Allosteric Inhibitory Molecular Recognition of a Photochromic Dye by a Digestive Enzyme: Dihydroindolizine makes α-chymotrypsin Photo-responsive

A Mutagen Acts as a Potent Reducing Agent of Glycated Hemoglobin: a Combined Ultrafast Electron Transfer and Computational Studies

Glycated hemoglobin (GHb) found in mammals undergoes irreversible damage when exposed to external redox agents, which is much more vulnerable than its normal counterpart hemoglobin (Hb). Besides the oxygen regulation throughout the body, Hb plays a vital role in balancing immunological health and the redox cycle. Photoinduced ultra-fast electron transfer phenomena actively participate in regulation of various kind of homeostasis involved in such biomacromolecules. In the present study we have shown that a well-known mutagen Ethidium Bromide (EtBr) reduces GHb in femtosecond time scale (efficiently) upon photoexcitation after efficient recognition in the biomolecule. We have performed similar experiment by colocalizing EtBr and Iron (Fe(III)) on the micellar surface as Hb mimic in order to study the excited state EtBr dynamics to rationalize the time scale obtained from EtBr in GHb and Hb. While other experimental techniques including Dynamic Light Scattering (DLS), Zeta potential, absorbance and emission spectroscopy have been employed for the confirmation of structural perturbation of GHb compared to Hb, a detailed computational studies involving molecular docking and density functional theory (DFT) have been employed for the explanation of the experimental observations.

A combined spectroscopic and molecular modeling Study on structure-function-dynamics under chemical modification: Alpha-chymotrypsin with formalin preservative

Enzyme function can be altered via modification of its amino acid residues, side chains and large-scale domain modifications. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of a covalent cross-linker formalin. Enzyme assay reveals reduced catalytic activity upon increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-Anilino-1-naphthalenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation of multiple ANS binding sites in the enzyme owing to modifications of its local amino acid residues. Molecular docking study on amino acid residue modifications in CHT also indicate towards the formation of multiple ANS binding site. The docking model also predicted no change in binding behavior for the substrate Ala-Ala-Phe-7-amido-4-methylcoumarin (AMC) at the active site upon formalin induced amino acid cross-linking.

Insights on the interaction mechanism of exemestane to three digestive enzymes by multi-spectroscopy and molecular docking

Exemestane is an irreversible steroidal aromatase inhibitor, typically used to treat breast cancer. As an anti-tumor drug, exemestane has more obvious side effects on the gastrointestinal tract. The purpose of this work is to investigate the combination of exemestane with three important digestive enzymes including pepsin (Pep), trypsin (Try) and α-Chymotrypsin (α-ChT) so as to analyze the mechanism of the gastrointestinal adverse effects causing by exemestane binding. Enzyme activity experiment showed that the enzyme activity of Pep was decreased in the presence of exemestane. Fluorescence spectra revealed that exemestane formed stable complexes with digestive enzymes, and the quenching mechanism of drug-digestive enzymes interaction were all static quenching. The binding constants of Pep, Try and α-ChT at 298 K were 2.34 × 10⁵, 1.45 × 10⁵, and 2.05 × 10⁵ M^-1, respectively. Synchronous fluorescence and 3D fluorescence spectroscopy showed that the conformation of exemestane was slightly changed after combining with digestive enzymes, and non-radiative energy transfer occurred. Circular dichroism results indicated that exemestane could change the secondary structure of digestive enzymes via increase the α-helix content and decrease in the β-sheet content. Thermodynamic parameters (ΔH⁰, ΔS⁰, and ΔG⁰) revealed that exemestane interacted with α-ChT through electrostatic force, and the binding force with Pep and Try was van der Waals interactions and hydrogen, which was basically consistent with the molecular docking results.

Thermodynamics, Kinetics and Mechanisms of Noncompetitive Allosteric Inhibition of Chymotrypsin by Dihydrolipoic Acid-Coated Gold Nanoclusters

Enzymes are an important class of biomacromolecules which catalyze many metabolic processes in living systems. Nanomaterials can be synthesized with tailored sizes as well as desired surface modifications, thus acting as promising enzyme regulators. Fluorescent gold nanoclusters (AuNCs) are a representative class of ultrasmall nanoparticles (USNPs) with sizes of ∼2 nm, smaller than most of proteins including enzymes. In this work, we chose α-chymotrypsin (ChT) and AuNCs as the model system. Activity assays and inhibition kinetics studies showed that dihydrolipoic acid (DHLA)-coated AuNCs (DHLA-AuNCs) had a high inhibitory potency (IC₅₀ = 3.4 μM) and high inhibitory efficacy (>80%) on ChT activity through noncompetitive inhibition mechanism. In distinct contrast, glutathione (GSH)-coated AuNCs (GSH-AuNCs) had no significant inhibition effects. Fluorescence spectroscopy, agarose gel electrophoresis and circular dichroism (CD) spectroscopy were conducted to explore the underlying mechanisms. A two-step interaction model was proposed. First, both DHLA-AuNCs and GSH-AuNCs might be bound to the positively charged sites of ChT through electrostatic forces. Second, further hydrophobic interactions occurred between three tyrosine residues of ChT and the hydrophobic carbon chain of DHLA, leading to a significant structural change thus to deactivate ChT on the allosteric site. On the contrary, no such interactions occurred with GSH of zwitterionic characteristic, which explained no inhibitory effect of GSH-AuNCs on ChT. To the best of our knowledge, this is the first example of the allosteric inhibition of ChT by nano regulators. These findings provide a fundamental basis for the design and development of nano regulators.

Enhanced Water Stability and Photoresponsivity in Metal-Organic Framework (MOF): A Potential Tool to Combat Drug-resistant Bacteria

In this work, we have successfully synthesized a bimetallic (Zinc and Cobalt) Zeolitic Imidazolate Framework (Zn50Co50-ZIF), a class in a wider microporous Metal-Organic Framework (MOF) family. The synthesized nanostructures maintain both water stability like ZIF-8 (solely Zn containing) and charge transfer electronic band in the visible optical spectrum as ZIF-67 (solely Co containing). Crystal structure from XRD, high resolution transmission electron microscopy (HRTEM) followed by elemental mapping (EDAX) confirm structural stability and omnipresence of the metal atoms (Zn and Co) across the nanomaterial with equal proportion. Existence of charge transfer state consistent with ZIF67 and intact ultrafast excited state dynamics of the imidazolate moiety in both ZIF-8 and ZIF-67, is evidenced from steady state and time resolved optical spectroscopy. The thermal and aqueous stabilities of Zn50Co50-ZIF are found to be better than ZIF-67 but comparable to ZIF-8 as evidenced by solubility, scanning electron microscopy (SEM) and XRD studies of the material in water. We have evaluated the photoinduced ROS generation by the mixed ZIF employing dichloro-dihydro-fluorescein diacetate (DCFH-DA) assay. We have also explored the potentiality of the synthesized material for the alternate remediation of methicillin resistant Staphylococcus aureus (MRSA) infection through the photoinduced reactive oxygen species (ROS) generation and methylene blue (MB) degradation kinetics.

Improvement of Photostability and NIR Activity of Cyanine Dye through Nanohybrid Formation: Key Information from Ultrafast Dynamical Studies

Near-infrared (NIR) light harvesting has enormous importance for different potential applications in the modern era of research. Some NIR cyanine dyes such as IR820 have achieved great success in energy harvesting and cancer therapy. However, their action is limited for low photostability, considerable thermal degradation, short circulation times, and nonspecific biodistribution. Our present study is an attempt to overcome such limitations by attaching a model cyanine dye IR820 with ZnO nanoparticles. We prepared an IR820-ZnO nanohybrid and characterized it using microscopic and optical spectroscopic tools. Thermogravimetric analysis depicted greater thermal stability of the IR820-ZnO nanohybrid compared to free dye. We explored the enhancement in the photostability of IR820 upon nanohybrid formation. We detected generation of photoinduced reactive oxygen species (ROS) such as superoxide, singlet oxygen, and so forth using appropriate molecular probes. The formation of IR820-ZnO nanohybrid reduced production of photoinduced singlet oxygen. However, it revealed an alternative trend in overall ROS formation (increases total ROS) under red light illumination. To correlate the enhanced photostability of IR820 on the ZnO surface, we explored excited-state dynamical processes at the interface in nanohybrids. We illustrated the photoinduced excited-state electron-transfer process from the lowest unoccupied molecular orbital of IR820 to the conduction band of ZnO. This photoelectron-transfer process enhances the production of ROS and decreases the formation of singlet oxygen that altogether leads to improvement in photostability and overall activity. A quencher of singlet oxygen sodium azide (NaN₃) was used to further confirm the direct association of singlet oxygen generation with the photostability issue of IR820. Also, ZnO is able to deliver the dye selectively in acidic environment, which suggests its diseased site-specific targeted activity. Our results provide promising improvement for potential use of IR820 through formation of a nanohybrid that could be translated for other NIR cyanine dyes.

Naja atra cardiotoxins enhance the protease activity of chymotrypsin

Snake venom cardiotoxins (CTXs) present diverse pharmacological functions. Previous studies have reported that CTXs affect the activity of some serine proteases, namely, chymotrypsin, subtilisin, trypsin, and acetylcholinesterase. To elucidate the mode of action of CTXs, the interaction of CTXs with chymotrypsin was thus investigated. It was found that Naja atra CTX isotoxins concentration-dependently enhanced chymotrypsin activity. The capability of CTX1 and CTX5 in increasing chymotrypsin activity was higher than that of CTX2, CTX3, and CTX4. Removal of the molecular beacon-bound CTXs by chymotrypsin, circular dichroism measurement, and acrylamide quenching of Trp fluorescence indicated that CTXs bound to chymotrypsin. Chemical modification of Lys, Arg, or Met residues of CTX1 attenuated its capability to enhance chymotrypsin activity without impairing their bond with chymotrypsin. Catalytically inactive chymotrypsin retained the binding affinity for native and modified CTX1. CTX1 and chemically modified CTX1 differently altered the global conformation of chymotrypsin and inactivated chymotrypsin. Moreover, CTX1 did not reduce the interaction of 2-(p-toluidino)-naphthalene-6-sulfonate (TNS) with chymotrypsin and inactivated chymotrypsin. Together with previous results revealing that TNS can bind at the hydrophobic region of active site in chymotrypsin, our data suggest that CTXs can enhance chymotrypsin activity by binding to the region outside the enzyme's active site.

Stimulus-Responsive Regulation of Enzyme Activity for One-Step and Multi-Step Syntheses

Multi-step biocatalytic reactions have gained increasing importance in recent years because the combination of different enzymes enables the synthesis of a broad variety of industrially relevant products. However, the more enzymes combined, the more crucial it is to avoid cross-reactivity in these cascade reactions and thus achieve high product yields and high purities. The selective control of enzyme activity, i.e., remote on-/off-switching of enzymes, might be a suitable tool to avoid the formation of unwanted by-products in multi-enzyme reactions. This review compiles a range of methods that are known to modulate enzyme activity in a stimulus-responsive manner. It focuses predominantly on in vitro systems and is subdivided into reversible and irreversible enzyme activity control. Furthermore, a discussion section provides indications as to which factors should be considered when designing and choosing activity control systems for biocatalysis. Finally, an outlook is given regarding the future prospects of the field.

Probing relaxation dynamics of a cationic lipid based non-viral carrier: a time-resolved fluorescence study

Lipid vesicles composed of cationic dioctadecyldimethylammonium bromide (DODAB) and neutral 1-monooleoyl-rac-glycerol (MO) are promising non-viral carriers of nucleic acids for delivery into cells. Among them, higher cell transfection efficiency was displayed by DODAB-rich vesicles than those enriched with MO. Structural relaxation of these mixed lipid vesicles plays a key role in their cell transfection efficiency because structural organization of the DODAB-rich vesicles are different from that of the MO-rich vesicles. Polarization-gated anisotropy in conjunction with picosecond resolved emission transients of a novel fluorophore 6-acetyl-(2-((4-hydroxycyclohexyl)(methyl)amino)naphthalene) (ACYMAN) has been employed to probe relaxation dynamics in pure DODAB vesicles, and in mixed vesicles of DODAB with varying content of MO. Both orientational relaxation of ACYMAN and relaxation dynamics of its local environment are retarded significantly in mixed lipid vesicles with increasing MO content, from a mole fraction (χ_MO) of 0.2 to that of 0.8 which is consistent with increased rigidity of the MO-rich (χ_MO > 0.5) vesicles relative to the DODAB-rich (χ_MO < 0.5) vesicles. Therefore, higher structural rigidity of the MO-rich vesicles (χ_MO > 0.5) gives rise to their lower cell transfection efficiency than the more flexible DODAB-rich (χ_MO < 0.5) vesicles as observed in previous in vivo studies (Biochim. Biophys. Acta, Biomembr., 2014, 1838, 2555–2567).

Lipid vesicles composed of cationic dioctadecyldimethylammonium bromide (DODAB) and neutral 1-monooleoyl-rac-glycerol (MO) are promising non-viral carriers of nucleic acids for delivery into cells.

Ultrafast dynamics-driven biomolecular recognition where fast activities dictate slow events

In general, biological macromolecules require significant dynamical freedom to carry out their different functions, including signal transduction, metabolism, catalysis and gene regulation. Effectors (ligands, DNA and external milieu, etc) are considered to function in a purely dynamical manner by selectively stabilizing a specific dynamical state, thereby regulating biological function. In particular, proteins in presence of these effectors can exist in several dynamical states with distinct binding or enzymatic activity. Here, we have reviewed the efficacy of ultrafast fluorescence spectroscopy to monitor the dynamical flexibility of various proteins in presence of different effectors leading to their biological activity. Recent studies demonstrate the potency of a combined approach involving picosecond-resolved Forster resonance energy transfer, polarisation-gated fluorescence and time-dependent stokes shift for the exploration of ultrafast dynamics in biomolecular recognition of various protein molecules. The allosteric protein-protein recognition following differential protein-DNA interaction is shown to be a consequence of some ultrafast segmental motions at the C-terminal of Gal repressor protein dimer with DNA operator sequences O_E and O_I. Differential ultrafast dynamics at the C-terminal of λ-repressor protein with two different operator DNA sequences for the protein-protein interaction with different strengths is also reviewed. We have also systemically briefed the study on the role of ultrafast dynamics of water molecules on the functionality of enzyme proteins alpha-chymotrypsin and deoxyribonuclease I. The studies on the essential ultrafast dynamics at the active site of the enzyme alpha-chymotrypsin by using an anthraniloyl fluorescent extrinsic probe covalently attached to the serine-195 residue for the enzymatic activity at homeothermic condition has also been reviewed. Finally, we have highlighted the evidence that a photoinduced dynamical event dictates the molecular recognition of a photochromic ligand, dihydroindolizine with the serine protease alpha-chymotrypsin and with a liposome (L-a-phosphatidylcholine).

Design of Thermochromic Polynorbornene Bearing Spiropyran Chromophore Moieties: Synthesis, Thermal Behavior and Dielectric Barrier Discharge Plasma Treatment

A new class of thermochromic polynorbornene with pendent spiropyran moieties has been synthesized. Functionalization of norbornene monomers with spirobenzopyran moieties has been achieved using Steglich esterification. These new monomeric materials were polymerized via Ring Opening Metathesis Polymerization (ROMP). In spite of their poor solubility, polynorbornenes with spirobenzopyran exhibited thermochromic behavior due to the conversion of their closed spiropyran moieties to the open merocyanine form. Moreover, these polymers displayed bathochromic shifts in their optical response, which was attributed to the J-aggregation of the attached merocyanine moieties that were associated with their high concentration in the polymeric chain. The surface of the obtained polymers was exposed to atmospheric pressure air Dielectric Barrier Discharge (DBD) plasma system, which resulted in the reduction of the surface porosity and converted some surface area into completely non-porous regions. Moreover, the plasma system created some areas with highly ordered J-aggregates of the merocyanine form in thread-like structures. This modification of the polymers’ morphology may alter their applications and allow for these materials to be potential candidates for new applications, such as non-porous membranes for reverse osmosis, nanofiltration, or molecular separation in the gas phase.

Essential Dynamics of an Effective Phototherapeutic Drug in a Nanoscopic Delivery Vehicle: Psoralen in Ethosomes for Biofilm Treatment

Appropriate localization of a drug and its structure/functional integrity in a delivery agent essentially dictates the efficacy of the vehicle and the medicinal activity of the drug. In the case of a phototherapeutic drug, its photoinduced dynamics becomes an added parameter. Here, we have explored the photoinduced dynamical events of a model phototherapeutic drug psoralen (PSO) in a potential delivery vehicle called an ethosome. Dynamic light scattering confirms the structural integrity of the ethosome vehicle after the encapsulation of PSO. Steady state and picosecond resolved polarization gated spectroscopy, including the well-known strategy of solvation and Förster resonance energy transfer, reveal the localization of the drug in the vehicle and the environment in the proximity of PSO. We have also investigated the efficacy of drug delivery to various individual bacteria (Gram-negative: Escherichia coli; Gram-positive: Staphylococcus aureus) and bacterial biofilms. Our optical and electron microscopic studies reveal a significant reduction in bacterial survival (∼70%) and the destruction of bacterial adherence following a change in the morphology of the biofilms after phototherapy. Our studies are expected to find relevance in the formulation of drug delivery agents in several skin diseases and biofilm formation in artificial implants.