5GO1

Structural, Functional characterization and discovery of novel inhibitors of Leishmania amazonensis Nucleoside Diphosphatase Kinase (NDK)

Summary for 5GO1

• Entry DOI: 10.2210/pdb5go1/pdb
• Descriptor: Nucleoside diphosphate kinase (2 entities in total)
• Functional Keywords: kinase, leishmania amazonensis, inhibitor, transferase
• Biological source: Leishmania amazonensis
• Total number of polymer chains: 1
• Total formula weight: 16714.08

Authors

Mishra, A.K.,Agnihotri, P.,Singh, S.P.,Pratap, J.V. (deposition date: 2016-07-26, release date: 2017-07-26, Last modification date: 2023-11-08)

Primary citation

Mishra, A.K.,Singh, N.,Agnihotri, P.,Mishra, S.,Singh, S.P.,Kolli, B.K.,Chang, K.P.,Sahasrabuddhe, A.A.,Siddiqi, M.I.,Pratap, J.V.
Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization.
J. Comput. Aided Mol. Des., 31:547-562, 2017

PubMed Abstract: Nucleoside diphosphate kinases (NDKs) are ubiquitous enzymes that catalyze the transfer of the γ-phosphate moiety from an NTP donor to an NDP acceptor, crucial for maintaining the cellular level of nucleoside triphosphates (NTPs). The inability of trypanosomatids to synthesize purines de novo and their dependence on the salvage pathway makes NDK an attractive target to develop drugs for the diseases they cause. Here we report the discovery of novel inhibitors for Leishmania NDK based on the structural and functional characterization of purified recombinant NDK from Leishmania amazonensis. Recombinant LaNDK possesses auto-phosphorylation, phosphotransferase and kinase activities with Histidine 117 playing an essential role. LaNDK crystals were grown by hanging drop vapour diffusion method in a solution containing 18% PEG-MME 500, 100 mM Bis-Tris propane pH 6.0 and 50 mM MgCl. It belongs to the hexagonal space group P622 with unit cell parameters a = b = 115.18, c = 62.18 Å and α = β = 90°, γ = 120°. The structure solved by molecular replacement methods was refined to crystallographic R-factor and R values of 22.54 and 26.52%, respectively. Molecular docking and dynamics simulation-based virtual screening identified putative binding compounds. Protein inhibition studies of selected hits identified five inhibitors effective at micromolar concentrations. One of the compounds showed ~45% inhibition of Leishmania promastigotes proliferation. Analysis of inhibitor-NDK complexes reveals the mode of their binding, facilitating design of new compounds for optimization of activities as drugs against leishmaniasis.

PubMed: 28551817
DOI: 10.1007/s10822-017-0022-9

Experimental method

X-RAY DIFFRACTION (2.5 Å)