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Vayssières M, Marechal N, Yun L, Lopez Duran B, Murugasamy NK, Fogg JM, Zechiedrich L, Nadal M, Lamour V. Structural basis of DNA crossover capture by Escherichia coli DNA gyrase. Science 2024; 384:227-232. [PMID: 38603484 PMCID: PMC11108255 DOI: 10.1126/science.adl5899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
DNA supercoiling must be precisely regulated by topoisomerases to prevent DNA entanglement. The interaction of type IIA DNA topoisomerases with two DNA molecules, enabling the transport of one duplex through the transient double-stranded break of the other, remains elusive owing to structures derived solely from single linear duplex DNAs lacking topological constraints. Using cryo-electron microscopy, we solved the structure of Escherichia coli DNA gyrase bound to a negatively supercoiled minicircle DNA. We show how DNA gyrase captures a DNA crossover, revealing both conserved molecular grooves that accommodate the DNA helices. Together with molecular tweezer experiments, the structure shows that the DNA crossover is of positive chirality, reconciling the binding step of gyrase-mediated DNA relaxation and supercoiling in a single structure.
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Affiliation(s)
- Marlène Vayssières
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Nils Marechal
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Long Yun
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Brian Lopez Duran
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Naveen Kumar Murugasamy
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Jonathan M. Fogg
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Marc Nadal
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Life Sciences, Université Paris Cité, Paris, France
| | - Valérie Lamour
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
- Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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Desai NC, Jadeja DJ, Jethawa AM, Ahmad I, Patel H, Dave BP. Design and synthesis of some novel hybrid molecules based on 4-thiazolidinone bearing pyridine-pyrazole scaffolds: molecular docking and molecular dynamics simulations of its major constituent onto DNA gyrase inhibition. Mol Divers 2024; 28:693-709. [PMID: 36750538 DOI: 10.1007/s11030-023-10612-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/23/2023] [Indexed: 02/09/2023]
Abstract
Due to multidrug resistance, microbial infections have become significant on a global level. As infections caused by several resistant bacteria and fungi severely harm mankind, scientists have developed new antibiotics to combat these infections. In order to develop novel antimicrobial agents, a series of 4-thiazolidinone-based 5-arylidene hybrids (5a-o) have been designed and synthesized to evaluate their antibacterial and antifungal activities. For the determination of the structure of a novel synthesized hybrid, various spectral techniques, e.g., IR, 1H NMR, 13C NMR, and Mass spectroscopy, were used. Two bacterial gram-negative (Escherichia coli and Pseudomonas aeruginosa), two gram-positive strains (Staphylococcus aureus and Streptococcus pyogenes), and one fungal strain (Candida albicans) were used to evaluate antimicrobial activity. Compounds 5c, 5g, and 5i were effective due to their MIC values of 62.5 μg/mL against tested bacterial strains (S. pyogenes (5c), P. aeruginosa (5g), and E. coli (5i), respectively.) and 250 μg/mL against C. albicans fungal strains, respectively. Additionally, molecular docking and 100 ns molecular dynamic simulations were carried out to investigate the stability of molecular contacts and to establish how the newly synthesized inhibitors fit together in the most stable conformations.
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Affiliation(s)
- Nisheeth C Desai
- Division of Medicinal Chemistry, Department of Chemistry, Maharaja Krishnakumarsinhji Bhavnagar University, Mahatma Gandhi Campus, Bhavnagar, 364 002, India.
| | - Dharmpalsinh J Jadeja
- Division of Medicinal Chemistry, Department of Chemistry, Maharaja Krishnakumarsinhji Bhavnagar University, Mahatma Gandhi Campus, Bhavnagar, 364 002, India
| | - Aratiba M Jethawa
- Division of Medicinal Chemistry, Department of Chemistry, Maharaja Krishnakumarsinhji Bhavnagar University, Mahatma Gandhi Campus, Bhavnagar, 364 002, India
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India
| | - B P Dave
- School of Science, Indrashil University, Rajpur, Kadi, Gujarat, 382740, India
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Harini M, Kavitha K, Prabakaran V, Krithika A, Dinesh S, Rajalakshmi A, Suresh G, Puvanakrishnan R, Ramesh B. Identification of apigenin-4'-glucoside as bacterial DNA gyrase inhibitor by QSAR modeling, molecular docking, DFT, molecular dynamics, and in vitro confirmation studies. J Mol Model 2024; 30:22. [PMID: 38170229 DOI: 10.1007/s00894-023-05813-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
CONTEXT It is well known that antibiotic resistance is a major health hazard. To eradicate antibiotic-resistant bacterial infections, it is essential to find a novel antibacterial agent. Hence, in this study, a quantitative structure-activity relationship (QSAR) model was developed using 43 DNA gyrase inhibitors, and 700 natural compounds were screened for their antibacterial properties. Based on molecular docking and absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies, the top three leads viz., apigenin-4'-glucoside, 8-deoxygartanin, and cryptodorine were selected and structurally optimized using density functional theory (DFT) studies. The optimized structures were redocked, and molecular dynamic (MD) simulations were performed. Binding energies were calculated by molecular mechanics/Poisson-Boltzmann surface area solvation (MM-PBSA). Based on the above studies, apigenin-4'-glucoside was identified as a potent antibacterial lead. Further in vitro confirmation studies were performed using the plant Lawsonia inermis containing apigenin-4'-glucoside to confirm the antibacterial activity. METHODS For QSAR modeling, 2D descriptors were calculated by PaDEL-Descriptors v2.21 software, and the model was developed using the DTClab QSAR tool. Docking was performed using PyRx v0.8 software. ORCA v5.0.1 computational package was used to optimize the structures. The job type used in optimization was equilibrium structure search using the DFT hybrid functional ORCA method B3LYP. The basis set was 6-311G (3df, 3pd) plus four polarization functions for all atoms. Accurate docking was performed for optimized leads using the iGEMDOCK v2.1 tool with a genetic algorithm by 10 solutions each of 80 generations. Molecular dynamic simulations were performed using GROMACS 2020.04 software with CHARMM36 all-atom force field.
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Affiliation(s)
- Manoharan Harini
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Kuppuswamy Kavitha
- PG & Research Department of Microbiology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Vadivel Prabakaran
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Anandan Krithika
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Shanmugam Dinesh
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Arumugam Rajalakshmi
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Gopal Suresh
- PG & Research Department of Microbiology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Rengarajulu Puvanakrishnan
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Balasubramanian Ramesh
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India.
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Pakeeraiah K, Mal S, Mahapatra M, Mekap SK, Sahu PK, Paidesetty SK. Schematic-portfolio of potent anti-microbial scaffolds targeting DNA gyrase: Unlocking ways to overcome resistance. Int J Biol Macromol 2024; 256:128402. [PMID: 38035955 DOI: 10.1016/j.ijbiomac.2023.128402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
Drug development process demands validation of specific drug target impeding the Multi Drug Resistance (MDR). DNA gyrase, as a bacterial target has been in trend for developing newer antibacterial candidates due to its absence in higher eukaryotes. The fluoroquinolones are the leading molecules in the drug discovery pipeline for gyrase inhibition due to its diversity. The fluoroquinolones like levofloxacin and moxifloxacin have been listed in class A drugs for treating MDR. Gatifloxacin and ciprofloxacin also proved its efficacy against MDR TB and MDR enteric fever in adults, whereas nemonoxacin can induce anti-MDR activity of other antibiotics already suggested by studies. Though fluoroquinolones already proved its effectiveness against gyrase, other molecules viz., benzothiazinone, phenyl pyrrolamide, substituted oxadiazoles, triazolopyrimidine, arylbenzothiazole, coumarinyl amino alcohols and ciprofloxacin uracil, can inhibit the target more precisely. The structure-activity-relationships of the different scaffolds along with their synthetic strategies have been deciphered in the current review. Also, the naturally occurring compounds along with their extraction procedure have also been highlighted as potent DNA gyrase inhibitors. In addition to fluoroquinolone, the natural compounds novobiocin and simocyclinone could also inhibit the gyrase, impressively which has been designed with the gyrase structure for better understanding. Herein, ongoing clinical development of some novel drugs possessing triazaacenaphthylenes, spiropyrimidinetriones, and oxazolidinone-quinolone hybrids have been highlighted which could further assist the future generation antibiotic development corroborating gyrase as a potential target against MDR pathogens.
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Affiliation(s)
- Kakarla Pakeeraiah
- Medicinal Chemistry Research Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar 751003, Odisha, India
| | - Suvadeep Mal
- Medicinal Chemistry Research Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar 751003, Odisha, India
| | - Monalisa Mahapatra
- Medicinal Chemistry Research Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar 751003, Odisha, India
| | - Suman Kumar Mekap
- School of Pharmacy and Life Sciences, Centurion University of technology and management, Bhubaneswar 752050, Odisha, India
| | - Pratap Kumar Sahu
- Department of Pharmacology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar 751003, Odisha, India
| | - Sudhir Kumar Paidesetty
- Medicinal Chemistry Research Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar 751003, Odisha, India.
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Kumar GS, Sobhia ME. Water network chemistry to exploit the nature of catalytic water molecules in Mtb DNA gyrase: a computational study to understand the binding mechanism of fluoroquinolones. J Biomol Struct Dyn 2024; 42:725-733. [PMID: 37121993 DOI: 10.1080/07391102.2023.2199869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/17/2023] [Indexed: 05/02/2023]
Abstract
The dynamics of DNA gyrase and mutants of DNA gyrA such as G88A, A90V, S91P, D94A, D94G, D94N, D94Y; and double-point mutant (S91P-D94G), are meticulously investigated using computational approaches. Molecular dynamics (MD) and hydration thermodynamics have shed light on the fundamental, mechanistic basis of mutations on the conformational stability of Quinolone Binding Pocket (QBP) of DNA gyrase. Analysis of MD results revealed the displacement of a single crystal water molecule (HOH201) from the catalytic site of wild-type (WT) and mutants of DNA gyrA. This prompted our research group to probe the five crystal water molecules present in the QBP of the enzyme using water thermodynamics. Hydration thermodynamics analysis revealed the displacement of HOH201 due to unstable thermodynamic signatures. Further, the analysis highlighted significant changes in thermodynamic signatures and locations of five crystal water hydration sites upon mutation. Integrated MD simulations and water thermodynamics provided promising insights into the conformational changes and inaccessibility of the catalytic water molecule that can influence the design of DNA gyrase inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- G Siva Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
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Zorman M, Hrast Rambaher M, Kokot M, Minovski N, Anderluh M. The overview of development of novel bacterial topoisomerase inhibitors effective against multidrug-resistant bacteria in an academic environment: From early hits to in vivo active antibacterials. Eur J Pharm Sci 2024; 192:106632. [PMID: 37949194 DOI: 10.1016/j.ejps.2023.106632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/29/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Antimicrobial resistance caused by the excessive and inappropriate use of antibacterial drugs is a global health concern. Currently, we are walking a fine line between the fact that most bacterial infections can still be cured with the antibiotics known so far, and the emergence of infections with bacteria resistant to several drugs at the same time, against which we no longer have an effective drug. Therefore, new antibacterial drugs are urgently needed to curb the hard-to-treat infections. Our group has developed new antibacterials from the class of novel bacterial topoisomerase inhibitors (NBTIs) that exhibit broad-spectrum antibacterial activity. This article reviews our efforts in developing highly potent NBTIs over the past decade. Following the discovery of an initial hit with potent enzyme inhibitory and broad-spectrum antibacterial activity, an extensive hit-to-lead campaign was conducted with the goal of optimizing physicochemical properties, reducing hERG inhibition, and maintaining antibacterial activity against both Gram-positive and Gram-negative bacteria, with a focus on methicillin-resistant Staphylococcus aureus (MRSA). This optimization strategy resulted in an amide-containing, focused NBTI library with compounds exhibiting potent antibacterial activity against Gram-positive bacteria, reduced hERG inhibition, no cardiotoxicity in in vivo zebrafish model, and favorable in vivo efficacy in a neutropenic murine thigh infection model for MRSA infections.
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Affiliation(s)
- Maša Zorman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia; Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1001, Slovenia
| | - Martina Hrast Rambaher
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Maja Kokot
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia; Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1001, Slovenia
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1001, Slovenia.
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia.
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Akili AWR, Hardianto A, Latip J, Permana A, Herlina T. Virtual Screening and ADMET Prediction to Uncover the Potency of Flavonoids from Genus Erythrina as Antibacterial Agent through Inhibition of Bacterial ATPase DNA Gyrase B. Molecules 2023; 28:8010. [PMID: 38138500 PMCID: PMC10745610 DOI: 10.3390/molecules28248010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence of antimicrobial resistance due to the widespread and inappropriate use of antibiotics has now become the global health challenge. Flavonoids have long been reported to be a potent antimicrobial agent against a wide range of pathogenic microorganisms in vitro. Therefore, new antibiotics development based on flavonoid structures could be a potential strategy to fight against antibiotic-resistant infections. This research aims to screen the potency of flavonoids of the genus Erythrina as an inhibitor of bacterial ATPase DNA gyrase B. From the 378 flavonoids being screened, 49 flavonoids show potential as an inhibitor of ATPase DNA gyrase B due to their lower binding affinity compared to the inhibitor and ATP. Further screening for their toxicity, we identified 6 flavonoids from these 49 flavonoids, which are predicted to have low toxicity. Among these flavonoids, erystagallin B (334) is predicted to have the best pharmacokinetic properties, and therefore, could be further developed as new antibacterial agent.
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Affiliation(s)
- Abd. Wahid Rizaldi Akili
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (A.W.R.A.); (A.H.); (A.P.)
| | - Ari Hardianto
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (A.W.R.A.); (A.H.); (A.P.)
| | - Jalifah Latip
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 46300, Malaysia;
| | - Afri Permana
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (A.W.R.A.); (A.H.); (A.P.)
| | - Tati Herlina
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (A.W.R.A.); (A.H.); (A.P.)
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Jakhar R, Khichi A, Kumar D, Sura K, Bhoomika, Dangi M, Chhillar AK. Development of pharmacophore model to identify potential DNA gyrase inhibitors. J Biomol Struct Dyn 2023; 41:10125-10135. [PMID: 36473713 DOI: 10.1080/07391102.2022.2153171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022]
Abstract
There is great concern in the medical community due to rapid increase in antibiotic resistance, causing 700,000 deaths annually worldwide. Therefore, there is paramount need to develop novel and innovative antibacterial agents active against resistant bacterial strains. DNA gyrase is a crucial enzyme in bacterial replication that is absent in eukaryotes, making it effective curative target for antibacterials. To identify potential DNA gyrase inhibitors by virtual screening of NCI database using a 3-step approach. A total of 271 compounds with known IC50 values against Escherichia coli DNA GyrA were selected to develop a pharmacophore model for dual screening approach to identify new potential hits from the NCI database. In the second step, the NCI database was also screened using in-house built NN-QSAR model. Molecular docking of common 5298 compounds screened from both methods were performed against E. coli DNA GyrA (PDB id- 6RKU), and 3004 compounds are reported to exhibit lower binding energies than ciprofloxacin (-6.77 Kcal/mol). The top three compounds (NCI371878, NCI371876 and NCI142159) reported with binding energy of -13.5, -13.19 and -13.03 Kcal/mol were further subjected to MD simulation studies for 100 ns supporting the stability of the docked complexes.
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Affiliation(s)
- Ritu Jakhar
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Alka Khichi
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Dev Kumar
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Kiran Sura
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Bhoomika
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Mehak Dangi
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
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Coba-Males MA, Lavecchia MJ, Alcívar-León CD, Santamaría-Aguirre J. Novel Fluoroquinolones with Possible Antibacterial Activity in Gram-Negative Resistant Pathogens: In Silico Drug Discovery. Molecules 2023; 28:6929. [PMID: 37836772 PMCID: PMC10574177 DOI: 10.3390/molecules28196929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 10/15/2023] Open
Abstract
Antibiotic resistance is a global threat to public health, and the search for new antibacterial therapies is a current research priority. The aim of this in silico study was to test nine new fluoroquinolones previously designed with potential leishmanicidal activity against Campylobacter jejuni, Escherichia coli, Neisseria gonorrhoeae, Pseudomonas aeruginosa, and Salmonella typhi, all of which are considered by the World Health Organization to resistant pathogens of global concern, through molecular docking and molecular dynamics (MD) simulations using wild-type (WT) and mutant-type (MT) DNA gyrases as biological targets. Our results showed that compound 9FQ had the best binding energy with the active site of E. coli in both molecular docking and molecular dynamics simulations. Compound 9FQ interacted with residues of quinolone resistance-determining region (QRDR) in GyrA and GyrB chains, which are important to enzyme activity and through which it could block DNA replication. In addition to compound 9FQ, compound 1FQ also showed a good affinity for DNA gyrase. Thus, these newly designed molecules could have antibacterial activity against Gram-negative microorganisms. These findings represent a promising starting point for further investigation through in vitro assays, which can validate the hypothesis and potentially facilitate the development of novel antibiotic drugs.
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Affiliation(s)
- Manuel Alejandro Coba-Males
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Salud Pública y Zoonosis (CIZ), Facultad de Ciencias Químicas (FCQ), Universidad Central del Ecuador, Quito 170521, Ecuador
| | - Martin J. Lavecchia
- CEQUINOR (UNLP-CONICET, CCT-La Plata, Associated with CICBA), Universidad Nacional de La Plata, La Plata 1900, Argentina;
| | | | - Javier Santamaría-Aguirre
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Salud Pública y Zoonosis (CIZ), Facultad de Ciencias Químicas (FCQ), Universidad Central del Ecuador, Quito 170521, Ecuador
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Mohammed HHH, Ali DME, Badr M, Habib AGK, Mahmoud AM, Farhan SM, Gany SSHAE, Mohamad SA, Hayallah AM, Abbas SH, Abuo-Rahma GEDA. Synthesis and molecular docking of new N4-piperazinyl ciprofloxacin hybrids as antimicrobial DNA gyrase inhibitors. Mol Divers 2023; 27:1751-1765. [PMID: 36152132 PMCID: PMC10415461 DOI: 10.1007/s11030-022-10528-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/11/2022] [Indexed: 11/24/2022]
Abstract
A series of N-4 piperazinyl ciprofloxacin derivatives as urea-tethered ciprofloxacin-chalcone hybrids 2a-j and thioacetyl-linked ciprofloxacin-pyrimidine hybrids 5a-i were synthesized. The target compounds were investigated for their antibacterial activity against S. aureus, P. aeruginosa, E. coli, and C. albicans strains, respectively. Ciprofloxacin derivatives 2a-j and 5a-i revealed broad antibacterial activity against either Gram positive or Gram negative strains, with MIC range of 0.06-42.23 µg/mL compared to ciprofloxacin with an MIC range of 0.15-3.25 µg/mL. Among the tested compounds, hybrids 2b, 2c, 5a, 5b, 5h, and 5i exhibited remarkable antibacterial activity with MIC range of 0.06-1.53 µg/mL against the tested bacterial strains. On the other hand, compounds 2c, 2e, 5c, and 5e showed comparable antifungal activity to ketoconazole against candida albicans with MIC range of 2.03-3.89 µg/mL and 2.6 µg/mL, respectively. Further investigations showed that some ciprofloxacin hybrids have inhibitory activity against DNA gyrase as potential molecular target compared to ciprofloxacin with IC50 range of 0.231 ± 0.01-7.592 ± 0.40 µM and 0.323 ± 0.02 µM, respectively. Docking studies of compounds 2b, 2c, 5b, 5c, 5e, 5h, and 5i on the active site of DNA gyrase (PDB: 2XCT) confirmed their ability to form stable complex with the target enzyme like that of ciprofloxacin.
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Affiliation(s)
- Hamada H H Mohammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sohag University, Sohag, 82524, Egypt.
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt.
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia City, 61768, Egypt.
| | | | - Mohamed Badr
- Department of Biochemistry, Faculty of Pharmacy, Menoufia University, Menoufia, Egypt
| | - Ahmed G K Habib
- Department of Biotechnology and Life Sciences, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt
| | - Abobakr Mohamed Mahmoud
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, New Minia City, 61768, Egypt
| | - Sarah M Farhan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, New Minia City, 61768, Egypt
| | | | - Soad A Mohamad
- Department of Pharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, Deraya University, New Minia, Minya, 61768, Egypt
| | - Alaa M Hayallah
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, El Fateh, 71526, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Sphinx University, New Assiut, Egypt
| | - Samar H Abbas
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Gamal El-Din A Abuo-Rahma
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt.
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia City, 61768, Egypt.
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11
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Bhowmick J, Nag M, Ghosh P, Rajmani RS, Chatterjee R, Karmakar K, Chandra K, Chatterjee J, Chakravortty D, Varadarajan R. A CcdB toxin-derived peptide acts as a broad-spectrum antibacterial therapeutic in infected mice. EMBO Rep 2023; 24:e55338. [PMID: 37166011 PMCID: PMC10328072 DOI: 10.15252/embr.202255338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/12/2023] Open
Abstract
The bacterial toxin CcdB (Controller of Cell death or division B) targets DNA Gyrase, an essential bacterial topoisomerase, which is also the molecular target for fluoroquinolones. Here, we present a short cell-penetrating 24-mer peptide, CP1-WT, derived from the Gyrase-binding region of CcdB and examine its effect on growth of Escherichia coli, Salmonella Typhimurium, Staphylococcus aureus and a carbapenem- and tigecycline-resistant strain of Acinetobacter baumannii in both axenic cultures and mouse models of infection. The CP1-WT peptide shows significant improvement over ciprofloxacin in terms of its in vivo therapeutic efficacy in treating established infections of S. Typhimurium, S. aureus and A. baumannii. The molecular mechanism likely involves inhibition of Gyrase or Topoisomerase IV, depending on the strain used. The study validates the CcdB binding site on bacterial DNA Gyrase as a viable and alternative target to the fluoroquinolone binding site.
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Grants
- Department of Biotechnology, Ministry of Science and Technology, India - Indian Institute of Science (DBT-IISc) partnership program
- BT/COE/34/SP15219/2015 Department of Biotechnology, Ministry of Science and Technology, India
- DT.20/11/2015 Department of Biotechnology, Ministry of Science and Technology, India
- Department of Science and Technology, Ministry of Science and Technology, India (DST FIST)
- Ministry of Education, India (MHRD)
- University Grants Commission, Ministry of Education, India (UGC Centre for Advanced Studies)
- Department of Biotechnology, Ministry of Science and Technology, India
- Ministry of Education, India (MHRD)
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Affiliation(s)
- Jayantika Bhowmick
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Manish Nag
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Pritha Ghosh
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Raju S Rajmani
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Ritika Chatterjee
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
| | - Kapudeep Karmakar
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
| | - Kasturi Chandra
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
| | - Jayanta Chatterjee
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
- School of BiologyIndian Institute of Science Education and Research Thiruvananthapuram (IISER TVM)ThiruvananthapuramIndia
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12
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Kamsri B, Pakamwong B, Thongdee P, Phusi N, Kamsri P, Punkvang A, Ketrat S, Saparpakorn P, Hannongbua S, Sangswan J, Suttisintong K, Sureram S, Kittakoop P, Hongmanee P, Santanirand P, Leanpolchareanchai J, Goudar KE, Spencer J, Mulholland AJ, Pungpo P. Bioisosteric Design Identifies Inhibitors of Mycobacterium tuberculosis DNA Gyrase ATPase Activity. J Chem Inf Model 2023; 63:2707-2718. [PMID: 37074047 DOI: 10.1021/acs.jcim.2c01376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Mutations in DNA gyrase confer resistance to fluoroquinolones, second-line antibiotics for Mycobacterium tuberculosis infections. Identification of new agents that inhibit M. tuberculosis DNA gyrase ATPase activity is one strategy to overcome this. Here, bioisosteric designs using known inhibitors as templates were employed to define novel inhibitors of M. tuberculosis DNA gyrase ATPase activity. This yielded the modified compound R3-13 with improved drug-likeness compared to the template inhibitor that acted as a promising ATPase inhibitor against M. tuberculosis DNA gyrase. Utilization of compound R3-13 as a virtual screening template, supported by subsequent biological assays, identified seven further M. tuberculosis DNA gyrase ATPase inhibitors with IC50 values in the range of 0.42-3.59 μM. The most active compound 1 showed an IC50 value of 0.42 μM, 3-fold better than the comparator ATPase inhibitor novobiocin (1.27 μM). Compound 1 showed noncytotoxicity to Caco-2 cells at concentrations up to 76-fold higher than its IC50 value. Molecular dynamics simulations followed by decomposition energy calculations identified that compound 1 occupies the binding pocket utilized by the adenosine group of the ATP analogue AMPPNP in the M. tuberculosis DNA gyrase GyrB subunit. The most prominent contribution to the binding of compound 1 to M. tuberculosis GyrB subunit is made by residue Asp79, which forms two hydrogen bonds with the OH group of this compound and also participates in the binding of AMPPNP. Compound 1 represents a potential new scaffold for further exploration and optimization as a M. tuberculosis DNA gyrase ATPase inhibitor and candidate anti-tuberculosis agent.
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Affiliation(s)
- Bundit Kamsri
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - 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
| | - 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
| | - 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, 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), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok 10210, 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
| | - Jiraporn Leanpolchareanchai
- Department of Pharmacy, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayuthaya Road,Rajathevi, Bangkok 10400, Thailand
| | - Kirsty E Goudar
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
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13
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Galvin CJ, Hobson M, Meng JX, Ierokomos A, Ivanov IE, Berger JM, Bryant Z. Single-molecule dynamics of DNA gyrase in evolutionarily distant bacteria Mycobacterium tuberculosis and Escherichia coli. J Biol Chem 2023; 299:103003. [PMID: 36775125 PMCID: PMC10130225 DOI: 10.1016/j.jbc.2023.103003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
DNA gyrase is an essential nucleoprotein motor present in all bacteria and is a major target for antibiotic treatment of Mycobacterium tuberculosis (MTB) infection. Gyrase hydrolyzes ATP to add negative supercoils to DNA using a strand passage mechanism that has been investigated using biophysical and biochemical approaches. To analyze the dynamics of substeps leading to strand passage, single-molecule rotor bead tracking (RBT) has been used previously to follow real-time supercoiling and conformational transitions in Escherichia coli (EC) gyrase. However, RBT has not yet been applied to gyrase from other pathogenically relevant bacteria, and it is not known whether substeps are conserved across evolutionarily distant species. Here, we compare gyrase supercoiling dynamics between two evolutionarily distant bacterial species, MTB and EC. We used RBT to measure supercoiling rates, processivities, and the geometries and transition kinetics of conformational states of purified gyrase proteins in complex with DNA. Our results show that E. coli and MTB gyrases are both processive, with the MTB enzyme displaying velocities ∼5.5× slower than the EC enzyme. Compared with EC gyrase, MTB gyrase also more readily populates an intermediate state with DNA chirally wrapped around the enzyme, in both the presence and absence of ATP. Our substep measurements reveal common features in conformational states of EC and MTB gyrases interacting with DNA but also suggest differences in populations and transition rates that may reflect distinct cellular needs between these two species.
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Affiliation(s)
- Cooper J Galvin
- Program in Biophysics, Stanford University, Stanford, California, USA; Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Matthew Hobson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Athena Ierokomos
- Program in Biophysics, Stanford University, Stanford, California, USA; Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Ivan E Ivanov
- Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zev Bryant
- Program in Biophysics, Stanford University, Stanford, California, USA; Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Structural Biology, Stanford University Medical Center, Stanford, California, USA.
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14
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Roney M, Issahaku AR, Forid MS, Huq AKMM, Soliman MES, Mohd Aluwi MFF, Tajuddin SN. In silico evaluation of usnic acid derivatives to discover potential antibacterial drugs against DNA gyrase B and DNA topoisomerase IV. J Biomol Struct Dyn 2023; 41:14904-14913. [PMID: 36995164 DOI: 10.1080/07391102.2023.2193996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/18/2023] [Indexed: 03/31/2023]
Abstract
Due to the rising increase in infectious diseases brought on by bacteria and anti-bacterial drug resistance, antibacterial therapy has become difficult. The majority of first-line antibiotics are no longer effective against numerous germs, posing a new hazard to global human health in the 21st century. Through the drug-likeness screening, 184 usnic acid derivatives were selected from an in-house database of 340 usnic acid compounds. The pharmacokinetics (ADMET) prediction produced fifteen hit compounds, of which the lead molecule was subsequently obtained through a molecular docking investigation. The lead compounds, labelled compound-277 and compound-276, respectively, with the substantial binding affinity towards the enzymes were obtained through further docking simulation on the DNA gyrase and DNA topoisomerase proteins. Additionally, molecular dynamic (MD) simulation was performed for 300 ns on the lead compounds in order to confirm the stability of the docked complexes and the binding pose discovered during docking tests. Due to their intriguing pharmacological characteristics, these substances may be promising therapeutic candidate for anti-bacterial medication.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Abdul Rashid Issahaku
- West African Centre for Computational Analysis, Accra, Ghana
- Molecular Bio-computation and Drug Design Laboratory, Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Md Shaekh Forid
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - A K M Moyeenul Huq
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Department of Pharmacy, School of Medicine, University of Asia Pacific, Dhaka, Bangladesh
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Saiful Nizam Tajuddin
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
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15
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Chattopadhyay G, Ahmed S, Srilatha NS, Asok A, Varadarajan R. Ter-Seq: A high-throughput method to stabilize transient ternary complexes and measure associated kinetics. Protein Sci 2023; 32:e4514. [PMID: 36382921 PMCID: PMC9793979 DOI: 10.1002/pro.4514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/01/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
Abstract
Regulation of biological processes by proteins often involves the formation of transient, multimeric complexes whose characterization is mechanistically important but challenging. The bacterial toxin CcdB binds and poisons DNA Gyrase. The corresponding antitoxin CcdA extracts CcdB from its complex with Gyrase through the formation of a transient ternary complex, thus rejuvenating Gyrase. We describe a high throughput methodology called Ter-Seq to stabilize probable ternary complexes and measure associated kinetics using the CcdA-CcdB-GyrA14 ternary complex as a model system. The method involves screening a yeast surface display (YSD) saturation mutagenesis library of one partner (CcdB) for mutants that show enhanced ternary complex formation. We also isolated CcdB mutants that were either resistant or sensitive to rejuvenation, and used surface plasmon resonance (SPR) with purified proteins to validate the kinetics measured using the surface display. Positions, where CcdB mutations lead to slower rejuvenation rates, are largely involved in CcdA-binding, though there were several notable exceptions suggesting allostery. Mutations at these positions reduce the affinity towards CcdA, thereby slowing down the rejuvenation process. Mutations at GyrA14-interacting positions significantly enhanced rejuvenation rates, either due to reduced affinity or complete loss of CcdB binding to GyrA14. We examined the effect of different parameters (CcdA affinity, GyrA14 affinity, surface accessibilities, evolutionary conservation) on the rate of rejuvenation. Finally, we further validated the Ter-Seq results by monitoring the kinetics of ternary complex formation for individual CcdB mutants in solution by fluorescence resonance energy transfer (FRET) studies.
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Affiliation(s)
- Gopinath Chattopadhyay
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
- Institute for Evolutionary Biology and Environmental SciencesUniversity of ZurichZurichSwitzerland
| | - Shahbaz Ahmed
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
- St. Jude Children's Research HospitalTennesseeUSA
| | | | - Aparna Asok
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
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16
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Abstract
The discovery of novel antibacterials devoid of cross resistance is of utmost importance. At the same time, biological pathways and processes suitable to be targeted are limited. At Actelion Pharmaceuticals we decided to work on novel bacterial topoisomerase inhibitors (NBTI) to discover new antibiotics with broad spectrum activity and limited resistance development for use against severe hospital infections. This paper summarizes the learnings and results of our efforts in the field, which led to the discovery of multiple chemical classes with potent Gram-negative activity and ultimately to the selection of several compounds that underwent preclinical profiling.
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Affiliation(s)
- Cornelia Zumbrunn
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil.
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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El-Kalyoubi S, Agili F, Zordok WA, El-Sayed ASA. Synthesis, In Silico Prediction and In Vitro Evaluation of Antimicrobial Activity, DFT Calculation and Theoretical Investigation of Novel Xanthines and Uracil Containing Imidazolone Derivatives. Int J Mol Sci 2021; 22:10979. [PMID: 34681643 PMCID: PMC8539769 DOI: 10.3390/ijms222010979] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 01/08/2023] Open
Abstract
Novel xanthine and imidazolone derivatives were synthesized based on oxazolone derivatives 2a-c as a key intermediate. The corresponding xanthine 3-5 and imidazolone derivatives 6-13 were obtained via reaction of oxazolone derivative 2a-c with 5,6-diaminouracils 1a-e under various conditions. Xanthine compounds 3-5 were obtained by cyclocondensation of 5,6-diaminouracils 1a-c with different oxazolones in glacial acetic acid. Moreover, 5,6-diaminouracils 1a-e were reacted with oxazolones 2a-c in presence of drops of acetic acid under fused condition yielding the imidazolone derivatives 6-13. Furthermore, Schiff base of compounds 14-16 were obtained by condensing 5,6-diaminouracils 1a,b,e with 4-dimethylaminobenzaldehyde in acetic acid. The structural identity of the resulting compounds was resolved by IR, 1H-, 13C-NMR and Mass spectral analyses. The novel synthesized compounds were screened for their antifungal and antibacterial activities. Compounds 3, 6, 13 and 16 displayed the highest activity against Escherichia coli as revealed from the IC50 values (1.8-1.9 µg/mL). The compound 16 displayed a significant antifungal activity against Candia albicans (0.82 µg/mL), Aspergillus flavus (1.2 µg/mL) comparing to authentic antibiotics. From the TEM microgram, the compounds 3, 12, 13 and 16 exhibited a strong deformation to the cellular entities, by interfering with the cell membrane components, causing cytosol leakage, cellular shrinkage and irregularity to the cell shape. In addition, docking study for the most promising antimicrobial tested compounds depicted high binding affinity against acyl carrier protein domain from a fungal type I polyketide synthase (ACP), and Baumannii penicillin- binding protein (PBP). Moreover, compound 12 showed high drug- likeness, and excellent pharmacokinetics, which needs to be in focus for further antimicrobial drug development. The most promising antimicrobial compounds underwent theoretical investigation using DFT calculation.
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Affiliation(s)
- Samar El-Kalyoubi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo 11651, Egypt
| | - Fatimah Agili
- Chemistry Department, Faculty of Science (Female Section), Jazan University, Jazan 82621, Saudi Arabia;
| | - Wael A. Zordok
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
| | - Ashraf S. A. El-Sayed
- Enzymology and Fungal Biotechnology, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
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20
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Rashdan HRM, Shehadi IA, Abdelrahman MT, Hemdan BA. Antibacterial Activities and Molecular Docking of Novel Sulfone Biscompound Containing Bioactive 1,2,3-Triazole Moiety. Molecules 2021; 26:molecules26164817. [PMID: 34443405 PMCID: PMC8399954 DOI: 10.3390/molecules26164817] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, a new synthetic 1,2,3-triazole-containing disulfone compound was derived from dapsone. Its chemical structure was confirmed using microchemical and analytical data, and it was tested for its in vitro antibacterial potential. Six different pathogenic bacteria were selected. MICs values and ATP levels were determined. Further, toxicity performance was measured using MicroTox Analyzer. In addition, a molecular docking study was performed against two vital enzymes: DNA gyrase and Dihydropteroate synthase. The results of antibacterial abilities showed that the studied synthetic compound had a strong bactericidal effect against all tested bacterial strains, as Gram-negative species were more susceptible to the compound than Gram-positive species. Toxicity results showed that the compound is biocompatible and safe without toxic impact. The molecular docking of the compound showed interactions within the pocket of two enzymes, which are able to stabilize the compound and reveal its antimicrobial activity. Hence, from these results, this study recommends that the established compound could be an outstanding candidate for fighting a broad spectrum of pathogenic bacterial strains, and it might therefore be used for biomedical and pharmaceutical applications.
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Affiliation(s)
- Huda R. M. Rashdan
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki, Cairo 12622, Egypt
- Correspondence:
| | - Ihsan A. Shehadi
- Chemistry Department, College of Science, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Mohamad T. Abdelrahman
- Radioisotopes Department, Nuclear Research Centre, Egyptian Atomic Energy Authority, Cairo 12311, Egypt;
| | - Bahaa A. Hemdan
- Water Pollution Research Department, Environmental Research Division, National Research Centre, 33 El Buhouth Street, Cairo 12622, Egypt;
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21
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Abo-Salem HM, Abd El Salam HA, Abdel-Aziem AM, Abdel-Aziz MS, El-Sawy ER. Synthesis, Molecular Docking, and Biofilm Formation Inhibitory Activity of Bis(Indolyl)Pyridines Analogues of the Marine Alkaloid Nortopsentin. Molecules 2021; 26:4112. [PMID: 34299385 PMCID: PMC8304590 DOI: 10.3390/molecules26144112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
An efficient and simple protocol for the synthesis of a new class of diverse bis(indolyl)pyridines analogues of the marine alkaloid nortopsentin has been reported. A one-pot four-component condensation of 3-cyanocarbomethylindole, various aldehyde, 3-acetylindole, and ammonium acetate in glacial acetic acid led to the formation of 2,6-bis(1H-indol-3-yl)-4-(substituted-phenyl)pyridine-5-carbonitriles. Additionally, 2,6-bis(1H-indol-3-yl)-4-(benzofuran) pyridine-5-carbonitriles were prepared via a one-pot four-component condensation of 3-cyanocarbomethylindole, various N-substituted-indole-3-aldehydes, 2-acetylbenzofuran, and ammonium acetate. The synthesized compounds were evaluated for their ability to inhibit biofilm formation against the Gram-positive bacterial reference strains Staphylococcus aureus ATCC 6538 and the Gram-negative strain Escherichia coli ATCC 25922. Some of the new compounds showed a marked selectivity against the Gram-positive and Gram-negative strains. Remarkably, five compounds 4b, 7a, 7c, 7d and 8e demonstrated good antibiofilm formation against S. aureus and E. coli. On the other hand, the release of reducing sugars and proteins from the treated bacterial strains over the untreated strains was considered to explain the disruption effect of the selected compound on the contact cells of S. aureus and E. coli. Out of all studied compounds, the binding energies and binding mode of bis-indole derivatives 7c and 7d were theoretically the best thymidylate kinase, DNA gyrase B and DNA topoisomerase IV subunit B inhibitors.
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Affiliation(s)
- Heba M. Abo-Salem
- Chemistry of Natural Compounds Department, National Research Centre, Dokki, Giza 12622, Egypt;
| | | | - Anhar M. Abdel-Aziem
- Chemistry Department, Faculty of Science (Girl’s Branch), Al-Azhar University, Cairo 11284, Egypt;
| | - Mohamed S. Abdel-Aziz
- Microbial Chemistry Department, Genetic Engineering and biotechnology Division, National Research Centre, Dokki, Giza 12622, Egypt;
| | - Eslam Reda El-Sawy
- Chemistry of Natural Compounds Department, National Research Centre, Dokki, Giza 12622, Egypt;
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22
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Alsayed SSR, Lun S, Payne A, Bishai WR, Gunosewoyo H. Facile synthesis and antimycobacterial activity of isoniazid, pyrazinamide and ciprofloxacin derivatives. Chem Biol Drug Des 2021; 97:1137-1150. [PMID: 33638304 PMCID: PMC8113106 DOI: 10.1111/cbdd.13836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/12/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022]
Abstract
Several rationally designed isoniazid (INH), pyrazinamide (PZA) and ciprofloxacin (CPF) derivatives were conveniently synthesized and evaluated in vitro against H37Rv Mycobacterium tuberculosis (M. tb) strain. CPF derivative 16 displayed a modest activity (MIC = 16 µg/ml) and was docked into the M. tb DNA gyrase. Isoniazid-pyrazinoic acid (INH-POA) hybrid 21a showed the highest potency in our study (MIC = 2 µg/ml). It also retained its high activity against the other tested M. tb drug-sensitive strain (DS) V4207 (MIC = 4 µg/ml) and demonstrated negligible cytotoxicity against Vero cells (IC50 ≥ 64 µg/ml). Four tested drug-resistant (DR) M. tb strains were refractory to 21a, similar to INH, whilst being sensitive to CPF. Compound 21a was also inactive against two non-tuberculous mycobacterial (NTM) strains, suggesting its selective activity against M. tb. The noteworthy activity of 21a against DS strains and its low cytotoxicity highlight its potential to treat DS M. tb.
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Affiliation(s)
- Shahinda S. R. Alsayed
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
| | - Shichun Lun
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, 1550, Orleans Street, Baltimore, Maryland, 21231-1044, United States
| | - Alan Payne
- School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, 1550, Orleans Street, Baltimore, Maryland, 21231-1044, United States
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland, 20815-6789, United States
| | - Hendra Gunosewoyo
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
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23
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Kowalczyk A, Paneth A, Trojanowski D, Paneth P, Zakrzewska-Czerwińska J, Stączek P. Thiosemicarbazide Derivatives Decrease the ATPase Activity of Staphylococcus aureus Topoisomerase IV, Inhibit Mycobacterial Growth, and Affect Replication in Mycobacterium smegmatis. Int J Mol Sci 2021; 22:ijms22083881. [PMID: 33918623 PMCID: PMC8069432 DOI: 10.3390/ijms22083881] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
Compounds targeting bacterial topoisomerases are of interest for the development of antibacterial agents. Our previous studies culminated in the synthesis and characterization of small-molecular weight thiosemicarbazides as the initial prototypes of a novel class of gyrase and topoisomerase IV inhibitors. To expand these findings with further details on the mode of action of the most potent compounds, enzymatic studies combined with a molecular docking approach were carried out, the results of which are presented herein. The biochemical assay for 1-(indol-2-oyl)-4-(4-nitrophenyl) thiosemicarbazide (4) and 4-benzoyl-1-(indol-2-oyl) thiosemicarbazide (7), showing strong inhibitory activity against Staphylococcus aureus topoisomerase IV, confirmed that these compounds reduce the ability of the ParE subunit to hydrolyze ATP rather than act by stabilizing the cleavage complex. Compound 7 showed better antibacterial activity than compound 4 against clinical strains of S. aureus and representatives of the Mycobacterium genus. In vivo studies using time-lapse microfluidic microscopy, which allowed for the monitoring of fluorescently labelled replisomes, revealed that compound 7 caused an extension of the replication process duration in Mycobacterium smegmatis, as well as the growth arrest of bacterial cells. Despite some similarities to the mechanism of action of novobiocin, these compounds show additional, unique properties, and can thus be considered a novel group of inhibitors of the ATPase activity of bacterial type IIA topoisomerases.
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Affiliation(s)
- Aleksandra Kowalczyk
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland;
| | - Agata Paneth
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
- Correspondence: (A.P.); (P.S.)
| | - Damian Trojanowski
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland; (D.T.); (J.Z.-C.)
| | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Łódź University of Technology, Żeromskiego 116, 90-924 Łódź, Poland;
- International Centre for Research on Innovative Biobased Materials (ICRI-BioM)—International Research Agenda, Łódź University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Jolanta Zakrzewska-Czerwińska
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland; (D.T.); (J.Z.-C.)
| | - Paweł Stączek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland;
- Correspondence: (A.P.); (P.S.)
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24
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Aroso RT, Guedes RC, Pereira MM. Synthesis of Computationally Designed 2,5(6)-Benzimidazole Derivatives via Pd-Catalyzed Reactions for Potential E. coli DNA Gyrase B Inhibition. Molecules 2021; 26:molecules26051326. [PMID: 33801316 PMCID: PMC7958342 DOI: 10.3390/molecules26051326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 11/16/2022] Open
Abstract
A pharmacophore model for inhibitors of Escherichia coli’s DNA Gyrase B was developed, using computer-aided drug design. Subsequently, docking studies showed that 2,5(6)-substituted benzimidazole derivatives are promising molecules, as they possess key hydrogen bond donor/acceptor groups for an efficient interaction with this bacterial target. Furthermore, 5(6)-bromo-2-(2-nitrophenyl)-1H-benzimidazole, selected as a core molecule, was prepared on a multi-gram scale through condensation of 4-bromo-1,2-diaminobenzene with 2-nitrobenzaldehyde using a sustainable approach. The challenging functionalization of the 5(6)-position was carried out via palladium-catalyzed Suzuki–Miyaura and Buchwald-Hartwig amination cross-coupling reactions between N-protected-5-bromo-2-nitrophenyl-benzimidazole and aryl boronic acids or sulfonylanilines, with yields up to 81%. The final designed molecules (2-(aminophen-2-yl)-5(6)-substituted-1H-benzimidazoles), which encompass the appropriate functional groups in the 5(6)-position according to the pharmacophore model, were obtained in yields up to 91% after acid-mediated N-boc deprotection followed by Pd-catalyzed hydrogenation. These groups are predicted to favor interactions with DNA gyrase B residues Asn46, Asp73, and Asp173, aiming to promote an inhibitory effect.
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Affiliation(s)
- Rafael T. Aroso
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal;
| | - Rita C. Guedes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Correspondence: (R.C.G.); (M.M.P.)
| | - Mariette M. Pereira
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal;
- Correspondence: (R.C.G.); (M.M.P.)
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25
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Mohammed HA, Khan RA, Abdel-Hafez AA, Abdel-Aziz M, Ahmed E, Enany S, Mahgoub S, Al-Rugaie O, Alsharidah M, Aly MSA, Mehany ABM, Hegazy MM. Phytochemical Profiling, In Vitro and In Silico Anti-Microbial and Anti-Cancer Activity Evaluations and Staph GyraseB and h-TOP-IIβ Receptor-Docking Studies of Major Constituents of Zygophyllum coccineum L. Aqueous-Ethanolic Extract and Its Subsequent Fractions: An Approach to Validate Traditional Phytomedicinal Knowledge. Molecules 2021; 26:molecules26030577. [PMID: 33499325 PMCID: PMC7866194 DOI: 10.3390/molecules26030577] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
Zygophyllum coccineum, an edible halophytic plant, is part of the traditional medicine chest in the Mediterranean region for symptomatic relief of diabetes, hypertension, wound healing, burns, infections, and rheumatoid arthritis pain. The current study aimed to characterize Z. coccineum phytoconstituents, and the evaluations of the anti-microbial-biofilm, and anti-cancers bioactivities of the plant’s mother liquor, i.e., aqueous-ethanolic extract, and its subsequent fractions. The in silico receptors interaction feasibility of Z. coccineum major constituents with Staph GyraseB, and human topoisomerase-IIβ (h-TOP-IIβ) were conducted to confirm the plant’s anti-microbial and anti-cancer biological activities. Thirty-eight secondary metabolites of flavonoids, stilbene, phenolic acids, alkaloids, and coumarin classes identified by LC-ESI-TOF-MS spectrometric analysis, and tiliroside (kaempferol-3-O-(6′′′′-p-coumaroyl)-glucoside, 19.8%), zygophyloside-F (12.78%), zygophyloside-G (9.67%), and isorhamnetin-3-O-glucoside (4.75%) were identified as the major constituents. A superior biofilm obliteration activity established the minimum biofilm eradication concentration (MBEC) for the chloroform fraction at 3.9–15.63 µg/mL, as compared to the positive controls (15.63–31.25 µg/mL) against all the microbial strains that produced the biofilm under study, except the Aspergillus fumigatus. The aqueous-ethanolic extract showed cytotoxic effects with IC50 values at 3.47, 3.19, and 2.27 µg/mL against MCF-7, HCT-116, and HepG2 cell-lines, respectively, together with the inhibition of h-TOP-IIβ with IC50 value at 45.05 ng/mL in comparison to its standard referral inhibitor (staurosporine, IC50, 135.33 ng/mL). This conclusively established the anti-cancer activity of the aqueous-ethanolic extract that also validated by in silico receptor-binding predicted energy levels and receptor-site docking feasibility of the major constituents of the plant’s extract. The study helped to authenticate some of the traditional phytomedicinal properties of the anti-infectious nature of the plant.
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Affiliation(s)
- Hamdoon A. Mohammed
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia;
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo 11371, Egypt;
- Correspondence: (H.A.M.); (R.A.K.); Tel.: +966-566-176-074 (H.A.M.)
| | - Riaz A. Khan
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia;
- Correspondence: (H.A.M.); (R.A.K.); Tel.: +966-566-176-074 (H.A.M.)
| | - Atef A. Abdel-Hafez
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia;
| | - Marwa Abdel-Aziz
- Regional Center for Mycology and Biotechnology (RCMB), Al-Azhar University, Cairo 11371, Egypt;
| | - Eman Ahmed
- Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt;
- Proteomics and Metabolomics Unit, Department of Basic Research, Children’s Cancer Hospital Egypt 57357, Cairo 11441, Egypt;
| | - Shymaa Enany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Sebaey Mahgoub
- Proteomics and Metabolomics Unit, Department of Basic Research, Children’s Cancer Hospital Egypt 57357, Cairo 11441, Egypt;
- Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Osamah Al-Rugaie
- Department of Basic Medical Sciences, College of Medicine and Medical Sciences, Qassim University, Unaizah, P.O. Box 991, Qassim 51911, Saudi Arabia;
| | - Mansour Alsharidah
- Department of Physiology, College of Medicine, Qassim University, Qassim 51452, Saudi Arabia;
| | | | - Ahmed B. M. Mehany
- Department of Zoology, Faculty of Science, Al-Azhar University, Cairo 11371, Egypt;
| | - Mostafa M. Hegazy
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo 11371, Egypt;
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26
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Tittal RK, Ghule VD, Yadav P, Lal K, Kumar A. Synthesis, antimicrobial potency with in silico study of Boc-leucine-1,2,3-triazoles. Steroids 2020; 161:108675. [PMID: 32531313 DOI: 10.1016/j.steroids.2020.108675] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022]
Abstract
A library of N-Boc protected Leucine-linked 1,4-disubstituted 1,2,3-triazoles was synthesized and fully characterized, in high yield via copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. In vitro antibacterial activity showed that compound 4h found to be more potent than the reference drug Ciprofloxacin (MIC: 0.0196 µmol/mL) against tested bacterial strains S. entrica, B. subtilis, S. aureus, E. coli and P. auroginosa with MIC: 0.0148, 0.0074, 0.0148, 0.0074, and 0.0074 µmol/mL, respectively and antifungal activity with MIC: 0.0148 µmol/mL as compared to reference drug Fluconazole (MIC: 0.0102 µmol/mL) against A. niger and C. albicans fungal strains. Further, the molecular docking study on 4h and its predecessor alkyne 3 by choosing E. coli topoisomerase II, DNA Gyrase (PDB ID: 1KZN) showed better binding with triazole than alkyne and these results were supported by DFT study using B3LYP/6-311G(d,p) basis set.
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Affiliation(s)
- Ram Kumar Tittal
- Department of Chemistry, National Institute of Technology Kurukshetra, Haryana 136119, India.
| | - Vikas D Ghule
- Department of Chemistry, National Institute of Technology Kurukshetra, Haryana 136119, India
| | - Pinki Yadav
- Department of Chemistry, Guru Jambheshwar University of Science & Technology (GJUS&T), Hisar, Haryana 12500, India
| | - Kashmiri Lal
- Department of Chemistry, Guru Jambheshwar University of Science & Technology (GJUS&T), Hisar, Haryana 12500, India.
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences, GJUS&T, Hisar, Haryana 12500, India
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27
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Hashem HE, Amr AEGE, Nossier ES, Elsayed EA, Azmy EM. Synthesis, Antimicrobial Activity and Molecular Docking of Novel Thiourea Derivatives Tagged with Thiadiazole, Imidazole and Triazine Moieties as Potential DNA Gyrase and Topoisomerase IV Inhibitors. Molecules 2020; 25:molecules25122766. [PMID: 32549386 PMCID: PMC7356696 DOI: 10.3390/molecules25122766] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/25/2022] Open
Abstract
To develop new antimicrobial agents, a series of novel thiourea derivatives incorporated with different moieties 2–13 was designed and synthesized and their biological activities were evaluated. Compounds 7a, 7b and 8 exhibited excellent antimicrobial activity against all Gram-positive and Gram-negative bacteria, and the fungal Aspergillus flavus with minimum inhibitory concentration (MIC) values ranged from 0.95 ± 0.22 to 3.25 ± 1.00 μg/mL. Furthermore, cytotoxicity studies against MCF-7 cells revealed that compounds 7a and 7b were the most potent with IC50 values of 10.17 ± 0.65 and 11.59 ± 0.59 μM, respectively. On the other hand, the tested compounds were less toxic against normal kidney epithelial cell lines (Vero cells). The in vitro enzyme inhibition assay of 8 displayed excellent inhibitory activity against Escherichia coli DNA B gyrase and moderate one against E. coli Topoisomerase IV (IC50 = 0.33 ± 1.25 and 19.72 ± 1.00 µM, respectively) in comparison with novobiocin (IC50 values 0.28 ± 1.45 and 10.65 ± 1.02 µM, respectively). Finally, the molecular docking was done to position compound 8 into the E. coli DNA B and Topoisomerase IV active pockets to explore the probable binding conformation. In summary, compound 8 may serve as a potential dual E. coli DNA B and Topoisomerase IV inhibitor.
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Affiliation(s)
- Heba E. Hashem
- Department of Chemistry, Faculty of Women, Ain Shams University, Heliopolis, Cairo 11457, Egypt; (H.E.H.); (E.M.A.)
| | - Abd El-Galil E. Amr
- Drug Exploration & Development Chair (DEDC), Pharmaceutical Chemistry Department, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Applied Organic Chemistry Department, National Research Center, Dokki 12622, Cairo, Egypt
- Correspondence: ; Tel.: +966-543074312
| | - Eman S. Nossier
- Pharmaceutical Medicinal Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11754, Egypt;
| | - Elsayed A. Elsayed
- Bioproducts Research Chair, Zoology Department, Faculty of Science, King Saud University, Riyadh 11451, Saudi Arabia;
- Chemistry of Natural and Microbial Products Department, National Research Centre, Dokki 12622, Cairo, Egypt
| | - Eman M. Azmy
- Department of Chemistry, Faculty of Women, Ain Shams University, Heliopolis, Cairo 11457, Egypt; (H.E.H.); (E.M.A.)
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Hassan AS, Askar AA, Naglah AM, Almehizia AA, Ragab A. Discovery of New Schiff Bases Tethered Pyrazole Moiety: Design, Synthesis, Biological Evaluation, and Molecular Docking Study as Dual Targeting DHFR/DNA Gyrase Inhibitors with Immunomodulatory Activity. Molecules 2020; 25:molecules25112593. [PMID: 32498469 PMCID: PMC7321065 DOI: 10.3390/molecules25112593] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 01/08/2023] Open
Abstract
A series of Bis-pyrazole Schiff bases (6a–d and 7a–d) and mono-pyrazole Schiff bases (8a–d and 9a–d) were designed and synthesized through the reaction of 5-aminopyrazoles 1a–d with aldehydes 2–5 using mild reaction condition with a good yield percentage. The chemical structure of newly formed Schiff bases tethered pyrazole core was confirmed based on spectral and experimental data. All the newly formed pyrazole Schiff bases were evaluated against eight pathogens (Gram-positive, Gram-negative, and fungi). The result exhibited that, most of them have good and broad activities. Among those, only six Schiff bases (6b, 7b, 7c, 8a, 8d, and 9b) displayed MIC values (0.97–62.5 µg/mL) compared to Tetracycline (15.62–62.5 µg/mL) and Amphotericin B (15.62–31.25 µg/mL), MBC values (1.94–87.5 µg/mL) and selectivity to tumor cell than normal cells. Immunomodulatory activities showed that the promising Schiff bases increase the immunomodulator effect of defense cell and the Schiff base 8a is the highest one by (Intra. killing activity = 136.5 ± 0.3%) having a pyrazole moiety as well as amide function (O=C-NH2) and piperidinyl core. Furthermore, the most potent one exhibited broad activity depending on both MIC and MBC values. Moreover, to study the mechanism of these pyrazole Schiff bases, two active Schiff bases 8a and 9b from six derivatives were introduced to study the enzyme assay as dihydrofolate reductase (DHFR) on E. coli organism and DNA gyrase with two different organisms, S. aureus and B. subtilis, to determine the inhibitory activities with lower values in the case of DNA gyrase (8a and 9b) or nearly as DHFR compound 9b, while pyrazole 8a showed excellent inhibitory against all enzyme assay. The molecular docking study against dihydrofolate reductase and DNA gyrase were performed to study the binding between active site in the pocket with the two Schiff bases (8a and 9b) that exhibited good binding affinity with different bond types as H-bonding, aren-aren, and arene-cation interaction as well as study the physicochemical and pharmacokinetic properties of the two active Schiff bases 8a and 9b.
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Affiliation(s)
- Ashraf S. Hassan
- Organometallic and Organometalloid Chemistry Department, National Research Centre, Dokki 12622, Cairo, Egypt
- Correspondence: (A.S.H.); (A.A.A.); (A.R.); Tel.: +20-100-664-5444 (A.S.H.); +20-101-081-5102 (A.A.A.); +20-100-934-1359 (A.R.)
| | - Ahmed A. Askar
- Botany and Microbiology Department, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
- Correspondence: (A.S.H.); (A.A.A.); (A.R.); Tel.: +20-100-664-5444 (A.S.H.); +20-101-081-5102 (A.A.A.); +20-100-934-1359 (A.R.)
| | - Ahmed M. Naglah
- Department of Pharmaceutical Chemistry, Drug Exploration and Development Chair (DEDC), College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.M.N.); (A.A.A.)
- Peptide Chemistry Department, National Research Centre, Dokki 12622, Cairo, Egypt
| | - Abdulrahman A. Almehizia
- Department of Pharmaceutical Chemistry, Drug Exploration and Development Chair (DEDC), College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.M.N.); (A.A.A.)
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed Ragab
- Chemistry Department, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
- Correspondence: (A.S.H.); (A.A.A.); (A.R.); Tel.: +20-100-664-5444 (A.S.H.); +20-101-081-5102 (A.A.A.); +20-100-934-1359 (A.R.)
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Gibson EG, Oviatt AA, Cacho M, Neuman KC, Chan PF, Osheroff N. Bimodal Actions of a Naphthyridone/Aminopiperidine-Based Antibacterial That Targets Gyrase and Topoisomerase IV. Biochemistry 2019; 58:4447-4455. [PMID: 31617352 PMCID: PMC7450530 DOI: 10.1021/acs.biochem.9b00805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Gyrase and topoisomerase IV are the targets of fluoroquinolone antibacterials. However, the rise in antimicrobial resistance has undermined the clinical use of this important drug class. Therefore, it is critical to identify new agents that maintain activity against fluoroquinolone-resistant strains. One approach is to develop non-fluoroquinolone drugs that also target gyrase and topoisomerase IV but interact differently with the enzymes. This has led to the development of the "novel bacterial topoisomerase inhibitor" (NBTI) class of antibacterials. Despite the clinical potential of NBTIs, there is a relative paucity of data describing their mechanism of action against bacterial type II topoisomerases. Consequently, we characterized the activity of GSK126, a naphthyridone/aminopiperidine-based NBTI, against a variety of Gram-positive and Gram-negative bacterial type II topoisomerases, including gyrase from Mycobacterium tuberculosis and gyrase and topoisomerase IV from Bacillus anthracis and Escherichia coli. GSK126 enhanced single-stranded DNA cleavage and suppressed double-stranded cleavage mediated by these enzymes. It was also a potent inhibitor of gyrase-catalyzed DNA supercoiling and topoisomerase IV-catalyzed decatenation. Thus, GSK126 displays a similar bimodal mechanism of action across a variety of species. In contrast, GSK126 displayed a variable ability to overcome fluoroquinolone resistance mutations across these same species. Our results suggest that NBTIs elicit their antibacterial effects by two different mechanisms: inhibition of gyrase/topoisomerase IV catalytic activity or enhancement of enzyme-mediated DNA cleavage. Furthermore, the relative importance of these two mechanisms appears to differ from species to species. Therefore, we propose that the mechanistic basis for the antibacterial properties of NBTIs is bimodal in nature.
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Affiliation(s)
- Elizabeth G. Gibson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
| | - Alexandria A. Oviatt
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
| | - Monica Cacho
- Department of Diseases of the Developing World, GlaxoSmithKline, Parque Tecnológico de Madrid, Calle de Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20982, United States
| | - Pan F. Chan
- Infectious Diseases Discovery, Medicines Opportunities Research Unit, GlaxoSmithKline, Collegeville, PA 19426, United States
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
- Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232, United States
- VA Tennessee Valley Healthcare System, Nashville, TN 37212, United States
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Kamsri P, Punkvang A, Hannongbua S, Suttisintong K, Kittakoop P, Spencer J, Mulholland AJ, Pungpo P. In silico study directed towards identification of the key structural features of GyrB inhibitors targeting MTB DNA gyrase: HQSAR, CoMSIA and molecular dynamics simulations. SAR QSAR Environ Res 2019; 30:775-800. [PMID: 31607177 DOI: 10.1080/1062936x.2019.1658218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/17/2019] [Indexed: 06/10/2023]
Abstract
Mycobacterium tuberculosis DNA gyrase subunit B (GyrB) has been identified as a promising target for rational drug design against fluoroquinolone drug-resistant tuberculosis. In this study, we attempted to identify the key structural feature for highly potent GyrB inhibitors through 2D-QSAR using HQSAR, 3D-QSAR using CoMSIA and molecular dynamics (MD) simulations approaches on a series of thiazole urea core derivatives. The best HQSAR and CoMSIA models based on IC50 and MIC displayed the structural basis required for good activity against both GyrB enzyme and mycobacterial cell. MD simulations and binding free energy analysis using MM-GBSA and waterswap calculations revealed that the urea core of inhibitors has the strongest interaction with Asp79 via hydrogen bond interactions. In addition, cation-pi interaction and hydrophobic interactions of the R2 substituent with Arg82 and Arg141 help to enhance the binding affinity in the GyrB ATPase binding site. Thus, the present study provides crucial structural features and a structural concept for rational design of novel DNA gyrase inhibitors with improved biological activities against both enzyme and mycobacterial cell, and with good pharmacokinetic properties and drug safety profiles.
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Affiliation(s)
- P Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University , Nakhon Phanon , Thailand
| | - A Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University , Nakhon Phanon , Thailand
| | - S Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University , Bangkok , Thailand
| | - K Suttisintong
- National Nanotechnology Center, NSTDA , Pathum Thani , Thailand
| | - P Kittakoop
- Chulabhorn Graduate Institute, Chemical Biology Program, Chulabhorn Royal Academy , Bangkok , Thailand
- Chulabhorn Research Institute , Bangkok , Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education , Bangkok , Thailand
| | - J Spencer
- School of Cellular and Molecular Medicine, University of Bristol , Bristol , UK
| | - A J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol , UK
| | - P Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University , Ubon Ratchathani , Thailand
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31
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Pisano MB, Kumar A, Medda R, Gatto G, Pal R, Fais A, Era B, Cosentino S, Uriarte E, Santana L, Pintus F, Matos MJ. Antibacterial Activity and Molecular Docking Studies of a Selected Series of Hydroxy-3-arylcoumarins. Molecules 2019; 24:E2815. [PMID: 31375003 PMCID: PMC6696357 DOI: 10.3390/molecules24152815] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 01/02/2023] Open
Abstract
Antibiotic resistance is one of the main public health concerns of this century. This resistance is also associated with oxidative stress, which could contribute to the selection of resistant bacterial strains. Bearing this in mind, and considering that flavonoid compounds are well known for displaying both activities, we investigated a series of hydroxy-3-arylcoumarins with structural features of flavonoids for their antibacterial activity against different bacterial strains. Active compounds showed selectivity against the studied Gram-positive bacteria compared to Gram-negative bacteria. 5,7-Dihydroxy-3-phenylcoumarin (compound 8) displayed the best antibacterial activity against Staphylococcus aureus and Bacillus cereus with minimum inhibitory concentrations (MICs) of 11 g/mL, followed by Staphylococcus aureus (MRSA strain) and Listeria monocytogenes with MICs of 22 and 44 g/mL, respectively. Moreover, molecular docking studies performed on the most active compounds against Staphylococcus aureus tyrosyl-tRNA synthetase and topoisomerase II DNA gyrase revealed the potential binding mode of the ligands to the site of the appropriate targets. Preliminary structure-activity relationship studies showed that the antibacterial activity can be modulated by the presence of the 3-phenyl ring and by the position of the hydroxyl groups at the coumarin scaffold.
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Affiliation(s)
- Maria Barbara Pisano
- Department of Medical Sciences and Public Health, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Amit Kumar
- Department of Electrical and Electronic Engineering, University of Cagliari, Via Marengo 2, 09123 Cagliari, Italy
| | - Rosaria Medda
- Department of Sciences of Life and Environment, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Gianluca Gatto
- Department of Electrical and Electronic Engineering, University of Cagliari, Via Marengo 2, 09123 Cagliari, Italy
| | - Rajesh Pal
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Antonella Fais
- Department of Sciences of Life and Environment, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy.
| | - Benedetta Era
- Department of Sciences of Life and Environment, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy.
| | - Sofia Cosentino
- Department of Medical Sciences and Public Health, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Eugenio Uriarte
- Department of Organic Chemistry, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Lourdes Santana
- Department of Organic Chemistry, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Francesca Pintus
- Department of Sciences of Life and Environment, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Maria João Matos
- Department of Organic Chemistry, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Jung-Schroers V, Jung A, Ryll M, Bauer J, Teitge F, Steinhagen D. Diagnostic methods for identifying different Aeromonas species and examining their pathogenicity factors, their correlation to cytotoxicity and adherence to fish mucus. J Fish Dis 2019; 42:189-219. [PMID: 30521094 DOI: 10.1111/jfd.12917] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 06/09/2023]
Abstract
Aeromonas spp. are ubiquitous in the aquatic environment, acting as facultative or obligate pathogens for fish. Identifying Aeromonas spp. is important for pathogenesis and prognosis in diagnostic cases but can be difficult because of their close relationship. Forty-four already characterized isolates of Aeromonas spp. were analysed by 16S rRNA gene sequencing, by gyrase B sequencing, by analysing their fatty acid profiles, by biochemical reactions and by MALDI-TOF MS. To determine their pathogenicity, cytotoxicity, adhesion to mucus and the expression of 12 virulence factors were tested. The susceptibility of the isolates towards 13 different antibiotics was determined. MALDI-TOF MS was found to be an acceptable identification method for Aeromonas spp. Although the method does not detect all species correctly, it is time-effective and entails relatively low costs and no other methods achieved better results. A high prevalence of virulence-related gene fragments was detected in almost all examined Aeromonas spp., especially in A. hydrophila and A. salmonicida, and most isolates exhibited a cytotoxic effect. Single isolates of A. hydrophila and A. salmonicida showed multiple resistance to antibiotics. These results might indicate the potentially pathogenic capacity of Aeromonas spp., suggesting a risk for aquatic animals and even humans, given their ubiquitous nature.
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Affiliation(s)
- Verena Jung-Schroers
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - Arne Jung
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| | - Martin Ryll
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| | - Julia Bauer
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - Felix Teitge
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - Dieter Steinhagen
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
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33
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Ansari A, Ali A, Asif M, Rauf MA, Owais M. Facile one-pot multicomponent synthesis and molecular docking studies of steroidal oxazole/thiazole derivatives with effective antimicrobial, antibiofilm and hemolytic properties. Steroids 2018; 134:22-36. [PMID: 29653115 DOI: 10.1016/j.steroids.2018.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/17/2018] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
A series of steroidal oxazole and thiazole derivatives have been synthesized employing thiosemicarbazide/semicarbazide hydrochloride and ethyl 2-chloroacetoacetate with a simple and facile one-pot multicomponent reaction pathway. The antimicrobial activity of newly synthesized compounds were evaluated against four bacterial strains namely Gram-negative (Escherichia coliand Pseudomonas aeruginosa) and Gram-positive bacteria (Staphylococcus aureus and Listeria monocytogenes) in addition to pathogenic fungi (Candida albicans and Cryptococcus neoformans). Bioactivity assay manifested that most of the compounds exhibited good antimicrobial activity. To provide additional insight into antimicrobial activity, the compounds were also tested for their antibiofilm activity against S. aureus biofilm. Moreover, molecular docking study shows binding of compounds with amino acid residues of DNA gyrase and glucosamine-6-phosphate synthase (promising antimicrobial target) through hydrogen bonding interactions. Hemolytic activity have been also investigated to ascertain the effect of compounds over RBC lysis and results indicate good prospects for biocompatibility. The expedient synthesis of steroidal heterocycles, effective antibacterial and antifungal behavior against various clinically relevant human pathogens, promising biocompatibility offer opportunities for further modification and potential applications as therapeutic agents.
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Affiliation(s)
- Anam Ansari
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India
| | - Abad Ali
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India; Organometallic Synthesis and Catalysis Group, Chemical Engineering Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411 008, Maharashtra, India
| | - Mohd Asif
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India
| | - Mohd Ahmar Rauf
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Owais
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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Klostermeier D. Why Two? On the Role of (A-)Symmetry in Negative Supercoiling of DNA by Gyrase. Int J Mol Sci 2018; 19:E1489. [PMID: 29772727 PMCID: PMC5983639 DOI: 10.3390/ijms19051489] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/09/2018] [Accepted: 05/12/2018] [Indexed: 11/17/2022] Open
Abstract
Gyrase is a type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme consists of two GyrA and two GyrB subunits. It is believed to introduce negative supercoils into DNA by converting a positive DNA node into a negative node through strand passage: First, it cleaves both DNA strands of a double-stranded DNA, termed the G-segment, and then it passes a second segment of the same DNA molecule, termed the T-segment, through the gap created. As a two-fold symmetric enzyme, gyrase contains two copies of all elements that are key for the supercoiling reaction: The GyrB subunits provide two active sites for ATP binding and hydrolysis. The GyrA subunits contain two C-terminal domains (CTDs) for DNA binding and wrapping to stabilize the positive DNA node, and two catalytic tyrosines for DNA cleavage. While the presence of two catalytic tyrosines has been ascribed to the necessity of cleaving both strands of the G-segment to enable strand passage, the role of the two ATP hydrolysis events and of the two CTDs has been less clear. This review summarizes recent results on the role of these duplicate elements for individual steps of the supercoiling reaction, and discusses the implications for the mechanism of DNA supercoiling.
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Affiliation(s)
- Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany.
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Germe T, Vörös J, Jeannot F, Taillier T, Stavenger RA, Bacqué E, Maxwell A, Bax BD. A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance. Nucleic Acids Res 2018; 46:4114-4128. [PMID: 29538767 PMCID: PMC5934680 DOI: 10.1093/nar/gky181] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/16/2018] [Accepted: 03/02/2018] [Indexed: 12/24/2022] Open
Abstract
Imidazopyrazinones (IPYs) are a new class of compounds that target bacterial topoisomerases as a basis for their antibacterial activity. We have characterized the mechanism of these compounds through structural/mechanistic studies showing they bind and stabilize a cleavage complex between DNA gyrase and DNA ('poisoning') in an analogous fashion to fluoroquinolones, but without the requirement for the water-metal-ion bridge. Biochemical experiments and structural studies of cleavage complexes of IPYs compared with an uncleaved gyrase-DNA complex, reveal conformational transitions coupled to DNA cleavage at the DNA gate. These involve movement at the GyrA interface and tilting of the TOPRIM domains toward the scissile phosphate coupled to capture of the catalytic metal ion. Our experiments show that these structural transitions are involved generally in poisoning of gyrase by therapeutic compounds and resemble those undergone by the enzyme during its adenosine triphosphate-coupled strand-passage cycle. In addition to resistance mutations affecting residues that directly interact with the compounds, we characterized a mutant (D82N) that inhibits formation of the cleavage complex by the unpoisoned enzyme. The D82N mutant appears to act by stabilizing the binary conformation of DNA gyrase with uncleaved DNA without direct interaction with the compounds. This provides general insight into the resistance mechanisms to antibiotics targeting bacterial type II topoisomerases.
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Affiliation(s)
- Thomas Germe
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Judit Vörös
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Frederic Jeannot
- Sanofi R&D, TSU Infectious Diseases, 1541 Avenue Marcel Mérieux, 69280 Marcy L’Etoile, France
| | - Thomas Taillier
- Sanofi R&D, TSU Infectious Diseases, 1541 Avenue Marcel Mérieux, 69280 Marcy L’Etoile, France
| | - Robert A Stavenger
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, 1250 Collegeville Road, Collegeville, PA 19426, USA
| | - Eric Bacqué
- Sanofi R&D, TSU Infectious Diseases, 1541 Avenue Marcel Mérieux, 69280 Marcy L’Etoile, France
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Benjamin D Bax
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
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Kumar S, Saini V, Maurya IK, Sindhu J, Kumari M, Kataria R, Kumar V. Design, synthesis, DFT, docking studies and ADME prediction of some new coumarinyl linked pyrazolylthiazoles: Potential standalone or adjuvant antimicrobial agents. PLoS One 2018; 13:e0196016. [PMID: 29672633 PMCID: PMC5908142 DOI: 10.1371/journal.pone.0196016] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/04/2018] [Indexed: 12/26/2022] Open
Abstract
The control of antimicrobial resistance (AMR) seems to have come to a dead end. The major consequences of the use and abuse of antibacterial drugs are the development of resistant strains due to genetic mutability of both pathogenic and nonpathogenic microorganisms. We, herein, report the synthesis, characterization and biological activities of coumarin-thiazole-pyrazole (CTP) molecular hybrids with an effort to explore and overcome the increasing antimicrobial resistance. The compounds were characterized by analyzing their IR, Mass, 1H and13C NMR spectral data and elemental analysis. The in vitro antimicrobial activity of the synthesized compounds was investigated against various pathogenic strains; the results obtained were further explained with the help of DFT and molecular orbital calculations. Compound 1b and 1f displayed good antimicrobial activity and synergistic effects when used with kanamycin and amphotericin B. Furthermore, in vitro cytotoxicity of compounds 1b and 1f were studied against HeLa cells (cervical cancer cell) and Hek-293 cells. The results of molecular docking study were used to better rationalize the action and prediction of the binding modes of these compounds.
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Affiliation(s)
- Sunil Kumar
- Department of Chemistry & Centre of Advance Studies in Chemistry, Panjab University, Chandigarhs, India
| | - Vikram Saini
- Department of Biotechnology, AIIMS- New Delhi, Delhi, India
| | - Indresh K. Maurya
- Department of Microbial Biotechnology, Panjab University, Chandigarh, India
| | | | - Mukesh Kumari
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
| | - Ramesh Kataria
- Department of Chemistry & Centre of Advance Studies in Chemistry, Panjab University, Chandigarhs, India
- * E-mail: (RK); (VK)
| | - Vinod Kumar
- Department of Chemistry, M. M. University, Mullana-Ambala, India
- * E-mail: (RK); (VK)
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Franco-Ulloa S, La Sala G, Miscione GP, De Vivo M. Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site. Int J Mol Sci 2018; 19:ijms19020453. [PMID: 29401640 PMCID: PMC5855675 DOI: 10.3390/ijms19020453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 11/19/2022] Open
Abstract
DNA gyrases are enzymes that control the topology of DNA in bacteria cells. This is a vital function for bacteria. For this reason, DNA gyrases are targeted by widely used antibiotics such as quinolones. Recently, structural and biochemical investigations identified a new class of DNA gyrase inhibitors called NBTIs (i.e., novel bacterial topoisomerase inhibitors). NBTIs are particularly promising because they are active against multi-drug resistant bacteria, an alarming clinical issue. Structural data recently demonstrated that these NBTIs bind tightly to a newly identified pocket at the dimer interface of the DNA–protein complex. In the present study, we used molecular dynamics (MD) simulations and docking calculations to shed new light on the binding of NBTIs to this site. Interestingly, our MD simulations demonstrate the intrinsic flexibility of this binding site, which allows the pocket to adapt its conformation and form optimal interactions with the ligand. In particular, we examined two ligands, AM8085 and AM8191, which induced a repositioning of a key aspartate (Asp83B), whose side chain can rotate within the binding site. The conformational rearrangement of Asp83B allows the formation of a newly identified H-bond interaction with an NH on the bound NBTI, which seems important for the binding of NBTIs having such functionality. We validated these findings through docking calculations using an extended set of cognate oxabicyclooctane-linked NBTIs derivatives (~150, in total), screened against multiple target conformations. The newly identified H-bond interaction significantly improves the docking enrichment. These insights could be helpful for future virtual screening campaigns against DNA gyrase.
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Affiliation(s)
- Sebastian Franco-Ulloa
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Giuseppina La Sala
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Gian Pietro Miscione
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
- IAS-5/INM-9 Computational Biomedicine Forschungszentrum Jülich Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
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Nastasă C, Vodnar DC, Ionuţ I, Stana A, Benedec D, Tamaian R, Oniga O, Tiperciuc B. Antibacterial Evaluation and Virtual Screening of New Thiazolyl-Triazole Schiff Bases as Potential DNA-Gyrase Inhibitors. Int J Mol Sci 2018; 19:ijms19010222. [PMID: 29324679 PMCID: PMC5796171 DOI: 10.3390/ijms19010222] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/21/2017] [Accepted: 01/09/2018] [Indexed: 01/18/2023] Open
Abstract
The global spread of bacterial resistance to drugs used in therapy requires new potent and safe antimicrobial agents. DNA gyrases represent important targets in drug discovery. Schiff bases, thiazole, and triazole derivatives are considered key scaffolds in medicinal chemistry. Fifteen thiazolyl-triazole Schiff bases were evaluated for their antibacterial activity, measuring the growth inhibition zone diameter, the minimum inhibitory concentration (MIC), and the minimum bactericidal concentration (MBC), against Gram-positive (Staphylococcus aureus, Listeria monocytogenes) and Gram-negative (Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa) bacteria. The inhibition of S. aureus and S. typhimurium was modest. Compounds B1, B2, and B9 showed a similar effect as ciprofloxacin, the antimicrobial reference, against L. monocytogenes. B10 displayed a better effect. Derivatives B1, B5–7, B9, and B11–15 expressed MIC values lower than the reference, against L. monocytogenes. B5, B6, and B11–15 strongly inhibited the growth of P. aeruginosa. All compounds were subjected to an in silico screening of the ADMET (absorption, distribution, metabolism, elimination, toxicity) properties. Molecular docking was performed on the gyrA and gyrB from L. monocytogenes. The virtual screening concluded that thiazolyl-triazole Schiff base B8 is the best drug-like candidate, satisfying requirements for both safety and efficacy, being more potent against the bacterial gyrA than ciprofloxacin.
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Affiliation(s)
- Cristina Nastasă
- Department of Pharmaceutical Chemistry, "Iuliu Haţieganu" University of Medicine and Pharmacy, 41 Victor Babeş Street, RO-400012 Cluj-Napoca, Romania.
| | - Dan C Vodnar
- Department of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 3-5 Mănăştur Street, RO-400372 Cluj-Napoca, Romania.
| | - Ioana Ionuţ
- Department of Pharmaceutical Chemistry, "Iuliu Haţieganu" University of Medicine and Pharmacy, 41 Victor Babeş Street, RO-400012 Cluj-Napoca, Romania.
| | - Anca Stana
- Department of Pharmaceutical Chemistry, "Iuliu Haţieganu" University of Medicine and Pharmacy, 41 Victor Babeş Street, RO-400012 Cluj-Napoca, Romania.
| | - Daniela Benedec
- Department of Pharmacognosy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 12 Ion Creangă Street, RO-400010 Cluj-Napoca, Romania.
| | - Radu Tamaian
- National Institute for Research and Development for Cryogenic and Isotopic Technologies, 4th Uzinei Street, RO-240050 Râmnicu Vâlcea, Romania.
- SC Biotech Corp SRL, 4th Uzinei Street, RO-240050 Râmnicu Vâlcea, Romania.
| | - Ovidiu Oniga
- Department of Pharmaceutical Chemistry, "Iuliu Haţieganu" University of Medicine and Pharmacy, 41 Victor Babeş Street, RO-400012 Cluj-Napoca, Romania.
| | - Brînduşa Tiperciuc
- Department of Pharmaceutical Chemistry, "Iuliu Haţieganu" University of Medicine and Pharmacy, 41 Victor Babeş Street, RO-400012 Cluj-Napoca, Romania.
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Hartmann S, Gubaev A, Klostermeier D. Binding and Hydrolysis of a Single ATP Is Sufficient for N-Gate Closure and DNA Supercoiling by Gyrase. J Mol Biol 2017; 429:3717-3729. [PMID: 29032205 DOI: 10.1016/j.jmb.2017.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 11/19/2022]
Abstract
Topoisomerases catalyze the relaxation, supercoiling, catenation, and decatenation of DNA. Gyrase is a bacterial topoisomerase that introduces negative supercoils into DNA in an ATP-dependent reaction. The enzyme consists of two GyrB subunits, containing the ATPase domains, and two GyrA subunits. Nucleotide binding to gyrase B GyrB causes closing of the N-gate in gyrase, which orients bound DNA for supercoiling. N-gate re-opening after ATP hydrolysis, at the end of the supercoiling reaction, resets the enzyme for subsequent catalytic cycles. Gyrase binds and hydrolyzes two ATP molecules per catalytic cycle. Here, we dissect the role of these two binding and hydrolysis events using gyrase with one ATP-binding- and hydrolysis-deficient subunit, or with one binding-competent, but hydrolysis-deficient ATPase domain. We show that binding of a single ATP molecule induces N-gate closure. Gyrase that can only bind and hydrolyze a single ATP undergoes opening and closing of the N-gate in synchrony with ATP hydrolysis, and promotes DNA supercoiling under catalytic conditions. In contrast, gyrase that can bind two ATP molecules, but hydrolyzes only one, only supercoils DNA under stoichiometric conditions. Here, ATP bound to the hydrolysis-deficient subunit keeps the N-gate closed after hydrolysis of the other ATP and prevents further turnovers. Gyrase with only one functional ATPase domain hydrolyzes ATP with a similar rate to wild-type, but its supercoiling efficiency is reduced. Binding and hydrolysis of the second ATP may thus ensure efficient coupling of the nucleotide cycle with the supercoiling reaction by stabilizing the closed N-gate and by acting as a timer for N-gate re-opening.
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Affiliation(s)
- Simon Hartmann
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Airat Gubaev
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany.
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Villa JK, Amador P, Janovsky J, Bhuyan A, Saldanha R, Lamkin TJ, Contreras LM. A Genome-Wide Search for Ionizing-Radiation-Responsive Elements in Deinococcus radiodurans Reveals a Regulatory Role for the DNA Gyrase Subunit A Gene's 5' Untranslated Region in the Radiation and Desiccation Response. Appl Environ Microbiol 2017; 83:e00039-17. [PMID: 28411225 PMCID: PMC5452802 DOI: 10.1128/aem.00039-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/07/2017] [Indexed: 12/19/2022] Open
Abstract
Tight regulation of gene expression is important for the survival of Deinococcus radiodurans, a model bacterium of extreme stress resistance. Few studies have examined the use of regulatory RNAs as a possible contributing mechanism to ionizing radiation (IR) resistance, despite their proffered efficient and dynamic gene expression regulation under IR stress. This work presents a transcriptome-based approach for the identification of stress-responsive regulatory 5' untranslated region (5'-UTR) elements in D. radiodurans R1 that can be broadly applied to other bacteria. Using this platform and an in vivo fluorescence screen, we uncovered the presence of a radiation-responsive regulatory motif in the 5' UTR of the DNA gyrase subunit A gene. Additional screens under H2O2-induced oxidative stress revealed the specificity of the response of this element to IR stress. Further examination of the sequence revealed a regulatory motif of the radiation and desiccation response (RDR) in the 5' UTR that is necessary for the recovery of D. radiodurans from high doses of IR. Furthermore, we suggest that it is the preservation of predicted RNA structure, in addition to DNA sequence consensus of the motif, that permits this important regulatory ability.IMPORTANCEDeinococcus radiodurans is an extremely stress-resistant bacterium capable of tolerating up to 3,000 times more ionizing radiation than human cells. As an integral part of the stress response mechanism of this organism, we suspect that it maintains stringent control of gene expression. However, understanding of its regulatory pathways remains incomplete to date. Untranslated RNA elements have been demonstrated to play crucial roles in gene regulation throughout bacteria. In this work, we focus on searching for and characterizing responsive RNA elements under radiation stress and propose that multiple levels of gene regulation work simultaneously to enable this organism to efficiently recover from exposure to ionizing radiation. The model we propose serves as a generic template to investigate similar mechanisms of gene regulation under stress that have likely evolved in other bacterial species.
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Affiliation(s)
- Jordan K Villa
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Paul Amador
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Justin Janovsky
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Arijit Bhuyan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas,USA
| | | | - Thomas J Lamkin
- Air Force Research Laboratory/XPRA Wright-Patterson AFB, Ohio, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas,USA
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Chan PF, Germe T, Bax BD, Huang J, Thalji RK, Bacqué E, Checchia A, Chen D, Cui H, Ding X, Ingraham K, McCloskey L, Raha K, Srikannathasan V, Maxwell A, Stavenger RA. Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase. Proc Natl Acad Sci U S A 2017; 114:E4492-E4500. [PMID: 28507124 PMCID: PMC5465892 DOI: 10.1073/pnas.1700721114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A paucity of novel acting antibacterials is in development to treat the rising threat of antimicrobial resistance, particularly in Gram-negative hospital pathogens, which has led to renewed efforts in antibiotic drug discovery. Fluoroquinolones are broad-spectrum antibacterials that target DNA gyrase by stabilizing DNA-cleavage complexes, but their clinical utility has been compromised by resistance. We have identified a class of antibacterial thiophenes that target DNA gyrase with a unique mechanism of action and have activity against a range of bacterial pathogens, including strains resistant to fluoroquinolones. Although fluoroquinolones stabilize double-stranded DNA breaks, the antibacterial thiophenes stabilize gyrase-mediated DNA-cleavage complexes in either one DNA strand or both DNA strands. X-ray crystallography of DNA gyrase-DNA complexes shows the compounds binding to a protein pocket between the winged helix domain and topoisomerase-primase domain, remote from the DNA. Mutations of conserved residues around this pocket affect activity of the thiophene inhibitors, consistent with allosteric inhibition of DNA gyrase. This druggable pocket provides potentially complementary opportunities for targeting bacterial topoisomerases for antibiotic development.
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Affiliation(s)
- Pan F Chan
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426;
| | - Thomas Germe
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Benjamin D Bax
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Jianzhong Huang
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Reema K Thalji
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Eric Bacqué
- Therapeutic Strategic Unit Infectious Diseases, Sanofi Research & Development, 69280, Marcy L'Etoile, France
| | - Anna Checchia
- Aptuit Center of Drug Discovery and Development, 37135, Verona, Italy
| | - Dongzhao Chen
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Haifeng Cui
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Xiao Ding
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Karen Ingraham
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Lynn McCloskey
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Kaushik Raha
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Velupillai Srikannathasan
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Robert A Stavenger
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426;
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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 QSAR Environ Res 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Preethi B, Shanthi V, Ramanathan K. Identification of Potential Therapeutics to Conquer Drug Resistance in Salmonella typhimurium: Drug Repurposing Strategy. BioDrugs 2017; 30:593-605. [PMID: 27761807 DOI: 10.1007/s40259-016-0200-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Salmonella typhimurium is the main cause of gastrointestinal illness in humans, and treatment options are decreasing because drug-resistant strains have emerged. OBJECTIVE The objective of this study was to use computational drug repurposing to identify a novel candidate with an effective mechanism of action to circumvent the drug resistance. METHODS We used the Mantra 2.0 database to initially screen drug candidates that share similar gene expression profiles to those of quinolones. Data were further reduced using pharmacophore mapping theory. Finally, we employed molecular-simulation studies to calculate the binding affinity of the screened candidates with DNA gyrase, alongside an analysis of side effects. RESULTS A total of 16 drug candidates from the Mantra 2.0 database were screened. The pharmacophoric features of the screened candidates were examined and nalidixic acid features compared using the PharamGist program. A total of 11 compounds with the highest pharmacophore score were considered for binding energy calculation. Finally, we analysed the side effects of the eight drug candidates that showed significant binding affinity in the simulation study. CONCLUSION Overall, flufenamic acid and sulconazole may be potential drug candidates that could be studied in vitro to assess their resistance profile against Salmonella enterica Typhimurium.
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Affiliation(s)
- Balasundaram Preethi
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Veerappapillai Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Karuppasamy Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
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Sanabria-Ríos DJ, Rivera-Torres Y, Rosario J, Gutierrez R, Torres-García Y, Montano N, Ortíz-Soto G, Ríos-Olivares E, Rodríguez JW, Carballeira NM. Chemical conjugation of 2-hexadecynoic acid to C5-curcumin enhances its antibacterial activity against multi-drug resistant bacteria. Bioorg Med Chem Lett 2015; 25:5067-71. [PMID: 26483137 PMCID: PMC4663078 DOI: 10.1016/j.bmcl.2015.10.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/06/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
The first total synthesis of a C5-curcumin-2-hexadecynoic acid (C5-Curc-2-HDA, 6) conjugate was successfully performed. Through a three-step synthetic route, conjugate 6 was obtained in 13% overall yield and tested for antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) strains. Our results revealed that 6 was active against eight MRSA strains at MICs that range between 31.3 and 62.5 μg/mL. It was found that the presence of 2-hexadecynoic acid (2-HDA, 4) in conjugate 6 increased 4-8-fold its antibacterial activity against MRSA strains supporting our hypothesis that the chemical connection of 4 to C5-curcumin (2) increases the antibacterial activity of 2 against Gram-positive bacteria. Combinational index (CIn) values that range between 1.6 and 2.3 were obtained when eight MRSA strains were treated with an equimolar mixture of 2 and 4. These results demonstrated that an antagonistic effect is taking place. Finally, it was investigated whether conjugate 6 can affect the replication process of S. aureus, since this compound inhibited the supercoiling activity of the S. aureus DNA gyrase at minimum inhibitory concentrations (MIC) of 250 μg/mL (IC50=100.2±13.9 μg/mL). Moreover, it was observed that the presence of 4 in conjugate 6 improves the anti-topoisomerase activity of 2 towards S. aureus DNA gyrase, which is in agreement with results obtained from antibacterial susceptibility tests involving MRSA strains.
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Affiliation(s)
- David J Sanabria-Ríos
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan 00919, Puerto Rico.
| | - Yaritza Rivera-Torres
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan 00919, Puerto Rico
| | - Joshua Rosario
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan 00919, Puerto Rico
| | - Ricardo Gutierrez
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan 00919, Puerto Rico
| | - Yeireliz Torres-García
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan 00919, Puerto Rico
| | - Nashbly Montano
- Department of Chemistry, University of Puerto Rico, Rio Piedras Campus, PO Box 23346, San Juan 00931-3346, Puerto Rico
| | - Gabriela Ortíz-Soto
- Department of Microbiology and Immunology, Universidad Central del Caribe School of Medicine, PO Box 60327, Bayamón 00960, Puerto Rico
| | - Eddy Ríos-Olivares
- Department of Microbiology and Immunology, Universidad Central del Caribe School of Medicine, PO Box 60327, Bayamón 00960, Puerto Rico
| | - José W Rodríguez
- Department of Microbiology and Immunology, Universidad Central del Caribe School of Medicine, PO Box 60327, Bayamón 00960, Puerto Rico
| | - Néstor M Carballeira
- Department of Chemistry, University of Puerto Rico, Rio Piedras Campus, PO Box 23346, San Juan 00931-3346, Puerto Rico
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Preethi B, Ramanathan K. Molecular level understanding of resistance to nalidixic acid in Salmonella enteric serovar typhimurium associates with the S83F sequence type. Eur Biophys J 2015; 45:35-44. [PMID: 26329667 DOI: 10.1007/s00249-015-1073-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 07/15/2015] [Accepted: 08/12/2015] [Indexed: 02/04/2023]
Abstract
Nalidixic acid is an antibiotic drug used for treatment of Salmonellosis, a gastrointestinal infection. DNA gyrase subunit A (GyrA) of Salmonella typhimurium is the drug target for nalidixic acid. Resistance of GyrA to nalidixic acid, because of a point mutation in S. typhimurium, was recently reported. Substitution of Phe in place of Ser at locus 83 in GyrA of S. typhimurium has been experimentally associated with nalidixic acid resistance. Despite recent efforts, the mechanism of this resistance is not well understood. In this investigation we used computational techniques to address this shortcoming. Our results showed that contact with residue Arg 91 is certainly important for efficient binding of nalidixic acid to the target protein, and that mutation of this residue results in 180° rotation of the antibiotic in its binding pocket, around its own long axis. It is hoped these findings may enable development of new antibiotics against resistant forms of Salmonella.
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Affiliation(s)
- B Preethi
- Industrial Biotechnology Division, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - K Ramanathan
- Industrial Biotechnology Division, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
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Hearnshaw SJ, Chung TTH, Stevenson CEM, Maxwell A, Lawson DM. The role of monovalent cations in the ATPase reaction of DNA gyrase. Acta Crystallogr D Biol Crystallogr 2015; 71:996-1005. [PMID: 25849408 PMCID: PMC4388272 DOI: 10.1107/s1399004715002916] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/10/2015] [Indexed: 11/25/2022]
Abstract
Four new crystal structures of the ATPase domain of the GyrB subunit of Escherichia coli DNA gyrase have been determined. One of these, solved in the presence of K(+), is the highest resolution structure reported so far for this domain and, in conjunction with the three other structures, reveals new insights into the function of this domain. Evidence is provided for the existence of two monovalent cation-binding sites: site 1, which preferentially binds a K(+) ion that interacts directly with the α-phosphate of ATP, and site 2, which preferentially binds an Na(+) ion and the functional significance of which is not clear. The crystallographic data are corroborated by ATPase data, and the structures are compared with those of homologues to investigate the broader conservation of these sites.
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Affiliation(s)
- Stephen James Hearnshaw
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
| | - Terence Tsz-Hong Chung
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
| | | | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
| | - David Mark Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
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47
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Abstract
DNA topoisomerases are enzymes that control the topology of DNA in all cells. There are two types, I and II, classified according to whether they make transient single- or double-stranded breaks in DNA. Their reactions generally involve the passage of a single- or double-strand segment of DNA through this transient break, stabilized by DNA-protein covalent bonds. All topoisomerases can relax DNA, but DNA gyrase, present in all bacteria, can also introduce supercoils into DNA. Because of their essentiality in all cells and the fact that their reactions proceed via DNA breaks, topoisomerases have become important drug targets; the bacterial enzymes are key targets for antibacterial agents. This article discusses the structure and mechanism of topoisomerases and their roles in the bacterial cell. Targeting of the bacterial topoisomerases by inhibitors, including antibiotics in clinical use, is also discussed.
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Perlmutter J, Forbes LT, Krysan DJ, Ebsworth-Mojica K, Colquhoun JM, Wang J, Dunman PM, Flaherty DP. Repurposing the antihistamine terfenadine for antimicrobial activity against Staphylococcus aureus. J Med Chem 2014; 57:8540-62. [PMID: 25238555 PMCID: PMC4207543 DOI: 10.1021/jm5010682] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Indexed: 01/28/2023]
Abstract
Staphylococcus aureus is a rapidly growing health threat in the U.S., with resistance to several commonly prescribed treatments. A high-throughput screen identified the antihistamine terfenadine to possess, previously unreported, antimicrobial activity against S. aureus and other Gram-positive bacteria. In an effort to repurpose this drug, structure-activity relationship studies yielded 84 terfenadine-based analogues with several modifications providing increased activity versus S. aureus and other bacterial pathogens, including Mycobacterium tuberculosis. Mechanism of action studies revealed these compounds to exert their antibacterial effects, at least in part, through inhibition of the bacterial type II topoisomerases. This scaffold suffers from hERG liabilities which were not remedied through this round of optimization; however, given the overall improvement in activity of the set, terfenadine-based analogues provide a novel structural class of antimicrobial compounds with potential for further characterization as part of the continuing process to meet the current need for new antibiotics.
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Affiliation(s)
- Jessamyn
I. Perlmutter
- Department
of Microbiology and Immunology, University
of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United
States
| | - Lauren T. Forbes
- Department
of Microbiology and Immunology, University
of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United
States
| | - Damian J. Krysan
- Department
of Pediatrics, University of Rochester Medical
Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Katherine Ebsworth-Mojica
- Department
of Microbiology and Immunology, University
of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United
States
- Department
of Pediatrics, University of Rochester Medical
Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Jennifer M. Colquhoun
- Department
of Microbiology and Immunology, University
of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United
States
| | - Jenna
L. Wang
- Specialized
Chemistry Center, Delbert M. Shankel Structural Biology Center, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United
States
| | - Paul M. Dunman
- Department
of Microbiology and Immunology, University
of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United
States
| | - Daniel P. Flaherty
- Specialized
Chemistry Center, Delbert M. Shankel Structural Biology Center, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United
States
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Bonasera JM, Asselin JAE, Beer SV. Identification of bacteria pathogenic to or associated with onion (Allium cepa) based on sequence differences in a portion of the conserved gyrase B gene. J Microbiol Methods 2014; 103:138-43. [PMID: 24925602 DOI: 10.1016/j.mimet.2014.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/01/2014] [Accepted: 06/01/2014] [Indexed: 11/17/2022]
Abstract
We have developed a method for the identification of Gram-negative bacteria, particularly members of the Enterobacteriaceae, based on sequence variation in a portion of the gyrB gene. Thus, we identified, in most cases to species level, over 1000 isolates from onion bulbs and leaves and soil in which onions were grown.
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Affiliation(s)
- Jean M Bonasera
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jo Ann E Asselin
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Steven V Beer
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA.
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Sandetskaya N, Naumann A, Hennig K, Kuhlmeier D. Specific enrichment of prokaryotic DNA using a recombinant DNA-binding protein. Anal Bioanal Chem 2014; 406:3755-62. [PMID: 24718438 DOI: 10.1007/s00216-014-7787-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/03/2014] [Accepted: 03/24/2014] [Indexed: 11/26/2022]
Abstract
Targeted enrichment of DNA is often necessary for its detection and characterization in complex samples. We describe the development and application of the novel molecular tool for the specific enrichment of prokaryotic DNA. A fused protein comprising the DNA-binding subunit of the bacterial topoisomerase II, gyrase, was expressed, purified, and immobilized on magnetic particles. We demonstrated the specific affinity of the immobilized protein towards bacterial DNA and investigated its efficiency in the samples with high background of eukaryotic DNA. The reported approach allowed for the selective isolation and further detection of as few as 5 pg Staphylococcus aureus DNA from the sample with 4 × 10(6)-fold surplus of human DNA. This method is a promising approach for the preparation of such type of samples, for example in molecular diagnostics of sepsis.
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Affiliation(s)
- Natalia Sandetskaya
- Nanotechnology Unit, Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstrasse 1, 04103, Leipzig, Germany,
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