	-0.21	-0.52	-0.17	-0.59	-0.49	-0.29
INH V	-0.33	-0.54	-0.30	-0.72	-0.50	-0.36SS

 

Table :3 Docking results of five drugs against β-keto acyl synthase- III

 

 

Crystal Structure of the Myobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Synthase III Protein Structure PDB CODE (1HZP)

 

STRUCTURE OF DESIGNED  LIGANDS:

 

Ligand	R
INH I	-Cl
INH II	NO2
INH III	OCH3
INH IV	4- OCH3 3-OH
INH V	3- NH2

 

Docking of designed ligands to β-ketoacyl-acyl carrier protein synthase III (mtFabH):

Docking of designed ligands (INH I-INH V) with β-ketoacyl-acyl carrier protein synthase III was performed using ARGUS LAB4.0. The algorithm exhaustively searches the entire rotational and translational space of the ligand with respect to the receptors. The various solutions evaluated by a score, which is equivalent to the absolute value of the total energy of the ligand in the protein environment. The best docking solutions ARGUS LAB score for each compound was considered. It was noted that ARGUS LAB scores of comp INH II and INH V was -8.68 and -8.86 respectively, which is greater than isoniazid drug score value -6.17. as shown in Table 3, Figures 2,3 and 4. The drug like activity of the ligand molecules are characterized using ADME properties. Isoniazid and designed compounds  satisfy Lipinski rule of 5 and ADME properties results are shown in Table 1& 2.

                                                             Energy level=  -8.86Kcal/mol

Fig :2 Molecular docking  in Argus Software(INH V)

Energy level=  -8.68Kcal/mol

Fig:3  Molecular docking  in Argus Software(INH II)

 

      Energy level=  -6.17Kcal/mol

Fig :4   Molecular docking  in Argus Software(ISONIAZID)

RESULT AND DISCUSSION:

Drug likeness:

All the designed compounds (INH I – INH V) showed zero violation of  Lipinski^’s rule of five, which indicates good bioactivity and bioavailability.

 

Docking:

Docking of designed ligands (INH I-INH V) with β-ketoacyl-acyl carrier protein synthase III was performed using ARGUS LAB4.0

 

Based on the literature, it has been found that pyrazolone linked isonicitinic acid hyrazide derivatives  can be used to target β-ketoacyl-acyl carrier protein synthase III. The energy values were calculated using Argus lab.  

 

Among all the designed ligands, the ligand II and V showed more binding energy values (-8.68 and -8.86 kcal/mol), which is greater than isoniazid drug score value -6.17 kcal/mol. as shown in Table 3.

 

CONCLUSION:

Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthase III (mtFabH) is a key condensing enzyme responsible for initiation of FAS II fatty acid biosynthetic pathway, and has emerged as an attractive new target for novel anti-tuberculosis agents in recent years.

It was observed that beta-ketoacyl acyl carrier protein synthase when docked with the compounds, give good scores,  also showed good result for ligand INH II  and INH V . The predicted potency of the five compounds with unknown potency showed that two ligands had very low activity value which ensures the potentiality of the compounds as good anti-tubercular drugs. In future research work we planned to synthesis these pyrazolone derivatives and screen for their in-vitro anti mycobacterial activity

                              

REFERENCES:

1        World Health Organization (WHO). Global Tuberculosis Control: A Short Update to the 2009 Report. WHO/HTM/TB/2009.426. WHO: Geneva, Switzerland, 2009. New address: P.J. Kocienski, School of Chemistry, University of Leeds, Leeds LS2 9JT, UK.

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6        Jayakumar, A.; Tai, M.H.; Huang, W.Y.; AlFeel, W.; Hsu, M.; AbuElheiga, L.; Chirala, S.S.;Wakil, S.J. Human fatty acid synthase: Properties and molecular cloning. Proc. Natl. Acad. Sci. USA1995, 92, 8695–8699.

7        Chirala, S.S.; Huang, W.Y.; Jayakumar, A.; Sakai, K.; Wakil, S.J. Animal fatty acid synthase:Functional mapping and cloning and expression of the domain I constituent activities.Proc. Natl. Acad. Sci. USA 1997, 94, 5588–5593.

8.       The Cord Factor: Structure, Biosynthesis and Application in Drug Research – Achilles Heel of Mycobacterium tuberculosis? Ayssar A. Elamin, Matthias Stehr and Mahavir Singh  Department of Gene Regulation and Differentiation,  Helmholtz Centre for Infection Research, Braunschweig Germa

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10.    Downloaded from http://www.acdlabs.com/resources/freeware/chemsketch/

11.    Molinspiration Cheminformatics. Molinspiration. [Internet]. 2010 [cited 2011 Mar 26]. Available from: http://www.molinspiration.com/cgi-bin/properties

12.    Research Collaboratory for Structural Bioinformatics. Protein Data Bank. [Internet]. 2011   [updated 2011 Mar 22; cited 2011 Mar 26]. Available from: http://www.pdb.org/

13.    ArgusLab 4.0.1, Mark A. THOMPSON, Planaria Software LLC, Seattle, WA, Downloaded from http://www.arguslab.com

 

 

 

Received on 26.04.2013       Modified on 11.05.2013

Accepted on 15.05.2013      © AJRC All right reserved