Platinum Binding Sites Research Articles

Abstract 2112: Structural characterization of transmembrane protein TMEM205

Abstract Cisplatin resistance is notorious in leading to therapeutic failure of many solid malignancies. Various resistance mechanisms have been proposed while many more are being added, based on the growing number of resistance-inducing genes identified. TMEM205 is an integral membrane protein with unknown function, but its intracellular level was found markedly elevated in cisplatin resistance cells, the mechanism of which is unknown. Here for the first time we characterized the molecular mechanism of TMEM205-mediated cisplatin resistance through structural and functional studies of TMEM205. The crystal structure of the full-length TMEM205 was obtained at 2.5 Å resolution and shows a 4-helix bundle with a highly hydrophilic tunnel. Strong anomalous signals were observed indicating platinum binding sites. Our structural and functional study of TMEM205 provides novel insight into the complexity of cisplatin resistance. Citation Format: Xiaoyun Bai, Di Xia. Structural characterization of transmembrane protein TMEM205 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2112.

Mass spectrometric studies on the interaction of cisplatin and insulin.

The interaction of antitumor drug, cisplatin (cis-[PtCl2(NH3)2], CDDP) with insulin from porcine pancreas has been investigated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and high resolution hybrid ion trap/time-of-flight mass spectrometry (MALIDI-TOF/TOF-MS and ESI-IT/TOF MS). The MALDI-TOF/TOF-MS results demonstrated that the presence of cisplatin complex resulted in the reduction of the disulfide bond in porcine pancreas after the incubations of the two substances were performed in vitro. It indicated that the presence of cisplatin would destroy the native configuration of insulin, which may lead to the inactivation of insulin. High resolution mass values and the characteristic isotopic pattern of the platinated insulin ions allowed the analysis of platinated mono-, di- and triadducts of cisplatin and insulin in the incubations under different conditions. The laser-induced dissociation of the monoadduct obtained in MALDI source was carried out and one platinum was found to bind to insulin B chain was determined. The platinum binding sites were further identified to be the N terminus (B chain), cysteine 7 (B chain) and cysteine 19 (B chain) residues by electrospray ionization tandem mass spectrometry. The identification of the interaction between insulin and cisplatin broadens the horizon of the knowledge in the interaction of the proteins and metallodrugs.

Prediction of Protein-Ligand Binding Sites for Cisplatin and Transplatin based on Hydrogen Bonds

Platinum compounds are very important to treatment of various malignant tumors. However, prediction of platinum-binding sites is very hard to be made. Nevertheless, hydrolysis of leaving groups bounded to platinum compounds plays an important role in delivering platinum to a target molecule. Herein, a study in silico provides an understanding of the molecular surface in atomic level of three-dimensional structure of cisplatin and transplatin and their binding-sites in order to offer some insights in drug designing. The goal of this work was to implement a new approach based on geometric and physicochemical parameters to find platinum-binding sites using parallel computing algorithms for graphics processing units (GPUs). These algorithms were tested and validated by analysing platinum-binding sites in five known proteins. The results indicated that these binding sites were predicted with significant success. In our analysis HexServer and PatchDock server did not find putative binding-sites for cisplatin and transplatin as we found for the five chosen proteins. Herein, we have shown that the present method have had a better prediction of platinum-binding site than HexServer and PatchDock methods.

Direct determination of the binding sites of cisplatin on insulin-like growth factor-1 by top-down mass spectrometry.

Cisplatin has been widely used in the chemotherapy of a variety of tumors, and the interactions of cisplatin with proteins play very important roles in its side effects and drug resistance, as well as its pharmacokinetics and the biodistribution. Insulin-like growth factor-1 (IGF-1) was found to be associated with the drug resistance of cisplatin. Here, the interaction between cisplatin and IGF-1 was investigated using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. IGF-1-Pt(NH3)Cl was the main mono-adduct and the trans labilization was important to the reaction between IGF-1 and cisplatin, while another special mono-adduct IGF-1-Pt(NH3)Cl2 was observed. The rapid and sensitive top-down mass spectrometry-based approach in linear ion trap mass spectrometer has been developed to identify the binding sites of cisplatin in IGF-1 directly without tedious enzyme digestion. Three binding sites (Met59, Arg56 and Cys6) of cisplatin in IGF-1 were determined. The results not only provide a rapid and efficient way to identify the platinum binding sites in proteins, but also indicate that the binding of cisplatin could promote the fragmentation of IGF-1 and the rupture of disulfide bond.

Mass spectrometric strategies to improve the identification of Pt(II)-modification sites on peptides and proteins.

To further explore the binding chemistry of cisplatin (cis-Pt(NH3)2Cl2) to peptides and also establish mass spectrometry (MS) strategies to quickly assign the platinum-binding sites, a series of peptides with potential cisplatin binding sites (Met(S), His(N), Cys(S), disulfide, carboxyl groups of Asp and Glu, and amine groups of Arg and Lys, were reacted with cisplatin, then analyzed by electron capture dissociation (ECD) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Radical-mediated side-chain losses from the charge-reduced Pt-binding species (such as CH3S(•) or CH3SH from Met, SH(•) from Cys, CO2 from Glu or Asp, and NH2(•) from amine groups) were found to be characteristic indicators for rapid and unambiguous localization of the Pt-binding sites to certain amino acid residues. The method was then successfully applied to interpret the top-down ECD spectrum of an inter-chain Pt-crosslinked insulin dimer, insulin + Pt(NH3)2 + insulin (>10 kDa). In addition, ion mobility MS shows that Pt binds to multiple sites in Substance P, generating multiple conformers, which can be partially localized by collisionally activated dissociation (CAD). Platinum(II) (Pt(II)) was found to coordinate to amine groups of Arg and Lys, but not to disulfide bonds under the conditions used. The coordination of Pt to Arg or Lys appears to arise from the migration of Pt(II) from Met(S) as shown by monitoring the reaction products at different pH values by ECD. No direct binding of cisplatin to amine groups was observed at pH 3 ~ 10 unless Met residues were present in the sequence, but noncovalent interactions between cisplatin hydrolysis and amination [Pt(NH3)4](2+) products and these peptides were found regardless of pH.

Characterization of Pt-protein complexes by nHPLC–ESI-LTQ MS/MS using a gel-based bottom-up approach

The suitability of in-gel digestion for the characterization of Pt-binding proteins by gel-based bottom-up MS approaches has been evaluated regarding the preservation of Pt-protein bonds during the process. Standard proteins (albumin, transferrin, carbonic anhydrase, myoglobin and cytochome c) incubated with cisplatin were separated by nrSDS-PAGE and in-gel trypsin-digested. The whole in-gel digestion protocol included treatment with reagents such as: ammonium bicarbonate, acetonitrile, formic acid, trypsin as enzyme and alternatively, dithiotreitol and iodoacetamide as reducing and alkylating agents. Digests were analyzed by nHPLC–ESI-LTQ-MS/MS and Pt-peptides were recognized in all the proteins studied on the basis of their isotopic pattern. Only when the reducing and alkylating reagents were used, the amount of detectable Pt-peptides decreased due to the high reactivity of thiol containing reagents towards Pt. Furthermore, the repeated use of acetonitrile could lead to the replacement of ligands originally attached to Pt by CN−, but does not affect the Pt-protein binding. Platinum-binding sites on the proteins were elucidated from the CID–MS/MS fragmentation spectra and assessed by evaluation of protein structures. Several histidines, cysteines and methionines were identified as platinum binding sites in the different standard proteins. Results were in accordance to those obtained with in-solution digestions.

The RING heterodimer BRCA1–BARD1 is a ubiquitin ligase inactivated by the platinum-based anticancer drugs

The breast cancer susceptibility protein 1 (BRCA1) participates in the maintenance of cells genomic integrity through DNA repair, cell cycle checkpoint, protein ubiquitination, and transcriptional regulation. The N-terminus of BRCA1 contains a RING domain that preferentially forms a heterodimeric complex with BARD1. The BRCA1-BARD1 RING complex has an E3 ubiquitin ligase activity that plays an essential role in response to DNA damage. Preclinical and clinical studies have recently revealed that structural changes to the heterodimer result in alterations to the BRCA1-mediated DNA repair pathways in cancer cells, and lead to hypersensitivity to several chemotherapeutic agents. It is of interest to approach the BRCA1 RING domain as a potentially molecular target for platinum-based drugs for cancer therapy. A previous study has shown that the anticancer drug cisplatin formed intramolecular and intermolecular BRCA1 adducts in which His117 was the primary platinum-binding site, and conferred conformational changes and induced thermostability. Here, we have studied the functional consequence of the in vitro platination of the BRCA1 RING domain by a number of platinum complexes. The BRCA1 ubiquitin ligase activity was inhibited by transplatin>cisplatin>oxaliplatin>carboplatin in that order. The consequences of the binding of the platinum complexes on the reactivity of the BRCA1 were also discussed. The data raised the possibility of selectively targeting the BRCA1 DNA repair for cancer therapy.

Shape Changes Induced by N-Terminal Platination of Ubiquitin by Cisplatin

The three-dimensional conformation of a protein is an important property and plays a key role in its biological activity. We show here that ion mobility-mass spectrometry (IM-MS) can be used to detect conformational changes in the protein ubiquitin in the gas phase induced by reaction with the anticancer drug cisplatin. The primary adduct was ubiquitin-{Pt(NH(3))(2)} under denaturing conditions. Up to three different conformations appear to be generated upon platination depending on the charge state. The collision cross-sections (Omega) for each conformation indicate that the conformations of the platinated protein are contracted in size compared with unmodified ubiquitin with generally smaller Omega values. Ion mobility-tandem MS allowed determination of the platinum binding site without a requirement for prior chromatographic separation. A rapid 30-min digestion of cisplatin-modified ubiquitin with trypsin allowed the platination site to be identified as the N-terminal methionine following low-energy collision-induced dissociation (CID) studies of the modified peptide. The data were generated using a Traveling-Wave based ion mobility-MS approach. Such cisplatin-induced shape changes may have a significant effect on its function in vivo. This work highlights the usefulness of the ion-mobility mass spectrometry technique for shedding new light on such protein interactions.

Coordination of platinum therapeutic agents to met-rich motifs of human copper transport protein1

Platinum therapeutic agents are widely used in the treatment of several forms of cancer. Various mechanisms for the transport of the drugs have been proposed including passive diffusion across the cellular membrane and active transport via proteins. The copper transport protein Ctr1 is responsible for high affinity copper uptake but has also been implicated in the transport of cisplatin into cells. Human hCtr1 contains two methionine-rich Mets motifs on its extracellular N-terminus that are potential platinum-binding sites: the first one encompasses residues 7-14 with amino acid sequence Met-Gly-Met-Ser-Tyr-Met-Asp-Ser and the second one spans residues 39-46 with sequence Met-Met-Met-Met-Pro-Met-Thr-Phe. In these studies, we use liquid chromatography and mass spectrometry to compare the binding interactions between cisplatin, carboplatin and oxaliplatin with synthetic peptides corresponding to hCtr1 Mets motifs. The interactions of cisplatin and carboplatin with Met-rich motifs that contain three or more methionines result in removal of the carrier ligands of both platinum complexes. In contrast, oxaliplatin retains its cyclohexyldiamine ligand upon platinum coordination to the peptide.

Rapid Cross-Linking of an RNA Internal Loop by the Anticancer Drug Cisplatin

Cisplatin is the most prominent member of a series of platinum(II) antitumor drugs that demonstrate activity based on binding to adjacent purines on genomic DNA. The interactions between cisplatin and alternate biomolecules, including chemically similar RNA, are less understood than are those for DNA. In order to investigate potential implications of platinum(II) drug binding to a structurally complex RNA, we have characterized the reaction between cisplatin and the internal loop of a 41-nucleotide subdomain derived from the U2:U6 spliceosomal RNAs. This "BBD" RNA subdomain consists of a hairpin structure containing a purine-rich asymmetric internal loop. Aquated cisplatin is found to cross-link G nucleobases on opposing sides of the internal loop, forming an intramolecular internal loop cross-link in BBD and an analogous intermolecular cross-link in a two-piece construct containing the same internal loop sequence. The two opposing guanine residues involved in the cross-link were identified via limited alkaline hydrolysis. The kinetics of aquated cisplatin binding to the BBD RNA, a related RNA hairpin, and its DNA hairpin analogue were investigated in an ionic background of 0.1 M NaNO(3) and 1 mM Mg(NO(3))(2). Both BBD and the RNA hairpin react 5-6-fold faster than the DNA hairpin, with calculated second-order rate constants of 2.0(2), 1.7(3), and 0.33(3) M(-1) s(-1), respectively, at 37 degrees C, pH 7.8. MALDI-MS data corroborate the biochemical studies and support a model in which kinetically preferred platinum binding sites compete with less reactive sites in these oligonucleotides. Taken together, these data indicate that cisplatin treatment has potential to create internal loop and other unusual cross-links in structurally complex RNAs, on a time scale that is relevant for RNA-dependent biological processes.

Top-Down Mass Spectrometric Approach for the Full Characterization of Insulin−Cisplatin Adducts

The interaction of the antitumor drug cisplatin with insulin was studied using a top-down mass spectrometric approach. In vitro incubations were prepared under acidic and physiological conditions at different insulin/cisplatin molar ratios for different incubation times. Size exclusion chromatography-inductively coupled plasma mass spectrometry (SEC-ICPMS) analysis enabled the specific detection of platinum containing species attributed to the binding of the drug to the protein. Further analysis through matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and nanoelectrospray ionization mass spectrometry using a linear ion trap (nESI-LIT-MS) allowed the identification of platinated mono-, di-, and even triadducts in the incubations. Platinum binding sites were identified by CID-MS(n) as B chain N-terminus, His5, and probably His10 residues, which turned out to be the same, regardless of the incubation conditions. Evidence on the binding of Pt to B chain Cys7 was also observed. Working with the LIT zoom scan mode provides enough resolution to discern the isotopic pattern for both precursor and fragment ions, allowing the differentiation of platinum-containing ions. The elucidation of platinum binding sites in a native protein through a top-down approach has been performed for the first time with this type of instrument.

DNA cleavage and binding selectivity of a heterodinuclear Pt–Cu(3-Clip-Phen) complex

The synthesis and nuclease activity of a new bifunctional heterodinuclear platinum–copper complex are reported. The design of this ditopic coordination compound is based on the specific mode of action of each component, namely, cisplatin and Cu(3-Clip-Phen), where 3-Clip-Phen is 1-(1,10-phenanthrolin-3-yloxy)-3-(1,10-phenanthrolin-8-yloxy)propan-2-amine. Cisplatin is not only able to direct the Cu(3-Clip-Phen) part to the GG or AG site, but also acts as a kinetically inert DNA anchor. The nuclease activity of this complex has been investigated on supercoiled DNA. The dinuclear compound is not only more active than Cu(3-Clip-Phen), but is also capable of inducing direct double-strand breaks. The sequence selectivity of the mononuclear platinum complex has been investigated by primer extension experiments, which reveal that its interaction with DNA occurs at the same sites as for cisplatin. The Taq polymerase recognizes the resulting DNA damage as different from that for unmodified cisplatin. The sequence-selective cleavage has been investigated by high-resolution gel electrophoresis on a 36-bp DNA fragment. Sequence-selective cleavages are observed in the close proximity of the platinum sites for the strand exhibiting the preferential platinum binding sites. The platinum moiety also coordinates to the other DNA strand, most likely leading only to mono guanine or adenine adducts.Electronic supplementary materialThe online version of this article (doi:10.1007/s00775-008-0346-y) contains supplementary material, which is available to authorized users.

Cisplatin biochemical mechanism of action: from cytotoxicity to induction of cell death through interconnections between apoptotic and necrotic pathways.

Although cisplatin, cis-diamminedichloroplatinum(II), has been successfully used in the chemotherapy of cancer for more than 25 years, its biochemical mechanism of action is still unclear. The current accepted paradigm about cisplatin mechanism of action is that the drug induces its cytotoxic properties through binding to nuclear DNA and subsequent interference with normal transcription, and/or DNA replication mechanisms. If cisplatin-DNA adducts are not efficiently processed by cell machinery, cytotoxic processes eventually end up in cell death. However, before cisplatin enters the cell it may bind to phospholipids and phosphatidylserine in the cell membrane. In addition, in the cytoplasm many potential platinum-binding sites are also available, including RNA and sulfur-containing biomolecules. Moreover, there is much evidence suggesting that the cytotoxic effects induced by binding of cisplatin to non-DNA targets (especially proteins) may contribute to its biochemical mechanism of action. On the other hand, it has been found that several factors such as the dose of drug as well as the metabolic condition of the cell subjected to cisplatin aggression, may determine that cancer cells die through apoptosis or necrosis. In fact, it has recently been reported that both mechanisms of cell demise work in concert so that within a population of tumour cells there is a continuum of possible modes of cell death.

Application of capillary electrophoresis-mass spectrometry for the investigation of the binding behavior of oxaliplatin to 5'-GMP in the presence of the sulfur-containing amino acid L-methionine.

Capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) has been used for investigating the influence of the sulfur containing amino acid L-methionine (L-Met) on the binding behavior of oxaliplatin (trans-R,R-diaminocyclohexane-(oxalato)platinum(II)) to 5'-GMP. L-Methionine competes with 5'-GMP for the platinum binding site and forms as well as 5'-GMP adducts with oxaliplatin. The formation of the prognosed complexes [Pt(DACH)(L-Met-S,N)]+ and [Pt(DACH)(5'-GMP)2]2- (DACH = 1,2-diaminocyclohexane) could be proved directly by using CE-ESI-MS. Furthermore, we could now bring forward proofs, that the coordination of 5'-GMP with oxaliplatin is inhibited by L-methionine and could show, that the 5'-GMP ligands of the [Pt(DACH) (5'-GMP)2]2- complex can be replaced slowly by L-methionine whereas methionine can not be replaced by GMP.

Unrestrained 5 ns molecular dynamics simulation of a cisplatin-DNA 1,2-GG adduct provides a rationale for the NMR features and reveals increased conformational flexibility at the platinum binding site

A 5 ns unrestrained molecular dynamics (MD) simulation of the DNA duplex d(GCCG∗G∗ATCGC)-d(GCGATCCGGC), bearing a cis-Pt(NH 3) 2 2+ unit crosslinking the two G∗ guanine bases, is reported. The MD trajectory was a posteriori correlated with NMR data determined for the same adduct, and it is shown that interproton distances and the characteristic chemical shifts are accounted for by the simulation. The simulation and its confrontation with the NMR data have confirmed the finding derived early from static models that the cytosine complementary to the 5′ G∗, C17, is mobile with respect to its adjacent bases. However, in contrast to our previous description of this mobility, which included rupture of the Watson-Crick hydrogen bonds and formation of non-Watson-Crick hydrogen bonds, the MD simulation indicated that the G∗4-C17 pair moves continuously along a trajectory roughly perpendicular to the local helix axis, with retention of all three Watson-Crick hydrogen bonds. The simulation indicated the reversible formation of a hydrogen bond between the 5′ oriented NH 3 ligand of platinum and the C3pG∗4 phosphate group, in accord with our former prediction. Furthermore, the simulation has disclosed previously undetected BI ⇌ BII transitions at the G∗5pA6 and A6pT7 steps, connected to formation/rupture of a hydrogen bond between the 3′ oriented NH 3 ligand of platinum and the N7 atom of A6. All these conformational equilibria affect the form of the minor groove and increase the conformational flexibility at the platination site, and are thus likely to facilitate recognition by cellular proteins.

X-ray structure of junctional adhesion molecule: structural basis for homophilic adhesion via a novel dimerization motif.

Junctional adhesion molecules (JAMs) are a family of immunoglobulin-like single-span transmembrane molecules that are expressed in endothelial cells, epithelial cells, leukocytes and myocardia. JAM has been suggested to contribute to the adhesive function of tight junctions and to regulate leukocyte trans migration. We describe the crystal structure of the recombinant extracellular part of mouse JAM (rsJAM) at 2.5 A resolution. rsJAM consists of two immunoglobulin-like domains that are connected by a conformationally restrained short linker. Two rsJAM molecules form a U-shaped dimer with highly complementary interactions between the N-terminal domains. Two salt bridges are formed in a complementary manner by a novel dimerization motif, R(V,I,L)E, which is essential for the formation of rsJAM dimers in solution and common to the known members of the JAM family. Based on the crystal packing and studies with mutant rsJAM, we propose a model for homophilic adhesion of JAM. In this model, U-shaped JAM dimers are oriented in cis on the cell surface and form a two-dimensional network by trans-interactions of their N-terminal domains with JAM dimers from an opposite cell surface.

Interaction of cis-diamminedichloroplatinum (II) with single-stranded DNA in the presence or absence of escherichia coli singlestranded binding protein

We have compared the mode of fixation in vitro of the antitumor drug cis-diamminedichloroplatinum (II) ( cis-DDP) to single-stranded M13mp10DNA either in the presence or absence of the Escherichia coli single-stranded binding protein (SSB). Platinum binding sites have been identified by taking advantage of their capacity to inhibit DNA replication of primed M13 DNA catalysed by E. coli DNA polymerase I large fragment. We report here that the presence of SSB increases the number of platinum-DNA lesions and alters their distribution. We also present evidence that SSB allows cis-DDP to bind to DNA sequences otherwise less accessible.

Coordination of 9-methyladenine to [ cis-Pt(NH 3) 2] 2+ and [Pt(dien)] 2+ as studied by proton NMR

Reaction products of 9-methyladenine (mAde) with [Pt(dien)Cl]Cl and cis-Pt(NH 3) 2Cl 2 have been separated using CM-Sephadex C25 cation exchange chromatography. NMR and UV characteristics are presented; the platinum binding sites were established by studying the pH dependence of the 1H-NMR chemical shifts and of UV difference absorption. It is shown that the N 1 atom of the ligand can be protonated in Pt(mAde- N7) adducts, while the N7 atom can be protonated in Pt(mAde- N1).

Ethidium bromide changes the nuclease-sensitive DNA binding sites of the antitumor drug cis-diamminedichloroplatinum(II).

Exonuclease III has been shown previously to reveal the binding sites of the antitumor drug cis-diamminedichloroplatinum(II) on DNA. Pretreatment of the same DNA with the intercalator ethidium bromide causes new platinum binding sites to be detected by the exonuclease III method. In particular, a 5'd(G6-D-G2)3' sequence in a 165-base-pair restriction fragment of plasmid pBR322 becomes a preferred site for exonuclease III-detectable cis-diamminedichloroplatinum(II)binding. This switching of nuclease-sensitive platinum binding to new sites by the influence of another drug, ethidium bromide, offers an explantation at the molecular level for the phenomenon of synergism in combination chemotherapy.

Location of platinum binding sites on bacteriorhodopsin by electron diffraction

A platinum-containing derivative of bacteriorhodopsin has been prepared by treating purple membranes with glycyl-L-methionatoplatinum. Low-dose electron diffraction was used to identify Pt binding sites in the 5.6 A resolution reconstruction of the bacteriorhodopsin unit cell in projection. This is a necessary first step in the use of the Pt derivative for identifying the parts of the amino acid sequence corresponding to the alpha helices in the bacteriorhodopsin structure and for obtaining phases for reflections out to 3.5 A resolution by the method of heavy-atom isomorphous replacement. The largest peak in a Fourier difference map between platinum-labeled and native purple membrane is larger than the spurious features expected to arise from errors in measurements of diffraction intensities.