Multistep Drug Intercalation: Molecular Dynamics and Free Energy Studies of the Binding of Daunomycin to DNA

The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes

Among all tools available to design new drugs, molecular dynamics (MD) simulations have become an essential technique. Initially developed to investigate molecular models with a limited number of atoms, computers now enable investigations of large macromolecular systems with a simulation time reaching the microsecond range. The reviewed articles cover four years of research to give an overview on the actual impact of MD on the current medicinal chemistry landscape with a particular emphasis on studies of ligand-protein interactions. With a special focus on studies combining computational approaches with data gained from other techniques, this review shows how deeply embedded MD simulations are in drug design strategies and articulates what the future of this technique could be.

Mechanism of amyloid-β fibril elongation

Amyloid-β is an intrinsically disordered protein that forms fibrils in the brains of patients with Alzheimer's disease. To explore factors that affect the process of fibril growth, we computed the free energy associated with disordered amyloid-β monomers being added to growing amyloid fibrils using extensive molecular dynamics simulations coupled with umbrella sampling. We find that the mechanisms of Aβ40 and Aβ42 fibril elongation have many features in common, including the formation of an obligate on-pathway β-hairpin intermediate that hydrogen bonds to the fibril core. In addition, our data lead to new hypotheses for how fibrils may serve as secondary nucleation sites that can catalyze the formation of soluble oligomers, a finding in agreement with recent experimental observations. These data provide a detailed mechanistic description of amyloid-β fibril elongation and a structural link between the disordered free monomer and the growth of amyloid fibrils and soluble oligomers.

Atomic level rendering of DNA-drug encounter

Computer simulations have been demonstrated to be important for unraveling atomic mechanisms in biological systems. In this study, we show how combining unbiased molecular dynamic simulations with appropriate analysis tools can successfully describe metal-based drug interactions with DNA. To elucidate the noncovalent affinity of cisplatin's family to DNA, we performed extensive all-atom molecular dynamics simulations (3.7 μs total simulation length). The results show that the parent drug, cisplatin, has less affinity to form noncovalent adducts in the major groove than its aquo complexes. Furthermore, the relative position in which the drugs enter the major groove is dependent on the compound's net charge. Based on the simulations, we estimated noncovalent binding free energies through the use of Markov state models. In addition, and to overcome the lack of experimental information, we employed two additional methods: Molecular Mechanics Poisson-Boltzmann Surface Area (MMPB-SA) and steered molecular dynamics with the Jarzynski estimator, with an overall good agreement between the three methods. All complexes show interaction energies below 3 kcal/mol with DNA but the charged hydrolysis products have slightly more favorable binding free energies than the parent drug. Moreover, this study sets the precedent for future unbiased DNA-ligand simulations of more complex binders.

P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape

Tyrosine kinases are regarded as excellent targets for chemical drug therapy of carcinomas. However, under strong purifying selection, drug resistance usually occurs in the cancer cells within a short term. Many cases of drug resistance have been found to be associated with secondary mutations in drug target, which lead to the attenuated drug-target interactions. For example, recently, an acquired secondary mutation, G2032R, has been detected in the drug target, ROS1 tyrosine kinase, from a crizotinib-resistant patient, who responded poorly to crizotinib within a very short therapeutic term. It was supposed that the mutation was located at the solvent front and might hinder the drug binding. However, a different fact could be uncovered by the simulations reported in this study. Here, free energy surfaces were characterized by the drug-target distance and the phosphate-binding loop (P-loop) conformational change of the crizotinib-ROS1 complex through advanced molecular dynamics techniques, and it was revealed that the more rigid P-loop region in the G2032R-mutated ROS1 was primarily responsible for the crizotinib resistance, which on one hand, impaired the binding of crizotinib directly, and on the other hand, shortened the residence time induced by the flattened free energy surface. Therefore, both of the binding affinity and the drug residence time should be emphasized in rational drug design to overcome the kinase resistance.

Cancers can eventually confer drug resistance to the continued medication. In most cases, mutations occurred in a drug target can attenuate the binding affinity of the drugs. Here, we studied the drug resistance mechanisms of the mutations G2032R in the ROS1 tyrosine kinase in fusion-type NSCLC. It is well known that the phosphate-binding loop (P-loop) plays a vital role in the binding of competitive inhibitors in tyrosine kinases, and numerous mutations have been found occurred around the P-loop, which may affect the binding/unbinding process of a drug. Free energy surfaces were constructed to characterize the impact of the mutation to the binding/unbinding process of a well-known NSCLC drug, crizotinib. Two advanced free energy calculation methods, namely funnel based well-tempered metadynamics and umbrella sampling based absolute binding free energy calculation achieved consistent results with the experimental data, suggesting that the rigid P-loop of the mutated target was mainly responsible for the crizotinib resistance to ROS1 tyrosine kinase.

Atomistic account of structural and dynamical changes induced by small binders in the double helix of a short DNA

Nucleic acids are flexible molecules and their dynamical properties play a key role in molecular recognition events. Small binders interacting with DNA fragments induce both structural and dynamical changes in the double helix. We study the dynamics of a DNA dodecamer and of its complexes with Hoechst 33258, which is a minor groove binder, and with the ethidium cation, which is an intercalator, by molecular dynamics simulation. The thermodynamics of DNA-drug interaction is evaluated in connection with the structure and the dynamics of the resulting complexes. We identify and characterize the relevant changes in the configurational distribution of the DNA helix and relate them to the corresponding entropic contributions to the binding free energy. The binder Hoechst locks the breathing motion of the minor groove inducing a reduction of the configurational entropy of the helix, which amounts to 20 kcal mol(-1). In contrast, intercalations with the ethidium cation enhance the flexibility of the double helix. We show that the balance between the energy required to deform the helix for the intercalation and the gain in configurational entropy is the origin of cooperativity in the binding of a second ethidium and of anti-cooperativity in the binding of a third one. The results of our study provide an understanding of the relation between structure, dynamics and energetics in the interaction between DNA fragments and small binders, highlighting the role of dynamical changes and consequent variation of the configurational entropy of the DNA double helix for both types of binders.

Mechanistic insight into ligand binding to G-quadruplex DNA

Specific guanine-rich regions in human genome can form higher-order DNA structures called G-quadruplexes, which regulate many relevant biological processes. For instance, the formation of G-quadruplex at telomeres can alter cellular functions, inducing apoptosis. Thus, developing small molecules that are able to bind and stabilize the telomeric G-quadruplexes represents an attractive strategy for antitumor therapy. An example is 3-(benzo[d]thiazol-2-yl)-7-hydroxy-8-((4-(2-hydroxyethyl)piperazin-1-yl)methyl)-2H-chromen-2-one (compound 1: ), recently identified as potent ligand of the G-quadruplex [d(TGGGGT)]4 with promising in vitro antitumor activity. The experimental observations are suggestive of a complex binding mechanism that, despite efforts, has defied full characterization. Here, we provide through metadynamics simulations a comprehensive understanding of the binding mechanism of 1: to the G-quadruplex [d(TGGGGT)]4. In our calculations, the ligand explores all the available binding sites on the DNA structure and the free-energy landscape of the whole binding process is computed. We have thus disclosed a peculiar hopping binding mechanism whereas 1: is able to bind both to the groove and to the 3' end of the G-quadruplex. Our results fully explain the available experimental data, rendering our approach of great value for further ligand/DNA studies.

Mutation induced conformational changes in genomic DNA from cancerous K562 cells influence drug-DNA binding modes

Normal human genomic DNA (N-DNA) and mutated DNA (M-DNA) from K562 leukemic cells show different thermodynamic properties and binding affinities on interaction with anticancer drugs; adriamycin (ADR) and daunomycin (DNM). Isothermal calorimetric thermograms representing titration of ADR/DNM with N-DNA and M-DNA on analysis best fitted with sequential model of four and three events respectively. From Raman spectroscopy it has been identified that M-DNA is partially transformed to A form owing to mutations and N-DNA on binding of drugs too undergoes transition to A form of DNA. A correlation of thermodynamic contribution and structural data reveal the presence of different binding events in drug and DNA interactions. These events are assumed to be representative of minor groove complexation, reorientation of the drug in the complex, DNA deformation to accommodate the drugs and finally intercalation. Dynamic light scattering and zeta potential data also support differences in structure and mode of binding of N and M DNA. This study highlights that mutations can manifest structural changes in DNA, which may influence the binding efficacy of the drugs. New generation of drugs can be designed which recognize the difference in DNA structure in the cancerous cells instead of their biochemical manifestation.

Recent advances in small organic molecules as DNA intercalating agents: synthesis, activity, and modeling

The interaction of small molecules with DNA plays an essential role in many biological processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study about the interaction of drug and DNA has a key role in pharmacology. Moreover, understanding the interactions of small molecules with DNA is of prime significance in the rational design of more powerful and selective anticancer agents. Two of the most important and promising targets in cancer chemotherapy include DNA alkylating agents and DNA intercalators. For these last the DNA recognition is a critical step in their anti-tumor action and the intercalation is not only one kind of the interactions in DNA recognition but also a pivotal step of several clinically used anti-tumor drugs such as anthracyclines, acridines and anthraquinones. To push clinical cancer therapy, the discovery of new DNA intercalators has been considered a practical approach and a number of intercalators have been recently reported. The intercalative binding properties of such molecules can also be harnessed as diagnostic probes for DNA structure in addition to DNA-directed therapeutics. Moreover, the problem of intercalation site formation in the undistorted B-DNA of different length and sequence is matter of tremendous importance in molecular modeling studies and, nowadays, three models of DNA intercalation targets have been proposed that account for the binding features of intercalators. Finally, despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. Therefore, a default protocol to identify DNA binding modes which uses a modified canonical DNA as receptor is needed.

Self-assembling doxorubicin-prodrug nanoparticles as siRNA drug delivery system for cancer treatment: in vitro and in vivo

The DOX-prodrug NPs can complex siRNA in pH 3 citrate buffer and have slight negative charges on the surface of NPs in pH 7.4 PBS.

Role of the protein in the DNA sequence specificity of the cleavage site stabilized by the camptothecin topoisomerase IB inhibitor: a metadynamics study

Camptothecin (CPT) is a topoisomerase IB (TopIB) selective inhibitor whose derivatives are currently used in cancer therapy. TopIB cleaves DNA at any sequence, but in the presence of CPT the only stabilized protein–DNA covalent complex is the one having a thymine in position −1 with respect to the cleavage site. A metadynamics simulation of two TopIB–DNA–CPT ternary complexes differing for the presence of a thymine or a cytosine in position −1 indicates the occurrence of two different drug’s unbinding pathways. The free-energy difference between the bound state and the transition state is large when a thymine is present in position −1 and is strongly reduced in presence of a cytosine, in line with the different drug stabilization properties of the two systems. Such a difference is strictly related to the changes in the hydrogen bond network between the protein, the DNA and the drug in the two systems, indicating a direct role of the protein in determining the specificity of the cleavage site sequence stabilized by the CPT. Calculations carried out in presence of one compound of the indenoisoquinoline family (NSC314622) indicate a comparable energy difference between the bound and the transition state independently of the presence of a thymine or a cytosine in position −1, in line with the experimental results.

Free energy profile and mechanism of self-assembly of peptide amphiphiles based on a collective assembly coordinate

By combining targeted molecular dynamics (TMD) simulations, umbrella sampling, and the weighted histogram analysis method (WHAM), we have calculated the potential of mean force (PMF) for the transition between the bound and free states of 90 peptide amphiphiles (PAs) in aqueous solution, with the bound state corresponding to a cylindrical micelle fiber. We specifically consider a collective reaction coordinate, the radius of gyration of the PAs, to describe assembly in this work. It is found that the free energy, enthalpy, and entropy differences between the free and bound states are -126 kcal/mol, -185 kcal/mol, and -190 cal/(mol K), respectively, for the self-assembly process. This indicates that the driving force to form the micelle structure is enthalpic. The enthalpic driving forces originate from several factors, including the conformational energy of PAs and the electrostatic and van der Waals interaction energy between solvent molecules and between solvent and PAs. Among these interactions, the solvent electrostatic interaction is the dominating one, contributing 54% of the total driving force. The PMF profile can be recognized as involving two stages of assembly: (1) PAs initially approach each other in mostly random configurations and loosely aggregate, resulting in significant desolvation and initiation of head-tail conformational reorganization; (2) PAs undergo a conformational disorder-to-order transition, including forming secondary structures that include more β-sheets and fewer random coils, along with tail-head core-shell alignment and condensation that leads to total exclusion of water from the core. The PMF decreases slowly in the first stage, but rapidly in the second. This study demonstrates a hierarchy of assembly steps in which PA structural changes, solvation, and redistribution of solvent molecules play significant roles in the PA self-assembly process.

Drug-DNA intercalation: from discovery to the molecular mechanism

The ability of small molecules to perturb the natural structure and dynamics of nucleic acids is intriguing and has potential applications in cancer therapeutics. Intercalation is a special binding mode where the planar aromatic moiety of a small molecule is inserted between a pair of base pairs, causing structural changes in the DNA and leading to its functional arrest. Enormous progress has been made to understand the nature of the intercalation process since its idealistic conception five decades ago. However, the biological functions were detected even earlier. In this review, we focus mainly on the acridine and anthracycline types of drugs and provide a brief overview of the development in the field through various experimental methods that led to our present understanding of the subject. Subsequently, we discuss the molecular mechanism of the intercalation process, free-energy landscapes, and kinetics that was revealed recently through detailed and rigorous computational studies.

Elucidation of the binding properties of a photosensitizer to salmon sperm DNA and its photobleaching processes by spectroscopic methods

Methylene blue (MB) is a tricyclic heteroaromatic photosensitizer with a promising application in the photodynamic therapy (PDT) for anticancer treatment. The binding properties of MB to salmon sperm DNA have been investigated by the measurements of absorption spectra, quenching experiments and the photobleaching processes. Remarkable hypochromic and bathochromic effects of MB in the presence of increasing amounts of DNA have been observed in the absorption spectra. The quenching of MB by the DNA bases obeys the Stern-Volmer equation and ferrocyanide quenching of MB in the absence and presence of DNA is also measured as extended experiments. Results from the above spectral measurements are all consistent with the intercalative binding mode of MB to DNA with the K b value of 5.6 × 10(3) M(-1). The photobleaching processes of MB and its DNA complex have also been studied, which indicate that the photobleaching of MB and its DNA complex proceed with different mechanisms and the reactive oxygen species are responsible for the self-sensitized photooxidation of MB.

Molecular mechanism of direct proflavine-DNA intercalation: evidence for drug-induced minimum base-stacking penalty pathway

DNA intercalation, a biophysical process of enormous clinical significance, has surprisingly eluded molecular understanding for several decades. With appropriate configurational restraint (to prevent dissociation) in all-atom metadynamics simulations, we capture the free energy surface of direct intercalation from minor groove-bound state for the first time using an anticancer agent proflavine. Mechanism along the minimum free energy path reveals that intercalation happens through a minimum base stacking penalty pathway where nonstacking parameters (Twist→Slide/Shift) change first, followed by base stacking parameters (Buckle/Roll→Rise). This mechanism defies the natural fluctuation hypothesis and provides molecular evidence for the drug-induced cavity formation hypothesis. The thermodynamic origin of the barrier is found to be a combination of entropy and desolvation energy.