Bioorganic & Medicinal Chemistry最新文献

{"title":"Designing peptide amphiphiles as novel antibacterials and antibiotic adjuvants against gram-negative bacteria","authors":"Huihua Xing ,&nbsp;Vanessa Loya-Perez ,&nbsp;Joshua Franzen ,&nbsp;Paul W. Denton ,&nbsp;Martin Conda-Sheridan ,&nbsp;Nathalia Rodrigues de Almeida","doi":"10.1016/j.bmc.2023.117481","DOIUrl":"10.1016/j.bmc.2023.117481","url":null,"abstract":"<div><p>Gram-negative strains are intrinsically resistant to most antibiotics due to the robust and impermeable characteristic of their outer membrane. Self-assembling cationic peptide amphiphiles (PAs) have the ability to disrupt bacteria membranes, constituting an excellent antibacterial alternative to small molecule drugs that can be used alone or as antibiotic adjuvants to overcome bacteria resistance. PA1 (C₁₆KHKHK), self-assembled into micelles, which exhibited low antibacterial activity against all strains tested, and showed strong synergistic antibacterial activity in combination with Vancomycin with a Fractional Inhibitory Concentration index (FIC<em>i</em>) of 0.15 against <em>E. coli.</em> The molecules, PA2 (C₁₆KRKR) and PA3 (C₁₆<span>AAAKRKR), also self-assembled into micelles, displayed a broad-spectrum antibacterial activity against all strains tested, and low susceptibility to resistance development over 21 days. Finally, PA1, PA 2 and PA3 displayed low cytotoxicity against mammalian cells, and PA2 showed a potent antibacterial activity and low toxicity in preliminary </span><em>in vivo</em> models using <em>G. mellonella</em>. The results show that PAs are a great platform for the future development of effective antibiotics to slow down the antibiotic resistance and can act as antibiotic adjuvants with synergistic mechanism of action, which can be repurposed for use with existing antibiotics commonly used to treat gram-positive bacteria to treat infections caused by gram-negative bacteria.</p></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"94 ","pages":"Article 117481"},"PeriodicalIF":3.5,"publicationDate":"2023-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41093439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selective modifications of lactose and N-acetyllactosamine with sulfate and aromatic bulky groups unveil unique structural insights in galectin-1-ligand recognition","authors":"Mora Massaro ,&nbsp;Alejandro J. Cagnoni ,&nbsp;Francisco J. Medrano ,&nbsp;Juan M. Pérez-Sáez ,&nbsp;Shuay Abdullayev ,&nbsp;Karima Belkhadem ,&nbsp;Karina V. Mariño ,&nbsp;Antonio Romero ,&nbsp;René Roy ,&nbsp;Gabriel A. Rabinovich","doi":"10.1016/j.bmc.2023.117480","DOIUrl":"10.1016/j.bmc.2023.117480","url":null,"abstract":"<div><p><span><span>Galectins, a family of endogenous glycan-binding proteins, play crucial roles in a broad range of physiological and pathological processes. Galectin-1 (Gal-1), a proto-type member of this family, is overexpressed in several cancers and plays critical roles in tumor-immune escape, </span>angiogenesis<span> and metastasis. Thus, generation of high-affinity Gal-1 inhibitors emerges as an attractive therapeutic approach for a wide range of neoplastic conditions. Small-molecule carbohydrate inhibitors based on lactose (Lac) and </span></span><em>N</em><span><span>-acetyllactosamine (LacNAc) structures have been tested showing different results. In this study, we evaluated Lac- and LacNAc-based compounds with specific chemical modifications at key positions as Gal-1 ligands by competitive solid-phase assays (SPA) and isothermal titration calorimetry<span> (ITC). Both assays showed excellent correlation, highlighting that lactosides bearing bulky aromatic groups at the anomeric carbon and sulfate groups at the O3′ position exhibited the highest binding affinities. To dissect the atomistic determinants for preferential affinity of the different tested Gal-1 ligands, </span></span>molecular docking simulations<span> were conducted and PRODIGY-LIG structure-based method was employed to predict binding affinity in protein–ligand complexes. Notably, calculated binding free energies derived from the molecular docking were in accordance with experimental values determined by SPA and ITC, showing excellent correlation between theoretical and experimental approaches. Moreover, this analysis showed that 3′-O-sulfate groups interact with residues of the Gal-1 subsite B, mainly with Asn33, while the ester groups of the aromatic anomeric group interact with Gly69 and Thr70 at Gal-1 subsite E, extending deeper into the pocket, which could account for the enhanced binding affinity. This study contributes to the rational design of highly optimized Gal-1 inhibitors to be further studied in cancer models and other pathologic conditions.</span></span></p></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"94 ","pages":"Article 117480"},"PeriodicalIF":3.5,"publicationDate":"2023-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41091586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of a potent and selective human AC2 inhibitor based on 7-deazapurine analogues of adefovir","authors":"Pavel Kraina ,&nbsp;Michal Česnek ,&nbsp;Eva Tloušťová ,&nbsp;Helena Mertlíková-Kaiserová ,&nbsp;Camryn J. Fulton ,&nbsp;Emily K. Davidson ,&nbsp;Brenton P. Smith ,&nbsp;Val J. Watts ,&nbsp;Zlatko Janeba","doi":"10.1016/j.bmc.2023.117508","DOIUrl":"10.1016/j.bmc.2023.117508","url":null,"abstract":"<div><p>Adefovir based acyclic nucleoside phosphonates were previously shown to modulate bacterial and, to a certain extent, human adenylate cyclases (mACs). In this work, a series of 24 novel 7-substituted 7-deazaadefovir analogues were synthesized in the form of prodrugs. Twelve analogues were single-digit micromolar inhibitors of <em>Bordetella pertussis</em> adenylate cyclase toxin with no cytotoxicity to J774A.1 macrophages. In HEK293 cell-based assays, compound <strong>14</strong> was identified as a potent (IC₅₀ = 4.45 μM), non-toxic, and selective mAC2 inhibitor (vs. mAC1 and mAC5). Such a compound represents a valuable addition to a limited number of small-molecule probes to study the biological functions of individual endogenous mAC isoforms.</p></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"95 ","pages":"Article 117508"},"PeriodicalIF":3.5,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of decoy oligonucleotide-warheaded chimeric molecules targeting STAT3","authors":"Po-Chang Shih ,&nbsp;Miyako Naganuma ,&nbsp;Genichiro Tsuji ,&nbsp;Yosuke Demizu ,&nbsp;Mikihiko Naito","doi":"10.1016/j.bmc.2023.117507","DOIUrl":"10.1016/j.bmc.2023.117507","url":null,"abstract":"<div><p><span><span><span><span>Proteolysis-targeting chimera (PROTAC) technology is a disruptive innovation in the drug<span> development community, and over 20 PROTAC molecules are currently under clinical evaluation. These PROTAC molecules contain small-molecule warheads that bind to target proteins. Recently, oligonucleotide-warheaded PROTACs have emerged as a promising new tool to degrade DNA-binding proteins such as transcription factors. In this study, we applied an oligonucleotide-warheaded PROTAC technology to induce the degradation of </span></span>signal transducer and activator of transcription 3 (STAT3), which is a hard-to-target protein. A double-stranded decoy </span>oligonucleotide<span> specific to STAT3 was conjugated to E3 binders (pomalidomide, VH032, and LCL161) to generate PROTAC molecules that recruited different E3 ubiquitin ligases </span></span>cereblon<span> (CRBN), von Hippel-Lindau (VHL), and inhibitor of apoptosis protein (IAP), respectively. One of the resulting PROTAC molecules, POM-STAT3, which recruits CRBN, potently induces STAT3 degradation. STAT3 degradation by POM-STAT3 was abolished by scrambling the oligonucleotide sequences of POM-STAT3 and by adding a double-stranded decoy oligonucleotide against STAT3 in a competitive manner, suggesting the significance of oligonucleotide sequences in STAT3 degradation. Moreover, POM-STAT3-induced STAT3 degradation was suppressed by the CRBN binder </span></span>thalidomide<span><span>, proteasome inhibitor </span>bortezomib<span>, E1 inhibitor MLN7243, and siRNA-mediated depletion of CRBN, indicating that STAT3 degradation is mediated by the ubiquitin-proteasome system, which involves CRBN as the responsible E3 ubiquitin ligase. Consistent with STAT3 degradation, NCI-H2087 cell viability<span> was severely reduced following POM-STAT3 treatment<span><span>. Thus, POM-STAT3 is a STAT3 degrader that potentially has cytocidal activity against cancer cells that are highly dependent on STAT3 signaling, which implies that inducing protein degradation by decoy oligonucleotide-warheaded PROTAC molecules could be harnessed to be therapeutic against </span>oncogenic transcription factors.</span></span></span></span></p></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"95 ","pages":"Article 117507"},"PeriodicalIF":3.5,"publicationDate":"2023-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expanding the squaramide library as mycobacterial ATP synthase inhibitors: Innovative synthetic pathway and biological evaluation","authors":"Jan Chasák ,&nbsp;Lauren Oorts ,&nbsp;Milan Dak ,&nbsp;Veronika Šlachtová ,&nbsp;Václav Bazgier ,&nbsp;Karel Berka ,&nbsp;Linda De Vooght ,&nbsp;Natalia Smiejkowska ,&nbsp;Kevin Van Calster ,&nbsp;Laurence Van Moll ,&nbsp;Davie Cappoen ,&nbsp;Paul Cos ,&nbsp;Lucie Brulíková","doi":"10.1016/j.bmc.2023.117504","DOIUrl":"10.1016/j.bmc.2023.117504","url":null,"abstract":"<div><p><span><span><span>Mycobacterial ATP synthase is a validated therapeutic target for combating drug-resistant tuberculosis. Inhibition of this </span>enzyme has been featured as an efficient strategy for the development of new </span>antimycobacterial agents<span> against drug-resistant pathogens. In this study, we synthesised and explored two distinct series of </span></span>squaric acid<span><span><span><span><span> analogues designed to inhibit mycobacterial ATP synthase. Among the extensive array of compounds investigated, members of the phenyl-substituted sub-library emerged as primary hits. To gain deeper insights into their mechanisms of action, we conducted advanced biological studies, focusing on the compounds displaying a direct binding of a nitrogen heteroatom to the phenyl ring, resulting in the highest potency. Our investigations into spontaneous mutants led to the validation of a single </span>point mutation within the atpB gene (Rv1304), responsible for encoding the ATP synthase </span>subunit a. This </span>genetic alteration sheds light on the molecular basis of resistance to squaramides. Furthermore, we explored the possibility of synergy between squaramides and the reference </span>drug<span><span> clofazimine using a checkerboard assay, highlighting the promising avenue for enhancing the effectiveness of existing </span>treatments through combined therapeutic approaches. This study contributes to the expansion of investigating squaramides as promising drug candidates in the ongoing battle against drug-resistant tuberculosis.</span></span></p></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"95 ","pages":"Article 117504"},"PeriodicalIF":3.5,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49687414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of structure–activity relationship of indol-3-yl-N-phenylcarbamic amides as potent STING inhibitors","authors":"Po-Wei Chang ,&nbsp;Jing-Ya Wang ,&nbsp;Wan-Ping Wang ,&nbsp;Wei-Cheng Huang ,&nbsp;Mine-Hsine Wu ,&nbsp;Jen-Shin Song ,&nbsp;Liuh-Yow Chen ,&nbsp;Chun-Wei Tung ,&nbsp;Ya-Hui Chi ,&nbsp;Shau-Hua Ueng","doi":"10.1016/j.bmc.2023.117502","DOIUrl":"10.1016/j.bmc.2023.117502","url":null,"abstract":"<div><p>A structure–activity relationship (SAR) study of stimulator of interferon gene (STING) inhibition was performed using a series of indol-3-yl-<em>N</em>-phenylcarbamic amides and indol-2-yl-<em>N</em>-phenylcarbamic amides. Among these analogs, compounds <strong>10</strong>, <strong>13</strong>, <strong>15</strong>, <strong>19</strong>, and <strong>21</strong> inhibited the phosphorylation of STING and interferon regulatory factor 3 (IRF3) to a greater extent than the reference compound, H-151. All five analogs showed stronger STING inhibition than H-151 on the 2′,3′-cyclic GMP-AMP-induced expression of interferon regulatory factors (IRFs) in a STING^R232 knock-in THP-1 reporter cell line. The half-maximal inhibitory concentration of the most potent compound, <strong>21</strong>, was 11.5 nM. The molecular docking analysis of compound <strong>21</strong> and STING combined with the SAR study suggested that the <em>meta</em>- and <em>para</em>-positions of the benzene ring of the phenylcarbamic amide moiety could be structurally modified by introducing halides or alkyl substituents.</p></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"95 ","pages":"Article 117502"},"PeriodicalIF":3.5,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49687413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aryl azoles based scaffolds for disrupting tumor microenvironment","authors":"Alberto Pla-López ,&nbsp;Paula Martínez-Colomina ,&nbsp;Laura Cañada-García ,&nbsp;Laura Fuertes-Monge ,&nbsp;Jose C. Orellana-Palacios ,&nbsp;Alejandro Valderrama-Martínez ,&nbsp;Marikena Pérez-Sosa ,&nbsp;Miguel Carda ,&nbsp;Eva Falomir","doi":"10.1016/j.bmc.2023.117490","DOIUrl":"10.1016/j.bmc.2023.117490","url":null,"abstract":"<div><p><span>Thirty-nine aryl azoles<span>, thirteen triazoles<span> and twenty-seven tetrazoles<span>, have been synthetized and biologically evaluated to determine their activity as tumor microenvironment disruptors. Antiproliferative studies have been performed on </span></span></span></span>tumor cell lines<span> HT-29, A-549 and MCF-7 and on non-tumor cell line HEK-293. It has been studied in HT-29 the expression levels of biological targets which are involved in tumor microenvironment processes, such as PD-L1, CD-47, c-Myc and VEGFR-2. In addition, antiproliferative activity<span><span> was evaluated when HT-29 were co-cultured with THP-1 monocytes and the secretion levels of IL-6 were also determined in these co-cultures. The </span>angiogenesis effect of some selected compounds on HMEC-1 was also evaluated as well as their action against vasculogenic mimicry on HEK-293. Compounds bearing an amino group in the phenyl ring and a halogen atom in the benzyl ring showed promising results as tumor microenvironment disrupting agents. The most outstanding compound decrease dramatically the population of HT-29 cells when co-cultured with THP-1 monocytes and the levels of IL-6 secreted, as well as it showed moderate effects over PD-L1, CD-47 and c-Myc.</span></span></p></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"95 ","pages":"Article 117490"},"PeriodicalIF":3.5,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49672185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design, synthesis and SAR of novel 7-azaindole derivatives as potential Erk5 kinase inhibitor with anticancer activity","authors":"Qin Zhang ,&nbsp;Xintao Gao ,&nbsp;Xiyu Duan ,&nbsp;Han Liang ,&nbsp;Mingyuan Gao ,&nbsp;Dianquan Dong ,&nbsp;Chuanlong Guo ,&nbsp;Longjiang Huang","doi":"10.1016/j.bmc.2023.117503","DOIUrl":"10.1016/j.bmc.2023.117503","url":null,"abstract":"<div><p>The extracellular signal-regulated kinase 5 (Erk5) signaling plays a crucial role in cancer, and regulating its activity may have potential in cancer chemotherapy. In this study, a series of novel 7-azaindole derivatives (<strong>4a-5o</strong>) were designed and synthesized. Their antitumor activities on human lung cancer A549 cells was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, 4′,6-diamidino-2-phenylindole (DAPI) staining and colony formation assay. Among them, compounds <strong>4a, 4 h, 5d</strong> and <strong>5j</strong> exhibited good anti-proliferative activity with the IC₅₀ values of 6.23 µg/mL, 8.52 µg/mL, 7.33 µg/mL and 4.56 µg/mL, respectively, equivalent to Erk5 positive control XMD8-92 (IC₅₀ = 5.36 µg/mL). The results of structure–activity relationships (SAR) showed that double bond on the piperidine ring and <em>N</em> atoms at the <em>N</em>7 position of 7-azaindole was essential for their antiproliferative activity. Furthermore, compounds <strong>4a</strong> and <strong>5j</strong> exhibited good inhibition on Erk5 kinase through Western blot analysis and possible action site of compounds with Erk5 kinase was elucidated by molecular docking.</p></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"95 ","pages":"Article 117503"},"PeriodicalIF":3.5,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49672187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design, synthesis and anticancer activity evaluation of 4-(3-1H-indazolyl)amino quinazoline derivatives as PAK4 inhibitors","authors":"Wei Han ,&nbsp;Yusang Yang ,&nbsp;Fan Yu ,&nbsp;Qianqian Li ,&nbsp;Anyao Liu ,&nbsp;Wenbo Xu ,&nbsp;Jiabin Li ,&nbsp;Xiaowen Xue","doi":"10.1016/j.bmc.2023.117501","DOIUrl":"10.1016/j.bmc.2023.117501","url":null,"abstract":"<div><p>A novel series of 4-(3-1<em>H</em>-indazolyl)amino quinazoline derivatives were developed as PAK4 inhibitors based on a scaffold hopping strategy. Compounds <strong>27e</strong>, <strong>27g</strong>, <strong>27i</strong> and <strong>27j</strong> were found to exhibit potent inhibitory activity against PAK4 (IC₅₀ = 10, 13, 11 and 9 nM, respectively). Subsequent cellular assay demonstrated that compound <strong>27e</strong> possessed the strongest antiproliferative activity against A549 cells with an IC₅₀ value of 0.61 μM, a little bit better than PF-3758309. Further anticancer mechanistic investigation revealed that compound <strong>27e</strong> significantly induced apoptosis of A549 cells in a concentration-dependent manner and blocked the cell cycle at phase G0/G1. A docking model between compound <strong>27e</strong> and PAK4 was proposed to elucidate its possible binding modes. As a promising PAK4 inhibitor, compound <strong>27e</strong> may serve as a candidate for the development of novel PAK4-targeted anticancer drug.</p></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"95 ","pages":"Article 117501"},"PeriodicalIF":3.5,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49672186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel genetically-encoded bicyclic peptide inhibitor of human urokinase-type plasminogen activator with better cross-reactivity toward the murine orthologue","authors":"Ylenia Mazzocato ,&nbsp;Stefano Perin ,&nbsp;Julia Morales-Sanfrutos ,&nbsp;Zhanna Romanyuk ,&nbsp;Stefano Pluda ,&nbsp;Laura Acquasaliente ,&nbsp;Giuseppe Borsato ,&nbsp;Vincenzo De Filippis ,&nbsp;Alessandro Scarso ,&nbsp;Alessandro Angelini","doi":"10.1016/j.bmc.2023.117499","DOIUrl":"10.1016/j.bmc.2023.117499","url":null,"abstract":"<div><p>The inhibition of human urokinase-type plasminogen activator (huPA), a serine protease that plays an important role in pericellular proteolysis, is a promising strategy to decrease the invasive and metastatic activity of tumour cells. However, the generation of selective small molecule huPA inhibitors has proven to be challenging due to the high structural similarity of huPA to other paralogue serine proteases. Efforts to generate more specific therapies have led to the development of cyclic peptide-based inhibitors with much higher selectivity against huPA. While this latter property is desired, the sparing of the orthologue murine poses difficulties for the testing of the inhibitor in preclinical mouse model. In this work, we have applied a Darwinian evolution-based approach to identify phage-encoded bicyclic peptide inhibitors of huPA with better cross-reactivity towards murine uPA (muPA). The best selected bicyclic peptide (UK132) inhibited huPA and muPA with <em>K</em>_i values of 0.33 and 12.58 µM, respectively. The inhibition appears to be specific for uPA, as UK132 only weakly inhibits a panel of structurally similar serine proteases. Removal or substitution of the second loop with one not evolved <em>in vitro</em> led to monocyclic and bicyclic peptide analogues with lower potency than UK132. Moreover, swapping of 1,3,5-<em>tris</em>-(bromomethyl)-benzene with different small molecules not used in the phage selection, resulted in an 80-fold reduction of potency, revealing the important structural role of the branched cyclization linker. Further substitution of an arginine in UK132 to a lysine resulted in a bicyclic peptide UK140 with enhanced inhibitory potency against both huPA (<em>K</em>_i = 0.20 µM) and murine orthologue (<em>K</em>_i = 2.79 µM). By combining good specificity, nanomolar affinity and a low molecular mass, the bicyclic peptide inhibitor developed in this work may provide a novel human and murine cross-reactive lead for the development of a potent and selective anti-metastatic therapy.</p></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"95 ","pages":"Article 117499"},"PeriodicalIF":3.5,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0968089623003474/pdfft?md5=63ef51ad1f70d68d7f0d911ba55a6156&pid=1-s2.0-S0968089623003474-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50160150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}