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.     

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.     

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.     

Does an all-sulphur analogue of heptamolybdate exist?

The complexes [MoX₄]²⁻ (M = Mo; X = O or S) exist as the monomeric tetrahedral species in aqueous alkaline solutions. Acidification of tetraoxomolybdate results in the condensation of the tetrahedral units via a series of polyoxomolybdates leading to the ultimate formation of the trioxide MoO₃. Heptamolybdate [Mo₇O₂₄]⁶⁻ is the first major polyanion of the acidification reaction. In contrast, acidification of tetrathiomolybdates leads to the formation of amorphous molybdenum trisulphide via a dinuclear Mo(V) complex. The formation of the dinuclear Mo(V) complex precludes the formation of any higher nuclearity Mo(VI)-S complexes in aqueous solution. Thus it is shown that the all-sulphur analogue of heptamolybdate [M0₇S₂₄]⁶⁻ does not exist in alkaline medium and also cannot be isolated from aqueous acidic medium     

Photonic crystals--a step towards integrated circuits for photonics.

The field of photonic crystals has, over the past few years, received dramatically increased attention. Photonic crystals are artificially engineered structures that exhibit a periodic variation in one, two, or three dimensions of the dielectric constant, with a period of the order of the pertinent light wavelength. Such structures in three dimensions should exhibit properties similar to solid-state electronic crystals, such as bandgaps, in other words wavelength regions where light cannot propagate in any direction. By introducing defects into the periodic arrangement, the photonic crystals exhibit properties analogous to those of solid-state crystals. The basic feature of a photonic bandgap was indeed experimentally demonstrated in the beginning of the 1990s, and sparked a large interest in, and in many ways revitalized, photonics research. There are several reasons for this attention. One is that photonic crystals, in their own right, offer a proliferation of challenging research tasks, involving a multitude of disciplines, such as electromagnetic theory, nanofabrication, semi-conductor technology, materials science, biotechnology, to name a few. Another reason is given by the somewhat more down-to-earth expectations that photonics crystals will create unique opportunities for novel devices and applications, and contribute to solving some of the issues that have plagued photonics such as large physical sizes, comparatively low functionality, and high costs. Herein, we will treat some basics of photonic crystal structures and discuss the state-of-the-art in fabrication as well give some examples of devices with unique properties, due to the use of photonic crystals. We will also point out some of the problems that still remain to be solved, and give a view on where photonic crystals currently stand.