In silico screening of antibacterial compounds from herbal sources against vibrio cholerae
Sabah Perveen, Hotam Singh Chaudhary
Department of Biotechnology, Madhav Institute of Technology and Science, Gwalior, Madhya Pradesh, India
|Date of Web Publication||31-Dec-2015|
Hotam Singh Chaudhary
Department of Biotechnology, MITS, Gwalior, Madhya Pradesh
Source of Support: None, Conflict of Interest: None
| Abstract|| |
Background: The prolonged use of antibiotic viz., tetracycline, quinolones, ampicillin, etc., to reduce the infection of cholera, may failed due to the emergence of new Vibrio cholerae antibiotics resistant strains. Moreover, these antibiotics even restricted for patient suffering from severe dehydration. Hence, there is a call to find an alternative therapeutics against V. cholerae. The natures serve different herbs in its lap which might contain several natural therapeutic compounds almost all diseases. Computer-aided designing is the initial steps for screening the novel inhibitors. Objective: To identify and evaluate natural compounds with low side effects with high efficacy against V. cholerae has been done. Materials and Methods: In silico screening, absorption, digestion, metabolism, and excretion (ADME), and docking of herbal compounds have been performed on to the target ToxT (transcriptional activator of V. cholerae). The compound with good ADME properties and drug-likeness property were subjected to docking. Results: From 70 herbal compounds, some compounds such as aloin, campesterol, lupeol, and ursolic acid showed a violation of the rule of five and compounds such as lupeol and beta carotene showed negative binding energy. Luteolin, catechin, brevifolin, etc., compounds were selected based on ADME, drug-likeness property, and docking studies. Conclusion: Two compounds named catechin and luteolin showed better inhibition properties against ToxT and good ADME and drug-likeness property were selected as a better lead molecule for drug development in future. The Genetic Optimization for Ligand Docking fitness score for catechin is 48.74 kcal/mol and luteolin 38.12 kcal/mol.
Keywords: Absorption, digestion, metabolism, and excretion, catechin, docking, luteolin, transcriptional activator ToxT
|How to cite this article:|
Perveen S, Chaudhary HS. In silico screening of antibacterial compounds from herbal sources against vibrio cholerae
. Phcog Mag 2015;11, Suppl S4:550-5
|How to cite this URL:|
Perveen S, Chaudhary HS. In silico screening of antibacterial compounds from herbal sources against vibrio cholerae
. Phcog Mag [serial online] 2015 [cited 2021 May 11];11, Suppl S4:550-5. Available from: http://www.phcog.com/text.asp?2015/11/44/550/172960
- Vibrio cholerae became antibiotic resistance and associated with several cholera epidemic and pandemic. Hence, there is a need to find an alternative therapeutics against V. cholerae. Many herbal compounds present in nature having high medicinal value. From in-silico study,found two compound Luteolin from Tulsi and Catechin from Green Tea which showed good binding energy and druggish property.
Abbreviations used: V. cholerae: Vibrio cholera, ADME: Absorption, digestion, metabolism and excretion, CT: Cholera toxin, TCP: Toxin co-regulated Pilus, GOLD: Genetic Optimization for Ligand Docking, Asp: Aspartic acid, Arg: Arginine, Lys: Lysine, Thr: Threonine, Tyr: Tyrosine, KEGG: Kyoto encyclopedia of Genes and Genomes.
| Introduction|| |
0Vibrio cholerae , the causative organism of cholera is a comma shaped, Gram-negative bacterium responsible for severe morbidity and mortality in developing countries of the world including South Asian countries. ,, It has been the culprit of seven pandemics of the world.  V. cholerae encompasses more than 200 serogroups, two of which are associated with cholera epidemic and pendemic. The studies of these V. cholerae serogroup O1 and O139 have led to the identification of several critical virulence factors such as cholera toxin (CT) and toxin co-regulated pilus (TCP). In addition, V. cholerae produces a major zinc-dependent metalloprotease known as hemagglutinin/protease. All the serogroups of V. cholerae except O1 and O139 are considered as non-O1 and non-O139, and most are nonpathogenic. However, some members of serogroup are capable of causing sporadic cases of moderate to severe gastroenteritis and extraintestinal infections in humans, despite the fact that the genes encoding TCP and CT are absent, thus raising increasing concern in endemic area. 
Many antibiotics use against V. cholerae such as tetracycline and fluoroquinolones, ciprofloxacin, ampicillin, nalidixic acid, and erythromycin. With time, the V. cholerae strains became resistant to these antibiotics, and this is evident from some recent cholera outbreaks. ,, In this current scenario, there is a demand to find a better therapeutics against V. cholerae. The best alternative is the bioactive natural compounds present in the lab of herbal plants. Importantly many herbal plants contain natural compounds of high medicinal value. Computer-aided methods are preliminary approach to screening novel therapeutic candidates and an emerging strategy to reduce many complexities of drug discovery process. Absorption, digestion, metabolism, and excretion (ADME) and drug-likeness properties of all biological active compounds present in nature can be easily found by the computer-aided method.  The study of receptor-ligand interaction is a fundamental concept of rational drug design and the prediction of such interactions by computational methods has highlighted the importance of structure-based drug discovery. 
There are many herbal compounds reported in the literature with medicinal value and may be used as therapeutics agent against V. cholerae. ,, The study is mainly focused on the screening of potential herbal compound which might inhibit the infection of targeted V. cholerae by computer-based studies.
| Materials And Methods|| |
0 Identification of potential ligands
Many herbal compounds having high medicinal value reported against V. cholerae.  Hence, an initial survey of 70 herbal compounds from 15 different plants was carried out from extensive review studies. The three-dimensional (3D) structure of these compounds is present in drug database such as PubChem, ChemSpider, and Kyoto Encyclopedia of Genes and Genomes, and the structures were retrieved from the PubChem  and ChemSpider. 
Absorption, digestion, metabolism, and excretion studies and screening of ligands
The ADME are the most important part of pharmacological studies of lead molecules, and these can be predicted by computational tools such as MedChem designer and OSIRIS property explorer. Hence, all the 70 ligands were tested for their ADME profile, drug-likeliness, drug score, and toxicity risks. MedChem designer was used for ADME profiling. The SDF file of ligands was uploaded in MedChem designer software and then calculated the ADME property. Computer programmer OSIRIS used for drug-likeliness, toxicity risks, and drug score.
MedChem designer is an advanced molecule design software application that combines an intuitive sketch interface with fast and accurate ADME property predictions from ADME Predictor software package.  It also predicts rule of five. Rule of five evaluate drug-likeliness property that would make it an orally active drug. Updated OSIRIS properties explorer help to search chemical structures by name, Simplified Molecular Input Line Entry System, CAS No., and calculates on-the-fly various drug-relevant properties whenever a structure is valid. Prediction results are valued and color coded. Properties with high risks of undesired effects like mutagenicity or a poor intestinal absorption are shown in red. Whereas a green color indicates drug-conform behavior. 
Selection of target protein and molecular docking
Transcriptional activator ToxT activates transcription for structural genes of CT and TCP virulence factors. Hence V. cholerae strain deficient for ToxT production lack expression of CT and TCP and thus could not cause disease. Thus, ToxT is now a novel and potent target in V. cholerae for drug designing.  The crystal structure of transcriptional activator ToxT (PDB ID: 3GBG) was retrieved from Protein Data Bank (PDB). The active site of this target protein is identified by Active Site Prediction (http://www.scfbio-iitd.res.in/dock/ActiveSite.jsp). The selected herbal compounds docked onto ToxT using Genetic Optimization for Ligand Docking (GOLD). GOLD uses a genetic algorithm for searching binding ligand conformational space and provides a score for binding residues. GOLD scores are used to rank poses. 
| Results|| |
The 70 herbal ligands are firstly screened on the basis of ADME studies. ADME prediction is done by MedChem designer. The result of ADME is tabulated in [Table 1]. The toxicity risk, drug-likeness, and drug score is calculated by computer programmer OSIRIS property explorer and the results are given in [Table 2]. After ADME studies of ligands we have found that many herbal compounds were suitable for drug development against V. cholerae. b-sitosterol from Aloe vera, lupeol from Ocimum tenuiflorum, brevifolin and ellagic acid from Punica granatum, catechin from green tea, luteolin from Tulsi, and many more showed better pharmacokinetic and drug-likeness properties. Using GOLD software, the docking of ligands to the target (PDB ID: 3GBG) has been done, and the GOLD fitness scores of all the ligands have been given in [Table 3].
|Table 1: ADME prediction of selected herbal compound by MedChem designer |
Click here to view
|Table 2: Toxicity risk, drug score, and drug-likeness are predicted by OSIRIS property explorer |
Click here to view
|Table 3: The GOLD score (kcal/mol) of various plant-derived compounds with ToxT of Vibrio cholerae |
Click here to view
On the basis of drug score, ADME and docking studies we have found luteolin and catechin as a best ligands which shows good drug-score, no toxicity risk, and best GOLD score.
| Discussions|| |
The outbreaks of cholera are critical because the organism is recently emerged as antibiotic resistant.  Hence, the discovery of an alternative treatment has profound scope and significance. Herbal compounds are the best alternative because of their high medicinal value. There are many herbal compounds present in the nature which has good druggish property and have some medicinal value. The traditional method of drug designing is time-consuming and complicated. There are many clinical and preclinical trials. One of the major reasons for drug failures is the poor drug-likeness and pharmacokinetic properties of lead compounds. Computer- aided drug designing method is a good and rapid method. It gives significant screening approach because it selects the lead molecules with good pharmacological and druggish properties. We have selected 70 herbal compounds from 15 different plants. The 3D structure of the ligands was retrieve from the drug database, PubChem, and ChemSpider. However, many ligands were found suitable as per Lipinski's rule of five [Table 1], Supplementary Data].
Another important concern in drug designing is the pharmacokinetics properties. The ADME study gives the property of drug such as ADME. The ADME profiling of selected ligand was done by MedChem designer, and the values are provided in [Table 1]. In silico toxicity prediction is the final step in any drug designing process. In this study, we have found that the predicted toxicity risks, drug-likeness, and drug score of some herbal compounds were suitable. b-sitosterol from A. vera, brevifolin from P. granatum, luteolin from Tulsi, catechin from green tea, and many more showed better pharmacokinetics property and drug score [Table 1] and [Table 2], Supplementary Material]. After this screening process, these ligands are found suitable for docking studies. All the herbal compounds were reported to have high medicinal value against different pathogens, and we have tested the efficiency of the same against V. cholerae by computer-aided approach.
There are two main virulence factors, CT and TCP in V. cholerae. The key protein involved in the virulence of V. cholerae is CT and TCP. The expression of both proteins is regulated by the transcriptional activator ToxT. Thus, the ToxT has been selected as a probable drug target. The crystal structure of ToxT (3GBG) was retrieved from PDB. The protein consists of a single chain. Chain A is the key domain consists of 260 amino acids residues, 4274 number of atoms, and 4313 number of bonds present. For interaction between ligand and target, the active site information is necessary. The active site was predicted by the online server Active Site Prediction. There were total 20 active cavities present in the target protein for docking. The docking study is carried out by GOLD. During docking studies, some compound did not give any fitness scores such as bergapten, gallate, and Nootkatone. The docking studies and the fitness score of all the selected ligands are given in [Table 3]. As the best catechin, active inhibitor present in green tea showed the fitness score 48.74. Similarly, the luteolin from Tulsi gave the fitness score 38.12. After docking the visualization of the result was done by LIGPLOT. The LIGPLOT program automatically generates schematic two-dimensional representations of protein-ligand complexes from standard PDB file input. The output is a color, or black-and-white, PostScript file giving a simple and informative representation of the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic interactions, and atom accessibilities. The program is completely general for any ligand and can also be used to show other types of interaction in proteins and nucleic acids. It gives the residues with which the ligand is binded with the target protein.  For ligand catechin, the main interacting residue is aspartic acid 167, arginine 92. Similarly for luteolin the main interacting residue is threonine 165, tyrosine 30, and lysine 95 in [Figure 1].
|Figure 1: Binding of ligand to the target residues. The main interacting residues of catechin (a) and the main interacting residues of luteolin (b). The residues of catechin are aspartic acid 167 (bond length 2.23 Å) and arginine-92 (bond length 2.47 Å). The residue of luteolin are lysine 95 (bond length 3.75, 3.53 Å), tyrosine 30 (bond length 3.54 Å), and threonine 165 (bond length 3.34 Å)|
Click here to view
| Conclusion|| |
The increase of multidrug resistant has led to the evolution of many notorious pathogens such as V. cholerae. This study concluded that the computer-based screening is an effective alternative for the remedies when all antibiotics seem to be failed. In silico ADME and toxicity studies help to identify the best ligand against the target. Several herbal compounds are screened against V. cholerae. It was found that herbal compounds such as catechin, luteolin shows good inhibitory action against ToxT (3GBG). However, the in vitro study is needed to perform to validate the computer-based result.
Financial support and sponsorship
Conflicts of interest
There are no conflicts of interest.
| References|| |
Hannan A, Humayun T, Hussain MB, Yasir M, Sikandar S. In vitro
antibacterial activity of onion (Allium cepa
) against clinical isolates of Vibrio cholerae
. J Ayub Med Coll Abbottabad 2010;22:160-3.
Kumar P, Mishra DK, Deshmukh DG, Jain M, Zade AM, Ingole KV, et al.
Haitian variant ctxB producing Vibrio cholerae
O1 with reduced susceptibility to ciprofloxacin is persistent in Yavatmal, Maharashtra, India, after causing a cholera outbreak. Clin Microbiol Infect 2014;20:O292-3.
Kumar P, Jain M, Goel AK, Bhadauria S, Sharma SK, Kamboj DV, et al.
A large cholera outbreak due to a new cholera toxin variant of the Vibrio cholerae
O1 El Tor biotype in Orissa, Eastern India. J Med Microbiol 2009;58(Pt 2):234-8.
Hannan A, Raja M, Arshad MU, Absar M. 'Gastro' of Mirpur Khas (Sindh) is resolved. J Ayub Med Coll Abbottabad 2008;20:10-2.
Tripathi R, Singh Naorem S, Dureja C, Haldar S, Mondal AK, Raychaudhuri S. VopF, a type III effector protein from a non-O1, non-O139 Vibrio cholerae
strain, demonstrates toxicity in a Saccharomyces cerevisiae
model. J Med Microbiol 2010;59(Pt 1):17-24.
Rafi S, Qureshi AH, Saeed W, Ali A, Ahmadani M, Khawaji SA. Changing epidemiology and sensitivity pattern of Vibrio cholera
at Rawalpindi. Pak J Med Sci 2004;20:357-60.
Jain M, Kumar P, Goel AK, Kamboj DV, Singh L. Class 1 integrons and SXT elements conferring multidrug resistance in Vibrio cholerae
O1 strains associated with a recent large cholera outbreak in Orissa, Eastern India. Int J Antimicrob Agents 2008;32:459-60.
Kumar P, Jain M, Goel AK, Kamboj DV, Kumar O. Tetracycline resistant V. cholerae
O1 biotype El Tor serotype Ogawa with classical ctxB from a recent cholera outbreak in Orissa, Eastern India. J Infect Public Health 2012;5:217-9.
Skariyachan S, Krishnan RS, Siddapa SB, Salian C, Bora P, Sebastian D. Computer aided screening and evaluation of herbal therapeutics against MRSA infections. Bioinformation 2011;7:222-33.
Lyskov S, Gray JJ. The RosettaDock server for local protein-protein docking. Nucleic Acids Res 2008;36:W233-8.
Praveen S, Saurabh M, Hemant S. To study the therapeutic role of Indian species in the treatment of gastrointestinal disease caused by Vibrio cholerae
. IJIRSET 2013;2:2371-5.
Yamasaki S, Asakura M, Neogi SB, Hinenoya A, Iwaoka E, Aoki S. Inhibition of virulence potential of Vibrio cholerae
by natural compounds. Indian J Med Res 2011;133:232-9.
Li Q, Cheng T, Wang Y, Bryant SH. PubChem as a public resource for drug discovery. Drug Discov Today 2010;15:1052-7.
Pence HE, Williams A. ChemSpider: An online chemical information resource. J Chem Educ 2010;87:1123-4.
van de Waterbeemd H, Gifford E. ADMET in silico
modelling: Towards prediction paradise? Nat Rev Drug Discov 2003;2:192-204.
Ertl P. Molecular structure input on the web. J Cheminform 2010;2:1.
Mondal SI, Khadka B, Akter A, Roy PK, Sultana R. Computer based screening for novel inhibitors against Vibrio cholerae
using NCI diversity set-II: An alternative approach by targeting transcriptional activator ToxT. Interdiscip Sci 2014;6:108-17.
Tjelvar O, Simon B. An Overview of Protein-ligand Docking Using GOLD. Cambridge Crystallographic Data Centre EMBO Workshop; 2014.
Kumar P, Mishra DK, Deshmukh DG, Jain M, Zade AM, Ingole KV, et al
. Vibrio cholerae
O1 Ogawa El Tor strains with the ctxB7 allele driving cholera outbreaks in south-western India in 2012. Infect Genet Evol 2014;25:93-6.
Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995;8:127-34.
| Authors|| |
Sabah Perveen is B.tech Biotechnology student.
Prof. Hotam Singh Chaudhary is M.tech biotechnology Asst. Prof. Madhav Institute of Technology and Science.
[Table 1], [Table 2], [Table 3]