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Staphylococcus epidermidis is one of the major causes of nosocomial infections around the globe that leads to a high rate of mortality and morbidity in both immunocompromised patients and preterm infants. Despite the alarming increase in multi-drug resistance, no promising vaccines are readily available against this pathogen. Thus, the present study is focused on designing a multi-epitope subunit vaccine using five antigenic proteins of S. epidermidis through an immunoinformatics approach. The final vaccine comprised B-cell, HTL, and CTL binding epitopes followed by Lipoprotein LprA adjuvant added at N-terminal to augment the immunogenicity. Physicochemical assessment of the vaccine reveals the antigenic and non-allergic nature. The vaccine structure was designed, refined, validated, and disulfide engineered to obtain the best model. Molecular docking and dynamics simulation of the proposed vaccine with toll-like receptors (TLR-2 and TLR-4) showed strong and stable interactions. MM-PBSA analysis was implemented as an efficient tool to determine the intermolecular binding free energies of the system. The vaccine was subjected to immune simulation to predict its immunogenic profile. In silico cloning suggested that the proposed vaccine can be expressed efficiently in E.coli. Furthermore, in vivo animal experiment is needed to determine the effectiveness of the in silico designed vaccine. Communicated by Ramaswamy H. Sarma

Staphylococcus epidermidis has emerged as a major contributor of nosocomial infections across the world. With the increased rate of emerging resistant and previously undefined infectious diseases, there is a growing need to develop a novel vaccine possessing required immunogenic properties. The adopted reverse vaccinology approach identified "IMPNQILTI" of LysM domain protein, "YSYTYTIDA" of staphylococcal secretory antigen SsaA, and "YNYDANTGQ" neutral metalloproteinaseas potential peptides for vaccine design. The 9-mer epitope of target proteins is antigenic, virulent, surface-exposed, non-allergenic, and conserved across various strains of S. epidermidis. Protein-protein interactions study indicated the involvement of target proteins in major biological pathways for S. epidermidis pathogenesis. Protein-peptide docking was performed, and population coverage analysis showed significant interactions of T-cell epitopes with the HLA-binding molecules while covering 90.58% of the world's population. Further, a multi-epitope vaccine of 177 amino acids long was constructed. Docking with Toll-like receptor (TLR-2) molecule confirmed the effective interaction of the vaccine with the receptor. The vaccine efficiency in generating an effective immune response in the host was evaluated by immune simulation. Finally, in silico cloning confirmed that the constructed vaccine can be efficiently expressed in E. coli. However, the designed vaccine needs experimental validation to determine the effectiveness and immunogenicity profile, which will ensure an active immunity against S. epidermidis.

Phloroglucinol and its derivatives possess wide array of biopotentials such as antimicrobial, antioxidant, anti-inflammatory, anticancer and anti-metastatic properties. In the present investigation, for the first time, we report the anticancer potential and pharmacokinetic properties of 2,4,6-triacetylphloroglucinol (TAPG) through anti-proliferative assay and its molecular interaction with human serum albumin (HSA). HSA – TAPG interaction was explored through steady-state fluorescence, time-resolved fluorescence (TRF), circular dichroism (CD), isothermal titration calorimetry (ITC) and computational approaches. TAPG showed significant cytotoxicity towards lung, breast, colon and cervical cancer cell lines with minimal effect on normal cells. In steady-state fluorescence, the binding of TAPG strongly quenched the intrinsic fluorescence of HSA through static quenching mechanism. This explains the ground-state complex formation which was also evidenced in lifetime measurements. At different molar concentrations of TAPG, the helical content of HSA decreased and thereby influenced the secondary structural content of protein. Calculation of binding constant through fluorescence and ITC studies revealed the reversible and moderate affinity of TAPG towards HSA which allows the compound to diffuse easily from circulatory system to target tissue. Thermodynamic parameters from ITC exhibited a negative enthalpy, positive entropy and negative free energy change for HSA – TAPG interaction. This elucidates the exothermic and spontaneous reaction of binding with involvement of electrostatic interactions. Molecular docking studies showed that TAPG formed interactions with polar residues of inner and outer cluster region of site I with more affinity than site II. It was also noticeable that TAPG interactions were more stable in site I than site II during 50 ns molecular dynamic simulation. Altogether, these results explain the favorable binding of TAPG with HSA which affects the drug distribution making it more bioavailable.

The proteins produced by the saliva and salivary glands of blood sucking arthropods play a vital role in transmission of the infected parasite to host and interfere the parasitic life cycle. The structure prediction of D7r1 and its active site leads to inhibition of hemostasis and inflammation in the host. D7r1 is a member of D7-related (D7r) salivary gland proteins that interferes various aspects of host physiology. Considering the significance of a protein, three dimensional structure of D7r1 model was generated by homology modeling and validated by PROCHECK, ERRAT, Verify-3D, RAMPAGE and Q mean server. The predicted structure has 96.9% of residues in the most favored region of the Ramachandran plot. The sequence and structural alignment between D7r1 and template 2PQL reveals that similar active site residues such as Ile42, Arg43, Tyr45, His56, Met57, Val60, Phe131, and Met156 involved in binding pocket formation. Further, a molecular dynamics simulation study was performed to reveal the prolonged stability of D7r1 protein. The essential dynamics which include PCA and FEL analysis were used to evaluate the conformational stability of D7r1. This combined molecular dynamics simulation and essential dynamics were used to provide comprehensive information of D7r1 and its active site prediction gain insights into the development of novel lead molecules for disrupting host-seeking behavior of mosquitoes.

A novel guaiane sesquiterpene derivative, guai-2-en-10α-ol, from Ulva fasciata Delile exhibits antimicrobial property. U. fasciata extract was reported to exhibit cytotoxicity against cancer. In the present study, we have studied the anticancer potential of the compound, guai-2-en-10α-ol, from U. fasciata. The compound showed selective cytotoxicity toward triple-negative breast cancer (TNBC) cell line (MDA MB-231) in a dose-dependent manner. In treated cells, the apoptotic hallmarks such as formation of apoptotic bodies, cell shrinkage, and nuclear condensation were observed. Many small molecules affect the function of cellular signaling pathways. As EGFR/PI3K/Akt pathway proteins are frequently altered in TNBC, we have studied the gene expression of key proteins of this pathway. The semiquantitative PCR results demonstrated the down-regulated expression of PDPK1 (positive regulator) and Akt (key activator) as well as up-regulated expression of PTEN (negative regulator), which suggested the interaction of guai-2-en-10α-ol with upstream protein. Further investigation showed the down-regulation of both PI3K and EGFR. As EGFR is the most upstream protein of the pathway, its protein level expression was investigated. Western blotting analysis confirmed the down-regulation of p-EGFR expression and activation of apoptosis upon compound treatment. Cell cycle analysis also evidenced the G1 phase arrest, which can be due to the inhibition of cell survival pathway. Computational studies showed the interaction of guai-2-en-10α-ol with Asp855 residue of EGFR kinase domain in active conformation. All these results demonstrate the anticancer potential of guai-2-en-10α-ol through EGFR/PI3K/Akt pathway.

Acinetobacter radioresistens PR8 produces extracellular lipase depending upon growth media. In present work we not only screened the nutrient sources but also investigated the causes for variation in productivity. The nutrient sources investigated are, groundnut oil, groundnut cake and fresh groundnut. Lower lipase productivity was observed on fresh ground nut in contrast to groundnut oil and groundnut cake. The lipase productivity was examined in the batch and parameters monitored were bacterial growth, enzyme activity, pH, lipids and protein concentration. The aflatoxin B1 and oxalic acid present in fresh groundnut were found to be responsible for lower lipase productivity. The interaction studies of oxalic acid and purified lipase was confirmed with CD spectra analysis, isothermal titration calorimetry studies and fluorescence quenching. Therefore, the importance of economical cheap groundnut cake with no aflatoxin B1 and oxalates are proposed to be used for optimum lipase production.

Fusobacterium nucleatum plays a key role in several diseases such as periodontitis, gingivitis, appendicitis, and inflammatory bowel disease (IBD). The development of antibiotic resistance by this bacterium demands novel therapeutic intervention. Our recent study has reported UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA) as one of the potential target proteins in F. nucleatum. In this study, we proposed two novel MurA inhibitors through in silico screening and evaluated their mode of inhibition by in vitro experiments. It was found that MurA structural arrangement (inside-out α/β barrel) was stabilized by L/FXXXG(A) motif-based interactions. The protein was maintained in an open or substrate-free conformation due to repulsive forces between two parallelly arranged positively charged residues of domain I and II. In this conformation, we identified six best compounds that held key interactions with the substrate-binding pocket via a structure-based virtual screening of natural and chemical compound libraries. However, among these, only orientin and quercetin-3-O-d-glucuronide (Q3G) showed better interaction capability through consistent H-bond occupancy and lowest binding free energy during molecular dynamic simulations. In vitro inhibition studies evidenced the mixed and uncompetitive mode of inhibition by orientin and Q3G, respectively, with purified MurA protein. This explains the binding of orientin in both open and closed (substrate-bound) conformations of MurA, and Q3G binding in only closed conformation. Therefore, the Q3G binding mode was predicted on a MurA-substrate complex, which highlighted its constant H-bond with Cys118, a phosphoenolpyruvate (PEP) interacting residue. This suggests that Q3G may interrupt the PEP binding, thereby inhibiting the MurA activity. Thus, the current study discusses the structure of MurA and demonstrates the inhibitory action of two novel compounds.

A new series of C4-N,N-dialkylaniline-substituted 4-aryl-4H-chromenes were synthesized, and their anti-proliferative properties were evaluated against human cancer cell lines, namely, laryngeal carcinoma (Hep2), lung adenocarcinoma (A549), and cervical cancer (HeLa). The best among them, the 4-aryl-4H-chromene with C4-1-phenylpiperidine substitution was selected for further structure activity relationship (SAR) studies. Among the derivatives, N,6-dimethyl-3-nitro-4-(4-(piperidine-1-yl)phenyl)-4H-chromene-2-amine 3k showed most potent cytotoxic activity against all three cancer cell lines. Toxicity studies revealed that the 4-aryl-4H-chromenes specifically target the cancer cell lines. Molecular docking studies of this compound revealed its efficient interaction with the active site of αβ-tubulin protein.

Identifying interactions between proteins in a complex is essential to analyze their role in various cellular activities and structural stability. Therefore, effective algorithms and computer programs are required for the better understanding of various interactions exist at the protein-protein interface. The protein inter-chain interaction (PICI) server was developed to identify these interaction sites and various interactions that contribute to the specificity and strength of the protein complex by using Protein Interaction Identification Algorithm (PIIA). The multi-parametric approach of this algorithm involves the interface area between the subunits, the atomic coordinate distance, the linearity of bonds, the orientation of aromatic side-chains, and physicochemical properties of the residues. Particular advantages of PICI include its ability to identify various strong and weak interactions, including those which have not been considered before by any other server. Representation of interface data in text tables, 3D interaction visualizer, colored sequence viewer, and a dynamic colored graphical matrix display makes it distinct from similar web servers. Users can analyze interactions within multi-chain proteins by their PDBids or by uploading a structure atomic coordinate file and can download the result in plain text or XML format. Availability: PICI is freely accessible at http://pici.bicpu.edu.in/

Marine bacterium, strain MB30 isolated from the deep sea sediment of Bay of Bengal, India, exhibited antimicrobial activity against human pathogenic bacteria. Based on the 16S rRNA sequence homology and subsequent phylogenetic tree analysis, the strain MB30 was identified as Staphylococcus sp. The bioactive metabolite produced by the strain MB30 was purified through silica gel column chromatography and preparative HPLC. Purified metabolite was further characterized by FT-IR, LC-MS and NMR analyses. On the basis of spectroscopic data, the metabolite was identified as pyrrole (1, 2, a) pyrazine 1, 4, dione, hexahydro 3-(2-methyl propyl) (PPDHMP). The PPDHMP exhibited in vitro anticancer potential against lung (A549) and cervical (HeLa) cancer cells in a dose-dependent manner with the IC50 concentration of 19.94 ± 1.23 and 16.73 ± 1.78 μg ml(-1) respectively. The acridine orange (AO)/ethidium bromide (EB) and 4,6-diamidino-2-phenylindole dihydrochloride (DAPI) staining of the IC50 concentration of PPDHMP-treated cancer cells exhibited an array of morphological changes such as nuclear condensation, cell shrinkage and formation of apoptotic bodies. The PPDHMP-treated cancer cells induced the progressive accumulation of fragmented DNA in a time-dependent manner. Based on the flow cytometric analysis, it has become evident that the compound was also effective in arresting the cell cycle at G1 phase. Further, the Western blotting analysis confirmed the down-regulation of cyclin-D1, cyclin dependent kinase (CDK-2), anti-apoptotic Bcl-2 family proteins (Bcl-2 and Bcl-xL), activation of caspase-9 and 3 with the cleavage of PARP. The PPDHMP-treated cancer cells also showed the inhibition of migration and invasive capacity of cancer cells. In the present investigation, for the first time, we have reported the extraction, purification and characterization of an anticancer metabolite, PPDHMP from a new marine bacterium, Staphylococcus sp. strain MB30.

Chloroquine (CQ) has been used for decades as the primary chemotherapeutic drug for the treatment of malaria. The emergence of drug resistance in Plasmodium falciparum has been considered to be because of the excessive use of antimalarial drugs worldwide. Moreover, the intense distribution and prevalence of chloroquine-resistant strains in endemic regions has aided the incidence of more complications to malaria treatment and control. Due to the lack of literature that portrays evident molecular mechanisms of drug resistance, it has been difficult to understand the drug resistance conferred by Plasmodium species. Intensive research on CQ drug resistance has identified the association of P. falciparum chloroquine resistance transporter protein (PfCRT), which belongs to the drug/metabolite transporter and EamA-like superfamily. Additionally, it has shown that K76 T mutation in PfCRT protein has mainly attributed to CQ resistance than other mutations. This study deals with the development of an in silico model of the PfCRT protein and its interaction with the CQ ligand molecule as well as the biochemical and biophysical characterization of the transmembrane domain 1 (TMD 1) peptide of the PfCRT protein. The physiochemical analysis of the PfCRT protein identified basic differences between the wild and mutant forms of the protein, as well as identifying the high hydrophobic nature of the mutant-type protein. The tertiary structure of the PfCRT protein was predicted and interaction with CQ revealed different active pocket binding regions in both the wild and mutant form of PfCRT proteins. The CQ2+ molecule interacts with TMD 10 of the wild-type PfCRT protein, whereas it interacts with TMD 1 of the mutant-type protein. Studies on the TMD 1 peptide revealed the insertion of the peptide in the micelles adopting stable alpha-helical structure. Binding studies with the CQ molecule detected high binding affinity toward the mutant-type TMD 1 peptide rather than the wild-type, thus confirming that the TMD 1 peptide is involved in substrate selectivity. Our findings help to characterize the structure of the PfCRT protein and the role played by the TMD 1 region in CQ resistance using in silico and biochemical approaches. Molecular docking and ligand binding studies confirm that TMD 1 is involved in substrate selectivity and aids in CQ efflux, thereby contributing to the parasite's CQ drug resistance mechanism.

Ptf1-p48 (Pancreas specific transcription factor 1a) is transcription regulatory protein known for the activation of exocrine specific genes. Downregulation of its expression formulates early stages of pancreatic adenocarcinoma as deduced by its association with oncogenic bHLH (Basic Helix–Loop–Helix) protein ID3 (Inhibitor of DNA binding 3) protein whose overexpression induces cytoplasmic mislocalization of Ptf1-p48. The precise mechanism and/or functional role of Ptf1-p48in promoting pancreatic cancer is vague. The structural features of the Ptf1-p48 and its dimerization with E47 (Transcription factor E2-alpha) and ID3 mediated by their HLH (Helix–Loop–Helix) domain were perceived through MD (Molecular Dynamics) simulations of 50 ns. The interactions formed by the HLH domain in both Ptf1-E47 and Ptf1-ID3 complexes are favored by the synergistic movement of their domain helices. Accordingly, in the Ptf1-E47 complex α7 of Ptf1-p48 and α1 helix of E47 along with the loop residues of their HLH domain exhibit transitions marked by inward movement toward each other and forms polar and charged interactions. In the Ptf1-ID3 complex, α8 of Ptf1-p48 moves toward the α3 helix of ID3 and forms hydrogen bonds. The interface analysis also reveals better interface in the Ptf1-p48 complex than the Ptf1-ID3 evident by energetics and number of hydrogen bonds. The interactions in each of these complexes, supported by angular displacement and mode vector analyzes, comprehensibly describe the considerable structural changes induced upon dimer formation. It thereby gives an insight into the interfaces that could help in designing of potential inhibitors for ID3 to curb the cancer cell growth.

A combinatorial library of eighteen C4-active methine-substituted 4H-chromenes were synthesized, and their anti-cancer properties were evaluated against four human cancer cell lines, namely laryngeal carcinoma (Hep2), lung adenocarcinoma (A549), colon carcinoma (HT-29) and cervical cancer (HeLa). Out of them, six displayed significant anti-proliferative activity. The best among them, the 4H-chromene with C4-malononitrile substitution, was selected for further structure–activity relationship studies. Six analogues were synthesized and subjected to in vitro studies on above four cancer cell lines. The best among them was subjected to detail in silico studies by binding with Bcl-2 protein, and the results corroborated those obtained from in vitro studies. Our findings show that the C4-malononitrile and C2-N-phenyl-substituted 4H-chromene are the most promising lead molecules for treatment of cancer.

Defects in the spindle assembly checkpoint (SAC) have been proposed to contribute to the chromosomal instability in human cancers. One of the major mechanisms underlying antimicrotubule drug (AMD) resistance involves acquired inactivation of SAC. Synuclein γ (SNCG), previously identified as a breast cancer–specific gene, is highly expressed in malignant cancer cells but not in normal epithelium. Here, we show that SNCG is sufficient to induce resistance to AMD-caused apoptosis in breast cancer cells and cancer xenografts. SNCG binds to spindle checkpoint kinase BubR1 and inhibits its kinase activity. Specifically, the C-terminal (Gln106-Asp127) of SNCG binds to the N-terminal TPR (tetratricopeptidelike folds) motif of BubR1. SNCG–BubR1 interaction induces a structure change of BubR1, attenuates its interaction with other key checkpoint proteins of Cdc20, and thus compromises SAC function. SNCG expression in breast cancers from patients with a neoadjuvant clinical trial showed that SNCG-positive tumors are resistant to chemotherapy-induced apoptosis. These data show that SNCG renders AMD resistance by inhibiting BubR1 activity and attenuating SAC function. Mol Cancer Ther; 13(3); 699–713. ©2014 AACR . This article is highlighted in the In This Issue feature, [p. 555][1] [1]: /lookup/volpage/13/555?iss=3

A series of N-methyl-3-nitro-4-(nitromethyl)-4H-chromen-2-amine derivatives 8 were synthesized from 2-((E)-2-nitrovinyl)phenol 7 and ((E)-N-methyl)-1-(methylthio)-2-nitroethenamine 5. The cytotoxic activity of these molecules was tested against two cancer cell lines namely HeLa (cervical cancer) and HEp-2 (epidermoid laryngeal carcinoma). Among them, two molecules (4H-chromenes 8h and 8i) displayed potent anti-proliferative activity with IC50 values of 115.04 and 18.96 μM for HeLa and 86.94 and 25.08 μM for Hep-2 cell lines, respectively. Morphological evaluation of the cell lines revealed that both 8h and 8i induce the apoptotic process. Molecular docking studies of all the 4H-chromenes 8 with anti-apoptotic Bcl-2, Bcl-w, and Bcl-xL proteins revealed that the 4H-chromenes 8h and 8i have good docking score and thus corroborated in vitro studies. Furthermore, evaluation of Lipinski and ADMET properties revealed their drug-like pharmacokinetic profiles. Thus, 4H-chromenes 8h and 8i exhibit promising anti-cancer properties and can be used as lead compounds for further development.

Secretory N-acyl homoserine lactones (AHLs) mediate quorum sensing (QS) in bacteria. AHLs are shown to be inhibitory for an unrelated group of bacteria and might mimic host signalling elements, thereby subverting the regulatory events in host cells. This study investigated the AHL produced by Acinetobacter baumannii and analysed its effect on other bacterial species and mammalian cells. Chemically characterized AHL had an m/z value of 325 with a molecular formula C18H31NO4 and showed its inhibitory potential against Staphylococcus aureus. Molecular docking studies identified D-alanine-D-alanine synthetase A, a cell wall synthesizing enzyme of S. aureus having a strong binding affinity towards AHL. Electron microscopy showed the disruption and sloughing off of the S. aureus cell wall when treated with AHL. In vitro experiments revealed that this bacteriostatic AHL showed time-dependent activity and induced apoptosis in cancer cell lines. This compound could be a potential structural backbone for constructing new AHL analogues against S. aureus. The findings emphasize the need to re-evaluate all previously characterized AHLs for any additional new biological functions other than QS.

Akt, a serine/threonine protein kinase, is often hyper activated in breast and prostate cancers, but with poor prognosis. Allosteric inhibitors regulate aberrant kinase activity by stabilizing the protein in inactive conformation. Several natural compounds have been reported as inhibitors for kinases. In this study, to identify potential natural allosteric inhibitor for Akt1, we generated a seven-point pharmacophore model and screened it through natural compound library. Quercetin-7-O-β-d-glucopyranoside or Q7G was found to be the best among selected molecules based on its hydrogen bond occupancy with key allosteric residues, persistent polar contacts and salt bridges that stabilize Akt1 in inactive conformation and minimum binding free energy during molecular dynamics simulation. Q7G induced dose-dependent inhibition of breast cancer cells (MDA MB-231) and arrested them in G1 and sub-G phase. This was associated with down-regulation of anti-apoptotic protein Bcl-2, up-regulation of cleaved caspase-3 and PARP. Expression of p-Akt (Ser473) was also down-regulated which might be due to Akt1 inhibition in inactive conformation. We further confirmed the Akt1 and Q7G interaction which was observed to have a dissociation constant (Kd) of 0.246μM. With these computational, biological and thermodynamic studies, we suggest Q7G as a lead molecule and propose for its further optimization.

Anomalous action of human acetylcholinesterase (hAChE) in Alzheimer's disease (AD) was restrained by various AChE inhibitors, of which the specific and potent lead candidate Donepezil is used for treating the disease AD. Besides the specificity, the observed undesirable side effects caused by Donepezil invoked the quest for new lead molecules with the increased potency and specificity for AChE. The present study elucidates the potency of six 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives to form a specific interaction with the peripheral anionic site and catalytic anionic subsite residues of hAChE. The NMSMs were prepared in good yield from 1,1-di(methylsulfanyl)-2-nitroethylene and primary amine (or) amino acid esters. In silico interaction analysis reveals specific and potent interactions between hAChE and selected ligand molecules. The site-specific interactions formed between these molecules also results in a conformational change in the orientation of active site residues of hAChE, which prevents them from being accessed by beta-amyloid protein (Aβ), which is a causative agent for amyloid plaque formation and acetylcholine (ACh). In silico interaction analysis between the ligand-bounded hAChE with Aß and ACh confirms this observation. The variation in the conformation of hAChE associated with the decreased ability of Aβ and ACh to access the respective functional residues of hAChE induced by the novel NMSMs favors their selection for in vivo analysis to present themselves as new members of hAChE inhibitors.

4H-chromenes are among the essential groups of biologically important compounds used as synthetic ligands for drug designing and discovery process. In this study, we have presented the single-crystal structure analysis of racemic 4H-chromene derivative namely N-methyl-3-nitro-4-(nitromethyl)-4H-chromen-2-amine. The optical rotation measurement data is supporting that the title compound is racemic in nature. The compound was crystallized in monoclinic crystal system in the non-centrosymmetric space group P21 with unit cell parameters a = 5.1041 (3), b = 7.7519 (4), c = 14.7974 (8), α = 90°, β = 97.088 (5)° and γ = 90°. The nitro group of title compound is disordered over two orientations (N3A/O4A/O5A & N3B/O4B/O5B) with the refined site-occupancy ratio of 0.626(6)/0.374(6). The structure was solved by direct methods using the program SHELXS-97 and refined by SHELXL-97 with the full-matrix least square procedure to a final R-value of 0.0429 and Goodness of Fit (GooF) of 0.982. The molecules in the unit cell are stabilized by N–H···O and C–H···O types of hydrogen bonds. The intermolecular hydrogen bonds are forming C (6) motifs, which is observed to contribute the crystal packing stability. Moreover, the intramolecular hydrogen bonds are forming S (6) motif essential to stabilize the molecular structure of title compound. Graph-set S (6) and C (6) motifs are involved in stability of the structure and packing respectively.

Checkpoint-1 kinase plays an important role in the G(2)M cell cycle control, therefore its inhibition by small molecules is of great therapeutic interest in oncology. In this paper, we have reported the virtual screening of an in-house library of 2499 pyranopyrazole derivatives against the ATP-binding site of Chk1 kinase using Glide 5.0 program, which resulted in six hits. All these ligands were docked into the site forming most crucial interactions with Cys87, Glu91 and Leu15 residues. From the observed results these ligands are suggested to be potent inhibitors of Chk1 kinase with sufficient scope for further elaboration.

Dimeric lactoglobulin molecules exist in the open conformation at basic pH, whereas they exist in the closed conformation at acidic pH, after undergoing the Tanford transition around neutral pH. Orthorhombic crystals consisting of molecules in the open conformation, grown close to neutral pH, undergo a water-mediated transformation when the relative humidity around the crystals is reduced. The two subunits in the dimer are related by a crystallographic twofold axis in the native crystals while the dimer is asymmetric in the low humidity form. Interestingly, one of the subunits in the dimer in the low humidity form is in an open conformation while the other is in a closed conformation. This is the first observation of such an asymmetric dimer. A hydrogen bond between the side chains of Gln35 and Tyr42 exists and the side chain of Glu89 is substantially buried in the closed subunit of the asymmetric unit, as in other structures with molecules in the closed conformation. However, the closure of the EF loop is not complete; its conformation can be described as half-closed. A comparison of different crystal structures of beta-lactoglobulin indicates that the conformation of the loops in the molecule is substantially influenced by other factors such as crystal packing, the pH, and the composition of the medium, while the change in the conformation of the EF loop follows the Tanford transition. The mutual disposition of the two subunits in the low humidity form is halfway between those in the open and closed structures. The present work further demonstrates that structural changes that occur during partial dehydration could mimic those that occur during the action of proteins.

The microbial polyketide, 2, 4-diacetylphloroglucinol (DAPG), exhibited a broad-spectrum of anti-leukemic, anti-lung, and anti-breast cancer properties. The aim of the present investigation was to study the interactive potentials of DAPG with the metastatic proteins such as MMP-2, MMP-9, and NF-κB and antiapoptotic Bcl-2 family proteins such as Bcl-2, Bcl-w, and Bcl-xL through in silico interaction and in vitro studies. The in silico modeling predicted high interactions of DAPG with the metastatic proteins, especially MMP-2, MMP-9, and NF-κB with the glide score of -7.028, -6.304, and -5.231, respectively. Similarly, the DAPG had weak interactions with the antiapoptotic Bcl-2, Bcl-w, and Bcl-xL with the glide score of -4.505, -3.839, and -4.003, respectively. The interaction studies further revealed the inhibition of MMP-2, MMP-9, and NF-κB activities with the low IC50 concentration of 5.82 ± 1.6, 6.74 ± 1.2, and 10.7 ± 1.5 μM respectively, in the presence of DAPG. Similarly, DAPG inhibited the Bcl-2, Bcl-xL and Bcl-w activities with the high IC50 concentration of 29.8 ± 1.9, 85.9 ± 2.7, and 97.4 ± 1.5 μM, respectively. These results correlate with the relatively high IC50 concentration of 16.3 ± 1.76, 7.67 ± 0.78, and 10.7 ± 0.96 μM in the Bcl-2-overexpressing HL-60, K562 and Raji leukemic cells than the metastatic A549 and MDA MB-231 cancer cells with the low IC50 concentration of 0.06 ± 0.02 and 0.08 ± 0.01 μM, respectively, compared to the healthy, human embryonic kidney (HEK-293) cells with the high IC50 concentration of 54.7 ± 1.43 μM. In summary, the affinity of DAPG with proteins are in the order of MMP-2 > MMP-9 > NF-κB > Bcl-2 > Bcl-xL > Bcl-w. Results presented in this study confirmed the high interaction of DAPG with the metastatic proteins than the antiapoptotic Bcl-2 family proteins.

A new series of chloroquinoline-4H-chromene conjugates incorporating piperizine or azipane tethers were synthesized and their anti-malarial activity were evaluated against two Plasmodium falciparum strains namely 3D7 chloroquine sensitive (CQS) and K1 chloroquine resistant (CQR). Chloroquine was used as the standard and also reference for comparison. The conjugates exhibit intense UV absorption with λmax located at 342 nm (log e=4.0), 254 nm (log e=4.2), 223 nm (log e=4.4) which can be used to spectrometrically track the molecules even in trace amounts. Among all the synthetic compounds, two molecules namely 6-nitro and N-piperazine groups incorporated 7d and 6-chloro and N-azapane incorporated 15b chloroquinoline-4H-chromene conjugates showed significant anti-malarial activity against two strains (3D7 and K1) of P. falciparum. These values are lesser than the values of standard antimalarial compound. Molecular docking results suggested that these two compounds showing strong binding affinity with P. falciparum lactate dehydrogenase (PfLDH) and also they occupy the co-factor position which indicated that they could be the potent inhibitors for dreadful disease malaria and specifically attack the glycolytic pathway in parasite for energy production.

Phenazine-1-carboxamide (PCN), a naturally occurring simple phenazine derivative isolated from Pseudomonas sp. strain PUP6, exhibited selective cytotoxic activity against lung (A549) and breast (MDA-MB-231) cancer cell lines in differential and dose-dependent manner compared to normal peripheral blood mononuclear cells. PCN-treated cancer cells showed the induction of apoptosis as evidenced by the release of low level of LDH, morphological characteristics, production of reactive oxygen species, loss of mitochondrial membrane potential (ΔΨm) and induction of caspase-3. At molecular level, PCN instigates apoptosis by mitochondrial intrinsic apoptotic pathway via the overexpression of p53, Bax, cytochrome C release and activation of caspase-3 with the inhibition of oncogenic anti-apoptotic proteins such as PARP and Bcl-2 family proteins (Bcl-2, Bcl-w and Bcl-xL). The in silico docking studies of PCN targeted against the anti-apoptotic members of Bcl-2 family proteins revealed the interaction of PCN with the BH3 domain, which might lead to the induction of apoptosis due to the inhibition of antiapoptotic proteins. Due to its innate inhibition potential of antiapoptotic Bcl-2 family proteins, PCN may be used as potent anticancer agent against both lung and breast cancer.

RecA protein is a crucial and central component of the homologous recombination and DNA repair machinery. Despite numerous studies on the protein, several issues concerning its action, including the allosteric regulation mechanism have remained unclear. Here we report, for the first time, a crystal structure of a complex of Mycobacterium smegmatis RecA (MsRecA) with dATP, which exhibits a fully ordered C-terminal domain, with a second dATP molecule bound to it. ATP binding is an essential step for all activities of RecA, since it triggers the formation of active nucleoprotein filaments. In the crystal filament, dATP at the first site communicates with a dATP of the second site of an adjacent subunit, through conserved residues, suggesting a new route for allosteric regulation. In addition, subtle but definite changes observed in the orientation of the nucleotide at the first site and in the positions of the segment preceding loop L2 as well as in the segment 102–105 situated between the 2 nt, all appear to be concerted and suggestive of a biological role for the second bound nucleotide.

The crystal structures of Mycobacterium smegmatis RecA (RecA Ms ) and its complexes with ADP, ATPγS, and dATP show that RecA Ms has an expanded binding site like that in Mycobacterium tuberculosis RecA, although there are small differences between the proteins in their modes of nucleotide binding. Nucleotide binding is invariably accompanied by the movement of Gln 196, which appears to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding loops. These observations provide a framework for exploring the known properties of the RecA proteins.

The crystal structure of the title compound 1',2',3',4'-tetrahydro-1,3-diphenyl-4-chlorospiro[2-pyrazoline-5,2-napthalen] 1'one has been determined. The structure consists of a pyrazoline ring, three aromatic rings and a tetralone moiety. All the aromatic rings are planar while the cyclohexonone ring of the tetralone moiety is in the distorted sofa conformation. The molecular packing is stabilized by C-H...O and C-H…π type inter molecular interactions.

A new rhizosphere soil bacterium that exhibits antimicrobial potential against human pathogens was isolated. On the basis of 16S ribosomal RNA nucleotide sequence homology and subsequent phylogenetic tree analysis, the strain PUW5 was identified as Pseudomonas putida. A bioactive metabolite was extracted and purified using silica gel column chromatography and preparative HPLC. Characterization of metabolite was done by employing Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR) and mass spectroscopy (MS). On the basis of spectroscopic data, the metabolite was structurally elucidated as 5-methyl phenazine-1-carboxylic acid betaine (MPCAB). The MPCAB exhibits selective cytotoxicity towards lung (A549) and breast (MDA MB-231) cancer cell lines in dose-dependent manner with IC50 value of 488.7±2.52 nM and 458.6±2.48 nM respectively. The MPCAB exhibited inhibition of cell viability, DNA synthesis, induced G1 cell cycle arrest and apoptosis in cancer cells. The docking and interaction studies confirmed the binding potential of MPCAB with Bcl-2 than Bcl-xL and Bcl-w proteins. These results strongly suggest that the MPCAB induces apoptosis in A549 and MDA MB-231 cancer cells through mitochondrial intrinsic pathway via activation of caspase-3 and down regulation of Bcl-2 protein.

Hsp90 is an important driver of stabilization and activation of several oncogenic proteins in many key pathways in oncogenesis, including HER2. The present study demonstrated that synuclein gamma (SNCG) prevents the protein degradation and protects the function of HER2 in the condition when the function of Hsp90 is blocked. Disruption of Hsp90 resulted in a significant degradation of HER2 and the loss of activity. However, SNCG completely recovered Hsp90 disruption-mediated losses of HER2 and the function. SNCG bound to HER2 in the presence and absence of Hsp90. Specifically, the C-terminal (Gln106-Asp127) of SNCG bound to the loop connecting αC helix and β4 sheet of the kinase domain of HER2. SNCG renders resistance to 17-AAG-induced tumor suppression in tumor xenograft. Crossing SNCG transgenic mice with HER2 mice stimulated HER2-induced tumor growth and rendered resistance to Hsp90 disruption. The present study indicates that SNCG protects Hsp90 client protein of HER2, and renders resistance to Hsp90 disruption.