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Prinsa, Saha S, Bulbul MZH, Ozeki Y, Alamri MA, Kawsar SMA. Flavonoids as potential KRAS inhibitors: DFT, molecular docking, molecular dynamics simulation and ADMET analyses. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:955-992. [PMID: 38647682 DOI: 10.1080/10286020.2024.2343821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024]
Abstract
KRAS mutations linked with cancer. Flavonoids were docked against KRAS G12C and G12D receptors. Abyssinone III, alpha naphthoflavone, beta naphthoflavone, abyssinone I, abyssinone II and beta naphthoflavone, genistin, daidzin showed good docking scores against KRAS G12C and G12D receptors, respectively. The MD simulation data revealed that Rg, RMSD, RMSF, and SASA values were within acceptable limits. Alpha and beta naphthoflavone showed good binding energies with KRAS G12C and G12D receptors. DFT and MEP analysis highlighted the nucleophilic and electrophilic zones of best-docked flavonoids. A novel avenue for the control of KRAS G12C and G12D mutations is made possible by flavonoids.
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Affiliation(s)
- Prinsa
- Department of Pharmaceutical Chemistry, Siddhartha Institute of Pharmacy, Near IT-Park, Dehradun, Uttarakhand, India
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Md Zahidul Haque Bulbul
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Yasuhiro Ozeki
- Graduate School of Nanobio Sciences, Yokohama City University, Yokohama, Japan
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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Ahad Hossain M, Sultana S, Alanazi MM, Hadni H, Bhat AR, Hasan I, Kawsar SM. In vitro antimicrobial, anticancer evaluation, and in silico studies of mannopyranoside analogs against bacterial and fungal proteins: Acylation leads to improved antimicrobial activity. Saudi Pharm J 2024; 32:102093. [PMID: 38737807 PMCID: PMC11087236 DOI: 10.1016/j.jsps.2024.102093] [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: 03/16/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024] Open
Abstract
Carbohydrate analogs are an important, well-established class of clinically useful medicinal agents that exhibit potent antimicrobial activity. Thus, we explored the various therapeutic potential of methyl α-D-mannopyranoside (MαDM) analogs, including their ability to synthesize and assess their antibacterial, antifungal, and anticancer properties; additionally, molecular docking, molecular dynamics simulation, and ADMET analysis were performed. The structure of the synthesized MαDM analogs was ascertained by spectroscopic techniques and physicochemical and elemental analysis. In vitro antimicrobial activity was assessed and revealed significant inhibitory effects, particularly against gram-negative bacteria along with the prediction of activity spectra for substances (PASS). Concurrently, MαDM analogs showed good results against antifungal pathogens and exhibited promising anticancer effects in vitro, demonstrating dose-dependent cytotoxicity against Ehrlich ascites carcinoma (EAC) cancer cells while sparing normal cells from compound 5, with an IC50 of 4511.65 µg/mL according to the MTT colorimetric assay. A structure-activity relationship (SAR) study revealed that hexose combined with the acyl chains of decanoyl (C-10) and benzenesulfonyl (C6H5SO2-) had synergistic effects on the bacteria and fungi that were examined. Molecular docking was performed against the Escherichia coli (6KZV) and Candida albicans (1EAG) proteins to acquire insights into the molecular interactions underlying the observed biological activities. The docking results were further supported by 100 ns molecular dynamics simulations, which provided a dynamic view of the stability and flexibility of complexes involving MαDM and its targets. In addition, ADMET analysis was used to evaluate the toxicological and pharmacokinetic profiles. Owing to their promising drug-like properties, these MαDM analogs exhibit potential as prospective therapeutic candidates for future development.
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Affiliation(s)
- Md. Ahad Hossain
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Shahin Sultana
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Mohammed M. Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ajmal R. Bhat
- Department of Chemistry, RTM Nagpur University, Nagpur 440033, India
| | - Imtiaj Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Sarkar M.A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
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Quayum ST, Esha NJI, Siraji S, Abbad SSA, Alsunaidi ZH, Almatarneh MH, Rahman S, Alodhayb AN, Alibrahim KA, Kawsar SM, Uddin KM. Exploring the effectiveness of flavone derivatives for treating liver diseases: Utilizing DFT, molecular docking, and molecular dynamics techniques. MethodsX 2024; 12:102537. [PMID: 38299040 PMCID: PMC10828815 DOI: 10.1016/j.mex.2023.102537] [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: 11/01/2023] [Accepted: 12/24/2023] [Indexed: 02/02/2024] Open
Abstract
In exploring nature's potential in addressing liver-related conditions, this study investigates the therapeutic capabilities of flavonoids. Utilizing in silico methodologies, we focus on flavone and its analogs (1-14) to assess their therapeutic potential in treating liver diseases. Molecular change calculations using density functional theory (DFT) were conducted on these compounds, accompanied by an evaluation of each analog's physiochemical and biochemical properties. The study further assesses these flavonoids' binding effectiveness and locations through molecular docking studies against six target proteins associated with human cancer. Tropoflavin and taxifolin served as reference drugs. The structurally modified flavone analogs (1-14) displayed a broad range of binding affinities, ranging from -7.0 to -9.4 kcal mol⁻¹, surpassing the reference drugs. Notably, flavonoid (7) exhibited significantly higher binding affinities with proteins Nrf2 (PDB:1 × 2 J) and DCK (PDB:1 × 2 J) (-9.4 and -8.1 kcal mol⁻¹) compared to tropoflavin (-9.3 and -8.0 kcal mol⁻¹) and taxifolin (-9.4 and -7.1 kcal mol⁻¹), respectively. Molecular dynamics (MD) simulations revealed that the docked complexes had a root mean square deviation (RMSD) value ranging from 0.05 to 0.2 nm and a root mean square fluctuation (RMSF) value between 0.35 and 1.3 nm during perturbation. The study concludes that 5,7-dihydroxyflavone (7) shows substantial promise as a potential therapeutic agent for liver-related conditions. However, further validation through in vitro and in vivo studies is necessary. Key insights from this study include:•Screening of flavanols and their derivatives to determine pharmacological and bioactive properties using ADMET, molinspiration, and pass prediction analysis.•Docking of shortlisted flavone derivatives with proteins having essential functions.•Analysis of the best protein-flavonoid docked complexes using molecular dynamics simulation to determine the flavonoid's efficiency and stability within a system.
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Affiliation(s)
- Syeda Tasnim Quayum
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Nusrat Jahan Ikbal Esha
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Siam Siraji
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Sanaa S. Al Abbad
- Department of Chemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Zainab H.A. Alsunaidi
- Department of Chemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | - Shofiur Rahman
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah N. Alodhayb
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khuloud A. Alibrahim
- Department of Chemistry, Princess Nora bint Abdulrahman University, College of Science, Riyadh, Al Riyadh, 11671, Saudi Arabia
| | - Sarkar M.A. Kawsar
- Lab of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong 4331, Bangladesh
| | - Kabir M. Uddin
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
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Yan X, Zhang A, Guan Y, Jiao J, Ghanim M, Zhang Y, He X, Shi R. Comparative Metabolome and Transcriptome Analyses Reveal Differential Enrichment of Metabolites with Age in Panax notoginseng Roots. PLANTS (BASEL, SWITZERLAND) 2024; 13:1441. [PMID: 38891250 PMCID: PMC11175106 DOI: 10.3390/plants13111441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/05/2024] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Panax notoginseng is a perennial plant well known for its versatile medicinal properties, including hepatoprotective, antioxidant, anti-inflammatory, anti-tumor, estrogen-like, and antidepressant characteristics. It has been reported that plant age affects the quality of P. notoginseng. This study aimed to explore the differential metabolome and transcriptome of 2-year (PN2) and 3-year-old (PN3) P. notoginseng plant root samples. Principal component analysis of metabolome and transcriptome data revealed major differences between the two groups (PN2 vs. PN3). A total of 1813 metabolites and 28,587 genes were detected in this study, of which 255 metabolites and 3141 genes were found to be differential (p < 0.05) between PN2 vs. PN3, respectively. Among differential metabolites and genes, 155 metabolites and 1217 genes were up-regulated, while 100 metabolites and 1924 genes were down-regulated. The KEGG pathway analysis revealed differentially enriched metabolites belonging to class lipids ("13S-hydroperoxy-9Z, 11E-octadecadionic acid", "9S-hydroxy-10E, 12Z-octadecadionic acid", "9S-oxo-10E, 12Z-octadecadionic acid", and "9,10,13-trihydroxy-11-octadecadionic acid"), nucleotides and derivatives (guanine and cytidine), and phenolic acids (chlorogenic acid) were found to be enriched (p < 0.05) in PN3 compared to PN2. Further, these differentially enriched metabolites were found to be significantly (p < 0.05) regulated via linoleic acid metabolism, nucleotide metabolism, plant hormone signal transduction, and arachidonic acid metabolism pathways. Furthermore, the transcriptome analysis showed the up-regulation of key genes MAT, DMAS, SDH, gallate 1-beta-glucosyltransferase, and beta-D-glucosidase in various plants' secondary metabolic pathways and SAUR, GID1, PP2C, ETR, CTR1, EBF1/2, and ERF1/2 genes observed in phytohormone signal transduction pathway that is involved in plant growth and development, and protection against the various stressors. This study concluded that the roots of a 3-year-old P. notoginseng plant have better metabolome and transcriptome profiles compared to a 2-year-old plant with importantly enriched metabolites and genes in pathways related to metabolism, plant hormone signal transduction, and various biological processes. These findings provide insights into the plant's dynamic biochemical and molecular changes during its growth that have several implications regarding its therapeutic use.
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Affiliation(s)
- Xinru Yan
- Yunnan Provincial Key Laboratory for Conservation and Utilization of In-Forest Resource, International Ecological Forestry Research Center of Kunming, Southwest Forestry University, Kunming 650224, China; (X.Y.); (A.Z.); (J.J.)
| | - Ao Zhang
- Yunnan Provincial Key Laboratory for Conservation and Utilization of In-Forest Resource, International Ecological Forestry Research Center of Kunming, Southwest Forestry University, Kunming 650224, China; (X.Y.); (A.Z.); (J.J.)
| | - Yiming Guan
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun 130112, China;
| | - Jinlong Jiao
- Yunnan Provincial Key Laboratory for Conservation and Utilization of In-Forest Resource, International Ecological Forestry Research Center of Kunming, Southwest Forestry University, Kunming 650224, China; (X.Y.); (A.Z.); (J.J.)
| | - Murad Ghanim
- Department of Entomology, Institute of Plant Protection, 68 Hamaccabim Road, Rishon LeZion 7505101, Israel;
| | - Yayu Zhang
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun 130112, China;
| | - Xiahong He
- Yunnan Provincial Key Laboratory for Conservation and Utilization of In-Forest Resource, International Ecological Forestry Research Center of Kunming, Southwest Forestry University, Kunming 650224, China; (X.Y.); (A.Z.); (J.J.)
| | - Rui Shi
- Yunnan Provincial Key Laboratory for Conservation and Utilization of In-Forest Resource, International Ecological Forestry Research Center of Kunming, Southwest Forestry University, Kunming 650224, China; (X.Y.); (A.Z.); (J.J.)
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5
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Khalaf MM, Abd El-Lateef HM, Gouda M, Abdelhamid AA, Abdelbaset M, Alsulami AH, Almarri MN, Abdou A. Designing, DFT, biological, & molecular docking analysis of new Iron(III) & copper(II) complexes incorporating 1-{[-(2-Hydroxyphenyl)methylene]amino}-5,5-diphenylimidazolidine-2,4-dione (PHNS). Comput Biol Chem 2024; 109:108031. [PMID: 38382408 DOI: 10.1016/j.compbiolchem.2024.108031] [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: 12/04/2023] [Revised: 01/25/2024] [Accepted: 02/10/2024] [Indexed: 02/23/2024]
Abstract
The exploration encompassed the synthesis and characterization of two innovative complexes, namely FePHNS and CuPHNS, employing a diverse array of analytical techniques such as elemental analysis, infrared and ultraviolet-visible spectroscopy, mass spectrometry, molar conductivity measurements, magnetic susceptibility assessments, and thermal analysis (TGA). In the spectral domain, infrared spectroscopy substantiated the tridentate ONS coordination of the PHNS ligand to the central metal atom. Thermal analysis offered valuable insights into the distribution and content of water molecules within the complexes. Density functional theory (DFT) calculations were harnessed to validate the molecular structures of both the PHNS ligand and its complex entities, providing an intricate comprehension of their quantum chemical parameters. The investigation extended to an evaluation of the in vitro antibacterial, antifungal, and antioxidant efficacy of the PHNS ligand and its complexes, revealing heightened biological activities for the complexes in comparison to the free PHNS ligand, notably with the CuPHNS complex demonstrating the highest activity, while the PHNS ligand exhibited the lowest. To delve into potential physiological activities, molecular docking studies were conducted, predicting the binding affinity of the compounds to proteins 2vf5 (Glucosamine-6-phosphate synthase in complex with glucosamine-6-phosphate) from Escherichia coli, 3cku (rate oxidase from Aspergillus flavus complexed with its inhibitor 8-azaxanthin and chloride) from Aspergillus flavus, and 5IJT (Crystal structure of Human Peroxiredoxin 2 Oxidized). The ensuing analysis of protein-ligand interactions and binding energies underscored the promising physiological activities of the investigated compounds, warranting further exploration for their potential in novel drug development.
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Affiliation(s)
- Mai M Khalaf
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia; Chemistry Department, Faculty of Science, Sohag University Sohag 82524, Egypt
| | - Hany M Abd El-Lateef
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia; Chemistry Department, Faculty of Science, Sohag University Sohag 82524, Egypt.
| | - Mohamed Gouda
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Antar A Abdelhamid
- Chemistry Department, Faculty of Science, Sohag University Sohag 82524, Egypt; Department of Chemistry, Faculty of Science, Al-Baha University, Al-Baha, Saudi Arabia
| | - Mohamed Abdelbaset
- Department of Chemistry, Faculty of Science, Al-Baha University, Al-Baha, Saudi Arabia; Chemistry Department, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - Abdulelah H Alsulami
- Chemistry Department, Faculty of Science and Arts in Baljurashi, Al-Baha University, Al-Baha, Saudi Arabia
| | - Mohammed N Almarri
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Aly Abdou
- Chemistry Department, Faculty of Science, Sohag University Sohag 82524, Egypt.
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Pedrinha VF, Santos LM, Gonçalves CP, Garcia MT, Lameira OA, Queiroga CL, Marcucci MC, Shahbazi MA, Sharma PK, Junqueira JC, Sipert CR, de Andrade FB. Effects of natural antimicrobial compounds propolis and copaiba on periodontal ligament fibroblasts, molecular docking, and in vivo study in Galleria mellonella. Biomed Pharmacother 2024; 171:116139. [PMID: 38198959 DOI: 10.1016/j.biopha.2024.116139] [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: 10/04/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
Root canal treatment addresses infectious processes that require control. Occasionally, the radicular pulp is vital and inflamed, presenting a superficial infection. To preserve pulpal remnants, conservative procedures have gained favor, employing anti-inflammatory medications. This study investigated the effects of propolis (PRO), and copaiba oil-resin (COR) associated with hydrocortisone (H) and compared their impact to that of Otosporin® concerning cytotoxic and genotoxic activity, cytokine detection, and toxicity in the Galleria mellonella model. Human periodontal ligament fibroblasts (PDLFs) were exposed to drug concentrations and evaluated by the MTT assay. Associations were tested from concentrations that did not compromise cell density. Genotoxicity was evaluated through micronucleus counting, while cytokines IL-6 and TGF-β1 were detected in the cell supernatant using ELISA. Molecular docking simulations were conducted, considering the major compounds identified in PRO, COR, and H. Increasing concentrations of PRO and COR were assessed for acute toxicity in Galleria mellonella model. Cellular assays were analyzed using one-way ANOVA followed by Tukey tests, while larval survivals were evaluated using the Log-rank (Mantel-Cox) test (α = 0.05). PRO and COR promoted PDLFs proliferation, even in conjunction with H. No changes in cell metabolism were observed concerning cytokine levels. The tested materials induce the release of AT1R, proliferating the PDFLs through interactions. PRO and COR had low toxicity in larvae, suggesting safety at tested levels. These findings endorse the potential of PRO and COR in endodontics and present promising applications across medical domains, such as preventive strategies in inflammation, shedding light on their potential development into commercially available drugs.
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Affiliation(s)
- Victor Feliz Pedrinha
- Department of Operative Dentistry, Endodontics and Dental Materials, Bauru School of Dentistry, University of São Paulo (FOB - USP), Bauru, São Paulo, Brazil; Department of Biomaterials and Biomedical Technology (BBT), University Medical Center Groningen (UMCG), University of Groningen, Groningen, the Netherlands.
| | - Letícia Martins Santos
- Department of Operative Dentistry, School of Dentistry, University of São Paulo (FO-USP), São Paulo, Brazil
| | | | - Maíra Terra Garcia
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos, São Paulo, Brazil
| | | | - Carmen Lucia Queiroga
- State University of Campinas, CPQBA, Division of Phytochemistry, Campinas, São Paulo, Brazil
| | - Maria Cristina Marcucci
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos, São Paulo, Brazil
| | - Mohammad-Ali Shahbazi
- Department of Biomaterials and Biomedical Technology (BBT), University Medical Center Groningen (UMCG), University of Groningen, Groningen, the Netherlands
| | - Prashant Kumar Sharma
- Department of Biomaterials and Biomedical Technology (BBT), University Medical Center Groningen (UMCG), University of Groningen, Groningen, the Netherlands
| | - Juliana Campos Junqueira
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos, São Paulo, Brazil
| | - Carla Renata Sipert
- Department of Operative Dentistry, School of Dentistry, University of São Paulo (FO-USP), São Paulo, Brazil
| | - Flaviana Bombarda de Andrade
- Department of Operative Dentistry, Endodontics and Dental Materials, Bauru School of Dentistry, University of São Paulo (FOB - USP), Bauru, São Paulo, Brazil
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Hosen MA, El Bakri Y, Rehman HM, Hashem HE, Saki M, Kawsar SMA. A computational investigation of galactopyranoside esters as antimicrobial agents through antiviral, molecular docking, molecular dynamics, pharmacokinetics, and bioactivity prediction. J Biomol Struct Dyn 2024; 42:1015-1030. [PMID: 37027788 DOI: 10.1080/07391102.2023.2198606] [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: 11/22/2022] [Accepted: 03/25/2023] [Indexed: 04/09/2023]
Abstract
One of the most common viral infections worldwide is the Human Papilloma Virus (HPV) which has been linked to cancer and other diseases in many countries. Monosaccharide esters are significant in the field of carbohydrate chemistry because they are efficient in the synthesis of pharmacologically active compounds. Therefore, the present study aimed to perform thermodynamic, molecular docking and molecular dynamics study of a series of previously designed monosaccharaides, methyl β-d-galactopyranoside (MGP, 1) esters (2-10) with along with their physicochemical and pharmacokinetic properties. We have optimized the MGP esters employing the DFT study at the B3LYP/6-311 + G (d,p) level of theory. The subsequent analysis also investigated the electronic energies, enthalpies, entropies, polarizability, and natural bond orbital (NBO) of these modified esters. Then, MGP esters were docked into CTX-M-15 extended-spectrum beta-lactamase from Escherichia coli (PDB: 4HBT) and E2 DNA-binding domain from human papillomavirus type 31 (PDB: 1A7G), and the results revealed that most of the esters can efficiently bind to the target. Desmond was used to doing molecular dynamics simulations at 200 ns in addition to molecular docking to look at the binding conformational stability of the protein-ligand complex. Based on RMSD and RMSF, it was determined that the stability of the protein-ligand combination was maintained during the whole 200 ns simulations for all compounds. Finally, a pharmacokinetic study suggests that modified esters of MGP exhibited better pharmacokinetic characteristics and were less hazardous than the parent drug. This work demonstrated that potential MGP esters can efficiently bind to 4HBT and 1A7G proteins and opened avenues for the development of newer antimicrobial agents that can target dangerous pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammed A Hosen
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Alnoorians Group of Institutes, Lahore, Pakistan
| | - Heba E Hashem
- Department of Chemistry, Faculty of Women, Ain Shams University, Cairo, Egypt
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sarkar M A Kawsar
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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8
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Ouassaf M, Bourougaa L, Al-Mijalli SH, Abdallah EM, Bhat AR, A. Kawsar SM. Marine-Derived Compounds as Potential Inhibitors of Hsp90 for Anticancer and Antimicrobial Drug Development: A Comprehensive In Silico Study. Molecules 2023; 28:8074. [PMID: 38138564 PMCID: PMC10871121 DOI: 10.3390/molecules28248074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Marine compounds constitute a diverse and invaluable resource for the discovery of bioactive substances with promising applications in the pharmaceutical development of anti-inflammatory and antibacterial agents. In this study, a comprehensive methodology was employed, encompassing pharmacophore modeling, virtual screening, in silico ADMET assessment (encompassing aspects of absorption, distribution, metabolism, excretion, and toxicity), and molecular dynamics simulations. These methods were applied to identify new inhibitors targeting the Hsp90 protein (heat shock protein 90), commencing with a diverse assembly of compounds sourced from marine origins. During the virtual screening phase, an extensive exploration was conducted on a dataset comprising 31,488 compounds sourced from the CMNPD database, characterized by a wide array of molecular structures. The principal objective was the development of structure-based pharmacophore models, a valuable approach when the pool of known ligands is limited. The pharmacophore model DDRRR was successfully constructed within the active sites of the Hsp90 crystal structure. Subsequent docking studies led to the identification of six compounds (CMNPD 22591, 9335, 10015, 360799, 15115, and 20988) demonstrating substantial binding affinities, each with values below -8.3 kcal/mol. In the realm of in silico ADMET predictions, five of these compounds exhibited favorable pharmacokinetic properties. Furthermore, molecular dynamics simulations and total binding energy calculations using MM-PBSA indicated that these marine-derived compounds formed exceptionally stable complexes with the Hsp90 receptor over a 100-nanosecond simulation period. These findings underscore the considerable potential of these novel marine compounds as promising candidates for anticancer and antimicrobial drug development.
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Affiliation(s)
- Mebarka Ouassaf
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra 707000, Algeria;
| | - Lotfi Bourougaa
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra 707000, Algeria;
| | - Samiah Hamad Al-Mijalli
- Department of Biology, College of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Emad M. Abdallah
- Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia;
| | - Ajmal R. Bhat
- Department of Chemistry, RTM Nagpur University, Nagpur 440033, India;
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh;
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Akter S, Alhatlani BY, Abdallah EM, Saha S, Ferdous J, Hossain ME, Ali F, Kawsar SMA. Exploring Cinnamoyl-Substituted Mannopyranosides: Synthesis, Evaluation of Antimicrobial Properties, and Molecular Docking Studies Targeting H5N1 Influenza A Virus. Molecules 2023; 28:8001. [PMID: 38138491 PMCID: PMC10745968 DOI: 10.3390/molecules28248001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The pursuit of innovative combinations for the development of novel antimicrobial and antiviral medications has garnered worldwide interest among scientists in recent times. Monosaccharides and their glycosides, such as methyl α-d-mannopyranoside derivatives, play a significant role in the potential treatment of viral respiratory pathologies. This study was undertaken to investigate and assess the synthesis and spectral characterization of methyl α-d-mannopyranoside derivatives 2-6, incorporating various aliphatic and aromatic groups. The investigation encompassed comprehensive in vitro antimicrobial screening, examination of physicochemical properties, molecular docking analysis, molecular dynamics simulations, and pharmacokinetic predictions. A unimolar one-step cinnamoylation reaction was employed under controlled conditions to produce methyl 6-O-cinnamoyl-α-d-mannopyranoside 2, demonstrating selectivity at the C-6 position. This represented a pivotal step in the development of potential antimicrobial derivatives based on methyl α-d-mannopyranoside. Subsequently, four additional methyl 6-O-cinnamoyl-α-d-mannopyranoside derivatives were synthesized with reasonably high yields. The chemical structures of these novel analogs were confirmed through a thorough analysis of their physicochemical properties, elemental composition, and spectroscopic data. In vitro antimicrobial assays were conducted against six bacterial strains and two fungal strains, revealing promising antifungal properties of these methyl α-d-mannopyranoside derivatives in comparison to their antibacterial activity. Moreover, cytotoxicity testing revealed that the compounds are less toxic. Further supporting these findings, molecular docking studies were performed against the H5N1 influenza A virus, indicating significant binding affinities and nonbonding interactions with the target protein 6VMZ. Notably, compounds 4 (-7.2) and 6 (-7.0) exhibited the highest binding affinities. Additionally, a 100 ns molecular dynamics simulation was conducted to assess the stability of the complex formed between the receptor 6VMZ and methyl α-d-mannopyranoside derivatives under in silico physiological conditions. The results revealed a stable conformation and binding pattern within the stimulating environment. In silico pharmacokinetic and toxicity assessments of the synthesized molecules were performed using Osiris software (version 2.9.1). Compounds 4 and 6 demonstrated favorable computational and pharmacological activities, albeit with a low drug score, possibly attributed to their higher molecular weight and irritancy. In conclusion, this study showcases the synthesis and evaluation of methyl α-d-mannopyranoside derivatives as promising candidates for antimicrobial and antifungal agents. Molecular docking and dynamics simulations, along with pharmacological predictions, contribute to our understanding of their potential therapeutic utility, although further research may be warranted to address certain pharmacological aspects.
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Affiliation(s)
- Sabina Akter
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh; (S.A.); (J.F.)
| | - Bader Y. Alhatlani
- Unit of Scientific Research, Applied College, Qassim University, Buraydah 52571, Saudi Arabia
| | - Emad M. Abdallah
- Department of Science Laboratories, College of Science and Arts, Qassim University, ArRass 51921, Saudi Arabia;
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun 248007, Uttarakhand, India;
| | - Jannatul Ferdous
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh; (S.A.); (J.F.)
| | - Md Emdad Hossain
- Wazed Miah Science Research Centre, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh;
| | - Ferdausi Ali
- Department of Microbiology, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh; (S.A.); (J.F.)
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10
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Kayes MR, Saha S, Alanazi MM, Ozeki Y, Pal D, Hadda TB, Legssyer A, Kawsar SM. Macromolecules: Synthesis, antimicrobial, POM analysis and computational approaches of some glucoside derivatives bearing acyl moieties. Saudi Pharm J 2023; 31:101804. [PMID: 37868643 PMCID: PMC10585311 DOI: 10.1016/j.jsps.2023.101804] [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: 09/07/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
Macromolecules i.e., carbohydrate derivatives are crucial to biochemical and medical research. Herein, we designed and synthesized eight methyl α-D-glucopyranoside (MGP) derivatives (2-8) in good yields following the regioselective direct acylation method. The structural configurations of the synthesized MGP derivatives were analyzed and verified using multiple physicochemical and spectroscopic techniques. Antimicrobial experiments revealed that almost all derivatives demonstrated noticeable antifungal and antibacterial efficacy. The synthesized derivatives showed minimum inhibitory concentration (MIC) values ranging from 0.75 µg/mL to 1.50 µg/mL and minimum bactericidal concentrations (MBCs) ranging from 8.00 µg/mL to 16.00 µg/mL. Compound 6 inhibited Ehrlich ascites carcinoma (EAC) cell proliferation by 10.36% with an IC50 of 2602.23 μg/mL in the MTT colorimetric assay. The obtained results were further rationalized by docking analysis of the synthesized derivatives against 4URO and 4XE3 receptors to explore the binding affinities and nonbonding interactions of MGP derivatives with target proteins. Compound 6 demonstrated the potential to bind with the target with the highest binding energy. In a stimulating environment, a molecular dynamics study showed that MGP derivatives have a stable conformation and binding pattern. The MGP derivatives were examined using POM (Petra/Osiris/Molinspiration) bioinformatics, and as a result, these derivatives showed good toxicity, bioavailability, and pharmacokinetics. Various antifungal/antiviral pharmacophore (Oδ-, O'δ-) sites were identified by using POM investigations, and compound 6 was further tested against other pathogenic fungi and viruses, such as Micron and Delta mutants of SARS-CoV-2.
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Affiliation(s)
- Mohammad R. Kayes
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, Uttarakhand 248007, India
| | - Mohammed M. Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-Ku, Yokohama 236-0027, Japan
| | - Dilipkumar Pal
- Department of Pharmaceutical Sciences, Guru Ghasidas Vishwavidyalaya (A Central University), C.G, 495009 Bilaspur, India
| | - Taibi B. Hadda
- BBEH and LACE Laboratories of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco
| | - Abdelkhaleq Legssyer
- BBEH and LACE Laboratories of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco
| | - Sarkar M.A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
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11
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Lotfi B, Mebarka O, Alhatlani BY, Abdallah EM, Kawsar SMA. Pharmacoinformatics and Breed-Based De Novo Hybridization Studies to Develop New Neuraminidase Inhibitors as Potential Anti-Influenza Agents. Molecules 2023; 28:6678. [PMID: 37764457 PMCID: PMC10534564 DOI: 10.3390/molecules28186678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/09/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza represents a profoundly transmissible viral ailment primarily afflicting the respiratory system. Neuraminidase inhibitors constitute a class of antiviral therapeutics employed in the management of influenza. These inhibitors impede the liberation of the viral neuraminidase protein, thereby impeding viral dissemination from the infected cell to host cells. As such, neuraminidase has emerged as a pivotal target for mitigating influenza and its associated complications. Here, we apply a de novo hybridization approach based on a breed-centric methodology to elucidate novel neuraminidase inhibitors. The breed technique amalgamates established ligand frameworks with the shared target, neuraminidase, resulting in innovative inhibitor constructs. Molecular docking analysis revealed that the seven synthesized breed molecules (designated Breeds 1-7) formed more robust complexes with the neuraminidase receptor than conventional clinical neuraminidase inhibitors such as zanamivir, oseltamivir, and peramivir. Pharmacokinetic evaluations of the seven breed molecules (Breeds 1-7) demonstrated favorable bioavailability and optimal permeability, all falling within the specified parameters for human application. Molecular dynamics simulations spanning 100 nanoseconds corroborated the stability of these breed molecules within the active site of neuraminidase, shedding light on their structural dynamics. Binding energy assessments, which were conducted through MM-PBSA analysis, substantiated the enduring complexes formed by the seven types of molecules and the neuraminidase receptor. Last, the investigation employed a reaction-based enumeration technique to ascertain the synthetic pathways for the synthesis of the seven breed molecules.
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Affiliation(s)
- Bourougaa Lotfi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 70700, Algeria;
| | - Ouassaf Mebarka
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 70700, Algeria;
| | - Bader Y. Alhatlani
- Unit of Scientific Research, Applied College, Qassim University, Buraydah 52571, Saudi Arabia
| | - Emad M. Abdallah
- Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia;
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh;
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12
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Hosen MA, Qais FA, Chtita S, Rahman IA, Almehdi AM, Ali F, Almalki FA, Hadda TB, Laaroussi H, Kawsar SMA. In silico and POM analysis for potential antimicrobial agents of thymidine analogs by using molecular docking, molecular dynamics and ADMET profiling. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 42:877-918. [PMID: 37235455 DOI: 10.1080/15257770.2023.2215839] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 04/19/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Abstract
Nucleoside analogs are an important, well-established class of clinically useful medicinal agents that exhibit potent antimicrobial activity. Thus, we designed to explore the synthesis and spectral characterization of 5'-O-(myristoyl)thymidine esters (2-6) for in vitro antimicrobial, molecular docking, molecular dynamics, SAR, and POM analyses. An unimolar myristoylation of thymidine under controlled conditions furnished the 5'-O-(myristoyl)thymidine and it was further converted into four 3'-O-(acyl)-5'-O-(myristoyl)thymidine analogs. The chemical structures of the synthesized analogs were ascertained by analyzing their physicochemical, elemental, and spectroscopic data. In vitro antimicrobial tests along with PASS, prediction indicated expectant antibacterial functionality of these thymidine esters compared to the antifungal activities. In support of this observation, their molecular docking studies have been performed against lanosterol 14α-demethylase (CYP51A1) and Aspergillus flavus (1R51) and significant binding affinities and non-bonding interactions were observed. The stability of the protein-ligand complexes was monitored by a 100 ns MD simulation and found the stable conformation and binding mode in a stimulating environment of thymidine esters. Pharmacokinetic predictions were studied to assess their ADMET properties and showed promising results in silico. SAR investigation indicated that acyl chains, lauroyl (C-12) and myristoyl (C-14), combined with deoxyribose, were most effective against the tested bacterial and fungal pathogens. The POM analyses provide the structural features responsible for their combined antibacterial/antifungal activity and provide guidelines for further modifications, with the aim of improving each activity and selectivity of designed drugs targeting potentially drug-resistant microorganisms. It also opens avenues for the development of newer antimicrobial agents targeting bacterial and fungal pathogens.
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Affiliation(s)
- Mohammed A Hosen
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Faizan A Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Ibrahim A Rahman
- Department of Chemistry, University of Sharjah, Sharjah, United Arab Emirates
| | - Ahmed M Almehdi
- Department of Chemistry, University of Sharjah, Sharjah, United Arab Emirates
| | - Ferdausi Ali
- Department of Microbiology, Faculty of Biological Science, University of Chittagong, Chittagong, Bangladesh
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Taibi B Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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13
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Design, Synthesis, In Silico and POM Studies for the Identification of the Pharmacophore Sites of Benzylidene Derivatives. Molecules 2023; 28:molecules28062613. [PMID: 36985587 PMCID: PMC10053039 DOI: 10.3390/molecules28062613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Due to the uneven distribution of glycosidase enzyme expression across bacteria and fungi, glycoside derivatives of antimicrobial compounds provide prospective and promising antimicrobial materials. Therefore, herein, we report the synthesis and characterization of six novel methyl 4,6-O-benzylidene-α-d-glucopyranoside (MBG) derivatives (2–7). The structures were ascertained using spectroscopic techniques and elemental analyses. Antimicrobial tests (zone of inhibition, MIC and MBC) were carried out to determine their ability to inhibit the growth of different Gram-positive, Gram-negative bacteria and fungi. The highest antibacterial activity was recorded with compounds 4, 5, 6 and 7. The compounds with the most significant antifungal efficacy were 4, 5, 6 and 7. Based on the prediction of activity spectra for substances (PASS), compounds 4 and 7 have promising antimicrobial capacity. Molecular docking studies focused on fungal and bacterial proteins where derivatives 3 and 6 exhibited strong binding affinities. The molecular dynamics study revealed that the complexes formed by these derivatives with the proteins L,D-transpeptidase Ykud and endoglucanase from Aspergillus niger remained stable, both over time and in physiological conditions. Structure–activity relationships, including in vitro and in silico results, revealed that the acyl chains [lauroyl-(CH3(CH2)10CO-), cinnamoyl-(C6H5CH=CHCO-)], in combination with sugar, were found to have the most potential against human and fungal pathogens. Synthetic, antimicrobial and pharmacokinetic studies revealed that MBG derivatives have good potential for antimicrobial activity, developing a therapeutic target for bacteria and fungi. Furthermore, the Petra/Osiris/Molinspiration (POM) study clearly indicated the presence of an important (O1δ−----O2δ−) antifungal pharmacophore site. This site can also be explored as a potential antiviral moiety.
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14
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Ahmmed F, Islam AU, Mukhrish YE, Bakri YE, Ahmad S, Ozeki Y, Kawsar SMA. Efficient Antibacterial/Antifungal Activities: Synthesis, Molecular Docking, Molecular Dynamics, Pharmacokinetic, and Binding Free Energy of Galactopyranoside Derivatives. Molecules 2022; 28:molecules28010219. [PMID: 36615413 PMCID: PMC9822152 DOI: 10.3390/molecules28010219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/13/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
The chemistry and biochemistry of carbohydrate esters are essential parts of biochemical and medicinal research. A group of methyl β-d-galactopyranoside (β-MGP, 1) derivatives was acylated with 3-bromobenzoyl chloride and 4-bromobenzoyl chloride in anhydrous N,N-dimethylformamide/triethylamine to obtain 6-O-substitution products, which were subsequently converted into 2,3,4-tri-O-acyl derivatives with different aliphatic and aromatic substituents. Spectroscopic and elemental data exploration of these derivatives confirmed their chemical structures. In vitro biological experiments against five bacteria and two fungi and the prediction of activity spectra for substances (PASS) revealed ascending antifungal and antibacterial activities compared with their antiviral activities. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) experiments were performed for two derivatives, 3 and 9, based on their antibacterial activities. Most of these derivatives showed >780% inhibition of fungal mycelial growth. Density functional theory (DFT) was used to calculate the chemical descriptors and thermodynamic properties, whereas molecular docking was performed against antibacterial drug targets, including PDB: 4QDI, 5A5E, 7D27, 1ZJI, 3K8E, and 2MRW, and antifungal drug targets, such as PDB: 1EA1 and 1AI9, to identify potential drug candidates for microbial pathogens. A 100 ns molecular dynamics simulation study revealed stable conformation and binding patterns in a stimulating environment by their uniform RMSD, RMSF, SASA, H-bond, and RoG profiles. In silico pharmacokinetic and quantitative structure−activity relationship (QSAR) calculations (pIC50 values 3.67~8.15) suggested that all the designed β-MGP derivatives exhibited promising results due to their improved kinetic properties with low aquatic and non-aquatic toxicities. These biological, structure−activity relationship (SAR) [lauroyl-(CH3(CH2)10CO-) group was found to have potential], and in silico computational studies revealed that the newly synthesized MGP derivatives are potential antibacterial/antifungal candidates and can serve as therapeutic targets for human and plant pathogens.
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Affiliation(s)
- Faez Ahmmed
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Anis Ul Islam
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Yousef E. Mukhrish
- Department of Chemistry, Faculty of Science, Jazan University, Jazan 45142, Saudi Arabia
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Lenin Prospect 76, 454080 Chelyabinsk, Russia
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Yokohama 236-0027, Japan
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
- Correspondence: ; Tel.: +88-01762717081
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15
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Salman M, Tariq A, Mustafa G, Javed MR, Naheed S, Qamar SA. Cyclo(L-Leucyl-L-Prolyl) from Lactobacillus coryniformis BCH-4 inhibits the proliferation of Aspergillus flavus: an in vitro to in silico approach. Arch Microbiol 2022; 204:267. [PMID: 35438350 DOI: 10.1007/s00203-022-02884-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/11/2022] [Accepted: 03/29/2022] [Indexed: 01/05/2023]
Abstract
Fungal spoilage led to a considerable economic loss of foodstuff which ultimately affects public health due to mycotoxins production. Moreover, the consumption of commercial antifungal drugs creates side effects and develops antifungal resistance. To overcome these challenges, the current work was aimed to investigate novel antifungal cyclic dipeptide (CDP) from Lactobacillus coryniformis (Loigolactobacillus coryniformis) BCH-4. CDPs have flexible, cyclic, and stable conformation. The proline-based CDPs provide additional structural compatibility and bio-functional values. Keeping in view, high-performance liquid chromatography (HPLC) was performed to explore cyclo(L-Leu-L-Pro) from L. coryniformis BCH-4. The HPLC detected concentration (135 ± 7.07 mg/mL) exhibited in vitro antifungal activity of 5.66 ± 0.57 mm (inhibitory zone) against Aspergillus flavus. Based on these results, cyclo(L-Leu-L-Pro) was used as a bioprotectant for selected food samples (grapes, lemon, cashew nuts, and almonds). A significant impact of cyclo(L-Leu-L-Pro) was observed in contrast with MRS broth (control) and cell-free supernatant. In silico molecular docking analysis of this CDP was carried out against FAD glucose dehydrogenase, dihydrofolate reductase, and urate oxidase of A. flavus as target proteins. Among these proteins, FAD glucose dehydrogenase exerted strong interactions with cyclo(L-Leu-L-Pro) having S-score of - 8.21. The results evaluated that the detected CDP has strong interactions with selected proteins, causing excellent growth inhibition of A. flavus. Therefore, cyclo(L-Leu-L-Pro) could be used as a potent bioprotectant against food-borne pathogenic fungi.
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Affiliation(s)
- Mahwish Salman
- Department of Biochemistry, Government College University, Faisalabad, Pakistan.
| | - Anam Tariq
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Shazia Naheed
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Sarmad Ahmad Qamar
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
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16
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Abyar Ghamsari P, Samadizadeh M. 4-Amino modified derivatives of cytidine towards interactions with the methyltransferase enzyme. MAIN GROUP CHEMISTRY 2022. [DOI: 10.3233/mgc-210185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
By the importance of exploring novel compounds for inhibiting the cancerous enzymes activities, this work was performed to recognize advantages of employing 4-amino modified derivatives of cytidine for participating in more efficient interactions with the methyltransferase (MTN) cancerous enzyme target. To this aim, four groups of modified models of cytidine were investigated in addition the original models to recognize the structural features and the corresponding activities. The 4-amino site of cytidine was functionalized by different carbon-based groups in linear and cyclic modes through a bridging peptide linkage. The models were optimized to reach the minimized energy structures by performing quantum chemical calculations and their interactions with the target were analyzed by performing molecular docking simulations. The obtained results of 4-amino modified derivatives of cytidine showed advantages of employing structural modifications to find structures with better molecular orbital based features. Formations of interacting complexes indicated that the additional of carbon-based groups helped to improve possibility of interactions between the substances in both of chemical and physical modes. As a remarkable achievement of this work, the model of cytidine with a phenyl group showed the best advantage of participating in interactions with the MTN target among all twenty five models of the investigated cytidine compounds.
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Affiliation(s)
- Parnia Abyar Ghamsari
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Marjaneh Samadizadeh
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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17
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Methyl β-D-galactopyranoside esters as potential inhibitors for SARS-CoV-2 protease enzyme: synthesis, antimicrobial, PASS, molecular docking, molecular dynamics simulations and quantum computations. Glycoconj J 2022; 39:261-290. [PMID: 35037163 PMCID: PMC8761875 DOI: 10.1007/s10719-021-10039-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 11/04/2022]
Abstract
Carbohydrate esters are significant in medicinal chemistry because of their efficacy for the synthesis of biologically active drugs. In the present study, methyl β-D-galactopyranoside (MGP) was treated with various acyl halides to produce 6-O-acyl MGP esters by direct acylation method with an excellent yield. To obtain newer products for antimicrobial assessment studies, the 6-O-MGP esters were further modified into 2,3,4-tri-O-acyl MGP esters containing a wide variety of functionalities in a single molecular framework. The chemical structures of the newly synthesized compounds were elucidated by analyzing their physicochemical, elemental, and spectroscopic data. In vitro antimicrobial testing against five bacteria and two fungi and the prediction of activity spectra for substances (PASS) revealed that these MGP estes have promising antifungal functionality compared to their antibacterial activities. The antimicrobial tests demonstrated that the compounds 3 and 10 were the most potent against Bacillus subtilis and Escherichia coli strains, with the minimum inhibitory concentration (MIC) values ranging from 0.352 ± 0.02 to 0.703 ± 0.01 mg/ml and minimum bactericidal concentration (MBC) values ranging from 0.704 ± 0.02 to 1.408 ± 0.04 mg/ml. Density functional theory (DFT) at the B3LYP/3-21G level of theory was employed to enumerate, frontier orbital energy, enthalpy, free energy, electronic energy, MEP, dipole moment which evaluated the effect of certain groups (aliphatic and aromatic) on drug properties. They discovered that all esters were more thermodynamically stable than the parent molecule. Molecular docking is performed using AutoDock Vina to determine the binding affinities and interactions between the MGP esters and the SARS-CoV-2 main protease. The modified esters strongly interact with the prime Cys145, His41, MET165, GLY143, THR26, and ASN142 residues. The MGP esters' shape and ability to form multiple electrostatic and hydrogen bonds with the active site match other minor-groove binders' binding modes. The molecular dynamics simulation validates the molecular docking results. The pharmacokinetic characterization of the optimized inhibitor demonstrates that these MGP esters appear to be safer inhibitors and a combination of in silico ADMET (absorption, distribution, metabolism, excretion, and toxicity) prediction and drug-likeness had promising results due to their improved kinetic properties. Structure activity relationships (SAR) study including in vitro and silico results revealed that the acyl chain, palmitoyl (C16) and 4-chlorobenzoyl (4.ClC6H4CO-) in combination with sugar were found the most potential activates against human and fungal pathogens. After all, our comprehensive computational and statistical analysis shows that these selected MGP esters can be used as potential inhibitors against the SARS-CoV-2.
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18
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Amin MR, Yasmin F, Hosen MA, Dey S, Mahmud S, Saleh MA, Emran TB, Hasan I, Fujii Y, Yamada M, Ozeki Y, Kawsar SMA. Synthesis, Antimicrobial, Anticancer, PASS, Molecular Docking, Molecular Dynamic Simulations & Pharmacokinetic Predictions of Some Methyl β-D-Galactopyranoside Analogs. Molecules 2021; 26:7016. [PMID: 34834107 PMCID: PMC8621697 DOI: 10.3390/molecules26227016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/07/2021] [Accepted: 11/12/2021] [Indexed: 11/27/2022] Open
Abstract
A series of methyl β-D-galactopyranoside (MGP, 1) analogs were selectively acylated with cinnamoyl chloride in anhydrous N,N-dimethylformamide/triethylamine to yield 6-O-substitution products, which was subsequently converted into 2,3,4-tri-O-acyl analogs with different acyl halides. Analysis of the physicochemical, elemental, and spectroscopic data of these analogs revealed their chemical structures. In vitro antimicrobial testing against five bacteria and two fungi and the prediction of activity spectra for substances (PASS) showed promising antifungal functionality comparing to their antibacterial activities. Minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) tests were conducted for four compounds (4, 5, 6, and 9) based on their activity. MTT assay showed low antiproliferative activity of compound 9 against Ehrlich's ascites carcinoma (EAC) cells with an IC50 value of 2961.06 µg/mL. Density functional theory (DFT) was used to calculate the thermodynamic and physicochemical properties whereas molecular docking identified potential inhibitors of the SARS-CoV-2 main protease (6Y84). A 150-ns molecular dynamics simulation study revealed the stable conformation and binding patterns in a stimulating environment. In-silico ADMET study suggested all the designed molecules to be non-carcinogenic, with low aquatic and non-aquatic toxicity. In summary, all these antimicrobial, anticancer and in silico studies revealed that newly synthesized MGP analogs possess promising antiviral activity, to serve as a therapeutic target for COVID-19.
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Affiliation(s)
- Md. Ruhul Amin
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh; (M.R.A.); (F.Y.); (M.A.H.)
| | - Farhana Yasmin
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh; (M.R.A.); (F.Y.); (M.A.H.)
| | - Mohammed Anowar Hosen
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh; (M.R.A.); (F.Y.); (M.A.H.)
| | - Sujan Dey
- Department of Microbiology, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (M.A.S.)
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (M.A.S.)
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
| | - Imtiaj Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Yuki Fujii
- School of Pharmaceutical Sciences, Nagasaki International University, 2825-7, Huis Ten Bosch-cho, Sasebo, Nagasaki 859-3298, Japan;
| | - Masao Yamada
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-ku, Yokohama 236-0027, Japan;
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-ku, Yokohama 236-0027, Japan;
| | - Sarkar Mohammad Abe Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh; (M.R.A.); (F.Y.); (M.A.H.)
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Harismah K, Hajali N, Mirzaei M, Salarrezaei E. Quantum processing of cytidine derivatives and evaluating their in silico interactions with the COVID-19 main protease. MAIN GROUP CHEMISTRY 2021. [DOI: 10.3233/mgc-210134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This work was performed by the importance of exploring possible medications for COVID-19 pandemic. In this regard, cytidine (Cyd) derivatives were investigated to reach a point to see their benefit of employing for the purpose. Each of halogenated models of Cyd including CydF, CydCl, CydBr, and CydI were investigated in addition to the original CydH model. Density functional theory (DFT) based quantum processing were performed to obtain stabilized structures in addition to evaluation of frontier molecular orbitals features. Next, molecular docking (MD) simulations were performed to reach a point of formations of interacting ligand-target complexes. Among the investigated models CydH and CydI were working better than other model for reaching the purpose of this work, in which the derived CydI model was indeed the ligand with the highest suitability for formation of ligand-target complexes. As a consequence, such ligands of original and halogenated Cyd models might work for inhibition of main protease (MPro) enzyme of COVID-19 based on the obtained meaningful vales for complex strengths in addition interacting with the amino acids of active site. More precisely, the CydI model could be proposed as promising ligand for showing the inhibitory effects towards the MPro target of COVID-19.
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Affiliation(s)
- Kun Harismah
- Department of Chemical Engineering, Faculty of Engineering, Universitas Muhammadiyah Surakarta, Surakarta, Indonesia
| | - Narjes Hajali
- Department of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mahmoud Mirzaei
- Medical Image & Signal Processing Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Salarrezaei
- Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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