Crystal to Hydrogel Transformation in S-Benzyl-L-Cysteine-Containing Cyclic Dipeptides - Nanostructure Elucidation and Applications.

Cyclic dipeptides (CDPs) are crucial building blocks for a range of functional nanomaterials due to their simple chemical structure and high molecular stability. In this investigation, we synthesized a set of S-benzyl-L-cysteine-based CDPs (designated as P1-P6) and thoroughly examined their self-assembly behavior in a methanol-water solvent to elucidate the relationship between their structure and gelation properties. The hydrophobicity of the amino acids within the CDPs was gradually increased. The present study employed a comprehensive array of analytical techniques, including NMR, FT-IR, AFM, thioflavin-T, congo-red CD, X-ray crystallography, and biophysical calculations like Hirshfield Surface analysis and DFT analysis. These methods revealed that in addition to hydrogen bonding, the hydrophobic nature of the amino acid side chain significantly influences the propensity of CDPs to form hydrogels. Each CDP yielded distinct nanofibrillar networks rich in ß-sheet structures, showcasing unique morphological features. Moreover, we explored the practical application of these CDP-based hydrogels in water purification by utilizing them to remove harmful organic dyes from contaminated water. This application underscores the potential of CDPs in addressing environmental challenges, offering a promising avenue for the future development of these materials in water treatment technologies.

Metal-Free Activation of Molecular Oxygen by Quaternary Ammonium-Based Ionic Liquid: A Detail Mechanistic Study.

Most oxidation processes in common organic synthesis and chemical biology require transition metal catalysts or metalloenzymes. Herein, we report a detailed mechanistic study of a metal-free oxygen (O2) activation protocol on benzylamine/alcohols using simple quaternary alkylammonium-based ionic liquids to produce products such as amide, aldehyde, imine, and in some cases, even aromatized products. NMR and various control experiments established the product formation and reaction mechanism, which involved the conversion of molecular oxygen into a hydroperoxyl radical via a proton-coupled electron transfer process. Detection of hydrogen peroxide in the reaction medium using colorimetric analysis supported the proposed mechanism of oxygen activation. Furthermore, first-principles calculations using density functional theory (DFT) revealed that reaction coordinates and transition state spin densities have a unique spin conversion of triplet oxygen leading to formation of singlet products via a minimum energy crossing point. In addition to DFT, domain-based local pair natural orbital coupled cluster, (DLPNO-CCSD(T)), and complete active space self-consistent field, CASSCF(20,14) methods complemented the above findings. Partial density of states analysis showed stabilization of π* orbital of oxygen in the presence of ionic liquid, making it susceptible to hydrogen abstraction in a mild, metal-free condition. Inductively coupled plasma atomic emission spectroscopic (ICP-AES) analysis of reactant and ionic liquids clearly showed the absence of any significant transition metal contamination. The current results described the origin of O2 activation within the context of molecular orbital (MO) theory and opened up a new avenue for the use of ionic liquids as inexpensive, multifunctional and high-performance alternative to metal-based catalysts for O2 activation.

Small-Molecule Cdc25A Inhibitors Protect Neuronal Cells from Death Evoked by NGF Deprivation and 6-Hydroxydopamine.

Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most common neurodegenerative diseases that are presently incurable. There have been reports of aberrant activation of cell cycle pathways in neurodegenerative diseases. Previously, we have found that Cdc25A is activated in models of neurodegenerative diseases, including AD and PD. In the present study, we have synthesized a small library of molecules targeting Cdc25A and tested their neuroprotective potential in cellular models of neurodegeneration. The Buchwald reaction and amide coupling were crucial steps in synthesizing the Cdc25A-targeting molecules. Several of these small-molecule inhibitors significantly prevented neuronal cell death induced by nerve growth factor (NGF) deprivation as well as 6-hydroxydopamine (6-OHDA) treatment. Lack of NGF signaling leads to neuron death during development and has been associated with AD pathogenesis. The NGF receptor TrkA has been reported to be downregulated at the early stages of AD, and its reduction is linked to cognitive failure. 6-OHDA, a PD mimic, is a highly oxidizable dopamine analogue that can be taken up by the dopamine transporters in catecholaminergic neurons and can induce cell death by reactive oxygen species (ROS) generation. Some of our newly synthesized molecules inhibit Cdc25A phosphatase activity, block loss of mitochondrial activity, and inhibit caspase-3 activation caused by NGF deprivation and 6-OHDA. Hence, it may be proposed that Cdc25A inhibition could be a therapeutic possibility for neurodegenerative diseases and these Cdc25A inhibitors could be effective treatments for AD and PD.

Cell-imaging studies of highly substituted oxazole derivatives as organelle targeting fluorophores (OTFPs).

The field of biomedical science has progressed enormously in the past decade. With the advent of newer diagnostic tools for imaging and detection, identification of root cause of a disease is now remarkably accurate and specific. Small organic fluorophores in these connections are in great demand currently for cellular organelle sensing and detecting, due to their non-invasiveness, excellent accuracy and bio-sensitivity. Small molecule fluorescence probes offer most potent area for biological sensing with diagnostic imaging ability. These organelle targetable fluorescent probes are produced through synthetic manipulations to get the desired, decent fluorescence properties. When a suitable organelle specific functional group is installed within these highly fluorescent scaffolds, then these molecules turn out to be as lysotracker, mitotracker and cytoplasm-stainer in mammalian cells with high efficiencies (high Pearson co-efficient factors). The present work demonstrated an environmentally benign (green) one-pot, sp3 C-H functionalization of highly substituted oxazole derivatives with excellent photophysical properties. These molecules were further modified by installing organelle specific targetable groups (sensors/detectors) which selectively localize in specific intra-cellular organelles.

ß-Sheet Induced Helical Self-Assembly Structure Formation by Dityrosine Dipeptide: Crystallographic Evidence and Other Biophysical Studies.

Self-assembled structures derived from short peptides are a versatile class of organic building blocks which have shown great potential in a wide range of domains. In the current study, side-chain protected dityrosine based short peptide (TP) was synthesized, and its conformation accompanied by a self-assembly pattern was investigated through several spectroscopic studies and single crystal X-ray analysis. The single crystal X-ray analysis of TP confirmed that it exhibited a ß-sheet pattern which further self-assembled to form ß-sheet-promoted helical architectures by various noncovalent interactions. To the best of our knowledge, this is the first crystallographic report of a side-chain protected dityrosine based short peptide adopting ß-sheet-promoted helical structures. Morphological analysis of TP also revealed ß-sheet as well as helical conformations. NMR study suggested that both amide hydrogens of TP are involved in intermolecular hydrogen bonding. Moreover, CD spectroscopy established the self-assembly phenomenon of TP in the solution state by showing both corresponding ß-sheet and α-helix bands. Hirshfeld surface analysis and DFT study also concluded similar results. These kinds of small peptide units mimicking important protein secondary structures like helical assembly would be of pivotal significance as they may act as small peptidomimetics, mimicking the protein "Hotspot" area.

S-Benzyl cysteine based cyclic dipeptide super hydrogelator: Enhancing efficacy of an anticancer drug via sustainable release.

Peptide-based low molecular weight supramolecular hydrogels hold promising aspects in various fields of application especially in biomaterial and biomedical sciences such as drug delivery, wound healing, tissue engineering, cell proliferation, and so on due to their extreme biocompatibility. Unlike linear peptides, cyclic peptides have more structural rigidity and tolerance to enzymatic degradation and high environmental stability which make them even better candidates for the above-said applications. Herein, a new small cyclic dipeptide (CDP) cyclo-(Leu-S-Bzl-Cys) (P1) consisting of L-leucine and S-benzyl protected L-cysteine was reported which formed a hydrogel at physiological conditions (at 37°C and pH = 7.46). The hydrogel formed from the cyclic dipeptide P1 showed very good tolerance towards environmental parameters such as pH and temperature and was seen to be stable for more than a year without any deformation. The hydrogel was thermoreversible and stable in the pH range 6-12. Mechanical strength of P1 hydrogel was measured by rheology experiments. Atomic force microscopy (AFM) and field emission scanning electron microscopy (FE-SEM) images revealed that, in aqueous solvents, P1 self-assembled into a highly cross-linked nanofibrillar network which immobilized water molecules inside the cages and formed the hydrogel. The self-assembled cyclic dipeptide acquired the antiparallel ß-sheet secondary structure, which was evident from CD and Fourier transform infrared (FT-IR) studies. The ß-sheet arrangement and formation of amyloid fibrils were further established by ThT binding assay. Furthermore, P1 was able to form a hydrogel in the presence of the anticancer drug 5-fluorouracil (5FU), and sustainable release of the drug from the hydrogel was measured in vitro. The hydrogelator P1 showed almost no cytotoxicity towards the human colorectal cancer cell line HCT116 up to a considerably high concentration and showed potential application in sustainable drug delivery. The co-assembly of 5FU and P1 hydrogel exhibited much better anticancer activity towards the HCT116 cancer cell line than 5FU alone and decreased the IC50 dose of 5FU to a much lower value.

Synthesis of N-Fused Triazole-Piperazine-Quinazolinones via One-Pot Tandem Click Reaction and Cross-Dehydrogenative Coupling.

Herein, a one-pot protocol to synthesize tetracyclic triazole-piperazine-quinazolinone-fused N-heterocyclic scaffolds is reported. In this strategy, a tandem approach of two highly efficient synthetic reactions, click and cross-dehydrogentive coupling reactions, with high atom economy were employed to obtain the target N-fused scaffolds. Being highly functional group tolerable, this method has broad substrate scope. Interestingly, some of these derivatives showed strong white solid-state fluorescence.

Synthetic and Computational Studies on RhIII-Catalyzed Redox-Neutral Cascade of Carbenoid Functionalization and Dephosphonylative Annulation.

A Rh(III)-catalyzed regioselective redox-neutral cascade process of carbenoid functionalization followed by dephosphonylative annulation of benzoic acids with α-diazo-ß-keto phosphonate has been realized, which led to the direct synthesis of a privileged 3-substituted isocoumarin scaffold. To the best of our knowledge, this is the first report of a complete redox neutral method to synthesize isocoumarins using C-H functionalization strategy. In the catalytic cycle of this reaction, there are two possible pathways for the C-C coupling between ortho-positioned carbon atom of benzoic acid and the diazo carbon atom: (i) concerted 1,2-aryl shift and (ii) stepwise metal-carbene formation followed by migratory insertion. DFT study has predicted that the concerted pathway has lower activation energy as compared to the stepwise pathway by 1.5 kcal/mol.

Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2.

Crystallization is the bottleneck in macromolecular crystallography; even when a protein crystallises, crystal packing often influences ligand-binding and protein-protein interaction interfaces, which are the key points of interest for functional and drug discovery studies. The human hypoxia-inducible factor prolyl hydroxylase 2 (PHD2) readily crystallises as a homotrimer, but with a sterically blocked active site. We explored strategies aimed at altering PHD2 crystal packing by protein modification and molecules that bind at its active site and elsewhere. Following the observation that, despite weak inhibition/binding in solution, succinamic acid derivatives readily enable PHD2 crystallization, we explored methods to induce crystallization without active site binding. Cyclic peptides obtained via mRNA display bind PHD2 tightly away from the active site. They efficiently enable PHD2 crystallization in different forms, both with/without substrates, apparently by promoting oligomerization involving binding to the C-terminal region. Although our work involves a specific case study, together with those of others, the results suggest that mRNA display-derived cyclic peptides may be useful in challenging protein crystallization cases.

Polysubstituted Imidazoles as LysoTracker Molecules: Their Synthesis via Iodine/H2O and Cell-Imaging Studies.

An iodine-catalyzed, environmentally benign one-pot methodology has been developed for the synthesis of diverse substituted imidazoles. This transition-metal-free, aerobic, water-mediated cyclization reaction is operationally simple and works well with different amines or aldehydes by multiple C-N bond formations with satisfactory yield. The methodology is regioselective as well as scalable. These imidazole derivatives show excellent fluorescence properties both in the solid and solution phase, which is further extended to live-cell imaging. Due to the suitable fluorescence properties of these scaffolds, lysosome-directing groups are incorporated in two of these derivatized imidazoles to track intracellular lysosomes. Successfully, those molecules show bright blue fluorescence while detecting lysosomes in human or murine cells and can be considered to be rapid lysosome-staining probes.

Cu-Catalyzed Direct Diversification of 2-(2-Bromophenyl)quinazolin-4(3H)-ones through Orthogonal Reactivity Modulation.

A modular strategy to obtain three different products from a single substrate was developed. The present methodology unveils new step-economical and cost-efficient routes to access diverse fused quinazolinoquinazolinone derivatives which are not prevalent in literature. Owing to the importance of quinazolinones in therapeutics, quick access to the arena of these scaffolds could be a valuable addition to the scientific domain of heterocyclic chemistry.

Solvent-Assisted Tyrosine-Based Dipeptide Forms Low-Molecular Weight Gel: Preparation and Its Potential Use in Dye Removal and Oil Spillage Separation from Water.

Low-molecular weight gelators (supramolecular, or simply molecular gels) are highly important molecular frameworks because of their potential application in drug delivery, catalysis, pollutant removal, sensing materials, and so forth. Herein, a small dipeptide composed of N-(tert-butoxycarbonyl)pentafluoro-l-phenylalanine and O-benzyl-l-tyrosine methyl ester was synthesized, and its gelation ability was investigated in different solvent systems. It was found that the dipeptide was unable to form gel with a single solvent, but a mixture of solvent systems was found to be suitable for the gelation of this dipeptide. Interestingly, water was found to be essential for gelation with the polar protic solvent, and long-chain hydrocarbon units such as, petroleum ether, kerosene, and diesel, were important for gelation with aromatic solvents. The structural insights of these gels were characterized by field-emission scanning electronic microscopy, atomic force microscopy, Fourier transform infrared analysis, and X-ray diffraction studies, and their mechanical strengths were characterized by rheological experiments. Both of the gels obtained from these two solvent systems were thermoreversible in nature, and these translucent gels had potential application for the treatment of waste water. The gel obtained from dipeptides with methanol-water was used to remove toxic dyes (crystal violet, Eriochrome Black T, and rhodamine B) from water. Furthermore, the gel obtained from dipeptide with assistance from toluene-petroleum ether was used as a phase-selective gelator for oil-spill recovery.

Efficient Detection of Early Events of α-Synuclein Aggregation Using a Cysteine Specific Hybrid Scaffold.

In this study, we have designed and synthesized a new hybrid ligand (SCG) that can selectively detect cysteine in the free and protein-bound states within minutes at the subnanomolar level. Photoinduced electron transfer was responsible for the visible color change as well as a large increase in steady state fluorescence. This detection was validated by using multiple model protein systems with differing cysteine environments and spatial arrangements. SCG was able to monitor the early events of the folding/aggregation kinetics of α-synuclein, a protein involved in the pathology of Parkinson's disease. The early events consisted of conformational fluctuations between different forms of the protein and oligomer formation. SCG was found to be effective in detecting early isomers of α-syn in vitro and in live cell environments.

Synthesis of Triazole-Substituted Quinazoline Hybrids for Anticancer Activity and a Lead Compound as the EGFR Blocker and ROS Inducer Agent.

A series of triazole-substituted quinazoline hybrid compounds were designed and synthesized for anticancer activity targeting epidermal growth factor receptor (EGFR) tyrosine kinase. Most of the compounds showed moderate to good antiproliferative activity against four cancer cell lines (HepG2, HCT116, MCF-7, and PC-3). Compound 5b showed good antiproliferative activity (IC50 = 20.71 µM) against MCF-7 cell lines. Molecular docking results showed that compound 5b formed hydrogen bond with Met 769 and Lys 721 and π-sulfur interaction with Met 742 of EGFR tyrosine kinase (PDB ID: 1M17). Compound 5b decreases the expression of EGFR and p-EGFR. It also induces apoptosis through reactive oxygen species generation, followed by the change in mitochondrial membrane potential.

Detection of Lysosome by a Fluorescent Heterocycle: Development of Fused Pyrido-Imidazo-Indole Framework via Cu-Catalyzed Tandem N-Arylation.

Fluorescent active small molecules for organelle-specific bioimaging are in great demand. We synthesized 20 different pyrido-imidazo-indole fused heterocycles (6-5-5-6 ring) via copper catalyzed tandem N-arylation reaction in moderate to good yields. Due to decent fluorescent property, lysosome-directing moieties were attached on two of these heterocycles. Delightfully, those molecules tracked lysosome with bright blue fluorescence and colocalized with a known lysosome marker (Lysotracker Red) in human/murine cells. Therefore, it may be considered as a rapid (10 min) lysosome staining probe.

Formation of Annular Protofibrillar Assembly by Cysteine Tripeptide: Unraveling the Interactions with NMR, FTIR, and Molecular Dynamics.

Both hydrogen-bonding and hydrophobic interactions play a significant role in molecular assembly, including self-assembly of proteins and peptides. In this study, we report the formation of annular protofibrillar structure (diameter ∼500 nm) made of a newly synthesized s-benzyl-protected cysteine tripeptide, which was primarily stabilized by hydrogen-bonding and hydrophobic interactions. Atomic force microscopy and field emission scanning electron microscopy analyses found small oligomers (diameter ∼60 nm) to bigger annular (outer diameter ∼300 nm; inner diameter, 100 nm) and protofibrillar structures after 1-2 days of incubation. Rotating-frame Overhauser spectroscopic (ROESY) analysis revealed the presence of several nonbonded proton-proton interactions among the residues, such as amide protons with methylene group, aromatic protons with tertiary butyl group, and methylene protons with tertiary butyl group. These added significant stability to bring the peptides closer to form a well-ordered assembled structure. Hydrogen-deuterium exchange NMR measurement further suggested that two individual amide protons among the three amide groups were strongly engaged with the adjacent tripeptide via H-bond interaction. However, the remaining amide proton was found to be exposed to solvent and remained noninteracting with other tripeptide molecules. In addition to chemical shift values, a significant change in amide bond vibrations of the tripeptide was found due to the formation of the self-assembled structure. The amide I mode of vibrations involving two amide linkages appeared at 1641 and 1695 cm-1 in the solid state. However, in the assembled state, the stretching band at 1695 cm-1 became broad and slightly shifted to ∼1689 cm-1. On the contrary, the band at 1641 cm-1 shifted to 1659 cm-1 and indicated that the -C═O bond associated with this vibration became stronger in the assembled state. These changes in Fourier transform infrared spectroscopy frequency clearly indicated changes in the amide backbone conformation and the associated hydrogen-bonding pattern due to the formation of the assembled structure. In addition to hydrogen bonding, molecular dynamics simulation indicated that the number of π-π interactions also increased with increasing number of tripeptides participated in the self-assembly process. Combined results envisaged a cross ß-sheet assembly unit consisting of four intermolecular hydrogen bonds. Such noncovalent peptide assemblies glued by hydrogen-bonding and other weak forces may be useful in developing nanocapsule and related materials.

Expedient synthesis of a phenanthro-imidazo-pyridine fused heteropolynuclear framework via CDC coupling: a new class of luminophores.

We herein report the design and synthesis of a group of fused phenanthro-imidazo[1,2-a]pyridine derivatives as a new class of luminescent materials through a Pd(ii) catalyzed intramolecular CDC (cross dehydrogenative coupling) reaction. This method thus unlocked a convenient & expedient way for the synthesis of a new molecular framework containing π-extended fused heteropolycycles. The heteropolycycles showed very good fluorescence properties both in solid and solution phases which were further utilized in live cell imaging. These kinds of molecules have potential to be used as therapeutic probes and also their solid state luminescence properties can be further utilized for making optoelectronic devices.

Neo-tanshinlactone D-ring modified novel analogues induce apoptosis in human breast cancer cell via DNA damage.

Neo-tanshinlactone (NTL) a natural product is known for its specificity and selectivity towards the breast cancer cells. By NTL D-ring modification approach, 13 new analogues were synthesized (1A-1M). Among them 1J showed the best anticancer activity in MCF-7 (ER+, PR+/-, HER2-), SKBR3 (ER-, PR-, HER2+) and MDA-MB-231 (ER-, PR-, HER2-) cells lines with IC50 value 11.98nM, 23.71nM, and 62.91nM respectively. 1J showed minor grove binding interaction with DNA at AT-rich region and induced DNA double strand breaks (DDSBs). This had triggered several key molecular events involving, activation of ATM, Chk2 and p53, reduction in mitochondrial potential (Δψm) leading to caspase-3 and PARP cleavage mediated apoptosis. These results along with other biochemical studies strongly suggest that novel NTL analogue 1J caused DNA cleavage mediated apoptosis in the breast cancer cells and this may serve as potential lead for future breast cancer treatment.

Envisaging Structural Insight of a Terminally Protected Proline Dipeptide by Raman Spectroscopy and Density Functional Theory Analyses.

The proline residue in a protein sequence generates constraints to its secondary structure as the associated torsion angles become a part of the heterocyclic ring. It becomes more significant when two consecutive proline residues link via amide linkage and produce additional configurational constraint to a protein's folding and stability. In the current manuscript we have illustrated conformation preference of a novel dipeptide, (R)-tert-butyl 2-((S)-2-(methoxycarbonyl)pyrrolidine-1-carbonyl)pyrrolidine-1-carboxylate. The dipeptide crystallized in the orthorhombic crystalline state and produced rod-shaped macroscopic material. The analysis of the crystal coordinates showed dihedral angles (φ, ψ) of the interlinked amide groups as (+72°, -147°) and the dihedral angles (φ, ψ) produced with the next carbonyl were (-68°, +151°), indicating polyglycine II (PGII) and polyproline II (PPII)-like helix states at the N- and C-terminals, respectively. These two states, PGII and PPII, are mirror image configurations and are expected to produce similar vibration bands from the associated carbonyl groups. However, the unique atomic arrangement in the molecule produces three carbonyl groups and one of them was very specific, being part of the main peptide linkage that connects both the pyrrolidine rings. The carbonyl group in the peptide bond exhibited a Raman vibration frequency at ∼1642 cm-1 and is considered a signatory Raman marker band for the peptide bond linking two heterochiral proline residues. The carbonyl group (t-Boc) at the N-terminal of the peptide showed a characteristic vibration at ∼1685 cm-1 and the C-terminal carbonyl group as a part of the ester showed a vibration signature at a significantly high frequency (1746 cm-1). Conformation analyses performed with density functional theory (DFT) calculations depicted that the dipeptide was stabilized in vacuum with dihedral angles (+72°, -154°) and (-72°, +151°) at the N- and C-terminals, respectively. Molecular dynamics (MD) simulation also showed that the peptide conformation having dihedral angles around (+75°, -150°) and (-75°, +150°) at the N- and C-terminals, respectively, was reasonably stable in water. Due to unique absence of the amide N-H, the peptide was ineffective in forming any intramolecular hydrogen bonding. MD investigation, however, revealed an intermolecular hydrogen bonding interaction with the water molecules, leading to its stability in aqueous solution. Metadynamics simulation analysis of the dipeptide in water also supported the PGII-PPII-like conformation at the N- and C-terminals, respectively, as the energetically stable conformation among the other possible combinations of conformations. The possible electronic transitions along with the HOMO-LUMO analysis further depicted the stability of the dipeptide in water and their possible absorption pattern. Time-dependent density functional theory (TDDFT) analysis showed strong negative rotatory strength of the dipeptide around 210 nm in water and acetonitrile, and it could be the source of experimentally observed high-amplitude negative absorption in the circular dichroism (CD) spectra around 200-203 nm. The very weak positive band (signature) in the region at ∼228 nm in CD spectra could also be correlated to the positive rotatory strength at 228 nm observed in ECD. To test the effect of such a dipeptide on a living cell, an MTT assay was performed and the result indicated no cytotoxic effect toward human hepatocellular carcinoma Hep G2 cancer cell lines.

Silver-catalysed azide-alkyne cycloaddition (AgAAC): assessing the mechanism by density functional theory calculations.

'Click reactions' are the copper catalysed dipolar cycloaddition reaction of azides and alkynes to incorporate nitrogens into a cyclic hydrocarbon scaffold forming a triazole ring. Owing to its efficiency and versatility, this reaction and the products, triazole-containing heterocycles, have immense importance in medicinal chemistry. Copper is the only known catalyst to carry out this reaction, the mechanism of which remains unclear. We report here that the 'click reactions' can also be catalysed by silver halides in non-aqueous medium. It constitutes an alternative to the well-known CuAAC click reaction. The yield of the reaction varies on the type of counter ion present in the silver salt. This reaction exhibits significant features, such as high regioselectivity, mild reaction conditions, easy availability of substrates and reasonably good yields. In this communication, the findings of a new catalyst along with the effect of solvent and counter ions will help to decipher the still obscure mechanism of this important reaction.