Dibyendu Dana - Academia.edu (original) (raw)

Papers by Dibyendu Dana

Bioorganic & Medicinal Chemistry Letters, May 1, 2023

An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Oncogenesis, 2013

Centrosomal kinase Nek2 is overexpressed in different cancers, yet how it contributes toward tumo... more Centrosomal kinase Nek2 is overexpressed in different cancers, yet how it contributes toward tumorigenesis remains poorly understood. dNek2 overexpression in a Drosophila melanogaster model led to upregulation of Drosophila Wnt ortholog wingless (Wg), and alteration of cell migration markers-Rho1, Rac1 and E-cadherin (Ecad)-resulting in changes in cell shape and tissue morphogenesis. dNek2 overexpression cooperated with receptor tyrosine kinase and mitogen-activated protein kinase signaling to upregulate activated Akt, Diap1, Mmp1 and Wg protein to promote local invasion, distant seeding and metastasis. In tumor cell injection assays, dNek2 cooperated with Ras and Src signaling to promote aggressive colonization of tumors into different adult fly tissues. Inhibition of the PI3K pathway suppressed the cooperation of dNek2 with other growth pathways. Consistent with our fly studies, overexpression of human Nek2 in A549 lung adenocarcinoma and HEK293T cells led to activation of the Akt...

Molecules

Cell cycle kinases represent an important component of the cell machinery that controls signal tr... more Cell cycle kinases represent an important component of the cell machinery that controls signal transduction involved in cell proliferation, growth, and differentiation. Nek2 is a mitotic Ser/Thr kinase that localizes predominantly to centrosomes and kinetochores and orchestrates centrosome disjunction and faithful chromosomal segregation. Its activity is tightly regulated during the cell cycle with the help of other kinases and phosphatases and via proteasomal degradation. Increased levels of Nek2 kinase can promote centrosome amplification (CA), mitotic defects, chromosome instability (CIN), tumor growth, and cancer metastasis. While it remains a highly attractive target for the development of anti-cancer therapeutics, several new roles of the Nek2 enzyme have recently emerged: these include drug resistance, bone, ciliopathies, immune and kidney diseases, and parasitic diseases such as malaria. Therefore, Nek2 is at the interface of multiple cellular processes and can influence num...

Molecules

Human cathepsin L belongs to the cathepsin family of proteolytic enzymes with primarily an endope... more Human cathepsin L belongs to the cathepsin family of proteolytic enzymes with primarily an endopeptidase activity. Although its primary functions were originally thought to be only of a housekeeping enzyme that degraded intracellular and endocytosed proteins in lysosome, numerous recent studies suggest that it plays many critical and specific roles in diverse cellular settings. Not surprisingly, the dysregulated function of cathepsin L has manifested itself in several human diseases, making it an attractive target for drug development. Unfortunately, several redundant and isoform-specific functions have recently emerged, adding complexities to the drug discovery process. To address this, a series of chemical biology tools have been developed that helped define cathepsin L biology with exquisite precision in specific cellular contexts. This review elaborates on the recently developed small molecule inhibitors and probes of human cathepsin L, outlining their mechanisms of action, and ...

Molecules (Basel, Switzerland), Jan 18, 2018

The practice of medicine is ever evolving. Diagnosing disease, which is often the first step in a... more The practice of medicine is ever evolving. Diagnosing disease, which is often the first step in a cure, has seen a sea change from the discerning hands of the neighborhood physician to the use of sophisticated machines to use of information gleaned from biomarkers obtained by the most minimally invasive of means. The last 100 or so years have borne witness to the enormous success story of allopathy, a practice that found favor over earlier practices of medical purgatory and homeopathy. Nevertheless, failures of this approach coupled with the omics and bioinformatics revolution spurred precision medicine, a platform wherein the molecular profile of an individual patient drives the selection of therapy. Indeed, precision medicine-based therapies that first found their place in oncology are rapidly finding uses in autoimmune, renal and other diseases. More recently a new renaissance that is shaping everyday life is making its way into healthcare. Drug discovery and medicine that starte...

PloS one, 2018

Although cirrhosis is a key risk factor for the development of hepatocellular carcinoma (HCC), mo... more Although cirrhosis is a key risk factor for the development of hepatocellular carcinoma (HCC), mounting evidence indicates that in a subset of patients presenting with non-alcoholic steatohepatitis (NASH) HCC manifests in the absence of cirrhosis. Given the sheer size of the ongoing non-alcoholic fatty liver disease (NAFLD) epidemic and the dismal prognosis associated with late-stage primary liver cancer there is an urgent need for HCC surveillance in the NASH population. Using serum levels of HCC biomarkers as vectors and biopsy-proven HCC or no HCC as outputs / binary classifier, a supervised learning campaign was undertaken to develop a minimally invasive technique for making a diagnosis of HCC in a clinically relevant model of NASH. Adult mice randomized to control diet or a fast food diet (FFD) were followed for up to 14 mo and serum level of a panel of HCC-relevant biomarkers was compared with liver biopsies at 3 and 14 mo. Both NAFLD Activity Score (NAS) and hepatic hydroxypr...

ABSTRACT The importance of a carefully regulated protein dephosphorylation event in cellular sign... more ABSTRACT The importance of a carefully regulated protein dephosphorylation event in cellular signaling by protein tyrosine phosphatases (PTPs) is well recognized. Indeed an anomalous level of PTP activities has been associated with a variety of aberrant cellular signaling and human diseases. As a result of this, potent and selective inhibitory agents of PTP enzymes are sought after by research communities across the globe. While there is considerable interest among academic researchers and pharmaceutical industries to develop non-covalent and reversible inhibitory agents of PTPs, the development of covalent inhibitory agents is plagued with presumption that they are not suitable candidates for drug discovery. This outcome is primarily due to the concern that such molecules could be immunogenic and serve as cellular toxic agents. The current success of covalent therapeutic agents in clinics, however, does not support this notion, and indicates that there is a need to reconsider this hypothesis with regard to the PTP-related drug discovery efforts. This review starts with a discussion of PTPs in general and provides an overview of reported covalent PTP inhibitors, highlighting their modes of interaction with enzymes. Finally, a brief perspective about the potential opportunities for the advancement of covalent inhibitors of PTPs in targeted PTP therapeutics is provided.

Human vaccines & immunotherapeutics, Jan 9, 2015

HLA-DR is the most commonly expressed and likely the most medically important human MHC class II,... more HLA-DR is the most commonly expressed and likely the most medically important human MHC class II, antigen presenting protein. In a normal immune response, HLA-DR binds to antigenic peptide and the HLA-DR/peptide complex binds to a T-cell receptor, thus contributing to T-cell activation and stimulation of an immune response against the antigen. When foreign antigen is not present, HLA-DR binds endogenous peptide which, under normal conditions does not stimulate an immune response. In most cases, the human peptide is CLIP, but a certain percentage of HLA-DR molecules will be present at the cell surface with other human peptides. We have recently shown that cell surface, CLIP/HLA-DR ratios are a measure of peptide heterogeneity, and in particular, changes in CLIP/HLA-DR ratios represent changes in the occupancy of HLA-DR by other, endogenous peptides. For example, treatment of cells with the HDAC inhibitor, Entinostat, leads to an upregulation of Cathepsin L1 and replacement of Catheps...

The importance of a carefully regulated protein dephosphorylation event in cellular signaling by ... more The importance of a carefully regulated protein dephosphorylation event in cellular signaling by protein tyrosine phosphatases (PTPs) is well recognized. Indeed an anomalous level of PTP activities has been associated with a variety of aberrant cellular signaling and human diseases. As a result of this, potent and selective inhibitory agents of PTP enzymes are sought after by research communities across the globe. While there is considerable interest among academic researchers and pharmaceutical industries to develop non-covalent and reversible inhibitory agents of PTPs, the development of covalent inhibitory agents is plagued with presumption that they are not suitable candidates for drug discovery. This outcome is primarily due to the concern that such molecules could be immunogenic and serve as cellular toxic agents. The current success of covalent therapeutic agents in clinics, however, does not support this notion, and indicates that there is a need to reconsider this hypothesi...

Rapid Communications in Mass Spectrometry, 2014

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry combined with isotope label... more Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry combined with isotope labeling methods are effective for protein and peptide quantification, but limited in their multiplexing capacity, cost-effectiveness and dynamic range. This study investigates MALDI-MS-based quantification of peptide phosphorylation without labeling, and aims to overcome the shot-to-shot variability of MALDI using a mathematical transformation and extended data acquisition times. A linear relationship between the reciprocal of phosphopeptide mole fraction and the reciprocal of phosphorylated-to-unphosphorylated signal ratio is derived, and evaluated experimentally using three separate phosphopeptide systems containing phosphorylated serine, threonine and tyrosine residues: mixtures of phosphopeptide and its des-phospho-analog with known stoichiometry measured by vacuum MALDI-linear ion trap mass spectrometry and fit to the linear model. The model is validated for quantifying in vitro phosphorylation assays with inhibition studies on Cdk2/cyclinA. Dynamic range of picomoles to femtomoles, good accuracy (deviations of 1.5-3.0% from expected values) and reproducibility (relative standard deviation (RSD) = 4.3-6.3%) are achieved. Inhibition of cyclin-dependent kinase phosphorylation by the classical inhibitors olomoucine and r-roscovitine was evaluated and IC50 values found to be in agreement with reported literature values. These results, achieved with single-point calibration, without isotope or chromatography, compare favorably to those arrived at using isotope dilution (p > 0.5 for accuracy). The mathematical relationship derived here can be applied to a method that we term Double Reciprocal Isotope-free Phosphopeptide Quantification (DRIP-Q), as a strategy for quantification of in vitro phosphorylation assays, the first MALDI-based, isotope- and calibration curve-free method of its type. These results also pave the way for further systematic studies investigating the effect of peptide composition and experimental conditions on quantitative, label-free MALDI.

Chemical Communications, 2014

A hybrid-design approach is undertaken to develop a highly potent and selective inhibitor of huma... more A hybrid-design approach is undertaken to develop a highly potent and selective inhibitor of human cathepsin L. Studies involving human breast carcinoma MDA-MB-231 cells establish that this inhibitor can successfully block intracellular cathepsin L activity, and retard the cell-migratory potential of these highly metastatic cells.

Tetrahedron Letters, 2013

ABSTRACT A reaction of diethyl phenylsulfonylmethylphosphonate with 2-arylacetaldehydes in the pr... more ABSTRACT A reaction of diethyl phenylsulfonylmethylphosphonate with 2-arylacetaldehydes in the presence of a catalytic excess of sodium hydride (1.1 equiv) yields allyl phenyl sulfones in excellent yield under mild reaction conditions. In contrast, when less than 1 equiv of sodium hydride (0.90 equiv) is used, the corresponding vinyl phenyl sulfones are obtained exclusively. The vinyl phenyl sulfones can be completely converted to allyl phenyl sulfones with only 0.2 equiv of NaH, suggesting that the second hydride involvement in the above transformation is catalytic. The regioselective control observed in these reactions offers a general method for synthesizing novel vinyl and allyl phenyl sulfones in one step from the same starting materials. The regioselectivity and stereoselectivity of this reaction, however, are not maintained when 2-alkylacetaldehydes are reacted with diethyl phenylsulfonylmethylphosphonate under identical reaction conditions. Our results indicate that an extended conjugation of the double bond in allylsulfones formed from the reaction of 2-arylacetaldehydes is required for the observed regio- and stereoselectivity. (c) 2013 Elsevier Ltd. All rights reserved.

Chemical Biology & Drug Design, 2012

A structure-based design approach has been applied to develop 2-(arylsulfonyl)oxiranes as potenti... more A structure-based design approach has been applied to develop 2-(arylsulfonyl)oxiranes as potential covalent inhibitors of protein tyrosine phosphatases. A detailed kinetic analysis of inactivation by these covalent inhibitors reveals that this class of compounds inhibits a panel of protein tyrosine phosphatases in a time- and dose-dependent manner, consistent with the covalent modification of the enzyme active site. An inactivation experiment in the presence of sodium arsenate, a known competitive inhibitor of protein tyrosine phosphatase, indicated that these inhibitors were active site bound. This finding is consistent with the mass spectrometric analysis of the covalently modified protein tyrosine phosphatase enzyme. Additional experiments indicated that these compounds remained inert toward other classes of arylphosphate-hydrolyzing enzymes, and alkaline and acid phosphatases. Cell-based experiments with human A549 lung cancer cell lines indicated that 2-(phenylsulfonyl)oxirane (1) caused an increase in intracellular pTyr levels in a dose-dependent manner thereby suggesting its cell-permeable nature. Taken together, the newly identified 2-(arylsulfonyl)oxiranyl moiety could serve as a novel chemotype for the development of activity-based probes and therapeutic agents against protein tyrosine phosphatase superfamily of enzymes.

Bioorganic & Medicinal Chemistry, 2013

Cysteine cathepsins are an important class of enzymes that coordinate a variety of important cell... more Cysteine cathepsins are an important class of enzymes that coordinate a variety of important cellular processes, and are implicated in various types of human diseases. However, small molecule inhibitors that are cell-permeable and non-peptidyl in nature are scarcely available. Herein the synthesis and development of sulfonyloxiranes as covalent inhibitors of cysteine cathepsins are reported. From a library of compounds, compound 5 is identified as a selective inhibitor of cysteine cathepsins. Live cell imaging and immunocytochemistry of metastatic human breast carcinoma MDA-MB-231 cells document the efficacy of compound 5 in inhibiting cysteine cathepsin activity in living cells. A cell-motility assay demonstrates that compound 5 is effective in mitigating the cell-migratory potential of highly metastatic breast carcinoma MDA-MB-231 cells.

Bioorganic & Medicinal Chemistry, 2013

Hepatitis C virus (HCV) NS5B polymerase is a key target for anti-HCV therapeutics development. He... more Hepatitis C virus (HCV) NS5B polymerase is a key target for anti-HCV therapeutics development. Herein, we report the synthesis and in vitro evaluation of anti-NS5B polymerase activity of a molecular hybrid of our previously reported lead compounds 1 (IC50=7.7 μM) and 2 (IC50=10.6 μM) as represented by hybrid compound 27 (IC50=6.7 μM). We have explored the optimal substituents on the terminal phenyl ring of the 3-phenoxybenzylidene moiety in 27, by generating a set of six analogs. This resulted in the identification of compound 34 with an IC50 of 2.6 μM. To probe the role of stereochemistry towards the observed biological activity, we synthesized and evaluated the D-isomers 41 (IC50=19.3 μM) and 45 (IC50=5.4 μM) as enantiomers of the l-isomers 27 and 34, respectively. The binding site of compounds 32 and 34 was mapped to palm pocket-I (PP-I) of NS5B. The docking models of 34 and 45 within the PP-I of NS5B were investigated to envisage the molecular mechanism of inhibition.

Bioorganic & Medicinal Chemistry Letters, May 1, 2023

An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Oncogenesis, 2013

Centrosomal kinase Nek2 is overexpressed in different cancers, yet how it contributes toward tumo... more Centrosomal kinase Nek2 is overexpressed in different cancers, yet how it contributes toward tumorigenesis remains poorly understood. dNek2 overexpression in a Drosophila melanogaster model led to upregulation of Drosophila Wnt ortholog wingless (Wg), and alteration of cell migration markers-Rho1, Rac1 and E-cadherin (Ecad)-resulting in changes in cell shape and tissue morphogenesis. dNek2 overexpression cooperated with receptor tyrosine kinase and mitogen-activated protein kinase signaling to upregulate activated Akt, Diap1, Mmp1 and Wg protein to promote local invasion, distant seeding and metastasis. In tumor cell injection assays, dNek2 cooperated with Ras and Src signaling to promote aggressive colonization of tumors into different adult fly tissues. Inhibition of the PI3K pathway suppressed the cooperation of dNek2 with other growth pathways. Consistent with our fly studies, overexpression of human Nek2 in A549 lung adenocarcinoma and HEK293T cells led to activation of the Akt...

Molecules

Cell cycle kinases represent an important component of the cell machinery that controls signal tr... more Cell cycle kinases represent an important component of the cell machinery that controls signal transduction involved in cell proliferation, growth, and differentiation. Nek2 is a mitotic Ser/Thr kinase that localizes predominantly to centrosomes and kinetochores and orchestrates centrosome disjunction and faithful chromosomal segregation. Its activity is tightly regulated during the cell cycle with the help of other kinases and phosphatases and via proteasomal degradation. Increased levels of Nek2 kinase can promote centrosome amplification (CA), mitotic defects, chromosome instability (CIN), tumor growth, and cancer metastasis. While it remains a highly attractive target for the development of anti-cancer therapeutics, several new roles of the Nek2 enzyme have recently emerged: these include drug resistance, bone, ciliopathies, immune and kidney diseases, and parasitic diseases such as malaria. Therefore, Nek2 is at the interface of multiple cellular processes and can influence num...

Molecules

Human cathepsin L belongs to the cathepsin family of proteolytic enzymes with primarily an endope... more Human cathepsin L belongs to the cathepsin family of proteolytic enzymes with primarily an endopeptidase activity. Although its primary functions were originally thought to be only of a housekeeping enzyme that degraded intracellular and endocytosed proteins in lysosome, numerous recent studies suggest that it plays many critical and specific roles in diverse cellular settings. Not surprisingly, the dysregulated function of cathepsin L has manifested itself in several human diseases, making it an attractive target for drug development. Unfortunately, several redundant and isoform-specific functions have recently emerged, adding complexities to the drug discovery process. To address this, a series of chemical biology tools have been developed that helped define cathepsin L biology with exquisite precision in specific cellular contexts. This review elaborates on the recently developed small molecule inhibitors and probes of human cathepsin L, outlining their mechanisms of action, and ...

Molecules (Basel, Switzerland), Jan 18, 2018

The practice of medicine is ever evolving. Diagnosing disease, which is often the first step in a... more The practice of medicine is ever evolving. Diagnosing disease, which is often the first step in a cure, has seen a sea change from the discerning hands of the neighborhood physician to the use of sophisticated machines to use of information gleaned from biomarkers obtained by the most minimally invasive of means. The last 100 or so years have borne witness to the enormous success story of allopathy, a practice that found favor over earlier practices of medical purgatory and homeopathy. Nevertheless, failures of this approach coupled with the omics and bioinformatics revolution spurred precision medicine, a platform wherein the molecular profile of an individual patient drives the selection of therapy. Indeed, precision medicine-based therapies that first found their place in oncology are rapidly finding uses in autoimmune, renal and other diseases. More recently a new renaissance that is shaping everyday life is making its way into healthcare. Drug discovery and medicine that starte...

PloS one, 2018

Although cirrhosis is a key risk factor for the development of hepatocellular carcinoma (HCC), mo... more Although cirrhosis is a key risk factor for the development of hepatocellular carcinoma (HCC), mounting evidence indicates that in a subset of patients presenting with non-alcoholic steatohepatitis (NASH) HCC manifests in the absence of cirrhosis. Given the sheer size of the ongoing non-alcoholic fatty liver disease (NAFLD) epidemic and the dismal prognosis associated with late-stage primary liver cancer there is an urgent need for HCC surveillance in the NASH population. Using serum levels of HCC biomarkers as vectors and biopsy-proven HCC or no HCC as outputs / binary classifier, a supervised learning campaign was undertaken to develop a minimally invasive technique for making a diagnosis of HCC in a clinically relevant model of NASH. Adult mice randomized to control diet or a fast food diet (FFD) were followed for up to 14 mo and serum level of a panel of HCC-relevant biomarkers was compared with liver biopsies at 3 and 14 mo. Both NAFLD Activity Score (NAS) and hepatic hydroxypr...

ABSTRACT The importance of a carefully regulated protein dephosphorylation event in cellular sign... more ABSTRACT The importance of a carefully regulated protein dephosphorylation event in cellular signaling by protein tyrosine phosphatases (PTPs) is well recognized. Indeed an anomalous level of PTP activities has been associated with a variety of aberrant cellular signaling and human diseases. As a result of this, potent and selective inhibitory agents of PTP enzymes are sought after by research communities across the globe. While there is considerable interest among academic researchers and pharmaceutical industries to develop non-covalent and reversible inhibitory agents of PTPs, the development of covalent inhibitory agents is plagued with presumption that they are not suitable candidates for drug discovery. This outcome is primarily due to the concern that such molecules could be immunogenic and serve as cellular toxic agents. The current success of covalent therapeutic agents in clinics, however, does not support this notion, and indicates that there is a need to reconsider this hypothesis with regard to the PTP-related drug discovery efforts. This review starts with a discussion of PTPs in general and provides an overview of reported covalent PTP inhibitors, highlighting their modes of interaction with enzymes. Finally, a brief perspective about the potential opportunities for the advancement of covalent inhibitors of PTPs in targeted PTP therapeutics is provided.

Human vaccines & immunotherapeutics, Jan 9, 2015

HLA-DR is the most commonly expressed and likely the most medically important human MHC class II,... more HLA-DR is the most commonly expressed and likely the most medically important human MHC class II, antigen presenting protein. In a normal immune response, HLA-DR binds to antigenic peptide and the HLA-DR/peptide complex binds to a T-cell receptor, thus contributing to T-cell activation and stimulation of an immune response against the antigen. When foreign antigen is not present, HLA-DR binds endogenous peptide which, under normal conditions does not stimulate an immune response. In most cases, the human peptide is CLIP, but a certain percentage of HLA-DR molecules will be present at the cell surface with other human peptides. We have recently shown that cell surface, CLIP/HLA-DR ratios are a measure of peptide heterogeneity, and in particular, changes in CLIP/HLA-DR ratios represent changes in the occupancy of HLA-DR by other, endogenous peptides. For example, treatment of cells with the HDAC inhibitor, Entinostat, leads to an upregulation of Cathepsin L1 and replacement of Catheps...

The importance of a carefully regulated protein dephosphorylation event in cellular signaling by ... more The importance of a carefully regulated protein dephosphorylation event in cellular signaling by protein tyrosine phosphatases (PTPs) is well recognized. Indeed an anomalous level of PTP activities has been associated with a variety of aberrant cellular signaling and human diseases. As a result of this, potent and selective inhibitory agents of PTP enzymes are sought after by research communities across the globe. While there is considerable interest among academic researchers and pharmaceutical industries to develop non-covalent and reversible inhibitory agents of PTPs, the development of covalent inhibitory agents is plagued with presumption that they are not suitable candidates for drug discovery. This outcome is primarily due to the concern that such molecules could be immunogenic and serve as cellular toxic agents. The current success of covalent therapeutic agents in clinics, however, does not support this notion, and indicates that there is a need to reconsider this hypothesi...

Rapid Communications in Mass Spectrometry, 2014

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry combined with isotope label... more Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry combined with isotope labeling methods are effective for protein and peptide quantification, but limited in their multiplexing capacity, cost-effectiveness and dynamic range. This study investigates MALDI-MS-based quantification of peptide phosphorylation without labeling, and aims to overcome the shot-to-shot variability of MALDI using a mathematical transformation and extended data acquisition times. A linear relationship between the reciprocal of phosphopeptide mole fraction and the reciprocal of phosphorylated-to-unphosphorylated signal ratio is derived, and evaluated experimentally using three separate phosphopeptide systems containing phosphorylated serine, threonine and tyrosine residues: mixtures of phosphopeptide and its des-phospho-analog with known stoichiometry measured by vacuum MALDI-linear ion trap mass spectrometry and fit to the linear model. The model is validated for quantifying in vitro phosphorylation assays with inhibition studies on Cdk2/cyclinA. Dynamic range of picomoles to femtomoles, good accuracy (deviations of 1.5-3.0% from expected values) and reproducibility (relative standard deviation (RSD) = 4.3-6.3%) are achieved. Inhibition of cyclin-dependent kinase phosphorylation by the classical inhibitors olomoucine and r-roscovitine was evaluated and IC50 values found to be in agreement with reported literature values. These results, achieved with single-point calibration, without isotope or chromatography, compare favorably to those arrived at using isotope dilution (p > 0.5 for accuracy). The mathematical relationship derived here can be applied to a method that we term Double Reciprocal Isotope-free Phosphopeptide Quantification (DRIP-Q), as a strategy for quantification of in vitro phosphorylation assays, the first MALDI-based, isotope- and calibration curve-free method of its type. These results also pave the way for further systematic studies investigating the effect of peptide composition and experimental conditions on quantitative, label-free MALDI.

Chemical Communications, 2014

A hybrid-design approach is undertaken to develop a highly potent and selective inhibitor of huma... more A hybrid-design approach is undertaken to develop a highly potent and selective inhibitor of human cathepsin L. Studies involving human breast carcinoma MDA-MB-231 cells establish that this inhibitor can successfully block intracellular cathepsin L activity, and retard the cell-migratory potential of these highly metastatic cells.

Tetrahedron Letters, 2013

ABSTRACT A reaction of diethyl phenylsulfonylmethylphosphonate with 2-arylacetaldehydes in the pr... more ABSTRACT A reaction of diethyl phenylsulfonylmethylphosphonate with 2-arylacetaldehydes in the presence of a catalytic excess of sodium hydride (1.1 equiv) yields allyl phenyl sulfones in excellent yield under mild reaction conditions. In contrast, when less than 1 equiv of sodium hydride (0.90 equiv) is used, the corresponding vinyl phenyl sulfones are obtained exclusively. The vinyl phenyl sulfones can be completely converted to allyl phenyl sulfones with only 0.2 equiv of NaH, suggesting that the second hydride involvement in the above transformation is catalytic. The regioselective control observed in these reactions offers a general method for synthesizing novel vinyl and allyl phenyl sulfones in one step from the same starting materials. The regioselectivity and stereoselectivity of this reaction, however, are not maintained when 2-alkylacetaldehydes are reacted with diethyl phenylsulfonylmethylphosphonate under identical reaction conditions. Our results indicate that an extended conjugation of the double bond in allylsulfones formed from the reaction of 2-arylacetaldehydes is required for the observed regio- and stereoselectivity. (c) 2013 Elsevier Ltd. All rights reserved.

Chemical Biology & Drug Design, 2012

A structure-based design approach has been applied to develop 2-(arylsulfonyl)oxiranes as potenti... more A structure-based design approach has been applied to develop 2-(arylsulfonyl)oxiranes as potential covalent inhibitors of protein tyrosine phosphatases. A detailed kinetic analysis of inactivation by these covalent inhibitors reveals that this class of compounds inhibits a panel of protein tyrosine phosphatases in a time- and dose-dependent manner, consistent with the covalent modification of the enzyme active site. An inactivation experiment in the presence of sodium arsenate, a known competitive inhibitor of protein tyrosine phosphatase, indicated that these inhibitors were active site bound. This finding is consistent with the mass spectrometric analysis of the covalently modified protein tyrosine phosphatase enzyme. Additional experiments indicated that these compounds remained inert toward other classes of arylphosphate-hydrolyzing enzymes, and alkaline and acid phosphatases. Cell-based experiments with human A549 lung cancer cell lines indicated that 2-(phenylsulfonyl)oxirane (1) caused an increase in intracellular pTyr levels in a dose-dependent manner thereby suggesting its cell-permeable nature. Taken together, the newly identified 2-(arylsulfonyl)oxiranyl moiety could serve as a novel chemotype for the development of activity-based probes and therapeutic agents against protein tyrosine phosphatase superfamily of enzymes.

Bioorganic & Medicinal Chemistry, 2013

Cysteine cathepsins are an important class of enzymes that coordinate a variety of important cell... more Cysteine cathepsins are an important class of enzymes that coordinate a variety of important cellular processes, and are implicated in various types of human diseases. However, small molecule inhibitors that are cell-permeable and non-peptidyl in nature are scarcely available. Herein the synthesis and development of sulfonyloxiranes as covalent inhibitors of cysteine cathepsins are reported. From a library of compounds, compound 5 is identified as a selective inhibitor of cysteine cathepsins. Live cell imaging and immunocytochemistry of metastatic human breast carcinoma MDA-MB-231 cells document the efficacy of compound 5 in inhibiting cysteine cathepsin activity in living cells. A cell-motility assay demonstrates that compound 5 is effective in mitigating the cell-migratory potential of highly metastatic breast carcinoma MDA-MB-231 cells.

Bioorganic & Medicinal Chemistry, 2013

Hepatitis C virus (HCV) NS5B polymerase is a key target for anti-HCV therapeutics development. He... more Hepatitis C virus (HCV) NS5B polymerase is a key target for anti-HCV therapeutics development. Herein, we report the synthesis and in vitro evaluation of anti-NS5B polymerase activity of a molecular hybrid of our previously reported lead compounds 1 (IC50=7.7 μM) and 2 (IC50=10.6 μM) as represented by hybrid compound 27 (IC50=6.7 μM). We have explored the optimal substituents on the terminal phenyl ring of the 3-phenoxybenzylidene moiety in 27, by generating a set of six analogs. This resulted in the identification of compound 34 with an IC50 of 2.6 μM. To probe the role of stereochemistry towards the observed biological activity, we synthesized and evaluated the D-isomers 41 (IC50=19.3 μM) and 45 (IC50=5.4 μM) as enantiomers of the l-isomers 27 and 34, respectively. The binding site of compounds 32 and 34 was mapped to palm pocket-I (PP-I) of NS5B. The docking models of 34 and 45 within the PP-I of NS5B were investigated to envisage the molecular mechanism of inhibition.