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Maryam, Rehman MU, Hussain I, Tayara H, Chong KT. A graph neural network approach for predicting drug susceptibility in the human microbiome. Comput Biol Med 2024; 179:108729. [PMID: 38955124 DOI: 10.1016/j.compbiomed.2024.108729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/04/2024] [Accepted: 06/08/2024] [Indexed: 07/04/2024]
Abstract
Recent studies have illuminated the critical role of the human microbiome in maintaining health and influencing the pharmacological responses of drugs. Clinical trials, encompassing approximately 150 drugs, have unveiled interactions with the gastrointestinal microbiome, resulting in the conversion of these drugs into inactive metabolites. It is imperative to explore the field of pharmacomicrobiomics during the early stages of drug discovery, prior to clinical trials. To achieve this, the utilization of machine learning and deep learning models is highly desirable. In this study, we have proposed graph-based neural network models, namely GCN, GAT, and GINCOV models, utilizing the SMILES dataset of drug microbiome. Our primary objective was to classify the susceptibility of drugs to depletion by gut microbiota. Our results indicate that the GINCOV surpassed the other models, achieving impressive performance metrics, with an accuracy of 93% on the test dataset. This proposed Graph Neural Network (GNN) model offers a rapid and efficient method for screening drugs susceptible to gut microbiota depletion and also encourages the improvement of patient-specific dosage responses and formulations.
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Affiliation(s)
- Maryam
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Mobeen Ur Rehman
- Khalifa University Center for Autonomous Robotic Systems (KUCARS), Khalifa University, United Arab Emirates
| | - Irfan Hussain
- Khalifa University Center for Autonomous Robotic Systems (KUCARS), Khalifa University, United Arab Emirates
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju, 54896, South Korea.
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea; Advances Electronics and Information Research Centre, Jeonbuk National University, Jeonju, 54896, South Korea.
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Bastos RS, de Aguiar CPO, Cruz JN, Ramos RS, Kimani NM, de Souza JSN, Chaves MH, de Freitas HF, Pita SSR, dos Santos CBR. Rational Approach toward COVID-19's Main Protease Inhibitors: A Hierarchical Biochemoinformatics Analysis. Int J Mol Sci 2024; 25:6715. [PMID: 38928422 PMCID: PMC11204165 DOI: 10.3390/ijms25126715] [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: 04/14/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
This study investigated the potential of selected compounds as inhibitors of SARS-CoV-2 Mpro through pharmacokinetic and toxicological analyses, molecular docking, and molecular dynamics simulations. In silico molecular docking simulations revealed promising ligands with favorable binding affinities for Mpro, ranging from -6.2 to -9.5 kcal/mol. Moreover, molecular dynamics simulations demonstrated the stability of protein-ligand complexes over 200 ns, maintaining protein secondary structures. MM-PBSA analysis revealed favorable interactions between ligands and Mpro, with negative binding energy values. Hydrogen bond formation capacity during molecular dynamics was confirmed, indicating consistent interactions with Mpro catalytic residues. Based on these findings, selected ligands show promise for future studies in developing COVID-19 treatments.
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Affiliation(s)
- Ruan S. Bastos
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Christiane P. O. de Aguiar
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - Jorddy N. Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Ryan S. Ramos
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Njogu M. Kimani
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya
- Natural Product Chemistry and Computational Drug Discovery Laboratory, Embu P.O. Box 6-60100, Kenya
| | - João S. N. de Souza
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil
| | - Mariana H. Chaves
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil
| | - Humberto F. de Freitas
- Laboratory of Bioinformatics and Molecular Modeling (LaBiMM), Federal University of Bahia, Av. Barão de Jeremoabo, 147, Pharmacy College, Ondina, Salvador 40170-115, BA, Brazil; (H.F.d.F.); (S.S.R.P.)
| | - Samuel S. R. Pita
- Laboratory of Bioinformatics and Molecular Modeling (LaBiMM), Federal University of Bahia, Av. Barão de Jeremoabo, 147, Pharmacy College, Ondina, Salvador 40170-115, BA, Brazil; (H.F.d.F.); (S.S.R.P.)
| | - Cleydson B. R. dos Santos
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
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Tahghighi A, Azerang P. Click chemistry beyond metal-catalyzed cycloaddition as a remarkable tool for green chemical synthesis of antifungal medications. Chem Biol Drug Des 2024; 103:e14555. [PMID: 38862260 DOI: 10.1111/cbdd.14555] [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: 12/13/2023] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
Click chemistry is widely used for the efficient synthesis of 1,4-disubstituted-1,2,3-triazole, a well-known scaffold with widespread biological activity in the pharmaceutical sciences. In recent years, this magic ring has attracted the attention of scientists for its potential in designing and synthesizing new antifungal agents. Despite scientific and medical advances, fungal infections still account for more than 1.5 million deaths globally per year, especially in people with compromised immune function. This increasing trend is definitely related to a raise in the incidence of fungal infections and prevalence of antifungal drug resistance. In this condition, an urgent need for new alternative antifungals is undeniable. By focusing on the main aspects of reaction conditions in click chemistry, this review was conducted to classify antifungal 1,4-disubstituted-1,2,3-triazole hybrids based on their chemical structures and introduce the most effective triazole antifungal derivatives. It was notable that in all reactions studied, Cu(I) catalysts generated in situ by the reduction in Cu(II) salts or used copper(I) salts directly, as well as mixed solvents of t-BuOH/H2O and DMF/H2O had most application in the synthesis of triazole ring. The most effective antifungal activity was also observed in fluconazole analogs containing 1,2,3-triazole moiety and benzo-fused five/six-membered heterocyclic conjugates with a 1,2,3-triazole ring, even with better activity than fluconazole. The findings of structure-activity relationship and molecular docking of antifungal derivatives synthesized with copper-catalyzed azide-alkyne cycloaddition (CuAAC) could offer medicinal chemistry scientists valuable data on designing and synthesizing novel triazole antifungals with more potent biological activities in their future research.
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Affiliation(s)
- Azar Tahghighi
- Medicinal Chemistry Laboratory, Department of Clinical Research, Pasteur Institute of Iran, Tehran, Iran
| | - Parisa Azerang
- Medicinal Chemistry Laboratory, Department of Clinical Research, Pasteur Institute of Iran, Tehran, Iran
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Abouzied AS, Huwaimel B, Alqarni S, Younes KM, Alshammari RE, Alshammari AH, Algharbi WF, Elkashlan AM. Sinefungin analogs targeting VP39 methyltransferase as potential anti-monkeypox therapeutics: a multi-step computational approach. Mol Divers 2024:10.1007/s11030-024-10875-z. [PMID: 38702561 DOI: 10.1007/s11030-024-10875-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/09/2024] [Indexed: 05/06/2024]
Abstract
The increasing spread of the Monkeypox virus (MPXV) presents a significant public health challenge, emphasising the urgent requirement for effective treatments. Our study focuses on the VP39 Methyltransferase enzyme of MPXV as a critical target for therapy. By utilising virtual screening, we investigated natural compounds with structural similarities to sinefungin, a broad-acting MTase inhibitor. From an initial set of 177 compounds, we identified three promising compounds-CNP0346326, CNP0343532, and CNP008361, whose binding scores were notably close to that of sinefungin. These candidates bonded strongly to the VP39 enzyme, hinting at a notable potential to impede the virus. Our rigorous computational assays, including re-docking, extended molecular dynamics simulations, and energetics analyses, validate the robustness of these interactions. The data paint a promising picture of these natural compounds as front-runners in the ongoing race to develop MPXV therapeutics and set the stage for subsequent empirical trials to refine these discoveries into actionable medical interventions.
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Affiliation(s)
- Amr S Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia.
- Medical and Diagnostic Research Center, University of Hail, 55473, Hail, Saudi Arabia.
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Medical and Diagnostic Research Center, University of Hail, 55473, Hail, Saudi Arabia
| | - Saad Alqarni
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
| | - Kareem M Younes
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Analytical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | | | | | | | - Akram M Elkashlan
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, El-Sadat, Egypt
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Balasundaram A, Ramireddy S, S UK, D TK, Tayubi IA, Zayed H, C GPD. A new horizon in the phosphorylated sites of AGA: the structural impact of C163S mutation in aspartylglucosaminuria through molecular dynamics simulation. J Biomol Struct Dyn 2024; 42:4313-4324. [PMID: 37334725 DOI: 10.1080/07391102.2023.2220798] [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: 03/18/2023] [Accepted: 05/28/2023] [Indexed: 06/20/2023]
Abstract
Aspartylglucosaminuria (AGU) is a lysosomal storage disorder caused by insufficient aspartylglucosaminidase (AGA) activity leading to chronic neurodegeneration. We utilized the PhosphoSitePlus tool to identify the AGA protein's phosphorylation sites. The phosphorylation was induced on the specific residue of the three-dimensional AGA protein, and the structural changes upon phosphorylation were studied via molecular dynamics simulation. Furthermore, the structural behaviour of C163S mutation and C163S mutation with adjacent phosphorylation was investigated. We have examined the structural impact of phosphorylated forms and C163S mutation in AGA. Molecular dynamics simulations (200 ns) exposed patterns of deviation, fluctuation, and change in compactness of Y178 phosphorylated AGA protein (Y178-p), T215 phosphorylated AGA protein (T215-p), T324 phosphorylated AGA protein (T324-p), C163S mutant AGA protein (C163S), and C163S mutation with Y178 phosphorylated AGA protein (C163S-Y178-p). Y178-p, T215-p, and C163S mutation demonstrated an increase in intramolecular hydrogen bonds, leading to greater compactness of the AGA forms. Principle component analysis (PCA) and Gibbs free energy of the phosphorylated/C163S mutation structures exhibit transition in motion/orientation than Wild type (WT). T215-p may be more dominant among these than the other studied phosphorylated forms. It might contribute to hydrolyzing L-asparagine functioning as an asparaginase, thereby regulating neurotransmitter activity. This study revealed structural insights into the phosphorylation of Y178, T215, and T324 in AGA protein. Additionally, it exposed the structural changes of the C163S mutation and C163S-Y178-p of AGA protein. This research will shed light on a better understanding of AGA's phosphorylated mechanism.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ambritha Balasundaram
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Sriroopreddy Ramireddy
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Udhaya Kumar S
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Thirumal Kumar D
- Faculty of Allied Health Sciences, Meenakshi Academy of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Iftikhar Aslam Tayubi
- Department of Computer Science, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hatem Zayed
- Department of Biomedical Sciences College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
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Opoku F, Govender P, Shonhai A, Simelane MB. Iso-mukaadial acetate and ursolic acid acetate bind to Plasmodium Falciparum heat shock protein 70: towards targeting parasite protein folding pathway. BMC Chem 2024; 18:55. [PMID: 38500145 PMCID: PMC10949600 DOI: 10.1186/s13065-024-01159-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024] Open
Abstract
Plasmodium falciparum is the most lethal malaria parasite. P. falciparum Hsp70 (PfHsp70) is an essential molecular chaperone (facilitates protein folding) and is deemed a prospective antimalarial drug target. The present study investigates the binding capabilities of select plant derivatives, iso-mukaadial acetate (IMA) and ursolic acid acetate (UAA), against P. falciparum using an in silico docking approach. The interaction between the ligands and PfHsp70 was evaluated using plasmon resonance (SPR) analysis. Molecular docking, binding free energy analysis and molecular dynamics simulations were conducted towards understanding the mechanisms by which the compounds bind to PfHsp70. The molecular docking results revealed ligand flexibilities, conformations and positions of key amino acid residues and protein-ligand interactions as crucial factors accounting for selective inhibition of Hsp70. The simulation results also suggest protein-ligand van der Waals forces as the driving force guiding the interaction of these compounds with PfHsp70. Of the two compounds, UAA and IMA bound to PfHsp70 within the micromolar range based on surface plasmon resonance (SPR) based binding assay. Our findings pave way for future rational design of new selective compounds targeting PfHsp70.
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Affiliation(s)
- Francis Opoku
- Department of Chemical Sciences (formerly Department of Applied Chemistry), University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Penny Govender
- Department of Chemical Sciences (formerly Department of Applied Chemistry), University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
| | - Addmore Shonhai
- Department of Biochemistry & Microbiology, University of Venda, Thohoyandou, South Africa
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Dhanabalan AK, Kumar P, Vasudevan S, Chworos A, Velmurugan D. Identification of a novel drug molecule for neurodegenerative disease from marine algae through in-silico analysis. J Biomol Struct Dyn 2024:1-10. [PMID: 38456260 DOI: 10.1080/07391102.2024.2322624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024]
Abstract
Cognitive functions are lost due to the rapid hydrolysis of acetylcholine including Acetylcholinesterase (AChE) and Butyrylcholinesterase (BChE). Marine algae-derived compounds were reported for their neuroprotective activities and hence they can be utilised for treating neurodegenerative ailments like Alzheimer's Disease and Parkinson's Disease which are due to the loss of cognitive functions. Major attention is currently paid to seaweeds due to their health benefits and high nutritional values. Sea weeds are of a rich sense of natural bioactive compounds which antioxidants, pharmaceutical compounds, flavonoids and alkaloids. They also contain a high amount of vitamins A, D, E, C and Ca, K, Mg and Fe. Regular consumption of a marine algae-based diet may boost immunities. In searching for natural cholinesterase inhibitors, the present study is focussed on some marine bioactive compounds reported from brown, red and green algae. Molecular docking studies have been carried out along with molecular dynamics simulations studies and binding energy calculations resulting in three best bioactive compounds when AChE is used as the target. The results are compared with cocrystal studies. Two best compounds, namely, Diphlorethohydroxycarmalol and Phlorofucofuroeckol from the brown seaweeds are identified as the potential lead compounds for neurodegenerative diseases, Alzheimer's and Parkinson's.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Praveen Kumar
- Research and Development Cell, AMET University, Kanathur, Tamil Nadu, India
| | - Saranya Vasudevan
- Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies Polish Academy of Sciences, Lodz, Poland
| | - Devadasan Velmurugan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
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Zhang T, Zhou C, Lv M, Yu J, Cheng S, Cui X, Wan X, Ahmad M, Xu B, Qin J, Meng X, Luo H. Trifluoromethyl quinoline derivative targets inhibiting HDAC1 for promoting the acetylation of histone in cervical cancer cells. Eur J Pharm Sci 2024; 194:106706. [PMID: 38244809 DOI: 10.1016/j.ejps.2024.106706] [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: 12/11/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/22/2024]
Abstract
Cervical cancer is the leading cause of death among gynecological malignant tumors, especially due to the poor prognosis of patients with advanced tumors due to recurrence, metastasis, and chemotherapy resistance. Therefore, exploring new antineoplastic drugs with high efficacy and low toxicity may bring new expectations in patients with cervical cancer. Natural products and their derivatives exert an antitumor activity. Therefore, in this work, combined with network pharmacology analysis and experimental validation, we investigated the anti-cervical cancer activity and molecular mechanism of a new trifluoromethyl quinoline (FKL) derivative in vivo and in vitro. FKL117 inhibited the proliferation of cervical cancer cells in a dose and time-dependent manner, induced apoptosis in HeLa cells, arrested the cell cycle in the G2/M phase, and regulated the expression of the apoptotic and cell cycle-related proteins Bcl-2, Bax, cyclin B1, and CDC2. We used online databases to obtain HDAC1 as one of the possible targets of FKL117 and the target binding and binding affinity were modeled by molecular docking. The results showed that FKL117 formed a hydrogen bond with HDAC1 and had good binding ability. We found that FKL117 targeted to inhibit the expression and function of HDAC1 and increased the acetylation of histone H3 and H4, which was also confirmed in vivo. The migration of HMGB1 from the nucleus to the cytoplasm further verified the above results. In conclusion, our study suggested that FKL117 might be used as a novel candidate for targeting the inhibition of HDAC1 against cervical cancer.
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Affiliation(s)
- Ting Zhang
- College of Clinical Medicine, Guizhou Medical University, Guiyang 550004, China; State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
| | - Changhua Zhou
- College of Clinical Medicine, Guizhou Medical University, Guiyang 550004, China; State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
| | - Mengfan Lv
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Jia Yu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Sha Cheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Xudong Cui
- Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Xinwei Wan
- Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Mashaal Ahmad
- Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Bixue Xu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Juan Qin
- College of Clinical Medicine, Guizhou Medical University, Guiyang 550004, China; The Maternal and Child Health Care Hospital of Guizhou Medical University, Guiyang, China.
| | - Xueling Meng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China.
| | - Heng Luo
- College of Clinical Medicine, Guizhou Medical University, Guiyang 550004, China; State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China.
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Krátký M, Nováčková K, Svrčková K, Švarcová M, Štěpánková Š. New 3-amino-2-thioxothiazolidin-4-one-based inhibitors of acetyl- and butyryl-cholinesterase: synthesis and activity. Future Med Chem 2024; 16:59-74. [PMID: 38047370 DOI: 10.4155/fmc-2023-0268] [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: 09/11/2023] [Accepted: 11/09/2023] [Indexed: 12/05/2023] Open
Abstract
Aim: 2-Thioxothiazolidin-4-one represents a versatile scaffold in drug development. The authors used it to prepare new potent acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitors that can be utilized, e.g., to treat Alzheimer's disease. Materials & methods: 3-Amino-2-thioxothiazolidin-4-one was modified at the amino group or active methylene, using substituted benzaldehydes. The derivatives were evaluated for inhibition of AChE and BChE (Ellman's method). Results & conclusion: The derivatives were obtained with yields of 52-94%. They showed dual inhibition with IC50 values from 13.15 μM; many compounds were superior to rivastigmine. The structure-activity relationship favors nitrobenzylidene and 3,5-dihalogenosalicylidene scaffolds. AChE was inhibited noncompetitively, whereas BChE was inhibited with a mixed type of inhibition. Molecular docking provided insights into molecular interactions. Each enzyme is inhibited by a different binding mode.
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Affiliation(s)
- Martin Krátký
- Department of Organic & Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 03, Hradec Králové, Czech Republic
| | - Karolína Nováčková
- Department of Organic & Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 03, Hradec Králové, Czech Republic
| | - Katarína Svrčková
- Department of Biological & Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Markéta Švarcová
- Department of Organic & Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 03, Hradec Králové, Czech Republic
- Department of Chemistry, Faculty of Science, J. E. Purkinje University, Pasteurova 3632/15, 400 96, Ústí nad Labem, Czech Republic
| | - Šárka Štěpánková
- Department of Biological & Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10, Pardubice, Czech Republic
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10
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Feyzi N, Ebadi A, Dastan D. Chimgin from Ferula haussknechtii as AChE inhibitor and confirmation of the absolute configuration. J Biomol Struct Dyn 2023:1-10. [PMID: 38109132 DOI: 10.1080/07391102.2023.2294176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/25/2023] [Indexed: 12/19/2023]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia worldwide and is classified as a neurodegenerative disorder. From a drug design perspective, natural products (NPs) are more drug-like and are highly compatible with biological systems compared to most synthetic libraries. NPs provide a more efficient and cost-effective approach to new drug discovery. However, the complexity of NPs makes their identification a challenging task. Chimgin, a bicyclic monoterpene with three chiral centers, exhibits a wide range of biological activity. Despite this, the exact structure of chimgin has remained unclear until now. In this study, we quantified the amount of chimgin in Ferula haussknechtii using analytical Reversed-phase high-pressure liquid chromatography equipped with photodiode array detector (RP-HPLC-PDA). Furthermore, we determined the absolute configuration of chimgin through electronic circular dichroism (ECD) spectroscopy and time-dependent density functional theory (TDDFT) calculations. Finally, we evaluated its inhibitory effect on AChE through in vitro and in silico studies. The extraction process yielded an output of 2.82 ± 0.10% with an exact amount of 0.62 ± 0.04 mg of chimgin per 100 g of plant. Based on the results of ECD and TDDFT calculation, the absolute configuration of chimgin was determined to be 1S, 2S, 4S. Chimgin exhibited an inhibitory effect on AChE with an IC50 of 37.43 µM and its mechanism of action was found to be competitive. HighlightsChimgin was isolated from the roots of Ferula haussknechtii.The amount of chimgin in the plant was determined by RP-HPLC-PDA.Its absolute configuration of chimgin was determined using ECD.In vitro acetylcholinesterase activity of the chimgin was evaluated.The docking and molecular dynamic simulation of chimgin was done.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neda Feyzi
- Department of Pharmacognosy, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ahmad Ebadi
- Department of Medicinal Chemistry, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Dara Dastan
- Department of Pharmacognosy, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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Huang L, Yu Q, Peng H, Zhen Z. Network pharmacology and molecular docking technology for exploring the effect and mechanism of Radix Bupleuri and Radix Paeoniae Alba herb-pair on anti-hepatitis: A review. Medicine (Baltimore) 2023; 102:e35443. [PMID: 38050220 PMCID: PMC10695497 DOI: 10.1097/md.0000000000035443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 09/08/2023] [Indexed: 12/06/2023] Open
Abstract
The Radix Bupleuri and Radix Paeoniae Alba herb-pair (RRH) are the most classic compatible drug pair for the treatment of hepatitis. However, the underlying mechanism remains unclear. Therefore, network pharmacology and molecular docking were conducted to investigate the prospective therapeutic constituents, targets, and pharmacological mechanisms of RRH in the treatment of hepatitis. The active components of RRH from the TCMSP database and disease-related targets from the OMIM, PharmGkb, GeneCards, TTD, and DrugBank databases were identified. The "drug-target-disease" network diagram and protein-protein interaction (PPI) network were constructed using Cytoscape (v3.8.0) and Online STRING 11.0. GO and KEGG pathway enrichment analyses were performed using R version 4.1.2, and molecular docking was performed to verify the results. We placed 176 overlapping cross genes into Online STRING 11.0 and obtained 14 core targets. A "Component-Target-GO-KEGG" network diagram was constructed, which was composed of 7 components, 14 targets, 10 biological processes, and 10 signal pathways. A total of 2413 GO biological processes and 174 KEGG pathways were explored for hepatitis treatment. Quercetin, kaempferol, isorhamnetin, and beta-sitosterol, which are the main bioactive components, were employed to bind the disease's hub targets, ensuring fulfillment of spatial and energy matching. The anti-hepatitis mechanism of RRH may be associated with several targets including RELA, AKT1, JUN, MAPK1, TP53, CCND1, MYC, NFKBIA, CDKN1A, and their respective signaling pathways. The main bioactive components in RRH, including quercetin, kaempferol, isorhamnetin, and beta-sitosterol, were used to bind the hub targets of the disease, which may provide insights into drug development for hepatitis.
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Affiliation(s)
- Long Huang
- Department of No. 1 Surgery, The first hospital affiliated to Anhui University of Traditional Chinese Medicine, Hefei, Anhui Province, China
| | - Qingsheng Yu
- Department of No. 1 Surgery, The first hospital affiliated to Anhui University of Traditional Chinese Medicine, Hefei, Anhui Province, China
| | - Hui Peng
- Department of No. 1 Surgery, The first hospital affiliated to Anhui University of Traditional Chinese Medicine, Hefei, Anhui Province, China
| | - Zhou Zhen
- Department of Surgery, The Second Hospital Affiliated to Anhui University of Traditional Chinese Medicine, Hefei, Anhui Province, China
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12
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Oliveira LPS, Lima LR, Silva LB, Cruz JN, Ramos RS, Lima LS, Cardoso FMN, Silva AV, Rodrigues DP, Rodrigues GS, Proietti-Junior AA, dos Santos GB, Campos JM, Santos CBR. Hierarchical Virtual Screening of Potential New Antibiotics from Polyoxygenated Dibenzofurans against Staphylococcus aureus Strains. Pharmaceuticals (Basel) 2023; 16:1430. [PMID: 37895901 PMCID: PMC10610096 DOI: 10.3390/ph16101430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/25/2023] [Accepted: 10/01/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a microorganism with high morbidity and mortality due to antibiotic-resistant strains, making the search for new therapeutic options urgent. In this context, computational drug design can facilitate the drug discovery process, optimizing time and resources. In this work, computational methods involving ligand- and structure-based virtual screening were employed to identify potential antibacterial agents against the S. aureus MRSA and VRSA strains. To achieve this goal, tetrahydroxybenzofuran, a promising antibacterial agent according to in vitro tests described in the literature, was adopted as the pivotal molecule and derivative molecules were considered to generate a pharmacophore model, which was used to perform virtual screening on the Pharmit platform. Through this result, twenty-four molecules were selected from the MolPort® database. Using the Tanimoto Index on the BindingDB web server, it was possible to select eighteen molecules with greater structural similarity in relation to commercial antibiotics (methicillin and oxacillin). Predictions of toxicological and pharmacokinetic properties (ADME/Tox) using the eighteen most similar molecules, showed that only three exhibited desired properties (LB255, LB320 and LB415). In the molecular docking study, the promising molecules LB255, LB320 and LB415 showed significant values in both molecular targets. LB320 presented better binding affinity to MRSA (-8.18 kcal/mol) and VRSA (-8.01 kcal/mol) targets. Through PASS web server, the three molecules, specially LB320, showed potential for antibacterial activity. Synthetic accessibility (SA) analysis performed on AMBIT and SwissADME web servers showed that LB255 and LB415 can be considered difficult to synthesize and LB320 is considered easy. In conclusion, the results suggest that these ligands, particularly LB320, may bind strongly to the studied targets and may have appropriate ADME/Tox properties in experimental studies.
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Affiliation(s)
- Lana P. S. Oliveira
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Lúcio R. Lima
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Network in Pharmaceutical Innovation, Federal University of Amapá, Macapá 68902-280, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal Univesity of Pará, Belém 66075-110, Brazil
| | - Luciane B. Silva
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal Univesity of Pará, Belém 66075-110, Brazil
| | - Jorddy N. Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Ryan S. Ramos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Luciana S. Lima
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Francy M. N. Cardoso
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Aderaldo V. Silva
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Dália P. Rodrigues
- Laboratory of Bacterial Enteric Pathogens, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21045-900, Brazil;
| | - Gabriela S. Rodrigues
- Graduate Program in Health Sciences, Institute of Collective Health, Federal University of Western Pará, Santarém 68270-000, Brazil; (G.S.R.); (G.B.d.S.)
| | - Aldo A. Proietti-Junior
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Gabriela B. dos Santos
- Graduate Program in Health Sciences, Institute of Collective Health, Federal University of Western Pará, Santarém 68270-000, Brazil; (G.S.R.); (G.B.d.S.)
| | - Joaquín M. Campos
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Institute of Biosanitary Research ibs. GRANADA, University of Granada, 18071 Granada, Spain;
| | - Cleydson B. R. Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Network in Pharmaceutical Innovation, Federal University of Amapá, Macapá 68902-280, Brazil
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13
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de Oliveira LHD, Cruz JN, Dos Santos CBR, de Melo EB. Multivariate QSAR, similarity search and ADMET studies based in a set of methylamine derivatives described as dopamine transporter inhibitors. Mol Divers 2023:10.1007/s11030-023-10724-5. [PMID: 37670118 DOI: 10.1007/s11030-023-10724-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/27/2023] [Indexed: 09/07/2023]
Abstract
The dopamine transporter (DAT), responsible for the regulation of dopaminergic neurotransmission, is implicated in the etiology of several neuropsychiatric disorders which, in turn, have contributed to high rates of disability and numerous deaths in recent years, significantly impacting the global health system. Although the research for new drugs for the treatment of neuropsychiatric disorders has evolved in recent years, the availability of DAT-selective drugs that do not generate the same psychostimulant effects observed in drugs of abuse remains scarce. Therefore, we performed a QSAR study based on a dataset of 36 methylamine derivatives described as DAT inhibitors. The model was obtained based only in descriptors derived from 2D structures, and it was validated and generated satisfactory results considering the metrics used for internal and external validation. Subsequently, a virtual screening step also based on 2D similarity was performed, where it was possible to identify a total of 1157 compounds. After a series of reductions of the set using toxicity filters, applicability domain evaluation, and pharmacokinetic properties in silico assessment, seven hit compounds were selected as the most promising to be used, in future studies, as new scaffolds for the development of new DAT inhibitors.
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Affiliation(s)
- Luiz Henrique Dias de Oliveira
- Theorical Medicinal and Environmental Chemistry Laboratory (LQMAT), Department of Pharmacy, Western Paraná State University (UNIOESTE), 2069 Universitária St., Cascavel, PR, 85819-110, Brazil
| | - Jorddy Neves Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, AP, 68902-280, Brazil
| | - Cleydson Breno Rodrigues Dos Santos
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, AP, 68902-280, Brazil
| | - Eduardo Borges de Melo
- Theorical Medicinal and Environmental Chemistry Laboratory (LQMAT), Department of Pharmacy, Western Paraná State University (UNIOESTE), 2069 Universitária St., Cascavel, PR, 85819-110, Brazil.
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14
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Hasan Mujahid M, Upadhyay TK, Upadhye V, Sharangi AB, Saeed M. Phytocompound identification of aqueous Zingiber officinale rhizome (ZOME) extract reveals antiproliferative and reactive oxygen species mediated apoptotic induction within cervical cancer cells: an in vitro and in silico approach. J Biomol Struct Dyn 2023:1-28. [PMID: 37639378 DOI: 10.1080/07391102.2023.2247089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/07/2023] [Indexed: 08/31/2023]
Abstract
The prevalence of cervical cancer in women is in the fourth position among various other types of cancer globally. Many established therapies, including surgery, chemotherapy, and immunomodulation, are present, but high levels of side effects cause mortality and morbidity among the patients. Zingiber officinale rhizome (ZOME) has been potentially used to cure a variety of ailments and diseases. The aqueous ZOME extract also contains ample phytochemical constituents having anticancer effects on different cancers. The cell viability of HeLa cells was evaluated using MTT assay with IC50 at 97 µg/mL. Furthermore, a significant level of ROS generation causes the apoptosis of the cells. Nuclear staining dye DAPI and Hoechst 33342 showed DNA's fragmented and condensed form. Propidium Iodide staining showed necrotic or late-apoptotic cells. While acidic organelle dye LysoTracker and MitoTracker dye along with dual staining showed significant results. In silico studies were carried out using identified phytochemicals from GC-MS analysis with pharmacokinetics properties (ADMET), and targeted toward receptor proteins for molecular docking. Ligands with high docked scores were subjected to molecular dynamics simulations at 310 K for 100 ns. In vitro and in silico investigations in our studies showed that aqueous ZOME extract can be used as an efficient therapy against cervical cancer treatment as it showed significant cytotoxic and antiproliferative effects toward the HeLa cell line.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Hasan Mujahid
- Department of Biotechnology, Parul Institute of Applied Sciences and Research and Development Cell, Parul University, Vadodara, Gujarat, India
| | - Tarun Kumar Upadhyay
- Department of Biotechnology, Parul Institute of Applied Sciences and Research and Development Cell, Parul University, Vadodara, Gujarat, India
| | - Vijay Upadhye
- Department of Biotechnology, Parul Institute of Applied Sciences and Research and Development Cell, Parul University, Vadodara, Gujarat, India
| | - Amit Baran Sharangi
- Department of Plantation, Spices, Medicinal & Aromatic Crops, BCKV-Agricultural University, Mohanpur, West Bengal, India
| | - Mohd Saeed
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
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15
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Kisiel-Nawrot E, Pindjakova D, Latocha M, Bak A, Kozik V, Suwinska K, Cizek A, Jampilek J, Zięba A. Towards Anticancer and Antibacterial Agents: Design and Synthesis of 1,2,3-Triazol-quinobenzothiazine Derivatives. Int J Mol Sci 2023; 24:13250. [PMID: 37686059 PMCID: PMC10487436 DOI: 10.3390/ijms241713250] [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: 07/25/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
In this paper, we describe a new method for synthesizing hybrid combinations of 1,2,3-triazoles with a tetracyclic quinobenzothiazinium system. The developed approach allowed for the production of a series of new azaphenothiazine derivatives with the 1,2,3-triazole system in different positions of the benzene ring. In practice, the methodology consists of the reaction of triazole aniline derivatives with thioquinanthrenediinium bis-chloride. The structure of the products was determined by 1H-NMR, 13C-NMR spectroscopy, and HR-MS spectrometry, respectively. Moreover, the spatial structure of the molecule and the arrangement of molecules in the crystal (unit cell) were determined by X-ray crystallography. The anticancer activity profiles of the synthesized compounds were tested in vitro against human cancer cells of the A549, SNB-19, and T47D lines and the normal NHDF cell line. Additional tests of antibacterial activity against methicillin-sensitive and methicillin-resistant staphylococci, vancomycin-sensitive and vancomycin-resistant enterococci, and two mycobacterial strains were also performed. In fact, the dependence of anticancer and antibacterial activity on the substituent type and its position in the quinobenzothiazinium system was observed. Furthermore, the distance-guided property evaluation was performed using principal component analysis (PCA) and hierarchical clustering analysis (HCA) on the pool of the calculated descriptors. Finally, the theoretically approximated partition coefficients (clogP) were (inter-)correlated with each other and cross-compared with the empirically specified logPTLC parameters.
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Affiliation(s)
- Ewa Kisiel-Nawrot
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Jagiellońska 4, 41-200 Sosnowiec, Poland
| | - Dominika Pindjakova
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Malgorzata Latocha
- Department of Cell Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Jedności 9, 41-200 Sosnowiec, Poland
| | - Andrzej Bak
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Violetta Kozik
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Kinga Suwinska
- Faculty of Mathematics and Natural Sciences, Cardinal Stefan Wyszyński University, K. Woycickiego 1/3, 01-938 Warszawa, Poland
| | - Alois Cizek
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic
| | - Josef Jampilek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10 Bratislava, Slovakia
| | - Andrzej Zięba
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Jagiellońska 4, 41-200 Sosnowiec, Poland
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16
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Naser SS, Singh D, Preetam S, Kishore S, Kumar L, Nandi A, Simnani FZ, Choudhury A, Sinha A, Mishra YK, Suar M, Panda PK, Malik S, Verma SK. Posterity of nanoscience as lipid nanosystems for Alzheimer's disease regression. Mater Today Bio 2023; 21:100701. [PMID: 37415846 PMCID: PMC10320624 DOI: 10.1016/j.mtbio.2023.100701] [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: 03/18/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023] Open
Abstract
Alzheimer's disease (AD) is a type of dementia that affects a vast number of people around the world, causing a great deal of misery and death. Evidence reveals a relationship between the presence of soluble Aβ peptide aggregates and the severity of dementia in Alzheimer's patients. The BBB (Blood Brain Barrier) is a key problem in Alzheimer's disease because it prevents therapeutics from reaching the desired places. To address the issue, lipid nanosystems have been employed to deliver therapeutic chemicals for anti-AD therapy in a precise and targeted manner. The applicability and clinical significance of lipid nanosystems to deliver therapeutic chemicals (Galantamine, Nicotinamide, Quercetin, Resveratrol, Curcumin, HUPA, Rapamycin, and Ibuprofen) for anti-AD therapy will be discussed in this review. Furthermore, the clinical implications of the aforementioned therapeutic compounds for anti-AD treatment have been examined. Thus, this review will pave the way for researchers to fashion therodiagnostics approaches based on nanomedicine to overcome the problems of delivering therapeutic molecules across the blood brain barrier (BBB).
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Affiliation(s)
- Shaikh Sheeran Naser
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Dibyangshee Singh
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Subham Preetam
- Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, 59053 Ulrika, Sweden
| | - Shristi Kishore
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand 834001, India
| | - Lamha Kumar
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Aditya Nandi
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Faizan Zarreen Simnani
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Anmol Choudhury
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Adrija Sinha
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark, Alison 2, 6400 Sønderborg, Denmark
| | - Mrutyunjay Suar
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Pritam Kumar Panda
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala, Sweden
| | - Sumira Malik
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Suresh K. Verma
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
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17
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Firdoos S, Dai R, Tahir RA, Khan ZY, Li H, Zhang J, Ni J, Quan Z, Qing H. In silico identification of novel stilbenes analogs for potential multi-targeted drugs against Alzheimer's disease. J Mol Model 2023; 29:209. [PMID: 37314512 DOI: 10.1007/s00894-023-05609-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/27/2023] [Indexed: 06/15/2023]
Abstract
CONTEXT Alzheimer's disease (AD) is a chronic progressive neurodegenerative syndrome, which adversely disturbs cognitive abilities as well as intellectual processes and frequently occurs in the elderly. Inhibition of cholinesterase is a valuable approach to upsurge acetylcholine concentrations in the brain and persuades the development of multi-targeted ligands against cholinesterases. METHODS The current study aims to determine the binding potential accompanied by antioxidant and anti-inflammatory activities of stilbenes-designed analogs against both cholinesterases (Acetylcholinesterase and butyrylcholinesterase) and neurotrophin targets for effective AD therapeutics. Docking results have shown that the WS6 compound exhibited the least binding energy - 10.1 kcal/mol with Acetylcholinesterase and - 7.8 kcal/mol with butyrylcholinesterase. The WS6 also showed a better binding potential with neurotrophin targets that are Brain-derived Neurotrophic Factor, Neurotrophin 4, Nerve Growth Factor, and Neurotrophin 3. The tested compounds particularly WS6 revealed significant antioxidant and anti-inflammatory activities through the comparative docking analysis with Fluorouracil and Melatonin as control drugs of antioxidants while Celecoxib and Anakinra as anti-inflammatory. The bioinformatics approaches including molecular docking calculations followed by the pharmacokinetics analysis and molecular dynamic simulations were accomplished to explore the capabilities of designed stilbenes as effective and potential leads. Root mean square deviation, root mean square fluctuations, and MM-GBSA calculations were performed through molecular dynamic simulations to extract the structural and residual variations and binding free energies through the 50-ns time scale.
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Affiliation(s)
- Sundas Firdoos
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, Beijing Institute of Technology (BIT), Beijing, 100081, People's Republic of China.
| | - Rongji Dai
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, Beijing Institute of Technology (BIT), Beijing, 100081, People's Republic of China.
| | - Rana Adnan Tahir
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Muzaffarabad, Pakistan
| | - Zahid Younas Khan
- Department of Computer Science and IT, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Hui Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Jun Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Zhenzhen Quan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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18
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Inhibition Kinetics and Theoretical Studies on Zanthoxylum chalybeum Engl. Dual Inhibitors of α-Glucosidase and α-Amylase. J Xenobiot 2023; 13:102-120. [PMID: 36976158 PMCID: PMC10059848 DOI: 10.3390/jox13010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Compounds from Zanthoxylum chalybeum Engl. were previously reported for inhibitory activities of amylase and glucosidase enzymatic action on starch as a preliminary study toward the establishment of a management strategy against postprandial hyperglycemia, however, the inhibitory kinetics and molecular interaction of these compounds were never established. A study was thus designed to establish the inhibitory kinetics and in silico molecular interaction of α-glucosidase and α-amylase with Z. chalybeum metabolites based on Lineweaver–Burk/Dixon plot analyses and using Molecular Operating Environment (MOE) software, respectively. Skimmianine (5), Norchelerythrine (6), 6-Acetonyldihydrochelerythrine (7), and 6-Hydroxy-N-methyldecarine (8) alkaloids showed mixed inhibition against both α-glucosidase and α-amylase with comparable Ki to the reference acarbose (p > 0.05) on amylase but significantly higher activity than acarbose on α-glucosidase. One phenolic 2,3-Epoxy-6,7-methylenedioxyconiferol (10) showed a competitive mode of inhibition both on amylase and glucosidase which were comparable (p > 0.05) to the activity of acarbose. The other compounds analyzed and displayed varied modes of inhibition between noncompetitive and uncompetitive with moderate inhibition constants included chaylbemide A (1), chalybeate B (2) and chalybemide C (3), fagaramide (4), ailanthoidol (9), and sesame (11). The important residues of the proteins α-glucosidase and α-amylase were found to have exceptional binding affinities and significant interactions through molecular docking studies. The binding affinities were observed in the range of −9.4 to −13.8 and −8.0 to −12.6 relative to the acarbose affinities at −17.6 and −20.5 kcal/mol on α-amylase and α-glucosidase residue, respectively. H-bonding, π-H, and ionic interactions were noted on variable amino acid residues on both enzymes. The study thus provides the basic information validating the application of extracts of Z. chalybeum in the management of postprandial hyperglycemia. Additionally, the molecular binding mechanism discovered in this study could be useful for optimizing and designing new molecular analogs as pharmacological agents against diabetes.
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