Towards Understanding the Structure, Dynamics and Bio-activity of Diabetic Drug Metformin

Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. In addition to that, metformin hydrochloride shows anti-tumour activities and increases the survival rate of patients suffering from certain types of cancer namely colorectal, breast, pancreas and prostate cancer. However, theoretical studies of structure and dynamics of metformin have not yet been fully explored. In this work, we investigate the characteristic structural and dynamical features of three mono-protonated forms of metformin hydrochloride with the help of experiments, quantum chemical calculations and atomistic molecular dynamics simulations. We validate our force field by comparing simulation results to that of the experimental findings. Nevertheless, we discover that the non-planar tautomeric form is the most stable. Metformin forms strong hydrogen bonds with surrounding water molecules and its solvation dynamics show unique features. Because of an extended positive charge distribution, metformin possesses features of being a permanent cationic partner toward several targets. We study its interaction and binding ability with DNA using UV spectroscopy, circular dichroism, fluorimetry and metadynamics simulation. We find a non-intercalating mode of interaction. Metformin feasibly forms a minor/major groove-bound state within a few tens of nanoseconds, preferably with AT rich domains. A significant decrease in the free-energy of binding is observed when it binds to a minor groove of DNA.Comment: 60 pages, 24 figure

Atom-efficient synthesis of a benchmark electrolyte for magnesium battery applications

The benchmark magnesium electrolyte, [Mg2Cl3]+ [AlPh4]−, can be prepared in a 100% atom-economic fashion by a ligand exchange reaction between AlCl3 and two molar equivalents of MgPh2. NMR and vibrational spectroscopy indicate that the reported approach results in a simpler ionic composition than the more widely adopted synthesis route of combining PhMgCl with AlCl3. Electrochemical performance has been validated by polarisation tests and cyclic voltammetry, which demonstrate excellent stability of electrolytes produced via this atom-efficient approach

Studying Hemoglobin and a Bare Metal-Porphyrin Complex Immobilized on Functionalized Silicon Surfaces Using Synchrotron X-ray Reflectivity

We evaluate here, using synchrotron X-ray reflectivity, hemoglobin adsorption characteristics on silicon substrates with varying chemical functionalities. Hemoglobin at isoelectronic point and at negative charge is immobilized on functionalized hydrophilic (hydroxyl, carboxylic, amine) and hydrophobic (alkylated) silicon surfaces for the study. As a control, the bare cofactor hemin (containing only the metal and porphyrin with no amino acid residues) is also studied under similar conditions. Ordered layers (grown using the Langmuir-Blodgett technique) are observed to be less affected by the surface chemistry compared to the multilayers formed by physical absorption. Surface chemistry and charge of the proteins are critical in controlling the protein adsorption characteristics on silicon, such as thickness (correlated to molecule size) and roughness. In this study, this is very well realized by varying both the hydrophobicity and hydrophilicity of the substrate. The fundamental studies discussed here provide us with a set of important guidelines as to how electrode surface functionalization can control molecular conformation/orientation, especially protein adsorption on the substrate. This in turn is expected to have a significant impact on the protein electrochemical function and response of biomolecular devices

Using porphyrin-amino acid pairs to model the electrochemistry of heme proteins: experimental and theoretical investigations

Quasi reversibility in electrochemical cycling between different oxidation states of iron is an often seen characteristic of iron containing heme proteins that bind dioxygen. Surprisingly, the system becomes fully reversible in the bare iron-porphyrin complex: hemin. This leads to the speculation that the polypeptide bulk (globin) around the iron-porphyrin active site in these heme proteins is probably responsible for the electrochemical quasi reversibility. To understand the effect of such polypeptide bulk on iron-porphyrin, we study the interaction of specific amino acids with the hemin center in solution. We choose three representative amino acids-histidine (a well-known iron coordinator in bio-inorganic systems), tryptophan (a well-known fluoroprobe for proteins), and cysteine (a redox-active organic molecule). The interactions of these amino acids with hemin are studied using electrochemistry, spectroscopy, and density functional theory. The results indicate that among these three, the interaction of histidine with the iron center is strongest. Further, histidine maintains the electrochemical reversibility of iron. On the other hand, tryptophan and cysteine interact weakly with the iron center but disturb the electrochemical reversibility by contributing their own redox active processes to the system. Put together, this study attempts to understand the molecular interactions that can control electrochemical reversibility in heme proteins. The results obtained here from the three representative amino acids can be scaled up to build a heme-amino acid interaction database that may predict the electrochemical properties of any protein with a defined polypeptide sequence

Methodologies for operando ATR-IR spectroscopy of magnesium battery electrolytes

We explore the suitability of operando attenuated total reflection infrared (ATR-IR) spectroscopy methodologies for the study of organoaluminate electrolytes for Mg battery applications. The "all-phenyl complex" in tetrahydrofuran (THF), with the molecular structure [Mg Cl ·6THF] [AlPh ] , is used as an exemplar electrolyte to compare two different spectroelectrochemical cell configurations. In one case, a Pt gauze is used as a working electrode, while in the second case, a thin (∼10 nm) Pt film working electrode is deposited directly on the surface of the ATR crystal. Spectroscopic measurements indicate substantial differences in the ATR-IR response for the two configurations, reflecting the different spatial arrangements of the working electrode with respect to the ATR sampling volume. The relative merits and potential pitfalls associated with the two approaches are discussed

Determination of Redox Sensitivity in Structurally Similar Biological Redox Sensors

Redox stimuli govern a variety of biological processes. The relative sensitivity of redox sensors plays an important role in providing a calibrated response to environmental stimuli and cellular homeostasis. This cellular machinery plays a crucial role in the human pathoge<i>n Mycobacterium tuberculosis</i> as it encounters diverse microenvironments in the host. The redox sensory mechanism in <i>M. tuberculosis</i> is governed by two component and one-component systems, alongside a class of transcription factors called the extra cytoplasmic function (ECF) σ factors. ECF σ factors that govern the cellular response to redox stimuli are negatively regulated by forming a complex with proteins called zinc associated anti-σ factors (ZAS). ZAS proteins release their cognate σ factor in response to oxidative stress. The relative sensitivity of the ZAS sensors to redox processes dictate the concentration of free ECF σ factors in the cell. However, factors governing the redox threshold of these sensors remain unclear. We describe here, the molecular characterization of three σ factor/ZAS pairsσ^L/RslA, σ^E/RseA, and σ^H/RshAusing a combination of biophysical and electrochemical techniques. This study reveals, conclusively, the differences in redox sensitivity in these proteins despite apparent structural similarity and rationalizes the hierarchy in the activation of the cognate ECF σ factors. Put together, the study provides a basis for examining sequence and conformational features that modulate redox sensitivity within the confines of a conserved structural scaffold. The findings provide the guiding principles for the design of intracellular redox sensors with tailored sensitivity and predictable redox thresholds, providing a much needed biochemical tool for understanding host–pathogen interaction

Unique Features of Metformin: A Combined Experimental, Theoretical, and Simulation Study of Its Structure, Dynamics, and Interaction Energetics with DNA Grooves

There are certain small molecules that exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as an antidiabetic drug for type-two diabetes. Recent lines of evidence of its role in antitumor activities and increasing the survival rates of cancer patients (namely, colorectal, breast, pancreas, and prostate cancer) are emerging. However, theoretical studies of the structure and dynamics of metformin have not yet been fully explored. In this work, we investigate the characteristic structural and dynamical features of three monoprotonated forms of metformin hydrochloride with the help of experiments, quantum chemical calculations, and atomistic molecular dynamics simulations. We validate our force field by comparing simulation results to those of the experimental findings. Energetics of proton transfer between two planar monoprotonated forms reveals a low energy barrier, which leads us to speculate a possible coexistence of them. Nevertheless, among the protonation states, we find that the nonplanar tautomeric form is the most stable. Our calculated values of the self-diffusion coefficient agree quantitatively with NMR results. Metformin forms strong hydrogen bonds with surrounding water molecules, and its solvation dynamics shows unique features. Because of an extended positive charge distribution, metformin possesses features of being a permanent cationic partner toward several targets. We study its interaction and binding ability with DNA using UV spectroscopy, circular dichroism, fluorimetry, and metadynamics simulation. We find a nonintercalative mode of interaction. Metformin feasibly forms a minor/major groove-bound state within a few tens of nanoseconds, preferably with AT-rich domains. A significant decrease in the free energy of binding is observed when it binds to a minor groove of DNA

Differentiating between ion transport and plating–stripping phenomena in magnesium battery electrolytes using operando Raman spectroscopy

Understanding metal plating–stripping and mass transport processes is necessary for the development of new electrolytes for post-lithium energy storage applications. Operando vibrational spectroscopy is a valuable analytical tool for this purpose, enabling structural and chemical changes at electrode–electrolyte interfaces to be probed dynamically, under battery cycling conditions. In this work we apply operando Raman spectroscopy to characterize the behavior of the Mg based "all phenyl complex" [Mg2Cl3]+[AlPh4]− in tetrahydrofuran (THF), an exemplar electrolyte for emerging Mg battery technologies. We demonstrate that the observed electrolyte Raman band intensities vary reversibly with electrochemical cycling due to anion migration in response to the applied electric field, while Mg plating and stripping can be monitored independently through the broad background scattering intensity. Spectral measurements across different sites of the platinum working electrode indicate that the ion transport response is spatially heterogeneous, while the plating and stripping response is ubiquitous