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Elitas M, Kalayci Demir G, Vural Kaymaz S. Mathematical Model for Growth and Rifampicin-Dependent Killing Kinetics of Escherichia coli Cells. ACS OMEGA 2023; 8:38452-38458. [PMID: 37867679 PMCID: PMC10586251 DOI: 10.1021/acsomega.3c05233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/21/2023] [Indexed: 10/24/2023]
Abstract
Antibiotic resistance is a global health threat. We urgently need better strategies to improve antibiotic use to combat antibiotic resistance. Currently, there are a limited number of antibiotics in the treatment repertoire of existing bacterial infections. Among them, rifampicin is a broad-spectrum antibiotic against various bacterial pathogens. However, during rifampicin exposure, the appearance of persisters or resisters decreases its efficacy. Hence, to benefit more from rifampicin, its current standard dosage might be reconsidered and explored using both computational tools and experimental or clinical studies. In this study, we present the mathematical relationship between the concentration of rifampicin and the growth and killing kinetics of Escherichia coli cells. We generated time-killing curves of E. coli cells in the presence of 4, 16, and 32 μg/mL rifampicin exposures. We specifically focused on the oscillations with decreasing amplitude over time in the growth and killing kinetics of rifampicin-exposed E. coli cells. We propose the solution form of a second-order linear differential equation for a damped oscillator to represent the mathematical relationship. We applied a nonlinear curve fitting solver to time-killing curve data to obtain the model parameters. The results show a high fitting accuracy.
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Affiliation(s)
- Meltem Elitas
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Istanbul 34956, Turkiye
| | - Guleser Kalayci Demir
- Faculty
of Engineering, Department of Electrical and Electronics Engineering, Dokuz Eylul University, Izmir 35397, Turkey
| | - Sumeyra Vural Kaymaz
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Istanbul 34956, Turkiye
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Liu L, Liu Y, Liu S, Nikandrova AA, Imamutdinova AN, Lukianov DA, Osterman IA, Sergiev PV, Zhang B, Zhang D, Li F, Sun C. Bioprospecting for the soil-derived actinobacteria and bioactive secondary metabolites on the Western Qinghai-Tibet Plateau. Front Microbiol 2023; 14:1247001. [PMID: 37886074 PMCID: PMC10599150 DOI: 10.3389/fmicb.2023.1247001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Introduction The increase in incidence of multidrug-resistant bacteria and the inadequacy of new antimicrobial drugs have led to a widespread outbreak of bacterial antimicrobial resistance. To discover new antibiotics, biodiversity, and novelty of culturable actinobacteria dwelled in soil of the Western Qinghai-Tibet Plateau were investigated. By integrating antibacterial assay with omics tools, Amycolatopsis sp. A133, a rare actinobacterial strain and its secondary metabolites were further studied. Method Culture-dependent method was used to obtain actinobacterial strains from two soil samples collected from Ali region in Qinghai-Tibet Plateau. The cultural extractions of representative strains were assayed against "ESKAPE" pathogens by paper-disk diffusion method and the double fluorescent protein reporter "pDualrep2" system. An Amycolatopsis strain coded as A133 was prioritized and its secondary metabolites were further analyzed and annotated by omics tools including antiSMASH and GNPS (Global Natural Social Molecular Networking). The predicted rifamycin analogs produced by Amycolatopsis sp. A133 were isolated and identified by chromatographic separation, such as Sephadex LH-20 and HPLC, and spectral analysis, such as NMR and UPLC-HRESI-MS/MS, respectively. Results A total of 406 actinobacteria strains affiliated to 36 genera in 17 families of 9 orders were isolated. Out of 152 representative strains, 63 isolates exhibited antagonistic activity against at least one of the tested pathogens. Among them, 7 positive strains were identified by the "pDualrep2" system as either an inhibitor of protein translation or DNA biosynthesis. The cultural broth of Amycolatopsis sp. A133 exhibited a broader antimicrobial activity and can induce expression of TurboRFP. The secondary metabolites produced by strain A133 was annotated as rifamycins and zampanolides by antiSMASH and GNPS analysis. Five members of rifamycins, including rifamycin W, protorifamycin I, rifamycin W-M1, proansamycin B, and rifamycin S, were purified and identified. Rifamycin W-M1, was found as a new member of the naturally occurring rifamycin group of antibiotics. Discussion Assisted by omics tools, the successful and highly efficient discovery of rifamycins, a group of clinically used antibiotics from actinobacteria in Ali area encouraged us to devote more energy to explore new antibiotics from the soils on the Western Tibetan Plateau.
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Affiliation(s)
- Lifang Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuyu Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shaowei Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Arina A. Nikandrova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arina N. Imamutdinova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Benyin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Dejun Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Feina Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
| | - Chenghang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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Rifamycin antibiotics and the mechanisms of their failure. J Antibiot (Tokyo) 2021; 74:786-798. [PMID: 34400805 DOI: 10.1038/s41429-021-00462-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Rifamycins are a class of antibiotics that were first discovered in 1957 and are known for their use in treating tuberculosis (TB). Rifamycins exhibit bactericidal activity against many Gram-positive and Gram-negative bacteria by inhibiting RNA polymerase (RNAP); however, resistance is prevalent and the mechanisms range from primary target modification and antibiotic inactivation to cytoplasmic exclusion. Further, phenotypic resistance, in which only a subpopulation of bacteria grow in concentrations exceeding their minimum inhibitory concentration, and tolerance, which is characterized by reduced rates of bacterial cell death, have been identified as additional causes of rifamycin failure. Here we summarize current understanding and recent developments regarding this critical antibiotic class.
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Shui T, Shi C, Jing Z, Yang D, Zhu J. Case Report: Rifampicin-Induced Thrombocytopenia in a Patient with Borderline Lepromatous Leprosy. Am J Trop Med Hyg 2020; 103:1441-1442. [PMID: 32748777 DOI: 10.4269/ajtmh.20-0211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Rifampicin is a highly effective antibacterial drug and an important component of multidrug therapy used to treat leprosy. Side effects of rifampicin are rare with the once-a-month dosage regimen of anti-leprosy multidrug therapy. Here, we report a case of rifampicin-induced thrombocytopenia during anti-leprosy treatment. Although rare, this potential side effect merits attention.
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Affiliation(s)
- Tiejun Shui
- Department of Leprosy Control, Yunnan Center for Disease Control and Prevention, Kunming, People's Republic of China
| | - Chao Shi
- Department of Leprosy, Shanghai Dermatology Hospital, Shanghai, People's Republic of China
| | - Zhichun Jing
- Department of Leprosy, Shanghai Dermatology Hospital, Shanghai, People's Republic of China
| | - Degang Yang
- Department of Leprosy, Shanghai Dermatology Hospital, Shanghai, People's Republic of China
| | - Jianyu Zhu
- Department of Leprosy, Shanghai Dermatology Hospital, Shanghai, People's Republic of China
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Potshangbam AM, Rathore RS, Nongdam P. Discovery of sulfone-resistant dihydropteroate synthase (DHPS) as a target enzyme for kaempferol, a natural flavanoid. Heliyon 2020; 6:e03378. [PMID: 32083215 PMCID: PMC7016458 DOI: 10.1016/j.heliyon.2020.e03378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/27/2019] [Accepted: 02/04/2020] [Indexed: 11/17/2022] Open
Abstract
Kaempferol is a ubiquitous flavonoid, found in various plants having a wide range of known pharmacological activities, including antioxidant, antiinflammatory, anticancer, antiallergic, antidiabetic, neuroprotective, cardioprotective and antimicrobial activities. Nonetheless various evidence suggest that kaempferol is also able to interact with many unknown therapeutic targets modulating signalling pathways, thus providing an opportunity to explore the potential target space of kaempferol. In this study, we have employed various ligand-based approaches to identify the potential targets of kaempferol, followed by validations using modelling and docking studies. Molecular dynamics, free energy calculations, volume and residue contact map analyses were made to delineate the cause of drug-resistance among mutants. We have discovered dihydropteroate synthase (DHPS) as a novel potential therapeutic target for kaempferol. Further studies employing molecular dynamics simulations and binding free energies indicate that kaempferol has potential to inhibit even the sulfone-resistant DHPS mutants, which makes it a very attractive antibiotic agent. The identification of natural-product based kaempferol opens up the door for the design of antibiotics in a quick and high throughput fashion for identifying antibiotic leads.
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Affiliation(s)
| | - Ravindranath Singh Rathore
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, India
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Bera S, Mondal D. Insights of synthetic analogues of anti-leprosy agents. Bioorg Med Chem 2019; 27:2689-2717. [PMID: 31103404 DOI: 10.1016/j.bmc.2019.04.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/15/2019] [Accepted: 04/26/2019] [Indexed: 02/05/2023]
Abstract
Today, the emergence of the phenomenon of drug or multidrug-resistance for community-associated diseases represents a major concern in the world. In these contexts, the chronic infectious disease, leprosy, grounded by a slow-growing bacterium called Mycobacterium leprae or Mycobacterium lepromatosis is a leadingcause of severe disfiguring skin sores and nerve damage in the arms, legs, and skin areas around the body. Even, over 200,000 new leprosy cases are being accounted every year along with the relapsed leprosy cases. Nonetheless, this has been considered a curable disease with a higher dose of multidrug therapy (MDT) for a long period of time. The prolonged action of a high dose of combination drugs administration may cause an adverse reaction that can significantly affect patient compliance, particularly the outbreak of multidrug-resistance in the infected person. To overcome these shortfalls or prevent the resistance-associated problems, researchers are diligently involved in the structural modifications of the clinically used anti-leprosy drugs or the allied compounds for the structure-antimycobacterial activity relationship study. This review article described the detailed synthesis and biological assays of different anti-leprosy compounds reported by several research groups.
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Affiliation(s)
- Smritilekha Bera
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat 382030, India.
| | - Dhananjoy Mondal
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat 382030, India
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Chaitanya S, Das M, Bhat P, Ebenezer M. Computational Modelling of Dapsone Interaction With Dihydropteroate Synthase inMycobacterium leprae; Insights Into Molecular Basis of Dapsone Resistance in Leprosy. J Cell Biochem 2015; 116:2293-303. [DOI: 10.1002/jcb.25180] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 03/31/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Sundeep Chaitanya
- Research Officer; Department of Laboratories; Molecular Biology and Immunology Division; The Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC); Karigiri; Vellore Tamil Nadu 632106 India
| | - Madhusmita Das
- Research Officer; Department of Laboratories; Molecular Biology and Immunology Division; The Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC); Karigiri; Vellore Tamil Nadu 632106 India
| | - Pritesh Bhat
- Applications Scientist; Schrodinger, Inc.; Near KMWA Vidya Niketan; Mahalakshmipuram; Bangalore 560 086 India
| | - Mannam Ebenezer
- The Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC); Karigiri; Vellore Tamil Nadu 632106 India
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Dhople AM, Williams SL. The activity of rifabutin against Mycobacterium leprae in armadillos. Int J Antimicrob Agents 1997; 9:169-73. [PMID: 9552713 DOI: 10.1016/s0924-8579(97)00048-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The activity of rifabutin (LM 427) against Mycobacterium leprae was evaluated in armadillos inoculated earlier with human-derived M. leprae. Rifabutin was administered daily at a dose of 6 mg/kg body weight/day. The effect of rifabutin on M. leprae harvested from armadillos was determined by measuring the intracellular levels of ATP (an indicator of metabolic activity) of M. leprae and also their ability to multiply in the mouse footpads and in vitro in DH medium. Within 2 weeks of initiating the treatment, ATP levels declined to 21% of the original (pre-treatment level) and these M. leprae failed to multiply in the footpads of mice as well as in the in vitro culture system. This suggests that rifabutin was able to kill all M. leprae within 2 weeks. After 8 weeks the treatment was terminated and results showed that M. leprae from the treated armadillos remained non-viable in the mouse footpad system as well as in the in vitro system, indicating bactericidal action of rifabutin. The results suggest that rifabutin can be a substitute for rifampin in the leprosy multi-drug therapy regimen.
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Affiliation(s)
- A M Dhople
- Department of Biological Sciences, Florida Institute of Technology, Melbourne 32901-6975, USA.
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Kenny MT. Effect of rifampin and its cyclopentyl analogue, MDL 473, on the expression of delayed type hypersensitivity to oxazolone. INTERNATIONAL JOURNAL OF IMMUNOPHARMACOLOGY 1987; 9:257-60. [PMID: 3583511 DOI: 10.1016/0192-0561(87)90100-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The purpose of this study was to determine the effect of rifampin and its cyclopentyl analogue, MDL 473, on delayed type hypersensitivity (DTH) using a murine model. Neither compound has any significant effect on DTH (as measured by ear swelling) to oxazolone when administered i.p. to BALB/c mice at doses of 1, 10, 50 or 100 mg/kg beginning 3 days before oxazolone sensitization and continuing until hapten challenge 5 days later. In contrast, sex and age matched controls receiving 200 mg hydrocortisone/kg i.p. beginning on the day of oxazolone sensitization and continuing to hapten challenge demonstrate a significant (P less than 0.001) abrogation of DTH.
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