3bgq › Citations

Docking study yields four novel inhibitors of the protooncogene Pim-1 kinase.

Pierce AC, Jacobs M, Stuver-Moody C
J Med Chem 51 1972-5 (2008)
Related entries: 3bgp, 3bgz

Cited: 64 times
EuropePMC logo PMID: 18290603

Abstract

To supplement the hits from a high throughput screen, docking was performed against Pim-1 kinase. Glide docking was augmented with a filter to require traditional or aromatic CH..O hydrogen bonds to the kinase hinge. Four diverse actives, of 96 molecules assayed, had K(i) values between 0.091 and 4.5 microM. This gives a 14-fold enrichment over the earlier HTS run, and the two crystal structures solved confirmed the binding modes predicted by docking.

Reviews - 3bgq mentioned but not cited (3)

  1. Molecular docking and structure-based drug design strategies. Ferreira LG, Dos Santos RN, Oliva G, Andricopulo AD. Molecules 20 13384-13421 (2015)
  2. The Development of CK2 Inhibitors: From Traditional Pharmacology to in Silico Rational Drug Design. Cozza G. Pharmaceuticals (Basel) 10 E26 (2017)
  3. Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory. Sugita M, Onishi I, Irisa M, Yoshida N, Hirata F. Molecules 26 E271 (2021)

Articles - 3bgq mentioned but not cited (9)

  1. A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series. Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP. J Chem Inf Model 51 2082-2089 (2011)
  2. Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets. Proctor EA, Yin S, Tropsha A, Dokholyan NV. Biophys. J. 102 144-151 (2012)
  3. Identification of the first inhibitor of the GBP1:PIM1 interaction. Implications for the development of a new class of anticancer agents against paclitaxel resistant cancer cells. Andreoli M, Persico M, Kumar A, Orteca N, Kumar V, Pepe A, Mahalingam S, Alegria AE, Petrella L, Sevciunaite L, Camperchioli A, Mariani M, Di Dato A, Novellino E, Scambia G, Malhotra SV, Ferlini C, Fattorusso C. J. Med. Chem. 57 7916-7932 (2014)
  4. Wogonin protects glomerular podocytes by targeting Bcl-2-mediated autophagy and apoptosis in diabetic kidney disease. Liu XQ, Jiang L, Li YY, Huang YB, Hu XR, Zhu W, Wang X, Wu YG, Meng XM, Qi XM. Acta Pharmacol Sin 43 96-110 (2022)
  5. Chemical space exploration based on recurrent neural networks: applications in discovering kinase inhibitors. Li X, Xu Y, Yao H, Lin K. J Cheminform 12 42 (2020)
  6. Crystal structure of pim1 kinase in complex with a pyrido[4,3-d]pyrimidine derivative suggests a unique binding mode. Lee SJ, Han BG, Cho JW, Choi JS, Lee J, Song HJ, Koh JS, Lee BI. PLoS ONE 8 e70358 (2013)
  7. A pharmacophore-guided deep learning approach for bioactive molecular generation. Zhu H, Zhou R, Cao D, Tang J, Li M. Nat Commun 14 6234 (2023)
  8. Identified Isosteric Replacements of Ligands' Glycosyl Domain by Data Mining. Zhang T, Jiang S, Li T, Liu Y, Zhang Y. ACS Omega 8 25165-25184 (2023)
  9. Inhibition of protein kinases by anticancer DNA intercalator, 4-butylaminopyrimido[4',5':4,5]thieno(2,3-b)quinoline. Rohit Kumar H, Kumar CS, Kiran Kumar HN, Advi Rao GM. Acta Pharm Sin B 7 303-310 (2017)


Reviews citing this publication (11)

  1. Computational methods in drug discovery. Sliwoski G, Kothiwale S, Meiler J, Lowe EW. Pharmacol. Rev. 66 334-395 (2014)
  2. PIM serine/threonine kinases in the pathogenesis and therapy of hematologic malignancies and solid cancers. Brault L, Gasser C, Bracher F, Huber K, Knapp S, Schwaller J. Haematologica 95 1004-1015 (2010)
  3. Docking and chemoinformatic screens for new ligands and targets. Kolb P, Ferreira RS, Irwin JJ, Shoichet BK. Curr. Opin. Biotechnol. 20 429-436 (2009)
  4. Why target PIM1 for cancer diagnosis and treatment? Magnuson NS, Wang Z, Ding G, Reeves R. Future Oncol 6 1461-1478 (2010)
  5. PIM1 kinase as a target for cancer therapy. Merkel AL, Meggers E, Ocker M. Expert Opin Investig Drugs 21 425-436 (2012)
  6. Docking Screens for Novel Ligands Conferring New Biology. Irwin JJ, Shoichet BK. J. Med. Chem. 59 4103-4120 (2016)
  7. Pim kinase inhibitors: a survey of the patent literature. Morwick T. Expert Opin Ther Pat 20 193-212 (2010)
  8. Docking screens: right for the right reasons? Kolb P, Irwin JJ. Curr Top Med Chem 9 755-770 (2009)
  9. Computational approaches in target identification and drug discovery. Katsila T, Spyroulias GA, Patrinos GP, Matsoukas MT. Comput Struct Biotechnol J 14 177-184 (2016)
  10. Insights from Pim1 structure for anti-cancer drug design. Ogawa N, Yuki H, Tanaka A. Expert Opin Drug Discov 7 1177-1192 (2012)
  11. Bioactive 2-pyridone-containing heterocycle syntheses using multicomponent reactions. Hurtado-Rodríguez D, Salinas-Torres A, Rojas H, Becerra D, Castillo JC. RSC Adv 12 34965-34983 (2022)

Articles citing this publication (41)

  1. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. Sastry GM, Adzhigirey M, Day T, Annabhimoju R, Sherman W. J. Comput. Aided Mol. Des. 27 221-234 (2013)
  2. Pharmacologic inhibition of Pim kinases alters prostate cancer cell growth and resensitizes chemoresistant cells to taxanes. Mumenthaler SM, Ng PY, Hodge A, Bearss D, Berk G, Kanekal S, Redkar S, Taverna P, Agus DB, Jain A. Mol. Cancer Ther. 8 2882-2893 (2009)
  3. Synthesis and evaluation of novel inhibitors of Pim-1 and Pim-2 protein kinases. Xia Z, Knaak C, Ma J, Beharry ZM, McInnes C, Wang W, Kraft AS, Smith CD. J. Med. Chem. 52 74-86 (2009)
  4. Pim-1 plays a pivotal role in hypoxia-induced chemoresistance. Chen J, Kobayashi M, Darmanin S, Qiao Y, Gully C, Zhao R, Yeung SC, Lee MH. Oncogene 28 2581-2592 (2009)
  5. Early role for IL-6 signalling during generation of induced pluripotent stem cells revealed by heterokaryon RNA-Seq. Brady JJ, Li M, Suthram S, Jiang H, Wong WH, Blau HM. Nat. Cell Biol. 15 1244-1252 (2013)
  6. Generation of receptor structural ensembles for virtual screening using binding site shape analysis and clustering. Osguthorpe DJ, Sherman W, Hagler AT. Chem Biol Drug Des 80 182-193 (2012)
  7. Ligand pose and orientational sampling in molecular docking. Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK. PLoS ONE 8 e75992 (2013)
  8. New potent dual inhibitors of CK2 and Pim kinases: discovery and structural insights. López-Ramos M, Prudent R, Moucadel V, Sautel CF, Barette C, Lafanechère L, Mouawad L, Grierson D, Schmidt F, Florent JC, Filippakopoulos P, Bullock AN, Knapp S, Reiser JB, Cochet C. FASEB J. 24 3171-3185 (2010)
  9. Isoxazolo[3,4-b]quinoline-3,4(1H,9H)-diones as unique, potent and selective inhibitors for Pim-1 and Pim-2 kinases: chemistry, biological activities, and molecular modeling. Tong Y, Stewart KD, Thomas S, Przytulinska M, Johnson EF, Klinghofer V, Leverson J, McCall O, Soni NB, Luo Y, Lin NH, Sowin TJ, Giranda VL, Penning TD. Bioorg. Med. Chem. Lett. 18 5206-5208 (2008)
  10. Kinase control of latent HIV-1 infection: PIM-1 kinase as a major contributor to HIV-1 reactivation. Duverger A, Wolschendorf F, Anderson JC, Wagner F, Bosque A, Shishido T, Jones J, Planelles V, Willey C, Cron RQ, Kutsch O. J. Virol. 88 364-376 (2014)
  11. The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors. Xiang Y, Hirth B, Asmussen G, Biemann HP, Bishop KA, Good A, Fitzgerald M, Gladysheva T, Jain A, Jancsics K, Liu J, Metz M, Papoulis A, Skerlj R, Stepp JD, Wei RR. Bioorg. Med. Chem. Lett. 21 3050-3056 (2011)
  12. Structure-based design of 3-aryl-6-amino-triazolo[4,3-b]pyridazine inhibitors of Pim-1 kinase. Grey R, Pierce AC, Bemis GW, Jacobs MD, Moody CS, Jajoo R, Mohal N, Green J. Bioorg. Med. Chem. Lett. 19 3019-3022 (2009)
  13. Discovery of CX-6258. A Potent, Selective, and Orally Efficacious pan-Pim Kinases Inhibitor. Haddach M, Michaux J, Schwaebe MK, Pierre F, O'Brien SE, Borsan C, Tran J, Raffaele N, Ravula S, Drygin D, Siddiqui-Jain A, Darjania L, Stansfield R, Proffitt C, Macalino D, Streiner N, Bliesath J, Omori M, Whitten JP, Anderes K, Rice WG, Ryckman DM. ACS Med Chem Lett 3 135-139 (2012)
  14. Drug efficiency indices for improvement of molecular docking scoring functions. García-Sosa AT, Hetényi C, Maran U. J Comput Chem 31 174-184 (2010)
  15. Inhibition of MicroRNA 195 Prevents Apoptosis and Multiple-Organ Injury in Mouse Models of Sepsis. Zheng D, Yu Y, Li M, Wang G, Chen R, Fan GC, Martin C, Xiong S, Peng T. J. Infect. Dis. 213 1661-1670 (2016)
  16. Clinical and therapeutic relevance of PIM1 kinase in gastric cancer. Yan B, Yau EX, Samanta S, Ong CW, Yong KJ, Ng LK, Bhattacharya B, Lim KH, Soong R, Yeoh KG, Deng N, Tan P, Lam Y, Salto-Tellez M, Singapore Gastric Cancer Consortium. Gastric Cancer 15 188-197 (2012)
  17. Synthesis, Pim kinase inhibitory potencies and in vitro antiproliferative activities of diversely substituted pyrrolo[2,3-a]carbazoles. Akué-Gédu R, Nauton L, Théry V, Bain J, Cohen P, Anizon F, Moreau P. Bioorg. Med. Chem. 18 6865-6873 (2010)
  18. A Novel Cinnamon-Related Natural Product with Pim-1 Inhibitory Activity Inhibits Leukemia and Skin Cancer. Kim JE, Son JE, Jeong H, Joon Kim D, Seo SK, Lee E, Lim TG, Kim JR, Chen H, Bode AM, Lee KW, Dong Z. Cancer Res. 75 2716-2728 (2015)
  19. Chemical space sampling by different scoring functions and crystal structures. Brooijmans N, Humblet C. J. Comput. Aided Mol. Des. 24 433-447 (2010)
  20. RASA: a rapid retrosynthesis-based scoring method for the assessment of synthetic accessibility of drug-like molecules. Huang Q, Li LL, Yang SY. J Chem Inf Model 51 2768-2777 (2011)
  21. Large scale meta-analysis of fragment-based screening campaigns: privileged fragments and complementary technologies. Kutchukian PS, Wassermann AM, Lindvall MK, Wright SK, Ottl J, Jacob J, Scheufler C, Marzinzik A, Brooijmans N, Glick M. J Biomol Screen 20 588-596 (2015)
  22. A Lewis Acid Catalyzed annulation to 2,1-benzisoxazoles. Otley KD, Ellman JA. J. Org. Chem. 79 8296-8303 (2014)
  23. Fragment-hopping-based discovery of a novel chemical series of proto-oncogene PIM-1 kinase inhibitors. Saluste G, Albarran MI, Alvarez RM, Rabal O, Ortega MA, Blanco C, Kurz G, Salgado A, Pevarello P, Bischoff JR, Pastor J, Oyarzabal J. PLoS ONE 7 e45964 (2012)
  24. Pim Kinase Inhibitors Evaluated with a Single-Molecule Engineered Nanopore Sensor. Harrington L, Alexander LT, Knapp S, Bayley H. Angew. Chem. Int. Ed. Engl. 54 8154-8159 (2015)
  25. A combination strategy to inhibit Pim-1: synergism between noncompetitive and ATP-competitive inhibitors. Mori M, Tintori C, Christopher RS, Radi M, Schenone S, Musumeci F, Brullo C, Sanità P, Delle Monache S, Angelucci A, Kissova M, Crespan E, Maga G, Botta M. ChemMedChem 8 484-496 (2013)
  26. Discovery and identification of PIM-1 kinase inhibitors through a hybrid screening approach. Shao M, Yuan Y, Yu K, Lei K, Zhu G, Chen L, Xiang M. Mol. Divers. 18 335-344 (2014)
  27. Identification of novel inhibitors for Pim-1 kinase using pharmacophore modeling based on a novel method for selecting pharmacophore generation subsets. Shahin R, Swellmeen L, Shaheen O, Aboalhaija N, Habash M. J. Comput. Aided Mol. Des. 30 39-68 (2016)
  28. Proposed Allosteric Inhibitors Bind to the ATP Site of CK2α. Brear P, Ball D, Stott K, D'Arcy S, Hyvönen M. J Med Chem 63 12786-12798 (2020)
  29. Biased retrieval of chemical series in receptor-based virtual screening. Brooijmans N, Cross JB, Humblet C. J. Comput. Aided Mol. Des. 24 1053-1062 (2010)
  30. Identification of quinones as novel PIM1 kinase inhibitors. Schroeder RL, Goyal N, Bratton M, Townley I, Pham NA, Tram P, Stone T, Geathers J, Nguyen K, Sridhar J. Bioorg. Med. Chem. Lett. 26 3187-3191 (2016)
  31. A PIM-1 Kinase Inhibitor Docking Optimization Study Based on Logistic Regression Models and Interaction Analysis. Ion GND, Nitulescu GM, Mihai DP. Life (Basel) 13 1635 (2023)
  32. A review on PIM kinases in tumors. Arrouchi H, Lakhlili W, Ibrahimi A. Bioinformation 15 40-45 (2019)
  33. Design of gp120 HIV-1 entry inhibitors by scaffold hopping via isosteric replacements. Iusupov IR, Curreli F, Spiridonov EA, Markov PO, Ahmed S, Belov DS, Manasova EV, Altieri A, Kurkin AV, Debnath AK. Eur J Med Chem 224 113681 (2021)
  34. Human papillomavirus insertions identify the PIM family of serine/threonine kinases as targetable driver genes in head and neck squamous cell carcinoma. Broutian TR, Jiang B, Li J, Akagi K, Gui S, Zhou Z, Xiao W, Symer DE, Gillison ML. Cancer Lett 476 23-33 (2020)
  35. Insights into the Interaction Mechanisms of the Proviral Integration Site of Moloney Murine Leukemia Virus (Pim) Kinases with Pan-Pim Inhibitors PIM447 and AZD1208: A Molecular Dynamics Simulation and MM/GBSA Calculation Study. Chen Q, Wang Y, Shi S, Li K, Zhang L, Gao J. Int J Mol Sci 20 (2019)
  36. Practical synthesis of 3-aryl anthranils via an electrophilic aromatic substitution strategy. Gao Y, Yang S, She M, Nie J, Huo Y, Chen Q, Li X, Hu XQ. Chem Sci 13 2105-2114 (2022)
  37. Selective inhibition of intestinal guanosine 3',5'-cyclic monophosphate signaling by small-molecule protein kinase inhibitors. Bijvelds MJC, Tresadern G, Hellemans A, Smans K, Nieuwenhuijze NDA, Meijsen KF, Bongartz JP, Ver Donck L, de Jonge HR, Schuurkes JAJ, De Maeyer JH. J. Biol. Chem. 293 8173-8181 (2018)
  38. Structural analysis of PIM1 kinase complexes with ATP-competitive inhibitors. Bogusz J, Zrubek K, Rembacz KP, Grudnik P, Golik P, Romanowska M, Wladyka B, Dubin G. Sci Rep 7 13399 (2017)
  39. Structure-Based Virtual Screening and De Novo Design of PIM1 Inhibitors with Anticancer Activity from Natural Products. Park H, Jeon J, Kim K, Choi S, Hong S. Pharmaceuticals (Basel) 14 275 (2021)
  40. Synthesis of 2,1-benzisoxazole-3(1H)-ones by base-mediated photochemical N-O bond-forming cyclization of 2-azidobenzoic acids. Dzhons DY, Budruev AV. Beilstein J Org Chem 12 874-881 (2016)
  41. Targeting Host PIM Protein Kinases Reduces Mayaro Virus Replication. Sugasti-Salazar M, Campos D, Valdés-Torres P, Galán-Jurado PE, González-Santamaría J. Viruses 14 422 (2022)


Quick links