Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase

Abstract

Thymidine monophosphate kinase (TMPK(mt)) is an essential enzyme for nucleotide metabolism in Mycobacterium tuberculosis, and thus an attractive target for novel antituberculosis agents. In this work, we have explored the chemical space around the 2',3'-bicyclic thymidine nucleus by designing and in silico screening of a virtual focused library selected via structure based methods to identify more potent analogs endowed with favorable ADME-related properties. In all the library members we have exchanged the ribose ring of the template with a cyclopentane moiety that is less prone to enzymatic degradation. In addition, we have replaced the six-membered 2',3'-ring by a number of five-membered and six-membered heterocyclic rings containing alternative proton donor and acceptor groups, to exploit the interaction with the carboxylate groups of Asp9 and Asp163 as well as with several cationic residues present in the vicinity of the TMPK(mt) binding site. The three-dimensional structure of the TMPK(mt) complexed with 5-hydroxymethyl-dUMP, an analog of dTMP, was employed to develop a QSAR model, to parameterize a scoring function specific for the TMPK(mt) target and to select analogues which display the highest predicted binding to the target. As a result, we identified a small highly focused combinatorial subset of bicyclic thymidine analogues as virtual hits that are predicted to inhibit the mycobacterial TMPK in the submicromolar concentration range and to display favorable ADME-related properties.

Synthesis and evaluation of 5′-modified thymidines and 5-hydroxymethyl-2′-deoxyuridines as Mycobacterium tuberculosis thymidylate kinase inhibitors

“…Furthermore, we showed that hydroxylation of the 5-methyl group of the TMP substrate (3) resulted in a moderately potent TMPKmt inhibitor instead of substrate [5]. Mainly based on inhibitory data reported by our group, Frecer et al recently reported on the combinatorial design and structure-based in silico screening of a virtual focused library of bicyclic thymidine analogs in an effort to identify more potent TMPKmt inhibitors [6]. In their study they used the threedimensional structure of TMPKmt complexed with 5-hydroxymethyl-dUMP (3) to develop a QSAR model, to parameterize a target-specific scoring function for TMPKmt and to select virtual hits which display the highest predicted binding to the target.…”

“…In this pilot study we decided to explore the importance of the proposed 5-CH 2 Figure 1 OH and 5'-modifications for TMPKmt inhibition. Selected promising TMPKmt inhibitors designed previously in our laboratory (1, 2, and 3) [4,5] or predicted by a QSAR model (4) [6]. K i exp and K i pre indicate experimental and predicted K i values, respectively.…”

<i>In silico</i> Design of Phosphonic Arginine and Hydroxamic Acid Inhibitors of <i>Plasmodium falciparum</i> M17 Leucyl Aminopeptidase with Favorable Pharmacokinetic Profile

“…This Computational approach successfully narrows the filter and accelerates the process to new lead compounds compared with traditional synthesis approach. This was observed for peptide and peptidomimetic inhibitors of HIV-1 [16,17] and hepatitis C (HCV) [15] virus proteases design, for combinatorial design of bicyclic thymidine analogues [22] and complexation structure-based design of thymidine analogues [21,23] inhibitors of Mycobacterium Tuberculosis (MTb) thymidine monophosphate kinase, to provide insight into selectivity of peptidomimetic inhibitors with modified statine core for pf Plasmepsin II over human Cathepsin D [18]. Recently a complete process starting from the complexation QSAR model and its derived 3D-QSAR four features Pharmacophore (PH4) model have successfully served to screen a large Virtual Library of 1.6 million compounds reaching one hundred orally bioavailable pyrrolidine carboxamide inhibitors of MTb enoyl acyl carrier protein reductase (InhA) [24].…”

“…The complexation methodology has been described largely accor-ding to a procedure successfully used to elaborate one descriptor QSAR models of viral, bacterial and protozoal protease-inhibitor complexes and from them to design peptidomimetic, hydroxylnaphthoic, thymidine, triclosan and pyrrolidine carboxamide derivative inhibitors [15,16,17,18,19,20,21,22,23,24].…”

Design of Thymidine Analogues Targeting Thymidilate Kinase ofMycobacterium tuberculosis

“…More recently attempts to replace the ribose ring with a phenyl [17] with no real improvement followed by a bicyclic sugar derivatives [18] reaching 3.5  μ M and later by a spacer ended by acyclic nucleoside analogues exploring edge to face interaction between the naphthyl group and Tyr39 has led to 0.27  μ M potency [19]. A Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of TMPK mt by Frecer et al [20] identified submicromolar concentration range inhibitors with favorable ADME profile.…”