Blocker-SELEX: a structure-guided strategy for developing inhibitory aptamers disrupting undruggable transcription factor interactions.

Despite the well-established significance of transcription factors (TFs) in pathogenesis, their utilization as pharmacological targets has been limited by the inherent challenges in modulating their protein interactions. The lack of defined small-molecule binding pockets and the nuclear localization of TFs do not favor the use of traditional tools. Aptamers possess large molecular weights, expansive blocking surfaces and efficient cellular internalization, making them compelling tools for modulating TF interactions. Here, we report a structure-guided design strategy called Blocker-SELEX to develop inhibitory aptamers (iAptamers) that selectively block TF interactions. Our approach leads to the discovery of iAptamers that cooperatively disrupt SCAF4/SCAF8-RNAP2 interactions, dysregulating RNAP2-dependent gene expression, which impairs cell proliferation. This approach is further applied to develop iAptamers blocking WDR5-MYC interactions. Overall, our study highlights the potential of iAptamers in disrupting pathogenic TF interactions, implicating their potential utility in studying the biological functions of TF interactions and in nucleic acids drug discovery.

Hydrogen peroxide enhanced photoinactivation of Candida albicans by a novel boron-dipyrromethene (BODIPY) derivative.

Photodynamic inactivation (PDI) has received increasing attention as a promising approach to combat Candida albicans infections. This study aimed to evaluate the synergistic effect of a new BODIPY (4,4-difluoro-boradiazaindacene) derivative and hydrogen peroxide on C. albicans. BDP-4L in combination with H2O2 demonstrated enhanced photokilling efficacy. In suspended cultures of C. albicans, the maximum decrease was 6.20 log and 2.56 log for PDI using BDP-4L (2.5 µM) with or without H2O2, respectively. For mature C. albicans biofilms, 20 µM BDP-4L plus H2O2 eradicated C. albicans, causing an over 6.7 log count reduction in biofilm-associated cells, while only a reduction of ~ 1 log count was observed when H2O2 was omitted. Scanning electron microscopy analysis and LIVE/DEAD assays suggested that PDI using BDP-4L plus H2O2 induced more damage to the cell membrane. Correspondingly, amplification of nucleic acids release was observed in biofilms treated with the combined PDI. Additionally, we also discovered that the addition of hydrogen peroxide potentiated the generation of 1O2 in PDI using the singlet oxygen sensor green probe. Collectively, BDP-4L combined with H2O2 presents a promising approach in the treatment of C. albicans infections.

Antifungal effect of a new photosensitizer derived from BODIPY on Candida albicans biofilms.

BACKGROUND: Photodynamic therapy (PDT) may be an alternative treatment of Candida albicans (C. albicans) infections. The aim of this study was to investigate the antifungal effect of PDT mediated by a new photosensitizer (PS) derived from BODIPY (BDP-4L) on C. albicans biofilms. METHODS: C. albicans biofilms were incubated with BDP-4L of different concentrations and then irradiated at the light doses of 1.8, 3.6, 5.4, 7.2 and 9.0 J/cm2. XTT reduction assay was conducted to determine the PS concentration and PDT parameters. Confocal light scanning microscopy (CLSM) and scanning electron microscope (SEM) were used to visualize and quantify the effect of BDP-4L on C. albicans biofilms after PDT. RESULTS: C. albicans biofilms were inactivated in light dose-dependent and PS concentration-dependent manners using BDP-4L as PS. Without irradiation, no inactivation effect was observed when PS concentrations varied from 5 µM to 80 µM. 40 µM PS with 3.6 J/cm2 irradiation resulted in a significant reduction of 83.8% in biofilm metabolic activities. CLSM assay demonstrated that cell viability was obviously inhibited by 82.6%. SEM images revealed ruptured and rough cell surface, indicating increased cell membrane permeability after PDT. CONCLUSIONS: Our results suggested that BDP-4L mediated PDT exhibited a favorable antifungal effect on C. albicans biofilms.

Discovery of Meso-(meta-Pyridinium) BODIPY Photosensitizers: In Vitro and In Vivo Evaluations for Antimicrobial Photodynamic Therapy.

Antimicrobial photodynamic therapy (aPDT) has emerged as a novel and promising approach for the treatment of pathogenic microorganism infections. The efficacy of aPDT depends greatly on the behavior of the photosensitizer. Herein, we report the design, preparation, antimicrobial photodynamic activities, as well as structure-activity relationships of a series of photosensitizers modified at the meso position of a 1,3,5,7-tetramethyl BODIPY scaffold with various pyridinyl and pyridinium moieties. The photodynamic antimicrobial activities of all photosensitizers have been tested against Staphylococcus aureus, Escherichia coli, Candida albicans, and Methicillin-resistant S. aureus (MRSA). The methyl meso-(meta-pyridinium) BODIPY photosensitizer (3c) possessed the highest phototoxicity against these pathogens at minimal inhibitory concentrations (MIC) ranging from 0.63 to 1.25 µM with a light dose of 81 J/cm2. Furthermore, 3c exhibited an impressive antimicrobial efficacy in S. aureus-infected mice wounds. Taken together, these findings suggest that 3c is a promising candidate as the antimicrobial photosensitizer for combating pathogenic microorganism infections.

Design, Synthesis and Biological Evaluation of Novel 1,2,5-Oxadiazol-3- Carboximidamide Derivatives as Indoleamine 2, 3-Dioxygenase 1 (IDO1) Inhibitors.

BACKGROUND AND OBJECTIVE: Indoleamine-2,3-dioxygenase 1 (IDO1), which catalyzes the degradation of L-tryptophan (L-Trp) to N-formyl kynurenine (NFK) in the first and rate-limiting step of Kynurenine (KYN) pathway has been identified as a promising therapeutic target for cancer immunotherapy. The small molecule Epacadostat developed by Incyte Corp is the most advanced IDO1 inhibitor in clinical trials. METHODS: In this study, various amidine derivatives were individually installed as the polar capping group onto the amino ethylene side chain to replace the sulfamoylamino moiety of Epacadostat to develop novel IDO1 inhibitors. A series of novel 1,2,5-oxadiazol-3-carboximidamide derivatives were designed, prepared, and evaluated for their inhibitory activities against human IDO1 enzyme and cellular IDO1. RESULTS: In vitro human IDO1 enzyme and cellular IDO1 assay results demonstrate that the inhibitory activities of compound 13a and 13b were comparable to Epacadostat, with the enzymatic IC50 values of 49.37nM and 52.12nM and cellular IC50 values of 12.34nM and 14.34nM, respectively. The anti-tumor efficacy of 13b is slightly better than Epacadosta in Lewis Lung Cancer (LLC) tumor-bearing mice model. CONCLUSION: 13b is a potent IDO1 inhibitor with therapeutic potential in tumor immunotherapy.

Anchoring BODIPY photosensitizers enable pan-microbial photoinactivation.

Photodynamic antimicrobial chemotherapy (PACT) is an effective strategy to inactivate pathogenic and resistant microbes. However, pan-microbial photoinactivation has hardly achieved. In this manuscript, we built anti-microbial PSs based on 2,6-diiodo-1,3,5,7-tetramethyl BODIPY (2I-BDP) using anchoring strategy through modifications on boron atom with bis-cationic moieties. With appropriate bis-cationic anchoring, we could achieve effective PACT for pan-microbial photoinactivation via straight forward modifications. Our studies suggested that integration of an efficient photosensitizer, good amphiphilicity, as well as tight interaction with microbial membrane could be essential for effective PACT.

Discovery of novel hydroxyamidine derivatives as indoleamine 2,3-dioxygenase 1 inhibitors with in vivo anti-tumor efficacy.

Indoleamine 2,3-dioxygenase 1 (IDO1) is closely associated with immune escape in many tumor tissues, and is considered to be a valuable therapeutic target in cancer immunotherapy. In this study, the modification of amino sidechain was performed with the hydroxyamidine core kept intact to optimize lead compound Epacadostat. 19 new compounds with hydrazide, thietane or sulfonamide moiety as polar capping group in sidechain were prepared and their IDO1 inhibitory activities were evaluated. Sulfonamide 3a showed potent IDO1 inhibition in both enzymatic and cellular assays with the IC50 value of 71 nM and EC50 value of 11 nM, respectively. Furthermore, in vivo Lewis lung cancer (LLC) allograft studies of 3a indicated that it handicapped the tumor growth with similar efficacy to Epacadostat. Molecular docking demonstrated that the change of polar capping group affords influence on the orientation of amino ethylene side chain and forms new hydrogen bonding.