Publications by authors named "Shailendra Asthana"

33 Publications

Identification and validation of potent Mycobacterial proteasome inhibitor from Enamine library.

J Biomol Struct Dyn 2021 May 6:1-11. Epub 2021 May 6.

Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi NCR, Sonepat, India.

As a consequence of present status of tuberculosis (TB) it is the obligation to develop novel targets and potential drugs so that rate of drug resistant TB can be declined. Mycobacterium proteasome is considered to be significant target for the purpose of drug designing as it is responsible for resisting the effect of NO (nitric oxide) immune system defence mechanism against the bacterial cells. Small compounds library from Enamine database has already been tested using virtual screening and molecular docking studies. Further a reanalysis with two picked out significant compounds Z1020863610, Z106766984 was carried out using molecular dynamic simulation studies and in vitro validations ( susceptibility assay, enzyme inhibition assay and MTT assay). outcome that two inhibiters were interacting at the active site pocket of receptor with high stability, was found to be very consistent with results. So it was conferred that compounds (Z1020863610, Z106766984) are potential lead for future process of drug development ( testing and clinical trials).Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1914173DOI Listing
May 2021

Wuhan to World: The COVID-19 Pandemic.

Front Cell Infect Microbiol 2021 30;11:596201. Epub 2021 Mar 30.

Translational Health Science and Technology Institute (THSTI), Faridabad, India.

COVID-19 is a Severe Acute Respiratory Syndrome (SARS), caused by SARS-CoV-2, a novel virus which belongs to the family . It was first reported in December 2019 in the Wuhan city of China and soon after, the virus and hence the disease got spread to the entire world. As of February 26, 2021, SARS-CoV-2 has infected ~112.20 million people and caused ~2.49 million deaths across the globe. Although the case fatality rate among SARS-CoV-2 patient is lower (~2.15%) than its earlier relatives, SARS-CoV (~9.5%) and MERS-CoV (~34.4%), the SARS-CoV-2 has been observed to be more infectious and caused higher morbidity and mortality worldwide. As of now, only the knowledge regarding potential transmission routes and the rapidly developed diagnostics has been guiding the world for managing the disease indicating an immediate need for a detailed understanding of the pathogen and the disease-biology. Over a very short period of time, researchers have generated a lot of information in unprecedented ways in the key areas, including viral entry into the host, dominant mutation, potential transmission routes, diagnostic targets and their detection assays, potential therapeutic targets and drug molecules for inhibiting viral entry and/or its replication in the host including cross-neutralizing antibodies and vaccine candidates that could help us to combat the ongoing COVID-19 pandemic. In the current review, we have summarized the available knowledge about the pathogen and the disease, COVID-19. We believe that this readily available knowledge base would serve as a valuable resource to the scientific and clinical community and may help in faster development of the solution to combat the disease.
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http://dx.doi.org/10.3389/fcimb.2021.596201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042280PMC
April 2021

Elucidation of Structural Determinants Delineates the Residues Playing Key Roles in Differential Dynamics and Selective Inhibition of Sirt1-3.

J Chem Inf Model 2021 Mar 19;61(3):1105-1124. Epub 2021 Feb 19.

Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India.

Sirt1-3 are the most studied sirtuins, playing a key role in caloric-dependent epigenetic modifications. Since they are localized in distinct cellular compartments and act differently under various pathological conditions, selective inhibition would be a promising strategy to understand their biological function and to discover effective therapeutics. Here, sirtuin's inhibitor Ex527* is used as a probe to speculate the possible root cause of selective inhibition and differential structural dynamics of Sirt1-3. Comparative energetics and mutational studies revealed the criticality of residues I279 and I316 for the Sirt1 selectivity toward Ex527*. Furthermore, essential dynamics and residue network analysis revealed that the side-chain reorientation in residue F190 due to nonconserved residue Y191 played a major role in the formation of an extended selectivity pocket in Sirt2. These changes at the dynamical and residual level, which impact the internal wiring significantly, might help in rationally designing selective inhibitors against Sirt1-3.
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http://dx.doi.org/10.1021/acs.jcim.0c01193DOI Listing
March 2021

Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1.

J Chem Inf Model 2021 01 12;61(1):358-384. Epub 2021 Jan 12.

NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India.

The dynamics and plasticity of the PD-1/PD-L1 axis are the bottlenecks for the discovery of small-molecule antagonists to perturb this interaction interface significantly. Understanding the process of this protein-protein interaction (PPI) is of fundamental biological interest in structure-based drug designing. Food and Drug Administration (FDA)-approved anti-PD-1 monoclonal antibodies (mAbs) are the first-in-class with distinct binding modes to access this axis clinically; however, their mechanistic aspects remain elusive. Here, we have unveiled the interactive interfaces with PD-L1 and mAbs to investigate the native plasticity of PD-1 at global (structural and dynamical) and local (residue side-chain orientations) levels. We found that the structural stability and coordinated C movements are increased in the presence of PD-1's binding partners. The rigorous analysis of these PPIs using computational biophysical approaches revealed PD-1's intrinsic plasticity, its concerted loops' movement (BC, FG, and CC'), distal side-chain motions, and the thermodynamic landscape, which are perturbed remarkably from its unbound to bound states. Based on intra-/inter-residues' contact networks and energetics, the have been identified that were found to be essential to arrest the dynamical motions of PD-1 significantly for the rational design of therapeutic agents by mimicking the mAbs mechanism.
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http://dx.doi.org/10.1021/acs.jcim.0c01080DOI Listing
January 2021

Identification and characterization of in vitro and in vivo fidarestat metabolites: Toxicity and efficacy evaluation of metabolites.

J Mass Spectrom 2021 Feb;56(2):e4694

Analytical Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India.

The progression of diabetic complications can be prevented by inhibition of aldose reductase and fidarestat considered to be highly potent. To date, metabolites of the fidarestat, toxicity, and efficacy are unknown. Therefore, the present study on characterization of hitherto unknown in vitro and in vivo metabolites of fidarestat using liquid chromatography-electrospray ionization tandem mass spectrometry (LC/ESI/MS/MS) is undertaken. In vitro and in vivo metabolites of fidarestat have been identified and characterized by using LC/ESI/MS/MS and accurate mass measurements. To identify in vivo metabolites, plasma, urine, and feces samples were collected after oral administration of fidarestat to Sprague-Dawley rats, whereas for in vitro metabolites, fidarestat was incubated in human S9 fraction, human liver microsomes, and rat liver microsomes. Furthermore, in silico toxicity and efficacy of the identified metabolites were evaluated. Eighteen metabolites have been identified. The main in vitro phase I metabolites of fidarestat are oxidative deamination, oxidative deamination and hydroxylation, reductive defluroniation, and trihydroxylation. Phase II metabolites are methylation, acetylation, glycosylation, cysteamination, and glucuronidation. Docking studies suggest that oxidative deaminated metabolite has better docking energy and conformation that keeps consensus with fidarestat whereas the rest of the metabolites do not give satisfactory results. Aldose reductase activity has been determined for oxidative deaminated metabolite (F-1), and it shows an IC50 value of 0.44 μM. The major metabolite, oxidative deaminated, did not show any cytotoxicity in H9C2, HEK, HEPG2, and Panc1 cell lines. However, in silico toxicity, the predication result showed toxicity in skin irritation and ocular irritancy SEV/MOD versus MLD/NON (v5.1) model for fidarestat and its all metabolites. In drug discovery and development research, it is distinctly the case that the potential for pharmacologically active metabolites must be considered. Thus, the active metabolites of fidarestat may have an advantage as drug candidates as many drugs were initially observed as metabolites.
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http://dx.doi.org/10.1002/jms.4694DOI Listing
February 2021

Japanese encephalitis virus capsid protein interacts with non-lipidated MAP1LC3 on replication membranes and lipid droplets.

J Gen Virol 2021 01 23;102(1). Epub 2020 Oct 23.

Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India.

Microtubule-associated protein 1 light chain 3 (MAP1LC3) is a protein with a well-defined function in autophagy, but still incompletely understood roles in several other autophagy-independent processess. Studies have shown MAP1LC3 is a host-dependency factor for the replication of several viruses. Japanese encephalitis virus (JEV), a neurotropic flavivirus, replicates on ER-derived membranes that are marked by autophagosome-negative non-lipidated MAP1LC3 (LC3-I). Depletion of LC3 exerts a profound inhibition on virus replication and egress. Here, we further characterize the role of LC3 in JEV replication, and through immunofluorescence and immunoprecipitation show that LC3-I interacts with the virus capsid protein in infected cells. This association was observed on capsid localized to both the replication complex and lipid droplets (LDs). JEV infection decreased the number of LDs per cell indicating a link between lipid metabolism and virus replication. This capsid-LC3 interaction was independent of the autophagy adaptor protein p62/Sequestosome 1 (SQSTM1). Further, no association of capsid was seen with the Gamma-aminobutyric acid receptor-associated protein family, suggesting that this interaction was specific for LC3. High-resolution protein-protein docking studies identified a putative LC3-interacting region in capsid, FTAL and other key residues that could mediate a direct interaction between the two proteins.
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http://dx.doi.org/10.1099/jgv.0.001508DOI Listing
January 2021

Development of potential proteasome inhibitors against .

J Biomol Struct Dyn 2020 Oct 19:1-15. Epub 2020 Oct 19.

Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India.

Tuberculosis (TB) has been recently declared as a health emergency because of sporadic increase in Multidrug-resistant Tuberculosis (MDR-TB) problem throughout the world. TB causing bacteria, has become resistant to the first line of treatment along with second line of treatment and drugs, which are accessible to us. Thus, there is an urgent need of identification of key targets and development of potential therapeutic approach(s), which can overcome the complications. In the present study, proteasome has been taken as a potential target as it is one of the key regulatory proteins in propagation. Further, a library of 400 compounds (small molecule) from Medicines for Malaria Venture (MMV) were screened against the target (proteasome) using molecular docking and simulation approach, and selected lead compounds were validated in model. In this study, we have identified two potent small molecules from the MMV Pathogen Box library, MMV019838 and MMV687146 with -9.8kcal/mol and -8.7kcal/mol binding energy respectively, which actively interact with the catalytic domain/active domain of proteasome and inhibit the growth in culture. Furthermore, the molecular docking and simulation study of MMV019838 and MMV687146 with proteasome show strong and stable interaction with compared to human proteasome and show no cytotoxicity effect. A better understanding of proteasome inhibition in in and model would eventually allow us to understand the molecular mechanism(s) and discover a novel and potent therapeutic agent against Tuberculosis. Active efflux of drugs mediated by efflux pumps that confer drug resistance is one of the mechanisms developed by bacteria to counter the adverse effects of antibiotics and chemicals. Efflux pump activity was tested for a specific compound MMV019838 which was showing good in silico results than MIC values. Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1835722DOI Listing
October 2020

Synthesis and evaluation of thiophene based small molecules as potent inhibitors of Mycobacterium tuberculosis.

Eur J Med Chem 2020 Dec 23;208:112772. Epub 2020 Aug 23.

Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, India. Electronic address:

Herein, we report the synthesis and anti-tubercular studies of novel molecules based on thiophene scaffold. We identified two novel small molecules 4a and 4b, which demonstrated 2-fold higher in vitro activity (MIC: 0.195 μM) compared to first line TB drug, isoniazid (0.39 μM). The identified leads demonstrated additive effect with front line TB drugs (isoniazid, rifampicin and levofloxacin) and synergistic effect with a recently FDA-approved drug, bedaquiline. Mechanistic studies (i) negated the role of Pks13 and (ii) suggested the involvement of KatG in the anti-tubercular activity of these identified leads.
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http://dx.doi.org/10.1016/j.ejmech.2020.112772DOI Listing
December 2020

Molecular mechanisms of interplay between autophagy and metabolism in cancer.

Life Sci 2020 Oct 5;259:118184. Epub 2020 Aug 5.

Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida 201313, India. Electronic address:

Autophagy is an essential mechanism of cellular degradation, a way to protect the cells under stress conditions, such as deprivation of nutrients, growth factors and cellular damage. However, in normal physiology autophagy plays a significant role in cancer cells. Current research is in progress to understand how autophagy and cancer cells go hand in hand to support cancer cell progression. The important aspect in cancer and autophagy is the interdependence of autophagy in the survival and progression of cancer cells. Autophagy is known to be a major cause of chemotherapeutic resistance in various cancer cell types. Therefore, inhibition of autophagy as an effective therapeutic approach is being actively studied and tested in clinical studies. Multiple metabolic pathways are linked with autophagy that could potentially be a significant target for chemotherapeutic strategy. The comprehension of the interconnection of autophagy with cancer metabolism can pave a novel findings for effective combinatorial therapeutic strategies.
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http://dx.doi.org/10.1016/j.lfs.2020.118184DOI Listing
October 2020

Bile acids mediated potential functional interaction between FXR and FATP5 in the regulation of Lipid Metabolism.

Int J Biol Sci 2020 14;16(13):2308-2322. Epub 2020 Jun 14.

Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India.

Perturbation in lipid homeostasis is one of the major bottlenecks in metabolic diseases, especially Non-alcoholic Fatty Liver Disease (NAFLD), which has emerged as a leading global cause of chronic liver disease. The bile acids (BAs) and their derivatives exert a variety of metabolic effects through complex and intertwined pathways, thus becoming the attractive target for metabolic syndrome treatment. To modulate the lipid homeostasis, the role of BAs, turn out to be paramount as it is essential for the absorption, transport of dietary lipids, regulation of metabolic enzymes and transporters that are essential for lipid modulation, flux, and excretion. The synthesis and transport of BAs (conjugated and unconjugated) is chiefly controlled by nuclear receptors and the uptake of long-chain fatty acids (LCFA) and BA conjugation via transporters. Among them, from studies, farnesoid X receptor (FXR) and liver-specific fatty acid transport protein 5 (FATP5) have shown convincing evidence for their key roles in lipid homeostasis and reversal of fatty liver disease substantially. BAs have a wider range of biological effects as they are identified as modulators for FXR and FATP5 both and therefore hold a significant promise for altering the lipid content in the treatment of a metabolic disorder. BAs also have received noteworthy interest in drug delivery research due to its peculiar physicochemical properties and biocompatibility. Here, we are highlighting the connecting possibility of BAs as an for FXR and for FATP5, paving an avenue to target them for designing synthetic small molecules for lipid homeostasis.
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http://dx.doi.org/10.7150/ijbs.44774DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7378638PMC
June 2020

Identification of an anti-SARS-CoV-2 receptor-binding domain-directed human monoclonal antibody from a naïve semisynthetic library.

J Biol Chem 2020 09 29;295(36):12814-12821. Epub 2020 Jul 29.

Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India

There is a desperate need for safe and effective vaccines, therapies, and diagnostics for SARS- coronavirus 2 (CoV-2), the development of which will be aided by the discovery of potent and selective antibodies against relevant viral epitopes. Human phage display technology has revolutionized the process of identifying and optimizing antibodies, providing facile entry points for further applications. Herein, we use this technology to search for antibodies targeting the receptor-binding domain (RBD) of CoV-2. Specifically, we screened a naïve human semisynthetic phage library against RBD, leading to the identification of a high-affinity single-chain fragment variable region (scFv). The scFv was further engineered into two other antibody formats (scFv-Fc and IgG1). All three antibody formats showed high binding specificity to CoV-2 RBD and the spike antigens in different assay systems. Flow cytometry analysis demonstrated specific binding of the IgG1 format to cells expressing membrane-bound CoV-2 spike protein. Docking studies revealed that the scFv recognizes an epitope that partially overlaps with angiotensin-converting enzyme 2 (ACE2)-interacting sites on the CoV-2 RBD. Given its high specificity and affinity, we anticipate that these anti-CoV-2 antibodies will be useful as valuable reagents for accessing the antigenicity of vaccine candidates, as well as developing antibody-based therapeutics and diagnostics for CoV-2.
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http://dx.doi.org/10.1074/jbc.AC120.014918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7476711PMC
September 2020

Proteome analysis revealed the essential functions of protein phosphatase PP2A in the induction of Th9 cells.

Sci Rep 2020 07 3;10(1):10992. Epub 2020 Jul 3.

Immuno-Biology Laboratory, Translational Health Science and Technology Institute (THSTI), 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, Haryana, 121 001, India.

Proteomic analysis identifies post-translational functions of proteins, which remains obscure in transcriptomics. Given the important functions of Th9 cells in anti-tumor immunity, we performed proteome analysis of Th9 cells to understand the involvement of proteins that might be crucial for the anti-tumor functions of Th9 cells. Here we performed a comprehensive proteomic analysis of murine Th0 and Th9 cells, and identified proteins that are enriched in Th9 cells. Pathway analysis identified an abundance of phosphoproteins in the proteome of Th9 cells as compared to Th0 cells. Among upregulated phosphoproteins, Ppp2ca (catalytic subunit of protein phosphatase, PP2A) was found to be highly enriched in Th9 cells. Although the role of PP2A has been shown to regulate the differentiation and functions of Th1, Th2, Th17 and Tregs, its role in the differentiation and functions of Th9 cells is not identified yet. Here we found that PP2A is required for the induction of Th9 cells, as PP2A inhibition leads to the suppression of IL-9 and expression of key transcription factors of Th9 cells. PP2A inhibition abrogates Th9 cell-mediated anti-tumor immune response in B16-OVA melanoma tumor model. Thus, we report that PP2A is essential for the differentiation and anti-tumor functions of Th9 cells.
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http://dx.doi.org/10.1038/s41598-020-67845-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7335106PMC
July 2020

A Review on the Progress and Prospects of Dengue Drug Discovery Targeting NS5 RNA- Dependent RNA Polymerase.

Curr Pharm Des 2020 ;26(35):4386-4409

Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad 502329, Telangana, India

Dengue virus (DENV) infection threatens the health and wellbeing of almost 100 million people in the world. Vectored by mosquitoes, DENV may cause a severe disease in human hosts called Dengue hemorrhagic fever (DHF)/Dengue shock syndrome (DSS), which is not preventable by any known drug. In the absence of a universally-accepted vaccine, a drug capable of inhibiting DENV multiplication is an urgent and unmet clinical need. Here we summarize inhibitory strategies by targeting either host biochemical pathways or virus-encoded proteins. A variety of approaches have been generated to design Directly-acting anti-virals or DAAs targeting different DENV proteins, with diverse success. Among them, DAAs targeting genome replicating viral enzymes have proven effective against many viruses including, Human Immuno-deficiency Virus and Hepatitis C Virus. DAAs may be derived either from existing compound libraries of novel molecules and plant secondary metabolites or devised through Computer-aided Drug design (CADD) methods. Here, we focus on compounds with reported DAA-activity against the DENV RNA-dependent RNA polymerase (RdRp), which replicate the viral RNA genome. The structure-activity relationship (SAR) and toxicity of the natural compounds, including secondary plant metabolites, have been discussed in detail. We have also tabulated novel compounds with known anti-RdRp activity. We concluded with a list of DAAs for which a co-crystal structure with RdRp is reported. Promising hit compounds are often discarded due to poor selectivity or unsuitable pharmacokinetics. We hope this review will provide a useful reference for further studies on the development of an anti-DENV drug.
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http://dx.doi.org/10.2174/1381612826666200523174753DOI Listing
February 2021

Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach.

J Biomol Struct Dyn 2020 May 20:1-19. Epub 2020 May 20.

Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster 3rd Milestone, Faridabad, Haryana, India.

The pandemic caused by novel coronavirus disease 2019 (COVID-19) infecting millions of populations worldwide and counting, has demanded quick and potential therapeutic strategies. Current approved drugs or molecules under clinical trials can be a good pool for repurposing through techniques to quickly identify promising drug candidates. The structural information of recently released crystal structures of main protease (M) in APO and complex with inhibitors, N3, and 13b molecules was utilized to explore the binding site architecture through Molecular dynamics (MD) simulations. The stable state of M was used to conduct extensive virtual screening of the aforementioned drug pool. Considering the recent success of HIV protease molecules, we also used anti-protease molecules for drug repurposing purposes. The identified top hits were further evaluated through MD simulations followed by the binding free energy calculations using MM-GBSA. Interestingly, in our screening, several promising drugs stand out as potential inhibitors of M. However, based on control (N3 and 13b), we have identified six potential molecules, Leupeptin Hemisulphate, Pepstatin A, Nelfinavir, Birinapant, Lypression and Octreotide which have shown the reasonably significant MM-GBSA score. Further insight shows that the molecules form stable interactions with residues, that are mainly conserved and can be targeted for structure- and pharmacophore-based designing. The pharmacokinetic annotations and therapeutic importance have suggested that these molecules possess drug-like properties and pave their way for studies.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1768151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7256355PMC
May 2020

Fluoresceinated Aminohexanol Tethered Inositol Hexakisphosphate: Studies on and and Docking with 2P1M Receptor.

ACS Omega 2020 Apr 13;5(16):9585-9597. Epub 2020 Apr 13.

Teri Deakin Nano Biotechnology Centre (TDNBC), Teri Gram, Gwal Pahari, Gurgaon- Faridabad Expressway, Gurugram, 122002 Haryana, India.

Inositol hexakisphosphate (InsP; phytic acid) is considered as the second messenger and plays a very important role in plants, animals, and human beings. It is the principal storage form of phosphorus in many plant tissues, especially in dry fruits, bran, and seeds. The resulting anion is a colorless species that plays a critical role in nutrition and is believed to cure many diseases. A fluoresceinated aminohexanol tethered inositol hexakisphosphate () had been synthesized earlier involving many complicated steps. We describe here a simple two-step synthesis of () and its characterization using different techniques such as matrix-assisted laser desorption ionization mass spectrometry, tandem mass spectrometry, and Fourier transform infrared, ultraviolet-visible, ultraviolet-fluorescence, H nuclear magnetic resonance (NMR), and two-dimensional NMR spectroscopies. The effect of () has been investigated in the model systems, and . Using Schrodinger software, computational studies on the binding of () with the protein 2P1M (Auxin-receptor TIR1-adaptor ASK1 complex) has revealed strong binding propensity with this compound. These studies on the fluoresceinated tethered phytic acid could have far reaching implications on its efficacy for human health and treatment of diseases (cancer/tumor and glioblastoma) and for understanding phosphorous recycling in the environment, especially for plant systems.
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http://dx.doi.org/10.1021/acsomega.0c00961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7191843PMC
April 2020

Common genetic variants associated with Parkinson's disease display widespread signature of epigenetic plasticity.

Sci Rep 2019 12 5;9(1):18464. Epub 2019 Dec 5.

Department of Neurology, University Clinic Bonn, Bonn, Germany.

Parkinson disease (PD) is characterized by a pivotal progressive loss of substantia nigra dopaminergic neurons and aggregation of α-synuclein protein encoded by the SNCA gene. Genome-wide association studies identified almost 100 sequence variants linked to PD in SNCA. However, the consequences of this genetic variability are rather unclear. Herein, our analysis on selective single nucleotide polymorphisms (SNPs) which are highly associated with the PD susceptibility revealed that several SNP sites attribute to the nucleosomes and overlay with bivalent regions poised to adopt either active or repressed chromatin states. We also identified large number of transcription factor (TF) binding sites associated with these variants. In addition, we located two docking sites in the intron-1 methylation prone region of SNCA which are required for the putative interactions with DNMT1. Taken together, our analysis reflects an additional layer of epigenomic contribution for the regulation of the SNCA gene in PD.
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http://dx.doi.org/10.1038/s41598-019-54865-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895091PMC
December 2019

A Common Tag Nucleotide Variant in Promoter Increases Risk for Hypertension via Enhanced Interactions With CREB (Cyclic AMP Response Element-Binding Protein) Transcription Factor.

Hypertension 2019 12 28;74(6):1448-1459. Epub 2019 Oct 28.

From the Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India (L.S., S.M., A.K., N.R.M.).

MMP (matrix metalloproteinase)-7-a potent extracellular matrix degrading enzyme-is emerging as a new regulator of cardiovascular diseases. However, potential contributions of genetic variations to hypertension remain unknown. In this study, we probed for the association of a tag single-nucleotide polymorphism in the promoter (-181A/G; rs11568818) with hypertension in an urban South Indian population (n=1501). The heterozygous AG genotype significantly increased risk for hypertension as compared with the wild-type AA genotype (odds ratio, 1.60 [95% CI, 1.25-2.06]; =2.4×10); AG genotype carriers also displayed significantly higher diastolic blood pressure and mean arterial pressure than wild-type AA individuals. The study was replicated in a North Indian population (n=949) (odds ratio, 1.52 [95% CI, 1.11-2.09]; =0.01). Transient transfection experiments using promoter-luciferase reporter constructs revealed that the variant -181G allele conferred greater promoter activity than the -181A allele. Computational prediction and structure-based conformational and molecular dynamics simulation studies suggested higher binding affinity for the CREB (cyclic AMP response element-binding protein) to the -181G promoter. In corroboration, overexpression/downregulation of CREB and chromatin immunoprecipitation experiments provided convincing evidence for stronger binding of CREB with the -181G promoter. The -181G promoter also displayed enhanced responses to hypoxia and epinephrine treatment. The higher promoter activity of -181G allele translated to increased MMP7 protein level, and - heterozygous individuals displayed elevated plasma MMP7 levels, which positively correlated with blood pressure. In conclusion, the A-181G promoter polymorphism increased MMP7 expression under pathophysiological conditions (hypoxic stress and catecholamine excess) via increased interactions with CREB and enhanced the risk for hypertension in its carriers.
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http://dx.doi.org/10.1161/HYPERTENSIONAHA.119.12960DOI Listing
December 2019

Combined treatment with cisplatin and the tankyrase inhibitor XAV-939 increases cytotoxicity, abrogates cancer-stem-like cell phenotype and increases chemosensitivity of head-and-neck squamous-cell carcinoma cells.

Mutat Res 2019 10 17;846:503084. Epub 2019 Aug 17.

Molecular Stress and Stem Cell Biology Group, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, Odisha 751024, India. Electronic address:

Cancer stem-like cells (CSCs) were reported to be linked with tumorigenesis, metastasis and resistant to chemo and radiotherapy in head and neck squamous cell carcinoma (HNSCC). In this study we investigated the role of CSCs in chemoresistance and abrogation of CSC mediated chemoresistance by combinatorial treatment with cisplatin and small molecule tankyrase inhibitor XAV-939. Two cisplatin-resistant HNSCC cells were generated by stepwise dose incremental strategy. We evaluated the chemoresistance, sphere forming capacity, extent of DNA damage and repair capacity in parental and cisplatin-resistant HNSCC cells. Furthermore, the abrogation of CSC mediated chemoresistance was evaluated in HNSCC cells with XAV-939 alone and in combination with cisplatin. It was observed that cisplatin-resistant HNSCC cell lines exhibited increase in chemoresistance, CSC phenotype and increased DNA repair capacity. We observed that combination of cisplatin and XAV-939 acts synergistically to abrogate chemoresistance by increasing DNA damage. Molecular docking study also revealed similar binding region that could contribute towards synergy predictions between cisplatin and XAV939. In conclusion, this study elucidated that combination of cisplatin and XAV-939 exerted cytotoxic and genotoxic effect to abrogate CSC mediated chemoresistance in HNSCC in synergistic manner.
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http://dx.doi.org/10.1016/j.mrgentox.2019.503084DOI Listing
October 2019

Conformational Characterization of Linker Revealed the Mechanism of Cavity Formation by 227G in BVDV RDRP.

J Phys Chem B 2019 07 11;123(29):6150-6160. Epub 2019 Jul 11.

Drug Discovery Research Center (DDRC) , Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster , 3rd Milestone, Faridabad-Gurgaon Expressway , Faridabad , Haryana 121001 , India.

RNA-dependent RNA polymerase (RdRp) is a relevant antiviral drug target. We investigated a potent benzimidazole inhibitor (227G; IC = 0.002 μM) against bovine viral diarrhea virus (BVDV) RdRp; however, its inhibition action was completely impaired in the presence of a resistant mutation, I261M. The binding of 227G in mutant RdRp affected the binding site loop conformations (especially Linker) that increased the volume of the binding site. It was also observed that the innate Linker's flexibility was retained, which was otherwise completely frozen in the wild-type complex. The functional role of Linker was hypothesized that it is a multidocking site for RNA template, inhibitors, and the other proteins involved in replication complex formation. The binding phenomenon requires significant molecular flexibility and the large-amplitude conformational dynamics of Linker, which is currently unknown. We observed a bidirectional "hinge"-like motion of Linker from crystal position, indicating its pronounced flexible behavior. This study underscores the importance of Linker's flexibility in the functionality of BVDV RdRp and proposes the template entrance site for selective anti-BVDV drug discovery.
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http://dx.doi.org/10.1021/acs.jpcb.9b01859DOI Listing
July 2019

Insights into structural dynamics of allosteric binding sites in HCV RNA-dependent RNA polymerase.

J Biomol Struct Dyn 2020 Apr 16;38(6):1612-1625. Epub 2019 May 16.

Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, India.

Inhibition of the viral RNA-dependent RNA polymerase (RdRp) to resolve chronic infection is a useful therapeutic strategy against Hepatitis C virus (HCV). Non-nucleoside inhibitors (NNIs) of RdRp are small molecules that bind tightly with allosteric sites on the enzyme, thereby inhibiting polymerase activity. A large number of crystal structures (176) were studied to establish the structure-activity relationship along with the mechanism of inhibition and resistance between HCV RdRp and NNIs at different allosteric sites. The structure and the associated dynamics are the blueprint to understand the function of the protein. We have implemented the ligand-based pharmacophore and molecular dynamic simulations to extract the possible local and global characteristics of RdRp upon NNI binding and the structural-dynamical features possessed by the known actives. Our results suggest that the NNI binding induces significant fluctuations at the atomic level which are critical for enzymatic activity, with minimal global structural alterations. Residue-wise mapping of interactions of NNIs at different sites exhibited some conserved interaction patterns of key amino acids and water molecules. Here, the structural insights are explored to understand the correlation between the dynamics of protein's subdomains and function at the molecular level, useful for genotype-specific rational designing of NNIs.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2019.1614480DOI Listing
April 2020

Molecular dynamics simulation reveals the possible druggable of USP7.

Oncotarget 2018 Sep 28;9(76):34289-34305. Epub 2018 Sep 28.

Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India.

The plasticity in Ubiquitin Specific Proteases (USP7) inducing conformational changes at important areas has highlighted an intricate mechanism, by which USP7 is regulated. Given the importance of USP7 in oncogenic pathways and immune-oncology, identification of USP7 inhibitors has attracted considerable interest. Despite substantial efforts, the discovery of deubiquitinases (DUBs) inhibitors, knowledge of their binding site and understanding the possible mechanism of action has proven particularly challenging. We disclose the most likely binding site of P5091 (a potent USP7 inhibitor), which reveal a cryptic allosteric site through extensive computational studies in an inhibitor dependent and independent manner. Overall, these findings demonstrate the tractability and druggability of USP7. Through a series of molecular dynamics simulations and detailed quantitative analysis, a dynamically stable allosteric binding site near catalytic center of the inactive state of USP7 (site partially absent in active state), along with two newly identified sites have been revealed, which opens the avenue for rational structure-guided inhibitor designing in USP7 specific-manner.
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http://dx.doi.org/10.18632/oncotarget.26136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6188144PMC
September 2018

Coumarin derivatives as promising xanthine oxidase inhibitors.

Int J Biol Macromol 2018 Dec 3;120(Pt A):1286-1293. Epub 2018 Sep 3.

Department of Mechanical, Chemical and Materials Engineering, University of Cagliari, via Marengo 2, 09123 Cagliari, Italy. Electronic address:

Xanthine oxidase (XO) is an interesting target for the synergic treatment of several diseases. Coumarin scaffold plays an important role in the design of efficient and potent inhibitors. In the current work, twenty 3-arylcoumarins and eight 3-heteroarylcoumarins were evaluated for their ability to inhibit XO. Among all the candidates, 5,7-dihydroxy-3-(3'-hydroxyphenyl)coumarin (compound 20) proved to be the best inhibitor with an IC of 2.13 μM, being 7-fold better than the reference compound, allopurinol (IC = 14.75 μM). To deeply understand the potential of this compound, the inhibition mode was also evaluated. Compound 20 showed an uncompetitive profile of inhibition. Molecular docking studies were carried out to analyze the interaction of compound 20 with the studied enzyme. The binding mode involving residues different from the catalytic site of the binding pocket, is compatible to the observed uncompetitive inhibition. Compound 20 was not cytotoxic at its IC value, as demonstrated by the viability of 99.1% in 3 T3 cells. Furthermore, pharmacokinetics and physicochemical properties were also calculated, which corroborated with the potential of the studied compounds as promising XO inhibitors.
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http://dx.doi.org/10.1016/j.ijbiomac.2018.09.001DOI Listing
December 2018

Potent Inhibition of Hepatitis E Virus Release by a Cyclic Peptide Inhibitor of the Interaction between Viral Open Reading Frame 3 Protein and Host Tumor Susceptibility Gene 101.

J Virol 2018 10 26;92(20). Epub 2018 Sep 26.

Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India

Hepatitis E virus (HEV) generally causes self-limiting acute viral hepatitis in normal individuals. It causes a more severe disease in immunocompromised persons and pregnant women. Due to the lack of an efficient cell culture system or animal model, the life cycle of the virus is understudied, few antiviral targets are known, and very few antiviral candidates against HEV infection have been identified. Inhibition of virus release is one possible antiviral development strategy, which limits the spread of the virus. Previous studies have demonstrated the essential role of the interaction between the PSAP motif of the viral open reading frame 3 protein (ORF3-PSAP) and the UEV domain of the host tumor susceptibility gene 101 (TSG101) protein (UEV-TSG101) in mediating the release of genotype 3 HEV. Cyclic peptide (CP) inhibitors of the interaction between the human immunodeficiency virus (HIV) gag-PTAP motif and UEV-TSG101 are known to block the release of HIV. Using a molecular dynamic simulation, we observed that both gag-PTAP and ORF3-PSAP motifs bind to the same site in UEV-TSG101 by hydrogen bonding. HIV-released inhibitory CPs also displayed binding to the same site in UEV-TSG101, indicating that they may compete with ORF3-PSAP or gag-PTAP for binding to UEV-TSG101. Two independent assays confirmed the ability of a cyclic peptide (CP11) to inhibit the ORF3-TSG101 interaction. CP11 treatment also reduced the release of both genotype 1 and genotype 3 HEV by approximately 90%, with a 50% inhibitory concentration (IC) of 2 μM. Thus, CP11 appears to be an attractive candidate for further validation of its anti-HEV properties. There is no specific therapy against hepatitis E virus (HEV)-induced hepatic and nonhepatic health problems. Prevention of the release of the progeny viruses from infected cells is an attractive strategy to limit the spread of the virus. Interactions between the viral open reading frame 3 and the host tumor susceptibility gene 101 proteins have been shown to be essential for the release of genotype 3 HEV from infected cells. In this study, we have identified a cyclic peptide inhibitor of the above-mentioned interaction and demonstrate the efficiency of the inhibitor in preventing virus release from infected cells. Thus, our findings uncover the possibility of developing a specific antiviral agent against HEV by blocking its release from infected cells.
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http://dx.doi.org/10.1128/JVI.00684-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158408PMC
October 2018

Scavenger receptor B type 1: expression, molecular regulation, and cholesterol transport function.

J Lipid Res 2018 07 2;59(7):1114-1131. Epub 2018 May 2.

Geriatric Research, Education, and Clinical Research Center (GRECC), Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304 and Division of Endocrinology, Gerontology, and Metabolism, Stanford University School of Medicine, Stanford, CA 94305

Cholesterol is required for maintenance of plasma membrane fluidity and integrity and for many cellular functions. Cellular cholesterol can be obtained from lipoproteins in a selective pathway of HDL-cholesteryl ester (CE) uptake without parallel apolipoprotein uptake. Scavenger receptor B type 1 (SR-B1) is a cell surface HDL receptor that mediates HDL-CE uptake. It is most abundantly expressed in liver, where it provides cholesterol for bile acid synthesis, and in steroidogenic tissues, where it delivers cholesterol needed for storage or steroidogenesis in rodents. SR-B1 transcription is regulated by trophic hormones in the adrenal gland, ovary, and testis; in the liver and elsewhere, SR-B1 is subject to posttranscriptional and posttranslational regulation. SR-B1 operates in several metabolic processes and contributes to pathogenesis of atherosclerosis, inflammation, hepatitis C virus infection, and other conditions. Here, we summarize characteristics of the selective uptake pathway and involvement of microvillar channels as facilitators of selective HDL-CE uptake. We also present the potential mechanisms of SR-B1-mediated selective cholesterol transport; the transcriptional, posttranscriptional, and posttranslational regulation of SR-B1; and the impact of gene variants on expression and function of human SR-B1. A better understanding of this unique pathway and SR-B1's role may yield improved therapies for a wide variety of conditions.
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http://dx.doi.org/10.1194/jlr.R083121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027903PMC
July 2018

Computational modeling suggests impaired interactions between NKX2.5 and GATA4 in individuals carrying a novel pathogenic D16N NKX2.5 mutation.

Oncotarget 2018 Mar 9;9(17):13713-13732. Epub 2018 Feb 9.

Division of Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.

, a homeobox containing gene, plays an important role in embryonic heart development and associated mutations are linked with various cardiac abnormalities. We sequenced the gene in 100 congenital heart disease (CHD) patients and 200 controls. Our analysis revealed a total of 7 mutations, 3 in intronic region, 3 in coding region and 1 in 3' UTR. Of the above mutations, one mutation was found to be associated with tetralogy of fallot (TOF) and two (rs2277923 and a novel mutation, D16N) were strongly associated with VSD. A novel missense mutation, D16N (p-value =0.009744), located in the tinman (TN) region and associated with ventricular septal defect (VSD), is the most significant findings of this study. Computational analysis revealed that D16N mutation is pathogenic in nature. Through the molecular modeling, docking and molecular dynamics simulation studies, we have identified the location of mutant D16N in and its interaction map with other partners at the atomic level. We found NKX2.5-GATA4 complex is stable, however, in case of mutant we observed significant conformational changes and loss of key polar interactions, which might be a cause of the pathogenic behavior. This study underscores the structural basis of D16N pathogenic mutation in the regulation of and how this mutation renders the structural-functional divergence that possibly leading towards the diseased state.
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http://dx.doi.org/10.18632/oncotarget.24459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862610PMC
March 2018

Presence of a consensus DNA motif at nearby DNA sequence of the mutation susceptible CG nucleotides.

Gene 2018 Jan 3;639:85-95. Epub 2017 Oct 3.

Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India. Electronic address:

Complexity in tissues affected by cancer arises from somatic mutations and epigenetic modifications in the genome. The mutation susceptible hotspots present within the genome indicate a non-random nature and/or a position specific selection of mutation. An association exists between the occurrence of mutations and epigenetic DNA methylation. This study is primarily aimed at determining mutation status, and identifying a signature for predicting mutation prone zones of tumor suppressor (TS) genes. Nearby sequences from the top five positions having a higher mutation frequency in each gene of 42 TS genes were selected from a cosmic database and were considered as mutation prone zones. The conserved motifs present in the mutation prone DNA fragments were identified. Molecular docking studies were done to determine putative interactions between the identified conserved motifs and enzyme methyltransferase DNMT1. Collective analysis of 42 TS genes found GC as the most commonly replaced and AT as the most commonly formed residues after mutation. Analysis of the top 5 mutated positions of each gene (210 DNA segments for 42 TS genes) identified that CG nucleotides of the amino acid codons (e.g., Arginine) are most susceptible to mutation, and found a consensus DNA "T/AGC/GAGGA/TG" sequence present in these mutation prone DNA segments. Similar to TS genes, analysis of 54 oncogenes not only found CG nucleotides of the amino acid Arg as the most susceptible to mutation, but also identified the presence of similar consensus DNA motifs in the mutation prone DNA fragments (270 DNA segments for 54 oncogenes) of oncogenes. Docking studies depicted that, upon binding of DNMT1 methylates to this consensus DNA motif (C residues of CpG islands), mutation was likely to occur. Thus, this study proposes that DNMT1 mediated methylation in chromosomal DNA may decrease if a foreign DNA segment containing this consensus sequence along with CG nucleotides is exogenously introduced to dividing cancer cells.
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http://dx.doi.org/10.1016/j.gene.2017.10.001DOI Listing
January 2018

A novel STK1-targeted small-molecule as an "antibiotic resistance breaker" against multidrug-resistant Staphylococcus aureus.

Sci Rep 2017 07 11;7(1):5067. Epub 2017 Jul 11.

Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, USA.

Ser/Thr protein kinase (STK1) plays a critical role in cell wall biosynthesis of and drug resistance in methicillin-resistant Staphylococcus aureus (MRSA). MRSA strains lacking STK1 become susceptible to failing cephalosporins, such as Ceftriaxone and Cefotaxime. STK1, despite being nonessential protein for MRSA survival, it can serve as an important therapeutic agent for combination therapy. Here, we report a novel small molecule quinazoline compound, Inh2-B1, which specifically inhibits STK1 activity by directly binding to its ATP-binding catalytic domain. Functional analyses encompassing in vitro growth inhibition of MRSA, and in vivo protection studies in mice against the lethal MRSA challenge indicated that at high concentration neither Inh2-B1 nor Ceftriaxone or Cefotaxime alone was able to inhibit the growth of bacteria or protect the challenged mice. However, the growth of MRSA was inhibited, and a significant protection in mice against the bacterial challenge was observed at a micromolar concentration of Ceftriaxone or Cefotaxime in the presence of Inh2-B1. Cell-dependent minimal to no toxicity of Inh2-B1, and its abilities to down-regulate cell wall hydrolase genes and disrupt the biofilm formation of MRSA clearly indicated that Inh2-B1 serves as a therapeutically important "antibiotic-resistance-breaker," which enhances the bactericidal activity of Ceftriaxone/Cefotaxime against highly pathogenic MRSA infection.
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http://dx.doi.org/10.1038/s41598-017-05314-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5505960PMC
July 2017

Protein kinase C-mediated sodium glucose transporter 1 activation in precondition-induced cardioprotection.

Drug Des Devel Ther 2016 14;10:2929-2938. Epub 2016 Sep 14.

Division of Medicinal Chemistry and Pharmacology, Indian Institute of Chemical Technology, Hyderabad, India; Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India.

The concept of cardioprotection through preconditioning against ischemia-reperfusion (I/R) injury is well known and established. However, among different proposed mechanisms regarding the concept of ischemic preconditioning, protein kinase C (PKC)-mediated cardioprotection through ischemic preconditioning plays a key role in myocardial I/R injury. Thus, this study was designed to find the relationship between PKC and sodium glucose transporter 1 (SGLT1) in preconditioning-induced cardioprotection, which is ill reported till now. By applying a multifaceted approach, we demonstrated that PKC activates SGLT1, which curbed oxidative stress and apoptosis against I/R injury. PKC activation enhances cardiac glucose uptake through SGLT1 and seems essential in preventing I/R-induced cardiac injury, indicating a possible cross-talk between PKC and SGLT1.
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http://dx.doi.org/10.2147/DDDT.S105482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5028101PMC
April 2017

Structure-Activity Relationship Study of Hydroxycoumarins and Mushroom Tyrosinase.

J Agric Food Chem 2015 Aug 11;63(32):7236-44. Epub 2015 Aug 11.

§Dipartimento di Scienze Biomediche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato, Cagliari, Italy.

The structure-activity relationships of four hydroxycoumarins, two with the hydroxyl group on the aromatic ring of the molecule and two with the hydroxyl group replacing hydrogen of the pyrone ring, and their interactions with mushroom tyrosinase were studied. These compounds displayed different behaviors upon action of the enzyme. The two compounds, ar-hydroxylated 6-hydroxycoumarin and 7-hydroxycoumarin, were both weak substrates of the enzyme. Interestingly, in both cases, the product of the catalysis was the 6,7-hydroxycoumarin, although 5,6- and 7,8-isomers could also theoretically be formed. Additionally, both were able to reduce the formation of dopachrome when tyrosinase acted on its typical substrate, L-tyrosine. Although none of the compounds that contained a hydroxyl group on the pyrone ring were substrates of tyrosinase, the 3-hydroxycoumarin was a potent inhibitor of the enzyme, and the 4-hydroxycoumarin was not an inhibitor. These results were compared with those obtained by in silico molecular docking predictions to obtain potentially useful information for the synthesis of new coumarin-based inhibitors that resemble the structure of the 3-hydroxycoumarin.
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http://dx.doi.org/10.1021/acs.jafc.5b02636DOI Listing
August 2015

A molecular analysis provides novel insights into androgen receptor signalling in breast cancer.

PLoS One 2015 17;10(3):e0120622. Epub 2015 Mar 17.

National Institute of Pathology, ICMR, Safdarjang Hospital, New Delhi, India.

Background: Androgen Receptor (AR) is an essential transcription factor for the development of secondary sex characteristics, spermatogenesis and carcinogenesis. Recently AR has been implicated in the development and progression of breast and prostate cancers. Although some of the functions of the AR are known but the mechanistic details of these divergent processes are still not clear. Therefore understanding the regulatory mechanisms of the functioning of the AR in ER-/AR+ breast cancer will provide many novel targets for the purpose of therapeutic intervention.

Methods/results: Using bioinformatics tools, we have identified 75 AR targets having prominent roles in cell cycle, apoptosis and metabolism. Herein, we validated 10 genes as AR targets by studying the regulation of these genes in MDA-MB-453 cell line on stimulation by androgens like 5α-dihydrotestosterone (DHT), using RT-qPCR and ChIP assay. It was observed that all the identified genes involved in cell cycle except MAD1L1 were found to be up regulated whereas expression of apoptosis related genes was decreased in response to DHT treatment. We performed an exhaustive, rigid-body docking between individual ARE and DNA binding domain (DBD) of the AR protein and it was found that novel residues K567, K588, K591 and R592 are involved in the process of DNA binding. To verify these specific DNA-protein interactions electrostatic energy term calculations for each residue was determined using the linearized Poisson-Boltzmann equation. Our experimental data showed that treatment of breast cancer cells with DHT promotes cell proliferation and decreases apoptosis. It was observed that bicalutamide treatment was able to reverse the effect of DHT.

Conclusion: Taken together, our results provide new insights into the mechanism by which AR promotes breast cancer progression. Moreover our work proposes to use bicalutamide along with taxanes as novel therapy for the treatment of TNBCs, which are positive for downstream AR signalling.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120622PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364071PMC
February 2016