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.     

Designing spirobifullerene core based three-dimensional cross shape acceptor materials with promising photovoltaic properties for high-efficiency organic solar cells

The development of organic electron acceptor materials is one of the key factors for realizing high-performance organic solar cells (OSCs). Nonfullerene electron acceptors, compared to traditional fullerene acceptor materials, have gained much impetus owing to their better optoelectronic tunabilities and lower cost, as well as higher stability. Therefore, 5 three-dimensional (3D) cross-shaped acceptor materials having a spirobifullerene core flanked with 2,1,3-benzothiadiazole are designed from a recently synthesized highly efficient acceptor molecule SF(BR) ₄ and are investigated in detail with regard to their use as acceptor molecules in OSCs. The density functional theory (DFT) and time-dependent DFT (TDDFT) calculations have been performed for the estimation of frontier molecular orbital (FMO) analysis, density of states analysis, reorganization energies of electron and hole, dipole moment, open-circuit voltage, photo-physical characteristics, and transition density matrix analysis. In addition, the structure-property relationship is studied, and the influence of end-capped acceptor modifications on photovoltaic, photo-physical, and electronic properties of newly selected molecules ( H1-H5 ) is calculated and compared with reference ( R ) acceptor molecule SF(BR) ₄ . The structural tailoring at terminals was found to effectively tune the FMO band gap, energy levels, absorption spectra, open-circuit voltage, reorganization energy, and binding energy value in selected molecules H1 to H5 . The 3D cross-shaped molecules H1 to H5 suppress the intermolecular aggregation in PTB7-Th blend, which leads to high efficiency of acceptor material H1 to H5 in OSCs. Consequently, better optoelectronic properties are achieved from designed molecules H1 to H5 . It is proposed that the conceptualized molecules are superior than highly efficient spirobifullerene core-based SF(BR) ₄ acceptor molecules and, thus, are recommended to experiments for future developments of highly efficient solar cells.     

Fermions in Odd Space-Time Dimensions: Back to Basics

It is a well-known feature of odd space-time dimensions d that there exist two inequivalent fundamental representations A and B of the Dirac gamma matrices. Moreover, the parity transformation swaps the fermion fields living in A and B. As a consequence, a parity-invariant Lagrangian can only be constructed by incorporating both the representations. Based upon these ideas and contrary to long-held belief, we show that in addition to a discrete exchange symmetry for the massless case, we can also define chiral symmetry provided the Lagrangian contains fields corresponding to both the inequivalent representations. We also study the transformation properties of the corresponding chiral currents under parity and charge-conjugation operations. We work explicitly in 2 + 1 dimensions and later show how some of these ideas generalize to an arbitrary number of odd dimensions.     

Infrared Spectroscopic Analysis of Chrysene and 1.2-Benzanthracence in Wax films

Chrysene and 1.2-benzanthracene are successfully doped in a solid wax film and their vibrational spectra in gooo--400cm^-1 are discussed. The harmonic frequencies and relative intensities of both the molecules observed in the film are compared with theoretical values calculated by the density functional theory （DFT） model as well as with the previous experimental data. The effects on spectra due to change of matrix and some additional bands observed in the wax film are also reported. Excellent agreement in the spectral positions and strengths between the experiments and DFT values are found.     

A quasilinearization method for a class of integro-differential equations with mixed nonlinearities

We develop an extended form of the quasilinearization method for an initial value problem involving a nonlinear integro-differential equation with mixed nonlinearities, occurring in distributed-infective and distributed-contact models. In fact, a monotone sequence of iterates converging uniformly and quadratically to a solution of the problem is obtained. Some interesting observations are presented.     

Parametric Quintic-Spline Approach to the Solution of a System of Fourth-Order Boundary-Value Problems

In this paper, we use parametric quintic splines to derive some consistency relations which are then used to develop a numerical method for computing the solution of a system of fourth-order boundary-value problems associated with obstacle, unilateral, and contact problems. It is known that a class of variational inequalities related to contact problems in elastostatics can be characterized by a sequence of variational inequations, which are solved using some numerical method. Numerical evidence is presented to show the applicability and superiority of the new method over other collocation, finite difference, and spline methods.     

Salt effects in the aqueous alkaline hydrolysis of N-hydroxyphthalimide. Kinetic evidence for the ion-pair formation

The effects of the concentrations of LiCl, NaCl, KCl, CsCl, Na₂CO₃, BaCl₂, and Me₄NCl on the rates of reactions of hydroxide ion with ionized N-hydroxyphthalimide (NHP) at 30°C and in a H₂O–MeCN solvent containing 98%, v/v, H₂O reveal a nonlinear increase in observed rate constants with increase in salt concentrations. The observed rate constants are highly sensitive to the valence state of cations and almost insensitive to the valence state of anions of the salts. These observations are explained in terms of ion-pair formation between cations and NHP^?.