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Zhang J, Jiang P, Wang S, Li M, Hao Z, Guan W, Pan J, Wu J, Zhang Y, Li H, Chen L, Yang B, Liu Y. Recent advances in the natural product analogues for the treatment of neurodegenerative diseases. Bioorg Chem 2024; 153:107819. [PMID: 39276492 DOI: 10.1016/j.bioorg.2024.107819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/30/2024] [Accepted: 09/08/2024] [Indexed: 09/17/2024]
Abstract
Neurodegenerative diseases (NDs) represent a hallmark of numerous incapacitating and untreatable conditions, the incidence of which is escalating swiftly, exemplified by Alzheimer's disease and Parkinson's disease. There is an urgent necessity to create pharmaceuticals that exhibit high efficacy and minimal toxicity in order to address these debilitating diseases. The structural complexity and diversity of natural products confer upon them a broad spectrum of biological activities, thereby significantly contributing to the history of drug discovery. Nevertheless, natural products present challenges in drug discovery, including time-consuming separation processes, low content, low bioavailability, and other related issues. To address these challenges, numerous analogs of natural products have been synthesized. This methodology enables the rapid synthesis of analogs of natural products with the potential to serve as lead compounds for drug development, thereby paving the way for the discovery of novel pharmaceuticals. This paper provides a summary of 127 synthetic analogues featuring various natural product structures, including flavonoids, alkaloids, coumarins, phenylpropanoids, terpenoids, polyphenols, and amides. The compounds are categorized based on their efficacy in treating various diseases. Furthermore, this article delves into the structure-activity relationship (SAR) of certain analogues, offering a thorough point of reference for the systematic development of pharmaceuticals aimed at addressing neurodegenerative conditions.
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Affiliation(s)
- Jinling Zhang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China; Research Institute of Medicine & Pharmacy, Qiqihar Medical University, Qiqihar 161006, China
| | - Peng Jiang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Shuping Wang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Mengmeng Li
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Zhichao Hao
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Wei Guan
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Juan Pan
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Jiatong Wu
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Yiqiang Zhang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Hua Li
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Bingyou Yang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China.
| | - Yan Liu
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China.
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Thakur S, Kumar D, Jaiswal S, Goel KK, Rawat P, Srivastava V, Dhiman S, Jadhav HR, Dwivedi AR. Medicinal chemistry-based perspectives on thiophene and its derivatives: exploring structural insights to discover plausible druggable leads. RSC Med Chem 2024:d4md00450g. [PMID: 39601022 PMCID: PMC11588141 DOI: 10.1039/d4md00450g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 10/27/2024] [Indexed: 11/29/2024] Open
Abstract
Thiophene is a privileged pharmacophore in medicinal chemistry owing to its diversified biological attributes. The thiophene moiety has been ranked 4th in the US FDA drug approval of small drug molecules, with around 7 drug approvals over the last decade. The present review covers USFDA-approved drugs possessing a thiophene ring system. Our analysis reveals that 26 drugs possessing thiophene nuclei have been approved under different pharmacological classes. The review further covers reported thiophene and its substituted analogues with diverse biological activities, including anti-diabetic, anticancer, anti-inflammatory, anticonvulsant, and antioxidant activity. Besides, a section is dedicated to appreciating the implications of structural bioinformatics in drug discovery. Additionally, the manuscript delves into structure-activity relationship studies to explore the chemical groups responsible for eliciting potential therapeutic activities. The review may provide invaluable insights for researchers working with thiophene nuclei in developing novel analogues with greater efficacy and fewer side effects.
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Affiliation(s)
- Shikha Thakur
- Pharmaceutical Chemistry Laboratory, Department of Pharmacy, Birla Institute of Technology and Sciences Pilani Pilani Campus, Vidya Vihar Pilani - 333031 RJ India
| | - Devendra Kumar
- School of Pharmacy, Narsee Monjee Institute of Management Studies (NMIMS) Dist. Dhule Maharashtra India
| | - Shivani Jaiswal
- Institute of Pharmaceutical Research, GLA University Mathura, 17 Km Stone, National Highway, Delhi-Mathura Road, P.O. Chaumuha Mathura-281406 Uttar Pradesh India
| | - Kapil Kumar Goel
- Department of Pharmaceutical Sciences, Gurukul Kangri (Deemed to Be University) Haridwar 249404 Uttarakhand India
| | - Pramod Rawat
- Graphic Era (Deemed to be University) Clement Town Dehradun-248002 India
- Graphic Era Hill University Clement Town Dehradun-248002 India
| | - Vivek Srivastava
- Amity Institute of Pharmacy Amity University Lucknow Campus Uttar Pradesh India
| | - Sonia Dhiman
- Centre for Research Impact & Outcome, Chitkara College of Pharmacy, Chitkara University Rajpura 140401 Punjab India
| | - Hemant R Jadhav
- Pharmaceutical Chemistry Laboratory, Department of Pharmacy, Birla Institute of Technology and Sciences Pilani Pilani Campus, Vidya Vihar Pilani - 333031 RJ India
| | - Ashish Ranjan Dwivedi
- Department of Medicinal Chemistry, GITAM School of Pharmacy, GITAM (deemed to be) University Hyderabad India
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Marinho MM, da Rocha MN, Magalhães EP, Ribeiro LR, Roberto CHA, de Queiroz Almeida-Neto FW, Monteiro ML, Nunes JVS, de Menezes RRPPB, Marinho ES, de Lima Neto P, Martins AMC, Dos Santos HS. Insights of potential trypanocidal effect of the synthetic derivative (2E)-1-(4-aminophenyl)-3-(2,4-dichlorophenyl)prop-2-en-1-one: in vitro assay, MEV analysis, quantum study, molecular docking, molecular dynamics, MPO analysis, and predictive ADMET. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:7797-7818. [PMID: 38722342 DOI: 10.1007/s00210-024-03138-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 04/30/2024] [Indexed: 10/04/2024]
Abstract
This study aims to evaluate the antitrypanosomiasis activity of a synthetic dichloro-substituted aminochalcone via in vitro assays against infected cell cultures, as well as a theoretical characterization of pharmacokinetics and pharmacodynamics against the protein targets of the evolutionary cycle of T. cruzi. The in vitro evaluation of parasite proliferation inhibition was performed via cytotoxicity analysis on mammalian host cells, effect on epimastigote and trypomastigote forms, and cell death analysis, while computer simulations characterized the electronic structure of (2E)-1-(4-aminophenyl)-3-(2,4-dichlorophenyl)prop-2-en-1-one (DCl), the mechanism of action against the proteins of the evolutionary cycle of T. cruzi: Cruzain, Trypanothione reductase, TcGAPDH, and CYP51 by molecular docking and dynamics and predictive pharmacokinetics by MPO-based ADMET. The in vitro tests showed that the DCl LC50 in order of 178.9 ± 23.9 was similar to the BZN, evidencing the effectiveness of chalcone against Trypomastigotes. Molecular docking and dynamics simulations suggest that DCl acts on the active site of the CYP51 receptor, with hydrogen interactions that showed a high degree of occupation, establishing a stable complex with the target. MPO analysis and ADMET prediction tests suggest that the compound presents an alignment between permeability and hepatic clearance, although it presents low metabolic stability. Chalcone showed stable pharmacodynamics against the CYP51 target, but can form reactive metabolites from N-conjugation and C = C epoxidation, as an indication of controlled oral dose, although the estimated LD50 rate > 500 mg/kg is a indicative of low incidence of lethality by ingestion, constituting a promising therapeutic strategy.
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Affiliation(s)
- Márcia Machado Marinho
- Department of Biological Chemistry, Regional University of Cariri, Crato, CE, Brazil
- Center for Exact Sciences and Technology, State University of Vale do Acaraú, Sobral, CE, Brazil
| | - Matheus Nunes da Rocha
- Center for Science and Technology, Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | - Emanuel Paula Magalhães
- Department of Clinical and Toxicological Analysis, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Lyanna Rodrigues Ribeiro
- Department of Clinical and Toxicological Analysis, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Caio Henrique Alexandre Roberto
- Center for Science and Technology, Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | | | - Marília Lopes Monteiro
- Department of Clinical and Toxicological Analysis, Federal University of Ceará, Fortaleza, CE, Brazil
| | - João Victor Serra Nunes
- Department of Clinical and Toxicological Analysis, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | - Emmanuel Silva Marinho
- Center for Science and Technology, Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | - Pedro de Lima Neto
- Department of Analytical Chemistry and Physical Chemistry, Federal University of Ceará, Campus do Pici, Fortaleza, CE, Brazil
| | - Alice Maria Costa Martins
- Department of Clinical and Toxicological Analysis, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Hélcio Silva Dos Santos
- Center for Exact Sciences and Technology, State University of Vale do Acaraú, Sobral, CE, Brazil.
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Oduselu GO, Elebiju OF, Ogunnupebi TA, Akash S, Ajani OO, Adebiyi E. Employing Hexahydroquinolines as PfCDPK4 Inhibitors to Combat Malaria Transmission: An Advanced Computational Approach. Adv Appl Bioinform Chem 2024; 17:83-105. [PMID: 39345873 PMCID: PMC11430315 DOI: 10.2147/aabc.s476404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 09/18/2024] [Indexed: 10/01/2024] Open
Abstract
Background Existing antimalarial drugs primarily target blood-stage parasites, but there is a need for transmission-blocking drugs to combat malaria effectively. Plasmodium falciparum Calcium-dependent Protein Kinase 4 (CDPK4) is a promising target for such drugs. This study employed advanced in silico analyses of hexahydroquinolines (HHQ) derivatives to identify PfCDPK4 inhibitors capable of disrupting malaria transmission. Structure-based virtual screening (SBVS) was employed to discover HHQ derivatives with the highest binding affinities against the 3D structure of PfCDPK4 (PDB 1D: 4QOX). Methods Interaction analysis of protein-ligand complexes utilized Discovery Studio Client, while druglikeness and ADMET properties were assessed using SwissADME and pkCSM web servers, respectively. Quantum mechanical calculations of the top hits were conducted using density functional theory (DFT), and GROMACS was employed to perform the molecular dynamics (MD) simulations. Binding free energy was predicted using the MMPBSA.py tool from the AMBER package. Results SBVS identified ten best hits possessing docking scores within the range of -11.2 kcal/mol and -10.6 kcal/mol, surpassing the known inhibitor, BKI-1294 (-9.9 kcal/mol). Among these, 4-[4-(Furan-2-carbonyl)piperazin-1-yl]-1-(naphthalen-2-ylmethyl)-2-oxo-4a,5,6,7,8,8a-hexahydroquinoline-3-carbonitrile (PubChem ID: 145784778) exhibited the highest binding affinity (-11.2 kcal/mol) against PfCDPK4. Conclusion Comparative analysis of this compound with BKI-1294 using advanced computational approaches demonstrated competitive potential. These findings suggest the potential of 4-[4-(Furan-2-carbonyl)piperazin-1-yl]-1-(naphthalen-2-ylmethyl)-2-oxo-4a,5,6,7,8,8a-hexahydroquinoline-3-carbonitrile as a promising PfCDPK4 inhibitor for disrupting malaria transmission. However, further experimental studies are warranted to validate its efficacy and safety profile.
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Affiliation(s)
- Gbolahan O Oduselu
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, OG, Nigeria
| | - Oluwadunni F Elebiju
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, OG, Nigeria
- Department of Chemistry, Covenant University, Ota, OG, Nigeria
| | - Temitope A Ogunnupebi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, OG, Nigeria
- Department of Chemistry, Covenant University, Ota, OG, Nigeria
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Olayinka O Ajani
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, OG, Nigeria
- Department of Chemistry, Covenant University, Ota, OG, Nigeria
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, OG, Nigeria
- African Center of Excellence in Bioinformatics & Data Intensive Science, Makerere University, Kampala, Uganda
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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5
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Arshad U, Shafiq N, Parveen S, Rashid M. Discovery of novel dihydro-pyrimidine hybrids: insight into the design, synthesis, biological evaluation and absorption, distribution, metabolism and excretion studies. Future Med Chem 2024; 16:1949-1969. [PMID: 39263831 PMCID: PMC11485738 DOI: 10.1080/17568919.2024.2389767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 07/24/2024] [Indexed: 09/13/2024] Open
Abstract
Aim: By keeping in aspects, the pharmacological potential of heterocyclic compounds, pyrimidine-based compounds were designed, synthesized and evaluated for α-amylase inhibitory potential.Materials & methods: Five new series 1a-l, 2a-d, 3a-d, 4a-d and 5a-d of 1,2,3,4-tetrahydroprimidine-5-carboxylate derivatives were designed by de novo method by taking Alogliptin as reference compound. Here in we describe synthesis and characterization of compounds as potential α-amylase inhibitor.Results: Structure activity relationship (SAR), in vitro analysis and molecular modelling approaches generate compounds 1 h, 1i, 1k and 4c as potential lead with good α-amylase inhibitory selection. However, compound 1k failed the criteria of optimization as drug lead by ADME studies while all other compounds showed optimum range for all in silico ADME parameters.Conclusion: Therefore, these compounds can serve as potential lead candidate in developing anti-diabetic therapy.
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Affiliation(s)
- Uzma Arshad
- Synthetic & Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University, Faisalabad, 38000, Pakistan
| | - Nusrat Shafiq
- Synthetic & Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University, Faisalabad, 38000, Pakistan
| | - Shagufta Parveen
- Synthetic & Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University, Faisalabad, 38000, Pakistan
| | - Maryam Rashid
- Synthetic & Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University, Faisalabad, 38000, Pakistan
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6
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Islam MR, Tayyeb JZ, Paul HK, Islam MN, Oduselu GO, Bayıl I, Abdellattif MH, Al‐Ahmary KM, Al‐Mhyawi SR, Zaki MEA. In silico analysis of potential inhibitors for breast cancer targeting 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1) catalyses. J Cell Mol Med 2024; 28:e18584. [PMID: 39135338 PMCID: PMC11319393 DOI: 10.1111/jcmm.18584] [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: 01/02/2024] [Revised: 05/12/2024] [Accepted: 05/22/2024] [Indexed: 08/16/2024] Open
Abstract
Breast cancer (BC) is still one of the major issues in world health, especially for women, which necessitates innovative therapeutic strategies. In this study, we investigated the efficacy of retinoic acid derivatives as inhibitors of 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1), which plays a crucial role in the biosynthesis and metabolism of oestrogen and thereby influences the progression of BC and, the main objective of this investigation is to identify the possible drug candidate against BC through computational drug design approach including PASS prediction, molecular docking, ADMET profiling, molecular dynamics simulations (MD) and density functional theory (DFT) calculations. The result has reported that total eight derivatives with high binding affinity and promising pharmacokinetic properties among 115 derivatives. In particular, ligands 04 and 07 exhibited a higher binding affinity with values of -9.9 kcal/mol and -9.1 kcal/mol, respectively, than the standard drug epirubicin hydrochloride, which had a binding affinity of -8.2 kcal/mol. The stability of the ligand-protein complexes was further confirmed by MD simulations over a 100-ns trajectory, which included assessments of hydrogen bonds, root mean square deviation (RMSD), root mean square Fluctuation (RMSF), dynamic cross-correlation matric (DCCM) and principal component analysis. The study emphasizes the need for experimental validation to confirm the therapeutic utility of these compounds. This study enhances the computational search for new BC drugs and establishes a solid foundation for subsequent experimental and clinical research.
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Affiliation(s)
- Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health SciencesDaffodil International UniversityDhakaBangladesh
| | - Jehad Zuhair Tayyeb
- Department of Clinical Biochemistry, College of MedicineUniversity of JeddahJeddahSaudi Arabia
| | - Hridoy Kumar Paul
- Department of PharmacyJashore University of Science and TechnologyJashoreBangladesh
| | | | | | - Imren Bayıl
- Department of bioinformatics and computational biologyGaziantep UniversityGaziantepTurkey
| | - Magda H. Abdellattif
- Department of Chemistry, Sciences CollegeUniversity College of Taraba, Taif UniversityTaifSaudi Arabia
| | | | - Saedah R. Al‐Mhyawi
- Department of Chemistry, College of ScienceUniversity of JeddahJeddahSaudi Arabia
| | - Magdi E. A. Zaki
- Department of Chemistry, College of ScienceImam Mohammad Ibn Saud Islamic University RiyadhRiyadhSaudi Arabia
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Al-Maqtari H, Hasan AH, Suleiman M, Ahmad Zahidi MA, Noamaan MA, Alexyuk P, Alexyuk M, Bogoyavlenskiy A, Jamalis J. Benzyloxychalcone Hybrids as Prospective Acetylcholinesterase Inhibitors against Alzheimer's Disease: Rational Design, Synthesis, In Silico ADMET Prediction, QSAR, Molecular Docking, DFT, and Molecular Dynamic Simulation Studies. ACS OMEGA 2024; 9:32901-32919. [PMID: 39100311 PMCID: PMC11292818 DOI: 10.1021/acsomega.4c03679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 08/06/2024]
Abstract
Acetylcholinesterase inhibitors (AChEIs) are crucial therapeutic targets for both the early and severe stages of Alzheimer's disease (AD). Chalcones and their chromone-based derivatives are well-known building blocks with anti-Alzheimer properties. This study synthesized 4-benzyloxychalcone derivatives and characterized their structures using IR, 1H NMR, 13C NMR, and HRMS. Additionally, the synthesized 4-benzyloxychalcone derivatives were tested for anti-acetylcholinesterase (AChE) activity. The synthesized compounds outperformed galantamine, which is used as a positive control against acetylcholinesterase. Utilizing an acetylcholinesterase (AChE) receptor (PDB ID: 4EY7)-chalcone derivative (12a-c), a molecular docking investigation was performed on the synthesized compounds. The goal was to predict the binding sites and energies of the derivatives with respect to the receptor amino acids. The dynamic behavior of the ligand-receptor complex resulting from the interaction of the best docking compounds 12a and 12c with the acetylcholinesterase receptor was used to analyze the stability via MD simulation. MM/GBSA and MM/PBSA were used to calculate free binding energies using snapshots from system trajectories. Advanced computational approaches incorporating long-range corrections were utilized to calculate the molecular characteristics of chalcone derivatives 12a-c at the DFT/wB97XD/6-311++G(d,p) level. We used the molecular electrostatic surface potential (MESP) with high-quality data and visualization to find the most active site in these molecules. Reactivity descriptors, including the condensed Fukui function, chemical hardness (η), dual descriptors, chemical potential (μ), and electrophilicity (ω), were calculated for the chalcone derivatives.
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Affiliation(s)
- Helmi
Mohammed Al-Maqtari
- Department
of Chemistry, Faculty of Science, Universiti
Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
- Department
of Chemistry, College of Education, Hodeidah
University, University
Street, Hodeidah, Yemen
| | - Aso Hameed Hasan
- Department
of Chemistry, Faculty of Science, Universiti
Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
- Department
of Chemistry, College of Science, University
of Garmian, Kalar 46021, Kurdistan Region, Iraq
| | - Mustapha Suleiman
- Department
of Chemistry, Faculty of Science, Universiti
Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
- Department
of Chemistry, Sokoto state university, Birnin Kebbi road, Sokoto 852101, Sokoto, Nigeria
| | - Muhammad Asraf Ahmad Zahidi
- Department
of Chemistry, Faculty of Science, Universiti
Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | - Mahmoud A. Noamaan
- Mathematics
Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Pavel Alexyuk
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Madina Alexyuk
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Andrey Bogoyavlenskiy
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Joazaizulfazli Jamalis
- Department
of Chemistry, Faculty of Science, Universiti
Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
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8
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Altıntop M, Sağlık Özkan BN, Özdemir A. Design, Synthesis, and Evaluation of New Pyrazolines As Small Molecule Inhibitors of Acetylcholinesterase. ACS OMEGA 2024; 9:31401-31409. [PMID: 39072133 PMCID: PMC11270571 DOI: 10.1021/acsomega.3c10490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 07/30/2024]
Abstract
In pursuit of identifying small molecule inhibitors of acetylcholinesterase (AChE), the synthesis of new 2-pyrazolines was performed efficiently. A modified spectrophotometric method was used to examine their inhibitory effects on AChE as well as butyrylcholinesterase. Four compounds (2a, 2g, 2j, and 2l) were identified as selective AChE inhibitors. Molecular docking studies were conducted to explore their potential interactions with the active site of AChE (PDB code: 4EY7). 1-(3-Nitrophenyl)-3-(thiophen-3-yl)-5-[4-(4-morpholinyl)phenyl]-2-pyrazoline (2l) exerted significant AChE inhibitory action with an IC50 value of 0.040 μM close to donepezil (IC50 = 0.021 μM). In addition to π-π interactions with Tyr341, Tyr124, and Trp86 residues, compound 2l was also capable of forming two hydrogen bonds and a salt bridge at the active site of AChE thanks to its nitro group at the meta position of the phenyl moiety linked to the N 1 position of the pyrazoline scaffold. The higher inhibitory effect of compound 2l on AChE when compared to other compounds in this series might be explained by these additional interactions. Based on the in vitro parallel artificial membrane permeability assay, compound 2l was found to have high blood-brain barrier permeability. In vitro and in silico studies suggest that compound 2l is a potent inhibitor of AChE, which is an important target for neurodegenerative disorders, particularly Alzheimer's disease.
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Affiliation(s)
- Mehlika
Dilek Altıntop
- Department of Pharmaceutical
Chemistry, Faculty of Pharmacy, Anadolu
University, 26470 Eskişehir, Turkey
| | | | - Ahmet Özdemir
- Department of Pharmaceutical
Chemistry, Faculty of Pharmacy, Anadolu
University, 26470 Eskişehir, Turkey
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9
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Yadav N, Kumar R, Sangwan S, Dhanda V, Rani R, Devi S, Duhan A, Sindhu J, Chauhan S, Malik VK, Yadav S, Banakar P. Design, Synthesis, Nematicidal Evaluation, and Molecular Docking Study of Pyrano[3,2- c]pyridones against Meloidogyne incognita. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15512-15522. [PMID: 38959331 DOI: 10.1021/acs.jafc.4c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Root-knot nematodes pose a serious threat to crops by affecting production and quality. Over a period of time, substantial work has been done toward the development of effective and environmentally benign nematicidal compounds. However, due to the inefficiencies of previously reported synthetics in achieving the target of safe, selective, and effective treatment, it is necessary to develop new efficacious and safer nematicidal agents considering human health and environment on top priority. This work aims to highlight the efficient and convenient l-proline catalyzed synthesis of pyrano[3,2-c]pyridone and their use as potential nematicidal agents. In vitro results of larval mortality and egg hatching inhibition revealed maximum nematicidal activity against Meloidogyne incognita from compounds 15b, 15m, and 15w with LC50 values of 28.8, 46.8, and 49.18 μg/mL at 48 h, respectively. Under similar conditions, pyrano[3,2-c]pyridones derivatives 15b (LC50 = 28.8 μg/mL) was found at par with LC50 (26.92 μg/mL) of commercial nematicide carbofuran. The in vitro results were further validated with in silico studies with the most active compound 15b nematicidal within the binding to the pocket of acetylcholine esterase (AChE). In docking, binding free energy values for compound 15b were found to be -6.90 kcal/mol. Results indicated that pyrano[3,2-c]pyridone derivatives have the potential to control M. incognita.
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Affiliation(s)
- Neelam Yadav
- Department of Chemistry, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Ravi Kumar
- Department of Chemistry, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
- MAP Section, Department of Genetics and Plant Breeding, Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
- Center for Bio-Nanotechnology, Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Sarita Sangwan
- Department of Chemistry, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Vidhi Dhanda
- Department of Chemistry, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Reena Rani
- Department of Chemistry, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Sheetu Devi
- Department of Chemistry, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Anil Duhan
- Department of Chemistry, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Jayant Sindhu
- Department of Chemistry, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Sonu Chauhan
- Department of Chemistry, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Vinod Kumar Malik
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Saroj Yadav
- Department of Nematology, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
| | - Prakash Banakar
- Center for Bio-Nanotechnology, Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
- Department of Nematology, Chaudhary Charan Singh Haryana Agricultural University Hisar, Haryana, India 125004
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10
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Abdalla Ali A, Mhamad SA, Hasan AH, Ahmad I, Abdullah SA, Jamil S, Patel H, Murugesan S, Jamalis J. Synthesis, biological evaluation and molecular modeling studies of modulated benzyloxychalcones as potential acetylcholinesterase inhibitors. J Biomol Struct Dyn 2024; 42:3604-3615. [PMID: 37293930 DOI: 10.1080/07391102.2023.2220032] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023]
Abstract
Acetylcholinesterase inhibitors (AChEIs) have become a significant target in the search for an efficient treatment of Alzheimer's disease. Chalcone-based compounds display a strong potency to hinder AChE. So, this study focused on the synthesis of a series of new chalcone derivatives with anti-cholinesterase potential and their structures were characterized based on spectroscopic methods including IR, 1H NMR, 13C NMR and HRMS. Chalcone derivatives were screened against AChE. Most of them exhibited potent inhibitory activity against AChE. Compound 11i showed the most potent activity toward acetylcholinesterase compared to the positive compound, Galantamine. Docking studies into the active site of the acetylcholinesterase enzyme ravealed the significant docking score of the synthesized compounds with docking score of -7.959 to -9.277 kcal/mol when compared to the co-crystallized ligand, Donepezil (-10.567 kcal/mol). The interaction's stability was further assessed using a conventional atomistic 100 ns dynamics simulation study, which revealed the conformational stability of representative compound 11i in the cavity of the acetylcholinesterase enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arman Abdalla Ali
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
- Tafan Preparatory School, General Directorate of Education of Sulaimani, Sulaimani, Kurdistan, Iraq
| | - Shakhawan Ahmad Mhamad
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
- Department of Chemistry, College of Education, University of Sulaimani, Sulaimani, Kurdistan, Iraq
| | - Aso Hameed Hasan
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
- Department of Chemistry, College of Science, University of Garmian, Kalar, Kurdistan, Iraq
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Siti Awanis Abdullah
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
| | - Shajarahtunnur Jamil
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Birla Institute of Technology & Science Pilani (BITS Pilani), Pilani, Rajasthan, India
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
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11
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Zhang XQ, Xiang YN, Qin T, Zou JP, Guo QW, Han ST, Zhang ZY, Liu WW, Ding G, Dong JQ, Shi DH. Design, synthesis and biological evaluation of bakuchiol derivatives as multi-target agents for the treatment of Alzheimer's disease. Fitoterapia 2024; 174:105867. [PMID: 38382891 DOI: 10.1016/j.fitote.2024.105867] [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: 11/04/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/23/2024]
Abstract
The concept of multi-target-directed ligands offers fresh perspectives for the creation of brand-new Alzheimer's disease medications. To explore their potential as multi-targeted anti-Alzheimer's drugs, eighteen new bakuchiol derivatives were designed, synthesized, and evaluated. The structures of the new compounds were elucidated by IR, NMR, and HRMS. Eighteen compounds were assayed for acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) in vitro using Ellman's method. It was shown that most of the compounds inhibited AChE and BuChE to varying degrees, but the inhibitory effect on AChE was relatively strong, with fourteen compounds showing inhibition of >50% at the concentration of 200 μM. Among them, compound 3g (IC50 = 32.07 ± 2.00 μM) and compound 3n (IC50 = 34.78 ± 0.34 μM) showed potent AChE inhibitory activities. Molecular docking studies and molecular dynamics simulation showed that compound 3g interacts with key amino acids at the catalytically active site (CAS) and peripheral anionic site (PAS) of acetylcholinesterase and binds stably to acetylcholinesterase. On the other hand, compounds 3n and 3q significantly reduced the pro-inflammatory cytokines TNF-α and IL-6 released from LPS-induced RAW 264.7 macrophages. Compound 3n possessed both anti-acetylcholinesterase activity and anti-inflammatory properties. Therefore, an in-depth study of compound 3n is expected to be a multi-targeted anti-AD drug.
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Affiliation(s)
- Xiao-Qing Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, People's Republic of China
| | - Yan-Nan Xiang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, People's Republic of China
| | - Tian Qin
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, People's Republic of China
| | - Jing-Pei Zou
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian-Wen Guo
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Shu-Tong Han
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, People's Republic of China
| | - Zhao-Yuan Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, People's Republic of China
| | - Wei-Wei Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, People's Republic of China
| | - Gang Ding
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, People's Republic of China.
| | - Jing-Quan Dong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, People's Republic of China.
| | - Da-Hua Shi
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, People's Republic of China.
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12
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Alam N, Islam M, Najnin H, Shakya S, Khan IM, Hossain MW, Zaidi R. Design and characterization of a binary CT complex of imidazole-oxyresveratrol: exploring its pharmacological and computational aspects. J Biomol Struct Dyn 2024; 42:1319-1335. [PMID: 37054451 DOI: 10.1080/07391102.2023.2199088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/30/2023] [Indexed: 04/15/2023]
Abstract
A new binary charge transfer (CT) complex between imidazole (IMZ) and oxyresveratrol (OXA) was synthesized and characterized experimentally and theoretically. The experimental work was carried out in solution and solid state in selected solvents such as chloroform (CHL), methanol (Me-OH), ethanol (Et-OH), and acetonitrile (AN). The newly synthesized CT complex (D1) has been characterized by various techniques such as UV-visible spectroscopy, FTIR, 1H-NMR, and powder-XRD. The 1:1 composition of D1 is confirmed by Jobs' method of continuous variation and spectrophotometric (at λmax 554 nm) methods at 298 K. The infrared spectra of D1 confirmed the existence of proton transfer hydrogen bond beside charge transfer interaction. These findings indicate that the cation and anion are joined together by the weak hydrogen bonding as N+-H-O-. Reactivity parameters strongly recommended that IMZ behaves as a good electron donor and OXA an efficient electron acceptor. Density functional theory (DFT) computations with basis set B3LYP/6-31G (d,p) was applied to support the experimental results. TD-DFT calculations gives HOMO (-5.12 eV) → LUMO (-1.14 eV) electronic energy gap (Δ E ) to be 3.80 eV. The bioorganic chemistry of D1 was well established after antioxidant, antimicrobial, and toxicity screening in Wistar rat. The type of interactions between HSA and D1 at the molecular level was studied through fluorescence spectroscopy. Binding constant along with the type of quenching mechanism, was investigated through the Stern-Volmer equation. Molecular docking demonstrated that D1 binds perfectly with human serum albumin and EGFR (1M17) and exposes free energy of binding (FEB) values of -295.2 and -283.3 kcal/mol, respectively. The D1 fits successfully into the minor groove of HAS and 1M17, the results of molecular docking show that the D1 binds perfectly with the HAS and 1M17, the higher value of binding energy shows stronger interaction between HAS and 1M17 with D1. Our synthesized complex shows good binding results with HAS compared to 1M17.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nisat Alam
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Maidul Islam
- Deparment of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh, India
| | - Hasina Najnin
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Sonam Shakya
- Deparment of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh, India
| | - Ishaat M Khan
- Deparment of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh, India
| | | | - Rana Zaidi
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
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13
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Hussen NH, Hamid SJ, Sabir MN, Hasan AH, Mohammed SJ, Shali AAK. Novel Penicillin Derivatives Against Selected Multiple-drug Resistant Bacterial Strains: Design, Synthesis, Structural Analysis, In Silico and In Vitro Studies. Curr Org Synth 2024; 21:684-703. [PMID: 37218207 DOI: 10.2174/1570179420666230510104319] [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: 12/16/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023]
Abstract
INTRODUCTION The rising numbers of multiple drug-resistant (MDR) pathogens and the consequent antibacterial therapy failure that resulted in severe medical conditions push to illustrate new molecules with extended activity against the resistant strains. In this manner, chemical derivatization of known antibiotics is proposed to save efforts in drug discovery, and penicillins serve as an ideal in this regard. METHODS Seven synthesized 6-aminopenicillanic acid-imine derivatives (2a-g) were structure elucidated using FT-IR, 1H NMR, 13C NMR, and MS spectroscopy. In silico molecular docking and ADMET studies were made. The analyzed compounds obeyed Lipinski's rule of five and showed promising in vitro bactericidal potential when assayed against E. coli, E. cloacae, P. aeruginosa, S. aureus, and A. baumannii. MDR strains using disc diffusion and microplate dilution techniques. RESULTS The MIC values were 8 to 32 μg/mL with more potency than ampicillin, explained by better membrane penetration and more ligand-protein binding capacity. The 2g entity was active against E. coli. This study was designed to find new active penicillin derivatives against MDR pathogens. CONCLUSION The products showed antibacterial activity against selected MDR species and good PHK, PHD properties, and low predicted toxicity, offering them as future candidates that require further preclinical assays.
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Affiliation(s)
- Narmin Hamaamin Hussen
- Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, University of Sulaimaniyah, Sulaimani, 46001, Kurdistan Region-Iraq, Iraq
| | - Shokhan Jamal Hamid
- Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, University of Sulaimaniyah, Sulaimani, 46001, Kurdistan Region-Iraq, Iraq
| | - Mohammed Nawzad Sabir
- Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, University of Sulaimaniyah, Sulaimani, 46001, Kurdistan Region-Iraq, Iraq
| | - Aso Hameed Hasan
- Department of Chemistry, College of Science, University of Garmian, Kalar, 46021, Kurdistan Region-Iraq, Iraq
| | - Sewara Jalal Mohammed
- Department of Chemistry, College of Science, University of Sulaimaniyah, Qlyasan Street, Sulaimani, 46001, Kurdistan Regional-Iraq, Iraq
| | - Aras Ahmed Kamal Shali
- Department of Biology, College of Science, University of Sulaimaniyah, Qlyasan Street, Sulaimani, 46001, Kurdistan Regional-Iraq, Iraq
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14
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Kawsar SMA, Munia NS, Saha S, Ozeki Y. In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Simulation Studies of Nucleoside Analogs for Drug Discovery- A Mini Review. Mini Rev Med Chem 2024; 24:1070-1088. [PMID: 37957918 DOI: 10.2174/0113895575258033231024073521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/26/2023] [Accepted: 09/22/2023] [Indexed: 11/15/2023]
Abstract
Nucleoside analogs have been widely used as antiviral, antitumor, and antiparasitic agents due to their ability to inhibit nucleic acid synthesis. Adenosine, cytidine, guanosine, thymidine and uridine analogs such as didanosine, vidarabine, remdesivir, gemcitabine, lamivudine, acyclovir, abacavir, zidovusine, stavudine, and idoxuridine showed remarkable anticancer and antiviral activities. In our previously published articles, our main intention was to develop newer generation nucleoside analogs with acylation-induced modification of the hydroxyl group and showcase their biological potencies. In the process of developing nucleoside analogs, in silico studies play an important role and provide a scientific background for biological data. Molecular interactions between drugs and receptors followed by assessment of their stability in physiological environments, help to optimize the drug development process and minimize the burden of unwanted synthesis. Computational approaches, such as DFT, FMO, MEP, ADMET prediction, PASS prediction, POM analysis, molecular docking, and molecular dynamics simulation, are the most popular tools to culminate all preclinical study data and deliver a molecule with maximum bioactivity and minimum toxicity. Although clinical drug trials are crucial for providing dosage recommendations, they can only indirectly provide mechanistic information through researchers for pathological, physiological, and pharmacological determinants. As a result, in silico approaches are increasingly used in drug discovery and development to provide mechanistic information of clinical value. This article portrays the current status of these methods and highlights some remarkable contributions to the development of nucleoside analogs with optimized bioactivity.
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Affiliation(s)
- Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Nasrin S Munia
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Premnagar, 248007, Dehradun, Uttarakhand, 248007, India
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-ku, Yokohama, 236-0027, Japan
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15
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Bogoyavlenskiy A, Zaitseva I, Alexyuk P, Alexyuk M, Omirtaeva E, Manakbayeva A, Moldakhanov Y, Anarkulova E, Imangazy A, Berezin V, Korulkin D, Hasan AH, Noamaan M, Jamalis J. Naturally Occurring Isorhamnetin Glycosides as Potential Agents Against Influenza Viruses: Antiviral and Molecular Docking Studies. ACS OMEGA 2023; 8:48499-48514. [PMID: 38144046 PMCID: PMC10734298 DOI: 10.1021/acsomega.3c08407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/26/2023]
Abstract
Influenza remains one of the most widespread infections, causing an annual illness in adults and children. Therefore, the search for new antiviral drugs is one of the priorities of practical health care. Eight isorhamnetin glycosides were purified from Persicaria species, characterized by nuclear magnetic resonance spectroscopy and mass spectrometry and then evaluated as potential agents against influenza virus. A comprehensive in vitro and in vivo assessment of the compounds revealed that compound 5 displayed the most potent inhibitory activity with an EC50 value of 1.2-1.3 μM, better than standard drugs (isorhamnetin 28.0-56.0 μM and oseltamivir 1.3-9.1 μM). Molecular docking results also revealed that compound 5 has the lowest binding energy (-10.7 kcal/mol) among the tested compounds and isorhamnetin (-8.1 kcal/mol). The ability of the isorhamnetin glycosides to suppress the reproduction of the influenza virus was studied on a model of a cell culture and chicken embryos. The ability of active compounds to influence the structure of the virion, as well as the activity of hemagglutinin and neuraminidase, has been demonstrated. Compound 1, 5, and 6 demonstrated the most effective inhibition of virus replication for all tested viruses. Molecular dynamics simulation techniques were run for 100 ns for compound 5 with two protein receptors Hem (1RUY) and Neu (3BEQ). These results revealed that the Hem-complex system acquired a relatively more stable conformation and even better descriptors than the other Neu-complex studied systems, suggesting that it can be an effective inhibiting drug toward hemagglutinin than neuraminidase inhibition. Based on the reported results, compound 5 can be a good candidate to be evaluated for effectiveness in preclinical testing.
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Affiliation(s)
- Andrey Bogoyavlenskiy
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Irina Zaitseva
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Pavel Alexyuk
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Madina Alexyuk
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Elmira Omirtaeva
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Adolat Manakbayeva
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Yergali Moldakhanov
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Elmira Anarkulova
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Anar Imangazy
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Vladimir Berezin
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Dmitry Korulkin
- Department
of Chemistry and Chemical Technology, al-Farabi
Kazakh National University, Almaty 050010, Kazakhstan
| | - Aso Hameed Hasan
- Department
of Chemistry, College of Science, University
of Garmian, Kalar, Kurdistan Region 46021, Iraq
| | - Mahmoud Noamaan
- Mathematics
Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Joazaizulfazli Jamalis
- Department
of Chemistry Faculty of Science, Universiti
Teknologi Malaysia, UTM Johor
Bahru, Johor 81310, Malaysia
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16
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N SD, Shivakumar, Kumar D U, Ghate SD, Dixit SR, Awasthi A, Revanasiddappa BC. Benzothiazole derivatives as p53-MDM2 inhibitors: in-silico design, ADMET predictions, molecular docking, MM-GBSA Assay, MD simulations studies. J Biomol Struct Dyn 2023:1-12. [PMID: 38111168 DOI: 10.1080/07391102.2023.2294836] [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: 07/04/2023] [Accepted: 12/09/2023] [Indexed: 12/20/2023]
Abstract
Breast cancer stands as the most prevalent malignancy among the female populace. One of the pivotal domains in the therapeutic landscape of breast cancer revolves around the precise targeting of the p53-MDM2 inhibitory pathway. The advent of p53-MDM2 inhibition in the context of developing treatments for breast cancer marks a significant stride. In the quest for enhancing the efficacy of p53-MDM2 inhibition against breast cancer, a new series of benzothiazole compounds (B1-B30) was designed through in-silico methodologies in the present work. Using Schrodinger Maestro, the compounds underwent molecular docking assessments against the p53-MDM2 target (PDB: 4OGT). Compared to reference compounds, B25 and B12 exhibited notably elevated glide scores. Extensive in-silico studies, including ADMET and toxicity evaluations, were performed to predict pharmacokinetics, drug likeness, and toxicity. All compounds adhered to Lipinski criteria, signifying favorable oral drug properties. The MM-GBSA analysis indicated consistent binding free energies. Molecular dynamics simulations for B25 over 200 ns assessed complex stability and interactions. In summary, these compounds exhibit potential for future cancer therapy medication development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shridhar Deshpande N
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, Karnataka, India
| | - Shivakumar
- Department of Chemistry, National Institute of Technology Karnataka, Mangalore, Karnataka, India
| | - Udaya Kumar D
- Department of Chemistry, National Institute of Technology Karnataka, Mangalore, Karnataka, India
| | - Sudeep D Ghate
- Center for Bioinformatics, Nitte (Deemed to be University), Deralakatte, Karnataka, India
| | - Sheshagiri R Dixit
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Karnataka, India
| | - Abhimanyu Awasthi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Karnataka, India
| | - B C Revanasiddappa
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, Karnataka, India
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17
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Alzamami A, Radwan EM, Abo-Elabass E, Behery ME, Alshwyeh HA, Al-Olayan E, Altamimi AS, Attallah NGM, Altwaijry N, Jaremko M, Saied EM. Novel 8-Methoxycoumarin-3-Carboxamides with potent anticancer activity against liver cancer via targeting caspase-3/7 and β-tubulin polymerization. BMC Chem 2023; 17:174. [PMID: 38041156 PMCID: PMC10693084 DOI: 10.1186/s13065-023-01063-5] [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: 08/01/2023] [Accepted: 10/23/2023] [Indexed: 12/03/2023] Open
Abstract
In the present study, we explored the potential of coumarin-based compounds, known for their potent anticancer properties, by designing and synthesizing a novel category of 8-methoxycoumarin-3-carboxamides. Our aim was to investigate their antiproliferative activity against liver cancer cells. Toward this, we developed a versatile synthetic approach to produce a series of 8-methoxycoumarin-3-carboxamide analogues with meticulous structural features. Assessment of their antiproliferative activity demonstrated their significant inhibitory effects on the growth of HepG2 cells, a widely studied liver cancer cell line. Among screened compounds, compound 5 exhibited the most potent antiproliferative activity among the screened compounds (IC50 = 0.9 µM), outperforming the anticancer drug staurosporine (IC50 = 8.4 µM), while showing minimal impact on normal cells. The flow cytometric analysis revealed that compound 5 induces cell cycle arrest during the G1/S phase and triggers apoptosis in HepG2 cells by increasing the percentage of cells arrested in the G2/M and pre-G1 phases. Annexin V-FITC/PI screening further supported the induction of apoptosis without significant necrosis. Further, compound 5 exhibited the ability to activate caspase3/7 protein and substantially inhibited β-tubulin polymerization activity in HepG2 cells. Finally, molecular modelling analysis further affirmed the high binding affinity of compound 5 toward the active cavity of β-tubulin protein, suggesting its mechanistic involvement. Collectively, our findings highlight the therapeutic potential of the presented class of coumarin analogues, especially compound 5, as promising candidates for the development of effective anti-hepatocellular carcinoma agents.
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Affiliation(s)
- Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Science, Shaqra University, AlQuwayiyah 11961, Sahqra, Saudi Arabia
| | - Eman M Radwan
- Chemistry Department (The Division of Organic Chemistry), Faculty of Science, Port-Said University, Port-Said, Egypt
| | - Eman Abo-Elabass
- Chemistry Department (The Division of Biochemistry), Faculty of Science, Port-Said University, Port-Said, Egypt
| | - Mohammed El Behery
- Chemistry Department (The Division of Biochemistry), Faculty of Science, Port-Said University, Port-Said, Egypt
| | - Hussah Abdullah Alshwyeh
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
- Basic & Applied Scientific Research Centre, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 31441, Dammam, Saudi Arabia
| | - Ebtesam Al-Olayan
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdulmalik S Altamimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, PO Box 173, 11942, Alkharj, Saudi Arabia
| | | | - Najla Altwaijry
- Department of Pharmaceutical Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, 11671, Riyadh, Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering, Smart-Health Initiative and Red Sea Research Center, King Abdullah University of Science and Technology, P.O. Box 4700, 23955-6900, Thuwal, Saudi Arabia.
| | - Essa M Saied
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt.
- Institute for Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany.
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18
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Zhou H, Jian Y, Shao Q, Guo F, Zhang M, Wan F, Yang L, Liu Y, Yang L, Li Y, Yang P, Li Z, Li S, Ding W. Development of Sustainable Insecticide Candidates for Protecting Pollinators: Insight into the Bioactivities, Selective Mechanism of Action and QSAR of Natural Coumarin Derivatives against Aphids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18359-18374. [PMID: 37965968 DOI: 10.1021/acs.jafc.3c03493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Plants employ abundant toxic secondary metabolites to withstand insect attack, while pollinators can tolerate some natural defensive compounds. Coumarins, as promising green alternatives to chemical insecticides, possess wide application prospects in the crop protection field. Herein, the bioactivities of 30 natural coumarin derivatives against Aphis gossypii were assessed and revealed that 6-methylcoumarin exhibited potent aphicidal activity against aphids but displayed no toxicity to honeybees. Additionally, using biochemical, bioinformatic, and molecular assays, we confirmed that the action mode of 6-methylcoumarin against aphids was by inhibiting acetylcholinesterase (AChE). Meanwhile, functional assays revealed that the difference in action site, which located in Lys585 in aphid AChE (equivalent to Val548 in honeybee AChE), was the principal reason for 6-methylcoumarin being toxic to aphids but safe to pollinators. This action site was further validated by mutagenesis data, which uncovered how 6-methylcoumarin was unique selective to the aphid over honeybee or mammalian AChE. Furthermore, a 2D-QSAR model was established, revealing that the central structural feature was H3m, which offers guidance for the future design of more potent coumarin compounds. This work provides a sustainable strategy to take advantage of coumarin analogues for pest management while protecting nontarget pollinators.
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Affiliation(s)
- Hong Zhou
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Yufan Jian
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Qingyi Shao
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Fuyou Guo
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Miao Zhang
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Fenglin Wan
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Liang Yang
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Ying Liu
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Li Yang
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Yanhong Li
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Pinglong Yang
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Zongquan Li
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Shili Li
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
| | - Wei Ding
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing 400715, P.R. China
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Kayes MR, Saha S, Alanazi MM, Ozeki Y, Pal D, Hadda TB, Legssyer A, Kawsar SM. Macromolecules: Synthesis, antimicrobial, POM analysis and computational approaches of some glucoside derivatives bearing acyl moieties. Saudi Pharm J 2023; 31:101804. [PMID: 37868643 PMCID: PMC10585311 DOI: 10.1016/j.jsps.2023.101804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
Macromolecules i.e., carbohydrate derivatives are crucial to biochemical and medical research. Herein, we designed and synthesized eight methyl α-D-glucopyranoside (MGP) derivatives (2-8) in good yields following the regioselective direct acylation method. The structural configurations of the synthesized MGP derivatives were analyzed and verified using multiple physicochemical and spectroscopic techniques. Antimicrobial experiments revealed that almost all derivatives demonstrated noticeable antifungal and antibacterial efficacy. The synthesized derivatives showed minimum inhibitory concentration (MIC) values ranging from 0.75 µg/mL to 1.50 µg/mL and minimum bactericidal concentrations (MBCs) ranging from 8.00 µg/mL to 16.00 µg/mL. Compound 6 inhibited Ehrlich ascites carcinoma (EAC) cell proliferation by 10.36% with an IC50 of 2602.23 μg/mL in the MTT colorimetric assay. The obtained results were further rationalized by docking analysis of the synthesized derivatives against 4URO and 4XE3 receptors to explore the binding affinities and nonbonding interactions of MGP derivatives with target proteins. Compound 6 demonstrated the potential to bind with the target with the highest binding energy. In a stimulating environment, a molecular dynamics study showed that MGP derivatives have a stable conformation and binding pattern. The MGP derivatives were examined using POM (Petra/Osiris/Molinspiration) bioinformatics, and as a result, these derivatives showed good toxicity, bioavailability, and pharmacokinetics. Various antifungal/antiviral pharmacophore (Oδ-, O'δ-) sites were identified by using POM investigations, and compound 6 was further tested against other pathogenic fungi and viruses, such as Micron and Delta mutants of SARS-CoV-2.
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Affiliation(s)
- Mohammad R. Kayes
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, Uttarakhand 248007, India
| | - Mohammed M. Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-Ku, Yokohama 236-0027, Japan
| | - Dilipkumar Pal
- Department of Pharmaceutical Sciences, Guru Ghasidas Vishwavidyalaya (A Central University), C.G, 495009 Bilaspur, India
| | - Taibi B. Hadda
- BBEH and LACE Laboratories of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco
| | - Abdelkhaleq Legssyer
- BBEH and LACE Laboratories of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco
| | - Sarkar M.A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
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Sabt A, Abdelraof M, Hamissa MF, Noamaan MA. Antibacterial Activity of Quinoline-Based Derivatives against Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa: Design, Synthesis, DFT and Molecular Dynamic Simulations. Chem Biodivers 2023; 20:e202300804. [PMID: 37933986 DOI: 10.1002/cbdv.202300804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/05/2023] [Indexed: 11/08/2023]
Abstract
Bacterial virulence becomes a significant challenge for clinical treatments, particularly those characterized as Multi-Drug-Resistant (MDR) strains. Therefore, the preparation of new compounds with active moieties could be a successful approach for eradication of MDR strains. For this purpose, newly synthesized quinoline compounds were prepared and tested for their antimicrobial activity against Methicillin-Resistant Staphylococcus Aureus (MRSA) and Pseudomonas Aeruginosa (PA). Among the synthesized derivatives, compounds 1-(quinolin-2-ylamino)pyrrolidine-2,5-dione (8) and 2-(2-((5-methylfuran-2-yl)methylene)hydrazinyl)quinoline (12) were shown to possess the highest antimicrobial activity with the minimum inhibitory concentration with the values of 5±2.2 and10±1.5 μg/mL towards Pseudomonas aeruginosa without any activity towards MRSA. Interestingly, compounds 2-(2-((1H-indol-3-yl)methylene)hydrazinyl)quinoline (13) and 2-(4-bromophenyl)-3-(quinolin-2-ylamino)thiazolidin-4-one (16c) showed significant inhibition activity against Staphylococcus aureus MRSA and Pseudomonas aeruginosa. Compound 13 (with indole moiety) particularly displayed excellent bactericidal activity with low MIC values 20±3.3 and 10±1.5 μg/mL against Staphylococcus aureus MRSA and Pseudomonas aeruginosa, respectively. Effects molecular modelling was used to determine the mode of action for the antimicrobial effect. The stability of complexes formed by docking and target-ligand pairing was evaluated using molecular dynamics simulations. The compounds were also tested for binding affinity to the target protein using MM-PBSA. Density-functional theory (DFT) calculations were also used to investigate the electrochemical properties of various compounds.
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Affiliation(s)
- Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Center, Dokki, Cairo, 12622, Egypt
| | - Mohamed Abdelraof
- Microbial Chemistry Department, Biotechnology Research Institute, National Research Center (NRC), 33 El Behouth St., Giza P.O., 12622, Egypt
| | - Mohamed Farouk Hamissa
- Department of Biomolecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic
| | - Mahmoud A Noamaan
- Mathematics Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
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21
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Suleiman M, Almalki FA, Ben Hadda T, Kawsar SMA, Chander S, Murugesan S, Bhat AR, Bogoyavlenskiy A, Jamalis J. Recent Progress in Synthesis, POM Analyses and SAR of Coumarin-Hybrids as Potential Anti-HIV Agents-A Mini Review. Pharmaceuticals (Basel) 2023; 16:1538. [PMID: 38004404 PMCID: PMC10675815 DOI: 10.3390/ph16111538] [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: 09/12/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
The human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), one of the deadliest pandemic diseases. Various mechanisms and procedures have been pursued to synthesise several anti-HIV agents, but due to the severe side effects and multidrug resistance spawning from the treatment of HIV/AIDS using highly active retroviral therapy (HAART), it has become imperative to design and synthesise novel anti-HIV agents. Literature has shown that natural sources, particularly the plant kingdom, can release important metabolites that have several biological, mechanistic and structural representations similar to chemically synthesised compounds. Certainly, compounds from natural and ethnomedicinal sources have proven to be effective in the management of HIV/AIDS with low toxicity, fewer side effects and affordability. From plants, fungi and bacteria, coumarin can be obtained, which is a secondary metabolite and is well known for its actions in different stages of the HIV replication cycle: protease, integrase and reverse transcriptase (RT) inhibition, cell membrane fusion and viral host attachment. These, among other reasons, are why coumarin moieties will be the basis of a good building block for the development of potent anti-HIV agents. This review aims to outline the synthetic pathways, structure-activity relationship (SAR) and POM analyses of coumarin hybrids with anti-HIV activity, detailing articles published between 2000 and 2023.
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Affiliation(s)
- Mustapha Suleiman
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia;
- Department of Chemistry, Sokoto State University, Birnin Kebbi Road, Sokoto 852101, Nigeria
| | - Faisal A. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Mecca 21955, Saudi Arabia; (F.A.A.); (T.B.H.)
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Mecca 21955, Saudi Arabia; (F.A.A.); (T.B.H.)
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, Oujda 60000, Morocco
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Subhash Chander
- Amity Institute of Phytochemistry & Phytomedicine, Amity University Uttar Pradesh, Noida 201313, India;
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Birla Institute of Technology & Science Pilani (BITS Pilani), Pilani Campus, Pilani 333031, India;
| | - Ajmal R. Bhat
- Department of Chemistry, R.T.M. Nagpur University, Nagpur 440033, India;
| | - Andrey Bogoyavlenskiy
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia;
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22
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Mashood Ahamed FM, Shakya B, Shakya S. Synthesis and characterization of a novel Mannich base benzimidazole derivative to explore interaction with human serum albumin and antimicrobial property: experimental and theoretical approach. J Biomol Struct Dyn 2023; 41:8701-8714. [PMID: 36284457 DOI: 10.1080/07391102.2022.2136757] [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: 07/29/2022] [Accepted: 10/09/2022] [Indexed: 10/31/2022]
Abstract
The novel Mannich base benzimidazole derivative (CB-1), 1-((1H-benzo[d]imidazol-1-yl)(3-chlorophenyl)methyl)-3-phenylurea) has been designed and synthesized by reacting benzimidazole, 3-chloro benzaldehyde, and N-Phenyl urea. CB-1 has been characterized by UV- Visible, FTIR, and 1H NMR. CB-1 was explored to study the interaction with the most abundant blood protein which involved in the role of transport of molecules (drugs), human serum albumin (HSA). Fluorescence results are evident for the presence of both dynamic and static quenching mechanisms in the binding of CB-1 to HSA. Antimicrobial screening were carried out against three bacteria and three fungi pathogens employing disc diffusion method. Molecular docking using AutoDock Vina tool further confirms the experimental binding interactions obtained from fluorescence. Density functional theory (DFT) with B3LYP/6-311G++ basis set was used for correlating theoretical data and obtaining optimized structures of CB-1 along with reactants with molecular electrostatic potential (MEP) map and HOMO→LUMO energy gap calculation. HIGHLIGHTSThe novel Mannich base benzimidazole derivative (CB-1) has been designed and synthesized by Mannich reaction.CB-1 has been characterized by UV- Visible, FTIR, and 1H NMR.Fluorescence quenching reveals that HSA binds to CB-1 via aromatic residues, which is corroborated by molecular docking.Antifungal and antibacterial activity was evaluated in comparison to Nystatin and Gentamicin standard drugs, respectively.DFT calculations support experimental data and provide HOMO-LUMO energy gap.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- F M Mashood Ahamed
- PG and Research Department of Chemistry, Jamal Mohamed College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, India
| | - Barkha Shakya
- Department of Zoology, Aligarh Muslim University, Aligarh, India
| | - Sonam Shakya
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
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23
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Ahmed S, Bhat AR, Rahiman AK, Dongre RS, Hasan AH, Niranjan V, C L, Sheikh SA, Jamalis J, Berredjem M, Kawsar SMA. Green synthesis, antibacterial and antifungal evaluation of new thiazolidine-2,4-dione derivatives: molecular dynamic simulation, POM study and identification of antitumor pharmacophore sites. J Biomol Struct Dyn 2023; 42:10635-10651. [PMID: 37768136 DOI: 10.1080/07391102.2023.2258404] [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: 05/12/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
In this study, a series of thiazolidine-2,4-dione derivatives 3a-i were synthesized and evaluated for antibacterial activity against Gram-positive and Gram-negative strains of Bacillus licheniformis, Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus. Newly prepared thiazolidine (TZD) derivatives were further screened separately for in vitro antifungal activity against cultures of fungal species, namely, Aspergillus niger, Alternaria brassicicola, Chaetomium murorum, Fusarium oxysporum, Lycopodium sp. and Penicillium notatum. The electron-donating substituents (-OH and -OCH3) and electron-withdrawing substituents (-Cl and -NO2) on the attached arylidene moieties of five-membered heterocyclic ring enhanced the broad spectrum of antimicrobial and antifungal activities. The molecular docking study has revealed that compound 3h strongly interacts with the catalytic residues of the active site of the β-carbonic anhydrase (P. aeruginosa) and has the best docking score. In silico pharmacokinetics studies showed the drug-likeness and non-toxic nature of the synthesized compounds, which indicates the combined antibacterial, antiviral and antitumor pharmacophore sites of the targeted drug. This work demonstrates that potential TZD derivatives bind to different types of bacterial and fungal pathogens for circumventing their activities and opens avenues for the development of newer drug candidates that can target bacterial and fungal pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sumeer Ahmed
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | - Ajmal R Bhat
- Department of Chemistry, RTM Nagpur University, Nagpur, India
| | - Aziz Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | | | - Aso Hameed Hasan
- Department of Chemistry, College of Science, University of Garmian, Kalar, Iraq
| | - Vidya Niranjan
- Department of Biotechnology, R V College of Engineering, Bengaluru, India
| | - Lavanya C
- Department of Biotechnology, R V College of Engineering, Bengaluru, India
| | - S A Sheikh
- Department of Physics, National Institute of Technology, Srinagar, Kashmir, India
| | - Joazaizulfazli Jamalis
- Faculty of Science, Department of Chemistry, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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Orabi MAA, Hasan AH, AbouZid SF, El Amir D, Hetta MH, Awadh AAA, Alqahtani OS, Hatano T, El-Shanawany MA. Nutritional, Antioxidant, Antimicrobial, and Anticholinesterase Properties of Phyllanthus emblica: A Study Supported by Spectroscopic and Computational Investigations. Metabolites 2023; 13:1013. [PMID: 37755293 PMCID: PMC10537340 DOI: 10.3390/metabo13091013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Dietary fruits and vegetables play a vital role as food and drugs and are the main sources of antioxidant defences against degenerative diseases, such as brain dysfunctions, cardiovascular diseases, immune system deteriorations, and cancers, brought on by oxidative damage. Phyllanthus emblica is a significant herbal remedy used in conventional medicine to recover lost strength and power. In this research, the potential value of Phyllanthus emblica as a food and drug is researched. The total phenolic, total flavonoid, and total tannin contents as well as the nutritional value, vitamin C, vitamin E, and mineral contents of different organs of P. emblica were evaluated. The antioxidant and antimicrobial activities of extracts and fractions of different organs of P. emblica were determined. A total of eleven flavonoids, simple phenolic, tannin-related phenolic, and tannin molecules were isolated from a hydroalcoholic extract of the leaves and fruits. The structures were identified by spectroscopic data and comparison with the literature values as gallic acid (1), naringenin 7-O-(6″-O-galloyl)-β-D-glucopyranoside (2), 3,3'-di-O-methyl ellagic acid-4'-O-β-d-glucopyranoside (3), 1-O-galloyl glycerol (4), 1,6-di-O-galloyl-β-d-glucopyranoside (5), flavogallonic acid bislactone (6), corilagin (7), ethyl gallate (8), urolithin M5 (9), (E)-p-coumaroyl-1-O-β-d-glucopyranoside (10), and 1,2,4,6-tetra-O-galloyl-β-d-glucopyranoside (11). Among them, compounds 3 and 10 are first isolated from the plant. Molecular docking was performed to investigate the comparative interactions between positive controls (galantamine and donepezil) and selected compounds utilizing acetylcholinesterase (4EY7) as a target receptor. Results exhibited the potency of these compounds against the target receptor. In summary, P. emblica has a wealth of minerals, vitamins C and E, and polyphenolic phytochemicals that may work together to treat infectious disease, prevent and/or treat oxidative-damage-related illnesses including Alzheimer's disease.
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Affiliation(s)
- Mohamed A. A. Orabi
- Department of Pharmacognosy, College of Pharmacy, Najran University, Najran 66454, Saudi Arabia;
| | - Aso Hameed Hasan
- Department of Chemistry, College of Science, University of Garmian, Kalar 46021, Kurdistan Region, Iraq;
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
| | - Sameh F. AbouZid
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt;
| | - Dalia El Amir
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt;
| | - Mona H. Hetta
- Department of Pharmacognosy, Faculty of Pharmacy, Fayoum University, Fayoum 63514, Egypt;
| | - Ahmed Abdullah Al Awadh
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 66454, Saudi Arabia;
| | - Omaish Salman Alqahtani
- Department of Pharmacognosy, College of Pharmacy, Najran University, Najran 66454, Saudi Arabia;
| | - Tsutomu Hatano
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Tsushima, Okayama 700-8530, Japan;
| | - Mohamed A. El-Shanawany
- Department of Pharmacognosy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City 11829, Egypt;
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25
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Hasan AH, Abdulrahman FA, Obaidullah AJ, Alotaibi HF, Alanazi MM, Noamaan MA, Murugesan S, Amran SI, Bhat AR, Jamalis J. Discovery of Novel Coumarin-Schiff Base Hybrids as Potential Acetylcholinesterase Inhibitors: Design, Synthesis, Enzyme Inhibition, and Computational Studies. Pharmaceuticals (Basel) 2023; 16:971. [PMID: 37513883 PMCID: PMC10385371 DOI: 10.3390/ph16070971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
To discover anti-acetylcholinesterase agents for the treatment of Alzheimer's disease (AD), a series of novel Schiff base-coumarin hybrids was rationally designed, synthesized successfully, and structurally characterized using Fourier transform infrared (FTIR), Nuclear magnetic resonance (NMR), and High-Resolution Mass Spectrometry (HRMS) analyses. These hybrids were evaluated for their potential inhibitory effect on acetylcholinesterase (AChE). All of them exhibited excellent inhibitory activity against AChE. The IC50 values ranged from 87.84 to 515.59 μg/mL; hybrids 13c and 13d with IC50 values of 0.232 ± 0.011 and 0.190 ± 0.004 µM, respectively, showed the most potent activity as acetylcholinesterase inhibitors (AChEIs). The reference drug, Galantamine, yielded an IC50 of 1.142 ± 0.027 µM. Reactivity descriptors, including chemical potential (μ), chemical hardness (η), electrophilicity (ω), condensed Fukui function, and dual descriptors are calculated at wB97XD/6-311++ G (d,p) to identify reactivity changes of the designed compounds. An in-depth investigation of the natural charge pattern of the studied compounds led to a deep understanding of the important interaction centers between these compounds and the biological receptors of AChE. The molecular electrostatic surface potential (MESP) of the most active site in these derivatives was determined using high-quality information and visualization. Molecular docking analysis was performed to predict binding sites and binding energies. The structure-activity-property relationship studies indicated that the proposed compounds exhibit good oral bioavailability properties. To explore the stability and dynamic behavior of the ligand-receptor complexes, molecular dynamics simulations (MDS) were performed for 100 ns on the two best docked derivatives, 13c and 13d, with the AChE (4EY7) receptor. A popular method for determining the free binding energies (MM/GBSA) is performed using snapshots taken from the systems' trajectories at 100 ns. These results revealed that the complex system of compound 13d acquired a relatively more stable conformation and exhibited better descriptors than the complex system of compound 13c and the Galantamine drug, suggesting its potential as an effective inhibiting drug. The binding free energy analysis revealed that the 13d-4EY7 complex exhibited greater stability with AChE receptors compared to other complexes.
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Affiliation(s)
- Aso Hameed Hasan
- Department of Chemistry, Faculty of Science, University Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
- Department of Chemistry, College of Science, University of Garmian, Kalar 46021, Kurdistan Region, Iraq
| | - Faruq Azeez Abdulrahman
- Department of Pharmacy, Kalar Private Technical Institute, Kalar 46021, Kurdistan Region, Iraq
| | - Ahmad J Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hadil Faris Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint AbdulRahman University, Riyadh 11671, Saudi Arabia
| | - Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mahmoud A Noamaan
- Mathematics Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Birla Institute of Technology & Science Pilani (BITS Pilani), Pilani Campus, Pilani 333031, Rajasthan, India
| | - Syazwani Itri Amran
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
| | - Ajmal R Bhat
- Department of Chemistry, R.T.M. Nagpur University, Nagpur 440033, Maharashtra, India
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, University Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
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26
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Bogoyavlenskiy A, Alexyuk M, Alexyuk P, Berezin V, Almalki FA, Ben Hadda T, Alqahtani AM, Ahmed SA, Dall'Acqua S, Jamalis J. Computer Analysis of the Inhibition of ACE2 by Flavonoids and Identification of Their Potential Antiviral Pharmacophore Site. Molecules 2023; 28:molecules28093766. [PMID: 37175179 PMCID: PMC10179817 DOI: 10.3390/molecules28093766] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In the present study, we investigated the antiviral activities of 17 flavonoids as natural products. These derivatives were evaluated for their in vitro antiviral activities against HIV and SARS-CoV-2. Their antiviral activity was evaluated for the first time based on POM (Petra/Osiris/Molispiration) theory and docking analysis. POM calculation was used to analyze the atomic charge and geometric characteristics. The side effects, drug similarities, and drug scores were also assumed for the stable structure of each compound. These results correlated with the experimental values. The bioinformatics POM analyses of the relative antiviral activities of these derivatives are reported for the first time.
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Affiliation(s)
- Andrey Bogoyavlenskiy
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Madina Alexyuk
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Pavel Alexyuk
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Vladimir Berezin
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, Oujda 60000, Morocco
| | - Alaa M Alqahtani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Stefano Dall'Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35121 Padova, Italy
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, UTM, Johor Bahru 81310, Johor, Malaysia
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Shakya S, Khan IM, Shakya B, Siddique YH, Varshney H, Jyoti S. Protective effect of the newly synthesized and characterized charge transfer (CT) complex against arecoline induced toxicity in third-instar larvae of transgenic Drosophila melanogaster (hsp70-lacZ)Bg9: experimental and theoretical mechanistic insights. J Mater Chem B 2023; 11:1262-1278. [PMID: 36648430 DOI: 10.1039/d2tb02362h] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Agents that suppress the toxic effect of arecoline (a chemical present in the Areca nut fruit) have become a need of the hour owing to its several harmful effects on human beings. Although some drug molecules have been developed for this purpose, yet, simple, easy to prepare, and economical molecules with remarkable potency are still a challenge to design. The present work thus becomes important as it involves the synthesis of a new charge transfer complex (CTC) material, which has, for the first time, been screened to investigate its effect on the toxic effects of arecoline. The newly designed material (CL), which is generated from the reaction between 2,4,6-trinitrophenol (TNP) and pyrazole (PYZ), has been crystallized by a slow evaporation method and characterized by employing spectral studies including single crystal X-ray crystallography. Spectrophotometry studies with the inclusion of the Benesi-Hildebrand equation reveal 1 : 1 stoichiometry and physical parameters of CL. Assays were used for determining the protective effect of CL against arecoline. CL was found to (dose-dependently) decrease β-galactosidase activity, damage in tissue and DNA damage caused by arecoline (80 μM) in the third-instar larvae of the transgenic Drosophila melanogaster (hsp70-lacZ)Bg9. The possible mechanism of this effect was explored through fluorescence and UV-vis spectroscopy. The possibility of suppression of arecoline action on the muscarinic acetylcholine receptor 1-G11 protein complex (found in the cell membrane) in the presence of CL was studied theoretically by molecular docking. Density functional theory (DFT) also theoretically supported various aspects of the designed material concerning the energy profile of the orbitals (HOMO-LUMO) as well as the energy minimized structure. Furthermore, time dependent (TD) DFT corroborated the electronic properties of the designed material.
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Affiliation(s)
- Sonam Shakya
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India.
| | - Ishaat M Khan
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India.
| | - Barkha Shakya
- Department of Zoology, Aligarh Muslim University, Aligarh 202002, India
| | | | - Himanshi Varshney
- Department of Zoology, Aligarh Muslim University, Aligarh 202002, India
| | - Smita Jyoti
- Department of Zoology, Aligarh Muslim University, Aligarh 202002, India
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Jabri Z, Thiruvalluvar AA, Sghyar R, Mague JT, Sabir S, Rodi YK, Anouar EH, Misbahi K, Sebbar NK, Essassi EM. Synthesis, structure elucidation, Hirshfeld surface analysis, DFT, and molecular docking of new 6-bromo-imidazo[4,5- b]pyridine derivatives as potential tyrosyl-tRNA synthetase inhibitors. J Biomol Struct Dyn 2023; 41:12347-12362. [PMID: 36744539 DOI: 10.1080/07391102.2023.2175258] [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: 09/24/2022] [Accepted: 01/02/2023] [Indexed: 02/07/2023]
Abstract
Novel 6-bromo-imidazo[4,5-b]pyridine derivatives (2-4, 5a-13a, and 6b, 8b-13b) have been synthesized based on a developed systematic approach involving the condensation of 5-Bromo-2,3-diaminopyridine with a suitable aromatic aldehyde in the presence of molecular iodine in water, followed by alkylation reactions using different alkyl dibromide agents. The synthesized compounds were characterized by the NMR spectroscopy technique. The structures of 8a, 9a, 12a, and 11b were confirmed using monocrystalline X-ray crystallography. Theoretical calculations have been carried out using DFT and TD-DFT methods at the B3LYP/6-31G++(d,p) level of theory. Intermolecular contacts between units of 8a, 9a, 12a, and 11b were determined through the Hirshfeld surface analysis. The molecular docking study has been performed to determine the binding affinity of 8a, 9a, 12a, and 11b into the binding site of S. aureus tyrosyl-tRNA synthetase as a target enzyme, and the results revealed that 9a is the most potent compound among the selected compounds with a binding affinity of -8.74 Kcal/mol.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zainab Jabri
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology Sidi Mohamed, Ben Abdallah University, Fez, BP, Morocco
| | | | - Riham Sghyar
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology Sidi Mohamed, Ben Abdallah University, Fez, BP, Morocco
| | - Joel T Mague
- Department of Chemistry, Tulane University New Orleans, LA, USA
| | - Safia Sabir
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology Sidi Mohamed, Ben Abdallah University, Fez, BP, Morocco
| | - Youssef Kandri Rodi
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology Sidi Mohamed, Ben Abdallah University, Fez, BP, Morocco
| | - El Hassane Anouar
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Saudi Arabia
| | - Khalid Misbahi
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology Sidi Mohamed, Ben Abdallah University, Fez, BP, Morocco
| | - Nada Kheira Sebbar
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
- Laboratory of Heterocyclic Organic Chemistry, Mohammed V University in Rabat, Rabat, Morocco
| | - El Mokhtar Essassi
- Laboratory of Heterocyclic Organic Chemistry, Mohammed V University in Rabat, Rabat, Morocco
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Salih RHH, Hasan AH, Hussen NH, Hawaiz FE, Hadda TB, Jamalis J, Almalki FA, Adeyinka AS, Coetzee LCC, Oyebamiji AK. Thiazole-Pyrazoline Hybrids as Potential Antimicrobial Agent: Synthesis, Biological Evaluation, Molecular Docking, DFT Studies and POM analysis. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135191] [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]
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A Review on Recent Approaches on Molecular Docking Studies of Novel Compounds Targeting Acetylcholinesterase in Alzheimer Disease. Molecules 2023; 28:molecules28031084. [PMID: 36770750 PMCID: PMC9921523 DOI: 10.3390/molecules28031084] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Alzheimer's disease (AD), a neurodegenerative brain disorder that affects millions of people worldwide, is characterized by memory loss and cognitive decline. Low levels of acetylcholine and abnormal levels of beta-amyloid, T protein aggregation, inflammation, and oxidative stress, have been associated with AD, and therefore, research has been oriented towards the cholinergic system and primarily on acetylcholinesterase (AChE) inhibitors. In this review, we are focusing on the discovery of AChE inhibitors using computer-based modeling and simulation techniques, covering the recent literature from 2018-2022. More specifically, the review discusses the structures of novel, potent acetylcholinesterase inhibitors and their binding mode to AChE, as well as the physicochemical requirements for the design of potential AChE inhibitors.
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Hasan AH, Shakya S, Hussain FHS, Murugesan S, Chander S, Pratama MRF, Jamil S, Das B, Biswas S, Jamalis J. Design, synthesis, anti-acetylcholinesterase evaluation and molecular modelling studies of novel coumarin-chalcone hybrids. J Biomol Struct Dyn 2023; 41:11450-11462. [PMID: 36591704 DOI: 10.1080/07391102.2022.2162583] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/19/2022] [Indexed: 01/03/2023]
Abstract
The major enzyme responsible for the hydrolytic breakdown of the neurotransmitter acetylcholine (ACh) is acetylcholinesterase (AChE). Acetylcholinesterase inhibitors (AChEIs) are the most prescribed class of medications for the treatment of Alzheimer's disease (AD) and dementia. The limitations of available therapy, like side effects, drug tolerance, and inefficacy in halting disease progression, drive the need for better, more efficacious, and safer drugs. In this study, a series of fourteen novel chalcone-coumarin derivatives (8a-n) were designed, synthesized and characterized by spectral techniques like FT-IR, NMR, and HR-MS. Subsequently, the synthesized compounds were tested for their ability to inhibit acetylcholinesterase (AChE) activity by Ellman's method. All tested compounds showed AChE inhibition with IC50 value ranging from 0.201 ± 0.008 to 1.047 ± 0.043 μM. Hybrid 8d having chloro substitution on ring-B of the chalcone scaffold showed relatively better potency, with IC50 value of 0.201 ± 0.008 μM compared to other members of the series. The reference drug, galantamine, exhibited an IC50 at 1.142 ± 0.027 μM. Computational studies revealed that designed compounds bind to the peripheral anionic site (PAS), the catalytic active site (CAS), and the mid-gorge site of AChE. Putative binding modes, ligand-enzyme interactions, and stability of the best active compound are studied using molecular docking, followed by molecular dynamics (MD) simulations. The cytotoxicity of the synthesised derivatives was determined using the MTT test at three concentrations (100 g/mL, 500 g/mL, and 1 mg/mL). None of the chemicals had a significant effect on the body at the highest dose of 1 mg/mL.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aso Hameed Hasan
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
- Department of Chemistry, College of Science, University of Garmian, Kalar, Kurdistan Region-Iraq, Iraq
| | - Sonam Shakya
- Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Faiq H S Hussain
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Erbil, Kurdistan Region-Iraq, Iraq
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Birla Institute of Technology & Science Pilani (BITS Pilani), Pilani, Rajasthan, India
| | - Subhash Chander
- Amity Institute of Phytochemistry and Phytomedicine, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India
| | - Mohammad Rizki Fadhil Pratama
- Doctoral Program of Pharmaceutical Sciences, Universitas Airlangga, Surabaya, East Java, Indonesia
- Department of Pharmacy, Universitas Muhammadiyah Palangkaraya, Palangka Raya, Central Kalimantan, Indonesia
| | - Shajarahtunnur Jamil
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
| | - Basundhara Das
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Translational Cancer & Stem Cell Research Laboratory, Noida, Uttar Pradesh, India
| | - Subhrajit Biswas
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Translational Cancer & Stem Cell Research Laboratory, Noida, Uttar Pradesh, India
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
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Miyan L, Adam AMA, Refat MS, Alsuhaibani AM. 2-aminopyrimidine-oxalic acid liquid–liquid charge-transfer interactions: Synthesis, spectroscopic characterizations, and the effect of temperature. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Al-Ghulikah HA, Mughal EU, Elkaeed EB, Naeem N, Nazir Y, Alzahrani AYA, Sadiq A, Shah SWA. Discovery of Chalcone Derivatives as Potential α-Glucosidase and Cholinesterase Inhibitors: Effect of Hyperglycemia in Paving a Path to Dementia. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Meesala G, Syeda AH, Varukolu M, Tigulla P. The charge transfer complex between 2, 3-diamino-5-bromopyridine and chloranilic acid: Preparation, spectroscopic characterization, DNA binding, and DFT/PCM analysis. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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35
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Potential inhibitory activity of phytoconstituents against black fungus: In silico ADMET, molecular docking and MD simulation studies. COMPUTATIONAL TOXICOLOGY 2022; 24:100247. [PMID: 36193218 PMCID: PMC9508704 DOI: 10.1016/j.comtox.2022.100247] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022]
Abstract
Mucormycosis or “black fungus” has been currently observed in India, as a secondary infection in COVID-19 infected patients in the post-COVID-stage. Fungus is an uncommon opportunistic infection that affects people who have a weak immune system. In this study, 158 antifungal phytochemicals were screened using molecular docking against glucoamylase enzyme of Rhizopus oryzae to identify potential inhibitors. The docking scores of the selected phytochemicals were compared with Isomaltotriose as a positive control. Most of the compounds showed lower binding energy values than Isomaltotriose (-6.4 kcal/mol). Computational studies also revealed the strongest binding affinity of the screened phytochemicals was Dioscin (-9.4 kcal/mol). Furthermore, the binding interactions of the top ten potential phytochemicals were elucidated and further analyzed. In-silico ADME and toxicity prediction were also evaluated using SwissADME and admetSAR online servers. Compounds Piscisoflavone C, 8-O-methylaverufin and Punicalagin exhibited positive results with the Lipinski filter and drug-likeness and showed mild to moderate of toxicity. Molecular dynamics (MD) simulation (at 300 K for 100 ns) was also employed to the docked ligand-target complex to explore the stability of ligand-target complex, improve docking results, and analyze the molecular mechanisms of protein-target interactions.
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Kawsar SMA, Almalki FA, Hadd TB, Laaroussi H, Khan MAR, Hosen MA, Mahmud S, Aounti A, Maideen NMP, Heidarizadeh F, Soliman SSM. Potential antifungal activity of novel carbohydrate derivatives validated by POM, molecular docking and molecular dynamic simulations analyses. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2123948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Faisal A. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Taibi Ben Hadd
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Muhammad A. R. Khan
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Mohammed A. Hosen
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Shafi Mahmud
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine –Dalgarno Centre for RNA Innovations, The Australian National University, Canberra, Australia
| | - Abdelouahed Aounti
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
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Taghour MS, Elkady H, Eldehna WM, El-Deeb N, Kenawy AM, Elkaeed EB, Alsfouk BA, Alesawy MS, Husein DZ, Metwaly AM, Eissa IH. Design, synthesis, anti-proliferative evaluation, docking, and MD simulations studies of new thiazolidine-2,4-diones targeting VEGFR-2 and apoptosis pathway. PLoS One 2022; 17:e0272362. [PMID: 36149902 PMCID: PMC9506633 DOI: 10.1371/journal.pone.0272362] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/18/2022] [Indexed: 11/19/2022] Open
Abstract
We report herein, the design and synthesis of thiazolidine-2,4-diones derivatives as new inhibitors for VEGFR-2. The designed members were assessed for their in vitro anticancer activity against four cancer cell lines; A549, Caco-2, HepG-2 and MDA-MB-231. Compound 14a showed the most potent effects against Caco-2, and HepG-2 cell lines (IC50 = of 1.5 and 31.5 μM, respectively). Next, the in vitro VEGFR-2 inhibitory activity, safety profiles and selectivity indices were examined for all the synthesized members against the normal Vero cell line. Compound 14a (the safest member against Caco-2 cell line) was further investigated for its ability to inhibit Caco-2 cells migration and healing. Moreover, the apoptotic induction of compound 14a against Caco-2 cell line was investigated by assessing against four apoptotic genes (Bcl2, Bcl-xl, TGF, and Survivin). The results revealed that compound 14a can exert apoptosis through significant reduction of Bcl2, Survivin, and TGF gene expression levels. Finally, deep computational studies including molecular docking, ADMET, toxicity studies, and MD simulation were carried out. Also, the DFT calculations were performed and discussed, and the results confirmed the inhibitory reactivity of 14a against VEGFR-2. Compound 14a is expected to be used as a potential lead in the development of new VEGFR-2 inhibitors with increased potency.
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Affiliation(s)
- Mohammed S. Taghour
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Hazem Elkady
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Nehal El-Deeb
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
- Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications (SRTA City), Alexandria, Egypt
| | - Ahmed M. Kenawy
- Nucleic Acids Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Bshra A. Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mohamed S. Alesawy
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Dalal Z. Husein
- Chemistry Department, Faculty of Science, New Valley University, El-Kharja, Egypt
| | - Ahmed M. Metwaly
- Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications (SRTA City), Alexandria, Egypt
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
- * E-mail: (IHE); (AMM)
| | - Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
- * E-mail: (IHE); (AMM)
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Salih RHH, Hasan AH, Hussein AJ, Samad MK, Shakya S, Jamalis J, Hawaiz FE, Pratama MRF. One-pot synthesis, molecular docking, ADMET, and DFT studies of novel pyrazolines as promising SARS-CoV-2 main protease inhibitors. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [PMCID: PMC9468527 DOI: 10.1007/s11164-022-04831-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyrazoline and its derivatives have numerous prominent pharmacological effects. Focusing on its anti-viral property, we have designed and synthesized three novel pyrazoline derivatives (A1–A3) through one-pot three components and characterized them using different spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, and UV). These compounds were evaluated against SARS-CoV-2 main protease utilizing in-silico molecular docking studies. The docking results displayed good inhibitory activity of the synthesized compounds. Among them, compound A2 was the most active against targeted protein. The drug-likeness and ADMET properties were predicted to have varied profiles but could still be developed, especially A2. DFT/TD-DFT calculations through B3LYP/6-311G++ level of theory were applied to provide comparable theoretical data along with MEP map and electronic energy gap of HOMO → LUMO.
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Affiliation(s)
- Rezan Huseen Hama Salih
- Department of Chemistry, College of Science, University of Garmian, Kalar, Kurdistan Region-Iraq 46021 Iraq
| | - Aso Hameed Hasan
- Department of Chemistry, College of Science, University of Garmian, Kalar, Kurdistan Region-Iraq 46021 Iraq
- Department of Chemistry, Faculty of Science, University Teknologi Malaysia, 81310 Johor Bahru, Johor Malaysia
| | - Awaz Jamil Hussein
- Department of Chemistry, College of Education, Salahaddin University, Erbil, Kurdistan Region-Iraq 44001 Iraq
| | - Mohammed Kareem Samad
- Department of Chemistry, College of Education, Salahaddin University, Erbil, Kurdistan Region-Iraq 44001 Iraq
| | - Sonam Shakya
- Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh, 202002 India
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, University Teknologi Malaysia, 81310 Johor Bahru, Johor Malaysia
| | - Farouq Emam Hawaiz
- Department of Chemistry, College of Education, Salahaddin University, Erbil, Kurdistan Region-Iraq 44001 Iraq
| | - Mohammad Rizki Fadhil Pratama
- Doctoral Program of Pharmaceutical Sciences, Universitas Airlangga, Jl Dr Ir Soekarno Kampus C UNAIR Mulyorejo, Surabaya, East Java 60115 Indonesia
- Department of Pharmacy, Universitas Muhammadiyah Palangkaraya, Jl RTA Milono Km 1.5 Pahandut, Palangka Raya, Central Kalimantan 73111 Indonesia
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Akkoc S, Karatas H, Muhammed MT, Kökbudak Z, Ceylan A, Almalki F, Laaroussi H, Ben Hadda T. Drug design of new therapeutic agents: molecular docking, molecular dynamics simulation, DFT and POM analyses of new Schiff base ligands and impact of substituents on bioactivity of their potential antifungal pharmacophore site. J Biomol Struct Dyn 2022:1-14. [DOI: 10.1080/07391102.2022.2111360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Senem Akkoc
- Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Süleyman Demirel University, Isparta, Türkiye
- Faculty of Engineering and Natural Sciences, Bahçeşehir University, Istanbul, Türkiye
| | - Halis Karatas
- Department of Chemistry, Faculty of Science, Erciyes University, Kayseri, Türkiye
| | - Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Süleyman Demirel University, Isparta, Türkiye
| | - Zülbiye Kökbudak
- Department of Chemistry, Faculty of Science, Erciyes University, Kayseri, Türkiye
| | - Ahmet Ceylan
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Erciyes University, Kayseri, Türkiye
| | - Faisal Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, Saudi Arabia
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Science, Mohammed Premier University, Oujda, Morocco
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Science, Mohammed Premier University, Oujda, Morocco
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Al-Hazmi GH, Ibrahim AA, Refat MS, Adam FA, Allam A, Shakya S, Alsuhaibani AM. Intermolecular charge-transfer complexes between chlorothiazide antihypertensive drug against iodine sigma and picric acid pi acceptors: DFT and molecular docking interaction study with Covid-19 protease. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100605] [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]
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Munia NS, Hosen MA, Azzam KMA, Al-Ghorbani M, Baashen M, Hossain MK, Ali F, Mahmud S, Shimu MSS, Almalki FA, Hadda TB, Laaroussi H, Naimi S, Kawsar SMA. Synthesis, antimicrobial, SAR, PASS, molecular docking, molecular dynamics and pharmacokinetics studies of 5'- O-uridine derivatives bearing acyl moieties: POM study and identification of the pharmacophore sites. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:1036-1083. [PMID: 35797068 DOI: 10.1080/15257770.2022.2096898] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/08/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Because of their superior antibacterial and pharmacokinetic capabilities, many nucleoside-based esters show potential against microorganisms, and may be used as pharmacological agents to address multidrug-resistant pathogenic problems. In this study, several aliphatic and aromatic groups were inserted to synthesize various 5'-O-decanoyluridine (2-5) and 5'-O-lauroyluridine derivatives (6-7) for antimicrobial, in silico computational, pharmacokinetic and POM (Petra/Osiris/Molinspiration). The chemical structures of the synthesized uridine derivatives were confirmed by physicochemical, elemental, and spectroscopic analyses. In vitro antimicrobial screening against five bacteria and two fungi, as well as the prediction of substance activity spectra (PASS), revealed that these uridine derivatives have promising antifungal properties when compared to the antibacterial activities. Density functional theory (DFT) was used to calculate the thermodynamic and physicochemical properties. Molecular docking was conducted against lanosterol 14a-demethylase CYP51A1 (3JUV) and Aspergillus flavus (1R4U) and revealed binding affinities and non-covalent interactions with the target. Then, a 150 ns molecular dynamic simulation was performed to confirm the behavior of the complex structure formed by microbial protein under in silico physiological conditions to examine its stability over time, which revealed a stable conformation and binding pattern in a stimulating environment of uridine derivatives. The acyl chain {CH3(CH2)9CO-} and {CH3(CH2)10CO-} in conjunction with sugar, was determined to have the most potent activity against bacterial and fungal pathogens in a structure-activity relationships (SAR) investigation. POM analyses were conducted with the presence of an antifungal (O δ- -- O' δ-) pharmacophore site. Overall, the present study might be useful for the development of uridine-based novel multidrug-resistant antimicrobial.
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Affiliation(s)
- Nasrin S Munia
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Mohammed A Hosen
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Khaldun M A Azzam
- Pharmacological and Diagnostic Research Center (PDRC), Department of Pharmaceutical Sciences, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, Jordan
| | - Mohammed Al-Ghorbani
- Department of Chemistry, Faculty of Science and Arts, Ulla, Taibah University, Medina, Saudi Arabia
| | - Mohammed Baashen
- Department of Chemistry, Science and Humanities College, Shaqra University, Shaqra, KSA
| | - Mohammed K Hossain
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong, Bangladesh
| | - Ferdausi Ali
- Department of Microbiology, Faculty of Biological Science, University of Chittagong, Chittagong, Bangladesh
| | - Shafi Mahmud
- Department of Genome Science, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Mst S S Shimu
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Taibi B Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Souad Naimi
- Department of Biological Sciences, Sanofi-Aventis, Vitry, France
| | - Sarkar M A Kawsar
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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Obaid RJ, Naeem N, Mughal EU, Al-Rooqi MM, Sadiq A, Jassas RS, Moussa Z, Ahmed SA. Inhibitory potential of nitrogen, oxygen and sulfur containing heterocyclic scaffolds against acetylcholinesterase and butyrylcholinesterase. RSC Adv 2022; 12:19764-19855. [PMID: 35919585 PMCID: PMC9275557 DOI: 10.1039/d2ra03081k] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/27/2022] [Indexed: 01/15/2023] Open
Abstract
Heterocycles are the key structures in organic chemistry owing to their immense applications in the biological, chemical, and pharmaceutical fields. Heterocyclic compounds perform various noteworthy functions in nature, medication, innovation etc. Most frequently, pure nitrogen heterocycles or various positional combinations of nitrogen, oxygen, and sulfur atoms in five or six-membered rings can be found. Inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes is a popular strategy for the management of numerous mental diseases. In this context, cholinesterase inhibitors are utilized to relieve the symptoms of neurological illnesses like dementia and Alzheimer's disease (AD). The present review focuses on various heterocyclic scaffolds and their role in designing and developing new potential AChE and BChE inhibitors to treat AD. Moreover, a detailed structure-activity relationship (SAR) has been established for the future discovery of novel drugs for the treatment of AD. Most of the heterocyclic motifs have been used in the design of new potent cholinesterase inhibitors. In this regard, this review is an endeavor to summarize the biological and chemical studies over the past decade (2010-2022) describing the pursuit of new N, O and S containing heterocycles which can offer a rich supply of promising AChE and BChE inhibitory activities.
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Affiliation(s)
- Rami J Obaid
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
| | - Nafeesa Naeem
- Department of Chemistry, University of Gujrat Gujrat-50700 Pakistan
| | | | - Munirah M Al-Rooqi
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
| | - Amina Sadiq
- Department of Chemistry, Govt. College Women University Sialkot-51300 Pakistan
| | - Rabab S Jassas
- Department of Chemistry, Jamoum University College, Umm Al-Qura University 21955 Makkah Saudi Arabia
| | - Ziad Moussa
- Department of Chemistry, College of Science, United Arab Emirates University P.O. Box 15551 Al Ain Abu Dhabi United Arab Emirates
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
- Department of Chemistry, Faculty of Science, Assiut University 71516 Assiut Egypt
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43
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In silico discovery of multi-targeting inhibitors for the COVID-19 treatment by molecular docking, molecular dynamics simulation studies, and ADMET predictions. Struct Chem 2022. [DOI: 10.1007/s11224-022-01996-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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