In silico Screening of Lead Molecule from Medicinal Plants for Bacterial Skin Disease- Impetigo

 

R. Sathish Kumar¹*, S. Navatheesh²

¹Assistant Professor, Department of Botany, PSG College of Arts and Science, Coimbatore.

²Department of Botany, PSG College of Arts and Science, Coimbatore.

 

ABSTRACT:

Skin disease is most common form of contagious infections occurs among all ages of people. Impetigo is one such skin infection than can spread from one person to another which appears as sores on the skin that are often covered by a thick dry honey-colored crust. Though the sores have no hurt, it has a tender feel when touched. Impetigo is usually caused by either Streptococcus or Staphylococcus bacteria, which are normally found on the skin and in the nose. When small cuts, scratches, or insect bites occur, these bacteria can get under the skin surface and cause infection. Children and adults can get impetigo, though children get it more often. The aim of this study is to identify the lead molecules to develop drug against impetigo from the medicinal plants. Here, the plants like Aloe vera, Curcuma longa, Lantana camara, and Euphorbia hirta are selected and docking was carried out to find the binding efficiency of the plant compounds with the antibacterial targets. Among Aloe vera showed significant result where 16 compounds were found active, those are carminic acid (11.83 Kcal/mol), 2-Anthroquine sulfonic acid (10.75 Kcal/mol), leucine (6.70 Kcal/mol), omannopyranosyltheronine (6.47 Kcal/mol), methionine (5.64 Kcal/mol) and carbobenzyloxyglycine (5.13 Kcal/mol). From the study it was concluded that compounds from Aloe vera could be used in future to develop a drug molecule using various computational and biotechnological techniques.

 

 

INTRODUCTION:

Impetigo is highly contagious bacterial skin infection, where the primary cause of impetigo is Staphylococcus aureus and group A beta-hemolytic Strep­tococcus pyogenes, or a combination of the two¹.Additionally, the anaerobic bacteria also might involve in the cause of infection. More than 11 million populations in United States are infected with S. Aureus annually. Especially the children of age two to five years are highly susceptible, however persons of any age can be affected in common².

One-third of travellers returning are liableto impetigo. Though many bacteria inhabit healthy skin in normal situation, the organisms like S. pyogenesand S. aureusoccasionally colonize the nasal, axillary, pharyngeal, or perineal areas and capable of provoking infection to susceptible skin types. The other factors for impetigo include skin trauma, hot, humid climates, poor hygiene, day care settings, crowding, mal­nutrition, diabetes mellitus and other medical comorbidities. The infections spreads to adjacent areas and form satellite lesions through autoinoculation via fingers, towels, or clothing, hence impetigo is said to be highly contagious².

 

Impetigo occurs in two forms as nonbullous (also known as impetigo conta­giosa) and bullous, where the former is most common representation, comprising 70% of cases⁴. Nonbullous is common form of impetigo⁵. It is usually caused by S. aureus, but S. pyogenescan also be involved, especially in warmer, more humid climates⁶. It normally begins as red macule that fastly becomes a vesicle⁷. Non­bullous impetigo can be further classified as primary or the more prevalent second­ary (common) form of infection, in which primary impetigo is a direct bacterial invasion of intact healthy skin and secondary (common) impetigo found in disrupted skin caused by trauma, eczema, insect bites, scabies, or herpetic outbreaks and other diseases. Patients of dia­betes or other underlying systemic condi­tions are also highly susceptible.

 

Impetigo initially forms a macula papular lesions that transi­t into thin-walled vesicles and rupture rapidly, leaving superficial, sometimes pru­ritic or painful erosions covered by the classic honey-colored crusts².

 

Bullous impetigo is caused only by S. aureus and is characterized by large, frag­ile, flaccid bullae that can rupture and ooze yellow fluid. It usually resolves within two to three weeks without scarring².Bul­lous impetigo is typically found on the trunk, face, axilla, and extremities, and in intertriginous (diaper) areas. It is the most common cause of ulcerative rash on the buttocks of infants. Systemic symptoms are uncommon but can include fever, diarrhoea, and weakness².

 

In the current era, plants are gaining greater importance for maintaining human health and it was reported that about 80% of world population have started utilizing plant sources for various ailments⁸. To the credit Sunitamentioned that plant based products are progressively beneficial in healthcare programs throughout the world⁹.The present study aims at screening the phytoconstituents of Aloevera, Curcumalonga, Lantana camara and Euphorbiahirta for antibacterial activity against the target dehydrosqualene synthase.

 

Aloe vera:

The plant A. vera belongs to the family Liliaceae, which iscommonly used as laxative and has the capability to cure variety of skin problems¹⁰. The extract of A. vera showed strong antibacterial activity against S.aureus¹¹.

 

Curcuma longa:

In Ayurvede, turmeric was prescribed to cure skin diseases¹²and possess various medicinal properties likeanti-fungal, anti-bacterial and anti-oxidant activities¹³.

 

Lantana camara:

Lantana camarais medicinal plant found throughout India. Leaves and roots of L. camara were reported for anti-bacterial activity against S.aureus¹⁴.

Euphorbia hirta:

The plant is native to India, commonly found on roadsides and wastelands¹⁵. The aerial part of the plant was reported for the presence offlavonoids likequercitrin, euphorbianin, leucocyanidol, camphol¹⁵. The methanol extract of E. hirta shows the anti-bacterial activity against S.aureus¹⁶.

 

From the above mentioned plants the present study has been designed to predict the binding efficiency of the compounds through docking analysis against the target proteindehydrosqualene synthase. The protein dehydrosqualene synthase involve in the synthesis of carotenoid pigment staphyloxanthinthrough which the organismS. aureusexhibit antioxidant property for its survivalinside the host cell¹⁷.Therefore targeting dehydrosqualene synthase might give an insight into the drug designing and development, which would avoid the drug resistance, a critical situation pose by the organismsat this period.

 

MATERIALS AND METHODS:

The 3D structure of protein target dehydrosqualenesynthase was retrieved from the protein data bank (PDB ID: 3ADZ). The phytochemical compounds of the selected plants (A. vera, C. longa, L. camara, E. hirta)were retrieved from the PubChem database. The compounds were predicted for the ADME-Toxicity through QikProp module of Schrodinger software. The active site for the protein was predicted using the LIGSITE and the active site residues are HIS18, SER17, SER19, SER21, TYR41, ARG45, ASP48, ALA134,ALA157, GLY161, GLN165, ASN168,ARG171, ARG265.At last, docking study was carried out in Glide module.

 

RESULTS AND DISCUSSION:

The interactions of phytochemical compounds with dehydrosqualenesynthase were tabulated representing its G-Score, number of hydrogen bonds, bond length and the interacting residues (Table 1). Among the plant compounds carminic acid from A. vera scored least G.score value of -11.83 Kcal/mol and had 8 hydrogen bonds. The residueARG45 had four interactions with bond length of 2.1, 2.5, 2.7 and 2.5Å, whereas the other four were observed with ARG171, GLN165 and ASN168. The residue ARG171 formed two hydrogen bonds of length 2.1 and 2.3Å.The interactions of carminic acid alone have been showed inFig.1 and the 2D structure of it was shown in Fig.2.

 

Next to it, curcuminglucuronide of Curcuma longahad G-score of -11.46 Kcal/mol and formed 4 hydrogen bonds of length 1.9, 2.4, 2.5 and 2.2Å with amino acid residues ARG45, ASN168, GLN165 and ASP48, respectively. The compounds hesperidine of C. longa and 2-anthroquine sulfonic acid of A. verashowed G. score of -10.89 and -10.75 Kcal/mol, each formed 4 and 3 hydrogen bonds. Hesperidine had two bonds with ASP48, both of 2.6Å, other two were formed with ASN168 and ARG45 of bond length 2.4 and 1.8Å. Quercitrin, a compound identified in E. hirta is the only compound possessing -8.91 Kcal/mol of G. score, whereas the compounds like cinnamic acid, eugenol and silybin had G. score in the range of -7 Kcal/mol. Omannopyranisylthreonine and D-ascorbic acid had -6.70 and -6.48 Kcal/mol of G. score, though the G. score were in the range of -6 Kcal/mol, the interactions were observed to be 10 number in each case, which is comparatively higher than the carminic acid and curcuminglucuronide. The very less G.score was observed with cpi-quercitrol and tanco-quercitrol, both having -4.68 and -4.67Kcal/mol, however, the interactions were found to be equal to carminic acid. The residues ARG45 and ARG171 were involved in bond formation, while SER19 in cpi-quercitrol formed single bond (2.6Å) and ARG265 in tano-quercitrol formed two hydrogen bonds of length 2.3 and 2.2Å, respectively. The compounds like L-ascorbic acid, n-cbz-1-threonine and n-carbobenzyloxyglycine had G.s core of -5.97,-5.59 and -5.13Kcal/mol.

 

Fig. 1: Screenshot of interactions with Dehydrosqualene synt hase and Carminic acid of Aloe vera

 

Note: Red colour molecule represents the ligand and Green colour molecule represents the residues; yellow dotted lines indicate the bond formation between the amino acid residue and ligand.

 

Table 1: Interactions of selected plant compounds with Dehydrosqualene synthase

 

Table 1 continued

 

The bond length is one of the important criteria to be noticed, however, most of the bonds formed in the present study are moderate and the interactive type is said to be mostly electrostatic. 2-anthroquine sulfonic acid is the only compound had bond length of 3.3Å which symbolizes its weak bond formation, besides the bond length in the range of 2.2-3.3 are said to be weaker. In general, the interaction types are mentioned as strongly covalent, mostly electrostatic and electrostatic dispersed based on the bond length 1.2-1.5, 1.5-2.2 and 2.2-3.3 Å, respectively. Even the bond angles are described as 170-180, >130 and >90. The present study also signifies from the interactions which were observed with the predicted active site residues. Lin et al. mentioned that interrupting the formation of carotenoid virulence factor staphyloxanthin resulted in noninfective form of Staph bacteria, thus targeting the dehydrosqualene synthase, first enzyme involve in the carotenoid and sterol biosynthesis, would make the bacteria to be susceptible for the host cell immune system¹⁸. The residues like ARG265, ASP52, ASP48, ASP172, ASN268 and ARG45 are reported to involvein the inhibition of the dehydrosqualene synthase¹⁹. In the present study also, the residues ARG265, ASP48, ASN268 and ARG45 are observed in the bond formation which indicated the efficiency of the plant molecules to inhibit the target dehydrosqualene synthase in a significant manner. The amino acid residues ASP48, ARG45 and ASP52 are crucial for second-half reaction and PPi ionization, therefore bond formation with these residues by the compound might inhibit the synthesis of carotenoids in the bacteria.

 

Fig.2:Chemical Structure of Carminicacid

 

CONCLUSION:

The present study indicates the efficient binding of plant compounds with the active amino acid residues of dehydrosqualene synthase, where the bond formation with the residues involve in the second-half of the reaction and PPi ionization signifies the ability of the plant compounds. The compound carminic acid had least G.score and the future perspective of the study would like molecular dynamics, ADME-Tox analysis and other drug likeness test will provide the significance of the plant compounds in treating the infectious and contagious diseases impetigo.

 

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Accepted on 21.08.2017        © RJPT All right reserved

Research J. Pharm. and Tech 2017; 10(11): 3687-3691.