3 Biotech

, 8:385 | Cite as

In silico insights into prediction and analysis of potential novel pyrrolopyridine analogs against human MAPKAPK-2: a new SAR-based hierarchical clustering approach

  • Kranthi Kumar Konidala
  • Uma Devi Bommu
  • Suneetha Yeguvapalli
  • Neeraja PabbarajuEmail author
Original Article


In the present study, we have focused on to elucidate potential bioactive pyrrolopyridine (PYP23) analogs against human mitogen-activated protein kinase-activated protein kinase-2 (MK-2). Here, in silico methods and computational systems biology tools were used as rational strategies to predict novel PYP23 analogs against the MK-2. Initially, crystal structure (PDB-ID: 2P3G) consists steriochemical conflicts were rectified by structure-optimization approaches using the Modeller program, and a new optimized-high resolution model was generated. The stereochemical qualities of the predicted MK-2 model were judged; these showed that the model was reliable for docking assessments. SAR-based bioactivity analysis showed that among the 197 datasets only 15 candidates contained bioactivity data and were accepted as probable MK-2 inhibitors. Virtual screening and docking strategies of dataset compounds against the ligand-binding domain of MK-2 recognized 13 composites containing high binding affinity than known compounds. Furthermore, the comparative structure clustering, in silico toxicogenomics and QSAR-based anticancer properties prediction approaches were successful in the recognition of five best potential compounds such as 60118340, 60118338, 60117736, 60118473 and 60118322, which have great anticancer and drug-likeness with non-toxicity class indices. Leu70, Glu139, Leu141, Glu145, Glu190, Thr206 and Asp207 were found to be novel hotspot residues prominently involved in H-bonds framing with ligands. Interestingly, they have shown better molecular similarity with known bioactive PYP inhibitors. Thus, predicted five compounds can useful as possible chemotherapeutic agents for MK-2 and show similar molecular actions like known PYP inhibitors. Overall, these streamlined new methods may have great potential to reveal possible ligands toward other molecular targets and biomarkers.


MAP kinase-activated protein kinase-2 Pyrrolopyrimidine inhibitors SAR-based bioassay clustering Virtual screening Ensemble docking ADMET analysis 



K. Kranthi Kumar (F1-17.1/2013-14/RGNF-2013-14-SC-AND-40670/(SAIII/Website)) and B. Uma Devi (F1–17.1/2012–13/RGNF-2012–13-SC-AND-32761/(SA-III/WEBSITE)) are thankful to University Grants Commission (UGC) New Delhi, India, for awarding research fellowship, Rajiv Gandhi National Fellowship (RGNF/SRF), to carry out this work.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

13205_2018_1405_MOESM1_ESM.docx (26 kb)
Supplementary material 1 (DOCX 25 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Kranthi Kumar Konidala
    • 1
  • Uma Devi Bommu
    • 2
  • Suneetha Yeguvapalli
    • 2
  • Neeraja Pabbaraju
    • 1
    Email author
  1. 1.Division of Molecular Physiology, Department of ZoologySri Venkateswara UniversityTirupatiIndia
  2. 2.Division of Cancer Informatics, Department of ZoologySri Venkateswara UniversityTirupatiIndia

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