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Goel KK, Thapliyal S, Kharb R, Joshi G, Negi A, Kumar B. Imidazoles as Serotonin Receptor Modulators for Treatment of Depression: Structural Insights and Structure-Activity Relationship Studies. Pharmaceutics 2023; 15:2208. [PMID: 37765177 PMCID: PMC10535231 DOI: 10.3390/pharmaceutics15092208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
Serotoninergic signaling is identified as a crucial player in psychiatric disorders (notably depression), presenting it as a significant therapeutic target for treating such conditions. Inhibitors of serotoninergic signaling (especially selective serotonin reuptake inhibitors (SSRI) or serotonin and norepinephrine reuptake inhibitors (SNRI)) are prominently selected as first-line therapy for the treatment of depression, which benefits via increasing low serotonin levels and norepinephrine by blocking serotonin/norepinephrine reuptake and thereby increasing activity. While developing newer heterocyclic scaffolds to target/modulate the serotonergic systems, imidazole-bearing pharmacophores have emerged. The imidazole-derived pharmacophore already demonstrated unique structural characteristics and an electron-rich environment, ultimately resulting in a diverse range of bioactivities. Therefore, the current manuscript discloses such a specific modification and structural activity relationship (SAR) of attempted derivatization in terms of the serotonergic efficacy of the resultant inhibitor. We also featured a landscape of imidazole-based development, focusing on SAR studies against the serotoninergic system to target depression. This study covers the recent advancements in synthetic methodologies for imidazole derivatives and the development of new molecules having antidepressant activity via modulating serotonergic systems, along with their SAR studies. The focus of the study is to provide structural insights into imidazole-based derivatives as serotonergic system modulators for the treatment of depression.
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Affiliation(s)
- Kapil Kumar Goel
- Department of Pharmaceutical Sciences, Gurukul Kangri (Deemed to Be University), Haridwar 249404, Uttarakhand, India
| | - Somesh Thapliyal
- Department of Pharmaceutical Sciences, HNB Garhwal University, Chauras Campus, Srinagar Garhwal 246174, Uttarakhand, India (G.J.)
| | - Rajeev Kharb
- Amity Institute of Pharmacy, Amity University, Noida 201313, Uttar Pradesh, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, HNB Garhwal University, Chauras Campus, Srinagar Garhwal 246174, Uttarakhand, India (G.J.)
| | - Arvind Negi
- Department of Bioproduct and Biosystems, Aalto University, 02150 Espoo, Finland
| | - Bhupinder Kumar
- Department of Pharmaceutical Sciences, HNB Garhwal University, Chauras Campus, Srinagar Garhwal 246174, Uttarakhand, India (G.J.)
- Department of Chemistry, Graphic Era (Deemed to Be University), Dehradun 248002, Uttarakhand, India
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Negi A, Kesari KK, Voisin-Chiret AS. Estrogen Receptor-α Targeting: PROTACs, SNIPERs, Peptide-PROTACs, Antibody Conjugated PROTACs and SNIPERs. Pharmaceutics 2022; 14:pharmaceutics14112523. [PMID: 36432713 PMCID: PMC9699327 DOI: 10.3390/pharmaceutics14112523] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Targeting selective estrogen subtype receptors through typical medicinal chemistry approaches is based on occupancy-driven pharmacology. In occupancy-driven pharmacology, molecules are developed in order to inhibit the protein of interest (POI), and their popularity is based on their virtue of faster kinetics. However, such approaches have intrinsic flaws, such as pico-to-nanomolar range binding affinity and continuous dosage after a time interval for sustained inhibition of POI. These shortcomings were addressed by event-driven pharmacology-based approaches, which degrade the POI rather than inhibit it. One such example is PROTACs (Proteolysis targeting chimeras), which has become one of the highly successful strategies of event-driven pharmacology (pharmacology that does the degradation of POI and diminishes its functions). The selective targeting of estrogen receptor subtypes is always challenging for chemical biologists and medicinal chemists. Specifically, estrogen receptor α (ER-α) is expressed in nearly 70% of breast cancer and commonly overexpressed in ovarian, prostate, colon, and endometrial cancer. Therefore, conventional hormonal therapies are most prescribed to patients with ER + cancers. However, on prolonged use, resistance commonly developed against these therapies, which led to selective estrogen receptor degrader (SERD) becoming the first-line drug for metastatic ER + breast cancer. The SERD success shows that removing cellular ER-α is a promising approach to overcoming endocrine resistance. Depending on the mechanism of degradation of ER-α, various types of strategies of developed.
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Affiliation(s)
- Arvind Negi
- Department of Bioproduct and Biosystems, Aalto University, 00076 Espoo, Finland
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
| | - Kavindra Kumar Kesari
- Department of Bioproduct and Biosystems, Aalto University, 00076 Espoo, Finland
- Department of Applied Physics, School of Science, Aalto University, 02150 Espoo, Finland
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
| | - Anne Sophie Voisin-Chiret
- CERMN (Centre d’Etudes et de Recherche sur le Médicament de Normandie), Normandie University UNICAEN, 14000 Caen, France
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
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Natural Products as Mcl-1 Inhibitors: A Comparative Study of Experimental and Computational Modelling Data. CHEMISTRY 2022. [DOI: 10.3390/chemistry4030067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The human myeloid leukemia cell differentiation protein (hMcl-1) is an anti-apoptotic multi-partner protein, belonging to the B-cell lymphoma-2 (Bcl-2) family of proteins. Studies have linked hMcl-1 alleviated expression with resistance to hemopoietic chemotherapeutics, which makes it a key drug target in blood cancers. However, most of the developed small- to medium-sized hMcl-1 inhibitors have typical off-target activity towards other members of the Bcl-2 family. To improve the hMcl-1 inhibitor design, especially exploring a suitable scaffold with pharmacophoric features, we focused on natural hMcl-1 inhibitors. To date, seven classes of natural compounds have been isolated, which display a low micromolar affinity for hMcl-1 and have limited biophysical studies. We screened hMcl-1 co-crystal structures, and identified nine co-crystal structures of hMcl-1 protein, which were later evaluated by multiple receptor conformations (which indicates that the differences between hMcl-1 in crystal structures are low (RMSD values between 0.52 and 1.13 Å, average RMSD of 0.638–0.888 Å, with a standard deviation of 0.102–0.185Å)), and multiple ligand conformations (which led to the selection of the PDB structure, 3WIX (RMSD value = 0.879 Å, standard deviation 0.116 Å), to accommodate various Mcl-1 ligands from a range of co-crystal PDB files) methods. Later, the three adopted docking methods were assessed for their ability to reproduce the conformation bound to the crystal as well as predict trends in Ki values based on calculated RMSD and docking energies. Iterative docking and clustering of the docked pose within ≤1.0 Å was used to evaluate the reproducibility of the adopted docking methods and compared with their experimentally determined hMcl-1 affinity data.
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Börzsei R, Zsidó BZ, Bálint M, Helyes Z, Pintér E, Hetényi C. Exploration of Somatostatin Binding Mechanism to Somatostatin Receptor Subtype 4. Int J Mol Sci 2022; 23:ijms23136878. [PMID: 35805885 PMCID: PMC9266823 DOI: 10.3390/ijms23136878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 02/04/2023] Open
Abstract
Somatostatin (also named as growth hormone-inhibiting hormone or somatotropin release-inhibiting factor) is a regulatory peptide important for the proper functioning of the endocrine system, local inflammatory reactions, mood and motor coordination, and behavioral responses to stress. Somatostatin exerts its effects via binding to G-protein-coupled somatostatin receptors of which the fourth subtype (SSTR4) is a particularly important receptor mediating analgesic, anti-inflammatory, and anti-depressant effects without endocrine actions. Thus, SSTR4 agonists are promising drug candidates. Although the knowledge of the atomic resolution-binding modes of SST would be essential for drug development, experimental elucidation of the structures of SSTR4 and its complexes is still awaiting. In the present study, structures of the somatostatin–SSTR4 complex were produced using an unbiased, blind docking approach. Beyond the static structures, the binding mechanism of SST was also elucidated in the explicit water molecular dynamics (MD) calculations, and key binding modes (external, intermediate, and internal) were distinguished. The most important residues on both receptor and SST sides were identified. An energetic comparison of SST binding to SSTR4 and 2 offered a residue-level explanation of receptor subtype selectivity. The calculated structures show good agreement with available experimental results and indicate that somatostatin binding is realized via prerequisite binding modes and an induced fit mechanism. The identified binding modes and the corresponding key residues provide useful information for future drug design targeting SSTR4.
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Affiliation(s)
- Rita Börzsei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
| | - Balázs Zoltán Zsidó
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
| | - Mónika Bálint
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
- Algonist Gmbh, 1030 Vienna, Austria
- PharmInVivo Ltd., 7624 Pécs, Hungary
| | - Erika Pintér
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
- Algonist Gmbh, 1030 Vienna, Austria
- PharmInVivo Ltd., 7624 Pécs, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
- Correspondence:
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Slater O, Kontoyianni M. A computational study of somatostatin subtype-4 receptor agonist binding. SN APPLIED SCIENCES 2022. [DOI: 10.1007/s42452-022-04968-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
AbstractThe somatostatin subtype-4 receptor (sst4) is highly expressed in neocortical and hippocampal areas, which are affected by amyloid beta accumulation. Sst4 agonists enhance downstream activity of amyloid beta peptide catabolism through neprilysin and may slow the progression of Alzheimer’s disease (AD). Sst4 is a G protein coupled receptor (GPCR), the structure of which has yet to be resolved. A newly constructed sst4 homology model, along with a previously reported model-built sst4 receptor structure, were used in the present study to gain insights into binding requirements of sst4 agonists employing a set of compounds patented by Boehringer Ingelheim. Besides aiming at delineating binding at the macromolecular level of these recently disclosed compounds, our objectives included the generation of a quantitative structure-activity relationship (QSAR) global model to explore the relationship between chemical structure and affinity. Through the implementation of model building, docking, and QSAR, plausible correlations between structural properties and the binding affinity are established. This study sheds light on understanding binding requirements at the sst4 receptor.
Graphical abstract
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Negi A, Voisin-Chiret AS. Strategies to reduce the On-target Platelet Toxicity of Bcl-xL Inhibitors: PROTACs, SNIPERs and Prodrug-based approaches. Chembiochem 2022; 23:e202100689. [PMID: 35263486 PMCID: PMC9311450 DOI: 10.1002/cbic.202100689] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/08/2022] [Indexed: 11/07/2022]
Abstract
Apoptosis is a highly regulated cellular process. Any alteration in apoptosis signaling results in disease states. Therefore, apoptosis proteins are prime targets in various therapies. Bcl-x L is an anti-apoptotic protein that prevents cellular apoptosis. Compared to other antiapoptotic proteins, expression of Bcl-x L is commonly observed in solid tumors and to an extent to some leukemias and lymphomas. Also, its overexpression is linked with survival, acquired resistance to other chemotherapeutics in cancer as well as in senescent cells, making it a potent anticancer and senolytic target. Therefore, various nanomolar range Bcl-x L inhibitors were studied. To a success, ABT-263 was identified as a Bcl-x L /Bcl-2 dual inhibitor but failed in the clinical trial (phase-II), due to on-target platelet toxicity, implying an expression of Bcl-x L protein is essential for human platelet survival. However, most of the presented designs of Bcl-x L inhibitors were based on conventional medicinal chemistry approaches using occupancy-derived pharmacology, therefore, other approaches were investigated. Most of the approaches developed to overcome the on-target platelet toxicity of Bcl-x L inhibitors were based on event-based pharmacology, such as pr oteolysis ta rgeting c himeras (PROTACs) and SNIPERs ( s pecific n on-genetic I AP-based p rotein er asers). However, PROTACs take advantage of 600 E3-ligases that are expressed differently based on cell type and, importantly less expressed in platelets. This paper also discussed the approaches that utilized the concept of the prodrugs, such as antibody-drug conjugates, phosphate prodrugs, dendrimer conjugate, and glycosylated conjugate. Various studies such as in vitro , in vivo , structure-activity relationship, and biophysical characterization of each inhibitor retrieved from these strategies are timely discussed in the paper.
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Affiliation(s)
- Arvind Negi
- Aalto-yliopisto, Bioproducts and Biosystems, Vuorimiehentie 1, 02150 Espoo Finland, 00530, Helsinki, FINLAND
| | - Anne Sophie Voisin-Chiret
- Caen University: Universite de Caen Normandie, Centre d' etudes et de recherche sur le medicament de normandie, FRANCE
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Dhara D, Dhara A, Bennett J, Murphy PV. Cyclisations and Strategies for Stereoselective Synthesis of Piperidine Iminosugars. CHEM REC 2021; 21:2958-2979. [PMID: 34713557 DOI: 10.1002/tcr.202100221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/31/2022]
Abstract
This personal account focuses on synthesis of polyhydroxylated piperidines, a subset of compounds within the iminosugar family. Cyclisations to form the piperidine ring include reductive amination, substitution via amines, iminium ions and cyclic nitrones, transamidification (N-acyl transfer), addition to alkenes, ring contraction and expansion, photoinduced electron transfer, multicomponent Ugi reaction and ring closing metathesis. Enantiomerically pure piperidines are obtained from chiral pool precursors (e. g. sugars, amino acids, Garner's aldehyde) or asymmetric reactions (e. g. epoxidation, dihydroxylation, aminohydroxylation, aldol, biotransformation). Our laboratory have contributed cascades based on reductive amination from glycosyl azide precursors as well as Huisgen azide-alkene cycloaddition. The latter's combination with allylic azide rearrangement has given substituted piperidines, including those with quaternary centres adjacent to nitrogen.
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Affiliation(s)
- Debashis Dhara
- School of Biological and Chemical Sciences, NUI Galway, University Road, Galway, H91 TK33, Ireland.,Unité de Chimie des Biomolécules, UMR 3523 CNRS, Institut Pasteur, Université de Paris, 28 rue du Dr Roux, 75015, Paris, France
| | - Ashis Dhara
- School of Biological and Chemical Sciences, NUI Galway, University Road, Galway, H91 TK33, Ireland
| | - Jack Bennett
- School of Biological and Chemical Sciences, NUI Galway, University Road, Galway, H91 TK33, Ireland
| | - Paul V Murphy
- School of Biological and Chemical Sciences, NUI Galway, University Road, Galway, H91 TK33, Ireland.,SSPC - The Science Foundation Ireland Research Centre for Pharmaceuticals, NUI Galway, University Road, Galway, H91 TK33, Ireland
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Fox KA, Chadda R, Cardona F, Barron S, McArdle P, Murphy PV. Building blocks from monosaccharides for synthesis of scaffolds, including macrocycles. Application of allylic azide rearrangement, azide-alkyne cycloaddition and ring closing metathesis. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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A Route to 1-Deoxynojirimycin and 1-Deoxymannojirimycin Derivatives with Quaternary Centers Adjacent to the Ring Nitrogen from Methyl α-d
-Mannopyranoside. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Negi A, Reilly CO, Jarikote DV, Zhou J, Murphy PV. Multi-targeting protein-protein interaction inhibitors: Evolution of macrocyclic ligands with embedded carbohydrates (MECs) to improve selectivity. Eur J Med Chem 2019; 176:292-309. [PMID: 31112891 DOI: 10.1016/j.ejmech.2019.04.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/01/2019] [Accepted: 04/24/2019] [Indexed: 10/26/2022]
Abstract
Compounds targeting multiple proteins can have synergistic effects and are therefore of interest in medicinal chemistry. At the same time, inhibiting protein-protein interactions (PPI) is increasingly desired in the treatment of disorders or diseases. The development of non-peptidomimetic inhibitors is still a challenge. Herein we investigate macrocyclic scaffolds with one or two embedded carbohydrates (MECs) that present amino acid side chains, or related isosteres, as pharmacophoric groups. Firstly, retroscreening of the previously reported eannaphane-40 (E40, 40), a MEC presenting two pharmacophoric groups, against a set of 55 receptor-subtypes led to a finding of sub-micromolar inhibitory activity for E40 against three serotonergic isoforms (5HT1A/2A/2B) as well as the Na+ channel and the NK-2 receptor. We synthesised MECs with an additional pharmacophoric group compared to E40, with a view to identifying compounds where the selectivity profile was altered among the protein hits from the retroscreening. MECs were produced based on scaffolds with two monosaccharide residues, leading to the incorporation of a third pharmacophoric group. Later, homology models were prepared for four proteins (5HT1A, 5HT2A, NK2 and site-2 of the sodium channel) whose 3D structure is unknown. Inverse docking of the synthesised compounds led to the selection of a new MEC (MEC-B) for protein binding assays. MEC-B was found to have its selectivity profile modulated, in line with docking prediction, compared to E40. MEC-B is dual inhibitor of both 5-HT1A and the sodium channel with improved selectivity for these proteins compared to 5-HT2A/2B/2C, 5-HT transporter and NK2 receptor. Thus, a new multitargeting compound, with an improved selectivity profile was identified, based on a MEC peptidomimetic scaffold.
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Affiliation(s)
- Arvind Negi
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Ciaran O Reilly
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Dilip V Jarikote
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Jian Zhou
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Paul V Murphy
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.
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N-Alkyl-1,5-dideoxy-1,5-imino-l-fucitols as fucosidase inhibitors: Synthesis, molecular modelling and activity against cancer cell lines. Bioorg Chem 2018; 84:418-433. [PMID: 30554081 DOI: 10.1016/j.bioorg.2018.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/23/2018] [Accepted: 12/03/2018] [Indexed: 12/22/2022]
Abstract
1,5-Dideoxy-1,5-imino-l-fucitol (1-deoxyfuconojirimycin, DFJ) is an iminosugar that inhibits fucosidases. Herein, N-alkyl DFJs have been synthesised and tested against the α-fucosidases of T. maritima (bacterial origin) and B. taurus (bovine origin). The N-alkyl derivatives were inactive against the bacterial fucosidase, while inhibiting the bovine enzyme. Docking of inhibitors to homology models, generated for the bovine and human fucosidases, was carried out. N-Decyl-DFJ was toxic to cancer cell lines and was more potent than the other N-alkyl DFJs studied.
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