Targeting PDE4A for therapeutic potential: exploiting drug repurposing approach through virtual screening and molecular dynamics

References

• Baell, J. B. (2016). Feeling nature’s PAINS: Natural products, natural product drugs, and pan assay interference compounds (PAINS). Journal of Natural Products, 79(3), 616–628. https://doi.org/10.1021/acs.jnatprod.5b00947
   PubMed Web of Science ®Google Scholar
• Bhat, A., Ray, B., Mahalakshmi, A. M., Tuladhar, S., Nandakumar, D., Srinivasan, M., Essa, M. M., Chidambaram, S. B., Guillemin, G. J., & Sakharkar, M. K. (2020). Phosphodiesterase-4 enzyme as a therapeutic target in neurological disorders. Pharmacological Research, 160, 105078. https://doi.org/10.1016/j.phrs.2020.105078
   PubMed Web of Science ®Google Scholar
• Biovia, D. S. (2017). Discovery studio visualizer. BIOVIA.
   Google Scholar
• Bopp, T., Becker, C., Klein, M., Klein-Hessling, S., Palmetshofer, A., Serfling, E., Heib, V., Becker, M., Kubach, J., Schmitt, S., Stoll, S., Schild, H., Staege, M. S., Stassen, M., Jonuleit, H., & Schmitt, E. (2007). Cyclic adenosine monophosphate is a key component of regulatory T cell–mediated suppression. The Journal of Experimental Medicine, 204(6), 1303–1310. https://doi.org/10.1084/jem.20062129
   PubMed Web of Science ®Google Scholar
• Cha, Y., Erez, T., Reynolds, I. J., Kumar, D., Ross, J., Koytiger, G., Kusko, R., Zeskind, B., Risso, S., Kagan, E., Papapetropoulos, S., Grossman, I., & Laifenfeld, D. (2018). Drug repurposing from the perspective of pharmaceutical companies. British Journal of Pharmacology, 175(2), 168–180. https://doi.org/10.1111/bph.13798
   PubMed Web of Science ®Google Scholar
• Cournia, Z., Chipot, C., Roux, B., York, D. M., & Sherman, W. (2021). Free energy methods in drug discovery—introduction. In Kira A. Armacost and David C. Thompson (Eds.), Free energy methods in drug discovery: Current state and future directions. ACS Publications (pp. 1–38).
   Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsl. Protein Crystallogr, 40, 82–92.
   Google Scholar
• D'Sa, C., Tolbert, L. M., Conti, M., & Duman, R. S. (2002). Regulation of cAMP‐specific phosphodiesterases type 4B and 4D (PDE4) splice variants by cAMP signaling in primary cortical neurons. Journal of Neurochemistry, 81(4), 745–757. https://doi.org/10.1046/j.1471-4159.2002.00878.x
   PubMed Web of Science ®Google Scholar
• Giembycz, M. A. (2001). Cilomilast: A second generation phosphodiesterase 4 inhibitor for asthma and chronic obstructive pulmonary disease. Expert Opinion on Investigational Drugs, 10(7), 1361–1379. https://doi.org/10.1517/13543784.10.7.1361
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (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>3.3.CO;2-L
   Web of Science ®Google Scholar
• Houslay, M. D., Schafer, P., & Zhang, K. Y. (2005). Keynote review: Phosphodiesterase-4 as a therapeutic target. Drug Discovery Today, 10(22), 1503–1519. https://doi.org/10.1016/S1359-6446(05)03622-6
   PubMed Web of Science ®Google Scholar
• Houslay, M. D., Scotland, G., Erdogan, S., Huston, E., Mackenzie, S., McCallum, J. F., McPhee, I., Pooley, L., Rena, G., Ross, A., Beard, M., Peder, A., Begg, F., Wilkinson, I., Yarwood, S., Ackerman, C., Houslay, E. S., Hoffman, R., Engels, P., Sullivan, M., & Bolger, G. (1997). Intracellular targeting, interaction with Src homology 3 (SH3) domains and rolipram-detected conformational switches in cAMP-specific PDE4A phosphodiesterase. Biochemical Society Transactions, 25(2), 374–381. https://doi.org/10.1042/bst0250374
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Jaidhan, B., Rao, P. S., & Apparao, A. (2014). Energy minimization and conformation analysis of molecules using steepest descent method. International Journal of Computer Science and Information Technologies, 5, 3525–3528.
   Google Scholar
• Kaplan, W., & Littlejohn, T. G. (2001). Swiss-PDB viewer (deep view). Briefings in Bioinformatics, 2(2), 195–197. https://doi.org/10.1093/bib/2.2.195
   PubMedGoogle Scholar
• Kawasumi, M., & Nghiem, P. (2007). Chemical genetics: Elucidating biological systems with small-molecule compounds. The Journal of Investigative Dermatology, 127(7), 1577–1584. https://doi.org/10.1038/sj.jid.5700853
   PubMed Web of Science ®Google Scholar
• Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., Oostenbrink, C., & Mark, A. E. (2011). An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7(12), 4026–4037. https://doi.org/10.1021/ct200196m
   PubMed Web of Science ®Google Scholar
• Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105(43), 9954–9960. https://doi.org/10.1021/jp003020w
   Web of Science ®Google Scholar
• Mazur, M., Karczewski, J., Lodyga, M., Żaba, R., & Adamski, Z. (2015). Inhibitors of phosphodiesterase 4 (PDE 4): A new therapeutic option in the treatment of psoriasis vulgaris and psoriatic arthritis. The Journal of Dermatological Treatment, 26(4), 326–328. https://doi.org/10.3109/09546634.2014.991267
   PubMed Web of Science ®Google Scholar
• Mohammad, T., Mathur, Y., & Hassan, M. I. (2021). InstaDock: A single-click graphical user interface for molecular docking-based virtual high-throughput screening. Briefings in Bioinformatics, 22(4), bbaa279. https://doi.org/10.1093/bib/bbaa279
   PubMed Web of Science ®Google Scholar
• Mohammad, T., Siddiqui, S., Shamsi, A., Alajmi, M. F., Hussain, A., Islam, A., Ahmad, F., & Hassan, M. I. (2020). Virtual screening approach to identify high-affinity inhibitors of serum and glucocorticoid-regulated kinase 1 among bioactive natural products: Combined molecular docking and simulation studies. Molecules, 25(4), 823. https://doi.org/10.3390/molecules25040823
   PubMed Web of Science ®Google Scholar
• Molina, C. E., Leroy, J., Richter, W., Xie, M., Scheitrum, C., Lee, I.-O., Maack, C., Rucker-Martin, C., Donzeau-Gouge, P., Verde, I., Llach, A., Hove-Madsen, L., Conti, M., Vandecasteele, G., & Fischmeister, R. (2012). Cyclic adenosine monophosphate phosphodiesterase type 4 protects against atrial arrhythmias. Journal of the American College of Cardiology, 59(24), 2182–2190. https://doi.org/10.1016/j.jacc.2012.01.060
   PubMed Web of Science ®Google Scholar
• Nagamine, Y., & Reich, E. (1985). Gene expression and cAMP. Proceedings of the National Academy of Sciences of the United States of America, 82(14), 4606–4610. https://doi.org/10.1073/pnas.82.14.4606
   PubMed Web of Science ®Google Scholar
• Nunes, I. K. D C., de Souza, E. T., Martins, I. R. R., Barbosa, G., Moraes Junior, M. O. D., Medeiros, M. D M., Silva, S. W. D., Balliano, T. L., da Silva, B. A., Silva, P. M. R., Carvalho, V. D F., Martins, M. A., & Lima, L. M. (2020). Discovery of sulfonyl hydrazone derivative as a new selective PDE4A and PDE4D inhibitor by lead-optimization approach on the prototype LASSBio-448: In vitro and in vivo preclinical studies. European Journal of Medicinal Chemistry, 204, 112492. https://doi.org/10.1016/j.ejmech.2020.112492
   PubMed Web of Science ®Google Scholar
• Papaleo, E., Mereghetti, P., Fantucci, P., Grandori, R., & De Gioia, L. (2009). Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case. Journal of Molecular Graphics & Modelling, 27(8), 889–899. https://doi.org/10.1016/j.jmgm.2009.01.006
   PubMed Web of Science ®Google Scholar
• Parasuraman, S. (2011). Prediction of activity spectra for substances. Journal of Pharmacology & Pharmacotherapeutics, 2(1), 52–53. https://doi.org/10.4103/0976-500X.77119
   PubMedGoogle Scholar
• Park, K. (2019). A review of computational drug repurposing. Translational and Clinical Pharmacology, 27(2), 59–63. https://doi.org/10.12793/tcp.2019.27.2.59
   PubMedGoogle Scholar
• Percival, M. D., Yeh, B., & Falgueyret, J.-P. (1997). Zinc dependent activation of cAMP-specific phosphodiesterase (PDE4A). Biochemical and Biophysical Research Communications, 241(1), 175–180. https://doi.org/10.1006/bbrc.1997.7542
   PubMed Web of Science ®Google Scholar
• Pushpakom, S., Iorio, F., Eyers, P. A., Escott, K. J., Hopper, S., Wells, A., Doig, A., Guilliams, T., Latimer, J., McNamee, C., Norris, A., Sanseau, P., Cavalla, D., & Pirmohamed, M. (2019). Drug repurposing: Progress, challenges and recommendations. Nature Reviews. Drug Discovery, 18(1), 41–58. https://doi.org/10.1038/nrd.2018.168
   PubMed Web of Science ®Google Scholar
• Schick, M. A., & Schlegel, N. (2022). Clinical implication of phosphodiesterase-4-inhibition. International Journal of Molecular Sciences, 23(3), 1209. https://doi.org/10.3390/ijms23031209
   PubMed Web of Science ®Google Scholar
• Shukla, R., & Tripathi, T. (2020). Molecular dynamics simulation of protein and protein–ligand complexes. In Dev Bukhsh Singh (Ed.), Computer-aided drug design (pp. 133–161). Nature Springer.
   Google Scholar
• Singh, S., Baker, Q. B., & Singh, D. B. (2022). Molecular docking and molecular dynamics simulation. Bioinformatics, 291–304.
   PubMedGoogle Scholar
• Stein, S. A. M., Loccisano, A. E., Firestine, S. M., & Evanseck, J. D. (2006). Principal components analysis: A review of its application on molecular dynamics data. Annual Reports in Computational Chemistry, 2, 233–261.
   Google Scholar
• Thompson, M. A., Britt, R. D., Kuipers, I., Stewart, A., Thu, J., Pandya, H. C., MacFarlane, P., Pabelick, C. M., Martin, R. J., & Prakash, Y. (2015). cAMP-mediated secretion of brain-derived neurotrophic factor in developing airway smooth muscle. Biochimica et Biophysica Acta, 1853(10 Pt A), 2506–2514. https://doi.org/10.1016/j.bbamcr.2015.06.008
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Tuteja, N. (2009). Signaling through G protein coupled receptors. Plant Signaling & Behavior, 4(10), 942–947. https://doi.org/10.4161/psb.4.10.9530
   PubMedGoogle Scholar
• Vagena, E., Ryu, J. K., Baeza-Raja, B., Walsh, N. M., Syme, C., Day, J. P., Houslay, M. D., & Baillie, G. S. (2019). A high-fat diet promotes depression-like behavior in mice by suppressing hypothalamic PKA signaling. Translational Psychiatry, 9(1), 141. https://doi.org/10.1038/s41398-019-0470-1
   PubMedGoogle Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Wang, H., Peng, M.-S., Chen, Y., Geng, J., Robinson, H., Houslay, M. D., Cai, J., & Ke, H. (2007). Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors. The Biochemical Journal, 408(2), 193–201. https://doi.org/10.1042/BJ20070970
   PubMedGoogle Scholar
• Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., … Wilson, M. (2018). DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Research, 46(D1), D1074–D1082. https://doi.org/10.1093/nar/gkx1037
   PubMed Web of Science ®Google Scholar
• Yunta, M. J. (2017). It is important to compute intramolecular hydrogen bonding in drug design. Am. J. Model. Optim, 5, 24–57.
   Google Scholar