References
- Abell, C., Scott, D. E., Ehebauer, M. T., Pukala, T., Marsh, M., Blundell, T. L., Venkitaraman, A. R., & Hyvönen, M. (2013). Using a fragment-based approach to target protein-protein interactions. ChemBioChem, 14(3), 332–342. https://doi.org/10.1002/cbic.201200521
- Almasoudi, H. H., Hakami, M. A., Alhazmi, A. Y., Makkawi, M., Alasmari, S., Alghamdi, Y. S., & Mashraqi, M. M. (2023). Unveiling the multitargeted repurposing potential of taxifolin (dihydroquercetin) in cervical cancer: An extensive MM\GBSA-based screening, and MD simulation study. Medical Oncology, 40(8), 218. https://doi.org/10.1007/s12032-023-02094-7
- Ansari, S. M., Coletta, A., Skeby, K. K., Sørensen, J., Schiøtt, B., Palmer, D. S., Ansari, S. M., Coletta, A., Skeby, K. K., & Sørensen, J. (2016). Allosteric-activation mechanism of bovine chymosin revealed by bias-exchange metadynamics and molecular dynamics simulations. The Journal of Physical Chemistry. B, 120(40), 10453–10462. https://doi.org/10.1021/acs.jpcb.6b07491
- Arencibia, J. M., Fröhner, W., Krupa, M., Pastor-Flores, D., Merker, P., Oellerich, T., Neimanis, S., Schmithals, C., Köberle, V., Süß, E., Zeuzem, S., Stark, H., Piiper, A., Odadzic, D., Schulze, J. O., & Biondi, R. M. (2017). An allosteric inhibitor scaffold targeting the PIF-pocket of atypical protein kinase C isoforms. ACS Chemical Biology, 12(2), 564–573. https://doi.org/10.1021/acschembio.6b00827
- Balendran, A., Biondi, R. M., Cheung, P. C. F., Casamayor, A., Deak, M., & Alessi, D. R. (2000). A 3-phosphoinositide-dependent protein kinase-1 (PDK1) docking site is required for the phosphorylation of protein kinase Cζ (PKCζ) and PKC- related kinase 2 by PDK1. The Journal of Biological Chemistry, 275(27), 20806–20813. https://doi.org/10.1074/jbc.M000421200
- Bayascas, J. R. (2008). Dissecting the role of the 3-phosphoinositide-dependent protein kinase-1 (PDK1) signalling pathways. Cell Cycle, 7(19), 2978–2982. https://doi.org/10.4161/cc.7.19.6810
- Beloglazkina, A., Zyk, N., Majouga, A., & Beloglazkina, E. (2020). Recent small-molecule inhibitors of the p53-MDM2 protein-protein interaction. Molecules (Basel, Switzerland), 25(5), 1211. https://doi.org/10.3390/MOLECULES25051211
- Bhat, H. R., Pandey, P. K., Ghosh, S. K., & Singh, U. P. (2013). Development of 4-aminoquinoline-1,3,5-triazine conjugates as potent antibacterial agent through facile synthetic route. Medicinal Chemistry Research, 22(10), 5056–5065. https://doi.org/10.1007/s00044-013-0521-8
- Biondi, R. M., Komander, D., Thomas, C. C., Lizcano, J. M., Deak, M., Alessi, D. R., & van Aalten, D. M. F. (2002). High resolution crystal structure of the human PDK1 catalytic domain defines the regulatory phosphopeptide docking site. The EMBO Journal, 21(16), 4219–4228. https://doi.org/10.1093/emboj/cdf437
- Busschots, K., Lopez-Garcia, L. A., Lammi, C., Stroba, A., Zeuzem, S., Piiper, A., Alzari, P. M., Neimanis, S., Arencibia, J. M., Engel, M., Schulze, J. O., & Biondi, R. M. (2012). Substrate-selective inhibition of protein kinase PDK1 by small compounds that bind to the PIF-pocket allosteric docking site. Chemistry & Biology, 19(9), 1152–1163. https://doi.org/10.1016/j.chembiol.2012.07.017
- Bussi, G., & Laio, A. (2020). Using metadynamics to explore complex free-energy landscapes. Nature Reviews Physics, 2(4), 200–212.https://doi.org/10.1038/s42254-020-0153-0
- Chaudhari, H. K., & Pahelkar, A. R. (2018). 3D QSAR, Docking, Molecular dynamics simulations and MM-GBSA studies of Extended Side Chain of the Antitubercular Drug (6S) 2-Nitro-6-{[4-(trifluoromethoxy) benzyl] oxy}-6,7-dihydro-5H-imidazo[2,1-b] [1,3] oxazine. Infectious Disorders Drug Targets, 19(2), 145–166. https://doi.org/10.2174/1871526518666181015145545
- Collins, B. J., Deak, M., Arthur, J. S. C., Armit, L. J., & Alessi, D. R. (2003). In vivo role of the PIF-binding docking site of PDK1 defined by knock-in mutation. The EMBO Journal, 22(16), 4202–4211. https://doi.org/10.1093/emboj/cdg407
- Cossar, P. J., Lewis, P. J., & McCluskey, A. (2020). Protein-protein interactions as antibiotic targets: A medicinal chemistry perspective. Medicinal Research Reviews, 40(2), 469–494. https://doi.org/10.1002/med.21519
- Cukuroglu, E., Engin, H. B., Gursoy, A., & Keskin, O. (2014). Hot spots in protein-protein interfaces: Towards drug discovery. Progress in Biophysics and Molecular Biology, 116(2–3), 165–173. https://doi.org/10.1016/j.pbiomolbio.2014.06.003
- Dettori, R., Sonzogni, S., Meyer, L., Lopez-Garcia, L. A., Morrice, N. A., Zeuzem, S., Engel, M., Piiper, A., Neimanis, S., Frödin, M., & Biondi, R. M. (2009). Regulation of the interaction between protein kinase C-related protein kinase 2 (PRK2) and its upstream kinase, 3-phosphoinositide-dependent protein kinase 1 (PDK1). The Journal of Biological Chemistry, 284(44), 30318–30327. https://doi.org/10.1074/jbc.M109.051151
- Engel, M., Hindie, V., Lopez-Garcia, L. A., Stroba, A., Schaeffer, F., Adrian, I., Imig, J., Idrissova, L., Nastainczyk, W., Zeuzem, S., Alzari, P. M., Hartmann, R. W., Piiper, A., & Biondi, R. M. (2006). Allosteric activation of the protein kinase PDK1 with low molecular weight compounds. The EMBO Journal, 25(23), 5469–5480. https://doi.org/10.1038/sj.emboj.7601416
- Feldman, R. I., Wu, J. M., Polokoff, M. A., Kochanny, M. J., Dinter, H., Zhu, D., Biroc, S. L., Alicke, B., Bryant, J., Yuan, S., Buckman, B. O., Lentz, D., Ferrer, M., Whitlow, M., Adler, M., Finster, S., Chang, Z., & Arnaiz, D. O. (2005). Novel small molecule inhibitors of 3-phosphoinositide-dependent kinase-1. The Journal of Biological Chemistry, 280(20), 19867–19874. https://doi.org/10.1074/jbc.M501367200
- Guo, W., Wisniewski, J. A., & Ji, H. (2014). Hot spot-based design of small-molecule inhibitors for protein-protein interactions. Bioorganic & Medicinal Chemistry Letters, 24(11), 2546–2554. https://doi.org/10.1016/j.bmcl.2014.03.095
- Jangid, K., Devi, B., Sahoo, A., Kumar, V., Dwivedi, A. R., Thareja, S., Kumar, R., & Kumar, V. (2023). Virtual screening and molecular dynamics simulation approach for the identification of potential multi-target directed ligands for the treatment of Alzheimer’s disease. Journal of Biomolecular Structure & Dynamics, 1–19. https://doi.org/10.1080/07391102.2023.2201838
- Johnson, M. C., Hu, Q., Lingardo, L., Ferre, R. A., Greasley, S., Yan, J., Kath, J., Chen, P., Ermolieff, J., & Alton, G. (2011). Novel isoquinolone PDK1 inhibitors discovered through fragment-based lead discovery. Journal of Computer-Aided Molecular Design, 25(7), 689–698. https://doi.org/10.1007/s10822-011-9456-7
- Kalash, L., Cresser-Brown, J., Habchi, J., Morgan, C., Miller, D. J., Glen, R. C., Allemann, R. K., Bender, A., Person, Q., Directive, W., State, M., Union, E., Authority, N., States, M., Control, Q., سینا, ا., Siderius, M., Shanmugham, A., England, P., … Bajouh, O. S. (2018). Discovery of a small-molecule inhibitor of specific serine residue BAD phosphorylation. Molecules, 23(5), E10505–E10514. https://doi.org/10.1073/pnas.1804897115
- Li, B., Rong, D., & Wang, Y. (2019). Targeting protein-protein interaction with covalent small-molecule inhibitors. Current Topics in Medicinal Chemistry, 19(21), 1872–1876. https://doi.org/10.2174/1568026619666191011163410
- Lingyan, J., Wang, W., & Georg, F. (2014). Targeting protein-protein interactions by small molecules. Annual Review of Pharmacology and Toxicology, 54, 435–456. https://doi.org/10.1007/978-981-13-0773-7
- Liu, W., Li, P., & Mei, Y. (2019). Discovery of SBF1 as an allosteric inhibitor targeting the PIF-pocket of 3-phosphoinositide-dependent protein kinase-1. Journal of Molecular Modeling, 25(7) . https://doi.org/10.1007/s00894-019-4069-5
- Macalino, S. J. Y., Basith, S., Clavio, N. A. B., Chang, H., Kang, S., & Choi, S. (2018). Evolution of in silico strategies for protein-protein interaction drug discovery. Molecules, 23(8), 1963. https://doi.org/10.3390/molecules23081963
- Mangani, S. (2013). Disruption of protein-protein interfaces: In search of new inhibitors. Springer. https://doi.org/10.1007/978-3-642-37999-4
- Pagare, P. P., Morris, A., Li, J., & Zhang, Y. (2021). MEDICINAL CHEMISTRY RESEARCH Development of structure-based pharmacophore to target the β-catenin-TCF protein-protein interaction. Medicinal Chemistry Research, 30(2), 429–439. https://doi.org/10.1007/s00044-020-02693-3
- Pastor-Flores, D., Schulze, J. O., Bahí, A., Giacometti, R., Ferrer-Dalmau, J., Passeron, S., Engel, M., Süss, E., Casamayor, A., & Biondi, R. M. (2013). PIF-pocket as a target for C. albicans Pkh selective inhibitors. ACS Chemical Biology, 8(10), 2283–2292. https://doi.org/10.1021/cb400452z
- Poulsen, A., Blanchard, S., Soh, C. K., Lee, C., Williams, M., Wang, H., & Dymock, B. (2012). Structure-based design of PDK1 inhibitors. Bioorganic & Medicinal Chemistry Letters, 22(1), 305–307. https://doi.org/10.1016/j.bmcl.2011.11.006
- Rehman, H. M., Sajjad, M., Ali, M. A., Gul, R., Naveed, M., Aslam, M. S., Shinwari, K., Bhinder, M. A., Ghani, M. U., Saleem, M., Rather, M. A., Ahmad, I., & Amin, A. (2023). Identification of RdRp inhibitors against SARS-CoV-2 through E-pharmacophore-based virtual screening, molecular docking and MD simulations approaches. International Journal of Biological Macromolecules, 237, 124169. https://doi.org/10.1016/J.IJBIOMAC.2023.124169
- Rettenmaier, T. J., Fan, H., Karpiak, J., Doak, A., Sali, A., Shoichet, B. K., & Wells, J. A. (2015). Small-molecule allosteric modulators of the protein kinase PDK1 from structure-based docking. Journal of Medicinal Chemistry, 58(20), 8285–8291. https://doi.org/10.1021/acs.jmedchem.5b01216.
- Rettenmaier, T. J., Sadowsky, J. D., Thomsen, N. D., Chen, S. C., Doak, A. K., Arkin, M. R., & Wells, J. A. (2014). A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1. Proceedings of the National Academy of Sciences of the United States of America, 111(52), 18590–18595. https://doi.org/10.1073/pnas.1415365112
- Sable, R., & Jois, S. (2015). Surfing the protein-protein interaction surface using docking methods: Application to the design of PPI inhibitors. Molecules, 20(6), 11569–11603. https://doi.org/10.3390/molecules200611569
- Sarkar, S., Gulati, K., Kairamkonda, M., Mishra, A., & Poluri, K. M. (2018). Elucidating Protein-protein Interactions through Computational Approaches and Designing Small Molecule Inhibitors against them for Various Diseases. Current Topics in Medicinal Chemistry, 18(20), 1719–1736. https://doi.org/10.2174/1568026618666181025114903
- Sarvagalla, S., Cheung, C. H. A., Tsai, J. Y., Hsieh, H. P., & Coumar, M. S. (2016). Disruption of protein-protein interactions: Hot spot detection, structure-based virtual screening and: In vitro testing for the anti-cancer drug target-survivin. RSC Advances, 6(38), 31947–31959. https://doi.org/10.1039/C5RA22927H
- Schrodinger Release 2021-3: Bioluminate, Schrodinger, LLC, New York, NY, 2021. (2015).
- Schulze, J. O., Saladino, G., Busschots, K., Neimanis, S., Süß, E., Odadzic, D., Zeuzem, S., Hindie, V., Herbrand, A. K., Lisa, M.-N., Alzari, P. M., Gervasio, F. L., & Biondi, R. M. (2016). Bidirectional allosteric communication between the ATP-binding site and the regulatory PIF pocket in PDK1 protein kinase. Cell Chemical Biology, 23(10), 1193–1205. https://doi.org/10.1016/j.chembiol.2016.06.017
- Schüttelkopf, A. W., & Van Aalten, D. M. F. (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
- Selvakumar, R., Anantha Krishnan, D., Ramakrishnan, C., Velmurugan, D., & Gunasekaran, K. (2020). Identification of novel NAD(P)H dehydrogenase [quinone] 1 antagonist using computational approaches. Journal of Biomolecular Structure & Dynamics, 38(3), 682–696. https://doi.org/10.1080/07391102.2019.1585291
- Sestito, S., & Rapposelli, S. (2019). A patent update on PDK1 inhibitors (2015-present). Expert Opinion on Therapeutic Patents, 29(4), 271–282. https://doi.org/10.1080/13543776.2019.1597852
- Shukla, S., Srivastava, R. S., Shrivastava, S. K., Sodhi, A., & Kumar, P. (2013). Synthesis, cytotoxic evaluation, docking and in silico pharmacokinetic prediction of 4-arylideneamino/cycloalkylidineamino 1, 2-naphthoquinone thiosemicarbazones. Journal of Enzyme Inhibition and Medicinal Chemistry, 28(6), 1192–1198. https://doi.org/10.3109/14756366.2012.721783
- Stockman, B. J., Kothe, M., Kohls, D., Weibley, L., Connolly, B. J., Sheils, A. L., Cao, Q., Cheng, A. C., Yang, L., Kamath, A. V., Ding, Y. H., & Charlton, M. E. (2009). Identification of allosteric PIF-pocket ligands for PDK1 using NMR-based fragment screening and 1H- 15N TROSY experiments. Chemical Biology & Drug Design, 73(2), 179–188. https://doi.org/10.1111/j.1747-0285.2008.00768.x
- Tkachenko, S. E. (2012). Library of Modulator of Protein-protein Interactions (PPI).
- Tran, Q. H., Nguyen, Q. T., Vo, N. Q. H., Mai, T. T., Tran, T. T. N., Tran, T. D., Le, M. T., Trinh, D. T. T., & Minh Thai, K. (2022). Structure-based 3D-Pharmacophore modeling to discover novel interleukin 6 inhibitors: An in silico screening, molecular dynamics simulations and binding free energy calculations. PloS One, 17(4), e0266632. https://doi.org/10.1371/JOURNAL.PONE.0266632
- Vennila, K. N., & Elango, K. P. (2022). Multimodal generative neural networks and molecular dynamics based identification of PDK1 PIF-pocket modulators. Molecular Systems Design & Engineering, 7(9), 1085–1092. https://doi.org/10.1039/D2ME00051B
- Verkhivker, G. M., Agajanian, S., Hu, G., & Tao, P. (2020). Allosteric regulation at the crossroads of new technologies: multiscale modeling, networks, and machine learning. Frontiers in Molecular Biosciences, 7, 136. https://doi.org/10.3389/fmolb.2020.00136
- Wang, X., Ni, D., Liu, Y., & Lu, S. (2021). Rational design of peptide-based inhibitors disrupting protein-protein interactions. Frontiers in Chemistry, 9(May), 682675. https://doi.org/10.3389/fchem.2021.682675
- Wang, L., Zhang, L., Li, L., Jiang, J., Zheng, Z., Shang, J., Wang, C., Chen, W., Bao, Q., Xu, X., Jiang, Z., Zhang, J., & You, Q. (2019). Small-molecule inhibitor targeting the Hsp90-Cdc37 protein-protein interaction in colorectal cancer. Science Advances, 5(9), eaax2277. https://doi.org/10.1126/SCIADV.AAX2277
- Xu, X., Chen, Y., Fu, Q., Ni, D., Zhang, J., Li, X., & Lu, S. (2019). The chemical diversity and structure-based discovery of allosteric modulators for the PIF-pocket of protein kinase PDK1. Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 361–374. https://doi.org/10.1080/14756366.2018.1553167