Madhurima Tiwari Sunita Gupta Prachi Bhargava


The discovery of antibiotics initiated the era of drug innovation and implementation for human and animal health. Very soon, antibiotic resistance started evolving due to over-prescription and heavy usage of drugs leading to deleterious side effects. However, using plant extracts or medicinal plants has emerged as a new approach to dealing with the current problem. One such medicinal plant Sisymbrium irio L. is widely used in Unani therapy as an antimicrobial, analgesic, antipyretic, antioxidant, anti-inflammatory, hepatoprotective, bronchoprotective etc. The phytochemicals extracted from the aerial part of the plant have been used as a natural compound library and screened against a well-known anti-bacterial drug target Dihydrofolate reductase (DHFR)  enzyme of Staphylococcus aureus. The top two phytochemicals with lower docking score along with the positive control were subjected to molecular dynamics (MD) simulation studies to examine the stabilities of the complexes over 100 ns, followed by binding free energy estimation. The Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) and Radius of Gyration (Rg) yielded established results throughout the MD run. Moreover, the derived phytochemicals exhibited lower binding free energy values than the positive control that can be tested for its in vitro efficacy, followed by further optimization to attain a potent therapeutic against S. aureus. Taken together, the present study suggests two promising phytochemicals derived from the aerial part of the plant S. irio with stable MD simulation results, strong binding affinity and no side effects.




Binding free energy, DHFR, Phytochemicals, Sisymbrium irio L.

Adwan, G., Abu-Shanab, B. & Adwan, K. (2010). Antibacterial activities of some plant extracts alone and in combination with different antimicrobials against multidrug-resistant Pseudomonas aeruginosa strains. Asian Pacific Journal of Tropical Medicine, 3(4), 266-269. https://doi.org/10.1016/S1995-7645(10)60064-8.
Aier, I., Varadwaj, P. & Raj, U. (2016). Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Scientific Reports, 6, 34984. https://doi.org/10.1038/srep34984.
Al Akeel, R., Al-Sheikh, Y., Mateen, A., Syed, R., Janardhan, K. & Gupta, VC. (2014). Evaluation of antibacterial activity of crude protein extracts from seeds of six different medical plants against standard bacterial strains. Saudi Journal of Biological Sciences, 21(2), 147–151. doi: 10.1016/j.sjbs.2013.09.003
Al-Jaber, NA. (2011). Phytochemical and biological studies of Sisymbriumirio L. Growing in Saudi Arabia. Journal of Saudi Chemical Society, 15(4), 345-350. https://doi.org/10.1016/j.jscs.2011.04.010
Al-Massarani, SM., El Gamal, A.A., Alam, P., Al-Sheddi, E.S., Al-Oqail, M.M. & Farshori, N.N. (2017). Isolation, biological evaluation and validated HPTLC-quantification of the marker constituent of the edible Saudi plant Sisymbriumirio L. Saudi Pharmaceutical Journal, 25(5), 750-759.https://doi.org/10.1016/j.jsps.2016.10.012
Al-Qudah, M.A. & Abu Zarga, M.H. (2010 a). Chemical constituents of Sisymbriumirio L. from Jordan. Natural Product Research, 24(5), 448-456.https://doi.org/10.10 80/14786410903388025
Al-Qudah, M.A. & Abu Zarga, M.H. (2010 b). Chemical composition of essential oils from aerial parts of Sisymbriumirio from Jordan. Journal of Chemistry, 7, 6-10. https://doi.org/10.1155/2010/973086
Alsaffar, D.F., Abbas, I.S. & Dawood, A.H. (2016). Investigation of the Main Alkaloid of London Rocket (Sisymbriumirio L) as a Wild Medicinal Plant Grown in Iraq. International Journal of Pharmaceutical Sciences Review and Research, 39, 279-281.
Alves, M.J., Froufe, H.J.C., Costa, A.F.T., Santos, A.F., Oliveira, L.G. & Osorio, S.R.M. (2014). Docking Studies in Target Proteins Involved in Antibacterial Action Mechanisms: Extending the Knowledge on Standard Antibiotics to Antimicrobial Mushroom Compounds. Molecules, 19(2), 1672-1678. https://doi.org/10.3390/molecules19021672.
Bourne, C.R., Barrow, E.W., Bunce, R.A., Bourne, P.C., Berlin, K.D. & Barrow, W.W. (2010). Inhibition of antibiotic-resistant Staphylococcus aureus by the broad-spectrum dihydrofolate reductase inhibitor RAB1. Antimicrobial agents and chemotherapy, 54(9), 3825-3833.https://doi.org/10.1128/AAC.00361-10.
Brady, G. P. & Stouten, P. F. (2000). Fast prediction and visualization of protein binding pockets with PASS. Journal of Computer-Aided Molecular Design, 14(4), 383–401. DOI: 10.1023/a: 1008124202956
DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on protein crystallography, 40, 82-92.
El-Sherbiny, Gamal M., Moghannem, S. A. & Sharaf, M. H. (2017). Antimicrobial activities and cytotoxicity of Sisymbrium irio L extract against multi-drug resistant bacteria (MDRB) and Candida albicans. International Journal of Current Microbiology and Applied Sciences, 6, 1-13. https://doi.org/10.20546/ijcmas.2017.604.001
Gupta, S., Lynn, A. M. & Gupta, V. (2018). Standardization of virtual-screening and post-processing protocols relevant to in-silico drug discovery. 3 Biotech, 8(12), 1-7.https://doi.org/10.1007/s13205-018-1523-5
Griffiths, D.W., Deighton, N., Birch, A.N., Patrian, B., Baur, R. & Städler, E. (2001). Identification of glucosinolates on the leaf surface of plants from the Cruciferae and other closely related species. Phytochemistry, 57(5), 693-700. https://doi.org/10.1016/S0031-9422(01)00138-8
Hailu, T., Gupta, R.K. & Rani, A. (2019). Sisymbriumirio L.: A Herb used in the Unani system of medicine for broad spectrum therapeutical applications. Indian Journal of Traditional Knowledge, 18(1), 140-143.http://nopr.niscair.res.in/handle/123456789/45672.
Jakalian, A., Jack, D. B. & Bayly, C. I. (2002). Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation. Journal of Computational Chemistry, 23(16), 1623-1641. DOI: 10.1002/jcc.10128
Khan, M.S., Javed, K. & Hasnain Khan, M. (1991). Chemical constituents of the aerial parts of Sisymbriumirio. Journal of the Indian Chemical Society, 68, 532 DOI: 10.5281/zenodo.6155010
Khoshoo, T.N. (1966). Biosystematics of Sisymbriumirio Complex XII: Distributional pattern. Caryologia, 19(2), 143-150. https://doi.org/10.1080/00087114.1966.10796212
Kim, S., Thiessen, P.A., Bolton, E., Chen, J., Fu, G., Gindulyte, A., Bryant, S. H. et al. (2016). PubChem substance and compound databases. Nucleic acids research, 44(D1), D1202-D1213.
Kobayashi, M., Kinjo, T., Koseki, Y., Bourne, C.R., Barrow, W.W. & Aoki, S. (2014). Identification of novel potential antibiotics against Staphylococcus using structure-based drug screening targeting dihydrofolate reductase. Journal of Chemical Information and Modeling, 54(4), 1242-1253. https://doi.org/10.1021/ci400686d.
Kroemer, R.T. (2007). Structure-Based Drug Design: Docking and Scoring. Current Protein Peptide Science, 8(4), 312-328. https://doi.org/10.2174/13892030 77813 69382
Kumalo, H. M., Bhakat, S. & Soliman, M.E.S. (2015). Theory and applications of covalent docking in drug discovery: Merits and pitfalls. Molecules, 20, 1984-2000. http://dx.doi.org/10.3390/molecules20021984.
Laskowski, R. A. & Swindells, M. B. (2011). LigPlotþ: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. DOI: 10.1021/ci200227u
Lev, E. (2003). Sisymbrium irio medicinal Substances in Jerusalem from early times to the present day Archaeopress. Oxford, UK, p. 62.
Li. X., Hilgers, M., Cunningham, M., Chen, Z., Trzoss, M., Zhang, J., Kohnen, L., Lam, T., Creighton, C., Kedar, G.C., Nelson, K. (2011). Structure-based design of new DHFR-based antibacterial agents: 7-aryl-2, 4-diaminoquinazolines. Bioorganic Chemistry Letters Medicinal, 21(18), 5171-5176. https://doi.org/10.1016/j.bmcl.2011.07.059.
Lindorff‐Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O. & Shaw, D. E. (2010). Improved side‐chain torsion potentials for the Amber ff99SB protein force field. Proteins: Structure, Function, and Bioinformatics, 78(8), 1950-1958. DOI: 10.1002/prot.22711.
Lobanov, M.Y., Bogatyreva, N.S. & Galzitskaya, O.V. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42, 623–628. https://doi.org/10.1134/S0026893308040195
Kumari, R. & Kumar, R., Open Source Drug Discovery Consortium & Lynn, A. (2014). g_mmpbsa A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951-1962. https://doi.org/10.1021/ci500020m.
Massova, I. & Kollman, P. A. (2000). Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspectives in Drug Discovery and Design, 18(1), 113-135.https://doi.org/10.1023/A:1008763014207
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry,30(16), 2785–2791. DOI: 10.1002/jcc.21256
O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T. & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3, 33. https://jcheminf.biomedcentral.com/articles/10.1186/17 58-2946-3-33.
Oefner, C., Parisi, S., Schulz, H., Lociuro, S. & Dale, G.E. (2009). Inhibitory properties and X-ray crystallographic study of the binding of AR-101, AR-102 and iclaprim in ternary complexes with NADPH and dihydrofolate reductase from Staphylococcus aureus. Acta Crystallographica Section D: Biological Crystallography, 65(8), 751-757. https://doi.org/10.1107/S0907444909013936
Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R. & Lindahl, E. (2013). GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845-854. DOI: 10.1093/bioinformatics/btt055
Ray, J., Creamer. R., Schroeder, J. & Murray, L. (2005). Moisture and temperature requirements for London rocket (Sisymbriumirio) emergence. Weed Science, 53(2), 187-192.  https://doi.org/10.1614/WS-04-150R1.
Sousa da Silva, A. W. & Vranken, W. F. (2012). ACPYPE-Antechamber python parser interface. BMC research notes, 5(1), 1-8.https://doi.org/10.1186/1756-0500-5-367.
Shabnam, B., Ziaur, R., Khalid, R. & Naveed, I. (2015). Biological screening of polarity-based extracts of leaves and seeds of Sisymbriumirio L. Pakistan Journal of Botany, 47, 301-305.
Shah, S., Rehmanullah, S. & Muhammad, Z. (2014). Pharmacognostic standardization and pharmacological study of Sisymbriumirio L. American Journal of Research Communication, 1(7), 241-253.
Singh, G., Soni, H., Tandon, S., Kumar. V., Babu, G., Gupta. V. & Chaudhuri, P. (2022). Identification of natural DHFR inhibitors in MRSA strains: Structure-based drug design study. Results in Chemistry, 26, 100292. https://doi.org/10.1016/j.rechem.2022.100292
Trott, O. & Olson, A J. (2010). Software news and update AutodockVina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. doi: 10.1002/jcc.21334.
Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E. & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291.
Vohora, S.B., Naqvi, S.A. & Kumar, I. (1980). Antipyretic, analgesic and antimicrobial studies on Sisymbriumirio. Planta Medica, 38(3), 255-259. DOI: 10.1055/s-2008-1074870.
Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157-1174.DOI: 10.1002/jcc.20035.
Research Articles

How to Cite

Virtual screening and molecular dynamics simulation studies to predict the binding of Sisymbrium irio L. derived phytochemicals against Staphylococcus aureus dihydrofolate reductase (DHFR). (2022). Journal of Applied and Natural Science, 14(4), 1297-1307. https://doi.org/10.31018/jans.v14i4.3641