Sadia Naz

Allosteric feedback inhibition of the committed step in amino acid biosynthetic pathways is a major concern for production of amino acids at industrial scale. Anthranilate synthase (AS) catalyzes the first reaction of tryptophan biosynthetic pathway found in microorganisms and is feedback inhibited by its own product i.e. tryptophan. Here, we identified new mutant sites in AS using computational mutagenesis approach. MD simulations (20 ns) followed by MMPBSA and per residue decomposition energy analysis identified seven amino acid residues with best binding affinity for tryptophan. All 19 mutant structures were generated for each identified amino acid residue followed by simulation to evaluate effect of mutation on protein stability. Later, molecular docking studies were employed to generate mutant-tryptophan complex and structures with binding energies (kcal/mol) much higher than wild-type AS were selected. Finally, two mutants i.e., S37W and S37H were identified on the basis of positive binding scores and loss of tryptophan binding inside pocket. Further, MD simulations run for 200 ns were performed over these mutant-tryptophan complexes followed by RMSD, RMSF, radius of gyration , solvent accessible surface area , intra-protein hydrogen bond numbers, principal component analysis, free energy landscape (FEL) and secondary structure analysis to rationale effect of mutations on stability of protein. Cross correlation analysis of mutant site amino acids (S37W) with key residues of catalytic site (G325, T326, H395 and G482) was done to evaluate the effect of mutations on catalytic site conformation. Current computational mutagenesis approach predicted two mutants S37W and S37H with proposed deregulated feedback inhibition by tryptophan and retained catalytic activity.

In this work, synthesis of graphene oxide (GO) and reduced graphene oxide (rGO) was realized through a modified Hummers route. Different concentrations (5 and 10 wt%) of Ag were doped in MoS ₂ and rGO using a hydrothermal technique. Synthesized Ag-MoS ₂ and Ag-rGO were evaluated through XRD that confirmed the hexagonal structure of MoS ₂ along with the transformation of GO to Ag-rGO as indicated by a shift in XRD peaks while Mo–O bonding and S=O functional groups were confirmed with FTIR. Morphological information of GO and formation of MoS ₂ nanopetals as well as interlayer spacing were verified through FESEM and HRTEM respectively. Raman analysis was employed to probe any evidence regarding defect densities of GO. Optical properties of GO, MoS ₂ , Ag-rGO, and Ag-MoS ₂ were visualized through UV–vis and PL spectroscopy. Prepared products were employed as nanocatalysts to purify industrial wastewater. Experimental results revealed that Ag-rGO and Ag-MoS ₂ showed 99% and 80% response in photocatalytic activity. Besides, the nanocatalyst (Ag-MoS ₂ and Ag-rGO) exhibited 6.05 mm inhibition zones against S. aureus gram positive (G+) and 3.05 mm for E. coli gram negative (G-) in antibacterial activity. To rationalize biocidal mechanism of Ag-doped MoS ₂ NPs and Ag-rGO, in silico molecular docking study was employed for two enzymes i.e. β -lactamase and D-alanine-D-alanine ligase B (ddlB) from cell wall biosynthetic pathway and enoyl-[acylcarrier-protein] reductase (FabI) from fatty acid biosynthetic pathway belonging to S. aureus . The present study provides evidence for the development of cost-effective, environment friendly and viable candidate for photocatalytic and antimicrobial applications.

Discovery of potent inhibitors of thymidine phosphorylase (TP) can offer appropriate approach in cancer treatment owing to it’s over expression in various human tumors compared to normal healthy tissues. Thymidine phosphorylase alongside 2-deoxy-D-ribose are reported as promoters of unwanted angiogenesis in cancerous cells. In this study, three new acrylic acid derivatives (1–3) have been isolated from ethyl acetate fraction of Achillea mellifolium. The characterization of these compounds (1–3) was done using UV, IR, 1 D and 2 D-NMR spectroscopy (¹H-NMR, ¹³C-NMR, HMBC, NOESY) and mass spectrometry. The structure of these acrylic acid derivatives were ethyl (E)-3-((1S,5R)-5-methoxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl)acrylate (1), methyl (E)-3-((1S,5R)-5-methoxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl)acrylate (2) and (4S,6R)-6-methoxy-3,5,5-trimethyl-4-((E)-3-oxobut-1-en-1-yl)cyclohex-2-en-1-one (3). Thymidine phosphorylase (TP) inhibition studies showed compound 3 as most active inhibitor of TP with IC₅₀ value 57.81 ± 3.41 while compound 1 and 2 showed IC₅₀ value as 158.9 ± 0.97 and 89.92 ± 0.37, respectively. In addition, molecular docking studies of compound (1–3) were performed to shed light on their binding interaction patterns for binding into active pocket of TP. Similarly, all compounds (1–3) were evaluated for their anti-oxidant potential showing anti-oxidant activities with IC₅₀ value ranging from 49.73 ± 0.41 to 79.81 ± 0.39. Later, these compound-protein (1–3) complexes were further subjected to MD simulations studies (50 ns) involving root mean square deviation, root mean square fluctuation, and secondary structure analysis to explore their binding mode stability inside active pocket. Communicated by Ramaswamy H. Sarma

Ongoing Coronavirus epidemic (COVID-19) identified first in Wuhan, China posed huge impact on public health and economy around the globe. Both cough and sneeze based droplets or aerosols encapsulated COVID-19 particles are responsible for air borne transmission of this virus and caused unexpected escalation and high mortality worldwide. Current study intends to investigate correlation of COVID-19 epidemic with meteorological parameters particularly, temperature, rainfall, humidity, and wind speed along with population size. Data set of COVID-19 for highly infected cities of Pakistan was collected from the official website of National Institute of health (NIH). Spearman’s rank (r s ) correlation coefficient test employed for data analysis revealed significant correlation between temperature minimum (TM), temperature average (TA), wind speed (WS) and population size (PS) with COVID-19 pandemic. Furthermore, receiver operating characteristics (ROC) curve was used to analyze the sensitivity of TA, WS, and PS on transmission rate of COVID-19 in selected cities of Pakistan. The results obtained for sensitivity and specificity analysis for all selected parameters signifies sensitivity and direct correlation of COVID-19 transmission with temperature variation, WS and PS. Positive correlation and strong association of PS parameter with COVID-19 pandemic suggested need of more strict actions and control measures for highly populated cities. These findings will be helpful for health regulatory authorities and policymakers to take specific measures to combat COVID-19 epidemic in Pakistan.

Discovery of new anti-tuberculosis drugs with novel mode of action is urgently needed. The tryptophan synthase is genetically validated enzyme that catalyzes last step of tryptophan biosynthetic pathway required for growth and survival of M. tuberculosis. Here, a ligand based pharmacophore model was built using molecular operating environment (MOE) software (version 2010.12) and validation of generated pharmacophoric features was done using active, inactive and decoy set of molecules. The generated pharmacophore model was used for screening of 7,523,972 drug like molecules of ZINC database. The best matches (rmsd α-subunit of tryptophan synthase from M. tuberculosis. The five hits were selected and validated through antituberculosis activity analysis. Finally a new inhibitor ZINC09150898 has been identified with best binding score -32.07 kcal/mol, showing 100% growth inhibition of M. tuberculosis (H37Rv strain) at 50 μg/ml. This identified inhibitor-protein complex was further subjected to MD simulations studies (50 ns) involving root mean square deviation, Root mean square fluctuation, secondary structure analysis and pocket interaction analysis to explore its binding mode stability inside active pocket. The binding free energies of inhibitor-protein complex through MM-PBSA analysis suggested that van der Waals interactions play vital role for retention of identified inhibitor inside the protein pocket. All these analyses confirmed retention of ligand inside pocket and no unfolding in protein structure was observed over explored time scale.