Discovery and development of novel salicylate synthase (MbtI) furanic inhibitors as antitubercular agents

We report on the virtual screening, synthesis, and biological evaluation of new furan derivatives targeting Mycobacterium tuberculosis salicylate synthase (MbtI). A receptor-based virtual screening procedure was applied to screen the Enamine database, identifying two compounds, I and III, endowed with a good enzyme inhibitory activity. Considering the most active compound I as starting point for the development of novel MbtI inhibitors, we obtained new derivatives based on the furan scaffold. Among the SAR performed on this class, compound 1a emerged as the most potent MbtI inhibitor reported to date (Ki = 5.3 μM). Moreover, compound 1a showed a promising antimycobacterial activity (MIC99 = 156 μM), which is conceivably related to mycobactin biosynthesis inhibition

New Chromane-Based Derivatives as Inhibitors of Mycobacterium tuberculosis Salicylate Synthase (MbtI): Preliminary Biological Evaluation and Molecular Modeling Studies

Tuberculosis is the leading cause of death from a single infectious agent worldwide; therefore, the need for new antitubercular drugs is desperate. The recently validated target salicylate synthase MbtI is the first enzyme involved in the biosynthesis of mycobactins, compounds able to chelate iron, an essential cofactor for the survival of Mycobacterium tuberculosis in the host. Here, we report on the synthesis and biological evaluation of chromane-based compounds as new potential inhibitors of MbtI. Our approach successfully allowed the identification of a novel lead compound (1), endowed with a promising activity against this enzyme (IC50 = 55 μM). Molecular modeling studies were performed in order to evaluate the binding mode of 1 and rationalize the preliminary structure-activity relationships, thus providing crucial information to carry out further optimization studies

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications

We report a computational approach that integrates structural bioinformatics, molecular modelling and systems biology to construct a drug-target network on a structural proteome-wide scale. The approach has been applied to the genome of Mycobacterium tuberculosis (M.tb), the causative agent of one of today's most widely spread infectious diseases. The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’. The TB-drugome reveals that approximately one-third of the drugs examined have the potential to be repositioned to treat tuberculosis and that many currently unexploited M.tb receptors may be chemically druggable and could serve as novel anti-tubercular targets. Furthermore, a detailed analysis of the TB-drugome has shed new light on the controversial issues surrounding drug-target networks [1]–[3]. Indeed, our results support the idea that drug-target networks are inherently modular, and further that any observed randomness is mainly caused by biased target coverage. The TB-drugome (http://funsite.sdsc.edu/drugome/TB) has the potential to be a valuable resource in the development of safe and efficient anti-tubercular drugs. More generally the methodology may be applied to other pathogens of interest with results improving as more of their structural proteomes are determined through the continued efforts of structural biology/genomics

Design and synthesis of potential antimicrobial agents

Chorismate mutase is one of the essential enzymes in the shikimate pathway and is key to the survival of the organism Mycobacterium tuberculosis. The x-ray crystal structure of this enzyme from Mycobacterium tuberculosis was manipulated to prepare an initial set of in silico protein models of the active site. Known inhibitors of the enzyme were docked into the active site using the flexible ligand / flexible active site side chains approach implemented in CAChe Worksystem (Fujitsu Ltd). The resulting complexes were refined by molecular dynamics studies in explicit water using Amber 9. This yielded a further set of protein models that were used for additional rounds of ligand docking. A binding hypothesis was established for the enzyme and this was used to screen a database of commercially available drug-like compounds. From these results new potential ligands were designed that fitted appropriately into the active site and matched the functional groups and binding motifs founds therein. Some of these compounds and close analogues were then synthesized and submitted for biological evaluation. As a separate part of this thesis, analogues of very active anti-tuberculosis pyridylcarboxamidrazone were also prepared. This was carried out by the addition and the deletion of the substitutions from the lead compound thereby preparing heteroaryl carboxamidrazone derivatives and related compounds. All these compounds were initially evaluated for biological activity against various gram positive organisms and then sent to the TAACF (USA) for screening against Mycobacterium tuberculosis. Some of the new compounds proved to be at least as potent as the original lead compound but less toxic

Ursolic acid as a potential inhibitor of mycobacterium tuberculosis cytochrome bc1 oxidase: a molecular modelling perspective.

Masters Degree. University of KwaZulu-Natal, Durban.Tuberculosis (TB) is a disease, caused by an infectious agent; Mycobacterium tuberculosis, which persists as a major problem globally, especially in developing countries such as Brazil, Indonesia, and South Africa. Individuals who are diabetic and human immunodeficiency virus (HIV) co-infected are at a higher risk of contracting TB. Hence, these risk factors are associated with a compromised immune system. Among these factors, various strains are involved in the pathogenesis of TB such as multidrug-resistant tuberculosis (MDR-TB) and extensively drugresistant tuberculosis (XDR-TB) strains. The emergence of these strains may result from failure to complete treatment within the stipulated period of six months. However, studies show that the protein QcrB; contributes more to TB pathogenesis. Therefore, there is an urgent need for the discovery of drugs that inhibit QcrB. The current FDA-approved anti-tubercular drugs such as, Lansoprazole sulfide (LSPZ) and Telacebec (Q203) which inhibit QcrB are bacteriostatic and have been linked to side effects including dementia, chronic kidney disease, and ischemic cardiac diseases [1], thus prompting a search for an alternative drug. Various natural compounds have been reported to possess several bioactivities that could be crucial in the management of tuberculosis (TB) disease. Warbugia salutaris, a medicinal plant has been found to exhibit inhibitory properties against M. tuberculosis. Numerous compounds are derived from W. salutaris. In this study, we focus solely on Ursolic acid (UA) and its derivative, Ursolic acid acetate (UAA). These two compounds possess antibacterial, anti-HIV, and antimycobacterial properties. This suggests that they could potentially possess inhibitory properties towards M.tuberculosis QcrB protein. In this study, computational methods are applied to investigate the inhibitory activity of UA and UAA on M. tuberculosis QcrB. Molecular Docking, Molecular Dynamics (MD) simulations, Radius of Gyration, Principal Component Analysis (PCA), and Molecular Mechanics-Generalized Born Surface Area (MM/GBSA) binding free energy calculations were performed in explicit solvent to accomplish our goal. The obtained results indicated that the (1) the binding of UA to QcrB induced a more stable and compacted conformation compared to LSPZ and Q203; (2) high total binding free energy estimated in the QcrB-UA system was due to numerous hydrophobic residues in the binding site of QcrB that interact with phenyl rings of UA resulting in hydrophobic packing. This implies that UA has a high binding affinity and, as a result, a strong inhibition of QcrB; (3) more H-bonds were observed in the QcrB-UA system than in the QcrBQ203 system; (4) rigidity was displayed mostly in Arg124 and Thr128; (5) Arg124 and Phe127 also contributed more to the total binding energy in QcrB-UA and QcrB-UAA. This implies that the ligands exert a high binding affinity in the porphyrin binding site than in the active site. The identification of a molecule that competes with the porphyrin ring for the binding site could be beneficial in QcrB pharmacological research; (6) UA could be a potential anti-tubercular agent through QcrB inhibition, although it is hepatotoxic within tolerable concentrations. However, observed potential hepatotoxicity was based on predictions. Although the preliminary findings of this report warrant further experimental validation, they lay a strong foundation for subsequent assessment and development of these natural compounds as antitubercular drugs.Some text in red font

An Indian effort towards affordable drugs: "generic to designer drugs"

This review discusses the progress of India from being one of the largest producers of generics to its coming of age and initiating novel drug development programs such as the Open Source Drug Discovery for tuberculosis. A few groups have also begun to emerge which focus their research on rational or structure based drug design. We discuss here some of the ongoing efforts in drug discovery in India primarily in national research institutions and academia

Design and synthesis of potential antimicrobial agents

Chorismate mutase is one of the essential enzymes in the shikimate pathway and is key to the survival of the organism Mycobacterium tuberculosis. The x-ray crystal structure of this enzyme from Mycobacterium tuberculosis was manipulated to prepare an initial set of in silico protein models of the active site. Known inhibitors of the enzyme were docked into the active site using the flexible ligand / flexible active site side chains approach implemented in CAChe Worksystem (Fujitsu Ltd). The resulting complexes were refined by molecular dynamics studies in explicit water using Amber 9. This yielded a further set of protein models that were used for additional rounds of ligand docking. A binding hypothesis was established for the enzyme and this was used to screen a database of commercially available drug-like compounds. From these results new potential ligands were designed that fitted appropriately into the active site and matched the functional groups and binding motifs founds therein. Some of these compounds and close analogues were then synthesized and submitted for biological evaluation. As a separate part of this thesis, analogues of very active anti-tuberculosis pyridylcarboxamidrazone were also prepared. This was carried out by the addition and the deletion of the substitutions from the lead compound thereby preparing heteroaryl carboxamidrazone derivatives and related compounds. All these compounds were initially evaluated for biological activity against various gram positive organisms and then sent to the TAACF (USA) for screening against Mycobacterium tuberculosis. Some of the new compounds proved to be at least as potent as the original lead compound but less toxic.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Computer Modelling of an Enzyme Reference Reaction for Empirical Valence Bond Simulation

It is extensively recognized that an enzyme functions through reducing the energy of activation of its elemental reaction and the catalytic effect of an enzyme is as a result of a change in activation free energy obtained relative to a reference reaction in water of the same mechanism. In this study, chorismate mutase which is an enzyme that catalyzes biochemical reactions for chorismate conversion to prephenate has been used as the model enzyme and its catalytic effect was investigated using Empirical Valence Bond method with the employment of Density Functional theory calculation to obtain its reference state reaction. It was found in this study that DFT has been able to produce good activation and reaction free energies compared to experimental values that can serve as a reference to investigate the enzymatic reaction of chorismate mutase and the enzyme’s catalytic effect was well analysed with EVB as the method was able to reproduce the enzyme’s activation and reaction free energies

In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks

Background Corynebacterium pseudotuberculosis (Cp) is a gram-positive bacterium that is classified into equi and ovis serovars. The serovar ovis is the etiological agent of caseous lymphadenitis, a chronic infection affecting sheep and goats, causing economic losses due to carcass condemnation and decreased production of meat, wool, and milk. Current diagnosis or treatment protocols are not fully effective and, thus, require further research of Cp pathogenesis. Results Here, we mapped known protein-protein interactions (PPI) from various species to nine Cp strains to reconstruct parts of the potential Cp interactome and to identify potentially essential proteins serving as putative drug targets. On average, we predict 16,669 interactions for each of the nine strains (with 15,495 interactions shared among all strains). An in silico sanity check suggests that the potential networks were not formed by spurious interactions but have a strong biological bias. With the inferred Cp networks we identify 181 essential proteins, among which 41 are non-host homologous. Conclusions The list of candidate interactions of the Cp strains lay the basis for developing novel hypotheses and designing according wet-lab studies. The non-host homologous essential proteins are attractive targets for therapeutic and diagnostic proposes. They allow for searching of small molecule inhibitors of binding interactions enabling modern drug discovery. Overall, the predicted Cp PPI networks form a valuable and versatile tool for researchers interested in Corynebacterium pseudotuberculosis