👤 Lee LC

Biomedical research benefits from the rapid growth and diversity of experimentally detected protein-protein interactions (PPIs) by gaining important biological insights. However, increasingly dense PPI networks can be challenging to interpret and apply. The 2025 update of the Integrated Interactions Database (IID) enhances accessibility and utility through several new features. We identify and incorporate network structural components from co-purified protein sets, as well as curated and predicted complexes, enabling users to explore network organization beyond binary interactions. Functional, pathway, and disease associations of these components can be analyzed, enabling interactions to be grouped into higher-order structures with known or provisional biological roles. Users can now filter interactions by five detection types: pairwise, co-purification, colocalization, proximity, and other evidence. To extend the value and information of predicted interactions, we include interaction interface predictions for 53 647 PPIs, generated using the MEGADOCK docking algorithm, adding molecular detail for structural biology and variant impact studies. Finally, we map PPIs to 15 immune cell types and 12 additional normal tissues, offering tissue-specific views of interaction networks increasingly relevant in disease and immunology research. IID 2025 now includes over 1 million experimentally detected human PPIs, representing an 83% increase from the previous release, alongside expanded non-human networks. The portal remains publicly available at https://ophid.utoronto.ca/iid. Show less

Site-specific bioconjugation techniques are extensively utilized in biological and biomedical fields to precisely label biomolecules with luminescent tags for direct visualization of their intracellular dynamics or with cytotoxic agents for the development of novel anticancer therapeutics. In this work, a series of cyclometalated iridium-(III) polypyridine complexes featuring a thioester moiety was designed as novel phosphorogenic probes for labeling N-terminal cysteine (N-Cys)-containing biomolecules. These thioester complexes were weakly emissive in solutions due to the presence of a low-lying nonradiative distorted triplet intraligand (³IL) state localized on the thioester unit, as elucidated by computational analyses. However, their emission intensities and singlet oxygen (¹O₂)-photosensitization efficiencies substantially increased upon reaction with l-Cys due to the conversion of the quenching thioester moiety to a nonquenching amide unit. Additionally, the thioester complexes exhibited high selectivity toward N-Cys and displayed significantly enhanced reactivity due to the electron-withdrawing iridium-(III) polypyridine moiety. The remarkable aminothiol-induced emission and ¹O₂-photosensitization turn-on of the thioester complexes were exploited for the development of intracellular Cys sensors and Cys-activatable photosensitizers for cancer-targeted photodynamic therapy. Furthermore, one of the thioester complexes was selected to react with various N-Cys-modified tumor-targeting peptides, yielding photofunctional iridium-(III)-peptide conjugates with high ¹O₂ generation efficiencies. These conjugates retained the tumor-targeting capabilities of the original peptides and showed high specificity for MDA-MB-231 cells compared to MCF-7 and HEK-293 cells, resulting in selective photocytotoxicity toward this triple-negative breast cancer cell line. We believe that our design approach will inspire the development of novel luminogenic thioester-based reagents for bioconjugation, bioimaging, and therapeutic applications. Show less

Photoactivatable systems have received considerable attention in the development of diagnostics and therapeutics due to their noninvasive nature and precise spatiotemporal control. Of particular interest is the 3,6-dithio-1,2,4,5-tetrazine (S,S-tetrazine) unit, which can not only act as a photolabile protecting group for constructing photoactivatable systems but also as a bioorthogonal scaffold that enables the inverse electron-demand Diels-Alder (IEDDA) cycloaddition reaction with strained alkynes. In this study, we designed and synthesised a cyclometallated iridium(iii) complex modified with a 3-chloro-6-thio-1,2,4,5-tetrazine moiety (1) for cysteine conjugation. The complex was conjugated with an integrin-targeting peptide c(RGDfC) to afford a tumour-targeting conjugate (1-RGD) for bioimaging and photoactivated therapy. An RGD-free analogue (2) was also prepared for comparison studies. Unlike common iridium(iii) complexes, excitation of conjugate 1-RGD and complex 2 resulted in weak emission and negligible singlet oxygen (¹O₂) generation due to the quenching effect of the tetrazine unit. Upon continuous light irradiation, the S,S-tetrazine moiety in conjugate 1-RGD and complex 2 underwent efficient photodissociation, yielding thiocyanate (3) and amide (4) complexes as photoproducts with increased emission intensities and enhanced ¹O₂ generation efficiencies. Interestingly, the IEDDA cycloaddition reaction of the S,S-tetrazine-containing conjugate 1-RGD and complex 2 with (1R,8S,9s)-bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN-OH) led to significant emission enhancement. Notably, conjugate 1-RGD showed higher cellular uptake and (photo)cytotoxicity (IC_50,dark = 26 μM, IC_50,light = 0.08 μM) in U87-MG cells, which overexpress integrin, compared to MCF-7 (IC_50,dark = 52 μM, IC_50,light = 0.22 μM) and HEK293 cells (IC_50,dark > 50 μM, IC_50,light = 1.3 μM) with lower integrin levels. This work will contribute to the development of photoactivatable transition metal complexes for cancer-targeted imaging and therapy. Show less

In this article, we report a novel targeting strategy involving the combination of an enzyme-instructed self-assembly (EISA) moiety and a strained cycloalkyne to generate large accumulation of bioorthogonal sites in cancer cells. These bioorthogonal sites can serve as activation triggers in different regions for transition metal-based probes, which are new ruthenium(II) complexes carrying a tetrazine unit for controllable phosphorescence and singlet oxygen generation. Importantly, the environment-sensitive emission of the complexes can be further enhanced in the hydrophobic regions offered by the large supramolecular assemblies, which is highly advantageous to biological imaging. Additionally, the (photo)cytotoxicity of the large supramolecular assemblies containing the complexes was investigated, and the results illustrate that cellular localization (extracellular and intracellular) imposes a profound impact on the efficiencies of photosensitizers. Show less

In this work we present the synthesis and characterization of six new ruthenium compounds with general formulae [Ru(L)(dppb)(bipy)]PF₆ and [Ru(L)(dppe)₂]PF₆ where L = salicylic acid (Sal), 4-aminosalicylic acid (AmSal) or 2,4-dihydroxybenzoic acid (DiSal), dppb = 1,4-bis(diphenylphosphino)butane, dppe = 1,2-bis(diphenylphosphino)ethane and bipy = 2,2'-bipyridine. The complexes were characterized by elemental analysis, molar conductivity, cyclic voltammetry, NMR, UV-vis and IR spectroscopies, and two by X-ray crystallography. The ³¹P{¹H} NMR spectra of the complexes with the general formula [Ru(L)(dppe)₂]PF₆ showed that the phosphorus signals are solvent-dependent. Aprotic solvents, which form strong hydrogen bonds with the complexes, inhibit the free rotation of the salicylic acid-based, modifying the diphosphine cone angles, leading to distortion of the phosphorus signals in the NMR spectra. The cytotoxicity of the complexes was evaluated in MCF-7, MDA-MB-231, SKBR3 human breast tumor cells, and MCF-10 non-tumor cell lines. The complexes with the structural formula [Ru(L)(dppe)₂]PF₆ were the most cytotoxic, and the complex [Ru(AmSal)(dppe)₂]PF₆ with L = 4-aminosalicylic acid ligand was the most selective for the MDA-MB-231 cell line. This complex interacts with the transferrin and induces apoptosis through the intrinsic pathway, as demonstrated by increased levels of proteins involved in apoptotic cell death. Show less

Title: Photofunctional cyclometallated iridium(III) polypyridine methylsulfone complexes as sulfhydryl-specific reagents for bioconjugation, bioimaging and photocytotoxic applications. Abstract: We report herein near-infrared (NIR)-emitting cyclometallated iridium(III) complexes bearing a heteroaromatic methylsulfone moiety as sulfhydryl-specific reagents; one of the complexes was conjugated to cysteine and cysteine-containing peptides and proteins for bioimaging and photocytotoxic applications. Show less

Luminescent cyclometallated iridium(III) complexes with a polyhedral oligomeric silsesquioxane (POSS) unit were designed as efficient theranostic agents that displayed tuneable organelle-targeting properties, minimal dark cytotoxicity and substantial photocytotoxicity even under hypoxic conditions. Show less

In this work, we demonstrate bioorthogonal control of the phosphorescence and singlet oxygen photosensitisation properties of new iridium(iii) tetrazine complexes by different reaction partners; the system was exploited for organelle-specific staining and modulated photocytotoxic activity applications. Show less

The triple-negative breast cancer subtype (TNBC) is highly aggressive and metastatic and corresponds to 15-20% of diagnosed cases. TNBC treatment is hampered, because these cells usually do not respond to hormonal therapy, and they develop resistance to chemotherapeutic drugs. On the other hand, the severe side effects of cisplatin represent an obstacle for its clinical use. Ruthenium (Ru)-based complexes have emerged as promising antitumor and antimetastatic substitutes for cisplatin. In this study, we demonstrated the effects of a Ru/biphosphine complex, containing gallic acid (GA) as a ligand, [Ru(GA)(dppe)₂]PF₆, hereafter called Ru(GA), on a TNBC cell line, and compared them to the effects in a nontumor breast cell line. Ru(GA) complex presented selective cytotoxicity against TNBC over nontumor cells, inhibited its migration and invasion, and induced apoptosis. These effects were associated with the increased amount of transferrin receptors (TfR) on tumor cells, compared to nontumor ones. Silencing of TfR decreased Ru(GA) effects on TNBC cells, demonstrating that these receptors were at least partially responsible for Ru(GA) delivery into tumor cells. The Ru(GA) compound must be further studied in different in vivo assays in order to investigate its antitumor properties and its toxicity in complex biological systems. Show less

A novel microwave-assisted synthetic method has been used to synthesise a series of mixed ligand ruthenium(II) compounds containing diimine as well as bidentate thiosemicarbazone ligands. The compounds contain the diimine 1,10-phenanthroline (phen) or 2,2'-bipyridine (bpy) and the thiosemicarbazone is derived from 9-anthraldehyde. Based on elemental analyses and spectroscopic data, the compounds are best formulated as [(phen)(2)Ru(thiosemicarbazone)](PF(6))(2) and [(phen)(2)Ru(thiosemicarbazone)](PF(6))(2) where thiosemicarbazone = 9-anthraldehydethiosemicarbazone, 9-anthraldehyde-N(4)-methylthiosemicarbazone, and 9-anthraldehyde-N(4)-ethylthiosemicarbazone. Fluorescence competition studies with ethidium bromide, along with viscometric measurements suggests that the complexes bind calf thymus DNA (CTDNA) relatively strongly via an intercalative mode possibly involving the aromatic rings of the diimine ligands. The complexes show good cytotoxic profiles against MCF-7 and MDA-MB-231 (breast adenocarcinoma) as well as HCT 116 and HT-29 (colorectal carcinoma) cell lines. Show less