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Bharathi, Roy KK. Structural basis for the binding of a selective inverse agonist AF64394 with the human G-protein coupled receptor 3 (GPR3). J Biomol Struct Dyn 2022; 40:10181-10190. [PMID: 34157950 DOI: 10.1080/07391102.2021.1940282] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The orphan class A G-protein coupled receptor 3 (GPR3) is highly expressed in brain and linked with various neuronal functions, and therefore, expected to play a vital role in the progression of Alzheimer's disease. In view of the lack of its experimental structure, we describe herein the three-dimensional structure and conformational dynamics of GPR3 complexed with the inverse agonist AF64394. The GPR3 model was predicted using the Iterative Threading ASSEmbly Refinement (I-TASSER) method. The Induced Fit Docking predicted two unique poses, Pose 1 and Pose 2, for AF64394, and then, molecular dynamics (MD) simulations followed by binding free-energy calculation revealed the Pose 1 as a very stable pose with the least fluctuation during the MD simulation while the Pose 2 underwent a significant fluctuation. The [1,2,4]triazolo[1,5-a]pyrimidine core was engaged in multiple hydrogen bonds (H-bonds), such as a water-mediated H-bond between the triazole nitrogen and T31, two direct H-bonds between the protonated triazole-ring nitrogen and V186 and T279, a direct H-bond between the secondary amine and V187. The phenyl substituent of AF64394 exhibited aromatic π-π stacking interactions with F97, F101, W43 and Y280. AF64394 showed a direct interaction with E28 and polar interactions with H96, T31 and T279. Throughout the MD simulation, the toggle switch residues, F120 and W260, remained in close contact, indicating that the GPR3 conformation represented an inactive state. The 4-(3-chloro-5-isopropoxyphenethyl) group resided near to the toggle switch residues. The insights gained here are expected to be useful in the structure-based design of new ligands targeting GPR3 modulation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharathi
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Kuldeep K Roy
- Department of Pharmaceutical Technology, School of Medical Sciences, Adamas University, Kolkata, India
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Khadse AN, Savsani HH, Chikhale RV, Ghuge RB, Prajapati DR, Kureshi G, Murumkar PR, Patel KV, Rajput SJ, Yadav MR. Design, synthesis and biological evaluation of Piperazinylanthranilamides as potential factor Xa inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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3
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Keshavarz MH, Shirazi Z, Mohajeri M. Simple method for assessment of activities of thrombin inhibitors through their molecular structure parameters. Comput Biol Med 2022; 146:105640. [DOI: 10.1016/j.compbiomed.2022.105640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022]
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Rodríguez DF, Durán-Osorio F, Duarte Y, Olivares P, Moglie Y, Dua K, Zacconi FC. Green by Design: Convergent Synthesis, Computational Analyses, and Activity Evaluation of New FXa Inhibitors Bearing Peptide Triazole Linking Units. Pharmaceutics 2021; 14:33. [PMID: 35056929 PMCID: PMC8780263 DOI: 10.3390/pharmaceutics14010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Green chemistry implementation has led to promising results in waste reduction in the pharmaceutical industry. However, the early sustainable development of pharmaceutically active compounds and ingredients remains a considerable challenge. Herein, we wish to report a green synthesis of new pharmaceutically active peptide triazoles as potent factor Xa inhibitors, an important drug target associated with the treatment of diverse cardiovascular diseases. The new inhibitors were synthesized in three steps, featuring cycloaddition reactions (high atom economy), microwave-assisted organic synthesis (energy efficiency), and copper nanoparticle catalysis, thus featuring Earth-abundant metals. The molecules obtained showed FXa inhibition, with IC50-values as low as 17.2 μM and no associated cytotoxicity in HEK293 and HeLa cells. These results showcase the environmental potential and chemical implications of the applied methodologies for the development of new molecules with pharmacological potential.
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Affiliation(s)
- Diego F. Rodríguez
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (D.F.R.); (F.D.-O.)
| | - Francisca Durán-Osorio
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (D.F.R.); (F.D.-O.)
| | - Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370035, Chile; (Y.D.); (P.O.)
| | - Pedro Olivares
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370035, Chile; (Y.D.); (P.O.)
| | - Yanina Moglie
- Departamento de Química INQUISUR, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca 8000, Argentina
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia;
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Flavia C. Zacconi
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (D.F.R.); (F.D.-O.)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Centro de Investigaciones en Nanotecnología y Materiales Avanzados, CIEN-UC, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
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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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Santana-Romo F, Lagos CF, Duarte Y, Castillo F, Moglie Y, Maestro MA, Charbe N, Zacconi FC. Innovative Three-Step Microwave-Promoted Synthesis of N-Propargyltetrahydroquinoline and 1,2,3-Triazole Derivatives as a Potential Factor Xa (FXa) Inhibitors: Drug Design, Synthesis, and Biological Evaluation. Molecules 2020; 25:molecules25030491. [PMID: 31979319 PMCID: PMC7037264 DOI: 10.3390/molecules25030491] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 12/22/2022] Open
Abstract
The coagulation cascade is the process of the conversion of soluble fibrinogen to insoluble fibrin that terminates in production of a clot. Factor Xa (FXa) is a serine protease involved in the blood coagulation cascade. Moreover, FXa plays a vital role in the enzymatic sequence which ends with the thrombus production. Thrombosis is a common causal pathology for three widespread cardiovascular syndromes: acute coronary syndrome (ACS), venous thromboembolism (VTE), and strokes. In this research a series of N-propargyltetrahydroquinoline and 1,2,3-triazole derivatives as a potential factor Xa (FXa) inhibitor were designed, synthesized, and evaluated for their FXa inhibitor activity, cytotoxicity activity and coagulation parameters. Rational design for the desired novel molecules was performed through protein-ligand complexes selection and ligand clustering. The microwave-assisted synthetic strategy of selected compounds was carried out by using Ullmann-Goldberg, N-propargylation, Mannich addition, Friedel-Crafts, and 1,3-dipolar cycloaddition type reactions under microwave irradiation. The microwave methodology proved to be an efficient way to obtain all novel compounds in high yields (73–93%). Furthermore, a thermochemical analysis, optimization and reactivity indexes such as electronic chemical potential (µ), chemical hardness (η), and electrophilicity (ω) were performed to understand the relationship between the structure and the energetic behavior of all the series. Then, in vitro analysis showed that compounds 27, 29–31, and 34 exhibited inhibitory activity against FXa and the corresponding half maximal inhibitory concentration (IC50) values were calculated. Next, a cell viability assay in HEK293 and HepG2 cell lines, and coagulation parameters (anti FXa, Prothrombin time (PT), activated Partial Thromboplastin Time (aPTT)) of the most active novel molecules were performed to determine the corresponding cytotoxicity and possible action on clotting pathways. The obtained results suggest that compounds 27 and 29 inhibited FXa targeting through coagulation factors in the intrinsic and extrinsic pathways. However, compound 34 may target coagulation FXa mainly by the extrinsic and common pathway. Interestingly, the most active compounds in relation to the inhibition activity against FXa and coagulation parameters did not show toxicity at the performed coagulation assay concentrations. Finally, docking studies confirmed the preferential binding mode of N-propargyltetrahydroquinoline and 1,2,3-triazole derivatives inside the active site of FXa.
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Affiliation(s)
- Fabián Santana-Romo
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago 7820436, Chile; (F.S.-R.); (F.C.); (N.C.)
| | - Carlos F. Lagos
- Chemical Biology & Drug Discovery Laboratory, Facultad de Medicina y Ciencia, Universidad San Sebastián, Lota 2465, Providencia 7510157, Santiago de Chile, Chile;
| | - Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile;
| | - Francisco Castillo
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago 7820436, Chile; (F.S.-R.); (F.C.); (N.C.)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago 7820436, Chile
| | - Yanina Moglie
- Departamento de Química, Instituto de Química del Sur (INQUISUR-CONICET), Universidad Nacional del Sur Avenida Alem 1253, Bahía Blanca B8000CPB, Argentina;
| | - Miguel A. Maestro
- Department of Chemistry—CICA, University of A Coruña, Campus da Zapateira, 15008A A Coruña, Spain;
| | - Nitin Charbe
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago 7820436, Chile; (F.S.-R.); (F.C.); (N.C.)
| | - Flavia C. Zacconi
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago 7820436, Chile; (F.S.-R.); (F.C.); (N.C.)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago 7820436, Chile
- Correspondence: ; Tel.: +56-2354-1150
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Papadaki S, Tselepis AD. Nonhemostatic Activities of Factor Xa: Are There Pleiotropic Effects of Anti-FXa Direct Oral Anticoagulants? Angiology 2019; 70:896-907. [PMID: 31010298 DOI: 10.1177/0003319719840861] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Factor Xa (FXa) is the key serine protease of the coagulation cascade as it is the point of convergence of the intrinsic and extrinsic pathways, leading to the formation of thrombin. Factor Xa is an established target of anticoagulation therapy, due to its central role in coagulation. Over the past years, several direct oral anticoagulants (DOACs) targeting FXa have been developed. Rivaroxaban, apixaban, and edoxaban are used in clinical practice for prevention and treatment of thrombotic diseases. Increasing evidence suggests that FXa exerts nonhemostatic cellular effects that are mediated mainly through protease-activated receptors-1 and -2 and are involved in pathophysiological conditions, such as atherosclerosis, inflammation, and fibrosis. Direct inhibition of FXa by DOACs could be beneficial in these conditions. This is a narrative review that focuses on the cellular effects of FXa in various cell types and conditions, as well as on the possible pleiotropic effects of FXa-targeting DOACs.
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Affiliation(s)
- Styliani Papadaki
- 1 Department of Chemistry, Atherothrombosis Research Centre/Laboratory of Biochemistry, University of Ioannina, Ioannina, Greece
| | - Alexandros D Tselepis
- 1 Department of Chemistry, Atherothrombosis Research Centre/Laboratory of Biochemistry, University of Ioannina, Ioannina, Greece
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8
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Ilin I, Lipets E, Sulimov A, Kutov D, Shikhaliev K, Potapov A, Krysin M, Zubkov F, Sapronova L, Ataullakhanov F, Sulimov V. New factor Xa inhibitors based on 1,2,3,4-tetrahydroquinoline developed by molecular modelling. J Mol Graph Model 2019; 89:215-224. [PMID: 30913501 DOI: 10.1016/j.jmgm.2019.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 10/27/2022]
Abstract
Factor Xa is a serine protease representing a crucial element in the coagulation process and an attractive target for anticoagulant therapy. At the present time there are several chemical classes of factor Xa inhibitors with proven activity. Furthermore, three factor Xa inhibitors have been approved for the medical use to date. However, therapy with these medications is accompanied by substantial adverse effects. In this background, the structure-based computational approach combining molecular docking and semiempirical quantum chemical calculations was applied for a search for new effective factor Xa inhibitors. We have undertaken a few virtual screening procedures to select potential candidates for synthesis and subsequent testing. The first screen of the focused library resulted in identifying 20 compounds among which 7 compounds showed the noticeable inhibition of factor Xa at maximal concentrations, allowed by solubility. The subsequent additional screens identified 20 additional candidates. Of these, 5 substances were shown to be capable of inhibiting factor Xa at 5 μM. The best two found 1,2,3,4-tetrahydroquinoline derivatives identified by means of modelling have demonstrated IC50 values in the micromolar range. One of them turned out to be selective factor Xa inhibitor over trypsin, factors IIa, IXa and XIa.
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Affiliation(s)
- Ivan Ilin
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia.
| | - Elena Lipets
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, 1 Samory Mashela Str., Moscow, 117997, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences Kosygina Str. 4, Moscow, 119334, Russia
| | - Alexey Sulimov
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia
| | - Danil Kutov
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia
| | - Khidmet Shikhaliev
- Voronezh State University, Universitetskaya Sq. 1, Voronezh, 394018, Russia
| | - Andrey Potapov
- Voronezh State University, Universitetskaya Sq. 1, Voronezh, 394018, Russia
| | - Michael Krysin
- Voronezh State University, Universitetskaya Sq. 1, Voronezh, 394018, Russia
| | - Fedor Zubkov
- Department of Organic Chemistry, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow, Russia
| | - Lyudmila Sapronova
- Department of Organic Chemistry, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow, Russia
| | - Fazoyl Ataullakhanov
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, 1 Samory Mashela Str., Moscow, 117997, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences Kosygina Str. 4, Moscow, 119334, Russia
| | - Vladimir Sulimov
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia
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9
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Kim PY, Yeh CH, Dale BJ, Leslie BA, Stafford AR, Fredenburgh JC, Hirsh J, Weitz JI. Mechanistic Basis for the Differential Effects of Rivaroxaban and Apixaban on Global Tests of Coagulation. TH OPEN 2018; 2:e190-e201. [PMID: 31249942 PMCID: PMC6524873 DOI: 10.1055/s-0038-1649507] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/26/2018] [Indexed: 02/07/2023] Open
Abstract
Rivaroxaban and apixaban are both small molecules that reversibly inhibit factor Xa. Compared with rivaroxaban, apixaban has minimal effects on the prothrombin time and activated partial thromboplastin time. To investigate this phenomenon, we used a factor Xa-directed substrate in a buffer system. Although rivaroxaban and apixaban inhibited factor Xa with similar K i values at equilibrium, kinetic measurements revealed that rivaroxaban inhibited factor Xa up to 4-fold faster than apixaban ( p < 0.001). Using a discontinuous chromogenic assay to monitor thrombin production by prothrombinase in a purified system, rivaroxaban was 4-fold more potent than apixaban (K i values of 0.7 ± 0.3 and 2.9 ± 0.5 nM, respectively; p = 0.02). Likewise, in thrombin generation assays in plasma, rivaroxaban prolonged the lag time and suppressed endogenous thrombin potential to a greater extent than apixaban. To characterize how the two inhibitors differ in recognizing factor Xa, inhibition of prothrombinase was monitored in real-time using a fluorescent probe for thrombin. The data were fit using a mixed-inhibition model and the individual association and dissociation rate constants were determined. The association rates for the binding of rivaroxaban to either free factor Xa or factor Xa incorporated into the prothrombinase complex were 10- and 1,193-fold faster than those for apixaban, respectively, whereas dissociation rates were about 3-fold faster. Collectively, these findings suggest that rivaroxaban and apixaban differ in their capacity to inhibit factor Xa and provide a plausible explanation for the observation that rivaroxaban has a greater effect on global tests of coagulation than apixaban.
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Affiliation(s)
- Paul Y Kim
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - Calvin H Yeh
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Brian J Dale
- Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Beverly A Leslie
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - Alan R Stafford
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - James C Fredenburgh
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - Jack Hirsh
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jeffrey I Weitz
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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10
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Bhunia SS, Saxena AK. Molecular modelling studies in explaining the higher GPVI antagonistic activity of the racemic 2-(4-methoxyphenylsulfonyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide than its enantiomers. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:783-799. [PMID: 29135287 DOI: 10.1080/1062936x.2017.1396247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 10/20/2017] [Indexed: 06/07/2023]
Abstract
The GPVI receptor on the platelets plays a major role in inhibiting arterial thrombosis with limited risk of bleeding and is considered a potential anti-thrombotic target for arterial thrombosis. In the reported anti-thrombotics, tetrahydropyridoindoles, the title compound was the best inhibitor of the collagen mediated platelet aggregation by antagonizing the platelet receptor GPVI. Interestingly, the racemic title compound showed better antagonism (IC50 racemate = 6.7 μM) than either of its enantiomers (IC50 S enantiomer = 25.3 μM; IC50 R enantiomer = 126.3 μM). In order to explain this, the molecular modelling approaches viz. site map analysis, protein-protein docking and molecular dynamics simulation were carried out, which led to the identification of a second binding site located near the primary antagonist binding site known to bind losartan. The induced fit docking studies for both the enantiomers at the primary and secondary binding sites showed that the S-enantiomer has better interactions at the primary binding site than the R-enantiomer, while the R-enantiomer has better interactions at the secondary site than the S-enantiomer. Hence, the overall interactions of the racemic compound containing equimolar mixture may be higher than any one of the enantiomers and may explain the higher activity than its enantiomers of the racemic compound.
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Affiliation(s)
- S S Bhunia
- a Division of Medicinal and Process Chemistry , CSIR-Central Drug Research Institute , Lucknow , India
| | - A K Saxena
- a Division of Medicinal and Process Chemistry , CSIR-Central Drug Research Institute , Lucknow , India
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11
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Abstract
Thrombosis is a complex process involving multiple pathways. Currently, therapy relies on the combination of two or more antithrombotic drugs, showing that inhibiting more than one target provides benefits in the prevention and treatment of thrombosis. This review focuses on structure-activity relationship studies of molecules possessing multiple actions against thrombosis, namely, dual inhibitors of coagulation, dual inhibitors of coagulation and platelet aggregation, and also dual inhibitors of platelet aggregation. EP217609 has just entered clinical trials, which raise the expectations on the multitarget strategy to prevent or treat thrombosis.
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12
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Patel NR, Patel DV, Murumkar PR, Yadav MR. Contemporary developments in the discovery of selective factor Xa inhibitors: A review. Eur J Med Chem 2016; 121:671-698. [PMID: 27322757 DOI: 10.1016/j.ejmech.2016.05.039] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/25/2016] [Accepted: 05/19/2016] [Indexed: 11/25/2022]
Abstract
Thrombosis is a leading cause of death in cardiovascular diseases such as myocardial infarction (MI), unstable angina and acute coronary syndrome (ACS) in the industrialized world. Venous thromboembolism is observed in about 1 million people every year in United States causing significant morbidity and mortality. Conventional antithrombotic therapy has been reported to have several disadvantages and limitations like inconvenience in oral administration, bleeding risks (heparin analogs), narrow therapeutic window and undesirable interactions with food and drugs (vitamin K antagonist-warfarin). The unmet medical demand for orally active safe anticoagulants has generated widespread interest among the medicinal chemists engaged in this field. To modulate blood coagulation, various enzymes involved in the coagulation process have received great attention as potential targets by various research groups for the development of oral anticoagulants. Among these enzymes, factor Xa (FXa) has remained the centre of attention in the last decade. Intensive research efforts have been made by various research groups for the development of small, safe and orally bioavailable FXa inhibitors. This review is an attempt to compile the research work of various researchers in the direction of development of FXa inhibitors reported since 2010 onward.
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Affiliation(s)
- Nirav R Patel
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Dushyant V Patel
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Mange Ram Yadav
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India.
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13
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Pharmacodynamics and potential synergistic effects of Mai-Luo-Ning injection on cardiovascular protection, based on molecular docking. Chin J Nat Med 2015; 13:815-822. [PMID: 26614456 DOI: 10.1016/s1875-5364(15)30085-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/20/2022]
Abstract
As a computer-assisted approach, molecular docking has been universally applied in drug research and development and plays an important role in the investigation and evaluation of herbal medicines. Herein, the method was used to estimate the pharmacodynamics of Mai-Luo-Ning injection, a traditional Chinese compound herbal prescription. Through investigating the interactions between several important proteins in cardiovascular system and characteristic components of the formula, its effect on cardiovascular protection was evaluated. Results showed the differences in the interactions between each component and the selected target proteins and revealed the possible mechanisms for synergistic effects of various characteristic components on cardiovascular protection. The study provided scientific evidence supporting the mechanistic study of the interactions among multi-components and targets, offering a general approach to investigating the pharmacodynamics of complicated materials in compound herbal prescriptions.
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Mena-Ulecia K, Tiznado W, Caballero J. Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA. PLoS One 2015; 10:e0142774. [PMID: 26599107 PMCID: PMC4657979 DOI: 10.1371/journal.pone.0142774] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/27/2015] [Indexed: 11/18/2022] Open
Abstract
Non-peptidic thrombin inhibitors (TIs; 177 compounds) with diverse groups at motifs P1 (such as oxyguanidine, amidinohydrazone, amidine, amidinopiperidine), P2 (such as cyanofluorophenylacetamide, 2-(2-chloro-6-fluorophenyl)acetamide), and P3 (such as phenylethyl, arylsulfonate groups) were studied using molecular modeling to analyze their interactions with S1, S2, and S3 subsites of the thrombin binding site. Firstly, a protocol combining docking and three dimensional quantitative structure-activity relationship was performed. We described the orientations and preferred active conformations of the studied inhibitors, and derived a predictive CoMSIA model including steric, donor hydrogen bond, and acceptor hydrogen bond fields. Secondly, the dynamic behaviors of some selected TIs (compounds 26, 133, 147, 149, 162, and 177 in this manuscript) that contain different molecular features and different activities were analyzed by creating the solvated models and using molecular dynamics (MD) simulations. We used the conformational structures derived from MD to accomplish binding free energetic calculations using MM-GBSA. With this analysis, we theorized about the effect of van der Waals contacts, electrostatic interactions and solvation in the potency of TIs. In general, the contents reported in this article help to understand the physical and chemical characteristics of thrombin-inhibitor complexes.
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Affiliation(s)
- Karel Mena-Ulecia
- Departamento de Química, Facultad de Ciencias Exactas, Universidad Andres Bello, Avenida República 252, Santiago, Chile
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - William Tiznado
- Departamento de Química, Facultad de Ciencias Exactas, Universidad Andres Bello, Avenida República 252, Santiago, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
- * E-mail: or
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15
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Prathipati P, Mizuguchi K. Integration of Ligand and Structure Based Approaches for CSAR-2014. J Chem Inf Model 2015; 56:974-87. [PMID: 26492437 DOI: 10.1021/acs.jcim.5b00477] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The prediction of binding poses and affinities is an area of active interest in computer-aided drug design (CADD). Given the documented limitations with either ligand or structure based approaches, we employed an integrated approach and developed a rapid protocol for binding mode and affinity predictions. This workflow was applied to the three protein targets of Community Structure-Activity Resource-2014 (CSAR-2014) exercise: Factor Xa (FXa), Spleen Tyrosine Kinase (SYK), and tRNA (guanine-N(1))-methyltransferase (TrmD). Our docking and scoring workflow incorporates compound clustering and ligand and protein structure based pharmacophore modeling, followed by local docking, minimization, and scoring. While the former part of the protocol ensures high-quality ligand alignments and mapping, the subsequent minimization and scoring provides the predicted binding modes and affinities. We made blind predictions of docking pose for 1, 5, and 14 ligands docked into 1, 2, and 12 crystal structures of FXa, SYK, and TrmD, respectively. The resulting 174 poses were compared with cocrystallized structures (1, 5, and 14 complexes) made available at the end of CSAR. Our predicted poses were related to the experimentally determined structures with a mean root-mean-square deviation value of 3.4 Å. Further, we were able to classify high and low affinity ligands with the area under the curve values of 0.47, 0.60, and 0.69 for FXa, SYK, and TrmD, respectively, indicating the validity of our approach in at least two of the three systems. Detailed critical analysis of the results and CSAR methodology ranking procedures suggested that a straightforward application of our workflow has limitations, as some of the performance measures do not reflect the actual utility of pose and affinity predictions in the biological context of individual systems.
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Affiliation(s)
- Philip Prathipati
- National Institutes of Biomedical Innovation, Health and Nutrition , 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation, Health and Nutrition , 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
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16
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Saxena M, Bhunia SS, Saxena AK. Molecular modelling studies on 2-substituted octahydropyrazinopyridoindoles for histamine H2 receptor antagonism. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:739-755. [PMID: 26461804 DOI: 10.1080/1062936x.2015.1088572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 08/26/2015] [Indexed: 06/05/2023]
Abstract
The human histamine H2 receptor (hH2HR) is a G-protein coupled receptor protein with seven transmembrane (TM)-spanning helices primarily involved in regulation of gastric acid secretion. Antagonists targeting hH2HR are useful in the treatment of hyperacidic conditions such as peptic ulcers, gastresophageal reflux disease and gastrointestinal bleeding. We have previously reported the antagonism of 2-substituted pyrazinopyridoindoles at the human histamine H1 receptor and mode of binding of these compounds at the hH1HR using in silico methods. Interestingly, some of the compounds in the series also showed promising activity towards hH2HR that prompted us to investigate the mode of binding of these compounds at hH2HR. In the absence of the crystal structure of hH2HR a homology model has been constructed using multiple sequence alignment, using the X-ray crystal structures of Turkey β1-adrenergic receptor (tβ1AR), Human histamine H1 receptor (hH1HR), Human β2-adrenergic receptor (hβ2AR) and Human D3 dopamine receptor (hD3R). The important residues for binding were depicted in TMIII, TMV, TMVI and TMVII by the homology modelled hH2HR for 2-substituted pyrazinopyridoindoles. A comparative study for deducing the selectivity regarding the binding towards hH1HR and hH2HR has been carried out, which may be useful in designing of selective hH1HR/hH2HR antagonists in these classes of compounds.
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Affiliation(s)
- M Saxena
- a Department of Chemistry , Amity University , Lucknow , India
| | - S S Bhunia
- b Global Institute of Pharmaceutical Education and Research , Kashipur , Uttarakhand , India
| | - A K Saxena
- c Division of Medicinal and Process Chemistry , CSIR Central Drug Research Institute , Lucknow , India
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17
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Application of Molecular Modeling to Development of New Factor Xa Inhibitors. BIOMED RESEARCH INTERNATIONAL 2015; 2015:120802. [PMID: 26484350 PMCID: PMC4592935 DOI: 10.1155/2015/120802] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 08/12/2015] [Accepted: 08/20/2015] [Indexed: 12/30/2022]
Abstract
In consequence of the key role of factor Xa in the clotting cascade and absence of its activity in the processes that do not affect coagulation, this protein is an attractive target for development of new blood coagulation inhibitors. Factor Xa is more effective and convenient target for creation of anticoagulants than thrombin, inhibition of which may cause some side effects. This study is aimed at finding new inhibitors of factor Xa by molecular computer modeling including docking SOL and postdocking optimization DISCORE programs. After validation of molecular modeling methods on well-known factor Xa inhibitors the virtual screening of NCI Diversity and Voronezh State University databases of ready-made low molecular weight species has been carried out. Seventeen compounds selected on the basis of modeling results have been tested experimentally in vitro. It has been found that 12 of them showed activity against factor Xa (IC50 = 1.8-40 μM). Based on analysis of the results, the new original compound was synthesized and experimentally verified. It shows activity against factor Xa with IC50 value of 0.7 μM.
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18
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Abdel-Azeim S, Oliva R, Chermak E, De Cristofaro R, Cavallo L. Molecular Dynamics Characterization of Five Pathogenic Factor X Mutants Associated with Decreased Catalytic Activity. Biochemistry 2014; 53:6992-7001. [DOI: 10.1021/bi500770p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Safwat Abdel-Azeim
- Kaust
Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department
of Sciences and Technologies, University “Parthenope” of Naples, Centro Direzionale Isola C4, 80133 Naples, Italy
| | - Edrisse Chermak
- Kaust
Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Raimondo De Cristofaro
- Hemostasis
Research Centre, Institute of Internal Medicine and Geriatrics, Catholic University School of Medicine, Rome, Italy
| | - Luigi Cavallo
- Kaust
Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Dipartimento
di Chimica e Biologia, University of Salerno, Via Papa Giovanni Paolo II, I-84084 Fisciano, Italy
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19
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Scott BM, Matochko WL, Gierczak RF, Bhakta V, Derda R, Sheffield WP. Phage display of the serpin alpha-1 proteinase inhibitor randomized at consecutive residues in the reactive centre loop and biopanned with or without thrombin. PLoS One 2014; 9:e84491. [PMID: 24427287 PMCID: PMC3888415 DOI: 10.1371/journal.pone.0084491] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/15/2013] [Indexed: 02/04/2023] Open
Abstract
In spite of the power of phage display technology to identify variant proteins with novel properties in large libraries, it has only been previously applied to one member of the serpin superfamily. Here we describe phage display of human alpha-1 proteinase inhibitor (API) in a T7 bacteriophage system. API M358R fused to the C-terminus of T7 capsid protein 10B was directly shown to form denaturation-resistant complexes with thrombin by electrophoresis and immunoblotting following exposure of intact phages to thrombin. We therefore developed a biopanning protocol in which thrombin-reactive phages were selected using biotinylated anti-thrombin antibodies and streptavidin-coated magnetic beads. A library consisting of displayed API randomized at residues 357 and 358 (P2-P1) yielded predominantly Pro-Arg at these positions after five rounds of thrombin selection; in contrast the same degree of mock selection yielded only non-functional variants. A more diverse library of API M358R randomized at residues 352-356 (P7-P3) was also probed, yielding numerous variants fitting a loose consensus of DLTVS as judged by sequencing of the inserts of plaque-purified phages. The thrombin-selected sequences were transferred en masse into bacterial expression plasmids, and lysates from individual colonies were screening for API-thrombin complexing. The most active candidates from this sixth round of screening contained DITMA and AAFVS at P7-P3 and inhibited thrombin 2.1-fold more rapidly than API M358R with no change in reaction stoichiometry. Deep sequencing using the Ion Torrent platform confirmed that over 800 sequences were significantly enriched in the thrombin-panned versus naïve phage display library, including some detected using the combined phage display/bacterial lysate screening approach. Our results show that API joins Plasminogen Activator Inhibitor-1 (PAI-1) as a serpin amenable to phage display and suggest the utility of this approach for the selection of "designer serpins" with novel reactivity and/or specificity.
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Affiliation(s)
- Benjamin M. Scott
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Wadim L. Matochko
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada
| | - Richard F. Gierczak
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Varsha Bhakta
- Canadian Blood Services, Research and Development, Hamilton, Ontario, Canada
| | - Ratmir Derda
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada
| | - William P. Sheffield
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Canadian Blood Services, Research and Development, Hamilton, Ontario, Canada
- * E-mail:
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20
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Cross S, Baroni M, Goracci L, Cruciani G. GRID-Based Three-Dimensional Pharmacophores I: FLAPpharm, a Novel Approach for Pharmacophore Elucidation. J Chem Inf Model 2012; 52:2587-98. [DOI: 10.1021/ci300153d] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simon Cross
- Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5
5NE, United Kingdom
| | - Massimo Baroni
- Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5
5NE, United Kingdom
| | - Laura Goracci
- Laboratory
for Chemometrics and Cheminformatics, Chemistry Department, University of Perugia, Via Elce di sotto 10, I-06123
Perugia, Italy
| | - Gabriele Cruciani
- Laboratory
for Chemometrics and Cheminformatics, Chemistry Department, University of Perugia, Via Elce di sotto 10, I-06123
Perugia, Italy
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21
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Saxena M, Bhunia SS, Saxena AK. Docking studies of novel pyrazinopyridoindoles class of antihistamines with the homology modelled H(1)-receptor. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 23:311-325. [PMID: 22463083 DOI: 10.1080/1062936x.2012.664561] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Histamine is an important neurotransmitter as it controls a multitude of physiological functions by activating specific receptors on target cells. It exerts its effects by binding to four different histamine receptors (H(1)-H(4)), which all belong to the large family of G protein-coupled receptors (GPCRs). Research and development of H(1) ligand has largely focused on antagonists which are used for their anti-allergy effects in the periphery. Recent understanding of the clinical importance of H(1) receptors in brain, however, suggests the pharmacotherapeutic potential of H(1) agonists in neurodegenerative and neuropsychiatric disorders. Despite the therapeutic importance of the H(1) receptor, for many years the molecular features of the H(1) receptor protein had been unknown. In view of the recently reported crystal structure of human H(1) receptor and in continuation of our work on 3D-pharmacophore on antihistamine H(1) and homology model of histamine H(1) receptor, docking studies have been carried out on some promising pyrazinopyridoindole class of antihistamine H(1), including two outliers, to validate our earlier reported models/hypotheses on H(1)-receptor, where a good explanation between estimated and observed activities has been obtained. In addition, the docking study also provided insights about the optimal activity of the outliers, for which no explanation was reported previously.
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Affiliation(s)
- M Saxena
- Department of Chemistry, Amity University, Lucknow, India.
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