Parameswaran Saravanan

Homology modeling and atomic level binding study of Leishmania MAPK with inhibitors.

The current therapy for leishmaniasis is not sufficient and it has two severe drawbacks, host-toxicity and drug resistance. The substantial knowledge of parasite biology is not yet translating into novel drugs for leishmaniasis. Based on this observation, a 3D structural model of Leishmania mitogen-activated protein kinase (MAPK) homologue has been developed, for the first time, by homology modeling and molecular dynamics simulation techniques. The model provided clear insight in its structure features, i.e. ATP binding pocket, phosphorylation lip, and common docking site. Sequence-structure homology recognition identified Leishmania CRK3 (LCRK3) as a distant member of the MAPK superfamily. Multiple sequence alignment and 3D structure model provided the putative ATP binding pocket of Leishmania with respect to human ERK2 and LCRK3. This analysis was helpful in identifying the binding sites and molecular function of the Leishmania specific MAPK homologue. Molecular docking study was performed on this 3D structural model, using different classes of competitive ATP inhibitors of LCRK3, to check whether they exhibit affinity and could be identified as Leishmania MAPK specific inhibitors. It is well known that MAP kinases are extracellular signal regulated kinases ERK1 and ERK2, which are components of the Ras-MAPK signal transduction pathway which is complexed with HDAC4 protein, and their inhibition is of significant therapeutic interest in cancer biology. In order to understand the mechanism of action, docking of indirubin class of molecules to the active site of histone deacetylase 4 (HDAC4) protein is performed, and the binding affinity of the protein-ligand interaction was computed. The new structural insights obtained from this study are all consistent with the available experimental data, suggesting that the homology model of the Leishmania MAPK and its ligand interaction modes are reasonable. Further the comparative molecular electrostatic potential and cavity depth analysis of Leishmania MAPK and human ERK2 suggested several important differences in its ATP binding pocket. Such differences could be exploited in the future for designing Leishmania specific MAPK inhibitors.

Identification of hotspot regions of MurB oxidoreductase enzyme using homology modeling, molecular dynamics and molecular docking techniques

Despite the availability of effective chemotherapy and a moderately protective vaccine, new anti-tuberculosis agents are urgently needed to decrease the global incidence of tuberculosis (TB) disease. The MurB gene belongs to the bacterial cell wall biosynthesis pathway and is an essential drug target in Mycobacterium tuberculosis (Mtb) that has no mammalian counterparts. Here, we present an integrated approach involving homology modeling, molecular dynamics and molecular docking studies on Mtb-MurB oxidoreductase enzyme. A homology model of Mtb-MurB enzyme was built for the first time in order to carry out structure-based inhibitor design. The accuracy of the model was validated using different techniques. The molecular docking study on this enzyme was undertaken using different classes of well known MurB inhibitors. Estimation of binding free energy by docking analysis indicated the importance of Tyr155, Arg156, Ser237, Asn241 and His304 residues within the Mtb-MurB binding pocket. Our computational analysis is in good agreement with experimental results of site-directed mutagenesis. The present study should therefore play a guiding role in the experimental design of Mtb-MurB inhibitors for in vitro/in vivo analysis.

Mitogen-activated protein kinase 4 of Leishmania parasite as a therapeutic target.

Protein kinases are important regulators of many different cellular processes such as transcriptional control, cell cycle progression and differentiation, and have drawn much attention as potential drug targets. Leishmania mexicana mitogen-activated protein kinase 4 (LmxMPK4) is crucial for the survival of the parasite. As the crystal structure of the enzyme is not known, we have used bioinformatics techniques to model LmxMPK4 structure. The current study reveals conservation of all sequence and structural motifs of LmxMPK4. Study shows mitogen-activated protein kinases are highly conserved throughout different Leishmania species and significant divergence is observed towards mammalian mitogen-activated protein kinases. Additionally, using virtual docking methods, we have identified inhibitors for LmxMPK4. The sequence and structure analysis results were helpful in identifying the ligand binding sites and molecular function of the Leishmania specific mitogen-activated protein kinase.

Studies on ornithine decarboxylase of Leishmania donovani: structure modeling and inhibitor docking

Leishmaniasis is a detrimental disease caused by the parasite Leishmania which has a unique redox metabolism involving trypanothione. Trypanothione delivers reducing equivalents which in turn saves the parasite from oxidative damage and is also utilized in the formation of deoxyribonucleotides. The polyamine biosynthesis pathway starts with the conversion of ornithine to spermidine, precursor of trypanothione, by ornithine decarboxylase. Thus, targeting ornithine decarboxylase would inhibit formation of spermidine and subsequently trypanothione, affecting the growth and survival of Leishmania. This enzyme could be a good drug target to combat leishmaniasis. In the current study, we have predicted the 3D structure of Leishmania donovani ornithine decarboxylase. Moreover, we have conducted structure-based virtual screening against the enzyme in an attempt to find potential leishmania-specific inhibitors. Interactions of the leishmanial enzyme with the inhibitors have also been investigated to identify functionally important residues.

Homology Modeling, Molecular Dynamics and Inhibitor Binding Study on MurD Ligase of Mycobacterium Tuberculosis

The cell wall of mycobacterium offers well validated targets which can be exploited for discovery of new lead compounds. MurC-MurF ligases catalyze a series of irreversible steps in the biosynthesis of peptidoglycan precursor, i.e. MurD catalyzes the ligation of D-glutamate to the nucleotide precursor UMA. The three dimensional structure of Mtb-MurD is not known and was predicted by us for the first time using comparative homology modeling technique. The accuracy and stability of the predicted Mtb-MurD structure was validated using Procheck and molecular dynamics simulation. Key interactions in Mtb-MurD were studied using docking analysis of available transition state inhibitors of E.coli-MurD. The docking analysis revealed that analogues of both L and D forms of glutamic acid have similar interaction profiles with Mtb-MurD. Further, residues His192, Arg382, Ser463, and Tyr470 are proposed to be important for inhibitor-(Mtb-MurD) interactions. We also identified few pharmacophoric features essential for Mtb-MurD ligase inhibitory activity and which can further been utilized for the discovery of putative antitubercular chemotherapy.

Synthesis of fused tetrahydropyrido[2,3-c]coumarin derivatives as potential inhibitors for dopamine d3 receptors, catalyzed by hydrated ferric sulfate

Fused furo- and pyrano-tetrahydropyrido[2,3-c]coumarin derivatives were synthesized using one-pot three component reactions between aromatic aldehydes, 3-aminocoumarins and cyclic enol ethers in the presence of 10 mol% hydrated ferric sulphate [Fe2(SO4)3·xH2O] in refluxing acetonitrile. The salient features of the present protocol are good yields, high diastereoselectivities, application to a wide range of substrates, using an inexpensive, readily available and recyclable catalyst and environmentally benign reaction conditions.

Targeting essential cell wall lipase Rv3802c for potential therapeutics against tuberculosis

Cell wall and lipid metabolism plays a vital role in the survival and infection of Mycobacterium tuberculosis. Increase in the incidences of life-threatening multidrug-resistant (MDR) and extreme drug-resistant (XDR) tuberculosis worsens the existing scenario and urge the need of new druggable targets and new drugs. Targeting Rv3802c, an essential cell wall lipase, can open up a new arsenal to fight the dreadful opportunistic pathogen. Our current study highlights the essentiality of Rv3802c. Its 3D structure is predicted for the first time which provides insight in identifying the ligand binding sites. Our analysis showed Rv3802c is highly conserved throughout mycobacterial species with no significant sequence homolog found in human proteome. Virtual screening followed by comparative docking studies of Rv3802c with its closest human structural homolog has been carried out to identify potential inhibitors effective towards mycobacterial proteins. Two diverse molecules from ZINC database, ZINC26726377 and ZINC43866786 have been identified as potential inhibitors effective towards Rv3802c based on the difference in predicted binding free energy of -3.99 and -3.28kcal/mol respectively. Rv3802c is a promising drug target and also a step towards understanding and targeting the pathogens cell wall and lipid metabolism simultaneously to combat tuberculosis.

Potential Selective Inhibitors against Rv0183 of Mycobacterium tuberculosis Targeting Host Lipid Metabolism

Tuberculosis is the second leading infectious killer with 9 million new cases in 2009. Extensive use of pathogen’s lipid metabolism especially in utilizing the host lipids and virulence highlights the importance of exported lipid‐catabolizing enzymes. Current study aims to emphasize the importance of Rv0183, an exported monoacylglycerol lipase, involved in metabolizing the host cell membrane lipids. Sequence analysis and homology modeling shows Rv0183 is highly conserved throughout mycobacterial species even in Mycobacterium leprae and also significantly divergent from mammalian lipases. Additionally, employing virtual screening using NCI diversity set and ZINC database with criteria of molecules with higher predicted free energy of binding toward Rv0183 than human lipase, potential inhibitors have been identified for Rv0183. A tautomer of ZINC13451138, known inhibitor for HIV‐1 integrase is the best hit with difference in free energy of binding of 8.72 kcal/mol. The sequence and structure analysis were helpful in identifying the ligand binding sites and molecular function of the mycobacterial specific monoacylglycerol lipase. Rv0183 represents a suitable and promising drug target and is also a step towards understanding dormancy development and reactivation, thereby addressing pathogen’s drug resistance. Experimental studies on the discovered potential inhibitors in this virtual screen should further validate the therapeutic utility of Rv0183.

First pharmacophore model of CCR3 receptor antagonists and its homology model-assisted, stepwise virtual screening.

CCR3, a G protein‐coupled receptor, plays a central role in allergic inflammation and is an important drug target for inflammatory diseases. To understand the structure–function relationship of CCR3 receptor, different computational techniques were employed, which mainly include: (i) homology modeling of CCR3 receptor, (ii) 3D‐quantitative pharmacophore model of CCR3 antagonists, (iii) virtual screening of small compound databases, and (iv) finally, molecular docking at the binding site of the CCR3 receptor homology model. Pharmacophore model was developed for the first time, on a training data set of 22 CCR3 antagonists, using catalystHypoRefine program. Best hypothesis (Hypo1) has three different chemical features: two hydrogen‐bond acceptors, one hydrophobic, and one ring aromatic. Hypo1 model was further validated using (i) 87 test set CCR3 antagonists, (ii) Cat Scramble randomization technique, and (iii) Decoy data set. Molecular docking studies were performed on modeled CCR3 receptor using 303 virtually screened hits, obtained from small compound database virtual screening. Finally, five hits were identified as potential leads against CCR3 receptor, which exhibited good estimated activities, favorable binding interactions, and high docking scores. These studies provided useful information on the structurally vital residues of CCR3 receptor involved in the antagonist binding, and their unexplored potential for the future development of potent CCR3 receptor antagonists.

Uridine monophosphate kinase as potential target for tuberculosis: From target to lead identification

Mycobacterium tuberculosis (Mtb) is a causative agent of tuberculosis (TB) disease, which has affected approximately 2 billion people worldwide. Due to the emergence of resistance towards the existing drugs, discovery of new anti-TB drugs is an important global healthcare challenge. To address this problem, there is an urgent need to identify new drug targets in Mtb. In the present study, the subtractive genomics approach has been employed for the identification of new drug targets against TB. Screening the Mtb proteome using the Database of Essential Genes (DEG) and human proteome resulted in the identification of 60 key proteins which have no eukaryotic counterparts. Critical analysis of these proteins using Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways database revealed uridine monophosphate kinase (UMPK) enzyme as a potential drug target for developing novel anti-TB drugs. Homology model of Mtb-UMPK was constructed for the first time on the basis of the crystal structure of E. coli-UMPK, in order to understand its structure-function relationships, and which would in turn facilitate to perform structure-based inhibitor design. Furthermore, the structural similarity search was carried out using physiological inhibitor UTP of Mtb-UMPK to virtually screen ZINC database. Retrieved hits were further screened by implementing several filters like ADME and toxicity followed by molecular docking. Finally, on the basis of the Glide docking score and the mode of binding, 6 putative leads were identified as inhibitors of this enzyme which can potentially emerge as future drugs for the treatment of TB.