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.     

A note on Hadwiger’s conjecture for W5-free graphs with independence number two

The Hadwiger number of a graph $G$, denoted $h\left(G\right)$, is the largest integer $t$ such that $G$ contains $K_t$ as a minor. A famous conjecture due to Hadwiger in 1943 states that for every graph $G$, $h\left(G\right)\ge \chi \left(G\right)$, where $\chi \left(G\right)$ denotes the chromatic number of $G$. Let $\alpha \left(G\right)$ denote the independence number of $G$. A graph is $H$-free if it does not contain the graph $H$ as an induced subgraph. In 2003, Plummer, Stiebitz and Toft proved that $h\left(G\right)\ge \chi \left(G\right)$ for all $H$-free graphs $G$ with $\alpha \left(G\right)\le 2$, where $H$ is any graph on four vertices with $\alpha \left(H\right)\le 2$, $H=C_5$, or $H$ is a particular graph on seven vertices. In 2010, Kriesell subsequently generalized the statement to include all forbidden subgraphs $H$ on five vertices with $\alpha \left(H\right)\le 2$. In this note, we prove that $h\left(G\right)\ge \chi \left(G\right)$ for all $W_5$-free graphs $G$ with $\alpha \left(G\right)\le 2$, where $W_5$ denotes the wheel on six vertices.     

Character of the thermal motion of water molecules according to the data on quasielastic incoherent scattering of slow neutrons

The paper discusses the applicability of quasi-crystalline approximation to describing the thermal motion of water molecules in their normal and supercooled states. The problem is subjected to the critical analysis of experimental data on incoherent scattering of slow neutrons based on theories developed by Singwi-Sjolander [1] and Oskotsky [2] modified to duly take into account the limited applicability range of diffusion approximation. The applicability conditions of quasi-crystalline approximation are shown to be consistently satisfied only when water is in supercooled state and within a narrow temperature range above the melting temperature.     

Inner derivations and norm equality

We characterize when the norm of the sum of two bounded operators on a Hilbert space is equal to the sum of their norms.