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Hu L, Lin J, Qin F, Xu L, Luo L. Exploring Sources, Biological Functions, and Potential Applications of the Ubiquitous Marine Cyclic Dipeptide: A Concise Review of Cyclic Glycine-Proline. Mar Drugs 2024; 22:271. [PMID: 38921582 PMCID: PMC11205142 DOI: 10.3390/md22060271] [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: 05/14/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Cyclic glycine-proline (cGP), a prevalent marine cyclic dipeptide, possesses a distinct pyrrolidine-2,5-dione scaffold, which contributes to the chemical diversity and broad bioactivities of cGP. The diverse sources from marine-related, endogenous biological, and synthetic pathways and the in vitro and in vivo activities of cGP are reviewed. The potential applications for cGP are also explored. In particular, the pivotal roles of cGP in regulating insulin-like growth factor-1 homeostasis, enhancing neuroprotective effects, and improving neurotrophic function in central nervous system diseases are described. The potential roles of this endogenous cyclic peptide in drug development and healthcare initiatives are also highlighted. This review underscores the significance of cGP as a fundamental building block in drug discovery with exceptional drug-like properties and safety. By elucidating the considerable value of cGP, this review aims to reignite interest in cGP-related research within marine medicinal chemistry and synthetic biology.
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Affiliation(s)
- Lei Hu
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Jing Lin
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Fei Qin
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Li Xu
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Lianzhong Luo
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
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2
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Warszycki D, Rueda M, Mordalski S, Kristiansen K, Satała G, Rataj K, Chilmonczyk Z, Sylte I, Abagyan R, Bojarski AJ. From Homology Models to a Set of Predictive Binding Pockets-a 5-HT 1A Receptor Case Study. J Chem Inf Model 2017; 57:311-321. [PMID: 28055203 PMCID: PMC5361891 DOI: 10.1021/acs.jcim.6b00263] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Despite its remarkable importance in the arena of drug design, serotonin 1A receptor (5-HT1A) has been elusive to the X-ray crystallography community. This lack of direct structural information not only hampers our knowledge regarding the binding modes of many popular ligands (including the endogenous neurotransmitter-serotonin), but also limits the search for more potent compounds. In this paper we shed new light on the 3D pharmacological properties of the 5-HT1A receptor by using a ligand-guided approach (ALiBERO) grounded in the Internal Coordinate Mechanics (ICM) docking platform. Starting from a homology template and set of known actives, the method introduces receptor flexibility via Normal Mode Analysis and Monte Carlo sampling, to generate a subset of pockets that display enriched discrimination of actives from inactives in retrospective docking. Here, we thoroughly investigated the repercussions of using different protein templates and the effect of compound selection on screening performance. Finally, the best resulting protein models were applied prospectively in a large virtual screening campaign, in which two new active compounds were identified that were chemically distinct from those described in the literature.
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Affiliation(s)
- Dawid Warszycki
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Street, 31-343 Kraków, Poland
| | - Manuel Rueda
- University of California, San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, 9500 Gilman Drive, MC 0747 La Jolla, CA 92093-0747, U.S
| | - Stefan Mordalski
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Street, 31-343 Kraków, Poland
| | - Kurt Kristiansen
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway
| | - Grzegorz Satała
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Street, 31-343 Kraków, Poland
| | - Krzysztof Rataj
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Street, 31-343 Kraków, Poland
| | - Zdzisław Chilmonczyk
- Department of Cell Biology, National Medicines Institute, 30/34 Chełmska Street, 00-725 Warszawa, Poland
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway
| | - Ruben Abagyan
- University of California, San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, 9500 Gilman Drive, MC 0747 La Jolla, CA 92093-0747, U.S
| | - Andrzej J. Bojarski
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Street, 31-343 Kraków, Poland
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3
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Borthwick AD. 2,5-Diketopiperazines: synthesis, reactions, medicinal chemistry, and bioactive natural products. Chem Rev 2012; 112:3641-716. [PMID: 22575049 DOI: 10.1021/cr200398y] [Citation(s) in RCA: 606] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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4
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Tabassum S, Al-Asbahy WM, Afzal M, Arjmand F, Bagchi V. Molecular drug design, synthesis and structure elucidation of a new specific target peptide based metallo drug for cancer chemotherapy as topoisomerase I inhibitor. Dalton Trans 2012; 41:4955-4964. [PMID: 22407358 DOI: 10.1039/c2dt12044e] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
To evaluate the biological preference of metallopeptide drugs in cancer cells, a new dinuclear copper(II) complex [Cu(2)(glygly)(2)(ppz)(H(2)O)(4)]·2H(2)O (1) (glygly = glycyl glycine anion and ppz = piperazine), was designed and synthesized as topoisomerase I inhibitor. The structural elucidation of the complex was done by elemental analysis, spectroscopic methods and single crystal X-ray diffraction. The in vitro DNA binding studies of complex 1 with CT DNA were carried out by employing different optical methods viz. UV-vis, fluorescence and circular dichroism. The molecular docking technique was also utilized to ascertain the mechanism and mode of action towards the molecular target DNA and enzymes. Complex 1 cleaves pBR322 DNA via an oxidative mechanism and strongly binds to the DNA minor groove. Furthermore, complex 1 exhibits significant inhibitory effects on the catalytic activity of topoisomerase I at a very low concentration, ~12.5 μM, in addition to its excellent SOD mimics (IC(50)~0.086 μM).
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Affiliation(s)
- Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh 202201, UP, India.
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5
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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6
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Pessoa‐Mahana H, Gajardo GR, Araya‐Maturana R, Cárcamo JK, Pessoa‐Mahana CD. Synthesis of 4‐Arylpiperazine Derivatives of Moclobemide: Potential Antidepressants with a Dual Mode of Action. SYNTHETIC COMMUN 2011. [DOI: 10.1081/scc-200025581] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hernán Pessoa‐Mahana
- a Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas , Universidad de Chile , Casilla 233, Santiago, 1, Chile
| | - Gonzalo Recabarren Gajardo
- a Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas , Universidad de Chile , Casilla 233, Santiago, 1, Chile
| | - Ramiro Araya‐Maturana
- a Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas , Universidad de Chile , Casilla 233, Santiago, 1, Chile
| | - Johann Kosche Cárcamo
- a Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas , Universidad de Chile , Casilla 233, Santiago, 1, Chile
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Zlatović MV, Sukalović VV, Schneider C, Roglić GM. Interaction of arylpiperazine ligands with the hydrophobic part of the 5-HT1A receptor binding site. Bioorg Med Chem 2006; 14:2994-3001. [PMID: 16403641 DOI: 10.1016/j.bmc.2005.12.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Revised: 12/04/2005] [Accepted: 12/09/2005] [Indexed: 11/23/2022]
Abstract
A flexible docking of a series of arylpiperazine derivatives with structurally different aryl part to the binding site of a model of human 5-HT1A receptor was exercised. The influence of structure and hydrophobic properties of aryl moiety on binding affinities was discussed and a model for ligand binding in the hydrophobic part of the binding site was proposed.
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Affiliation(s)
- Mario V Zlatović
- Faculty of Chemistry, University of Belgrade, PO Box 158, 11000 Belgrade, Serbia and Montenegro.
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8
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Influence of N-1 substituent properties on binding affinities of arylpiperazines to the binding site of 5-HT1A receptor. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2006. [DOI: 10.2298/jsc0611125z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Serotonin receptors (5-HTRs), especially the 5-HT1A subtype, have been the subject of intensive research for the past decade, due to their function in human physiology. Several structurally different classes of ligands are known to bind to the 5-HT1A receptor, but arylpiperazine derivatives are among the most important ligands. In the work, docking analyses were used to explain the binding affinities of a series of ligands with different N-1 substituent. All ligands had in common the arylpiperazine structure, while the N-1 subsistent was modified to investigate the influence of ligand structure on its binding affinity. The shape and size, as well as the rigidity of the subsistents were altered to investigate the possible effects on the formation of the receptor - ligand complex.
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9
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Fanelli F, De Benedetti PG. Computational Modeling Approaches to Structure−Function Analysis of G Protein-Coupled Receptors. Chem Rev 2005; 105:3297-351. [PMID: 16159154 DOI: 10.1021/cr000095n] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute and Department of Chemistry, University of Modena and Reggio Emilia, via Campi 183, 41100 Modena, Italy.
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10
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Kamei K, Maeda N, Katsuragi-Ogino R, Koyama M, Nakajima M, Tatsuoka T, Ohno T, Inoue T. New piperidinyl- and 1,2,3,6-tetrahydropyridinyl-pyrimidine derivatives as selective 5-HT1A receptor agonists with highly potent anti-ischemic effects. Bioorg Med Chem Lett 2005; 15:2990-3. [PMID: 15914001 DOI: 10.1016/j.bmcl.2005.04.059] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Accepted: 04/22/2005] [Indexed: 11/30/2022]
Abstract
A series of new piperidinyl- and 1,2,3,6-tetrahydropyridinyl-pyrimidine derivatives were synthesized. Among these compounds, 4-methyl-2-(1,2,3,6-tetrahydropyridin-4-yl)pyrimidine derivative 23 (SUN N5147) exhibited sub-nanomolar affinity for 5-HT1A receptor with 1000-fold selectivity over both dopamine D2 and alpha1-adrenergic receptors and remarkable neuroprotective activity in a transient middle cerebral artery occlusion (t-MCAO) model.
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Affiliation(s)
- Katsuhide Kamei
- Daiichi Suntory Biomedical Research Co., Ltd, 1-1-1, Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka 618-8513, Japan.
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11
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Benzimidazole derivatives. Part 5: design and synthesis of new benzimidazole-arylpiperazine derivatives acting as mixed 5-HT1A/5-HT3 ligands. Bioorg Med Chem 2005; 12:5181-91. [PMID: 15351401 DOI: 10.1016/j.bmc.2004.07.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Accepted: 07/09/2004] [Indexed: 12/01/2022]
Abstract
A series of new mixed benzimidazole-arylpiperazine derivatives were designed by incorporating in general structure III the pharmacophoric elements of 5-HT(1A) and 5-HT(3) receptors. Compounds 1-11 were synthesized and evaluated for binding affinity at both serotoninergic receptors, all of them exhibiting high 5-HT(3)R affinity (K(i)=10-62nM), and derivatives with an o-alkoxy group in the arylpiperazine ring showing nanomolar affinity for the 5-HT(1A)R (K(i)=18-150nM). Additionally, all the synthesized compounds were selective over alpha(1)-adrenergic and dopamine D(2) receptors (K(i)>1000-10,000nM). Compound 3 was selected for further pharmacological characterization due to its interesting binding profile as mixed 5-HT(1A)/5-HT(3) ligand with high affinity for both receptors (5-HT(1A): K(i)=18.0nM, 5-HT(3): K(i)=27.2nM). In vitro and in vivo findings suggest that this compound acts as a partial agonist at 5-HT(1A)Rs and as a 5-HT(3)R antagonist. This novel mixed 5-HT(1A)/5-HT(3) ligand was also effective in preventing the cognitive deficits induced by muscarinic receptor blockade in a passive avoidance learning test, suggesting a potential interest in the treatment of cognitive dysfunction.
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12
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Chapter 6.2 Six-membered ring systems: Diazines and benzo derivatives. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s0959-6380(05)80055-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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13
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López-Rodríguez ML, Ayala D, Viso A, Benhamú B, de La Pradilla RF, Zarza F, Ramos JA. Synthesis and structure–activity relationships of a new model of arylpiperazines. Part 7: Study of the influence of lipophilic factors at the terminal amide fragment on 5-HT1A affinity/selectivity. Bioorg Med Chem 2004; 12:1551-7. [PMID: 15018929 DOI: 10.1016/j.bmc.2003.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2003] [Accepted: 12/09/2003] [Indexed: 12/01/2022]
Abstract
The influence of lipophilic factors at the amide fragment of a new series of (+/-)-7a-alkyl-2-[4-(4-arylpiperazin-1-yl)butyl]-1,3-dioxoperhydropyrrolo[1,2-c]imidazoles 2 and of (+/-)-7a-alkyl-2-[(4-arylpiperazin-1-yl)methyl]-1,3-dioxoperhydropyrrolo[1,2-c]imidazoles 3 has been studied. Variations of logP have been carried out by introducing different hydrocarbonated substituents (R(1)) at the position 7a of the bicyclohydantoin, namely the non-pharmacophoric part. All the new compounds exhibit high potency for the 5-HT(1A) receptor; however, affinities for the alpha(1) receptor are high for compounds 2a-l while compounds 3a-f are selective over this adrenergic receptor. On the other hand, differences in logP do not notably affect the K(i) values for the above receptors.
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Affiliation(s)
- María L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense, E-28040 Madrid, Spain.
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14
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López-Rodríguez ML, Benhamú B, Morcillo MJ, Tejada I, Avila D, Marco I, Schiapparelli L, Frechilla D, Del Río J. Design and synthesis of new benzimidazole-arylpiperazine derivatives acting as mixed 5-HT1A/5-HT3 ligands. Bioorg Med Chem Lett 2003; 13:3177-80. [PMID: 12951088 DOI: 10.1016/s0960-894x(03)00706-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A series of new benzimidazole-arylpiperazine derivatives III were designed, synthesized and evaluated for binding affinity at serotoninergic 5-HT(1A) and 5-HT(3) receptors. Compound IIIc was identified as a novel mixed 5-HT(1A)/5-HT(3) ligand with high affinity for both serotonin receptors and excellent selectivity over alpha(1)-adrenergic and dopamine D(2) receptors. This compound was characterized as a partial agonist at 5-HT(1A)Rs and a 5-HT(3)R antagonist, and was effective in preventing the cognitive deficits induced by muscarinic receptor blockade in a passive avoidance learning test.
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Affiliation(s)
- María L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense, E-28040 Madrid, Spain.
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