Insight into the binding mechanism of imipenem to human serum albumin by spectroscopic and computational approaches

Integrated spectroscopic and computational analyses unravel the molecular interaction of pesticide azinphos-methyl with bovine beta-lactoglobulin

Organophosphorus are typically hazardous chemicals used in the pharmaceutical, agricultural, and other industries. They pose a serious risk to human life and can be fatal upon direct exposure. Hence, studying the interaction between such compounds with proteins is crucial for environmental, health, and food safety. In this study, we investigated the interaction mechanism between azinphos-methyl (AZM) and β-lactoglobulin (BLG) at pH 7.4 using a combination of biophysical techniques. Intrinsic fluorescence investigations revealed that BLG fluorescence was quenched in the presence of increasing AZM concentrations. The quenching mechanism was identified as static, as evidenced by a decrease in the fluorescence quenching constant (1.25 × 104, 1.18 × 104, and 0.86 × 104 M-1) with an increase in temperatures. Thermodynamic calculations (ΔH > 0; ΔS > 0) affirmed the formation of a complex between AZM and BLG through hydrophobic interactions. The BLG's secondary structure was found to be increased due to AZM interaction. Ultraviolet -visible spectroscopy data showed alterations in BLG conformation in the presence of AZM. Molecular docking highlighted the significant role of hydrophobic interactions involving residues such as Val43, Ile56, Ile71, Val92, Phe105, and Met107 in the binding between BLG and AZM. A docking energy of -6.9 kcal mol-1, and binding affinity of 1.15 × 105 M-1 suggest spontaneous interaction between AZM and BLG with moderate to high affinity. These findings underscore the potential health risks associated with the entry of AZM into the food chain, emphasizing the need for further consideration of its impact on human health.

Addressing the interaction of stem bromelain with different anionic surfactants, below, at and above the critical micelle concentration (cmc) in phosphate buffer at pH 7: Physicochemical, spectroscopic, & molecular docking study

The structural stability and therapeutic activity of Stem Bromelain (BM) have been explored by unravelling the interaction of stem BM in presence of two different types of anionic surfactants namely, bile salts, NaC and NaDC and the conventional anionic surfactants, SDDS and SDBS, below, at and above the critical micelle concentration (cmc) in aqueous phosphate buffer of pH 7. Different physicochemical parameters like, surface excess (Γcmc), minimum area of surfactants at air water interface (Amin) etc. are calculated from tensiometry both in absence and presence of BM. Several inflection points (C1, C2 and C3) have been found in tensiometry profile of surfactants in presence of BM due to the conformational change of BM assisted by surfactants. Similar observation also found in isothermal titration calorimetry (ITC) profiles where the enthalpy of micellization (ΔH0obs) of surfactants in absence and presence of BM have calculated. Further, steady state absorption and fluorescence spectra monitoring the tryptophan (Trp) emission of free BM and in presence of all the surfactants at three different temperatures (288.15 K, 298.15 K, and 308.15 K) reveal the nature of fluorescence quenching of BM in presence of bile salts/surfactants. Time resolved fluorescence studies at room temperature also support to determine the several quenching parameters. The binding constant (Kb) of BM with all the surfactants and free energy of binding (∆G0 of bile salts/surfactants with BM at different temperatures have been calculated exploiting steady state fluorescence technique. It is observed that, the binding of NaC with BM is greater as compared to other surfactants while Stern-Volmer quenching constant (KSV) is found greater in presence of SDBS as compared with others which supports the surface tension and ITC data with the fact that surface activity of surfactant(s) is decreasing with the binding of the surfactants at the core or binding pocket of BM. Circular Dichroism (CD) study shows the stability of secondary structure of BM in presence of NaC and NaDC below C3, while BM lost its structural stability even at very low surfactant concentration of SDDS and SDBS which also supports the more involvement of bile salts in binding rather than surfactants. The molecular docking studies have also been substantiated for better understanding the several experimental investigations interaction of BM with the bile salts/surfactants.

Implication of Caffeic Acid for the Prevention and Treatment of Alzheimer's Disease: Understanding the Binding with Human Transferrin Using In Silico and In Vitro Approaches

In present times, a switch from chemical molecules towards natural products is taking place, and the latter is being increasingly explored in the management of diseases due to their broad range of therapeutic potential. Consumption of coffee is thought to reduce Alzheimer's disease (AD); however, the mechanism is still unexplored. Primarily, it is thought that components of coffee are the key players in making it a neuroprotectant. Caffeic acid (CA) is found in high quantities in coffee; thus, it is being increasingly explored to decipher its neuroprotection by various mechanisms. Iron is a toxic element in a free form capable of causing oxidative damage and ultimately contributing to the pathogenesis of AD. Thus, maintaining the proper iron levels is vital and human transferrin (Htf), a glycoprotein, is a key player in this aspect. In this work, we explored the binding mechanism of CA with Htf at the atomistic level, employing molecular docking and extensive molecular dynamics simulation (MD) approaches coupled with spectroscopic techniques in a bid to decipher the mode of interaction of CA with Htf. Molecular docking results demonstrated a strong binding affinity between CA and Htf. Furthermore, MD study highlighted the Htf-CA complex's stability and the ligand's minimal impact on Htf's overall structure. In silico approaches were further backed up by experimental approaches. Strong binding of CA with Htf was ascertained by UV-visible and fluorescence spectroscopy observations. Together, the study provides a comprehensive understanding of the Htf-CA interaction, adding to the knowledge of the use of CA in the treatment of AD, thereby adding another feather to its already known neuroprotective role.

The weakened physiological functions of human serum albumin in presence of polystyrene nanoplastics

Due to the widespread presence of nanoplastics (NPs) in daily essentials and drinking water, the potential adverse effects of NPs on human health have become a global concern. Human serum albumin (HSA), the most abundant and multi-functional protein in plasma, has been chosen to understand the biological effects of NPs after entering the blood. The esterase activity and the transport of bisphenol A in the presence of polystyrene nanoplastics (PSNPs) under physiological conditions (pH 4.0 and 7.4) have been investigated to evaluate the possible biological effects. The interactions between PSNPs and HSA have also been systematically studied by multispectral methods and dynamic light scattering techniques. The esterase activity of HSA presented a decreased trend with increasing PSNPs; conversely, higher permeabilities are accompanied by higher amounts of PSNPs. Compared with the unchanged hydrodynamic diameter and weaker interactions at pH 7.4, stronger binding between HSA and PSNPs at pH 4.0 led to a significant increase in the particle size of the PSNPs-HSA complex. The quenching mechanism belonged to the static quenching type. The electrostatic force is proposed to be the dominant factor for PSNPs binding to HSA. The work provides some information about the toxicity of NPs when exposed to humans.

Spectroscopic insights with molecular docking and molecular dynamic simulation studies of anticancer drug 5-Fluorouracil targeting human pyruvate kinase m2

This study was conducted to test the efficacy of 5-fluorouracil (5-FU) as an anticancer drug against the human pyruvate kinase isozyme M2 (PKM2) using spectroscopic, molecular docking and molecular dynamic simulation studies. PKM2 fluorescence quenching studies in the presence of 5-FU performed at three different temperatures indicates dynamic quenching processes with single-set of binding (n ≈ 1) profile. The biomolecular quenching constants (kq) and the effective binding constants (Kb) obtained are shown to increase with temperature. The calculated enthalpy (ΔH) and entropy changes (ΔS) are estimated to be -118.06 kJ/mol and 146.14 kJ/mol/K respectively, which suggest the possible mode of interaction as electrostatic and hydrogen bonding. Further, these values were used to estimate the free energy changes (ΔG) and that increases with temperature. The negative ΔG values clearly indicates spontaneous binding process that stabilizes the complex formed between 5-FU and PKM2. Far-UV CD spectra of PKM2 in the presence of 5-FU shows decrease in α-helix contents which point towards the destabilization of secondary structure that weakens the biological activity of PKM2. The intrinsic fluorescence study and circular dichroism (CD) spectra showed minor conformational changes of PKM2 in the presence of 5-FU. Additionally, the results obtained from molecular docking and all-atom molecular dynamic simulation study supports the insight of the spectroscopic binding studies, and strengthens the dynamic stability of the complex between 5-FU and PKM2 through H-bonding. This study establishes a paradigm of 5-FU-PKM2 complexation and the efficacy of 5-FU that compromises the biological activity of the targeted PKM2.Communicated by Ramaswamy H. Sarma.

Investigating the effect of pH on the interaction of cypermethrin with human serum albumin: Insights from spectroscopic and molecular dynamics simulation studies

To efficiently combat the negative consequences of the utilization of pesticides and hazardous substances with biomolecules, it is crucial to comprehend the features of the corresponding compounds. In this study, interactions between cypermethrin (CYP) and HSA at neutral and acidic pH were investigated using a set of spectroscopic and computational tools, such as UV/VIS's absorption spectroscopy, fluorescence, Fourier-transform infrared (FTIR) spectroscopy, molecular docking, and molecular dynamics. Furthermore, the effect of CYP on the HSA thermal stability was investigated. The increase in the CYP concentration at acidic and neutral pH resulted in static HSA fluorescence quenching. In the interaction between HSA and CYP at both pH, increasing the temperature led to a decrease in the Stern-Volmer quenching constant and the binding constant. We also revealed that with increasing CYP concentration, the melting temperature of HSA increases at both pH values.

Interaction between gastric enzyme pepsin and tetradecyltrimethylammonium bromide in presence of sodium electrolytes: Exploration of micellization behavior

Pepsin is a proteolytic enzyme used in the treatment of digestive disorders. In this study, we investigated the physicochemical properties of the tetradecyltrimethylammonium bromide (TTAB) and pepsin protein mixture in various sodium salt media within a temperature range of 300.55-320.55 K with 5 K intervals. The conductometric study of the TTAB+pepsin mixture revealed a reduction in the critical micelle concentration (CMC) in electrolyte media. The micellization of TTAB was delayed in the presence of pepsin. The CMC of the TTAB + pepsin mixture was found to depend on the concentrations of electrolytes and protein, as well as the temperature variations. The aggregation of the TTAB+pepsin mixture was hindered as a function of [pepsin] and increasing temperatures, while micellization was promoted in aqueous electrolyte solutions. The negative free energy changes (∆Gm0) indicated the spontaneous aggregation of the TTAB+pepsin mixture. Changes in enthalpy, entropy, molar heat capacities, transfer properties, and enthalpy-entropy compensation variables were calculated and illustrated rationally. The interaction forces between TTAB and pepsin protein in the experimental solvents were primarily hydrophobic and electrostatic (ion-dipole) in nature. An analysis of molecular docking revealed hydrophobic interactions as the main stabilizing forces in the TTAB-pepsin complex.

Aggregation phenomena and physico-chemical properties of tetradecyltrimethylammonium bromide and protein (bovine serum albumin) mixture: Influence of electrolytes and temperature

It is important for biological, pharmaceutical, and cosmetic industries to understand how proteins and surfactants interact. Herein, the interaction of bovine serum albumin (BSA) with tetradecyltrimethylammonium bromide (TTAB) in different inorganic salts (KCl, K2SO4, K3PO4.H2O) has been explored through the conductivity measurement method at different temperatures (300.55 to 325.55 K) with a specific salt concentration and at a fixed temperature (310.55 K) using different salts concentrations. The extent of micelle ionization (α) and different thermodynamic parameters associated with BSA and TTAB mixtures in salt solutions were calculated. Evaluation of the magnitudes of ∆Hm0 and ∆Sm0 showed that the association was exothermic and primarily an enthalpy-operated process in all cases at lower contents of BSA, but the system became endothermic, and entropy driven in the presence of K3PO4.H2O at a relatively higher concentration of BSA. The enthalpy-entropy compensation variables were determined, which explained the types and nature of interactions between TTAB and BSA in salt media. Molecular docking analysis revealed that the main stabilizing factors in the BSA-TTAB complex are electrostatic and hydrophobic interactions. These findings aligned with the significant results obtained from the conductometry method regarding the nature and characteristics of binding forces observed between BSA and TTAB.

Study of Amiloride Binding to Human Serum Albumin: Insights from Thermodynamic, Spectroscopic, and Molecular Docking Investigations

This study was undertaken to investigate the interaction between the sodium channel blocker amiloride (AML) and human serum albumin (HSA). A combination of multi-spectroscopic techniques and computational methods were employed to identify the AML binding site on HSA and the forces responsible for the formation of the HSA-AML complex. Our findings revealed that AML specifically binds to Sudlow's site II, located in subdomain IIIA of HSA, and that the complex formed is stabilized using van der Waals hydrogen-bonding and hydrophobic interactions. FRET analysis showed that the distance between AML and Trp214 was optimal for efficient quenching. UV-Vis spectroscopy and circular dichroism indicated minor changes in the structure of HSA after AML binding, and molecular dynamics simulations (MDS) conducted over 100 ns provided additional evidence of stable HSA-AML-complex formation. This study enhances understanding of the interaction between AML and HSA and the mechanism responsible.

Predicting Volume of Distribution in Neonates: Performance of Physiologically Based Pharmacokinetic Modelling

The volume of distribution at steady state (Vss) in neonates is still often estimated through isometric scaling from adult values, disregarding developmental changes beyond body weight. This study aimed to compare the accuracy of two physiologically based pharmacokinetic (PBPK) Vss prediction methods in neonates (Poulin & Theil with Berezhkovskiy correction (P&T+) and Rodgers & Rowland (R&R)) with isometrical scaling. PBPK models were developed for 24 drugs using in-vitro and in-silico data. Simulations were done in Simcyp (V22) using predefined populations. Clinical data from 86 studies in neonates (including preterms) were used for comparison, and accuracy was assessed using (absolute) average fold errors ((A)AFEs). Isometric scaling resulted in underestimated Vss values in neonates (AFE: 0.61), and both PBPK methods reduced the magnitude of underprediction (AFE: 0.82-0.83). The P&T+ method demonstrated superior overall accuracy compared to isometric scaling (AAFE of 1.68 and 1.77, respectively), while the R&R method exhibited lower overall accuracy (AAFE: 2.03). Drug characteristics (LogP and ionization type) and inclusion of preterm neonates did not significantly impact the magnitude of error associated with isometric scaling or PBPK modeling. These results highlight both the limitations and the applicability of PBPK methods for the prediction of Vss in the absence of clinical data.

Inhibitory potential of N-acetylaspartate against protein glycation, AGEs formation and aggregation: Implication of brain osmolyte in glycation-related complications

Protein glycation and aggregation have a pivotal role in many diseases including diabetes and neurodegenerative disorders. N-acetyl aspartate (NAA), an osmolyte derived from L-aspartic acid, is one of the most abundant metabolites in the mammalian brain. Although NAA is supposed to be a substitute for a neuronal marker, its function is not fully elucidated. Herein, we have investigated the effect of NAA on glycation, AGEs formation and aggregation of irisin. AGE-specific fluorescence showed the strong inhibition of AGEs formation in the presence of NAA, demonstrating its anti-glycating property. The aggregates present in MG-modified irisin were also reduced by NAA, which was confirmed by Thioflavin T fluorescence and fluorescence microscopy. Further, for the explanation of the strong anti-glycating potential of NAA, the interaction between irisin and NAA was also examined. Interaction studies involving steady-state fluorescence and molecular docking demonstrated that hydrogen bonding and salt bridges by NAA stabilize the irisin. It was found that glycation-prone residues i.e., lysine and arginine are specifically involved in the interaction which might prevent them from getting modified during the process of glycation. This study for the first time reported the antiglycating potential of NAA which can be implicated in the therapeutic management of various glycation-related complications.

A flaw in applying the FRET technique to evaluate the distance between ligands and tryptophan residues in human serum albumin: Proposal of correction

Due to its primordial function as a drug carrier, human serum albumin (HSA) is extensively studied regarding its binding affinity with developing drugs. Förster resonance energy transfer (FRET) is frequently applied as a spectroscopic molecular ruler to measure the distance between the binding site and the ligand. In this work, we have shown that most of the published results that use the FRET technique to estimate the distance from ligands to the binding sites do not corroborate the crystallography data. By comparing the binding affinity of dansyl-proline with HSA and ovotransferrin, we demonstrated that FRET explains the quenching provoked by the interaction of ligands in albumin. So, why does the distance calculation via FRET not corroborate the crystallography data? We have shown that this inconsistency is related to the fact that a one-to-one relationship between donor and acceptor is not present in most experiments. Hence, the quenching efficiency used for calculating energy transfer depends on distance and binding constant, which is inconsistent with the correct application of FRET as a molecular ruler. We have also shown that the indiscriminate attribution of 2/3 to the relative orientation of transition dipoles of the acceptor and donor (κ²) generates inconsistencies. We proposed corrections based on the experimental equilibrium constant and theoretical orientation of transition dipoles to correct the FRET results.

Unveiling the binding details and esterase-like activity effect of methyl yellow on human serum albumin: spectroscopic and simulation study

The food sector uses methyl yellow (MY) extensively as a colorant. The primary transporter in vivo that influences MY absorption, metabolism, distribution, and excretion is human serum albumin (HSA). Exploring the binding process and looking at how HSA and MY work physiologically at the molecular level is therefore very important. Experiments using steady-state fluorescence and fluorescence lifetimes proved that HSA and MY's quenching mechanisms were static. The HSA-MY complex's binding constant was estimated using thermodynamic parameters to be around 10⁴ M^-1. The hydrophobic forces were a major factor in the binding process, as evidenced by the negative ΔG, positive ΔH, and ΔS, which suggested that this contact was spontaneous. Site tests showed that MY linked to HSA's site I. Circular dichroism and three-dimensional fluorescence analysis revealed that the 1.33% α-helix content dropped and the amino acid microenvironment altered. While HSA's protein surface hydrophobicity decreased when engaging MY, the binding of MY to HSA reduced in the presence of urea. The stability of the system was assessed using molecular modeling. Additionally, HSA's esterase-like activity decreased when MY was present, and Ibf/Phz affected the inhibition mechanism of MY on HSA. These findings offer a distinctive perspective for comprehending the structure and functioning of HSA and evaluating the safety of MY.

The Formation of β-Cyclodextrin Complexes with Levofloxacin and Ceftriaxone as an Approach to the Regulation of Drugs’ Pharmacokinetic

The study has been devoted to the complexation of hydroxypropyl-β-cyclodextrin (HPCD) with antibacterial drugs, namely, ceftriaxone (CT) and levofloxacin (LV), which are used to treat respiratory diseases, including bacterial infections of the respiratory tract. FTIR and NMR spectroscopic investigations have shown that the LV–HPCD complex is formed mainly due to the inclusion of the aromatic fragment of LV into the HPCD cavity; while the CT–HPCD complex is realized on the HPCD surface. Being a more hydrophobic molecule, LV forms ten times stronger complexes with HPCD than does CT: K_disLV-HPCD ~ 10^–3 M, while K_disCT-HPCD ~10^–2 M at pH 7.4. It has been shown that, for singly charged forms of the drugs, the complexes are two times more stable. Fluorescence spectroscopy has been employed to study the thermodynamic parameters for the interaction of dosage forms with human serum albumin. Negative values of ΔH and ΔS of the reaction have indicated both hydrogen bonding and van der Waals interactions during the complexation of both drugs with human serum albumin. It has been found that the protein is ~4 times more strongly bound to LV at 37°C as compared with CT. The data obtained will make it possible to improve the characteristics of the studied drugs and bring the methods of treating severe forms of respiratory diseases to a new level.

Celecoxib, Glipizide, Lapatinib, and Sitagliptin as potential suspects of aggravating SARS-CoV-2 (COVID-19) infection: a computational approach

COVID-19 caused by SARS-CoV-2 has emerged as a potential threat to human life, especially to people suffering from chronic diseases. In this study, we investigated the ability of selected FDA-approved drugs to inhibit TACE (tumor necrosis factor α converting enzyme), which is responsible for the shedding of membrane-bound ACE2 (angiotensin-converting enzyme2) receptors into soluble ACE2. The inhibition of TACE would lead to an increased population of membrane-bound ACE2, which would facilitate ACE2-Spike protein interaction and viral entry. A total of 50 drugs prescribed in treating various chronic diseases in Saudi Arabia were screened by performing molecular docking using AutoDock4.2. Based on docking energy (≤ -9.00 kcal mol^-1), four drugs (Celecoxib, Glipizide, Lapatinib, and Sitagliptin) were identified as potential inhibitors of TACE, with binding affinities up to 10⁶-10⁷ M^-1. Analysis of the molecular docking suggests that these drugs were bound to TACE's catalytic domain and interact with the key residues such as His405, Glu406, and His415, which are involved in active site Zn²⁺ ion chelation. Molecular dynamics simulation was performed to confirm the stability of TACE-drugs complexes. RMSD (root mean square deviation), RMSF (root mean square fluctuation), Rg (radius of gyration), and SASA (solvent accessible surface area) were within the acceptable limits. Free energy calculations using Prime-MM/GBSA suggest that Celecoxib formed the most stable complex with TACE, followed by Glipizide, Sitagliptin, and Lapatinib. The finding of this study suggests a mechanism for drugs to aggravate SARS-CoV-2 infection and hence high mortality in patients suffering from chronic diseases.Communicated by Ramaswamy H. Sarma.

Exploration of the binding between cuminol and bovine serum albumin through spectroscopic, molecular docking and molecular dynamics methods

Cuminol (4-Isopropylbenzyl alcohol), found in the essential oils of several plant sources, is an important constituent of several cosmetics formulations. The interaction of cuminol with model plasma protein bovine serum albumin was studied in this paper. The experimental studies were mainly carried out using fluorescence spectrophotometry aided with UV visible and CD spectroscopies. Intrinsic fluorescence measurements showed that there was a weak binding between cuminol and BSA. The mechanism of binding involved static quenching with around 1:1 binding. The binding was chiefly supported by hydrophobic forces although a little contribution of hydrogen bonding was also found in the interaction and the values of enthalpy change were negative with positive entropy change. The secondary structure of BSA didn't change significantly in presence of low concentrations of cuminol, however, partial unfolding of the former taken place when the concentration of the latter increased. Molecular docking analyses showed cuminol binds at the intersection of subdomains IIA and IIIA, i.e. its binding site is in between Sudlow sites I and II. Molecular dynamics simulations results have shown that BSA forms a stable complex with cuminol and the structure of the former didn't change much in presence of later. Communicated by Ramaswamy H. Sarma.

Unravelling Binding of Human Serum Albumin with Galantamine: Spectroscopic, Calorimetric, and Computational Approaches

Human serum albumin (HSA), an abundant plasma protein, binds to various ligands, acting as a transporter for numerous endogenous and exogenous substances. Galantamine (GAL), an alkaloid, treats cognitive decline in mild to moderate Alzheimer's disease and other memory impairments. A vital step in pharmacological profiling involves the interaction of plasma protein with the drugs, and this serves as an essential platform for pharmaceutical industry advancements. This study is carried out to understand the binding mechanism of GAL with HSA using computational and experimental approaches. Molecular docking revealed that GAL preferentially occupies Sudlow's site I, i.e., binds to subdomain IIIA. The results unveiled that GAL binding does not induce any conformational change in HSA and hence does not compromise the functionality of HSA. Molecular dynamics simulation (250 ns) deciphered the stability of the HSA-GAL complex. We performed the fluorescence binding and isothermal titration calorimetry (ITC) to analyze the actual binding of GAL with HSA. The results suggested that GAL binds to HSA with a significant binding affinity. ITC measurements also delineated thermodynamic parameters associated with the binding of GAL to HSA. Altogether, the present study deciphers the binding mechanism of GAL with HSA.

Albumin-Mediated Size Exclusion Chromatography: The Apparent Molecular Weight of PSMA Radioligands as Novel Parameter to Estimate Their Blood Clearance Kinetics

A meticulously adjusted pharmacokinetic profile and especially fine-tuned blood clearance kinetics are key characteristics of therapeutic radiopharmaceuticals. We, therefore, aimed to develop a method that allowed the estimation of blood clearance kinetics in vitro. For this purpose, ¹⁷⁷Lu-labeled PSMA radioligands were subjected to a SEC column with human serum albumin (HSA) dissolved in a mobile phase. The HSA-mediated retention time of each PSMA ligand generated by this novel 'albumin-mediated size exclusion chromatography' (AMSEC) was converted to a ligand-specific apparent molecular weight (MW_app), and a normalization accounting for unspecific interactions between individual radioligands and the SEC column matrix was applied. The resulting normalized MW_app,norm. could serve to estimate the blood clearance of renally excreted radioligands by means of their influence on the highly size-selective process of glomerular filtration (GF). Based on the correlation between MW and the glomerular sieving coefficients (GSCs) of a set of plasma proteins, GSC_calc values were calculated to assess the relative differences in the expected GF/blood clearance kinetics in vivo and to select lead candidates among the evaluated radioligands. Significant differences in the MW_app,norm. and GSC_calc values, even for stereoisomers, were found, indicating that AMSEC might be a valuable and high-resolution tool for the preclinical selection of therapeutic lead compounds for clinical translation.

Antioxidant and antimicrobial potential of two extracts from Capparis spinosa L. and Rumex nervosus and molecular docking investigation of selected major compounds

The present study examined the phytochemical composition, antioxidant, antimicrobial properties, and molecular docking of different solvents extracts (methanol and water) of two medicinal plants, namely, Capparis spinosa L (CS) and Rumex nervosus (RN). Phytochemical analysis showed that total phenol, flavonoids, alkaloids, and vitamin C were significantly (P ≤ 0.05) higher in the methanolic extract of both plants than in other solvents. However, tannin content was significantly (P ≤ 0.05) high in the water extract for both plants. Chloroform and acetone extracts were significantly lower in phytochemicals than other solvents, therefore excluded in this study. GC–MS analysis showed one dominant compound in CS (isopropyl isothiocyanate) and two in RN (pyrogallol and palmitic acid). The antioxidant methods applied (DPPH, ABTS, β-Carotene/linoleic acid assay, and reducing the power) showed that the methanolic extract of CS exerted higher activity in methanolic extract but lower than that of BHA standard. The methanolic extract of both plants inhibited the bacterial pathogens when a minimum inhibitory concentration (MIC) method was applied, compared to water extract with RN-methanolic extract had a lower inhibition concentration than CS-methanolic extract. The molecular interactions study revealed that the palmitic acid and pyrogallol interacted with the receptors' active site. This work concluded that CS and RN showed a remarkable antioxidant and antibacterial effect with the high antimicrobial activity of RN extract.

Inhibiting Cyclin-Dependent Kinase 6 by Taurine: Implications in Anticancer Therapeutics

Cyclin-dependent kinase 6 (CDK6) is linked with a cyclin partner and plays a crucial role in the early stages of cancer development. It is currently a potential drug target for developing therapeutic molecules targeting cancer therapy. Here, we have identified taurine as an inhibitor of CDK6 using combined in silico and experimental studies. We performed various experiments to find the binding affinity of taurine with CDK6. Molecular docking analysis revealed critical residues of CDK6 that are involved in taurine binding. Fluorescence measurement studies showed that taurine binds to CDK6 with a significant binding affinity, with a binding constant of K = 0.7 × 10⁷ M^-1 for the CDK6-taurine complex. Enzyme inhibition assay suggested taurine as a good inhibitor of CDK6 possessing an IC₅₀ value of 4.44 μM. Isothermal titration calorimetry analysis further confirmed a spontaneous binding of taurine with CDK6 and delineated the thermodynamic parameters for the CDK6-taurine system. Altogether, this study established taurine as a CDK6 inhibitor, providing a base for using taurine and its derivatives in CDK6-associated cancer and other diseases.

PROTEIN BINDING CHARACTERISTICS OF YOHIMBINE, A NATURAL INDOLE ALKALOID BASED DRUG FOR ERECTILE DYSFUNCTION

Even to this day, talking about sexual-dysfunctions largely remains a taboo. Hence less studies were recorded and fewer remedies given. Erectile dysfunction (ED) is one of the most commonly treated psychological disorders which leads to major distress, interpersonal limitation and reduces the quality of life & marriage. This study aimed to assess a plant-derived molecule, Yohimbine (Yoh, a β-carboline indole-alkaloid; often used for ED treatment) and its potential binding phenomenon with hemoglobin (Hb). Successful binding of the Yoh with Hb is evident from spectroscopic and molecular-docking results. Yoh quenched the fluorescence of Hb efficiently through 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 to be spontaneous and attributed by entropy-driven exothermic-binding. Non-polyelectrolytic factor was the core, dominating factor. The structural aspects have been deciphered through infra-red 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 modeling data. This study reveals the detailed interaction pattern and molecular mechanism of Hb-Yoh binding; correlating the structure-function relationship for the first time; therefore, holds enormous importance from the standpoint of rational and efficient drug-designing & development.

Investigating binding mechanism of thymoquinone to human transferrin, targeting Alzheimer's disease therapy

Iron deposition in the central nervous system (CNS) is one of the causes of neurodegenerative diseases. Human transferrin (hTf) acts as an iron carrier present in the blood plasma, preventing it from contributing to redox reactions. Plant compounds and their derivatives are frequently being used in preventing or delaying Alzheimer's disease (AD). Thymoquinone (TQ), a natural product has gained popularity because of its broad therapeutic applications. TQ is one of the significant phytoconstituent of Nigella sativa. The binding of TQ to hTf was determined by spectroscopic methods and isothermal titration calorimetry. We have observed that TQ strongly binds to hTf with a binding constant (K) of 0.22 × 10⁶ M^-1 and forming a stable complex. In addition, isothermal titration calorimetry revealed the spontaneous binding of TQ with hTf. Molecular docking analysis showed key residues of the hTf that were involved in the binding to TQ. We further performed a 250 ns molecular dynamics simulation which deciphered the dynamics and stability of the hTf-TQ complex. Structure analysis suggested that the binding of TQ doesn't cause any significant alterations in the hTf structure during the course of simulation and a stable complex is formed. Altogether, we have elucidated the mechanism of binding of TQ with hTf, which can be further implicated in the development of a novel strategy for AD therapy.

Antimicrobial Activity of Dihydroisocoumarin Isolated from Wadi Lajab Sediment-Derived Fungus Penicillium chrysogenum: In Vitro and In Silico Study

Antibiotic resistance is considered a major health concern globally. It is a fact that the clinical need for new antibiotics was not achieved until now. One of the most commonly prescribed classes of antibiotics is β-Lactam antibiotics. However, most bacteria have developed resistance against β-Lactams by producing enzymes β-Lactamase or penicillinase. The discovery of new β-Lactamase inhibitors as new antibiotics or antibiotic adjuvants is essential to avoid future catastrophic pandemics. In this study, five dihydroisocoumarin: 6-methoxy mellein (1); 5,6-dihydroxymellein (2); 6-hydroxymellein (3); 4-chloro-6-hydroxymellein (4) and 4-chloro-5,6-di-hydroxymellein (5) were isolated from Wadi Lajab sediment-derived fungus Penicillium chrysogenum, located 15 km northwest of Jazan, KSA. The elucidation of the chemical structures of the isolated compounds was performed by analysis of their NMR, MS. Compounds 1–5 were tested for antibacterial activities against Gram-positive and Gram-negative bacteria. All of the compounds exhibited selective antibacterial activity against Gram-positive bacteria Staphylococcus aureus and Bacillus licheniformis except compound 3. The chloro-dihydroisocoumarin derivative, compound 4, showed potential antimicrobial activities against all of the tested strains with the MIC value between 0.8–5.3 μg/mL followed by compound 5, which exhibited a moderate inhibitory effect. Molecular docking data showed good affinity with the isolated compounds to β-Lactamase enzymes of bacteria; NDM-1, CTX-M, OXA-48. This work provides an effective strategy for compounds to inhibit bacterial growth or overcome bacterial resistance.

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.

Tetranectin targeting by epigallocatechin gallate suppresses colon cancer cell proliferation

Tetranectin is a serum protein that binds to plasminogen and enhances its proteolytic activation, which underlies the involvement of tetranectin in the development of several carcinomas including colon cancer. In the present study, structure-based in silico screening of natural products showed that epigallocatechin gallate with anticancer effects binds to tetranectin. Binding to epigallocatechin gallate to tetranectin was confirmed by intrinsic fluorescence quenching assays and isothermal titration calorimetry. Furthermore, epigallocatechin gallate efficiently inhibited the activity of tetranectin to enhance the activation of plasminogen. We also found that tetranectin enhanced the proliferation of CT-26 colon cancer cells. Epigallocatechin gallate showed its cytotoxic effect on CT-26 cells due to its binding to tetranectin and the consequent suppression of the cell proliferation. These results demonstrate that the anticancer effect of epigallocatechin gallate is mediated, at least in part, by inhibiting tetranectin as a binding target.

Mo(VI) Potential Metallodrugs: Explaining the Transport and Cytotoxicity by Chemical Transformations

The transport and cytotoxicity of molybdenum-based drugs have been explained with the concept of chemical transformation, a very important idea in inorganic medicinal chemistry that is often overlooked in the interpretation of the biological activity of metal-containing systems. Two monomeric, [MoO₂(L¹)(MeOH)] (1) and [MoO₂(L²)(EtOH)] (2), and two mixed-ligand dimeric Mo^VIO₂ species, [{MoO₂(L^1-2)}₂(μ-4,4'-bipy)] (3-4), were synthesized and characterized. The structures of the solid complexes were solved through SC-XRD, while their transformation in water was clarified by UV-vis, ESI-MS, and DFT. In aqueous solution, 1-4 lead to the penta-coordinated [MoO₂(L^1-2)] active species after the release of the solvent molecule (1 and 2) or removal of the 4,4'-bipy bridge (3 and 4). [MoO₂(L^1-2)] are stable in solution and react with neither serum bioligand nor cellular reductants. The binding affinity of 1-4 toward HSA and DNA were evaluated through analytical and computational methods and in both cases a non-covalent interaction is expected. Furthermore, the in vitro cytotoxicity of the complexes was also determined and flow cytometry analysis showed the apoptotic death of the cancer cells. Interestingly, μ-4,4'-bipy bridged complexes 3 and 4 were found to be more active than monomeric 1 and 2, due to the mixture of species generated, that is [MoO₂(L^1-2)] and the cytotoxic 4,4'-bipy released after their dissociation. Since in the cytosol neither the reduction of Mo^VI to Mo^V/IV takes place nor the production of reactive oxygen species (ROS) through Fenton-like reactions of 1-4 with H₂O₂ occurs, the mechanism of cytotoxicity should be attributable to the direct interaction with DNA that happens with a minor-groove binding which results in cell death through an apoptotic mechanism.

Mutation in the CX3C Motif of G Protein Disrupts Its Interaction with Heparan Sulfate: A Calorimetric, Spectroscopic, and Molecular Docking Study

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection in children and infants. To date, there is no effective vaccine available against RSV. Heparan sulfate is a type of glycosaminoglycan that aids in the attachment of the RSV to the host cell membrane via the G protein. In the present study, the effect of amino acid substitution on the structure and stability of the ectodomain G protein was studied. Further, it was investigated whether mutation (K117A) in the CX3C motif of G protein alters the binding with heparan sulfate. The point mutation significantly affects the conformational stability of the G protein. The mutant protein showed a low binding affinity with heparan sulfate as compared to the wild-type G protein, as determined by fluorescence quenching, isothermal titration calorimetry (ITC), and molecular docking studies. The low binding affinity and decreased stability suggested that this mutation may play an important role in prevention of attachment of virion to the host cell receptors. Collectively, this investigation suggests that mutation in the CX3C motif of G protein may likely improve the efficacy and safety of the RSV vaccine.

The Antiproliferative and Apoptotic Effects of a Novel Quinazoline Carrying Substituted-Sulfonamides: In Vitro and Molecular Docking Study

In order to investigate for a new effective and safe anticancer drug, we synthesized a novel series of quinazoline containing biologically active substituted-sulfonamide moiety at 3- position 4a-n. The structure of the newly prepared compounds was proved by microanalysis, IR, ¹H-NMR, ¹³C-NMR and mass spectral data. All the synthesized compounds were evaluated for their in vitro cytotoxic activity in numerous cancer cell lines including A549, HepG-2, LoVo and MCF-7 and normal HUVEC cell line. The two most active compounds 4d and 4f were then tested for their apoptosis induction using DNA content and Annexin V-FITC/PI staining. Moreover, apoptosis initiation was also confirmed using RT-PCR and Western blot. To further understand the binding preferences of quinazoline sulfonamides, docking simulations were used. Among the fourteen new synthesized compounds, we found that compounds 4d and 4f exerted the strongest cytotoxicity against MCF-7 cells with an IC₅₀ value of 2.5 and 5 μM, respectively. Flow cytometry data revealed the ability of compounds 4d and 4f to mediate apoptosis and arrest cell cycle growth at G1 phase. Furthermore, RT-PCR and Western blot results suggested that both 4d and 4f activates apoptotic cell death pathway in MCF-7 cells. Molecular docking assessments indicated that compounds 4d and 4f fit perfectly into Bcl2's active site. Based on the biological properties, we conclude that both compounds 4d and 4f could be used as a new type of anticancer agent, which provides a scientific basis for further research into the treatment of cancer.

Novel sulphonamide-bearing methoxyquinazolinone derivatives as anticancer and apoptosis inducers: synthesis, biological evaluation and in silico studies

We synthesised a new series of sulphonamide-bearing quinazolinone derivatives 5-18 and evaluated their in vitro cytotoxicity in various cancer cell lines (A549, HepG-2, LoVo and MCF-7) and in normal human cells (HUVEC). Compounds 6 and 10 exhibited the higher activity against all the cancer cell lines compared with 5-flourourcil as positive control. The ability of the most promising compounds 6 and 10 to induce cell cycle arrest and apoptosis in breast cancer (MCF-7) cells was evaluated by flow cytometry. Reverse transcriptase-polymerase chain reaction and western blotting were used to evaluate the expression of apoptosis-related markers. We found that the 2-tolylthioacetamide derivative 6 and the 3-ethyl phenyl thioacetamide derivative 10 exhibited cytotoxic activity comparable to that of 5-fluorouracil as reference drug in MCF-7 and LoVo colon cancer cells. Cell cycle analysis showed a concentration-dependent accumulation of cells in the sub-G1 phase upon treatment with both compounds. The Annexin V-fluorescein isothiocyanate/propidium iodide assay showed that the compounds 6 and 10 increased the early and late apoptosis cell death modes in a dose-dependent manner. These compounds downregulated the expression of B-cell lymphoma-2 (Bcl-2), while increasing that of p53, Bcl-2-like protein 4, and caspase-7, at the mRNA and protein levels. Molecular docking of compounds 6 and 10 with Bcl-2 predicted them to show moderate − high binding affinity (6: −7.5 kcal/mol, 10: −7.9 kcal/mol) and interactions with key central substrate cavity residues. Overall, compounds 6 and 10 were found to be promising anticancer and apoptosis-inducing agents.

Structural Characterization of Ectodomain G Protein of Respiratory Syncytial Virus and Its Interaction with Heparan Sulfate: Multi-Spectroscopic and In Silico Studies Elucidating Host-Pathogen Interactions

The global burden of disease caused by a respiratory syncytial virus (RSV) is becoming more widely recognized in young children and adults. Heparan sulfate helps in attaching the virion through G protein with the host cell membrane. In this study, we examined the structural changes of ectodomain G protein (edG) in a wide pH range. The absorbance results revealed that protein maintains its tertiary structure at physiological and highly acidic and alkaline pH. However, visible aggregation of protein was observed in mild acidic pH. The intrinsic fluorescence study shows no significant change in the λ_max except at pH 12.0. The ANS fluorescence of edG at pH 2.0 and 3.0 forms an acid-induced molten globule-like state. The denaturation transition curve monitored by fluorescence spectroscopy revealed that urea and GdmCl induced denaturation native (N) ↔ denatured (D) state follows a two-state process. The fluorescence quenching, molecular docking, and 50 ns simulation measurements suggested that heparan sulfate showed excellent binding affinity to edG. Our binding study provides a preliminary insight into the interaction of edG to the host cell membrane via heparan sulfate. This binding can be inhibited using experimental approaches at the molecular level leading to the prevention of effective host–pathogen interaction.

Cytotoxicity and molecular docking analysis of racemolactone I, a new sesquiterpene lactone isolated from Inula racemosa

CONTEXT

Traditionally, Inula racemosa Hook. f. (Asteraceae) has been reported to be effective in cancer treatment which motivated the authors to explore the plant for novel anticancer compounds.

OBJECTIVE

To isolate and characterize new cytotoxic phytoconstituents from I. racemosa roots.

MATERIALS AND METHODS

The column chromatography of I. racemosa ethyl acetate extract furnished a novel sesquiterpene lactone whose structure was established by NMR (1D/2D), ES-MS and its cytotoxic properties were assessed on HeLa, MDAMB-231, and A549 cell lines using MTT and LDH (lactate dehydrogenase) assays. Further, morphological changes were analyzed by flow cytometry, mitochondrial membrane potential, AO-EtBr dual staining, and comet assay. Molecular docking and simulation were performed using Glide and Desmond softwares, respectively, to validate the mechanism of action.

RESULTS

The isolated compound was identified as racemolactone I (compound 1). Amongst the cell lines tested, considerable changes were observed in HeLa cells. Compound 1 (IC50 = 0.9 µg/mL) significantly decreased cell viability (82%) concomitantly with high LDH release (76%) at 15 µg/mL. Diverse morphological alterations along with significant increase (9.23%) in apoptotic cells and decrease in viable cells were observed. AO-EtBr dual staining also confirmed the presence of 20% apoptotic cells. A gradual decrease in mitochondrial membrane potential was observed. HeLa cells showed significantly increased comet tail length (48.4 µm), indicating broken DNA strands. In silico studies exhibited that compound 1 binds to the active site of Polo-like kinase-1 and forms a stable complex.

CONCLUSIONS

Racemolactone I was identified as potential anticancer agent, which can further be confirmed by in vivo investigations.

Concatenation of molecular docking and molecular simulation of BACE-1, γ-secretase targeted ligands: in pursuit of Alzheimer's treatment

INTRODUCTION

Alzheimer's disease (AD), the most predominant cause of dementia, has evolved tremendously with an escalating frequency, mainly affecting the elderly population. An effective means of delaying, preventing, or treating AD is yet to be achieved. The failure rate of dementia drug trials has been relatively higher than in other disease-related clinical trials. Hence, multi-targeted therapeutic approaches are gaining attention in pharmacological developments.

AIMS

As an extension of our earlier reports, we have performed docking and molecular dynamic (MD) simulation studies for the same 13 potential ligands against beta-site APP cleaving enzyme 1 (BACE-1) and γ-secretase as a therapeutic target for AD. The In-silico screening of these ligands as potential inhibitors of BACE-1 and γ-secretase was performed using AutoDock enabled PyRx v-0.8. The protein-ligand interactions were analyzed in Discovery Studio 2020 (BIOVIA). The stability of the most promising ligand against BACE-1 and γ-secretase was evaluated by MD simulation using Desmond-2018 (Schrodinger, LLC, NY, USA).

RESULTS

The computational screening revealed that the docking energy values for each of the ligands against both the target enzymes were in the range of -7.0 to -10.1 kcal/mol. Among the 13 ligands, 8 (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed binding energies of ≤-8 kcal/mol against BACE-1 and γ-secretase. For the selected enzyme targets, BACE-1 and γ-secretase, 6Z5 displayed the lowest binding energy of -10.1 and -9.8 kcal/mol, respectively. The MD simulation study confirmed the stability of BACE-6Z5 and γ-secretase-6Z5 complexes and highlighted the formation of a stable complex between 6Z5 and target enzymes.

CONCLUSION

The virtual screening, molecular docking, and molecular dynamics simulation studies revealed the potential of these multi-enzyme targeted ligands. Among the studied ligands, 6Z5 seems to have the best binding potential and forms a stable complex with BACE-1 and γ-secretase. We recommend the synthesis of 6Z5 for future in-vitro and in-vivo studies.

Exploring the binding mechanism and adverse toxic effects of persistent organic pollutant (dicofol) to human serum albumin: A biophysical, biochemical and computational approach

The organochlorine pesticide dicofol (DCF), a persistent organic pollutant, is used as acaricide worldwide. Considering its large consumption in the agriculture sector and potential toxic effects such as endocrine disruption, carcinogenicity, and environmental persistence are detrimental to human health. To take an extensive evaluation of its potential toxicity, the current study was aimed to explore the binding mechanism and adverse effect of DCF on human serum albumin (HSA) by using an array of biophysical techniques (UV-visible, fluorescence, 3D fluorescence, and circular dichroism spectroscopy), isothermal titration calorimetric (ITC), computational methods and biochemical approaches. Fluorescence quenching and UV-Visible spectra of the HSA-DCF system confirmed static quenching mechanism and complex formation between HSA and DCF. The thermodynamics results from ITC revealed DCF-HSA interaction was exothermic and spontaneous and involved hydrophobic interactions and hydrogen bonding. The esterase activity of HSA displayed constant V_max and elevated K_m values confirming DCF-HSA competitive interaction. Circular dichroism spectra results revealed structural changes in HSA protein on interaction with DCF. Furthermore, molecular-specific site marker and molecular modelling results affirmed that the binding Site of DCF is Site I of HSA. A significant carbonyl content level in DCF-HSA system suggested protein structure damage. This work is likely to add a better understanding of DCF toxicity in human health and helpful in fortifying the check on food safety.

Myricetin inhibits breast and lung cancer cells proliferation via inhibiting MARK4

Identifying novel molecules as potential kinase inhibitors are gaining significant attention globally. The present study suggests Myricetin as a potential inhibitor of microtubule-affinity regulating kinase (MARK4), adding another molecule to the existing list of anticancer therapeutics. MARK4 regulates initial cell division steps and is a potent druggable target for various cancers. Structure-based docking with 100 ns molecular dynamics simulation depicted activity of Myricetin in the active site pocket of MARK4 and the formation of a stable complex. The fluorescence-based assay showed excellent affinity of Myricetin to MARK4 guided by static and dynamic quenching. Moreover, the assessment of enthalpy change (∆H) and entropy change (∆S) delineated electrostatic interactions as a dominant force in the MARK4-myricetin interaction. Isothermal titration calorimetric measurements revealed spontaneous binding of Myricetin with MARK4. Further, the kinase assay depicted significant inhibition of MARK4 by Myricetin with IC₅₀  = 3.11 µM. Additionally, cell proliferation studies established that Myricetin significantly inhibited the cancer cells (MCF-7 and A549) proliferation, and inducing apoptosis. This study provides a solid rationale for developing Myricetin as a promising anticancer molecule in the MARK4 mediated malignancies.

Inhibition and interactions of alpha-amylase by daucosterol from the peel of Chinese water chestnut (Eleocharis dulcis)

The alpha-amylase inhibitory effect of daucosterol purified from the peel of Chinese water chestnut (CWC), a common Chinese vegetable, was assessed. The alpha-amylase inhibitory properties were elucidated by enzyme inhibition, fluorescence quenching and molecular docking experiments. It was found that three saponins from CWC peel exhibited potent inhibitory activity on alpha-amylase and daucosterol was found to be the main inhibitory factor against alpha-amylase with a mixed-type mode. Strong fluorescence quenching of alpha-amylase was observed under static fluorescence quenching with hydrophobic interactions with daucosterol. Molecular docking revealed that the conformation of daucosterol in the high-affinity sites I and II of alpha-amylase was optimum, and hydrophobic interactions were produced by daucosterol aglycone, and hydrogen bonding by the β-D-glucopyranosyl residue. Ingested daucosterol suppressed the elevation of blood glucose levels through inhibition of alpha-amylase in the small intestine in starch-loaded mice. This study provides data supporting the potential benefit of daucosterol from CWC peel in the treatment of diabetes.

High-Throughput Screening and Molecular Dynamics Simulation of Natural Product-like Compounds against Alzheimer's Disease through Multitarget Approach

Alzheimer’s disease (AD) is a progressive neurological disorder that affects 50 million people. Despite this, only two classes of medication have been approved by the FDA. Therefore, we have planned to develop therapeutics by multitarget approach. We have explored the library of 2029 natural product-like compounds for their multi-targeting potential against AD by inhibiting AChE, BChE (cholinergic pathway) MAO-A, and MOA-B (oxidative stress pathway) through in silico high-throughput screening and molecular dynamics simulation. Based on the binding energy of these target enzymes, approximately 189 compounds exhibited a score of less than −10 kcal/mol against all targets. However, none of the control inhibitors exhibited a binding affinity of less than −10 kcal/mol. Among these, the top 10 hits of compounds against all four targets were selected for ADME-T analysis. As a result, only F0850-4777 exhibited an acceptable range of physicochemical properties, drug-likeness, pharmacokinetics, and suitability for BBB permeation with high GI-A and non-toxic effects. The molecular dynamics study confirmed that F0850-4777 remained inside the binding cavity of targets in a stable conformation throughout the simulation and Prime-MM/GBSA study revealed that van der Waals’ energy (ΔG_vdW) and non-polar solvation or lipophilic energy (ΔG_{Sol_Lipo}) contribute favorably towards the formation of a stable protein–ligand complex. Thus, F0850-4777 could be a potential candidate against multiple targets of two pathophysiological pathways of AD and opens the doors for further confirmation through in vitro and in vivo systems.

Identification of Butyrylcholinesterase and Monoamine Oxidase B Targeted Ligands and their Putative Application in Alzheimer's Treatment: A Computational Strategy

BACKGROUND

With the burgeoning worldwide aging population, the incidence of Alzheimer's disease (AD) and its associated disorders is continuously rising. To appraise other relevant drug targets that could lead to potent enzyme targeting, 13 previously predicted ligands (shown favorable binding with AChE (acetylcholinesterase) and GSK-3 (glycogen synthase kinase) were screened for targeting 3 different enzymes, namely butyrylcholinesterase (BChE), monoamine oxidase A (MAO-A), and monoamine oxidase B (MAO-B) to possibly meet the unmet medical need of better AD treatment.

MATERIALS AND METHODS

The study utilized in silico screening of 13 ligands against BChE, MAO-A and MAOB using PyRx-Python prescription 0.8. The visualization of the active interaction of studied compounds with targeted proteins was performed by Discovery Studio 2020 (BIOVIA).

RESULTS

The computational screening of studied ligands revealed the docking energies in the range of -2.4 to -11.3 kcal/mol for all the studied enzymes. Among the 13 ligands, 8 ligands (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed the binding energies of ≤ -8.0 kcal/mol towards BChE, MAO-A and MAO-B. The ligand 6Z5 was found to be the most potent inhibitor of BChE and MAO-B, with a binding energy of -9.7 and -10.4 kcal mol, respectively. Molecular dynamics simulation of BChE-6Z5 and MAO-B-6Z5 complex confirmed the formation of a stable complex.

CONCLUSION

Our computational screening, molecular docking, and molecular dynamics simulation studies revealed that the above-mentioned enzymes targeted ligands might expedite the future design of potent anti-AD drugs generated on this chemical scaffold.

Elucidation of molecular interactions of theaflavin monogallate with camel milk lactoferrin: detailed spectroscopic and dynamic simulation studies

Lactoferrin is a heme-binding multifunctional glycoprotein known for iron transportation in the blood and also contributes to innate immunity. In this study, the interaction of theaflavin monogallate, a polyphenolic component of black tea, with camel milk lactoferrin was studied using various biophysical and computational techniques. Fluorescence quenching at different temperatures suggests that theaflavin monogallate interacted with lactoferrin by forming a non-fluorescent complex, i.e., static quenching. Theaflavin monogallate shows a significant affinity towards lactoferrin with a binding constant of ∼10⁴–10⁵ M⁻¹ at different temperatures. ANS binding shows that the binding of polyphenol resulted in the burial of hydrophobic domains of lactoferrin. Moreover, thermodynamic parameters (ΔH, ΔS and ΔG) suggested that the interaction between protein and polyphenol was entropically favored and spontaneous. Circular dichroism confirmed there was no alteration in the secondary structure of lactoferrin. The energy transfer efficiency (FRET) from lactoferrin to theaflavin was found to be approximately 50%, with a distance between protein and polyphenol of 2.44 nm. Molecular docking shows that the binding energy of lactoferrin–theaflavin monogallate interaction was −9.7 kcal mol⁻¹. Theaflavin monogallate was bound at the central cavity of lactoferrin and formed hydrogen bonds with Gln89, Tyr192, Lys301, Ser303, Gln87, and Val250 of lactoferrin. Other residues, such as Tyr82, Tyr92, and Tyr192, were involved in hydrophobic interactions. The calculation of various molecular dynamics simulations parameters indicated the formation of a stable complex between protein and polyphenol. This study delineates the binding mechanism of polyphenol with milk protein and could be helpful in milk formulations and play a key role in the food industry.

Lactoferrin is a heme-binding multifunctional glycoprotein known for iron transportation in the blood and also contributes to innate immunity.

Probe into the Molecular Mechanism of Ibuprofen Interaction with Warfarin Bound to Human Serum Albumin in Comparison to Ascorbic and Salicylic Acids: Allosteric Inhibition of Anticoagulant Release

The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned randomly and distant from the binary complex (HSA-warfarin) in a physiologically relevant concentration. The results obtained from both approaches indicated that s-ibuprofen and ascorbic acid both displayed allosteric effects on the release of warfarin from HSA. Although ascorbic acid aided in warfarin release, leading to destabilization of HSA, ibuprofen demonstrated a stabilizing effect on releasing the anticoagulant drug through several noncovalent interactions, including hydrophobic, electrostatic, and hydrogen-bonding interactions with the protein. The calculated binding free energy and energy contribution of involved residues using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method, along with root mean square deviation (RMSD) values, protein gyration, and free energy surface (FES) mapping of the protein, provided valuable details on the nature of the interactions of each drug on the release of warfarin from HSA. These results can provide important information on the mechanisms of anticoagulant release that has not been revealed in molecular details previously.