Computational identification of potential lead molecules targeting rho receptor of Neisseria gonorrhoeae

References

• Alirol, E., Wi, T. E., Bala, M., Bazzo, M. L., Chen, X.-S., Deal, C., Dillon, J.-A R., Kularatne, R., Heim, J., Hooft van Huijsduijnen, R., Hook, E. W., Lahra, M. M., Lewis, D. A., Ndowa, F., Shafer, W. M., Tayler, L., Workowski, K., Unemo, M., & Balasegaram, M. (2017). Multidrug-resistant gonorrhea: A research and development roadmap to discover new medicines. PLOS Medicine, 14(7), e1002366–12. https://doi.org/10.1371/journal.pmed.1002366
   PubMed Web of Science ®Google Scholar
• Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
   PubMed Web of Science ®Google Scholar
• Amala, M., Rajamanikandan, S., Prabhu, D., Surekha, K., & Jeyakanthan, J. (2019). Identification of anti-filarial leads against Aspartate semialdehyde dehydrogenase of Wolbachia endosymbiont of Brugia malayi: Combined molecular docking and molecular dynamics approaches. J Biomol Struct Dyn, 37(2), 394–410. https://doi.org/10.1080/07391102.2018.1427633
   PubMed Web of Science ®Google Scholar
• Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., de Castro, E., Duvaud, S., Flegel, V., Fortier, A., Gasteiger, E., Grosdidier, A., Hernandez, C., Ioannidis, V., Kuznetsov, D., Liechti, R., Moretti, S., Mostaguir, K., Redaschi, N., Rossier, G., Xenarios, I., & Stockinger, H. (2012). ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research, 40(Web Server issue), W597–W603. https://doi.org/10.1093/nar/gks400
   PubMedGoogle Scholar
• Becke, A. D. (1993). Density functional thermochemistry III. The role of exact exchange. The Journal of Chemical Physics, 98(7), 5648–5652. https://doi.org/10.1063/1.464913
   Web of Science ®Google Scholar
• Berendsen, H. J. C., Grigera, J. R., & Straatsma, T. P. (1987). The missing term in effective pair potentials. The Journal of Physical Chemistry, 91(24), 6269–6271. https://doi.org/10.1021/j100308a038
   Web of Science ®Google Scholar
• Botella, L., Vaubourgeix, J., Livny, J., & Schnappinger, D. (2017). Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death. Nature Communication, 8, 14731.
   PubMed Web of Science ®Google Scholar
• Christen, M., Hunenberger, P. H., Bakowies, D., Baron, R., Burgi, R., Geerke, D. P., Heinz, T. N., Kastenholz, M. A., Krautler, V., Oostenbrink, C., Peter, C., Trzesniak, D., & van Gunsteren, W. F. (2005). The GROMOS software for biomolecular simulation: GROMOS05. Journal of Computational Chemistry, 26(16), 1719–1751. https://doi.org/10.1002/jcc.20303
   PubMed Web of Science ®Google Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science : a Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N_log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• D'Heygère, F., Rabhi, M., & Boudvillain, M. (2013). Phyletic distribution and conservation of the bacterial transcription termination factor Rho. Microbiology (Reading, England), 159(Pt 7), 1423–1436. https://doi.org/10.1099/mic.0.067462-0
   PubMedGoogle Scholar
• Galvin, S. R., & Cohen, M. S. (2004). The role of sexually transmitted diseases in HIV transmission. Nature Reviews. Microbiology, 2(1), 33–42. https://doi.org/10.1038/nrmicro794
   PubMed Web of Science ®Google Scholar
• Goldberg, A. R., & Hurwitz, J. (1972). Studies on termination of in vitro ribonucleic acid synthesis by rho factor. Journal of Biological Chemistry, 247(17), 5637–5645. https://doi.org/10.1016/S0021-9258(20)81150-8
   PubMed Web of Science ®Google Scholar
• Gutierrez, P., Kozlov, G., Gabrielli, L., Elias, D., Osborne, M. J., Gallouzi, I. E., & Gehring, K. (2007). Solution structure of YaeO, a Rho-specific inhibitor of transcription termination. Journal of Biological Chemistry, 282(32), 23348–23353. https://doi.org/10.1074/jbc.M702010200
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H., & Fraaije, J. C. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Hill, S. A., Masters, T. L., & Wachter, J. (2016). Gonorrhea - an evolving disease of the new millennium. Microbial Cell (Graz, Austria), 3(9), 371–389. https://doi.org/10.15698/mic2016.09.524
   PubMed Web of Science ®Google Scholar
• Humbert, M. V., & Christodoulides, M. (2019). Atypical, yet not infrequent, infections with Neisseria species. Pathogens, 9(1), 10–27. https://doi.org/10.3390/pathogens9010010
   PubMed Web of Science ®Google Scholar
• Hussain, A. S., Shanthi, V., Sheik, S. S., Jeyakanthan, J., Selvarani, P., & Sekar, K. (2002). PDB Goodies-a web-based GUI to manipulate the Protein Data Bank file . Acta Crystallographica. Section D, Biological Crystallography, 58(Pt 8), 1385–1386. https://doi.org/10.1107/s090744490200985x
   PubMedGoogle Scholar
• Iwahara, J., Esadze, A., & Zandarashvili, L. (2015). Physicochemical properties of ion pairs of Biological Macromolecules. Biomolecules, 5(4), 2435–2463. https://doi.org/10.3390/biom5042435
   PubMed Web of Science ®Google Scholar
• Karplus, M. (2002). Molecular dynamics simulations of biomolecules. Accounts of Chemical Research, 35(6), 321–323. https://doi.org/10.1021/ar020082r
   PubMed Web of Science ®Google Scholar
• Kidd, S., & Workowski, K. A. (2015). Management of Gonorrhea in Adolescents and Adults in the United States. Clinical Infectious Diseases, 16, S785–S801.
   Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK – a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Lee, C., Yang, W., & Parr, R. G. (1988). Development of the Colle-salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37(2), 785–789. https://doi.org/10.1103/PhysRevB.37.785
   PubMed Web of Science ®Google Scholar
• LenZ, J. D., & Dillard, J. P. (2018). Pathogenesis of Neisseria gonorrhoeae and the host defense in ascending infections of human fallopian tube. Frontiers in Immunology, 9, 1–18. https://doi.org/10.3389/fimmu.2018.02710
   PubMed Web of Science ®Google Scholar
• LigPrep. (2020). Schrödinger, LLC.
   Google Scholar
• Lionta, E., Spyrou, G., Vassilatis, D. K., & Cournia, Z. (2014). Structure-based virtual screening for drug discovery: principles, applications and recent advances. Current Topics in Medicinal Chemistry, 14(16), 1923–1938. https://doi.org/10.2174/1568026614666140929124445
   PubMed Web of Science ®Google Scholar
• Lowery-Goldhammer, C., & Richardson, J. P. (1974). An RNA-dependent nucleoside triphosphate phosphohydrolase (ATPase) associated with rho termination factor. Proceedings of the National Academy of Sciences of the United States of America, 71(5), 2003–2007. https://doi.org/10.1073/pnas.71.5.2003
   PubMed Web of Science ®Google Scholar
• Mitra, P., Ghosh, G., Hafeezunnisa, M., & Sen, R. (2017). Rho protein: Roles and mechanisms. Annual Review of Microbiology, 71, 687–709. https://doi.org/10.1146/annurev-micro-030117-020432
   PubMed Web of Science ®Google Scholar
• Patel, J., & Mazumdar, V. S. (2019). The current status of sexually transmitted infections/reproductive tract infections in Vadodara city: Health-care provider perspective. Indian Journal of Community Medicine : official Publication of Indian Association of Preventive & Social Medicine, 44(3), 247–251. https://doi.org/10.4103/ijcm.IJCM_382_18
   PubMed Web of Science ®Google Scholar
• Patil, M. (2012). Ectopic pregnancy after infertility treatment. Journal of Human Reproductive Sciences, 5(2), 154–165. https://doi.org/10.4103/0974-1208.101011
   PubMedGoogle Scholar
• Peters, J. M., Vangeloff, A. D., & Landick, R. (2011). Bacterial transcription terminators: The RNA 3'-end chronicles. Journal of Molecular Biology, 412(5), 793–813. https://doi.org/10.1016/j.jmb.2011.03.036
   PubMed Web of Science ®Google Scholar
• Piszczek, J., St Jean, R., & Khaliq, Y. (2015). Gonorrhea: Treatment update for an increasingly resistant organism. Canadian Pharmacists Journal : CPJ = Revue Des Pharmaciens du Canada : RPC, 148(2), 82–89. https://doi.org/10.1177/1715163515570111
   PubMedGoogle Scholar
• Prabhu, D., Rajamanikandan, S., Saritha, P., & Jeyakanthan, J. (2019). Evolutionary significance and functional characterization of Streptomycin adenylyltransferase from Serratia marcescens. Journal of Biomolecular Structure and Dynamics, 29, 1–14.
   Google Scholar
• Prabhu, D., Vidhyavathi, R., & Jeyakanthan, J. (2017). Computational identification of potent inhibitors for Streptomycin 3″-adenylyltransferase of Serratia marcescens . Microbial Pathogenesis, 103, 94–106. https://doi.org/10.1016/j.micpath.2016.12.015
   PubMed Web of Science ®Google Scholar
• Prime, Schrödinger, LLC, New York, NY (2020).
   Google Scholar
• Protein Preparation Wizard. (2020). Schrödinger, LLC, New York.
   Google Scholar
• QikProp. (2020). Schrödinger, LLC.
   Google Scholar
• Quillin, J., & Seifert, H. S. (2018). Neisseria gonorrhoeae host adaptation and pathogenesis. Nature Reviews. Microbiology, 16(4), 226–240. https://doi.org/10.1038/nrmicro.2017.169
   PubMed Web of Science ®Google Scholar
• Rajamanikandan, S., Jeyakanthan, J., & Srinivasan, P. (2017a). Binding mode exploration of LuxR-thiazolidinedione analogues, e-pharmacophore-based virtual screening in the designing of LuxR inhibitors and its biological evaluation. Journal of Biomolecular Structure & Dynamics, 35(4), 897–916. https://doi.org/10.1080/07391102.2016.1166455
   PubMed Web of Science ®Google Scholar
• Rajamanikandan, S., Jeyakanthan, J., & Srinivasan, P. (2017b). Discovery of potent inhibitors targeting Vibrio harveyi LuxR through shape and e-pharmacophore based virtual screening and its biological evaluation. Microbial Pathogenesis, 103, 40–56. https://doi.org/10.1016/j.micpath.2016.12.003
   PubMed Web of Science ®Google Scholar
• Ray-Soni, A., Bellecourt, M. J., & Landick, R. (2016). Mechanisms of bacterial transcription termination: All good things must end. Annual Review of Biochemistry, 85, 319–347. https://doi.org/10.1146/annurev-biochem-060815-014844
   PubMed Web of Science ®Google Scholar
• Rowley, J., Vander Hoorn, S., Korenromp, E., Low, N., Unemo, M., & Abu-Raddad, L. L. (2019). Global and regional estimates of the prevalence and incidence of four curable sexually transmitted infections in 2016. WHO Bulletin.
   Google Scholar
• Schuttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Seifert, E. (2014). OriginPro 9.1: Scientific data analysis and graphing software-software review. Journal of Chemical Information and Modeling, 54(5), 1552 https://doi.org/10.1021/ci500161d
   PubMed Web of Science ®Google Scholar
• Sherman, W., Day, T., Jacobson, M. P., Friesner, R. A., & Farid, R. (2006). Novel procedure for modeling ligand/receptor induced fit effect. Journal of Medicinal Chemistry, 49(2), 534–553. https://doi.org/10.1021/jm050540c
   PubMed Web of Science ®Google Scholar
• Skordalakes, E., & Berger, J. M. (2003). Structure of the Rho transcription terminator: Mechanism of mRNA recognition and helicase loading. Cell, 114(1), 135–146. https://doi.org/10.1016/s0092-8674(03)00512-9
   PubMed Web of Science ®Google Scholar
• Surekha, K., Prabhu, D., Richard, M., Nachiappan, M., Biswal, J., & Jeyakanthan, J. (2016). Investigation of vital pathogenic target orotate phosphoribosyltransferases (OPRTase) from Thermus thermophilus HB8: Phylogenetic and molecular modeling approach. Gene, 583(2), 102–111. https://doi.org/10.1016/j.gene.2016.02.006
   PubMed Web of Science ®Google Scholar
• Unemo, M. (2015). Current and future antimicrobial treatment of gonorrhoea – the rapidly evolving Neisseria gonorrhoeae continues to challenge. BMC Infectious Diseases, 15(1), 15. https://doi.org/10.1186/s12879-015-1029-2
   PubMedGoogle Scholar
• Virtual Screening Workflow (2020). Schrödinger, LLC, New York.
   Google Scholar
• Xu, D., & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal, 101(10), 2525–2534. https://doi.org/10.1016/j.bpj.2011.10.024
   PubMed Web of Science ®Google Scholar
• Zwiefka, A., Kohn, H., & Widger, W. R. (1993). Transcription termination factor rho: The site of bicyclomycin inhibition in Escherichia coli. Biochemistry, 32(14), 3564–3570. https://doi.org/10.1021/bi00065a007
   PubMed Web of Science ®Google Scholar