Atomic level and structural understanding of natural ligands inhibiting Helicobacter pylori peptide deformylase through ligand and receptor based screening, SIFT, molecular dynamics and DFT – a structural computational approach

References

• Antczak, C., Shum, D., Escobar, S., Bassit, B., Kim, E., Seshan, V. E., Wu, N., Yang, G., Ouerfelli, O., Li, Y.-M., Scheinberg, D. A., & Djaballah, H. (2007). High-throughput identification of inhibitors of human mitochondrial peptide deformylase. Journal of Biomolecular Screening, 12(4), 521–535. https://doi.org/10.1177/1087057107300463
   PubMedGoogle Scholar
• Apfel, C., Banner, D. W., Bur, D., Dietz, M., Hirata, T., Hubschwerlen, C., Locher, H., Page, M. G., Pirson, W., Rossé, G., & Specklin, J. L. (2000). Hydroxamic acid derivatives as potent peptide deformylase inhibitors and antibacterial agents. Journal of Medicinal Chemistry, 43(12), 2324–2331. https://doi.org/10.1021/jm000018k
   PubMed Web of Science ®Google Scholar
• Apfel, C., Banner, D. W., Bur, D., Dietz, M., Hubschwerlen, C., Locher, H., Marlin, F., Masciadri, R., Pirson, W., & Stalder, H. (2001). 2-(2-Oxo-1,4-dihydro-2H-quinazolin-3-yl)- and 2-(2,2-dioxo-1,4-dihydro-2H-2lambda6-benzo[1,2,6]thiadiazin-3-yl)-N-hydroxy-acetamides as potent and selective peptide deformylase inhibitors. Journal of Medicinal Chemistry, 44(12), 1847–1852. https://doi.org/10.1021/jm000352g
   PubMed Web of Science ®Google Scholar
• Axten, J. M., Medina, J. R., Blackledge, C. W., Duquenne, C., Grant, S. W., Bobko, M. A., Peng, T., Miller, W. H., Pinckney, T., Gallagher, T. F., Kulkarni, S., Lewandowski, T., Van Aller, G. S., Zonis, R., Ward, P., & Campobasso, N. (2012). Acylprolinamides: A new class of peptide deformylase inhibitors with in vivo antibacterial activity. Bioorganic & Medicinal Chemistry Letters, 22(12), 4028–4032. https://doi.org/10.1016/j.bmcl.2012.04.086
   PubMed Web of Science ®Google Scholar
• Barge, S., Jade, D., Ayyamperumal, S., Manna, P., Borah, J., Nanjan, C. M. J., Nanjan, M. J., & Talukdar, N. C. (2021). Potential inhibitors for FKBP51: An in silico study using virtual screening, molecular docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2021.1994877
   Google Scholar
• Becker, A., Schlichting, I., Kabsch, W., Schultz, S., & Wagner, A. F. (1998). Structure of peptide deformylase and identification of the substrate binding site. The Journal of Biological Chemistry, 273(19), 11413–11416. https://doi.org/10.1074/jbc.273.19.11413
   PubMed Web of Science ®Google Scholar
• Bendjeddou, A., Abbaz, T., Gouasmia, A., & Villemin, D. (2016). Molecular structure, HOMO-LUMO, MEP and Fukui function analysis of some TTF-donor substituted molecules using DFT (B3LYP) calculations. International Research Journal of Pure and Applied Chemistry, 12(1), 1–9. https://doi.org/10.9734/IRJPAC/2016/27066
   Google Scholar
• Boularot, A., Giglione, C., Artaud, I., & Meinnel, T. (2004). Structure-activity relationship analysis and therapeutic potential of peptide deformylase inhibitors. Current Opinion in Investigational Drugs (London, England: 2000), 5(8), 809–822.
   PubMedGoogle Scholar
• Cai, J., Han, C., Hu, T., Zhang, J., Wu, D., Wang, F., Liu, Y., Ding, J., Chen, K., Yue, J., Shen, X., & Jiang, H. (2006). Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: Reverse docking, enzymatic assay, and X-ray crystallography validation. Protein Science : A Publication of the Protein Society, 15(9), 2071–2081. https://doi.org/10.1110/ps.062238406
   PubMed Web of Science ®Google Scholar
• Casalvieri, K. A., Matheson, C. J., Backos, D. S., & Reigan, P. (2020). Molecular docking of substituted pteridinones and pyrimidines to the ATP-binding site of the N-terminal domain of RSK2 and associated MM/GBSA and molecular field datasets. Data in Brief, 29, 105347. https://doi.org/10.1016/j.dib.2020.105347
   PubMed Web of Science ®Google Scholar
• Chen, D. Z., Patel, D. V., Hackbarth, C. J., Wang, W., Dreyer, G., Young, D. C., Margolis, P. S., Wu, C., Ni, Z. J., Trias, J., White, R. J., & Yuan, Z. (2000). Actinonin, a naturally occurring antibacterial agent, is a potent deformylase inhibitor. Biochemistry, 39(6), 1256–1262. https://doi.org/10.1021/bi992245y
   PubMed Web of Science ®Google Scholar
• Chinnasamy, S., Nagamani, S., & Muthusamy, K. (2015). Zn2+ ion of the snake venom metalloproteinase (SVMP) plays a critical role in ligand binding: A molecular dynamics simulation study. RSC Advances, 5(86), 70566–70576. https://doi.org/10.1039/C5RA14693C
   Web of Science ®Google Scholar
• Chinnasamy, S., Selvaraj, G., Kaushik, A. C., Kaliamurthi, S., Chandrabose, S., Singh, S. K., Thirugnanasambandam, R., Gu, K., & Wei, D.-Q. (2020). Molecular docking and molecular dynamics simulation studies to identify potent AURKA inhibitors: Assessing the performance of density functional theory, MM-GBSA and mass action kinetics calculations. Journal of Biomolecular Structure & Dynamics, 38(14), 4325–4335. https://doi.org/10.1080/07391102.2019.1674695
   PubMed Web of Science ®Google Scholar
• Cui, K., Lu, W., Zhu, L., Shen, X., & Huang, J. (2013). Caffeic acid phenethyl ester (CAPE), an active component of propolis, inhibits Helicobacter pylori peptide deformylase activity. Biochemical and Biophysical Research Communications, 435(2), 289–294. https://doi.org/10.1016/j.bbrc.2013.04.026
   PubMed Web of Science ®Google Scholar
• Deng, Z., Chuaqui, C., & Singh, J. (2004). Structural interaction fingerprint (SIFt): A novel method for analyzing three-dimensional protein-ligand binding interactions . Journal of Medicinal Chemistry, 47(2), 337–344. https://doi.org/10.1021/jm030331x
   PubMed Web of Science ®Google Scholar
• Eda, S. R., & Jinka, R. (2019). Combined e-pharmacophore based screening and docking of PI3 kinase with potential inhibitors from a database of natural compounds. Bioinformation, 15(10), 709–715. https://doi.org/10.6026/97320630015709
   PubMed Web of Science ®Google Scholar
• Esther, M., Vijayakumar, S., Kumar, A., Subramanian, M., & Manogar, P. (2017). Molecular docking, ADMET analysis and dynamics approach to potent natural inhibitors against sex hormone binding globulin in male infertility. Pharmacognosy Journal, 9(6s), s35–s43. https://doi.org/10.5530/pj.2017.6s.155
   Google Scholar
• Ferrari, A. M., Degliesposti, G., Sgobba, M., & Rastelli, G. (2007). Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors. Bioorganic & Medicinal Chemistry, 15(24), 7865–7877. https://doi.org/10.1016/j.bmc.2007.08.019
   PubMed Web of Science ®Google Scholar
• Fieulaine, S., Alves de Sousa, R., Maigre, L., Hamiche, K., Alimi, M., Bolla, J.-M., Taleb, A., Denis, A., Pagès, J.-M., Artaud, I., Meinnel, T., & Giglione, C. (2016). A unique peptide deformylase platform to rationally design and challenge novel active compounds. Scientific Reports, 6(1), 35429. https://doi.org/10.1038/srep35429
   PubMedGoogle Scholar
• Fiolhais, C., Nogueira, F., & Marques, M. A. (2003). A primer in density functional theory (Vol. 620). Springer.
   Google Scholar
• Ganesan, V., Kamal, C., Venkatesh, V., Govindaraju, M., Mary, Y. S., Armaković, S., Armaković, S., Kaya, S., & Panicker, C. Y. (2018). Molecular dynamic simulations, ALIE surface, Fukui functions geometrical, molecular docking and vibrational spectra studies of tetra chloro p and m -xylene. Journal of Molecular Structure, 1171, 253–267. https://doi.org/10.1016/j.molstruc.2018.06.001
   Web of Science ®Google Scholar
• Gao, J., Cheng, Y., Cui, W., Zhang, F., Zhang, H., Du, Y., & Ji, M. (2012). Prediction of the binding modes between macrolactin N and peptide deformylase from Staphylococcus aureus by molecular docking and molecular dynamics simulations. Medicinal Chemistry Research, 22(6), 2889–2901. https://doi.org/10.1007/s00044-012-0303-8
   Web of Science ®Google Scholar
• Gázquez, J. (2006). Hardness and softness in density functional theory. In K. D. Sen (Ed.), Chemical hardness. Structure and bonding (Vol 80, pp. 27–43). Springer. https://doi.org/10.1007/BFb0036798
   Google Scholar
• Gece, G. (2008). The use of quantum chemical methods in corrosion inhibitor studies. Corrosion Science, 50(11), 2981–2992. https://doi.org/10.1016/j.corsci.2008.08.043
   Web of Science ®Google Scholar
• Geppert, H., Vogt, M., & Bajorath, J. (2010). Current trends in ligand-based virtual screening: Molecular representations, data mining methods, new application areas, and performance evaluation. Journal of Chemical Information and Modeling, 50(2), 205–216. https://doi.org/10.1021/ci900419k
   PubMed Web of Science ®Google Scholar
• Giglione, C., Pierre, M., & Meinnel, T. (2000). Peptide deformylase as a target for new generation, broad spectrum antimicrobial agents. Molecular Microbiology, 36(6), 1197–1205. https://doi.org/10.1046/j.1365-2958.2000.01908.x
   PubMed Web of Science ®Google Scholar
• Groche, D., Becker, A., Schlichting, I., Kabsch, W., Schultz, S., & Wagner, A. F. (1998). Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site. Biochemical and Biophysical Research Communications, 246(2), 342–346. https://doi.org/10.1006/bbrc.1998.8616
   PubMed Web of Science ®Google Scholar
• Grujić, M., & Renko, M. (2002). Aminopeptidase inhibitors bestatin and actinonin inhibit cell proliferation of myeloma cells predominantly by intracellular interactions. Cancer Letters, 182(2), 113–119. https://doi.org/10.1016/s0304-3835(02)00086-1
   PubMed Web of Science ®Google Scholar
• Guilloteau, J. P., Mathieu, M., Giglione, C., Blanc, V., Dupuy, A., Chevrier, M., Gil, P., Famechon, A., Meinnel, T., & Mikol, V. (2002). The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: A platform for the structure-based design of antibacterial agents. Journal of Molecular Biology, 320(5), 951–962. https://doi.org/10.1016/S0022-2836(02)00549-1
   PubMed Web of Science ®Google Scholar
• Gupta, S., & Bajaj, A. V. (2018). Extra precision glide docking, free energy calculation and molecular dynamics studies of 1,2-diarylethane derivatives as potent urease inhibitors. Journal of Molecular Modeling, 24(9), 261. https://doi.org/10.1007/s00894-018-3787-4
   PubMed Web of Science ®Google Scholar
• Hackbarth, C. J., Chen, D. Z., Lewis, J. G., Clark, K., Mangold, J. B., Cramer, J. A., Margolis, P. S., Wang, W., Koehn, J., Wu, C., Lopez, S., Withers, G., Gu, H., Dunn, E., Kulathila, R., Pan, S.-H., Porter, W. L., Jacobs, J., Trias, J., … Yuan, Z. (2002). N-alkyl urea hydroxamic acids as a new class of peptide deformylase inhibitors with antibacterial activity. Antimicrobial Agents and Chemotherapy, 46(9), 2752–2764. https://doi.org/10.1128/AAC.46.9.2752-2764.2002
   PubMed Web of Science ®Google Scholar
• Hernick, M., & Fierke, C. (2010). Mechanisms of metal-dependent hydrolases in metabolism. In H.-W. Liu (Ed.), Comprehensive natural products II (pp. 547–581). Elsevier. https://doi.org/10.1016/B978-008045382-8.00178-7
   Google Scholar
• Hu, Y., Zhang, M., Lu, B., & Dai, J. (2016). Helicobacter pylori and antibiotic resistance, A continuing and intractable problem. Helicobacter, 21(5), 349–363. https://doi.org/10.1111/hel.12299
   PubMed Web of Science ®Google Scholar
• Huang, J., Van Aller, G. S., Taylor, A. N., Kerrigan, J. J., Liu, W.-S., Trulli, J. M., Lai, Z., Holmes, D., Aubart, K. M., Brown, J. R., & Zalacain, M. (2006). Phylogenomic and biochemical characterization of three Legionella pneumophila polypeptide deformylases. Journal of Bacteriology, 188(14), 5249–5257. https://doi.org/10.1128/jb.00866-05
   PubMed Web of Science ®Google Scholar
• Hussan, K. P S., Parambil, H., Hamza, S., Parameswaran, A., Thayyil, M., & Muraleedharan, K. (2020). DFT and molecular docking studies of a set of non-steroidal anti-inflammatory drugs: Propionic acid derivatives. In S. R. De Lazaro, L. H. Da Silveira Lacerda & R. A. P. Ribeiro (Eds.), Density functional theory calculations. IntechOpen. https://doi.org/10.5772/intechopen.93828
   Google Scholar
• IARC Monographs on the Evaluation of Carcinogenic Risks to Humans. (1994). Schistosomes, liver flukes and Helicobacter pylori. IARC Working group on the evaluation of carcinogenic risks to humans. Lyon, 7–14 June 1994. IARC Monographs on the Evaluation of Carcinogenic Risks to Humans, 61, 1–241.
   PubMedGoogle Scholar
• IARC Working Group on the Evaluation of Carcinogenic Risks to Humans. (2012). Biological agents. Volume 100 B. A review of human carcinogens. IARC Monographs on the Evaluation of Carcinogenic Risks to Humans, 100(Pt B):1–441.
   Google Scholar
• Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012). ZINC: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 52(7), 1757–1768. https://doi.org/10.1021/ci3001277
   PubMed Web of Science ®Google Scholar
• Israelachvili, J. N. (2011). Strong intermolecular forces: Covalent and coulomb interactions. In J. N. Israelachvili (Ed.), Intermolecular and surface forces (3rd ed., pp. 53–70). Academic Press. https://doi.org/10.1016/B978-0-12-375182-9.10003-X
   Google Scholar
• Jain, R., Chen, D., White, R., Patel, D., & Yuan, Z. (2005). Bacterial Peptide deformylase inhibitors: A new class of antibacterial agents. Current Medicinal Chemistry, 12(14), 1607–1621. https://doi.org/10.2174/0929867054367194
   PubMed Web of Science ®Google Scholar
• Jaiprakash, N. S., Firoz, A. K. K., & Devanand, B. S. (2015). Peptide deformylase: A new target in antibacterial, antimalarial and anticancer drug discovery. Current Medicinal Chemistry, 22(2), 214–236. https://doi.org/10.2174/0929867321666140826115734
   PubMed Web of Science ®Google Scholar
• Jang, C., Yadav, D. K., Subedi, L., Venkatesan, R., Venkanna, A., Afzal, S., Lee, E., Yoo, J., Ji, E., Kim, S. Y., & Kim, M.-H. (2018). Identification of novel acetylcholinesterase inhibitors designed by pharmacophore-based virtual screening, molecular docking and bioassay. Scientific Reports, 8(1), 14921. https://doi.org/10.1038/s41598-018-33354-6
   PubMedGoogle Scholar
• Kalirajan, R., Pandiselvi, A., Gowramma, B., & Balachandran, P. (2019). In-silico design, ADMET screening, MM-GBSA binding free energy of some novel isoxazole substituted 9-anilinoacridines as HER2 inhibitors targeting breast cancer. Current Drug Research Reviews, 11(2), 118–128. https://doi.org/10.2174/2589977511666190912154817
   PubMedGoogle Scholar
• Kataria, R., & Khatkar, A. (2019). In-silico design, synthesis, ADMET studies and biological evaluation of novel derivatives of chlorogenic acid against urease protein and H. pylori bacterium. BMC Chemistry, 13(1), 41. https://doi.org/10.1186/s13065-019-0556-0
   PubMedGoogle Scholar
• Kataria, R., & Khatkar, A. (2019). Molecular docking, synthesis, kinetics study, structure-activity relationship and ADMET analysis of morin analogous as Helicobacter pylori urease inhibitors. BMC Chemistry, 13(1), 45. https://doi.org/10.1186/s13065-019-0562-2
   PubMedGoogle Scholar
• Khan, M. F., Verma, G., Akhtar, W., Shaquiquzzaman, M., Akhter, M., Rizvi, M., & Alam, M. (2016). Pharmacophore modeling, 3D-QSAR, docking study and ADME prediction of Acyl 1,3,4-thiadiazole amides and sulfonamides as antitubulin agents. Arabian Journal of Chemistry, 12(8), 5000–5018. https://doi.org/10.1016/j.arabjc.2016.11.004
   Google Scholar
• Kikiowo, B., Ogunleye, A. J., Inyang, O. K., Adelakun, N. S., Omotuyi, O. I., Metibemu, D. S., David, T. I., Oludoyi, O. O., & Ijatuyi, T. T. (2020). Flavones scaffold of Chromolaena odorata as a potential xanthine oxidase inhibitor: Induced fit docking and ADME studies. BioImpacts, 10(4), 227–234. https://doi.org/10.34172/bi.2020.29
   PubMed Web of Science ®Google Scholar
• Kreusch, A., Spraggon, G., Lee, C. C., Klock, H., McMullan, D., Ng, K., Shin, T., Vincent, J., Warner, I., Ericson, C., & Lesley, S. A. (2003). Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: Snapshots of the oxygen sensitivity of peptide deformylase. Journal of Molecular Biology, 330(2), 309–321. https://doi.org/10.1016/s0022-2836(03)00596-5
   PubMed Web of Science ®Google Scholar
• Lin, P., Hu, T., Hu, J., Yu, W., Han, C., Zhang, J., Qin, G., Yu, K., Götz, F., Shen, X., Jiang, H., & Qu, D. (2010). Characterization of peptide deformylase homologues from Staphylococcus epidermidis. Microbiology (Reading, England), 156(Pt 10), 3194–3202. https://doi.org/10.1099/mic.0.038174-0
   PubMedGoogle Scholar
• Ma, Y.-C., Yang, B., Wang, X., Zhou, L., Li, W.-Y., Liu, W.-S., Lu, X.-H., Zheng, Z.-H., Ma, Y., & Wang, R.-L. (2019). Identification of novel inhibitor of protein tyrosine phosphatases delta: Structure-based pharmacophore modeling, virtual screening, flexible docking, molecular dynamics simulation, and post-molecular dynamics analysis. Journal of Biomolecular Structure and Dynamics, 38(15), 1–22. https://doi.org/10.1080/07391102.2019.1682050
   Google Scholar
• Mandal, R. S., & Das, S. (2015). In silico approach towards identification of potential inhibitors of Helicobacter pylori DapE. Journal of Biomolecular Structure & Dynamics, 33(7), 1460–1473. https://doi.org/10.1080/07391102.2014.954272
   PubMed Web of Science ®Google Scholar
• Marondedze, E. F., Govender, K. K., & Govender, P. P. (2020). Ligand-based pharmacophore modelling and virtual screening for the identification of amyloid-beta diagnostic molecules. Journal of Molecular Graphics & Modelling, 101, 107711. https://doi.org/10.1016/j.jmgm.2020.107711
   PubMed Web of Science ®Google Scholar
• Nain, Z., Sayed, S. B., Karim, M. M., Islam, M. A., & Adhikari, U. K. (2020). Energy-optimized pharmacophore coupled virtual screening in the discovery of quorum sensing inhibitors of LasR protein of Pseudomonas aeruginosa. Journal of Biomolecular Structure & Dynamics, 38(18), 5374–5388. https://doi.org/10.1080/07391102.2019.1700168
   PubMed Web of Science ®Google Scholar
• Nayak, C., Chandra, I., & Singh, S. K. (2019). An in silico pharmacological approach toward the discovery of potent inhibitors to combat drug resistance HIV-1 protease variants. Journal of Cellular Biochemistry, 120(6), 9063–9081. https://doi.org/10.1002/jcb.28181
   PubMed Web of Science ®Google Scholar
• Oliveira, L. M., Araújo, J. S., Costa, D. B., Santos, M., Santos, A. F., & Leite, F. H. A. (2018). Virtual screening for the selection of new candidates to Trypanosoma cruzi farnesyl pyrophosphate synthase inhibitors. Journal of the Brazilian Chemical Society, 29, 2554–2568.
   Web of Science ®Google Scholar
• Oostenbrink, C., Villa, A., Mark, A. E., & van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25(13), 1656–1676. https://doi.org/10.1002/jcc.20090
   PubMed Web of Science ®Google Scholar
• Padmaja, L., Ravikumar, C., Sajan, D., Hubert, J. I., Jayakumar, V. S., Pettit, G. R., & Faurskov, N. O. (2009). Density functional study on the structural conformations and intramolecular charge transfer from the vibrational spectra of the anticancer drug combretastatin-A2. Journal of Raman Spectroscopy, 40(4), 419–428. https://doi.org/10.1002/jrs.2145
   Web of Science ®Google Scholar
• Parr, R. G. (1980). Density functional theory of atoms and molecules. In K. Fukui & B. Pullman (Eds.), Horizons of quantum chemistry (pp. 5–15). Springer.
   Google Scholar
• Pichota, A., Duraiswamy, J., Yin, Z., Keller, T. H., Alam, J., Liung, S., Lee, G., Ding, M., Wang, G., Chan, W. L., Schreiber, M., Ma, I., Beer, D., Ngew, X., Mukherjee, K., Nanjundappa, M., Teo, J. W. P., Thayalan, P., Yap, A., … Cynamon, M. (2008). Peptide deformylase inhibitors of Mycobacterium tuberculosis: Synthesis, structural investigations, and biological results. Bioorganic & Medicinal Chemistry Letters, 18(24), 6568–6572. https://doi.org/10.1016/j.bmcl.2008.10.040
   PubMed Web of Science ®Google Scholar
• Ragusa, S., Blanquet, S., & Meinnel, T. (1998). Control of peptide deformylase activity by metal cations. Journal of Molecular Biology, 280(3), 515–523. https://doi.org/10.1006/jmbi.1998.1883
   PubMed Web of Science ®Google Scholar
• Rajagopalan, P. T., Datta, A., & Pei, D. (1997). Purification, characterization, and inhibition of peptide deformylase from Escherichia coli. Biochemistry, 36(45), 13910–13918. https://doi.org/10.1021/bi971155v
   PubMed Web of Science ®Google Scholar
• Rampogu, S., Zeb, A., Baek, A., Park, C., Son, M., & Lee, K. W. (2018). Discovery of potential plant-derived peptide deformylase (PDF) inhibitors for multidrug-resistant bacteria using computational studies. Journal of Clinical Medicine, 7(12), 563. https://doi.org/10.3390/jcm7120563
   PubMed Web of Science ®Google Scholar
• Ranjith, P. K., Al-Abdullah, E. S., Al-Omary, F. A. M., El-Emam, A. A., Anto, P. L., Sheena, M. Y., Armaković, S., Armaković, S. J., Zitko, J., Dolezal, M., & Van Alsenoy, C. (2017). FT-IR and FT-Raman characterization and investigation of reactive properties of N-(3-iodo-4-methylphenyl)pyrazine-2-carboxamide by molecular dynamics simulations and DFT calculations. Journal of Molecular Structure, 1136, 14–24. https://doi.org/10.1016/j.molstruc.2017.01.079
   Web of Science ®Google Scholar
• Raza, H., Abbas, Q., Hassan, M., Eo, S. H., Ashraf, Z., Kim, D., Phull, A. R., Kim, S. J., Kang, S. K., & Seo, S. Y. (2017). Isolation, characterization, and in silico, in vitro and in vivo antiulcer studies of isoimperatorin crystallized from Ostericum koreanum. Pharmaceutical Biology, 55(1), 218–226. https://doi.org/10.1080/13880209.2016.1257641
   PubMed Web of Science ®Google Scholar
• Sangeetha, K., Aravindakshan, K., & Hussan, K. P S. (2017). Insight into the theoretical and experimental studies of 1-phenyl-3-methyl-4-benzoyl-5-pyrazolone N (4)-methyl- N (4)- phenylthiosemicarbazone – A potential NLO material. Journal of Molecular Structure, 1150, 135–145. https://doi.org/10.1016/j.molstruc.2017.08.078
   Web of Science ®Google Scholar
• Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Segall, M., Lindan, P., Probert, M., Pickard, C., Hasnip, P., Clark, S., & Payne, M. (2002). First-principles simulation: Ideas, illustrations and the CASTEP code. Journal of Physics: Condensed Matter, 14(11), 2717–2744. https://doi.org/10.1088/0953-8984/14/11/301
   Web of Science ®Google Scholar
• Shelley, J., Cholleti, A., Frye, L., Greenwood, J., Timlin, M., & Uchimaya, M. (2008). Epik: A software program for pK( a ) prediction and protonation state generation for drug-like molecules. Journal of Computer-Aided Molecular Design, 21(12), 681–691. https://doi.org/10.1007/s10822-007-9133-z
   Web of Science ®Google Scholar
• Siddique, O., Ovalle, A., Siddique, A. S., & Moss, S. F. (2018). Helicobacter pylori Infection: An update for the internist in the age of increasing global antibiotic resistance. The American Journal of Medicine, 131(5), 473–479. https://doi.org/10.1016/j.amjmed.2017.12.024
   PubMed Web of Science ®Google Scholar
• Singh, S. B., Genilloud, O., & Peláez, F. (2010). Terrestrial microorganisms – filamentous bacteria. In H.-W. Liu (Ed.), Comprehensive natural products II (pp. 109–140). Elsevier. https://doi.org/10.1016/B978-008045382-8.00036-8
   Google Scholar
• Smith, K. J., Petit, C. M., Aubart, K., Smyth, M., McManus, E., Jones, J., Fosberry, A., Lewis, C., Lonetto, M., & Christensen, S. B. (2003). Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species. Protein Science: A Publication of the Protein Society, 12(2), 349–360. https://doi.org/10.1110/ps.0229303
   PubMed Web of Science ®Google Scholar
• Stockwell, B. R. (2004). Exploring biology with small organic molecules. Nature, 432(7019), 846–854. https://doi.org/10.1038/nature03196
   PubMed Web of Science ®Google Scholar
• Sureshkumar, B., Mary, Y. S., Panicker, C. Y., Suma, S., Armaković, S., Armaković, S. J., Van Alsenoy, C., & Narayana, B. (2020). Quinoline derivatives as possible lead compounds for anti-malarial drugs: Spectroscopic, DFT and MD study. Arabian Journal of Chemistry, 13(1), 632–648. https://doi.org/10.1016/j.arabjc.2017.07.006
   Web of Science ®Google Scholar
• Syed, A. (2016). Molecular docking studies of sesquiterpenoids against Helicobacter pylori peptide deformylase. British Journal of Pharmaceutical Research, 10, 1–7.
   Google Scholar
• Thorarensen, A., Deibel, M. R., Rohrer, D. C., Vosters, A. F., Yem, A. W., Marshall, V. D., Lynn, J. C., Bohanon, M. J., Tomich, P. K., Zurenko, G. E., Sweeney, M. T., Jensen, R. M., Nielsen, J. W., Seest, E. P., & Dolak, L. A. (2001). Identification of novel potent hydroxamic acid inhibitors of peptidyl deformylase and the importance of the hydroxamic acid functionality on inhibition. Bioorganic & Medicinal Chemistry Letters, 11(11), 1355–1358. https://doi.org/10.1016/s0960-894x(01)00242-6
   PubMed Web of Science ®Google Scholar
• Tripathy, S., Azam, M. A., Jupudi, S., & Sahu, S. K. (2018). Pharmacophore generation, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on benzamide analogues as FtsZ inhibitors. Journal of Biomolecular Structure & Dynamics, 36(12), 3218–3230. https://doi.org/10.1080/07391102.2017.1384401
   PubMed Web of Science ®Google Scholar
• Tshibangu-Kabamba, E., & Yamaoka, Y. (2021). Helicobacter pylori infection and antibiotic resistance – from biology to clinical implications. Nature Reviews Gastroenterology & Hepatology, 18(9), 613–629. https://doi.org/10.1038/s41575-021-00449-x
   PubMed Web of Science ®Google Scholar
• Vanajothi, R., Hemamalini, V., Jeyakanthan, J., & Premkumar, K. (2020). Ligand-based pharmacophore mapping and virtual screening for identification of potential discoidin domain receptor 1 inhibitors. Journal of Biomolecular Structure & Dynamics, 38(9), 2800–2808. https://doi.org/10.1080/07391102.2019.1640132
   PubMed Web of Science ®Google Scholar
• Wenzel, R. P., & Edmond, M. B. (2000). Managing antibiotic resistance. The New England Journal of Medicine, 343(26), 1961–1963. https://doi.org/10.1056/nejm200012283432610
   PubMed Web of Science ®Google Scholar
• Xu, Y., Lai, L., Gabrilove, J., & Scheinberg, D. (1998). Antitumor activity of actinonin in vitro and in vivo. Clinical Cancer Research : An Official Journal of the American Association for Cancer Research, 4(1), 171–176.
   PubMed Web of Science ®Google Scholar