Discovery of anticancer compound possessing potential to bind γ-secretase catalytic subunit and inhibit notch promoter activity.

Gamma secretase (GS) is an important therapeutic target in anticancer drug discovery. Increased GS activity activates notch signaling pathway which is associated with cancer stemness and drug resistance in cancer cells. A total of 69,075 natural and their derivative compounds were screened to identify the lead compound on the basis of in silico GS catalytic domain binding potential and in vitro selective anticancer efficacy. STOCK1N-23234 showed higher dock score (-11.82) compared to DAPT (-9.2) in molecular docking experiment and formed hydrogen bond with the key amino acid (Asp385) involve in catalysis process. Molecular dynamics (MD) simulation parameters (RMSD, RMSF, Rg, SASA and hydrogen bond formation) revealed that the STOTCK1N-23234 formed structurally and energetically stable complex with the GS catalytic domain with lower binding energy (-22.79 kcal/mol) compared to DAPT (-16.22 kcal/mol). STOCK1N-23234 showed better toxicity (up to 60%) against colon and breast cancer cells (HCT-116 and MDA-MB-453) at 1-70 µM concentration. Interestingly, STOCK1N-23234 did not showed cytotoxicity against human normal breast cells (MCF-10A). STOCK1N-23234 treatment significantly decreased sphere formation, notch promoter activity, and transcription of notch target genes (Hes-1 and Hey-1) in HCT-116 cells derived colonosphere. Confocal microscopy revealed that STOTCK1N-23234 treatment at test concentration induced apoptosis related morphological changes, reduced mitochondria membrane potential and increased reactive oxygen species production in HCT-116 cells compared to non-treated cells. In conclusion, STOCK1N-23234 is a novel lead natural anticancer compound which requires in depth validation in cancer preclinical models.Communicated by Ramaswamy H. Sarma.

Immunodominant conserved moieties on spike protein of SARS-CoV-2 renders virulence factor for the design of epitope-based peptide vaccines.

The outbreak of novel SARS-CoV-2 virion has wreaked havoc with a high prevalence of respiratory illness and high transmission due to a vague understanding of the viral antigenicity, augmenting the dire challenge to public health globally. This viral member necessitates the expansion of diagnostic and therapeutic tools to track its transmission and confront it through vaccine development. Therefore, prophylactic strategies are mandatory. Virulent spike proteins can be the most desirable candidate for the computational design of vaccines targeting SARS-CoV-2, followed by the meteoric development of immune epitopes. Spike protein was characterized using existing bioinformatics tools with a unique roadmap related to the immunological profile of SARS-CoV-2 to predict immunogenic virulence epitopes based on antigenicity, allergenicity, toxicity, immunogenicity, and population coverage. Applying in silico approaches, a set of twenty-four B lymphocyte-based epitopes and forty-six T lymphocyte-based epitopes were selected. The predicted epitopes were evaluated for their intrinsic properties. The physico-chemical characterization of epitopes qualifies them for further in vitro and in vivo analysis and pre-requisite vaccine development. This study presents a set of screened epitopes that bind to HLA-specific allelic proteins and can be employed for designing a peptide vaccine construct against SARS-CoV-2 that will confer vaccine-induced protective immunity due to its structural stability. Supplementary Information: The online version contains supplementary material available at 10.1007/s13337-023-00852-9.

Every lid swelling is not stye: A rare presentation of scrub typhus eschar.

A 17-year-old female patient presented to us with complaints of diffuse swelling in her left upper eyelid with preauricular lymphadenopathy for three days. She was diagnosed with a case of hordeolum externum and was treated on the same line. However, during follow-up, she developed a mild- to moderate-grade fever, which did not subside with treatment. On further investigation, her IgM rapid ELISA for Scrub typhus was positive, which was further confirmed by the Weil-Fellix test (OXK=1:360). She was treated with systemic doxycycline. Within a week, her fever returned to normal baseline, with resolution of local eye lid swelling, and her black scab was also gone. We have reported a case of scrub typhus as a rare manifestation with lid swelling and subsequently eschar formation on the upper eye lid. The patient was promptly treated with oral antibiotics without any morbidity.

Natural bone inspired core-shell triple-layered gel/PCL/gel 3D printed scaffolds for bone tissue engineering.

Despite technological advancements in bone tissue engineering, it is still a challenge to fabricate a scaffold with high bioactivity as well as high mechanical strength that can promote osteogenesis as well as bear load. Here we developed a 3D printed gel-polymer multi-layered hybrid scaffold. The innermost layer is porous gel-based framework made of gelatin/carboxymethyl-chitin/nano-hydroxyapatite and is cryogenically 3D printed. Further, the second and middle layer of micro-engineered polycaprolactone (PCL) is infused in the gel with controlled penetration and tuneable coating thickness. The PCL surface is further coated with a third and final thin layer of gel matrix used for the first layer. This triple-layered structure demonstrates compression strength and modulus of 13.07 ± 1.15 MPa and 21.8 ± 0.82 MPa, respectively, post 8 weeks degradation which is >3000% and >700% than gel scaffold. It also shows degradation of 6.84 ± 0.70% (83% reduction than gel scaffold) after 12 weeks and swelling of 69.09 ± 6.83% (81% reduction) as compared to gel scaffolds. Further, nearly 300%, 250%, 50%, and 440% increase in cellular attachment, proliferation, protein generation, and mineralization, respectively are achieved as compared to only PCL scaffolds. Thus, these hybrid scaffolds offer high mechanical strength, slow degradation rate, high bioactivity, and high osteoconductivity. These multifunctional scaffolds have potential for reconstructing non-load-bearing bone defects like sinus lift, jaw cysts, and moderate load-bearing like reconstructing hard palate, orbital palate, and other craniomaxillofacial bone defects.

Designing of neoepitopes based vaccine against breast cancer using integrated immuno and bioinformatics approach.

Cancer is characterized by genetic instability due to accumulation of somatic mutations in the genes which generate neoepitopes (mutated epitopes) for targeting by Cytotoxic T lymphocytes (CTL). Breast cancer has a high transformation rate with unique composition of mutational burden and neoepitopes load that open a platform to designing a neoepitopes-based vaccine. Neoepitopes-based therapeutic cancer vaccines designed by neoantigens have shown to be feasible, nontoxic, and immunogenic in cancer patients. Stimulation of CTL by neoepitope-based vaccine of self-antigenic proteins plays a key role in distinguishing cancer cells from normal cells and selectively targets only malignant cells. A neoepitopes-based vaccine to combat breast cancer was designed by combining immunology and bioinformatics approaches. The vaccine construct was assembled by the fusion of CTL neoepitopes, helper sequences (used for better separation of the epitopes), and adjuvant together with linkers. The neoepitopes were identified from somatic mutations in the MUC16, TP53, RYR2, F5, DNAH17, ASPM, and ABCA13 self-antigenic proteins. The vaccine construct was undertaken to study the immune simulations (IS), physiochemical characteristics (PP), molecular docking (MD) and simulations, and cloning in appropriate vector. Together, these parameters establish safety, stability, and a strong binding affinity against class I MHC molecules capable of inducing a complete immune response against breast cancer cells.Communicated by Ramaswamy H. Sarma.

Rationalizing mineral gypsum use through microbially enriched municipal solid waste compost for amelioration and regaining productivity potential of degraded alkali soils.

Reclamation of alkali soils to harness their productivity potential is more complex due to the presence of excess sodium ions, poor hydraulic conductivity and infiltration rate, resulting in poor plant growth and crop productivity. Sodic soil reclamation using inorganic ameliorants like mineral gypsum or phosphogypsum is beyond the reach of small and marginal farmers having alkali soils because of their higher market prices and shortage of availability. Conjoint use of inorganic and organic amendments can be a pragmatic solution for improving soil physico-chemical and biological properties and sustaining crop productivity. Municipal solid waste compost (MSWC) available in abundant quantity if enriched with the efficient halophilic microbial consortium and used in conjunction with a reduced dose of gypsum can be a cost-effective approach for sustainable reclamation of alkali soils and harnessing their productivity potential. Hence, a field experiment was conducted on a high alkali soil (pH2 9.2 ± 0.10), electrical conductivity (EC) 1.14 ± 0.12 dS m-1, exchangeable sodium percentage 48 ± 2.50 and organic carbon (0.30%) was conducted during 2018-19 to 2020-21 to study the combined effect inorganic and organic (enriched municipal solid waste compost (EMSWC)) amendments on amelioration of alkali soils and sustaining productivity of rice-wheat cropping system. Application of gypsum @ 25% GR + enriched MSW compost @ 10 t ha-1 (T6) showed significant improvement in soil physico-chemical and biological properties over the sole application of organic (T3 and T4), inorganic (T2) and control (T1). A significant improvement in soil fertility status in terms of available nitrogen and micronutrients as well as CO3, HCO3, Cl, Ca and Mg content were recorded with the combined application of organic and inorganic soil amendments (T5 and T6) over the sole application of mineral gypsum. Soil microbial biomass carbon (MBC), nitrogen (MBN) and phosphorus (MBP) improved significantly due to the application of EMSWC with gypsum over the application of gypsum only. Grain yield of rice and wheat increased significantly (P < 0.05) owing to the application of a reduced dose of gypsum (25% GR) and EMSWC @ 10 t ha-1 (T6) with values of 5.55 and 3.83 t ha-1, respectively over rest of the treatments. Three years economic analysis of the study revealed that treatments T6 and T5 gave the highest positive net return whereas it was lowest in treatment T1 and negative in treatment T2. The highest benefit-to-cost ratio (B:C) was obtained in treatments T6 and T5 which were significantly higher compared to the rest of the treatments.

Investigation of barriers and mitigation strategies to blockchain technology implementation in construction industry: an interpretive structural modeling approach.

Blockchain technology has emerged as a promising solution for enhancing transparency, efficiency, and security in various industries, including construction. However, implementing blockchain in the construction industry faces several barriers that hinder its widespread adoption. To fill this gap, this study is aimed at identifying and discussing the key barriers to implementing blockchain in the construction industry. The study employs a four-phase methodology. In the first phase, barriers are identified through a comprehensive literature review and supplemented with semi-structured interviews with different stakeholders, identifying critical barriers. The second phase involves data collection from ten construction experts, while the third phase utilizes the interpretive structural modeling (ISM) technique for data analysis. In the fourth phase, ten effective strategies are formulated to tackle the identified barriers and their interdependencies. The results reveal the overall structure of barriers and classify them into four groups based on driving and dependence power using the cross-impact matrix multiplication applied to the classification (MICMAC) technique. The identified barriers include a lack of collaboration in consortium formation, insufficient capacity and performance, and regulatory uncertainty, which hinders blockchain implementation in the construction industry. The research findings provide valuable information for policymakers on the overall structure with barriers and implementation in India and other countries with similar situations. Additionally, the management implications of the results were analyzed to facilitate the effective implementation of measures to overcome the obstacles and increase the level of blockchain adoption in the construction industry.

Anti-proliferative, apoptosis inducing, and antioxidant potential of Callistemon lanceolatus bark extracts: an in vitro and in silico study.

The present study reports anticancer and antioxidant activities of Callistemon lanceolatus bark extracts. Anticancer activity was studied against MDA-MB-231 cells. Antioxidant assessment of the chloroform and methanol extracts showed considerable free radical scavenging, metal ion chelating, and reducing power potential. Chloroform extract exhibited potent inhibition of cancer cell proliferation in MTT assay (IC50 9.6 µg/ml) and promoted programmed cell death. Reactive oxygen species (ROS) generation, mitochondria membrane potential (MMP) disruption ability, and nuclear morphology changes were studied using H2-DCFDA, JC-1, and Hoechst dyes, respectively, using confocal microscopy. Apoptotic cells exhibited fragmented nuclei, increased ROS generation, and altered MMP in dose- and time-dependent manner. Chloroform extract upregulated the BAX-1 and CASP3 mRNA expression coupled with downregulation of BCL-2 gene. Further, in silico docking of phytochemicals present in C. lanceolatus with anti-apoptotic Bcl-2 protein endorsed apoptosis by its inhibition and thus corroborated the experimental findings. Obatoclax, a known inhibitor of Bcl-2 was used as a reference compounds.

Specific Genetic Polymorphisms Contributing in Differential Binding of Gliadin Peptides to HLA-DQ and TCR to Elicit Immunogenicity in Celiac Disease.

Immunogenicity of gliadin peptides in celiac disease (CD) is majorly determined by the pattern of molecular interactions with HLA-DQ and T-cell receptors (TCR). Investigation of the interactions between immune-dominant gliadin peptides, DQ protein, and TCR are warranted to unravel the basis of immunogenicity and variability contributed by the genetic polymorphisms. Homology modeling of HLA and TCR done using Swiss Model and iTASSER, respectively. Molecular interactions of eight common deamidated immune-dominant gliadin with HLA-DQ allotypes and specific TCR gene pairs were evaluated. Docking of the three structures was performed with ClusPro2.0 and ProDiGY was used to predict binding energies. Effects of known allelic polymorphisms and reported susceptibility SNPs were predicted on protein-protein interactions. CD susceptible allele, HLA-DQ2.5 was shown to have considerable binding affinity to 33-mer gliadin (ΔG = - 13.9; Kd = 1.5E - 10) in the presence of TRAV26/TRBV7. Higher binding affinity was predicted (ΔG = - 14.3, Kd = 8.9E - 11) when TRBV28 was replaced with TRBV20 paired with TRAV4 suggesting its role in CD predisposition. SNP rs12722069 at HLA-DQ8 that codes Arg76α forms three H-bonds with Glu12 and two H-bonds with Asn13 of DQ2 restricted gliadin in the presence of TRAV8-3/TRBV6. None of the HLA-DQ polymorphisms was found to be in linkage disequilibrium with reported CD susceptibility markers. Haplotypic presentations of rs12722069-G, rs1130392-C, rs3188043-C and rs4193-A with CD reported SNPs were observed in sub-ethnic groups. Highly polymorphic sites of HLA alleles and TCR variable regions could be utilized for better risk prediction models in CD. Therapeutic strategies by identifying inhibitors or blockers targeting specific gliadin:HLA-DQ:TCR binding sites could be investigated.

Flavonoids as emerging notch signaling pathway modulators in cancer.

Notch signaling is an evolutionary conserved pathway important for the developmental processes and implicated in the tumor formation. Notch signaling pathway (NSP) inhibitors have been tested in clinical trials alone or in combination with the chemotherapy but none got clinical approval due to severe toxicity in patients. Flavonoids inhibit NSP by inhibiting notch receptor cleavage and/or inhibiting transcriptional regulation by Notch intracellular domain (NICD). Interestingly, some flavonoids are reported to inhibit NSP by mediating the microRNA expression. NSP inhibitory flavonoid(s) in combination with standard therapy is might be an effective strategy in cancer treatment.

Conservation Tillage and Waste Crop Residue Based Zinc Fortification in Rice and Wheat under Reclaimed Sodic Soils: Progress toward Nutrient Circularity and Sustainability.

Nearly 50% of the population across the globe is at risk of malnutrition with respect to zinc (Zn) in areas where a cereal based dietary system dominates. The present study estimated daily Zn intake in humans through field experiments in reclaimed sodic soil, utilizing waste crop residue (CR) in conservation tillage where CR played a vital role in enhancing Zn uptake in rice and wheat grains. Zn dynamics, its bioavailability, interaction with soil properties, and plausible contribution in dietary intake were studied extensively to supplement the research. A higher mobility factor (2.70%) and plant available Zn resulted in its higher uptake in rice (58.2 mg kg-1) and wheat (67.2 mg kg-1) under zero tillage in rice followed by zero tillage in wheat where CR was retained on the surface (ZTR-ZTW+CR). Daily Zn intake was found to be maximum (0.651 mg kg-1 day-1) under ZTR-ZTW+CR, demonstrating zinc sufficiency. Thus, this study may help in formulating actionable policies for combating both nutritional security and environmental hazards due to CR burning.

Discovery of differentially expressed novel miRNAs in breast normal cells and their putative targets.

MicroRNAs (miRNAs) play critical role in normal breast development and their altered expression may lead to breast cancer. Identification of new miRNAs allows us to understand the normal physiological process and associated disease pathophysiology. In the present study we identify the novel miRNAs in withaferin A treated breast normal cells (MCF-10A) using small RNA sequencing. The pathophysiological potential of the identified miRNAs was checked by studying their expression pattern in MDA-MB-231 and MCF-7 breast cancer cells using qRT-PCR technique. The secondary/tertiary structure of the identified miRNAs, target gene enrichment in Gene Ontology terms and KEGG pathway, miRNA-mRNA interaction of the sorted target genes, miRNA-mRNA/miRNA-argonaute protein/miRNA-mRNA-argonaute protein interaction and stability, were studied using bioinformatics tools/software, and molecular dynamics simulations. Hsa-miR-N88585 and hsa-miR-N461089 were identified and validated as novel miRNAs in normal breast cells. Up-expression of identified miRNAs in MDA-MB-231 and MCF-7 cells indicates their oncogenic nature. Identified target genes were enriched in classical signaling pathways (AMPK and Ras) and important GO terms. PLXDC2, BHLHE40, ARMC8, and PECAM1, CDC27, KCNK3 genes were sorted as putative targets for hsa-miR-N88585 and hsa-miR-N461089, respectively. MD simulation revealed stable hsa-miR-N88585/hsa-miR-N461089-AGO protein complex formation which indicates their further processing. In conclusion, the study identifies hsa-miR-N88585 and hsa-miR-N461089 as novel miRNAs in breast normal cells which are significantly inversely expressed in breast cancer cells. Further experiments are required to study the role of identified novel miRNAs in normal breast development and pathophysiology of breast cancer.

Assessing thermo-physical products' efficiency in the building and construction industry: a bibliometric analysis approach.

This study aims to assess the performance of thermophysical materials in the construction and building industry to establish the necessary academic basis for the interpretation of trends, developments, and status in this research field. The Scopus database contains 159 papers on this topic, which were published between 1968 and 2021 and originated in 60 countries. The International Organization for Standardization published significant information on thermal insulating materials, merchandize, elements, and applications. Several forms of insulation currently exist: (i) solid-state foam insulation composed of fibers, grains, and matrix; (ii) liquid-state insulation that encloses humidity within the filling; and (iii) gasifier form, which incorporates air, steam, or alternative gases. To reduce the amount of energy demanded, thermal insulation materials must be extended, current solutions must be modified, and new materials must be developed. Because high-temperature thermal insulation materials have more complex working conditions than alternative materials, their application requires further consideration.

Hesperidin potentially interacts with the catalytic site of gamma-secretase and modifies notch sensitive genes and cancer stemness marker expression in colon cancer cells and colonosphere.

Gamma secretase (GS) produces Notch Intracellular Domain (NICD) by trans-membrane cleavage of notch receptor. The NICD enters the nucleus and activates the notch signaling pathway (NSP) by activating notch-responsive gene transcription. Hyperactivation of NSP is related to cancer aggressiveness, therapy resistance, and poor therapy outcome, and decreased overall disease-free survival in patients. Till date, none of the GS inhibitors (GSI) has been clinically approved due to their toxicity in patients. Thus in the present study, we explored the GS catalytic site binding potential of hesperidin (natural flavone glycoside) and its effect on notch responsive gene expression in HCT-116 cells. Molecular docking, MM-GBSA binding energy calculations, and molecular dynamics (MD) simulation experiments were performed to study the GS catalytic site binding potential of hesperidin. The compound showed better GS catalytic site binding potential at the active site compared to experimentally validated GSI, N-N-(3, 5-Difluorophenacetyl)-L-alanyl-S-phenylglycine t-butyl ester (DAPT) in molecular docking and MM-GBSA experiments. MD simulation results showed that hesperidin forms stable and energetically favorable complex with gamma secretase in comparison to standard inhibitor (DAPT)-GS complex. Further, in vitro experiments showed that hesperidin inhibited cell growth and sphere formation potential in HCT-116 cells. Further, hesperidin treatment altered notch responsive genes (Hes1, Hey1, and E-cad) and cancer stemness/self-renewal markers expression at transcription levels. In conclusion, hesperidin produces toxicity in HCT-116 cells and decreases colonosphere formation by inhibiting transcription of notch signaling pathway target genes and stemness markers.Communicated by Ramaswamy H. Sarma.

Novel Eubacterium rectale inhibitor from Coriandrum sativum L. for possible prevention of colorectal cancer: a computational approach.

This research aims to screen out the effective bioactive compounds from Coriander (Coriandrum sativum L.), which may be novel potential inhibitors of Eubacterium rectale for the prevention of colorectal cancer (CRC). A series of 8 coriander-derived chemical compounds previously assessed for their anti-inflammatory, antioxidant, and antidiabetic activities were tested against Carbohydrate ABC transporter substrate-binding protein and compared to the standard inhibitor Acarbose, to support their use as novel Eubacterium rectale inhibitors. Herein, these derivatives were submitted to a thorough analysis of docking studies, in which detailed interactions of the selected phytocompounds with carbohydrate ABC transporter substrate-binding protein were revealed. Molecular docking analysis recommends Rutin, Gallocatechin, and Epigallocatechin as the most potential Eubacterium rectale inhibitors among the eight selected phytochemical compounds. Subsequently, the stability of the three selected phytochemical complexes was checked using molecular dynamics (MD) simulation at 100 ns and Molecular Mechanics combined with Poisson-Boltzmann Surface Area (MM-PBSA). The results show quite good stability for Rutin and Gallocatechin. In silico ADMET prediction was performed on the selected compounds, and the findings revealed a reasonably good ADMET profile for both Rutin and Gallocatechin. The current findings predict that Gallocatechin could be a better CRC preventive natural compound, and, further in vitro, in vivo and clinical studies may confirm its therapeutic potential.Communicated by Ramaswamy H. Sarma.

Withaniasomnifera phytochemicals possess SARS-CoV-2 RdRp and human TMPRSS2 protein binding potential.

Abstract: Coronavirus disease-19 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has infected approximately 26 million people and caused more than 6 million deaths globally. Spike (S)-protein on the outer surface of the virus uses human trans-membrane serine protease-2 (TMPRSS2) to gain entry into the cell. Recent reports indicate that human dipeptidyl peptidase-4 inhibitors (DPP4 or CD26) could also be utilized to check the S-protein mediated viral entry into COVID-19 patients. RNA dependent RNA polymerase (RdRp) is another key virulence protein of SARS-CoV-2 life cycle. The study aimed to identify the potential anti-SARS-CoV-2 inhibitors present in Withania somnifera (Solanaceae) using computer aided drug discovery approach. Molecular docking results showed that flavone glycoside, sugar alcohol, and flavonoid present in W. somnifera showed - 11.69, - 11.61, - 10.1, - 7.71 kcal/mole binding potential against S-protein, CD26, RdRp, and TMPRSS2 proteins. The major standard inhibitors of the targeted proteins (Sitagliptin, VE607, Camostat mesylate, and Remdesivir) showed the - 7.181, - 6.6, - 5.146, and - 7.56 kcal/mole binding potential. Furthermore, the lead phytochemicals and standard inhibitors bound and non-bound RdRp and TMPRSS2 proteins were subjected to molecular dynamics (MD) simulation to study the complex stability and change in protein conformation. The result showed energetically favorable and stable complex formation in terms of RMSD, RMSF, SASA, Rg, and hydrogen bond formation. Drug likeness and physiochemical properties of the test compounds exhibited satisfactory results. Taken together, the present study suggests the presence of potential anti-SARS-CoV-2 phytochemicals in W. somnifera that requires further validation in in vitro and in vivo studies. Supplementary information: The online version contains supplementary material available at 10.1007/s42535-022-00404-4.

Multifaceted 3D-QSAR analysis for the identification of pharmacophoric features of biphenyl analogues as aromatase inhibitors.

Aromatase, a cytochrome P450 enzyme, is responsible for the conversion of androgens to estrogens, which fuel the multiplication of cancerous cells. Inhibition of estrogen biosynthesis by aromatase inhibitors (AIs) is one of the highly advanced therapeutic approach available for the treatment of estrogen-positive breast cancer. Biphenyl moiety aids lipophilicity to the conjugated scaffold and enhances the accessibility of the ligand to the target. The present study is focused on the investigation of, the mode of binding of biphenyl with aromatase, prediction of ligand-target binding affinities, and pharmacophoric features essential for favorable for aromatase inhibition. A multifaceted 3D-QSAR (SOMFA, Field and Gaussian) along with molecular docking, molecular dynamic simulations and pharmacophore mapping were performed on a series of biphenyl bearing molecules (1-33) with a wide range of aromatase inhibitory activity (0.15-920 nM). Among the generated 3D-QSAR models, the Force field-based 3D-QSAR model (R2 = 0.9151) was best as compared to SOMFA and Gaussian Field (R2=0.7706, 0.9074, respectively). However, all the generated 3D-QSAR models were statistically fit, robust enough, and reliable to explain the variation in biological activity in relation to pharmacophoric features of dataset molecules. A four-point pharmacophoric features with three acceptor sites (A), one aromatic ring (R) features, AAAR_1, were obtained with the site and survival score values 0.890 and 4.613, respectively. The generated 3D-QSAR plots in the study insight into the structure-activity relationship of dataset molecules, which may help in the designing of potent biphenyl derivatives as newer inhibitors of aromatase.Communicated by Ramaswamy H. Sarma.

Naringin dihydrochalcone potentially binds to catalytic domain of matrix metalloproteinase-2: molecular docking, MM-GBSA, and molecular dynamics simulation approach.

Matrix metalloproteinase-2 (MMP2), an extracellular matrix remodulating protein's increased activity causes cancer-metastasis. Potential MMP2 inhibitors showed sever side-effects in clinical trials. Present study is focused on identification natural MMP2 inhibitor by applying molecular docking, MM-GBSA binding energy estimation and molecular dynamics (MD) simulations. Commercially available flavonoid compound library was used to screen the molecules potentially binding with catalytic domain of MMP2 protein compared to standard MMP2 inhibitor ARP100. Naringin dihydrochalcone (NDC) showed interaction with the important residues (His120, Leu82 and Val117) present at the MMP2 catalytic domain in comparison to known inhibitor ARP100 (dock score ≈ -13 and -8 kcal/mole respectively). Lower ligand-protein binding energy (-67.31 kcal/mole) obtained in MM-GBSA and the MD simulation trajectory analysis showed significant stable and energetically favourable binding of NDC at the catalytic site of MMP2. In conclusion, anti-metastatic potential of NDC should be validated in in vitro and in vivo experiments.

Rutin Potentially Binds the Gamma Secretase Catalytic Site, Down Regulates the Notch Signaling Pathway and Reduces Sphere Formation in Colonospheres.

Rutin, a natural flavonol, can modulate molecular signaling pathways and has considerable potential in cancer treatment. However, little is known about the effect of rutin on the notch signaling pathway (NSP) in cancer and cancer stem-like cells. In this study, we explored the effect of rutin on gamma secretase (GS, a putative notch signaling target) inhibition mediated NICD (Notch Intracellular Domain) production in colon cancer cells. Molecular docking, MM-GBSA, and Molecular dynamics (MD) simulation experiments were performed to check rutin's GS catalytic site binding potential. The HCT-116 colon cancer and cancer stem-like cells (colonospheres) were utilized to validate the in silico findings. The NICD production, notch promoter assay, expression of notch target genes, and cancer stemness/self-renewal markers were studied at molecular levels. The results were compared with the Notch-1 siRNA transfected test cells. The in silico study revealed GS catalytic site binding potential in rutin. The in vitro results showed a decreased NICD formation, an altered notch target gene (E-cad, Hes-1, and Hey-1) expression, and a reduction in stemness/self-renewal markers (CD44, c-Myc, Nanog, and Sox2) in test cells in a time and dose-dependent manner. In conclusion, rutin inhibits the notch signaling pathway and reduces the stemness/self-renewal property in colon cancer cells and the colonospheres by targeting gamma secretase. The clinical efficacy of rutin in combination therapy in colon cancer may be studied in the future.

Acarbose Potentially Binds to the Type I Peptide Deformylase Catalytic Site and Inhibits Bacterial Growth: An In Silico and In Vitro Study.

BACKGROUND: In bacteria, peptide deformylase (PDF), a metalloenzyme, removes N-formyl methionine from a nascent protein, which is a critical step in the protein maturation process. The enzyme is ubiquitously present in bacteria and possesses therapeutic target potential. Acarbose, an FDA-approved antidiabetic drug, is an alpha-glucosidase inhibitor of microbial origin. Clinical studies indicate that acarbose administration in humans can alter gut microbiota. As per the best of our knowledge, the antibacterial potential of acarbose has not been reported. OBJECTIVE: The present study aimed to check the binding ability of acarbose to the catalytic site of E. coli PDF and assess its in vitro antibacterial activity. METHODS: Molecular docking, molecular dynamic (MD) simulation, and MM-PBSA experiments were performed to study the binding potential of the catalytic site, and a disc diffusion assay was also employed to assess the antibacterial potential of acarbose. RESULTS: Acarbose was found to form a hydrogen bond and interact with the metal ion present at the catalytic site. The test compound showed a better docking score in comparison to the standard inhibitor of PDF. MD simulation results showed energetically stable acarbose-PDF complex formation in terms of RMSD, RMSF, Rg, SASA, and hydrogen bond formation throughout the simulation period compared to the actinonin-PDF complex. Furthermore, MM-PBSA calculations showed better binding free energy (ΔG) of acarbose PDF than the actinonin-PDF complex. Moreover, acarbose showed in vitro antibacterial activity. CONCLUSION: Acarbose forms conformational and thermodynamically stable interaction with the E. coli peptide deformylase catalytic site. Results of the present work necessitate in-depth antimicrobial potential studies on the effect of acarbose on drug resistance and nonresistant bacteria.