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Wiedemeyer SJA, Wu G, Pham TLP, Lang-Henkel H, Perez Urzua B, Whisstock JC, Law RHP, Steinmetzer T. Synthesis and Structural Characterization of Macrocyclic Plasmin Inhibitors. ChemMedChem 2023; 18:e202200632. [PMID: 36710259 DOI: 10.1002/cmdc.202200632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023]
Abstract
Two series of macrocyclic plasmin inhibitors with a C-terminal benzylamine group were synthesized. The substitution of the N-terminal phenylsulfonyl group of a previously described inhibitor provided two analogues with sub-nanomolar inhibition constants. Both compounds possess a high selectivity against all other tested trypsin-like serine proteases. Furthermore, a new approach was used to selectively introduce asymmetric linker segments. Two of these compounds inhibit plasmin with Ki values close to 2 nM. For the first time, four crystal structures of these macrocyclic inhibitors could be determined in complex with a Ser195Ala microplasmin mutant. The macrocyclic core segment of the inhibitors binds to the open active site of plasmin without any steric hindrance. This binding mode is incompatible with other trypsin-like serine proteases containing a sterically demanding 99-hairpin loop. The crystal structures obtained experimentally explain the excellent selectivity of this inhibitor type as previously hypothesized.
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Affiliation(s)
- Simon J A Wiedemeyer
- Department of Pharmacy Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Guojie Wu
- Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology, Monash University, Melbourne, 3800, Australia
| | - T L Phuong Pham
- Department of Pharmacy Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Heike Lang-Henkel
- Department of Pharmacy Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Benjamin Perez Urzua
- Department of Cellular and Molecular Biology Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - James C Whisstock
- Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology, Monash University, Melbourne, 3800, Australia
| | - Ruby H P Law
- Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology, Monash University, Melbourne, 3800, Australia
| | - Torsten Steinmetzer
- Department of Pharmacy Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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Verma S, Ravichandiran V, Ranjan N, Flora SJS. Recent Advances in Therapeutic Applications of Bisbenzimidazoles. Med Chem 2021; 16:454-486. [PMID: 31038072 DOI: 10.2174/1573406415666190416120801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/19/2019] [Accepted: 04/08/2019] [Indexed: 12/16/2022]
Abstract
Nitrogen-containing heterocycles are one of the most common structural motifs in approximately 80% of the marketed drugs. Of these, benzimidazoles analogues are known to elicit a wide spectrum of pharmaceutical activities such as anticancer, antibacterial, antiparasitic, antiviral, antifungal as well as chemosensor effect. Based on the benzimidazole core fused heterocyclic compounds, crescent-shaped bisbenzimidazoles were developed which provided an early breakthrough in the sequence-specific DNA recognition. Over the years, a number of functional variations in the bisbenzimidazole core have led to the emergence of their unique properties and established them as versatile ligands against several classes of pathogens. The present review provides an overview of diverse pharmacological activities of the bisbenzimidazole analogues in the past decade with a brief account of its development through the years.
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Affiliation(s)
- Smita Verma
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli, 229010, India.,National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Vishnuvardh Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli, 229010, India
| | - Swaran J S Flora
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli, 229010, India
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Bhaduri S, Ranjan N, Arya DP. An overview of recent advances in duplex DNA recognition by small molecules. Beilstein J Org Chem 2018; 14:1051-1086. [PMID: 29977379 PMCID: PMC6009268 DOI: 10.3762/bjoc.14.93] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
As the carrier of genetic information, the DNA double helix interacts with many natural ligands during the cell cycle, and is amenable to such intervention in diseases such as cancer biogenesis. Proteins bind DNA in a site-specific manner, not only distinguishing between the geometry of the major and minor grooves, but also by making close contacts with individual bases within the local helix architecture. Over the last four decades, much research has been reported on the development of small non-natural ligands as therapeutics to either block, or in some cases, mimic a DNA–protein interaction of interest. This review presents the latest findings in the pursuit of novel synthetic DNA binders. This article provides recent coverage of major strategies (such as groove recognition, intercalation and cross-linking) adopted in the duplex DNA recognition by small molecules, with an emphasis on major works of the past few years.
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Affiliation(s)
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research (NIPER), Raebareli 122003, India
| | - Dev P Arya
- NUBAD, LLC, 900B West Faris Rd., Greenville 29605, SC, USA.,Clemson University, Hunter Laboratory, Clemson 29634, SC, USA
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Sergeev AV, Kirsanova OV, Loiko AG, Nomerotskaya EI, Gromova ES. Detection of DNA Methylation by Dnmt3a Methyltransferase using Methyl-Dependent Restriction Endonucleases. Mol Biol 2018. [DOI: 10.1134/s0026893318020139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Koval VS, Arutyunyan AF, Salyanov VL, Klimova RR, Kushch AA, Rybalkina EY, Susova OY, Zhuze AL. DNA sequence-specific ligands. XVII. Synthesis, spectral properties, virological and biochemical studies of fluorescent dimeric bisbenzimidazoles DBA(n). Bioorg Med Chem 2018; 26:2302-2309. [PMID: 29602675 DOI: 10.1016/j.bmc.2018.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/10/2018] [Indexed: 02/07/2023]
Abstract
A series of DNA minor groove binding fluorescent dimeric bisbenzimidazoles DBA(n) bearing linkers of various length were synthesized and their biochemical and antiviral activities were evaluated. Their antiviral activity was assessed in model cell systems infected with human herpes simplex virus (HSV-1) and cytomegalovirus (CMV). Compounds DBA(1) and DBA(7) demonstrated in vitro inhibitory properties towards HSV-1, and DBA(7) completely blocked the viral infection. Compound DBA(11) displayed the in vitro therapeutic activity towards both HSV-1 and CMV. All of the DBA(n) could fluoresce, were well soluble in water, not cytotoxic to a concentration of 240 µM, penetrated well into cell nuclei by binding to DNA and could inhibit topo-I at low micromolecular concentrations.
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Affiliation(s)
- Vasiliy S Koval
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova St. 32, Moscow 119991, Russia
| | - Albert F Arutyunyan
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova St. 32, Moscow 119991, Russia
| | - Victor L Salyanov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova St. 32, Moscow 119991, Russia
| | - Regina R Klimova
- Ivanovsky Institute of Virology, Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow 123098, Russia
| | - Alla A Kushch
- Ivanovsky Institute of Virology, Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow 123098, Russia
| | - Ekaterina Yu Rybalkina
- Institute of Carcinogenesis, FSBI "N.N. Blokhin National Medical Research Center of Oncology", The Ministry of Health of the Russian Federation, Kashirskoye Av., 24, Moscow, Russia
| | - Olga Yu Susova
- Institute of Carcinogenesis, FSBI "N.N. Blokhin National Medical Research Center of Oncology", The Ministry of Health of the Russian Federation, Kashirskoye Av., 24, Moscow, Russia
| | - Alexei L Zhuze
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova St. 32, Moscow 119991, Russia.
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Kostyuk SV, Kvasha MA, Khrabrova DA, Kirsanova OV, Ershova ES, Malinovskaya EM, Veiko NN, Ivanov AA, Koval VS, Zhuze AL, Tashlitsky VH, Umriukhin PE, Kutsev SI, Gromova ES. Symmetric dimeric bisbenzimidazoles DBP(n) reduce methylation of RARB and PTEN while significantly increase methylation of rRNA genes in MCF-7 cancer cells. PLoS One 2018; 13:e0189826. [PMID: 29329300 PMCID: PMC5766121 DOI: 10.1371/journal.pone.0189826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 12/01/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Hypermethylation is observed in the promoter regions of suppressor genes in the tumor cancer cells. Reactivation of these genes by demethylation of their promoters is a prospective strategy of the anticancer therapy. Previous experiments have shown that symmetric dimeric bisbenzimidazoles DBP(n) are able to block DNA methyltransferase activities. It was also found that DBP(n) produces a moderate effect on the activation of total gene expression in HeLa-TI population containing epigenetically repressed avian sarcoma genome. PRINCIPAL FINDINGS It is shown that DBP(n) are able to penetrate the cellular membranes and accumulate in breast carcinoma cell MCF-7, mainly in the mitochondria and in the nucleus, excluding the nucleolus. The DBP(n) are non-toxic to the cells and have a weak overall demethylation effect on genomic DNA. DBP(n) demethylate the promoter regions of the tumor suppressor genes PTEN and RARB. DBP(n) promotes expression of the genes RARB, PTEN, CDKN2A, RUNX3, Apaf-1 and APC "silent" in the MCF-7 because of the hypermethylation of their promoter regions. Simultaneously with the demethylation of the DNA in the nucleus a significant increase in the methylation level of rRNA genes in the nucleolus was detected. Increased rDNA methylation correlated with a reduction of the rRNA amount in the cells by 20-30%. It is assumed that during DNA methyltransferase activity inhibition by the DBP(n) in the nucleus, the enzyme is sequestered in the nucleolus and provides additional methylation of the rDNA that are not shielded by DBP(n). CONCLUSIONS/SIGNIFICANCE It is concluded that DBP (n) are able to accumulate in the nucleus (excluding the nucleolus area) and in the mitochondria of cancer cells, reducing mitochondrial potential. The DBP (n) induce the demethylation of a cancer cell's genome, including the demethylation of the promoters of tumor suppressor genes. DBP (n) significantly increase the methylation of ribosomal RNA genes in the nucleoli. Therefore the further study of these compounds is needed; it could lead to the creation of new anticancer agents.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Pavel E. Umriukhin
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- P.K. Anokhin Institute of Normal Physiology, Moscow, Russia
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Melkina OE, Koval VS, Ivanov AA, Zhuze AL, Zavilgelsky GB. DNA sequence-specific dimeric bisbenzimidazoles DBP(n) and DBPA(n) as inhibitors of H-NS silencing in bacterial cells. Microbiol Res 2017; 207:75-82. [PMID: 29458871 DOI: 10.1016/j.micres.2017.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/07/2017] [Accepted: 11/12/2017] [Indexed: 11/16/2022]
Abstract
DNA sequence-specific fluorescent dimeric bisbenzimidazoles DBP(n) and DBPA(n), noncovalently interacting with A-T pairs in the minor groove of double-stranded DNA were used for studying and monitoring the expression of histone-like H-NS-dependent promoters. Histone-like H-NS selectively binds to AT-rich segments of DNA and silences a large number of genes in bacterial chromosomes. The H-NS-dependent promoters of Quorum Sensing (QS)-regulated lux operons of the marine bacteria mesophilic Aliivibrio fischeri, psychrophilic Aliivibrio logei were used. Escherichia coli lux biosensors were constructed by cloning fragments bearing QS-regulated promoters into the vector, thereby placing each fragment upstream of the promoterless Photorhabdus luminescens luxCDABE genes. It was shown that the dimeric bisbenzimidazoles DBP(n) and DBPA(n) counteract the H-NS silencing activity. Thus, the presence of DBP(n) or DBPA(n) in the medium leads to an approximately 10-100-fold increase in the level of transcription of QS promoters in E. coli hns+. The largest decrease in the level of H-NS repression was observed using ligands containing a linker with a length of ca. 18Å, such as DBP(2) and DBPA(2). Ligands containing linkers with n=1 and 3 are an order of magnitude less active; ligands with n=4 are inactive. DBPA(2) exhibits activity starting with a concentration of 0.5μM; the minimum concentration of DBP(2) is 5-7 times higher. It is suggested that A-T pairs located at five nucleotide pair intervals, which correspond to the linker length in highly active ligands with n=2, play a key role in the structure of H-NS-binding sites in QS-regulated promoters.
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Affiliation(s)
- Olga E Melkina
- State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), Moscow, 117545, Russia
| | - Vasilii S Koval
- Engelhardt Institute of Molecular Biology, Moscow, 119991, Russia
| | - Alexander A Ivanov
- Emanuel Institute of Biochemical Physics RAS, Kosygin st., 4, Moscow, 119334, Russia
| | - Alexei L Zhuze
- Engelhardt Institute of Molecular Biology, Moscow, 119991, Russia
| | - Gennadii B Zavilgelsky
- State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), Moscow, 117545, Russia.
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Koval VS, Ivanov AA, Salyanov VI, Stomakhin AA, Oleinikov VA, Zhuze AL. DNA sequence-specific ligands: XVI. Series of the DBP(n) fluorescent dimeric bisbenzimidazoles with 1,4-piperazine-containing linkers. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s106816201702008x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fang XJ, Jeyakkumar P, Avula SR, Zhou Q, Zhou CH. Design, synthesis and biological evaluation of 5-fluorouracil-derived benzimidazoles as novel type of potential antimicrobial agents. Bioorg Med Chem Lett 2016; 26:2584-8. [DOI: 10.1016/j.bmcl.2016.04.036] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/31/2016] [Accepted: 04/15/2016] [Indexed: 12/11/2022]
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