Bioorganic Chemistry Laboratory



Selected Publications
  1. Nibedita Ghosh *, Lal Mohan Kundu * "A reagent-free, sequence-dependent in situ peptide self-cyclization strategy under physiological condition " European Journal of Medicinal Chemistry Reports 12 (2024) 100236 https://doi.org/10.1016/j.ejmcr.2024.100236
  2. Pallabi Paul, Hirakjyoti Roy, Gourav Bhattacharjee, Neeharika Baruah and Lal Mohan Kundu* "Amine-Rich Carbon Dots Synthesized from Kappa-Carrageenan and l-Lysine as a Dual Probe for Detection of Folic Acid and Tumor-Targeted Delivery of Therapeutics " ACS Applied Bio Materials 2024 doi: 10.1021/acsabm.4c00678
  3. Paul, P., Das, H., Horo, H., Kundu, L.M. "DNA-Based Hydrogel in Drug Delivery." Biomaterial-based Hydrogels. Springer, Singapore. Springer. (Book Chapter 2024). doi.org/10.1007/978-981-99-8826-6_11.
  4. Katare A, Sharma S, Horo H, Bhowmick S, Kundu LM*. Mandal B* "An investigation on the effects of both amine grafting and blending with biodegradable chitosan membrane for CO2 capture from CO2/N2 gas mixtures." Chemical Engineering Journal, 2023.
  5. Horo H, Das H, Bhattacharjee G, Kundu L M. “Chitosan-derived Biomaterials in Cancer Therapeutics and Biomedical Imaging.” RSC. (Book Chapter 2022). doi.org/10.1039/9781839166235-00497.
  6. Ghosh N and Kundu L. M.* "Breaker peptides against amyloid-β aggregation: a potential therapeutic strategy for Alzheimer's disease." Future Medicinal Chemistry 2021.
  7. Ghosh N and Kundu L. M.* "In-situ side-chain peptide cyclization as a breaker strategy against the amyloid aggregating peptide." Bioorganic & Medicinal Chemistry 2021, 33, 116017.
    Abstract:
    Accumulation and deposition of misfolded amyloid β (Aβ) peptide outside the nerve cells are one of the major causes of Alzheimer's disease (AD). To date, one of the promising therapeutic strategies for AD is to block the early steps associated with the aggregation of Aβ peptide. We have developed synthetic breaker peptides derived from the original Aβ sequences that undergo self-cyclization in situ. We have focussed and replaced Val-18 (of Aβ) by side-chain modified glutamic acid (Glu-OBn) to generate adequate turn through in-situ peptide cyclization to disrupt the β-sheet structure of Aβ. The disruption of amyloid fibril formation and the mechanism of the 'inhibition of aggregation' were studied by various biophysical methods, such as ThT-assay, TEM, Congo-red birefringence study. CD and FTIR spectroscopy were used to characterize the conformational change during the aggregation process. Results suggest that designed breaker peptides may be useful to inhibit and disrupt not only Aβ peptide but related peptides that undergo aggregation.
  8. Horo, H.; Bhattacharya, S.; Mandal, B.; Kundu, L. M*. “Synthesis of functionalized silk-coated chitosan-gold nanoparticles and microparticles for target-directed delivery of antitumor agents” Carbohydrate polymers 2021, 117659.
    Abstract:
    Chemically modified biopolymers derived nanomaterials have shown great potential in drug delivery and live-cell imaging. We have developed two materials, doxorubicin-loaded chitosan-gold nanoparticles and beads, both embedded with functionalized silk fibroin. Nanoparticles with size 8 ± 3 nm were synthesized using chitosan as reducing and stabilizing agent. Beads with 900-1000 µm size were formulated by the ionic gelation technique. Both the materials were coated with functionalized silk fibroin for targeted and sustained drug release properties. The coated materials showed retarded drug release compared to the uncoated ones. The cytotoxicity was assessed in HeLa cell lines, which demonstrated a maximum dose-dependent decrease in cell viability for the cells treated with folate conjugated silk fibroin coated nanoparticles. The live-cell imaging of the nanoparticles unveiled the increased cellular uptake of the coated materials by seven folds than the uncoated ones. Thus, functionalized SF coated materials can be effective drug delivery tools for targeted and sustained drug release.
  9. Das S.; Thakur K. K.; Kunnumakkara A.B. and Kundu L. M.* "Development of a Cleavable Biotin‐Drug Conjugate Hydrogelator for the Controlled and Dual Delivery of Anticancer Drugs." Chemistry Select 2021, 6, 13, 3256-3261
    Abstract:
    Hydrogels based drug delivery has found extensive application recently. In most of the cases, polymers and peptide based hydrogels were used in drug delivery. In this report, we have developed a hydrogelator containing an anti‐tumor agent 5‐Fluorouracil (5‐Fu). The design comprised of a photo‐responsive prodrug of 5‐Fu covalently conjugated to an essential nutrient, biotin (vitamin B7), providing the hydrogelator high biocompatibility. The synthesized molecule formed hydrogel at pH 7. The hydrogel also can effectively entrap another water‐soluble chemotherapeutic agent doxorubicin hydrochloride (DOX). The release of 5‐Fu was observed in a light dependent manner whereas sustained release of DOX was recorded from the hydrogel. The controlled and sustained release of both the drugs were monitored by UV‐Vis, fluorescence spectroscopy and 1H NMR study. Such 5‐Fu‐biotin gel could be useful as a dual drug carrier for effective delivery of two hydrophilic antitumor agents simultaneously
  10. Verma, R., Kundu, L. M., & Pandey, L. M. (2021). "Decontamination of distillery spent wash through advanced oxidation methods." In Advanced Oxidation Processes for Effluent Treatment Plants (pp. 103-117). Elsevier. (Book Chapter)
    Abstract:
    Distillery industries play an important role in the world economy, but they also generate highly polluted wastewater, called spent wash. This spent wash contains high COD (110,000–190,000 mg L− 1), BOD (50,000–90,000 mg L− 1), and melanoidins such as nonbiodegradable coloring compounds. In the last few decades, advanced oxidation processes (AOPs) have been applied successfully to remove color and degrade pollutants from wastewater. The AOPs generate very powerful oxidants such as hydroxyl radicals, which are generated from ozone (O3), hydrogen peroxide (H2O2), photocatalysis, the Fenton process, and a combination of ultraviolet (UV) radiation. These •OH free radicals oxidize organic and inorganic compounds present in wastewater and decompose them. These methods are recognized as highly efficient for the treatment of recalcitrant water with low biodegradability and high chemical efficiency. They also have great potential to treat the highly polluted distillery spent wash. In comparison to the other treatment processes, AOPs are simple, fast, efficient, and nonselective. Thus, these methods can be applied along with other treatment processes, either in the pretreatment or the final treatment step. In this chapter, the fundamentals and applications of various AOPs relevant to the decontamination of distillery spent wash are discussed. The applications and effectiveness of various AOPs toward decolorization and COD removal from distillery spent wash are mainly discussed.
  11. Himali Horo, Sini Porathoor, Ruchi Anand and Lal Mohan Kundu* “A combinatorial approach involving E. coli cytosine deaminase and 5-fluorocytosine-nanoparticles as an enzyme-prodrug therapeutic method for highly substrate selective in situ generation of 5-fluorouracil.” Journal of Drug Delivery Science and Technology 2020, 58, 101799.
    Abstract:
    Enzyme-prodrug combination is a recognized therapeutic strategy for the treatment of cancer cells. Cytosine deaminases (CD) are non-mammalian proteins perceived to convert the prodrug 5-fluorocytosine (5-FC), into the active antitumor agent 5-fluorouracil (5-FU). In this study, we have synthesized 5-FC as well as 5-FU loaded chitosan-silver nanoparticles in a green synthesis approach, with high yield. The size of the nanoparticles was ascertained to be below 25 nm, thus proficient in penetrating cells. Investigation in human breast carcinoma cell line MDA-MB-468 manifested potent cytotoxicity for 5-FU nanoparticles as compared to the prodrug, 5-FC nanoparticles. E. coli CD (ECD) effectively hydrolyzes 5-FC into 5-FU but was inert to silver nanoparticles as well as 5-FU loaded nanoparticles.
  12. Soumi Das, Kamalesh Verma, Vikash Kumar Dubey and Lal Mohan Kundu* “Fabrication of nanoparticles from a synthesized peptide amphiphile as a versatile therapeutic cargo for high antiproliferative activity in tumor cells” Bioorganic Chemistry 2020, 94, 103440.
    Abstract:
    Nanoparticles with encapsulated small molecules have attained vital importance in anticancer research. Peptide-based nanoparticles show their versatility in drug delivery due to their excellent biocompatibility and nontoxic nature. We demonstrate here the design and fabrication of peptide-based nanoparticles as dual-therapeutic cargo for the controlled release of hydrophilic 5-Fluorouracil (5Fu) and hydrophobic camptothecin (CPT), simultaneously. The covalent conjugation of 5Fu with the peptide, through a stimuli-responsive linker, provided better control over the release of 5Fu and dramatically reduced the possibility of leaching of the small molecule. As anticipated, the peptide-5Fu nanoparticles were efficient to encapsulate a second chemotherapeutic molecule CPT in its hydrophobic region. The stimuli-responsive release of 5Fu was carefully monitored by HPLC, NMR, and UV–visible spectroscopy. On the other hand, the release of the hydrophobic drug CPT from the nanoparticles was determined to be in a diffusion-controlled fashion. Assessment of performance in human cervical HeLa cell lines demonstrated the peptide-drug nanoparticles to be highly nontoxic. Whereas, the simultaneous release of the two antitumor agents, in a controlled manner, resulting in rapid antiproliferation of the tumor cells.
  13. Verma, R., Sharma, S., Kundu, L. M., & Pandey, L. M* "Experimental investigation of molasses as a sole nutrient for the production of an alternative metabolite biosurfactant." Journal of Water Process Engineering 2020, 38, 101632
    Abstract:
    In this study, sugarcane molasses was explored as a sole source of nutrients for the production of a value added product (biosurfactant) using an isolated strain Bacillus subtilis RSL-2. The biosurfactant production (maximum) was scrutinized by response surface methodology-central composite design (RSM-CCD), considering molasses as the carbon source (1–5 % w/v), pH (4–8) and temperature (25–45 °C), as the input parameters. At the optimized condition, remarkable biosurfactant concentration and surface tension were obtained as 12.34 ± 0.1 g/L and 24.09 ± 0.11 mN/m, respectively. The critical micelle concentration of the produced biosurfactant was found to be 80 mg/L. The produced biosurfactant was identified to be lipopeptide in nature and reduced the surface tension of water from 72.80 ± 0.5 mN/m to 24.09 ± 0.11 mN/m. The produced biosurfactant showed excellent surface activities, and thermal and colloidal stability. The present study endorsed the suitability of molasses as a suitable substrate (media) for the remarkable production of biosurfactant.
  14. Kamalesh Verma, Debanjan Kundu, Lal Mohan Kundu, Ashish Kumar Singh and Vikash Kumar Dubey* “Folding and stability of recombinant azoreductase enzyme from Chromobacterium violaceum.” Enzyme and Microbial Technology 2019, 131, 109433.
    Abstract:
    Azoreductase from Chromobacterium violaceum was characterized biophysically using experimental and computational tools. The in-silico docking and cross-linking experiments using glutaraldehyde suggest dimeric nature of the enzyme. The enzyme structure was modelled and also studied using circular dichroism (CD) spectroscopy which suggests 40% α- helix, 30% β- sheet and 30% random coils. In the modelled structure of the azoreductase, the cofactor flavin mononucleotide (FMN) binding energy was -3.8 kJ/mol. The binding of FMN affects the azoreductase-cofactor complex stability. The stability-folding studies indicate that the cofactor, FMN is required for folding, stability and activity. Overall, the data provides interesting insight into stability and biophysical parameters of the azoreductase protein.
  15. Soumi Das, Himali Horo,Upashi Goswami and Lal Mohan Kundu* “Synthesis of a Peptide Conjugated 5-Fluorouracil Gelator Prodrug for Photo-Controlled Release of the Antitumor Agent” ChemistrySelect 2019, 4, 6778 –6783
    Abstract:
    Widely used chemotherapeutic agent 5‐fluorouracil (5‐Fu) exhibits adverse effects by damaging the normal cells. Controlled delivery and release of such antitumor drugs is essential for better treatment. Herein, a low molecular weight peptide‐drug conjugate for the photo‐controlled delivery of 5‐Fu is demonstrated. 5‐Fu is covalently attached with a short peptide through a photo‐cleavable linker. With a careful choice of the peptide sequence, the peptide‐drug conjugate was able to form a hydrogel within a narrow pH window (pH 6.0 ‐ 8.0). MTT assay of the peptide‐drug conjugate in HeLa cells inferred almost no cytotoxicity up to a high concentration of 110 μg/mL. The gelator prodrug releases 5‐Fu in a controlled, does‐dependent manner under irradiation. The characterizations and controlled release of the drug were investigated using various analytical techniques including FTIR, HPLC and UV‐visible spectroscopy whereas, morphology of the gel was studied by FESEM. The gelation behaviour and rheology of the conjugate was also studied in details. Such covalently peptide‐conjugated 5‐Fu gel could be useful for effective delivery of antitumor agent.
  16. Himali Horo, Soumi Das, Bishnupada Mandal and Lal Mohan Kundu* "Development of a photoresponsive chitosan conjugated prodrug nano-carrier for controlled delivery of antitumor drug 5-fluorouracil" Int.J.Biol.Macromol. 2019, 121, 1070-1076
    Abstract:
    Controlled drug delivery offers improved therapeutic efficacy of the drugs while minimizing side effects. Biocompatible polymers and nanomaterials have emerged as effective carriers for the controlled delivery of drugs. We have synthesized a prodrug of 5-fluorouracil (5FU) covalently conjugated to low molecular weight chitosan (LMWC) via a photocleavable linker. The conjugate was designed to be cleaved under 365 nm UV-A radiations, which is regarded as relatively safe for the cells and release 5FU in a dose-dependent manner. The conjugate showed enhanced water solubility compared to LMWC and forms hydrogel and DMSO gel. The conjugate polymer was also fabricated into nanoparticles by ionic gelation technique. The size of the nanoparticles was found to be in the range 70-90 nm, thus should have the ability to penetrate into living cells. In vitro release study of 5FU from the conjugate showed controlled release of the antitumor drug over time. The synthesized nanoparticles and the gel, therefore, could be a good model for controlled release of antitumor drugs.
  17. Kamalesh Verma, Gundappa Saha,Lal Mohan Kundu, Vikash Kumar Dubey*"Biochemical characterization of a stable azoreductase enzyme from Chromobacterium violaceum: Application in industrial effluent dye degradation" Int.J.Biol.Macromol. 2019, 121, 1011-1018
    Abstract:
    The presence of dye, including azo functional group (NN) containing dyes, in industrial waste water is one of the major causes of water pollution. This report showcases the functional role of azoreductase from Chromobacterium violaceum (MTCC No: 2656) as a valuable enzyme for degradation of azo dyes. The enzyme was cloned, expressed, purified and biochemically characterized and further tested for degradation efficiency of azo group containing dyes like methyl red, amaranth and methyl orange. The degraded azo dye products (metabolites) resulted by the action of azoreductase enzyme had reduced toxicity on fibroblast cell lines (L929) as compared to raw and intact dye. Further, good stability of the enzyme makes it more suitable for various applications related to the degradation and decolourisation of effluent dyes.
  18. K Radhakrishnan, Soumi Das and Lal Mohan Kundu* "Synthesis of Size-Expanded Nucleobase Analogues for Artificial Base-Pairing Using a Ligand-Free, Microwave-Assisted Copper(I)-Catalyzed Reaction" Chemistry Select 2018, 3(46), 13098-13102
    Abstract:
    Quinazolines is an important class of natural products. Size‐expanded isocytosine analogues or 2‐aminoquinazolinones have found significance as pharmaceutically active compounds, for the expansion of genetic alphabets and as biomolecular probes. With an aim for further biomolecular applications, a library of functionalized isocytosine analogues have been synthesized in a one‐pot, microwave‐directed reaction. Syntheses were carried out using simple reactants such as ortho‐halo aromatic carboxylic acids and guanidine hydrochloride, in absence of any additional ligand. The usefulness of the methodology could be justified by the diversity of the compounds synthesized, containing functional groups, natural nucleobases, fluorophores or peptide bonds.
  19. Soumi Das, Himali Horo and Lal Mohan Kundu* “Biopolymers and Peptide Based materials for Targeted Antitumor Drug Delivery: An Overview” Nov Appro Drug Des Dev. 2018, 4(4),555643
    Abstract:
    Targeted antitumor drug delivery seeks to concentrate the antitumor drugs only in the affected tissues sparing the normal tissues, so that the drug efficacy is increased, and side effects are minimized. Various cancer cell targeting moieties are physically immobilized or covalently conjugated to the delivery systems in order to carry the system specifically to the tumour site. This review mainly focuses on the various types of targeting moieties and role of biodegradable polymers and their nanoparticles in site specific delivery of antitumor drugs.
  20. Laxmi Narayana Burgula and Lal Mohan Kundu* "Direct Chemoselective Synthesis of N-3-Substituted Pyrimidinones in a Microwave-Assisted Method" Synth.Commun. 2015, 45, 1342-1353
    Abstract:
    Synthesis of selectively N-3-substituted pyrimidine nucleobases or pyrimidinones has always been a challenge because of poor regioselectivity and chemoselectivity. In this article we demonstrate a single-step, de novo synthesis of selectively N-3-substituted modified pyrimidinones. We have developed a microwave-assisted methodology for direct, chemoselective alkylation, benzylation, and arylation of C-5 and C-6 substituted pyrimidine nucleobases selectively at the N-3 position. The reactions were found to proceed, with high efficiency, without the requirement of solvent and were complete within 10–15 min of irradiation. The efficiency of the method was further improved by addition of a Lewis acid, which not only increases the yield significantly but also accelerates the reaction rate.
  21. K. Radhakrishnan, N. Sarma and Lal Mohan Kundu*"Direct synthesis of 5 and 6 substituted 2-aminopyrimidines as potential non-natural base pairs" RSC Adv. 2014, 4, 15087-15090
    Abstract:
    A series of 2-aminopyrimidine derivatives, substituted at 5- and 6-positions, were synthesized. The reaction was carried out in a single step by treatment of the corresponding β-ketoester or β- aldehydoester with guanidine hydrochloride in the presence of K 2 CO 3 , in a microwave-assisted method without the requirement of solvent. A unique 1 : 1 co-crystal structure was obtained which shows that a 6-phenyl-2-aminopyrimidinone forms a strong nucleobase-pair with cytosine, involving three hydrogen bonds. The base-pair was found to be as strong as that of natural guanine:cytosine (G:C), signifying the potential application of the synthesized derivatives. Additionally, we also report a second co-crystal involving 5-isopropyl-6-methyl-2-aminopyrimidinone and cytosine in a 1 : 1 ratio, which also shows strong base-pairing properties.
  22. K. Radhakrishnan, Laxmi Narayana Burgula and Lal Mohan Kundu*"Watson-Crick and Hoogsteen tri-base pairing: a co-crystal structure of a 2 : 1 complex of 6-isopropyluracil and adenine nucleobases" RSC Adv. 2013, 3, 7282-7284
    Abstract:
    The formation of a tri-base pairing from free nucleobases is rare. A co-crystal structure obtained from an equimolar mixture of 6-isopropyluracil and adenine shows the formation of a tri-base pairing, where one molecule of free adenine is adhered to two molecules of the free pyrimidine nucleobase, involving both Watson–Crick and Hoogsteen base-pairing interactions.
  23. Laxmi Narayana Burgula, K. Radhakrishnan, Lal Mohan Kundu*"Synthesis of modified uracil and cytosine nucleobases using a microwave-assisted method" Tet. Lett. 2012, 53, 2639-2642
    Abstract:
    Modified nucleobases and nucleic acids have found many biological and pharmaceutical applications. Here we report a microwave-directed synthesis of a variety of modified uracil and cytosine nucleobases with high yields under solvent-free conditions. The reaction yields were further improved by addition of Lewis acid. The crystal structures of 5-isopropyl-6-methyluracil and 6-phenyluracil were also determined.
  24. H. Tsukada, L. M. Kundu, Y. Matsuoka, N. Kanayama, T. Takarada*, M. Maeda"Quantitative single-nucleotide polymorphism analysis in secondary-structured DNA by affinity capillary electrophoresis using a polyethylene glycol-peptide nucleic acid block copolymer"Anal. Biochem. 2013, 433, 150-152
  25. L. M. Kundu, H. Tsukada, Y. Matsuoka, N. Kanayama, T. Takarada*, M. Maeda"Estimation of Binding Constants of Peptide Nucleic Acid and Secondary-Structured DNA by Affinity Capillary Electrophoresis"Anal. Chem. 2012, 84, 5204-5209
  26. L.M. Kundu, G. R. Loppnow*''Direct Detection of 8-oxo-Deoxyguanosine using Resonance Raman Spectroscopy" Photochem. Photobiol. 2007, 83, 600-602.
  27. L.M. Kundu, U. Linne, M. Marahiel, T. Carell*"RNA Is More UV Resistant than DNA: The Formation of UV-Induced DNA Lesions is Strongly Sequence and Conformation Dependent" Chem. Eur. J. 2004, 10, 5697-5705
  28. L.M. Kundu, L.T. Burgdorf, O. Kleiner, A. Batschauer, T. Carell*"Thymine Dimer Containing Molecular Beacons for the Investigation of Photolyase Activity in Cell Extracts" ChemBioChem 2002, 3, 1053-1060.
  29. T. Carell*, L.T. Burgdorf, L.M. Kundu, M. Cichon,"The Mechanism of Action of Photolyase" Curr. Opin. Chem. Biol. 2001, 5, 491-498.