LP-118 is a novel B-cell lymphoma 2 / extra-large inhibitor that demonstrates efficacy in models of venetoclax-resistant chronic lymphocytic leukemia.

Patients with chronic lymphocytic leukemia (CLL) respond well to initial treatment with the Bcell lymphoma 2 (BCL2) inhibitor venetoclax. Upon relapse, they often retain sensitivity to BCL2 targeting, but durability of response remains a concern. We hypothesize that targeting both BCL2 and B-cell lymphoma-extra large (BCLXL) will be a successful strategy to treat CLL, including for patients who relapse on venetoclax. To test this hypothesis, we conducted a pre-clinical investigation of LP-118, a highly potent inhibitor of BCL2 with moderate BCLXL inhibition to minimize platelet toxicity. This study demonstrated that LP-118 induces efficient BAK activation, cytochrome C release, and apoptosis in both venetoclax naïve and resistant CLL cells. Significantly, LP-118 is effective in cell lines expressing the BCL2 G101V mutation and in cells expressing BCLXL but lacking BCL2 dependence. Using an immunocompetent mouse model, Eµ-TCL1, LP-118 demonstrates low platelet toxicity, which hampered earlier BCLXL inhibitors. Finally, LP-118 in the RS4;11 and OSU-CLL xenograft models results in decreases in tumor burden and survival advantage, respectively. These results provide a mechanistic rationale for the evaluation of LP-118 for the treatment of venetoclax responsive and relapsed CLL.

Genome-wide identification and expression analysis of WRKY transcription factors in pearl millet (Pennisetum glaucum) under dehydration and salinity stress.

BACKGROUND: Plants have developed various sophisticated mechanisms to cope up with climate extremes and different stress conditions, especially by involving specific transcription factors (TFs). The members of the WRKY TF family are well known for their role in plant development, phytohormone signaling and developing resistance against biotic or abiotic stresses. In this study, we performed a genome-wide screening to identify and analyze the WRKY TFs in pearl millet (Pennisetum glaucum; PgWRKY), which is one of the most widely grown cereal crops in the semi-arid regions. RESULTS: A total number of 97 putative PgWRKY proteins were identified and classified into three major Groups (I-III) based on the presence of WRKY DNA binding domain and zinc-finger motif structures. Members of Group II have been further subdivided into five subgroups (IIa-IIe) based on the phylogenetic analysis. In-silico analysis of PgWRKYs revealed the presence of various cis-regulatory elements in their promoter region like ABRE, DRE, ERE, EIRE, Dof, AUXRR, G-box, etc., suggesting their probable involvement in growth, development and stress responses of pearl millet. Chromosomal mapping evidenced uneven distribution of identified 97 PgWRKY genes across all the seven chromosomes of pearl millet. Synteny analysis of PgWRKYs established their orthologous and paralogous relationship among the WRKY gene family of Arabidopsis thaliana, Oryza sativa and Setaria italica. Gene ontology (GO) annotation functionally categorized these PgWRKYs under cellular components, molecular functions and biological processes. Further, the differential expression pattern of PgWRKYs was noticed in different tissues (leaf, stem, root) and under both drought and salt stress conditions. The expression pattern of PgWRKY33, PgWRKY62 and PgWRKY65 indicates their probable involvement in both dehydration and salinity stress responses in pearl millet. CONCLUSION: Functional characterization of identified PgWRKYs can be useful in delineating their role behind the natural stress tolerance of pearl millet against harsh environmental conditions. Further, these PgWRKYs can be employed in genome editing for millet crop improvement.

Fabrication of biobeads expressing heavy metal-binding protein for removal of heavy metal from wastewater.

Heavy metals, being toxic in nature, are one of the most persistent problems in wastewater. Unabated discharge of large amount of heavy metals into water bodies are known to cause several environmental and health impacts. Biological remediation processes like microbial remediation and phytoremediation are proved to be very effective in the reduction of heavy metal pollutants in wastewater. To circumvent the issues involved several peptides and proteins are being explored. Metal-binding capacity, accumulation, and tolerance of heavy metals in bacteria can be upsurge by overexpressing the genes which code for metal-binding proteins. In the present study, an attempt has been made to bioremediate heavy metal toxicity by overexpressing metal-binding proteins. Two expression cassettes harboring top4 metal-binding protein (T4MBP) and human metallothionein 3 (HMP3) were designed under the control of constitutive CaMV 35S promoter and transformed into E.coli TBI cells. E.coli over expressing HMP3 and T4MBP were immobilized in biobeads which were explored for the detoxification of water contaminated with copper and cadmium. Effects on the concentration of heavy metal before and after treatment with beads were estimated with the help of ICP-OES. Noteworthy results were obtained in the case of copper with 87.2% decrease in its concentration after treatment with biobeads. Significant decrement of 32.8% and 27.3% was found in case of zinc and cadmium, respectively. Mechanisms of binding of proteins with heavy metals were further validated by molecular modeling and metal-binding analysis. HMP3 protein was found to be more efficient in metal accumulation as compared with T4MBP. The fabricated biobeads in this study definitely offer an easy and user-handy approach towards the treatment of toxic wastewater.

Phenothiazines and phenoxazines: as electron transfer mediators for ferritin iron release.

Intracellular ferritin stores iron as ferrihydrite and releases it for various cellular metabolic activities. The reductive approach, one of the possible mechanisms of iron mobilization from ferritin nanocages, requires electron transfer (ET) from reducing agent(s) to the protein encapsulated iron. In vitro, the rate of ET from the physiological reducing agent, NADH, to mineralized ferritin is very slow resulting in a smaller amount of iron release. Therefore, medically relevant phenothiazine (TH/MB/MG/TDB) and phenoxazine (BCB/CRV/NB) dyes were used as ET mediators to facilitate the electron relay and to evaluate their iron releasing ability from ferritin. These dyes have earlier been exploited as ET mediators during electrocatalysis and in the treatment of methemoglobinemia. With the exception of MG, the midpoint potentials (E1/2) and NADH oxidizing abilities of these dyes dictated by their structure and the reaction conditions along with the dye-ferritin interaction govern the kinetics of reductive iron mobilization. A greater amount of iron release was observed in the case of TH, BCB and CRV. In comparison to neutral pH, acidic pH altered E1/2 and protein conformation leading to enhanced iron mobilization, whereas dissolved O2 and the photosensitizing effect of dyes were found to have a negligible impact. In analogy to in vitro, the acidic environment of the lysosome may bring about similar changes in the reducing agents/dye mediators/ferritin to facilitate the iron release process in vivo. Following Marcus theory, our current observations suggest that the dyes with E1/2 values well separated from those of the reducing agents and ferritin's mineral core can be exploited to facilitate iron release during iron overload conditions.

Pharmacophore modeling and molecular dynamics approach to identify putative DNA Gyrase B inhibitors for resistant tuberculosis.

One of the major mechanisms followed by the therapeutic agents to target the causative organism of TB, mycobacterium tuberculosis (Mtb), involves disruption of the replication cycle of the pathogen DNA. The process involves two steps that occur simultaneously, ie, breakage and reunion of DNA at gyrase A (GyrA) domain and ATP hydrolysis at gyrase B (GyrB) domain. Current therapy for multi-drug resistant TB involves FDA approved, Fluoroquinolone-based antibiotics, which act by targeting the replication process at GyrA domain. However, resistance against fluoroquinolones due to mutations in the GyrA domain has limited the use of this therapy and shifted the focus of the research community on the GyrB domain. Thus, this study involves in silico designing of chemotherapeutic agents for resistant TB by targeting GyrB domain. In the current study, a pharmacophore model for GyrB domain was generated using reported inhibitors. It was utilized as a query search against three commercial databases to identify GyrB domain inhibitors. Additionally, a qualitative Hip-Hop pharmacophore model for GyrA was also developed on the basis of some marketed fluoroquinolone-based GyrA inhibitors, to remove non-selective gyrase inhibitors obtained in virtual screening. Further, molecular dynamic simulations were carried out to determine the stability of the obtained molecules in complex with both the domains. Finally, Molecular mechanics with generalized Born and surface area solvation score was calculated to determine the binding affinity of obtained molecule with both domains to determine the selectivity of the obtained molecules that resulted in seven putative specific inhibitors of GyrB domain.

Releasing iron from ferritin protein nanocage by reductive method: The role of electron transfer mediator.

BACKGROUND: Ferritin detoxifies excess of free Fe(II) and concentrates it in the form of ferrihydrite (Fe2O3·xH2O) mineral. When in need, ferritin iron is released for cellular metabolic activities. However, the low solubility of Fe(III) at neutral pH, its encapsulation by stable protein nanocage and presence of dissolved O2 limits in vitro ferritin iron release. METHODS: Physiological reducing agent, NADH (E1/2 = -330 mV) was inefficient in releasing the ferritin iron (E1/2 = +183 mV), when used alone. Thus, current work investigates the role of low concentration (5-50 µM) of phenazine based electron transfer (ET) mediators such as FMN, PYO - a redox active virulence factor secreted by Pseudomonas aeruginosa and PMS towards iron mobilization from recombinant frog M ferritin. RESULTS: The presence of dissolved O2, resulting in initial lag phase and low iron release in FMN, had little impact in case of PMS and PYO, reflecting their better ET relay ability that facilitates iron mobilization. The molecular modeling as well as fluorescence studies provided further structural insight towards interaction of redox mediators on ferritin surface for electron relay. CONCLUSIONS: Reductive mobilization of iron from ferritin is dependent on the relative rate of NADH oxidation, dissolved O2 consumption and mineral core reduction, which in turn depends on E1/2 of these mediators and their interaction with ferritin. GENERAL SIGNIFICANCE: The current mechanism of in vitro iron mobilization from ferritin by using redox mediators involves different ET steps, which may help to understand the iron release pathway in vivo and to check microbial growth.

Comparative molecular dynamics studies of heterozygous open reading frames of DNA polymerase eta (η) in pathogenic yeast Candida albicans.

Genomic instability in Candida albicans is believed to play a crucial role in fungal pathogenesis. DNA polymerases contribute significantly to stability of any genome. Although Candida Genome database predicts presence of S. cerevisiae DNA polymerase orthologs; functional and structural characterizations of Candida DNA polymerases are still unexplored. DNA polymerase eta (Polη) is unique as it promotes efficient bypass of cyclobutane pyrimidine dimers. Interestingly, C. albicans is heterozygous in carrying two Polη genes and the nucleotide substitutions were found only in the ORFs. As allelic differences often result in functional differences of the encoded proteins, comparative analyses of structural models and molecular dynamic simulations were performed to characterize these orthologs of DNA Polη. Overall structures of both the ORFs remain conserved except subtle differences in the palm and PAD domains. The complementation analysis showed that both the ORFs equally suppressed UV sensitivity of yeast rad30 deletion strain. Our study has predicted two novel molecular interactions, a highly conserved molecular tetrad of salt bridges and a series of π-π interactions spanning from thumb to PAD. This study suggests these ORFs as the homologues of yeast Polη, and due to its heterogeneity in C. albicans they may play a significant role in pathogenicity.

S95C substitution in CuZn-SOD of Ipomoea carnea: impact on the structure, function and stability.

Superoxide dismutase (SOD) in general is a unique homo-dimeric enzyme that can scavenge toxic superoxide radicals by dismutation reaction. In IcSOD (Ipomoea carnea SOD), the presence of cysteine (Cys) plays an essential role in protein behaviour. This study analysed the role of Cys in modulating the stability and kinetic properties of IcSOD. To investigate the significance of the dimeric structure in modulating the structure/function relationship of CuZn-SODs, we have substituted a conserved serine by cysteine (Ser95Cys) in Ipomoea carnea CuZn-SOD. The results demonstrate that this mutation leads to an increase in dimeric strength, as reflected by size exclusion chromatography, differential scanning calorimetry, and high-temperature circular dichroism spectroscopy measurements. The mutant form, as compared to the native enzyme, shows a relatively low tendency to form aggregates but encountered a reduction in both dismutase and peroxidase activities. This study provides new mechanistic insight into the role of free cysteine in CuZn-SODs and such mutation may be used to increase dimeric strength. Protein docking and molecular dynamics simulations further demonstrate that Ser95Cys substitution in Ipomoea carnea CuZn-SOD leads to the creation of a new subunit interface resulting in increased dimeric strength of the protein.

Overexpression of human peroxisomal enoyl-CoA delta isomerase2 HsPECI2, an ortholog of bamboo expressed during gregarious flowering alters salinity stress responses and polar lipid content in tobacco.

Peroxisomal enoyl-CoA delta isomerase2 (PECI2) is one of the key enzymes that has critical role in lipid metabolism and plant development during salt stress. Seven out of ten tobacco plants overexpressing human PECI2 (HsPECI2) with PTS1-sequence showed hypersensitivity to salt. Under salt-stress, T2 transformed plants (HsPECI2) displayed reduced primary root, delayed shoot-growth, and visibly smaller rosette leaves turning pale yellow as compared to the pKYLX71 vector control plant. Also, we found altered reactive oxygen species (ROS) levels and reduced catalase activity in 100mM sodium chloride (NaCl) treated HsPECI2 transformed plant compared with the pKYLX71 counterpart. ESI-MS/MS data showed that the polar lipids were differentially modulated upon salt treatment in HsPECI2 transformed and pKYLX71 plants as compared with the respective untreated counterpart. Notably, the levels of monogalactosyldiacylglycerol and phosphatidic acid varied significantly, whereas phosphatidylcholine, phosphatidylserine and digalactosyldiacylglycerol contents were moderately upregulated. In parallel, abscisic acid (ABA) responsiveness assay confirmed insensitivity of HsPECI2 transformed plant towards ABA. Overall our data proclaim that HsPECI2 play multifunctional role in normal development and response to salinity stress apart from its primary role in ß-oxidation.

Doxorubicin inhibits E. coli division by interacting at a novel site in FtsZ.

The increase in antibiotic resistance has become a major health concern in recent times. It is therefore essential to identify novel antibacterial targets as well as discover and develop new antibacterial agents. FtsZ, a highly conserved bacterial protein, is responsible for the initiation of cell division in bacteria. The functions of FtsZ inside cells are tightly regulated and any perturbation in its functions leads to inhibition of bacterial division. Recent reports indicate that small molecules targeting the functions of FtsZ may be used as leads to develop new antibacterial agents. To identify small molecules targeting FtsZ and inhibiting bacterial division, we screened a U.S. FDA (Food and Drug Administration)-approved drug library of 800 molecules using an independent computational, biochemical and microbial approach. From this screen, we identified doxorubicin, an anthracycline molecule that inhibits Escherichia coli division and forms filamentous cells. A fluorescence-binding assay shows that doxorubicin interacts strongly with FtsZ. A detailed biochemical analysis demonstrated that doxorubicin inhibits FtsZ assembly and its GTPase activity through binding to a site other than the GTP-binding site. Furthermore, using molecular docking, we identified a probable doxorubicin-binding site in FtsZ. A number of single amino acid mutations at the identified binding site in FtsZ resulted in a severalfold decrease in the affinity of FtsZ for doxorubicin, indicating the importance of this site for doxorubicin interaction. The present study suggests the presence of a novel binding site in FtsZ that interacts with the small molecules and can be targeted for the screening and development of new antibacterial agents.

Molecular modeling and identification of novel glucokinase activators through stepwise virtual screening.

The glucose phosphorylating enzyme glucokinase (GK) is a 50kD monomeric protein having 465 amino acids. It maintains glucose homeostasis inside cells, acts as a glucose sensor in pancreatic ß-cells and as a rate controlling enzyme for hepatic glucose clearance and glycogen synthesis. It has two binding sites, one for binding d-glucose and the other for a putative allosteric activator named glucokinase activator (GKA). The GKAs interact with the same region of the GK enzyme that is commonly affected by naturally occurring mutations in humans. However, many GKAs do not bind to GK in the absence of glucose. Recently, it has been reported that GKAs are highly effective in patients with type 2 diabetes mellitus. In this milieu a molecular modeling study has been carried out on three natural variants of GK that lie in the GKA binding site and are known to cause maturity onset diabetes of young (MODY). Additionally, a 10ns molecular dynamics simulation was done on each of the modeled variant in order to explore the flexibility of this site. Subsequently, a systematic virtual screening study was done to identify compounds which can bind with high affinity at GKA binding site of mutant GK.

Development of constrained tamoxifen mimics and their antiproliferative properties against breast cancer cells.

An efficient synthesis of a new series of tamoxifen mimics is described by employing iodine catalyzed ipsocyclization strategy followed by Suzuki coupling. A molecular docking studies of the synthesized compounds 11a-n and 12 in estrogen receptor (ER-α) showed that the scaffolds are fitting well in the groove, thereby suggesting them as promising antiproliferative agents for estrogen dependent breast cancer lines. All compounds were tested in vitro against breast cancer cell lines-ER positive, MCF-7; ER negative, MDA-MB-231; and control mammary epithelial cells, MEpiC. The biological results showed that most of the compounds are active against MCF-7 with IC50 values less than 6.5µM which corroborate the results of molecular docking studies.