101
|
Rodrigues ET, Peretti P, Bezerra RM, Biancardi MF, Sousa FFO, Mendes EP, Dutra JBR, Silveira CCR, Castro CH, Cruz JN, Santos CBR, Santos FCA, Pinheiro MT. Pharmacological Characteristics of the Hydroethanolic Extract of Acmella oleracea (L) R. K. Jansen Flowers: ADME/Tox In Silico and In Vivo Antihypertensive and Chronic Toxicity Evaluation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2023; 2023:1278720. [PMID: 37159592 PMCID: PMC10163967 DOI: 10.1155/2023/1278720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
Acmella oleracea (L.) R. K. Jansen, popularly known as jambu in Northern Brazil, is widely used in folk medicine and local cuisine. Its consumption in different ways reinforces the need for safety assessments. In this study, the major compounds found in the hydroethanolic extract of A. oleracea flowers (EHFAO) were characterized by ultra-performance liquid mass spectrometry (UHPLC-ESI-QTOF-MS/MS). The effects of oral administration of 100/mg/kg of EHFAO extract over 60 days in male spontaneously hypertensive (SHR) and Wistar (WR) rats and the in silico ADME/Tox predictions, lipophilicity, and water solubility were accomplished for the compounds identified. Spilanthol was detected as the foremost major compound at a concentration of 97.7%, followed by 1.53% scopoletin and 0.77% d-limonene. The treatment with EHFAO did not alter the animals´ weight over the studied period. Moderate alterations were observed solely in the hepatic enzymes AST (WR = 97 UI/L and SHR = 150 UI/L ∗ p < 0.05) and ALT (WR = 55 UI/L and SHR = 95 UI/L ∗ p < 0.05), while no relevant histopathological alterations were found. The in-silico study confirmed the in vivo findings, as the identified compounds were considered highly bioactive orally, due to their drug similarity profiles, adequate lipid solubility, bioavailability, and pharmacokinetics. Therefore, the chronic treatment with EHFAO was found safe at the concentration of 100/mg/kg, with no interference in the blood pressure levels neither appreciable toxic effects.
Collapse
Affiliation(s)
- Emanuelle T. Rodrigues
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Paulo Peretti
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Roberto M. Bezerra
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Laboratory of Atomic Absorption and Bioprospecting, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Manoel F. Biancardi
- Department of Histology, Embryology and Cell Biology, Laboratory of Microscopy Applied to Reproduction, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Francisco F. O. Sousa
- Laboratory of Quality Control and Bromatology, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Elizabeth P. Mendes
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - João B. R. Dutra
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
- Integrated Laboratory of Cardiovascular and Neurological Pathophysiology, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Carla C. R. Silveira
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
- Integrated Laboratory of Cardiovascular and Neurological Pathophysiology, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Carlos H. Castro
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
- Integrated Laboratory of Cardiovascular and Neurological Pathophysiology, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Jorddy N. Cruz
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Cleydson B. R. Santos
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Fernanda C. A. Santos
- Laboratory of Atomic Absorption and Bioprospecting, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Mayara T. Pinheiro
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| |
Collapse
|
102
|
Shehta W, Agili F, Farag B, Youssif S, Almehmadi SJ, Elfeky SM, El-Kalyoubi S. Synthesis and in vitro study of pyrimidine-phthalimide hybrids as VEGFR2 inhibitors with antiproliferative activity. Future Med Chem 2023; 15:661-677. [PMID: 37125606 DOI: 10.4155/fmc-2023-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Aim: Thalidomide, a once notorious sedative, is now clinically used as an antitumor agent. We aimed to use it as a lead compound for designing pyrimidine-phthalimide hybrids. Materials & methods: Nucleophilic substitution reaction of thalidomide analog 4 with primary and/or secondary aliphatic amines afforded pyrimidine-phthalimide hybrids 5a-g, 6 and 7a-d. Results & conclusion: Compound 7c showed high antiproliferative activity against four cell lines: HepG-2 (IC50: 7.86 ± 0.5 μM), MCF-7 (IC50: 2.77 ± 0.1 μM), HCT-116 (IC50: 5.73 ± 0.4 μM) and PC-3 (IC50: 8.32 ± 0.5 μM), with selective cytotoxicity for WI-38 (IC50: 43.2 ± 2.56 μM). 7c arrested MCF-7 cells at S phase of the cell cycle and increased the total apoptotic cells by 50-fold. 7c inhibited VEGFR2 in vitro (IC50: 0.130 ± 0.02 μM). 7c was capable of binding at the VEGFR2 binding site, forming hydrogen bond interactions with Asp1046 and Glu885 in a similar way to sorafenib.
Collapse
Affiliation(s)
- Wael Shehta
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Fatimah Agili
- Department of Chemistry, Faculty of Science (Girls Section), Jazan University, Jazan, 45142, Saudi Arabia
| | - Basant Farag
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Shaker Youssif
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Samar J Almehmadi
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Mecca, 24451, Saudi Arabia
| | - Sherin M Elfeky
- Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 355516, Egypt
| | - Samar El-Kalyoubi
- Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Port Said University, Port Said, 42511, Egypt
| |
Collapse
|
103
|
Hu E, Li Z, Li T, Yang X, Ding R, Jiang H, Su H, Cheng M, Yu Z, Li H, Tang T, Wang Y. A novel microbial and hepatic biotransformation-integrated network pharmacology strategy explores the therapeutic mechanisms of bioactive herbal products in neurological diseases: the effects of Astragaloside IV on intracerebral hemorrhage as an example. Chin Med 2023; 18:40. [PMID: 37069580 PMCID: PMC10108474 DOI: 10.1186/s13020-023-00745-5] [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: 12/16/2022] [Accepted: 04/02/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The oral bioavailability and blood-brain barrier permeability of many herbal products are too low to explain the significant efficacy fully. Gut microbiota and liver can metabolize herbal ingredients to more absorbable forms. The current study aims to evaluate the ability of a novel biotransformation-integrated network pharmacology strategy to discover the therapeutic mechanisms of low-bioavailability herbal products in neurological diseases. METHODS A study on the mechanisms of Astragaloside IV (ASIV) in treating intracerebral hemorrhage (ICH) was selected as an example. Firstly, the absorbed ASIV metabolites were collected by a literature search. Next, the ADMET properties and the ICH-associated targets of ASIV and its metabolites were compared. Finally, the biotransformation-increased targets and biological processes were screened out and verified by molecular docking, molecular dynamics simulation, and cell and animal experiments. RESULTS The metabolites (3-epi-cycloastragenol and cycloastragenol) showed higher bioavailability and blood-brain barrier permeability than ASIV. Biotransformation added the targets ASIV in ICH, including PTK2, CDC42, CSF1R, and TNF. The increased targets were primarily enriched in microglia and involved in cell migration, proliferation, and inflammation. The computer simulations revealed that 3-epi-cycloastragenol bound CSF1R and cycloastragenol bound PTK2 and CDC42 stably. The In vivo and in vitro studies confirmed that the ASIV-derived metabolites suppressed CDC42 and CSF1R expression and inhibited microglia migration, proliferation, and TNF-α secretion. CONCLUSION ASIV inhibits post-ICH microglia/macrophage proliferation and migration, probably through its transformed products to bind CDC42, PTK2, and CSF1R. The integrated strategy can be used to discover novel mechanisms of herbal products or traditional Chinses medicine in treating diseases.
Collapse
Affiliation(s)
- En Hu
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Zhilin Li
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Teng Li
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Xueping Yang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Ruoqi Ding
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Haoying Jiang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Hong Su
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Menghan Cheng
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Zhe Yu
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Haigang Li
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, Hunan, People's Republic of China, 410219
| | - Tao Tang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008.
| | - Yang Wang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008.
| |
Collapse
|
104
|
Flores RMA, Pantaleão SQ, Araujo SC, Malpartida HMG, Honorio KM. Structural analysis of factors related to FAM3C/ILEI dimerization and identification of inhibitor candidates targeting cancer treatment. Comput Biol Chem 2023; 104:107869. [PMID: 37068312 DOI: 10.1016/j.compbiolchem.2023.107869] [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: 12/22/2022] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023]
Abstract
FAM3 is a superfamily of four cytokines that maintain a single globular structure β -β -α of three classes: FAM3A, B, C and D. FAM3C was the first member of this family related to cancer and is functionally characterized as an essential factor for the epithelial-mesenchymal transition (EMT), leading to late delays in tumor progression. Due to its crucial role in EMT and metastasis, FAM3C has been termed an interleukin-like EMT (ILEI) inducer. There are several studies on the part of FAM3C in the progression of cancer and other diseases. However, little is known about its cellular receptors and possible inhibitors. In this study, based on in silico approaches, we performed structural analyses of factors related to FAM3C/ILEI dimerization. We also identified four possible inhibitor candidates, expected to be exciting prototypes and could be submitted to future biological tests targeting cancer treatment.
Collapse
Affiliation(s)
| | - Simone Queiroz Pantaleão
- Center for Mathematics, Computing, and Cognition, Federal University of ABC, 09210-170 Santo André, SP, Brazil
| | - Sheila Cruz Araujo
- Center for Sciences Natural and Human, Federal University of ABC, 09210-170 Santo André, SP, Brazil
| | | | - Kathia Maria Honorio
- Center for Sciences Natural and Human, Federal University of ABC, 09210-170 Santo André, SP, Brazil; School of Arts, Sciences and Humanities, University of São Paulo, 03828-0000 São Paulo, SP, Brazil.
| |
Collapse
|
105
|
Nisa N, Rasmita B, Arati C, Uditraj C, Siddhartha R, Dinata R, Bhanushree B, Bidanchi RM, Manikandan B, Laskar SA, Abinash G, Pori B, Roy VK, Gurusubramanian G. Repurposing of phyto-ligand molecules from the honey bee products for Alzheimer's disease as novel inhibitors of BACE-1: small molecule bioinformatics strategies as amyloid-based therapy. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:51143-51169. [PMID: 36808033 DOI: 10.1007/s11356-023-25943-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/10/2023] [Indexed: 04/16/2023]
Abstract
Alzheimer's disease (AD) is one of the neurodegenerative diseases, manifesting dementia, spatial disorientation, language, cognitive, and functional impairment, mainly affects the elderly population with a growing concern about the financial burden on society. Repurposing can improve the traditional progress of drug design applications and could speed up the identification of innovative remedies for AD. The pursuit of potent anti-BACE-1 drugs for AD treatment has become a pot boiler topic in the recent past and to instigate the design of novel improved inhibitors from the bee products. Drug-likeness characteristics (ADMET: absorption, distribution, metabolism, excretion, and toxicity), docking (AutoDock Vina), simulation (GROMACS), and free energy interaction (MM-PBSA, molecular mechanics Poisson-Boltzmann surface area) analyses were performed to identify the lead candidates from the bee products (500 bioactives from the honey, royal jelly, propolis, bee bread, bee wax, and bee venom) for Alzheimer's disease as novel inhibitors of BACE-1 (beta-site amyloid precursor protein cleaving enzyme (1) receptor using appropriate bioinformatics tools. Forty-four bioactive lead compounds were screened from the bee products through high throughput virtual screening on the basis of their pharmacokinetic and pharmacodynamics characteristics, showing favorable intestinal and oral absorption, bioavailability, blood brain barrier penetration, less skin permeability, and no inhibition of cytochrome P450 inhibitors. The docking score of the forty-four ligand molecules was found to be between -4 and -10.3 kcal/mol, respectively, exhibiting strong binding affinity to BACE1 receptor. The highest binding affinity was observed in the rutin (-10.3 kcal/mol), 3,4-dicaffeoylquinic acid (-9.5 kcal/mol), nemorosone (-9.5 kcal/mol), and luteolin (-8.9 kcal/mol). Furthermore, these compounds demonstrated high total binding energy -73.20 to -105.85 kJ/mol), and low root mean square deviation (0.194-0.202 nm), root mean square fluctuation (0.0985-0.1136 nm), radius of gyration (2.12 nm), number of H-bonds (0.778-5.436), and eigenvector values (2.39-3.54 nm2) in the molecular dynamic simulation, signifying restricted motion of Cα atoms, proper folding and flexibility, and highly stable with compact of the BACE1 receptor with the ligands. Docking and simulation studies concluded that rutin, 3,4-dicaffeoylquinic acid, nemorosone, and luteolin are plausibly used as novel inhibitors of BACE1 to combat AD, but further in-depth experimental investigations are warranted to prove these in silico findings.
Collapse
Affiliation(s)
- Nisekhoto Nisa
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Borgohain Rasmita
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Chettri Arati
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Chetia Uditraj
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | - Roy Dinata
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Baishya Bhanushree
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | - Bose Manikandan
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Saeed Ahmed Laskar
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Giri Abinash
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Buragohain Pori
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Vikas Kumar Roy
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | |
Collapse
|
106
|
Malik MS, Faazil S, Alsharif MA, Sajid Jamal QM, Al-Fahemi JH, Banerjee A, Chattopadhyay A, Pal SK, Kamal A, Ahmed SA. Antibacterial Properties and Computational Insights of Potent Novel Linezolid-Based Oxazolidinones. Pharmaceuticals (Basel) 2023; 16:ph16040516. [PMID: 37111273 PMCID: PMC10143092 DOI: 10.3390/ph16040516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The mounting evidence of bacterial resistance against commonly prescribed antibiotics warrants the development of new antibacterial drugs on an urgent basis. Linezolid, an oxazolidinone antibiotic, is a lead molecule in designing new oxazolidinones as antibacterial agents. In this study, we report the antibacterial potential of the novel oxazolidinone-sulphonamide/amide conjugates that were recently reported by our research group. The antibacterial assays showed that, from the series, oxazolidinones 2 and 3a exhibited excellent potency (MIC of 1.17 μg/mL) against B. subtilis and P. aeruginosa strains, along with good antibiofilm activity. Docking studies revealed higher binding affinities of oxazolidinones 2 and 3a compared to linezolid, which were further validated by molecular dynamics simulations. In addition to this, other computational studies, one-descriptor (log P) analysis, ADME-T and drug likeness studies demonstrated the potential of these novel linezolid-based oxazolidinones to be taken forward for further studies.
Collapse
|
107
|
Zargar S, Wani TA. Food Toxicity of Mycotoxin Citrinin and Molecular Mechanisms of Its Potential Toxicity Effects through the Implicated Targets Predicted by Computer-Aided Multidimensional Data Analysis. Life (Basel) 2023; 13:life13040880. [PMID: 37109409 PMCID: PMC10142723 DOI: 10.3390/life13040880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
The mycotoxin citrinin, which can contaminate food, is a major global concern. Citrinin is regarded as an inevitable pollutant in foods and feed since fungi are widely present in the environment. To identify contentious toxicity and lessen its severity by understanding the targets of citrinin in the human body and the impacted biosynthetic pathways, we analyzed the production of citrinin from Aspergillus flavus and Penicillium notatum and used a thorough bioinformatics analysis to characterize the toxicity and predict genes and protein targets for it. The predicted median fatal dosage (LD50) for citrinin was 105 mg/kg weight, and it belonged to toxicity class 3 (toxic if swallowed). Citrinin was found to be well absorbed by human intestinal epithelium and was a Pgp nonsubstrate (permeability glycoprotein), which means that once it is absorbed, it cannot be pumped out, hence leading to bioconcentration or biomagnification in the human body. The main targets of toxicity were casp3, TNF, IL10, IL1B, BAG3, CCNB1, CCNE1, and CDC25A, and the biological pathways implicated were signal transduction involved in DNA damage checkpoints, cellular and chemical responses to oxidative stress, DNA damage response signal transduction by P53, stress-activated protein kinase signaling cascade, netrin–UNC5B signaling, PTEN gene regulation, and immune response. Citrinin was linked to neutrophilia, squamous cell carcinoma, Fanconi anemia, leukemia, hepatoblastoma, and fatty liver diseases. The transcription factors E2F1, HSF1, SIRT1, RELA, NFKB, JUN, and MYC were found to be responsible. When data mining was performed on citrinin targets, the top five functional descriptions were a cell’s response to an organic cyclic compound, the netrin–UNC5B signaling pathway, lipids and atherosclerosis, thyroid cancer, and controlling the transcription of the PTEN gene.
Collapse
|
108
|
Morita R, Shigeta Y, Harada R. Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score. J Comput Aided Mol Des 2023; 37:217-225. [PMID: 36943644 DOI: 10.1007/s10822-023-00502-8] [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: 01/17/2023] [Accepted: 03/05/2023] [Indexed: 03/23/2023]
Abstract
Membrane proteins are attractive targets for drug discovery due to their crucial roles in various biological processes. Studying the binding poses of amphipathic molecules to membrane proteins is essential for understanding the functions of membrane proteins and docking simulations can facilitate the screening of protein-ligand complexes at low computational costs. However, identifying docking poses for a ligand in non-aqueous environments such as lipid bilayers can be challenging. To address this issue, we propose a new docking score called logP-corrected membrane docking (LoCoMock) score. To screen putative protein-ligand complexes embedded in a membrane, the LoCoMock score considers the affinity between a target ligand and the membrane. It combines the docking score of the protein-ligand complex with the logP of the target ligand. In demonstrations using several model ligands, the LoCoMock score screened more putative complexes than the conventional docking score. As extended docking, the LoCoMock score makes it possible to screen membrane proteins more effectively as drug targets than the conventional docking.
Collapse
Affiliation(s)
- Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8577, Tsukuba, Ibaraki, Japan.
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8577, Tsukuba, Ibaraki, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8577, Tsukuba, Ibaraki, Japan.
| |
Collapse
|
109
|
Bulygina LA, Khrushcheva NS, Nelyubina YV, Dorovatovskii P, Strelkova TV, Alexeev MS, Mandegani Z, Nabavizadeh SM, Kuznetsov NY. Bilateral metalloheterocyclic systems based on palladacycle and piperidine-2,4-dione pharmacophores. Org Biomol Chem 2023; 21:2337-2354. [PMID: 36825470 DOI: 10.1039/d3ob00022b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The design of molecules with effective anticancer properties constructed from both dually active metal complex and organic fragments is a novel trend in medicinal chemistry. This concept suggests the impact of a drug on several biological targets or the synergistic action of both fragments as a single unit. We propose that the combination of a Pd-metallocomplex fragment and an organic unit can be an interesting model for anticancer drug discovery. The first phase in the development of such suggested molecules is the synthesis of bilateral metallosystems containing bioactive 6-substituted piperidin-2-one and a palladated N-phenylpyrazolic fragment. Both fragments were incorporated into one molecule through the fused pyrazole-piperidine-2-one unit followed by pyrazol-directed cyclopalladation of the phenyl-group with Pd(OAc)2. An effect of acceleration of the rate of the palladation by NH-lactam was observed. The synthesized hybrid palladacycles have been characterized and tested for their cytotoxic activity on three cancerous cell lines as PPh3 complexes, revealing structures with potential for further development and structural optimization.
Collapse
Affiliation(s)
- Ludmila A Bulygina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov st. 28, 119991 Moscow, Russian Federation.
| | - Natalya S Khrushcheva
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov st. 28, 119991 Moscow, Russian Federation.
| | - Yulia V Nelyubina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov st. 28, 119991 Moscow, Russian Federation.
| | - Pavel Dorovatovskii
- National Research Centre "Kurchatov Institute", 123182, Akademika Kurchatova pl., 1, Moscow, Russian Federation
| | - Tatiana V Strelkova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov st. 28, 119991 Moscow, Russian Federation.
| | - Michael S Alexeev
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov st. 28, 119991 Moscow, Russian Federation. .,A.V. Topchiev Institute of Petrochemical Synthesis, Leninsky Prospect 29, 119991, Moscow, Russian Federation
| | - Zeinab Mandegani
- Professor Rashidi Laboratory of Organometallic Chemistry, Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71467-13565, Iran
| | - S Masoud Nabavizadeh
- Professor Rashidi Laboratory of Organometallic Chemistry, Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71467-13565, Iran
| | - Nikolai Yu Kuznetsov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov st. 28, 119991 Moscow, Russian Federation. .,A.V. Topchiev Institute of Petrochemical Synthesis, Leninsky Prospect 29, 119991, Moscow, Russian Federation
| |
Collapse
|
110
|
Dvorácskó S, Dimmito MP, Sebastiani J, La Regina G, Silvestri R, Pieretti S, Stefanucci A, Tömböly C, Mollica A. Rimonabant-Based Compounds Bearing Hydrophobic Amino Acid Derivatives as Cannabinoid Receptor Subtype 1 Ligands. ACS Med Chem Lett 2023; 14:479-486. [PMID: 37077391 PMCID: PMC10108392 DOI: 10.1021/acsmedchemlett.3c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
In this study, 1H-pyrazole-3-carboxylic acids related to the cannabinoid type 1 (CB1) receptor antagonist rimonabant were amidated with valine or tert-leucine, and the resulting acids were further diversified as methyl esters, amides, and N-methyl amides. In vitro receptor binding and functional assays demonstrated a wide series of activities related to the CB1 receptors (CB1Rs). Compound 34 showed a high CB1R binding affinity (K i = 6.9 nM) and agonist activity (EC50 = 46 nM; E max = 135%). Radioligand binding and [35S]GTPγS binding assays also demonstrated its selectivity and specificity to CB1Rs. Moreover, in vivo experiments revealed that 34 was slightly more effective than the CB1 agonist WIN55,212-2 in the early phase of the formalin test, indicating a short duration of the analgesic effect. Interestingly, in a mouse model of zymosan-induced hindlimb edema, 34 was able to maintain the percentage of paw volume below 75% for 24 h following subcutaneous injection. After intraperitoneal administration, 34 increased the food intake of mice, suggesting potential activity on CB1Rs.
Collapse
Affiliation(s)
- Szabolcs Dvorácskó
- Laboratory of Chemical Biology, Institute of Biochemistry, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary
- Department of Medicinal Chemistry, University of Szeged, 6720 Szeged, Hungary
| | - Marilisa Pia Dimmito
- Department of Pharmacy, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Jessica Sebastiani
- Laboratory Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giuseppe La Regina
- Laboratory Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Romano Silvestri
- Laboratory Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Stefano Pieretti
- National Centre for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Azzurra Stefanucci
- Department of Pharmacy, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Csaba Tömböly
- Laboratory of Chemical Biology, Institute of Biochemistry, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Adriano Mollica
- Department of Pharmacy, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| |
Collapse
|
111
|
Sciacca C, Cardullo N, Pulvirenti L, Di Francesco A, Muccilli V. Evaluation of honokiol, magnolol and of a library of new nitrogenated neolignans as pancreatic lipase inhibitors. Bioorg Chem 2023; 134:106455. [PMID: 36913880 DOI: 10.1016/j.bioorg.2023.106455] [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: 12/27/2022] [Revised: 02/16/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
Obesity is a complex disease defined as an excessive amount of body fat. It is considered a risk factor for several pathologies; therefore, there is an increasing interest in its treatment. Pancreatic lipase (PL) plays a key role in fat digestion, and its inhibition is a preliminary step in the search for anti-obesity agents. For this reason, many natural compounds and their derivatives are studied as new PL inhibitors. This study reports the synthesis of a library of new compounds inspired by two natural neolignans, honokiol (1) and magnolol (2) and bearing amino or nitro groups linked to a biphenyl core. The synthesis of unsymmetrically substituted biphenyls was achieved through an optimisation of the Suzuki-Miyaura cross-coupling reaction followed by the insertion of allyl chains, thus furnishing the O- and/or N-allyl derivatives, and finally, a sigmatropic rearrangement yielding in some cases, the C-allyl analogues. Magnolol, honokiol and the twenty-one synthesised biphenyls were evaluated for their in vitro inhibitory activity toward PL. Three compounds (15b, 16 and 17b) were more effective inhibitors than the natural neolignans (magnolol IC50 = 158.7 µM and honokiol IC50 = 115.5 µM) with IC50 of 41-44 µM. Detailed studies through kinetics suggested better inhibitory activity of the synthetic analogues compared with the natural 1 and 2. Magnolol (Ki = 614.3 µM; K'i of 140.9 µM) and the synthetic biphenyls 15b (Ki = 286.4 µM; K'i = 36.6 µM) and 16 (Ki = 176.2 µM; K'i = 6.4 µM) are mixed-type inhibitors, whereas honokiol (Ki = 674.8 µM) and 17b (Ki = 249 µM) are competitive inhibitors. Docking studies corroborated these findings, showing the best fitting for intermolecular interaction between biphenyl neolignans and PL. The above outcomes highlighted how the proposed structures could be considered interesting candidates for future studies for the development of more effective PL inhibitors.
Collapse
Affiliation(s)
- Claudia Sciacca
- Department of Chemical Sciences, University of Catania, V.le A. Doria 6. 95125, Catania, Italy
| | - Nunzio Cardullo
- Department of Chemical Sciences, University of Catania, V.le A. Doria 6. 95125, Catania, Italy
| | - Luana Pulvirenti
- Department of Chemical Sciences, University of Catania, V.le A. Doria 6. 95125, Catania, Italy
| | - Antonella Di Francesco
- Department of Chemical Sciences, University of Catania, V.le A. Doria 6. 95125, Catania, Italy
| | - Vera Muccilli
- Department of Chemical Sciences, University of Catania, V.le A. Doria 6. 95125, Catania, Italy.
| |
Collapse
|
112
|
Acar Çevik U, Celik I, İnce U, Maryam Z, Ahmad I, Patel H, Özkay Y, Asım Kaplancıklı Z. Synthesis, Biological Evaluation, and Molecular Modeling Studies of New 1,3,4-Thiadiazole Derivatives as Potent Antimicrobial Agents. Chem Biodivers 2023; 20:e202201146. [PMID: 36764924 DOI: 10.1002/cbdv.202201146] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/14/2023] [Accepted: 02/10/2023] [Indexed: 02/12/2023]
Abstract
In this work, the synthesis, characterization, and biological activities of a new series of 1,3,4-thiadiazole derivatives were investigated. The structures of final compounds were identified using 1 H-NMR, 13 C-NMR, elemental analysis, and HRMS. All the new synthesized compounds were then screened for their antimicrobial activity against four types of pathogenic bacteria and one fungal strain, by application of the MIC assays, using Ampicilin, Gentamycin, Vancomycin, and Fluconazole as standards. Among the compounds, the MIC values of 4 and 8 μg/mL of the compounds 3f and 3g, respectively, are remarkable and indicate that these compounds are good candidates for antifungal activity. The docking experiments were used to identify the binding forms of produced ligands with sterol 14-demethylase to acquire insight into relevant proteins. The MD performed about 100 ns simulations to validate selected compounds' theoretical studies. Finally, using density functional theory (DFT) to predict reactivity, the chemical characteristics and quantum factors of synthesized compounds were computed. These results were then correlated with the experimental data. Furthermore, computational estimation was performed to predict the ADME properties of the most active compound 3f.
Collapse
Affiliation(s)
- Ulviye Acar Çevik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, 26470, Turkey
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, 38039, Turkey
| | - Ufuk İnce
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Erciyes University, Kayseri, 38039, Turkey
| | - Zahra Maryam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, 26470, Turkey
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Yusuf Özkay
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, 26470, Turkey
| | - Zafer Asım Kaplancıklı
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, 26470, Turkey
| |
Collapse
|
113
|
Munir R, Zaib S, Zia-ur-Rehman M, Hussain N, Chaudhry F, Younas MT, Zahra FT, Tajammul Z, Javid N, Dera AA, Ogaly HA, Khan I. Ultrasound-Assisted Synthesis of Piperidinyl-Quinoline Acylhydrazones as New Anti-Alzheimer's Agents: Assessment of Cholinesterase Inhibitory Profile, Molecular Docking Analysis, and Drug-like Properties. Molecules 2023; 28:molecules28052131. [PMID: 36903376 PMCID: PMC10004187 DOI: 10.3390/molecules28052131] [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: 02/05/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Alzheimer's disease (AD) is one of the progressive neurological disorders and the main cause of dementia all over the world. The multifactorial nature of Alzheimer's disease is a reason for the lack of effective drugs as well as a basis for the development of new structural leads. In addition, the appalling side effects such as nausea, vomiting, loss of appetite, muscle cramps, and headaches associated with the marketed treatment modalities and many failed clinical trials significantly limit the use of drugs and alarm for a detailed understanding of disease heterogeneity and the development of preventive and multifaceted remedial approach desperately. With this motivation, we herein report a diverse series of piperidinyl-quinoline acylhydrazone therapeutics as selective as well as potent inhibitors of cholinesterase enzymes. Ultrasound-assisted conjugation of 6/8-methyl-2-(piperidin-1-yl)quinoline-3-carbaldehydes (4a,b) and (un)substituted aromatic acid hydrazides (7a-m) provided facile access to target compounds (8a-m and 9a-j) in 4-6 min in excellent yields. The structures were fully established using spectroscopic techniques such as FTIR, 1H- and 13C NMR, and purity was estimated using elemental analysis. The synthesized compounds were investigated for their cholinesterase inhibitory potential. In vitro enzymatic studies revealed potent and selective inhibitors of AChE and BuChE. Compound 8c showed remarkable results and emerged as a lead candidate for the inhibition of AChE with an IC50 value of 5.3 ± 0.51 µM. The inhibitory strength of the optimal compound was 3-fold higher compared to neostigmine (IC50 = 16.3 ± 1.12 µM). Compound 8g exhibited the highest potency and inhibited the BuChE selectively with an IC50 value of 1.31 ± 0.05 µM. Several compounds, such as 8a-c, also displayed dual inhibitory strength, and acquired data were superior to the standard drugs. In vitro results were further supported by molecular docking analysis, where potent compounds revealed various important interactions with the key amino acid residues in the active site of both enzymes. Molecular dynamics simulation data, as well as physicochemical properties of the lead compounds, supported the identified class of hybrid compounds as a promising avenue for the discovery and development of new molecules for multifactorial diseases, such as Alzheimer's disease (AD).
Collapse
Affiliation(s)
- Rubina Munir
- School of Chemistry, University of the Punjab, Lahore 54590, Pakistan
- Department of Chemistry, Kinnaird College for Women, Lahore 54000, Pakistan
- Correspondence: (R.M.); (S.Z.); (I.K.)
| | - Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
- Correspondence: (R.M.); (S.Z.); (I.K.)
| | | | - Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain P.O. Box 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi P.O. Box 144534, United Arab Emirates
| | - Faryal Chaudhry
- Department of Chemistry, Kinnaird College for Women, Lahore 54000, Pakistan
| | - Muhammad Tayyab Younas
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Fatima Tuz Zahra
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Zainab Tajammul
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Noman Javid
- Chemistry Department (C-Block), Forman Christian College, Ferozepur Road, Lahore 54600, Pakistan
| | - Ayed A. Dera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia
| | - Hanan A. Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha 61421, Saudi Arabia
- Biochemistry and Molecular Biology Department, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Imtiaz Khan
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Correspondence: (R.M.); (S.Z.); (I.K.)
| |
Collapse
|
114
|
Laraoui H, Lanez E, Zegheb N, Adaika A, Lanez T, Benkhaled M. Anti‐Diabetic Activity of Flavonol Glucosides From
Fumana montana
Pomel: In vitro Analysis, In Silico Docking, ADMET Prediction, and Molecular Dynamics Simulations. ChemistrySelect 2023. [DOI: 10.1002/slct.202204512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Habiba Laraoui
- Faculty of Matter Sciences Department of chemistry LCCE Laboratory University of Batna 5000 Batna Algeria
- Faculty of Exact and Natural Sciences Department of Matter Sciences University of Biskra BP 145 RP 07000 Biskra Algeria
| | - Elhafnaoui Lanez
- Department of Biochemistry University of El Oued 39000 El Oued Algeria
- Chemistry Department VTRS Laboratory University of El Oued B.P.789 39000 El Oued Algeria
| | - Nadjiba Zegheb
- Chemistry Department VTRS Laboratory University of El Oued B.P.789 39000 El Oued Algeria
| | - Aicha Adaika
- Chemistry Department VTRS Laboratory University of El Oued B.P.789 39000 El Oued Algeria
| | - Touhami Lanez
- Chemistry Department VTRS Laboratory University of El Oued B.P.789 39000 El Oued Algeria
| | - Mohammed Benkhaled
- Faculty of Matter Sciences Department of chemistry LCCE Laboratory University of Batna 5000 Batna Algeria
| |
Collapse
|
115
|
Bender O, Celik I, Dogan R, Atalay A, Shoman ME, Ali TFS, Beshr EAM, Mohamed M, Alaaeldin E, Shawky AM, Awad EM, Ahmed ASF, Younes KM, Ansari M, Anwar S. Vanillin-Based Indolin-2-one Derivative Bearing a Pyridyl Moiety as a Promising Anti-Breast Cancer Agent via Anti-Estrogenic Activity. ACS OMEGA 2023; 8:6968-6981. [PMID: 36844536 PMCID: PMC9948168 DOI: 10.1021/acsomega.2c07793] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The structure-based design introduced indoles as an essential motif in designing new selective estrogen receptor modulators employed for treating breast cancer. Therefore, here, a series of synthesized vanillin-substituted indolin-2-ones were screened against the NCI-60 cancer cell panel followed by in vivo, in vitro, and in silico studies. Physicochemical parameters were evaluated with HPLC and SwissADME tools. The compounds demonstrated promising anti-cancer activity for the MCF-7 breast cancer cell line (GI = 6-63%). The compound with the highest activity (6j) was selective for the MCF-7 breast cancer cell line (IC50 = 17.01 μM) with no effect on the MCF-12A normal breast cell line supported by real-time cell analysis. A morphological examination of the used cell lines confirmed a cytostatic effect of compound 6j. It inhibited both in vivo and in vitro estrogenic activity, triggering a 38% reduction in uterine weight induced by estrogen in an immature rat model and hindering 62% of ER-α receptors in in vitro settings. In silico molecular docking and molecular dynamics simulation studies supported the stability of the ER-α and compound 6j protein-ligand complex. Herein, we report that indolin-2-one derivative 6j is a promising lead compound for further pharmaceutical formulations as a potential anti-breast cancer drug.
Collapse
Affiliation(s)
- Onur Bender
- Biotechnology
Institute, Ankara University, 06135 Ankara, Turkey
| | - Ismail Celik
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, 38280 Kayseri, Turkey
| | - Rumeysa Dogan
- Biotechnology
Institute, Ankara University, 06135 Ankara, Turkey
| | - Arzu Atalay
- Biotechnology
Institute, Ankara University, 06135 Ankara, Turkey
| | - Mai E. Shoman
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Taha F. S. Ali
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Eman A. M. Beshr
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Mahmoud Mohamed
- Department
of Pharmacognosy, College of Clinical Pharmacy, Al Baha University, 65528 Al Baha, Saudi Arabia
| | - Eman Alaaeldin
- Department
of Pharmaceutics, Faculty of Pharmacy, Minia
University, 61519 Minia, Egypt
- Department
of Clinical Pharmacy, Faculty of Pharmacy, Deraya University, 61111 Minia, Egypt
| | - Ahmed M. Shawky
- Science
and Technology Unit (STU), Umm Al-Qura University, 21955 Makkah, Saudi Arabia
- Central
Laboratory for Micro-analysis, Minia University, 61519 Minia, Egypt
| | - Eman M. Awad
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Al-Shaimaa F. Ahmed
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Kareem M. Younes
- Department
of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442 Hail, Saudi Arabia
- Analytical Chemistry Department, Faculty of Pharmacy, Cairo University, El-Kasr El-Aini Street, ET-11562 Cairo, Egypt
| | - Mukhtar Ansari
- Department
of Clinical Pharmacy, College of Pharmacy, University of Hail, 81442 Hail, Saudi Arabia
| | - Sirajudheen Anwar
- Department
of Pharmacology and Toxicology, College of Pharmacy, University of Hail, 81442 Hail, Saudi Arabia
| |
Collapse
|
116
|
Zhang J, Gai J, Ma H, Tang J, Yang C, Zu G. Understanding the molecular mechanism of Ginkgo Folium-Forsythiae Fructus for cerebral atherosclerosis treatment using network pharmacology and molecular docking. Medicine (Baltimore) 2023; 102:e32823. [PMID: 36800633 PMCID: PMC9936039 DOI: 10.1097/md.0000000000032823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Cerebral atherosclerosis (CA) is a chronic disease caused by multiple infarcts and atrophy causing nerve degenerative syndrome. Ginkgo Folium (GF) and Forsythiae Fructus (FF) have shown positive effects on vascular protection, but their relationship with CA is unclear. This study aimed to identify the potential CA targets and mechanisms of action of GF-FF, using network pharmacology. OBJECTIVE This study used network pharmacology and molecular docking to examine the potential targets and pharmacological mechanism of GF-FF on CA. METHODS Using the traditional Chinese medicine systems pharmacology database and analysis platform, components were screened and corresponding targets were predicted using boundary values and Swiss Target Prediction. Using Cytoscape 3.8.0, a network was established between GF-FF components and CA targets. We extracted disease genes and constructed a network of targets based on the protein-protein interaction networks functional enrichment analysis database. Using Metascape, the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes of the enriched targets were determined. AutoDock Vina was used to perform molecular docking. RESULTS Twenty-three active ingredients of GF-FF were confirmed to treat CA, covering 109 targets, of which 48 were CA-related. Luteolin, bicuculline, sesamin, kaempferol, quercetin, and ginkgolide B were the vital active compounds, and EGFR, CYP2E1, CREB1, CYP19A1, PTGS2, PPARG, PPARA, ESR1, MMP9, MAPK14, MAPK8, and PLG were the major targets. The molecular docking showed that these compounds and targets exhibited good intercalation. These 48 protein targets produced effects on CA by modulating pathways such as "apoptosis-multiple species," "IL-17 signaling pathway," and "relaxin signaling pathway." CONCLUSIONS As predicted by network pharmacology, GF-FF exerts anti-tumor effects through multiple components and targets for treatment of CA, providing new clinical ideas for CA treatment.
Collapse
Affiliation(s)
- Jinfei Zhang
- Department of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jialin Gai
- Department of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Hengqin Ma
- Department of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jiqin Tang
- Department of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
- * Correspondence: Jiqin Tang, Department of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China (e-mail: )
| | - Chuntao Yang
- Hospital Management Office, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Guoxiu Zu
- Department of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| |
Collapse
|
117
|
Antonijevic M, Charou D, Ramos I, Valcarcel M, Gravanis A, Villace P, Callizot N, Since M, Dallemagne P, Charalampopoulos I, Rochais C. Design, synthesis and biological characterization of novel activators of the TrkB neurotrophin receptor. Eur J Med Chem 2023; 248:115111. [PMID: 36645981 DOI: 10.1016/j.ejmech.2023.115111] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/07/2023] [Accepted: 01/08/2023] [Indexed: 01/11/2023]
Abstract
Numerous studies have been published about the implication of the neurotrophin brain-derived neurotrophic factor (BDNF) and its receptor TrkB in the pathogenesis of several neurodegenerative conditions such as Alzheimer's disease, Parkinson's disease, Multiple Sclerosis and motor neuron disease. BDNF activates the TrkB receptor with high potency and specificity, promoting neuronal survival, differentiation and synaptic plasticity. Based on the main structural characteristics of LM22A-4, a previously published small molecule that acts as activator of the TrkB receptor, we have designed and synthesized a small data set of compounds. The lead idea for the design of the new compounds was to modify the third position of the LM22A-4, by introducing different substitutions in order to obtain compounds which will have not only better physicochemical properties but selective activity as well. ADME and toxicity profiles of molecules have been evaluated as well as their biological properties through the TrkB receptor and affinity to promote neurite differentiation.
Collapse
Affiliation(s)
| | - Despoina Charou
- Department of Pharmacology, Medical School, University of Crete, Heraklion, Greece; Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas (IMBB-FORTH), Heraklion, Greece
| | | | | | - Achille Gravanis
- Department of Pharmacology, Medical School, University of Crete, Heraklion, Greece; Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas (IMBB-FORTH), Heraklion, Greece
| | | | | | - Marc Since
- Normandie Univ., UNICAEN, CERMN, 14000, Caen, France
| | | | - Ioannis Charalampopoulos
- Department of Pharmacology, Medical School, University of Crete, Heraklion, Greece; Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas (IMBB-FORTH), Heraklion, Greece
| | | |
Collapse
|
118
|
Synthesis and evaluation of anti-yellow fever virus activity of new 6-aryl-3-R-amino-1,2,4-triazin-5(4H)-ones. Eur J Med Chem 2023; 248:115117. [PMID: 36657300 DOI: 10.1016/j.ejmech.2023.115117] [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: 11/08/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
Yellow fever disease is one of public health concerns in the tropics. Despite its significant medicinal and economic impact among large groups of the population, there is a lack of effective treatment against yellow fever. In this regard, here we describe the synthesis of a series of new 6-aryl-3-R-amino-1,2,4-triazin-5(4H)-ones and evaluation of their in vitro inhibitory activity against yellow fever virus. Among all tested compounds 4 derivatives possessing strong inhibitory activity at μM concentrations were identified. All the active compounds revealed a good toxicity profile. These facts make the compounds interesting candidates for further evaluation of their efficacy in the treatment of yellow fever virus infection in vivo.
Collapse
|
119
|
Chemical and Biological Review of Endophytic Fungi Associated with Morus sp. (Moraceae) and In Silico Study of Their Antidiabetic Potential. Molecules 2023; 28:molecules28041718. [PMID: 36838706 PMCID: PMC9968060 DOI: 10.3390/molecules28041718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
The chronic nature of diabetes mellitus motivates the quest for novel agents to improve its management. The scarcity and prior uncontrolled utilization of medicinal plants have encouraged researchers to seek new sources of promising compounds. Recently, endophytes have presented as eco-friendly leading sources for bioactive metabolites. This article reviewed the endophytic fungi associated with Morus species and their isolated compounds, in addition to the biological activities tested on their extracts and chemical constituents. The relevant literature was collected from the years 2008-2022 from PubMed and Web of Science databases. Notably, no antidiabetic activity was reported for any of the Morus-associated endophytic fungal extracts or their twenty-one previously isolated compounds. This encouraged us to perform an in silico study on the previously isolated compounds to explore their possible antidiabetic potential. Furthermore, pharmacokinetic and dynamic stability studies were performed on these compounds. Upon molecular docking, Colletotrichalactone A (14) showed a promising antidiabetic activity due to the inhibition of the α-amylase local target and the human sodium-glucose cotransporter 2 (hSGT2) systemic target with safe pharmacokinetic features. These results provide an in silico interpretation of the possible anti-diabetic potential of Morus endophytic metabolites, yet further study is required.
Collapse
|
120
|
Olczak A, Pawlak T, Kałużyńska S, Gobis K, Korona-Głowniak I, Suśniak K, Zaborowski M, Szczesio M. Structure and Microbiological Activity of 1 H-benzo[ d]imidazole Derivatives. Int J Mol Sci 2023; 24:ijms24043319. [PMID: 36834732 PMCID: PMC9961232 DOI: 10.3390/ijms24043319] [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: 12/20/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 02/10/2023] Open
Abstract
Three new crystal structures of 1H-benzo[d]imidazole derivatives were determined. In the structures of these compounds, an identical system of hydrogen bonds, C(4), was observed. Solid-state NMR was applied for testing the quality of the obtained samples. All of these compounds were tested for in vitro antibacterial activity against Gram-positive bacteria and Gram-negative bacteria, as well as antifungal activity, by checking their selectivity. ADME calculations indicate that the compounds can be tested as potential drugs.
Collapse
Affiliation(s)
- Andrzej Olczak
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Science, Sienkiewicza 112, 90-363 Lodz, Poland
- Correspondence:
| | - Sylwia Kałużyńska
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Katarzyna Gobis
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gen. Hallera Ave. 107, 80-416 Gdańsk, Poland
| | - Izabela Korona-Głowniak
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Lublin, Chodźki Street 1, 20-093 Lublin, Poland
| | - Katarzyna Suśniak
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Lublin, Chodźki Street 1, 20-093 Lublin, Poland
| | - Marcin Zaborowski
- Dean Office’s, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 114, 90-543 Lodz, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| |
Collapse
|
121
|
Abdel-Mohsen HT, El Kerdawy AM, Petreni A, Supuran CT. Novel benzenesulfonamide-thiouracil conjugates with a flexible N-ethyl acetamide linker as selective CA IX and CA XII inhibitors. Arch Pharm (Weinheim) 2023; 356:e2200434. [PMID: 36372524 DOI: 10.1002/ardp.202200434] [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: 08/12/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/15/2022]
Abstract
Novel benzenesulfonamide derivatives linked to diverse functionalized thiouracils through a flexible N-ethyl acetamide linker were designed and synthesized as carbonic anhydrase (CA) inhibitors. The synthesized candidates demonstrated a potent inhibitory activity against four different CA isoforms in the nanomolar range. Compound 10d showed more than twofold higher potency than the reference AAZ against CA II with Ki of 5.65 and 12 nM, respectively. Moreover, compounds 10d and 20 revealed potent activity against CA IX with Ki of 18.1 and 14.2 nM, respectively. In addition, 10c, 10d, 11b, 11c, and 20 demonstrated high potency against the CA XII isozyme with a Ki range of 4.18-4.8 nM. Most of the synthesized derivatives displayed preferential selectivity toward the CA IX and CA XII isoforms over CA I and CA II. Compounds 11a and 20 exhibited favorable selectivity toward CA IX over CA II with a selectivity index (SI) of 14.36 and 16.62, respectively, and toward CA XII over CA II with SI of 71.01 and 51.19, respectively. Molecular docking simulations showed that the synthesized conjugates adopted comparable binding modes in the CA I, CA II, CA IX, and CA XII isoforms, involving the deep fitting of the sulfonamide moiety in the base of the CA active site via chelation of the Zn2+ ion and H-bond interaction with the key amino acids Thr199 and/or Thr200. Moreover, the N-ethyl acetamide flexible linker enables the substituted thiouracils and fused thiouracil tail to achieve multiple interactions with the surrounding hydrophobic and hydrophilic regions.
Collapse
Affiliation(s)
- Heba T Abdel-Mohsen
- Department of Chemistry of Natural and Microbial Products, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Cairo, Egypt
| | - Ahmed M El Kerdawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt.,Department of Pharmaceutical Chemistry, School of Pharmacy, Newgiza University (NGU), Cairo, Egypt
| | - Andrea Petreni
- Department NEUROFARBA-Pharmaceutical and Nutraceutical Section, Università degli Studi di Firenze, University of Firenze, Firenze, Italy
| | - Claudiu T Supuran
- Department NEUROFARBA-Pharmaceutical and Nutraceutical Section, Università degli Studi di Firenze, University of Firenze, Firenze, Italy
| |
Collapse
|
122
|
Jain P, Sudandira Doss C. Identification of potential andrographolide-based drug candidate against Keap1-Nrf2 pathway through rigorous cheminformatics screening. Mol Divers 2023; 27:341-356. [PMID: 35467270 DOI: 10.1007/s11030-022-10435-3] [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: 12/07/2021] [Accepted: 04/05/2022] [Indexed: 12/01/2022]
Abstract
The Keap1-Nrf2 [Kelch-like ECH-associated protein-1-Nuclear factor erythroid-2-related factor-2] regulatory pathway plays a vital role in the protection of cells by regulating transcription of antioxidant and detoxification genes. Andrographolide (AGP) regulates the Keap1-Nrf2 pathway by inhibiting the Keap1 protein. To identify a more potent AGP analog as a therapeutic agent against Keap1 protein, in this work, cheminformatics analysis of 237 AGP analogs was carried out. Amongst these, five AGP analogs were screened through virtual screening followed by their molecular docking analysis against Keap1 protein, which revealed greater binding affinities (binding energy = - 4.15 to - 5.59 kcal/mol) for the shortlisted AGP analogs compared to AGP (binding energy = - 4.02 kcal/mol). Pharmacophore mapping indicated 14 spatial features, including 3 hydrogen bond acceptors and 11 hydrophobic, while ADME analysis established the potential of all five analogs as orally-active drug-like candidates based on Lipinski's rule of five. We also examined the chemical reactivity of AGP and the shortlisted AGP analogs using DFT analysis, which revealed that except for one analog (AGP_A2) all are more chemically reactive than AGP. Further, molecular dynamics simulation analysis and MM/GBSA evidenced that AGP_A1 (PubchemID-123361152), AGP_A3 (PubchemID-58209855) and AGP_A4 (PubchemID-101362374) are the best drug like candidates compared to AGP and have greater potential to activate the Keap1-Nrf2 pathway by inhibiting the Keap1 protein.
Collapse
Affiliation(s)
- Priyanka Jain
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C Sudandira Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| |
Collapse
|
123
|
Ghannam IAY, El Kerdawy AM, Mounier MM, Abo-Elfadl MT, Ali IH. Novel 2-oxo-2-phenylethoxy and benzyloxy diaryl urea hybrids as VEGFR-2 inhibitors: Design, synthesis, and anticancer evaluation. Arch Pharm (Weinheim) 2023; 356:e2200341. [PMID: 36398495 DOI: 10.1002/ardp.202200341] [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: 06/25/2022] [Revised: 09/11/2022] [Accepted: 10/07/2022] [Indexed: 11/19/2022]
Abstract
Two series of diaryl urea derivatives, 6a-k and 7a-n, were synthesized. All the newly synthesized compounds were tested against the NCI (US) cancer cell lines via SRB assay. The p-chloro-m-trifluoromethyl phenyl derivatives 6e-g and 7e-g showed the most potent cytotoxic activity with a GI50 value range of 1.2-15.9 µM. Furthermore, the p-fluorobenzyloxy diaryl urea derivative 7g revealed the most potent cytotoxicity against eight cancer cell lines in the MTT assay with IC50 values below 5 µM. Compounds 6a-k and 7a-n were tested for their vascular endothelial growth factor receptor-2 (VEGFR-2) kinase inhibitory activities. The p-chloro-m-trifluoromethyl diaryl urea benzyloxy derivatives 7e-i and the p-methoxydiaryl urea benzyloxy derivatives 7k, 7l, and 7n were found to be the most active compounds as VEGFR-2 inhibitors in the benzyloxy series 7, with an IC50 range of 0.09-4.15 µM. In the 2-oxo-2-phenylethoxy series 6, compounds 6e-g and 6i were reported with IC50 values of 0.94, 0.54, 2.71, and 4.81 µM, respectively. Moreover, compounds 7e and 7g induced apoptosis, causing cell cycle arrest in the G2/M phase. In addition, 7g showed an antimigratory effect in A-375 cells and inhibited the VEGFR-2 expression in an immunohistofluorescence study. Molecular docking simulations on VEGFR-2 as well as ADME properties prediction were also performed.
Collapse
Affiliation(s)
- Iman A Y Ghannam
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Egypt
| | - Ahmed M El Kerdawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt.,Department of Pharmaceutical Chemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Egypt
| | - Marwa M Mounier
- Department of Pharmacognosy, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Egypt
| | - Mahmoud T Abo-Elfadl
- Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences, National Research Centre, Dokki, Egypt.,Biochemistry Department, Biotechnology Research Institute, National Research Centre, Dokki, Egypt
| | - Islam H Ali
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Egypt
| |
Collapse
|
124
|
Costa RKM, Souza LMP, Silva RS, Souza FR, Pimentel AS. The reconciliation between the experimental and calculated octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using atomistic molecular dynamics: an open question. J Biomol Struct Dyn 2023; 41:11510-11517. [PMID: 36715129 DOI: 10.1080/07391102.2023.2173298] [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: 11/09/2022] [Accepted: 12/26/2022] [Indexed: 01/31/2023]
Abstract
The octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) was investigated using atomistic molecular dynamics simulations via thermodynamic integration and multistate Bennett acceptance ratio methods. The GAFF and CHARMM36 force fields were used with six water models widely used in molecular dynamics simulations. The OPC4 water model provided the best agreement with the experimental octanol-water partition coefficient of DPPC using the two force fields. However, there is still plenty of room for improvement in water models with correct estimation of surface tension that uses better and suitable non-bonded interaction parameters between water-water and water-DPPC. The Gibbs free energy of transferring DPPC from octanol to water phase was calculated to be 19.8 ± 0.3 and 20.2 ± 0.3 kcal mol-1, giving a partition coefficient of 14.5 ± 0.4 and 14.8 ± 0.3 for the GAFF and CHARMM36 force fields, respectively. This study reinforces the importance of developing new water models that reproduce experimental surface tensions to reconcile the water-water and water-DPPC non-bonded interactions and the existing discrepancy between experimental measurements of amphiphilic molecules that are important in many areas of scientific applications and industry such as biophysics, surfactant, colloids, membranes, medicine, nanotechnology, and food and pharmaceutical industries, and so on. It raises two important open questions: Is the experimental octanol-water partition coefficient of DPPC reliable? Or is its calculation accurate using the OPC4 water model? With respect to the experimental measurements, there may be non-treated aspects such as the formation of aggregates in aqueous phase and limit of detection of the applied method. And, in the calculation, some effects are not possible to be considered in a correct way or viable time such as calculating quantum effects, sampling all conformations, considering phase transitions, and correctly evaluating the intermolecular forces to estimate an accurate surface tension.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | | | - Rudielson Santos Silva
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Felipe Rodrigues Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - André Silva Pimentel
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
125
|
Phytochemical Characterization of Pterocephalus frutescens with In-Silico Evaluation as Chemotherapeutic Medicine and Oral Pharmacokinetics Prediction Study. Sci Pharm 2023. [DOI: 10.3390/scipharm91010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Virtual screening of the potential lead chemotherapeutic phytochemicals from medicinal plants has useful application in the field of in-silico modelling and computer-based drug design by orienting and scoring ligands in the active binding site of a target protein. The phytochemical investigation of the Pterocephalus frutescens extract in n-butanol resulted in the isolation and structure elucidation of three iridoids and four flavonoids which were identified as Geniposide (1), Geniposidic acid (2), Nepetanudoside C (3), Isovitexin (4), Luteolin-7-O-glucoside (5) Isoorientin (6) and Orientin (7), respectively. Molecular docking studies were used to compare the binding energies of the isolated phytochemicals at four biological cancer-relevant targets; namely, aromatase, carbonic anhydrase IX, fatty acid synthase, and topoisomerase II-DNA complex. The docking study concluded that the isolated compounds have promising cytotoxic activities, in particular, Luteolin-7-O-glucoside (5) and Orientin (7) which exhibited high binding affinities among the isolated compounds at the active sites of the target enzymes; Aromatase (−8.73 Kcal/mol), and Carbonic anhydrase IX (−8.92 Kcal/mol), respectively, surpassing the corresponding binding scores of the co-crystallized ligands and the reference drugs at these target enzymes. Additionally, among the isolated compounds, Luteolin-7-O-glucoside (5) showed the most outstanding binding affinities at the active sites of the target enzymes; Fatty acid synthase, and Topisomerase II-DNA complex with binding scores of −6.82, and −7.99 Kcal/mol, respectively. Finally, the SwissADME online web tool predicted that most of these compounds possessed acceptable oral bioavailability and drug likeness characteristics.
Collapse
|
126
|
Adewumi AT, Oluyemi WM, Adekunle YA, Adewumi N, Alahmdi MI, Soliman MES, Abo‐Dya NE. Propitious Indazole Compounds as β‐ketoacyl‐ACP Synthase Inhibitors and Mechanisms Unfolded for TB Cure: Integrated Rational Design and MD Simulations. ChemistrySelect 2023. [DOI: 10.1002/slct.202203877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Adeniyi T. Adewumi
- Molecular Bio-computation and Drug Design Laboratory School of Health Sciences University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
| | - Wande M. Oluyemi
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
- Department of Pharmaceutical and Medicinal Chemistry College of Pharmacy Afe Babalola University Ado-Ekiti Ekiti State Nigeria
- Laboratory for Natural Products and Biodiscovery Research Pharmaceutical Chemistry Department Faculty of Pharmacy University of Ibadan Nigeria
| | - Yemi A. Adekunle
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
- Laboratory for Natural Products and Biodiscovery Research Pharmaceutical Chemistry Department Faculty of Pharmacy University of Ibadan Nigeria
- Centre for Natural Products Discovery (CNPD) School of Pharmacy and Biomolecular Sciences Liverpool John Moores University Liverpool L3 3AF United Kingdom
| | - Nonhlanhla Adewumi
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
- Department of Chemistry Faculty of Applied and Computer Sciences Vaal University Vanderbijl Park South Africa
- Chemical research Laboratory BetaChem Pty Ltd ERF5 Producta Road, Driemanskap, Heidelberg 1441 Gauteng South Africa
| | - Mohamed Issa Alahmdi
- Department of Chemistry Faculty of Science University of Tabuk, Tabuk, 7149 Saudi Arabia
| | - Mahmoud E. S. Soliman
- Molecular Bio-computation and Drug Design Laboratory School of Health Sciences University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
| | - Nader E. Abo‐Dya
- Department of Pharmaceutical Chemistry Faculty of Pharmacy Tabuk University Tabuk 71491 Saudi Arabia
- Department of Pharmaceutical Organic Chemistry Faculty of Pharmacy Zagazig University Zagazig 44519 Egypt
| |
Collapse
|
127
|
Pyae NYL, Maiuthed A, Phongsopitanun W, Ouengwanarat B, Sukma W, Srimongkolpithak N, Pengon J, Rattanajak R, Kamchonwongpaisan S, Ei ZZ, Chunhacha P, Wilasluck P, Deetanya P, Wangkanont K, Hengphasatporn K, Shigeta Y, Rungrotmongkol T, Chamni S. N-Containing α-Mangostin Analogs via Smiles Rearrangement as the Promising Cytotoxic, Antitrypanosomal, and SARS-CoV-2 Main Protease Inhibitory Agents. Molecules 2023; 28:molecules28031104. [PMID: 36770770 PMCID: PMC9919084 DOI: 10.3390/molecules28031104] [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: 12/09/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
New N-containing xanthone analogs of α-mangostin were synthesized via one-pot Smiles rearrangement. Using cesium carbonate in the presence of 2-chloroacetamide and catalytic potassium iodide, α-mangostin (1) was subsequently transformed in three steps to provide ether 2, amide 3, and amine 4 in good yields at an optimum ratio of 1:3:3, respectively. The evaluation of the biological activities of α-mangostin and analogs 2-4 was described. Amine 4 showed promising cytotoxicity against the non-small-cell lung cancer H460 cell line fourfold more potent than that of cisplatin. Both compounds 3 and 4 possessed antitrypanosomal properties against Trypanosoma brucei rhodesiense at a potency threefold stronger than that of α-mangostin. Furthermore, ether 2 gave potent SARS-CoV-2 main protease inhibition by suppressing 3-chymotrypsinlike protease (3CLpro) activity approximately threefold better than that of 1. Fragment molecular orbital method (FMO-RIMP2/PCM) indicated the improved binding interaction of 2 in the 3CLpro active site regarding an additional ether moiety. Thus, the series of N-containing α-mangostin analogs prospectively enhance druglike properties based on isosteric replacement and would be further studied as potential biotically active chemical entries, particularly for anti-lung-cancer, antitrypanosomal, and anti-SARS-CoV-2 main protease applications.
Collapse
Affiliation(s)
- Nan Yadanar Lin Pyae
- Pharmaceutical Sciences and Technology Program, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
| | - Arnatchai Maiuthed
- Department of Pharmacology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Centre of Biopharmaceutical Science for Healthy Ageing, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Bongkot Ouengwanarat
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
| | - Warongrit Sukma
- Pharmaceutical Sciences and Technology Program, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
| | - Nitipol Srimongkolpithak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Jutharat Pengon
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Roonglawan Rattanajak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Zin Zin Ei
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Preedakorn Chunhacha
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Patcharin Wilasluck
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peerapon Deetanya
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kittikhun Wangkanont
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki, Japan
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supakarn Chamni
- Pharmaceutical Sciences and Technology Program, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: ; Tel.: +662-218-8357
| |
Collapse
|
128
|
Afzal M, Hassan SS, Sohail S, Camps I, Khan Y, Basharat Z, Karim A, Aurongzeb M, Irfan M, Salman M, Morel CM. Genomic landscape of the emerging XDR Salmonella Typhi for mining druggable targets clpP, hisH, folP and gpmI and screening of novel TCM inhibitors, molecular docking and simulation analyses. BMC Microbiol 2023; 23:25. [PMID: 36681806 PMCID: PMC9860245 DOI: 10.1186/s12866-023-02756-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/03/2023] [Indexed: 01/22/2023] Open
Abstract
Typhoid fever is transmitted by ingestion of polluted water, contaminated food, and stool of typhoid-infected individuals, mostly in developing countries with poor hygienic environments. To find novel therapeutic targets and inhibitors, We employed a subtractive genomics strategy towards Salmonella Typhi and the complete genomes of eight strains were primarily subjected to the EDGAR tool to predict the core genome (n = 3207). Human non-homology (n = 2450) was followed by essential genes identification (n = 37). The STRING database predicted maximum protein-protein interactions, followed by cellular localization. The virulent/immunogenic ability of predicted genes were checked to differentiate drug and vaccine targets. Furthermore, the 3D models of the identified putative proteins encoded by the respective genes were constructed and subjected to druggability analyses where only "highly druggable" proteins were selected for molecular docking and simulation analyses. The putative targets ATP-dependent CLP protease proteolytic subunit, Imidazole glycerol phosphate synthase hisH, 7,8-dihydropteroate synthase folP and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gpmI were screened against a drug-like library (n = 12,000) and top hits were selected based on H-bonds, RMSD and energy scores. Finally, the ADMET properties for novel inhibitors ZINC19340748, ZINC09319798, ZINC00494142, ZINC32918650 were optimized followed by binding free energy (MM/PBSA) calculation for ligand-receptor complexes. The findings of this work are expected to aid in expediting the identification of novel protein targets and inhibitors in combating typhoid Salmonellosis, in addition to the already existing therapies.
Collapse
Affiliation(s)
- Muneeba Afzal
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar, KP 25000 Pakistan
| | - Syed Shah Hassan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building “Expansão”, 8th floor room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ 21040-361 Brazil
- Jamil-Ur-Rehman Center for Genome Research, PCMD-ICCBS, University of Karachi, Karachi, Sindh 75270 Pakistan
| | - Saman Sohail
- Department of Chemistry, Islamia College Peshawar, Peshawar, KP 25000 Pakistan
| | - Ihosvany Camps
- Laboratório de Modelagem Computacional, LaModel, Instituto de Ciências Exatas - ICEx. Universidade Federal de Alfenas - UNIFAL-MG, Alfenas, Minas Gerais Brazil
- High Performance & Quantum Computing Labs, Waterloo, Canada
| | - Yasmin Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Zarrin Basharat
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Asad Karim
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Muhammad Aurongzeb
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Muhammad Irfan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Muhammad Salman
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar, KP 25000 Pakistan
| | - Carlos M. Morel
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building “Expansão”, 8th floor room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ 21040-361 Brazil
| |
Collapse
|
129
|
QSAR, molecular docking, and molecular dynamics simulation–based design of novel anti-cancer drugs targeting thioredoxin reductase enzyme. Struct Chem 2023. [DOI: 10.1007/s11224-022-02111-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
130
|
Galantamine Based Novel Acetylcholinesterase Enzyme Inhibitors: A Molecular Modeling Design Approach. Molecules 2023; 28:molecules28031035. [PMID: 36770702 PMCID: PMC9919016 DOI: 10.3390/molecules28031035] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
Acetylcholinesterase (AChE) enzymes play an essential role in the development of Alzheimer's disease (AD). Its excessive activity causes several neuronal problems, particularly psychopathies and neuronal cell death. A bioactive pose on the hAChE B site of the human acetylcholinesterase (hAChE) enzyme employed in this investigation, which was obtained from the Protein Data Bank (PDB ID 4EY6), allowed for the prediction of the binding affinity and free binding energy between the protein and the ligand. Virtual screening was performed to obtain structures similar to Galantamine (GNT) with potential hAChE activity. The top 200 hit compounds were prioritized through the use of filters in ZincPharmer, with special features related to the pharmacophore. Critical analyses were carried out, such as hierarchical clustering analysis (HCA), ADME/Tox predictions, molecular docking, molecular simulation studies, synthetic accessibility (SA), lipophilicity, water solubility, and hot spots to confirm the stable binding of the two promising molecules (ZINC16951574-LMQC2, and ZINC08342556-LMQC5). The metabolism prediction, with metabolites M3-2, which is formed by Glutathionation reaction (Phase II), M1-2, and M2-2 formed from the reaction of S-oxidation and Aliphatic hydroxylation (Phase I), were both reactive but with no side effects. Theoretical synthetic routes and prediction of synthetic accessibility for the most promising compounds are also proposed. In conclusion, this study shows that in silico modeling can be used to create new drug candidate inhibitors for hAChE. The compounds ZINC16951574-LMQC2, and ZINC08342556-LMQC5 are particularly promising for oral administration because they have a favorable drug-likeness profile, excellent lipid solubility, high bioavailability, and adequate pharmacokinetics.
Collapse
|
131
|
Kenney DH, Paffenroth RC, Timko MT, Teixeira AR. Dimensionally reduced machine learning model for predicting single component octanol-water partition coefficients. J Cheminform 2023; 15:9. [PMID: 36658606 PMCID: PMC9854055 DOI: 10.1186/s13321-022-00660-1] [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: 09/26/2022] [Accepted: 11/25/2022] [Indexed: 01/20/2023] Open
Abstract
MF-LOGP, a new method for determining a single component octanol-water partition coefficients ([Formula: see text]) is presented which uses molecular formula as the only input. Octanol-water partition coefficients are useful in many applications, ranging from environmental fate and drug delivery. Currently, partition coefficients are either experimentally measured or predicted as a function of structural fragments, topological descriptors, or thermodynamic properties known or calculated from precise molecular structures. The MF-LOGP method presented here differs from classical methods as it does not require any structural information and uses molecular formula as the sole model input. MF-LOGP is therefore useful for situations in which the structure is unknown or where the use of a low dimensional, easily automatable, and computationally inexpensive calculations is required. MF-LOGP is a random forest algorithm that is trained and tested on 15,377 data points, using 10 features derived from the molecular formula to make [Formula: see text] predictions. Using an independent validation set of 2713 data points, MF-LOGP was found to have an average [Formula: see text] = 0.77 ± 0.007, [Formula: see text] = 0.52 ± 0.003, and [Formula: see text] = 0.83 ± 0.003. This performance fell within the spectrum of performances reported in the published literature for conventional higher dimensional models ([Formula: see text] = 0.42-1.54, [Formula: see text] = 0.09-1.07, and [Formula: see text] = 0.32-0.95). Compared with existing models, MF-LOGP requires a maximum of ten features and no structural information, thereby providing a practical and yet predictive tool. The development of MF-LOGP provides the groundwork for development of more physical prediction models leveraging big data analytical methods or complex multicomponent mixtures.
Collapse
Affiliation(s)
- David H. Kenney
- grid.268323.e0000 0001 1957 0327Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609 USA
| | - Randy C. Paffenroth
- grid.268323.e0000 0001 1957 0327Department of Mathematical Sciences, Worcester Polytechnic Institute, Worcester, MA 01609 USA
| | - Michael T. Timko
- grid.268323.e0000 0001 1957 0327Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609 USA
| | - Andrew R. Teixeira
- grid.268323.e0000 0001 1957 0327Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609 USA
| |
Collapse
|
132
|
Oyeyemi IT, Adewole KE, Gyebi GA. In silico prediction of the possible antidiabetic and anti-inflammatory targets of Nymphaea lotus-derived phytochemicals and mechanistic insights by molecular dynamics simulations. J Biomol Struct Dyn 2023; 41:12225-12241. [PMID: 36645154 DOI: 10.1080/07391102.2023.2166591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/01/2023] [Indexed: 01/17/2023]
Abstract
Nymphaea lotus is used traditionally for the treatment of diabetes and its complications. However, the mode of action and the likely bioactive phytochemicals involved are not yet fully explored. GC-MS analysis was employed to identify the inherent compounds in N. lotus leaves. To gain an insight into the antidiabetic mode of action of this plant, the identified phytochemicals were subjected to computational studies against four molecular targets of diabetes, dipeptidyl peptidase-4, glycogen synthase kinase 3, NADPH oxidase (NOX), sodium-glucose co-transporter-2, and one target of inflammation, cyclooxygenase-2. Compounds with notable binding affinity were subjected to druggability test. Results from molecular docking showed that seven of the compounds investigated exhibited druggability properties and had outstanding binding affinity values for these targets relative to values obtained for the respective standards of each of the targets. Analysis of the MD trajectories from a 100 ns atomistic run shows that the integrities of the complex systems were more stable and preserved throughout the simulation than the unbound protein. These results indicated that the antidiabetic and anti-inflammatory effects of these compounds might be via the inhibition of these targets, laying the foundation for further studies, such as in vitro and in vivo studies to fully validate the anti-diabetic agents from this plant.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | | | - Gideon Ampoma Gyebi
- Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nasarawa, Nigeria
- NpsBC-Cr: Natural Products and Structural (Bio-Chem)-Informatics Computing Research Lab, Bingham University, Karu, Nasarawa, Nigeria
| |
Collapse
|
133
|
Dulsat J, López-Nieto B, Estrada-Tejedor R, Borrell JI. Evaluation of Free Online ADMET Tools for Academic or Small Biotech Environments. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020776. [PMID: 36677832 PMCID: PMC9864198 DOI: 10.3390/molecules28020776] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/27/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
For a new molecular entity (NME) to become a drug, it is not only essential to have the right biological activity also be safe and efficient, but it is also required to have a favorable pharmacokinetic profile including toxicity (ADMET). Consequently, there is a need to predict, during the early stages of development, the ADMET properties to increase the success rate of compounds reaching the lead optimization process. Since Lipinski's rule of five, the prediction of pharmacokinetic parameters has evolved towards the current in silico tools based on empirical approaches or molecular modeling. The commercial specialized software for performing such predictions, which is usually costly, is, in many cases, not among the possibilities for research laboratories in academia or at small biotech companies. Nevertheless, in recent years, many free online tools have become available, allowing, more or less accurately, for the prediction of the most relevant pharmacokinetic parameters. This paper studies 18 free web servers capable of predicting ADMET properties and analyzed their advantages and disadvantages, their model-based calculations, and their degree of accuracy by considering the experimental data reported for a set of 24 FDA-approved tyrosine kinase inhibitors (TKIs) as a model of a research project.
Collapse
|
134
|
Novel hybrid molecules based on triazole-quinoline as potential anticancer agents: screening on MCF-7 cell line, docking studies, and pharmacokinetics evaluation. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2023. [DOI: 10.1007/s13738-022-02737-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
135
|
New N4-Donor Ligands as Supramolecular Guests for DNA and RNA: Synthesis, Structural Characterization, In Silico, Spectrophotometric and Antimicrobial Studies. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28010400. [PMID: 36615615 PMCID: PMC9823393 DOI: 10.3390/molecules28010400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/05/2023]
Abstract
The present work reports the synthesis of new N4-donor compounds carrying p-xylyl spacers in their structure. Different Schiff base aliphatic N-donors were obtained synthetically and subsequently evaluated for their ability to interact with two models of nucleic acids: calf-thymus DNA (CT-DNA) and the RNA from yeast Saccharomyces cerevisiae (herein simply indicated as RNA). In more detail, by condensing p-xylylenediamine and a series of aldehydes, we obtained the following Schiff base ligands: 2-thiazolecarboxaldehyde (L1), pyridine-2-carboxaldehyde (L2), 5-methylisoxazole-3-carboxaldehyde (L3), 1-methyl-2-imidazolecarboxaldehyde (L4), and quinoline-2-carboxaldehyde (L5). The structural characterisation of the ligands L1-L5 (X-ray, 1H NMR, 13C NMR, elemental analysis) and of the coordination polymers {[CuL1]PF6}n (herein referred to as Polymer1) and {[AgL1]BF4}n, (herein referred to as Polymer2, X-ray, 1H NMR, ESI-MS) is herein described in detail. The single crystal X-ray structures of complexes Polymer1 and Polymer2 were also investigated, leading to the description of one-dimensional coordination polymers. The spectroscopic and in silico evaluation of the most promising compounds as DNA and RNA binders, as well as the study of the influence of the 1D supramolecular polymers Polymer1 and Polymer2 on the proliferation of Escherichia coli bacteria, were performed in view of their nucleic acid-modulating and antimicrobial applications. Spectroscopic measurements (UV-Vis) combined with molecular docking calculations suggest that the thiazolecarboxaldehyde derivative L1 is able to bind CT-DNA with a mechanism different from intercalation involving the thiazole ring in the molecular recognition and shows a binding affinity with DNA higher than RNA. Finally, Polymer2 was shown to slow down the proliferation of bacteria much more effectively than the free Ag(I) salt.
Collapse
|
136
|
Yue J, Li Y, Li F, Zhang P, Li Y, Xu J, Zhang Q, Zhang C, He X, Wang Y, Liu Z. Discovery of Mcl-1 inhibitors through virtual screening, molecular dynamics simulations and in vitro experiments. Comput Biol Med 2023; 152:106350. [PMID: 36493735 DOI: 10.1016/j.compbiomed.2022.106350] [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: 09/13/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
As a member of the B-cell lymphoma 2 (Bcl-2) protein family, the myeloid leukemia cell differentiation protein (Mcl-1) can inhibit apoptosis and plays an active role in the process of tumor escape from apoptosis. Therefore, inhibition of Mcl-1 protein can effectively promote the apoptosis of tumor cells and may also reduce tumor cell resistance to drugs targeting other anti-apoptotic proteins. This research is dedicated to the development of Mcl-1 inhibitors, aiming to provide more references for lead compounds with different scaffolds for the development of targeted anticancer drugs. We obtained a series of small molecules with a common core skeleton through molecular docking from Specs database and searched the core structure in ZINC database for more similar small molecules. Collecting these small molecules for preliminary experimental screening, we found a batch of active compounds, and selected two small molecules with the strongest inhibitory activity on B16F10 cells: compound 7 and compound 1. Their IC50s are 7.86 ± 1.25 and 24.72 ± 1.94 μM, respectively. These two compounds were also put into cell scratch test for B16F10 cells and cell viability assay of other cell lines. Furthermore, through molecular dynamics (MD) simulation analysis, we found that compound 7 formed strong binding with the key P2, P3 pocket and ARG 263 of Mcl-1. Finally, ADME results showed that compound 7 performs well in terms of drug similarity. In conclusion, this study provides hits with co-scaffolds that may aid in the design of effective clinical drugs targeting Mcl-1 and the future drug development.
Collapse
Affiliation(s)
- Jianda Yue
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yaqi Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fengjiao Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Peng Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yimin Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jiawei Xu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Qianqian Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Cheng Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China
| | - Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| |
Collapse
|
137
|
Nuha D, Evren AE, Kapusiz Ö, Gül ÜD, Gundogdu-Karaburun N, Karaburun AÇ, Berber H. Design, synthesis, and antimicrobial activity of novel coumarin derivatives: An in-silico and in-vitro study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
138
|
Molecule generation toward target protein (SARS-CoV-2) using reinforcement learning-based graph neural network via knowledge graph. NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS 2023; 12:13. [PMID: 36627927 PMCID: PMC9817447 DOI: 10.1007/s13721-023-00409-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/23/2022] [Accepted: 12/31/2022] [Indexed: 01/07/2023]
Abstract
AI-driven approaches are widely used in drug discovery, where candidate molecules are generated and tested on a target protein for binding affinity prediction. However, generating new compounds with desirable molecular properties such as Quantitative Estimate of Drug-likeness (QED) and Dopamine Receptor D2 activity (DRD2) while adhering to distinct chemical laws is challenging. To address these challenges, we proposed a graph-based deep learning framework to generate potential therapeutic drugs targeting the SARS-CoV-2 protein. Our proposed framework consists of two modules: a novel reinforcement learning (RL)-based graph generative module with knowledge graph (KG) and a graph early fusion approach (GEFA) for binding affinity prediction. The first module uses a gated graph neural network (GGNN) model under the RL environment for generating novel molecular compounds with desired properties and a custom-made KG for molecule screening. The second module uses GEFA to predict binding affinity scores between the generated compounds and target proteins. Experiments show how fine-tuning the GGNN model under the RL environment enhances the molecules with desired properties to generate 100 % valid and 100 % unique compounds using different scoring functions. Additionally, KG-based screening reduces the search space of generated candidate molecules by 96.64 % while retaining 95.38 % of promising binding molecules against SARS-CoV-2 protein, i.e., 3C-like protease (3CLpro). We achieved a binding affinity score of 8.185 from the top rank of generated compound. In addition, we compared top-ranked generated compounds to Indinavir on different parameters, including drug-likeness and medicinal chemistry, for qualitative analysis from a drug development perspective. Supplementary Information The online version contains supplementary material available at 10.1007/s13721-023-00409-2.
Collapse
|
139
|
A Convergent Multicomponent Synthesis, Spectral Analysis, Molecular Modelling and Docking Studies of Novel 2H-pyrido[1,2-a]pyrimidine-2,4(3H)-dione Derivatives as Potential Anti-Cervical Cancer Agents. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
140
|
Ozcan I, Akkoc S, Alici H, Capanlar S, Sahin O, Tahtaci H. Novel Thioether-Bridged 2,6-Disubstituted and 2,5,6-Trisubstituted Imidazothiadiazole Analogues: Synthesis, Antiproliferative Activity, ADME, and Molecular Docking Studies. Chem Biodivers 2023; 20:e202200884. [PMID: 36445849 DOI: 10.1002/cbdv.202200884] [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: 09/19/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
In this study, starting from 2-amino-1,3,4-thiadiazole derivatives (3-5), a new series of 2,6-disubstituted (compounds 7-15) and 2,5,6-trisubstituted (compounds 16-33) imidazo[2,1-b][1,3,4]-thiadiazole derivatives were synthesized using cyclization and Mannich reaction mechanisms, respectively. All synthesized compounds were characterized by 1 H-NMR, 13 C-NMR, FT-IR, elemental analysis, and mass spectroscopy techniques. Also, X-ray diffraction analysis were used for compounds 4, 7, 11, 17, and 19. The cytotoxic effects of the new compounds on the viability of colon cancer cells (DLD-1), lung cancer cells (A549), and liver cancer cells (HepG2) were investigated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method in vitro. Compound 15 was found to be the most potent anticancer drug candidate in this series with an IC50 value of 3.63 μM against HepG2 for 48 h. Moreover, the absorption, distribution, metabolism, and excretion (ADME) parameters of the synthesized compounds were calculated and thus, their potential to be safe drugs was evaluated. Finally, to support the biological activity experiments, molecular docking studies of these compounds were carried out on three different target cancer protein structures (PDB IDs: 5ETY, 1M17, and 3GCW), and the amino acids that play key roles in the binding of the compounds to these proteins were determined.
Collapse
Affiliation(s)
- Ibrahim Ozcan
- Karabuk University, Faculty of Science, Department of Chemistry, 78050, Karabuk, Türkiye
| | - Senem Akkoc
- Süleyman Demirel University, Faculty of Pharmacy, Department of Basic Pharmaceutical Sciences, 32260, Isparta, Türkiye.,Bahcesehir University, Faculty of Engineering and Natural Sciences, 34353, Istanbul, Türkiye
| | - Hakan Alici
- Zonguldak Bülent Ecevit University, Faculty of Science, Department of Physics, 67100, Zonguldak, Türkiye
| | - Seval Capanlar
- Zonguldak Bülent Ecevit University, Faculty of Science, Department of Chemistry, 67100, Zonguldak, Türkiye
| | - Onur Sahin
- Sinop University, Faculty of Health Sciences, Department of Occupational Health & Safety, 57000, Sinop, Türkiye
| | - Hakan Tahtaci
- Karabuk University, Faculty of Science, Department of Chemistry, 78050, Karabuk, Türkiye
| |
Collapse
|
141
|
Luo J, Wen W, Chen J, Zeng X, Wang P, Xu S. Differences in tissue distribution ability of evodiamine and dehydroevodiamine are due to the dihedral angle of the molecule stereo-structure. Front Pharmacol 2023; 14:1109279. [PMID: 37089948 PMCID: PMC10117637 DOI: 10.3389/fphar.2023.1109279] [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: 11/27/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Introduction: This researcher focused at the evodiamine and dehydroevodiamine tissue distribution and structure-pharmacokinetics (PK) relationship after intravenous injection in mice. Methods: Using a transmembrane transport experiment, the permeability of evodiamine and dehydroevodiamine on Caco-2 cells was evaluated. The tissue distribution and pharmacokinetics (PK) of evodiamine and dehydroevodiamine in mice were studied. To comprehend the connection between structure and tissue distribution, physicochemical property evaluations and molecular electrostatic potential (MEP) calculations were performed. Results: Dehydroevodiamine's Papp values in vitro were 10-5 cm/s, whereas evodiamine's were 10-6 cm/s. At a dose of 5 mg/kg, the brain concentration of dehydroevodiamine was 6.44 times more than that of evodiamine. By MEP or physicochemical measures, the permeability difference between evodiamine and dehydroevodiamine is unaffected. The dihedral angle of the stereo-structure appears to be the main cause of the difference in tissue distribution ability between evodiamine and dehydroevodiamine. Discussion: Dehydroevodiamine has a dihedral angle of 3.71° compared to 82.34° for evodiamine. Dehydroevodiamine can more easily pass through the phospholipid bilayer than evodiamine because it has a more planar stereo-structure. Dehydroevodiamine is therefore more likely to pass cross the blood-brain barrier and enter the brain in a tissue-specific manner.
Collapse
Affiliation(s)
- Jie Luo
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Wen Wen
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jie Chen
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xiaobo Zeng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Ping Wang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- *Correspondence: Ping Wang, ; Shijun Xu,
| | - Shijun Xu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- *Correspondence: Ping Wang, ; Shijun Xu,
| |
Collapse
|
142
|
Rathod SB, Prajapati PB, Pal R, Mansuri MF. AMPA GluA2 subunit competitive inhibitors for PICK1 PDZ domain: Pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and ADME studies. J Biomol Struct Dyn 2023; 41:336-351. [PMID: 34809533 DOI: 10.1080/07391102.2021.2006086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PICK1 (Protein interacting with C kinase-1) plays a key role in the regulation of intracellular trafficking of AMPA GluA2 subunit that is linked with synaptic plasticity. PICK1 is a scaffolding protein and binds numerous proteins through its PDZ domain. Research showed that synaptic plasticity is altered upon disrupting the GluA2-PDZ interactions. Inhibiting PDZ and GluA2 binding lead to beneficial effects in the cure of neurological diseases thus, targeting PDZ domain is proposed as a novel therapeutic target in such diseases. For this, various classes of synthetic peptides were tested. Though small organic molecules have been utilized to prevent these interactions, the number of such molecules is inadequate. Hence, in this study, ten molecular libraries containing large number of molecules were screened against the PDZ domain using pharmacophore-based virtual screening to find the best hits for the PDZ domain. Molecular docking and molecular dynamics simulation studies revealed that Hit_II is a potent inhibitor for the PDZ domain and confirm the allosteric nature of Hit_III. Additionally, ADME analysis suggests the drug-likeness of both Hit_II and Hit_III. This study suggests that tested hits may have potency against the PDZ domain and can be considered effective to treat neurological disorders.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shravan B Rathod
- Department of Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat, India
| | - Pravin B Prajapati
- Department of Chemistry, Sheth M. N. Science College, Patan, Gujarat, India
| | - Ranjan Pal
- Department of Medical Genetics, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Mohmedyasin F Mansuri
- Department of Microbiology, Smt. S. M. Panchal Science College, Talod, Gujarat, India
| |
Collapse
|
143
|
Khakpash M, Esfahanizadeh M, Mahboubi-Rabbani M, Amidi S, Kobarfard F. Synthesis and Biological Evaluation of Novel Thiadiazole Derivatives as Antiplatelet Agents. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2023; 22:e141846. [PMID: 38655234 PMCID: PMC11036646 DOI: 10.5812/ijpr-141846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/29/2023] [Accepted: 12/19/2023] [Indexed: 04/26/2024]
Abstract
A novel series of thiadiazole compounds was synthesized through the reaction of thiosemicarbazone intermediates with 2, 3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ). The antiplatelet activity of the synthesized compounds was evaluated using an aggregation test with adenosine diphosphate (ADP) and arachidonic acid (AA) as platelet aggregation inducers. Among the synthesized analogs, compound 3b exhibited the most potent inhibition of platelet aggregation induced by ADP (half maximal inhibitory concentration [IC50] = 39 ± 11 µM). Molecular docking studies of 3b revealed hydrogen bonds between the nitrogen of the thiadiazole ring and Lys280. The tolyl ring exhibited hydrophobic interactions with Tyr105, similar to the antagonist co-crystallized with P2Y12 (PDB ID: 4NTJ). These compounds have the potential to serve as lead molecules for designing P2Y12 inhibitors.
Collapse
Affiliation(s)
- Mahsima Khakpash
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marjan Esfahanizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Mahboubi-Rabbani
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Salimeh Amidi
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Kobarfard
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
144
|
Shi K, Wang Y, Xiao Y, Tu J, Zhou Z, Cao G, Liu Y. Therapeutic effects and mechanism of Atractylodis rhizoma in acute lung injury: Investigation based on an Integrated approach. Front Pharmacol 2023; 14:1181951. [PMID: 37168993 PMCID: PMC10164760 DOI: 10.3389/fphar.2023.1181951] [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: 03/08/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023] Open
Abstract
Acute lung injury (ALI) is characterized by an excessive inflammatory response. Atractylodes lancea (Thunb.) DC. is a traditional chinese medicine with good anti-inflammatory activity that is commonly used clinically for the treatment of lung diseases in China; however, its mechanism of against ALI is unclear. We clarified the therapeutic effects of ethanol extract of Atractylodis rhizoma (EEAR) on lipopolysaccharide (LPS)-induced ALI by evaluation of hematoxylin-eosin (HE) stained sections, the lung wet/dry (W/D) ratio, and levels of inflammatory factors as indicators. We then characterized the chemical composition of EEAR by ultra-performance liquid chromatography and mass spectrometry (UPLC-MS) and screened the components and targets by network pharmacology to clarify the signaling pathways involved in the therapeutic effects of EEAR on ALI, and the results were validated by molecular docking simulation and Western blot (WB) analysis. Finally, we examined the metabolites in rat lung tissues by gas chromatography and mass spectrometry (GC-MS). The results showed that EEAR significantly reduced the W/D ratio, and tumor necrosis factor-α (TNF-α), interleukin-1 beta (IL-1β), interleukin-6 (IL-6) levels in the lungs of ALI model rats. Nineteen components of EEAR were identified and shown to act synergetically by regulating shared pathways such as the mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K)-protein kinase B (AKT) signaling pathways. Ferulic acid, 4-methylumbelliferone, acetylatractylodinol, atractylenolide I, and atractylenolide III were predicted to bind well to PI3K, AKT and MAPK1, respectively, with binding energies < -5 kcal/mol, although only atractylenolide II bound with high affinity to MAPK1. EEAR significantly inhibited the phosphorylation of PI3K, AKT, p38, and ERK1/2, thus reducing protein expression. EEAR significantly modulated the expression of metabolites such as D-Galactose, D-Glucose, serine and D-Mannose. These metabolites were mainly concentrated in the galactose and amino acid metabolism pathways. In conclusion, EEAR alleviates ALI by inhibiting activation of the PI3K-AKT and MAPK signaling pathways and regulating galactose metabolism, providing a new direction for the development of drugs to treat ALI.
Collapse
Affiliation(s)
- Kun Shi
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yan Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yangxin Xiao
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Jiyuan Tu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Center for Hubei TCM Processing Technology Engineering, Wuhan, China
| | - Zhongshi Zhou
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Center for Hubei TCM Processing Technology Engineering, Wuhan, China
| | - Guosheng Cao
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Center for Hubei TCM Processing Technology Engineering, Wuhan, China
- *Correspondence: Guosheng Cao, ; Yanju Liu,
| | - Yanju Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Center for Hubei TCM Processing Technology Engineering, Wuhan, China
- *Correspondence: Guosheng Cao, ; Yanju Liu,
| |
Collapse
|
145
|
Yilmaz ZN, Dede B. Synthesis, characterization of a novel molecule containing imine group, investigation of its quantum chemical, molecular docking and ADME properties. J Biomol Struct Dyn 2022; 40:13727-13737. [PMID: 34709142 DOI: 10.1080/07391102.2021.1993339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this study, a novel Schiff base, 2-[(4-dimethylamino-benzylidene)-amino]-3-(4-hydroxy-phenyl)-propionic acid (DMAT) was synthesized as a result of the condensation reaction of N,N-dimethylamino benzaldehyde and L-tyrosine. The structure of the molecule obtained was characterized by 1H- and 13C-NMR, FTIR, UV-Vis spectroscopy and elemental analysis. Density functional theory (DFT) was used to calculate the optimized geometry, vibrational wavenumbers and electronic parameters at the B3LYP level using 6-311 G(d,p) basis set. In addition, 1H- and 13C-NMR, FTIR and UV-Vis data of the DMAT molecule were calculated with the same DFT/B3LYP/6-311G(d,p) trinity and the spectra obtained from these calculations were compared to the experimental data. The interactions of the DMAT molecule with vascular endothelial growth factor receptor-2 (VEGFR-2) and β-ketoacyl synthase (KAS III) proteins were investigated by molecular docking studies. The results obtained were then compared with the molecular docking results of the selected drug active substances Regorafenib and Isoniazid molecules. The best interaction was between DMAT-VEGFR-2 with -8.30 and -1586.97 kcal/mol binding energy and full fitness score, respectively. In addition, ADME properties of the DMAT molecule were examined and some drug-likeness, physicochemical, lipophilicity and pharmacokinetic properties of this molecule were determined. The ADME and Lipinski parameters of the DMAT molecule exhibited good drug-likeness properties.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Zeliha Nur Yilmaz
- Faculty of Science & Art, Department of Chemistry, Süleyman Demirel University, Isparta, Turkey
| | - Bülent Dede
- Faculty of Science & Art, Department of Chemistry, Süleyman Demirel University, Isparta, Turkey
| |
Collapse
|
146
|
Chandel S, Singh R, Gautam A, Ravichandiran V. Screening of Azadirachta indica phytoconstituents as GSK-3β inhibitor and its implication in neuroblastoma: molecular docking, molecular dynamics, MM-PBSA binding energy, and in-vitro study. J Biomol Struct Dyn 2022; 40:12827-12840. [PMID: 34569452 DOI: 10.1080/07391102.2021.1977705] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glycogen synthase kinase-3 (GSK-3), a constitutively active serine/threonine kinase, primary regulator of various cellular activities varying from glycogen metabolism to cell proliferation and regulation. GSK-3β is associated with the pathogenesis of numerous human diseases, including cancer, metabolic disorder, and Alzheimer's disease. In this study, Azadirachta indica compounds were selected and further screened on the BOILED-Egg model. The compounds showing good GIT absorption were docked with the crystal structure of GSK-3β. The compounds with high docking score were submitted for the molecular dynamic simulation (MDS) and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA). Based upon the MDS and MM-PBSA study, gedunin showed the highest binding energy throughout the MDS process. Gedunin was isolated from the Azadirachta indica, and its efficacy on GSK-3β inhibition was studied in the human neuroblastoma (SH-SY5Y) cells. Gedunin induced apoptosis and anti-proliferative activity by arresting G2/M phase, as evident by cell-cycle analysis. From immunoblot study, gedunin significantly enhanced the expression of an inhibitory form of GSK-3β (p-GSK-3β Ser9) in concentration-dependent manner. Our findings demonstrate that gedunin may act as an effective GSK-3β inhibitor suggesting that this compound may be used for the management of neuroblastoma. Further preclinical and clinical investigation is desirable.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shivani Chandel
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| |
Collapse
|
147
|
Chaudhary M, Sehgal D. In silico identification of natural antiviral compounds as a potential inhibitor of chikungunya virus non-structural protein 3 macrodomain. J Biomol Struct Dyn 2022; 40:11560-11570. [PMID: 34355667 DOI: 10.1080/07391102.2021.1960195] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chikungunya Virus (CHIKV) is having a major impact on humans with potentially life-threatening and debilitating arthritis. The lack of a specific antiviral drug against the CHIKV disease has created an alarming situation to identify or develop potent chemical molecules for its remedial measures. Antiviral therapies for viral diseases are generally expensive and have adverse side effects. Plant-based antiviral natural compounds are the most suitable and best alternative of current antiviral drugs because of less toxicity. In the present study, non-structural protein 3 macrodomain (nsP3MD) of the CHIKV that is essential for virus replication has been selected for anti CHIKV drug target. The compounds were identified using molecular docking, virtual screening and further evaluated by molecular dynamics (MD) simulation studies. The binding mechanism of each compound was analyzed considering the stability and energetic parameter. We have found six plant-based natural antiviral compounds Baicalin, Rutaecarpine, Amentoflavone, Apigetrin, Luteoloside, and Baloxavir as strong inhibitors of nsP3MD of CHIKV. ADMET prediction and target analysis of the selected compounds showed drug likeliness of these compounds. MD simulation studies indicated energetically favorable complex formation between nsP3MD and the selected antiviral compounds. Furthermore, the structural effects on these substitutions were analyzed using the principles of each trajectory, which validated the interaction studies. Our analysis suggests a very high probability of these compounds to inhibit nsP3MD of CHIKV and could be evaluated for Chikungunya fever drug development. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Meenakshi Chaudhary
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
| | - Deepak Sehgal
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
| |
Collapse
|
148
|
Hamdy AK, Sakamoto T, Toma T, Sakamoto M, Abourehab MAS, Otsuka M, Fujita M, Tateishi H, Radwan MO. New Insights into the Structural Requirements of Isatin-Derived Pro-Apoptotic Agents against Acute Myeloid Leukemia. Pharmaceuticals (Basel) 2022; 15:ph15121579. [PMID: 36559030 PMCID: PMC9784816 DOI: 10.3390/ph15121579] [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: 12/01/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Searching for bioactive compounds within the huge chemical space is like trying to find a needle in a haystack. Isatin is a unique natural compound which is endowed with different bio-pertinent activities, especially in cancer therapy. Herein, we envisaged that adopting a hybrid strategy of isatin and α,β-unsaturated ketone would afford new chemical entities with strong chemotherapeutic potential. Of interest, compounds 5b and 5g demonstrated significant antiproliferative activities against different cancer genotypes according to NCI-60 screening. Concomitantly, their IC50 against HL-60 cells were 0.38 ± 0.08 and 0.57 ± 0.05 µM, respectively, demonstrating remarkable apoptosis and moderate cell cycle arrest at G1 phase. Intriguingly, an impressive safety profile for 5b was reflected by a 37.2 times selectivity against HL-60 over PBMC from a healthy donor. This provoked us to further explore their mechanism of action by in vitro and in silico tools. Conclusively, 5b and 5g stand out as strong chemotherapeutic agents that hold clinical promise against acute myeloid leukemia.
Collapse
Affiliation(s)
- Ahmed K. Hamdy
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Takashi Sakamoto
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Tsugumasa Toma
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Masaharu Sakamoto
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Mohammed A. S. Abourehab
- Department of Pharmaceutics, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Department of Drug Discovery, Science Farm, Ltd., Kumamoto 862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Correspondence: (M.F.); (H.T.); (M.O.R.)
| | - Hiroshi Tateishi
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Correspondence: (M.F.); (H.T.); (M.O.R.)
| | - Mohamed O. Radwan
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Giza 12622, Egypt
- Correspondence: (M.F.); (H.T.); (M.O.R.)
| |
Collapse
|
149
|
Wu W, Sung YS, Tomat E. Thiol-Reactive Arylsulfonate Masks for Phenolate Donors in Antiproliferative Iron Prochelators. Inorg Chem 2022; 61:19974-19982. [PMID: 36455205 PMCID: PMC10188280 DOI: 10.1021/acs.inorgchem.2c03250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Tridentate thiosemicarbazones, among several families of iron chelators, have shown promising results in anticancer drug discovery because they target the increased need for iron that characterizes malignant cells. Prochelation strategies, in which the chelator is released under specific conditions, have the potential to avoid off-target metal binding (for instance, in the bloodstream) and minimize unwanted side effects. We report a prochelation approach that employs arylsulfonate esters to mask the phenolate donor of salicylaldehyde-based chelators. The new prochelators liberate a tridentate thiosemicarbazone intracellularly upon reaction with abundant nucleophile glutathione (GSH). A 5-bromo-substituted salicylaldehyde thiosemicarbazone (STC4) was selected for the chelator unit because of its antiproliferative activity at low micromolar levels in a panel of six cancer cell lines. The arylsulfonate prochelators were assessed in vitro with respect to their stability, ability to abolish metal binding, and reactivity in the presence of GSH. Cell-based assays indicated that the arylsulfonate-masked prochelators present higher antiproliferative activities relative to the parent compound after 24 h. The activation and release of the chelator intracellularly were corroborated by assays of cytosolic iron binding and iron supplementation effects as well as cell cycle analysis. This study introduces the 1,3,4-thiadiazole sulfonate moiety to mask the phenolate donor of an iron chelator and impart good solubility and stability to prochelator constructs. The reactivity of these systems can be tuned to release the chelator at high glutathione levels, as encountered in several cancer phenotypes.
Collapse
Affiliation(s)
- Wangbin Wu
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Yu-Shien Sung
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Elisa Tomat
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| |
Collapse
|
150
|
Tivari S, Singh PK, Singh PP, Srivastava V. Visible light-induced photoredox catalyzed C-N coupling of amides with alcohols. RSC Adv 2022; 12:35221-35226. [PMID: 36540212 PMCID: PMC9730743 DOI: 10.1039/d2ra07065k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/02/2022] [Indexed: 03/23/2024] Open
Abstract
A visible-light-mediated method for the construction of N-monoalkylated products from easily available benzamides and benzyl alcohol in the presence of eosin Y has been developed. The reaction proceeded smoothly, for a wide range of derivatives of benzamides and benzyl alcohols, to give the desired products in good to excellent yields. Biological studies, such as those on drug-likeness and molecular docking, are carried out on the molecules.
Collapse
Affiliation(s)
- Shraddha Tivari
- Department of Chemistry, CMP Degree College, University of Allahabad Prayagraj-211002 Uttar Pradesh India
| | - Pravin K Singh
- Department of Chemistry, CMP Degree College, University of Allahabad Prayagraj-211002 Uttar Pradesh India
| | - Praveen P Singh
- Department of Chemistry, United College of Engineering & Research Naini Prayagraj-211010 Uttar Pradesh India
| | - Vishal Srivastava
- Department of Chemistry, CMP Degree College, University of Allahabad Prayagraj-211002 Uttar Pradesh India
| |
Collapse
|