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Pakamwong B, Thongdee P, Kamsri B, Phusi N, Taveepanich S, Chayajarus K, Kamsri P, Punkvang A, Hannongbua S, Sangswan J, Suttisintong K, Sureram S, Kittakoop P, Hongmanee P, Santanirand P, Leanpolchareanchai J, Spencer J, Mulholland AJ, Pungpo P. Ligand-Based Virtual Screening for Discovery of Indole Derivatives as Potent DNA Gyrase ATPase Inhibitors Active against Mycobacterium tuberculosis and Hit Validation by Biological Assays. J Chem Inf Model 2024. [PMID: 38993154 DOI: 10.1021/acs.jcim.4c00511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Mycobacterium tuberculosis is the single most important global infectious disease killer and a World Health Organization critical priority pathogen for development of new antimicrobials. M. tuberculosis DNA gyrase is a validated target for anti-TB agents, but those in current use target DNA breakage-reunion, rather than the ATPase activity of the GyrB subunit. Here, virtual screening, subsequently validated by whole-cell and enzyme inhibition assays, was applied to identify candidate compounds that inhibit M. tuberculosis GyrB ATPase activity from the Specs compound library. This approach yielded six compounds: four carbazole derivatives (1, 2, 3, and 8), the benzoindole derivative 11, and the indole derivative 14. Carbazole derivatives can be considered a new scaffold for M. tuberculosis DNA gyrase ATPase inhibitors. IC50 values of compounds 8, 11, and 14 (0.26, 0.56, and 0.08 μM, respectively) for inhibition of M. tuberculosis DNA gyrase ATPase activity are 5-fold, 2-fold, and 16-fold better than the known DNA gyrase ATPase inhibitor novobiocin. MIC values of these compounds against growth of M. tuberculosis H37Ra are 25.0, 3.1, and 6.2 μg/mL, respectively, superior to novobiocin (MIC > 100.0 μg/mL). Molecular dynamics simulations of models of docked GyrB:inhibitor complexes suggest that hydrogen bond interactions with GyrB Asp79 are crucial for high-affinity binding of compounds 8, 11, and 14 to M. tuberculosis GyrB for inhibition of ATPase activity. These data demonstrate that virtual screening can identify known and new scaffolds that inhibit both M. tuberculosis DNA gyrase ATPase activity in vitro and growth of M. tuberculosis bacteria.
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Affiliation(s)
- Bongkochawan Pakamwong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Paptawan Thongdee
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Bundit Kamsri
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Naruedon Phusi
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Somjintana Taveepanich
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Kampanart Chayajarus
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Pharit Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand
| | - Auradee Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jidapa Sangswan
- Department of Biological Science, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Khomson Suttisintong
- National Nanotechnology Center, NSTDA, 111 Thailand Science Park, Klong Luang, Pathum Thani 12120, Thailand
| | - Sanya Sureram
- Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - Prasat Kittakoop
- Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok 10210, Thailand
| | - Poonpilas Hongmanee
- Division of Clinical Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Pitak Santanirand
- Division of Clinical Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | | | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Pornpan Pungpo
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
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Qiu X, Zhang Q, Li Z, Zhang J, Liu H. Revealing the Interaction Mechanism between Mycobacterium tuberculosis GyrB and Novobiocin, SPR719 through Binding Thermodynamics and Dissociation Kinetics Analysis. Int J Mol Sci 2024; 25:3764. [PMID: 38612573 PMCID: PMC11011931 DOI: 10.3390/ijms25073764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
With the rapid emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), various levels of resistance against existing anti-tuberculosis (TB) drugs have developed. Consequently, the identification of new anti-TB targets and drugs is critically urgent. DNA gyrase subunit B (GyrB) has been identified as a potential anti-TB target, with novobiocin and SPR719 proposed as inhibitors targeting GyrB. Therefore, elucidating the molecular interactions between GyrB and its inhibitors is crucial for the discovery and design of efficient GyrB inhibitors for combating multidrug-resistant TB. In this study, we revealed the detailed binding mechanisms and dissociation processes of the representative inhibitors, novobiocin and SPR719, with GyrB using classical molecular dynamics (MD) simulations, tau-random acceleration molecular dynamics (τ-RAMD) simulations, and steered molecular dynamics (SMD) simulations. Our simulation results demonstrate that both electrostatic and van der Waals interactions contribute favorably to the inhibitors' binding to GyrB, with Asn52, Asp79, Arg82, Lys108, Tyr114, and Arg141 being key residues for the inhibitors' attachment to GyrB. The τ-RAMD simulations indicate that the inhibitors primarily dissociate from the ATP channel. The SMD simulation results reveal that both inhibitors follow a similar dissociation mechanism, requiring the overcoming of hydrophobic interactions and hydrogen bonding interactions formed with the ATP active site. The binding and dissociation mechanisms of GyrB with inhibitors novobiocin and SPR719 obtained in our work will provide new insights for the development of promising GyrB inhibitors.
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Affiliation(s)
- Xiaofei Qiu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; (X.Q.); (Z.L.); (J.Z.)
| | - Qianqian Zhang
- Faculty of Applied Science, Macao Polytechnic University, Macao SAR, China;
| | - Zhaoguo Li
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; (X.Q.); (Z.L.); (J.Z.)
| | - Juan Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; (X.Q.); (Z.L.); (J.Z.)
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao SAR, China;
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Lougiakis N, Sakalis N, Georgiou M, Marakos P, Pouli N, Skaltsounis AL, Mavrogonatou E, Pratsinis H, Kletsas D. Synthesis, cytotoxic activity evaluation and mechanistic investigation of novel 3,7-diarylsubstituted 6-azaindoles. Eur J Med Chem 2023; 261:115804. [PMID: 37729693 DOI: 10.1016/j.ejmech.2023.115804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
A number of new disubstituted 6-azaindoles have been designed and synthesized bearing a crucial structural modification in respect to an analogous antiproliferative hit compound. The synthesis was performed using 2-amino-3-nitro-4-picoline, that was suitably modified and converted to 7-chloro-3-iodo-6-azaindole and this central scaffold was used for successive Suzuki-type couplings, to result in the target compounds. The evaluation of the cytotoxic activity was performed against four human cancer cell lines, as well as a normal human fibroblast strain. Certain compounds possessed strong anticancer activity without affecting normal cells. At subcytotoxic concentrations for cancer cells, these compounds displayed an anti-proliferative effect by arresting the cells at the G2/M phase of the cell cycle, which could be associated with the observed decrease in the phosphorylation levels of the MEK1- ERK1/2 pathway and/or the activation of the p53-p21WAF1 axis.
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Affiliation(s)
- Nikolaos Lougiakis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece.
| | - Nikolaos Sakalis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
| | - Maria Georgiou
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
| | - Panagiotis Marakos
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
| | - Nicole Pouli
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
| | - Alexios-Leandros Skaltsounis
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
| | - Eleni Mavrogonatou
- Laboratory of Cell Proliferation and Ageing, Institute of Biosciences and Applications, NCSR ''Demokritos'', 15310, Athens, Greece
| | - Harris Pratsinis
- Laboratory of Cell Proliferation and Ageing, Institute of Biosciences and Applications, NCSR ''Demokritos'', 15310, Athens, Greece
| | - Dimitris Kletsas
- Laboratory of Cell Proliferation and Ageing, Institute of Biosciences and Applications, NCSR ''Demokritos'', 15310, Athens, Greece
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Baweja S, Kalal B, Kumar Mitra P, Maity S. Competing Excited-State Hydrogen and Proton-Transfer Processes in 6-Azaindole-S 3,4 and 2,6-Diazaindole-S 3,4 Clusters (S=H 2 O, NH 3 ). Chemphyschem 2023:e202300270. [PMID: 37671972 DOI: 10.1002/cphc.202300270] [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: 04/17/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/07/2023]
Abstract
Excited state hydrogen (ESHT) and proton (ESPT) transfer reaction pathways in the three and four solvent clusters of 6-azaindole (6AI-S3,4 ) and 2,6-diazaindole (26DAI-S3,4 )(S=H2 O, NH3 ) were computationally investigated to understand the fate of photo-excited biomolecules. The ESHT energy barriers in (H2 O)3 complexes (39.6-41.3 kJmol-1 ) were decreased in (H2 O)4 complexes (23.1-20.2 kJmol-1 ). Lengthening the solvent chain lowered the barrier because of the relaxed transition states geometries with reduced angular strains. Replacing the water molecule with ammonia drastically decreased the energy barriers to 21.4-21.3 kJmol-1 in (NH3 )3 complexes and 8.1-9.5 kJ mol-1 in (NH3 )4 complexes. The transition states were identified as Ha atom attached to the first solvent molecule. The formation of stronger hydrogen bonds in (NH3 )3,4 complexes resulted in facile ESHT reaction than that in the (H2 O)3,4 complexes. The ESPT energy barriers in 6AI-S3,4 and 26DAI-S3,4 were found to range between 40-73 kJmol-1 . The above values were significantly higher than that of the ESHT processes and hence are considered as a minor channel in the process. The effect of N(2) insertion was explored for the very first time in the isolated solvent clusters using local vibrational mode analysis. In DAI-S4 , the higher Ka (Ha ⋯Sa ) values depicted the increased photoacidity of the N(1)-Ha group which may facilitate the hydrogen transfer reaction. However, the increased N(6)⋯Hb bond length elevated the reaction barriers. Therefore, in the ESHT reaction channel, the co-existence of two competing factors led to a marginal/no change in the overall energy barriers due to the N(2) insertion. In the ESPT reaction pathway, the energy barriers showed notable increase upon N(2) insertion because of the increased N(6)⋯Hb bond length.
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Affiliation(s)
- Simran Baweja
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Bhavika Kalal
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Prajoy Kumar Mitra
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Surajit Maity
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
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5
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Alov P, Al Sharif M, Najdenski H, Pencheva T, Tsakovska I, Zaharieva MM, Pajeva I. New Potential Pharmacological Targets of Plant-Derived Hydroxyanthraquinones from Rubia spp. Molecules 2022; 27:molecules27103274. [PMID: 35630751 PMCID: PMC9145346 DOI: 10.3390/molecules27103274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023] Open
Abstract
The increased use of polyphenols nowadays poses the need for identification of their new pharmacological targets. Recently, structure similarity-based virtual screening of DrugBank outlined pseudopurpurin, a hydroxyanthraquinone from Rubia cordifolia spp., as similar to gatifloxacin, a synthetic antibacterial agent. This suggested the bacterial DNA gyrase and DNA topoisomerase IV as potential pharmacological targets of pseudopurpurin. In this study, estimation of structural similarity to referent antibacterial agents and molecular docking in the DNA gyrase and DNA topoisomerase IV complexes were performed for a homologous series of four hydroxyanthraquinones. Estimation of shape- and chemical feature-based similarity with (S)-gatifloxacin, a DNA gyrase inhibitor, and (S)-levofloxacin, a DNA topoisomerase IV inhibitor, outlined pseudopurpurin and munjistin as the most similar structures. The docking simulations supported the hypothesis for a plausible antibacterial activity of hydroxyanthraquinones. The predicted docking poses were grouped into 13 binding modes based on spatial similarities in the active site. The simultaneous presence of 1-OH and 3-COOH substituents in the anthraquinone scaffold were emphasized as relevant features for the binding modes’ variability and ability of the compounds to strongly bind in the DNA-enzyme complexes. The results reveal new potential pharmacological targets of the studied polyphenols and help in their prioritization as drug candidates and dietary supplements.
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Affiliation(s)
- Petko Alov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (P.A.); (M.A.S.); (T.P.); (I.T.)
| | - Merilin Al Sharif
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (P.A.); (M.A.S.); (T.P.); (I.T.)
| | - Hristo Najdenski
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (H.N.); (M.M.Z.)
| | - Tania Pencheva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (P.A.); (M.A.S.); (T.P.); (I.T.)
| | - Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (P.A.); (M.A.S.); (T.P.); (I.T.)
| | - Maya Margaritova Zaharieva
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (H.N.); (M.M.Z.)
| | - Ilza Pajeva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (P.A.); (M.A.S.); (T.P.); (I.T.)
- Correspondence:
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6
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Pakamwong B, Thongdee P, Kamsri B, Phusi N, Kamsri P, Punkvang A, Ketrat S, Saparpakorn P, Hannongbua S, Ariyachaokun K, Suttisintong K, Sureram S, Kittakoop P, Hongmanee P, Santanirand P, Spencer J, Mulholland AJ, Pungpo P. Identification of Potent DNA Gyrase Inhibitors Active against Mycobacterium tuberculosis. J Chem Inf Model 2022; 62:1680-1690. [PMID: 35347987 DOI: 10.1021/acs.jcim.1c01390] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mycobacterium tuberculosis DNA gyrase manipulates the DNA topology using controlled breakage and religation of DNA driven by ATP hydrolysis. DNA gyrase has been validated as the enzyme target of fluoroquinolones (FQs), second-line antibiotics used for the treatment of multidrug-resistant tuberculosis. Mutations around the DNA gyrase DNA-binding site result in the emergence of FQ resistance in M. tuberculosis; inhibition of DNA gyrase ATPase activity is one strategy to overcome this. Here, virtual screening, subsequently validated by biological assays, was applied to select candidate inhibitors of the M. tuberculosis DNA gyrase ATPase activity from the Specs compound library (www.specs.net). Thirty compounds were identified and selected as hits for in vitro biological assays, of which two compounds, G24 and G26, inhibited the growth of M. tuberculosis H37Rv with a minimal inhibitory concentration of 12.5 μg/mL. The two compounds inhibited DNA gyrase ATPase activity with IC50 values of 2.69 and 2.46 μM, respectively, suggesting this to be the likely basis of their antitubercular activity. Models of complexes of compounds G24 and G26 bound to the M. tuberculosis DNA gyrase ATP-binding site, generated by molecular dynamics simulations followed by pharmacophore mapping analysis, showed hydrophobic interactions of inhibitor hydrophobic headgroups and electrostatic and hydrogen bond interactions of the polar tails, which are likely to be important for their inhibition. Decreasing compound lipophilicity by increasing the polarity of these tails then presents a likely route to improving the solubility and activity. Thus, compounds G24 and G26 provide attractive starting templates for the optimization of antitubercular agents that act by targeting DNA gyrase.
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Affiliation(s)
- Bongkochawan Pakamwong
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Paptawan Thongdee
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Bundit Kamsri
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Naruedon Phusi
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Pharit Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand
| | - Auradee Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand
| | - Sombat Ketrat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | | | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kanchiyaphat Ariyachaokun
- Department of Biological Science, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Khomson Suttisintong
- National Nanotechnology Center, NSTDA, 111 Thailand Science Park, Klong Luang, Pathum Thani 12120, Thailand
| | - Sanya Sureram
- Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Prasat Kittakoop
- Chulabhorn Research Institute, Bangkok 10210, Thailand
- Chulabhorn Graduate Institute, Chemical Biology Program, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok 10300, Thailand
| | - Poonpilas Hongmanee
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Pitak Santanirand
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
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7
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Frejat FOA, Cao Y, Wang L, Zhai H, Abdelazeem AH, Gomaa HAM, Youssif BGM, Wu C. New 1,2,4-oxadiazole/pyrrolidine hybrids as topoisomerase IV and DNA gyrase inhibitors with promising antibacterial activity. Arch Pharm (Weinheim) 2022; 355:e2100516. [PMID: 35363388 DOI: 10.1002/ardp.202100516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 11/09/2022]
Abstract
A series of hybridized pyrrolidine compounds with a 1,2,4-oxadiazole moiety were synthesized to develop effective molecules against the enzymes DNA gyrase and topoisomerase IV (Topo IV). Compounds 8-20 were developed based on a previously disclosed series of compounds from our lab, but with small structural modifications in the hopes of increasing the compounds' biological activity. In comparison to novobiocin, with IC50 = 170 nM, the findings of the DNA gyrase inhibitory assay revealed that compounds 16 and 17 were the most potent of all synthesized derivatives, with IC50 values of 180 and 210 nM, respectively. Compound 17 had the strongest inhibitory effect against Escherichia coli Topo IV of all the synthesized compounds, with an IC50 value of 13 µM, which was comparable to novobiocin (IC50 = 11 µM). Therefore, hybrids 16 and 17 appeared to be potential dual-target inhibitors. In the minimal inhibitory concentration (MIC) assays, compound 17 outperformed ciprofloxacin against E. coli, with an MIC of 55 ng/ml, compared to 60 ng/ml for ciprofloxacin. Finally, the docking study, along with the in vitro experiments, supports our promising approach to effectively develop potent leads for further optimization as dual DNA gyrase and Topo IV inhibitors.
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Affiliation(s)
- Firas O A Frejat
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, People's Republic of China.,Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Zhengzhou, People's Republic of China
| | - Yaquan Cao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, People's Republic of China.,Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Zhengzhou, People's Republic of China
| | - Lihong Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, People's Republic of China.,Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Zhengzhou, People's Republic of China
| | - Hongjin Zhai
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, People's Republic of China.,Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Zhengzhou, People's Republic of China
| | - Ahmed H Abdelazeem
- Department of Medicinal Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt.,Pharmacy Department, College of Pharmacy, Riyadh Elm University, Riyadh, Saudi Arabia
| | - Hesham A M Gomaa
- Pharmacology Department, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Chunli Wu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, People's Republic of China.,Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Zhengzhou, People's Republic of China
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8
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Abstract
Bacterial resistance to antibiotics threatens our progress in healthcare, modern medicine, food production and ultimately life expectancy. Antibiotic resistance is a global concern, which spreads rapidly across borders and continents due to rapid travel of people, animals and goods. Derivatives of metabolically stable pyrazole nucleus are known for their wide range of pharmacological properties, including antibacterial activities. This review highlights recent reports of pyrazole derivatives targeting different bacterial strains focusing on the drug-resistant variants. Pyrazole derivatives target different metabolic pathways of both Gram-positive and Gram-negative bacteria.
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9
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Rajput S, Kaur R, Jain N. Pd and photoredox dual catalysis assisted decarboxylative ortho-benzoylation of N-phenyl-7-azaindoles. Org Biomol Chem 2022; 20:1453-1461. [DOI: 10.1039/d1ob02338a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Directing group assisted decarboxylative ortho-benzoylation of N-aryl-7-azaindoles with α-keto acids has been achieved by synergistic visible light promoted photoredox and palladium catalysis. The approach tenders rapid entry to aryl ketone...
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10
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Modi G, Marqus GM, Vippila MR, Gollapalli DR, Kim Y, Manna AC, Chacko S, Maltseva N, Wang X, Cullinane RT, Zhang Y, Kotler JLM, Kuzmic P, Zhang M, Lawson AP, Joachimiak A, Cheung A, Snider BB, Rothstein DM, Cuny GD, Hedstrom L. The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections. ACS Infect Dis 2021; 7:3062-3076. [PMID: 34590817 DOI: 10.1021/acsinfecdis.1c00342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many bacterial pathogens, including Staphylococcus aureus, require inosine 5'-monophosphate dehydrogenase (IMPDH) for infection, making this enzyme a promising new target for antibiotics. Although potent selective inhibitors of bacterial IMPDHs have been reported, relatively few have displayed antibacterial activity. Here we use structure-informed design to obtain inhibitors of S. aureus IMPDH (SaIMPDH) that have potent antibacterial activity (minimal inhibitory concentrations less than 2 μM) and low cytotoxicity in mammalian cells. The physicochemical properties of the most active compounds were within typical Lipinski/Veber space, suggesting that polarity is not a general requirement for achieving antibacterial activity. Five compounds failed to display activity in mouse models of septicemia and abscess infection. Inhibitor-resistant S. aureus strains readily emerged in vitro. Resistance resulted from substitutions in the cofactor/inhibitor binding site of SaIMPDH, confirming on-target antibacterial activity. These mutations decreased the binding of all inhibitors tested, but also decreased catalytic activity. Nonetheless, the resistant strains had comparable virulence to wild-type bacteria. Surprisingly, strains expressing catalytically inactive SaIMPDH displayed only a mild virulence defect. Collectively these observations question the vulnerability of the enzymatic activity of SaIMPDH as a target for the treatment of S. aureus infections, suggesting other functions of this protein may be responsible for its role in infection.
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Affiliation(s)
- Gyan Modi
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Gary M. Marqus
- Graduate Program in Chemistry, Brandeis University, Waltham Massachusetts 02453, United States
| | - Mohana Rao Vippila
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Health Building 2, 4849 Calhoun Rd., Houston, Texas 77204, United States
| | | | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Adhar C. Manna
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Shibin Chacko
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xingyou Wang
- Graduate Program in Chemistry, Brandeis University, Waltham Massachusetts 02453, United States
| | - Ryan T. Cullinane
- Department of Biochemistry, Brandeis University, Massachusetts 02453, United States
| | - Yubo Zhang
- Department of Biochemistry, Brandeis University, Massachusetts 02453, United States
| | - Judy L. M. Kotler
- Graduate Program in Biochemistry and Biophysics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Petr Kuzmic
- BioKin Ltd., Watertown, Massachusetts 02472, United States
| | - Minjia Zhang
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Ann P. Lawson
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60367, United States
| | - Ambrose Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Barry B. Snider
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - David M. Rothstein
- David Rothstein Consulting, LLC, Lexington, Massachusetts 02421, United States
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Health Building 2, 4849 Calhoun Rd., Houston, Texas 77204, United States
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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11
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Sawano T, Matsui T, Koga M, Ishikawa E, Takeuchi R. Iridium-catalyzed C3-selective asymmetric allylation of 7-azaindoles with secondary allylic alcohols. Chem Commun (Camb) 2021; 57:9684-9687. [PMID: 34555140 DOI: 10.1039/d1cc03968g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The development of efficient synthetic methods of 7-azaindoles has been desired due to the useful biological activities and physical properties. We report the first example of the iridium-catalyzed C3-selective asymmetric allylation of 7-azaindoles with racemic secondary allylic alcohols to give only branched allylation products in good to high yields with high enantioselectivity (up to >99.5% ee). Allylic alcohols and 7-azaindoles with a variety of functional groups including halogen and heteroaromatic groups are compatible with the reaction conditions. Furthermore, transformations of the obtained allylation products are demonstrated without a significant loss of enantiomeric excess.
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Affiliation(s)
- Takahiro Sawano
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan.
| | - Takeshi Matsui
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan.
| | - Marina Koga
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan.
| | - Eri Ishikawa
- Department of Applied Chemistry, Chubu University, 1200 Matsumoto-cho, Kasugai 487-8501, Japan.
| | - Ryo Takeuchi
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan.
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12
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A Fine-Tuned Lipophilicity/Hydrophilicity Ratio Governs Antibacterial Potency and Selectivity of Bifurcated Halogen Bond-Forming NBTIs. Antibiotics (Basel) 2021; 10:antibiotics10070862. [PMID: 34356782 PMCID: PMC8300687 DOI: 10.3390/antibiotics10070862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022] Open
Abstract
Herein, we report the design of a focused library of novel bacterial topoisomerase inhibitors (NBTIs) based on innovative mainly monocyclic right-hand side fragments active against DNA gyrase and Topo IV. They exhibit a very potent and wide range of antibacterial activity, even against some of the most concerning hard-to-treat pathogens for which new antibacterials are urgently needed, as reported by the WHO and CDC. NBTIs enzyme activity and whole cell potency seems to depend on the fine-tuned lipophilicity/hydrophilicity ratio that governs the permeability of those compounds through the bacterial membranes. Lipophilicity of NBTIs is apparently optimal for passing through the membrane of Gram-positive bacteria, but the higher, although not excessive lipophilicity and suitable hydrophilicity seems to determine the passage through Gram-negative bacterial membranes. However, due to the considerable hERG inhibition, which is still at least two orders of magnitude away from MICs, continued optimization is required to realize their full potential.
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13
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Carpio Arévalo JM, Amorim JC. An in-silico analysis reveals 7,7'-bializarin as a promising DNA gyrase B inhibitor on Gram-positive and Gram-negative bacteria. Comput Biol Med 2021; 135:104626. [PMID: 34246160 DOI: 10.1016/j.compbiomed.2021.104626] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 10/21/2022]
Abstract
Bacterial diseases are considered by the World Health Organization to be one of the greatest threats to public health worldwide, mainly due to the increasingly frequent resistance to traditional antibiotics. Estimates from the World Bank indicate that the annual global economic impacts of antibiotic resistance will reach US$1.0-3.4 trillion by 2030. With this, the demand for studies aiming at the discovery of new antibiotics or molecules that may play a synergistic role within the spectrum of drug-resistant bacteria is of fundamental importance. In this in silico study, ligands generated from anthraquinones with established antibacterial activity were evaluated as potential inhibitors of the DNA gyrase subunit B of two species of Gram-positive and two Gram-negative bacteria. The main result of molecular docking-based virtual screening reveals several anthraquinones with remarkable binding energies, of which 7,7'-bializarin (ZINC000004783172) exhibited the highest value for all DNA gyrases subunit B studied and formed stable complexes, as evidenced by molecular dynamics simulations. Collectively, the results presented here reveal the potential of this molecule to bind tightly to the active site of DNA gyrases subunit B of Escherichia coli, Salmonella enterica (subtype typhi), Enterococcus faecalis, and Staphylococcus aureus, and therefore represents a promising candidate for further in vitro testing aimed at evaluating its antibacterial effect.
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Affiliation(s)
- Juan Marcelo Carpio Arévalo
- Academic Unit of Health and Wellness, Catholic University of Cuenca, De Las Américas y Humboldt Avenue, Cuenca, Azuay, Ecuador.
| | - Juliana Carolina Amorim
- Academic Unit of Health and Wellness, Catholic University of Cuenca, De Las Américas y Humboldt Avenue, Cuenca, Azuay, Ecuador.
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14
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Ligand-based pharmacophore modelling, in silico virtual screening, molecular docking and molecular dynamic simulation study to identify novel Francisella tularensis ParE inhibitors. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01274-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Structure-based drug repurposing to inhibit the DNA gyrase of Mycobacterium tuberculosis. Biochem J 2020; 477:4167-4190. [PMID: 33030198 DOI: 10.1042/bcj20200462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
Drug repurposing is an alternative avenue for identifying new drugs to treat tuberculosis (TB). Despite the broad-range of anti-tubercular drugs, the emergence of multi-drug-resistant and extensively drug-resistant strains of Mycobacterium tuberculosis (Mtb) H37Rv, as well as the significant death toll globally, necessitates the development of new and effective drugs to treat TB. In this study, we have employed a drug repurposing approach to address this drug resistance problem by screening the drugbank database to identify novel inhibitors of the Mtb target enzyme, DNA gyrase. The compounds were screened against the ATPase domain of the gyrase B subunit (MtbGyrB47), and the docking results showed that echinacoside, doxorubicin, epirubicin, and idarubicin possess high binding affinities against MtbGyrB47. Comprehensive assessment using fluorescence spectroscopy, surface plasmon resonance spectroscopy (SPR), and circular dichroism (CD) titration studies revealed echinacoside as a potent binder of MtbGyrB47. Furthermore, ATPase, and DNA supercoiling assays exhibited an IC50 values of 2.1-4.7 µM for echinacoside, doxorubicin, epirubicin, and idarubicin. Among these compounds, the least MIC90 of 6.3 and 12 μM were observed for epirubicin and echinacoside, respectively, against Mtb. Our findings indicate that echinacoside and epirubicin targets mycobacterial DNA gyrase, inhibit its catalytic cycle, and retard mycobacterium growth. Further, these compounds exhibit potential scaffolds for optimizing novel anti-mycobacterial agents that can act on drug-resistant strains.
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16
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Kannaboina P, Mondal K, Laha JK, Das P. Recent advances in the global ring functionalization of 7-azaindoles. Chem Commun (Camb) 2020; 56:11749-11762. [PMID: 32935671 DOI: 10.1039/d0cc04264a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The 7-azaindole building block has attracted considerable interest in the field of drug discovery in the current portfolio. Because of their powerful medicinal properties, the development of synthetic, elegant techniques for the functionalization of 7-azaindoles continues to be an active area of research. Advances in metal-catalyzed chemistry have recently supported the successful development of a number of novel and effective methods for functionalization of the 7-azaindole template. This review reports state-of-the-art functionalization chemistry of 7-azaindoles with an aspiration to highlight the global ring functionalization of 7-azaindoles that are potential as pharmacophores for various therapeutic targets. Other relevant reviews focused on 7-azaindole synthesis, properties and applications have also been reported. However, none of these reviews have been dedicated to the results achieved in the field of metal-catalyzed cross-coupling/C-H bond functionalized reactions. So we wish to discuss and summarize the advances made since 2011 in this field toward 7-azaindole functionalization.
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Affiliation(s)
- Prakash Kannaboina
- Department of Chemistry, Indian Institute of Technology (Indian School of Mines) Dhanbad, Dhanbad-826004, India.
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17
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Hu Y, Shi H, Zhou M, Ren Q, Zhu W, Zhang W, Zhang Z, Zhou C, Liu Y, Ding X, Shen HC, Yan SF, Dey F, Wu W, Zhai G, Zhou Z, Xu Z, Ji Y, Lv H, Jiang T, Wang W, Xu Y, Vercruysse M, Yao X, Mao Y, Yu X, Bradley K, Tan X. Discovery of Pyrido[2,3- b]indole Derivatives with Gram-Negative Activity Targeting Both DNA Gyrase and Topoisomerase IV. J Med Chem 2020; 63:9623-9649. [PMID: 32787097 DOI: 10.1021/acs.jmedchem.0c00768] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rise of multidrug resistant (MDR) Gram-negative (GN) pathogens and the decline of available antibiotics that can effectively treat these severe infections are a major threat to modern medicine. Developing novel antibiotics against MDR GN pathogens is particularly difficult as compounds have to permeate the GN double membrane, which has very different physicochemical properties, and have to circumvent a plethora of resistance mechanisms such as multiple efflux pumps and target modifications. The bacterial type II topoisomerases DNA gyrase (GyrA2B2) and Topoisomerase IV (ParC2E2) are highly conserved targets across all bacterial species and validated in the clinic by the fluoroquinolones. Dual inhibitors targeting the ATPase domains (GyrB/ParE) of type II topoisomerases can overcome target-based fluoroquinolone resistance. However, few ATPase inhibitors are active against GN pathogens. In this study, we demonstrated a successful strategy to convert a 2-carboxamide substituted azaindole chemical scaffold with only Gram-positive (GP) activity into a novel series with also potent activity against a range of MDR GN pathogens. By systematically fine-tuning the many physicochemical properties, we identified lead compounds such as 17r with a balanced profile showing potent GN activity, high aqueous solubility, and desirable PK features. Moreover, we showed the bactericidal efficacy of 17r using a neutropenic mouse thigh infection model.
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Affiliation(s)
| | | | | | - Qingcheng Ren
- WuXi AppTec (Wuhan) Co., Ltd., No. 666 Gaoxin Road, Wuhan East Lake High-tech Development Zone, Hubei 430075, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wen Wang
- MicuRx Pharmaceuticals, Inc. (Shanghai), Floor 3, Building B, 1976 Middle Gaoke Road, Shanghai 201210, China
| | - Yunhua Xu
- MicuRx Pharmaceuticals, Inc. (Shanghai), Floor 3, Building B, 1976 Middle Gaoke Road, Shanghai 201210, China
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18
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Discovery of novel multi-substituted benzo-indole pyrazole schiff base derivatives with antibacterial activity targeting DNA gyrase. Bioorg Chem 2020; 99:103807. [DOI: 10.1016/j.bioorg.2020.103807] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/25/2020] [Accepted: 03/28/2020] [Indexed: 01/14/2023]
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19
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Second-generation 4,5,6,7-tetrahydrobenzo[ d]thiazoles as novel DNA gyrase inhibitors. Future Med Chem 2020; 12:277-297. [PMID: 32043377 DOI: 10.4155/fmc-2019-0127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: DNA gyrase and topoisomerase IV are essential bacterial enzymes, and in the fight against bacterial resistance, they are important targets for the development of novel antibacterial drugs. Results: Building from our first generation of 4,5,6,7-tetrahydrobenzo[d]thiazole-based DNA gyrase inhibitors, we designed and prepared an optimized series of analogs that show improved inhibition of DNA gyrase and topoisomerase IV from Staphylococcus aureus and Escherichia coli, with IC50 values in the nanomolar range. Importantly, these inhibitors also show improved antibacterial activity against Gram-positive strains. Conclusion: The most promising inhibitor, 29, is active against Enterococcus faecalis, Enterococcus faecium and S. aureus wild-type and resistant strains, with minimum inhibitory concentrations between 4 and 8 μg/ml, which represents good starting point for development of novel antibacterials.
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20
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Azam MA, Thathan J, Jupudi S. Pharmacophore modeling, atom based 3D-QSAR, molecular docking and molecular dynamics studies on Escherichia coli ParE inhibitors. Comput Biol Chem 2019; 84:107197. [PMID: 31901788 DOI: 10.1016/j.compbiolchem.2019.107197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 10/25/2022]
Abstract
ATP dependent ParE enzyme is as an attractive target for the development of antibacterial agents. Atom based 3D-QSAR model AADHR.187 was developed based on the thirty eight Escherichia coli ParE inhibitors. The generated model showed statistically significant coefficient of determinations for the training (R2 = 0.985) and test (R2 = 0.86) sets. The cross-validated correlation coefficient (q2) was 0.976. The utility of the generated model was validated by the enrichment study. The model was also validated with structurally diverse external test set of ten compounds. Contour plot analysis of the generated model unveiled the chemical features necessary for the E. coli ParE enzyme inhibition. Extra-precision docking result revealed that hydrogen bonding and ionic interactions play a major role in ParE protein-ligand binding. Binding free energy was computed for the data set inhibitors to validate the binding affinity. A 30-ns molecular dynamics simulation showed high stability and effective binding of inhibitor 34 within the active site of ParE enzyme. Using the best fitted model AADHR.187, pharmacophore-based high-throughput virtual screening was performed to identify virtual hits. Based on the above studies three new molecules are proposed as E. coli ParE inhibitors with high binding affinity and favourable ADME properties.
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Affiliation(s)
- Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1).
| | - Janarthanan Thathan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1)
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1)
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21
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Synthesis, Docking Studies, and In Vitro Evaluation of Some Novel Thienopyridines and Fused Thienopyridine-Quinolines as Antibacterial Agents and DNA Gyrase Inhibitors. Molecules 2019; 24:molecules24203650. [PMID: 31658631 PMCID: PMC6832920 DOI: 10.3390/molecules24203650] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/03/2019] [Accepted: 10/06/2019] [Indexed: 01/05/2023] Open
Abstract
A series of novel thienopyridines and pyridothienoquinolines (3a,b–14) was synthesized, starting with 2-thioxo-1,2-dihydropyridine-3-carbonitriles 1a and 1b. All compounds were evaluated for their in vitro antimicrobial activity against six bacterial strains. Compounds 3a,b, 4a, 5b, 6a,b, 7a, 9b, 12b, and 14 showed significant growth inhibition activity against both Gram-positive and Gram-negative bacteria compared with the reference drug. The most active compounds (4a, 7a, 9b, and 12b) against Staphylococcus aureus were also tested for their in vitro inhibitory action on methicillin-resistant Staphylococcus aureus (MRSA). The tested compounds showed promising inhibition activity, with the performance of 12b being equal to gentamicin and that of 7a exceeding it. Moreover, the most promising compounds were also screened for their Escherichia coli DNA gyrase inhibitory activity, compared with novobiocin as a reference DNA gyrase inhibitor. The results revealed that compounds (3a, 3b, 4a, 9b, and 12b) had the highest inhibitory capacity, with IC50 values of 2.26–5.87 µM (that of novobiocin is equal to 4.17 µM). Docking studies were performed to identify the mode of binding of the tested compounds to the active site of E. coli DNA gyrase B.
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22
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Design, synthesis and molecular modeling studies of new series of s-triazine derivatives as antimicrobial agents against multi-drug resistant clinical isolates. Bioorg Chem 2019; 89:103013. [DOI: 10.1016/j.bioorg.2019.103013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/08/2019] [Accepted: 05/24/2019] [Indexed: 01/13/2023]
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23
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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.
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24
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Wang J, Zhao C, Tu J, Yang H, Zhang X, Lv W, Zhai H. Design of novel quinoline-aminopiperidine derivatives as Mycobacterium tuberculosis (MTB) GyrB inhibitors: an in silico study. J Biomol Struct Dyn 2018; 37:2913-2925. [DOI: 10.1080/07391102.2018.1498806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Juan Wang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, PR China
| | - Chenxi Zhao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, PR China
| | - Jing Tu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, PR China
| | - Hong Yang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, PR China
| | - Xiaoyun Zhang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, PR China
| | - Wenjuan Lv
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, PR China
| | - Honglin Zhai
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, PR China
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25
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Ivanova АE, Burgart YV, Saloutin VI. 3-Polyfluoroalkyl-1,5-diphenylpyrazoles in Suzuki Cross-Coupling Reactions. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1070428018080250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Lessing T, van Mark H, Müller TJJ. Substituted 1H-1,2,3-Triazol-4-yl-1H-pyrrolo[2,3-b]pyridines by De Novo One-Pot Ring-Forming Coupling/Cyclization/Desilylation Cu Alkyne/Azide Cycloaddition (AAC) Sequence. Chemistry 2018; 24:8974-8979. [PMID: 29726615 DOI: 10.1002/chem.201801632] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Indexed: 11/06/2022]
Abstract
Substituted 1H-1,2,3-triazol-4-yl-pyrrolo[2,3-b]pyridines are efficiently prepared by a one-pot coupling/cyclization/desilylation Cu alkyne/azide cycloaddition (CuAAC) sequence in the sense of a consecutive three-component fashion. The key feature of this new de novo formation of azole and triazole anellation is the sequentially Pd/Cu-catalyzed process employing tri(iso-propyl)silyl (TIPS) butadiyne as a four-carbon building block. In addition, the sequence can be expanded in a four-component fashion also employing the in situ formation of the required azides.
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Affiliation(s)
- Timo Lessing
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, d-40225, Düsseldorf, Germany
| | - Hauke van Mark
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, d-40225, Düsseldorf, Germany
| | - Thomas J J Müller
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, d-40225, Düsseldorf, Germany
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27
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McGarry DH, Cooper IR, Walker R, Warrilow CE, Pichowicz M, Ratcliffe AJ, Salisbury AM, Savage VJ, Moyo E, Maclean J, Smith A, Charrier C, Stokes NR, Lindsay DM, Kerr WJ. Design, synthesis and antibacterial properties of pyrimido[4,5-b]indol-8-amine inhibitors of DNA gyrase. Bioorg Med Chem Lett 2018; 28:2998-3003. [PMID: 30122228 DOI: 10.1016/j.bmcl.2018.05.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/24/2018] [Accepted: 05/26/2018] [Indexed: 01/12/2023]
Abstract
According to the World Health Organization (WHO), approximately 1.7 million deaths per year are caused by tuberculosis infections. Furthermore, it has been predicted that, by 2050, antibacterial resistance will be the cause of approximately 10 million deaths annually if the issue is not tackled. As a result, novel approaches to treating broad-spectrum bacterial infections are of vital importance. During the course of our wider efforts to discover unique methods of targeting multidrug-resistant (MDR) pathogens, we identified a novel series of amide-linked pyrimido[4,5-b]indol-8-amine inhibitors of bacterial type II topoisomerases. Compounds from the series were highly potent against gram-positive bacteria and mycobacteria, with excellent potency being retained against a panel of relevant Mycobacterium tuberculosis drug-resistant clinical isolates.
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Affiliation(s)
- David H McGarry
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom.
| | - Ian R Cooper
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - Rolf Walker
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | | | - Mark Pichowicz
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | | | | | | | - Emmanuel Moyo
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - John Maclean
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - Andrew Smith
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - Cédric Charrier
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - Neil R Stokes
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - David M Lindsay
- Department of Pure and Applied Chemistry, University of Strathclyde, WestCHEM, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - William J Kerr
- Department of Pure and Applied Chemistry, University of Strathclyde, WestCHEM, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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Benedetto Tiz D, Kikelj D, Zidar N. Overcoming problems of poor drug penetration into bacteria: challenges and strategies for medicinal chemists. Expert Opin Drug Discov 2018; 13:497-507. [PMID: 29566560 DOI: 10.1080/17460441.2018.1455660] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Bacterial cell walls and membranes provide essential protection for bacteria against environmental influences. Different bacteria possess different cell envelopes and understanding each of these structures is crucial for the design of effective antibacterial drugs whose targets are intracellular. Optimal properties of drugs that are required for their entry into bacteria are still hard to predict. The guidelines that are suitable and well established for the penetration of a drug into eukaryotic cells are poorly adaptable to the complex world of pathogens. Areas covered: The factors that govern the penetration of anti-infection drugs into bacteria are examined and the available strategies to overcome this therapeutically very important barrier are reviewed. The areas covered include optimization of the physicochemical properties of compounds, utilization of iron-chelating compounds, i.e. siderophores, the use of efflux pump inhibitors, and of carriers such as liposomes. Expert opinion: Although several rules governing permeation have recently been proposed for effective antibacterial drugs, none of them has been so far established as the 'golden' rule. Thus, new research is needed to find a more general approach on how to increase the concentration of antibacterial compounds in bacterial cells.
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Affiliation(s)
| | - Danijel Kikelj
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | - Nace Zidar
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
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29
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Pan C, Wang Y, Wu C, Yu JT. Iridium-catalyzed C–H phosphoramidation of N-aryl-7-azaindoles with phosphoryl azides. Org Biomol Chem 2018; 16:3711-3715. [DOI: 10.1039/c8ob00776d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An iridium-catalyzed C–H phosphoramidation of N-aryl-7-azaindoles with phosphoryl azides was developed, affording a series of 7-azaindole phenylphosphoramidates.
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Affiliation(s)
- Changduo Pan
- School of Chemical & Environmental Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Yun Wang
- School of Chemical & Environmental Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Chao Wu
- School of Chemical & Environmental Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Jin-Tao Yu
- School of Petrochemical Engineering
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology
- Changzhou University
- Changzhou 213164
- P. R. China
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30
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Jeon M, Park J, Dey P, Oh Y, Oh H, Han S, Um SH, Kim HS, Mishra NK, Kim IS. Site-Selective Rhodium(III)-Catalyzed C−H Amination of 7-Azaindoles with Anthranils: Synthesis and Anticancer Evaluation. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700800] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mijin Jeon
- School of Pharmacy; Sungkyunkwan University; Suwon 16419 Republic of Korea
| | - Jihye Park
- School of Pharmacy; Sungkyunkwan University; Suwon 16419 Republic of Korea
| | - Prasanta Dey
- School of Pharmacy; Sungkyunkwan University; Suwon 16419 Republic of Korea
| | - Yongguk Oh
- School of Pharmacy; Sungkyunkwan University; Suwon 16419 Republic of Korea
| | - Hyunjung Oh
- School of Pharmacy; Sungkyunkwan University; Suwon 16419 Republic of Korea
| | - Sangil Han
- School of Pharmacy; Sungkyunkwan University; Suwon 16419 Republic of Korea
| | - Sung Hee Um
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University; School of Medicine; Suwon 16419 Republic of Korea
| | - Hyung Sik Kim
- School of Pharmacy; Sungkyunkwan University; Suwon 16419 Republic of Korea
| | | | - In Su Kim
- School of Pharmacy; Sungkyunkwan University; Suwon 16419 Republic of Korea
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31
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Azam MA, Thathan J. Pharmacophore generation, atom-based 3D-QSAR and molecular dynamics simulation analyses of pyridine-3-carboxamide-6-yl-urea analogues as potential gyrase B inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:275-296. [PMID: 28399673 DOI: 10.1080/1062936x.2017.1310131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 03/20/2017] [Indexed: 06/07/2023]
Abstract
DNA gyrase subunit B (GyrB) is an attractive drug target for the development of antibacterial agents with therapeutic potential. In the present study, computational studies based on pharmacophore modelling, atom-based QSAR, molecular docking, free binding energy calculation and dynamics simulation were performed on a series of pyridine-3-carboxamide-6-yl-urea derivatives. A pharmacophore model using 49 molecules revealed structural and chemical features necessary for these molecules to inhibit GyrB. The best fitted model AADDR.13 was generated with a coefficient of determination (r²) of 0.918. This model was validated using test set molecules and had a good r² of 0.78. 3D contour maps generated by the 3D atom-based QSAR revealed the key structural features responsible for the GyrB inhibitory activity. Extra precision molecular docking showed hydrogen bond interactions with key amino acid residues of ATP-binding pocket, important for inhibitor binding. Further, binding free energy was calculated by the MM-GBSA rescoring approach to validate the binding affinity. A 10 ns MD simulation of inhibitor #47 showed the stability of the predicted binding conformations. We identified 10 virtual hits by in silico high-throughput screening. A few new molecules were also designed as potent GyrB inhibitors. The information obtained from these methodologies may be helpful to design novel inhibitors of GyrB.
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Affiliation(s)
- M A Azam
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy (A Constituent College of Jagadguru Sri Sivarathreeswara University, Mysuru) , Tamil Nadu , India
| | - J Thathan
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy (A Constituent College of Jagadguru Sri Sivarathreeswara University, Mysuru) , Tamil Nadu , India
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32
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Discovery of substituted oxadiazoles as a novel scaffold for DNA gyrase inhibitors. Eur J Med Chem 2017; 130:171-184. [DOI: 10.1016/j.ejmech.2017.02.046] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 01/06/2023]
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33
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Synthesis, molecular docking, antimycobacterial and antimicrobial evaluation of new pyrrolo[3,2-c]pyridine Mannich bases. Eur J Med Chem 2017; 131:275-288. [PMID: 28340368 DOI: 10.1016/j.ejmech.2017.03.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/05/2017] [Accepted: 03/10/2017] [Indexed: 11/23/2022]
Abstract
In this report, we describe the synthesis and biological evaluation of a new series of pyrrolo[3,2-c]pyridine Mannich bases (7a-v). The Mannich bases were obtained in good yields by one-pot three component condensation of pyrrolo[3,2-c]pyridine scaffold (6a-c) with secondary amines and excess of formaldehyde solution in AcOH. The chemical structures of the compounds were characterized by 1H NMR, 13C NMR, LC/MS and elemental analysis. Single crystal X-ray diffraction has been recorded for compound 7k ([C23H29ClN4]+2, H2O). The in vitro antimicrobial activities of the compounds were evaluated against various bacterial and fungal strains using Agar diffusion method and Broth micro dilution method. Compounds 7e, 7f, 7r, 7t, and 7u were showed good Gram-positive antibacterial activity against S. aureus, B. flexus, C. sporogenes and S. mutans. Furthermore, in vitro antimycobacterial activity was evaluated against Mycobacterium tuberculosis H37Rv (ATCC 27294) using MABA. Compounds 7r, 7t, and 7u were showed good antitubercular activity against Mtb (MIC ≥6.25 μg/mL). Among the tested compounds, 1-((4-chloro-2-(cyclohexylmethyl)-1H-pyrrolo[3,2-c]pyridin-3-yl)methyl)piperidine-3-carboxamide (7t) was showed excellent antimycobacterial activity against Mtb (MIC <0.78 μg/mL) and low cytotoxicity against the HEK-293T cell line (SI >>25). Molecular docking of the active compounds against glutamate racemase (MurI) and Mtb glutamine synthetase were explained the structure-activity observed in vitro.
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34
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Molecular insights on analogs of imidazo[1,2-a]pyridine, azaindole, and pyridylurea towards ParE using pharmacophore modeling, molecular docking, and dynamic simulation. Struct Chem 2017. [DOI: 10.1007/s11224-017-0919-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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35
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Priyanka, Singh V, Ekta, Katiyar D. Synthesis, antimicrobial, cytotoxic and E. coli DNA gyrase inhibitory activities of coumarinyl amino alcohols. Bioorg Chem 2017; 71:120-127. [PMID: 28196603 DOI: 10.1016/j.bioorg.2017.01.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/01/2017] [Accepted: 01/29/2017] [Indexed: 12/20/2022]
Abstract
Here we report the in vitro antimicrobial activity (minimum inhibitory concentration) of fourteen coumarinyl amino alcohols 2-16 against eight bacterial strains and two fungi. Among these compounds 4, 8, 12, 15 and 16 showed moderate to good microbial inhibition with MIC values varied from 6.25 to 25μg/mL. The most promising compounds were also evaluated for their in vitro cytotoxic and E. coli DNA gyrase inhibitory activities along with the two 7-oxy-4-methyl coumarinyl amino alcohol derivatives 17 and 18, which were found to be the most potent in in vitro antimicrobial screening in our previous study. All the active compounds, including 17 and 18, were also docked into the E. coli DNA gyrase ATP binding site (PDB ID: 1KZN) to investigate their binding interactions. Of these compound 17 has shown maximum binding energy value of -6.13kcal/mol.
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Affiliation(s)
- Priyanka
- Department of Chemistry, MMV, Banaras Hindu University, Varanasi 221005, India
| | - Vineeta Singh
- Department of Biotechnology, Institute of Engineering and Technology, Lucknow 226021, India
| | - Ekta
- Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi 221005, India
| | - Diksha Katiyar
- Department of Chemistry, MMV, Banaras Hindu University, Varanasi 221005, India.
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36
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Tomašič T, Mirt M, Barančoková M, Ilaš J, Zidar N, Tammela P, Kikelj D. Design, synthesis and biological evaluation of 4,5-dibromo-N-(thiazol-2-yl)-1H-pyrrole-2-carboxamide derivatives as novel DNA gyrase inhibitors. Bioorg Med Chem 2017; 25:338-349. [DOI: 10.1016/j.bmc.2016.10.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/27/2016] [Accepted: 10/29/2016] [Indexed: 11/25/2022]
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37
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El-Hiti GA, Smith K, Hegazy AS, Masmali AM, Kariuki BM. Crystal structure of 3-tert-butyl-7-azadioxindole, C11H14N2O2. Z KRIST-NEW CRYST ST 2016. [DOI: 10.1515/ncrs-2016-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractC11H14N2O2, orthorhombic, P212121 (no. 19), a = 7.3227(3) Å, b = 10.9955(4) Å, c = 26.3709(9) Å, V = 2123.30(14) Å3, Z = 8, Rgt(F) = 0.0372, wRref(F2) = 0.0907, T = 150 K.
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Affiliation(s)
- Gamal A. El-Hiti
- 1Cornea Research Chair, Department of Optometry, College of Applied Medical Sciences, King Saud University, P. O. Box 10219, Riyadh 11433, Saudi Arabia
| | - Keith Smith
- 2School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom of Great Britain and Northern Ireland
| | - Amany S. Hegazy
- 2School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom of Great Britain and Northern Ireland
| | - Ali M. Masmali
- 1Cornea Research Chair, Department of Optometry, College of Applied Medical Sciences, King Saud University, P. O. Box 10219, Riyadh 11433, Saudi Arabia
| | - Benson M. Kariuki
- 2School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom of Great Britain and Northern Ireland
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38
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Singla P, Luxami V, Paul K. Pyrrolo[2,3- b]pyridine Derivatives: Synthesis and Preliminary Evaluation of their Calf Thymus DNA Binding Properties. ChemistrySelect 2016. [DOI: 10.1002/slct.201600801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Prinka Singla
- School of Chemistry and Biochemistry; Thapar University; Patiala- 147001 India
| | - Vijay Luxami
- School of Chemistry and Biochemistry; Thapar University; Patiala- 147001 India
| | - Kamaldeep Paul
- School of Chemistry and Biochemistry; Thapar University; Patiala- 147001 India
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39
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Chaudhari K, Surana S, Jain P, Patel HM. Mycobacterium Tuberculosis (MTB) GyrB inhibitors: An attractive approach for developing novel drugs against TB. Eur J Med Chem 2016; 124:160-185. [PMID: 27569197 DOI: 10.1016/j.ejmech.2016.08.034] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/03/2016] [Accepted: 08/17/2016] [Indexed: 01/24/2023]
Abstract
New classes of drugs are needed to treat tuberculosis (TB) in order to combat the emergence of resistance (MDR and XDR) to existing agents and shorten the duration of therapy. Mycobacterial DNA gyrase B subunit has been identified to be one of the potentially under exploited drug targets in the field of antitubercular drug discovery. In the present review, we discussed the synthesis, structural optimization and docking study of effective potent DNA gyrase inhibitor against M. tuberculosis, with improved properties such as enhanced activity against MDR strains, reduced toxicity. Based on this progress, if we can successfully leverage the opportunities in this target, there is hope that we will be able to raise novel gyrase inhibitor in earnest in the long.
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Affiliation(s)
- Kavita Chaudhari
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India
| | - Pritam Jain
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India.
| | - Harun M Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India.
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40
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Li Y, Wong YL, Ng FM, Liu B, Wong YX, Poh ZY, Liu S, Then SW, Lee MY, Ng HQ, Huang Q, Hung AW, Cherian J, Hill J, Keller TH, Kang C. Escherichia coli Topoisomerase IV E Subunit and an Inhibitor Binding Mode Revealed by NMR Spectroscopy. J Biol Chem 2016; 291:17743-53. [PMID: 27365392 PMCID: PMC5016168 DOI: 10.1074/jbc.m116.737429] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/29/2016] [Indexed: 11/06/2022] Open
Abstract
Bacterial topoisomerases are attractive antibacterial drug targets because of their importance in bacterial growth and low homology with other human topoisomerases. Structure-based drug design has been a proven approach of efficiently developing new antibiotics against these targets. Past studies have focused on developing lead compounds against the ATP binding pockets of both DNA gyrase and topoisomerase IV. A detailed understanding of the interactions between ligand and target in a solution state will provide valuable information for further developing drugs against topoisomerase IV targets. Here we describe a detailed characterization of a known potent inhibitor containing a 9H-pyrimido[4,5-b]indole scaffold against the N-terminal domain of the topoisomerase IV E subunit from Escherichia coli (eParE). Using a series of biophysical and biochemical experiments, it has been demonstrated that this inhibitor forms a tight complex with eParE. NMR studies revealed the exact protein residues responsible for inhibitor binding. Through comparative studies of two inhibitors of markedly varied potencies, it is hypothesized that gaining molecular interactions with residues in the α4 and residues close to the loop of β1-α2 and residues in the loop of β3-β4 might improve the inhibitor potency.
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Affiliation(s)
- Yan Li
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Ying Lei Wong
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Fui Mee Ng
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Boping Liu
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Yun Xuan Wong
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Zhi Ying Poh
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Shuang Liu
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Siew Wen Then
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Michelle Yueqi Lee
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Hui Qi Ng
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Qiwei Huang
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Alvin W Hung
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Joseph Cherian
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Jeffrey Hill
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Thomas H Keller
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - CongBao Kang
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
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41
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Isolation and characterization of 2-hydroxy-9,10-anthraquinone from Streptomyces olivochromogenes (ERINLG-261) with antimicrobial and antiproliferative properties. REVISTA BRASILEIRA DE FARMACOGNOSIA-BRAZILIAN JOURNAL OF PHARMACOGNOSY 2016. [DOI: 10.1016/j.bjp.2015.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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42
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Synthesis and evaluation of biological activities of new sulfonamide and carbamate derivatives of 1H-pyrrolo[2,3-b]pyridine (7-azaindole). RESEARCH ON CHEMICAL INTERMEDIATES 2016. [DOI: 10.1007/s11164-016-2547-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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43
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Zidar N, Tomašič T, Macut H, Sirc A, Brvar M, Montalvão S, Tammela P, Ilaš J, Kikelj D. New N-phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATPase inhibitors of DNA gyrase. Eur J Med Chem 2016; 117:197-211. [PMID: 27100032 DOI: 10.1016/j.ejmech.2016.03.079] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/25/2016] [Accepted: 03/26/2016] [Indexed: 12/26/2022]
Abstract
Following the withdrawal of novobiocin, the introduction of a new ATPase inhibitor of DNA gyrase to the clinic would add the first representative of this mechanistic class to the antibacterial pipeline. This would be of great importance because of the well-known problems associated with antibacterial resistance. Using structure-based design and starting from the recently determined crystal structure of the N-phenyl-4,5-dibromopyrrolamide inhibitor-DNA gyrase B complex, we have prepared 28 new N-phenyl-4,5-dibromopyrrolamides and N-phenylindolamides and evaluated them against DNA gyrase from Escherichia coli. The most potent compound was 2-((4-(4,5-dibromo-1H-pyrrole-2-carboxamido)phenyl)amino)-2-oxoacetic acid (9a), with an IC50 of 0.18 μM against E. coli gyrase. A selected set of compounds was evaluated against DNA gyrase from Staphylococcus aureus and against topoisomerase IV from E. coli and S. aureus, but the activities were weaker. The binding affinity of 2-((4-(4,5-dibromo-1H-pyrrole-2-carboxamido)phenyl)amino)-2-oxoacetic acid (9a) to E. coli gyrase was studied using surface plasmon resonance. In the design of the present series, the focus was on the optimisation of biological activities of compounds - especially by varying their size, the position and orientation of key functional groups, and their acid-base properties. The structure-activity relationship (SAR) was examined and the results were rationalised with molecular docking.
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Affiliation(s)
- Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.
| | - Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Helena Macut
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Anja Sirc
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Matjaž Brvar
- National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
| | - Sofia Montalvão
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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44
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Bobesh KA, Renuka J, Srilakshmi RR, Yellanki S, Kulkarni P, Yogeeswari P, Sriram D. Replacement of cardiotoxic aminopiperidine linker with piperazine moiety reduces cardiotoxicity? Mycobacterium tuberculosis novel bacterial topoisomerase inhibitors. Bioorg Med Chem 2015; 24:42-52. [PMID: 26678175 DOI: 10.1016/j.bmc.2015.11.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/20/2015] [Accepted: 11/28/2015] [Indexed: 11/26/2022]
Abstract
Recently numerous non-fluoroquinolone-based bacterial type II topoisomerase inhibitors from both the GyrA and GyrB classes have been reported as antibacterial agents. Inhibitors of the GyrA class include aminopiperidine-based novel bacterial type II topoisomerase inhibitors (NBTIs). However, inhibition of the cardiac ion channel remains a serious liability for the aminopiperidine based NBTIs. In this paper we replaced central aminopiperidine linker with piperazine moiety and tested for its biological activity. We developed a series of twenty four compounds with a piperazine linker 1-(2-(piperazin-1-yl)ethyl)-1,5-naphthyridin-2(1H)-one, by following a multistep protocol. Among them compound 4-(2-(7-methoxy-2-oxo-1,5-naphthyridin-1(2H)-yl)ethyl)-N-(4-nitrophenyl)piperazine-1-carboxamide (11) was the most promising inhibitor with Mycobacterium tuberculosis (MTB) DNA gyrase enzyme supercoiling IC50 of 0.29±0.22μM, with a good MTB MIC of 3.45μM. These kind of compounds retains good potency and showed reduced cardiotoxicity compared to aminopiperidines.
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Affiliation(s)
- Karyakulam Andrews Bobesh
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawaharnagar, Hyderabad 500078, India
| | - Janupally Renuka
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawaharnagar, Hyderabad 500078, India
| | - Rudraraju Reshma Srilakshmi
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawaharnagar, Hyderabad 500078, India
| | - Swapna Yellanki
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Zephase Therapeutics (an Incubated Company at the Dr Reddy's Institute of Life Sciences), University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India
| | - Pushkar Kulkarni
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Zephase Therapeutics (an Incubated Company at the Dr Reddy's Institute of Life Sciences), University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India
| | - Perumal Yogeeswari
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawaharnagar, Hyderabad 500078, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawaharnagar, Hyderabad 500078, India.
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45
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Li Y, Wong YX, Poh ZY, Wong YL, Lee MY, Ng HQ, Liu B, Hung AW, Cherian J, Hill J, Keller TH, Kang C. NMR structural characterization of the N-terminal active domain of the gyrase B subunit from Pseudomonas aeruginosa and its complex with an inhibitor. FEBS Lett 2015; 589:2683-9. [PMID: 26272827 DOI: 10.1016/j.febslet.2015.07.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/08/2015] [Accepted: 07/26/2015] [Indexed: 01/18/2023]
Abstract
The N-terminal ATP binding domain of the DNA gyrase B subunit is a validated drug target for antibacterial drug discovery. Structural information for this domain (pGyrB) from Pseudomonas aeruginosa is still missing. In this study, the interaction between pGyrB and a bis-pyridylurea inhibitor was characterized using several biophysical methods. We further carried out structural analysis of pGyrB using NMR spectroscopy. The secondary structures of free and inhibitor bound pGyrB were obtained based on backbone chemical shift assignment. Chemical shift perturbation and NOE experiments demonstrated that the inhibitor binds to the ATP binding pocket. The results of this study will be helpful for drug development targeting P. aeruginosa.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Yun Xuan Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Zhi Ying Poh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Boping Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Joseph Cherian
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
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46
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Chennakesava Rao K, Easwaramoorthi K, Arun Y, Balachandran C, Muralidhara Rao KS, Govindhan M, Emi N, Prakasam T, Perumal PT. Synthesis of BF₃ catalyzed Mannich derivatives with excellent ee from phenylpropanolamine, study of their antimicrobial activity and molecular docking. Bioorg Med Chem Lett 2015; 25:4232-8. [PMID: 26296475 DOI: 10.1016/j.bmcl.2015.07.096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/05/2015] [Accepted: 07/31/2015] [Indexed: 01/31/2023]
Abstract
Antimicrobial agents 4a-g and 5a-g with very good potency were synthesized with 100% ee from phenylpropanolamine (norephedrine) by BF3 catalyzed three components one pot Mannich reaction in good yields. Obtained compounds were characterized using spectral techniques. Antimicrobial study of these compounds revealed a good to very high potential activity against tested microbes when compared to standard antimicrobial drugs streptomycin and ketoconazole. These synthesized compounds exhibited significant minimum inhibitory concentration (MIC) values against Gram positive and Gram negative bacteria. Amongst compound 4b, 4c, 4d, 4e, 5a, and 5e exhibited very high potent MIC values against tested twelve bacteria and three fungi when compared to control. When subjected to molecular docking, in silico studies revealed significant binding energies ranging from -7.06 to -8.90 kcal/mol for all obtained compounds towards target receptor DNA topoisomerase IV and amongst compounds 4b and 4d have shown maximum binding energies 8.70 and 8.90 kcal/mol, respectively.
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Affiliation(s)
- K Chennakesava Rao
- Organic Chemistry Division, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, Tamil Nadu, India; R&D Center, Malladi Drugs & Pharmaceuticals Ltd, Poonamalle, Chennai 600124, Tamil Nadu, India
| | - K Easwaramoorthi
- R&D Center, Malladi Drugs & Pharmaceuticals Ltd, Poonamalle, Chennai 600124, Tamil Nadu, India
| | - Y Arun
- Organic Chemistry Division, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, Tamil Nadu, India
| | - C Balachandran
- Department of Hematology, Fujita Health University, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - K S Muralidhara Rao
- R&D Center, Malladi Drugs & Pharmaceuticals Ltd, Poonamalle, Chennai 600124, Tamil Nadu, India
| | - M Govindhan
- Department of Chemistry, Anna University, Guindy, Chennai 600020, Tamil Nadu, India
| | - Nobuhiko Emi
- Department of Hematology, Fujita Health University, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - T Prakasam
- R&D Center, Malladi Drugs & Pharmaceuticals Ltd, Poonamalle, Chennai 600124, Tamil Nadu, India
| | - P T Perumal
- Organic Chemistry Division, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, Tamil Nadu, India.
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47
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Azam MA, Thathan J, Jubie S. Dual targeting DNA gyrase B (GyrB) and topoisomerse IV (ParE) inhibitors: A review. Bioorg Chem 2015; 62:41-63. [PMID: 26232660 DOI: 10.1016/j.bioorg.2015.07.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 01/03/2023]
Abstract
GyrB and ParE are type IIA topoisomerases and found in most bacteria. Its function is vital for DNA replication, repair and decatenation. The highly conserved ATP-binding subunits of DNA GyrB and ParE are structurally related and have been recognized as prime candidates for the development of dual-targeting antibacterial agents with broad-spectrum potential. However, no natural product or small molecule inhibitors targeting ATPase catalytic domain of both GyrB and ParE enzymes have succeeded in the clinic. Moreover, no inhibitors of these enzymes with broad-spectrum antibacterial activity against Gram-negative pathogens have been reported. Availability of high resolution crystal structures of GyrB and ParE made it possible for the design of many different classes of inhibitors with dual mechanism of action. Among them benzimidazoles, benzothiazoles, thiazolopyridines, imidiazopyridazoles, pyridines, indazoles, pyrazoles, imidazopyridines, triazolopyridines, pyrrolopyrimidines, pyrimidoindoles as well as related structures are disclosed in literatures. Unfortunately most of these inhibitors are found to be active against Gram-positive pathogens. In the present review we discuss about studies on novel dual targeting ATPase inhibitors.
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Affiliation(s)
- Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of JSS University, Mysore), Udhagamandalam 643001, Tamil Nadu, India.
| | - Janarthanan Thathan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of JSS University, Mysore), Udhagamandalam 643001, Tamil Nadu, India
| | - Selvaraj Jubie
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of JSS University, Mysore), Udhagamandalam 643001, Tamil Nadu, India
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48
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Zidar N, Macut H, Tomašič T, Brvar M, Montalvão S, Tammela P, Solmajer T, Peterlin Mašič L, Ilaš J, Kikelj D. N-Phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATP Competitive DNA Gyrase B Inhibitors: Design, Synthesis, and Evaluation. J Med Chem 2015; 58:6179-94. [PMID: 26126187 DOI: 10.1021/acs.jmedchem.5b00775] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacterial DNA gyrase is a well-known and validated target in the design of antibacterial drugs. However, inhibitors of its ATP binding subunit, DNA gyrase B (GyrB), have so far not reached clinical use. In the present study, three different series of N-phenyl-4,5-dibromopyrrolamides and N-phenylindolamides were designed and prepared as potential DNA gyrase B inhibitors. The IC50 values of compounds on DNA gyrase from Escherichia coli were in the low micromolar range, with the best compound, (4-(4,5-dibromo-1H-pyrrole-2-carboxamido)benzoyl)glycine (18a), displaying an IC50 of 450 nM. For this compound, a high-resolution crystal structure in complex with E. coli DNA gyrase B was obtained, revealing details of its binding mode within the active site. The binding affinities of three compounds with GyrB were additionally evaluated by surface plasmon resonance, and the results were in good agreement with the determined enzymatic activities. For the most promising compounds, the inhibitory activities against DNA gyrase from Staphylococcus aureus and topoisomerases IV from E. coli and S. aureus were determined. Antibacterial activities of the most potent compounds of each series were evaluated against two Gram-positive and two Gram-negative bacterial strains. The results obtained in this study provide valuable information on the binding mode and structure-activity relationship of N-phenyl-4,5-dibromopyrrolamides and N-phenylindolamides as promising classes of ATP competitive GyrB inhibitors.
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Affiliation(s)
- Nace Zidar
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Helena Macut
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Matjaž Brvar
- ‡National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
| | - Sofia Montalvão
- §Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Päivi Tammela
- §Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Tom Solmajer
- ‡National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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49
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Tomašič T, Katsamakas S, Hodnik Ž, Ilaš J, Brvar M, Solmajer T, Montalvão S, Tammela P, Banjanac M, Ergović G, Anderluh M, Peterlin Mašič L, Kikelj D. Discovery of 4,5,6,7-Tetrahydrobenzo[1,2-d]thiazoles as Novel DNA Gyrase Inhibitors Targeting the ATP-Binding Site. J Med Chem 2015; 58:5501-21. [PMID: 26098163 DOI: 10.1021/acs.jmedchem.5b00489] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial DNA gyrase and topoisomerase IV are essential enzymes that control the topological state of DNA during replication and validated antibacterial drug targets. Starting from a library of marine alkaloid oroidin analogues, we identified low micromolar inhibitors of Escherichia coli DNA gyrase based on the 5,6,7,8-tetrahydroquinazoline and 4,5,6,7-tetrahydrobenzo[1,2-d]thiazole scaffolds. Structure-based optimization of the initial hits resulted in low nanomolar E. coli DNA gyrase inhibitors, some of which exhibited micromolar inhibition of E. coli topoisomerase IV and of Staphylococcus aureus homologues. Some of the compounds possessed modest antibacterial activity against Gram positive bacterial strains, while their evaluation against wild-type, impA and ΔtolC E. coli strains suggests that they are efflux pump substrates and/or do not possess the physicochemical properties necessary for cell wall penetration. Our study provides a rationale for optimization of this class of compounds toward balanced dual DNA gyrase and topoisomerase IV inhibitors with antibacterial activity.
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Affiliation(s)
- Tihomir Tomašič
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Sotirios Katsamakas
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.,‡Faculty of Health Sciences, School of Pharmacy, Department of Pharmaceutical Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Žiga Hodnik
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Matjaž Brvar
- §Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Tom Solmajer
- §Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Sofia Montalvão
- ∥Faculty of Pharmacy, Centre for Drug Research, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Päivi Tammela
- ∥Faculty of Pharmacy, Centre for Drug Research, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Mihailo Banjanac
- ⊥Galapagos Istraživački Ctr D.o.o, Prilaz Baruna Filipovića 29, HR-10000 Zagreb, Croatia
| | - Gabrijela Ergović
- ⊥Galapagos Istraživački Ctr D.o.o, Prilaz Baruna Filipovića 29, HR-10000 Zagreb, Croatia
| | - Marko Anderluh
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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50
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Shahavar Sulthana S, Arul Antony S, Balachandran C, Syed Shafi S. Thiophene and benzodioxole appended thiazolyl-pyrazoline compounds: Microwave assisted synthesis, antimicrobial and molecular docking studies. Bioorg Med Chem Lett 2015; 25:2753-7. [PMID: 26028159 DOI: 10.1016/j.bmcl.2015.05.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 04/29/2015] [Accepted: 05/14/2015] [Indexed: 12/29/2022]
Abstract
A novel series of thiophene and benzodioxole appended thiazolyl-pyrazoline derivatives have been designed, synthesized and evaluated against different bacteria and fungi. The antimicrobial activity of the synthesized compounds were screened using MIC method and were proved synthesized compounds 7o, 7r and 7t to show good antimicrobial activity against bacteria and fungi. In silico molecular docking studies revealed that all the synthesized molecules showed good binding energy toward the target receptor DNA topoisomerase IV, ranging from -10.42 to -11.66 kcal/mol.
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Affiliation(s)
- S Shahavar Sulthana
- PG & Research Department of Chemistry, Presidency College, Chennai 600 005, India
| | - S Arul Antony
- PG & Research Department of Chemistry, Presidency College, Chennai 600 005, India.
| | - C Balachandran
- Division of Microbiology and Cancer Biology, Entomology Research Institute, Loyola College, Chennai 600034, India
| | - S Syed Shafi
- Department of Chemistry, Thiruvalluvar University, Serkadu, Vellore 632 115, India.
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