Identification of new snake venom zinc Metalloproteinase inhibitor using docking studies from Plectanthus amboinicus

 

Subramaniam Sivakumar*, Manju P

Department of Biochemistry, Sri Sankara Arts and Science College (Autonomous), Enathur – 631561.

 

ABSTRACT:

Snake bites cause considerable morbidity and mortality worldwide. Snake bite can require intensive care since they are life-threatening injuries.  India found to have the highest snakebite mortality in the world.  World Health Organization (WHO) estimates place the number of bites to be 83,000 per annum with 11,000 deaths.  Snake bite is one of the most neglected public health issues. Metalloproteinases are among the most abundant toxins in many Viperidae venoms. Snake venom zinc metalloproteinase (SVMP) causes haemorrhage.  It also induces skeletal muscle damage and microvessel disruption.  In the present study, strategy was planned to identify the drug against SVMP through bioinformatics tools.  Docking was carried out between SVMP and chemical compounds retrieved from Plectanthus amboinicus.  From the docking score two chemical compounds namely beta-sitosterol beta-D glucoside and euscaphic compound were selected with highest scores 5886 and 5180 respectively.  By applying Lipinski’s rule of five, euscaphic compound found to be effective druggable inhibitor against SVMP enzyme. 

 

 

 

INTRODUCTION:

Throughout the world, snake bites remain life-threatening injuries^1-4, sometimes requiring intensive care⁵. Similar to malaria, dengue hemorrhagic fever, tuberculosis, and parasitic diseases, the risk of snake bite is always present¹. In 2009, the World Health Organization (WHO) added snake bites to the list of neglected tropical diseases, which includes dengue hemorrhagic fever, cholera, and Japanese encephalitis. The mortality associated with snake bites is much greater than that of other neglected tropical diseases^1,6.  Snake venom metalloproteinases (SVMPs) are the primary factors responsible for hemorrhage and may also interfere with the hemostatic system, thus facilitating loss of blood from the vasculature of the prey⁷.   

 

In addition to hemorrhage, venom metalloproteinases induce skeletal muscle damage, myonecrosis, which seems to be secondary to the ischemia that ensues in muscle tissue as a consequence of bleeding and reduced perfusion. Microvessel disruption by metalloproteinases also impairs skeletal muscle regeneration, being therefore responsible of fibrosis and permanent tissue loss after snake bites⁸.

 

The world health organization (WHO) estimated that 80% of the population of developing countries depend on traditional medicines mostly plant drugs for their primary health care needs. Also, modern pharmacopoeia still contains at least 25% of drug derived from plants and many others are synthetic analogous build on prototype compounds isolated from medicinal plants. They are used for wide range of health-related applications from common cold to memory improvement and treatment of poisonous snake bites, enhancements of general immunity etc., India is the one of the major countries inhabited by a large number of tribal communities who possess precious and unique knowledge about the use of wild plants for treating human ailments^9,10.

 

Plectranthus amboinicus (Karpooravalli in tamil) is a tender fleshy perennial plant in the family Lamiaceae with oregano like flavor and odor, reported for many traditional uses, especially for the treatment of cough, sore throat and other nasal congestion. It is also used for a range of other problems such as infection, rheumatism and flatulence^10,11. Plectranthus amboinicus Benth may be used for treating poisonous snake bites, and relieving symptoms such as headache, flatulence, vomiting, diarrhea and fever.  Metalloproteinases are among the most abundant toxins in many Viperidae venoms. Snake venom zinc metalloproteinase (SVMP) causes haemorrhage.  It also induces skeletal muscle damage and microvessel disruption.  The aim of the study is to identify the active principle from Plectanthus amboinicus, a medicinal plant used in folk medicine to treat snake bite. In the present study, strategy was planned to identify the drug against SVMP through bioinformatics tools. 

 

METHODOLOGY:

Retrieval of Protein sequence of snake venom:

Protein sequence of snake venom metalloproteinase was retrieved from Uniprot¹² database.

 

Chemical constituent retrieval from Plectanthus amboinicus:

Eighteen chemical constituents present in Plectanthus amboinicus were retrieved from literature of Roshan et al., 2010¹¹.

 

Prediction of Tertiary structure of snake venom metalloproteinase:

Tertiary structure of snake venom metalloproteinase was achieved using CPH Model¹³ server.

 

Preparation of list of ligands from Pubchem against snake venom metalloproteinase:

List of ligands from Plectanthus amboinicus against snake venom metalloproteinase were identified from Pubchem. The structure and smile formats of ligands were collected from pubchem.

 

Docking of snake venom metalloproteinase with ligands:

The collected structure of ligands and structure of snake venom metalloproteinase were subjected into PatchDock¹⁴ server for docking.

 

Selection of best ligands:

Best ligand was selected on the basis of docking score and Lipinski’s rule of five.

 

RESULTS AND DISCUSSION:

Snake venom metalloproteinase is an important constituent present in higher concentration of about 30% in snake venom. Protein sequence for SVMP was retrieved from Uniprot database with Id P30431.  Eighteen chemical constituents from the plant Plectanthus amboinicus extracted retrieved from Roshan et al., (2010) study which are 6-methoxy-genkawanin, apigenin, butylaniside, carvacrol, beta-caryophylle, chrysoeriol, 1,8-cineole, cirsimaritin, crategolic, p-cymene, eriodictyol, ethylsalicylate, euscaphic, limonene, luteolin, myrcene, oleanolic, oxaloacetate, pinenes, pomolic, quercetin, salvigenin, selenene, beta-sitosterol beta-D-glucoside, taxifolin, terpinen-4ol, terpinene, tetrahydroxyurs 12-en-28oic, thymol, tormentic acid, ursolic acid and verbenone. The tertiary structure for SVMP was predicted using CPH Model which was shown in figure-1.  The tertiary structures for eighteen chemical constituents were retrieved from Pubchem database.  

 

Docking was carried out between SVMP and eighteen chemical compounds using PatchDock server.  The docking scores represented in table-1.  From the docking scores of eighteen phytochemical compounds, two chemical compounds namely beta-sitosterol beta-D glucoside and euscaphic compound selected with highest scores 5886 and 5180 respectively.  The docked images of the selected phytochemicals depicted in figure-2.

 

Molinspiration¹⁵ online tool was utilized to predict molecular properties of beta-sitosterol beta-D glucoside and euscaphic compound.  From the molinspiration results, it was concluded that euscaphic compound is the best inhibitor of snake venom metalloproteinase because none of the violation regarding Lipinski’s rule of five¹⁶ rules exhibited by it.  Through the present study, the plant Plectanthus amboinicus has the ability to inhibit snake venom metalloproteinase determined through in-silico study.  However, these findings should be confirmed with wetlab studies before ascertaining the effectiveness of chemical compound as drug.

 

Figure-1: Tertiary structure of SVMP.

 

Figure -2: Docked structures of two phytochemicals

 

Table-1: Docked score of phytochemicals from the plant Plectanthus amboinicus

 

 

Table - 2: Molinspiration results of Beta-sitosterol beta-D glucoside and euscaphic.

Sl. No.	Drug name	Log P value	TPSA	N atoms	Hydrogen bond acceptor	Hydrogen bond donor	No. of violation of Lipinski’s rule of five
01	Beta-sitosterol beta-D glucoside	7.15	99.38	41	6	4	2
02	Euscaphic	4.93	97.98	35	5	4	0

 

 

 

CONFLICT OF INTEREST:

The authors declare no conflict of interest.

 

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Received on 18.05.2017          Accepted on 11.08.2017        

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