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Bhunia SS, Saxena AK. Efficiency of Homology Modeling Assisted Molecular Docking in G-protein Coupled Receptors. Curr Top Med Chem 2021; 21:269-294. [PMID: 32901584 DOI: 10.2174/1568026620666200908165250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Molecular docking is in regular practice to assess ligand affinity on a target protein crystal structure. In the absence of protein crystal structure, the homology modeling or comparative modeling is the best alternative to elucidate the relationship details between a ligand and protein at the molecular level. The development of accurate homology modeling (HM) and its integration with molecular docking (MD) is essential for successful, rational drug discovery. OBJECTIVE The G-protein coupled receptors (GPCRs) are attractive therapeutic targets due to their immense role in human pharmacology. The GPCRs are membrane-bound proteins with the complex constitution, and the understanding of their activation and inactivation mechanisms is quite challenging. Over the past decade, there has been a rapid expansion in the number of solved G-protein-coupled receptor (GPCR) crystal structures; however, the majority of the GPCR structures remain unsolved. In this context, HM guided MD has been widely used for structure-based drug design (SBDD) of GPCRs. METHODS The focus of this review is on the recent (i) developments on HM supported GPCR drug discovery in the absence of GPCR crystal structures and (ii) application of HM in understanding the ligand interactions at the binding site, virtual screening, determining receptor subtype selectivity and receptor behaviour in comparison with GPCR crystal structures. RESULTS The HM in GPCRs has been extremely challenging due to the scarcity in template structures. In such a scenario, it is difficult to get accurate HM that can facilitate understanding of the ligand-receptor interactions. This problem has been alleviated to some extent by developing refined HM based on incorporating active /inactive ligand information and inducing protein flexibility. In some cases, HM proteins were found to outscore crystal structures. CONCLUSION The developments in HM have been highly operative to gain insights about the ligand interaction at the binding site and receptor functioning at the molecular level. Thus, HM guided molecular docking may be useful for rational drug discovery for the GPCRs mediated diseases.
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Affiliation(s)
- Shome S Bhunia
- Global Institute of Pharmaceutical Education and Research, Kashipur, Uttarakhand, India
| | - Anil K Saxena
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow 226031, India
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Szczepańska K, Pockes S, Podlewska S, Höring C, Mika K, Latacz G, Bednarski M, Siwek A, Karcz T, Nagl M, Bresinsky M, Mönnich D, Seibel U, Kuder KJ, Kotańska M, Stark H, Elz S, Kieć-Kononowicz K. Structural modifications in the distal, regulatory region of histamine H 3 receptor antagonists leading to the identification of a potent anti-obesity agent. Eur J Med Chem 2021; 213:113041. [PMID: 33261900 DOI: 10.1016/j.ejmech.2020.113041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/07/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023]
Abstract
A series of 4-pyridylpiperazine derivatives with varying regulatory region substituents proved to be potent histamine H3 receptor (H3R) ligands in the nanomolar concentration range. The most influential modification that affected the affinity toward the H3R appeared by introducing electron-withdrawing moieties into the distal aromatic ring. In order to finally discuss the influence of the characteristic 4-pyridylpiperazine moiety on H3R affinity, two Ciproxifan analogues 2 and 3 with a slight modification in their basic part were obtained. The replacement of piperazine in 3 with piperidine in compound 2, led to slightly reduced affinity towards the H3R (Ki = 3.17 and 7.70 nM, respectively). In fact, 3 showed the highest antagonistic properties among all compounds in this series, hence affirming our previous assumptions, that the 4-pyridylpiperazine moiety is the key element for suitable interaction with the human histamine H3 receptor. While its structural replacement to piperidine is also tolerated for H3R binding, the heteroaromatic 4-pyridyl moiety seems to be essential for proper ligand-receptor interaction. The putative protein-ligand interactions responsible for their high affinity were demonstrated using molecular modeling techniques. Furthermore, selectivity, intrinsic activity at the H3R, as well as drug-like properties of ligands were evaluated using in vitro methods. Moreover, pharmacological in vivo test results of compound 9 (structural analogue of Abbott's A-331440) clearly indicate that it may affect the amount of calories consumed, thus act as an anorectic compound.
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Affiliation(s)
- Katarzyna Szczepańska
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków, 30-688, Poland
| | - Steffen Pockes
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany.
| | - Sabina Podlewska
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków, 30-688, Poland; Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, Kraków, 31-343, Poland
| | - Carina Höring
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Kamil Mika
- Department of Department of Pharmacological Screening, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków, 30-688, Poland
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków, 30-688, Poland
| | - Marek Bednarski
- Department of Department of Pharmacological Screening, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków, 30-688, Poland
| | - Agata Siwek
- Department of Pharmacobiology, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków, 30-688, Poland
| | - Tadeusz Karcz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków, 30-688, Poland
| | - Martin Nagl
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Merlin Bresinsky
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Denise Mönnich
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Ulla Seibel
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Kamil J Kuder
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków, 30-688, Poland
| | - Magdalena Kotańska
- Department of Department of Pharmacological Screening, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków, 30-688, Poland
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Sigurd Elz
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Katarzyna Kieć-Kononowicz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków, 30-688, Poland.
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3
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Novel potent (dihydro)benzofuranyl piperazines as human histamine receptor ligands - Functional characterization and modeling studies on H 3 and H 4 receptors. Bioorg Med Chem 2020; 30:115924. [PMID: 33333448 DOI: 10.1016/j.bmc.2020.115924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/28/2020] [Accepted: 12/01/2020] [Indexed: 01/18/2023]
Abstract
Histamine acts through four different receptors (H1R-H4R), the H3R and H4R being the most explored in the last years as drug targets. The H3R is a potential target to treat narcolepsy, Parkinson's disease, epilepsy, schizophrenia and several other CNS-related conditions, while H4R blockade leads to anti-inflammatory and immunomodulatory effects. Our group has been exploring the dihydrobenzofuranyl-piperazines (LINS01 series) as human H3R/H4R ligands as potential drug candidates. In the present study, a set of 12 compounds were synthesized from adequate (dihydro)benzofuran synthons through simple reactions with corresponding piperazines, giving moderate to high yields. Four compounds (1b, 1f, 1g and 1h) showed high hH3R affinity (pKi > 7), compound 1h being the most potent (pKi 8.4), and compound 1f showed the best efficiency (pKi 8.2, LE 0.53, LLE 5.85). BRET-based assays monitoring Gαi activity indicated that the compounds are potent antagonists. Only one compound (2c, pKi 7.1) presented high affinity for hH4R. In contrast to what was observed for hH3R, it showed partial agonist activity. Docking experiments indicated that bulky substituents occupy a hydrophobic pocket in hH3R, while the N-allyl group forms favorable interactions with hydrophobic residues in the TM2, 3 and 7, increasing the selectivity towards hH3R. Additionally, the importance of the indole NH in the interaction with Glu5.46 from hH4R was confirmed by the modeling results, explaining the affinity and agonistic activity of compound 2c. The data reported in this work represent important findings for the rational design of future compounds for hH3R and hH4R.
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Silva DR, Barigye SJ, Santos-Garcia L, Fontes Ferreira da Cunha E. Molecular Modelling of Potential Candidates for the Treatment of Depression. Mol Inform 2019; 38:e1900024. [PMID: 31131991 DOI: 10.1002/minf.201900024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/07/2019] [Indexed: 12/22/2022]
Abstract
A lot of research initiatives in the last decades have been focused on the search of new strategies to treat depression. However, despite the availability of various antidepressants, current treatment is still far from ideal. Unwanted side effects, modest response rates and the slow onset of action are the main shortcomings. As a strategy to improve symptomatic relief and response rates, the dual modulation of the serotonin transporter and the histamine H3 receptor by a single chemical entity has been proposed in the literature. Accordingly, this work aims to elucidate key structural features responsible for the dual inhibitory activity of the hexahydro-pyrrolo-isoquinoline derivatives. For this purpose, two approaches were employed, four-dimensional quantitative structure-activity relationship (4D-QSAR) and molecular docking. The 4D-QSAR models for both receptors allowed the identification of the pharmacophore groups critical for the modelled biological activity, whereas the binding mode of this class of compounds to the human serotonin transporter was assessed by molecular docking. The findings can be applicable to design new antidepressants.
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Affiliation(s)
- Daniela Rodrigues Silva
- Department of Chemistry, Universidade Federal de Lavras, P.O. Box 3037, 37200-000, Lavras, MG, Brazil
| | - Stephen J Barigye
- Department of Chemistry, McGill University, 801 Sherbrooke Street W., Montréal, QC, Canada, H3 A 0B8
| | - Letícia Santos-Garcia
- Department of Chemistry, Universidade Federal de Lavras, P.O. Box 3037, 37200-000, Lavras, MG, Brazil
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Vass M, Podlewska S, de Esch IJP, Bojarski AJ, Leurs R, Kooistra AJ, de Graaf C. Aminergic GPCR-Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data. J Med Chem 2018; 62:3784-3839. [PMID: 30351004 DOI: 10.1021/acs.jmedchem.8b00836] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The aminergic family of G protein-coupled receptors (GPCRs) plays an important role in various diseases and represents a major drug discovery target class. Structure determination of all major aminergic subfamilies has enabled structure-based ligand design for these receptors. Site-directed mutagenesis data provides an invaluable complementary source of information for elucidating the structural determinants of binding of different ligand chemotypes. The current study provides a comparative analysis of 6692 mutation data points on 34 aminergic GPCR subtypes, covering the chemical space of 540 unique ligands from mutagenesis experiments and information from experimentally determined structures of 52 distinct aminergic receptor-ligand complexes. The integrated analysis enables detailed investigation of structural receptor-ligand interactions and assessment of the transferability of combined binding mode and mutation data across ligand chemotypes and receptor subtypes. An overview is provided of the possibilities and limitations of using mutation data to guide the design of novel aminergic receptor ligands.
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Affiliation(s)
- Márton Vass
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Sabina Podlewska
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Department of Drug Design and Pharmacology , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Sosei Heptares , Steinmetz Building, Granta Park, Great Abington , Cambridge CB21 6DG , U.K
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Khanfar MA, Reiner D, Hagenow S, Stark H. Design, synthesis, and biological evaluation of novel oxadiazole- and thiazole-based histamine H 3R ligands. Bioorg Med Chem 2018; 26:4034-4046. [PMID: 29960729 DOI: 10.1016/j.bmc.2018.06.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 02/06/2023]
Abstract
Histamine H3 receptor (H3R) is largely expressed in the CNS and modulation of the H3R function can affect histamine synthesis and liberation, and modulate the release of many other neurotransmitters. Targeting H3R with antagonists/inverse agonists may have therapeutic applications in neurodegenerative disorders, gastrointestinal and inflammatory diseases. This prompted us to design and synthesize azole-based H3R ligands, i.e. having oxadiazole- or thiazole-based core structures. While ligands of oxadiazole scaffold were almost inactive, thiazole-based ligands were very potent and several exhibited binding affinities in a nanomolar concentration range. Ligands combining 4-cyanophenyl moiety as arbitrary region, para-xylene or piperidine carbamoyl linkers, and/or pyrrolidine or piperidine basic heads were found to be the most active within this series of thiazole-based H3R ligands. The most active ligands were in silico screened for ADMET properties and drug-likeness. They fulfilled Lipinski's and Veber's rules and exhibited potential activities for oral administration, blood-brain barrier penetration, low hepatotoxicity, combined with an overall good toxicity profile.
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Affiliation(s)
- Mohammad A Khanfar
- Heinrich Heine University Düsseldorf, Institute of Pharmaceutical and Medicinal Chemistry, Universitaetsstr. 1, 40225 Duesseldorf, Germany; Faculty of Pharmacy, University of Jordan, P.O Box 13140, Amman 11942, Jordan; College of Pharmacy, Alfaisal University, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia
| | - David Reiner
- Heinrich Heine University Düsseldorf, Institute of Pharmaceutical and Medicinal Chemistry, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Stefanie Hagenow
- Heinrich Heine University Düsseldorf, Institute of Pharmaceutical and Medicinal Chemistry, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Holger Stark
- Heinrich Heine University Düsseldorf, Institute of Pharmaceutical and Medicinal Chemistry, Universitaetsstr. 1, 40225 Duesseldorf, Germany.
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7
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Structural insights into serotonin receptor ligands polypharmacology. Eur J Med Chem 2018; 151:797-814. [DOI: 10.1016/j.ejmech.2018.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 02/03/2023]
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8
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Computer-Aided Drug Design Approaches to Study Key Therapeutic Targets in Alzheimer’s Disease. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-1-4939-7404-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Kuder KJ, Łażewska D, Kaleta M, Latacz G, Kottke T, Olejarz A, Karcz T, Fruziński A, Szczepańska K, Karolak-Wojciechowska J, Stark H, Kieć-Kononowicz K. Synthesis and biological activity of novel tert-amylphenoxyalkyl (homo)piperidine derivatives as histamine H 3R ligands. Bioorg Med Chem 2017; 25:2701-2712. [PMID: 28372935 DOI: 10.1016/j.bmc.2017.03.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/13/2017] [Accepted: 03/15/2017] [Indexed: 12/25/2022]
Abstract
As a continuation of our search for novel histamine H3 receptor ligands a series of twenty new tert-amyl phenoxyalkylamine derivatives (2-21) was synthesized. Compounds of four to eight carbon atoms spacer alkyl chain were evaluated on their binding properties at human histamine H3 receptor (hH3R). The highest affinities were observed for pentyl derivatives 6-8 (Ki=8.8-23.4nM range) and among them piperidine derivative 6 with Ki=8.8nM. Structures 6, 7 were also classified as antagonists in cAMP accumulation assay (with EC50=157 and 164nM, respectively). Moreover, new compounds were also evaluated for anticonvulsant activity in Antiepileptic Screening Program (ASP) at National Institute of Neurological Disorders and Stroke (USA). Seven compounds (2-4, 9, 11, 12 and 20) showed anticonvulsant activity at maximal electroshock (MES) test in the dose of 30mg/kg at 0.5h. In the subcutaneous pentetrazole (scMET) test compound 4 showed protection at 100 and 300mg/kg dose at mice, however compounds showed high neurotoxicity in rotarod test at used doses. Also, molecular modeling studies were undertaken, to explain affinity of compounds at hH3R (taking into the consideration X-ray analysis of compound 18). In order to estimate "drug-likeness" of selected compounds in silico and experimental evaluation of lipophilicity, metabolic stability and cytotoxicity was performed.
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Affiliation(s)
- Kamil J Kuder
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Dorota Łażewska
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Maria Kaleta
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Tim Kottke
- Institute of Pharmaceutical Chemistry, Biozentrun, ZAFES, Frankfurt/Main 60438, Germany
| | - Agnieszka Olejarz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Tadeusz Karcz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Andrzej Fruziński
- Institute of General and Ecological Chemistry, Technical University of Łódź, Żeromskiego 116 str., Łódź 90-924, Poland
| | - Katarzyna Szczepańska
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Janina Karolak-Wojciechowska
- Institute of General and Ecological Chemistry, Technical University of Łódź, Żeromskiego 116 str., Łódź 90-924, Poland
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Universitaetsstr. 1, Düsseldorf 40225, Germany
| | - Katarzyna Kieć-Kononowicz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland.
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10
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Minovski N, Novič M. Integrated in Silico Methods for the Design and Optimization of Novel Drug Candidates. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although almost fully automated, the discovery of novel, effective, and safe drugs is still a long-term and highly expensive process. Consequently, the need for fleet, rational, and cost-efficient development of novel drugs is crucial, and nowadays the advanced in silico drug design methodologies seem to effectively meet these issues. The aim of this chapter is to provide a comprehensive overview of some of the current trends and advances in the in silico design of novel drug candidates with a special emphasis on 6-fluoroquinolone (6-FQ) antibacterials as potential novel Mycobacterium tuberculosis DNA gyrase inhibitors. In particular, the chapter covers some of the recent aspects of a wide range of in silico drug discovery approaches including multidimensional machine-learning methods, ligand-based and structure-based methodologies, as well as their proficient combination and integration into an intelligent virtual screening protocol for design and optimization of novel 6-FQ analogs.
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11
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Kiss R, Keserű GM. Structure-based discovery and binding site analysis of histamine receptor ligands. Expert Opin Drug Discov 2016; 11:1165-1185. [DOI: 10.1080/17460441.2016.1245288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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12
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Łażewska D, Jończyk J, Bajda M, Szałaj N, Więckowska A, Panek D, Moore C, Kuder K, Malawska B, Kieć-Kononowicz K. Cholinesterase inhibitory activity of chlorophenoxy derivatives-Histamine H3 receptor ligands. Bioorg Med Chem Lett 2016; 26:4140-5. [PMID: 27445168 DOI: 10.1016/j.bmcl.2016.04.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/16/2016] [Accepted: 04/20/2016] [Indexed: 12/28/2022]
Abstract
In recent years, multitarget-directed ligands have become an interesting strategy in a search for a new treatment of Alzheimer's disease. Combination of both: a histamine H3 receptor antagonist/inverse agonist and a cholinesterases inhibitor in one molecule could provide a new therapeutic opportunity. Here, we present biological evaluation of histamine H3 receptor ligands-chlorophenoxyalkylamine derivatives against cholinesterases: acetyl- and butyrylcholinesterase. The target compounds showed cholinesterase inhibitory activity in a low micromolar range. The most potent in this group was 1-(7-(4-chlorophenoxy)heptyl)homopiperidine (18) inhibiting the both enzymes (EeAChE IC50=1.93μM and EqBuChE IC50=1.64μM). Molecular modeling studies were performed to explain the binding mode of 18 with histamine H3 receptor as well as with cholinesterases.
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Affiliation(s)
- Dorota Łażewska
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Jakub Jończyk
- Department of Physicochemical Drug Analysis, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Marek Bajda
- Department of Physicochemical Drug Analysis, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Natalia Szałaj
- Department of Physicochemical Drug Analysis, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Anna Więckowska
- Department of Physicochemical Drug Analysis, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Dawid Panek
- Department of Physicochemical Drug Analysis, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Caitlin Moore
- Department of Physicochemical Drug Analysis, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Kamil Kuder
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Barbara Malawska
- Department of Physicochemical Drug Analysis, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
| | - Katarzyna Kieć-Kononowicz
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland.
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13
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Panula P, Chazot PL, Cowart M, Gutzmer R, Leurs R, Liu WLS, Stark H, Thurmond RL, Haas HL. International Union of Basic and Clinical Pharmacology. XCVIII. Histamine Receptors. Pharmacol Rev 2016; 67:601-55. [PMID: 26084539 DOI: 10.1124/pr.114.010249] [Citation(s) in RCA: 362] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Histamine is a developmentally highly conserved autacoid found in most vertebrate tissues. Its physiological functions are mediated by four 7-transmembrane G protein-coupled receptors (H1R, H2R, H3R, H4R) that are all targets of pharmacological intervention. The receptors display molecular heterogeneity and constitutive activity. H1R antagonists are long known antiallergic and sedating drugs, whereas the H2R was identified in the 1970s and led to the development of H2R-antagonists that revolutionized stomach ulcer treatment. The crystal structure of ligand-bound H1R has rendered it possible to design new ligands with novel properties. The H3R is an autoreceptor and heteroreceptor providing negative feedback on histaminergic and inhibition on other neurons. A block of these actions promotes waking. The H4R occurs on immuncompetent cells and the development of anti-inflammatory drugs is anticipated.
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Affiliation(s)
- Pertti Panula
- Department of Anatomy, and Neuroscience Center, University of Helsinki, Finland (P.P.); School of Biological and Biomedical Sciences, University of Durham, United Kingdom (P.L.C.); AbbVie, Inc. North Chicago, Illinois (M.C.); Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany (R.G.); Department of Medicinal Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands (R.L.); Ziarco Pharma Limited, Canterbury, United Kingdom (W.L.S.L.); Institute of Pharmaceutical and Medical Chemistry and Institute of Neurophysiology, Medical Faculty, Westfalische-Wilhelms-University, Muenster, Germany (H.L.H.); Heinrich-Heine-University Duesseldorf, Germany (H.S.); and Janssen Research & Development, LLC, San Diego, California (R.L.T.)
| | - Paul L Chazot
- Department of Anatomy, and Neuroscience Center, University of Helsinki, Finland (P.P.); School of Biological and Biomedical Sciences, University of Durham, United Kingdom (P.L.C.); AbbVie, Inc. North Chicago, Illinois (M.C.); Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany (R.G.); Department of Medicinal Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands (R.L.); Ziarco Pharma Limited, Canterbury, United Kingdom (W.L.S.L.); Institute of Pharmaceutical and Medical Chemistry and Institute of Neurophysiology, Medical Faculty, Westfalische-Wilhelms-University, Muenster, Germany (H.L.H.); Heinrich-Heine-University Duesseldorf, Germany (H.S.); and Janssen Research & Development, LLC, San Diego, California (R.L.T.)
| | - Marlon Cowart
- Department of Anatomy, and Neuroscience Center, University of Helsinki, Finland (P.P.); School of Biological and Biomedical Sciences, University of Durham, United Kingdom (P.L.C.); AbbVie, Inc. North Chicago, Illinois (M.C.); Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany (R.G.); Department of Medicinal Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands (R.L.); Ziarco Pharma Limited, Canterbury, United Kingdom (W.L.S.L.); Institute of Pharmaceutical and Medical Chemistry and Institute of Neurophysiology, Medical Faculty, Westfalische-Wilhelms-University, Muenster, Germany (H.L.H.); Heinrich-Heine-University Duesseldorf, Germany (H.S.); and Janssen Research & Development, LLC, San Diego, California (R.L.T.)
| | - Ralf Gutzmer
- Department of Anatomy, and Neuroscience Center, University of Helsinki, Finland (P.P.); School of Biological and Biomedical Sciences, University of Durham, United Kingdom (P.L.C.); AbbVie, Inc. North Chicago, Illinois (M.C.); Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany (R.G.); Department of Medicinal Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands (R.L.); Ziarco Pharma Limited, Canterbury, United Kingdom (W.L.S.L.); Institute of Pharmaceutical and Medical Chemistry and Institute of Neurophysiology, Medical Faculty, Westfalische-Wilhelms-University, Muenster, Germany (H.L.H.); Heinrich-Heine-University Duesseldorf, Germany (H.S.); and Janssen Research & Development, LLC, San Diego, California (R.L.T.)
| | - Rob Leurs
- Department of Anatomy, and Neuroscience Center, University of Helsinki, Finland (P.P.); School of Biological and Biomedical Sciences, University of Durham, United Kingdom (P.L.C.); AbbVie, Inc. North Chicago, Illinois (M.C.); Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany (R.G.); Department of Medicinal Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands (R.L.); Ziarco Pharma Limited, Canterbury, United Kingdom (W.L.S.L.); Institute of Pharmaceutical and Medical Chemistry and Institute of Neurophysiology, Medical Faculty, Westfalische-Wilhelms-University, Muenster, Germany (H.L.H.); Heinrich-Heine-University Duesseldorf, Germany (H.S.); and Janssen Research & Development, LLC, San Diego, California (R.L.T.)
| | - Wai L S Liu
- Department of Anatomy, and Neuroscience Center, University of Helsinki, Finland (P.P.); School of Biological and Biomedical Sciences, University of Durham, United Kingdom (P.L.C.); AbbVie, Inc. North Chicago, Illinois (M.C.); Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany (R.G.); Department of Medicinal Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands (R.L.); Ziarco Pharma Limited, Canterbury, United Kingdom (W.L.S.L.); Institute of Pharmaceutical and Medical Chemistry and Institute of Neurophysiology, Medical Faculty, Westfalische-Wilhelms-University, Muenster, Germany (H.L.H.); Heinrich-Heine-University Duesseldorf, Germany (H.S.); and Janssen Research & Development, LLC, San Diego, California (R.L.T.)
| | - Holger Stark
- Department of Anatomy, and Neuroscience Center, University of Helsinki, Finland (P.P.); School of Biological and Biomedical Sciences, University of Durham, United Kingdom (P.L.C.); AbbVie, Inc. North Chicago, Illinois (M.C.); Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany (R.G.); Department of Medicinal Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands (R.L.); Ziarco Pharma Limited, Canterbury, United Kingdom (W.L.S.L.); Institute of Pharmaceutical and Medical Chemistry and Institute of Neurophysiology, Medical Faculty, Westfalische-Wilhelms-University, Muenster, Germany (H.L.H.); Heinrich-Heine-University Duesseldorf, Germany (H.S.); and Janssen Research & Development, LLC, San Diego, California (R.L.T.)
| | - Robin L Thurmond
- Department of Anatomy, and Neuroscience Center, University of Helsinki, Finland (P.P.); School of Biological and Biomedical Sciences, University of Durham, United Kingdom (P.L.C.); AbbVie, Inc. North Chicago, Illinois (M.C.); Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany (R.G.); Department of Medicinal Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands (R.L.); Ziarco Pharma Limited, Canterbury, United Kingdom (W.L.S.L.); Institute of Pharmaceutical and Medical Chemistry and Institute of Neurophysiology, Medical Faculty, Westfalische-Wilhelms-University, Muenster, Germany (H.L.H.); Heinrich-Heine-University Duesseldorf, Germany (H.S.); and Janssen Research & Development, LLC, San Diego, California (R.L.T.)
| | - Helmut L Haas
- Department of Anatomy, and Neuroscience Center, University of Helsinki, Finland (P.P.); School of Biological and Biomedical Sciences, University of Durham, United Kingdom (P.L.C.); AbbVie, Inc. North Chicago, Illinois (M.C.); Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany (R.G.); Department of Medicinal Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands (R.L.); Ziarco Pharma Limited, Canterbury, United Kingdom (W.L.S.L.); Institute of Pharmaceutical and Medical Chemistry and Institute of Neurophysiology, Medical Faculty, Westfalische-Wilhelms-University, Muenster, Germany (H.L.H.); Heinrich-Heine-University Duesseldorf, Germany (H.S.); and Janssen Research & Development, LLC, San Diego, California (R.L.T.)
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14
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Kuder K, Łażewska D, Latacz G, Schwed JS, Karcz T, Stark H, Karolak-Wojciechowska J, Kieć-Kononowicz K. Chlorophenoxy aminoalkyl derivatives as histamine H(3)R ligands and antiseizure agents. Bioorg Med Chem 2015; 24:53-72. [PMID: 26690914 DOI: 10.1016/j.bmc.2015.11.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/12/2015] [Accepted: 11/19/2015] [Indexed: 12/20/2022]
Abstract
A series of twenty new chlorophenoxyalkylamine derivatives (9-28) was synthesized and evaluated on their binding properties at the human histamine H3 receptor (hH3R). The spacer alkyl chain contained five to seven carbon atoms. The highest affinities have shown the 4-chloro substituted derivatives 10 and 25 (Ki=133 and 128 nM, respectively) classified as antagonists in cAMP accumulation assay (EC50=72 and 75 nM, respectively). Synthesized compounds were also evaluated for anticonvulsant activity in Antiepileptic Screening Program (ASP) at National Institute of Neurological Disorders and Stroke (USA). Two compounds (4-chloro substituted derivatives: 20 and 26) were the most promising and showed in the MES seizure model in rats (after ip administration) ED50 values of 14 mg/kg and 13.18 mg/kg, respectively. Protective indexes (PI=TD50/ED50) were 3.2 for 20 and 3.8 for 26. Moreover, molecular modeling and docking studies were undertaken to explain affinity at hH3R of target compounds, and the experimentally and in silico estimation of properties like lipophilicity and metabolism was performed. Antiproliferative effects have been also investigated in vitro for selected compounds (10 and 25). These compounds neither possessed significant antiproliferative and antitumor activity, nor modulated CYP3A4 activity up to concentration of 10 μM.
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Affiliation(s)
- Kamil Kuder
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Technology and Biotechnology of Drugs, Medyczna 9, 30-688 Kraków, Poland
| | - Dorota Łażewska
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Technology and Biotechnology of Drugs, Medyczna 9, 30-688 Kraków, Poland
| | - Gniewomir Latacz
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Technology and Biotechnology of Drugs, Medyczna 9, 30-688 Kraków, Poland
| | - Johannes Stephan Schwed
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Tadeusz Karcz
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Technology and Biotechnology of Drugs, Medyczna 9, 30-688 Kraków, Poland
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Janina Karolak-Wojciechowska
- Institute of General and Ecological Chemistry, Technical University of Łódź, Żeromskiego 116 Str., 90-924 Łódź, Poland
| | - Katarzyna Kieć-Kononowicz
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Technology and Biotechnology of Drugs, Medyczna 9, 30-688 Kraków, Poland.
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15
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Sadek B, Stark H. Cherry-picked ligands at histamine receptor subtypes. Neuropharmacology 2015; 106:56-73. [PMID: 26581501 DOI: 10.1016/j.neuropharm.2015.11.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 12/17/2022]
Abstract
Histamine, a biogenic amine, is considered as a principle mediator of multiple physiological effects through binding to its H1, H2, H3, and H4 receptors (H1-H4Rs). Currently, the HRs have gained attention as important targets for the treatment of several diseases and disorders ranging from allergy to Alzheimer's disease and immune deficiency. Accordingly, medicinal chemistry studies exploring histamine-like molecules and their physicochemical properties by binding and interacting with the four HRs has led to the development of a diversity of agonists and antagonists that display selectivity for each HR subtype. An overview on H1-R4Rs and developed ligands representing some key steps in development is provided here combined with a short description of structure-activity relationships for each class. Main chemical diversities, pharmacophores, and pharmacological profiles of most innovative H1-H4R agonists and antagonists are highlighted. Therefore, this overview should support the rational choice for the optimal ligand selection based on affinity, selectivity and efficacy data in biochemical and pharmacological studies. This article is part of the Special Issue entitled 'Histamine Receptors'.
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Affiliation(s)
- Bassem Sadek
- Department of Pharmacology and Therapeutics, College of Medicine & Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, United Arab Emirates.
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitaetsstr. 1, 40225 Düsseldorf, Germany
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16
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Nikolic K, Agbaba D, Stark H. Pharmacophore modeling, drug design and virtual screening on multi-targeting procognitive agents approaching histaminergic pathways. J Taiwan Inst Chem Eng 2015. [DOI: 10.1016/j.jtice.2014.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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Whittaker CAP, Patching SG, Esmann M, Middleton DA. Ligand orientation in a membrane-embedded receptor site revealed by solid-state NMR with paramagnetic relaxation enhancement. Org Biomol Chem 2015; 13:2664-8. [DOI: 10.1039/c4ob02427c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paramagnetic relaxation-enhanced solid-state NMR reveals a ouabain analogue with an inverted orientation in the Na,K-ATPase inhibitory site.
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Affiliation(s)
| | | | - Mikael Esmann
- Department of Biomedicine
- Aarhus University
- Aarhus
- Denmark
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18
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Wingen K, Stark H. Scaffold variations in amine warhead of histamine H₃ receptor antagonists. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 10:e483-9. [PMID: 24451638 DOI: 10.1016/j.ddtec.2013.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The histamine H₃ receptor (H₃R) is involved in numerous regulatory neurotransmission processes and there-fore, is a prominent target for centrally occurring disease with some promising clinical candidates. Previous research resulted in the identification of a core pharmacophore blueprint for H₃R antagonists/inverse agonists, which when inserted in a molecule, mostly ensures acceptable affinity. Nevertheless, variations of scaffold and peripheral areas can increase potency and pharmacokinetic profile of drug candidates. The variations in amine scaffolds of antagonists for this aminergic GPCR are of special importance.
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19
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Kooistra AJ, Kuhne S, de Esch IJP, Leurs R, de Graaf C. A structural chemogenomics analysis of aminergic GPCRs: lessons for histamine receptor ligand design. Br J Pharmacol 2014; 170:101-26. [PMID: 23713847 DOI: 10.1111/bph.12248] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 04/26/2013] [Accepted: 05/03/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND AND PURPOSE Chemogenomics focuses on the discovery of new connections between chemical and biological space leading to the discovery of new protein targets and biologically active molecules. G-protein coupled receptors (GPCRs) are a particularly interesting protein family for chemogenomics studies because there is an overwhelming amount of ligand binding affinity data available. The increasing number of aminergic GPCR crystal structures now for the first time allows the integration of chemogenomics studies with high-resolution structural analyses of GPCR-ligand complexes. EXPERIMENTAL APPROACH In this study, we have combined ligand affinity data, receptor mutagenesis studies, and amino acid sequence analyses to high-resolution structural analyses of (hist)aminergic GPCR-ligand interactions. This integrated structural chemogenomics analysis is used to more accurately describe the molecular and structural determinants of ligand affinity and selectivity in different key binding regions of the crystallized aminergic GPCRs, and histamine receptors in particular. KEY RESULTS Our investigations highlight interesting correlations and differences between ligand similarity and ligand binding site similarity of different aminergic receptors. Apparent discrepancies can be explained by combining detailed analysis of crystallized or predicted protein-ligand binding modes, receptor mutation studies, and ligand structure-selectivity relationships that identify local differences in essential pharmacophore features in the ligand binding sites of different receptors. CONCLUSIONS AND IMPLICATIONS We have performed structural chemogenomics studies that identify links between (hist)aminergic receptor ligands and their binding sites and binding modes. This knowledge can be used to identify structure-selectivity relationships that increase our understanding of ligand binding to (hist)aminergic receptors and hence can be used in future GPCR ligand discovery and design.
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Affiliation(s)
- A J Kooistra
- Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands
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20
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Wittmann HJ, Seifert R, Strasser A. Mathematical analysis of the sodium sensitivity of the human histamine H3 receptor. In Silico Pharmacol 2014; 2:1. [PMID: 27502620 PMCID: PMC4644138 DOI: 10.1186/s40203-014-0001-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/28/2014] [Indexed: 11/22/2022] Open
Abstract
Purpose It was shown by several experimental studies that some G protein coupled receptors (GPCR) are sensitive to sodium ions. Furthermore, mutagenesis studies or the determination of crystal structures of the adenosine A2A or δ-opioid receptor revealed an allosteric Na+ binding pocket near to the highly conserved Asp2.50. Within a previous study, the influence of NaCl concentration onto the steady-state GTPase activity at the human histamine H3 receptor (hH3R) in presence of the endogenous histamine or the inverse agonist thioperamide was analyzed. The purpose of the present study was to examine and quantify the Na+-sensitivity of hH3R on a molecular level. Methods To achieve this, we developed a set of equations, describing constitutive activity and the different ligand-receptor equilibria in absence or presence of sodium ions. Furthermore, in order to gain a better understanding of the ligand- and Na+-binding to hH3R on molecular level, we performed molecular dynamic (MD) simulations. Results The analysis of the previously determined experimental steady-state GTPase data with the set of equations presented within this study, reveals that thioperamide binds into the orthosteric binding pocket of the hH3R in absence or presence of a Na+ in its allosteric binding site. However, the data suggest that thioperamide binds preferentially into the hH3R in absence of a sodium ion in its allosteric site. These experimental results were supported by MD simulations of thioperamide in the binding pocket of the inactive hH3R. Furthermore, the MD simulations revealed two different binding modes for thioperamide in presence or absence of a Na+ in its allosteric site. Conclusion The mathematical model presented within this study describes the experimental data regarding the Na+-sensitivity of hH3R in an excellent manner. Although the present study is focused onto the Na+-sensitivity of the hH3R, the resulting equations, describing Na+- and ligand-binding to a GPCR, can be used for all other ion-sensitive GPCRs.
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Affiliation(s)
- Hans-Joachim Wittmann
- Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, Regensburg, 93040, Germany
| | - Roland Seifert
- Institute of Pharmacology, Medical School of Hannover, Carl-Neuberg-Straße 1, Hannover, 30625, Germany
| | - Andrea Strasser
- Department of Pharmaceutical and Medicinal Chemistry II, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, Regensburg, 93040, Germany.
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21
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Nikolic K, Filipic S, Agbaba D, Stark H. Procognitive properties of drugs with single and multitargeting H3 receptor antagonist activities. CNS Neurosci Ther 2014; 20:613-23. [PMID: 24836924 DOI: 10.1111/cns.12279] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/07/2014] [Accepted: 04/07/2014] [Indexed: 01/01/2023] Open
Abstract
The histamine H3 receptor (H3 R) is an important modulator of numerous central control mechanisms. Novel lead optimizations for H3 R antagonists/inverse agonists involved studies of structure-activity relationships, cross-affinities, and pharmacokinetic properties of promising ligands. Blockade of inhibitory histamine H3 autoreceptors reinforces histaminergic transmission, while antagonism of H3 heteroreceptors accelerates the corticolimbic liberation of acetylcholine, norepinephrine, glutamate, dopamine, serotonin and gamma-aminobutyric acid (GABA). The H3 R positioned at numerous neurotransmission crossroads indicates therapeutic applications of small-molecule H3 R modulators in a number of psychiatric and neurodegenerative diseases with various clinical candidates available. Dual target drugs displaying H3 R antagonism/inverse agonism with inhibition of acetylcholine esterase (AChE), histamine N-methyltransferase (HMT), or serotonin transporter (SERT) are novel class of procognitive agents. Main chemical diversities, pharmacophores, and pharmacological profiles of procognitive agents acting as H3 R antagonists/inverse agonists and dual H3 R antagonists/inverse agonists with inhibiting activity on AChE, HMT, or SERT are highlighted here.
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Affiliation(s)
- Katarina Nikolic
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Belgrade, Belgrade, Serbia
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22
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Darras FH, Pockes S, Huang G, Wehle S, Strasser A, Wittmann HJ, Nimczick M, Sotriffer CA, Decker M. Synthesis, biological evaluation, and computational studies of Tri- and tetracyclic nitrogen-bridgehead compounds as potent dual-acting AChE inhibitors and hH3 receptor antagonists. ACS Chem Neurosci 2014; 5:225-42. [PMID: 24422467 DOI: 10.1021/cn4002126] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Combination of AChE inhibiting and histamine H3 receptor antagonizing properties in a single molecule might show synergistic effects to improve cognitive deficits in Alzheimer's disease, since both pharmacological actions are able to enhance cholinergic neurotransmission in the cortex. However, whereas AChE inhibitors prevent hydrolysis of acetylcholine also peripherally, histamine H3 antagonists will raise acetylcholine levels mostly in the brain due to predominant occurrence of the receptor in the central nervous system. In this work, we designed and synthesized two novel classes of tri- and tetracyclic nitrogen-bridgehead compounds acting as dual AChE inhibitors and histamine H3 antagonists by combining the nitrogen-bridgehead moiety of novel AChE inhibitors with a second N-basic fragment based on the piperidinylpropoxy pharmacophore with different spacer lengths. Intensive structure-activity relationships (SARs) with regard to both biological targets led to compound 41 which showed balanced affinities as hAChE inhibitor with IC50 = 33.9 nM, and hH3R antagonism with Ki = 76.2 nM with greater than 200-fold selectivity over the other histamine receptor subtypes. Molecular docking studies were performed to explain the potent AChE inhibition of the target compounds and molecular dynamics studies to explain high affinity at the hH3R.
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Affiliation(s)
| | | | - Guozheng Huang
- Pharmazeutische und Medizinische Chemie, Institut für
Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Sarah Wehle
- Pharmazeutische und Medizinische Chemie, Institut für
Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | | | | | - Martin Nimczick
- Pharmazeutische und Medizinische Chemie, Institut für
Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Christoph A. Sotriffer
- Pharmazeutische und Medizinische Chemie, Institut für
Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Michael Decker
- Pharmazeutische und Medizinische Chemie, Institut für
Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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23
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Ng HW, Laughton CA, Doughty SW. Molecular dynamics simulations of the adenosine A2a receptor in POPC and POPE lipid bilayers: effects of membrane on protein behavior. J Chem Inf Model 2014; 54:573-81. [PMID: 24460123 DOI: 10.1021/ci400463z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Analysis of 300 ns (ns) molecular dynamics (MD) simulations of an adenosine A2a receptor (A2a AR) model, conducted in triplicate, in 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) and 1-palmitoyl-2-oleoylphosphatidylethanolamine (POPE) bilayers reveals significantly different protein dynamical behavior. Principal component analysis (PCA) shows that the dissimilarities stem from interhelical rather than intrahelical motions. The difference in the hydrophobic thicknesses of these simulated lipid bilayers is potentially a significant reason for the observed difference in results. The distinct lipid headgroups might also lead to different molecular interactions and hence different protein loop motions. Overall, the A2a AR shows higher mobility and flexibility in POPC as compared to POPE.
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Affiliation(s)
- Hui Wen Ng
- School of Pharmacy, University of Nottingham Malaysia Campus , Jalan Broga, 43500 Semenyih, Selangor, Malaysia
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24
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Levoin N, Labeeuw O, Krief S, Calmels T, Poupardin-Olivier O, Berrebi-Bertrand I, Lecomte JM, Schwartz JC, Capet M. Determination of the binding mode and interacting amino-acids for dibasic H3 receptor antagonists. Bioorg Med Chem 2013; 21:4526-9. [DOI: 10.1016/j.bmc.2013.05.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/16/2013] [Accepted: 05/21/2013] [Indexed: 12/28/2022]
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25
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Ng HW, Laughton CA, Doughty SW. Molecular dynamics simulations of the adenosine A2a receptor: structural stability, sampling, and convergence. J Chem Inf Model 2013; 53:1168-78. [PMID: 23514445 DOI: 10.1021/ci300610w] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Molecular dynamics (MD) simulations of membrane-embedded G-protein coupled receptors (GPCRs) have rapidly gained popularity among the molecular simulation community in recent years, a trend which has an obvious link to the tremendous pharmaceutical importance of this group of receptors and the increasing availability of crystal structures. In view of the widespread use of this technique, it is of fundamental importance to ensure the reliability and robustness of the methodologies so they yield valid results and enable sufficiently accurate predictions to be made. In this work, 200 ns simulations of the A2a adenosine receptor (A2a AR) have been produced and evaluated in the light of these requirements. The conformational dynamics of the target protein, as obtained from replicate simulations in both the presence and absence of an inverse agonist ligand (ZM241385), have been investigated and compared using principal component analysis (PCA). Results show that, on this time scale, convergence of the replicates is not readily evident and dependent on the types of the protein motions considered. Thus rates of inter- as opposed to intrahelical relaxation and sampling can be different. When studied individually, we find that helices III and IV have noticeably greater stability than helices I, II, V, VI, and VII in the apo form. The addition of the inverse agonist ligand greatly improves the stability of all helices.
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Affiliation(s)
- Hui Wen Ng
- School of Pharmacy, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
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26
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Lounnas V, Ritschel T, Kelder J, McGuire R, Bywater RP, Foloppe N. Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery. Comput Struct Biotechnol J 2013; 5:e201302011. [PMID: 24688704 PMCID: PMC3962124 DOI: 10.5936/csbj.201302011] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/26/2013] [Accepted: 02/08/2013] [Indexed: 12/20/2022] Open
Abstract
The past decade has witnessed a paradigm shift in preclinical drug discovery with structure-based drug design (SBDD) making a comeback while high-throughput screening (HTS) methods have continued to generate disappointing results. There is a deficit of information between identified hits and the many criteria that must be fulfilled in parallel to convert them into preclinical candidates that have a real chance to become a drug. This gap can be bridged by investigating the interactions between the ligands and their receptors. Accurate calculations of the free energy of binding are still elusive; however progresses were made with respect to how one may deal with the versatile role of water. A corpus of knowledge combining X-ray structures, bioinformatics and molecular modeling techniques now allows drug designers to routinely produce receptor homology models of increasing quality. These models serve as a basis to establish and validate efficient rationales used to tailor and/or screen virtual libraries with enhanced chances of obtaining hits. Many case reports of successful SBDD show how synergy can be gained from the combined use of several techniques. The role of SBDD with respect to two different classes of widely investigated pharmaceutical targets: (a) protein kinases (PK) and (b) G-protein coupled receptors (GPCR) is discussed. Throughout these examples prototypical situations covering the current possibilities and limitations of SBDD are presented.
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Affiliation(s)
- Valère Lounnas
- CMBI, NCMLS Radboud University, Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
| | - Tina Ritschel
- Computational Drug Discovery, CMBI, NCMLS, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
| | - Jan Kelder
- Beethovengaarde 97, 5344 CD Oss, The Netherlands
| | - Ross McGuire
- BioAxis Research BV, Pivot Park, Molenstraat 110, 5342 CC Oss, The Netherlands
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27
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Docking and MD study of histamine H4R based on the crystal structure of H1R. J Mol Graph Model 2013; 39:1-12. [DOI: 10.1016/j.jmgm.2012.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/09/2012] [Accepted: 10/13/2012] [Indexed: 01/06/2023]
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28
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Bajda M, Kuder KJ, Łażewska D, Kieć-Kononowicz K, Więckowska A, Ignasik M, Guzior N, Jończyk J, Malawska B. Dual-Acting Diether Derivatives of Piperidine and Homopiperidine with Histamine H3 Receptor Antagonistic and Anticholinesterase Activity. Arch Pharm (Weinheim) 2012; 345:591-7. [DOI: 10.1002/ardp.201200018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 03/16/2012] [Accepted: 03/21/2012] [Indexed: 12/28/2022]
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29
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Heifetz A, Morris GB, Biggin PC, Barker O, Fryatt T, Bentley J, Hallett D, Manikowski D, Pal S, Reifegerste R, Slack M, Law R. Study of Human Orexin-1 and -2 G-Protein-Coupled Receptors with Novel and Published Antagonists by Modeling, Molecular Dynamics Simulations, and Site-Directed Mutagenesis. Biochemistry 2012; 51:3178-97. [DOI: 10.1021/bi300136h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - G. Benjamin Morris
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Oliver Barker
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Tara Fryatt
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Jonathan Bentley
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - David Hallett
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | | | - Sandeep Pal
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Rita Reifegerste
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Mark Slack
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Richard Law
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
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30
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Combinatorial support vector machines approach for virtual screening of selective multi-target serotonin reuptake inhibitors from large compound libraries. J Mol Graph Model 2012; 32:49-66. [DOI: 10.1016/j.jmgm.2011.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/30/2011] [Accepted: 09/01/2011] [Indexed: 12/13/2022]
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31
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Bordi F, Rivara S, Dallaturca E, Carmi C, Pala D, Lodola A, Vacondio F, Flammini L, Bertoni S, Ballabeni V, Barocelli E, Mor M. Dibasic biphenyl H3 receptor antagonists: Steric tolerance for a lipophilic side chain. Eur J Med Chem 2012; 48:214-30. [DOI: 10.1016/j.ejmech.2011.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/07/2011] [Accepted: 12/10/2011] [Indexed: 10/14/2022]
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32
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Seddon G, Lounnas V, McGuire R, van den Bergh T, Bywater RP, Oliveira L, Vriend G. Drug design for ever, from hype to hope. J Comput Aided Mol Des 2012; 26:137-50. [PMID: 22252446 PMCID: PMC3268973 DOI: 10.1007/s10822-011-9519-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 12/05/2011] [Indexed: 01/28/2023]
Abstract
In its first 25 years JCAMD has been disseminating a large number of techniques aimed at finding better medicines faster. These include genetic algorithms, COMFA, QSAR, structure based techniques, homology modelling, high throughput screening, combichem, and dozens more that were a hype in their time and that now are just a useful addition to the drug-designers toolbox. Despite massive efforts throughout academic and industrial drug design research departments, the number of FDA-approved new molecular entities per year stagnates, and the pharmaceutical industry is reorganising accordingly. The recent spate of industrial consolidations and the concomitant move towards outsourcing of research activities requires better integration of all activities along the chain from bench to bedside. The next 25 years will undoubtedly show a series of translational science activities that are aimed at a better communication between all parties involved, from quantum chemistry to bedside and from academia to industry. This will above all include understanding the underlying biological problem and optimal use of all available data.
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Affiliation(s)
- G Seddon
- Adelard Institute, Manchester, UK
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33
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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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34
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Istyastono EP, Nijmeijer S, Lim HD, van de Stolpe A, Roumen L, Kooistra AJ, Vischer HF, de Esch IJP, Leurs R, de Graaf C. Molecular determinants of ligand binding modes in the histamine H(4) receptor: linking ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) models to in silico guided receptor mutagenesis studies. J Med Chem 2011; 54:8136-47. [PMID: 22003888 DOI: 10.1021/jm201042n] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The histamine H(4) receptor (H(4)R) is a G protein-coupled receptor (GPCR) that plays an important role in inflammation. Similar to the homologous histamine H(3) receptor (H(3)R), two acidic residues in the H(4)R binding pocket, D(3.32) and E(5.46), act as essential hydrogen bond acceptors of positively ionizable hydrogen bond donors in H(4)R ligands. Given the symmetric distribution of these complementary pharmacophore features in H(4)R and its ligands, different alternative ligand binding mode hypotheses have been proposed. The current study focuses on the elucidation of the molecular determinants of H(4)R-ligand binding modes by combining (3D) quantitative structure-activity relationship (QSAR), protein homology modeling, molecular dynamics simulations, and site-directed mutagenesis studies. We have designed and synthesized a series of clobenpropit (N-(4-chlorobenzyl)-S-[3-(4(5)-imidazolyl)propyl]isothiourea) derivatives to investigate H(4)R-ligand interactions and ligand binding orientations. Interestingly, our studies indicate that clobenpropit (2) itself can bind to H(4)R in two distinct binding modes, while the addition of a cyclohexyl group to the clobenpropit isothiourea moiety allows VUF5228 (5) to adopt only one specific binding mode in the H(4)R binding pocket. Our ligand-steered, experimentally supported protein modeling method gives new insights into ligand recognition by H(4)R and can be used as a general approach to elucidate the structure of protein-ligand complexes.
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Affiliation(s)
- Enade P Istyastono
- Department of Pharmacochemistry, Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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35
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Walter M, Kottke T, Stark H. The histamine H₄ receptor: targeting inflammatory disorders. Eur J Pharmacol 2011; 668:1-5. [PMID: 21741967 DOI: 10.1016/j.ejphar.2011.06.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 06/07/2011] [Accepted: 06/15/2011] [Indexed: 01/14/2023]
Abstract
The discovery of the histamine H(4) receptor has added a new chapter to the century of extensive biogenic amine research. The human histamine H(4) receptor is mainly expressed in cells of the human immune system (e.g. mast cells, eosinophils, monocytes, dendritic cells, T cells) and mediates several effects on chemotaxis with numerous cell types. The distinct expression pattern and the immunomodulatory role highlight its physiological relevance in inflammatory and immunological processes. Inflammatory conditions, e.g. allergy, asthma and autoimmune diseases, were for a long time thought to be mainly mediated by activation of the histamine H(1) receptor subtype. However, in the treatment of diseases as chronic pruritus, asthma and allergic rhinitis the use of histamine H(1) receptor antagonists is unsatisfying. Selective H(4) receptor ligands and/or synergism of histamine H(1) and H(4) receptor modulation may be more effective in such pathophysiological conditions. Promising preclinical studies underline its role as an attractive target in the treatment of inflammatory and autoimmune disorders. Meanwhile, first histamine H(4) receptor antagonist has reached clinical phases for the treatment of respiratory diseases.
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Affiliation(s)
- Miriam Walter
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, ZAFES/LiFF/CMP/ICNF, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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36
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Receptor-specific functional efficacies of alkyl imidazoles as dual histamine H3/H4 receptor ligands. Eur J Pharmacol 2011; 654:200-8. [DOI: 10.1016/j.ejphar.2010.12.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 11/18/2010] [Accepted: 12/15/2010] [Indexed: 11/23/2022]
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37
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Wijtmans M, de Graaf C, de Kloe G, Istyastono EP, Smit J, Lim H, Boonnak R, Nijmeijer S, Smits RA, Jongejan A, Zuiderveld O, de Esch IJP, Leurs R. Triazole ligands reveal distinct molecular features that induce histamine H4 receptor affinity and subtly govern H4/H3 subtype selectivity. J Med Chem 2011; 54:1693-703. [PMID: 21348462 DOI: 10.1021/jm1013488] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The histamine H(3) (H(3)R) and H(4) (H(4)R) receptors attract considerable interest from the medicinal chemistry community. Given their relatively high homology yet widely differing therapeutic promises, ligand selectivity for the two receptors is crucial. We interrogated H(4)R/H(3)R selectivities using ligands with a [1,2,3]triazole core. Cu(I)-assisted "click chemistry" was used to assemble diverse [1,2,3]triazole compounds (6a-w and 7a-f), many containing a peripheral imidazole group. The imidazole ring posed some problems in the click chemistry putatively due to Cu(II) coordination, but Boc protection of the imidazole and removal of oxygen from the reaction mixture provided effective strategies. Pharmacological studies revealed two monosubstituted imidazoles (6h,p) with <10 nM H(4)R affinities and >10-fold H(4)R/H(3)R selectivity. Both compounds possess a cycloalkylmethyl group and appear to target a lipophilic pocket in H(4)R with high steric precision. The use of the [1,2,3]triazole scaffold is further demonstrated by the notion that simple changes in spacer length or peripheral groups can reverse the selectivity toward H(3)R. Computational evidence is provided to account for two key selectivity switches and to pinpoint a lipophilic pocket as an important handle for H(4)R over H(3)R selectivity.
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Affiliation(s)
- Maikel Wijtmans
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Exact Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
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38
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Sander K, Kottke T, Weizel L, Stark H. Kojic acid derivatives as histamine H(3) receptor ligands. Chem Pharm Bull (Tokyo) 2011; 58:1353-61. [PMID: 20930404 DOI: 10.1248/cpb.58.1353] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The histamine H(3) receptor (H(3)R) is a promising target in the development of new compounds for the treatment of mainly centrally occurring diseases. However, emerging novel therapeutic concepts have been introduced and some indications in the H(3)R field, e.g. migraine, pain or allergic rhinitis, might take advantage of peripherally acting ligands. In this work, kojic acid-derived structural elements were inserted into a well established H(3)R antagonist/inverse agonist scaffold to investigate the bioisosteric potential of γ-pyranones with respect to the different moieties of the H(3)R pharmacophore. The most affine compounds showed receptor binding in the low nanomolar concentration range. Evaluation and comparison of kojic acid-containing ligands and their corresponding phenyl analogues (3-7) revealed that the newly integrated scaffold greatly influences chemical properties (S Log P, topological polar surface area (tPSA)) and hence, potentially modifies the pharmacokinetic profile of the different derivatives. Benzyl-1-(4-(3-(piperidin-1-yl)propoxy)phenyl)methanamine ligands 3 and 4 belong to the centrally acting diamine-based class of H(3)R antagonist/inverse agonist, whereas kojic acid analogues 6 and 7 might act peripherally. The latter compounds state promising lead structures in the development of H(3)R ligands with a modified profile of action.
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Affiliation(s)
- Kerstin Sander
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, ZAFES/CMP/ICNF, Frankfurt/Main, Germany
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39
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Walter M, von Coburg Y, Isensee K, Sander K, Ligneau X, Camelin JC, Schwartz JC, Stark H. Azole derivatives as histamine H3 receptor antagonists, Part I: Thiazol-2-yl ethers. Bioorg Med Chem Lett 2010; 20:5879-82. [DOI: 10.1016/j.bmcl.2010.07.098] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 07/23/2010] [Accepted: 07/25/2010] [Indexed: 11/29/2022]
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40
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Azole derivatives as histamine H3 receptor antagonists, Part 2: C–C and C–S coupled heterocycles. Bioorg Med Chem Lett 2010; 20:5883-6. [DOI: 10.1016/j.bmcl.2010.07.109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 07/23/2010] [Accepted: 07/25/2010] [Indexed: 11/24/2022]
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41
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Comparison of the pharmacological properties of human and rat histamine H(3)-receptors. Biochem Pharmacol 2010; 80:1437-49. [PMID: 20688049 DOI: 10.1016/j.bcp.2010.07.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 07/20/2010] [Accepted: 07/23/2010] [Indexed: 11/20/2022]
Abstract
Ligand pharmacology of histamine H(3)-receptors is species-dependent. In previous studies, two amino acids in transmembrane domain 3 (TM III) were shown to play a significant role. In this study, we characterized human and rat histamine H(3)-receptors (hH(3)R and rH(3)R, respectively), co-expressed with mammalian G proteins in Sf9 insect cell membranes. We compared a series of imidazole-containing H(3)R ligands in radioligand binding and steady-state GTPase assays. H(3)Rs similarly coupled to Gα(i/o)-proteins. Affinities and potencies of the agonists histamine, N(α)-methylhistamine and R-(α)-methylhistamine were in the same range. Imetit was only a partial agonist. The pharmacology of imetit and proxifan was similar at both species. However, impentamine was more potent and efficacious at rH(3)R. The inverse agonists ciproxifan and thioperamide showed higher potency but lower efficacy at rH(3)R. Clobenpropit was not species-selective. Strikingly, imoproxifan was almost full agonist at hH(3)R, but an inverse agonist at rH(3)R. Imoproxifan was docked into the binding pocket of inactive and active hH(3)R- and rH(3)R-models and molecular dynamic simulations were performed. Imoproxifan bound to hH(3)R and rH(3)R in E-configuration, which represents the trans-isomer of the oxime-moiety as determined in crystallization studies, and stabilized active hH(3)R-, but inactive rH(3)R-conformations. Large differences in electrostatic surfaces between TM III and TM V cause differential orientation of the oxime-moiety of imoproxifan, which then differently interacts with the rotamer toggle switch Trp(6.48) in TM VI. Collectively, the substantial species differences at H(3)Rs are explained at a molecular level by the use of novel H(3)R active-state models.
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Sander K, Kottke T, Hoffend C, Walter M, Weizel L, Camelin JC, Ligneau X, Schneider EH, Seifert R, Schwartz JC, Stark H. First Metal-Containing Histamine H3 Receptor Ligands. Org Lett 2010; 12:2578-81. [DOI: 10.1021/ol100419y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kerstin Sander
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Tim Kottke
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Claas Hoffend
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Miriam Walter
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Lilia Weizel
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Jean-Claude Camelin
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Xavier Ligneau
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Erich H. Schneider
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Roland Seifert
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Jean-Charles Schwartz
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Holger Stark
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, Biocenter, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany, Bioprojet-Biotech, 4 Rue du Chesnay-Beauregard, 35762 Saint Grégoire Cedex, France, University of Regensburg, Department of Pharmacology and Toxicology, Universitätsstrasse 1, 93053 Regensburg, Germany, and Medical School of Hannover, Institute of Pharmacology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
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Homology modelling of the human adenosine A2B receptor based on X-ray structures of bovine rhodopsin, the beta2-adrenergic receptor and the human adenosine A2A receptor. J Comput Aided Mol Des 2010; 23:807-28. [PMID: 19757091 DOI: 10.1007/s10822-009-9299-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Accepted: 08/12/2009] [Indexed: 10/20/2022]
Abstract
A three-dimensional model of the human adenosine A2B receptor was generated by means of homology modelling, using the crystal structures of bovine rhodopsin, the beta2-adrenergic receptor, and the human adenosine A2A receptor as templates. In order to compare the three resulting models, the binding modes of the adenosine A2B receptor antagonists theophylline, ZM241385, MRS1706, and PSB601 were investigated. The A2A-based model was much better able to stabilize the ligands in the binding site than the other models reflecting the high degree of similarity between A2A and A2B receptors: while the A2B receptor shares about 21% of the residues with rhodopsin, and 31% with the beta2-adrenergic receptor, it is 56% identical to the adenosine A2A receptor. The A2A-based model was used for further studies. The model included the transmembrane domains, the extracellular and the intracellular hydrophilic loops as well as the terminal domains. In order to validate the usefulness of this model, a docking analysis of several selective and nonselective agonists and antagonists was carried out including a study of binding affinities and selectivities of these ligands with respect to the adenosine A2A and A2B receptors. A common binding site is proposed for antagonists and agonists based on homology modelling combined with site-directed mutagenesis and a comparison between experimental and calculated affinity data. The new, validated A2B receptor model may serve as a basis for developing more potent and selective drugs.
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Sander K, von Coburg Y, Camelin JC, Ligneau X, Rau O, Schubert-Zsilavecz M, Schwartz JC, Stark H. Acidic elements in histamine H(3) receptor antagonists. Bioorg Med Chem Lett 2010; 20:1581-4. [PMID: 20138762 DOI: 10.1016/j.bmcl.2010.01.089] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022]
Abstract
Antagonists of the human histamine H(3) receptor (hH(3)R) often contain a second basic moiety, which is well known to boost affinity on this histamine receptor subtype. Here, we prepared compounds with acidic moieties of different pK(a) values to figure out that the hH(3)R tolerates these functionalities when added to a common pharmacophore blueprint. Depending on the acidic, electronic and steric features the designed ligands showed hH(3)R affinities in the nanomolar concentration range. Additionally, selected ligands were tested but failed as dual acting hH(3)R/hPPAR (human peroxisome proliferator-activated receptor) ligands.
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Affiliation(s)
- Kerstin Sander
- Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, ZAFES/LiFF/CMP, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
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Langham JJ, Cleves AE, Spitzer R, Kirshner D, Jain AN. Physical binding pocket induction for affinity prediction. J Med Chem 2009; 52:6107-25. [PMID: 19754201 DOI: 10.1021/jm901096y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Computational methods for predicting ligand affinity where no protein structure is known generally take the form of regression analysis based on molecular features that have only a tangential relationship to a protein/ligand binding event. Such methods have limited utility when structural variation moves beyond congeneric series. We present a novel approach based on the multiple-instance learning method of Compass, where a physical model of a binding site is induced from ligands and their corresponding activity data. The model consists of molecular fragments that can account for multiple positions of literal protein residues. We demonstrate the method on 5HT1a ligands by training on a series with limited scaffold variation and testing on numerous ligands with variant scaffolds. Predictive error was between 0.5 and 1.0 log units (0.7-1.4 kcal/mol), with statistically significant rank correlations. Accurate activity predictions of novel ligands were demonstrated using a validation approach where a small number of ligands of limited structural variation known at a fixed time point were used to make predictions on a blind test set of widely varying molecules, some discovered at a much later time point.
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Affiliation(s)
- James J Langham
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158-9001, USA
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2,4-Diaminopyrimidines as histamine H4 receptor ligands—Scaffold optimization and pharmacological characterization. Bioorg Med Chem 2009; 17:7186-96. [DOI: 10.1016/j.bmc.2009.08.059] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 08/26/2009] [Accepted: 08/28/2009] [Indexed: 11/21/2022]
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Strasser A. Molecular modeling and QSAR-based design of histamine receptor ligands. Expert Opin Drug Discov 2009; 4:1061-75. [DOI: 10.1517/17460440903264972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Kolb P, Ferreira RS, Irwin JJ, Shoichet BK. Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol 2009; 20:429-36. [PMID: 19733475 DOI: 10.1016/j.copbio.2009.08.003] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 08/05/2009] [Indexed: 12/13/2022]
Abstract
Computer-based docking screens are now widely used to discover new ligands for targets of known structure; in the last two years alone, the discovery of ligands for more than 20 proteins has been reported. Recently, investigators have also turned to predicting new substrates for enzymes of unknown function, taking docking in a wholly new direction. Increasingly, the hit rates, the true-positives, and the false-positives from the docking screens are being compared to those from empirical, high-throughput screens, revealing the strengths, weaknesses, and complementarities of both techniques. The recent efflorescence of GPCR structures has made these quintessential drug targets available to structure-based approaches. Consistent with their 'druggability', the docking screens have returned high hit rates and potent molecules. Finally, in the last several years, an approach almost exactly opposite to docking has also appeared; this pharmacological network approach begins not with the structure of the target but rather those of drug molecules and asks, given a pattern of chemistry in the ligands, what targets may a particular drug bind to? This method, which returns to an older, pharmacology logic, has been surprisingly successful in predicting new 'off-targets' for established drugs.
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Affiliation(s)
- Peter Kolb
- Dept of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Room 508D, San Francisco, CA 94158-2550, United States
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Rai BK, Tawa GJ, Katz AH, Humblet C. Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: Application to H3 antagonists. Proteins 2009; 78:457-73. [DOI: 10.1002/prot.22571] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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New vistas in GPCR 3D structure prediction. J Mol Model 2009; 16:183-91. [PMID: 19551412 DOI: 10.1007/s00894-009-0533-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 05/06/2009] [Indexed: 10/20/2022]
Abstract
Human G-protein coupled receptors (hGPCRs) comprise the most prominent family of validated drug targets. More than 50% of approved drugs reveal their therapeutic effects by targeting this family. Accurate models would greatly facilitate the process of drug discovery and development. However, 3-D structure prediction of GPCRs remains a challenge due to limited availability of resolved structure. The X-ray structures have been solved for only four such proteins. The identity between hGPCRs and the potential templates is mostly less than 30%, well below the level at which sequence alignment can be done regularly. In this study, we analyze a large database of human G-protein coupled receptors that are members of family A in order to optimize usage of the available crystal structures for molecular modeling of hGPCRs. On the basis of our findings in this study, we propose to regard specific parts from the trans-membrane domains of the reference receptor helices as appropriate template for constructing models of other GPCRs, while other residues require other techniques for their remodeling and refinement. The proposed hypothesis in the current study has been tested by modeling human beta2-adrenergic receptor based on crystal structures of bovine rhodopsin (1F88) and human A2A adenosine receptor (3EML). The results have shown some improvement in the quality of the predicted models compared to Modeller software.
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