Role of salt bridge dynamics in inter domain recognition of human impdh isoforms: An insight to inhibitor topology for isoform-ii

Hridoy R. Bairagya, Bishnu P. Mukhopadhyay, Asim K. Bera

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13 Scopus citations


Inosine monophosphate dehydrogenase (IMPDH) enzyme involves in the biosynthesis pathway of guanosine nucleotide. Type II isoform of the enzyme is selectively upregulated in neoplastic fast replicating lymphocytes and CML cancer cells. The hIMPDH-II is an excellent target for antileukemic agent. The detailed investigation during MD-Simulation (15 ns) of three different unliganded structures (1B3O, 1JCN and 1JR1) have clearly explored the salt bridge mediated stabilization of inter or intra domain (catalytic domains IN, with res. Id. 28–111 and 233–504, whereas two CBS domains C1, C2 are 112–171 and 172–232) in IMPDH enzyme which are mostly inaccessible in their X-rays structures. The salt bridge interaction in IN—C1 inter-domain of hIMPDH-I, IN—C2 of IMPDH-II and C1—IC of nhIMPDH-II are discriminative features among the isoforms. The IN—C2 recognition in hIMPDH-II (1B3O) is missing in type-I isoform (1JCN). The salt bridge interaction D232—K238 at the surface of protein and the involvement of three conserved water molecules or the hydrophilic centers (WA232OD1, WB232OD2 and W238NZ) to those acidic and basic residues seem to be unique in hIMPDH-II. The hydrophilic susceptibility, geometrical and electronic consequences of this salt bridge interaction could be useful to design the topology of specific inhibitor for hIMPDH-II which may not be effective for hIMPDH-I. Possibly, the aliphatic ligand containing carboxyl, amide or hydrophilic groups with flexible structure may be implicated for hIMPDH-II inhibitor design using the conserved water mimic drug design protocol.

Original languageEnglish (US)
Pages (from-to)441-462
Number of pages22
JournalJournal of Biomolecular Structure and Dynamics
Issue number3
StatePublished - Dec 2011
Externally publishedYes

Bibliographical note

Funding Information:
H.R.B. acknowledge and thankful to C.S.I.R. (Council of Scientific and Industrial Research, Govt. of India) for providing Senior Research Fellowship (SRF). B. P. M. acknowledge and thankful to Department of Biotechnology (Govt. of India) for providing Super Micro Computer and overhead charges. B. P. M. and H. R. B. also thankful to National Institute of Technology-Durgapur for providing the research facility in the Department of Chemistry.


  • Dynamics of salt bridges
  • IMPDH isoforms
  • Inhibitor topology
  • Inter and intra domain recognition


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