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Shafiq N, Shahzad N, Rida F, Ahmad Z, Nazir HA, Arshad U, Zareen G, Attiq N, Parveen S, Rashid M, Ali B. One-pot multicomponent synthesis of novel pyridine derivatives for antidiabetic and antiproliferative activities. Future Med Chem 2023; 15:1069-1089. [PMID: 37503685 DOI: 10.4155/fmc-2023-0132] [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: 07/29/2023] Open
Abstract
Background: Due to the close relationship of diabetes with hypertension reported in various research, a set of pyridine derivatives with US FDA-approved drug cores were designed and integrated by artificial intelligence. Methods: Novel pyridines were designed and synthesized. Compounds MNS-1-MNS-4 were evaluated for their structure and were screened for their in vitro antidiabetic (α-amylase) activity and anticancer (HepG2) activity by methyl thiazolyl tetrazolium assay. Comparative 3D quantitative structure-activity relationship analysis and pharmacophore generation were carried out. Results: The study revealed MNS-1 and MNS-4 as good alternatives to acarbose as antidiabetic agents, and MNS-2 as a more viable, better alternative to doxorubicin in the methyl thiazolyl tetrazolium assay. Conclusion: This combination of studies identifies new and more active analogs of existing FDA-approved drugs for the treatment of diabetes.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Nabeel Shahzad
- Department of Chemistry, University of WAH, Wah Cantt, 44700, Pakistan
| | - Fatima Rida
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Zaheer Ahmad
- Department of Chemistry, University of WAH, Wah Cantt, 44700, Pakistan
| | - Hafiza Ayesha Nazir
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Uzma Arshad
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Gul Zareen
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Naila Attiq
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Shagufta Parveen
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Maryam Rashid
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Basharat Ali
- Department of Chemistry, Khawaja Fareed University of Engineering & Information Technology, Rahim Yar Khan, Punjab, 64200, Pakistan
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Rossino G, Orellana I, Caballero J, Schepmann D, Wünsch B, Rui M, Rossi D, González-Avendaño M, Collina S, Vergara-Jaque A. New Insights into the Opening of the Occluded Ligand-Binding Pocket of Sigma1 Receptor: Binding of a Novel Bivalent RC-33 Derivative. J Chem Inf Model 2019; 60:756-765. [DOI: 10.1021/acs.jcim.9b00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Giacomo Rossino
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Ivana Orellana
- Center for Bioinformatics and Molecular Simulation, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
| | - Julio Caballero
- Center for Bioinformatics and Molecular Simulation, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
| | - Dirk Schepmann
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, Correnstrasse 48, 48149 Münster, Germany
| | - Bernhard Wünsch
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, Correnstrasse 48, 48149 Münster, Germany
| | - Marta Rui
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Mariela González-Avendaño
- Center for Bioinformatics and Molecular Simulation, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Ariela Vergara-Jaque
- Center for Bioinformatics and Molecular Simulation, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
- Multidisciplinary Scientific Nucleus, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
- Millennium Nucleus of Ion Channels-associated Diseases (MiNICAD), Santiago, Chile
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Ossa F, Schnell JR, Ortega-Roldan JL. A Review of the Human Sigma-1 Receptor Structure. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 964:15-29. [PMID: 28315262 DOI: 10.1007/978-3-319-50174-1_3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The Sigma-1 Receptor (S1R) is a small, ligand-regulated integral membrane protein involved in cell homeostasis and the cellular stress response. The receptor has a multitude of protein and small molecule interaction partners with therapeutic potential. Newly reported structures of the human S1R in ligand-bound states provides essential insights into small molecule binding in the context of the overall protein structure. The structure also raises many interesting questions and provides an excellent starting point for understanding the molecular tricks employed by this small membrane receptor to modulate a large number of signaling events. Here, we review insights from the structures of ligand-bound S1R in the context of previous biochemical studies and propose, from a structural viewpoint, a set of important future directions.
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Affiliation(s)
- Felipe Ossa
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jason R Schnell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - José Luis Ortega-Roldan
- School of Biosciences, University of Kent, Stacey Building, Room 215B, Canterbury, CT2 7NJ, UK
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Insight into the Structural Determinants of Imidazole Scaffold-Based Derivatives as TNF-α Release Inhibitors by in Silico Explorations. Int J Mol Sci 2015; 16:20118-38. [PMID: 26307982 PMCID: PMC4613192 DOI: 10.3390/ijms160920118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/10/2015] [Accepted: 07/30/2015] [Indexed: 01/29/2023] Open
Abstract
Presently, 151 widely-diverse pyridinylimidazole-based compounds that show inhibitory activities at the TNF-α release were investigated. By using the distance comparison technique (DISCOtech), comparative molecular field analysis (CoMFA), and comparative molecular similarity index analysis (CoMSIA) methods, the pharmacophore models and the three-dimensional quantitative structure-activity relationships (3D-QSAR) of the compounds were explored. The proposed pharmacophore model, including two hydrophobic sites, two aromatic centers, two H-bond donor atoms, two H-bond acceptor atoms, and two H-bond donor sites characterizes the necessary structural features of TNF-α release inhibitors. Both the resultant CoMFA and CoMSIA models exhibited satisfactory predictability (with Q2 (cross-validated correlation coefficient) = 0.557, R2ncv (non-cross-validated correlation coefficient) = 0.740, R2pre (predicted correlation coefficient) = 0.749 and Q2 = 0.598, R2ncv = 0.767, R2pre = 0.860, respectively). Good consistency was observed between the 3D-QSAR models and the pharmacophore model that the hydrophobic interaction and hydrogen bonds play crucial roles in the mechanism of actions. The corresponding contour maps generated by these models provide more diverse information about the key intermolecular interactions of inhibitors with the surrounding environment. All these models have extended the understanding of imidazole-based compounds in the structure-activity relationship, and are useful for rational design and screening of novel 2-thioimidazole-based TNF-α release inhibitors.
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Hechinger M, Leonhard K, Marquardt W. What is Wrong with Quantitative Structure–Property Relations Models Based on Three-Dimensional Descriptors? J Chem Inf Model 2012; 52:1984-93. [DOI: 10.1021/ci300246m] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- M. Hechinger
- AVT-Process
Systems Engineering and ‡Chair of Technical Thermodynamics, RWTH Aachen University, 52064 Aachen, Germany
| | - K. Leonhard
- AVT-Process
Systems Engineering and ‡Chair of Technical Thermodynamics, RWTH Aachen University, 52064 Aachen, Germany
| | - W. Marquardt
- AVT-Process
Systems Engineering and ‡Chair of Technical Thermodynamics, RWTH Aachen University, 52064 Aachen, Germany
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Caballero J, Zilocchi S, Tiznado W, Rossi D, Collina S. Models of the pharmacophoric pattern and affinity trend of methyl 2-(aminomethyl)-1-phenylcyclopropane-1-carboxylate derivatives as σ1ligands. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.614243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Kortagere S, Ekins S. Troubleshooting computational methods in drug discovery. J Pharmacol Toxicol Methods 2010; 61:67-75. [PMID: 20176118 DOI: 10.1016/j.vascn.2010.02.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 02/11/2010] [Indexed: 10/19/2022]
Abstract
Computational approaches for drug discovery such as ligand-based and structure-based methods, are increasingly seen as an efficient approach for lead discovery as well as providing insights on absorption, distribution, metabolism, excretion and toxicity (ADME/Tox). What is perhaps less well known and widely described are the limitations of the different technologies. We have therefore presented a troubleshooting approach to QSAR, homology modeling, docking as well as hybrid methods. If such computational or cheminformatics methods are to become more widely used by non-experts it is critical that such limitations are brought to the user's attention and addressed during their workflows. This could improve the quality of the models and results that are obtained.
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Affiliation(s)
- Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA.
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Mercer SL, Shaikh J, Traynor JR, Matsumoto RR, Coop A. Nitrile analogs of meperidine as high affinity and selective sigma-1 receptor ligands. Eur J Med Chem 2008; 43:1304-8. [PMID: 17988766 PMCID: PMC2486414 DOI: 10.1016/j.ejmech.2007.09.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 09/25/2007] [Accepted: 09/27/2007] [Indexed: 11/22/2022]
Abstract
A series of N-substituted-4-cyano-4-phenylpiperidine analogs were synthesized and evaluated for binding affinity at opioid receptors and showed no affinity. The series similarity to previously reported sigma ligands prompted analysis at sigma receptors to determine the SAR for affinity at sigma receptors. Within the N-substituent series the saturated analogs showed increased affinity at both sigma receptors. Optimal chain length in the N-arylalkyl series for sigma(1) and sigma(2) receptors proved to be N-propylphenyl; extension to a four carbon chain dramatically decreased affinity at both receptors. Substituents in the 4-position affect only sigma(1) affinity; no change in affinity at sigma(2) was shown. The N-isobutyl, N-phenylpropyl, and N-benzyl analogs are worth pursuing due to their good affinity and selectivity at the sigma(1) receptor, whereas the N-benzyl analog exhibits the greatest selectivity for sigma(1).
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Affiliation(s)
- Susan L. Mercer
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, USA
| | - Jamaluddin Shaikh
- Department of Pharmacology, University of Mississippi, 303 Faser Hall, University, MS 38677, USA
| | - John R. Traynor
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rae R. Matsumoto
- Department of Pharmacology, University of Mississippi, 303 Faser Hall, University, MS 38677, USA
| | - Andrew Coop
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, USA
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Hou T, McLaughlin W, Lu B, Chen K, Wang W. Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. J Proteome Res 2006; 5:32-43. [PMID: 16396493 DOI: 10.1021/pr0502267] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The SH3 domain of the human protein amphiphysin-1, which plays important roles in clathrin-mediated endocytosis, actin function and signaling transduction, can recognize peptide motif PXRPXR (X is any amino acid) with high affinity and specificity. We have constructed a complex structure of the amphiphysin-1 SH3 domain and a high-affinity peptide ligand PLPRRPPRA using homology modeling and molecular docking, which was optimized by molecular dynamics (MD). Three-dimensional quantitative structure-affinity relationship (3D-QSAR) analyses on the 200 peptides with known binding affinities to the amphiphysin-1 SH3 domain was then performed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The best CoMSIA model showed promising predictive power, giving good predictions for about 95% of the peptides in the test set (absolute prediction errors less than 1.0). It was used to validate peptide-SH3 binding structure and provide insight into the structural requirements for binding of peptides to SH3 domains. Finally, MD simulations were performed to analyze the interaction between the SH3 domain and another peptide GFPRRPPPRG that contains with the PXRPXsR (s represents residues with small side chains) motif. MD simulations demonstrated that the binding conformation of GFPRRPPPRG is quite different from that of PLPRRPPRAA especially the four residues at the C terminal, which may explain why the CoMSIA model cannot give good predictions on the peptides of the PXRPXsR motif. Because of its efficiency and predictive power, the 3D-QSAR model can be used as a scoring filter for predicting peptide sequences bound to SH3 domains.
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Affiliation(s)
- Tingjun Hou
- Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0319, USA
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Laggner C, Schieferer C, Fiechtner B, Poles G, Hoffmann RD, Glossmann H, Langer T, Moebius FF. Discovery of high-affinity ligands of sigma1 receptor, ERG2, and emopamil binding protein by pharmacophore modeling and virtual screening. J Med Chem 2005; 48:4754-64. [PMID: 16033255 DOI: 10.1021/jm049073+] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ERG2, emopamil binding protein (EBP), and sigma-1 receptor (sigma(1)) are enzymes of sterol metabolism and an enzyme-related protein, respectively, that share high affinity for various structurally diverse compounds. To discover novel high-affinity ligands, pharmacophore models were built with Catalyst based upon a series of 23 structurally diverse chemicals exhibiting K(i) values from 10 pM to 100 microM for all three proteins. In virtual screening experiments, we retrieved drugs that were previously reported to bind to one or several of these proteins and also tested 11 new hits experimentally, of which three, among them raloxifene, had affinities for sigma(1) or EBP of <60 nM. When used to search a database of 3525 biochemicals of intermediary metabolism, a slightly modified ERG2 pharmacophore model successfully retrieved 10 substrate candidates among the top 28 hits. Our results indicate that inhibitor-based pharmacophore models for sigma(1), ERG2, and EBP can be used to screen drug and metabolite databases for chemically diverse compounds and putative endogenous ligands.
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Affiliation(s)
- Christian Laggner
- Institute of Pharmacy, Department of Pharmaceutical Chemistry, and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
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