Drug design and identification of potent leads against Mycobacterium tuberculosis thymidine monophosphate kinase

Antiviral chemotherapy often relies on nucleoside analogues, which, once phophorylated by intracellular kinases, target viral polymerases impeding DNA synthesis. In contrast, nucleoside analogues are much less explored as antibacterial drugs. Thymidine monophosphate kinase from Mycobacterium tuberculosis (TMPKmt), which is essential to DNA replication, was selected as a promising target for the design of new inhibitors. This review describes stepwise modifications of the TMPKmt substrate, guided by the feedback of enzyme assays and crystallographic analysis to afford potent enzyme inhibitors some of which also exhibited antitubercular activity. More importantly, several of the reported thymidine analogues provided a deeper understanding of the structure and catalytic mechanism of this intriguing enzyme

Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes

Identification of Novel Compounds with Anti-Mycobacterial Activity Using in Silico Screening and Pharmacophore Modeling Targeting Mycobacterium Thymidine Monophosphate Kinase

The increasing prevalence of drug-resistant tuberculosis (TB), which is resistant to effective multiple antibiotic, remains a major public health menace. The Mycobacterium tuberculosis (M. tuberculosis) thymidine monophosphate kinase (mtTMPK), which is an essential enzyme for the maintenance of the thymidine triphosphate pools, is considered a potential enzymatic target for the development of effective antibiotics against TB. In this study, I attempted to identify novel compounds with anti-mycobacterial activity specifically targeting mtTMPK. I performed in silico structure-based drug screening (SBDS) with a large-scale virtual compound library (6,192,932 compounds) and phramacophore-based in silico screening with a compound library of 461,383 compounds. I then evaluated the inhibitory effects of candidate compounds on model mycobacteria strains. As a result, I found that compounds K10, KTP3, KTPS1, and KTPS2, completely inhibited the growth of Mycobacterium vanbaalenii (M. vanbaalenii) and/or Mycobacterium smegmatis (M. smegmatis). In addition, I experimentally demonstrated that two compounds (KTPS1 and KTPS2) directly inhibitedmtTMPK catalytic activity to some extent. Moreover, the most potent chemical compounds, KTPS1, did not exhibit any significant toxic effects on the growth of model intestinal bacteria (Escheichila coli: E. coli) and several mammalian cells. The structural and experimental information regarding these chemical compounds is likely useful for the development of novel antibiotics for the treatment of TB.九州工業大学博士学位論文 学位記番号:情工博甲第298号 学位授与年月日:平成27年3月25日1. Introduction|2. Results|3. Discussion|4. Conclusion|5. Materials and methods九州工業大学平成26年

Anticancer and antibiotic leads from marine organis

During the past three decades, the development of marine natural products as drug leads has become a promising avenue for research. As our efforts towards the discovery of anticancer and antibiotic drug leads from marine organisms, modifications of anticancer drug candidate kahalalide F, isolations of new peptides from the mollusk, Elysia rufescens and anticancer drug leads from the NCI repository, as well as chemical regulation of antibiotic production from marine Pseudomonas aeruginosa were investigated. Kahalalide F (KF) is a potent anticancer lead isolated from the herbivorous marine mollusk E. rufescens and its algal diet Bryopsis pennata. Our semisynthesis approach was aimed to improve the efficacy or prolong the half-life resulted in 15 KF analogues. These analogues included eight elongation products with nonpolar amino acid residues, four analogues with modified amino group at the Orn residue, one dehydration product of KF, and two new cyclization products of kahalalide G. All the analogues are being evaluated by Wayne State University for solid tumor cytotoxicity. In the course of the isolation of KF as starting material for its analogues, nine new and 10 known peptides were isolated from E. rufescens. However, only five structures were determined and the remaining four structures could not be assigned due to limited sample amounts (less than 1 mg). Future work will focus on the structure assignment using FTMS amino acid sequence analysis or 700 MHz NMR. During the screening of anticancer drug leads from the NCI repository, 27 extracts from marine organisms were tested, and 12 known compounds including tetracyclic aromatic alkaloids, diterpenoids and pyrroloaminopropylimidazole alkaloids were purified. Bioassay-guided isolation from marine P. aeruginosa collected in the Gulf of Mexico afforded 15 known antibiotics including two phenazines, six 2-alkyl-4-quinolones, and seven rhamnolipids. 2-Nonyl-4(1H)-quinolone and 2-(1-nonenyl)-4(1H)-quinolone displayed potent antimalarial activity, which was first reported here. Based on the metabolic profile of antibiotics from P. aeruginosa, chemical regulation and its impact on the yield of these metabolites were investigated. Treatment of P. aeruginosa with sceptrin and co-culturing with another Pseudomonas sp. increased antibiotic production significantly. This could be attributed to the activation of antibiotic biosynthetic gene expression under stress conditions

QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni.

Schistosomiasis is a neglected tropical disease that affects millions of people worldwide. Thioredoxin glutathione reductase of Schistosoma mansoni (SmTGR) is a validated drug target that plays a crucial role in the redox homeostasis of the parasite. We report the discovery of new chemical scaffolds against S. mansoni using a combi-QSAR approach followed by virtual screening of a commercial database and confirmation of top ranking compounds by in vitro experimental evaluation with automated imaging of schistosomula and adult worms. We constructed 2D and 3D quantitative structure-activity relationship (QSAR) models using a series of oxadiazoles-2-oxides reported in the literature as SmTGR inhibitors and combined the best models in a consensus QSAR model. This model was used for a virtual screening of Hit2Lead set of ChemBridge database and allowed the identification of ten new potential SmTGR inhibitors. Further experimental testing on both shistosomula and adult worms showed that 4-nitro-3,5-bis(1-nitro-1H-pyrazol-4-yl)-1H-pyrazole (LabMol-17) and 3-nitro-4-{[(4-nitro-1,2,5-oxadiazol-3-yl)oxy]methyl}-1,2,5-oxadiazole (LabMol-19), two compounds representing new chemical scaffolds, have high activity in both systems. These compounds will be the subjects for additional testing and, if necessary, modification to serve as new schistosomicidal agents

3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents

Tuberculosis (TB) is the primary cause of mortality among infectious diseases. Mycobacterium tuberculosis monophosphate kinase (TMPKmt) is essential to DNA replication. Thus, this enzyme represents a promising target for developing new drugs against TB. In the present study, the receptor-independent, RI, 4D-QSAR method has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 81 thymidine analogues, and two corresponding subsets, reported as inhibitors of TMPKmt. The resulting optimized models are not only statistically significant with r (2) ranging from 0.83 to 0.92 and q (2) from 0.78 to 0.88, but also are robustly predictive based on test set predictions. The most and the least potent inhibitors in their respective postulated active conformations, derived from each of the models, were docked in the active site of the TMPKmt crystal structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. Moreover, the QSAR models provide insights regarding a probable mechanism of action of the analogues.CAPES Foundationfederal scientific agency of BrazilNational Institutes of Health (NIH)[1 R21 GM075775