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Nunes B, Cagide F, Fernandes C, Borges A, Borges F, Simões M. Efficacy of Novel Quaternary Ammonium and Phosphonium Salts Differing in Cation Type and Alkyl Chain Length against Antibiotic-Resistant Staphylococcus aureus. Int J Mol Sci 2023; 25:504. [PMID: 38203676 PMCID: PMC10778626 DOI: 10.3390/ijms25010504] [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: 11/17/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Antibacterial resistance poses a critical public health threat, challenging the prevention and treatment of bacterial infections. The search for innovative antibacterial agents has spurred significant interest in quaternary heteronium salts (QHSs), such as quaternary ammonium and phosphonium compounds as potential candidates. In this study, a library of 49 structurally related QHSs was synthesized, varying the cation type and alkyl chain length. Their antibacterial activities against Staphylococcus aureus, including antibiotic-resistant strains, were evaluated by determining minimum inhibitory/bactericidal concentrations (MIC/MBC) ≤ 64 µg/mL. Structure-activity relationship analyses highlighted alkyl-triphenylphosphonium and alkyl-methylimidazolium salts as the most effective against S. aureus CECT 976. The length of the alkyl side chain significantly influenced the antibacterial activity, with optimal chain lengths observed between C10 and C14. Dose-response relationships were assessed for selected QHSs, showing dose-dependent antibacterial activity following a non-linear pattern. Survival curves indicated effective eradication of S. aureus CECT 976 by QHSs at low concentrations, particularly compounds 1e, 3e, and 5e. Moreover, in vitro human cellular data indicated that compounds 2e, 4e, and 5e showed favourable safety profiles at concentrations ≤ 2 µg/mL. These findings highlight the potential of these QHSs as effective agents against susceptible and resistant bacterial strains, providing valuable insights for the rational design of bioactive QHSs.
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Affiliation(s)
- Bárbara Nunes
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal; (B.N.); (A.B.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- CIQUP-IMS, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal (C.F.); (F.B.)
| | - Fernando Cagide
- CIQUP-IMS, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal (C.F.); (F.B.)
| | - Carlos Fernandes
- CIQUP-IMS, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal (C.F.); (F.B.)
| | - Anabela Borges
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal; (B.N.); (A.B.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Fernanda Borges
- CIQUP-IMS, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal (C.F.); (F.B.)
| | - Manuel Simões
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal; (B.N.); (A.B.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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Avraham M, Steinberg D, Barak T, Shalish M, Feldman M, Sionov RV. Improved Anti-Biofilm Effect against the Oral Cariogenic Streptococcus mutans by Combined Triclosan/CBD Treatment. Biomedicines 2023; 11:biomedicines11020521. [PMID: 36831057 PMCID: PMC9953046 DOI: 10.3390/biomedicines11020521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Streptococcus mutans is a Gram-positive bacterium highly associated with dental caries, and it has a strong biofilm-forming ability, especially in a sugar-rich environment. Many strategies have been undertaken to prevent dental caries by targeting these bacteria. Recently, we observed that a sustained-release varnish containing triclosan and cannabidiol (CBD) was more efficient than each compound alone in preventing biofilm formation by the fungus Candida albicans, which is frequently involved in oral infections together with S. mutans. It was therefore inquiring to study the effect of this drug combination on S. mutans. We observed that the combined treatment of triclosan and CBD had stronger anti-bacterial and anti-biofilm activity than each compound alone, thus enabling the use of lower concentrations of each drug to achieve the desired effect. The combined drug treatment led to an increase in the SYTO 9low, propidium iodide (PI)high bacterial population as analyzed by flow cytometry, indicative for bacteria with disrupted membrane. Both triclosan and CBD induced membrane hyperpolarization, although there was no additive effect on this parameter. HR-SEM images of CBD-treated bacteria show the appearance of elongated and swollen bacteria with several irregular septa structures, and upon combined treatment with triclosan, the bacteria took on a swollen ellipse and sometimes oval morphology. Increased biofilm formation was observed at sub-MIC concentrations of each compound alone, while combining the drugs at these sub-MIC concentrations, the biofilm formation was prevented. The inhibition of biofilm formation was confirmed by CV biomass staining, MTT metabolic activity, HR-SEM and live/dead together with exopolysaccharide (EPS) staining visualized by spinning disk confocal microscopy. Importantly, the concentrations required for the anti-bacterial and anti-biofilm activities toward S. mutans were non-toxic to the normal Vero epithelial cells. In conclusion, the data obtained in this study propose a beneficial role of combined triclosan/CBD treatment for potential protection against dental caries.
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Affiliation(s)
- Maayan Avraham
- Faculty of Dental Medicine, Ein Kerem Campus, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Division of Biotechnology, Strauss Campus, Hadassah Academic College, Jerusalem 9514223, Israel
| | - Doron Steinberg
- Faculty of Dental Medicine, Ein Kerem Campus, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Tamar Barak
- Faculty of Dental Medicine, Ein Kerem Campus, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Hadassah Medical Center, Department of Orthodontics, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Miriam Shalish
- Hadassah Medical Center, Department of Orthodontics, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Mark Feldman
- Faculty of Dental Medicine, Ein Kerem Campus, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ronit Vogt Sionov
- Faculty of Dental Medicine, Ein Kerem Campus, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Correspondence:
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Valencia J, Rubio V, Puerto G, Vasquez L, Bernal A, Mora JR, Cuesta SA, Paz JL, Insuasty B, Abonia R, Quiroga J, Insuasty A, Coneo A, Vidal O, Márquez E, Insuasty D. QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis. Antibiotics (Basel) 2022; 12:antibiotics12010061. [PMID: 36671262 PMCID: PMC9854539 DOI: 10.3390/antibiotics12010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, a series of novel quinolinone-based thiosemicarbazones were designed in silico and their activities tested in vitro against Mycobacterium tuberculosis (M. tuberculosis). Quantitative structure-activity relationship (QSAR) studies were performed using quinolinone and thiosemicarbazide as pharmacophoric nuclei; the best model showed statistical parameters of R2 = 0.83; F = 47.96; s = 0.31, and was validated by several different methods. The van der Waals volume, electron density, and electronegativity model results suggested a pivotal role in antituberculosis (anti-TB) activity. Subsequently, from this model a new series of quinolinone-thiosemicarbazone 11a-e was designed and docked against two tuberculosis protein targets: enoyl-acyl carrier protein reductase (InhA) and decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1). Molecular dynamics simulation over 200 ns showed a binding energy of -71.3 to -12.7 Kcal/mol, suggesting likely inhibition. In vitro antimycobacterial activity of quinolinone-thiosemicarbazone for 11a-e was evaluated against M. bovis, M. tuberculosis H37Rv, and six different strains of drug-resistant M. tuberculosis. All compounds exhibited good to excellent activity against all the families of M. tuberculosis. Several of the here synthesized compounds were more effective than the standard drugs (isoniazid, oxafloxacin), 11d and 11e being the most active products. The results suggest that these compounds may contribute as lead compounds in the research of new potential antimycobacterial agents.
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Affiliation(s)
- Jhesua Valencia
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Vivian Rubio
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Gloria Puerto
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Luisa Vasquez
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Anthony Bernal
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
| | - Sebastian A. Cuesta
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Cercado de Lima 15081, Peru
| | - Braulio Insuasty
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Jairo Quiroga
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Alberto Insuasty
- Grupo de Investigación en Materiales Funcionales Nanoestructurados, Universidad CESMAG, Pasto 520003, Colombia
| | - Andres Coneo
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Oscar Vidal
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Edgar Márquez
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
| | - Daniel Insuasty
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
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Investigation of Major Flavonoids from Artemisia argyi as a Potential COVID-19 Drug: Molecular Docking and DFT Calculations. CRYSTALS 2022. [DOI: 10.3390/cryst12070990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Flavonoids from natural products are well-identified as potential antiviral agents in the treatment of SARS-CoV-2 (COVID-19) infection and related diseases. However, some major species of flavonoids from Chinese traditional folk medicine, such as of Artemisia argyi (A. argyi), have not been evaluated yet. Here, we choose five major flavonoids obtained from A. argyi, namely, Jaceosidin (1), Eupatilin (2), Apigenin (3), Eupafolin (4), and 5,6-Dihydroxy-7,3′,4′-trimethoxyflavone (5), compared to the well-studied Baicalein (6), as potential inhibitors analogs for COVID-19 by computational modeling strategies. The frontier molecular orbitals (FMOs), chemical reactivity descriptors, and electrostatic surface potential (ESP) were performed by density functional theory (DFT) calculations. Additionally, these flavonoids were docked on the main protease (PDB: 6LU7) of SARS-CoV-2 to evaluate the binding affinities. Computational analysis predicted that all of these compounds show a high affinity and might serve as potential inhibitors to SARS-CoV-2, among which compound (5) exhibits the least binding energy (−155.226 kcal/mol). The high binding affinity could be enhanced by increasing the electron repulsion due to the valence shell electron pair repulsion model (VSEPR). Consequently, the major flavonoids in Artemisia argyi have a significant ability to reduce the deterioration of COVID-19 in the terms of DFT calculations and molecular docking.
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Oliveros R. DA, Machado RA, Mora JR. Quantitative structure–property relationship analysis of the spectrochemical series by employing electronic descriptors from DFT calculations. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2040629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Deivi A. Oliveros R.
- Facultad de Ciencias, Universidad Central de Venezuela, Escuela de Química, Caracas, Venezuela
| | - Rubén A. Machado
- Centro de Química, Laboratorio de Química de Metales de Transición, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - José R. Mora
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito, Instituto de Simulación Computacional, Quito, Ecuador
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Mahmud MS, Hossain MS, Ahmed ATMF, Islam MZ, Sarker ME, Islam MR. Antimicrobial and Antiviral (SARS-CoV-2) Potential of Cannabinoids and Cannabis sativa: A Comprehensive Review. Molecules 2021; 26:7216. [PMID: 34885798 PMCID: PMC8658882 DOI: 10.3390/molecules26237216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Antimicrobial resistance has emerged as a global health crisis and, therefore, new drug discovery is a paramount need. Cannabis sativa contains hundreds of chemical constituents produced by secondary metabolism, exerting outstanding antimicrobial, antiviral, and therapeutic properties. This paper comprehensively reviews the antimicrobial and antiviral (particularly against SARS-CoV-2) properties of C. sativa with the potential for new antibiotic drug and/or natural antimicrobial agents for industrial or agricultural use, and their therapeutic potential against the newly emerged coronavirus disease (COVID-19). Cannabis compounds have good potential as drug candidates for new antibiotics, even for some of the WHO's current priority list of resistant pathogens. Recent studies revealed that cannabinoids seem to have stable conformations with the binding pocket of the Mpro enzyme of SARS-CoV-2, which has a pivotal role in viral replication and transcription. They are found to be suppressive of viral entry and viral activation by downregulating the ACE2 receptor and TMPRSS2 enzymes in the host cellular system. The therapeutic potential of cannabinoids as anti-inflammatory compounds is hypothesized for the treatment of COVID-19. However, more systemic investigations are warranted to establish the best efficacy and their toxic effects, followed by preclinical trials on a large number of participants.
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Affiliation(s)
- Md Sultan Mahmud
- Faculty of Textile Engineering, Bangladesh University of Textiles, Dhaka 1208, Bangladesh; (M.S.M.); (A.T.M.F.A.); (M.Z.I.)
| | - Mohammad Sorowar Hossain
- Biomedical Research Foundation, Dhaka 1230, Bangladesh;
- School of Environment and Life Sciences, Independent University, Dhaka 1229, Bangladesh
| | - A. T. M. Faiz Ahmed
- Faculty of Textile Engineering, Bangladesh University of Textiles, Dhaka 1208, Bangladesh; (M.S.M.); (A.T.M.F.A.); (M.Z.I.)
| | - Md Zahidul Islam
- Faculty of Textile Engineering, Bangladesh University of Textiles, Dhaka 1208, Bangladesh; (M.S.M.); (A.T.M.F.A.); (M.Z.I.)
| | - Md Emdad Sarker
- Faculty of Textile Engineering, Bangladesh University of Textiles, Dhaka 1208, Bangladesh; (M.S.M.); (A.T.M.F.A.); (M.Z.I.)
| | - Md Reajul Islam
- Faculty of Textile Engineering, Bangladesh University of Textiles, Dhaka 1208, Bangladesh; (M.S.M.); (A.T.M.F.A.); (M.Z.I.)
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Hanif N, Tyas TA, Hidayati L, Dinelsa FF, Provita D, Kinnary NR, Prasetiawan FM, Khalik GA, Mubarok Z, Tohir D, Setiawan A, Farid M, Kurnianda V, Murni A, de Voogd NJ, Tanaka J. Oxy-Polybrominated Diphenyl Ethers from the Indonesian Marine Sponge, Lamellodysidea herbacea: X-ray, SAR, and Computational Studies. Molecules 2021; 26:molecules26216328. [PMID: 34770740 PMCID: PMC8588277 DOI: 10.3390/molecules26216328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022] Open
Abstract
Polybrominated diphenyl ether (PBDE) compounds, derived from marine organisms, originate from symbiosis between marine sponges and cyanobacteria or bacteria. PBDEs have broad biological spectra; therefore, we analyzed structure and activity relationships of PBDEs to determine their potential as anticancer or antibacterial lead structures, through reactions and computational studies. Six known PBDEs (1–6) were isolated from the sponge, Lamellodysdiea herbacea; 13C NMR data for compound 6 are reported for the first time and their assignments are confirmed by their theoretical 13C NMR chemical shifts (RMSE < 4.0 ppm). Methylation and acetylation of 1 (2, 3, 4, 5-tetrabromo-6-(3′, 5′-dibromo-2′-hydroxyphenoxy) phenol) at the phenol functional group gave seven molecules (7–13), of which 10, 12, and 13 were new. New crystal structures for 8 and 9 are also reported. Debromination carried out on 1 produced nine compounds (1, 2, 14, 16–18, 20, 23, and 26) of which 18 was new. Debromination product 16 showed a significant IC50 8.65 ± 1.11; 8.11 ± 1.43 µM against human embryonic kidney (HEK293T) cells. Compounds 1 and 16 exhibited antibacterial activity against Gram-positive Staphylococcus aureus and Gram-negative Klebsiella pneumoniae with MID 0.078 µg/disk. The number of four bromine atoms and two phenol functional groups are important for antibacterial activity (S. aureus and K. pneumoniae) and cytotoxicity (HEK293T). The result was supported by analysis of frontier molecular orbitals (FMOs). We also propose possible products of acetylation and debromination using analysis of FMOs and electrostatic charges and we confirm the experimental result.
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Affiliation(s)
- Novriyandi Hanif
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
- Correspondence: ; Tel.: +62-(251)-862-4567
| | - Trianda Ayuning Tyas
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
- Department of Chemistry, Biology, and Marine Science, University of the Ryukyus, Nishihara 903-0213, Okinawa, Japan; (V.K.); (J.T.)
| | - Lestari Hidayati
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
| | - Fabians Faisal Dinelsa
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
| | - Dian Provita
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
| | - Nyimas Ratna Kinnary
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
| | - Fauzi Muhamad Prasetiawan
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
| | - Gibral Abdul Khalik
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
| | - Zaki Mubarok
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
| | - Dudi Tohir
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
| | - Andi Setiawan
- Department of Chemistry, Lampung University, Bandar Lampung 35145, Indonesia;
| | - Muhamad Farid
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia; (T.A.T.); (L.H.); (F.F.D.); (D.P.); (N.R.K.); (F.M.P.); (G.A.K.); (Z.M.); (D.T.); (M.F.)
| | - Viqqi Kurnianda
- Department of Chemistry, Biology, and Marine Science, University of the Ryukyus, Nishihara 903-0213, Okinawa, Japan; (V.K.); (J.T.)
| | - Anggia Murni
- Tropical Biopharmaca Research Center, IPB University, Bogor 16128, Indonesia;
| | - Nicole J. de Voogd
- Institute of Environmental Sciences (CML) Leiden University, P.O. Box 9518, 2300 RA Leiden, The Netherlands;
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Junichi Tanaka
- Department of Chemistry, Biology, and Marine Science, University of the Ryukyus, Nishihara 903-0213, Okinawa, Japan; (V.K.); (J.T.)
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Guzmán-Ávila R, Avelar M, Márquez EA, Rivera-Leyva JC, Mora JR, Flores-Morales V, Rivera-Islas J. Synthesis, In Vitro, and In Silico Analysis of the Antioxidative Activity of Dapsone Imine Derivatives. Molecules 2021; 26:molecules26195747. [PMID: 34641292 PMCID: PMC8510498 DOI: 10.3390/molecules26195747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
Dapsone (DDS) is an antibacterial drug with well-known antioxidant properties. However, the antioxidant behavior of its derivatives has not been well explored. In the present work, the antioxidant activity of 10 dapsone derivatives 4-substituted was determined by an evaluation in two in vitro models (DPPH radical scavenging assay and ferric reducing antioxidant power). These imine derivatives 1-10 were obtained through condensation between DDS and the corresponding aromatic aldehydes 4-substuited. Three derivatives presented better results than DDS in the determination of DPPH (2, 9, and 10). Likewise, we have three compounds with better reducing activity than dapsone (4, 9, and 10). In order to be more insight, the redox process, a conceptual DFT analysis was carried out. Molecular descriptors such as electronic distribution, the total charge accepting/donating capacity (I/A), and the partial charge accepting/donating capacity (ω+/ω-) were calculated to analyze the relative donor-acceptor capacity through employing a donor acceptor map (DAM). The DFT calculation allowed us to establish a relationship between GAPHOMO-LUMO and DAM with the observed antioxidant effects. According to the results, we concluded that compounds 2 and 3 have the lowest Ra values, representing a good antioxidant behavior observed experimentally in DPPH radical capturing. On the other hand, derivatives 4, 9, and 10 display the best reducing capacity activity with the highest ω- and Rd values. Consequently, we propose these compounds as the best antireductants in our DDS imine derivative series.
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Affiliation(s)
- Ricardo Guzmán-Ávila
- Laboratorio 4, Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Mexico; (R.G.-Á.); (J.C.R.-L.)
| | - Mayra Avelar
- Laboratorio de Síntesis Asimétrica y Bioenergética (LSAyB), Ingeniería Química (UACQ), Universidad Autónoma de Zacatecas, Campus XXI Km 6 Carr. Zac-Gdl, Zacatecas 98160, Mexico;
| | - Edgar A. Márquez
- Grupo de Investigación en Química y Biología, Departamento de Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia 1569, Barranquilla Atlántico 081007, Colombia;
| | - Julio C. Rivera-Leyva
- Laboratorio 4, Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Mexico; (R.G.-Á.); (J.C.R.-L.)
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170901, Ecuador;
| | - Virginia Flores-Morales
- Laboratorio de Síntesis Asimétrica y Bioenergética (LSAyB), Ingeniería Química (UACQ), Universidad Autónoma de Zacatecas, Campus XXI Km 6 Carr. Zac-Gdl, Zacatecas 98160, Mexico;
- Correspondence: (V.F.-M.); (J.R.-I.); Tel.: +52-4929-256-690 (V.F.-M.); +52-7773-2970-00 (J.R.-I.)
| | - Jesús Rivera-Islas
- Laboratorio 4, Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Mexico; (R.G.-Á.); (J.C.R.-L.)
- Correspondence: (V.F.-M.); (J.R.-I.); Tel.: +52-4929-256-690 (V.F.-M.); +52-7773-2970-00 (J.R.-I.)
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9
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Anchique L, Alcázar JJ, Ramos-Hernandez A, Méndez-López M, Mora JR, Rangel N, Paz JL, Márquez E. Predicting the Adsorption of Amoxicillin and Ibuprofen on Chitosan and Graphene Oxide Materials: A Density Functional Theory Study. Polymers (Basel) 2021; 13:1620. [PMID: 34067695 PMCID: PMC8156938 DOI: 10.3390/polym13101620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 01/23/2023] Open
Abstract
The occurrence, persistence, and accumulation of antibiotics and non-steroidal anti-inflammatory drugs (NSAIDs) represent a new environmental problem due to their harmful effects on human and aquatic life. A suitable absorbent for a particular type of pollutant does not necessarily absorb other types of compounds, so knowing the compatibility between a particular pollutant and a potential absorbent before experimentation seems to be fundamental. In this work, the molecular interactions between some pharmaceuticals (amoxicillin, ibuprofen, and tetracycline derivatives) with two potential absorbers, chitosan and graphene oxide models (pyrene, GO-1, and coronene, GO-2), were studied using the ωB97X-D/6-311G(2d,p) level of theory. The energetic interaction order found was amoxicillin/chitosan > amoxicillin/GO-1 > amoxicillin/GO-2 > ibuprofen/chitosan > ibuprofen/GO-2 > ibuprofen/GO-1, the negative sign for the interaction energy in all complex formations confirms good compatibility, while the size of Eint between 24-34 kcal/mol indicates physisorption processes. Moreover, the free energies of complex formation were negative, confirming the spontaneity of the processes. The larger interaction of amoxicillin Gos, compared to ibuprofen Gos, is consistent with previously reported experimental results, demonstrating the exceptional predictability of these methods. The second-order perturbation theory analysis shows that the amoxicillin complexes are mainly driven by hydrogen bonds, while van der Waals interactions with chitosan and hydrophobic interactions with graphene oxides are modelled for the ibuprofen complexes. Energy decomposition analysis (EDA) shows that electrostatic energy is a major contributor to the stabilization energy in all cases. The results obtained in this work promote the use of graphene oxides and chitosan as potential adsorbents for the removal of these emerging pollutants from water.
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Affiliation(s)
- Leonardo Anchique
- Programa de Química, Grupo Química Supramolecular Aplicada, Facultad de Ciencias Básicas, Semillero Electroquímica Aplicada, Universidad del Atlántico, Barranquilla 081001, Colombia; (L.A.); (A.R.-H.)
| | - Jackson J. Alcázar
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Casilla 306, Santiago 6094411, Chile;
| | - Andrea Ramos-Hernandez
- Programa de Química, Grupo Química Supramolecular Aplicada, Facultad de Ciencias Básicas, Semillero Electroquímica Aplicada, Universidad del Atlántico, Barranquilla 081001, Colombia; (L.A.); (A.R.-H.)
| | - Maximiliano Méndez-López
- Departamento de Química y Biología, Facultad de Ciencias Exactas, Grupo de Investigaciones en Química y Biología, Universidad del Norte, Carrera 51B, Km 5, vía Puerto Colombia, Barranquilla 081007, Colombia
| | - José R. Mora
- Departamento de Ingeniería Química, Grupo de Química Computacional y Teórica (QCT-USFQ), Diego de Robles y Vía Interoceánica, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Norma Rangel
- TecNM/Instituto Tecnológico de Aguascalientes-División de Estudios de Posgrado e Investigación, Ave. Adolfo López Mateos #1801Ote. Fracc. Bona Gens, Aguascalientes 20256, Mexico;
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Cercado de Lima 15081, Peru;
| | - Edgar Márquez
- Departamento de Química y Biología, Facultad de Ciencias Exactas, Grupo de Investigaciones en Química y Biología, Universidad del Norte, Carrera 51B, Km 5, vía Puerto Colombia, Barranquilla 081007, Colombia
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10
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Computational study of the binding mode, action mechanism and potency of pregabalin through molecular docking and quantum mechanical descriptors. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Cuesta SA, Mora JR, Márquez EA. In Silico Screening of the DrugBank Database to Search for Possible Drugs against SARS-CoV-2. Molecules 2021; 26:1100. [PMID: 33669720 PMCID: PMC7923184 DOI: 10.3390/molecules26041100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
Coronavirus desease 2019 (COVID-19) is responsible for more than 1.80 M deaths worldwide. A Quantitative Structure-Activity Relationships (QSAR) model is developed based on experimental pIC50 values reported for a structurally diverse dataset. A robust model with only five descriptors is found, with values of R2 = 0.897, Q2LOO = 0.854, and Q2ext = 0.876 and complying with all the parameters established in the validation Tropsha's test. The analysis of the applicability domain (AD) reveals coverage of about 90% for the external test set. Docking and molecular dynamic analysis are performed on the three most relevant biological targets for SARS-CoV-2: main protease, papain-like protease, and RNA-dependent RNA polymerase. A screening of the DrugBank database is executed, predicting the pIC50 value of 6664 drugs, which are IN the AD of the model (coverage = 79%). Fifty-seven possible potent anti-COVID-19 candidates with pIC50 values > 6.6 are identified, and based on a pharmacophore modelling analysis, four compounds of this set can be suggested as potent candidates to be potential inhibitors of SARS-CoV-2. Finally, the biological activity of the compounds was related to the frontier molecular orbitals shapes.
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Affiliation(s)
- Sebastián A. Cuesta
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Colegio Politécnico, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170901, Ecuador;
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Colegio Politécnico, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170901, Ecuador;
| | - Edgar A. Márquez
- Grupo de Investigaciones en Química y Biología, Departamento de Química y Biología, Facultad de Ciencias Exactas, Universidad del Norte, Carrera 51B, Km 5, vía Puerto Colombia, Barranquilla 081007, Colombia
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12
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Appell M, Compton DL, Evans KO. Predictive Quantitative Structure-Activity Relationship Modeling of the Antifungal and Antibiotic Properties of Triazolothiadiazine Compounds. Methods Protoc 2020; 4:mps4010002. [PMID: 33375476 PMCID: PMC7838911 DOI: 10.3390/mps4010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 11/23/2022] Open
Abstract
Predictive models were developed using two-dimensional quantitative structure activity relationship (QSAR) methods coupled with B3LYP/6-311+G** density functional theory modeling that describe the antimicrobial properties of twenty-four triazolothiadiazine compounds against Aspergillus niger, Aspergillus flavus and Penicillium sp., as well as the bacteria Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa. B3LYP/6-311+G** density functional theory calculations indicated the triazolothiadiazine derivatives possess only modest variation between the frontier orbital properties. Genetic function approximation (GFA) analysis identified the topological and density functional theory derived descriptors for antimicrobial models using a population of 200 models with one to three descriptors that were crossed for 10,000 generations. Two or three descriptor models provided validated predictive models for antifungal and antibiotic properties with R2 values between 0.725 and 0.768 and no outliers. The best models to describe antimicrobial activities include descriptors related to connectivity, electronegativity, polarizability, and van der Waals properties. The reported method provided robust two-dimensional QSAR models with topological and density functional theory descriptors that explain a variety of antifungal and antibiotic activities for structurally related heterocyclic compounds.
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Affiliation(s)
- Michael Appell
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University St., Peoria, IL 61604, USA
- Correspondence:
| | - David L. Compton
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, 1815 N. University St., Peoria, IL 61604, USA; (D.L.C.); (K.O.E.)
| | - Kervin O. Evans
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, 1815 N. University St., Peoria, IL 61604, USA; (D.L.C.); (K.O.E.)
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13
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Toor HG, Banerjee DI, Chauhan JB. In Silico Evaluation of Human Cathelicidin LL-37 as a Novel Therapeutic Inhibitor of Panton-Valentine Leukocidin Toxin of Methicillin-Resistant Staphylococcus aureus. Microb Drug Resist 2020; 27:602-615. [PMID: 33983855 DOI: 10.1089/mdr.2020.0196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Incidence of drug resistance in clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) is attributed to its diverse repertoire of virulence factors. Of these virulence determinants, Panton-Valentine Leukocidin (PVL) has been experimentally validated as a prospective drug target due to its conspicuous and comprehensive role in nosocomial infections. This study encompassed an in silico approach to elucidate the antimicrobial potentiality of human cathelicidin LL-37 against PVL toxin of MRSA. Molecular docking studies of LL-37 and its segments with the PVL toxin subunits LukS and LukF were carried out using PatchDock server and the results were refined using FireDock server. The paramount ligand-receptor combination was selected and analyzed based on diverse parametric attributes and compared with the commercial inhibitors of PVL viz. Andrimid, Beclobrate, Beta-sitosterol, Diathymosulfone, and Probucol to determine the most potent inhibitor among them. Our results elucidated that the interaction of LL-37 with the LukS subunit of PVL toxin (minimum global energy of -61.82 kcal/mol) depicted 34 molecular interactions, while the commercial PVL inhibitors depicted fewer and insubstantial interactions. SWISS-ADME (Absorption, Distribution, Metabolism, and Excretion) and ToxinPred analysis of LL-37 further corroborated its null potency of toxicity in systemic milieu. The results obtained may credit this study as basis for the development of LL-37 as a potential inhibitor against virulent MRSA toxins, thereby exalting the treatment regimes for nosocomial infections in health care facilities worldwide.
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Affiliation(s)
- Himanshu G Toor
- P.G. Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), Sardar Patel University, Anand, India
| | - Devjani I Banerjee
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Jenabhai B Chauhan
- P.G. Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), Sardar Patel University, Anand, India
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