Capecitabine as a minor groove binder of DNA: molecular docking,molecular dynamics,and multi-spectroscopic studies

The interaction mechanism and binding mode of capecitabine with ctDNA was extensively investigated using docking and molecular dynamics simulations, fluorescence and circular dichroism (CD) spectroscopy, DNA thermal denaturation studies, and viscosity measurements. The possible binding mode and acting forces on the combination between capecitabine and DNA had been predicted through molecular simulation. Results indicated that capecitabine could relatively locate stably in the G-C base-pairs-rich DNA minor groove by hydrogen bond and several weaker nonbonding forces. Fluorescence spectroscopy and fluorescence lifetime measurements confirmed that the quenching was static caused by ground state complex formation. This phenomenon indicated the formation of a complex between capecitabine and ctDNA. Fluorescence data showed that the binding constants of the complex were approximately 2 × 10⁴ M^?1. Calculated thermodynamic parameters suggested that hydrogen bond was the main force during binding, which were consistent with theoretical results. Moreover, CD spectroscopy, DNA melting studies, and viscosity measurements corroborated a groove binding mode of capecitabine with ctDNA. This binding had no effect on B-DNA conformation.     

Experimental and computational studies on the effects of valganciclovir as an antiviral drug on calf thymus DNA

DNA-binding properties of an antiviral drug, valganciclovir (valcyte) was studied by using emission, absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, and computational studies. The drug bound to calf thymus DNA (ct-DNA) in a groove-binding mode. The calculated binding constant of UV-vis, K_a, is comparable to groove-binding drugs. Competitive fluorimetric studies with Hoechst 33258 showed that valcyte could displace the DNA-bound Hoechst 33258. The drug could not displace intercalated methylene blue from DNA double helix. Furthermore, the induced detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity confirm the groove-binding mode. In addition, an integrated molecular docking was employed to further investigate the binding interactions between valcyte and calf thymus DNA.     

DNA-binding study of anticancer drug cytarabine by spectroscopic and molecular docking techniques

The interaction of anticancer drug cytarabine with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multispectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove-binding mode, while the binding constant of UV-vis and the number of binding sites were 4.0 ± 0.2 × 10⁴ L mol^?1 and 1.39, respectively. The fluorimetric studies showed that the reaction between the drugs with CT-DNA is exothermic. Circular dichroism spectroscopy was employed to measure the conformational change of DNA in the presence of cytarabine. Furthermore, the drug induces detectable changes in its viscosity for DNA interaction. The molecular modeling results illustrated that cytarabine strongly binds to groove of DNA by relative binding energy of docked structure ?20.61 KJ mol^?1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the interaction of small molecular pollutants and drugs with biomacromolecules for clarifying the molecular mechanism of toxicity or side effect in vivo.     

DNA binding studies of antibiotic drug cephalexin using spectroscopic and molecular docking techniques

The purpose of this study was to explore an accurate characterization of the binding interaction of antibiotic drug cephalexin with calf thymus DNA (CT-DNA) as a relevant biological target by using UV absorption, fluorescence spectroscopy and circular dichroism (CD) in vitro under simulated physiological conditions (pH = 7.4) and also through a molecular modeling study. The results showed that the drug interacts with the DNA helix via a minor groove binding mode. The thermodynamic parameters were calculated and showed that the reaction between the drug and CT-DNA was exothermic. In addition, the drug enforced traceable changes in the viscosity of DNA. The molecular modeling results indicated that cephalexin forcefully binds to the minor groove of DNA with a relative binding energy of ?21.02?kJ mol^?1. The obtained theoretical results were in good agreement with those obtained from experimental studies.     

Spectroscopic and computational approaches to unravel the mode of binding between a isoflavone,biochanin-A and calf thymus DNA

In the present study, attempt was made to explore the interaction between biochanin-A (BioA) and calf thymus DNA (ctDNA) by employing fluorescence spectroscopy, absorption spectroscopy, circular dichroism (CD), DNA melting studies, viscosity measurements, and molecular modeling methods. A well-known fluorescence probe, acridine orange (AO) was used in the present study in order to enhance the emission intensity of weakly fluorescent ctDNA. Quenching in emission intensity of ctDNA-AO system was observed in the presence of different concentrations of BioA, suggesting that BioA has interacted with ctDNA. The hyperchromic effect observed upon the addition of BioA in the absorption spectra of ctDNA-AO without any shift in its absorption maximum revealed that BioA was bound to ctDNA through groove mode of binding. Further the groove mode of binding of BioA to ctDNA was confirmed by DNA melting studies, viscosity measurements, and molecular docking studies. The results of fluorescence measurements that were carried out at different temperature indicated that the BioA has quenched the emission intensity of ctDNA-AO through static mode of quenching mechanism. Thermodynamic parameters revealed that the BioA-ctDNA-AO system was stabilized by van der Waals forces and hydrogen bonding. The effect of binding of BioA on the conformation of ctDNA was examined by circular dichroism studies.     

Spectroscopic and molecular docking studies on the interaction of antiviral drug nevirapine with calf thymus DNA

The interaction of calf thymus DNA with nevirapine at physiological pH was studied by using absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, salt effect studies and computational methods. The drug binds to ct-DNA in a groove binding mode, as shown by slight variation in the viscosity of ct-DNA. Furthermore, competitive fluorimetric studies with Hoechst 33258 indicate that nevirapine binds to DNA via groove binding. Moreover, the structure of nevirapine was optimized by DFT calculations and was used for the molecular docking calculations. The molecular docking results suggested that nevirapine prefers to bind on the minor groove of ct-DNA.     

Interaction of procarbazine with calf thymus DNA—a biophysical and molecular docking study

Interaction of procarbazine (PCZ) with calf thymus DNA was studied using biophysical and molecular docking studies. Procarbazine was to interact with DNA with a binding constant of 6.52 × 10³ M⁻¹ as calculated using ultraviolet‐visible spectroscopy. To find out the binding mode, molecular docking was performed that predicted PCZ to interact with DNA through groove binding mode with binding affinity of −6.7 kcal/mole. To confirm the groove binding nature, different experiments were performed. Dye displacement assays confirmed the non‐intercalative binding mode. Procarbazine displaced Hoechst dye from the minor groove of DNA while it was unable to displace intercalating dyes. There was no increase in the viscosity of DNA solution in presence of PCZ. Also, negligible change in the secondary structure of DNA was observed in presence of PCZ as evident by circular dichroism spectra. Procarbazine caused decrease in the melting temperature of DNA possibly because of decrease in the stability of DNA caused by groove binding interaction of PCZ with DNA.     

DNA-binding affinity,cytotoxicity, apoptosis,cell cycle inhibition and molecular docking studies of a new stilbene derivative

Stilbene derivatives have been found to possess promising anticancer activities against human cancer cell lines in vitro. In the present study, we have investigated cytotoxic, apoptosis induction and DNA binding activity of new stilbene derivative, (E)-1-(4-Chlorophenyl)-4,5-diphenyl-2-[4-(4-methoxystryl)phenyl]-1H-imidazol (STIM) on K562 chronic myeloid leukemia cell line. Via MTT assay STIM demonstrated cytotoxic activity against K562 cell line with IC₅₀ value of 150?µM. Apoptosis, as the mechanism of cell death, was evaluated by morphological study and flow cytometric analysis. In vitro DNA binding property of STIM has been studied by vital spectroscopic techniques, which indicated that STIM interact with ctDNA through groove binding mode and binding constant (K_b) was estimated to be 6.9?×?10⁴?M^?1. Docking studies revealed that hydrophobic is the most important interaction in STIM-DNA complex, and that the ligand (STIM) interacts with DNA via groove binding mode and the bindiyspng energy was calculated as ?13.37?kcal/mol. Taken together, the present study suggests that STIM exhibits anticancer effect on K562 cell line through the induction of apoptosis as well as cell cycle arrest at Sub-G1 phase and also can bind to double helix DNA in vitro.     

Incorporating replacement free energy of binding‐site waters in molecular docking

Binding‐site water molecules play a crucial role in protein‐ligand recognition, either being displaced upon ligand binding or forming water bridges to stabilize the complex. However, rigorously treating explicit binding‐site waters is challenging in molecular docking, which requires to fully sample ensembles of waters and to consider the free energy cost of replacing waters. Here, we describe a method to incorporate structural and energetic properties of binding‐site waters into molecular docking. We first developed a solvent property analysis (SPA) program to compute the replacement free energies of binding‐site water molecules by post‐processing molecular dynamics trajectories obtained from ligand‐free protein structure simulation in explicit water. Next, we implemented a distance‐dependent scoring term into DOCK scoring function to take account of the water replacement free energy cost upon ligand binding. We assessed this approach in protein targets containing important binding‐site waters, and we demonstrated that our approach is reliable in reproducing the crystal binding geometries of protein‐ligand‐water complexes, as well as moderately improving the ligand docking enrichment performance. In addition, SPA program (free available to academic users upon request) may be applied in identifying hot‐spot binding‐site residues and structure‐based lead optimization. Proteins 2014; 82:1765–1776. © 2014 Wiley Periodicals, Inc.     

Intercalation of a flavonoid,silibinin into DNA base pairs: Experimental and theoretical approach

Polyphenols are secondary plant metabolites, which have received much attention because of their potential health benefits. Silibinin (SIL) is a well‐known naturally occurring flavonolignan, which is extensively used in treating a wide variety of diseases as a dietary supplement as well as a prescribed drug. The mechanism of binding of SIL to calf thymus DNA (ctDNA) was investigated by employing multispectroscopic techniques, viz., absorption, fluorescence, and circular dichroism besides viscosity measurements and docking studies. Analysis of fluorescence results indicated that SIL has interacted with ctDNA and quenched its intensity through static quenching mechanism. The binding constant at room temperature was found to be 2.48×10⁴ mol^?1, suggesting moderate binding affinity between SIL and ctDNA. The hypochromicity observed in the absorption spectra of ctDNA in the presence of SIL revealed the intercalation of SIL into ctDNA base pairs. Further, the intercalative mode of binding between SIL and ctDNA was confirmed by viscosity measurements and molecular docking studies. The outcome of present study helps to decipher the interaction mechanism between SIL and DNA at physiological pH, which further assists in the design of a new analogue for better therapeutic effects.     

Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge

Abstract

Ribosomal RNA K-turn motifs are asymmetric internal loops characterized by a sharp bend in the phosphodiester backbone resulting in “V” shaped structures, recurrently observed in ribosomes and showing a high degree of sequence conservation. We have carried out extended explicit solvent molecular dynamics simulations of selected K-turns, in order to investigate their intrinsic structural and dynamical properties. The simulations reveal an unprecedented dynamical flexibility of the K-turns around their X-ray geometries. The K-turns sample, on the nanosecond timescale, different conformational substates. The overall behavior of the simulations suggests that the sampled geometries are essentially isoenergetic and separated by minimal energy barriers. The nanosecond dynamics of isolated K-turns can be qualitatively considered as motion of two rigid helix stems controlled by a very flexible internal loop which then leads to substantial hinge-like motions between the two stems. This internal dynamics of K-turns is strikingly different for example from the bacterial 5S rRNA Loop E motif or BWYV frameshifting pseudoknot which appear to be rigid in the same type of simulations. Bistability and flexibility of K-turns was also suggested by several recent biochemical studies. Although the results of MD simulations should be considered as a qualitative picture of the K-turn dynamics due to force field and sampling limitations, the main advantage of the MD technique is its ability to investigate the region close to K-turn riboso- mal-like geometries. This part of the conformational space is not well characterized by the solution experiments due to large-scale conformational changes seen in the experiments. We suggest that K-turns are well suited to act as flexible structural elements of ribosomal RNA. They can for example be involved in mediation of large-scale motions or they can allow a smooth assembling of the other parts of the ribosome.     

Insight into the binding modes and inhibition mechanisms of adamantyl-based 1,3-disubstituted urea inhibitors in the active site of the human soluble epoxide hydrolase

Soluble epoxide hydrolase (sEH) is a promising new target for treating hypertension and inflammation. Considerable efforts have been devoted to develop novel inhibitors. In this study, the binding modes and interaction mechanisms of a series of adamantyl-based 1,3-disubstituted urea inhibitors were investigated by molecular docking, molecular dynamics simulations, binding free energy calculations, and binding energy decomposition analysis. Based on binding affinity, the most favorable binding mode was determined for each inhibitor. The calculation results indicate that the total binding free energy (ΔG_TOT, the sum of enthalpy ΔG_MM-GB/SA, and entropy ?TΔS) presents a good correlation with the experimental inhibitory activity (IC₅₀, r²?=?.99). The van der Waals energy contributes most to the total binding free energy (ΔG_TOT). A detailed discussion on the interactions between inhibitors and those residues located in the active pocket is made based on hydrogen bond and binding modes analysis. According to binding energy decomposition, the residues Asp333 and Trp334 contribute the most to binding free energy in all systems. Furthermore, Hip523 plays a major role in determining this class of inhibitor-binding orientations. Combined with the results of hydrogen bond analysis and binding free energy, we believe that the conserved hydrogen bonds play a role only in anchoring the inhibitors to the exact site for binding and the number of hydrogen bonds may not directly relate to the binding free energy. The results we obtained will provide valuable information for the design of high potency sEH inhibitors.     

Designing of benzothiazole derivatives as promising EGFR tyrosine kinase inhibitors: a pharmacoinformatics study

Abstract

Benzothiazole derivatives represent an important class of therapeutic chemical agents and are widely used for interesting biological activities and therapeutic functions including anticancer, antitumor and antimicrobial. In this study, we have performed similarity/substructure-based search of eMolecule database to find out promising benzothiazole derivatives as EGFR tyrosine kinase inhibitors. Several screening criteria that included molecular docking, pharmacokinetics and synthetic accessibility were used on initially derived about 7000 molecules consisting of benzothiazole as major component. Finally, four molecules were found to be promising EGFR tyrosine kinase inhibitors. The best docked pose of each molecule was considered for binding interactions followed by molecular dynamics (MD) and binding energy calculation. Molecular docking clearly showed the final proposed derivatives potential to form a number of binding interactions. MD simulation trajectories undoubtedly indicated that the EGFR protein becomes stable when proposed derivatives bind to the receptor cavity. Strong binding affinity was found for all molecules toward the EGFR which was substantiated by the binding energy calculation using the MM-PBSA approach. Therefore, proposed benzothiazole derivatives may be promising EGFR tyrosine kinase inhibitors for potential application as cancer therapy.

Communicated by Ramaswamy H. Sarma     

Insights into mechanism of pyrido[2,3‐d]pyrimidines as DYRK1A inhibitors based on molecular dynamic simulations

DYRK1A is characterized by the early development and regulation of neuronal proliferation, and its over expression gives rise to neurological abnormalities. As the promising DYRK1A inhibitors, the binding mechanism between DYRK1A and pyrido[2,3‐d]pyrimidines derivatives at molecular level are still veiled. In this article, it was achieved to get the structural insights into pyrido[2,3‐d]pyrimidines derivatives as DYRK1A inhibitors by means of comprehensive computational approaches involving molecular docking, molecular dynamics simulation, free energy calculation, and energy decomposition analysis. The calculated energy values were highly consistent with the experimental activities. Based on the individual energy terms analysis, the van der Waals interaction was the major leading force in the DYRK1A–ligand interaction. Lys188 was the important residue that formed the hydrogen bond, which improved the inhibitory activity. Furthermore, four novel inhibitors with higher predicted activity were designed based on the obtained findings and confirmed by molecular simulations. Our study is expected to provide significant drug design strategy for the development of more promising DYRK1A inhibitors. Proteins 2016; 84:1108–1123. © 2016 Wiley Periodicals, Inc.     

DNA‐binding activity and cytotoxic and cell‐cycle arrest properties of some new coumarin derivatives: a multispectral and computational investigation

Coumarins are the most important class of natural compounds found widely in various plants. Many coumarin derivatives with different biological and pharmacological activities have been synthesized. In this study, the antiapoptotic and cytotoxic effects and DNA‐binding properties of some synthetic coumarin derivatives (4b, 4d, 4f, 4 g (DBP‐g), 4 h and 4j) against K562 cell lines were investigated using different techniques. MTT assay indicated that the DBP‐g compound was more active than other derivatives, with a IC₅₀ value of 55 μM, and therefore this compound was chosen for further investigation. Apoptosis induction was assessed using acridine orange/ethidium bromide double‐staining and cell‐cycle analysis. In addition, in vitro DNA‐binding studies were carried out using ultraviolet–visible light absorption and fluorescence spectroscopy, as well as viscosity measurement and molecular modelling studies. In vitro results indicated that DBP‐g interacted with DNA through a groove‐binding mode with a binding constant (K_b) of 1.17 × 10⁴ M^?1. In agreement with other experimental data, molecular docking studies showed that DBP‐g is a minor groove binder. Overall, it can be concluded that DBP‐g could be used as an effective and novel chemotherapeutic agent.     

Comparative molecular docking and simulation analysis of molnupiravir and remdesivir with SARS-CoV-2 RNA dependent RNA polymerase (RdRp)

Treatment of SARS-CoV-2 targeting its RNA dependent RNA polymerase (RdRp) is of current interest. Remdesivir has been approved for the treatment of COVID-19 around the world. However, the drug has been linked with pharmacological limitations like adverse effects and reduced efficiency. Nevertheless, recent advancements have depicted molnupiravir as an effective therapeutic agent to target the SARS-CoV-2 RdRp. The drug has cleared both in vitro and in vivo screening. It is in phase-III clinical trial. Nonetheless, there are no data on themolecular binding interaction of molnupiravir with RdRp. Therefore, it is of interest to report the binding interaction of molnupiravir using molecular docking. It is also of interest to show its stability during interaction using molecular dynamics and binding free energy calculations along with drug likeliness and pharmacokinetic properties in comparison with remdesivir.     

Lysozyme binding with sulfa group of antibiotics: Comparative binding thermodynamics and computational study

Protein–drug binding study addresses a broad domain of biological problems associating molecular functions to physiological processes composing and modifying safe and coherent drug therapeutics. Comparison of the binding and thermodynamic aspect of sulfa drugs, sulfamethazine (SMZ) and sulfadiazine (SDZ) with the protein, lysozyme (Lyz) was carried out using spectroscopic, molecular docking, and dynamic simulation studies. The fluorescence quenching and apparent binding constant for the binding reaction were calculated to be in the order of 10⁴ M⁻¹, slightly higher for SMZ as compared to that of SDZ and the binding stoichiometry values show 1:1 drug binding with each protein molecule. The binding was an enthalpy-driven spontaneous exothermic reaction favored by a negative enthalpy and a positive entropy contribution for both the complexes. The binding from the fluorescence quenching data suggests a static quenching mechanism dominated by non-polyelectrolytic components. Synchronous fluorescence denoted a conformational change in the tryptophan moiety of the protein. Molecular docking and dynamic simulation study provided a clearer view of the interaction pattern, where the drug resides on the binding pocket of the protein structure. Overall the protein, Lyz binding of SMZ was slightly more favored over SDZ.     

Structure prediction and molecular dynamics simulations of a G-protein coupled receptor: human CCR2 receptor

CC chemokine receptor type-2 (CCR2) is a member of G-protein coupled receptors superfamily, expressed on the cell surface of monocytes and macrophages. It binds to the monocyte chemoattractant protein-1, a CC chemokine, produced at the sites of inflammation and infection. A homology model of human CCR2 receptor based on the recently available C-X-C chemokine recepor-4 crystal structure has been reported. Ligand information was used as an essential element in the homology modeling process. Six known CCR2 antagonists were docked into the model using simple and induced fit docking procedure. Docked complexes were then subjected to visual inspection to check their suitability to explain the experimental data obtained from site directed mutagenesis and structure-activity relationship studies. The homology model was refined, validated, and assessed for its performance in docking-based virtual screening on a set of CCR2 antagonists and decoys. The docked complexes of CCR2 with the known antagonists, TAK779, a dual CCR2/CCR5 antagonist, and Teijin-comp1, a CCR2 specific antagonist were subjected to molecular dynamics (MD) simulations, which further validated the binding modes of these antagonists. B-factor analysis of 20?ns MD simulations demonstrated that Cys190 is helpful in providing structural rigidity to the extracellular loop (EL2). Residues important for CCR2 antagonism were recognized using free energy decomposition studies. The acidic residue Glu291 from TM7, a conserved residue in chemokine receptors, is favorable for the binding of Teijin-comp1 with CCR2 by ΔG of ?11.4?kcal/mol. Its contribution arises more from the side chains than the backbone atoms. In addition, Tyr193 from EL2 contributes ?0.9?kcal/mol towards the binding of the CCR2 specific antagonist with the receptor. Here, the homology modeling and subsequent molecular modeling studies proved successful in probing the structure of human CCR2 chemokine receptor for the structure-based virtual screening and predicting the binding modes of CCR2 antagonists.     

Deoxyribonuclease I Inhibitory Properties,Molecular Docking and Molecular Dynamics Simulations of 1-(Pyrrolidin-2-yl)propan-2-one Derivatives

Deoxyribonuclease I (DNase I) inhibitory properties of two 1-(pyrrolidin-2-yl)propan-2-one derivatives were examined in vitro. Determined IC₅₀ values of 1-[1-(4-methoxyphenyl)pyrrolidin-2-yl]propan-2-one ( 1 ) (192.13±16.95 μM) and 1-[1-(3,4,5-trimethoxyphenyl)pyrrolidin-2-yl]propan-2-one ( 2 ) (132.62±9.92 μM) exceed IC₅₀ value of crystal violet, used as a positive control, 1.89- and 2.73-times, respectively. Compounds are predicted to be nontoxic and to have favorable pharmacokinetic profiles, with high gastrointestinal absorption and blood-brain barrier permeability. Molecular docking and molecular dynamics simulations suggest that interactions with Glu 39, Glu 78, Arg 111, Pro 137, Asp 251 and His 252 are an important factor for inhibitors affinity toward the DNase I. Determined inhibitory properties along with predicted ADMET profiles and observed interactions would be beneficial for the discovery of new active 1-(pyrrolidin-2-yl)propan-2-one-based inhibitors of DNase I.     

Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues

Experimental studies (M. Mandal, B. Boese, J.E. Barrick, W.C. Winkler and R.R. Breaker, Riboswitches control fundamental biochemical pathways in bacillus subtilis and other bacteria, Cell 113 (2003), pp. 577–586) demonstrated that, besides recognising guanine with high specificity, guanine riboswitch could also bind guanine analogues, but the alteration of every functionalised position on the guanine heterocycle could cause a substantial loss of binding affinity. To investigate the nature of guanine riboswitch recognising metabolites, molecular docking and molecular dynamics simulation were carried out on diverse guanine analogues. The calculation results reveal that (1) most guanine analogues could bind to guanine riboswitch at the same binding pocket, with identical orientations and dissimilar binding energies, which is related to the positions of the functional groups; (2) the two tautomers of xanthine adopt different binding modes, and the enol-tautomer shows similar binding mode and affinity of hypoxanthine, which agrees well with the experimental results and (3) the riboswitch could form stable complexes with guanine analogues by hydrogen bonding contacts with U51 and C74. Particularly, U51 plays an important role in stabilising the complexes.