Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Coumarins: antifungal effectiveness and future therapeutic scope

Molecular Diversity - The antifungals that are in current clinical practice have a high occurrence of a side effect and multidrug resistance (MDR). Researchers across the globe are trying to...     

Amine‐blocked polyisocyanates. I. Synthesis of novel N‐methylaniline‐blocked polyisocyanates and deblocking studies using hot‐stage fourier transform infrared spectroscopy

A series of substituted N‐methylaniline‐blocked polyisocyanates based on 4,4′‐methylenebis(phenyl isocyanate) and poly(tetrahydrofuran) were prepared and characterized thoroughly with FTIR, ¹H NMR, and ¹³C NMR spectroscopy methods. Compared with unsubstituted N‐methylaniline, a blocking agent with an electron‐releasing substituent at the para position took a shorter time, whereas those with an electron‐releasing substituent at the ortho position or an electron‐withdrawing substituent at the ortho and para positions took longer times for the blocking reaction. The thermal dissociation reactions of blocked polyisocyanates were carried out with an FTIR spectrophotometer attached to hot‐stage accessories under dynamic and isothermal conditions. The dynamic method was used to determine the deblocking temperature, and the isothermal method was used to calculate the deblocking kinetics and activation parameters. The cure times of blocked polyisocyanates with hydroxyl‐terminated polybutadiene were also determined. The deblocking temperatures, the results of cure‐time studies, and the kinetic parameters revealed that the thermal dissociation of the N‐methylaniline‐blocked polyisocyanates was retarded by electron‐donating substituents and facilitated by electron‐withdrawing substituents. The action of N‐methylanilines as blocking agents for isocyanate was explained by the formation of a four‐center, intramolecularly hydrogen‐bonded ring structure during the thermal dissociation of the blocked polyisocyanates. The formation of such a hydrogen‐bonded ring structure was confirmed and supported by variable‐temperature ¹H NMR studies and entropy parameters, respectively. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1557–1570, 2007     

Deformations of complex structures on Γ/SL 2(C)

LetG be a connected complex semisimple Lie group. Let Γ be a cocompact lattice inG. In this paper, we show that whenG isSL ₂(C), nontrivial deformations of the canonical complex structure onX exist if and only if the first Betti number of the lattice Γ is non-zero. It may be remarked that for a wide class of arithmetic groups Γ, one can find a subgroup Γ′ of finite index in Γ, such that Γ′/[Γ′,Γ′] is finite (it is a conjecture of Thurston that this is true for all cocompact lattices inSL(2, C)). We also show thatG acts trivially on the coherent cohomology groupsH ⁱ(Γ/G, O) for anyi≥0.     

Phonon structure and dynamics of boron nitride single wall nanotube

We report a detailed study of the phonon properties of hexagonal boron nitride (BN) monolayers as well as nanotubes by using De Launay type of angular force model. The force constants used for calculation of phonon dispersion relations of the nanotube are derived from those for the monolayers of hexagonal by employing force constant method. These force constants have been modified to include the effect of curvature of the tubule. The results are then used to derive the phonon dispersion relations for (10,10) BN nanotubes using ‘zone-folding’ method. Calculated phonon modes are in good agreement with the experimental values obtained so far, for (10,10) armchair BN nanotubes.     

Physics possibilities at India-based Neutrino Observatory

In this talk I review the physics possible at India-based Neutrino Observatory (INO). I discuss the improvement in the precision of currently known quantities and the possibility measuring the presently unknown quantities.     

Cyclic networks with general blocking and starvation

We introducegeneral starvation and consider cyclic networks withgeneral blocking and starvation (GBS). The mechanism of general blocking allows the server to process a limited number of jobs when the buffer downstream is full, and that of general starvation allows the server to perform a limited number of services in anticipation of jobs that are yet to arrive. The two main goals of this paper are to investigate how the throughput of cyclic GBS networks is affected by varying (1) the total number of jobsJ, and (2) the buffer allocationk=(k₁..., k_m) subject to a fixed total buffer capacityK=k ₁ +... + k_m. In particular, we obtain sufficient conditions for the throughput to be symmetric inJ and to be maximized whenJ=K/2. We also show that the equal buffer allocation is optimal under the two regimes of light or heavy usage. In order to establish these results, we obtain several intermediate structural properties of the throughput, using duality, reversibility, and concavity, which are of independent interest.Research supported in part by NSF Grant No. ECS-8919818.