1
|
Le D, Akiyama T, Weiss D, Kim M. Dissociation kinetics of small-molecule inhibitors in Escherichia coli is coupled to physiological state of cells. Commun Biol 2023; 6:223. [PMID: 36841892 PMCID: PMC9968327 DOI: 10.1038/s42003-023-04604-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Bioactive small-molecule inhibitors represent a treasure chest for future drugs. In vitro high-throughput screening is a common approach to identify the small-molecule inhibitors that bind tightly to purified targets. Here, we investigate the inhibitor-target binding/unbinding kinetics in E. coli cells using a benzimidazole-derivative DNA inhibitor as a model system. We find that its unbinding rate is not constant but depends on cell growth rate. This dependence is mediated by the cellular activity, forming a feedback loop with the inhibitor's activity. In accordance with this feedback, we find cell-to-cell heterogeneity in inhibitor-target interaction, leading to co-existence of two distinct subpopulations: actively growing cells that dissociate the inhibitors from the targets and non-growing cells that do not. We find similar heterogeneity for other clinical DNA inhibitors. Our studies reveal a mechanism that couples inhibitor-target kinetics to cell physiology and demonstrate the significant effect of this coupling on drug efficacy.
Collapse
Affiliation(s)
- Dai Le
- Department of Physics, Emory University, Atlanta, GA, 30322, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Tatsuya Akiyama
- Department of Physics, Emory University, Atlanta, GA, 30322, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - David Weiss
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
- Antibiotic Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, GA, 30322, USA.
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA.
- Antibiotic Research Center, Emory University, Atlanta, GA, 30322, USA.
| |
Collapse
|
2
|
Poornashree M, Kumar H, Ajmeer R, Jain R, Jain V. Dual role of Nrf2 in cancer: molecular mechanisms, cellular functions and therapeutic interventions. Mol Biol Rep 2023; 50:1871-1883. [PMID: 36513865 DOI: 10.1007/s11033-022-08126-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Nrf2 regulates oxidative stress, which is essential for cellular function. Fundamental initiation of Nrf2 in many malignancies increases prosurvival genes & endorses tumour cell propagation via metabolic reprogramming, suppression of tumour programmed cell death, & increased cancer stem cell self-renewal potential. More specifically, Nrf2 has been associated with cancer cell chemoresistance, radioresistance & inflammation-induced carcinogenesis. METHODS AND RESULTS: Many Nrf2 inhibitors have been revealed for tumour treatment and targeting Nrf2 could be an effective cancer therapeutic method. Before spreading, cancer cells adapt to their surroundings. Cancer cells usually have mutations in tumor suppressor genes. In a variety of malignancies, somatic mutations & other anomalies in the Nrf2 genes, as well as renowned cancer suppressor genes including TP53, CDKN2A, PTEN & PIK3CA, have been found. In tumour cells, somatic mutations in the Nrf2 genes, as well as additional mechanisms that affect Nrf2 binding, and produce aberrant Nrf2 activation. Uncontrolled Nrf2 causes tumour cells to become resistant to antineoplastic drugs & reactive oxygen species (ROS), as well as guiding them toward metabolic reprogramming. CONCLUSIONS: As a result, Nrf2 has been studied as potential malignancy treatment target. We covered the pathways, mechanisms, and dual characteristics of Nrf2 in malignancy in this article. We also discussed how Nrf2 inhibitors are targeted against cancer in this review.
Collapse
Affiliation(s)
- M Poornashree
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, 570015, Mysuru, India
| | - Hitesh Kumar
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, 570015, Mysuru, India
| | - Ramkishan Ajmeer
- Central Drugs Standard Control Organization, East Zone, 700020, Kolkata, West Bengal, India
| | - Rupshee Jain
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, 570015, Mysuru, India
| | - Vikas Jain
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, 570015, Mysuru, India.
| |
Collapse
|
3
|
Wu K, Peng X, Chen M, Li Y, Tang G, Peng J, Peng Y, Cao X. Recent progress of research on anti‐tumor agents using benzimidazole as the structure unit. Chem Biol Drug Des 2022; 99:736-757. [DOI: 10.1111/cbdd.14022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Kaiyue Wu
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Xiaoyu Peng
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Miaojia Chen
- Department of Pharmacy the first People's Hospital Pingjiang Yueyang Hunan China
| | - Yang Li
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Guotao Tang
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Junmei Peng
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Yuanyuan Peng
- School of Electrical and Automation Engineering East China Jiaotong University Nanchang 330000 China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| |
Collapse
|
4
|
Li R, Ma Y, Hu X, Wu W, Wu X, Dong C, Shi S, Lin Y. [Ru(phen) 2podppz] 2+ significantly inhibits glioblastoma growth in vitro and vivo with fewer side-effects than cisplatin. Dalton Trans 2021; 49:8864-8871. [PMID: 32602487 DOI: 10.1039/d0dt01877e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To overcome the acquired resistance and the significant side-effects of the reported drugs, four new ruthenium(ii) complexes with alkynyl (Ru1, Ru2, Ru3, Ru4) were designed and synthesized. Ru1, Ru2, Ru3 and Ru4 were characterized by ESI-MS, 1H NMR, 1H-1H COSY NMR and elemental analysis. Compared with Ru2, Ru3, Ru4 and cisplatin, the anti-tumor experiments in vitro and vivo confirmed that Ru1 could most effectively inhibit tumor growth. In the experiments of safety evaluation in vivo, Ru1 could avoid any detectable side-effects compared with cisplatin. DNA binding experiments and cell cycle experiments showed that Ru1 exhibited the strongest DNA binding ability and interfered with the cell cycle by inserting DNA to inhibit tumor growth. The study demonstrated that Ru1 had the potential to be an exciting new drug candidate for glioblastoma treatment.
Collapse
Affiliation(s)
- Ruihao Li
- Shanghai East Hospital, Shanghai Key Lab of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, 1239 Siping Road, 200092 Shanghai, P. R. China.
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Abstract
The transcription factor NRF2 (nuclear factor erythroid 2-related factor 2) triggers homeostatic responses against a plethora of environmental or endogenous deviations in redox metabolism, inflammation, proteostasis, etc. Therefore, pharmacological activation of NRF2 is a promising therapeutic strategy for several chronic diseases that are underlined by low-grade oxidative inflammation and dysregulation of redox metabolism, such as neurodegenerative, cardiovascular, and metabolic diseases. While NRF2 activation is useful in inhibiting carcinogenesis, its inhibition is needed in constituted tumors where NRF2 provides a survival advantage in the challenging tumor niche. This review describes the electrophilic and non-electrophilic NRF2 activators with clinical projection in various chronic diseases. We also analyze the status of NRF2 inhibitors, which are for the moment in a proof-of-concept stage. Advanced in silico screening and medicinal chemistry are expected to provide new or repurposing small molecules with increased potential for fostering the development of targeted NRF2 modulators. The nuclear factor erythroid 2 (NFE2)-related factor 2 (NRF2) is rapidly degraded by proteasomes under a basal condition in a Keap1-dependent manner. ROS oxidatively modifies Keap1 to release NRF2 and allow its nuclear translocation. Here it binds to the antioxidant response element to regulate gene transcription. An alternative mechanism controlling NRF2 stability is glycogen synthase kinase 3 (GSK-3)-induced phosphorylation. Indicated in blue are NRF2-activating and NRF2-inhibiting drugs.
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Seddek A, Annamalai T, Tse-Dinh YC. Type IA Topoisomerases as Targets for Infectious Disease Treatments. Microorganisms 2021; 9:E86. [PMID: 33401386 PMCID: PMC7823277 DOI: 10.3390/microorganisms9010086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/13/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022] Open
Abstract
Infectious diseases are one of the main causes of death all over the world, with antimicrobial resistance presenting a great challenge. New antibiotics need to be developed to provide therapeutic treatment options, requiring novel drug targets to be identified and pursued. DNA topoisomerases control the topology of DNA via DNA cleavage-rejoining coupled to DNA strand passage. The change in DNA topological features must be controlled in vital processes including DNA replication, transcription, and DNA repair. Type IIA topoisomerases are well established targets for antibiotics. In this review, type IA topoisomerases in bacteria are discussed as potential targets for new antibiotics. In certain bacterial pathogens, topoisomerase I is the only type IA topoisomerase present, which makes it a valuable antibiotic target. This review will summarize recent attempts that have been made to identify inhibitors of bacterial topoisomerase I as potential leads for antibiotics and use of these inhibitors as molecular probes in cellular studies. Crystal structures of inhibitor-enzyme complexes and more in-depth knowledge of their mechanisms of actions will help to establish the structure-activity relationship of potential drug leads and develop potent and selective therapeutics that can aid in combating the drug resistant bacterial infections that threaten public health.
Collapse
Affiliation(s)
- Ahmed Seddek
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
8
|
Howard KC, Dennis EK, Watt DS, Garneau-Tsodikova S. A comprehensive overview of the medicinal chemistry of antifungal drugs: perspectives and promise. Chem Soc Rev 2020; 49:2426-2480. [PMID: 32140691 DOI: 10.1039/c9cs00556k] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The emergence of new fungal pathogens makes the development of new antifungal drugs a medical imperative that in recent years motivates the talents of numerous investigators across the world. Understanding not only the structural families of these drugs but also their biological targets provides a rational means for evaluating the merits and selectivity of new agents for fungal pathogens and normal cells. An equally important aspect of modern antifungal drug development takes a balanced look at the problems of drug potency and drug resistance. The future development of new antifungal agents will rest with those who employ synthetic and semisynthetic methodology as well as natural product isolation to tackle these problems and with those who possess a clear understanding of fungal cell architecture and drug resistance mechanisms. This review endeavors to provide an introduction to a growing and increasingly important literature, including coverage of the new developments in medicinal chemistry since 2015, and also endeavors to spark the curiosity of investigators who might enter this fascinatingly complex fungal landscape.
Collapse
Affiliation(s)
- Kaitlind C Howard
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
| | | | | | | |
Collapse
|
9
|
Gram-negative synergy and mechanism of action of alkynyl bisbenzimidazoles. Sci Rep 2019; 9:14171. [PMID: 31578425 PMCID: PMC6775084 DOI: 10.1038/s41598-019-48898-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/15/2019] [Indexed: 01/08/2023] Open
Abstract
Bisbenzimidazoles with terminal alkynyl linkers, selective inhibitors of bacterial topoisomerase I, have been evaluated using bacterial cytological profiling (BCP) to ascertain their mechanism of action and screened for synergism to improve Gram-negative bacterial coverage. Principal component analysis of high throughput fluorescence images suggests a dual-mechanism of action affecting DNA synthesis and cell membrane integrity. Fluorescence microscopy of bacteria challenged with two of the alkynyl-benzimidazoles revealed changes in the cellular ultrastructure that differed from topoisomerase II inhibitors including induction of spheroplasts and membrane lysis. The cytoskeleton recruitment enzyme inhibitor A22 in combination with one of the alkynyl-benzimidazoles was synergistic against Acinetobacter baumannii and Escherichia coli. Gram-positive coverage remained unchanged in the A22-alkynyl bisbenzimidazole combination. Efflux inhibitors were not synergistic, suggesting that the Gram-negative outer membrane was a significant barrier for alkynyl-bisbenzimidazole uptake. Time-kill assays demonstrated the A22-bisbenzimidazole combination had a similar growth inhibition curve to that of norfloxacin in E.coli. Bisbenzimidazoles with terminal alkynyl linkers likely impede bacterial growth by compromising cell membrane integrity and by interfering with DNA synthesis against Gram-positive pathogens and in the synergistic combination against Gram-negative pathogens including E. coli and multidrug-resistant A. baumanii.
Collapse
|
10
|
Yi L, Lü X. New Strategy on Antimicrobial-resistance: Inhibitors of DNA Replication Enzymes. Curr Med Chem 2019; 26:1761-1787. [PMID: 29110590 DOI: 10.2174/0929867324666171106160326] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/31/2017] [Accepted: 10/30/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Antimicrobial resistance is found in all microorganisms and has become one of the biggest threats to global health. New antimicrobials with different action mechanisms are effective weapons to fight against antibiotic-resistance. OBJECTIVE This review aims to find potential drugs which can be further developed into clinic practice and provide clues for developing more effective antimicrobials. METHODS DNA replication universally exists in all living organisms and is a complicated process in which multiple enzymes are involved in. Enzymes in bacterial DNA replication of initiation and elongation phases bring abundant targets for antimicrobial development as they are conserved and indispensable. In this review, enzyme inhibitors of DNA helicase, DNA primase, topoisomerases, DNA polymerase and DNA ligase were discussed. Special attentions were paid to structures, activities and action modes of these enzyme inhibitors. RESULTS Among these enzymes, type II topoisomerase is the most validated target with abundant inhibitors. For type II topoisomerase inhibitors (excluding quinolones), NBTIs and benzimidazole urea derivatives are the most promising inhibitors because of their good antimicrobial activity and physicochemical properties. Simultaneously, DNA gyrase targeted drugs are particularly attractive in the treatment of tuberculosis as DNA gyrase is the sole type II topoisomerase in Mycobacterium tuberculosis. Relatively, exploitation of antimicrobial inhibitors of the other DNA replication enzymes are primeval, in which inhibitors of topo III are even blank so far. CONCLUSION This review demonstrates that inhibitors of DNA replication enzymes are abundant, diverse and promising, many of which can be developed into antimicrobials to deal with antibioticresistance.
Collapse
Affiliation(s)
- Lanhua Yi
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| |
Collapse
|
11
|
Activators and Inhibitors of NRF2: A Review of Their Potential for Clinical Development. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:9372182. [PMID: 31396308 PMCID: PMC6664516 DOI: 10.1155/2019/9372182] [Citation(s) in RCA: 344] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/26/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023]
Abstract
The transcription factor NRF2 (nuclear factor erythroid 2-related factor 2) triggers the first line of homeostatic responses against a plethora of environmental or endogenous deviations in redox metabolism, proteostasis, inflammation, etc. Therefore, pharmacological activation of NRF2 is a promising therapeutic approach for several chronic diseases that are underlined by oxidative stress and inflammation, such as neurodegenerative, cardiovascular, and metabolic diseases. A particular case is cancer, where NRF2 confers a survival advantage to constituted tumors, and therefore, NRF2 inhibition is desired. This review describes the electrophilic and nonelectrophilic NRF2 activators with clinical projection in various chronic diseases. We also analyze the status of NRF2 inhibitors, which at this time provide proof of concept for blocking NRF2 activity in cancer therapy.
Collapse
|
12
|
Guo L, Wang H, Wang Y, Feng L. Facile core–shell nanoparticles with controllable antibacterial activity assembled by chemical and biological molecules. Biomater Sci 2019; 7:5528-5534. [DOI: 10.1039/c9bm01367a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A newly switchable antibacterial self-assembly was developed by conjugated polymer nanoparticles, DNA, Hoechst 33258 and deoxyribonuclease I.
Collapse
Affiliation(s)
- Lixia Guo
- School of Chemistry and Chemical Engineering
- Shanxi University
- Taiyuan
- P.R. China
| | - Haoping Wang
- School of Chemistry and Chemical Engineering
- Shanxi University
- Taiyuan
- P.R. China
| | - Yunxia Wang
- School of Chemistry and Chemical Engineering
- Shanxi University
- Taiyuan
- P.R. China
| | - Liheng Feng
- School of Chemistry and Chemical Engineering
- Shanxi University
- Taiyuan
- P.R. China
| |
Collapse
|
13
|
Cuadrado A, Manda G, Hassan A, Alcaraz MJ, Barbas C, Daiber A, Ghezzi P, León R, López MG, Oliva B, Pajares M, Rojo AI, Robledinos-Antón N, Valverde AM, Guney E, Schmidt HHHW. Transcription Factor NRF2 as a Therapeutic Target for Chronic Diseases: A Systems Medicine Approach. Pharmacol Rev 2018; 70:348-383. [DOI: 10.1124/pr.117.014753] [Citation(s) in RCA: 329] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
|
14
|
Chandrika NT, Shrestha SK, Ranjan N, Sharma A, Arya DP, Garneau-Tsodikova S. New Application of Neomycin B-Bisbenzimidazole Hybrids as Antifungal Agents. ACS Infect Dis 2018; 4:196-207. [PMID: 29227087 PMCID: PMC5971066 DOI: 10.1021/acsinfecdis.7b00254] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alkylated aminoglycosides and bisbenzimidazoles have previously been shown to individually display antifungal activity. Herein, we explore for the first time the antifungal activity (in liquid cultures and in biofilms) of ten alkylated aminoglycosides covalently linked to either mono- or bisbenzimidazoles. We also investigate their toxicity against mammalian cells, their hemolytic activity, and their potential mechanism(s) of action (inhibition of fungal ergosterol biosynthetic pathway and/or reactive oxygen species (ROS) production). Overall, many of our hybrids exhibited broad-spectrum antifungal activity. We also found them to be less cytotoxic to mammalian cells and less hemolytic than the FDA-approved antifungal agents amphotericin B and voriconazole, respectively. Finally, we show with our best derivative (8) that the mechanism of action of our compounds is not the inhibition of ergosterol biosynthesis, but that it involves ROS production in yeast cells.
Collapse
Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sanjib K. Shrestha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Nihar Ranjan
- Department of Chemistry, Clemson University, 219 Hunter Laboratories, Clemson, South Carolina 29634, United States
| | - Anindra Sharma
- Department of Chemistry, Clemson University, 219 Hunter Laboratories, Clemson, South Carolina 29634, United States
| | - Dev P. Arya
- Department of Chemistry, Clemson University, 219 Hunter Laboratories, Clemson, South Carolina 29634, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| |
Collapse
|
15
|
Ranjan N, Kellish P, King A, Arya DP. Impact of Linker Length and Composition on Fragment Binding and Cell Permeation: Story of a Bisbenzimidazole Dye Fragment. Biochemistry 2017; 56:6434-6447. [PMID: 29131946 DOI: 10.1021/acs.biochem.7b00929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Small molecules that modulate biological functions are targets of modern day drug discovery efforts. In a common platform fragment-based drug discovery, two fragments that bind to adjacent sites on a target are identified and are then linked together using different linkers to identify the linkage for optimum activity. What are not known from these studies are the effects these linkers, which typically contain C, H, and O atoms, have on the properties of the individual fragment. Herein, we investigate such effects in a bisbenzimidazole fragment whose derivatives have a wide range of therapeutic applications in nucleic acid recognition, sensing, and photodynamic therapy and as cellular probes. We report a dramatic effect of linker length and composition of alkynyl (clickable) Hoechst 33258 derivatives in target binding and cell uptake. We show that the binding of Hoechst 33258-modeled bisbenzimidazoles (1-9) that contain linkers of varying lengths (3-21 atoms) display length- and composition-dependent variation in B-DNA stabilization using a variety of spectroscopic methods. For a dodecamer DNA duplex, the thermal stabilization varied from 0.3 to 9.0 °C as the linker length increased from 3 to 21 atoms, respectively. Compounds with linker lengths of ≤11 atoms (such as compounds 1 and 5) are localized in the nucleus, while compounds with long linkers (such as compounds 8 and 9) are distributed in the extranuclear space, as well, with possible interactions with extranuclear targets. These findings provide insights into future drug design by revealing how linkers can influence the biophysical and cellular properties of individual drug fragments.
Collapse
Affiliation(s)
- Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
| | - Patrick Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
| | - Ada King
- NUBAD LLC , 900 B West Faris Road, Greenville, South Carolina 29605, United States
| | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States.,NUBAD LLC , 900 B West Faris Road, Greenville, South Carolina 29605, United States
| |
Collapse
|
16
|
Ranjan N, Story S, Fulcrand G, Leng F, Ahmad M, King A, Sur S, Wang W, Tse-Dinh YC, Arya DP. Selective Inhibition of Escherichia coli RNA and DNA Topoisomerase I by Hoechst 33258 Derived Mono- and Bisbenzimidazoles. J Med Chem 2017; 60:4904-4922. [DOI: 10.1021/acs.jmedchem.7b00191] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Nihar Ranjan
- Laboratory
of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Sandra Story
- NUBAD LLC, 900B West Faris
Road, Greenville, South Carolina 29605, United States
| | - Geraldine Fulcrand
- Department
of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular
Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department
of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular
Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Muzammil Ahmad
- Genome
Instability and Chromatin Remodeling Section, Lab of Genetics, National
Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, United States
| | - Ada King
- NUBAD LLC, 900B West Faris
Road, Greenville, South Carolina 29605, United States
| | - Souvik Sur
- Laboratory
of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Weidong Wang
- Genome
Instability and Chromatin Remodeling Section, Lab of Genetics, National
Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, United States
| | - Yuk-Ching Tse-Dinh
- Department
of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular
Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Dev P. Arya
- Laboratory
of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
- NUBAD LLC, 900B West Faris
Road, Greenville, South Carolina 29605, United States
| |
Collapse
|
17
|
Zhang ZH, Chen Y, Yan XJ, Sun Y, Yang XM, Cai XY, You S. Synthesis and evaluation of novel urea and amide derivatives of 2-amino-4-phenylthiazole as potential antibacterial agents. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1910-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
18
|
DNA topoisomerase I and DNA gyrase as targets for TB therapy. Drug Discov Today 2017; 22:510-518. [DOI: 10.1016/j.drudis.2016.11.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 11/20/2022]
|
19
|
Ranjan N, Arya DP. Linker dependent intercalation of bisbenzimidazole-aminosugars in an RNA duplex; selectivity in RNA vs. DNA binding. Bioorg Med Chem Lett 2016; 26:5989-5994. [PMID: 27884695 PMCID: PMC6201841 DOI: 10.1016/j.bmcl.2016.10.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 01/08/2023]
Abstract
Neomycin and Hoechst 33258 are two well-known nucleic acid binders that interact with RNA and DNA duplexes with high affinities respectively. In this manuscript, we report that covalent attachment of bisbenzimidazole unit derived from Hoechst 33258 to neomycin leads to intercalative binding of the bisbenzimidazole unit (oriented at 64-74° with respected to the RNA helical axis) in a linker length dependent manner. The dual binding and intercalation of conjugates were supported by thermal denaturation, CD, LD and UV-Vis absorption experiments. These studies highlight the importance of linker length in dual recognition by conjugates, for effective RNA recognition, which can lead to novel ways of recognizing RNA structures. Additionally, the ligand library screens also identify DNA and RNA selective compounds, with compound 9, containing a long linker, showing a 20.3°C change in RNA duplex Tm with only a 13.0°C change in Tm for the corresponding DNA duplex. Significantly, the shorter linker in compound 3 shows almost the reverse trend, a 23.8°C change in DNA Tm, with only a 9.1°C change in Tm for the corresponding RNA duplex.
Collapse
Affiliation(s)
- Nihar Ranjan
- Laboratory of Bioorganic and Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States
| | - Dev P Arya
- Laboratory of Bioorganic and Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States.
| |
Collapse
|
20
|
Synthesis and investigation of novel benzimidazole derivatives as antifungal agents. Bioorg Med Chem 2016; 24:3680-6. [PMID: 27301676 DOI: 10.1016/j.bmc.2016.06.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 01/02/2023]
Abstract
The rise and emergence of resistance to antifungal drugs by diverse pathogenic fungal strains have resulted in an increase in demand for new antifungal agents. Various heterocyclic scaffolds with different mechanisms of action against fungi have been investigated in the past. Herein, we report the synthesis and antifungal activities of 18 alkylated mono-, bis-, and trisbenzimidazole derivatives, their toxicities against mammalian cells, as well as their ability to induce reactive oxygen species (ROS) in yeast cells. Many of our bisbenzimidazole compounds exhibited moderate to excellent antifungal activities against all tested fungal strains, with MIC values ranging from 15.6 to 0.975μg/mL. The fungal activity profiles of our bisbenzimidazoles were found to be dependent on alkyl chain length. Our most potent compounds were found to display equal or superior antifungal activity when compared to the currently used agents amphotericin B, fluconazole, itraconazole, posaconazole, and voriconazole against many of the strains tested.
Collapse
|
21
|
Targeting bacterial topoisomerase I to meet the challenge of finding new antibiotics. Future Med Chem 2016; 7:459-71. [PMID: 25875873 DOI: 10.4155/fmc.14.157] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Resistance of bacterial pathogens to current antibiotics has grown to be an urgent crisis. Approaches to overcome this challenge include identification of novel targets for discovery of new antibiotics. Bacterial topoisomerase I is present in all bacterial pathogens as a potential target for bactericidal topoisomerase poison inhibitors. Recent efforts have identified inhibitors of bacterial topoisomerase I with antibacterial activity. Additional research on the mode of action and binding site of these inhibitors would provide further validation of the target and establish that bacterial topoisomerase I is druggable. Bacterial topoisomerase I is a potentially high value target for discovery of new antibiotics. Demonstration of topoisomerase I as the cellular target of an antibacterial compound would provide proof-of-concept validation.
Collapse
|
22
|
Nahar S, Ranjan N, Ray A, Arya DP, Maiti S. Potent inhibition of miR-27a by neomycin-bisbenzimidazole conjugates. Chem Sci 2015; 6:5837-5846. [PMID: 29861909 PMCID: PMC5947510 DOI: 10.1039/c5sc01969a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/07/2015] [Indexed: 12/27/2022] Open
Abstract
miRNAs are important components of regulatory networks that control gene expression and have implications in various diseases including cancer. Targeting oncogenic miRNAs with small molecules is currently being explored to develop cancer therapeutics. Here, we report the development of dual binding neomycin-bisbenzimidazole conjugates that target oncogenic miR-27a with high affinity (Ka = 1.2 to 7.4 × 108 M-1). These conjugates bring significant reduction (∼65% at 5 μM) in mature miRNA levels and penetrate easily in the cells where they localise both in the cytoplasm and the nucleus. Cell cycle analysis showed significant increase in the G0/G1 phase (∼15%) and decrease in the S phase (∼7%) upon treatment with neomycin-bisbenzimidazole conjugates, suggesting inhibition of cell proliferation. Using the conjugation approach, we show that moderately binding ligands can be covalently combined into high affinity binders. This study also highlights the role of linker optimization in designing high affinity ligands for miR-27a targeting.
Collapse
Affiliation(s)
- Smita Nahar
- Academy of Scientific and Innovative Research (AcSIR) , Anusandhan Bhawan, 2 Rafi Marg , New Delhi-110001 , India
- CSIR-Institute of Genomics and Integrative Biology , Mathura Road , Delhi-110020 , India . ; ; Tel: +91-11-2766-6156
| | - Nihar Ranjan
- Department of Chemistry , Clemson University , Clemson , SC 29634 , USA
| | - Arjun Ray
- Academy of Scientific and Innovative Research (AcSIR) , Anusandhan Bhawan, 2 Rafi Marg , New Delhi-110001 , India
- CSIR-Institute of Genomics and Integrative Biology , Mathura Road , Delhi-110020 , India . ; ; Tel: +91-11-2766-6156
| | - Dev P Arya
- Department of Chemistry , Clemson University , Clemson , SC 29634 , USA
| | - Souvik Maiti
- Academy of Scientific and Innovative Research (AcSIR) , Anusandhan Bhawan, 2 Rafi Marg , New Delhi-110001 , India
- CSIR-Institute of Genomics and Integrative Biology , Mathura Road , Delhi-110020 , India . ; ; Tel: +91-11-2766-6156
- CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune , 411008 , India . ;
| |
Collapse
|