Uttam Pal

Melatonin inhibits matrix metalloproteinase‐9 activity by binding to its active site

The zinc‐dependent matrix metalloproteinases (MMPs) are key enzymes associated with extracellular matrix (ECM) remodeling; they play critical roles under both physiological and pathological conditions. MMP‐9 activity is linked to many pathological processes, including rheumatoid arthritis, atherosclerosis, gastric ulcer, tumor growth, and cancer metastasis. Specific inhibition of MMP‐9 activity may be a promising target for therapy for diseases characterized by dysregulated ECM turnover. Potent MMP‐9 inhibitors including an indole scaffold were recently reported in an X‐ray crystallographic study. Herein, we addressed whether melatonin, a secretory product of pineal gland, has an inhibitory effect on MMP‐9 function. Gelatin zymographic analysis showed a significant reduction in pro‐ and active MMP‐9 activity in vitro in a dose‐ and time‐dependent manner. In addition, a human gastric adenocarcinoma cell line (AGS) exhibited a reduced (~50%) MMP‐9 expression when incubated with melatonin, supporting an inhibitory effect of melatonin on MMP‐9. Atomic‐level interaction between melatonin and MMP‐9 was probed with computational chemistry tools. Melatonin docked into the active site cleft of MMP‐9 and interacted with key catalytic site residues including the three histidines that form the coordination complex with the catalytic zinc as well as proline 421 and alanine 191. We hypothesize that under physiological conditions, tight binding of melatonin in the active site might be involved in reducing the catalytic activity of MMP‐9. This finding could provide a novel approach to physical docking of biomolecules to the catalytic site of MMPs, which inhibits this protease, to arrest MMP‐9‐mediated inflammatory signals.

Novel Anti-inflammatory Activity of Epoxyazadiradione against Macrophage Migration Inhibitory Factor INHIBITION OF TAUTOMERASE AND PROINFLAMMATORY ACTIVITIES OF MACROPHAGE MIGRATION INHIBITORY FACTOR

Background: Macrophage migration inhibitory factor (MIF) is responsible for proinflammatory reactions in many infectious and non-infectious diseases. Results: Epoxyazadiradione, a limonoid, inhibits the tautomerase activity of both human and malarial MIF and prevents MIF-induced proinflammatory reactions. Conclusion: Epoxyazadiradione bears therapeutic potential against MIF-induced proinflammatory reactions. Significance: This novel molecule is a significant addition in the discovery of anti-inflammatory drugs. Macrophage migration inhibitory factor (MIF) is responsible for proinflammatory reactions in various infectious and non-infectious diseases. We have investigated the mechanism of anti-inflammatory activity of epoxyazadiradione, a limonoid purified from neem (Azadirachta indica) fruits, against MIF. Epoxyazadiradione inhibited the tautomerase activity of MIF of both human (huMIF) and malaria parasites (Plasmodium falciparum (PfMIF) and Plasmodium yoelii (PyMIF)) non-competitively in a reversible fashion (Ki, 2.11–5.23 μm). Epoxyazadiradione also significantly inhibited MIF (huMIF, PyMIF, and PfMIF)-mediated proinflammatory activities in RAW 264.7 cells. It prevented MIF-induced macrophage chemotactic migration, NF-κB translocation to the nucleus, up-regulation of inducible nitric-oxide synthase, and nitric oxide production in RAW 264.7 cells. Epoxyazadiradione not only exhibited anti-inflammatory activity in vitro but also in vivo. We tested the anti-inflammatory activity of epoxyazadiradione in vivo after co-administering LPS and MIF in mice to mimic the disease state of sepsis or bacterial infection. Epoxyazadiradione prevented the release of proinflammatory cytokines such as IL-1α, IL-1β, IL-6, and TNF-α when LPS and PyMIF were co-administered to BALB/c mice. The molecular basis of interaction of epoxyazadiradione with MIFs was explored with the help of computational chemistry tools and a biological knowledgebase. Docking simulation indicated that the binding was highly specific and allosteric in nature. The well known MIF inhibitor (S,R)-3-(4-hydroxyphenyl)-4,5-dihydro-5-isoxazole acetic acid methyl ester (ISO-1) inhibited huMIF but not MIF of parasitic origin. In contrast, epoxyazadiradione inhibited both huMIF and plasmodial MIF, thus bearing an immense therapeutic potential against proinflammatory reactions induced by MIF of both malaria parasites and human.

Synthesis and bio-evaluation of human macrophage migration inhibitory factor inhibitor to develop anti-inflammatory agent

Macrophage migration inhibitory factor (MIF), a pro-inflammatory cytokine, is involved in the development of an array of inflammatory disorders including rheumatoid arthritis, inflammatory bowel disease, psoriasis, multiple sclerosis and sepsis. The synthesis of MIF-inhibitor is a rationale approach to develop novel anti-inflammatory agent to treat multitude of inflammatory diseases. In this work, we have synthesized and evaluated MIF-inhibitory activity of a series of small molecules containing isoxazoline skeleton. Mode of binding of this inhibitor to human MIF (huMIF) was determined by docking studies. The synthesized molecules inhibit tautomerase activity of huMIF. The anti-inflammatory activity of the most active inhibitor, 4-((3-(4-hydroxy-3-methoxyphenyl)-4, 5-dihydroisoxazol-5-yl) methoxy) benzaldehyde (4b) was evaluated against huMIF-induced inflammation in a cellular model (RAW 264.7 cell). Compound 4b significantly inhibits huMIF-mediated NF-κB translocation to the nucleus, up-regulation of inducible nitric oxide synthase and nitric oxide production in RAW 264.7 cell which are the markers for inflammation. The compound 4b is not cytotoxic as evident from cell viability assay. Hence, the compound 4b has potential to be a novel anti-inflammatory agent.

Dipeptide derived from benzylcystine forms unbranched nanotubes in aqueous solution

The essence of modern nanotechnology is manifested in the formation of well-ordered nanostructures by a process of self-association. Peptides are among the most useful building blocks for organic bionanostructures such as nanotubes, nanospheres, nanotapes, nanofibrils, and other different ordered structures at the nanoscale. Peptides are biocompatible, chemically diverse, and much more stable and can be readily synthesized on a large scale. Also, they have diverse application in biosensors, tissue engineering, drug delivery, etc. Here, we report a short cystine-based dipeptide, which spontaneously self-associates to form straight, unbranched nanotubes. Such self-assembled nanobiomaterials provide a novel possibility of designing new functional biomaterials with potential applications in nanobiotechnology. The formation of nanotubes in solution state has been demonstrated by atomic force microscopy and scanning electron microscopy. Infrared absorption and circular dichroism demonstrated the intermolecular β-sheet-like backbone hydrogen bonding in juxtaposing and stacking of aromatic side chains.

Cα-H carries information of a hydrogen bond involving the geminal hydroxyl group: a case study with a hydrogen-bonded complex of 1,1,1,3,3,3-hexafluoro-2-propanol and tertiary amines.

Experimental measurement of the contribution of H-bonding to intermolecular and intramolecular interactions that provide specificity to biological complex formation is an important aspect of macromolecular chemistry and structural biology. However, there are very few viable methods available to determine the energetic contribution of an individual hydrogen bond to binding and catalysis in biological systems. Therefore, the methods that use secondary deuterium isotope effects analyzed by NMR or equilibrium or kinetic isotope effect measurements are attractive ways to gain information on the H-bonding properties of an alcohol system, particularly in a biological environment. Here, we explore the anharmonic contribution to the C-H group when the O-H group of 1,1,1,3,3,3-hexafluoro-2-propanol (HFP) forms an intermolecular H-bond with the amines by quantum mechanical calculations and by experimentally measuring the H/D effect by NMR. Within the framework of density functional theory, ab initio calculations were carried out for HFP in its two different conformational states and their H-bonded complexes with tertiary amines to determine the (13)C chemical shielding, change in their vibrational equilibrium distances, and the deuterium isotope effect on (13)C2 (secondary carbon) of HFP upon formation of complexes with tertiary amines. When C2-OH was involved in hydrogen bond formation (O-H as hydrogen donor), it weakened the geminal C2-H bond; it was reflected in the NMR chemical shift, coupling constant, and the equilibrium distances of the C-H bond. The first derivative of nuclear shielding at C2 in HFP was -48.94 and -50.73 ppm Å(-1) for anti and gauche conformations, respectively. In the complex, the values were -50.28 and -50.76 ppm Å(-1), respectively. The C-H stretching frequency was lower than the free monomer, indicating enhanced anharmonicity in the C-H bond in the complex form. In chloroform, HFP formed a complex with the amine; δC2 was 69.107 ppm for HFP-triethylamine and 68.766 ppm for HFP-d2-triethylamine and the difference in chemical shift, the ΔδC2 was 341 ppb. The enhanced anharmonicity in the hydrogen-bonded complex resulted in a larger vibrational equilibrium distance in C-H/D bonds. An analysis with the Morse potential function indicated that the enhanced anharmonicity encountered in the bond was the origin of a larger isotope effect and the equilibrium distances. Change in vibrational equilibrium distance and the deuterium isotope effect, as observed in the complex, could be used as parameters in monitoring the strength of the H-bond in small model systems with promising application in biomacromolecules.

Sequence Complexity of Amyloidogenic Regions in Intrinsically Disordered Human Proteins

An amyloidogenic region (AR) in a protein sequence plays a significant role in protein aggregation and amyloid formation. We have investigated the sequence complexity of AR that is present in intrinsically disordered human proteins. More than 80% human proteins in the disordered protein databases (DisProt+IDEAL) contained one or more ARs. With decrease of protein disorder, AR content in the protein sequence was decreased. A probability density distribution analysis and discrete analysis of AR sequences showed that ∼8% residue in a protein sequence was in AR and the region was in average 8 residues long. The residues in the AR were high in sequence complexity and it seldom overlapped with low complexity regions (LCR), which was largely abundant in disorder proteins. The sequences in the AR showed mixed conformational adaptability towards α-helix, β-sheet/strand and coil conformations.

pKa determination of D-ribose by Raman spectroscopy.

Determination of the pKa of OH groups present in D-ribose is crucial in order to elucidate the origin and mechanism of many catalytic processes that involve the ribose unit. However, there is hardly any reports about the experimental pKa of the OH group due to the lack of an appropriate method. In this study we investigated the protonation state of OH groups in D-ribose by introducing C-D labeling and measuring the changes in the isolated C-D frequency in several isotopologues of the compound with pH. The large shift in the νC-D of D-ribose-C1-D in ionized condition compared to other deuterium-substituted D-riboses (e.g., D-ribose-C2-D, D-ribose-C3-D, etc.) confirmed that the C1-OH group preferred ionization, and the ionization pKa was 11.8. Both the ionized and the unionized structures of D-ribose preferred the pyranose conformation, which was supported by (13)C NMR experiments. Electronic redistribution via resonance and intramolecular hydrogen-bond formation were proposed to account for the stabilization of the ionized structure.

Potent anticancer activity of cystine-based dipeptides and their interaction with serum albumins

BackgroundCancer is a severe threat to the human society. In the scientific community worldwide cancer remains a big challenge as there are no remedies as of now. Cancer is quite complicated as it involves multiple signalling pathways and it may be caused by genetic disorders. Various natural products and synthetic molecules have been designed to prevent cell proliferation. Peptide-based anticancer drugs, however, are not explored properly. Though peptides have their inherent proteolytic instability, they could act as anticancer agents.ResultsIn this present communication a suitably protected cystine based dipeptide and its deprotected form have been synthesized. Potent anticancer activities were confirmed by MTT assay (a laboratory test and a standard colorimetric assay, which measures changes in colour, for measuring cellular proliferation and phase contrast images. The IC50 value, a measure of the effectiveness of a compound in inhibiting biological or biochemical function, of these compounds ranges in the sub-micromolar level. The binding interactions with serum albumins (HSA and BSA) were performed with all these molecules and all of them show very strong binding at sub-micromolar concentration.ConclusionsThis study suggested that the cystine-based dipeptides were potential anticancer agents. These peptides also showed very good binding with major carrier proteins of blood, the serum albumins. We are currently working on determining the detailed mechanism of anticancer activity of these molecules.

Identification of modes of interactions between 9-aminoacridine hydrochloride hydrate and serum proteins by low and high resolution spectroscopy and molecular modeling

Photophysical studies on binding interactions of a therapeutically important drug, 9-aminoacridine hydrochloride hydrate (9AA-HCl) with serum proteins, bovine serum albumin (BSA) and human serum albumin (HSA), have been performed using several low and high resolution spectroscopic techniques in conjunction with molecular modeling, which disclose some salient features of such interactions in ground and excited sates. The studies reveal that although 9AA-HCl forms ground state complexes with both BSA and HSA, their individual modes of binding interaction are quite different. Its resonance energy transfer efficiency is 79% and 72% with BSA and HSA respectively. It undergoes photoinduced electron transfer (PET) with BSA, but both PET and excited state proton transfer simultaneously with HSA, which are confirmed further by laser flash photolysis studies coupled with a magnetic field. Thermodynamic analyses indicate that the binding of 9AA-HCl with BSA and HSA is controlled primarily by changes in enthalpy and entropy, respectively, with corresponding binding stoichiometries of 1:1 and 1:2, respectively. Circular dichroism spectra depict some structural changes of both the serum proteins while interacting with 9AA-HCl. Docking analyses unveil the crucial role of the disparity between the cavity sizes of the proteins which might be the foremost reason behind the differential behavior of the drug towards BSA and HSA. The binding site pocket of HSA to be docked with 9AA-HCl is 1.7 times larger in dimensions than that of BSA, which facilitates HSA to bind with 9AA-HCl with higher stoichiometry compared to BSA. These differences in binding modes as well as affinities have been further confirmed by saturation transfer difference (STD) NMR experiments which show the ligand 9AA-HCl binds to BSA with higher affinity compared to HSA. In addition, unlike BSA, HSA can accommodate more than one ligand, which corroborates well with docking and fluorescence studies.

Conformation and cytotoxicity of a tetrapeptide constellated with alternative D- and L-proline

Proline containing peptides are highly important due to their natural abundance in various secondary structural elements like turns (β turn and γ turn etc.) in proteins. Here the conformation, cytotoxicity and structure of a unique tetrapeptide composed of alternative D- and L-proline residues are discussed. The peptide showed a polyproline II like conformation in dilute aqueous solution. The aqueous solution of the peptide self-assembled to form spheroidal oligomers with a diameter of ∼90 nm. The morphological features were confirmed by bright field confocal images, TEM analysis and AFM. The alternative D- and L-proline residues in the peptide showed toxicity towards cancer cell lines and ∼50% cell death was recorded against three different types of cancer cells (Neura 2a, HEK 293 and Hep G2).