Molecular interactions of AL3818 (anlotinib) to human serum albumin as revealed by spectroscopic and molecular docking studies

Interaction of Cecropin A (1-7) Analogs with DNA Analyzed by Multi-spectroscopic Methods

Cecropin A (1-7) is a cationic antimicrobial peptide which contain lots of basic amino acids. To understand the effect of basic amino acids on cecropin A (1-7), analogues CA2, CA3 and CA4 which have more arginine or lysine at the N-terminal or C-terminal were designed and synthesized. The interaction of cecropin A (1-7) and its analogs with DNA was studied using ultraviolet-visible spectroscopy, fluorescence spectroscopy and circular dichroism spectroscopy. Multispectral analysis showed that basic amino acids improved the interaction between the analogues and DNA. The interaction between CA4 and DNA is most pronounced. Fluorescence spectrum indicated that Ksv value of CA4 is 1.19 × 105  L mol-1 compared to original peptide cecropin A (1-7) of 3.73 × 104  L mol-1. The results of antimicrobial experiments with cecropin A (1-7) and its analogues showed that basic amino acids enhanced the antimicrobial effect of the analogues. The antimicrobial activity of CA4 against E. coli was eightfold higher than that of cecropin A (1-7). The importance of basic amino acid in peptides is revealed and provides useful information for subsequent studies of antimicrobial peptides.

Impacts of Halogen Substitutions on Bisphenol A Compounds Interaction with Human Serum Albumin: Exploring from Spectroscopic Techniques and Computer Simulations

Bisphenol A (BPA) is an endocrine-disrupting compound, and the binding mechanism of BPA with carrier proteins has drawn widespread attention. Halogen substitutions can significantly impact the properties of BPA, resulting in various effects for human health. Here, we selected tetrabromobisphenol A (TBBPA) and tetrachlorobisphenol A (TCBPA) to investigate the interaction between different halogen-substituted BPAs and human serum albumin (HSA). TBBPA/TCBPA spontaneously occupied site I and formed stable binary complexes with HSA. Compared to TCBPA, TBBPA has higher binding affinity to HSA. The effect of different halogen substituents on the negatively charged surface area of BPA was an important reason for the higher binding affinity of TBBPA to HSA compared to TCBPA. Hydrogen bonds and van der Waals forces were crucial in the TCBPA-HSA complex, while the main driving factor for the formation of the TBBPA-HSA complex was hydrophobic interactions. Moreover, the presence of TBBPA/TCBPA changed the secondary structure of HSA. Amino acid residues such as Lys199, Lys195, Phe211, Arg218, His242, Leu481, and Trp214 were found to play crucial roles in the binding process between BPA compounds and HSA. Furthermore, the presence of halogen substituents facilitated the binding of BPA compounds with HSA.

Elucidation of binding dynamics of tyrosine kinase inhibitor tepotinib, to human serum albumin, using spectroscopic and computational approach

Tepotinib (TPT), an anticancer drug, is a fibroblast growth factor receptor inhibitor approved by the FDA for the chemotherapy of urothelial carcinoma. The binding of anticancer medicines to HSA can affect their pharmacokinetics and pharmacodynamics. The absorption, fluorescence emission, circular dichroism, molecular docking, and simulation studies were used to evaluate the binding relationship between TPT and HSA. The absorption spectra exhibited a hyperchromic effect upon the interaction of TPT with HSA. The Stern-Volmer and binding constant of the HSA-TPT complex demonstrates that fluorescence quenching is triggered by a static rather than a dynamic process. Further, the displacement assays and molecular docking results revealed that TPT preferred binding to site III of HSA. Circular dichroism spectroscopy confirmed that TPT binding to HSA induces conformational changes and reduces α-helical content. The thermal CD spectra reveal that tepotinib enhances protein's stability in the temperature range of 20 to 90 °C. The findings of MDS studies provide further evidence for the stability of the HSA-TPT complex. Consequently, the findings of the present investigation provide a clear picture of the impacts of TPT on HSA interaction. These interactions are thought to make the microenvironment around HSA more hydrophobic than in its native state.

Structural change study of pepsin in the presence of spermidine trihydrochloride: Insights from spectroscopic to molecular dynamics methods

Spermidine is an aliphatic polyamine that directs a set of biological processes. This work aimed to use UV-Vis spectroscopy, fluorescence spectroscopy, thermal stability, kinetic methods, docking, and molecular dynamic simulations to examine the influence of spermidine trihydrochloride (SP) on the structure and function of pepsin. The results of the fluorescence emission spectra indicated that spermidine could quench pepsin's intrinsic emission in a static quenching process, resulting in the formation of the pepsin-spermidine complex. The results discovered that spermidine had a strong affinity to the pepsin structure because of its high binding constant. The obtained results from spectroscopy and molecular dynamic approaches showed the binding interaction between spermidine and pepsin, induced micro-environmental modifications around tryptophan residues that caused a change in the tertiary and secondary structure of the enzyme. FTIR analysis showed hypochromic effects in the spectra of amide I and II and redistribution of the helical structure. Moreover, the molecular dynamic (MD) and docking studies confirmed the experimental data. Both experimental and molecular dynamics simulation results clarified that electrostatic bond interactions were dominant forces.

Evaluation the binding of chlorogenic acid with bovine serum albumin: Spectroscopic methods, electrochemical and molecular docking

Chlorogenic acid(CGA) is the common active phenolic acid in Chinese medicinal materials such as honeysuckle and eucommia. It is a class of small molecules with multiple activities such as antioxidant, inhibiting cancer cells, lowering blood sugar and lowering blood pressure. In this paper, UV-vis spectroscopy, fluorescence spectroscopy, circular dichroism, molecular dynamics simulation and cyclic voltammetry (CV) electrochemical analysis were used to investigate the mechanism about interaction between CGA and BSA. Based on fluorescence quenching analysis, CGA quenched the inherent fluorescence of BSA remarkably through a static mechanism. The obtained value of binding constant (K_b = 5.75 × 10⁵ L·mol^-1) revealed a high binding affinity between CGA and BSA. The simulated molecular docking showed that hydrophobic force were also involved in the interaction between BSA and CGA. This paper also investigate the effect of temperature and metal ions on the binding of CGA and BSA. When the temperature increased, the binding of BSA and CGA was destroyed. Metal ions affect both the structure of BSA and the combination of BSA and CGA. By studying the mechanism of CGA interaction with BSA, we elucidated the storage and transport mechanism of CGA in vivo under simulated human environment and temperature conditions.

Interaction of bifunctional peptide-carbazole complexes with DNA and antimicrobial activity

Two peptide-carbazole conjugates, CTAT and CNLS, were designed and synthesized using carbazole Schiff base to modify the cell membrane penetrating peptide TAT (47-57) and the nuclear localization peptide NLS at the N terminus. The interaction with ctDNA was investigated by multispectral and agarose gel electrophoresis. And the effects of CNLS and CTAT on the G-quadruplex structure were explored by circular dichroism titration experiments. The results show that both CTAT and CNLS interact with ctDNA in a minor groove binding manner. Both conjugates bind more tightly to DNA than the individual substances CIBA, TAT and NLS. In addition, CTAT and CNLS are capable of unfolding parallel G-quadruplex structures and are potential G-quadruplex unfolding agents. Finally, broth microdilution was performed to test the antimicrobial activity of the peptides. The results showed that CTAT and CNLS had a 4-fold increase in antimicrobial activity compared with the parent peptides TAT and NLS. They could exert antimicrobial activity by disrupting the integrity of cell membrane bilayer and binding to DNA, and could be used as novel antimicrobial peptides for the development of novel antimicrobial antibiotics.

Study on the interaction of two quinazoline derivatives as novel PI3K/mTOR dual inhibitors and anticancer agents to human serum albumin utilizing spectroscopy and docking

Interactions of human serum albumin (HSA) with two structurally similar quinazoline derivatives, S₁ and S₂ , which are potential anticancer drugs acting on PI3K/mTOR targets, were investigated in vitro utilizing multiple spectroscopy as well as molecular docking. The fluorescence quenching study demonstrated that HSA fluorescence could be statically quenched by S₁ and S₂ through the formation of an HSA-drug complex. Furthermore, the details of the binding site number, binding constant, as well as the thermodynamic parameters, were estimated at 298, 303, and 310 K. The results revealed that hydrogen bond interactions, as well as van der Waals forces, were the predominant factors responsible for binding HSA to S₁ or S₂ . Synchronous fluorescence and ultraviolet (UV) absorption spectra suggested that S₁ and S₂ had little effect on the polarity of the microenvironment and conformation of HSA. Energy transfer from HSA to S₁ or S₂ most probably occurred. The docking study revealed that S₁ and S₂ were able to bind to the hydrophobic cavity that was located in the HSA subdomain IIA and formed varying numbers of hydrogen bonds with amino acid residues nearby. Due to the subtle difference in the chemical structure, the binding of S₁ and S₂ to HSA was slightly different.

Spectroscopic, molecular docking and dynamic simulation studies of binding between the new anticancer agent olmutinib and human serum albumin

In this study, the interaction between human serum albumin (HSA), which is the key bio-distributor of exogenous and endogenous compounds in the human bloodstream, and HM61713 (Olmutinib; OMB), which is used as an anticancer drug, is examined by multiple spectroscopic techniques (steady-state fluorescence, UV spectrophotometry, synchronous, and 3 D fluorescence) combined with molecular docking and molecular dynamic simulation investigations. The fluorescence results clearly demonstrated quenching in HSA fluorescence in the existence of OMB indicating the formation of complex and have also shown that the interaction is static. Fluorescence spectroscopy was used to obtain the binding constant values that revealed a strong interaction between the HSA and OMB at 298 K with a binding constant of 7.39x10⁴ M^-1 suggesting strong interaction. OMB binds to HSA at site I (IIA). Electrostatic forces and H-bonding were the main binding forces of main bonding between HSA and OMB as revealed by docking and thermodynamic results.Communicated by Ramaswamy H. Sarma.

Spectroscopic and computational investigation of the interaction between the new anticancer agent enasidenib and human serum albumin

Enasidenib (EDB) is a new therapeutic agent for the treatment of adult patients with relapsed or refractory acute myeloid leukemia (AML) with an isocitrate dehydrogenase-2 (IDH2) mutation. This research aimed at utilizing experimental and theoretical approaches to characterize the binding mechanism between EDB and human serum albumin (HSA). Formation of an EDB-HSA static complex was demonstrated by quenching of the HSA intrinsic fluorescence by EDB. Using well known mathematical relations (e.g. Stern-Volmer and Lineweaver-Burk equations), the recorded EDB-HSA fluorescence data were interpreted and revealed binding constants in the magnitude order of 10⁴ M^-1 for the different investigated temperatures. These determined results were taken into further mathematical calculations to reveal the thermodynamic properties of EDB-HSA binding. Results demonstrated that spontaneous EDB and HSA binding takes place led by electrostatic forces. Computational docking studies have further confirmed the latter finding showing that EDB fits into the HSA Sudlow site I. Molecular dynamic simulation was performed to calculate the root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R_g) and hydrogen bond parameters for the EDB-HSA complex.

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.

Comprehensive insights into the interactions of dicyclohexyl phthalate and its metabolite to human serum albumin

Phthalate esters (PAEs) are a type of persistent organic pollutants and have received widespread concerns due to their adverse effects on human health. Dicyclohexyl phthalate (DCHP) and its metabolite monocyclohexyl phthalate (MCHP) were selected to explore the mechanism for interaction of PAEs with human serum albumin (HSA) through molecular docking and several spectroscopic techniques. The results showed that DCHP/MCHP can spontaneously occupy site I to form a binary complex with HSA, and DCHP exhibited higher binding affinity to HSA than MCHP. At 298 K, the binding constants (K_b) of DCHP and MCHP to HSA were 24.82 × 10⁴ and 1.04 × 10⁴ M^-1, respectively. Hydrogen bonds and van der Waals forces were the major driving forces in DCHP/MCHP-HSA complex. The presence of DCHP/MCHP induced the secondary structure changes in HSA, and the pi electrons of the benzene ring skeleton of DCHP/MCHP played a key role in this binding processes. Exposure of DCHP/MCHP to TM4 cells revealed that interactions between PAEs and serum albumin can affect their cytotoxicity; DCHP showed higher toxicity than MCHP. The binding affinity of PAEs with HSA may be a valuable parameter for rapid assessment of their toxicity to organisms.

Effect of local anesthetic drug procaine hydrochloride on the conformational stability of bovine hemoglobin: Multi-spectroscopic and computational approaches

The interaction between bovine hemoglobin (BHb) and local anesthetic drug procaine hydrochloride (PCH) was examined by spectroscopic and computational studies. Intrinsic fluorescence analysis explored the ground-state complex formation in the binding of PCH with BHb through static quenching mechanism. The binding constants (K_b) are 29.38 × 10³, 22.54 × 10³ and 17.99 × 10³ M^-1 at 288, 298 and 308 K, respectively, and the ratio of BHb:PCH was 1:1 in the interaction mechanism of PCH and BHb. The acquired thermodynamic parameters (ΔH⁰, ΔG⁰ and ΔS⁰) demonstrated that interaction mechanism is spontaneous and enthalpy driven. The van der Waals forces and hydrogen bonding have been played a predominant role in the binding mechanism. The UV-vis spectroscopy validates the ground-state complexation between PCH and BHb and the binding constant (K_b) has been evaluated utilizing Benesi-Hildebrand equation. Fluorescence resonance energy transfer (FRET) results have demonstrated that the distance between donor (BHb) and acceptor (PCH) is very short (2.34 nm) suggesting a significant probability to energy transfer from BHb to PCH. Synchronous fluorescence results revealed that the alteration in the micro-environment of Tyrosine (Tyr) is more than tryptophan (Trp) residues suggesting that PCH molecule is close to Tyr residue. The secondary structure alterations were confirmed by CD, 3-D fluorescence and FT-IR spectroscopic measurements. Moreover, computational analyses further corroborated that PCH molecules are closer to Tyr residues as compared to Trp residues of BHb during the interaction process. The BHb-PCH complexes may contribute to a deeper understanding of the metabolism of drug, blood circulation process and may help to illustrate the relationship between functions and structure of BHb.Communicated by Ramaswamy H. Sarma.

Estimation of internal human daily intakes of organophosphate esters using one-compartment toxicokinetic model in the whole blood from Hebei Province, China

To evaluate the human health risks attributed by organophosphate ester (OPE) exposure, it is very important to estimate the daily intakes (DIs) of OPEs in human. In this study, the DIs of OPEs were estimated using a simplified one-compartment toxicokinetic model based on their total clearance rates in human and their whole blood concentrations. Thirty paired human whole blood and plasma samples were collected from participants in Hengshui, Hebei Province, China. The detection frequencies of most OPEs in the whole blood were lower than 50.0%. Thus, the OPE levels in whole blood were converted from the corresponding plasma levels using the fractions of OPEs in plasma (F_p), which were estimated from an in vitro partition assay and the values were in the range of 0.52-0.98. The measured whole blood concentrations of triphenyl phosphate (TPHP) and tris(chloroethyl) phosphate (TCEP) were comparable to those converted from the plasma concentrations, suggesting that the conversion method was reliable. The estimated total DIs of TPHP, TCEP, and tris(2-chloroisopropyl) phosphate were 1-30 times of those derived by the external exposure method, which usually excluded many exposure sources. The estimated human health risks based on the DIs indicated that the carcinogenic and non-carcinogenic effects of OPEs for the participants in Hengshui, Hebei Province, China, were negligible. This study recommended a more reliable and simpler method to estimate the human health risks attributed to the exposure of OPEs.

Evaluation of the interaction of novel tyrosine kinase inhibitor apatinib mesylate with bovine serum albumin using spectroscopies and theoretical calculation approaches

Apatinib mesylate (APM), a novel tyrosine kinase inhibitor, has been applied in treating various cancers. In the present study, the binding mechanism of APM with bovine serum albumin (BSA) was studied by making use of various spectroscopic and theoretical calculation approaches to provide theoretical support for further studying its pharmacokinetics and metabolism. The results from fluorescence experiments showed that the quenching mechanism of BSA induced by APM was static quenching and the APM-BSA complex with the stoichiometry of 1:1 was formed during binding reaction. Moreover, the findings also showed that the binding process of APM to BSA was spontaneous and enthalpy-driven, and the mainly driving forces were hydrogen bonding, van der Waals as well as hydrophobic interactions. From the outcomes of the competitive experiments, it can be found that the binding site was primarily nestled in sub-domain IIIA of BSA (site II) which was in line with the results of molecular docking. An appreciable decline in α-helix content of BSA can be observed from the FT-IR data, meaning that the conformational change of BSA occurred after binding with APM, this phenomenon can be corroborated by the results of UV-vis, synchronous fluorescence and 3D fluorescence studies. Furthermore, the effect of some metal ions (e.g. K⁺, Co²⁺, Ni²⁺, Fe³⁺) on the binding constant of APM to BSA was explored.Communicated by Ramaswamy H. Sarma.

Biomolecular interactions and binding dynamics of tyrosine kinase inhibitor erdafitinib, with human serum albumin

Erdafitinib is an approved tyrosine kinase inhibitor that inhibits fibroblast growth factor receptor. It has been described as one of the potent anti-tumor drugs especially for the treatment of urothelial carcinoma. In this study, we have investigated the binding dynamics of erdafitinib with human serum albumin (HSA) using multiple spectroscopic techniques. The outcome of the results suggests the occurrence of static quenching during the interaction of HSA with erdafitinib which leads to the formation of non-fluorescent HSA-erdafitinib ground state complex. Formation of HSA-erdafitinib complex was also confirmed from the findings of absorption spectral analysis. The changes in microenvironment around hydrophobic domains (especially tryptophan and tyrosine) were deciphered from fluorescence spectroscopy which was further confirmed by synchronous spectral analysis. In order to gain insight into the binding site of erdafitinib in HSA, molecular docking combined with competitive displacement assay was performed. The modified form of Stern Volmer equation was used to estimate various binding parameters including number of binding sites. The findings are indicative of a single binding site (n = 1) with binding constant in the order of 10⁴. The negative values of thermodynamic parameters like ΔG, ΔH and ΔS were suggestive of the binding reaction being spontaneous and exothermic, while the hydrogen bonds and Van der Waals interactions being the major forces present between HSA and erdafitinib. Circular dichroism spectral analysis revealed the alterations in the conformation of HSA structure and reduction in its α-helical content.Communicated by Ramaswamy H. Sarma[Formula: see text].

Estimating renal and hepatic clearance rates of organophosphate esters in humans: Impacts of intrinsic metabolism and binding affinity with plasma proteins

The renal and hepatic clearance rates of organophosphate esters (OPEs) in humans were estimated. Six OPEs and their corresponding diester metabolites (mOPEs) were quantified respectively in 30 paired human plasma and urine samples collected in Hengshui, Hebei province, China. The renal clearance rate (CL_renal) of triphenyl phosphate (TPHP), tris(chloroethyl) phosphate (TCEP) and tris(1,3-dichloro-isopropyl) phosphate (TDCIPP) was estimated to be 68.9, 50.9 and 33.3 mL/kg/day, respectively, while it was not calculated for other three OPEs due to the low detection frequencies in human samples. To estimate the clearance rates of the target OPEs, hepatic clearance rates (CL_h) of OPEs were extrapolated from their in vitro intrinsic clearance data in human liver microsomes (CL_HLM). The calculated CL_h values of TCEP and TDCIPP were comparable to their CL_renal, indicating that the in vitro extrapolation method was suitable for estimating the clearance rates of OPEs. The higher binding affinity of TDCIPP with plasma proteins could reduce its renal clearance. The estimated half-lives of Cl-OPEs in human were longer than those of the aryl- and alkyl-OPEs. This study provided a feasible in vitro method to predict the clearance and half-lives of OPEs in human, which is significant for their accurate health risk assessment.

Spectroscopic and molecular docking studies reveal binding characteristics of nazartinib (EGF816) to human serum albumin

The interactions of novel anti-cancer therapeutic agents with the different plasma and tissue components, specifically serum albumins, have lately gained considerable attention due to the significant influence of such interactions on the pharmacokinetics and/or -dynamics of this important class of therapeutics. Nazartinib (EGF 816; NAZ) is a new anti-cancer candidate proposed as a third-generation epidermal growth factor receptor tyrosine kinase inhibitor that is being developed and clinically tested for the management of non-small cell lung cancer. The current study aimed to characterize the interaction between NAZ and human serum albumin (HSA) using experimental and theoretical approaches. Experimental results of fluorescence quenching of HSA induced by NAZ revealed the development of a statically formed complex between NAZ and HSA. Interpretation of the observed fluorescence data using Stern-Volmer, Lineweaver-Burk and double-log formulae resulted in binding constants for HSA-NAZ complex in the range of (2.34-2.81) × 10⁴ M^-1 over the studied temperatures. These computed values were further used to elucidate thermodynamic attributes of the interaction, which showed that NAZ spontaneously binds to HSA with a postulated electrostatic force-driven interaction. This was further verified by theoretical examination of the NAZ docking on the HSA surface that revealed an HSA-NAZ complex where NAZ is bound to HSA Sudlow site I driven by hydrogen bonding in addition to electrostatic forces in the form of pi-H bond. The HSA binding pocket for NAZ was shown to encompass ARG 257, ARG 222, LYS 199 and GLU 292 with a total binding energy of -25.59 kJ mol^-1.

Spectroscopic and molecular docking studies reveal binding characteristics of nazartinib (EGF816) to human serum albumin

The interactions of novel anti-cancer therapeutic agents with the different plasma and tissue components, specifically serum albumins, have lately gained considerable attention due to the significant influence of such interactions on the pharmacokinetics and/or -dynamics of this important class of therapeutics. Nazartinib (EGF 816; NAZ) is a new anti-cancer candidate proposed as a third-generation epidermal growth factor receptor tyrosine kinase inhibitor that is being developed and clinically tested for the management of non-small cell lung cancer. The current study aimed to characterize the interaction between NAZ and human serum albumin (HSA) using experimental and theoretical approaches. Experimental results of fluorescence quenching of HSA induced by NAZ revealed the development of a statically formed complex between NAZ and HSA. Interpretation of the observed fluorescence data using Stern-Volmer, Lineweaver-Burk and double-log formulae resulted in binding constants for HSA-NAZ complex in the range of (2.34-2.81) × 10⁴ M^-1 over the studied temperatures. These computed values were further used to elucidate thermodynamic attributes of the interaction, which showed that NAZ spontaneously binds to HSA with a postulated electrostatic force-driven interaction. This was further verified by theoretical examination of the NAZ docking on the HSA surface that revealed an HSA-NAZ complex where NAZ is bound to HSA Sudlow site I driven by hydrogen bonding in addition to electrostatic forces in the form of pi-H bond. The HSA binding pocket for NAZ was shown to encompass ARG 257, ARG 222, LYS 199 and GLU 292 with a total binding energy of -25.59 kJ mol^-1.