Mode of interaction of altretamine with calf thymus DNA: biophysical insights.

Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 103 M-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK-1 mol-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.[Formula: see text]HighlightsAltretamine binds CT-DNA which is enthalpically driven with Ka of the order of 103Insignificant conformational change is observed due to DNA-altretamine complexationAltretamine binds favorably with A-T rich sequences in the minor groove of CT-DNAMechanistic insights obtained based on thermodynamic signaturesCommunicated by Ramaswamy H. Sarma.

Mechanistic physicochemical insights into glycation and drug binding by serum albumin: Implications in diabetic conditions.

The drug binding ability of serum albumin might get affected as a result of its glycation under diabetic conditions. It requires not only an understanding of the effect of glycation of the protein upon association with the drug, but also calls for an assessment of structure-property-energetics relationships. A combination of ultrasensitive calorimetric, spectroscopic and chromatographic approach has been employed to correlate thermodynamic signatures with recognition, conformation and mechanistic details of the processes involved. An important observation from this work is that 3-(dansylamino) phenyl boronic acid (DnsPBA) assay cannot always determine the extent of glycation as evidenced by MALDI-TOF mass spectra of glycated HSA due to its selectivity for 1,2 or 1,3 cis-diol structures which may be absent in certain AGEs. Protein gets modified post glycation with the formation of advanced glycation end products (AGEs), which are monitored to be targeted by the guanidine group present in anti-diabetic drugs. AGEs formed in the third and fourth week of glycation are significant in the recognition of anti-diabetic drugs. The results with metformin and aminoguanidine suggest that the extent of binding depends upon the number of guanidine group(s) in the drug molecule. Open chain molecules having guanidine group(s) exhibit stronger affinity towards glycated HSA than closed ring entities like naphthalene or pyridine moiety. The observation that the drug binding ability of HSA is not adversely affected, rather strengthened upon glycation, has implications in diabetic conditions. A rigorous structure-property-energetics correlation based on thermodynamic signatures and identification of functional groups on drugs for recognition by HSA are essential in deriving guidelines for rational drug design addressing diabetes.

Unraveling diverse action of triton X-100 and methimazole on lysozyme fibrillation/aggregation: Physicochemical insights.

Identification of functionalities responsible for prevention of fibrillation in proteins is important to design effective drugs in addressing neurodegenerative diseases. We have used nonionic surfactant triton X-100 (TX-100) and antithyroid drug methimazole (MMI) to understand mechanistic aspects of action of these molecules having different functionalities on hen egg-white lysozyme at different stages of fibrillation. After establishing the nucleation, elongation and maturation stages of fibrillation of protein at 57 °C, energetics of interactions with these molecules have been determined by using isothermal titration calorimetry. Differential scanning calorimetry has permitted assessment of thermal stability of the protein at these stages, with or without these molecular entities. The enthalpies of interaction of TX-100 and MMI with protein fibrils suggest importance of hydrogen bonding and polar interactions in their effectiveness towards prevention of fibrils. TX-100, in spite of several polar centres, is unable to prevent fibrillation, rather it promotes. MMI is able to establish polar interactions with interacting strands of the protein and disintegrate fibrils. A rigorous comparison with inhibitors reported in literature highlights importance -OH and >CO functionalities in fibrillation prevention. Even though MMI has hydrogen bonding centres, its efficiency as inhibitor falls after the inhibited lysozyme fibrils further interact and form amorphous aggregates.

Physicochemical Insights into the Role of Drug Functionality in Fibrillation Inhibition of Bovine Serum Albumin.

To revert amyloid fibrils to their native state is a challenge in finding a solution to prevent neurodegenerative diseases. We have adopted a structure-property-energetics correlation-based approach with drugs (5-fluorouracil and hydroxyurea) having multiple hydrogen-bond donors and acceptors as inhibitors targeting different stages of bovine serum albumin fibrillation. We present here a quantitative comprehensive biophysical approach for identifying functionalities in molecules, which offers this feature in terms of polarity and hydrogen bonding. Our objective of identifying the functionality on a drug molecule that establishes effective intermolecular hydrogen bonding with ß-strands of protein fibrils was achieved by combined calorimetric, spectroscopic, volumetric, and microscopic correlations. Relationships have been established among thermodynamic signatures, F19-NMR chemical shifts, hydrodynamic diameters, and thermal expansion coefficients to demonstrate that the open-chain molecule is a better inhibitor of fibrillation, but its efficiency decreases with the formation of amorphous aggregates, as compared to the molecule having a uracil ring. The results have provided quantitative insights into the role of polarity and hydrogen bonding in prevention of the fibrillation process. The approach adopted here highlights the physical chemistry underlying such biologically important processes and hence has significance in deriving guidelines for rational drug design.

Anticancer altretamine recognition by bovine serum albumin and its role as inhibitor of fibril formation: Biophysical insights.

Binding of anticancer drug altretamine with bovine serum albumin (BSA) and its inhibitory effect on fibrillation of the protein has been studied by using a combination of spectroscopic and calorimetric methods. Altretamine is observed to bind with BSA with a moderate binding affinity of the order of 105, which is weakly temperature dependent. Circular dichroism, fluorescence spectroscopic and dynamic light scattering methods have been employed to monitor the conformational change in the protein. Time correlated single photon counting measurements have confirmed ground state complexation of the drug with the protein. Docking studies have led to identification of binding sites on BSA at site III in domain IB. Thioflavin T (ThT) fluorescence emission has been used as a tool to monitor the formation of fibrils/aggregates in BSA. It is observed that anticancer drug altretamine can also act as an inhibitor of fibrillation in BSA and hence can be useful in the treatment of neuro-degenerative diseases. Differential scanning calorimetry has been employed to study the thermal transitions of BSA at different stages of the fibrillation process with and without altretamine to obtain insights into the extent of stabilisation provided by the drug to the protein in native, nucleation/elongation and matured state in the fibrillation process.

Physicochemical Insights into the Stabilization of Stressed Lysozyme and Glycine Homopeptides by Sorbitol.

Understanding the mode of action of osmolytes on the protein with and without stressed conditions still requires experimental proof. In this direction, we have studied the interactions of a model protein hen egg white lysozyme (HEWL) and some homopeptides with sorbitol and a mixture of [dodecyltrimethylammonium bromide (DTAB) + sorbitol] by using a combination of high sensitivity calorimetry, density, sound velocity, and conductivity measurements with spectroscopic support. The physical chemistry underlying these interactions has been addressed on the basis of the energetics of interactions and other physicochemical properties. These results have highlighted that, even though the number of -CONH groups increases in higher homopeptides, the hydrophobic effect of - CH2 groups in the peptides dominates. Further, the counteraction of the deleterious effects of DTAB by sorbitol is due to the strengthened DTAB-sorbitol interactions rather than the indirect effect of the osmolyte via preferential exclusion. The results provide insights into the nature of interactions of the protein as well as some of the building blocks with the (DTAB + osmolyte) mixture which helped in understanding the mode of action of the osmolyte. Detailed physicochemical insights into the mode of action of stress counteracting agents on the protein and its destabilizer are needed to develop strategies to achieve optimum stability and activity of proteins under such conditions.