Computational metallomics of the anticancer drug cisplatin

Unraveling Copper Exchange in the Atox1-Cu(I)-Mnk1 Heterodimer: A Simulation Approach

Copper, an essential metal for various cellular processes, requires tight regulation to prevent cytotoxicity. Intracellular pathways crucial for maintaining optimal copper levels involve soluble and membrane transporters, namely, metallochaperones and P-type ATPases, respectively. In this study, we used a simulation workflow based on free-energy perturbation (FEP) theory and parallel bias metadynamics (PBMetaD) to predict the Cu(I) exchange mechanism between the human Cu(I) chaperone, Atox1, and one of its two physiological partners, ATP7A. ATP7A, also known as the Menkes disease protein, is a transmembrane protein and one of the main copper-transporting ATPases. It pumps copper into the trans-Golgi network for the maturation of cuproenzymes and is also essential for the efflux of excess copper across the plasma membrane. In this analysis, we utilized the nuclear magnetic resonance (NMR) structure of the Cu(I)-mediated complex between Atox1 and the first soluble domain of the Menkes protein (Mnk1) as a starting point. Independent free-energy simulations were conducted to investigate the dissociation of both Atox1 and Mnk1. The calculations revealed that the two dissociations require free energy values of 6.3 and 6.2 kcal/mol, respectively, following a stepwise dissociation mechanism.

On the mechanism of action of arsenoplatins: arsenoplatin-1 binding to a B-DNA dodecamer

The reaction of Pt-based anticancer agents with arsenic trioxide affords robust complexes known as arsenoplatins. The prototype of this family of anticancer compounds is arsenoplatin-1 (AP-1) that contains an As(OH)2 fragment linked to a Pt(II) moiety derived from cisplatin. Crystallographic and spectrometric studies of AP-1 binding to a B-DNA double helix dodecamer are presented here, in comparison with cisplatin and transplatin. Results reveal that AP-1, cisplatin and transplatin react differently with the DNA model system. Notably, in the AP-1/DNA systems, the Pt-As bond can break down with time and As-containing fragments can be released. These results have implications for the understanding of the mechanism of action of arsenoplatins.

Development of Integrated Bioorthogonal Self-Catalyzed NO Donor/Platinum(IV) Prodrugs for Synergistical Intervention against Triple-Negative Breast Cancer

The platinum(IV) prodrug strategy is attractive for the synergistic antitumor effect. High levels (>400 nM) of nitric oxide (NO) exert promising cancer inhibition effects via multiple mechanisms. Herein, we designed and synthesized a new group of integrated bioorthogonal self-catalyzed NO donor/Pt(IV) prodrugs bearing long alkyl chains to enhance the stability in circulation, while the cytoplasmic reductants trigger cascade activation to release Pt and NO in tumor cells. Specifically, compound 10c exhibited an improved stability, favorable pharmacokinetic properties (AUC(0-t) of 2210.10 h*ng/mL), potent anti-triple-negative breast cancer (TNBC) effects (71.08% tumor growth inhibition (TGI) against the MDA-MB-231 xenograft model), potent in vivo anti-TNBC lung metastasis activity, and acceptable low toxicity. Importantly, NO released from 10c leads to the S-nitrosation of metal transporters Atox1&ATP7a in TNBC cells, which increases the Pt retention and inhibits lysyl oxidase, generating synergistic tumoricidal and antimetastatic activity. These results may inspire further study on the synergistical therapy of Pt and NO for the treatment of TNBC.

Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations

The initial phases of drug discovery - in silico drug design - could benefit from first principle Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations in explicit solvent, yet many applications are currently limited by the short time scales that this approach can cover. Developing scalable first principle QM/MM MD interfaces fully exploiting current exascale machines - so far an unmet and crucial goal - will help overcome this problem, opening the way to the study of the thermodynamics and kinetics of ligand binding to protein with first principle accuracy. Here, taking two relevant case studies involving the interactions of ligands with rather large enzymes, we showcase the use of our recently developed massively scalable Multiscale Modeling in Computational Chemistry (MiMiC) QM/MM framework (currently using DFT to describe the QM region) to investigate reactions and ligand binding in enzymes of pharmacological relevance. We also demonstrate for the first time strong scaling of MiMiC-QM/MM MD simulations with parallel efficiency of ∼70% up to >80,000 cores. Thus, among many others, the MiMiC interface represents a promising candidate toward exascale applications by combining machine learning with statistical mechanics based algorithms tailored for exascale supercomputers.

Predicting 195 Pt NMR Chemical Shifts in Water-Soluble Inorganic/Organometallic Complexes with a Fast and Simple Protocol Combining Semiempirical Modeling and Machine Learning

Water-soluble Pt complexes are the key components in medicinal chemistry and catalysis. The well-known cisplatin family of anticancer drugs and industrial hydrosylilation catalysts are two leading examples. On the molecular level, the activity mechanisms of such complexes mostly involve changes in the Pt coordination sphere. Using ¹⁹⁵ Pt NMR spectroscopy for operando monitoring would be a valuable tool for uncovering the activity mechanisms; however, reliable approaches for the rapid correlation of Pt complex structure with ¹⁹⁵ Pt chemical shifts are very challenging and not available for everyday research practice. While NMR shielding is a response property, molecular 3D structure determines NMR spectra, as widely known, which allows us to build up 3D structure to ¹⁹⁵ Pt chemical shift correlations. Accordingly, we present a new workflow for the determination of lowest-energy configurational/conformational isomers based on the GFN2-xTB semiempirical method and prediction of corresponding chemical shifts with a Machine Learning (ML) model tuned for Pt complexes. The workflow was designed for the prediction of ¹⁹⁵ Pt chemical shifts of water-soluble Pt(II) and Pt(IV) anionic, neutral, and cationic complexes with halide, NO₂ ^- , (di)amino, and (di)carboxylate ligands with chemical shift values ranging from -6293 to 7090 ppm. The model offered an accuracy (normalized root-mean-square deviation/RMSD) of 1.08 %/145.02 ppm on the held-out test set.

Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective

The dissociation rate (k off) associated with ligand unbinding events from proteins is a parameter of fundamental importance in drug design. Here we review recent major advancements in molecular simulation methodologies for the prediction of k off. Next, we discuss the impact of the potential energy function models on the accuracy of calculated k off values. Finally, we provide a perspective from high-performance computing and machine learning which might help improve such predictions.

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.

Frontiers of metal-coordinating drug design

Introduction: The occurrence of metal ions in biomolecules is required to exert vital cellular functions. Metal-containing biomolecules can be modulated by small-molecule inhibitors targeting their metal-moiety. As well, the discovery of cisplatin ushered the rational discovery of metal-containing-drugs. The use of both drug types exploiting metal-ligand interactions is well established to treat distinct pathologies. Therefore, characterizing and leveraging metal-coordinating drugs is a pivotal, yet challenging, part of medicinal chemistry.Area covered: Atomic-level simulations are increasingly employed to overcome the challenges met by traditional drug-discovery approaches and to complement wet-lab experiments in elucidating the mechanisms of drugs' action. Multiscale simulations, allow deciphering the mechanism of metal-binding inhibitors and metallo-containing-drugs, enabling a reliable description of metal-complexes in their biological environment. In this compendium, the authors review selected applications exploiting the metal-ligand interactions by focusing on understanding the mechanism and design of (i) inhibitors targeting iron and zinc-enzymes, and (ii) ruthenium and gold-based anticancer agents targeting the nucleosome and aquaporin protein, respectively.Expert opinion: The showcased applications exemplify the current role and the potential of atomic-level simulations and reveal how their synergic use with experiments can contribute to uncover fundamental mechanistic facets and exploit metal-ligand interactions in medicinal chemistry.

Reactions of cisplatin and cis-[PtI2(NH3)2] with molecular models of relevant protein sidechains: A comparative analysis

Quite surprisingly, cisplatin and cis-[PtI₂(NH₃)₂] were found to manifest significant differences in their reactions with the model protein lysozyme. We decided to explore whether these differences recur when reacting these two Pt compounds with other proteins. Notably, ESI-MS measurements carried out on cytochrome c nicely confirmed the reaction pattern observed for lysozyme. This prompted us to exploit a computational DFT approach to disclose the molecular basis of such behavior. We analyzed comparatively the reactions of cis-[PtCl₂(NH₃)₂] and cis-[PtI₂(NH₃)₂] with appropriate molecular models (Ls) of the sidechains of relevant aminoacids. We found that when Pt(II) complexes are reacted with sulfur ligands both quickly lose their halide ligands and then the resulting cis-[Pt(L)₂(NH₃)₂] species loses ammonia upon reaction with a ligand excess. In the case of imidazole, again cis-[PtCl₂(NH₃)₂] and cis-[PtI₂(NH₃)₂] quickly lose their halide ligands but the resulting cis-[Pt(L)₂(NH₃)₂] species does not lose ammonia by reaction with excess imidazole. These results imply that the two platinum complexes manifest a significantly different behavior in their reaction with representative small molecules in agreement with what observed in the case of model proteins. It follows that the protein itself must play a crucial role in triggering the peculiar reactivity of cis-[PtI₂(NH₃)₂] and in governing the nature of the formed protein adducts. The probable reasons for the observed behavior are critically commented and discussed.

Role of Metastasis-Related Genes in Cisplatin Chemoresistance in Gastric Cancer

The role of metastasis-related genes in cisplatin (CDDP) chemoresistance in gastric cancer is poorly understood. Here, we examined the expression of four metastasis-related genes (namely, c-met, HMGB1, RegIV, PCDHB9) in 39 cases of gastric cancer treated with neoadjuvant therapy with CDDP or CDDP+5-fluorouracil and evaluated its association with CDDP responsiveness. Comparison of CDDP-sensitive cases with CDDP-resistant cases, the expression of c-met, HMGB1, and PCDHB9 was correlated with CDDP resistance. Among them, the expression of HMGB1 showed the most significant correlation with CDDP resistance in multivariate analysis. Treatment of TMK-1 and MKN74 human gastric cancer cell lines with ethyl pyruvate (EP) or tanshinone IIA (TAN), which are reported to inhibit HMGB1 signaling, showed a 4–5-fold increase in inhibition by CDDP. Treatment with EP or TAN also suppressed the expression of TLR4 and MyD88 in the HMGB1 signal transduction pathway and suppressed the activity of NFκB in both cell lines. These results suggest that the expression of these cancer metastasis-related genes is also related to anticancer drug resistance and that suppression of HMGB1 may be particularly useful for CDDP sensitization.

The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin

The composition of the plasma membrane of malignant cells is thought to influence the cellular uptake of cisplatin and to take part in developing resistance to this widespread anti-cancer drug. In this work we study the permeation of cisplatin through the model membranes of normal and cancer cells using molecular dynamics simulations. A special attention is paid to lipid asymmetry and cholesterol content of the membranes. The loss of lipid asymmetry, which is common for cancer cells, leads to a decrease in their permeability to cisplatin by one order of magnitude in comparison to the membranes of normal cells. The change in the cholesterol molar ratio from 0% to 33% also decreases the permeability of the membrane by approximately one order of magnitude. The permeability of pure DOPC membrane is 5-6 orders of magnitude higher than one of the membranes with realistic lipid composition, which makes it as an inadequate model for the studies of drug permeability.

Effect of cisplatin on the transport activity of PII-type ATPases

Cisplatin (cis-diamminedichlorido-Pt(ii)) is extensively used as a chemotherapeutic agent against various types of tumors. However, cisplatin administration causes serious side effects, including nephrotoxicity, ototoxicity and neurotoxicity. It has been shown that cisplatin can interact with P-type ATPases, e.g., Cu⁺-ATPases (ATP7A and ATP7B) and Na⁺,K⁺-ATPase. Cisplatin-induced inhibition of Na⁺,K⁺-ATPase has been related to the nephrotoxic effect of the drug. To investigate the inhibitory effects of cisplatin on the pumping activity of P_II-type ATPases, electrical measurements were performed on sarcoplasmic reticulum Ca²⁺-ATPase (SERCA) and Na⁺,K⁺-ATPase embedded in vesicles/membrane fragments adsorbed on a solid-supported membrane. We found that cisplatin inhibits SERCA and Na⁺,K⁺-ATPase only when administered without a physiological reducing agent (GSH); in contrast, inhibition was also observed in the case of Cu⁺-ATPases in the presence of 1 mM GSH. Our results indicate that cisplatin is a much stronger inhibitor of SERCA (with an IC₅₀ value of 1.3 μM) than of Na⁺,K⁺-ATPase (with an IC₅₀ value of 11.1 μM); moreover, cisplatin inhibition of Na⁺,K⁺-ATPase is reversible, whereas it is irreversible in the case of SERCA. In the absence of a physiological substrate, while Cu⁺-ATPases are able to translocate cisplatin, SERCA and Na⁺,K⁺-ATPase do not perform ATP-dependent cisplatin displacement.

Labile Pd-sulphur and Pt-sulphur bonds in organometallic palladium and platinum complexes [(COD)M(alkyl)(S-ligand)]n+-A speciation study

Reaction of various sulphur ligands L (SEt^-, SPh^-, SC₆F₄H-4^-, SEt₂, StBu₂, SnBu₂, DMSO, DPSO) with the precursors [(COD)M(R)Cl] (COD=1,5-cyclooctadiene, M=Pd or Pt; R=methyl (Me) or benzyl (Bn); DMSO=dimethyl sulfoxide; DPSO=diphenyl sulfoxide) allowed isolation and characterisation of mononuclear neutral (n=0) or cationic (n=1) complexes [(COD)Pt(R)(L)]ⁿ⁺. Reaction of l-cysteine (HCys) with [(COD)Pt(Me)Cl] under similar conditions gave the binuclear cationic complex in [{(COD)Pt(Me)}₂(μ-Cys)]Cl. Detailed NMR spectroscopy and single crystal X-ray diffraction in the case of [(COD)Pt(Me)(SEt₂)][SbF₆] and [(COD)Pt(Me)(DMSO)][SbF₆] reveal markedly labilised Pt-S bonds as a consequence of the highly covalent Pt-C bonds of the R coligands in these organometallic species. Cationic charge (n=1) seems to lower the Pt-S bond strength further. Consequently, most of these complexes are not stable long-term in aqueous DMF (N,N-dimethylformamide) solutions. This made the evaluation of their antiproliferative properties towards HT-29 colon carcinoma and MCF-7 breast adenocarcinoma cell lines impossible. Only the two complexes [(COD)Pt(R)(SC₆F₄H-4)] with R=Me or SC₆F₄H-4 coligands could be tested with the R=Me complex showing promising activity (in the range of cisplatin), while the R=SC₆F₄H-4 derivative is largely inactive, as were the phosphane complexes [(dppe)Pt(SC₆F₄H-4)₂] (dppe=1,2-bis(diphenylphosphino)ethane), cis-[(PPh₃)₂Pt(SC₆F₄H-4)₂] and cis-[(PPh₃)₂PtCl₂] which were tested for comparison. In turn, our findings might pave the way to new Pt anti-cancer drugs with largely reduced unwanted depletion of incorporated drugs and reduced side-effects from binding to S-containing biomolecules.