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Mousavi H, Rimaz M, Zeynizadeh B. Practical Three-Component Regioselective Synthesis of Drug-Like 3-Aryl(or heteroaryl)-5,6-dihydrobenzo[ h]cinnolines as Potential Non-Covalent Multi-Targeting Inhibitors To Combat Neurodegenerative Diseases. ACS Chem Neurosci 2024; 15:1828-1881. [PMID: 38647433 DOI: 10.1021/acschemneuro.4c00055] [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] [Indexed: 04/25/2024] Open
Abstract
Neurodegenerative diseases (NDs) are one of the prominent health challenges facing contemporary society, and many efforts have been made to overcome and (or) control it. In this research paper, we described a practical one-pot two-step three-component reaction between 3,4-dihydronaphthalen-1(2H)-one (1), aryl(or heteroaryl)glyoxal monohydrates (2a-h), and hydrazine monohydrate (NH2NH2•H2O) for the regioselective preparation of some 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnoline derivatives (3a-h). After synthesis and characterization of the mentioned cinnolines (3a-h), the in silico multi-targeting inhibitory properties of these heterocyclic scaffolds have been investigated upon various Homo sapiens-type enzymes, including hMAO-A, hMAO-B, hAChE, hBChE, hBACE-1, hBACE-2, hNQO-1, hNQO-2, hnNOS, hiNOS, hPARP-1, hPARP-2, hLRRK-2(G2019S), hGSK-3β, hp38α MAPK, hJNK-3, hOGA, hNMDA receptor, hnSMase-2, hIDO-1, hCOMT, hLIMK-1, hLIMK-2, hRIPK-1, hUCH-L1, hPARK-7, and hDHODH, which have confirmed their functions and roles in the neurodegenerative diseases (NDs), based on molecular docking studies, and the obtained results were compared with a wide range of approved drugs and well-known (with IC50, EC50, etc.) compounds. In addition, in silico ADMET prediction analysis was performed to examine the prospective drug properties of the synthesized heterocyclic compounds (3a-h). The obtained results from the molecular docking studies and ADMET-related data demonstrated that these series of 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines (3a-h), especially hit ones, can really be turned into the potent core of new drugs for the treatment of neurodegenerative diseases (NDs), and/or due to the having some reactionable locations, they are able to have further organic reactions (such as cross-coupling reactions), and expansion of these compounds (for example, with using other types of aryl(or heteroaryl)glyoxal monohydrates) makes a new avenue for designing novel and efficient drugs for this purpose.
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Affiliation(s)
- Hossein Mousavi
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran 19395-3697, Iran
| | - Behzad Zeynizadeh
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
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Almeida RL, Maltarollo VG, Coelho FGF. Overcoming class imbalance in drug discovery problems: Graph neural networks and balancing approaches. J Mol Graph Model 2024; 126:108627. [PMID: 37801808 DOI: 10.1016/j.jmgm.2023.108627] [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: 06/27/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
This research investigates the application of Graph Neural Networks (GNNs) to enhance the cost-effectiveness of drug development, addressing the limitations of cost and time. Class imbalances within classification datasets, such as the discrepancy between active and inactive compounds, give rise to difficulties that can be resolved through strategies like oversampling, undersampling, and manipulation of the loss function. A comparison is conducted between three distinct datasets using three different GNN architectures. This benchmarking research can steer future investigations and enhance the efficacy of GNNs in drug discovery and design. Three hundred models for each combination of architecture and dataset were trained using hyperparameter tuning techniques and evaluated using a range of metrics. Notably, the oversampling technique outperforms eight experiments, showcasing its potential. While balancing techniques boost imbalanced dataset models, their efficacy depends on dataset specifics and problem type. Although oversampling aids molecular graph datasets, more research is needed to optimize its usage and explore other class imbalance solutions.
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Affiliation(s)
- Rafael Lopes Almeida
- Graduate Program in Electrical Engineering - Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, 31270-901, MG, Brazil
| | - Vinícius Gonçalves Maltarollo
- Department of Pharmaceutical Products - Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, 31270-901, MG, Brazil.
| | - Frederico Gualberto Ferreira Coelho
- Department of Electronical Engineering - Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, 31270-901, MG, Brazil
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Mathew B, Ravichandran V, Raghuraman S, Rangarajan TM, Abdelgawad MA, Ahmad I, Patel HM, Kim H. Two dimensional-QSAR and molecular dynamics studies of a selected class of aldoxime- and hydroxy-functionalized chalcones as monoamine oxidase-B inhibitors. J Biomol Struct Dyn 2023; 41:9256-9266. [PMID: 36411738 DOI: 10.1080/07391102.2022.2146198] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/05/2022] [Indexed: 11/23/2022]
Abstract
Candidates generated from unsaturated ketone (chalcone) demonstrated as strong, reversible and specific monoamine oxidase-B (MAO-B) inhibitory activity. For the research on MAO-B inhibition, our team has synthesized and evaluated a panel of aldoxime-chalcone ethers (ACE) and hydroxylchalcones (HC). The MAO-B inhibitory activity of several candidates is in the micro- to nanomolar range in these series. The purpose of this research was to develop predictive QSAR models and look into the relation between MAO-B inhibition by aldoxime and hydroxyl-functionalized chalcones. It was shown that the molecular descriptors ETA Shape P, MDEO-12, ETA dBetaP, SpMax1 Bhi and ETA EtaP B are significant in the inhibitory action of the MAO-B target. Using the current 2D QSAR models, potential chalcone-based MAO-B inhibitors might be created. The lead molecules were further analyzed by the detailed molecular dynamics study to establish the stability of the ligand-enzyme complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, India
| | | | - Seenivasan Raghuraman
- Department of Pharmaceutical Chemistry, Unity College of Pharmacy, Bhongir, Telangana, India
| | - T M Rangarajan
- Department of Chemistry, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Mohamed A Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf, Saudi Arabia
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Harun M Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Hoon Kim
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon, Republic of Korea
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Tahir A, Siddiqi AR, Maryam A, Chaitanya Vedithi S, Blundell TL. Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis. J Biomol Struct Dyn 2023:1-14. [PMID: 37814544 DOI: 10.1080/07391102.2023.2264394] [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: 03/27/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
Ostrinia furnacalis is a species of moth in the Crambidae family that is harmful to maize and other corn crops in Southeast Asia and the Western Pacific regions. Ostrinia furnacalis causes devastating losses to economically important corn fields. The β-N-acetyl-D-hexosaminidase is an essential enzyme in O. furnacalis and its substrate binding +1 active site is different from that of the plants and humans β-N-acetyl-D-hexosaminidases. To develop environment-friendly insecticides against OfHex1, we conducted structure-guided computational insecticide discovery to identify potential inhibitors that can bind the active site and inhibit the substrate binding and activity of the enzyme. We adopted a three-pronged strategy to conduct virtual screening using Glide and virtual screening workflow (VSW) in Schrödinger Suite-2022-3, against crystal structures of OfHex1 (PDB Id:3NSN), its homologue in humans (PDB Id: 1NP0) and Alphafold model of β-N-acetyl-D-hexosaminidase from Trichogramma pretiosum, an egg parasitoid that protects the crops from O. furnacalis. A library of 20,313 commercially available and "insecticide-like" compounds was extracted from published literature. LigPrep enabled 44,943 ready-to-dock conformers generation. Glide docking revealed 18 OfHex1-specific hits that were absent in human and T. pretiosum screens. Reference docking was conducted using inhibitors/natural ligands in the crystal structures and hits with better docking scores than the reference were selected for MD simulations using Desmond to understand the stability of hit-target interactions. We noted five compounds that bound to OfHex1 TMX active-site based on their docking scores, consistent binding as noted by MD simulations and their insecticide/pesticide likeliness as noted by the Comprehensive Pesticide Likeness Analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adeena Tahir
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Arooma Maryam
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Sundeep Chaitanya Vedithi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Heart and Lung Research Institute (HLRI), Cambridge, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Heart and Lung Research Institute (HLRI), Cambridge, United Kingdom
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Abstract
Proper elucidation of drug-target interaction is one of the most significant steps at the early stages of the drug development research. Computer-aided drug design tools have substantial contribution to this stage. In this chapter, we specifically concentrate on the computational methods widely used to develop reversible inhibitors for monoamine oxidase (MAO) isozymes. In this context, current computational techniques in identifying the best drug candidates showing high potency are discussed. The protocols of structure-based drug design methodologies, namely, molecular docking, in silico screening, and molecular dynamics simulations, are presented. Employing case studies of safinamide binding to MAO B, we demonstrate how to use AutoDock 4.2.6 and NAMD software packages.
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Affiliation(s)
- Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey.
| | - Safiye Sağ Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, Istanbul, Turkey
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Jadoon R, Aamir Javed M, Saeed Jan M, Ikram M, Mahnashi MH, Sadiq A, Shahid M, Rashid U. Design, synthesis, in-vitro, in-vivo and ex-vivo pharmacology of thiazolidine-2,4-dione derivatives as selective and reversible monoamine oxidase-B inhibitors. Bioorg Med Chem Lett 2022; 76:128994. [PMID: 36162779 DOI: 10.1016/j.bmcl.2022.128994] [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: 05/17/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 11/02/2022]
Abstract
Neurodegenerative ailments are a diverse set of syndromes distinguished by gradual deterioration of the structure as well as functions of the central nervous system or peripheral nervous system. Alzheimer's disease (AD) and Parkinson's disease (PD) have no cure, common, and are high prevalent neurodegenerative pathologies. In current research, rationally designed thiazolidine-2,4-dione based analogs were synthesized and tested for their inhibition potential against two isoforms of monoamine oxidase (MAO-A / MAO-B). Structure activity relationships were explored. Pyridinyl and thiazolyl hydrazone derivative 43 and 44 with IC50 value of 0.013 µM and 0.008 µM (selectivity 228 / 226 times) exhibited higher potency than reference drug safinamide. Most active compounds showed BBB penetration in PAMPA in-vitro assay. Except nitro derivative 41, all compounds were non-neurotoxic in the studied concentration. Molecular docking studies supported the in-vitro experimental results and the selectivity by comparing the binding energy values against both MAO-A and MAO-B isoforms. All the results of current research suggest compounds 43 and 44 may serve as promising candidates for further research for treatment of neurodegenerative diseases.
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Affiliation(s)
- Ridha Jadoon
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, 22060 Abbottabad, Pakistan
| | - Muhammad Aamir Javed
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, 22060 Abbottabad, Pakistan
| | - Muhammad Saeed Jan
- Department of Pharmacy, The Professional Institute of Health Sciences, Mardan, KP, Pakistan
| | - Muhammad Ikram
- Department of Pharmacy, COMSATS University Islamabad, Abbottabad Campus, 22060 Abbottabad, Pakistan
| | - Mater H Mahnashi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Najran University, Najran, Saudi Arabia
| | - Abdul Sadiq
- Department of Pharmacy, University of Malakand, 18000 Chakdara, KP, Pakistan
| | - Muhammad Shahid
- Department of Pharmacy, Institute of Integrative Biosciences, CECOS University of IT and Emerging Sciences, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Umer Rashid
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, 22060 Abbottabad, Pakistan.
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The hop cones (Humulus lupulus L.): Chemical composition, antioxidant properties and molecular docking simulations. J Herb Med 2022. [DOI: 10.1016/j.hermed.2022.100566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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