Multispectroscopic and Theoretical Investigation on the Binding Interaction of a Neurodegenerative Drug, Lobeline with Human Serum Albumin: Perturbation in Protein Conformation and Hydrophobic-Hydrophilic Surface.

Lobeline (LOB), a naturally occurring alkaloid, has a broad spectrum of pharmacological activities and therapeutic potential, including applications in central nervous system disorders, drug misuse, multidrug resistance, smoking cessation, depression, and epilepsy. LOB represents a promising compound for developing treatments in various medical fields. However, despite extensive pharmacological profiling, the biophysical interaction between the LOB and proteins remains largely unexplored. In the current article, a range of complementary photophysical and cheminformatics methodologies were applied to study the interaction mechanism between LOB and the carrier protein HSA. Steady-state fluorescence and fluorescence lifetime experiments confirmed the static-quenching mechanisms in the HSA-LOB system. "K" (binding constant) of the HSA-LOB system was determined to be 105 M-1, with a single preferable binding site in HSA. The forces governing the HSA-LOB stable complex were analyzed by thermodynamic parameters and electrostatic contribution. The research also investigated how various metal ions affect complex binding. Site-specific binding studies depict Site I as probable binding in HSA by LOB. We conducted synchronous fluorescence, 3D fluorescence, and circular dichroism studies to explore the structural alteration occurring in the microenvironment of amino acids. To understand the robustness of the HSA-LOB complex, we used theoretical approaches, including molecular docking and MD simulations, and analyzed the principal component analysis and free energy landscape. These comprehensive studies of the structural features of biomolecules in ligand binding are of paramount importance for designing targeted drugs and delivery systems.

On the traditional medicinal plants and plant-derived natural drugs used by indigenous people of Nagaland, India.

An ethnobotanical documentation on the medicinal plants used by local people of Nagaland (North-east India) has been presented here. The study explored 33 plant species (with their local names, indigenous applications, sources/origins, parts of plants used, bioactive compounds present, process of preparing medicines from the plants) belonging to 28 families have been reviewed thoroughly. Some examples are, Catharanthus roseus (Tsuinrinaro, Periwinkle), Acacia pennata (Chakrangaing, Ballikhadira), Adhatoda vasica (Kicharangnaro, Malabar-nut), Ageratum conzyoides (Imchenriza, Billy-goat-weed,/Tropical-white-weed), Alstonia scholaris (Lazarongpang, Blackboard), Rauvolfia serpentina (Per-mozutong, Indian-snakeroot), etc. Plant based drugs are very popular and effective in Nagaland from ancient times but thorough-documentation with scientific-background of effectiveness, active chemical-compounds present, their action-mechanism, etc., are still scanty. Such review can be of useful for pharmacologist, phyto-chemists to a broad group of researchers and may lead to discovery of new sources of novel medicines through traditional therapeutic knowledge.

Mechanistic investigation into the binding property of Yohimbe towards natural polymeric DNAs.

DNA interactions with multivalent ligand(s) have increasingly become the subject of substantial research. For several small molecules with therapeutic potential, nucleic acids serve as their primary molecular target. Such interaction has been shown to affect transcription or replication, ultimately leading to apoptotic cell death. As a result, researchers are becoming increasingly interested in understanding how small molecules interact with DNA making it possible to develop new, DNA-specific drugs. The bioactive indole alkaloid, Yohimbe (Yohimbine; Yh) has been broadly studied in pharmacological properties while its binding mode to DNA has not been explicated so far. This study adopted molecular modelling and multi-spectroscopic methods to investigate the interaction between Yohimbine and herring testes (HT DNA) in physiological conditions. Minor hypochromic and bathochromic shifts of fluorescence intensity were observed, suggesting the binding of Yh to HT DNA. The Scatchard plot analyses using the McGhee-von Hipple method revealed non-cooperative binding and affinities in the range of 105 M-1. The thermodynamic parameters suggested exothermic binding, which was favoured by negative enthalpy and positive entropy changes from temperature-dependent fluorescence experiments. Salt-dependent fluorescence suggested that the interaction between the ligand and DNA was governed by non-polyelectrolytic forces. The results of iodide quenching, urea denaturation assay, dye displacement, and in silico molecular docking, suggested groove binding of Yh to HT DNA. Thus, the groove binding mechanism of interaction was validated by both biophysical and computational techniques. The structural elucidation and energetic profiling of Yh's interaction with naturally occurring polymeric DNA can be useful to the development of DNA-targeted therapeutics.

Structural Insight into Groove Binding of Yohimbine with Calf Thymus DNA: A Spectroscopic, Calorimetric, and Computational Approach.

A variety of anticancer and antibacterial drugs target DNA as one of their primary intracellular targets. Understanding ligand-DNA interactions and developing new, promising bioactive molecules for clinical use are greatly aided by elucidating the interaction between small molecules and natural polymeric DNAs. Small molecules' ability to attach to and inhibit DNA replication and transcription provides more information on how drugs impact the expression of genes. Yohimbine has been broadly studied in pharmacological properties, while its binding mode to DNA has not been explicated so far. In this study, an attempt was made to explore the interaction between Yohimbine (YH) and calf thymus (CT-DNA) by using varying thermodynamics and in silico approaches. Minor hypochromic and bathochromic shifts of fluorescence intensity were observed, suggesting the binding of YH to CT-DNA. The Scatchard plot analysis using the McGhee-von Hipple method revealed noncooperative binding and affinities in the range of 105 M-1. The binding stoichiometry value is 2:1 (2 molecules of YH were span by 1 base pair) and was determined by Job's plot. The thermodynamic parameters suggested exothermic binding, which was favored by negative enthalpy and positive entropy changes from both isothermal titration calorimetry and temperature-dependent fluorescence experiment. Salt-dependent fluorescence suggested that the interaction between the ligand and DNA was governed by nonpolyelectrolytic forces. Kinetics experiment confirmed the static type of quenching. The results of iodide quenching, urea denaturation assay, dye displacement, DNA melting, and in silico molecular docking (MD) suggested groove binding of YH to CT-DNA. Circular dichroism spectra confirmed minimal perturbation of CT-DNA with YH binding via groove region. Therefore, the groove binding mechanism of interaction was validated by biophysical techniques and in silico, MD approaches. The findings supported here may contribute to the development of new YH therapeutics possessing better efficacy and lesser side effects.

Biophysical and molecular modeling evidences for the binding of sulfa molecules with hemoglobin.

The molecular mechanism of the heme protein, hemoglobin (Hb) interaction with sulfa molecule, sulfadiazine (SDZ) has been investigated through spectroscopic, neutron scattering and molecular modeling techniques. Absorption and emission spectroscopic studies showed that SDZ molecules were bound to Hb protein, non-cooperatively. The binding affinityof SDZ-Hb complex at standard experimental condition was evaluated to be around (4.2 ± 0.07) ×104, M-1with 1:1 stoichiometry. Drug induced structural perturbation of the 3 D protein moiety was confirmed through circular dichroism (CD), synchronous fluorescence and small angle neutron scattering methods. From the temperature dependent spectrofluorometric studies, the negative standard molar Gibbs energy change suggested the spontaneity of the reaction. The negative enthalpy and positive entropy change(s) indicated towards the involvement of both electrostatic and hydrophobic forces during the association process. Salt dependent fluorescence study revealed major contributions from non-poly-electrolytic forces. Molecular modeling studies determined the probable binding sites, types of interaction involved and the conformational alteration of the compactness of the Hb structure upon interaction with SDZ molecule. Overall, the study provides detailed insights into the binding mechanism of SDZ antibiotics to Hb protein.Communicated by Ramaswamy H. Sarma.

Application of Drug Aggregation to Solubilize Antimicrobial Compound and Enhancing its Bioavailability.

With the progress and advancement in discovery of novel antimicrobial drugs, efficient solubility plays an important component for a drug to express its out-turn effectively. A biocompatible neutral/non-ionic surfactant, Triton X-100 (Tx-100), was successfully employed to solubilize an antibiotic drug, sulfamethazine (SMZ), through micellization process. The association process of Tx-100 toward SMZ was confirmed through the characteristic spectral change in absorption and emission spectroscopy. The morphological behavior of the complex was studied from small angle neutron scattering (SANS). Changes in size(s) and charge(s) of the micelles were monitored using zeta (z) potential technique. This present study emphasized the molecular mechanism and characteristics of Tx-100 as an effective drug solubilizing and carrier agent. Thus, the drug-loaded micellar system can enhance cellular uptake and increase the antibacterial effects of drugs in the biological system(s). Schematic illustration of drug-surfactant micelle formation and target release of drug at the targeted site.

Protein-binding characteristics of yohimbine, a natural indole alkaloid-based drug for erectile dysfunction.

Even today, talking about sexual dysfunction largely remains a taboo. Therefore less studies have been recorded and fewer remedies given. Erectile dysfunction (ED) is one of the most commonly treated psychological disorders that leads to major distress, interpersonal limitation and reduces the quality of life and marriage. This study aimed to assess a plant-derived molecule, yohimbine (Yoh; a ß-carboline indole alkaloid often used for ED treatment) and its potential binding phenomenon with haemoglobin (Hb). Successful binding of Yoh with Hb is evident from spectroscopic and molecular-docking results. Yoh quenched the fluorescence of Hb efficiently through a static mode. The binding affinity was in the order of 105 M-1 with 1:1 stoichiometry. Thermodynamic analyses concluded that the protein-ligand association was spontaneous and was attributed to entropy-driven exothermic binding. Nonpolyelectrolytic factor was the core, dominating factor. Structural aspects were deciphered through infrared spectroscopy and computational methods. The giant 3D-protein moiety was significantly perturbed through drug binding. Hydrophobic forces and hydrogen bonding participation were stipulated by molecular modelling data. This study reveals the detailed interaction pattern and molecular mechanism of Hb-Yoh binding, correlating the structure-function relationship for the first time, and therefore holds enormous importance from the standpoint of rational and efficient drug design and development.

Lysozyme binding with sulfa group of antibiotics: Comparative binding thermodynamics and computational study.

Protein-drug binding study addresses a broad domain of biological problems associating molecular functions to physiological processes composing and modifying safe and coherent drug therapeutics. Comparison of the binding and thermodynamic aspect of sulfa drugs, sulfamethazine (SMZ) and sulfadiazine (SDZ) with the protein, lysozyme (Lyz) was carried out using spectroscopic, molecular docking, and dynamic simulation studies. The fluorescence quenching and apparent binding constant for the binding reaction were calculated to be in the order of 104 M-1 , slightly higher for SMZ as compared to that of SDZ and the binding stoichiometry values show 1:1 drug binding with each protein molecule. The binding was an enthalpy-driven spontaneous exothermic reaction favored by a negative enthalpy and a positive entropy contribution for both the complexes. The binding from the fluorescence quenching data suggests a static quenching mechanism dominated by non-polyelectrolytic components. Synchronous fluorescence denoted a conformational change in the tryptophan moiety of the protein. Molecular docking and dynamic simulation study provided a clearer view of the interaction pattern, where the drug resides on the binding pocket of the protein structure. Overall the protein, Lyz binding of SMZ was slightly more favored over SDZ.

Deciphering binding affinity, energetics, and base specificity of plant alkaloid Harmane with AT and GC hairpin duplex DNA.

Insights into binding efficacy and thermodynamic aspects of small molecules are important for rational drug designing and development. Here, the interaction of Harmane (Har), a very important bioactive indole alkaloid, with AT and GC hairpin duplex-DNAs has been reported using various biophysical tools. Detailed molecular mechanism with special emphasis on binding nature, base specificity, and thermodynamics have been elucidated via probing nucleic acids with varying base compositions. Har bound to both the DNA strands exhibited hypochromic effect in absorbance whereas bathochromic and hypochromic effects in fluorescence spectra. The binding constants estimated were in the order of 105 M-1 (higher for GC sequence compared with AT) with 1:1 stoichiometry. Noncooperative binding mode has been observed via intercalation in both the cases. The thermodynamic profile was obtained from temperature-dependent fluorescence experiments. Both Har-AT and Har-GC complexations were exothermic in nature associated with positive entropy and negative enthalpy changes. Salt-dependent studies revealed that the binding interaction was governed by nonpolyelectrolytic and hydrophobic interaction forces. The ligand-induced structural perturbation of the DNA structures was evident from the circular dichroism data. Molecular modelling data indicated towards the involvement of hydrophobic forces and hydrogen bonding.

Heme Protein Binding of Sulfonamide Compounds: A Correlation Study by Spectroscopic, Calorimetric, and Computational Methods.

Protein-ligand interaction studies are useful to determine the molecular mechanism of the binding phenomenon, leading to the establishment of the structure-function relationship. Here, we report the binding of well-known antibiotic sulfonamide drugs (sulfamethazine, SMZ; and sulfadiazine, SDZ) with heme protein myoglobin (Mb) using spectroscopic, calorimetric, ζ potential, and computational methods. Formation of a 1:1 complex between the ligand and Mb through well-defined equilibrium was observed. The binding constants obtained between Mb and SMZ/SDZ drugs were on the order of 104 M-1. SMZ with two additional methyl (-CH3) substitutions has higher affinity than SDZ. Upon drug binding, a notable loss in the helicity (via circular dichroism) and perturbation of the three-dimensional (3D) protein structure (via infrared and synchronous fluorescence experiments) were observed. The binding also indicated the dominance of non-polyelectrolytic forces between the amino acid residues of the protein and the drugs. The ligand-protein binding distance signified high probability of energy transfer between them. Destabilization of the protein structure upon binding was evident from differential scanning calorimetry results and ζ potential analyses. Molecular docking presented the best probable binding sites of the drugs inside protein pockets. Thus, the present study explores the potential binding characteristics of two sulfonamide drugs (with different substitutions) with myoglobin, correlating the structural and energetic aspects.

Targeting Natural Polymeric DNAs with Harmane: An Insight into Binding and Thermodynamic Interaction Through Biophysical Approach.

DNA is one of the major molecular targets for a broad range of anticancer drugs. Hence, interaction studies involving cellular DNA and small molecules can be highly beneficial as they often lead to rational and efficient drug design. In this study, the binding interaction of Harmane (a naturally occurring, bioactive indole alkaloid) with two natural polymeric DNAs, that is, Calf thymus (CT) DNA and Herring testis (HT) DNA has been elucidated using biophysical techniques. A ground state, 1:1 complexation, was revealed by steady-state fluorescence spectroscopy. The thermodynamic profile and energetics of the associated reaction were evaluated by temperature-dependent fluorescence spectroscopy. The spontaneity of the binding was confirmed by the negative ΔG° values in both cases. Negative enthalpy change, along with stronger positive entropic contribution, indicated the dominant electrostatic nature of the interaction and finally the entropy-driven exothermic binding process throughout. Salt-dependent studies further demonstrated the significant contribution of electrostatic interactions in ligand binding toward DNA. Infrared data substantiated the structural information of the said interactions, leading to the exploration of the structure-function relationship.

Sulfonamide drugs: structure, antibacterial property, toxicity, and biophysical interactions.

Sulfonamide (or sulphonamide) functional group chemistry (SN) forms the basis of several groups of drug. In vivo sulfonamides exhibit a range of pharmacological activities, such as anti-carbonic anhydrase and anti-t dihydropteroate synthetase allowing them to play a role in treating a diverse range of disease states such as diuresis, hypoglycemia, thyroiditis, inflammation, and glaucoma. Sulfamethazine (SMZ) is a commonly used sulphonamide drug in veterinary medicine that acts as an antibacterial compound to treat livestock diseases such as gastrointestinal and respiratory tract infections. Sulfadiazine (SDZ) is another frequently employed sulphonamide drug that is used in combination with the anti-malarial drug pyrimethamine to treat toxoplasmosis in warm-blooded animals. This study explores the research findings and the work behaviours of SN (SMZ and SDZ) drugs. The areas covered include SN drug structure, SN drug antibacterial activity, SN drug toxicity, and SN environmental toxicity.

Conformational flexibility influences degree of hydration of nucleic acid hybrids.

Four nucleic acid duplexes-DNA/RNA hybrid, RNA/DNA hybrid, RNA duplex, and DNA duplex-were studied under molecular crowding conditions of osmolytes. Destabilization of duplexes (ΔΔG°(25)) indicated that the ΔΔG°(25) values of hybrids were intermediate between those of DNA and RNA duplexes. In the presence of polyethylene glycol 200, the ΔΔG°(25) values were estimated to be +3.0, +3.5, +3.5, and +4.1 kcal mol(-1) for the DNA duplex, DNA/RNA hybrid, RNA/DNA hybrid, and RNA duplex, respectively. Differences in the number of water molecules taken up (-Δn(w)) upon duplex formations between 0 and 37 °C (Δ(-Δn(w))) were estimated to be 44.8 and 59.7 per duplex structure for the DNA/RNA and RNA/DNA hybrids, respectively. While the Δ(-Δn(w)) value for the DNA/RNA hybrid was intermediate between those of the DNA (26.1) and RNA (59.2) duplexes, the value for RNA/DNA hybrid was close to that of RNA duplex. These differences in the thermodynamic parameters and hydration are probably a consequence of the enhanced global flexibility of the RNA/DNA hybrid structure relative to the DNA/RNA hybrid structure observed in molecular dynamics simulations. This molecular crowding study provides information not only on hydration but also on the flexibility of the conformation of nucleic acid duplexes.

Effect of locked nucleic acid modifications on the thermal stability of noncanonical DNA structure.

We studied the kinetic and thermodynamic effects of locked nucleic acid (LNA) modifications on parallel and antiparallel DNA duplexes. The LNA modifications were introduced at cytosine bases of the pyrimidine strand. Kinetic parameters evaluated from melting and annealing curves showed that the association and dissociation rate constants for the formation of the LNA-modified parallel duplex at 25.0 °C were 3 orders of magnitude larger and 6 orders of magnitude smaller, respectively, than that of the unmodified parallel duplex. The activation energy evaluated from the temperature-dependent rate constants was largely altered by the LNA modifications, suggesting that the LNA modifications affected a prenucleation event in the folding process. Moreover, thermodynamic parameters showed that the extent of stabilization by the LNA modification for parallel duplexes (3.6 kcal mol(-1) per one modification) was much more significant than that of antiparallel duplexes (1.6 kcal mol(-1)). This large stabilization was due to the decrease in ΔH° that was more favorable than the decrease in TΔS°. These quantitative parameters demonstrated that LNA modification specifically stabilized the noncanonical parallel duplex. On the basis of these observations, we succeeded to stabilize the parallel duplex by LNA modification at the physiological pH. These results can be useful in the rational design of functional molecules such as more effective antisense and antigene strands, more sensitive strands for detection of target DNA and RNA strands, and molecular switches responding to solution pH.

Mechanistic studies on oxidation of hydrogen peroxide by an oxo-bridged diiron complex in aqueous acidic media.

A novel Raman spectroscopic model for the dinuclear iron site in ribonucleotide reductase and met-hemerythrin, [Fe2(micro-O)(phen)4(H2O)2]4+, 1, (phen = 1,10-phenanthroline) quantitatively oxidizes hydrogen peroxide to dioxygen via an inner-sphere electron transfer pathway. Although 1 deprotonates to form [Fe2(micro-O)(phen)4(H2O)(OH)]3+ (2) and [Fe2(micro-O)(phen)4(OH)2]2+ (3) in aqueous media, neither 2 nor 3 is reactive in oxidising H2O2. In the presence of excess phen, no phen-releasing equilibria from , and exist. Kinetic evidence of the generation of a (micro-1,2 peroxo)diiron(III,III) intermediate, prior to electron transfer, were obtained. Significant rate retardation in D2O media suggests proton coupled electron transfer (PCET) in the rate determining step of the title redox reaction.

Mechanistic studies on oxidation of L-ascorbic acid by an oxo-bridged diiron complex in aqueous acidic media.

[Fe2(micro-O)(phen)4(H2O)2]4+ (1) (Fig. 1, phen = 1,10-phenanthroline) equilibrates with [Fe2(micro-O)(phen)4(H2O)(OH)]3+ (2) and [Fe2(micro-O)(phen)4(OH)2]2+ (3) in aqueous solution in the presence of excess phen, where no phen-releasing equilibria from 1, 2 and 3 exist. 1 quantitatively oxidizes ascorbic acid (H2A) to dehydroascorbic acid (A) in the pH range 3.00-5.50 in the presence of excess phen, which buffers the reaction within 0.05 pH units and ensures complete formation of end iron product ferroin, [Fe(phen)3]2+. The reactive species are 1, 2 and HA- and the reaction proceeds through an initial 1 : 1 inner-sphere adduct formation between 1 and 2 with HA-, followed by a rate limiting outer-sphere one electron one proton (electroprotic) transfer from a second HA- to the ascorbate-unbound iron(III).

Mechanistic studies on oxidation of hydrazine by a mu-oxo diiron(III,III) complex in aqueous acidic media-proton coupled electron transfer.

[Fe2(mu-O)(phen)4(H2O)2]4+ (1), one of the simplest mu-oxo diiron(III) complexes, quantitatively oxidises hydrazine to dinitrogen and itself is reduced to two moles of ferroin, [Fe(phen)3]2+ in presence of excess phenanthroline. The weak dibasic acid, 1 (pKa1= 3.71 +/- 0.05 and pKa2= 5.28 +/- 0.10 at 25.0 degrees C, I= 1.0 mol dm(-3)(NaNO3)) and its conjugate bases, [Fe2(mu-O)(phen)4(H2O)(OH)]3+ (2) and [Fe2(mu-O)(phen)4(OH)2]2+ (3) are involved in the redox process with the reactivity order 1 > 2 > 3 whereas N2H4 and not N2H5+ was found to be reactive in the pH interval studied 3.45-5.60. Cyclic voltammetric studies indicate poor oxidizing capacity of the title substitution-labile diiron complex, yet it oxidizes N2H4 with a moderate rate--a proton coupled electron transfer (1e, 1H+) drags the energetically unfavourable reaction to completion. The rate retardation in D2O media is substantially higher at higher pH due to the increasing basicity of the oxo-ligand in the order 3 > 2 > 1. Marcus calculations result an unacceptably high one-electron self-exchange rate for the iron center indicating an inner-sphere nature of the electron-transfer.