1
|
Sohail M, Rahman HMAU, Asghar MN. Drug-ionic surfactant interactions: density, sound speed, spectroscopic, and electrochemical studies. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:735-747. [PMID: 37943328 DOI: 10.1007/s00249-023-01689-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/14/2023] [Indexed: 11/10/2023]
Abstract
The failure of antibiotics against infectious diseases has become a global health issue due to the incessant use of antibiotics in the community and a lack of entry of new antibacterial drugs onto the market. The limited knowledge of biophysical interactions of existing antibiotics with bio-membranes is one of the major hurdles to design and develop more effective antibiotics. Surfactant systems are the simplest biological membrane models that not only mimic the cell membrane functions but are also used to investigate the biophysical interactions between pharmaceutical drugs and bio-membranes at the molecular level. In this work, volumetric and acoustic studies were used to investigate the molecular interactions of moxifloxacin (MXF), a potential antibacterial drug, with ionic surfactants (dodecyl-tri-methyl-ammonium bromide (DTAB), a cationic surfactant and sodium dodecyl sulfate (SDS), an anionic surfactant) under physiological conditions (phosphate buffer, pH 7.4) at T = 298.15-313.15 K at an interval of 5 K. Various volumetric and acoustic parameters were computed from the density and sound speed data and interpreted in terms of MXF-ionic surfactant interaction using electrostriction effect and co-sphere overlap model. Absorption spectroscopy and cyclic voltammetry were further used to determine the binding, partitioning, and related free energies of MXF with ionic micelles.
Collapse
Affiliation(s)
- Muhammad Sohail
- Department of Chemistry, Forman Christian College (A Chartered University), Lahore, 54600, Pakistan
| | | | - Muhammad Nadeem Asghar
- Department of Chemistry, Forman Christian College (A Chartered University), Lahore, 54600, Pakistan.
| |
Collapse
|
2
|
Ashraf MV, Pant S, Khan MAH, Shah AA, Siddiqui S, Jeridi M, Alhamdi HWS, Ahmad S. Phytochemicals as Antimicrobials: Prospecting Himalayan Medicinal Plants as Source of Alternate Medicine to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:881. [PMID: 37375828 DOI: 10.3390/ph16060881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Among all available antimicrobials, antibiotics hold a prime position in the treatment of infectious diseases. However, the emergence of antimicrobial resistance (AMR) has posed a serious threat to the effectiveness of antibiotics, resulting in increased morbidity, mortality, and escalation in healthcare costs causing a global health crisis. The overuse and misuse of antibiotics in global healthcare setups have accelerated the development and spread of AMR, leading to the emergence of multidrug-resistant (MDR) pathogens, which further limits treatment options. This creates a critical need to explore alternative approaches to combat bacterial infections. Phytochemicals have gained attention as a potential source of alternative medicine to address the challenge of AMR. Phytochemicals are structurally and functionally diverse and have multitarget antimicrobial effects, disrupting essential cellular activities. Given the promising results of plant-based antimicrobials, coupled with the slow discovery of novel antibiotics, it has become highly imperative to explore the vast repository of phytocompounds to overcome the looming catastrophe of AMR. This review summarizes the emergence of AMR towards existing antibiotics and potent phytochemicals having antimicrobial activities, along with a comprehensive overview of 123 Himalayan medicinal plants reported to possess antimicrobial phytocompounds, thus compiling the existing information that will help researchers in the exploration of phytochemicals to combat AMR.
Collapse
Affiliation(s)
- Mohammad Vikas Ashraf
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Shreekar Pant
- Centre for Biodiversity Studies, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - M A Hannan Khan
- Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Ali Asghar Shah
- Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Sazada Siddiqui
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | - Mouna Jeridi
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | | | - Shoeb Ahmad
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| |
Collapse
|
3
|
Rep V, Štulić R, Koštrun S, Kuridža B, Crnolatac I, Radić Stojković M, Paljetak HČ, Perić M, Matijašić M, Raić-Malić S. Novel tetrahydropyrimidinyl-substituted benzimidazoles and benzothiazoles: synthesis, antibacterial activity, DNA interactions and ADME profiling. RSC Med Chem 2022; 13:1504-1525. [PMID: 36561067 PMCID: PMC9749923 DOI: 10.1039/d2md00143h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/12/2022] [Indexed: 12/25/2022] Open
Abstract
A series of tetrahydropyrimidinyl-substituted benzimidazoles attached to various aliphatic or aromatic residues via phenoxymethylene were synthesised to investigate their antibacterial activities against selected Gram-positive and Gram-negative bacteria. The influence of the type of substituent at the C-3 and C-4 positions of the phenoxymethylene linker on the antibacterial activity was observed, showing that the aromatic moiety improved the antibacterial potency. Of all the evaluated compounds, benzoyl-substituted benzimidazole derivative 15a was the most active compound, particularly against the Gram-negative pathogens E. coli (MIC = 1 μg mL-1) and M. catarrhalis (MIC = 2 μg mL-1). Compound 15a also exhibited the most promising antibacterial activity against sensitive and resistant strains of S. pyogenes (MIC = 2 μg mL-1). Significant stabilization effects and positive induced CD bands strongly support the binding of the most biologically active benzimidazoles inside the minor grooves of AT-rich DNA, in line with docking studies. The predicted physico-chemical and ADME properties lie within drug-like space except for low membrane permeability, which needs further optimization. Our findings encourage further development of novel structurally related 5(6)-tetrahydropyrimidinyl substituted benzimidazoles in order to optimize their antibacterial effect against common respiratory pathogens.
Collapse
Affiliation(s)
- Valentina Rep
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
| | - Rebeka Štulić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
| | - Sanja Koštrun
- Selvita d.o.oPrilaz baruna Filipovića 2910000 ZagrebCroatia
| | - Bojan Kuridža
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Ivo Crnolatac
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Marijana Radić Stojković
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Hana Čipčić Paljetak
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Mihaela Perić
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Mario Matijašić
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
| |
Collapse
|
4
|
Serine Metabolism Tunes Immune Responses To Promote Oreochromis niloticus Survival upon Edwardsiella tarda Infection. mSystems 2021; 6:e0042621. [PMID: 34427522 PMCID: PMC8407201 DOI: 10.1128/msystems.00426-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Overactive immune response is a critical factor triggering host death upon bacterial infection. However, the mechanism behind the regulation of excessive immune responses is still largely unknown, and the corresponding control and preventive measures are still to be explored. In this study, we find that Nile tilapia, Oreochromis niloticus, that died from Edwardsiella tarda infection had higher levels of immune responses than those that survived. Such immune responses are strongly associated with metabolism that was altered at 6 h postinfection. By gas chromatography-mass spectrometry-based metabolome profiling, we identify glycine, serine, and threonine metabolism as the top three of the most impacted pathways, which were not properly activated in the fish that died. Serine is one of the crucial biomarkers. Exogenous serine can promote O. niloticus survival both as a prophylactic and therapeutic upon E. tarda infection. Our further analysis revealed exogenous serine flux into the glycine, serine, and threonine metabolism and, more importantly, the glutathione metabolism via glycine. The increased glutathione synthesis could downregulate reactive oxygen species. Therefore, these data together suggest that metabolic modulation of immune responses is a potential preventive strategy to control overactive immune responses. IMPORTANCE Bacterial virulence factors are not the only factors responsible for host death. Overactive immune responses, such as cytokine storm, contribute to tissue injury that results in organ failure and ultimately the death of the host. Despite the recent development of anti-inflammation strategies, the way to tune immune responses to an appropriate level is still lacking. We propose that metabolic modulation is a promising approach in tuning immune responses. We find that the metabolomic shift at as early as 6 h postinfection can be predictive of the consequences of infection. Serine is a crucial biomarker whose administration can promote host survival upon bacterial infection either in a prophylactic or therapeutic way. Further analysis demonstrated that exogenous serine promotes the synthesis of glutathione, which downregulates reactive oxygen species to dampen immune responses. Our study exemplifies that the metabolite(s) is a potential therapeutic reagent for overactive immune response during bacterial infection.
Collapse
|
5
|
Yitayeh L, Gize A, Kassa M, Neway M, Afework A, Kibret M, Mulu W. Antibiogram Profiles of Bacteria Isolated from Different Body Site Infections Among Patients Admitted to GAMBY Teaching General Hospital, Northwest Ethiopia. Infect Drug Resist 2021; 14:2225-2232. [PMID: 34163187 PMCID: PMC8214533 DOI: 10.2147/idr.s307267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/13/2021] [Indexed: 11/23/2022] Open
Abstract
Background Infections with multi-drug resistant (MDR) bacteria are serious threats to many low-income countries associated with overuse and misuse of antibiotics. This study determined the antibiogram profiles of bacteria isolated from different body site infections among patients admitted to GAMBY Teaching General Hospital, Bahir Dar, Northwest Ethiopia. Methods A hospital-based cross-sectional study was done between November 2015 and May 2018. Various clinical specimens were sampled from patients and analyzed for aerobic bacterial isolation and Kirby–Bauer disk diffusion susceptibility testing. Chi-square test was calculated to see association among variables, and P-value <0.05 was taken as a cutoff value for statistical significance. Results From the 716 clinical specimens processed, 134 (18.7%) were culture-positive for aerobic bacterial pathogens. Culture-confirmed positivity was higher in ear discharge (27.3%) and urine (26.3%) samples. The prevalence of infection was significantly highest among females (P = 0.001). Escherichia coli 63 (47.4%) and 10 (7.4%) of Klebsiella spp. from Gram-negative bacteria were the predominant bacterial isolates, while Staphylococcus saprophyticus 17 (12.6%) and S. aureus 14 (10.4%) were from Gram-positive bacteria. Overall, 61.8% of the isolates were found to be MDR. The proportion of MDR among Klebsiella spp., S. aureus and E. coli isolates was 90.9%, 60.9% and 50%, respectively. Gram-positive bacteria demonstrated 20%, 48.6% and 100% of resistance against norfloxacin, ciprofloxacin and clindamycin, respectively. Gram-negative bacteria also revealed from 20% resistance for the antibiotic nitrofurantoin and 100% of resistance for ampicillin and penicillin. Conclusion Infections with bacterial isolates resistant to the majority of antibiotics are a major issue in the study area. Most of the identified bacteria were resistant to the routinely used antibiotics, and MDR isolates are alarmingly high. Therefore, clinicians should practice rational choice of antibiotics and treatment should be guided by antimicrobial susceptibility testing.
Collapse
Affiliation(s)
| | - Addisu Gize
- Department of Microbiology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Melkayehu Kassa
- Department of Microbiology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Misrak Neway
- GAMBY Teaching General Hospital, Bahir Dar, Ethiopia
| | | | - Mulugeta Kibret
- Department of Biology, Science College, Bahir Dar University, Bahir Dar, Ethiopia
| | - Wondemagegn Mulu
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| |
Collapse
|
6
|
Selas A, Martin-Encinas E, Fuertes M, Masdeu C, Rubiales G, Palacios F, Alonso C. A patent review of topoisomerase I inhibitors (2016-present). Expert Opin Ther Pat 2021; 31:473-508. [PMID: 33475439 DOI: 10.1080/13543776.2021.1879051] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Topoisomerases are important targets for therapeutic improvement in the treatment of some diseases, including cancer. Inhibitors and poisons of topoisomerase I can limit the activity of this enzyme in its enzymatic cycle. This fact implies an anticancer effect of these drugs, since most cancer cells are characterized by both a higher activity of topoisomerase I and a higher replication rate compared to non-cancerous cells. Clinically approved inhibitors include camptothecin (CPT) and its derivatives. However, their limitations have encouraged different research groups to prepare new compounds, proof of which are the numerous research works and patents, some of them in the last five years. AREAS COVERED This review covers patent literature on topoisomerase I inhibitors and their application published between 2016-present. EXPERT OPINION The highest contribution toward patent development has been obtained from academics or small biotechnology companies. The most important fields of innovation include the preparation of prodrugs or inhibitors combined with other agents, as biocompatible polymers or antibodies. A promising development of topoisomerase I inhibitors is expected in the next years, directed to the treatment of diverse diseases, specifically toward different types of cancer and infectious diseases, among others.
Collapse
Affiliation(s)
- Asier Selas
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Endika Martin-Encinas
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Maria Fuertes
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Carme Masdeu
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Francisco Palacios
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Concepción Alonso
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| |
Collapse
|
7
|
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
|
8
|
Sinha D, Kiianitsa K, Sherman DR, Maizels N. Rapid, direct detection of bacterial topoisomerase 1-DNA adducts by RADAR/ELISA. Anal Biochem 2020; 608:113827. [PMID: 32738213 DOI: 10.1016/j.ab.2020.113827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 10/23/2022]
Abstract
Topoisomerases are proven drug targets, but antibiotics that poison bacterial Topoisomerase 1 (Top1) have yet to be discovered. We have developed a rapid and direct assay for quantification of Top1-DNA adducts that is suitable for high throughput assays. Adducts are recovered by "RADAR fractionation", a quick, convenient approach in which cells are lysed in chaotropic salts and detergent and nucleic acids and covalently bound adducts then precipitated with alcohol. Here we show that RADAR fractionation followed by ELISA immunodetection can quantify adducts formed by wild-type and mutant Top1 derivatives encoded by two different bacterial pathogens, Y. pestis and M. tuberculosis, expressed in E. coli or M. smegmatis, respectively. For both enzymes, quantification of adducts by RADAR/ELISA produces results comparable to the more cumbersome classical approach of CsCl density gradient fractionation. The experiments reported here establish that RADAR/ELISA assay offers a simple way to characterize Top1 mutants and analyze kinetics of adduct formation and repair. They also provide a foundation for discovery and optimization of drugs that poison bacterial Top1 using standard high-throughput approaches.
Collapse
Affiliation(s)
- Devapriya Sinha
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - Kostantin Kiianitsa
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA.
| | - David R Sherman
- Department of Microbiology, University of Washington, 815 Republican St., Seattle, WA, 98102, USA
| | - Nancy Maizels
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA; Department of Biochemistry, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| |
Collapse
|
9
|
Hussein EM, Alsantali RI, Morad M, Obaid RJ, Altass HM, Sayqal A, Abourehab MAS, Elkhawaga AA, Aboraia ASM, Ahmed SA. Bioactive fluorenes. Part III: 2,7-dichloro-9 H-fluorene-based thiazolidinone and azetidinone analogues as anticancer and antimicrobial against multidrug resistant strains agents. BMC Chem 2020; 14:42. [PMID: 32596690 PMCID: PMC7315563 DOI: 10.1186/s13065-020-00694-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/17/2020] [Indexed: 11/27/2022] Open
Abstract
Background Thiazoles, thiazolidinones and azetidinones are highly ranked amongst natural and synthetic heterocyclic derivatives due to their great pharmaceutical potential. Results New thiazolidinone and azetidinone class of bioactive agents based on 4-(2,7-dichloro-9H-fluoren-4-yl)thiazole moiety have been successfully synthesized. 4-(2,7-dichloro-9H-fluoren-4-yl)thiazol-2-amine was synthesized and allowed to react with various aryl/heteroaryl aldehydes to afford the corresponding Schiff base intermediates. The target thiazolidinone and azetidinone analogues have derived from Schiff bases by their reactions with thioglycolic acid and chloroacetyl chloride, respectively. The newly synthesized compounds were then evaluated for their antimicrobial activity against some multidrug resistant strains and examined for cytotoxic activity against normal lung fibroblast (WI-38), human lung carcinoma (A549), and human breast carcinoma (MDA-MB-231) cell lines to develop a novel class of fluorene-based bioactive agents. The mode of action and the binding interaction of the synthesized compound with the active sites of dihydrofolate reductase enzyme were well identified by fluorescence-activated cell sorting (FACS) analysis and molecular docking study. Conclusion Some of the synthesized compounds showed remarkable activity against A-549 and MDA-MB-231 when compared to Taxol, which was used as a reference drug. 2,7-dichloro-9H-fluorene-based azetidinones are more efficient as antimicrobial and anticancer agents compared to dichloro-9H-fluorene-based thiazolidinones derivatives.![]()
Collapse
Affiliation(s)
- Essam M Hussein
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, 21955 Saudi Arabia.,Chemistry Department, Faculty of Science, Assiut University, Assiut, 71516 Egypt
| | - Reem I Alsantali
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, 21955 Saudi Arabia.,Department of Pharmaceutical Chemistry, Pharmacy College, Taif University, 888, Taif, Saudi Arabia
| | - Moataz Morad
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, 21955 Saudi Arabia
| | - Rami J Obaid
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, 21955 Saudi Arabia
| | - Hatem M Altass
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, 21955 Saudi Arabia
| | - Ali Sayqal
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, 21955 Saudi Arabia
| | - Mohamed A S Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Amal A Elkhawaga
- Department of Medical Microbiology & Immunology, Faculty of Medicine Assiut University, Assiut, 71516 Egypt
| | - Ahmed S M Aboraia
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut, 71516 Egypt
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, 21955 Saudi Arabia.,Chemistry Department, Faculty of Science, Assiut University, Assiut, 71516 Egypt
| |
Collapse
|
10
|
Tiwari PB, Chapagain PP, Seddek A, Annamalai T, Üren A, Tse-Dinh YC. Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development. ChemMedChem 2020; 15:623-631. [PMID: 32043806 PMCID: PMC7133791 DOI: 10.1002/cmdc.201900721] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/11/2022]
Abstract
A topoisomerase-DNA transient covalent complex can be a druggable target for novel topoisomerase poison inhibitors that represent a new class of antibacterial or anticancer drugs. Herein, we have investigated molecular features of the functionally important Escherichia coli topoisomerase I (EctopoI)-DNA covalent complex (EctopoIcc) for molecular simulations, which is very useful in the development of new antibacterial drugs. To demonstrate the usefulness of our approach, we used a model small molecule (SM), NSC76027, obtained from virtual screening. We examined the direct binding of NSC76027 to EctopoI as well as inhibition of EctopoI relaxation activity of this SM via experimental techniques. We then performed molecular dynamics (MD) simulations to investigate the dynamics and stability of EctopoIcc and EctopoI-NSC76027-DNA ternary complex. Our simulation results show that NSC76027 forms a stable ternary complex with EctopoIcc. EctopoI investigated here also serves as a model system for investigating a complex of topoisomerase and DNA in which DNA is covalently attached to the protein.
Collapse
Affiliation(s)
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
| | - Ahmed Seddek
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Thirunavukkarasu Annamalai
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, DC 20057, USA
| | - Yuk-Ching Tse-Dinh
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
11
|
Abstract
Antibacterial agents are a group of materials that selectively destroy bacteria by interfering with bacterial growth or survival. With the emergence of resistance phenomenon of bacterial pathogens to current antibiotics, new drugs are frequently entering into the market along with the existing drugs, and the alternative compounds with antibacterial functions are being explored. Due to the advantages of their inherent biochemical and biophysical properties including precise targeting ability, biocompatibility, biodegradability, long blood circulation time, and low cytotoxicity, biomolecules such as peptides, carbohydrates, and nucleic acids have huge potential for the antimicrobial application and have been extensively studied in recent years. In this review, antimicrobial therapeutic agents composed of three kinds of functional biological molecules were summarized. In addition, the research progress of antibacterial mechanism, chemical modification, and nanoparticle coupling of those biomolecules were also discussed.
Collapse
|
12
|
Gutti G, Arya K, Singh SK. Latent Tuberculosis Infection (LTBI) and Its Potential Targets: An Investigation into Dormant Phase Pathogens. Mini Rev Med Chem 2019; 19:1627-1642. [PMID: 31241015 DOI: 10.2174/1389557519666190625165512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/06/2018] [Accepted: 05/28/2018] [Indexed: 11/22/2022]
Abstract
One-third of the world's population harbours the latent tuberculosis infection (LTBI) with a lifetime risk of reactivation. Although, the treatment of LTBI relies significantly on the first-line therapy, identification of novel drug targets and therapies are the emerging focus for researchers across the globe. The current review provides an insight into the infection, diagnostic methods and epigrammatic explanations of potential molecular targets of dormant phase bacilli. This study also includes current preclinical and clinical aspects of tubercular infections and new approaches in antitubercular drug discovery.
Collapse
Affiliation(s)
- Gopichand Gutti
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.) Varanasi-221005 (U.P.), India
| | - Karan Arya
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.) Varanasi-221005 (U.P.), India
| | - Sushil Kumar Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.) Varanasi-221005 (U.P.), India
| |
Collapse
|
13
|
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
|
14
|
Cao N, Tan K, Annamalai T, Joachimiak A, Tse-Dinh YC. Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site. Nucleic Acids Res 2019; 46:7296-7308. [PMID: 29905859 PMCID: PMC6101483 DOI: 10.1093/nar/gky492] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/25/2018] [Indexed: 12/18/2022] Open
Abstract
We have obtained new crystal structures of Mycobacterium tuberculosis topoisomerase I, including structures with ssDNA substrate bound to the active site, with and without Mg2+ ion present. Significant enzyme conformational changes upon DNA binding place the catalytic tyrosine in a pre-transition state position for cleavage of a specific phosphodiester linkage. Meanwhile, the enzyme/DNA complex with bound Mg2+ ion may represent the post-transition state for religation in the enzyme's multiple-step DNA relaxation catalytic cycle. The first observation of Mg2+ ion coordinated with the TOPRIM residues and DNA phosphate in a type IA topoisomerase active site allows assignment of likely catalytic role for the metal and draws a comparison to the proposed mechanism for type IIA topoisomerases. The critical function of a strictly conserved glutamic acid in the DNA cleavage step was assessed through site-directed mutagenesis. The functions assigned to the observed Mg2+ ion can account for the metal requirement for DNA rejoining but not DNA cleavage by type IA topoisomerases. This work provides new structural insights into a more stringent requirement for DNA rejoining versus cleavage in the catalytic cycle of this essential enzyme, and further establishes the potential for selective interference of DNA rejoining by this validated TB drug target.
Collapse
Affiliation(s)
- Nan Cao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| | - Kemin Tan
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| |
Collapse
|
15
|
Mycobacterium tuberculosis topoisomerases and EthR as the targets for new anti-TB drugs development. Future Med Chem 2019; 11:2193-2203. [DOI: 10.4155/fmc-2018-0232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The significant increase in the detection of drug-resistant strains of Mycobacterium tuberculosis caused an urgent need for the discovery new antituberculosis drugs. Development of bioinformatics and computational sciences enabled the progress of new strategies leading to design, discovery and identification of a series of interesting drug candidates. In this short review, we would like to present recently discovered compounds targeting important mycobacterial proteins: DNA topoisomerases and the transcriptional repressor of EthA monooxygenase – EthR.
Collapse
|
16
|
Li D, Wang Q, Zhou B, Zhuge Q, Lv B. Small DNA circles as bacterial topoisomerase I inhibitors. RSC Adv 2019; 9:18415-18419. [PMID: 35515216 PMCID: PMC9064831 DOI: 10.1039/c9ra02398d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/06/2019] [Indexed: 11/21/2022] Open
Abstract
Bacterial topoisomerase I is a potential target during the course of antibacterial drug therapy. In our studies, specifically designed small DNA circles with high bending stress were synthesized. It is demonstrated that small DNA circles showed high inhibitory effect on the activity of bacterial topoisomerase I and the single-stranded regions associated with bending deformation in DNA circles are believed to be the crucial factor for trapping the enzymes and decreasing the effective concentration of the topoisomerases in the reaction solution. In addition, the DNA circles showed high thermal stability and excellent nuclease resistance. In consideration of the low cytotoxicity of DNA-based biopharmaceuticals, our results may provide a new idea for the future design and optimization of DNA-based therapeutic agents for antibacterial therapy.
Collapse
Affiliation(s)
- Dawei Li
- College of Biology and the Environment, Nanjing Forestry University 159 Longpan Road Nanjing 210037 China
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University 159 Longpan Road Nanjing 210037 China
| | - Qiang Wang
- College of Biology and the Environment, Nanjing Forestry University 159 Longpan Road Nanjing 210037 China
| | - Bing Zhou
- College of Biology and the Environment, Nanjing Forestry University 159 Longpan Road Nanjing 210037 China
| | - Qiang Zhuge
- College of Biology and the Environment, Nanjing Forestry University 159 Longpan Road Nanjing 210037 China
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University 159 Longpan Road Nanjing 210037 China
| | - Bei Lv
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Science and Chemistry, Jiangsu Second Normal University Nanjing 210013 China
| |
Collapse
|
17
|
PPEF: A bisbenzimdazole potent antimicrobial agent interacts at acidic triad of catalytic domain of E. coli topoisomerase IA. Biochim Biophys Acta Gen Subj 2019; 1863:1524-1535. [PMID: 31145964 DOI: 10.1016/j.bbagen.2019.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/20/2019] [Accepted: 05/23/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Topoisomerase is a well known target to develop effective antibacterial agents. In pursuance of searching novel antibacterial agents, we have established a novel bisbenzimidazole (PPEF) as potent E. coli topoisomerase IA poison inhibitor. METHODS In order to gain insights into the mechanism of action of PPEF and understanding protein-ligand interactions, we have produced wild type EcTopo 67 N-terminal domain (catalytic domain) and its six mutant proteins at acidic triad (D111, D113, E115). The DDE motif is replaced by alanine (A) to create three single mutants: D111A, D113A, E115A and three double mutants: D111A-D113A, D113A-E115A and D111A-E115A. RESULTS Calorimetric study of PPEF with single mutants showed 10 fold lower affinity than that of wild type EcTopo 67 (7.32 × 106 M-1for wild type, 0.89 × 106 M-1for D111A) and 100 fold lower binding with double mutant D113A-E115A (0.02 × 106 M-1) was observed. The mutated proteins showed different CD signature as compared to wild type protein. CD and fluorescence titrations were done to study the interaction between EcTopo 67 and ligands. Molecular docking study validated that PPEF has decreased binding affinity towards mutated enzymes as compared to wild type. CONCLUSION The overall study reveals that PPEF binds to D113 and E115 of acidic triad of EcTopo 67. Point mutations decrease binding affinity of PPEF towards DDE motif of topoisomerase. GENERAL SIGNIFICANCE This study concludes PPEF as poison inhibitor of E. coli Topoisomerase IA, which binds to acidic triad of topoisomerase IA, responsible for its function. PPEF can be considered as therapeutic agent against bacteria.
Collapse
|
18
|
Kaur H, Singh J, Narasimhan B. Indole hybridized diazenyl derivatives: synthesis, antimicrobial activity, cytotoxicity evaluation and docking studies. BMC Chem 2019; 13:65. [PMID: 31384812 PMCID: PMC6661771 DOI: 10.1186/s13065-019-0580-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023] Open
Abstract
Background In search of effective antimicrobial and cytotoxic agents, a series of indole hybridized diazenyl derivatives (DS-1 to DS-21) was efficiently prepared by condensation of diazotized p-aminoacetophenone with indole or nitroindole followed by reaction with different aromatic/heteroaromatic amines of biological significance. The synthesized derivatives were characterized by various spectroscopic techniques. Methodology The antimicrobial evaluation of DS-1 to DS-23 was done by tube dilution method against various pathogenic bacterial and fungal strains. The active antimicrobial derivatives were further evaluated for cytotoxicity against human lung carcinoma cell line (HCT-116), breast cancer cell line (MDAMB231), leukemic cancer cell line (K562), and normal cell line (HEK293) by MTT assay using doxorubicin as the standard drug. The test derivatives were additionally docked for the B-subunit of enzyme DNA gyrase from E. coli at the ATPase binding site to study the molecular interactions using Schrodinger maestro v11.5 software. Results and discussion Most of the synthesized derivatives have shown high activity against Gram-negative bacteria particularly E. coli and K. pneumonia with MIC ranging from 1.95 to 7.81 μg/ml. The derivatives have demonstrated very less activity against tested Gram positive bacterial and fungal strains. The derivatives DS-14 and DS-20 have been found to active against breast cancer cell line and human colon carcinoma cell line having IC50 in the range of 19–65 µg/ml. All the derivatives were found to less potent against leukemic cancer cell line. The synthesized derivatives have revealed their safety by exhibiting very less cytotoxicity against the normal cell line (HEK-293) with IC50 > 100 µg/ml. Most of the active derivatives have shown good docking scores in comparison to the standard drugs against DNA gyrase from E. coli. Further ADME predictions by Qikprop module of the Schrodinger confirmed these molecules have drug like properties. Conclusion The derivatives DS-14 and DS-20 have shown potential against Gram-negative bacteria and breast cancer cell line and can be used as a lead for rational drug designing of the antimicrobial and cytotoxic agents. .
Collapse
Affiliation(s)
- Harmeet Kaur
- 1Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001 India
| | - Jasbir Singh
- 2College of Pharmacy, Postgraduate Institute of Medical Sciences, Rohtak, 124001 India
| | | |
Collapse
|
19
|
Mills M, Tse-Dinh YC, Neuman KC. Direct observation of topoisomerase IA gate dynamics. Nat Struct Mol Biol 2018; 25:1111-1118. [PMID: 30478267 PMCID: PMC6379066 DOI: 10.1038/s41594-018-0158-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/31/2018] [Indexed: 12/18/2022]
Abstract
Type IA topoisomerases cleave single-stranded DNA and relieve negative supercoils in discrete steps corresponding to the passage of the intact DNA strand through the cleaved strand. Although type IA topoisomerases are assumed to accomplish this strand passage via a protein-mediated DNA gate, opening of this gate has never been observed. We developed a single-molecule assay to directly measure gate opening of the Escherichia coli type IA topoisomerases I and III. We found that after cleavage of single-stranded DNA, the protein gate opens by as much as 6.6 nm and can close against forces in excess of 16 pN. Key differences in the cleavage, ligation, and gate dynamics of these two enzymes provide insights into their different cellular functions. The single-molecule results are broadly consistent with conformational changes obtained from molecular dynamics simulations. These results allowed us to develop a mechanistic model of interactions between type IA topoisomerases and single-stranded DNA.
Collapse
Affiliation(s)
- Maria Mills
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yuk-Ching Tse-Dinh
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
20
|
Cinelli MA. Topoisomerase 1B poisons: Over a half-century of drug leads, clinical candidates, and serendipitous discoveries. Med Res Rev 2018; 39:1294-1337. [PMID: 30456874 DOI: 10.1002/med.21546] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/17/2022]
Abstract
Topoisomerases are DNA processing enzymes that relieve supercoiling (torsional strain) in DNA, are necessary for normal cellular division, and act by nicking (and then religating) DNA strands. Type 1B topoisomerase (Top1) is overexpressed in certain tumors, and the enzyme has been extensively investigated as a target for cancer chemotherapy. Various chemical agents can act as "poisons" of the enzyme's religation step, leading to Top1-DNA lesions, DNA breakage, and eventual cellular death. In this review, agents that poison Top1 (and have thus been investigated for their anticancer properties) are surveyed, including natural products (such as camptothecins and indolocarbazoles), semisynthetic camptothecin and luotonin derivatives, and synthetic compounds (such as benzonaphthyridines, aromathecins, and indenoisoquinolines), as well as targeted therapies and conjugates. Top1 has also been investigated as a therapeutic target in certain viral and parasitic infections, as well as autoimmune, inflammatory, and neurological disorders, and a summary of literature describing alternative indications is also provided. This review should provide both a reference for the medicinal chemist and potentially offer clues to aid in the development of new Top1 poisons.
Collapse
Affiliation(s)
- Maris A Cinelli
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| |
Collapse
|
21
|
Abstract
Bacterial Topoisomerase I is a potential target for the identification of novel topoisomerase poison inhibitors that could provide leads for a new class of antibacterial compounds. Here we describe in detail a fluorescence-based cleavage assay that is successfully used in HTS for the discovery of bacterial topoisomerase Ι poisons.
Collapse
|
22
|
Badshah SL, Ullah A. New developments in non-quinolone-based antibiotics for the inhibiton of bacterial gyrase and topoisomerase IV. Eur J Med Chem 2018; 152:393-400. [DOI: 10.1016/j.ejmech.2018.04.059] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 04/23/2018] [Accepted: 04/29/2018] [Indexed: 01/06/2023]
|
23
|
Abstract
Antibiotics have saved millions of lives over the past decades. However, the accumulation of so many antibiotic resistance genes by some clinically relevant pathogens has begun to lead to untreatable infections worldwide. The current antibiotic resistance crisis will require greater efforts by governments and the scientific community to increase the research and development of new antibacterial drugs with new mechanisms of action. A major challenge is the identification of novel microbial targets, essential for in vivo growth or pathogenicity, whose inhibitors can overcome the currently circulating resistome of human pathogens. In this article, we focus on the potential high value of bacterial transcriptional regulators as targets for the development of new antibiotics, discussing in depth the molecular role of these regulatory proteins in bacterial physiology and pathogenesis. Recent advances in the search for novel compounds that inhibit the biological activity of relevant transcriptional regulators in pathogenic bacteria are reviewed.
Collapse
|
24
|
Discovery of novel bacterial topoisomerase I inhibitors by use of in silico docking and in vitro assays. Sci Rep 2018; 8:1437. [PMID: 29362471 PMCID: PMC5780498 DOI: 10.1038/s41598-018-19944-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023] Open
Abstract
Topoisomerases are important targets for antibacterial and anticancer therapies. Bacterial topoisomerase I remains to be exploited for antibiotics that can be used in the clinic. Inhibitors of bacterial topoisomerase I may provide leads for novel antibacterial drugs against pathogens resistant to current antibiotics. TB is the leading infectious cause of death worldwide, and new TB drugs against an alternative target are urgently needed to overcome multi-drug resistance. Mycobacterium tuberculosis topoisomerase I (MtbTopI) has been validated genetically and chemically as a TB drug target. Here we conducted in silico screening targeting an active site pocket of MtbTopI. The top hits were assayed for inhibition of MtbTopI activity. The shared structural motif found in the active hits was utilized in a second round of in silico screening and in vitro assays, yielding selective inhibitors of MtbTopI with IC50s as low as 2 µM. Growth inhibition of Mycobacterium smegmatis by these compounds in combination with an efflux pump inhibitor was diminished by the overexpression of recombinant MtbTopI. This work demonstrates that in silico screening can be utilized to discover new bacterial topoisomerase I inhibitors, and identifies a novel structural motif which could be explored further for finding selective bacterial topoisomerase I inhibitors.
Collapse
|
25
|
Yang Z, Jiang T, Zhong H, Kang Y. Bulge oligonucleotide as an inhibitory agent of bacterial topoisomerase I. J Enzyme Inhib Med Chem 2018; 33:319-323. [PMID: 29281935 PMCID: PMC6009931 DOI: 10.1080/14756366.2017.1419218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bacterial topoisomerase I (Btopo I) was defined as potential target for discovery of new antibacterial compounds. Various oligonucleotides containing bulge structure were designed and synthesised as inhibitors to Btopo I in this investigation. The results of this study demonstrated that the designed oligonucleotides display high inhibitory efficiency on the activity of Btopo I and the inhibitory effect could be modulated by the amount of bulge DNA bases. The most efficient one among them showed an IC50 value of 63.1 nM in its inhibition on the activity of Btopo I. In addition, our studies confirmed that the designed oligonucleotide would induce irreversible damages to Btopo I and without any effects occur to eukaryotic topoisomerase I. It is our hope that the results provided in these studies could provide a novel way to inhibit Btopo I.
Collapse
Affiliation(s)
- Zhaoqi Yang
- a School of Pharmaceutical Sciences , Jiangnan University , Jiangsu , People's Republic of China.,b Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University , Jiangsu , People's Republic of China
| | - Tuoyu Jiang
- b Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University , Jiangsu , People's Republic of China
| | - Hanshi Zhong
- b Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University , Jiangsu , People's Republic of China
| | - Yu Kang
- b Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University , Jiangsu , People's Republic of China
| |
Collapse
|
26
|
Abstract
DNA topoisomerases are proven therapeutic targets of antibacterial agents. Quinolones, especially fluoroquinolones, are the most successful topoisomerase-targeting antibacterial drugs. These drugs target type IIA topoisomerases in bacteria. Recent structural and biochemical studies on fluoroquinolones have provided the molecular basis for both their mechanism of action, as well as the molecular basis of bacterial resistance. Due to the development of drug resistance, including fluoroquinolone resistance, among bacterial pathogens, there is an urgent need to discover novel antibacterial agents. Recent advances in topoisomerase inhibitors may lead to the development of novel antibacterial drugs that are effective against fluoroquinolone-resistant pathogens. They include type IIA topoisomerase inhibitors that either interact with the GyrB/ParE subunit or form nick-containing ternary complexes. In addition, several topoisomerase I inhibitors have recently been identified. Thus, DNA topoisomerases remain important targets of antibacterial agents.
Collapse
|
27
|
|
28
|
Domingos LC, Moreira MVL, Keller KM, Viana FAB, Melo MM, Soto-Blanco B. Simultaneous quantification of gatifloxacin, moxifloxacin, and besifloxacin concentrations in cornea and aqueous humor by LC-QTOF/MS after topical ocular dosing. J Pharmacol Toxicol Methods 2017; 83:87-93. [DOI: 10.1016/j.vascn.2016.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/27/2016] [Accepted: 09/22/2016] [Indexed: 10/21/2022]
|
29
|
Bansal S, Bajaj P, Pandey S, Tandon V. Topoisomerases: Resistance versus Sensitivity, How Far We Can Go? Med Res Rev 2016; 37:404-438. [PMID: 27687257 DOI: 10.1002/med.21417] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/04/2016] [Accepted: 08/29/2016] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases are ubiquitously present remarkable molecular machines that help in altering topology of DNA in living cells. The crucial role played by these nucleases during DNA replication, transcription, and recombination vis-à-vis less sequence similarity among different species makes topoisomerases unique and attractive targets for different anticancer and antibacterial drugs. However, druggability of topoisomerases by the existing class of molecules is increasingly becoming questationable due to resistance development predominated by mutations in the corresponding genes. The current scenario facing a decline in the development of new molecules further comprises an important factor that may challenge topoisomerase-targeting therapy. Thus, it is imperative to wisely use the existing inhibitors lest with this rapid rate of losing grip over the target we may not go too far. Furthermore, it is important not only to design new molecules but also to develop new approaches that may avoid obstacles in therapies due to multiple resistance mechanisms. This review provides a succinct account of different classes of topoisomerase inhibitors, focuses on resistance acquired by mutations in topoisomerases, and discusses the various approaches to increase the efficacy of topoisomerase inhibitors. In a later section, we also suggest the possibility of using bisbenzimidazoles along with efflux pump inhibitors for synergistic bactericidal effects.
Collapse
Affiliation(s)
- Sandhya Bansal
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Priyanka Bajaj
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Stuti Pandey
- Department of Chemistry, University of Delhi, New Delhi, India
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.,Department of Chemistry, University of Delhi, New Delhi, India
| |
Collapse
|
30
|
Yu X, Zhang M, Annamalai T, Bansod P, Narula G, Tse-Dinh YC, Sun D. Synthesis, evaluation, and CoMFA study of fluoroquinophenoxazine derivatives as bacterial topoisomerase IA inhibitors. Eur J Med Chem 2016; 125:515-527. [PMID: 27689733 DOI: 10.1016/j.ejmech.2016.09.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 09/16/2016] [Accepted: 09/17/2016] [Indexed: 10/21/2022]
Abstract
New antibacterial agents with novel target and mechanism of action are urgently needed to combat problematic bacterial infections and mounting antibiotic resistances. Topoisomerase IA represents an attractive and underexplored antibacterial target, as such, there is a growing interest in developing selective and potent topoisomerase I inhibitors for antibacterial therapy. Based on our initial biological screening, fluoroquinophenoxazine 1 was discovered as a low micromolar inhibitor against E. coli topoisomerase IA. In the literature, fluoroquinophenoxazine analogs have been investigated as antibacterial and anticancer agents, however, their topoisomerase I inhibition was relatively underexplored and there is little structure-activity relationship (SAR) available. The good topoisomerase I inhibitory activity of 1 and the lack of SAR prompted us to design and synthesize a series of fluoroquinophenoxazine analogs to systematically evaluate the SAR and to probe the structural elements of the fluoroquinophenoxazine core toward topoisomerase I enzyme target recognition. In this study, a series of fluoroquinophenoxazine analogs was designed, synthesized, and evaluated as topoisomerase I inhibitors and antibacterial agents. Target-based assays revealed that the fluoroquinophenoxazine derivatives with 9-NH2 and/or 6-substituted amine functionalities generally exhibited good to excellent inhibitory activities against topoisomerase I with IC50s ranging from 0.24 to 3.9 μM. Notably, 11a bearing the 6-methylpiperazinyl and 9-amino motifs was identified as one of the most potent topoisomerase I inhibitors (IC50 = 0.48 μM), and showed broad spectrum antibacterial activity (MICs = 0.78-7.6 μM) against all the bacteria strains tested. Compound 11g with the 6-bipiperidinyl lipophilic side chain exhibited the most potent antituberculosis activity (MIC = 2.5 μM, SI = 9.8). In addition, CoMFA analysis was performed to investigate the 3D-QSAR of this class of fluoroquinophenoxazine derivatives. The constructed CoMFA model produced reasonable statistics (q2 = 0.688 and r2 = 0.806). The predictive power of the developed model was obtained using a test set of 7 compounds, giving a predictive correlation coefficient r2pred of 0.767. Collectively, these promising data demonstrated that fluoroquinophenoxazine derivatives have the potential to be developed as a new chemotype of potent topoisomerase IA inhibitors with antibacterial therapeutic potential.
Collapse
Affiliation(s)
- Xufen Yu
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, HI 96720, USA
| | - Mingming Zhang
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, HI 96720, USA
| | | | - Priyanka Bansod
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Gagandeep Narula
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, HI 96720, USA.
| |
Collapse
|
31
|
Small-Molecule Inhibitors Targeting Topoisomerase I as Novel Antituberculosis Agents. Antimicrob Agents Chemother 2016; 60:4028-36. [PMID: 27114277 DOI: 10.1128/aac.00288-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/15/2016] [Indexed: 01/30/2023] Open
Abstract
Bacterial topoisomerase functions are required for regulation of DNA supercoiling and overcoming the DNA topological barriers that are encountered during many vital cellular processes. DNA gyrase and topoisomerase IV of the type IIA bacterial topoisomerase family are important clinical targets for antibacterial therapy. Topoisomerase I, belonging to the type IA topoisomerase family, has recently been validated as a potential antitubercular target. The topoisomerase I activity has been shown to be essential for bacterial viability and infection in a murine model of tuberculosis. Mixture-based combinatorial libraries were screened in this study to identify novel bacterial topoisomerase I inhibitors. Using positional-scanning deconvolution, selective small-molecule inhibitors of bacterial topoisomerase I were identified starting from a polyamine scaffold. Antibacterial assays demonstrated that four of these small-molecule inhibitors of bacterial topoisomerase I are bactericidal against Mycobacterium smegmatis and Mycobacterium tuberculosis The MICs for growth inhibition of M. smegmatis increased with overexpression of recombinant M. tuberculosis topoisomerase I, consistent with inhibition of intracellular topoisomerase I activity being involved in the antimycobacterial mode of action.
Collapse
|
32
|
Abstract
DNA gyrase and topoisomerase IV are type IIA bacterial topoisomerases that are targeted by highly effective antibiotics. However, resistance via multiple mechanisms arises to limit the efficacies of these drugs. Continued research on type IIA bacterial topoisomerases has provided novel approaches to counter the most common resistance mechanism for utilization of these proven targets in antibacterial therapy. Bacterial topoisomerase I is being explored as an alternative target that is not expected to show cross-resistance. Dual targeting or combination therapy could be strategies for circumventing the development of resistance to topoisomerase-targeting antibiotics. Bacterial topoisomerases are high-value bactericidal targets that could continue to be exploited for antibacterial therapy, if new tactics to counter resistance can be adopted.
Collapse
|
33
|
Yang Z, Jiang T, Zhong H, Liu Y. Portion mismatch in duplex oligonucleotides as inhibitors of bacterial topoisomerase I. RSC Adv 2016. [DOI: 10.1039/c6ra23304j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The activities of bacterial topoisomerase I can be modulated by non-perfect match duplex oligonucleotides.
Collapse
Affiliation(s)
- Zhaoqi Yang
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province
- School of Food Science and Technology
- Jiangnan University
- China
- School of Pharmaceutical Sciences
| | - Tuoyu Jiang
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province
- School of Food Science and Technology
- Jiangnan University
- China
| | - Hanshi Zhong
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province
- School of Food Science and Technology
- Jiangnan University
- China
| | - Yuanfa Liu
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province
- School of Food Science and Technology
- Jiangnan University
- China
| |
Collapse
|
34
|
Tan K, Cao N, Cheng B, Joachimiak A, Tse-Dinh YC. Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold. J Mol Biol 2015; 428:182-193. [PMID: 26655023 DOI: 10.1016/j.jmb.2015.11.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 01/17/2023]
Abstract
The DNA topoisomerase I enzyme of Mycobacterium tuberculosis (MtTOP1) is essential for the viability of the organism and survival in a murine model. This topoisomerase is being pursued as a novel target for the discovery of new therapeutic agents for the treatment of drug-resistant tuberculosis. In this study, we succeeded in obtaining a structure of MtTOP1 by first predicting that the C-terminal region of MtTOP1 contains four repeated domains that do not involve the Zn-binding tetracysteine motifs seen in the C-terminal domains of Escherichia coli topoisomerase I. A construct (amino acids A2-T704), MtTOP1-704t, that includes the N-terminal domains (D1-D4) and the first predicted C-terminal domain (D5) of MtTOP1 was expressed and found to retain DNA cleavage-religation activity and catalyze single-stranded DNA catenation. MtTOP1-704t was crystallized, and a structure of 2.52Å resolution limit was obtained. The structure of the MtTOP1 N-terminal domains has features that have not been observed in other previously available bacterial topoisomerase I crystal structures. The first C-terminal domain D5 forms a novel protein fold of a four-stranded antiparallel β-sheet stabilized by a crossing-over α-helix. Since there is only one type IA topoisomerase present in Mycobacteriaceae and related Actinobacteria, this subfamily of type IA topoisomerase may be required for multiple functions in DNA replication, transcription, recombination, and repair. The unique structural features observed for MtTOP1 may allow these topoisomerase I enzymes to carry out physiological functions associated with topoisomerase III enzyme in other bacteria.
Collapse
Affiliation(s)
- Kemin Tan
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.
| | - Nan Cao
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Bokun Cheng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
| |
Collapse
|