1
|
Rathod S, Dey S, Pawar S, Dhavale R, Choudhari P, Rajakumara E, Mahuli D, Bhagwat D, Tamboli Y, Sankpal P, Mali S, More H. Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study. J Biomol Struct Dyn 2024; 42:5178-5196. [PMID: 37340697 DOI: 10.1080/07391102.2023.2225099] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/09/2023] [Indexed: 06/22/2023]
Abstract
The cases of bacterial multidrug resistance are increasing every year and becoming a serious concern for human health. Multidrug efflux pumps are key players in the formation of antibiotic resistance, which transfer out a broad spectrum of drugs from the cell and convey resistance to the host. Efflux pumps have significantly reduced the efficacy of the previously available antibiotic armory, thereby increasing the frequency of therapeutic failures. In gram-negative bacteria, the AcrAB-TolC efflux pump is the principal transporter of the substrate and plays a major role in the formation of antibiotic resistance. In the current work, advanced computer-aided drug discovery approaches were utilized to find hit molecules from the library of biogenic chalcones against the bacterial AcrB efflux pump. The results of the performed computational studies via molecular docking, drug-likeness prediction, pharmacokinetic profiling, pharmacophore mapping, density functional theory, and molecular dynamics simulation study provided ZINC000004695648, ZINC000014762506, ZINC000014762510, ZINC000095099506, and ZINC000085510993 as stable hit molecules against the AcrB efflux pumps. Identified hits could successfully act against AcrB efflux pumps after optimization as lead molecules.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Sreenath Dey
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Swaranjali Pawar
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Rakesh Dhavale
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Deepak Mahuli
- Department of Pharmacology, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Durgacharan Bhagwat
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Yasinalli Tamboli
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Poournima Sankpal
- Department of Pharmaceutical Chemistry, Ashokrao Mane College of Pharmacy, Kolhapur, MS, India
| | - Sachin Mali
- Department of Pharmaceutics, Y. D. Mane College of Pharmacy, Kagal, MS, India Kolhapur
| | - Harinath More
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| |
Collapse
|
2
|
Martin ALAR, Pereira RLS, Rocha JE, Farias PAM, Freitas TS, Caldas FRDL, Figueredo FG, Sampaio NFL, Oliveira-Tintino CDDM, Tintino SR, da Hora GCA, Lima MCP, de Menezes IRA, Carvalho DT, Coutinho HDM, Fonteles MMF. Unlocking bacterial defense: Exploring the potent inhibition of NorA efflux pump by coumarin derivatives in Staphylococcus aureus. Microb Pathog 2024; 190:106608. [PMID: 38503396 DOI: 10.1016/j.micpath.2024.106608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
The occurrence of bacterial resistance has been increasing, compromising the treatment of various infections. The high virulence of Staphylococcus aureus allows for the maintenance of the infectious process, causing many deaths and hospitalizations. The MepA and NorA efflux pumps are transporter proteins responsible for expelling antimicrobial agents such as fluoroquinolones from the bacterial cell. Coumarins are phenolic compounds that have been studied for their diverse biological actions, including against bacteria. A pharmacokinetic in silico characterization of compounds C10, C11, C13, and C14 was carried out according to the principles of Lipinski's Rule of Five, in addition to searching for similarity in ChemBL and subsequent search for publications in CAS SciFinder. All compounds were evaluated for their in vitro antibacterial and modulatory activity against standard and multidrug-resistant Gram-positive and Gram-negative strains. The effect of coumarins C9, C10, C11, C13, and C14 as efflux pump inhibitors in Staphylococcus aureus strains was evaluated using the microdilution method (MepA or NorA) and fluorimetry (NorA). The behavior of coumarins regarding the efflux pump was determined from their interaction properties with the membrane and coumarin-protein using molecular docking and molecular dynamics simulations. Only the isolated coumarin compound C13 showed antibacterial activity against standard strains of Staphylococcus aureus and Escherichia coli. However, the other tested coumarins showed modulatory capacity for fluoroquinolone and aminoglycoside antibacterials. Compounds C10, C13, and C14 were effective in reducing the MIC of both antibiotics for both multidrug-resistant strains, while C11 potentiated the effect of norfloxacin and gentamicin for Gram-positive and Gram-negative bacteria and only norfloxacin for Gram-negative. Only coumarin C14 produced synergistic effects when associated with ciprofloxacin in MepA-carrying strains. All tested coumarins have the ability to inhibit the NorA efflux pump present in Staphylococcus aureus, both in reducing the MIC and inducing increased ethidium bromide fluorescence emission in fluorimetry. The findings of this study offer an atomistic perspective on the potential of coumarins as active inhibitors of the NorA pump, highlighting their specific mode of action mainly targeting protein inhibition. In molecular docking, it was observed that coumarins are capable of interacting with various amino acid residues of the NorA pump. The simulation showed that coumarin C10 can cross the bilayer; however, the other coumarins interacted with the membrane but were unable to cross it. Coumarins demonstrated their potentiating role in the effect of norfloxacin through a dual mechanism: efflux pump inhibition through direct interaction with the protein (C9, C10, C11, and C13) and increased interaction with the membrane (C10 and C13). In the context of pharmacokinetic prediction studies, the studied structures have a suitable chemical profile for possible oral use. We suggest that coumarin derivatives may be an interesting alternative in the future for the treatment of resistant bacterial infections, with the possibility of a synergistic effect with other antibacterials, although further studies are needed to characterize their therapeutic effects and toxicity.
Collapse
Affiliation(s)
- Ana Luíza A R Martin
- Department of Physiology and Pharmacology, Federal University of Ceará - UFC, 60430-160, Fortaleza, Brazil; Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil; School of Medicine, Medical Education Institute - IDOMED, 63048-080, Juazeiro do Norte, Brazil
| | | | - Janaína Esmeraldo Rocha
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil
| | - Pablo A M Farias
- School of Medicine, Medical Education Institute - IDOMED, 63048-080, Juazeiro do Norte, Brazil; CECAPE College, 63024-015, Juazeiro do Norte, Brazil
| | - Thiago S Freitas
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil
| | | | - Fernando G Figueredo
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil; School of Medicine, Medical Education Institute - IDOMED, 63048-080, Juazeiro do Norte, Brazil
| | - Nadghia Figueiredo Leite Sampaio
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil; School of Medicine, Medical Education Institute - IDOMED, 63048-080, Juazeiro do Norte, Brazil
| | | | - Saulo Relison Tintino
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil
| | | | | | - Irwin Rose A de Menezes
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil
| | - Diogo T Carvalho
- School of Pharmacy, Federal University of Alfenas - UNIFAL, 37130-001, Alfenas, Brazil
| | - Henrique D M Coutinho
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil.
| | - Marta M F Fonteles
- Department of Physiology and Pharmacology, Federal University of Ceará - UFC, 60430-160, Fortaleza, Brazil
| |
Collapse
|
3
|
Menon DN, Leite IDAB, Ramsdorf MTDA, Chagas LDS, Arroyo SA, dos Santos AC, Kassuya CAL, Mota JDS, de Barros ME. Effect of ethanolic extracts from Piperaceae leaves on the reduction of skin necrosis and wound healing in an animal model of degloving injuries. Acta Cir Bras 2023; 38:e387223. [PMID: 37909597 PMCID: PMC10637343 DOI: 10.1590/acb387223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/24/2023] [Indexed: 11/03/2023] Open
Abstract
PURPOSE To assess the effect of the ethanolic extract of the leaves of three species of plants from the Piperaceae family on reducing necrosis and enhancing wound healing in an animal model of degloving injuries. METHODS The animals were divided into six groups, each consisting of six animals: sham, negative control, EEPA (Piper amalago ethanolic extract), EEPG (Piper glabratum ethanolic extract), EEPV (Piper vicosanum ethanolic extract), and positive control receiving hyperbaric oxygenation. The animals underwent surgery to induce excision wounds, and the extent of cutaneous necrosis was evaluated using graphic software, while wound healing was assessed through histopathology. RESULTS Skin necrosis percentage area was: sham group = 62.84% 6.38; negative control group = 63.03% 4.11; P. vicosanum = 40.80% 4.76 p < 0.05; P. glabratum 32.97% 4.01 p < 0.01; P. amalago = 32.40% 4.61 p < 0.01; hyperbaric oxygenation = 33.21% 4.29 p < 0.01. All treated groups showed higher collagen deposition and less intense, plus predominantly mononuclear inflammatory infiltrate, suggesting improved healing process. CONCLUSIONS The three tested extracts demonstrated efficacy in reducing the extent of cutaneous necrosis caused by degloving injuries and also showed evidence of improvement in the wound healing process.
Collapse
Affiliation(s)
- Douglas Neumar Menon
- Universidade Federal da Grande Dourados – Health Science Department – Dourados (MS) – Brazil
- Universidade Federal da Grande Dourados – General Surgery – Dourados (MS) – Brazil
| | | | | | | | - Sahra Amaral Arroyo
- Universidade Federal da Grande Dourados – Health Science Department – Dourados (MS) – Brazil
| | | | | | - Jonas da Silva Mota
- Universidade Estadual de Mato Grosso do Sul – Chemistry Department – Dourados (MS) – Brazil
| | | |
Collapse
|
4
|
Cavalcante CHL, Almeida-Neto FWDQ, da Rocha MN, Bandeira PN, de Menezes RRPPB, Paula Magalhães E, Sampaio TL, Marinho ES, Marinho MM, Maria Costa Martins A, Dos Santos HS. Antichagasic evaluation, molecular docking and ADMET properties of the chalcone (2 E)-3-(2-fluorophenyl)-1-(2-hydroxy- 3,4,6-trimethoxyphenyl)prop-2-en-1-one against Trypanosoma cruzi. J Biomol Struct Dyn 2023; 41:7463-7479. [PMID: 36120936 DOI: 10.1080/07391102.2022.2123394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/02/2022] [Indexed: 10/14/2022]
Abstract
Characterized as a neglected disease, Chagas disease is an infection that, in the current scenario, affects about 8 million people per year, with a higher incidence in underdeveloped countries, Chagas is responsible for physiological disabilities that result in impacts that are slightly reflected in world socioeconomic stability. Although treatments are based on drugs such as Benznidazole, the pathology lacks a continuous treatment method with low toxicological incidence. The present study estimates the anti-chagasic activity of the synthetic chalcone CPN2F based on the alignment between in vitro tests and structural classification in silico studies, molecular docking and ADMET studies. The in vitro tests showed a reduction in the protozoan metabolism in host cells (LLC-MK2). At the same time, the molecular docking models evaluate this growth inhibition through the synergistic effect associated with Benznida- zole against validated therapeutic target key stages (Cruzaine TcGAPDH and Trypanothione reductase) of the Trypanosoma cruzi development cycle. The in silico prediction results reveal an alignment between pharmacokinetic attributes, such as renal absorption and release, which allow the preparation of CPN2F as an antichagasic drug with a low incidence of organic toxicity.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Carlos Henrique Leitão Cavalcante
- Postgraduate Program in Biotechnology - PPGB-Renorbio, State University of Ceara, Fortaleza, CE, Brazil
- Federal Institute of Education and Technology of Ceara, Maracanau, CE, Brazil
| | | | - Matheus Nunes da Rocha
- Center for Science and Technology, Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | - Paulo Nogueira Bandeira
- Center for Exact Sciences and Technology, State University of Vale do Acaraú, Sobral, CE, Brazil
| | | | - Emanuel Paula Magalhães
- Department of Clinical and Toxicological Analysis, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Tiago Lima Sampaio
- Department of Clinical and Toxicological Analysis, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | - Márcia Machado Marinho
- Center for Exact Sciences and Technology, State University of Vale do Acaraú, Sobral, CE, Brazil
| | - Alice Maria Costa Martins
- Department of Clinical and Toxicological Analysis, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Hélcio Silva Dos Santos
- Postgraduate Program in Biotechnology - PPGB-Renorbio, State University of Ceara, Fortaleza, CE, Brazil
- Center for Science and Technology, Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE, Brazil
- Center for Exact Sciences and Technology, State University of Vale do Acaraú, Sobral, CE, Brazil
| |
Collapse
|