Ru(ii)-Polypyridyl-1,8-naphthalimide Tröger's bases have undergone detailed biological profiling to unravel their mechanism of cellular uptake, cellular trafficking and cellular responses to photoexcitation.

Correction for 'Time-resolved infra-red studies of photo-excited porphyrins in the presence of nucleic acids and in HeLa tumour cells: insights into binding site and electron transfer dynamics' by Paraic M. Keane et al., Phys. Chem. Chem. Phys., 2022, 24, 27524-27531, https://doi.org/10.1039/D2CP04604K.

Correction for ‘Time-resolved infra-red studies of photo-excited porphyrins in the presence of nucleic acids and in HeLa tumour cells: insights into binding site and electron transfer dynamics’ by Páraic M. Keane et al. , Phys. Chem. Chem. Phys. , 2022, 24 , 27524–27531, https://doi.org/10.1039/D2CP04604K.

Cationic porphyrins based on the 5,10,15,20-meso-(tetrakis-4-N-methylpyridyl) core (TMPyP4) have been studied extensively over many years due to their strong interactions with a variety of nucleic acid structures, and their potential use as photodynamic therapeutic agents and telomerase inhibitors. In this paper, the interactions of metal-free TMPyP4 and Pt(II)TMPyP4 with guanine-containing nucleic acids are studied for the first time using time-resolved infrared spectroscopy (TRIR). In D2O solution (where the metal-free form exists as D2TMPyP4) both compounds yielded similar TRIR spectra (between 1450-1750 cm-1) following pulsed laser excitation in their Soret B-absorption bands. Density functional theory calculations reveal that vibrations centred on the methylpyridinium groups are responsible for the dominant feature at ca. 1640 cm-1. TRIR spectra of D2TMPyP4 or PtTMPyP4 in the presence of guanosine 5'-monophosphate (GMP), double-stranded {d(GC)5}2 or {d(CGCAAATTTGCG)}2 contain negative-going signals, 'bleaches', indicative of binding close to guanine. TRIR signals for D2TMPyP4 or PtTMPyP bound to the quadruplex-forming cMYC sequence {d(TAGGGAGGG)}2T indicate that binding occurs on the stacked guanines. For D2TMPyP4 bound to guanine-containing systems, the TRIR signal at ca. 1640 cm-1 decays on the picosecond timescale, consistent with electron transfer from guanine to the singlet excited state of D2TMPyP4, although IR marker bands for the reduced porphyrin/oxidised guanine were not observed. When PtTMPyP is incorporated into HeLa tumour cells, TRIR studies show protein binding with time-dependent ps/ns changes in the amide absorptions demonstrating TRIR's potential for studying light-activated molecular processes not only with nucleic acids in solution but also in biological cells.

Abstract Clinical data demonstrates increased antigen presentation diversity is an important factor in determining response rates to checkpoint inhibitors. In addition to tumor mutational burden, increased HLA heterozygosity and HLA evolutionary diversity are non-overlapping factors which further diversify the immunopeptidome and improve clinical response to checkpoint therapies. Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an enzyme that trims peptides loaded into classical and nonclassical MHC Class I molecules. Human genome-wide association studies have identified single nucleotide polymorphisms within ERAP1 that are associated with immune-related diseases, such as ankylosing spondylitis, providing human genetic validation for ERAP1's role in human disease and antigen presentation. Further, ablation of mouse ERAAP modifies the immunopeptidome, resulting in improved immunogenicity, generation of CD8+ T cell responses and tumor growth inhibition. Grey Wolf Therapeutics have developed highly potent and selective ERAP1 inhibitors. These inhibitors demonstrate significant modulation of the cancer-related antigen repertoire across diverse ERAP1 and HLA genotypes and cancer-type backgrounds, both in vitro and in vivo. These changes in the antigen repertoire drive changes in T cell activation and response, leading to increased T cell infiltration into CT26 syngeneic tumors and T cell receptor (TCR) diversification when combined with anti-PD-1. We have identified immune related markers that are modulated following ERAP1 inhibition in syngeneic tumor models which have the potential to be used as biomarkers. Importantly, ERAP1 inhibitor induced immunopeptidome and T cell changes lead to significant tumor growth inhibition in syngeneic mouse models when combined with anti-PD-1. In parallel, we have demonstrated the ability of ERAP1 inhibitor induced novel cancer associated antigens to stimulate human CD8+ T cell responses. Extensive assessment of the potential of ERAP1 inhibitors to enhance tumor immune responses in combination with additional therapies (e.g. chemotherapy and radiotherapy), across different tumor microenvironments, is ongoing. These data provide the foundation from which we plan to explore the potential of our first-in-class ERAP1 inhibitor development candidate in the clinic. Citation Format: Andrew Leishman, Fergus Poynton, Nicola Ternette, Elisa Lori, Camila de Almeida, Henry Leonard, Emma Reeves, Edd James, Kristopher Clark, Carmen Tong, Jason Shiers, Martin Quibell, Peter Ian Joyce. First in class inhibitors of ERAP1 have the potential to be a transformative immunotherapy in oncology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1715.

Abstract Immune checkpoint therapy has changed the cancer treatment paradigm, however the majority of patients respond poorly to T cell checkpoint blockade alone. Emerging evidence suggests factors that increase the diversity of the immunopeptidome such as high tumor mutation burden and HLA-I evolutionary divergence (HED), improve clinical response to checkpoint blockade providing an impetus to develop strategies that increase the presentation of cancer associated antigens to the immune system. Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an aminopeptidase that trims peptides loaded into classical and nonclassical MHC molecules. Human genome-wide association studies have identified single nucleotide polymorphisms within ERAP1 that are associated with immune-related diseases, such as ankylosing spondylitis, providing human genetic validation for ERAP1's role in human disease and antigen presentation. Furthermore, in mice, genetic ablation, reduction or pharmacological inhibition of ERAP1 changes the immune repertoire, creating novel antigens with improved immunogenicity that lead to the generation of productive CD8 T cell responses and tumor growth inhibition in various syngeneic models. We have generated and profiled highly potent, species cross reactive and selective ERAP1 inhibitors through a suite of in vitro and in vivo assays to develop these as novel immunotherapy agents. In vitro CETSA measurements show potent cellular target engagement that correlates with in vitro SPR and enzyme potency. Using the model antigen SIINFEKL and Class I MHC expression as key pharmacodynamic measurements, we demonstrate Class I modulation in vitro and in vivo in line with published data from ERAP1 knockout mice. These assays are being used to elucidate the kinetics and temporal dynamics of the antigen change to optimise dosing schedules for in vivo studies. Implementation of our immunopeptidomics pipeline has demonstrated treatment with ERAP1 inhibitors both generate novel antigens in vitro and in vivo and lead to profound and consistent increased overall immunopeptidome length in mouse and human cells. To establish the functional consequence of these changes, we developed a human primary T cell immunogenicity platform. The immunogenic potential of these novel cancer associated antigens has been confirmed by the ability to stimulate IFNγ production in naïve T cells and suggests responses to these antigens could reinvigorate anti-tumor responses. Extensive assessment of mouse and human CD8 T cells responses is ongoing, in order to characterise and select Grey Wolf Therapeutics' first lead ERAP1 inhibitor for use as monotherapy or in combination with other immunotherapies such as checkpoint blockade. Citation Format: Jamie Ware, Patrick McIntyre, Kristopher Clark, Carmen Tong, Jason Shiers, Elisa Lori, Camila de Almeida, Emma Reeves, Henry Leonard, Alihussein Remtulla, Michael Ford, Nicola Ternette, Fergus Poynton, Edd James, Lesley Young, Martin Quibell, Peter I. Joyce. Potent oral ERAP1 inhibitors modify the immunopeptidome in vivo and are novel immunotherapy agents [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5551.

Background Clinical data demonstrates increased antigen presentation diversity is a key factor in determining response rates to checkpoint inhibitors.1 In addition to tumour mutational burden/microsatellite instability, increased HLA heterozygosity and HLA evolutionary diversity are non-overlapping factors recently identified to further diversify the immunopeptidome and improve clinical response to checkpoint therapies.2 3 Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an enzyme that trims peptides loaded into classical and nonclassical class I MHC molecules.4 5 Ablation of mouse ERAAP modifies the immunopeptidome, resulting in improved immunogenicity, generation of CD8 T cell responses and tumor growth inhibition.6 7 Recently identified selective small molecules potently inhibit ERAP1 across key species and haplotypes.8 We report the further profiling of lead candidate ERAP1 inhibitors in human primary T cell in vitro assays and in vivo tumor models in mice. Methods Human cancer cell lines treated with ERAP1 inhibitors in vitro or in vivo in xenograft mouse models were assessed by immunopeptidomics9 to profile peptide repertoire changes. Novel or upregulated peptides were also tested in human immunogenicity assays. FACS analysis of T cells stimulated with Tyrosinase mRNA transfected human dendritic cells ± ERAP1 inhibition was to assess T cell repertoire changes. ERAP1 inhibitor and anti PD-1 mAb combination was assessed in syngeneic mouse tumor models to investigate tumour growth inhibition and PD end-points (e.g. IHC). Results Analysis of human cervical, lung, colorectal and melanoma cell lines carrying distinct HLA haplotypes demonstrates a consistent and profound effect of ERAP1 inhibition on the immunopeptidome. Novel and upregulated cancer associated antigens identified in association with multiple different HLA-A and B alleles stimulate IFNγ production in primary naïve human T cell immunogenicity assays. The impact of ERAP1 inhibition on the T cell repertoire to the melanoma antigen tyrosinase is ongoing. The combination of ERAP1 inhibitor and anti PD-1 mAb led to significant tumor growth inhibition in the CT26 syngeneic mouse tumor model that correlated with increased infiltration of T cells to the tumor. Further PD end-points to be analysed include immune gene array and TCR Vbeta repertoire. Conclusions Grey Wolf ERAP1 inhibitors significantly modify the immunopeptidome both in vitro and in vivo across a broad range of HLA and tumor types. Combination of these inhibitors with anti PD-1 leads to significant T cell infiltration and tumor growth inhibition. Thus, ERAP1 mediated modulation of the immunopeptidome has the potential to drive anti tumor T cell responses and be a transformative immunotherapy. References Rizvi N, Hellmann MD, Snyder A, et al. Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer. Science. 2015;348(6230):124–128. Chowell D, Morris LGT, Grigg CM, et al. Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy. Science 2018;359 (6375):582–587. Chowell D, Krishna C, Pierini F, et al. Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy. Nature Medicine 2019;25(11):1715–1720. Shastri N, Nagarajan N, Lind KC, et al. Monitoring peptide processing for MHC class I molecules in the endoplasmic reticulum. Curr Opin Immunol 2014; 26:123–127. Mpakali A, Maben Z, Stern LJ, et al. Molecular pathways for antigenic peptide generation by ER aminopeptidase 1. Mol Immunol 2018; 13:50–57. James E, Bailey I, Sugiyarto G, et al. Induction of protective antitumor immunity through attenuation of ERAAP function. J Immunol 2013;190(11):5839–5846. Manguso RT, Pope HW, Zimmer MD, et al. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature 2017;547(7664):413–418. Leonard, H Remtulla A, Poynton F, et al. AACR Annual Meeting 2020. Purcell AW, Ramarathinam SH, Ternette N. Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics. Nat Protoc 2019;14(6):1687–1707.

Ruthenium polypyridyl complexes which can sensitise the photo-oxidation of nucleic acids and other biological molecules show potential for photo-therapeutic applications. In this article a combination of transient visible absorption (TrA) and time-resolved infra-red (TRIR) spectroscopy are used to compare the photo-oxidation of guanine by the enantiomers of [Ru(TAP)2(dppz)]2+ in both polymeric {poly(dG-dC), poly(dA-dT) and natural DNA} and small mixed-sequence duplex-forming oligodeoxynucleotides. The products of electron transfer are readily monitored by the appearance of a characteristic TRIR band centred at ca. 1700 cm-1 for the guanine radical cation and a band centered at ca. 515 nm in the TrA for the reduced ruthenium complex. It is found that efficient electron transfer requires that the complex be intercalated at a G-C base-pair containing site. Significantly, changes in the nucleobase vibrations of the TRIR spectra induced by the bound excited state before electron transfer takes place are used to identify preferred intercalation sites in mixed-sequence oligodeoxynucleotides and natural DNA. Interestingly, with natural DNA, while it is found that quenching is inefficient in the picosecond range, a slower electron transfer process occurs, which is not found with the mixed-sequence duplex-forming oligodeoxynucleotides studied.

Ultrafast time-resolved infrared (TRIR) is used to report on the binding site of the [Ru(phen)(2)(dppz)](2+) "light-switch" complex with both bimolecular (Oxytricha nova telomere) and intramolecular (human telomere) guanine-quadruplex structures in both K+ and Na+ containing solutions. TRIR permits the simultaneous monitoring both of the "dark" and "bright" states of the complex and of the quadruplex nucleobase bases, the latter via a Stark effect induced by the excited state of the complex. These data are used to establish the contribution of guanine base stacking and loop interactions to the binding site of this biologically relevant DNA structure in solution. A particularly striking observation is the strong thymine signal observed for the Na+ form of the human telomere sequence, which is expected to be in the anti-parallel conformation.

Nanomedicine is a multidisciplinary research field with an integration of traditional sciences such as chemistry, physics, biology and materials science. The application of nanomedicine for lung diseases as a relatively new area of interdisciplinary science has grown rapidly over the last 10 years. Promising research outcomes suggest that nanomedicine will revolutionise the practice of medicine, through the development of new approaches in therapeutic agent delivery, vaccine development and nanotechnology-based medical detections. Nano-based approaches in the diagnosis and treatment of lung diseases will, in the not too distant future, change the way we practise medicine. This review will focus on the current trends and developments in the clinical translation of nanomedicine for lung diseases, such as in the areas of lung cancer, cystic fibrosis, asthma, bacterial infections and COPD.

Key to the development of DNA-targeting phototherapeutic drugs is determining the interplay between the photoactivity of the drug and its binding preference for a target sequence. For the photooxidising lambda-[Ru(TAP)2(dppz)] 2+ (Ʌ-1) complex bound to either d{T1C2G3G4C5G6C7C8G9A10}2 (G9) or d{TCGGCGCCIA}2 (I9), the Xray crystal structures shows the dppz intercalated at the terminal T1C2;G9A10 step or T1C2;I9A10 step. Thus substitution of the G9 nucleobase by inosine does not affect intercalation in the solid state although with I9 the dppz is more deeply inserted. In solution it is found that the extent of guanine photo-oxidation, and the rate of back electron transfer, as determined by ps and ns time-resolved infrared and transient visible absorption spectroscopy, is enhanced in I9, despite it containing the less oxidisable inosine. This is attributed to the nature of the binding in the minor groove due to the absence of an NH2 group. Similar behaviour and the same binding site in the crystal.are found for d{TTGGCGCCAA}2 (A9), In solution we propose that intercalation occurs at the C2G3;C8I9 or T2G3;C8A9 steps, respectively, with G3 the likely target for photo-oxidation. This demonstrates how changes in the minor groove (in this case removal of an NH2 group) can facilitate binding of Ru(II)dppz complexes and hence influence any sensitised reactions occurring at these sites. No similar enhancement of photooxidation on binding to I9 is found for the delta enantiomer. Introduction Recent studies have shown that inosine is responsible for several important effects in nucleic acid chemistry. For example biological diversity has been linked to posttranscriptional RNA editing which involves the deamination of adenosine to inosine. In double-stranded nucleic acids inosine forms Watson Crick base-pairs with cytosine and can therefore replace guanine. However substitution of a GC base-pair with an IC has been found to influence the thermal stability of DNA in a highly sequence dependent manner and replacing guanosine with inosine is also reported to influence the structural conformation of DNA beyond the local site of substitution. Another conspicuous feature of this process is that, while the groups in the major groove of B-DNA are similar for GC and IC they are quite different in the minor groove. In fact, the minor groove surfaces of I-C and A-T are closely similar (Figure 1). This may have important consequences for the non-covalent binding of drugs and other small molecules and this has been demonstrated for compounds such as the pluramycin family of alkylating compounds, daunomycin, quinoxaline antibiotics and echinomycin. Ruthenium polypyridyl complexes have been shown to be avid binders to DNA with potential applications for imaging and for phototherapeutics. Particularly important amongst these are complexes containing the dipyridophenazine (dppz) ligand, which can intercalate between the base pairs of DNA. Some of these act as DNA ‘light switches’. Others, such as [Ru(TAP)2(dppz)] (1, Figure 1) (TAP = 1,4,5,8-tetraaza-phenanthrene), may photooxidise guanine by one-electron transfer to the photoexcited complex. The TAP ligand can also form covalent adducts with guanine under certain conditions, while 1 and its modified analogues have recently been shown to cause light-induced cytotoxicity against HeLa cancer cells. Understanding the mechanism of photosensitised DNA damage, and therefore developing targeted drug therapies, requires accurate knowledge of where and how the sensitiser is bound in the DNA. In this regard X-ray crystallography can provide critical information about the interactions in the binding site and is increasingly proving very informative in defining the mode and geometry of binding of polypyridyl Ru(II)dppz complexes. This was recently demonstrated for [Ru(TAP)2(dppz)] (-1) where X-ray crystallography of the isosteric -[Ru(phen)2(dppz)] bound to the oligodeoxynucleotides (ODNs) d{CCGGTACCGG}2 or d{CCGGATCCGG}2 proved to be an excellent guide to the preferred binding site and hence the electron transfer properties monitored by transient spectroscopy in solution. In a further important development, we reported the first time-resolved infrared (TRIR) study performed directly in the crystal, where [a] P. M. Keane, J. P. Hall, S. P. Gurung, C. J. Cardin Department of Chemistry, University of Reading, Whiteknights, Reading, RG66AD, UK E-mail: c.j.cardin@reading.ac.uk [b] P. M. Keane, F. E. Poynton, B. C. Poulsen, T. Gunnlaugsson, J. M. Kelly School of Chemistry, Trinity College Dublin, Dublin 2, Ireland E-mail: keanepa@tcd.ie, jmkelly@tcd.ie [c] J. P. Hall, S. P. Gurung Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK [d] F. E. Poynton, B. C. Poulsen, T. Gunnlaugsson Trinity Biomedical Sciences Institute, Pearse St., Dublin 2, Ireland [e] I. P. Clark, I. V. Sazanovich, M. Towrie Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratories, Didcot, Oxfordshire, OX11 0QX, UK [f] S. J. Quinn School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland Email: susan.quinn@ucd.ie Supporting information for this article is given via a link at the end of the document. 10.1002/chem.201701447 Chemistry A European Journal This article is protected by copyright. All rights reserved.

Ruthenium(II) [Ru(II)] polypyridyl complexes have been the focus of intense investigations since work began exploring their supramolecular interactions with DNA. In recent years, there have been considerable efforts to translate this solution-based research into a biological environment with the intention of developing new classes of probes, luminescent imaging agents, therapeutics and theranostics. In only 10 years the field has expanded with diverse applications for these complexes as imaging agents and promising candidates for therapeutics. In light of these efforts this review exclusively focuses on the developments of these complexes in biological systems, both in cells and in vivo, and hopes to communicate to readers the diversity of applications within which these complexes have found use, as well as new insights gained along the way and challenges that researchers in this field still face.

Key to the development of DNA-targeting phototherapeutic drugs is determining the interplay between the photoactivity of the drug and its binding preference for a target sequence. For the photo-oxidising lambda-[Ru(TAP)2 (dppz)]2+ (Λ-1) (dppz=dipyridophenazine) complex bound to either d{T1 C2 G3 G4 C5 G6 C7 C8 G9 A10 }2 (G9) or d{TCGGCGCCIA}2 (I9), the X-ray crystal structures show the dppz intercalated at the terminal T1 C2 ;G9 A10 step or T1 C2 ;I9 A10 step. Thus substitution of the G9 nucleobase by inosine does not affect intercalation in the solid state although with I9 the dppz is more deeply inserted. In solution it is found that the extent of guanine photo-oxidation, and the rate of back electron-transfer, as determined by pico- and nanosecond time-resolved infrared and transient visible absorption spectroscopy, is enhanced in I9, despite it containing the less oxidisable inosine. This is attributed to the nature of the binding in the minor groove due to the absence of an NH2 group. Similar behaviour and the same binding site in the crystal are found for d{TTGGCGCCAA}2 (A9). In solution, we propose that intercalation occurs at the C2 G3 ;C8 I9 or T2 G3 ;C8 A9 steps, respectively, with G3 the likely target for photo-oxidation. This demonstrates how changes in the minor groove (in this case removal of an NH2 group) can facilitate binding of RuII dppz complexes and hence influence any sensitised reactions occurring at these sites. No similar enhancement of photooxidation on binding to I9 is found for the delta enantiomer.

School of Chemistry, Trinity College Dub Ireland. E-mail: jmkelly@tcd.ie Trinity Biomedical Sciences Institute (TBSI) Dublin, Dublin 2, Ireland Department of Chemistry, University of Rea Diamond Light Source, Harwell Science and OX11 0QX, UK Central Laser Facility, Research Complex Laboratory, Oxfordshire, OX11 0QX, UK School of Chemistry, University College Dub The School of Chemical Sciences, Dublin C conor.long@dcu.ie † Electronic supplementary information XRD spectra, spectra (UV-Vis, emission animations of vibrational modes of the CCDC 1038710. For ESI and crystallogr format see DOI: 10.1039/c5sc04514b Cite this: Chem. Sci., 2016, 7, 3075

Strikingly different TRIR spectra are recorded for the complex in D2O or CD3CN or when DNA-bound.