A combined spectroscopic, docking and molecular dynamics simulation approach to probing binding of a Schiff base complex to human serum albumin

Synthesis and isolation of metalloprotein on a super water-repellent umbrella-shaped pillar array with double re-entrant structure

This paper reports the generation of microdroplets on a water-repellent device equipped with an array of tiny umbrella-shaped pillar structures. The microdroplets were used for chemical synthesis, docking, and crystallization of a functional protein. The umbrella-shaped water-repellent devices were easily fabricated from SU-8 by soft micro-electromechanical systems technology, which would suit mass production. We used simulations to visually clarify how water and methanol were repelled and quantitatively determined the umbrella-shaped structure's water-repellency by measuring a microdroplet's contact angle. Pillar array devices reduce the amount of reagents used in chemical synthesis experiments and facilitate chemical analysis. Furthermore, the reaction speed in microdroplets is often faster. The synthesis of a Zn(II) complex, which usually takes 4 h in a beaker, was completed in less than 120 s. The reaction inside the microdroplets was observed with a high-speed camera, and the products were identified by optical analysis. A metal complex and protein were docked and crystallized in microdroplets on the water-repellent device. The crystallization was observed under an optical microscope, producing beautiful single protein crystals. The metal complex and protein docking was confirmed by elemental analysis of the crystals.

A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma

BACKGROUND

Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32).

AIM

The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL.

METHODOLOGY

Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds.

RESULT

MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies.

CONCLUSION

Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.

Bovine β-casein binding studies of a Schiff base ligand: fluorescence and circular dichroism approaches

In this study, a Schiff base derived from a heterocyclic moiety was synthesized and characterized. The in vitro binding behaviour of this ligand with β-casein (β-CN) was investigated using biophysical techniques. For evaluation, thermodynamics variables of interactions between the Schiff base ligand and β-CN, such as fluorescence at different temperatures, were measured. The results showed that the Schiff base ligand possessed considerable associated binding to β-CN and that the procedure was enthalpy driven. The β-CN conformation was also changed to give a further unfolded structure. Fluorescence resonance energy transfer was used to estimate the interval between donor (β-CN) and acceptor (Schiff base ligand). All these experimental results proposed that β-CN might act as carrier protein for the Schiff base ligand to deliver it to the target molecules.

Synthesis and Characterization of Cobalt(II) and Manganese(II) Schiff Base Complexes: Metal Effect on the Binding Affinity with β-Casein

In this study, two metal Schiff base complexes (cobalt(II) and manganese(II), were synthesized and characterized by ¹H-NMR and FT-IR analyses. The in vitro binding behavior of this complexes with β-Casein (β-CN) was investigated by using biophysical techniques. For evaluation the thermodynamics parameters of interaction between Schiff base complexes and β-CN,the fluorescence data at different temperatures were done. The results showed that the intrinsic fluorescence of the β-CN was quenched by increasing the complexes through the dynamic quenching mechanism. Also, these complexes demonstrated a considrable binding affinity to β-CN and the process is mainly entropy driven. Fluorescence resonance energy transfer was used in order to estimating the distance between donor (β-CN) and acceptor (complex). Results demonstrated that the sequence of tendency of the complexes to β-CN was as follows: Mn-Schiff base complex > Co-Schiff base complex. All these experimental results propose that β-CN might act as carrier protein for Co(II) and Mn (II) complexes to deliver it to the target molecules.

Structural-Dependent N,O-Donor Imine-Appended Cu(II)/Zn(II) Complexes: Synthesis, Spectral, and in Vitro Pharmacological Assessment

Four mononuclear bioefficient imine-based coordination complexes, [(L ¹ ) ₂ Cu], [(L ¹ ) ₂ Zn], [(L ² )Cu(H ₂ O)], and [(L ² )Zn(H ₂ O)], were synthesized using ligands [L ¹ = 2-(((3-hydroxynaphthalen-2-yl)methylene)amino)-2-methylpropane-1,3-diol and L ² = 4-(1-((1,3-dihydroxy-2-methylpropan-2-yl)imino)ethyl)benzene-1,3-diol]. The formation of the complexes was ascertained by elemental analysis, Fourier transform infrared, ¹H NMR, ¹³C NMR, electrospray ionization-mass spectroscopy, electron paramagnetic resonance, and thermogravimetric analysis. The comparative binding propensity profiles of the above-synthesized complexes with the DNA/human serum albumin (HSA) were investigated via UV absorption, fluorescence, and Förster resonance energy-transfer studies. On the basis of extended conjugation and planarity, L ¹ complexes exhibited superior bioactivity with greater calculated DNA binding constant values, (K _b) 2.9444 × 10³ [(L ¹ ) ₂ Cu] and 2.2693 × 10³ [(L ¹ ) ₂ Zn], as compared to L ² complexes, 1.793 × 10³ [(L ² )Cu(H ₂ O)] and 9.801 × 10² [(L ² )Zn(H ₂ O)]. The competitive displacement assay of complexes was performed by means of fluorogenic dyes (EtBr and Hoechst), which corroborates the occurrence of minor groove binding because of the enhanced displacement activity with Hoechst 33258. The minor groove binding of the [(L ¹ ) ₂ Cu] complex is further confirmed by the molecular docking study. Moreover, the HSA study demonstrated effective static quenching of complexes with substantial K _sv values. The [(L ¹ ) ₂ Cu] complex was found to have pronounced cleavage efficiency as evaluated from sodium dodecyl sulfate polyacrylamide gel electrophoresis electrophoresis. Furthermore, in vitro antioxidant activity against 2,2-diphenyl-1-picrylhydrazyl and superoxide radicals further proclaimed the remarkable bioefficiency of compounds, which make them promising as active chemotherapeutic agents.

Selective binding of pyrene in subdomain IB of human serum albumin: Combining energy transfer spectroscopy and molecular modelling to understand protein binding flexibility

The ability of human serum albumin (HSA) to bind medium-sized hydrophobic molecules is important for the distribution, metabolism, and efficacy of many drugs. Herein, the interaction between pyrene, a hydrophobic fluorescent probe, and HSA was thoroughly investigated using steady-state and time-resolved fluorescence techniques, ligand docking, and molecular dynamics (MD) simulations. A slight quenching of the fluorescence signal from Trp214 (the sole tryptophan residue in the protein) in the presence of pyrene was used to determine the ligand binding site in the protein, using Förster's resonance energy transfer (FRET) theory. The estimated FRET apparent distance between pyrene and Trp214 was 27Å, which was closely reproduced by the docking analysis (29Å) and MD simulation (32Å). The highest affinity site for pyrene was found to be in subdomain IB from the docking results. The calculated equilibrium structure of the complex using MD simulation shows that the ligand is largely stabilized by hydrophobic interaction with Phe165, Phe127, and the nonpolar moieties of Tyr138 and Tyr161. The fluorescence vibronic peak ratio I₁/I₃ of bound pyrene inside HSA indicates the presence of polar effect in the local environment of pyrene which is less than that of free pyrene in buffer. This was clarified by the MD simulation results in which an average of 5.7 water molecules were found within 0.5nm of pyrene in the binding site. Comparing the fluorescence signals and lifetimes of pyrene inside HSA to that free in buffer, the high tendency of pyrene to form dimer was almost completely suppressed inside HSA, indicating a high selectivity of the binding pocket toward pyrene monomer. The current results emphasize the ability of HSA, as a major carrier of several drugs and ligands in blood, to bind hydrophobic molecules in cavities other than subdomain IIA which is known to bind most hydrophobic drugs. This ability stems from the nature of the amino acids forming the binding sites of the protein that can easily adapt their shape to accommodate a variety of molecular structures.

DNA and HSA interaction of Vanadium (IV), Copper (II), and Zinc (II) complexes derived from an asymmetric bidentate Schiff-base ligand: multi spectroscopic, viscosity measurements, molecular docking, and ONIOM studies

The interaction of three complexes [Zn(II), Cu(II), and V(IV)] derived from an asymmetric bidentate Schiff-base ligand with DNA and HSA was studied using fluorescence quenching, UV-Vis spectroscopy, viscosity measurements, and computational methods [molecular docking and our Own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM)]. The obtained results revealed that the DNA and HSA affinities for binding of the synthesized compounds follow as V(IV) > Zn(II) > Cu(II) and Zn(II) > V(IV) > Cu(II), respectively. The distance between these compounds and HSA was obtained based on the Förster's theory of non-radiative energy transfer. Furthermore, computational molecular docking was carried out to investigate the DNA- and HSA-binding pose of the compounds. Molecular docking calculations showed that H-bond, hydrophobic, and π-cation interactions have dominant role in stability of the compound-HSA complexes. ONIOM method was utilized to investigate the HSA binding of the compounds more precisely in which molecular-mechanics method (UFF) and semi-empirical method (PM6) were selected for the low layer and the high layer, respectively. The results show that the structural parameters of the compounds changed along with binding, indicating the strong interaction between the compounds with HSA and DNA. Viscosity measurements as well as computational docking data suggest that all metal complexes interact with DNA, presumably by groove-binding mechanism.

Interaction between Pin1 and its natural product inhibitor epigallocatechin-3-gallate by spectroscopy and molecular dynamics simulations

The binding of epigallocatechin-3-gallate (EGCG) to wild type Pin1 in solution was studied by spectroscopic methods and molecular dynamics simulations in this research to explore the binding mode and inhibition mechanism. The binding constants and number of binding sites per Pin1 for EGCG were calculated through the Stern-Volmer equation. The values of binding free energy and thermodynamic parameters were calculated and indicated that hydrogen bonds, electrostatic interaction and Van der Waals interaction played the major role in the binding process. The alterations of Pin1 secondary structure in the presence of EGCG were confirmed by far-UV circular dichroism spectra. The binding model at atomic-level revealed that EGCG was bound to the Glu12, Lys13, Arg14, Met15 and Arg17 in WW domain. Furthermore, EGCG could also interact with Arg69, Asp112, Cys113 and Ser114 in PPIase domain.

Synthesis, characterization and biological application of four novel metal-Schiff base complexes derived from allylamine and their interactions with human serum albumin: Experimental, molecular docking and ONIOM computational study

Novel metal-based drug candidate including VOL2, NiL2, CuL2 and PdL2 have been synthesized from 2-hydroxy-1-allyliminomethyl-naphthalen ligand and have been characterized by means of elemental analysis (CHN), FT-IR and UV-vis spectroscopies. In addition, (1)H and (13)C NMR techniques were employed for characterization of the PdL2 complex. Single-crystal X-ray diffraction technique was utilized to characterise the structure of the complexes. The Cu(II), Ni(II) and Pd(II) complexes show a square planar trans-coordination geometry, while in the VOL2, the vanadium center has a distorted tetragonal pyramidal N2O3 coordination sphere. The HSA-binding was also determined, using fluorescence quenching, UV-vis spectroscopy, and circular dichroism (CD) titration method. The obtained results revealed that the HSA affinity for binding the synthesized compounds follows as PdL2>CuL2>VOL2>NiL2, indicating the effect of metal ion on binding constant. The distance between these compounds and HSA was obtained based on the Förster's theory of non-radiative energy transfer. Furthermore, computational methods including molecular docking and our Own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) were carried out to investigate the HSA-binding of the compounds. Molecular docking calculation indicated the existence of hydrogen bond between amino acid residues of HSA and all synthesized compounds. The formation of the hydrogen bond in the HSA-compound systems leads to their stabilization. The ONIOM method was utilized in order to investigate HSA binding of compounds more precisely in which molecular mechanics method (UFF) and semi empirical method (PM6) were selected for the low layer and the high layer, respectively. The results show that the structural parameters of the compounds changed along with binding to HSA, indicating the strong interaction between the compounds and HSA. The value of binding constant depends on the extent of the resultant changes. This should be mentioned that both theoretical methods calculated the Kb values in the same sequence and are in a good agreement with the experimental data.

Comparative study of the effects of the structurally similar flavonoids quercetin and taxifolin on the therapeutic behavior of alprazolam

After a meal rich in plant products, dietary flavonoids can be detected in plasma as serum albumin bound conjugates. Flavonoid–albumin binding is expected to control the bioavailability of drugs. In this study, the binding of alprazolam (ALP) and human serum albumin (HSA) has been investigated in the absence and presence of two flavonoids with similar structures, quercetin (QUER) and taxifolin (TAX), by means of fluorescence spectroscopy, chemometrics, and molecular dynamics simulation. Our results show that ALP has the ability to quench the intrinsic fluorescence of HSA. This quenching is affected by flavonoids. The presence of QUER and TAX decreased the quenching constants, binding constants, and equilibrium constants associated with ALP binding to HSA. The effect of ALP and both flavonoids on the conformation of HSA was analyzed using synchronous fluorescence spectroscopy. Our results indicate a conformational change of HSA with the addition of ligands. The molecular dynamics study makes an important contribution to understanding the effect of the binding of ALP, QUER, and TAX on conformational changes of HSA and modification of its tertiary structure in the absence and presence of flavonoids. All of these results may have relevant consequences in rationalizing the interferences of common food and drugs.

Molecular simulation study of the specific combination between four kinds of phthalic acid esters and human serum albumin

The interaction between endocrine disruptor phthalic acid esters (PAEs) and human serum albumin (HSA) was studied by fluorescence spectroscopy and molecular modeling methods. The efficiency of energy transfer and the distance between HSA and PAEs were calculated. The results showed that all of the four kinds of PAEs could quench the intrinsic fluorescence of the HSA, with the mechanisms of static quenching and non-radiative energy transfer. Molecular docking study and thermodynamic analysis revealed that the binding behavior was mainly governed by hydrophobic force. And the results of site marker competitive experiments and modeling method suggested that the four PAEs would mainly bind to the HSA in sub-domain IIIA, which demonstrated that the experimental results could coordinate with the theoretical results. Molecular dynamic simulation (MD) revealed that HSA did have a slight conformational change when it bound with PAEs. It also verified the greater stability of HSA-PAEs complex compared to free protein.

Microfluidic synthesis of chiral salen Mn(ii) and Co(ii) complexes containing lysozyme

Efficient microfluidic synthesis of chiral salen Mn(ii) and Co(ii) complexes containing lysozyme was achieved.

Interaction between the Natural Components in Danhong Injection (DHI) with Serum Albumin (SA) and the Influence of the Coexisting Multi-Components on the SaB-BSA Binding System: Fluorescence and Molecular Docking Studies

Danhong injection (DHI) is a widely used Chinese Materia Medica standardized product for the clinical treatment of ischemic encephalopathy and coronary heart disease. The bindings of eight natural components in DHI between bovine serum albumin (BSA) were studied by fluorescence spectroscopy technology and molecular docking. According to the results, the quenching process of salvianolic acid B and hydroxysafflor yellow A was a static quenching procedure through the analysis of quenching data by the Stern-Volmer equation, the modified Stern-Volmer equation, and the modified Scatchard equation. Meanwhile, syringin (Syr) enhanced the fluorescence of BSA, and the data were analyzed using the Lineweaver-Burk equation. Molecular docking suggested that all of these natural components bind to serum albumin at the site I location. Further competitive experiments of SaB confirmed the result of molecular docking studies duo to the displacement of warfarin by SaB. Base on these studies, we selected SaB as a research target because it presented the strongest binding ability to BSA and investigated the influence of the multi-components coexisting in DHI on the interaction between the components of the SaB-BSA binding system. The participation of these natural components in DHI affected the interaction between the components of the SaB-BSA system. Therefore, when DHI is used in mammals, SaB is released from serum albumin more quickly than it is used alone. This work would provide a new experiment basis for revealing the scientific principle of compatibility for Traditional Chinese Medicine.

Molecular modeling and multispectroscopic studies of the interaction of mesalamine with bovine serum albumin

The interaction of mesalamine (5-aminosalicylic acid (5-ASA)) with bovine serum albumin (BSA) was investigated by fluorescence quenching, absorption spectroscopy, circular dichroism (CD) techniques, and molecular docking. Thermodynamic parameters (ΔH<0 and ΔS 0) indicated that the hydrogen bond and electrostatic forces played the major role in the binding of 5-ASA to BSA. The results of CD and UV-vis spectroscopy showed that the binding of this drug to BSA induces some conformational changes in BSA. Displacement experiments predicted that the binding of 5-ASA to BSA is located within domain III, Sudlows site 2, that these observations were substantiated by molecular docking studies. In addition, the docking result shows that the 5-ASA in its anionic form mainly interacts with Gln-416 residue through one hydrogen bond between H atom of 5-ASA anion and the adjacent O atom of the hydroxyl group of Gln-416.