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Hussein YT, Azeez YH. DFT analysis and in silico exploration of drug-likeness, toxicity prediction, bioactivity score, and chemical reactivity properties of the urolithins. J Biomol Struct Dyn 2023; 41:1168-1177. [PMID: 34931599 DOI: 10.1080/07391102.2021.2017350] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Urolithins (Uro) are human microflora-derived metabolites of ellagic acid and ellagitannins. It has been shown to be a powerful modulator of oxidative stress, agents with potential anti-inflammatory, antiproliferative, and antiaging properties. The present study aimed to explore the drug-likeness, toxicity, and bioactivity score of urolithins that were required to be considered oral drug-active using the web-based softwares, Molinspiration, and protox_II. In addition, the chemical reactivity descriptors of the urolithins (Uro A, Uro B, Uro, C, Uro D) were also determined through density functional (DFT) calculations. Furthermore, electrostatic potential (MEP), natural bonds orbitals (NBO), HOMO-LUMO energies, chemical reactivity descriptors, dipole moment, and Fukui functions of all the urolithins were investigated by resorting the conceptual of DFT at the M06-2X/6-311++G (d, p) basis set as a tool to analyse and comprehend the molecular interaction. The results showed that all the urolithins comply with the Lipinski's rule of five and have biological activity. According to the toxicity predictions, Uro A, Uro C, and Uro D belong to class 4 while Uro B belongs to class 6. The chemical reactivity and stability features of the investigated compounds were evaluated using global chemical reactivity descriptors calculated from the Frontier Molecular Orbitals (FMOs) energies gap, which revealed that the stability order of the molecules was Uro B > Uro C > Uro D > Uro A. The present findings indicate that the urolithins could be a promising candidate for development into a therapeutic medication.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yousif Taha Hussein
- Medical Laboratory Science, Technical College of Applied Sciences, Research Center, Sulaimani Polytechnic University, Sulaimani, Iraq
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Anitha K, Nataraj A, Narayana B. DFT Investigation, Chemical Reactivity Identification and Molecular Docking of 2( E)˗1˗(3˗Bromothiophene˗2˗yl)˗3˗(Furan˗2˗yl)Prop˗2˗en˗1˗one. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2138920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- K. Anitha
- Department of Physics, SRM Institute of Science and Technology, Chennai, Tamilnadu, India
| | - A. Nataraj
- Department of Physics, SRM Institute of Science and Technology, Chennai, Tamilnadu, India
| | - Badiadka Narayana
- Department of Studies in Chemistry, Mangalore University, Mangalagangotri, Mangalore, Karnataka, India
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Elwahy AHM, Eid EM, Abdel-Latif SA, Hassaneen HME, Abdelhamid IA. Design, Synthesis, DFT, TD-DFT/PCM Calculations, and Molecular Docking Studies on the Anti-COVID-19, and Anti-SARS Activities of Some New Bis-Thiazoles and Bis-Thiadiazole. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2117204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
| | - Elshimaa M. Eid
- Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
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Sattari Alamdar S, Foroughifar N, Shahi M, Balali E. Synthesis, Biological Activitiy and DFT Study of New Azaphenalene Derivatives. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2089700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Somayeh Sattari Alamdar
- Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Department of Organic Chemistry, Islamic Azad University, Tehran, Iran
| | - Naser Foroughifar
- Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Department of Organic Chemistry, Islamic Azad University, Tehran, Iran
| | - Masoumeh Shahi
- Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Department of Organic Chemistry, Islamic Azad University, Tehran, Iran
| | - Ebrahim Balali
- Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Department of Organic Chemistry, Islamic Azad University, Tehran, Iran
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Chandrasekaran R, Murugavel S, Silambarasan T. Computer Aided Drug Design of 1,2,3-Triazole Fused Bioactive Derivative Targeting Glucosamine-6-Phosphate Synthase (GlmS) – XRD, Computational Crystallography, and Molecular Simulation Approach. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2067196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- RaviKumar Chandrasekaran
- Department of Physics, Thanthai Periyar EVR Government Polytechnic College, Vellore, Tamil Nadu, India
| | - Saminathan Murugavel
- Department of Physics, Thanthai Periyar Government Institute of Technology, Vellore, Tamil Nadu, India
| | - Tamilselvan Silambarasan
- Department of Microbiology, School of Allied Health Sciences, VIMS Campus, Vinayaka Missions Research Foundation (Deemed University), Salem, Tamil Nadu, India
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Pooja K, Fatima A, Sharma A, Garima K, Savita S, Kumar M, Verma I, Siddiqui N, Javed S. Experimental, theoretical, hirschfeld surface, electronic excitation and molecular docking studies on fomepizole(4-Methyl-1H-pyrazole). J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Alkhimova LE, Sharov AV, Burkhanova TM, Babashkina MG, Safin DA. Ambroxol: Insight into the Crystal Structure, Hirshfeld Surface Analysis and Computational Study. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2049323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Larisa E. Alkhimova
- Advanced Materials for Industry and Biomedicine laboratory, Kurgan State University, Kurgan, Russian Federation
- University of Tyumen, Tyumen, Russian Federation
| | - Artem V. Sharov
- Advanced Materials for Industry and Biomedicine laboratory, Kurgan State University, Kurgan, Russian Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University Named after the First President of Russia B.N. Yeltsin, Ekaterinburg, Russian Federation
| | - Tatyana M. Burkhanova
- Advanced Materials for Industry and Biomedicine laboratory, Kurgan State University, Kurgan, Russian Federation
- University of Tyumen, Tyumen, Russian Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University Named after the First President of Russia B.N. Yeltsin, Ekaterinburg, Russian Federation
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Damir A. Safin
- Advanced Materials for Industry and Biomedicine laboratory, Kurgan State University, Kurgan, Russian Federation
- University of Tyumen, Tyumen, Russian Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University Named after the First President of Russia B.N. Yeltsin, Ekaterinburg, Russian Federation
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Zothantluanga JH, Abdalla M, Rudrapal M, Tian Q, Chetia D, Li J. Computational Investigations for Identification of Bioactive Molecules from Baccaurea ramiflora and Bergenia ciliata as Inhibitors of SARS-CoV-2 M pro. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2046613] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- James H. Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Shandong Province, PR China
| | - Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education Research, Pune, Maharashtra, India
| | - Qiang Tian
- Department of Senile Neurology, The Central Hospital of Taian, Taian, Shandong, PR China
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Jin Li
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Shandong Province, PR China
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Devasia J, Chinnam S, Khatana K, Shakya S, Joy F, Rudrapal M, Nizam A. Synthesis, DFT and In Silico Anti-COVID Evaluation of Novel Tetrazole Analogues. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2036778] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jyothis Devasia
- Department of Chemistry, CHRIST (Deemed to be University), Bengaluru, Karnataka, India
| | - Sampath Chinnam
- Department of Chemistry, M. S. Ramaiah Institute of Technology (Visvesvaraya Technological University, Belgaum), Bengaluru, Karnataka, India
| | - Kavita Khatana
- Department of Applied Sciences (Chemistry), IIMT College of Polytechnic, Greater Noida, Uttar Pradesh, India
| | - Sonam Shakya
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Francis Joy
- Department of Chemistry, CHRIST (Deemed to be University), Bengaluru, Karnataka, India
| | - Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Pune, Maharashtra, India
| | - Aatika Nizam
- Department of Chemistry, CHRIST (Deemed to be University), Bengaluru, Karnataka, India
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Ganga M, Kalaivanan C, Sankaran KR. Synthesis, SC-XRD, DFT Investigation and Hirshfeld Surface Analysis of 1-Neopentyl-2,4,5-Triphenyl-1H-Imidazole Derivatives. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2038217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- M. Ganga
- Department of Chemistry, Annamalai University, Chidambaram, Tamil Nadu, India
| | - C. Kalaivanan
- Department of Chemistry, K. Ramakrishnan College of Technology, Tiruchirapalli, Tamil Nadu, India
| | - K. R. Sankaran
- Department of Chemistry, Annamalai University, Chidambaram, Tamil Nadu, India
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Abd El Ghani GE, Elmorsy MA, Ibrahim ME. Docking Studies on Some Synthesized 5H-Chromeno[4,3-b]Pyridin-5-One Derivatives for Breast Cancer. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2038216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Mohammad A. Elmorsy
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mona E. Ibrahim
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, Egypt
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Fatima A, Khanum G, Verma I, Butcher RJ, Siddiqui N, Srivastava SK, Javed S. Synthesis, Characterization, Crystal Structure, Hirshfeld Surface, Electronic Excitation, Molecular Docking, and DFT Studies on 2-Amino Thiophene Derivative. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2032769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, MP, India
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao Ambedkar University, Agra, UP, India
| | - Ghazala Khanum
- S.O.S in Chemistry, Jiwaji University, Gwalior, MP, India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, UP, India
| | - Ray J. Butcher
- Department of Chemistry, Howard University, Washington, DC, USA
| | | | | | - Saleem Javed
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao Ambedkar University, Agra, UP, India
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Zaki YH, Abdelhamid AO, Sayed AR, Mohamed HS. Synthesis of 1,3,4-Thiadiazole Derivatives Using Hydrazonoyl Bromide: Molecular Docking and Computational Studies. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2027791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yasser H. Zaki
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni‑Suef, Egypt
- Department of Chemistry, Faculty of Science and Humanity Studies at Al-Quwayiyah, Shaqra University, Al-Quwayiyah, Saudi Arabia
| | | | - Abdelwahed R. Sayed
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni‑Suef, Egypt
- Department of Chemistry, Faculty of Science, King Faisal University, Al-Hofuf, Al-Ahsa, Saudi Arabia
| | - Hussein S. Mohamed
- Department of Chemistry of Medicinal and Aromatic Plants, Research Institute of Medicinal and Aromatic Plants (RIMAB), Beni-Suef University, Beni-Suef, Egypt
- Department of Basic Sciences, Higher Technological Institute in Beni-Suef, Beni-Suef, Egypt
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