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.     

Synthesis and characterization of isotopically enriched methylmercury (CH3201Hg+)

A simple procedure for the synthesis of an important standard, isotopically enriched methylmercury, which is not commercially available, has been established successfully. The isotopically enriched standard synthesized is utilized in conventional isotope dilution mass spectrometry (IDMS), as well as in speciated IDMS (SIDMS), for determination of the true concentration of methylmercury in environmental samples. The CH₃²⁰¹Hg⁺ standard has been synthesized from commercially available ²⁰¹HgO and tetramethyltin. The synthesis time required is 1 h at 60°C. The product is highly pure, yielding more than 90% as ²⁰¹Hg in CH₃²⁰¹Hg⁺. Hazardous dimethylmercury does not occur during this synthesis procedure. The product synthesized was analyzed using high‐performance liquid chromatography coupled with inductively coupled plasma mass spectrometry (ICP‐MS) and ICP‐MS alone in order to determine its concentration, isotopic composition and purity. The stability of the product was also evaluated for over 6 months and found to be stable at 4°C in the dark. The isotopically enriched methylmercury synthesized can be used in SIDMS and IDMS analyses as a standard. Copyright © 2003 John Wiley & Sons, Ltd.     

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.