Recent: 2009 - Present

   ● A Systematic Review of the Efficacy and Safety of Favipiravir (Avigan) for the Treatment of Novel COVID-19 Infections ●Bag*, Subhendu Sekhar; Sinha, Sayantan; and Saito, Isao  ● Medical Research Archives 2020, XX, XX (In Press).

Abstract: The first SARS-CoV-19 infection was detected in the Wuhan city, Hubei province, in China around December 2019. Since then, the world has seen death dance due to the pandemic caused by the spreading of SARS-CoV-19 infections. Unlike SARS-CoV and MERS-CoV, SARS-CoV-2 infects humans and causes the severe acute respiratory syndrome. The spread of infection has caused disease in over 8.1 million people across the globe. However, more than 439 thousand deaths are reported as on 16^th June 2020. As a result, the pandemic has put the health care system across the world under grave challenges. The added disadvantage is the stress and unavailability of drugs/vaccines or therapeutics to treat the infection. Presently countries across the globe are trying to stop the spread of the virus by initiating lockdowns and also providing supportive care to patients through supplemental oxygen and mechanical ventilation. Scientists worldwide are engaged in research to understand SARS-CoV-2 pathogenicity and to obtain a rapid solution of the pandemic, with utmost sincerity. Recently with the revelation of SARS-CoV-2 genetic makeup, it has been possible to compare the genome structure of SERS-CoV and MERS-CoV with its mutated neighbor. This study helped scientists to locate potential drug targets in SARS-CoV-2, which are SARS-CoV-2 main protease 3CL^pro, papin like protease PL^pro and CoV-2 RNA dependent RNA polymerase (RdRp). These drug targets have opened up the window for screening and selecting the existing potential antiviral drugs as a process of drug repurposing. One such drug is Favipiravir marketed under the brand name Avigan by Fujifilm, Japan. Avigan is an RdRp inhibitor and reported to target the SARS-CoV-2 RdRp and therefore inhibit the viral replication. Recently in the month of April, Fujifilm has initiated the phase-II clinical trial of Avigan against CoV-2 infections in collaboration with Japanese hospitals,Brigham and Women's Hospital, Massachusetts General Hospital, and the University of Massachusetts Medical School. Therefore, at this crucial time, the scientific community must come up with adequate and detailed understanding regarding the interaction of Avigan with CoV-2 as well as the patients infected with the virus. Hence we decided to write this review to focus on a thorough and in-depth knowledge of the mechanistic role of Avigan in interacting with RdRp of CoV-2. We also focus on the pharmacokinetic characteristics of Avigan and potential drug-drug interaction. We believe this review would attract the attention of the scientific community for further development of new drug therapeutics for COVID-19.

 

   ● Wastewater an Emerging Source of Spreading COVID-19 Infections in India: A Recent Perspective● Bag*, Subhendu Sekhar and Sinha, Sayantan● Current Science 2020, XX, XX (Under Review).

Abstract: Epidemics caused form infectious pathogens are known since the prehistoric era. The first report was around 3000 B.C. when an unknown disease was noticed amongst villagers residing in today's 'Hamim Mangha’ and ‘Miaoigao’ located in northeastern China province. The entire village population of all age groups was locked in a house and set to fire to contain the spread of the disease. However, since then, many such cases have haunted the world population over the years. In the initial days till 1860, people did not have any idea about pathogens creating infections. It was in 1860 Luis Pasteur related the pathogenicity of puerperal fever and the pyogenic vibrio. This was the first incident when the world came to know about infectious bacteria. Thirty-two years after, in 1892, Dmitri Ivanovsk had discovered the virus for the first time. However, the first case of human infection from the virus was reported only in 1901 as a spread of Yellow fever 1, which was also the first viral pandemic reported. Therefore, viral diseases and related deaths are not new to the world community. Some of the fatal viral epidemics which have tested and threatened the world at times are Influenza (Spanish flu etc.), haemorrhagic fever, Chikungunya, Monkey pox, Small pox etc. In the last two decades, the world has also witnessed a few fatal pandemics like: Ebola viral disease, Nipah viral infections, and SARS related diseases.

 

   ● Inhibiting the Pathogenicity of SARS-CoV-2 with a Designer Fluorescent Carbon Quantum Dot (FL-ASCQD): A Concept● Bag*, Subhendu Sekhar and Sinha, Sayantan● Medicinal Chemistry 2020, XX, XX (Under Review).  

Abstract: The world is paralyzed by the infection of SARS-CoV-2 (novel coronavirus) at present. The disease caused by this virus is officially declared as COVID-19 by WHO. Scientists worldwide are trying to develop a drug/vaccine that can eradicate this disease. However, the present treatment avenue is only a supportive medication coming out as a drug repurposing protocol. In this concept paper we would like to propose the synthesis of an antiviral biogenic fluorescent Carbon Quantum Dot (FL-ASCQD) as a promising nanomedicine that can be effective in COVID-19 cure. The nanomedicine surface is engineered with Angiotensin 2 protein and HSPG receptor mimic linked with an antiviral drug isolated from False Daisy leaf extract. The nanomedicine is expected to show a multi-functional property such as to (a) stop entry of SARS-CoV-2 into host cell via attachment with HSPG mimick on the surface of the nanomedicine, (b) inhibit viral replication through the interaction of attached antiviral drug with viral RdRp enzyme, (c) sense the SARS-CoV-2 via a change in fluorescent photophysical response. Thus, this nanomedicine would find potential application as a promising drug, sensor of SARS-CoV-2, anti-SARS-CoV-2 protective layer in masks, and also as disinfectant for SARS virus/MDR laden wastewater.

   ● SARS-CoV-2 from Host Cell Entry, Pathogenicity to Possible Remediation of the Infection Caused: An Overview● Bag*, Subhendu Sekhar and Sinha, Sayantan●  2020, XX, XX (Communicated).

Abstract: Six months have passed and we are still fighting with COVID-19 pandemic situation. We do not have any specific drugs to treat COVID-19, however looking at the pace of current research worldwide we believe that “The DAY” is not a long way when the world gets COVID-19 drug/vaccine. In many countries where the infection started spreading at the initial moment has now started to recover and regain their daily life style with precautions. However other countries are still emerged under the crisis. SARS-CoV-2 is extremely pathogenic and its rate of infection is nearly uncontrollable. The only ray of hope is the comparatively lower fatality rate. We got the motivation of writing this review thinking that as we have now been sustaining with COVID-19 for a good time period it is important for us to know our enemy in a better way so that we can take proper precautions and also do not panic unnecessarily or get frustrated from hoax presumptions. This review discuses about the life cycle, pathogenicity of SARS-CoV-2. Also we have discussed in details about the clinical syndromes that a COVID-19 patient develops and the possible medications that will be given based on the severity of the clinical presentation. We have also discussed about the most important drug targets and drug candidates that promises resolution of COVID-19.
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   ● Stabilization of an Abasic Site Paired Against an Unnatural Triazolyl Nitrobenzene Nucleoside● Bag*, Subhendu Sekhar; Sinha, Sayantan; Gogoi, Hiranya; Datta, Subhashis; Kundu, Rajen; Talukdar, Sangita● Biophysical Chemistry 2020, XX, XX (In Press).

Abstract: An abasic site is the most frequently observed among the various forms of DNA lesions in genomic DNA. If left unrepaired, an abasic site might turn out to be a principle cause for deleterious mutations and can be threat to cellular survival. Thus, to keep cellular integrity and measure the extent of DNA damage, recognition and stabilization of the abasic sites (apurinic/apyrimidinic site = Ap) are essential. Further, it is crucial to detect and stabilise the abasic site for towards the development of new diagnostics and chemotherapeutics. Herein, we report the stabilization of an abasic DNA duplex wherein the abasic site paired against a novel unnatural nucleoside, triazolylnitrobenzene (TNBBAc). This nucleoside is bulky and exhibits, high polarizability and good stacking propensity. Robust hetero-pair stabilization is another feature of it. Therefore, it is interesting to study the stabilization of an abasic DNA containing a synthesized triazolylnitrobenzene nucleoside TNBBAc We planned to study the thermal as well as the thermodynamic origin of abasic DNA stabilization by our synthesized oligonucleotide probe containing TNBBAc nucleoside. We observed that the nucleoside TNBBAc offered good thermal stabilization of a TNBBAc- duplex via strong intercalative stacking interaction alongside an abasic site. The UV-visible spectroscopic study supported the intercalative stacking interaction. The stabilization though is marginal, but it would shed light on the design of bases of significant volume to stabilize abasic DNA to a greater extent.
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   ● Extended fluorescent uridine analogues: Synthesis, photo-physical properties and selective interaction with BSA protein● Ardhapure, Ajaykumar V.; Gayakhe, Vijay; Bhilare, Shatrughn; Kapdi*; Anant R.;  Bag*, Subhendu Sekhar;  Sanghvi,Yogesh S.;  Gunturu, Krishna Chaitanya● New Journal of Chemistry 2020, XX, XX (Under Revision).

Abstract: The improvement in fluorescent property of 2’-deoxyuridine was brought about by the installation of (hetero)aromatic moieties at the C–5 position of uridine directly or via alkenyl/phenyl/styryl linkers to create a library of biologically useful fluorescent nucleosides. The synthesis of these extended nucleoside analogues was carried out using Suzuki-Miyaura and Heck alkenylation reactions. A comparison of the photophysical properties allowed the identification of nucleosides 1g and 1h to exhibit the highest quantum yields in an aqueous solution. Studies on the binding interaction of the most promising fluorescent analogues, 1g and 1h, with serum albumin proteins showed excellent selectivity towards BSA protein over α-amylase. Docking studies were also performed to predict the specific binding site of the nucleosides to BSA.

   78. ● Triazolyl C-Nucleosides via the Intermediacy of β-1'-ethynyl-2'-deoxyriboside Derived from a Nicholas Reaction:  Synthesis, Photophysical Property and Interaction with BSA†● Bag*, Subhendu Sekhar; Das, Suman, K.● J. Org. Chem. 2018, XX, XX (Under Revision).

Abstract: We report the design and synthesis of triazolyl donor/acceptor unnatural C-nucleosides via alkyne (sugar)—azide (aromatic) 1, 3-dipolar cyclo-addition reaction as a key step and studies on their photophysical properties. We have chosen β-1'-ethynyl-2'-deoxy riboside as a precursor to synthesize triazolyl-C-nucleoside. Overcoming the difficulties, we obtained β-1'-ethynyl riboside as a major product following a Co₂(CO)₈ catalyzed intramolecular Nicholas reaction. The 1,3-diaxial interaction is the driving force for the α to β-anomeric conversion while performing cobalt complexation followed by oxidation to afford β-1'-ethynyl riboside as the major product. A Cu(I)-catalyzed click reaction between different aromatic donor/acceptor azides and β-1'-ethynyl riboside generated the desired unnatural triazolyl donor-acceptor aromatic C-nucleosides (^cTB_Do/Ac) within 30 minutes. Single crystal X-ray structure shows the puckered conformation of sugar as C2'-endo/C3'-exo. Studies on the photophysical properties suggested good fluorophoric as well as solvatochromic characteristics of these nucleosides. Two of the synthesized nucleosides, ^cTAnthB_Do and ^cTPyB_Do, are found to interact with BSA as the only protein via a generation of enhanced fluorescence signal. The designed bases, thus, might find applications in stabilizing a DNA and in the biophysical study thereof, if a pair of such donor acceptor C-nucleosides are incorporated into a DNA sequence.
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77.● Pyrenylthioureayl Alanine as a Switch-on Fluorescent Sensor for Hg(II) Ions● Bag*, Subhendu Sekhar; De, Suranjan● Chemistry Select. 2018, 3, 11758-11764.

Abstract: Fluorescence sensing of heavy metal ion such as mercury is highly important because of its adverse effects on biological systems and on environment. Toward this end, we report herein a new and novel pyrenylthioureayl alanine amino acid (1, ^PyTUAla) as an efficient  switch-on fluorescent sensor for sensing of Hg²⁺ ion in semi-aqueous solvent system (7:3 H₂O:ACN). The probe also shows binding interaction with Cu²⁺ ion with an enhancement of emission. In both the cases 1:2 metal-ligand binding stoichiometry is evident from Job’s plot analyses. The detection limit is found to be 93 nM with a very high association (10¹⁰ M^-1) constant for Hg²⁺ ion.  The UV-visible absorption, IR-spectroscopic study, NMR titration, and a theoretical calculation supported the probe’s binding to Hg²⁺ ion through the coordination with two sulphur atoms of two iminothioureayl moieties of two pyrenylthioureayl alanines.
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76.● Synergized AgNPs formation using microwave in a bio-mediated route: Studies on particle aggregation and electrocatalytic sensing of ascorbic acid from biological entities● Dash, S. R.; Bag, S. S.; Golder, K. A.● J. Electroanal. Chem. 2018, 827, 181–192.

Abstract: Psidium guajava leaves are laden with potential reducing analytes namely quercitin, chlorogenic acid, D‑glucose, ascorbic acid and capping agents like citric acid. This work reported on the one-pot synthesis of AgNPs by these analytes extracted in an aqueous medium and the synthesis rate was synergized by microwave (MW). The synergy between the MW input powers and disintegration of capping agents leading to particle aggregation was explored. The modified electrode (AgNPs (pH 9.5)/GPE) exhibited a reduction in charge transfer resistance from 3.2 to 0.453 kΩ. A single electron reaction (Tafel slope 103 mV/decade, α=0.57) of ascorbic acid (AA, 0.380 V vs. Ag/AgCl) was found in a phosphate buffer media (pH 7.2) and, AA oxidation was diffusion control at AA≤150 μM and activation control at 150≤AA≤2000 μM. Dopamine and uric acid couldn't interfere the response current of the chronoamperometric test of AgNPs(pH 9.5)/GPE and, the (peak)separation potential of 0.272 and 1.114 V was found for AA-dopamine and AA-uric acid. The limit of detection and sensitivities of AgNPs(pH 9.5)/GPE were estimated as 14.63 μM and, 0.719 (diffusion control) and 0.390 (activation control) μA/cm2·μM. The concentration of AA in S. edule and Z. mauritiana extract determined using AgNPs(pH 9.5)/GPE well matched with high performance liquid chromatography.
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75.●Relay FRET Event in a Designed Trichromophoric Pentapeptide Containing o-, m-Aromatic-Amino Acid Scaffold ● Bag*, Subhendu Sekhar; Yashmeen, Afsana● Chem. Commun. 2018, 54, 9765-9768.

Abstract: The concept of relay FRET event is established in a designed trichromophoric pentapeptide containing o-,m-aromatic amino acid scaffold in the backbone as a novel a β-turn mimetic β-sheet folding nucleator. This system would find applications in studying fundamental processes involving interbiomolecular interactions in chemical biology.

73.●Green Synthesis of Silver Nanoparticle using Sechium Edule Fruit Aqueous Extract and Study of Antimicrobial and Catalytic Activity ● Bag*, Subhendu Sekhar; Banerjee, Ankita; Singh, Anu;  Golder, Animes Kumar; Bora, Anupama  ● Current Nanomaterials, 2018, (In Press).

Abstract: A cost effective and environment friendly biomimetic green synthesis of silver nanoparticles from the aqueous extract of Chayote squash is demonstrated. In north eastern region of India chayote is known as Squash and used for benefit for stomach. Therefore, we have used, for the first time, the Squash vegetable extract which is widely available, cheap and has antioxidant properties for the synthesis of stable silver nanoparticles. The formation of silver nanoparticles is tested by various spectroscopic techniques like, UV–Vis, FTIR-spectroscopy and X-ray diffraction (XRD). The advantage of our method lies on the fact that squash acts both as a reducing agent and a stabilizer of silver nanoparticles. The carbohydrate and the fiber part are most probably acts as stabilizers. The synthesized nanoparticles are found to show antimicrobial activity and catalytic activity toward the reduction of methylene blue. The reduction of methylene blue by Ag-NPs in presence of sechium edule aqueous extract is attributed to the electron relay effect.

67.●Sensing the Chemical Cleavage of Fluorescent β-Lactams via FRET/Exciplex or Excimer Emission● Bag,* Subhendu Sekhar; Afsana Yashmeen● J. Phochem.Photobiol. A:Chemistry 2017, 353, 464-468.

Abstract: We report herein the design, synthesis of C6-triazolyl donor-acceptor fluorescent penicilines. Two of the fluorescent penicilines have been utilized for studying the photophysical outcome after ring cleavage by an external fluoregenic amine as nucleophile. Thus, the chemical cleavage of β-lactam rings is signaled by interesting photophysical phenomena-dual path to exciplex emission or via excimer emission.

 

66.●Uracil-Amino Acid as a Scaffold for β-Sheet Peptidomimetics: Study of Photophysics and interaction with BSA Protein  ● Bag,* Subhendu Sekhar; Afsana Yashmeen● Bioorganic and Medicinal Chemistry Letters 2017,  27, 5387.

Abstract: We report herein the uracil-di-aza-amino acid (U^rAA) as a new family of molecular scaffold to induce β-hairpin structure with H-bonded β-sheet conformation in a short peptide. This has been demonstrated in two conceptual fluorescent pentapeptides wherein triazolylpyrenyl alanine and/or triazolylmethoxynapthyl alanine (^TPyAla_Do and/or ^TMNapAla_Do) are embedded into two arms of the uracil-amino acid via an intervening leucine. Conformational analysis by CD, IR, variable temperature and 2D NMR spectroscopy reveals the β-hairpin structures for both the peptides. Study of photophysical property reveals that the pentapeptide containing fluorescent triazolyl unnatural amino acids ^TMNapAla_Do and ^TPyAla_Do at the two termini exhibits dual path entry to exciplex emission-either via FRET from ^TMNapAla^Do to ^TPyAla^Do or via direct excitation of a FRET acceptor, ^TPyAla_Do. The other pentapeptide with ^TPyAla_Do/ ^TPyAla_Do pair shows excimer emission. Furthermore, both the peptides maintaining their fundamental photophysics are found to interact with BSA as only a test biomolecule.

65.●Use of Azido Naphthalimide Carboxylic Acids as Fluorescent Template with Built-in Photo-reactive Group and Flexible Linker Simplifies Protein Labeling Study: Applications in Selective Tagging of HCAII and Penicillin Binding Proteins  ● Basak, Amit;   Singha, Monisha;  Roy,  Sayantani; Pandey, Satya Deo;  Bag, Subhendu Sekhar;  Bhattacharya,  Prabuddha; Das,  Mainak; Ghosh, Anindya Sundar;  Ray, Debashis  ● Chemical Communications 2017, 53, 13015 (Outside Back Cover Page; DOI: 10.1039/C7CC08209F).

Abstract: The work describes the synthesis of azidonaphthalimide carboxylic acids acting as fluorescent template with built-in photo-reactive group and linker thus simplifying the design of protein labeling agents. These were separately connected to selectivity hands like a sulfonamide and ampicillin for successful labeling/detection of HCAII and PBPs respectively.

 

64.●Tetrazolylpyrene Unnatural Nucleoside as a Human Telomeric Multimeric G-Quadruplex Selective Switch-On Fluorescent Sensor ● Bag,* Subhendu Sekhar; Manoj Kumar Pradhan, Talukdar, Sangita● Organic and Biomolecular Chemistry 2017, 15, 10145.

Abstract: We want to report herein the specific sensing of dimeric H45 G-quadruplex DNA via a fluorescence light-up response using fluorescent tetrazolyl pyrene nucleoside (^TzPyB_Do) as probe. The strong binding of the probe via intercalative stacking interaction inside the connecting loop of two G-quadruplex units of H45 and discrimination to other monomeric and long DNA duplexes are accompanied by a drastic enhancement of emission intensity without compromising the conformation and stability.

 

63.●Isothiocyanyl Alanine as a Synthetic Intermediate for the Synthesis of Thioureayl Alanines and Subsequent Aminotetrazolyl Alanines ● Bag,* Subhendu Sekhar; Suranjan De● The Journal of Organic Chemistry 2017, 82, 12276.

Abstract: The synthesis of unnatural amino acids with small side-chain functionalities usable for further transformations is highly demanding for the expansion of the genetic code and other possible biotechnological applications. Toward this end, we wanted to report the utility of an unexplored unnatural amino acid, isothiocyanyl alanine (^NCSAla = Ita), for the synthesis of another class of unnatural amino acids, thioureayl alanines (^TUAla = Tua). The synthesis of a third class of unnatural amino acids, amino tetrazolyl alanines (^ATzAla = Ata), in very good yield was subsequently achieved utilizing thioureayl alanines. Thus, a variety of aliphatic- and aromatic-substituted thioureayl alanines and aromatic-substituted amino tetrazolyl alanines were successfully synthesized in good to excellent yields. The photophysical properties of three of the fluorescent unnatural amino acids from two classes were also studied and presented herein.

62.●Axially Chiral Amino Acid Scaffold as an Efficient Fluorescent Discriminator of Methanol-Ethanol● Bag,* Subhendu Sekhar; Jana, Subhashis● New Journal of Chemistry 2017, 41, 13391-13398.

Abstract: We report a unique fluorescence sensor based on an axially chiral unnatural triazolyl aromatic amino acid scaffold (^ArTAA) for discrimination of methanol from ethanol via a switch on fluorescence response. All the three sensors, simple scaffold (^ArTAA), mono- (PyAm-^ArTAA) and bis-pyrenyl- (Py₂Am-^ArTAA) amides, show similar sensitivity and detection limit ranging from 0.5%-2.1 v/v% of ethanol. The solid films of these sensors are also found to be effective in sensing ethanol vapour via generation of distinct and enhanced fluorescence signal. All our experimental results suggest the role of axial chirality of the hairpin-shaped scaffold in differential solvation guided H-bonding interaction and discriminating between ethanol and methanol with a switch-on fluorescence response.

 

61.●Trifunctional fluorescent unnatural nucleoside: Label free detection of T-T/C-C base mismatches, abasic site and bulge DNA● Bag,* Subhendu Sekhar; Manoj Kumar Pradhan, Talukdar, Sangita● J. Photochem. Photobiol. B 2017, 173, 165-169.

Abstract: The detection and targeting of both the mismatched and abasic DNA is highly important which would ultimately help in designing new diagnostics and chemotherapeutics. Furthermore,  sensing and targeting the bulge sequence with a fluorescent probe would be useful to study the role of bulges in nucleic acid function or could have significant therapeutic potential. Thus, detection of specific bulges by small fluorescent molecules is an attractive research area since the past several years. Many attempts have been made to prepare such compounds. We report herein a label free strategy for the detection of pyrimidine base mismatches (T/T and C/C), sensing of abasic site, and pyrimidine base bulge DNA using an unnatural tetrazolylpyrene nucleoside (^TzPyB_Do) as a bare fluorescent probe. The H-bonding/hydrophobic force mediated interactions allow the sensing of all three deformed DNA via an enhancement of fluorescence signal using our simple “Just-Mix and Read” strategy.  The binding of the probe to all the three deformed DNA duplexes is accompanied by an increase in the thermal melting stability of the deformed DNA. That the probe binds efficiently to the minor groove near the deformed site was evident from spectroscopic study. All the spectral evidences open up a multitude of possibilities for using our probe, tetrazolylpyrene nucleoside, as an efficient fluorescent light-up bio-probe for label free DNA detection.

 

60.●Design, Synthesis and Photophysical Property of a Doubly Widened Fused-Triazolyl-Phenanthrene Unnatural Nucleoside● Bag,* Subhendu Sekhar; Das, Suman Kalyan● Chemistry Select 2017, 2, 3577-3583.

Abstract: Fused Triazolyl Phenanthrene! is presented as a new generation of doubly widened hydrophobic unnatural nucleobase surrogate having interesting photphysical property with chrysene type emission. Theoretical study based on Molecular dynamics simulation using Schrodinger Macromodel and DFT reveal its potential stacking propensity in a duplex DNA without compromising the right-handed B-form helical conformations with C2'-endo/C3'-exo sugar disposition. Thus, the novel FTPhen is expected to find wide applications  in chemistry, biotechnology and DNA-based material design.

59.●A Bio-synthesis Route to nearly spherical AgNPs using Chayote fruit extract ● Rao, Ch. Venkatanarasimha;  Bag, Subhendu Sekhar; Golder^, Animes Kumar ● Environmental Progress & Sustainable Energy 2017, 36, 192.

Abstract: Silver nanoparticles (AgNPs) were biosynthesized using the aqueous extract of Chayote fruit that served as both reducing and capping agents. The synthesis route of AgNPs reported here is rather ecofriendly, cost-effective and energy-saving, and the reduction process didn’t need any additional chemicals apart from AgNO₃ as the metal precursor. The formation of AgNPs was confirmed using UV-vis and Atomic absorption spectroscopies and X-ray diffraction (XRD). While the particle size was analyzed by Transmission Electron Microscopy (TEM), Atomic Force Microscopy (AFM) and Dynamic light scattering (DLS). The growth of AgNPs mostly occurred during the nucleation period, and after that the natural capping agents inhibited AgNPs destabilization in the aqueous media as evidenced by zeta potential and also supported by Thermogravimetric analysis. The particles were of bi-crystalline in nature with the predominant face-centered cubic crystal of AgNPs. The hydrodynamic diameter of 72.8 nm of AgNPs measured by DLS was around 1.6 times greater than TEM images found after 24 h of reaction with more than 99% yield. The biosynthesized AgNPs were tested for the inactivation of Bacillus subtilis and Escherichia coli using the disc diffusion method. Furthermore, AgNPs were found to be highly effective against pathogenic fungi Aspergillus thermomutans and showed the maximum inhibition zone of 78 mm. The electron spin resonance (ESR) spectra of AgNPs confirmed that the free radical formed were one of the actions for microbial inactivation.

 

58.●Bis-Pyridobenzene as A Fluorescence Light-up Sensor for Hg²⁺Ion in Water● Ghosh, Ujjal, Bag,* Subhendu Sekhar; Mukherjee,* Chandan● Sensors & Actuators: B. Chemical 2017, 238, 903.

Abstract: Heavy metal ion such as mercury is a highly toxic in all its oxidation states in the environment. Mercury exposure causes a variety of adverse environmental and health problems, such as brain damage, neurological disorder, damage of immune system etc. Mercuric ions (Hg2+) being highly water-soluble are easily bioavailable for humans and animals through ingestion leading to many of the physiological problems. Thus, continued alarm over mercury pollution has prompted increasing interest in the design of new fluorescent probe for mercury detection in biological and environmental samples. Therefore, we synthesize meta-di-4-methylpyridyl benzene (m-DPB) core as a possible fluorescent probe for Hg2+ detection. The probe shows a dual fluorescence emission at long wavelength region (350, 425 nm) indicating its potential use as a probe in aqueous medium which could be utilized for sensing of metal ions. Herein, we report the synthesis of that new and novel fluorescence probe and its use in switch-on sensing of Hg2+ ion. The probe is very simple in design and is found to be highly sensitive for sensing Hg2+ ion in the presence of other interfering metal cations with a high binding constant for 1:1 probe-Hg2+ complexation and high sensitivity (1 M) in water. All the observations are evident from the absorption and fluorescence spectroscopic studies. A theoretical calculation and NMR titration suggest that the probe binds Hg2+ through the coordination with two pyridyl nitrogens.

57.●Hybridization Accompanying FRET Event in Labeled Natural Nucleoside-Unnatural Nucleoside Containing Chimeric DNA Duplexes ● Bag*, Subhendu Sekhar; Das, Suman Kalyan; Pradhan, Monoj Kumar; Jana, Subhashis● Journal of Photochemistry & Photobiology, B: Biology 2016, 162, 669-673.

Abstract: Förster resonance energy transfer (FRET) is a highly efficient strategy in illuminating the structures, structural changes and dynamics of DNA, proteins and other biomolecules and thus is being widely utilized in studying such phenomena, in designing molecular/biomolecular probes for monitoring the hybridization event of two single stranded DNA to form duplex, in gene detection and in many other sensory applications in chemistry, biology and material sciences. Moreover, FRET can give information about the positional status of chromophores within the associated biomolecules with much more accuracy than other methods can yield. Toward this end, we want to report here the ability of fluorescent unnatural nucleoside, triazolylphenanthrene (TPhenBDo) to show FRET interaction upon hybridization with fluorescently labeled natural nucleosides, PerU or OxoPyU or PerU, forming two stable chimeric DNA duplexes. The pairing selectivity and the thermal duplex stability of the chimeric duplexes are higher than any of the duplexes with natural nucleoside formed. The hybridization results in a Förster resonance energy transfer (FRET) from donor triazolylphenanthrene of TPhenBDo to acceptor oxopyrene of OxoPyU and/or to perylene chromophore of PerU, respectively, in two chimeric DNA duplexes. Therefore, we have established the FRET process in two chimeric DNA duplexes wherein a fluorescently labeled natural nucleoside (OxoPyU or PerU) paired against an unnatural nucleoside (TPhenBDo) without sacrificing the duplex stability and B-DNA conformation. The hybridization accompanying FRET event in these classes of interacting fluorophores is new. Moreover, there is no report of such designed system of chimeric DNA duplex. Our observed phenomenon and the design can potentially be exploited in designing more of such efficient FRET pairs for useful application in the detection and analysis of biomolecular interactions and in material science application.

 

56. Book Chapter: ●Design of Environmentally Sensitive Fluorescent Nucleosides and Their Applications● Bag*, Subhendu Sekhar; Saito, Isao;  ● In Fluorescent Analogues of Biomolecular Building Blocks: Design and Applications, Eds. Tor, Yitzhak; Wilhelmsson, Marcus. Publisher: John Wiley & Sons (2016). (ISBN: 978-1-118-17586-6).

55.●Mechanistic studies on Garratt-Braverman Cyclization: Solving the Diradical-Cycloaddition Puzzle ● Das, Joyee; Bag,* Subhendu Sekhar; Basak*, Amit● J. Org. Chem. 2016, 81(11), 4623.

Abstract: In this work, we present the results of extensive multi prong studies involving fate of deuterium labeled substrates, EPR, trapping experiments and LA-LDI mass spectrometry to sort out the controversies relating to the mechanism of Garratt-Braverman cyclization in two systems, namely bis-propargyl sulfones and ethers. The results are in conformity with a diradical mechamism for the sulfone, while for the ether, the anionic [4+2] appears to be the preferred pathway. This shows that the mechanistic pathway towards GB cyclization is dependent upon the nature of hetero atom (O or S in sulfone) bridging the propargyl arms.

 

54.●Synthesis and Photophysical Properties of Triazolyl-Donor/Acceptor Chomophores Decorated Unnatural Amino Acids and Application of Triazolylperylene Amino Acid in Sensing BSA● Bag,* Subhendu Sekhar; Jana, Subhashis;  Pradhan, Manoj Kumar● Bioorg. Med. Chem. 2016, 24(16), 3579.

Abstract: The research in the field of design and synthesis of unnatural amino acids is growing at a fast space for the increasing demand of proteins of potential therapeutics and many other diversified novel functional applications. Thus, we report herein the design and synthesis of microenvironment sensitive fluorescent triazolyl unnatural amino acids (UNAA) decorated with donor and/or acceptor aromatic chromophores via click chemistry. The synthesized fluorescent amino acids show interesting solvatochromic characteristic and/or intramolecular charge transfer (ICT) feature as is revealed from the UV-visible, fluorescence photophysical properties and DFT/TDDFT calculation. HOMO-LUMO distribution shows that the emissive states of some of the amino acids are characterized with more significant electron redistribution between the triazolyl moiety and the aromatic chromophores linked to it leading to modulated emission property. A pair of donor-acceptor amino acid shows interesting photophysical interaction property indicating a FRET quenching event. Furthermore, one of the amino acid, triazolyl-perylene amino acid, has been exploited for studying interaction with BSA and found that it is able to sense BSA with an enhancement of fluorescence intensity. We envisage that our investigation is of importance for the development of new fluorescent donor-acceptor unnatural amino acids a pair of which can be exploited for generating fluorescent peptidomimetic probe of interesting photophysical property for applications in studying peptide-protein interaction.

53.●Donor/Acceptor Chromophores Decorated Triazolyl Unnatural Nucleosides: Synthesis, Photophysical Properties and Study of Interaction with BSA● Bag,* Subhendu Sekhar; Talukdar, Sangita; Das, Suman Kalyan;  Pradhan, Manoj Kumar; Mukherjee, Soumen ● Org. Biomol. Chem. 2016, 14, 5088.

Abstract: Much efforts have been put forth to develop non-natural, stable, hydrophobic base pairs of orthogonal recognition properties and study their effect on DNA duplex stabilisation. Our continuous efforts on the design of fluorescent unnatural biomolecular building blocks lead us to the synthesis of few triazolyl donor/acceptor unnatural nucleosides via azide-alkyne 1,3-dipolar cycloaddition reaction as a key step which we want to report herein. We have studied their photophysical properties and found interesting solvatochromic fluorescence for two of such nucleosides. Photophysical interactions among two donor-acceptor β-nucleosides as well as a pair of α/β- nucleosides have also been evaluated. Furthermore, we exploited one of the fluorescent nucleoside in studying interaction with BSA with the help of UV-visible and steady state fluorescence technique. Our design concept based on the hypothesis that a pair of such donor/acceptor nucleoside might involve in p-stacking as well as in photophysical interaction leading to stabilization of DNA duplex if such nucleosides can be incorporated into short oligonucleotide sequences. Therefore, the designed bases may find application in the biophysical study in the context of DNA.

52.●Trichromophoric Pentapeptide: Impact of β-Sheet Conformation on Dual Path to Excimer Emission and Sensing of BSA Protein ● Bag,* Subhendu Sekhar; Jana, Subhashis; Pradhan, Manoj Kumar; Pal, Sunit● RSC Advances 2016, 6, 72654.
 

Abstract: We are reporting a dual door entry system to excimer emission in a designed triazolo amino acid scaffolded (^ArTAA) trichromophoric b-sheet pentapeptide. In our design, two fluorescent unnatural amino acids (^TPyAla_Do) are embedded into two arms of a novel chromophoric scaffold, ^ArTAA, via an intervening natural amino acid, leucine. The unnatural fluorescent pentapeptide shows an excimer emission either via Förster resonance energy transfer (FRET) from the scaffold (^ArTAA) acting as donor or via direct excitation of an acceptor chromophore, ^TPyAla_Do. Moreover, it serves as an effective fluorescence light-up probe for studying protein-peptide interaction. This is a new generation probe which would provide fundamental guidelines to design more of such conceptual fluorescent peptide-probe that would hold great promise for application in chemical biology.

 

51.●Regioselective and Stereoselective Route to N2-β-Tetrazolyl Unnatural Nucleosides via S_N2 Reaction at the Anomeric Center of Hoffer’s Chlorosugar● Bag,* Subhendu Sekhar; Talukdar, Sangita;  Anjali S.J.● Bioorg. Med. Chem. Lett. 2016, 26(8), 2044-2050.
 

Abstract: We are reporting a regioselective and stereospecific route to N2--tetrazolyl aromatic donor/acceptor unnatural nucleosides as new class of possible DNA base analogues. The SN2 substitution reaction at the anomeric center of Hoffer’s chlorosugar with various 5-substituted aromatic tetrazoles in THF in presence of K2CO3 proceeds with regioselectivity at N2-tetrazoes and stereospecificity at -chlorosugar with very good yield. The stereoelectronic and steric effects play a crucial role for the observed outcome which is also supported from a theoretical (DFT) study. The methodology is simple, eco-compatible and the tetrazolyl unnatural nucleosides might find applications in decorating DNA for various biotechnological and DNA based material science applications.

50.●Synthesis of Functionalized Pyrazoles via Vanadium-Catalyzed C-N Dehydrogenative Cross-Coupling and Fluorescence Switch-On Sensing of BSA Protein● Sar, Dinabandhu;  Bag, Raghunath; Yashmeen, Afsana; Bag,* Subhendu Sekhar; Punniyamurthy,* Tharmalingam ● Organic Letters, 2015, 17(21), 5308-5311.
 

Abstract: Vanadium-catalyzed C-N dehydrogenative cross-coupling of alkenyl hydrazones leading to functionalized pyrazoles is described in a 1:1 mixture of toluene : H₂O using air as the terminal oxidant. The use of the commercial non-toxic VOSO₄ as a recyclable catalyst, mild reaction conditions, scalability and the broad substrate scope are the significant practical features. Some of the product pyrazoles exhibit interesting photophysical properties. Fluorescence light-up sensing of BSA Protein by one of the pyrazole is also highlighted.

49.●Triazolo-β-Aza-ε-Amino Acid and Its Aromatic Analogue as Novel Scaffolds for β-turn Peptidomimetics● Bag, Subhendu Sekhar*; Jana, Subhashis; Yashmeen, Afsana; De, Suranjan● Chemical Communication, 2015, 51, 5242 (Emerging Investigators Issue).

Abstract: Triazolo-β-aza-e-amino acid and its aromatic analogue (^AlTAA/^ArTAA) in peptide backbone mark a novel class of conformationally constrained molecular scaffolds to induce β-turn conformations. This was demonstrated for ^AlTAA in a Leu-enkephalin analogue and in a designed pentapeptide wherein FRET process was established. Restricted rotation induced chirality and turn conformation into the achiral aromatic scaffold, ^ArTAA, which in a short tripeptide backbone acted as a b-turn mimic as a b-sheet nucleator.

48.●Wavelength Shifting Oligonucleotide Probe for the Detection of Adenosine of a Target DNA with Enhanced Fluorescence Signal● Bag, Subhendu Sekhar*; Pradhan, Manoj K.; Das, Suman K.;  Jana, Subhashis; Bag, Raghunath● Bioorganic & Medicinal Chemistry Letters, 2014, 24, 4678.

Abstract: The modulated photophysical property of strong electronically coupled naphthyl uridine linked via a single C-C bond was explored in DNA detection via wavelength shifting and enhanced fluorescence emission by a simple Just-Mix & Read strategy of homogeneous DNA detection.

47.●Design and Synthesis of Triazolyl-Donor/Acceptor Unnatural Nucleosides and Oligonucleotide Probes Containing Triazolyl-Phenanthrene Nucleoside●Bag, Subhendu Sekhar*; Talukdar, Sangita;  Das, Suman Kalyan● Current Protocols in Nucleic Acids Chemistry 2014, 58:1.32.1-1.32.27.

Abstract: In the context of abasic DNA or DNA duplex stabilization several unnatural nucleosidic/non-nucleosidic base surrogates have been reported.  Toward this end, we have designed and synthesized triazolyl-aromatic donor chomophore as unnatural nucleoside analogs. These modifications display markedly higher thermal stabilization of abasic DNA duplex in comparison to the stabilization offered by other nucleoside/non-nucleoside base surrogates reported in the literature. The same oligonucleotide probe containing triazolylphenanthrene nucleotide also offers very good stability of the self-pair duplex via p-p stacking interaction and hetero pair duplex via charge transfer interaction when paired against triazolyl acceptor aromatic nucleoside.  Moreover, the probe in the reverse sequence containing triazolylphenanthrene nucleotide showed FRET efficiency in a chimeric DNA duplex. The triazolyl nucleotides would expectedly show stability toward exonuclease activity. This unit describes protocol for chemical synthesis of unnatural triazolyl nucleosides and one oligonucleotide probe. This unit also provides a summary of various thermal and photophysical applications of triazolylphenantherene containing oligonucleotides. Curr. Protoc. Nucleic Acid Chem. 58:1.32.1-1.32.27 @2014 by John Wiley & Sons, Inc.

46.●Dual Door Entry to Exciplex Emission in A Chimeric DNA Duplex Containing Non-nucleoside-Nucleoside Pair●Bag, Subhendu Sekhar*; Talukdar, Sangita;  Kundu, Rajen; Saito, Isao; Jana, Subhashis● Chemical Communications 2014, 50, 829.

Abstract: Better Dual door entry to exciplex formation was established in a chimeric DNA duplex wherein a fluorescent non-nucleosidic base surrogate (^OxoPyS) paired against a fluorescent nucleosidic base surrogate (^TPhenB_Do). Packing of nucleobases via intercalative stacking interaction led to an exciplex emission either via FRET from donor ^TPhenB_Do or direct excitation of FRET acceptor ^OxoPyS.

45.●Triazolyl-Donor/Acceptor Chromophore Decorated Unnatural Amino Acids and Peptides: FRET Event in β-Turn Conformation●Bag, Subhendu Sekhar*; Jana, Subhashis; Yashmeen Afsana; Senthilkumar, K; Bag, Raghunath● Chemical Communications 2014, 50, 433.

Abstract: The β-turn conformation and FRET process were established in the designed tripeptide containing fluorescent triazolyl donor and acceptor unnatural amino acids separated by a natural alanine.

44.●Unnatural triazolyl nucleoside stabilizes an abasic site containing DNA duplex equally as the stabilization of a natural A-T pair●Bag, Subhendu Sekhar*; Kundu, Rajen; Sangita Talukdar ● RSC Advances 2013, 3, 21352.

Abstract: Better than reported abasic duplex stabilization was achieved with novel triazolylphenanthrene nucleoside ^TPhenB_Do. The large surface area, polarizability and strong stacking propensity of triazolylphenanthrene play a major role to offer thermal stabilization of ^TPhenB_Do-F duplex comparable to that of a natural A-T pair via strong intercalative stacking interaction.

43.●Sensing of micellar microenvironment  with dual fluorescent probe, triazolylpyrene (^TNDMBPy) ●Bag, Subhendu Sekhar*; Kundu, Rajen ● Journal of Fluorescence 2013, 23, 939-938.

Abstract: We report a dual fluorescent triazolylpyrene (^TNDMBPy) as an efficient fluorescent light-up probe of various micellar microenvironments. The absorption spectra of ^TNDMBPy in an aqueous solution of varying surfactant concentration, CTAB, SDS and TX-100 showed that as the surfactant concentration was increased the absorbance increased with no shift in wavelength maxima. The increase of absorbance in each surfactant solution with increase in surfactant concentration was due to the enhanced solubilization of ^TNDMBPy in surfactant solutions. Our investigations based on steady state and time resolved fluorescence techniques showed that the probe reports the microenvironment of ionic surfactant solutions (CTAB and SDS) via dual emission (LE and ICT) at low surfactant concentration. The ICT band showed a blue shifting pattern with enhanced intensity that disappeared as the concentration of surfactant increases (> 1 mM for CTAB and > 3 mM for SDS). In non-ionic surfactant (Triton X-100) solution, the fluorophore showed dual emission with dominant ICT behaviour over LE emission at low concentration (up to 0.35 mM). In reverse micelle we observed a blue shifted ICT band with no LE band with increasing molar concentration of water. We found 100 nm blue shifting when we moved from R = 0 to R = 7, where R is the molar ratio of water to TX-100 (R = [H2O]/[TX-100]). The blue shifting of ICT band is because of the movement of the probe from hydrophilic core to hydrophobic core (surface) of the reverse micelle. Thus from the steady-state fluorescence study it was observed that the ICT band of the probe, ^TNDMBPy was more influenced by the micellar environment in comparison to the LE band. This difference in behaviour of the fluorophore is probably because of varying extent of hydrophobic/hydrogen bonding interactions experienced by the probe and its relative disposition inside the various micellar nanocores.

 

42.●Triazolyl-Donor/Acceptor Sensing of biomolecules and label free discrimination of DNA containing a triple T-C/T-G mismatch pair with a fluorescence light-up probe, triazolylpyrene (^TNDMBPy) ●Bag, Subhendu Sekhar*; Kundu, Rajen; Jana Subhashis ● Tetrahedron Lett. 2013, 54, 2627-2632.

Abstract: Binding to the minor groove of calf-thymus DNA (ct-DNA) and strong binding in hydrophobic pocket of bovine serum albumin (BSA), switched-on the fluorescence of smart fluorescent probe, triazolylpyrene (TNDMBPy). Also, a novel label free strategy was adopted to detect DNA base mismatch via the generation of distinct fluorescence signal at visible region utilizing the same probe.

41.●Solvatochromic fluorescent cyanophenoxazine: design, synthesis, photophysical properties and fluorescence light-up sensing of ct-DNA ●Bag, Subhendu Sekhar*; Ghorai, Samir; Jana, Subhashis; Mukherjee,* Chandan ● RSC Advances 2013, 3, 5374–5377.

Abstract: We report our new methodology on the Mn2+-catalysed synthesis of donor/acceptor substituted classical fluorescent phenoxazine which showed high solvatochromic emission property and ct-DNA sensing efficiency via light-up fluorescence response.

40.●Triazolyl-Donor/Acceptor Chromophores Decorated Unnatural Nucleosides and Oligonucleotides with Duplex Stability Comparable to that of Natural A/T Pair ●Bag, Subhendu Sekhar*; Talukdar, Sangita; Matsumoto, Katsuhiko; Kundu, Rajen ● The Journal of Organic Chemistry 2013, 78, 278.

Abstract: We report the design and synthesis of triazolyl donor/acceptor unnatural nucleosides via click chemistry and the studies on the duplex stabilization of DNA containing two of such new nucleoside. The observed duplex stabilization among the self-pair/hetero-pair has been found to be comparable to that of a natural A/T pair. Our observations on the comparable duplex stabilization has been explained based on possible π-π stacking and/or charge transfer interactions between the pairing partners. The evidence of ground state charge transfer complexation came from the UV-visible spectra and the static quenching of fluorescence in a hetero-pair. We also have exploited one of our unnatural DNAs in stabilizing abasic DNA.

32.●Installation/Modulation of the Emission Response via Click Reaction● Bag, Subhendu Sekhar*; Kundu, Rajen● The Journal of Organic Chemistry 2011, 76(9), 3348-3356.

Abstract: We have demonstrated the installation of a fluorescence property into a non-fluorescent precursor and modulation of an emission response of a pyrene fluorophore via click reaction. The synthesized fluorophores show different solvatochromicity and/or intramolecular charge transfer (ICT) feature as is revealed from the UV-visible, fluorescence photophysical properties of these fluorophores, and DFT/TDDFT calculation. We observed that some of the synthesized fluorophores showed purely ICT character while emission from some of them arose from LE state. A structure-less and solvent polarity-sensitive dual emission behavior was observed for one of the triazolyl-pyrene fluorophores that contains an electron donating –NMe2 substituent (fluorophore, 7a). Conversely, triazolyl-pyrene with an electron-withdrawing –CN group (fluorophore, 7b) showed a solvent polarity-independent vibronic emission. The effect of ICT on the photophysical properties of these fluorophores were studied by fluorescence emission spectra, and DFT/TDDFT calculations. Fluorescence life times were also measured in different solvents. All of our findings revealed the delicate interplay of structure and emission properties and thus having broader general utility. As the CT to LE intensity ratio can be employed as a sensing index, the dual emissive fluorophore can be utilized in designing molecular recognition system too. We envisage that our investigation is of importance for the development of new fluorophores with predetermined photophysical properties that may find a wide range of applications in chemistry, biology, and in material sciences.

31.●Click-Reagent Version of Sonogashira Coupling Protocol to Conjugated Fluorescent Alkynes with No or Reduced Homocoupling● Bag, Subhendu Sekhar*; Kundu, Rajen; Das, Manas● The Journal of Organic Chemistry Note 2011, 76(7), 2332-2337.

Abstract: A click-reagent version of the Sonogashira-coupling protocol has been developed. Diarylalkynes with donor and/or acceptor substituents have been synthesized via this protocol at moderate to excellent yields and with no or drastically reduced quantities of undesired homocoupled side products. This protocol is green-solvent compatible, air-insensitive, and effective under microwave conditions.

 

28.●Suppressed b-Effect of Silicon in 3-Silylated Monocyclic b-Lactams: The Role of Antiaromaticity● Bag, Subhendu Sekhar*; Kundu, Rajen; Basak, Amit; Slania, Zdenek● Organic Letters 2009, 11(24),  5722-5725.

Abstract: The b-stabilizing effect of silicon substituent at C-3 on a C-4 cation and a radical in the 2-azetidinone systems is studied using NMR kinetics. While the b-effect is virtually nonexistent in the case of a cation, a foiled b-effect (only a 3-fold rate enhancement) is obsd. for a radical intermediate.  From both the exptl. and theor. studies, it is demonstrated that antiaromaticity is playing the prime role in suppressing the b-stabilizing effect of silicon.

27.●A novel enediynyl peptide inhibitor of furin that blocks processing of proPDGF-A, B and proVEGF-C● Basak, Ajoy; Khatib, Abdel-Majid; Mohottalage, Dayani; Basak, Sarmistha; Kolajova, Maria; Bag, Subhendu Sekhar; Basak, Amit● PLoS One  2009,  4(11),  No pp.

Abstract: Background: Furin represents a crucial member of secretory mammalian subtilase, the Proprotein Convertase (PC) or Proprotein Convertase Subtilisin/Kexin (PCSK) superfamily.  It has been linked to cancer, tumorgenesis, viral and bacterial pathogenesis.  As a result it is considered a major target for intervention of these diseases.  Methodol./Principal Findings: Herein, we report, for the first time, the synthesis and biol. evaluation of a newly designed potent furin inhibitor that contains a highly reactive beta-turn inducing and radical generating "enediynyl amino acid" (Eda) moiety.  "Eda" was inserted between P1 and P1' residues of hfurin98-112 peptide, derived from the primary cleavage site of furin's own prodomain.  The resulting hexadecapeptide deriv. inhibited furin in vitro with IC50 .apprx.40 nM when measured against the fluorogenic substrate Boc-RVRR-MCA.  It also inhibited furin-mediated cleavage of a fluorogenic peptide derived from hSARS-CoV spike protein with IC50 .apprx.193 nM.  Addnl. it also blocked furin-processing of growth factors proPDGF-A, B and VEGF-C that are linked to tumor genesis and cancer.  CD study showed that this inhibitor displayed a predominantly beta-turn structure while western blots confirmed its ability to protect furin protein from self degrdn.  Conclusion/Significance: These findings imply its potential as a therapeutic agent for intervention of cancer and other furin-assocd. diseases.

26.●Pyrene-labeled deoxyguanosine as a fluorescence sensor to discriminate single and double stranded DNA structures: Design of ends free molecular beacons● Matsumoto, Katsuhiko; Shinohara, Yuta; Bag, Subhendu Sekhar; Takeuchi, Yoshiki; Morii, Takashi; Saito, Yoshio; Saito Isao ● Bioorganic & Medicinal Chemistry Letters, 2009, 19, 6392-6395.

Abstract: A novel fluorescent DNA probe containing pyrene-labeled C8 alkylamino-substituted 2′-deoxyguanosine was designed in order to discriminate single stranded and double stranded regions in DNA. This fluorescent sensor was used for the design of practically useful 3′- and 5′-ends free self-quenched molecular beacon (MB). Unique MB detectable by pyrene excimer fluorescence was also demonstrated.

25.●Fluorescence switching of photochromic vinylpyrene-substituted 2'-deoxyguanosine● Saito, Yoshio; Matsumoto, Katsuhiko; Takeuchi, Yoshiki; Bag, Subhendu Sekhar; Kodate, Satoshi; Morii, Takashi; Saito, Isao● Tetrahedron Letters  2009,  50(13),  1403-1406. 

Abstract: We synthesized C8-vinylpyrene-substituted 2'-deoxyguanosine and studied the photoregulated reversible E-Z isomerization.  When E-isomer was irradiated with visible light (>420 nm), E- to Z-isomerization took place very rapidly, while upon irradn. with UV-light (.apprx.365 nm), Z-isomer was converted to E-isomer.  When Z-isomer was illuminated with 365-400 nm light, no fluorescence was obsd., while E-isomer showed a very strong fluorescence emission, indicating that ^VPyG could be a useful fluorescence switching mol.

2006 - 2008

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24.●Ends free and self-quenched molecular beacon with pyrene labeled pyrrolocytidine in the middle of the stem● Saito, Yoshio; Shinohara, Yuta; Bag, Subhendu Sekhar; Takeuchi, Yoshiki; Matsumoto, Katsuhiko; Saito, Isao● Tetrahedron  2009,  65(4),  934-939. 

Abstract: Pyrene labeled pyrrolocytidine was incorporated into an oligonucleotide to construct ends free and self-quenched mol. beacon in which the fluorophore contg. pyrrolocytidine was placed in the middle of the stem and used for the detection of a target DNA with an excellent efficiency.

23.●Design of an ultimate quencher free molecular beacon containing pyrrolocytidine-guanine base pair● Saito, Yoshio; Shinohara, Yuta; Bag, Subhendu Sekhar; Takeuchi, Yoshiki; Matsumoto, Katsuhiko; Saito, Isao● Nucleic Acids Symposium Series 2008, 52(1), 361-362. 

Abstract: A novel quencher free mol. beacon was designed in which fluorophore-labeled pyrrolocytidine was placed away from the stem terminal.  This new type of MB was used for the detection of a target DNA with an excellent efficiency.

22.●Design of an efficient self-quenched molecular beacon for SNPs genotyping● Saito, Yoshio; Numajiri, Kyoko; Bag, Subhendu Sekhar; Mizuno, Erika; Saito, Isao. ●Nucleic Acids Symposium Series 2008, 52(1),  359-360. 

Abstract: Quencher free mol. beacon with an excellent signal to noise ratio was designed and used for SNPs genotyping.

21.●Fluorometric sensing of conformational switching of DNA; the use of fluorescence labeled C8-alkylamino substituted 2'-deoxyguanosine● Saito, Yoshio; Matsumoto, Katsuhiko; Bag, Subhendu Sekhar; Misawa, Akihiro; Saito, Isao●  Nucleic Acids Symposium Series 2008,  52(1),  357-358.

Abstract: C8-alkylamino substituted 2'-deoxyguanosine was incorporated into a DNA sequence and then labeled with pyrene.  The conformational change from B- to Z-form was monitored using CD and fluorescence spectroscopy for both labeled and unlabeled ODNs.

20.●C8-alkynyl- and alkylamino substituted 2'-deoxyguanosines: a universal linker for nucleic acids modification● Saito, Yoshio; Matsumoto, Katsuhiko; Bag, Subhendu Sekhar; Ogasawara, Shinzi; Fujimoto, Kenzo; Hanawa, Kazuo; Saito, Isao●    Tetrahedron  2008,  64(16),  3578-3588. 

Abstract: Incorporation of modified nucleosides with a flexible universal linker is of great value for post-synthetic modification of nucleic acids.  Thus, C8-alkynyl- and alkylamino substituted 2'-deoxyguanosines I and II (x = 1,2,3,4) were synthesized for the first time and incorporated into short oligonucleotide sequences.  The preference for syn conformation of these C8-substituted 2'-deoxyguanosines and the stability of the duplexes were discussed.  The stabilizing effect of Z-DNA has also been examd. 

19.●Synthesis of C8-alkylamino substituted 2'-deoxyguanosine● Saito, Yoshio; Matsumoto, Katsuhiko; Bag, Subhendu Sekhar; Ogasawara, Shinji; Suzuka, Isamu; Saito, Isao● Nucleic Acids Symposium Series  2007,   (51),  147-148. 

Abstract: Synthesis of C8-alkynyl- and alkylamino substituted 2'-deoxyguanosine, e.g. I, is described.  Protected alkynyl-amines are coupled with 8-bromo-2'-deoxyguanosine by a Pd(0)-mediate Sonogashira coupling protocol.  Hydrogenation of alkynyl derivs. over 10% Pd/C under atm. pressure gave 8-alkylamino guanosine derivs. in nearly quant. yields. 

18.●Design of dual-labeled oligonucleotide probes for SNPs genotyping● Saito, Yoshio; Bag, Subhendu Sekhar; Kodate, Satoshi; Suzuka, Isamu; Saito, Isao● Nucleic Acids Symposium Series 2007,   (51),  23-24. 

Abstract: Our effort in designing base-discriminating fluorescence nucleosides (BDF), leads us to develop dual-labeled oligonucleotide probe in which the BDF nucleoside, PyU/2-AntU act as the donor sepd. by a defined base pair distance from the acceptor, fluorescein, attached to 5'-end of the probe.  Thus, a longer wavelength emission from acceptor might allow the probe to be used for SNP typing in chip based detection technol. or in cell.

17.●Anthracene based base-discriminating fluorescent oligonucleotide probes for SNPs typing: Synthesis and photophysical properties● Saito, Yoshio; Motegi, Kaori; Bag, Subhendu Sekhar; Saito, Isao● Bioorganic & Medicinal Chemistry  2008,  16(1),  107-113. 

Abstract: 2- And 9-Anthracenecarboxamide labeled 2'-deoxyuridines were synthesized and their photophys. properties were examd.  These oligonucleotide probes are capable of detecting adenine base on a target DNA sequence.  It was also found that 2-anthracene based oligonucleotide probe is more efficient than the corresponding 9-anthracene based oligonucleotide in the application for DNA chip based SNP detection, due to its longer emission wavelength and high fluorescence intensity.

 

16.●Design of a novel G-quenched molecular beacon: A simple and efficient strategy for DNA sequence analysis● Saito, Yoshio; Mizuno, Erika; Bag, Subhendu Sekhar; Suzuka, Isamu; Saito, Isao● Chemical Communications 2007,  (43),  4492-4494. (Highlited as Chemical Biology Research Article 2007, 12.)

Abstract: G-quenched MBs are devised from readily available starting materials and used for sequence specific DNA detection with high efficiency.

15.●Synthesis and properties of acridone-labeled base-discriminating fluorescent (BDF) nucleosides● Saito, Yoshio; Hanawa, Kazuo; Bag, Subhendu Sekhar; Motegi, Kaori; Saito, Isao● Nucleic Acids Symposium Series  2006,   (50),  181-182. 

Abstract: We have developed novel acridone-labeled BDF probe which showed its potential in recognizing opposite matched base from its target sequence via enhancement of fluorescence intensity.  This probe emit at a longer wavelength than previously reported pyrene-labeled BDF probe and thus can be used in DNA chip.

14.●Synthesis of perylene-labeled base-discriminating fluorescent (BDF) nucleoside and its fluorescence properties● Bag, Subhendu Sekhar; Saito, Yoshio; Hanawa, Kazuo; Hayasi, Keigo; Kodate, Satoshi; Suzuka, Isamu; Saito, Isao● Nucleic Acids Symposium Series  2006,   (50),  179-180. 

Abstract: We have synthesized perylene labeled BDF probe and its photophys. properties were explored.  Perylene labeled oligonucleotide probe is capable of detecting cytosine from its target mismatch sequence by enhancement of fluorescence intensity.

13.●Dual-labeled oligonucleotide probe for sensing adenosine via FRET: A novel alternative to SNPs genotyping● Saito, Yoshio; Bag, Subhendu Sekhar; Kusakabe, Yuichi; Nagai, Chiharu; Matsumoto, Katsuhiko; Mizuno, Erika; Kodate, Satoshi; Suzuka, Isamu; Saito, Isao● Chemical Communications 2007,   (21),  2133-2135. 

Abstract: A novel FRET based strategy for DNA sequence anal. utilizing base-discriminating fluorescence (BDF) nucleosides (^PyU or ^2-AntU) as donor in the dual-labeled oligonucleotide probe is reported.  Emission from acceptor (5'-FAM) was obsd. upon excitation at the donor only when paired with adenine on the complementary target sequence.

12.●Highly selective fluorescent nucleobases for designing base-discriminating fluorescent probes● Saito, Isao; Saito, Yoshio; Hanawa, Kazuo; Hayashi, Keigo; Motegi, Kaori; Bag, Subhendu Sekhar; Dohno, Chikara; Ichiba, Tomohisa; Tainaka, Kazuki; Okamoto, Akimitsu● Pure and Applied Chemistry 2006,  78(12),  2305-2312. 

Abstract: There is increasing interest in single nucleotide polymorphism (SNP) typing since they can be used as markers to identify the genes that underlie complex diseases and to realize the full potential of pharmacogenomics in analyzing variable response to drugs.  Among the different methodologies for SNP genotyping, the homogeneous assay is more amenable than the heterogeneous one.  In this article, we will describe some of our most recently developed novel base-discriminating fluorescent (BDF) nucleosides useful for homogeneous SNP typing.  Our novel concept led to the investigation of a new type of pyrene-labeled BDF nucleosides ^PyU, ^PyC, ^8pyA, and ^MePydA, which emitted strong fluorescence only when the bases opposite the BDF bases are A, G, T, and C, resp.  The DNA probes contg. four different BDF bases enabled us to distinguish single-base alterations by simply mixing with a sample soln. of target DNA.  An example of SNP typing of c-Ha-ras SNP sequence has also been demonstrated.  Detection of base insertion in insertion/deletion (indel) polymorphisms using pyrene excimer fluorescent probe has also been explored.

11.●Intelligent fluorescent nucleoside in sensing cytosine base: Importance of hydrophobic nature of perylene fluorophore● Bag, Subhendu Sekhar; Saito, Yoshio; Hanawa, Kazuo; Kodate, Satoshi; Suzuka, Isamu; Saito, Isao. ● Bioorganic & Medicinal Chemistry Letters  2006,  16(24),  6338-6341. 

Abstract: Fluorescence response upon hybridization of perylene labeled oligonucleotide probes depends on the microenvironment experienced by the perylene fluorophore.  In mismatched duplex (^PerU-C), enhanced fluorescence was obsd. while in matched duplex (^PerU-A) fluorescence intensity decreased considerably.  This observation will be a promising research effort in giving rise to a new powerful tool in detection of SNP.

10. ●Acridone-labeled base-discriminating fluorescence (BDF) nucleoside: synthesis and their photophysical properties● Saito, Yoshio; Hanawa, Kazuo; Kawasaki, Naomi; Bag, Subhendu Sekhar; Saito, Isao. ●  Chemistry Letters  2006,  35(10),  1182-1183. 

Abstract: Acridone-labeled BDF bases ^AcA and ^AcU were incorporated into oligonucleotides (ODNs) and their photophys. properties were evaluated.  The BDF probe containing ^AcA is extremely powerful in recognizing opposite base T via enhancement of the fluorescence intensity.  Furthermore, they emit strong fluorescence at a longer wavelength than previously reported pyrene-labeled BDF probes and thus can be used for the detection of SNPs.

 

2000-2005

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9.  ●Design and synthesis of a novel enediynyl pentapeptide with predominantly b-turn structural motif and its potential as a fluorescence-based chemosensor● Basak, Amit; Bag, Subhendu Sekhar; Basak, Ajoy●  Bioorganic & Medicinal Chemistry  2005,  13(12),  4096-4102.  

Abstract: A novel enediynyl pentapeptide in the protected form 1 was synthesized and characterized.  It exists predominantly in b-turn structural motif as revealed by variable temperature. NMR and CD spectroscopy.  In the presence of transition metal ions and gold nanoparticles, the fluorescence intensity of the peptide got enhanced with remarkable quantum yield with the Z-enediynyl w-amino acid acting as a fluorophoric reporter.  The interesting photophysical behaviors with alkali and alkaline earth metal ions are also reported.

8.  ●The effect of charge-transfer complexation/p-stacking interactions in lowering the activation barrier of the Bergman Cyclization● Basak, Amit; Bag, Subhendu Sekhar; Das, Amit K● European Journal of Organic Chemistry  2005,   (7),  1239-1245. 

Abstract: To elaborate the concept of weak interactions and their effect on Bergman Cyclization (BC), several 1,2-dikynyl benzenes incorporating various combinations of donor and acceptor units in the two arms of the enediynes were designed and synthesized, and their charge-transfer interactions followed by UV/Vis spectroscopy.  The thermal reactivities, as studied by DSC, show an increase in reactivity for the donor/acceptor or donor/donor combinations relative to the acceptor/acceptor pair.  Such an increase in reactivity can be explained on the basis of intramol. charge transfer and p-stacking interactions between the two arms, which may lower the distance between the two acetylenic ends.

7. ●Purification, characterization and some studies on secondary structure of tannase from Aspergillus awamori Nakazawa● Mahapatra, Kalyani; Nanda, Ranjan Kumar; Bag, Subhendu Sekhar; Banerjee, Rintu; Pandey, Ashok; Szakacs, George● Process Biochemistry (Oxford, United Kingdom) 2005, 40(10), 3251-3254.

Abstract: Tannase (EC 3.1.1.20) (I) of A. awamori Nakazawa was purified and characterized. Optimal conditions of prodn. were detd. using varying substrate combinations and studying fermn. on various media combinations. Fermn. was carried out for 46 h for optimum enzyme prodn. Enzyme samples were obtained from the broth after fermn. by acetone pptn. of the supernatant followed by gel filtration chromatog. The properties of purified I were investigated. The optimum temp. and pH were investigated and the effects of urea, surfactants, and chelators were studied. I from this new isolate exhibited optimum activity at 35 and pH 5.0. Urea concns. of >3M were inhibitory. Increasing concns. of sodium lauryl sulfate (SLS) also led to a decrease in activity, with 2% SLS being inhibitory. Increasing concns. of EDTA also had an inhibitory effect on I. I was found to be a glycoprotein. CD anal. of purified fractions of I indicated that the .beta.-sheet structure was predominant indicating its globular nature.

6.  ●Effect of Remote Trigonal Carbons on the Kinetics of Bergman Cyclization: Synthesis and Chemical Reactivity of Pyridazinedione-Based Enediynes●  Basak, Amit; Bag, Subhendu Sekhar; Majumder, Pooja Anjali; Das, Amit Kumar; Bertolasi, Valerio● Journal of Organic Chemistry  2004,  69(20),  6927-6930. 

Abstract: The synthesis and chem. reactivity of pyridazinedione-based enediynes (1, 2) are described.  Both of these enediynes, namely the dihydro compd. 1 and its corresponding tetrahydro analog 2, were prepd. by double N,O-alkylation of the corresponding heterocyclic system with the acyclic enediynyl dibromide 8 in good yields.  Their single-crystal X-ray structures revealed similar c, d distances (distance between the acetylenic carbons undergoing covalent connection in Bergman cyclization).  Interestingly, these mols. undergo Bergman cyclization at different rates, and the reactivity is shown to be dependent upon the state of hybridization of C-4 and C-5 atoms of the parent heterocyclic ring.

5.  ●Molecular recognition in b-lactams: The crystal packing in 4-sulfonyl b -lactams●  Basak, Amit; Bag, Subhendu Sekhar; Mazumdar, Pooja Anjali; Bertolasi, Valerio; Das, Amit Kumar● Journal of Chemical Research  2004,   (5),  318-321.  

Abstract: Single crystal x-ray structures of 4-Ph sulfonyl 2-azetidinone 1, a 1:2 conglomerate of the corresponding 3-Me (trans) and 3,3-di-Me derivs., and 3-acetoxymethyl 1,4-di-Ph 2-azetidinone revealed interesting variation in crystal packing dictated by H-bonding and hydrophobic interactions which may be responsible for mol. recognition in b-lactams.

4.  ●Synthesis and reactivity of enediynyl amino acids and peptides: a novel concept in lowering the activation energy of Bergman cyclisation by H-bonding and electrostatic interactions● Basak Amit; Bag, Subhendu Sekhar; Bdour Hussam M. M. Chemical communications 2003,  (20),  2614-5.

Abstract: Novel enediynyl amino acids and peptides 3 and 5-8 were synthesized and their thermal reactivity towards Bergman cyclization studied and compared with the earlier reported amino acid 4, which demonstrated, for the first time, the effect of H-bonding and electrostatic interactions in lowering the activation energy of Bergman cyclization.

3.  ●Chelation-Controlled Bergman Cyclization: Synthesis and Reactivity of Enediynyl Ligands ● Basak, Amit; Mandal, Subrata; Bag, Subhendu Sekhar● Chemical Reviews 2003,  103(10),  4077-4094. 

      Abstract: A review with 150 references.

2.  ●Synthesis, reactivity and conformational preferences of novel enediynyl peptides: a possible scaffold for b-sheet capping turns● Basak, Amit; Rudra, Kakali Rani; Bag, Subhendu Sekhar; Basak, Ajoy●  Journal of the Chemical Society, Perkin Transactions 1  2002,   (15),  1805-1809. 

Abstract: Novel enediynyl tripeptides 2(a-c) in fully protected forms have been prepd. via a sequence of palladium(0)-based Sonogashira coupling.  The thermal reactivity of these peptides was shown to be dependent upon the nature of the side chain in the amino acids.  Anal. of the CD-spectra of these peptides as well as the variation of chem. shifts with temp. revealed the presence of a b-sheet nucleating conformation in equil. with a conformation induced by H-bond formation between the CO and NH belonging to the enediynyl amino acid.