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Rani A, Aslam M, Khan J, Pandey G, Singh P, Maharia RS, Nand B. Computational Insights into Chromene/pyran Derivatives: Molecular Docking, ADMET Studies, DFT Calculations, and MD Simulations as Promising Candidates for Parkinson's Disease. Chem Biodivers 2024:e202400920. [PMID: 38818615 DOI: 10.1002/cbdv.202400920] [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: 04/12/2024] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024]
Abstract
Parkinson's disease (PD) is a neurodegenerative condition characterized by both motor and non-motor symptoms. Although PD is commonly associated with a decline of dopaminergic neurons in the substantia nigra, other diagnostic criteria and biomarkers also exist. In the search for novel therapeutic agents, chromene and pyran derivatives have shown potential due to their diverse pharmacological activities. This study utilizes a comprehensive computational approach to investigate the viability of chromene/pyran compounds as potential treatments for PD. The drug-likeness characteristics of these molecules were analyzed using ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) studies. Molecular docking was performed against PDB ID: 2V5Z. The best three molecules chosen were compound 7, compound 24, and compound 67 have a binding energy of -6.7, -8.6, and -10.9 kcal/mol. Molecules demonstrating positive blood-brain barrier permeability, good solubility, and favorable binding affinity were further evaluated using Density Functional Theory (DFT) calculations and Molecular Dynamics (MD) simulations to assess their electronic structure and stability. DFT calculations indicated that molecule 82 has a dipole moment of 15.70 D. RMSD and RMSF results confirmed the stability of the complexes over a 100 ns simulation, with a maximum of 3 hydrogen bonds formed.
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Affiliation(s)
- Anjali Rani
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, 110021, Delhi, India
- Department of Chemistry, SRM Institute of Science and Technology, Delhi-NCR Campus, 201204, Modinagar, Uttar Pradesh, India
| | - Mohd Aslam
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, 110021, Delhi, India
- Department of Chemistry, SRM Institute of Science and Technology, Delhi-NCR Campus, 201204, Modinagar, Uttar Pradesh, India
| | - Javed Khan
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, 110021, Delhi, India
- Department of Chemistry, SRM Institute of Science and Technology, Delhi-NCR Campus, 201204, Modinagar, Uttar Pradesh, India
| | - Garima Pandey
- Department of Chemistry, SRM Institute of Science and Technology, Delhi-NCR Campus, 201204, Modinagar, Uttar Pradesh, India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, 110021, Delhi, India
| | - R S Maharia
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, 110021, Delhi, India
| | - Bhaskara Nand
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, 110021, Delhi, India
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Naseem S, Khan S, Hussain S, Mirza MU, Ashraf M, Shafiq Z, Trant JF. Synthesis, biological evaluation, and molecular docking study of xanthene-linked thiosemicarbazones as cholinesterase inhibitors. J Biomol Struct Dyn 2023:1-15. [PMID: 37948312 DOI: 10.1080/07391102.2023.2274981] [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: 03/07/2023] [Accepted: 10/18/2023] [Indexed: 11/12/2023]
Abstract
This study delineates the design and synthesis of a series of xanthene-based thiosemicarbazones that show low μM inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), crucial enzymes associated with, among others, Alzheimer's Disease (AD) pathology. Despite FDA-approved AChE inhibitors being frontline treatments for AD, there remains a need for agents exhibiting improved efficacy and selectivity. Our synthesized series demonstrate meaningful inhibition against AChE (IC50 ranging from 4.2 to 62 μM). These compounds exhibit comparatively lower potency against BChE (IC50 values between 64 and 315 μM), showcasing a pronounced AChE selectivity compared to physostigmine. The selectivity index for the compounds between the two targets does vary between 0.02 and 0.75 highlighting that even minor structural differences can have drastic effects on protein interactions. Molecular docking insights further substantiated these observations, revealing the importance of the xanthene scaffold for AChE-binding and the aryl R2 moiety for BChE interactions. Notably, some compounds demonstrated dual enzyme targeting, emphasizing their interactions could be exploited for developing monotherapies against cholinesterase-associated neurodegenerative afflictions like AD. Collectively, these findings suggest that xanthene-based thiosemicarbazones are a promising and highly accessible scaffold that deserve further investigative exploration in the cholinesterase inhibitor therapeutic landscape.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saira Naseem
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Samra Khan
- Department of Chemistry and Biochemistry, University of Windsor, Canada
| | - Safdar Hussain
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Muhammad Ashraf
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
- Department of Pharmaceutical & Medicinal Chemistry, Universitat Bonn, Bonn, Germany
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Canada
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Pouramiri B, Rashidi M, Lotfi S, Mohammadi M, Rabiei K. Biological Evaluation of Anti-Cholinesterase Activity, in Silico Molecular Docking Studies, and DFT Calculations of Green Synthesized Thiadiazolo[3,2-a]pyrimidine Derivatives. Chem Biodivers 2023; 20:e202301193. [PMID: 37869899 DOI: 10.1002/cbdv.202301193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/17/2023] [Accepted: 10/22/2023] [Indexed: 10/24/2023]
Abstract
A series of [1,3,4] thiadiazolo[3,2-a]pyrimidine-6-carboxylate derivatives 4(a-n) have been designed and synthesized as inhibitors of acetylcholinesterase (AChE). Synthesizing of thiadiazolo[3,2-a] pyrimidines was carried out in a single step, one-pot reaction using aromatic aldehydes, ethyl acetoacetate and different derivatives of 1,3,4-thiadiazoles (with molar ratio of 1 : 2 : 1, respectively) in conjunction with the catalyst, anhydrous iron(III) chloride by a grinding method under solvent-free conditions at room temperature. The in-vitro studies exhibited good potency for inhibiting AChE comparable with donepezil as the reference drug. The best results were obtained by Ethyl 2-(4-nitroophenyl)-7-methyl-5-(pyridin-3-yl)-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidine-6-carboxylate 4n with IC50 value of 0.082±0.001 μM which was comparable with AChE inhibitory effects of donepezil (IC50 =0.079 μM).
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Affiliation(s)
- Behjat Pouramiri
- Department of Organic Chemistry, Qom University of Technology, Qom
| | - Mohsen Rashidi
- Department of Chemistry, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, 37195 Qom, Iran
| | - Safa Lotfi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | | | - Khadijeh Rabiei
- Department of Organic Chemistry, Qom University of Technology, Qom
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Mutahir S, Khan MA, Mushtaq M, Deng H, Naglah AM, Almehizia AA, Al-Omar MA, Alrayes FI, Kalmouch A, El-Mowafi SA, Refat MS. Investigations of Electronic, Structural, and In Silico Anticancer Potential of Persuasive Phytoestrogenic Isoflavene-Based Mannich Bases. Molecules 2023; 28:5911. [PMID: 37570881 PMCID: PMC10421429 DOI: 10.3390/molecules28155911] [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: 06/18/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Isoflavenes have received the greatest research attention among the many groups of phytoestrogens. In this study, various isoflavene-based Mannich bases were selected for their theoretical studies. The purpose of this research was to discover the binding potential of all the designated Mannich bases acting as inhibitors against cancerous proteins EGFR, cMet, hTrkA, and HER2 (PDB codes: 5GTY, 3RHK, 6PL2, and 7JXH, respectively). For their virtual screening, DFT calculations and molecular docking studies were undertaken using in silico software. Docking studies predicted that ligands 5 and 15 exhibited the highest docking score by forming hydrogen bonds within the active pocket of protein 6PL2, ligands 1 and 15 both with protein 3RHK, and 7JXH, 12, and 17 with protein 5GTY. Rendering to the trends in polarizability and dipole moment, the energy gap values (0.2175 eV, 0.2106 eV) for the firm conformers of Mannich bases (1 and 4) replicate the increase in bioactivity and chemical reactivity. The energy gap values (0.2214 eV and 0.2172 eV) of benzoxazine-substituted isoflavene-based Mannich bases (9 and 10) reflect the increase in chemical potential due to the most stable conformational arrangements. The energy gap values (0.2188 eV and 0.2181 eV) of isoflavenes with tertiary amine-based Mannich bases (14 and 17) reflect the increase in chemical reactivity and bioactivity due to the most stable conformational arrangements. ADME was also employed to explore the pharmacokinetic properties of targeted moieties. This study revealed that these ligands have a strong potential to be used as drugs for cancer treatment.
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Affiliation(s)
- Sadaf Mutahir
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
- Department of Chemistry, University of Sialkot, Sialkot 51300, Pakistan
| | - Muhammad Asim Khan
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
- Department of Chemistry, University of Sialkot, Sialkot 51300, Pakistan
| | - Maryam Mushtaq
- Department of Chemistry, University of Sialkot, Sialkot 51300, Pakistan
| | - Haishan Deng
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ahmed M. Naglah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdulrahman A. Almehizia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohamed A. Al-Omar
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Faris Ibrahim Alrayes
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Atef Kalmouch
- Peptide Chemistry Department, Chemical Industries Research Institute, National Research Centre, Cairo 12622, Egypt
| | - Shaima A. El-Mowafi
- Peptide Chemistry Department, Chemical Industries Research Institute, National Research Centre, Cairo 12622, Egypt
| | - Moamen S. Refat
- Department of Chemistry, Faculty of Science, Port Said University, Port Said 42526, Egypt
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Mutahir S, Khan MA, Almehizia AA, Abouzied AS, Khalifa NE, Naglah AM, Deng H, Refat MS, Khojali WMA, Huwaimel B. Design, Synthesis, Characterization and Computational Studies of Mannich Bases Oxadiazole Derivatives as New Class of Jack Bean Urease Inhibitors. Chem Biodivers 2023; 20:e202300241. [PMID: 37344354 DOI: 10.1002/cbdv.202300241] [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: 02/18/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 06/23/2023]
Abstract
Mannich bases consisting of 1,3,4-oxadiazole-2-thione (3 a-3 l) bearing various substituents were synthesized and found potent jack bean urease inhibitors. The prepared compounds showed significantly good inhibitory activities with IC50 values from 9.45±0.05 to 267.42±0.23 μM. The compound 3 k containing 4-chlorophenyl (-R) and 4-hydroxyphenyl (-R') was most active with IC50 9.45±0.05 μM followed by 3 e (IC50 22.52±0.15 μM) in which -R was phenyl and -R' was isopropyl group. However, when both -R and -R' were either 4-chlorophenyl groups (3 l) or only -R' was 4-nitrophenyl (3 i), both compounds were found inactive. The detailed binding affinities of the produced compounds with protein were explored through molecular docking and data-supported in-vitro enzyme inhibition profiles. Drug likeness was confirmed by in silico ADME investigations and molecular orbital analysis (HOMO-LUMO) and electrostatic potential maps were got from DFT calculations. ESP maps exposed that there are two potential binding sites with the most positive and most negative parts.
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Affiliation(s)
- Sadaf Mutahir
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, China
| | - Muhammad Asim Khan
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, China
| | - Abdulrahman Abdulaziz Almehizia
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Amr Salah Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, 81442, Saudi Arabia
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NODCAR), Giza, 12553, Egypt
| | - Nasrin Eldirdiri Khalifa
- Department of pharmaceutics, College of Pharmacy, University of Hail, Hail, 81442, Saudi Arabia
- Department of pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum, 11115, Sudan
| | - Ahmed Mohamed Naglah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Haishan Deng
- School of Pharmacy, Nanjing University of Traditional Chinese Medicine, Nanjing, 210094, China
| | - Moamen Salaheldeen Refat
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Weam Mohamed Ali Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, 81442, Saudi Arabia
- Department of pharmaceutical chemistry, faculty of pharmacy, Omdurman Islamic University, Omdurman, 14415, Sudan
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, 81442, Saudi Arabia
- Medical and Diagnostic Research Center, University of Hail, Hail, 81442, Saudi Arabia
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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: 19] [Impact Index Per Article: 19.0] [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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Sain S, Jaiswal S, Jain S, Misra N, Srivastava A, Jendra R, Kishore D, Dwivedi J, Wabaidur SM, Islam MA, Sharma S. Synthesis and Theoretical Studies of Biologically Active Thieno Nucleus Incorporated Tri and Tetracyclic Nitrogen Containing Heterocyclics Scaffolds via Suzuki Cross-Coupling Reaction. Chem Biodivers 2022; 19:e202200540. [PMID: 36310125 DOI: 10.1002/cbdv.202200540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/25/2022] [Indexed: 12/27/2022]
Abstract
A new series of thieno nucleus embellished trinuclear (19, 20) and tetranuclear (21-24) nitrogen heteroaryl have been synthesized by the Suzuki cross-coupling reaction using bis(triphenylphosphine)palladium(II) dichloride. All the synthesized compounds were characterized by IR, 1 H-NMR, 13 CNMR and Mass spectral properties. In vitro antibacterial studies of the synthesized compound were conducted using broth microdilution assay employing Gram-positive and Gram-negative strains and half-maximal inhibitory concentration (IC50 ) was determined. The result showed that compound 20 possess best antibacterial activity against S. aureus and E. coli with IC50 values of 60 μg mL-1 and 90 μg mL-1 . Further to determine the mode of antibacterial action, compounds 20 and 21 were examined for in vitro bacterial dehydrogenase inhibitory assay. To understand the binding affinity of the synthesized compounds, the docking study was performed in the bacterial dehydrogenase enzyme by AutoDock Vina software and structure was confirmed by Discovery Studio Visualizer. All the synthesized compounds were docked in a good manner within the active sites of the bacterial dehydrogenase enzyme and exhibited good binding energies.
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Affiliation(s)
- Shalu Sain
- Department of Chemistry, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Shivangi Jaiswal
- Department of Chemistry, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Sonika Jain
- Department of Chemistry, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Namita Misra
- Thakur H. N. Singh, PG College, Prayagraj, Uttar Pradesh, 211016, India
| | - Anamika Srivastava
- Department of Chemistry, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Ra Jendra
- Department of Chemistry, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Dharma Kishore
- Department of Chemistry, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Jaya Dwivedi
- Department of Chemistry, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | | | - Mohammad Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health University of Manchester, Manchester, United Kingdom
| | - Swapnil Sharma
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
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Chaudhry F, Munir R, Ashraf M, Mehr-un-Nisa, Huma R, Malik N, Hussain S, Ali Munawar M, Ain Khan M. Exploring Facile Synthesis and Cholinesterase Inhibiting Potential of Heteroaryl Substituted Imidazole Derivatives for the Treatment of Alzheimer’s Disease. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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