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Research Article

Structural refinement and prediction of potential CCR2 antagonists through validated multi-QSAR modeling studies

ORCID Icon, ORCID Icon, , ORCID Icon & ORCID Icon
Pages 75-94 | Received 30 Oct 2017, Accepted 12 Dec 2017, Published online: 03 Jan 2018

References

  • Abbadie, C., Lindia, J. A., Cumiskey, A. M., Peterson, L. B., Mudgett, J. S., Bayne, E. K., … Forrest, M. J. (2003). Impaired neuropathic pain responses in mice lacking the chemokine receptor CCR2. Proceedings of the National Academy of Sciences of the United States of America, 100, 7947–7952. doi:10.1073/pnas.1331358100
  • Adhikari, N., Amin, S. A., Saha, A., & Jha, T. (2017). Combating breast cancer with non-steroidal aromatase inhibitors (NSAIs): Understanding the chemico-biological interactions through comparative SAR/QSAR study. European Journal of Medicinal Chemistry, 137, 365–438. doi:10.1016/j.ejmech.2017.05.041
  • Amin, S. A., Adhikari, N., Jha, T., & Gayen, S. (2016a). First molecular modeling report on novel arylpyrimidine kynurenine monooxygenase inhibitors through multi-QSAR analysis against Huntington’s disease: A proposal to chemists! Bioorganic and Medicinal Chemistry Letters, 26, 5712–5718. doi:10.1016/j.bmcl.2016.10.058
  • Amin, S. A., Adhikari, N., Jha, T., & Gayen, S. (2016b). Exploring structural requirements of unconventional Knoevenagel-type indole derivatives as anticancer agents through comparative QSAR modeling approaches. Canadian Journal of Chemistry, 94, 637–644. doi:10.1139/cjc-2016-0050
  • Amin, S. A., Adhikari, N., Bhargava, S., Jha, T., & Gayen, S. (2017). Designing potential antitrypanosomal thiazol-2-ethylamines through predictive regression based and classification based QSAR analyses. Current Drug Discovery Technology, 14, 39–52. doi:10.2174/1570163813666161117144137
  • Amin, S. A., Adhikari, N., Gayen, S., & Jha, T. (2017). An integrated ligand-based modelling approach to explore the structure-property relationships of influenza endonuclease inhibitors. Structural Chemistry, 28, 1663–1678. doi:10.1007/s11224-017-0933-z
  • Amin, S. A., Adhikari, N., Gayen, S., & Jha, T. (2017). First report on the structural exploration and prediction of new BPTES analogs as glutaminase inhibitors. Journal of Molecular Structure, 1143, 49–64. doi:10.1016/j.molstruc.2017.04.020
  • Amin, S. A., Bhargava, S., Adhikari, N., Gayen, S., & Jha, T. (2017). Exploring pyrazolo[3,4-d]pyrimidine phosphodiesterase 1 (PDE1) inhibitors: A predictive approach combining comparative validated multiple molecular modelling techniques. Journal of Biomolecular Structure and Dynamics, 1–19.doi:10.1080/07391102.2017.1288659
  • Awasthi, M., Amin, S. A., Shukla, V., Jain, S., Patil, U. K., & Gayen, S. (2016). Structural requirements of some derivatives based on natural alkaloid lycorine for their dengue inhibitory activity to accelerate dengue drug discovery efforts. Indian Journal of Natural Product and Resources, 7, 221–228.
  • Biovia, D. S. (2016). Discovery Studio. San Diego, CA: Author . Retrieved fromhttps://www.accelrys.com
  • Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983). Charmm – A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4, 187–217. doi:10.1002/jcc.540040211
  • Bush, B., & Nachbar, R., Jr (1993). Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA. Journal of Computer-Aided Molecular Design, 7, 587–619. doi:10.1007/BF00124364
  • Cai, C., McComsey, D. F., Hou, C., O’Neill, J. C., Opas, E., McKenney, S., … Sui, Z. (2014). Discovery and SAR of 5-aminooctahydrocyclopentapyrrole-3a-carboxamides as potent CCR2 antagonists. Bioorganic & Medicinal Chemistry Letters, 24, 1239–1242. doi:10.1016/j.bmcl.2013.05.024
  • Chan, C. K., Kuo, M. L., Yeh, K. W., Ou, L. S., Chen, L. C., Yao, T. C., & Huang, J. L. (2009). Sequential evaluation of serum monocyte chemotactic protein 1 among asymptomatic state and acute exacerbation and remission of asthma in children. Journal of Asthma, 46, 225–228. doi:10.1080/02770900802553805
  • Chem Draw Ultra 8.0. (2015). Cambridge soft corporation: USA. Retrieved from http://www.cambridgesoft.com
  • Cramer, R. D., Patterson, D. E., & Bunce, J. D. (1988). Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. Journal of the American Chemical Society, 110, 5959–5967. doi:10.1021/ja00226a005
  • Dawson, T. C., Kuziel, W. A., Osahar, T. A., & Maeda, N. (1999). Absence of CC chemokine receptor-2 reduces atherosclerosis in apolipoprotein E-deficient mice. Atherosclerosis, 143, 205–211. doi:10.1016/S0021-9150(98)00318-9
  • Debnath, A. K. (2002). Pharmacophore mapping of a series of 2,4-diamino-5-deazapteridine inhibitors of mycobacterium avium complex dihydrofolate reductase. Journal of Medicinal Chemistry, 45, 41–53. doi:10.1021/jm010360c
  • Devinyak, O., Havrylyuk, D., & Lesyk, R. (2014). 3D-MoRSE descriptors explained. Journal of Molecular Graphics and Modelling, 54, 194–203. doi:10.1016/j.jmgm.2014.10.006
  • DRAGON 6.0. (2001). TALETE SRL: Italy. Retrieved from http://www.talete.mi.it/products/dragon_description.htm
  • Fawcett, T. (2006). An introduction to ROC analysis. Pattern Recognition Letters, 27, 861–874. doi:10.1016/j.patrec.2005.10.010
  • Fife, B. T., Huffnagle, G. B., Kuziel, W. A., & Karpus, W. J. (2000). Cc chemokine receptor 2 is critical for induction of experimental autoimmune encephalomyelitis. The Journal of Experimental Medicine, 192, 899–905. doi:10.1084/jem.192.6.899
  • Fisher, S. R. A., Genetiker, S., Fisher, R. A., Genetician, S., Fisher, R. A., & Généticien, S. (1960). The design of experiments. Edinburgh: Oliver and Boyd.
  • Gasteiger, J., Sadowski, J., Schuur, J., Selzer, P., Steinhauer, L., & Steinhauer, V. (1996). Chemical information in 3D space. Journal of Chemical Information and Computer Science, 36, 1030–1037. doi:10.1021/ci960343+
  • Golbraikh, A., & Tropsha, A. (2002). Beware of q2! Journal of Molecular Graphics and Modelling, 20, 269–276. doi:10.1016/S1093-3263(01)00123-1
  • Gong, J. H., Ratkay, L. G., Waterfield, J. D., & Clark-Lewis, I. (1997). An antagonist of monocyte chemoattractant protein 1 (MCP-1) inhibits arthritis in the MRL- lpr mouse model. The Journal of Experimental Medicine, 186, 131–137. doi:10.1084/jem.186.1.131
  • Gonza’lez, M. P., Ga’ndara, Z., Fall, Y., & Go’mez, G. (2008). Radial distribution function descriptors for predicting affinity for vitamin D receptor. European Journal of Medicinal Chemistry, 43, 1360–1365. doi:10.1016/j.ejmech.2007.10.020
  • Halder, A. K., Amin, S. A., Jha, T., & Gayen, S. (2017). Insight into the structural requirements of pyrimidine-based phosphodiesterase 10A (PDE10A) inhibitors by multiple validated 3D QSAR approaches. SAR and QSAR in Environmental Research, 28, 253–273. doi:10.1080/1062936X.2017.1302991
  • Hemmer, M. C., Steinhauer, V., & Gasteiger, J. (1999). Deriving the 3D structure of organic molecules from their infrared spectra. Vibrational Spectroscopy, 19, 151–164. doi:10.1016/S0924-2031(99)00014-4
  • Hocking, R. R. (1976). The analysis and selection of variables in linear regression. Biometrics, 32, 1–49. doi:10.2307/2529336
  • Islam, M. A., & Pillay, T. S. (2015). Exploration of the structural requirements of HIV-protease inhibitors using pharmacophore, virtual screening and molecular docking approaches for lead identification. Journal of Molecular Graphics and Modelling, 56, 20–30. doi:10.1016/j.jmgm.2014.11.015
  • Klebe, G., Abraham, U., & Mietzner, T. (1994). Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. Journal of Medicinal Chemistry, 37, 4130–4146. doi:10.1021/jm00050a010
  • Klon, A. E., Lowrie, J. F., & Diller, D. J. (2006). Improved naïve bayesian modeling of numerical data for absorption, distribution, metabolism and excretion (ADME) property prediction. Journal of Chemical Information and Modelling, 46, 1945–1956. doi:10.1021/ci0601315
  • Laing, K. J., & Secombes, C. J. (2004). Chemokines. Developmental & Comparative Immunology, 28, 443–460. doi:10.1016/j.dci.2003.09.006
  • Lanter, J. C., Markotan, T. P., Zhang, X., Subasinghe, N., Kang, F. A., Hou, C., … Sui, Z. (2011). The discovery of novel cyclohexylamide CCR2 antagonists. Bioorganic & Medicinal Chemistry Letters, 21, 7496–7501. doi:10.1016/j.bmcl.2011.09.113
  • Liu, L. L., Lu, J., Lu, Y., Zheng, M. Y., Luo, X. M., Zhu, W. L., … Chen, K. X. (2014). Novel Bayesian classification models for predicting compounds blocking hERG potassium channels. Acta Pharmacologica Sinica, 35, 1093–1102. doi:10.1038/aps.2014.35
  • Mitra, I., Saha, A., & Roy, K. (2010). Exploring quantitative structure–activity relationship (QSAR) studies of antioxidant phenolic compounds obtained from traditional Chinese medicinal plants. Molecular Simulation, 36, 1067–1079. doi:10.1080/08927022.2010.503326
  • Ojha, P. K., & Roy, K. (2011). Comparative QSARs for antimalarial endochins: Importance of descriptor-thinning and noise reduction prior to feature selection. Chemometrics and Intelligent Laboratory Systems, 109, 146–161. doi:10.1016/j.chemolab.2011.08.007
  • Pavadai, E., El Mazouni, F., Wittlin, S., de Kock, C., Phillips, M. A., & Chibale, K. (2016). Identification of new human malaria parasite plasmodium falciparum dihydroorotate dehydrogenase inhibitors by pharmacophore and structure-based virtual screening. Journal of Chemical Information and Modelling, 56, 548–562. doi:10.1021/acs.jcim.5b00680
  • Pease, J., & Horuk, R. (2012). Chemokine receptor antagonists. Journal of Medicinal Chemistry, 55, 9363–9392. doi:10.1021/jm300682j
  • Pourbasheer, E., Aalizadeh, R., ShokouhiTabar, S., Ganjali, M. R., Norouzi, P., & Shadmanesh, J. (2014). 2D and 3D quantitative structure–activity relationship study of hepatitis C virus NS5B polymerase inhibitors by comparative molecular field analysis and comparative molecular similarity indices analysis methods. Journal of Chemical Information and Modeling., 54, 2902–2914. doi:10.1021/ci500216c
  • Roy, K., Kar, S., & Ambure, P. (2015). On a simple approach for determining applicability domain of QSAR models. Chemometrics and Intelligent Laboratory Systems, 145, 22–29. doi:10.1016/j.chemolab.2015.04.013
  • Ruster, C., & Wolf, G. (2008). The role of chemokines and chemokine receptors in diabetic nephropathy. Frontiers in Bioscience, 13, 944–955. doi:10.2741/2734
  • Sakkiah, S., Thangapandian, S., John, S., Kwon, Y. J., & Lee, K. W. (2010). 3D QSAR pharmacophore based virtual screening and molecular docking for identification of potential HSP90 inhibitors. European Journal of Medicinal Chemistry, 45, 2132–2140. doi:10.1016/j.ejmech.2010.01.016
  • Schuur, J. H., Selzer, P., & Gasteiger, J. (1996). The coding of the three-dimensional structure of molecules by molecular transforms and its application to structure-spectra correlations and studies of biological activity. Journal of Chemical Information and Computer Science, 36, 334–344. doi:10.1021/ci950164c
  • Strunz, A. K., Zweemer, A. J., Weiss, C., Schepmann, D., Junker, A., Heitman, L. H., … Wünsch, B. (2015). Synthesis and biological evaluation of spirocyclic antagonists of CCR2 (chemokine CC receptor subtype 2). Bioorganic & Medicinal Chemistry, 23, 4034–449. doi:10.1016/j.bmc.2015.02.019
  • Subasinghe, N. L., Lanter, J., Markotan, T., Opas, E., McKenney, S., Crysler, C., … Sui, Z. (2013). A novel series of N-(azetidin-3-yl)-2-(heteroarylamino) acetamide CCR2 antagonists. Bioorganic & Medicinal Chemistry Letters, 23, 1063–1069. doi:10.1016/j.bmcl.2012.12.017
  • SYBYL-X 2.0. (2015). USA: Certara. Retrieved from http://www.certara.com
  • Szollosi, D. E., Ghoneim, O. A., Manzoor, M. K., Dhuguru, J., & Edafiogho, I. O. (2016). Novel piperazino-enaminones suppress pro-inflammatory cytokines and inhibit chemokine receptor CCR2. Inflammation, 39, 2053–2061. doi:10.1007/s10753-016-0443-y
  • The simple, user-friendly and reliable online standalone tools. Retrieved December 1, 2016, from https://dtclab.webs.com/software-tools
  • Todeschini, R., & Consonni, V. (2009). Molecular Descriptors for Chemoinformatics (Vol. 2). Germany: Weinheim WILEY-VCH.10.1002/9783527628766
  • Vilums, M., Zweemer, A. J., Barmare, F., van der Gracht, A. M., Bleeker, D. C., Yu, Z., … IJzerman, A. P. (2015). When structure-affinity relationships meet structure-kinetics relationships: 3-((Inden-1-yl)amino)-1-isopropyl-cyclopentane-1-carboxamides as CCR2 antagonists. European Journal of Medicinal Chemistry, 93, 121–134. doi:10.1016/j.ejmech.2015.01.063
  • Xia, M., Hou, C., DeMong, D. E., Pollack, S. R., Pan, M., Brackley, J. A., … Wachter, M. (2007). Synthesis, structure−activity relationship and in vivo antiinflammatory efficacy of substituted dipiperidines as CCR2 antagonists. Journal of Medicinal Chemistry, 50, 5561–5563. doi:10.1021/jm070902b
  • Xia, M., Hou, C., DeMong, D., Pollack, S., Pan, M., Brackley, J., … Wachter, M. (2008). Substituted dipiperidine alcohols as potent CCR2 antagonists. Bioorganic & Medicinal Chemistry Letters, 18, 3562–3564. doi:10.1016/j.bmcl.2008.05.010
  • Xia, M., Hou, C., DeMong, D., Pollack, S., Pan, M., Singer, M., … Wachter, M. (2008). Synthesis and structure-activity relationship of 7-azaindole piperidine derivatives as CCR2 antagonists. Bioorganic & Medicinal Chemistry Letters, 18, 6468–6470. doi:10.1016/j.bmcl.2008.10.061
  • Xue, C. B., Wang, A., Han, Q., Zhang, Y., Cao, G., Feng, H., … Metcalf, B. (2011). Discovery of INCB8761/PF-4136309, a potent, selective, and orally bioavailable CCR2 antagonist. ACS Medicinal Chemistry Letters, 2, 913–918. doi:10.1021/ml200199c
  • Zweemer, A. J., Bunnik, J., Veenhuizen, M., Miraglia, F., Lenselink, E. B., Vilums, M., … Heitman, L. H. (2014). Discovery and mapping of an intracellular antagonist binding site at the chemokine receptor CCR2. Molecular Pharmacology, 86, 358–368. doi:10.1124/mol.114.093328

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