Skip to main content
SpringerLink
Log in

Identification of ligand efficient, fragment-like hits from an HTS library: structure-based virtual screening and docking investigations of 2H- and 3H-pyrazolo tautomers for Aurora kinase A selectivity

  • Published:
Journal of Computer-Aided Molecular Design Aims and scope Submit manuscript

Abstract

Furanopyrimidine 1 (IC50 = 273 nM, LE = 0.36, LELP = 10.28) was recently identified by high-throughput screening (HTS) of an in-house library (125,000 compounds) as an Aurora kinase inhibitor. Structure-based hit optimization resulted in lead molecules with in vivo efficacy in a mouse tumour xenograft model, but no oral bioavailability. This is attributed to “molecular obesity”, a common problem during hit to lead evolution during which degradation of important molecular properties such as molecular weight (MW) and lipophilicity occurs. This could be effectively tackled by the right choice of hit compounds for optimization. In this regard, ligand efficiency (LE) and ligand efficiency dependent lipophilicity (LELP) indices are more often used to choose fragment-like hits for optimization. To identify hits with appropriate LE, we used a MW cut-off <250, and pyrazole structure to filter HTS library. Next, structure-based virtual screening using software (Libdock and Glide) in the Aurora A crystal structure (PDB ID: 3E5A) was carried out, and the top scoring 18 compounds tested for Aurora A enzyme inhibition. This resulted in the identification of a novel tetrahydro-pyrazolo-isoquinoline hit 7 (IC50 = 852 nM, LE = 0.44, LELP = 8.36) with fragment-like properties suitable for further hit optimization. Moreover, hit 7 was found to be selective for Aurora A (Aurora B IC50 = 35,150 nM) and the possible reasons for selectivity investigated by docking two tautomeric forms (2H- and 3H-pyrazole) of 7 in Auroras A and B (PDB ID: 4AF3) crystal structures. This docking study shows that the major 3H-pyrazole tautomer of 7 binds in Aurora A stronger than in Aurora B.

Graphical Abstract

A series of in silico filters were applied to HTS library compounds, followed by biochemical testing identified aurora A selective hit 7 with fragment-like characters suitable for further development.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Abbreviations

ΔG:

Binding free energy

CLogP:

Calculated logarithm of partition coefficient

HTS:

High-throughput screening

LE:

Ligand efficiency

LELP:

Ligand efficiency dependent lipophilicity

NHAC:

Non hydrogen atom count

SBVS:

Structure-based virtual screening

taut-1:

Tautomer-1

taut-2:

Tautomer-2

References

  1. Hann MM (2011) Molecular obesity, potency and other addictions in drug discovery. MedChemComm 2:349–355

    Article  CAS  Google Scholar 

  2. Perola E (2010) An analysis of the binding efficiencies of drugs and their leads in successful drug discovery programs. J Med Chem 53(7):2986–2997

    Article  CAS  Google Scholar 

  3. Hann MM, Keseru GM (2012) Finding the sweet spot: the role of nature and nurture in medicinal chemistry. Nature Rev Drug Discov 11(5):355–365

    Article  CAS  Google Scholar 

  4. Lobell M, Hendrix M, Hinzen B, Keldenich J, Meier H, Schmeck C, Schohe-Loop R, Wunberg T, Hillisch A (2006) In silico ADMET traffic lights as a tool for the prioritization of HTS hits. ChemMedChem 1(11):1229–1236

    Article  CAS  Google Scholar 

  5. Erlanson DA (2012) Introduction to fragment-based drug discovery. Top Curr Chem 317:1–32

    Article  CAS  Google Scholar 

  6. Leach AR, Hann MM (2011) Molecular complexity and fragment-based drug discovery: ten years on. Curr Opin Chem Biol 15(4):489–496

    Article  CAS  Google Scholar 

  7. Bembenek SD, Tounge BA, Reynolds CH (2009) Ligand efficiency and fragment-based drug discovery. Drug Discov Today 14(5–6):278–283

    Article  CAS  Google Scholar 

  8. Orita M, Ohno K, Niimi T (2009) Two ‘Golden Ratio’ indices in fragment-based drug discovery. Drug Discov Today 14(5–6):321–328

    Article  CAS  Google Scholar 

  9. Noble ME, Endicott JA, Johnson LN (2004) Protein kinase inhibitors: insights into drug design from structure. Science 303(5665):1800–1805

    Article  CAS  Google Scholar 

  10. Kollareddy M, Zheleva D, Dzubak P, Brahmkshatriya PS, Lepsik M, Hajduch M (2012) Aurora kinase inhibitors: progress towards the clinic. Invest New Drugs 30(6):2411–2432

    Article  CAS  Google Scholar 

  11. Fu J, Bian M, Jiang Q, Zhang C (2007) Roles of Aurora kinases in mitosis and tumorigenesis. Mol Cancer Res 5(1):1–10

    Article  CAS  Google Scholar 

  12. Carmena M, Earnshaw WC (2003) The cellular geography of aurora kinases. Nature Rev Mol Cell Biol 4(11):842–854

    Article  CAS  Google Scholar 

  13. Cheung CH, Coumar MS, Chang JY, Hsieh HP (2011) Aurora kinase inhibitor patents and agents in clinical testing: an update (2009–10). Expert Opin Ther Pat 21(6):857–884

    Article  CAS  Google Scholar 

  14. Coumar MS, Tsai MT, Chu CY, Uang BJ, Lin WH, Chang CY, Chang TY, Leou JS, Teng CH, Wu JS, Fang MY, Chen CH, Hsu JT, Wu SY, Chao YS, Hsieh HP (2010) Identification, SAR studies, and X-ray co-crystallographic analysis of a novel furanopyrimidine aurora kinase A inhibitor. ChemMedChem 5(2):255–267

    Article  CAS  Google Scholar 

  15. Coumar MS, Chu CY, Lin CW, Shiao HY, Ho YL, Reddy R, Lin WH, Chen CH, Peng YH, Leou JS, Lien TW, Huang CT, Fang MY, Wu SH, Wu JS, Chittimalla SK, Song JS, Hsu JT, Wu SY, Liao CC, Chao YS, Hsieh HP (2010) Fast-forwarding hit to lead: aurora and epidermal growth factor receptor kinase inhibitor lead identification. J Med Chem 53(13):4980–4988

    Article  CAS  Google Scholar 

  16. Wu JM, Chen CT, Coumar MS, Lin WH, Chen ZJ, Hsu JT, Peng YH, Shiao HY, Chu CY, Wu JS, Lin CT, Chen CP, Hsueh CC, Chang KY, Kao LP, Huang CY, Chao YS, Wu SY, Hsieh HP, Chi YH (2013) Aurora kinase inhibitors reveal mechanisms of HURP in nucleation of centrosomal and kinetochore microtubules. Proc Natl Acad Sci USA 110(19):E1779–E1787

    Article  CAS  Google Scholar 

  17. Shiao HY, Coumar MS, Chang CW, Ke YY, Chi YH, Chu CY, Sun HY, Chen CH, Lin WH, Fung KS, Kuo PC, Huang CT, Chang KY, Lu CT, Hsu JT, Chen CT, Jiaang WT, Chao YS, Hsieh HP (2013) Optimization of ligand and lipophilic efficiency to identify an in vivo active Furano-Pyrimidine Aurora Kinase Inhibitor. J Med Chem 56(13):5247–5260

    Article  CAS  Google Scholar 

  18. Accelrys Software Inc. (2011) Discovery Studio Modelling Environment, Release 3.1, Accelry Software Inc

  19. Maestro, version 9.2 (2011) Schrödinger, LLC, York N

  20. LigPrep, version 2.5 (2012) Schrödinger, LLC, York N

  21. Glide, version 5.8 (2012) Schrödinger, LLC, York N

  22. Prime, version 3.0 (2011) Schrödinger, LLC, York N

  23. Lin WH, Song JS, Chang TY, Chang CY, Fu YN, Yeh CL, Wu SH, Huang YW, Fang MY, Lien TW, Hsieh HP, Chao YS, Huang SF, Tsai SF, Wang LM, Hsu JT, Chen YR (2008) A cell-based high-throughput screen for epidermal growth factor receptor pathway inhibitors. Anal Biochem 377(1):89–94

    Article  CAS  Google Scholar 

  24. Kumar H, Saini D, Jain S, Jain N (2013) Pyrazole scaffold: a remarkable tool in the development of anticancer agents. Eur J Med Chem 70:248–258

    Article  CAS  Google Scholar 

  25. Coumar MS, Leou JS, Shukla P, Wu JS, Dixit AK, Lin WH, Chang CY, Lien TW, Tan UK, Chen CH, Hsu JT, Chao YS, Wu SY, Hsieh HP (2009) Structure-based drug design of novel Aurora kinase A inhibitors: structural basis for potency and specificity. J Med Chem 52(4):1050–1062

    Article  CAS  Google Scholar 

  26. Zhao B, Smallwood A, Yang J, Koretke K, Nurse K, Calamari A, Kirkpatrick RB, Lai Z (2008) Modulation of kinase-inhibitor interactions by auxiliary protein binding: crystallography studies on Aurora A interactions with VX-680 and with TPX2. Protein Sci 17(10):1791–1797

    Article  CAS  Google Scholar 

  27. Ke YY, Coumar MS, Shiao HY, Wang WC, Chen CW, Song JS, Chen CH, Lin WH, Wu SH, Hsu JTA, Chang CM, Hsieh HP (2014) Ligand efficiency based approach for efficient virtual screening of compound libraries. Eur J Med Chem 83:226–235

  28. Shultz MD (2013) Setting expectations in molecular optimizations: strengths and limitations of commonly used composite parameters. Bioorg Med Chem Lett 23(21):5980–5991

    Article  CAS  Google Scholar 

  29. Cavasotto CN, Ortiz MA, Abagyan RA, Piedrafita FJ (2006) In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells. Bioorg Med Chem Lett 16(7):1969–1974

    Article  CAS  Google Scholar 

  30. Fabian MA, Biggs WH 3rd, Treiber DK, Atteridge CE, Azimioara MD, Benedetti MG, Carter TA, Ciceri P, Edeen PT, Floyd M, Ford JM, Galvin M, Gerlach JL, Grotzfeld RM, Herrgard S, Insko DE, Insko MA, Lai AG, Lelias JM, Mehta SA, Milanov ZV, Velasco AM, Wodicka LM, Patel HK, Zarrinkar PP, Lockhart DJ (2005) A small molecule-kinase interaction map for clinical kinase inhibitors. Nature Biotechnol 23(3):329–336

    Article  CAS  Google Scholar 

  31. Kusakabe K, Ide N, Daigo Y, Tachibana Y, Itoh T, Yamamoto T, Hashizume H, Hato Y, Higashino K, Okano Y, Sato Y, Inoue M, Iguchi M, Kanazawa T, Ishioka Y, Dohi K, Kido Y, Sakamoto S, Yasuo K, Maeda M, Higaki M, Ueda K, Yoshizawa H, Baba Y, Shiota T, Murai H, Nakamura Y (2013) Indazole-based potent and cell-active Mps1 kinase inhibitors: rational design from pan-kinase inhibitor anthrapyrazolone (SP600125). J Med Chem 56(11):4343–4356

    Article  CAS  Google Scholar 

  32. Bearss DJ (2011) Shining the light on aurora-a kinase as a drug target in pancreatic cancer. Mol Cancer Ther 10(11):2012

    Article  CAS  Google Scholar 

  33. Elkins JM, Santaguida S, Musacchio A, Knapp S (2012) Crystal structure of human aurora B in complex with INCENP and VX-680. J Med Chem 55(17):7841–7848

    Article  CAS  Google Scholar 

  34. Instant JChem, version 6.1, ChemAxon Ltd, Budapest (2013)

  35. Dodson CA, Kosmopoulou M, Richards MW, Atrash B, Bavetsias V, Blagg J, Bayliss R (2010) Crystal structure of an Aurora-A mutant that mimics Aurora-B bound to MLN8054: insights into selectivity and drug design. Biochem J 427(1):19–28

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Financial support from the Science and Engineering Research Board (SR/FT/LS-64/2011 for MSC), and Department of Biotechnology (DBT-JRF/2012-13/80 for SS), India, National Health Research Institutes and National Science Council (NSC-101-2325-B-400-003 and NSC-101-2113-M-400-002-MY4 for HPH; NSC-102-2113-M-400-003-MY3, for HYS), Taiwan are gratefully acknowledged.

Author information

Authors and Affiliations

  1. Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, 605014, Puducherry, India

    Sailu Sarvagalla, Vivek Kumar Singh & Mohane Selvaraj Coumar

  2. Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, 350, Miaoli County, Taiwan, ROC

    Yi-Yu Ke, Hui-Yi Shiao, Wen-Hsing Lin, Hsing-Pang Hsieh & John T. A. Hsu

Authors
  1. Sailu Sarvagalla
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vivek Kumar Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yi-Yu Ke
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hui-Yi Shiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Wen-Hsing Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hsing-Pang Hsieh
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. John T. A. Hsu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Mohane Selvaraj Coumar
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mohane Selvaraj Coumar.

Additional information

Sailu Sarvagalla, Vivek Kumar Singh, Yi-Yu Ke contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

10822_2014_9807_MOESM1_ESM.doc

Supplementary material 1 Supplementary data associated with this article can be found in the online version. These data include, list of Aurora kinase inhibitors in clinical development, hits identified from SBVS, compound characterization data and kinase selectivity profile of hit 7 are provided. (DOC 887 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sarvagalla, S., Singh, V.K., Ke, YY. et al. Identification of ligand efficient, fragment-like hits from an HTS library: structure-based virtual screening and docking investigations of 2H- and 3H-pyrazolo tautomers for Aurora kinase A selectivity. J Comput Aided Mol Des 29, 89–100 (2015). https://doi.org/10.1007/s10822-014-9807-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10822-014-9807-2

Keywords

Search

Navigation