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Mycoplasma pneumoniae type 2a strain 309 is a simplest known bacterium and is the primary cause of community acquired pneumonia in the children . It mainly causes severe atypical pneumonia as well as several other non-pulmonary manifestations such as neurological, hepatic, hemolytic anemia, cardiac diseases and polyarthritis. The size of M. pneumoniae genome (Accession number: NC_016807.1 ) is relatively smaller as compared to other bacteria and contains 707 functional proteins, in which 204 are classified as hypothetical proteins (HPs) because of the unavailability of experimentally validated functions. The functions of the HPs were predicted by integrating a variety of protein classification systems, motif discovery tools as well as methods that are based on characteristic features obtained from the protein sequence and metabolic pathways. The probable functions of 83HPs were predicted successfully. The accuracy of the diverse tools used in the adopted pipeline was evaluated on the basis of statistical techniques of Receiver Operating Characteristic (ROC), which indicated the reliability of the functional predictions. Furthermore, the virulent HPs present in the set of 83 functionally annotated proteins were predicted by using the Bioinformatics tools and the conformational behaviours of the proteins with highest virulence scores were studied by using the molecular dynamics (MD) simulations. This study will facilitate in the better understanding of various drug resistance and pathogenesis mechanisms present in the M. pneumoniae and can be utilized in designing of better therapeutic agents. [ABSTRACT FROM AUTHOR]

Abstract: A quantum-chemical mechanistic investigation of the multistep mechanism of the one pot annular conversion of pentacyclo-undecane (PCU) cage lactam formation was carried out using density functional theory (DFT) level with the B3LYP hybrid functional in both the gas phase and with the self consistent reaction-field (SCRF) solvent model with the 6-31+G(d) basis set. The kinetic and thermodynamic properties of all species involved were investigated. The theoretical results suggest that the final product obtained is both thermodynamically and kinetically preferred. Moreover, the observed rate determining step compared favourably to the experimentally observed intermediate that was isolated before. [Copyright &y& Elsevier]

The lysosomal storage disorders are a group of 50 unique inherited diseases characterized by unseemly lipid storage in lysosomes. These malfunctions arise due to genetic mutations that result in deficiency or reduced activities of the lysosomal enzymes, which are responsible for catabolism of biological macromolecules. Sly syndrome or mucopolysaccharidosis type VII is a lysosomal storage disorder associated with the deficiency of β-glucuronidase (EC 3.2.1.31) that catalyzes the hydrolysis of β- d -glucuronic acid residues from the non-reducing terminal of glycosaminoglycan. The effects of the disease causing mutations on the framework of the sequences and structure of β-glucuronidase (GUSBp) were analyzed utilizing a variety of bioinformatic tools. These analyses showed that 211 mutations may result in alteration of the biological activity of GUSBp, including previously experimentally validated mutations. Finally, we refined 90 disease causing mutations, which presumably cause a significant impact on the structure, function, and stability of GUSBp. Stability analyses showed that mutations p.Phe208Pro, p.Phe539Gly, p.Leu622Gly, p.Ile499Gly and p.Ile586Gly caused the highest impact on GUSBp stability and function because of destabilization of the protein structure. Furthermore, structures of wild type and mutant GUSBp were subjected to molecular dynamics simulation to examine the relative structural behaviors in the explicit conditions of water. In a broader view, the use of in silico approaches provided a useful understanding of the effect of single point mutations on the structure-function relationship of GUSBp. [ABSTRACT FROM AUTHOR]

Abstract: The present work involves the study of the conformational profile of bombesin using different computational procedures used to explore the configurational space based on molecular dynamics simulations. Specifically, the present study describes the effect of using Berendsen''s versus Langevin''s thermostat and on the other hand, the use of the multicanonical replica exchange molecular dynamics as compared to standard molecular dynamics. In these simulations the solvent was modeled using the Onufriev, Bashford and Case implementation of Generalized Born procedure. The detailed computational analysis agrees well with the aggregated information previously reported in the NMR study of the peptide in a mixture of trifluoroethanol/water. Present results show a clear preference for the peptide to attain a helical structure on the segment 6–14, with a tendency to adopt a α-helix at the C-terminus aligning the aromatic residues Trp8 and His12 together with Gln7, known to be important for peptide mediated activation. Finally, the three methodologies used in the present work yield similar structural results, although a detailed analysis reveals biases that need to be considered when performing this kind of studies. [Copyright &y& Elsevier]

Abstract: A detailed study on the cycloaddition reactions of cross-conjugated enaminones 1 and 9 with dimethyl acetylenedicarboxylate (DMAD) and ketenes is described. The reactions provide a variety of pyran (4, 11), pyran-2-one 14 and pyrrol-3-ylidene 8 derivatives having great pharmacological and medicinal significance. Moreover, the preferred formation of product 8 over 7 has been explained on the basis of molecular dynamics (MD) simulations performed on the intermediate 5 in the gas phase. The synthetic potential of enaminones 9 has further been explored by treating them with Lawesson''s reagent (LR) and trapping the in situ generated enaminothiones 16 with some acrylates 17 leading to the formation of thiopyran derivatives 19. To the best of our knowledge, this is the first report in which cross-conjugated enaminothiones 16 have been utilized in cycloaddition reactions. [Copyright &y& Elsevier]

• Functional annotation of 1000 hypothetical proteins using Bioinformatics' techniques. • Categorization of annotated HPs into enzymes, transport, and other cellular activities. • Classification of putative virulence factors. • Structure-based functional analyses of the classified virulent HPs. • Molecular Dynamic (MD) simulation-based assessment of the predicted structure stability. The emergence of the drug-resistant mechanisms in Mycobacterium tuberculosis poses the biggest challenges to the current therapeutic measures, which necessitates the identification of new drug targets. The Hypothetical Proteins (HPs), a class of functionally uncharacterized proteins, may provide a new class of undiscovered therapeutic targets. The genome of M. tuberculosis contains 1000 HPs with their sequences were analyzed using a variety of bioinformatics tools and the functional annotations were performed. The functions of 662 HPs were successfully predicted and further classified 483 HPs as enzymes, 141 HPs were predicted to be involved in the diverse cellular mechanisms and 38 HPs may function as transporters and carriers proteins. Furthermore, 28 HPs were predicted to be virulent in nature. Amongst them, the HP P95201, HP P9WM79, HP I6WZ30, HP I6 × 9T8, HP P9WKP3, and HP P9WK89 showed the highest virulence scores. Therefore, these proteins were subjected to extensive structure analyses and dynamics of their conformations were investigated using the principles of molecular dynamics simulations, each for a 150 ns time scale. This study provides a deeper understanding of the undiscovered drug targets and the generated outputs will facilitate the process of drug design and discovery against the infection of M. tuberculosis. [ABSTRACT FROM AUTHOR]

MAP/microtubule affinity-regulating kinase 4 (MARK4) plays a central role in the cellular physiology, and it is inseparably linked with many human diseases including cancer, diet induced obesity, type2 diabetes and neurodegenerative disorders. Here, we studied the interaction of PKR-inhibitor with two variants of human MARK4. One variant is named as MARK4-F1 which has 59 N-terminal residues along with kinase domain while another variant is MARK4-F2 which has kinase domain only. Molecular-docking, molecular dynamics (MD) simulation and fluorescence-binding studies were undertaken to understand the role of N-terminal 59-residues in the binding of substrate/inhibitors. Molecular docking studies revealed that the PKR-inhibitor binds in the large hydrophobic cavity of the kinase domain of MARK4 through several hydrophobic and hydrogen-bonded interactions. Furthermore, MD simulation showed a stable parameters for the complexes of both MARK4-F1 and MARK4-F2 to PKR-inhibitor with marginal difference in their binding affinities. A significant decrease in the fluorescence intensity of MARK4 was observed on successive addition of the PKR-inhibitor. Using fluorescence data we have calculated the binding-affinity and the number of binding site of PKR-inhibitor to the MARK4. A significantly high binding affinity was observed for the PKR-inhibitor to the MARK4 variants. However, there is no any significant difference in the binding affinity of PKR-inhibitor to the MARK4 variants was observed, indicating that 59 N-terminal residues of MARK4-F1 are not playing a crucial role in the ligand binding. The present study will provide an insights into designing of new PKR-inhibitor derivative as potent and selective therapeutic agent against many life threatening diseases which are associated with MARK4. [ABSTRACT FROM AUTHOR]

Abstract: 1,2,3-Triazole tethered β-lactam and 7-chloroquinoline bifunctional hybrids were synthesized and evaluated as potential antimalarial agents. Activity against cultured Plasmodium falciparum was dependent on the N-substituent of the β-lactam ring as well as the presence of bis-triazole at the C-3 position. The observed activity profiles were further substantiated by docking studies via inhibition of P. falciparum dihydrofolate reductase (PfDHFR), a potential target for the development of new anti-malarials. [Copyright &y& Elsevier]