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.

Spectroscopic and computational study of the interaction of Pt(II) pyrrole-imine chelates with human serum albumin

Three bis(pyrrolide-imine) Pt(II) chelates were synthesised and characterized with different bridging alkyl groups, specifically 2-hydroxypropyl (1), 2,2-dimethylpropyl (2), and 1,2-(S,S)-(+)-cyclohexyl (3). Novel compounds 1 and 2 were analysed by single-crystal X-ray diffraction (space group P1̄). The asymmetric unit of 1 comprises three independent molecules linked by hydrogen bonds involving the OH groups, forming a trimeric supramolecular structure. The Pt(II) chelates were reacted with human serum albumin (HSA) to investigate how the ligand bound to the Pt(II) ion influences the compound's affinity for HSA. Fluorescence quenching data obtained for native HSA and HSA bound to site-specific probes (warfarin, subdomain IIA; ibuprofen, subdomain IIIA) indicated that the three Pt(II) chelates bind close enough (within ∼30 Å) to Trp-214 to quench its intrinsic fluorescence. The bimolecular quenching constant (kq) was 103-104 -fold higher than the maximum diffusion-controlled collision constant in water (1010 M s-1) at 310 K, while the affinity constants, Ka, ranged from ∼5 × 103 to ∼5 × 105 at 310 K, and followed the order 1 > 3 > 2. The reactions of 1 and 3 with HSA were enthalpically driven, while that for 2 was entropically driven. Macromolecular docking simulations (Glide XP) and binding site specificity assays employing site-specific probes and UV-vis CD spectroscopy indicated that 1 and 2 target Sudlow's site II in subdomain IIIA, minimally perturbing the tertiary structure of the protein. Well-resolved induced CD signals from 1 and 2 bound to HSA in subdomain IIIA were adequately simulated by hybrid QM:MM TD-DFT methods. We conclude that the structure of the bis(pyrrolide-imine) Pt(II) chelate measurably affects its uptake by HSA without detectable decomposition or demetallation. Such compounds could thus serve as metallodrug candidates capable of utilising an HSA-mediated cellular uptake pathway.

Delineating the cascade of molecular events in protein aggregation triggered by Glyphosate, aminomethylphosphonic acid, and Roundup in serum albumins

The molecular basis of protein unfolding on exposure to the widely used herbicide, Glyphosate (GLY), its metabolite aminomethylphosphonic acid (AMPA), and the commercial formulation Roundup have been probed using human and bovine serum albumins (HSA and BSA). Protein solutions were exposed to chemical stress at set experimental conditions. The study proceeds with spectroscopic and imaging tools. Steady-state and time-resolved fluorescence (TRF) measurements indicated polarity changes with the possibility of forming a ground-state complex. Atomic force microscopy imaging results revealed the formation of fibrils from BSA and dimer, trimer, and tetramer forms of oligomers from HSA under the chemical stress of GLY. In the presence of AMPA, serum albumins (SAs) form a compact network of oligomers. The compact network of oligomers was transformed into fibrils for HSA with increasing concentrations of AMPA. In contrast, Roundup triggered the formation of amorphous aggregates from SAs. Analysis of the Raman amide I band of all aggregates showed a significant increase in antiparallel β-sheet fractions at the expense of α-helix. The highest percentage, 24.6%, of antiparallel β-sheet fractions was present in amorphous aggregate formed from HSA under the influence of Roundup. These results demonstrated protein unfolding, which led to the formation of oligomers and fibrils.

Biochemical interaction of human hemoglobin with ionic liquids of noscapinoids: Spectroscopic and computational approach

In this work, we have developed noscapine based ionic liquids i.e., Noscapine (MeNOS) and 9-Bromonoscapine (MeBrNOS) as cation supported with bis(trifluoromethylsulfonyl)amide (NTf₂^-) as anion. We have reported the mechanism of binding interaction between noscapine based ILs and human hemoglobin (Hb) using various spectroscopic and computational techniques. The corresponding thermodynamics studies showed that the binding is exothermic in nature and major forces responsible for binding are Van der waals and hydrogen bonding interaction. The fluorescence spectra showed that the intensity of Hb decreases in the presence of [MeNOS]NTf₂ and [MeBrNOS]NTf₂ both shows static quenching. The secondary structural changes in Hb were observed and calculated by using CD spectroscopy. Molecular docking studies revealed that both the ILs show strong binding in β1 fragment of the tetrameric structure of Hb, but the binding of [MeNOS]NTf₂ is relatively stronger than [MeBrNOS]NTf₂ and the results are supported by MD simulations.

Probing the interaction between 7-geranyloxycoumarin and bovine serum albumin: Spectroscopic analyzing and molecular docking study

7-Geranyloxycoumarin (auraptene; AUR), as a potent phytochemical, is the naturally abundant prenyloxycoumarin found in many genera of the Rutaceae family. As the interaction with serum albumins may play a crucial role in identifying their pharmacological properties, we investigated AUR binding profile with bovine serum albumin (BSA) by experimental and computational methods. Binding constant, binding site, mode of binding, and the BSA structural change upon AUR addition, were studied. UV-vis spectroscopy results and fluorescence quenching analysis proposed that AUR can form the ground state complex with BSA. Meantime, thermodynamic parameters (negative ΔH and ΔS values) revealed that hydrogen bonds and van der Waals interactions play major role, as intermolecular forces, in the AUR-BSA complex formation. Synchronous fluorescence spectra and circular dichroism (CD) data showed that the secondary structure of BSA did not change significantly in the presence of AUR. Moreover, molecular docking results showed that AUR binds to the subdomain IIIB of BSA.

How hydrophilic group affects drug-protein binding modes: Differences in interaction between sirtuins inhibitors Tenovin-1/Tenovin-6 and human serum albumin

Introduction of hydrophilic groups can improve the solubility of leading drugs but inevitably affect their interaction with proteins. This study selected sirtuin inhibitors Tenovin-1 (T1) and Tenovin-6 (T6) as drug models to determine differences in binding mode to human serum albumin (HSA). T1 and T6 quenched the endogenous fluorescence of HSA via static quenching mechanism. Introduction of hydrophilic groups greatly reduced the binding constant, i.e., from 1.302 × 10⁴ L mol^-1 for the HSA-T6 system to 0.128 × 10⁴ L mol^-1 for the HSA-T1 system. HSA-T1 system was mainly driven by electrostatic interactions while that of HSA-T6 system was hydrophobic interaction and both systems were spontaneous reactions. Site marker experiments and molecular docking indicated that both systems mainly bound to the hydrophobic site I of HSA. Molecular dynamics (MD) simulation analysis further revealed that Tyr148, Tyr150 and Arg257 residues played a key role in this recognition process for both systems. In particular, T6 maintained additional several hydrogen bonds with the surrounding residues. T1 had almost no effect on the esterase-like activity of HSA, but T6 inhibited the hydrolysis of p-NPA. Furthermore, differential scanning calorimetry (VP-DSC), circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy confirmed that HSA in the T6 system undergone a more significant conformational transition than that in the T1 system.

Insight into the binding of glycerol with myoglobin: Spectroscopic and MD simulation approach

Stability of proteins plays a significant role not only in their biological function but also in medical science and protein engineering. Since proteins are only stable in special conditions, maintaining their stability and function in biological and biotechnological applications may pose serious challenges. Osmolytes provide a general method of shielding proteins from the unfolding and aggregation caused by extreme stress on the environment. In such studies, the researchers used spectroscopic and simulation approaches to study the alterations of the myoglobin structure and stability in glycerol presence. Experimental results showed a stability improvement of the complex myoglobin-glycerol. After the addition of glycerol resulting in the initiation of hydrogen bonds and higher levels of hydrophobicity, the increase of the T_m was observed. The static mode quenching observed in this study. Van der Waals forces and hydrogen bindings had a decisive and significant role concerning the stability of protein which was consistent with the modeling results. Molecular dynamics simulation showed that the glycerol presence could enhance myoglobin stability. The consistency between the theoretical studies and experimental findings demonstrates that the method proposed in this study could provide a useful method for protein-ligand complex investigations.

Mechanism and inhibition kinetics of peptide P13 as thrombin inhibitor

Excessive coagulation can easily lead to arterial and venous thrombosis, which is the main reason for the evolution of myocardial infarction and cerebrovascular accidents. As a key coagulation factor for the coagulation pathway, thrombin has become a remarkable target for the control of thrombosis. The synthesized peptide P13 with amino acid sequence of N-RGDAGFAGDDAPR was expected to be an inhibitor with higher antithrombotic activity. The results showed that the IC₅₀ (50% inhibition of thrombin activity) of the peptide P13 was determined by colorimetric method to be 115 µM. And enzyme kinetic experiments showed that P13 was a competitive inhibitor of thrombin with K_i = 106 µM. Fluorescence spectra and three-dimensional fluorescence showed that P13 could alter the secondary structure of thrombin and the microenvironment of certain chromogenic amino acids. P13 can spontaneously bind with thrombin exosite 1 in the form of 1:1 mainly through hydrogen bonding and van der Waals force. And the optimal docking mode of P13 and thrombin was revealed by molecular docking with "-CDOCKER_Energy" of 178.679 kcal mol^-1. This study revealed P13 may become a potential anticoagulant drug widely used after further studies in preclinical and clinical trials.

Experimental and theoretical investigations on the interaction of l-methionine molecules with α-chymotrypsin in the aqueous solution using various methods

l-Methionine (l-Met) is one of the necessary amino acids that play unparalleled roles, influencing both the protein structure and metabolism. Understanding the interactions between proteins and small molecules can be realized by various perspectives, and this is significant for the progression of basic sciences and drug development. In this study, the variations in the stability, function, and structure of α-Chymotrypsin (α-Chy) in the presence of l-Met were investigated using spectroscopic and computational approaches. The results of the UV-vis absorption demonstrated that α-Chy had a maximum peak at 280 nm due to the Trp residue. Hyperchromism shift was seen in the presence of l-Met. Ground state system was formed in the presence of l-Met, as confirmed by the fluorescence studies. Fluorescence variations also revealed static quenching. The CD spectra also represented the alteration of the enzyme with an increase in the α-helix and a decrease in the β-sheet. The activity of α-Chy was incremented in the presence of l-Met. Therefore, l-Met served as an activator. Molecular docking results also indicated a negative amount for the Gibbs free energy of the binding of l-Met to the enzyme. α-Chy became more stable in the presence of l-Met, based on the molecular dynamics simulation.

Insight into the delivery channel and selectivity of multiple binding sites in bovine serum albumin towards naphthalimide-polyamine derivatives

Naphthalimide derivatives are types of small-molecule anticancer drug candidates; however, their negative factors and potential side effects make their application limited. The pharmacophores select a direct access into the tumor cells as the first choice; this can reduce the side effect of the anti-cancer drugs on the normal cells. Herein, the delivery and binding of the naphthalimide-polyamine complex assisted by the bovine serum albumin (BSA) protein have been studied by combining several molecular dynamic simulations. The plausible transportation channels and the most favorable pathways for the delivery of the naphthalimide-polyamine complex to two drug sites (DSI and DSII), their thermodynamic and dynamic properties and the mechanisms have been discussed in detail. The residues His287 and Phe394 acted as guards in the DSI and DSII, respectively, which played a gating-switch role by flipping the ring from open to close during the compound delivery. The binding mode, binding energy and substituent effects have been also identified. The two drug sites have different preferences towards the compound with the electron-withdrawing and electron-donating substituents, and their strong interactions are more sensitive to the number of the substituent groups. The naphthalimide-polyamine complexes are more likely to choose DSI, both thermodynamically and dynamically, as compared to DSII. This selective specificity of these two drug sites manipulated by the electron-withdrawing and electron-donating substituents is quite promising for the design of new naphthalimide drugs.

Insight Into the Binding Mechanism of p53/pDIQ-MDMX/MDM2 With the Interaction Entropy Method

The study of the p53-MDMX/MDM2 binding sites is a research hotspot for tumor drug design. The inhibition of p53-targeted MDMX/MDM2 has become an effective approach in anti-tumor drug development. In this paper, a theoretically rigorous and computationally accurate method, namely, the interaction entropy (IE) method, combined with the polarized protein-specific charge (PPC) force field, is used to explore the difference in the binding mechanism between p53-MDMX and p53-MDM2. The interaction of a 12mer peptide inhibitor (pDIQ), which is similar to p53 in structure, with MDMX/MDM2 is also studied. The results demonstrate that p53/pDIQ with MDM2 generates a stronger interaction than with MDMX. Compared to p53, pDIQ has larger binding free energies with MDMX and MDM2. According to the calculated binding free energies, the differences in the binding free energy among the four complexes that are obtained from the combination of PPC and IE are more consistent with the experimental values than with the results from the combination of the non-polarizable AMBER force field and IE. In addition, according to the decomposition of the binding free energy, the van der Waals (vdW) interactions are the main driving force for the binding of the four complexes. They are also the main source of the weaker binding affinity of p53/pDIQ-MDMX relative to p53/pDIQ-MDM2. Compared with p53-MDMX/MDM2, according to the analysis of the residue decomposition, the predicated total residue contributions are higher in pDIQ-MDMX/MDM2 than in p53-MDMX/MDM2, which explains why pDIQ has higher binding affinity than p53 with MDMX/MDM2. The current study provides theoretical guidance for understanding the binding mechanisms and designing a potent dual inhibitor that is targeted to MDMX/MDM2.

Exploring the binding pattern between pepsin and deferasirox using detailed experimental and computer simulation methods

Steady-state fluorescence spectroscopy indicated that a ground state complex was formed between deferasirox (DFX) and pepsin. The binding parameters and thermodynamic parameters of pepsin-DFX complex formation suggested the presence of only one high affinity binding site in the binding process of DFX and pepsin and that the binding process was hydrogen bond dominated. According to the MD simulation optimal pepsin-DFX binding model analysis, the binding force between DFX and pepsin was mainly hydrogen bonding, and the hydrophobic interaction was supplemented. Synchronous fluorescence spectroscopy and 3D fluorescence spectroscopy indicated that the binding of DFX to pepsin had minor effect on the protein structure and function. Circular dichroism spectra showed that DFX had no significant effect on the main secondary structure of pepsin. MD analysis also showed that DFX did not affect the looseness of pepsin and the overall secondary structure, but it affected the amino acid residue sequence Leu48-Ala49-Cys50-Ser51-Asp52. Pepsin enzyme activity test showed that the addition of DFX had a slight enhancement effect on the activity of pepsin. Combined with the MD results, DFX bound to pepsin and was closer to the pepsin active site Asp-215, which may affect the electrical environment of Asp-215 residues and enhance the activity of pepsin.

Insights into the binding mechanism of BODIPY-based photosensitizers to human serum albumin: A combined experimental and computational study

Photodynamic therapy (PDT) is a noninvasive and effective approach in clinical cancer treatments. Boron-dipyrromethene (BODIPY)-based derivatives have emerged as novel and promising photosensitizers (PSs) in PDT, attributed to their strong near-infrared singlet oxygen luminescence emissions and high photostabilities. However, the binding mechanism of BODIPY derivatives to proteins, key for their therapeutic and biomedical applications is still poorly understood. Here, we investigated the molecular interactions of two 2, 6-diiodo-BODIPY derivatives with human serum albumin (HSA) using combined experimental and computational techniques. Our spectroscopic results showed that both BODIPY derivatives formed stable complexes with HSA. Strikingly, the BODIPY/HSA complexes exhibited notably enhanced water solubility and singlet oxygen generation efficiency with respect to the BODIPY alone. Furthermore, molecular docking, molecular dynamics simulations, and binding free energy calculations provided the structural and energetic insights into the binding mechanism of BODIPY-based derivatives to HSA. Our work demonstrated that conjugation of BODIPYs with HSA may be a promising strategy to enhance the performance of BODIPY-based PSs, and the combination of computational and experimental techniques is expected to play key roles in the design and development of novel PSs with improved bioavailability and biocompatibility for cancer therapeutic applications.

A general microwave synthesis of metal (Ni, Cu, Zn) selenide nanoparticles and their competitive interaction with human serum albumin

Simple microwave irradiation technique was used to synthesize a series of selenide nanoparticles (platelet-like NiSe nanoparticles, uniform CuSe nanorods, and distorted ZnSe nano-hexagons) and their competitive interaction with human serum albumin was studied.