Molecular modelling studies of DNA damage recognition

How DNA repair proteins search and recognise the rare sites of damage from the massive numbers of normal DNA remains poorly understood. FapydG (2,6-diamino-4-hydroxy-5-formamidopyrimidine) is one of the most prevalent guanine derived lesions involving opening of the imidazole ring. It is typically repaired by formamidopyrimidine-DNA glycosylase (Fpg) as an initial step in base excision repair; if not repaired, the lesion generates a G: C -+ T: A transversion. Unfortunately, studies on the recognition of FapydG have been hindered by difficulties to synthesise and incorporate the FapydG residue into a DNA duplex. Crystal structures of Fpg-DNA complexes have demonstrated three common recognition events: the protein specifically binding to the extrahelical lesion, bending DNA centred on the damaged base, and flipping the damage into the pocket. Thus, molecular modelling and dynamics simulation have been used to gather dynamical information of those recognition events for damaged and undamaged DNA. The simulations were initially performed when FapydG or G occurs in several dodecamer B-DNA sequences in aqueous solution, then inside the lesion-recognition pocket of Fpg, and during the flipping pathway from the helical stack to an extrahelical position. The influence of the damage on DNA stability and flexibility was first investigated. Energetic analysis revealed that damage to DNA does appear to destabilise the duplex. DNA curvature analysis and a novel combined method of the principal component analysis (PCA) and the Mahalanobis distance (DM) indicated that damaged DNA can adopt the observed protein-bound conformation with lower energetic penalties than its normal counterpart. Results of these studies have provided the validation of DNA bending enhancement by the FapydG lesion. It also suggested that intrinsic DNA bending could be a principal element of how the repair protein locates the lesion from vast expanse of normal bases. Considering the specific recognition of FapydG by Fpg, the aF-/39 loop of the Fpg enzyme may function as a gatekeeping to accommodate the lesion while denying the normal base. Remarkably fluctuating movement of the flipped G residue and the aF-ß9 loop is due to the formation of the non-specific Fpg/G complex with a lower binding energy by 8.4 kcal/mol compared to the specific Fpg/FapydG complex. Free-energy profiles for both damaged and undamaged base flipping were generated from the umbrella sampling simulations and the Weight Histogram Analysis Method (WHAM). An energy barrier for flipping the damage out from the helix is 2.7 kcal/mol higher than its equivalent G and the lesion is highly stabilised inside the pocket. In contrast, G flipping seems to be rapidly rotated out and into the duplex without the formation of a specific complex. These studies could unravel a potentially comprehensive process of the repair protein to find and recognise the lesion through the slow kinetic pathway in which the more deformable damaged DNA is initially located by the protein; the protein subsequently compresses the duplex into an appropriate angle and direction to form a specific protein-DNA complex prior to being flipped and repaired

Molecular modelling studies of DNA damage recognition

How DNA repair proteins search and recognise the rare sites of damage from the massive numbers of normal DNA remains poorly understood. FapydG (2,6-diamino-4-hydroxy-5-formamidopyrimidine) is one of the most prevalent guanine derived lesions involving opening of the imidazole ring. It is typically repaired by formamidopyrimidine-DNA glycosylase (Fpg) as an initial step in base excision repair; if not repaired, the lesion generates a G: C -+ T: A transversion. Unfortunately, studies on the recognition of FapydG have been hindered by difficulties to synthesise and incorporate the FapydG residue into a DNA duplex. Crystal structures of Fpg-DNA complexes have demonstrated three common recognition events: the protein specifically binding to the extrahelical lesion, bending DNA centred on the damaged base, and flipping the damage into the pocket. Thus, molecular modelling and dynamics simulation have been used to gather dynamical information of those recognition events for damaged and undamaged DNA. The simulations were initially performed when FapydG or G occurs in several dodecamer B-DNA sequences in aqueous solution, then inside the lesion-recognition pocket of Fpg, and during the flipping pathway from the helical stack to an extrahelical position. The influence of the damage on DNA stability and flexibility was first investigated. Energetic analysis revealed that damage to DNA does appear to destabilise the duplex. DNA curvature analysis and a novel combined method of the principal component analysis (PCA) and the Mahalanobis distance (DM) indicated that damaged DNA can adopt the observed protein-bound conformation with lower energetic penalties than its normal counterpart. Results of these studies have provided the validation of DNA bending enhancement by the FapydG lesion. It also suggested that intrinsic DNA bending could be a principal element of how the repair protein locates the lesion from vast expanse of normal bases. Considering the specific recognition of FapydG by Fpg, the aF-/39 loop of the Fpg enzyme may function as a gatekeeping to accommodate the lesion while denying the normal base. Remarkably fluctuating movement of the flipped G residue and the aF-ß9 loop is due to the formation of the non-specific Fpg/G complex with a lower binding energy by 8.4 kcal/mol compared to the specific Fpg/FapydG complex. Free-energy profiles for both damaged and undamaged base flipping were generated from the umbrella sampling simulations and the Weight Histogram Analysis Method (WHAM). An energy barrier for flipping the damage out from the helix is 2.7 kcal/mol higher than its equivalent G and the lesion is highly stabilised inside the pocket. In contrast, G flipping seems to be rapidly rotated out and into the duplex without the formation of a specific complex. These studies could unravel a potentially comprehensive process of the repair protein to find and recognise the lesion through the slow kinetic pathway in which the more deformable damaged DNA is initially located by the protein; the protein subsequently compresses the duplex into an appropriate angle and direction to form a specific protein-DNA complex prior to being flipped and repaired

Adverse events related to herbal products used by patients presenting at emergency departments

Herbal medications are gaining popularity in many countries. Although most can be used without any problem, serious toxicities do occur. Adverse events can be anticipated when herbal medications are used at excessive dose, long-term, for non-approved indications or by patients who are using multiple medications. Adverse events should be anticipated when these herbal medications with identified pharmacological effects or toxic ingredients are used. Healthcare professionals need to discuss or advise patients regarding their use. Physician-obtained medication histories towards specific herbal product use could provide relevant pharmacologic information and uncover cases of adverse events or toxicity from the used herbal products

3D-QSAR modelling dataset of bioflavonoids for predicting the potential modulatory effect on P-glycoprotein activity

The data is obtained from exploring the modulatory activities of bioflavonoids on P-glycoprotein function by ligand-based approaches. Multivariate Linear-QSAR models for predicting the induced/inhibitory activities of the flavonoids were created. Molecular descriptors were initially used as independent variables and a dependent variable was expressed as pFAR. The variables were then used in MLR analysis by stepwise regression calculation to build the linear QSAR data. The entire dataset consisted of 23 bioflavonoids was used as a training set. Regarding the obtained MLR QSAR model, R of 0.963, R2=0.927, Radj2=0.900, SEE=0.197, F=33.849 and q2=0.927 were achieved. The true predictabilities of QSAR model were justified by evaluation with the external dataset (Table 4). The pFARs of representative flavonoids were predicted by MLR QSAR modelling. The data showed that internal and external validations may generate the same conclusion

Multitarget-Based Virtual Screening for Identification of Herbal Substances toward Potential Osteoclastic Targets

Osteoporosis is a complex bone disease indicating porous bone with low bone mass density and fragility. Cathepsin K, V-ATPase, and αVβ3 integrin are exhibited as novel targets for osteoporosis treatment. Our preliminary study uses a state-of-the-art method, including target-based virtual screening and clustering methods to determine promising candidates with multitarget properties. Phytochemicals with osteoprotective properties from the literature are used to elucidate the molecular interactions toward three targets. The binding scores of compounds are normalized and rescored. The K-means and hierarchical clustering methods are applied to filter and define the promising compounds, and the silhouette analysis is supposed to validate the clustering method. We explore 108 herbal compounds by virtual screening and the cluster approach, and find that rutin, sagittatoside A, icariin, and kaempferitrin showed strong binding affinities against Cathepsin K, V-ATPase, and αVβ3 integrin. Dockings of candidates toward three targets also provide the protein-ligand interactions and crucial amino acids for binding. Our study provides a straightforward and less time-consuming approach to exploring the new multitarget candidates for further investigations, using a combination of in silico methods

Tentative Peptide‒Lipid Bilayer Models Elucidating Molecular Behaviors and Interactions Driving Passive Cellular Uptake of Collagen-Derived Small Peptides

Collagen contains hydroxyproline (Hyp), which is a unique amino acid. Three collagen-derived small peptides (Gly-Pro-Hyp, Pro-Hyp, and Gly-Hyp) interacting across a lipid bilayer (POPC model membrane) for cellular uptakes of these collagen-derived small peptides were studied using accelerated molecular dynamics simulation. The ligands were investigated for their binding modes, hydrogen bonds in each coordinate frame, and mean square displacement (MSD) in the Z direction. The lipid bilayers were evaluated for mass and electron density profiles of the lipid molecules, surface area of the head groups, and root mean square deviation (RMSD). The simulation results show that hydrogen bonding between the small collagen peptides and plasma membrane plays a significant role in their internalization. The translocation of the small collagen peptides across the cell membranes was shown. Pro-Hyp laterally condensed the membrane, resulting in an increase in the bilayer thickness and rigidity. Perception regarding molecular behaviors of collagen-derived peptides within the cell membrane, including their interactions, provides the novel design of specific bioactive collagen peptides for their applications

Potential Anti-Alzheimer Agents from Guanidinyl Tryptophan Derivatives with Activities of Membrane Adhesion and Conformational Transition Inhibitions

Guanidinyl tryptophan derivatives TGN1, TGN2, TGN3, and TGN4 were synthesized, and these compounds were shown to possess in vitro inhibitory activity for amyloid aggregation in a previous study. Nevertheless, the influence of the TGN series of compounds on the binding and permeation behaviors of an Aβ monomer to the cell membranes was not elucidated. In this study, we investigated the effect of compounds in the TGN series on the behavior of an Aβ monomer regarding its toxicity toward the bilayer lipid membrane using molecular dynamics (MD) simulation. MD simulations suggest that TGN4 is a potential agent that can interfere with the movement of the Aβ monomer into the membrane. The MM-GBSA result demonstrated that TGN4 exhibits the highest affinity to the Aβ1–42 monomer but has the lowest affinity to the bilayer. Moreover, TGN4 also contributes to a decrease in the binding affinity between the Aβ1–42 monomer and the POPC membrane. Regarding the results of the binding mode and conformational analyses, a high number of amino-acid residues were shown to provide the binding interactions between TGN4 and the Aβ1–42 monomer. TGN4 also reduces the conformational transition of the Aβ1–42 monomer by means of interacting with the monomer. The present study presents molecular-level insights into how the TGN series of compounds affect the membrane adsorption and the conformational transition of the Aβ1–42 monomer, which could be valuable for the further development of new anti-Alzheimer agents

Destabilization of DNA duplexes by oxidative damage at guanine: implications for lesion recognition and repair

We have used molecular dynamics simulations to study the structure and dynamics of a range of DNA duplexes containing the 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapydG) lesion that can result from oxidative damage at guanine. Compared to the corresponding undamaged DNA duplexes, FapydG-containing duplexes show little gross structural changes—the damaged base remains stacked in to the DNA double helix and retains hydrogen bonds to its cytosine partner. However, the experimentally observed reduction in DNA stability that accompanies lesion formation can be explained by a careful energetic analysis of the simulation data. Irrespective of the nature of the base pairs on either side of the lesion site, conversion of a guanine to a FapydG base results in increased dynamical flexibility in the base (but not in the DNA as a whole) that significantly weakens its hydrogen-bonding interactions. Surprisingly, the stacking interactions with its neighbours are not greatly altered. The formamido group adopts a non-planar conformation that can interact significantly and in a sequence-dependent manner with its 3′-neighbour. We conclude that the recognition of FapydG lesions by the repair protein formamidopyrimidine-DNA glycosylase probably does not involve the protein capturing an already-extrahelical FapydG base, but rather it relies on detecting alterations to the DNA structure and flexibility created by the lesion site

Insight into the molecular mechanism of P-glycoprotein mediated drug toxicity induced by bioflavonoids: an integrated computational approach

In this work, molecular docking, pharmacophore modeling and molecular dynamics (MD) simulation were rendered for the mouse P-glycoprotein (P-gp) (code: 4Q9H) and bioflavonoids; amorphigenin, chrysin, epigallocatechin, formononetin and rotenone including a positive control; verapamil to identify protein–ligand interaction features including binding affinities, interaction characteristics, hot-spot amino acid residues and complex stabilities. These flavonoids occupied the same binding site with high binding affinities and shared the same key residues for their binding interactions and the binding region of the flavonoids was revealed that overlapped the ATP binding region with hydrophobic and hydrophilic interactions suggesting a competitive inhibition mechanism of the compounds. Root mean square deviations (RMSDs) analysis of MD trajectories of the protein–ligand complexes and NBD2 residues, and ligands pointed out these residues were stable throughout the duration of MD simulations. Thus, the applied preliminary structure-based molecular modeling approach of interactions between NBD2 and flavonoids may be gainful to realize the intimate inhibition mechanism of P-gp at NBD2 level and on the basis of the obtained data, it can be concluded that these bioflavonoids have the potential to cause herb–drug interactions or be used as lead molecules for the inhibition of P-gp (as anti-multidrug resistance agents) via the NBD2 blocking mechanism in future