1
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Masand VH, Al-Hussain S, Alzahrani AY, Al-Mutairi AA, Sultan Alqahtani A, Samad A, Alafeefy AM, Jawarkar RD, Zaki MEA. Unveiling dynamics of nitrogen content and selected nitrogen heterocycles in thrombin inhibitors: a ceteris paribus approach. Expert Opin Drug Discov 2024; 19:991-1009. [PMID: 38898679 DOI: 10.1080/17460441.2024.2368743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Despite the progress in comprehending molecular design principles and biochemical processes associated with thrombin inhibition, there is a crucial need to optimize efforts and curtail the recurrence of synthesis-testing cycles. Nitrogen and N-heterocycles are key features of many anti-thrombin drugs. Hence, a pragmatic analysis of nitrogen and N-heterocycles in thrombin inhibitors is important throughout the drug discovery pipeline. In the present work, the authors present an analysis with a specific focus on understanding the occurrence and distribution of nitrogen and selected N-heterocycles in the realm of thrombin inhibitors. RESEARCH DESIGN AND METHODS A dataset comprising 4359 thrombin inhibitors is used to scrutinize various categories of nitrogen atoms such as ring, non-ring, aromatic, and non-aromatic. In addition, selected aromatic and aliphatic N-heterocycles have been analyzed. RESULTS The analysis indicates that ~62% of thrombin inhibitors possess five or fewer nitrogen atoms. Substituted N-heterocycles have a high occurrence, like pyrrolidine (23.24%), pyridine (20.56%), piperidine (16.10%), thiazole (9.61%), imidazole (7.36%), etc. in thrombin inhibitors. CONCLUSIONS The majority of active thrombin inhibitors contain nitrogen atoms close to 5 and a combination of N-heterocycles like pyrrolidine, pyridine, piperidine, etc. This analysis provides crucial insights to optimize the transformation of lead compounds into potential anti-thrombin inhibitors.
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Affiliation(s)
- Vijay H Masand
- Department of Chemistry, Vidya Bharati Mahavidyalaya, Amravati, India
| | - Sami Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdullah Y Alzahrani
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail Asser, Saudi Arabia
| | - Aamal A Al-Mutairi
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Arwa Sultan Alqahtani
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdul Samad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil, Iraq
| | - Ahmed M Alafeefy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Universiti Teknologi MARA [UiTM], Bandar Puncak Alam, Selangor, Malaysia
| | - Rahul D Jawarkar
- Department of Medicinal Chemistry and Drug Discovery, Dr Rajendra Gode Institute of Pharmacy, Amravati, India
| | - Magdi E A Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
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2
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Velcicky J, Janser P, Gommermann N, Brenneisen S, Ilic S, Vangrevelinghe E, Stiefl N, Boettcher A, Arnold C, Malinverni C, Dawson J, Murgasova R, Desrayaud S, Beltz K, Hinniger A, Dekker C, Farady CJ, Mackay A. Discovery of Potent, Orally Bioavailable, Tricyclic NLRP3 Inhibitors. J Med Chem 2024; 67:1544-1562. [PMID: 38175811 DOI: 10.1021/acs.jmedchem.3c02098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
NLRP3 is a molecular sensor recognizing a wide range of danger signals. Its activation leads to the assembly of an inflammasome that allows for activation of caspase-1 and subsequent maturation of IL-1β and IL-18, as well as cleavage of Gasdermin-d and pyroptotic cell death. The NLRP3 inflammasome has been implicated in a plethora of diseases including gout, type 2 diabetes, atherosclerosis, Alzheimer's disease, and cancer. In this publication, we describe the discovery of a novel, tricyclic, NLRP3-binding scaffold by high-throughput screening. The hit (1) could be optimized into an advanced compound NP3-562 demonstrating excellent potency in human whole blood and full inhibition of IL-1β release in a mouse acute peritonitis model at 30 mg/kg po dose. An X-ray structure of NP3-562 bound to the NLRP3 NACHT domain revealed a unique binding mode as compared to the known sulfonylurea-based inhibitors. In addition, NP3-562 shows also a good overall development profile.
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Affiliation(s)
- Juraj Velcicky
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Philipp Janser
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | | | - Slavica Ilic
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | | | | | | | | | - Janet Dawson
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | | | - Karen Beltz
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | - Carien Dekker
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | - Angela Mackay
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
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3
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Meyer ST, Fernandes S, Anderson RE, Pacherille A, Toms B, Kerr WG, Chisholm JD. Structure-Activity Studies on Bis-Sulfonamide SHIP1 Activators. Molecules 2023; 28:8048. [PMID: 38138538 PMCID: PMC10745928 DOI: 10.3390/molecules28248048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
The SH2-containing inositol polyphosphate 5-phosphatase 1 (SHIP1) enzyme opposes the activity of PI3K and therefore is of interest in the treatment of inflammatory disorders. Recent results also indicate that SHIP1 promotes phagolysosomal degradation of lipids by microglia, suggesting that the enzyme may be a target for the treatment of Alzheimer's disease. Therefore, small molecules that increase SHIP1 activity may have benefits in these areas. Recently we discovered a bis-sulfonamide that increases the enzymatic activity of SHIP1. A series of similar SHIP1 activators have been synthesized and evaluated to determine structure-activity relationships and improve in vivo stability. Some new analogs have now been found with improved potency. In addition, both the thiophene and the thiomorpholine in the parent structure can be replaced by groups without a low valent sulfur atom, which provides a way to access activators that are less prone to oxidative degradation.
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Affiliation(s)
- Shea T. Meyer
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Sandra Fernandes
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | - Angela Pacherille
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Bonnie Toms
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - William G. Kerr
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - John D. Chisholm
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
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4
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Kamel EM, Tawfeek AM, El-Bassuony AA, Lamsabhi AM. Mechanistic aspects of reactive metabolite formation in clomethiazole catalyzed biotransformation by cytochrome P450 enzymes. Org Biomol Chem 2023; 21:7158-7172. [PMID: 37609887 DOI: 10.1039/d3ob01014g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Clomethiazole (CLM), a sedative and anticonvulsant drug, is commonly employed for the treatment of alcohol withdrawal syndrome because it suppresses cytochrome P450 (P450) activity associated with the generation of free radicals and liver damage. The catalyzed biotransformation of thiazole-containing drugs by P450 is known to afford reactive metabolites. These metabolites can alter the biological functions of macromolecules and result in toxicity and adverse drug interactions. Multitargeted molecular modeling and quantum chemical DFT calculations were performed to explore the binding modes and molecular mechanisms underlying the mechanism-based inactivation (MBI) of P450 by CLM. The mechanistic details associated with reactive metabolite formation from further metabolic processes were extensively assessed. Seven possible routes were proposed for CLM-P450 biotransformation including CLM hydroxylation, sulfoxidation, N-oxidation, CN epoxidation (oxaziridine formation), and CC epoxidation. The results revealed a degree of preference for the C-N epoxidation pathway because of the low energy requirements of its rate-determining step (8.74 and 10.07 kcal mol-1 for LS and HS states, respectively). A kinetic competition for the CLM-methyl hydroxylation pathway was detected because the H-abstraction energy barrier was relatively comparable to the thermodynamically prevailing oxaziridine formation rate-determining step (12.58 and 14.52 kcal mol-1 for quartet and doublet states, respectively). Our studies assessed the mechanisms of covalent nucleophilic epoxide adduct formation through nucleophilic addition, hydrolysis of epoxidation products, and nonenzymatic degradation. CLM was shown to display P450-inhibitory activity by forming covalent adducts rather than further metabolization to reactive metabolites. The outcomes of molecular docking allowed assessing the binding profile of CLM with three human P450 isozymes, namely, CYP2E1, CYP3A4, and CYP2D6.
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Affiliation(s)
- Emadeldin M Kamel
- Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt.
| | - Ahmed M Tawfeek
- Chemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ashraf A El-Bassuony
- Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt.
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, Madrid 28049, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
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5
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Apaza Ticona L, Sánchez Sánchez-Corral J, Flores Sepúlveda A, Soriano Vázquez C, Hernán Vieco C, Rumbero Sánchez Á. Novel 1,2,4-oxadiazole compounds as PPAR-α ligand agonists: a new strategy for the design of antitumour compounds. RSC Med Chem 2023; 14:1377-1388. [PMID: 37484563 PMCID: PMC10357926 DOI: 10.1039/d3md00063j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/22/2023] [Indexed: 07/25/2023] Open
Abstract
Modulation of PPAR-α by natural ligands is a novel strategy for the development of anticancer therapies. A series of 16 compounds based on the structure of 3-(pyridin-3-yl)-5-(thiophen-3-yl)-1,2,4-oxadiazole (natural compound) with antitumour potential were designed and synthesised. The cytotoxicity and PPAR agonist activity of these synthetic 1,2,4-oxadiazoles were evaluated in the A-498 and DU 145 tumour cell lines. Preliminary biological evaluation showed that most of these synthetic 1,2,4-oxadiazoles are less cytotoxic (sulforhodamine B assay) than the positive control WY-14643. Regarding the PPAR-α modulation, compound 16 was the most active, with EC50 = 0.23-0.83 μM (PPAR-α). Additionally, compound 16 had a similar activity to the natural compound (EC50 = 0.18-0.77 μM) and was less toxic in the RPTEC and WPMY-1 cell lines (non-tumour cells) (CC50 = 81.66-92.67 μM) than the natural compound. Looking at the link between chemical structure and activity, our study demonstrates that changes to the natural 1,2,4-oxadiazole at the level of the thiophenyl residue can lead to new agonists of PPAR-α with promising anti-tumour activity.
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Affiliation(s)
- Luis Apaza Ticona
- Organic Chemistry Unit, Department of Chemistry in Pharmaceutical Sciences, Faculty of Pharmacy, Universidad Complutense of Madrid Plaza Ramón y Cajal s/n 28040 Madrid Spain
- Department of Organic Chemistry, Faculty of Sciences, University Autónoma of Madrid Cantoblanco 28040 Madrid Spain
| | | | | | - Carmen Soriano Vázquez
- Faculty of Pharmacy, Universidad Complutense of Madrid Plaza Ramón y Cajal s/n 28040 Madrid Spain
| | - Carmen Hernán Vieco
- Faculty of Pharmacy, Universidad Complutense of Madrid Plaza Ramón y Cajal s/n 28040 Madrid Spain
| | - Ángel Rumbero Sánchez
- Department of Organic Chemistry, Faculty of Sciences, University Autónoma of Madrid Cantoblanco 28040 Madrid Spain
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Gannam ZTK, Jamali H, Kweon OS, Herrington J, Shillingford SR, Papini C, Gentzel E, Lolis E, Bennett AM, Ellman JA, Anderson KS. Defining the structure-activity relationship for a novel class of allosteric MKP5 inhibitors. Eur J Med Chem 2022; 243:114712. [PMID: 36116232 PMCID: PMC9830533 DOI: 10.1016/j.ejmech.2022.114712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 01/13/2023]
Abstract
Mitogen-activated protein kinase (MAPK) phosphatase 5 (MKP5) is responsible for regulating the activity of the stress-responsive MAPKs and has been put forth as a potential therapeutic target for a number of diseases, including dystrophic muscle disease a fatal rare disease which has neither a treatment nor cure. In previous work, we identified Compound 1 (3,3-dimethyl-1-((9-(methylthio)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl)thio)butan-2-one) as the lead compound of a novel class of MKP5 inhibitors. In this work, we explore the structure-activity relationship for inhibition of MKP5 through modifications to the scaffold and functional groups present in 1. A series of derivative compounds was designed, synthesized, and evaluated for inhibition of MKP5. In addition, the X-ray crystal structures of six enzyme-inhibitor complexes were solved, further elucidating the necessary requirements for MKP5 inhibition. We found that the parallel-displaced π-π interaction between the inhibitor three-ring core and Tyr435 is critical for modulating potency, and that modifications to the core and functionalization at the C-9 position are essential for ensuring proper positioning of the core for this interaction. These results lay the foundation from which more potent MKP5 allosteric inhibitors can be developed for potential therapeutics towards the treatment of dystrophic muscle disease.
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Affiliation(s)
- Zira T K Gannam
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Haya Jamali
- Department of Chemistry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Oh Sang Kweon
- Department of Chemistry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - James Herrington
- Yale Center for Molecular Discovery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | | | - Christina Papini
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Erik Gentzel
- Department of Chemistry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Elias Lolis
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Anton M Bennett
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA; Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Jonathan A Ellman
- Department of Chemistry, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06520, USA.
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7
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Xue Y, Zhang L, Zhang L, Sun W, Fang Z, Leng Y, Li M, Ren X, Zhang R, Zhang Y, Chen L, Wang H. Danshensu prevents thrombosis by inhibiting platelet activation via SIRT1/ROS/mtDNA pathways without increasing bleeding risk. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 104:154271. [PMID: 35777120 DOI: 10.1016/j.phymed.2022.154271] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/01/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Coronary thrombosis and its correlated disorders are main healthcare problems globally. The therapeutic effects of current treatments involving antiplatelet drugs are not fully satisfactory. Danshensu (DSS) is an important monomer obtained from Salvia miltiorrhiza roots that have been widely employed for vascular diseases in medicinal practices. Nonetheless, the underlying mechanisms of DSS are not fully unraveled. PURPOSE The objective of this study was to penetrate the antithrombotic and antiplatelet mechanisms of DSS. METHODS Network pharmacology assay was used to forecast the cellular mechanisms of DSS for treating thrombosis. The work focused the impacts of DSS on platelet activation by analyzing aggregation and adhesion in vitro. Flow cytometry, western blotting, CM-H2DCFDA staining and mitochondrial function assays were performed to reveal the molecular mechanisms. The model of common carotid artery thrombus induced by ferric chloride was established. The wet weight of thrombus was measured, and the thrombosis was observed by hematoxylin and eosin (H&E) staining, in order to support the inhibitory effect of DSS on thrombosis. RESULTS Data mining found the antithrombotic effect of DSS is related to platelet activation and the core target is silent information regulator 1 (SIRT1). We confirmed that DSS dose-dependently inhibited platelet activation in vitro. DSS was further demonstrated to induce the expression of SIRT1 and decreased reactive oxygen species (ROS) burden and thereby prevented mitochondrial dysfunction. Mitochondrial function tests further indicated that DSS prevented mitochondrial DNA (mtDNA) release, which induced activation of platelet in a dendritic cell specific intercellular-adhesion-molecule-3 grabbing non-integrin (DC-SIGN)-dependent manner. In carotid artery injury model induced by ferric chloride, DSS inhibited the development of carotid arterial thrombosis. More encouragingly, in tail bleeding time assay, DSS did not augment bleeding risk. CONCLUSION These findings indicated that DSS effectively inhibited platelet activation by depressing the collection of ROS and the release of platelet mtDNA without arousing hemorrhage risk. DSS might represent a promising candidate drug for thrombosis and cardiovascular disease therapeutics.
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Affiliation(s)
- Yuejin Xue
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China
| | - Liyuan Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China
| | - Lusha Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China
| | - Wei Sun
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China
| | - Zhirui Fang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China
| | - Yuze Leng
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China
| | - Mengyao Li
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China
| | - Xiuyun Ren
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China
| | - Rui Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China
| | - Yingxue Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China
| | - Lu Chen
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Tianjin Key Laboratory of Traditional Chinese Medicine Pharmacology, 301617 Tianjin, China; Tianjin State Key Laboratory of Modern Chinese Medicine, 301617 Tianjin, China; Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China.
| | - Hong Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formula, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China; Tianjin Key Laboratory of Traditional Chinese Medicine Pharmacology, 301617 Tianjin, China; Tianjin State Key Laboratory of Modern Chinese Medicine, 301617 Tianjin, China; School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, 301617 Tianjin, China.
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8
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Liu S, Hirao H. Energy Decomposition Analysis of the Nature of Coordination Bonding at the Heme Iron Center in Cytochrome P450 Inhibition. Chem Asian J 2022; 17:e202200360. [PMID: 35514038 DOI: 10.1002/asia.202200360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/26/2022] [Indexed: 11/11/2022]
Abstract
Drug compounds or their metabolic intermediates (MIs) sometimes inhibit the function of cytochrome P450 enzymes (P450s) by forming a coordination bond with the Fe(III) heme or Fe(II) heme of P450s. Such inhibition is one of the major causes of drug-drug interactions (DDIs), a subject of longstanding academic and practical interest. However, such coordination bonding is not fully understood at the quantum mechanical level, thus hampering rational improvement of the accuracy of DDI-related predictions. In this work, we employed density functional theory (DFT) and the generalized Kohn-Sham energy decomposition analysis (GKS-EDA) scheme to investigate the nature of the coordination bonding formed in the reversible and quasi-irreversible inhibition of P450s. The GKS-EDA results highlighted a previously unrecognized role of the electron correlation effect in P450 inhibition. The correlation effect tends to be larger in Fe(II) complexes of MI-type inhibitors and is particularly prominent for the nitrosoalkane ligand. An additional natural bond orbital (NBO) analysis provided insight into the relative significance of the σ donation and π backdonation effects in various heme-inhibitor complexes.
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Affiliation(s)
- Shuyang Liu
- The Chinese University of Hong Kong - Shenzhen, School of Life and Health Sciences, CHINA
| | - Hajime Hirao
- The Chinese University of Hong Kong - Shenzhen, School of Life and Health Sciences, …, Shenzhen, CHINA
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9
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Monooxygenase- and Dioxygenase-Catalyzed Oxidative Dearomatization of Thiophenes by Sulfoxidation, cis-Dihydroxylation and Epoxidation. Int J Mol Sci 2022; 23:ijms23020909. [PMID: 35055091 PMCID: PMC8777831 DOI: 10.3390/ijms23020909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
Enzymatic oxidations of thiophenes, including thiophene-containing drugs, are important for biodesulfurization of crude oil and drug metabolism of mono- and poly-cyclic thiophenes. Thiophene oxidative dearomatization pathways involve reactive metabolites, whose detection is important in the pharmaceutical industry, and are catalyzed by monooxygenase (sulfoxidation, epoxidation) and dioxygenase (sulfoxidation, dihydroxylation) enzymes. Sulfoxide and epoxide metabolites of thiophene substrates are often unstable, and, while cis-dihydrodiol metabolites are more stable, significant challenges are presented by both types of metabolite. Prediction of the structure, relative and absolute configuration, and enantiopurity of chiral metabolites obtained from thiophene enzymatic oxidation depends on the substrate, type of oxygenase selected, and molecular docking results. The racemization and dimerization of sulfoxides, cis/trans epimerization of dihydrodiol metabolites, and aromatization of epoxides are all factors associated with the mono- and di-oxygenase-catalyzed metabolism of thiophenes and thiophene-containing drugs and their applications in chemoenzymatic synthesis and medicine.
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10
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Jaladanki CK, Khatun S, Gohlke H, Bharatam PV. Reactive Metabolites from Thiazole-Containing Drugs: Quantum Chemical Insights into Biotransformation and Toxicity. Chem Res Toxicol 2021; 34:1503-1517. [PMID: 33900062 DOI: 10.1021/acs.chemrestox.0c00450] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Drugs containing thiazole and aminothiazole groups are known to generate reactive metabolites (RMs) catalyzed by cytochrome P450s (CYPs). These RMs can covalently modify essential cellular macromolecules and lead to toxicity and induce idiosyncratic adverse drug reactions. Molecular docking and quantum chemical hybrid DFT study were carried out to explore the molecular mechanisms involved in the biotransformation of thiazole (TZ) and aminothiazole (ATZ) groups leading to RM epoxide, S-oxide, N-oxide, and oxaziridine. The energy barrier required for the epoxidation is 13.63 kcal/mol, that is lower than that of S-oxidation, N-oxidation, and oxaziridine formation (14.56, 17.90, and 20.20, kcal/mol respectively). The presence of the amino group in ATZ further facilitates all the metabolic pathways, for example, the barrier for the epoxidation reaction is reduced by ∼2.5 kcal/mol. Some of the RMs/their isomers are highly electrophilic and tend to form covalent bonds with nucleophilic amino acids, finally leading to the formation of metabolic intermediate complexes (MICs). The energy profiles of these competitive pathways have also been explored.
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Affiliation(s)
- Chaitanya K Jaladanki
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Samima Khatun
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.,Forschungszentrum Jülich GmbH, John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
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11
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Mirzaei MS, Ivanov MV, Taherpour AA, Mirzaei S. Mechanism-Based Inactivation of Cytochrome P450 Enzymes: Computational Insights. Chem Res Toxicol 2021; 34:959-987. [PMID: 33769041 DOI: 10.1021/acs.chemrestox.0c00483] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mechanism-based inactivation (MBI) refers to the metabolic bioactivation of a xenobiotic by cytochrome P450s to a highly reactive intermediate which subsequently binds to the enzyme and leads to the quasi-irreversible or irreversible inhibition. Xenobiotics, mainly drugs with specific functional units, are the major sources of MBI. Two possible consequences of MBI by medicinal compounds are drug-drug interaction and severe toxicity that are observed and highlighted by clinical experiments. Today almost all of these latent functional groups (e.g., thiophene, furan, alkylamines, etc.) are known, and their features and mechanisms of action, owing to the vast experimental and theoretical studies, are determined. In the past decade, molecular modeling techniques, mostly density functional theory, have revealed the most feasible mechanism that a drug undergoes by P450 enzymes to generate a highly reactive intermediate. In this review, we provide a comprehensive and detailed picture of computational advances toward the elucidation of the activation mechanisms of various known groups with MBI activity. To this aim, we briefly describe the computational concepts to carry out and analyze the mechanistic investigations, and then, we summarize the studies on compounds with known inhibition activity including thiophene, furan, alkylamines, terminal acetylene, etc. This study can be reference literature for both theoretical and experimental (bio)chemists in several different fields including rational drug design, the process of toxicity prevention, and the discovery of novel inhibitors and catalysts.
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Affiliation(s)
- M Saeed Mirzaei
- Department of Organic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran 67149-67346
| | - Maxim V Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Avat Arman Taherpour
- Department of Organic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran 67149-67346.,Medical Biology Research Centre, University of Medical Sciences, Kermanshah, Iran 67149-67346
| | - Saber Mirzaei
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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12
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Focused structure-activity relationship profiling around the 2-phenylindole scaffold of a cannabinoid type-1 receptor agonist-positive allosteric modulator: site-III aromatic-ring congeners with enhanced activity and solubility. Bioorg Med Chem 2020; 28:115727. [PMID: 33065437 DOI: 10.1016/j.bmc.2020.115727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/06/2020] [Accepted: 08/19/2020] [Indexed: 12/31/2022]
Abstract
Specific tuning of cannabinoid 1 receptor (CB1R) activity by small-molecule allosteric modulators is a therapeutic modality with multiple properties inherently advantageous to therapeutic applications. We previously generated a library of unique CB1R positive allosteric modulators (PAMs) derived from GAT211, which has three pharmacophoric sites critical to its ago-PAM activity. To elaborate our CB1R PAM library, we report the rational design and molecular-pharmacology profiling of several 2-phenylindole analogs modified at the "site-III" aromatic ring. The comprehensive structure-activity relationship (SAR) investigation demonstrates that attaching small lipophilic functional groups on the ortho-position of the GAT211 site-III phenyl ring could markedly enhance CB1R ago-PAM activity. Select site-III modifications also improved GAT211's water solubility. The SAR reported both extends the structural diversity of this compound class and demonstrates the utility of GAT211's site-III for improving the parent compound's drug-like properties of potency and/or aqueous solubility.
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13
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Jaladanki CK, Gahlawat A, Rathod G, Sandhu H, Jahan K, Bharatam PV. Mechanistic studies on the drug metabolism and toxicity originating from cytochromes P450. Drug Metab Rev 2020; 52:366-394. [DOI: 10.1080/03602532.2020.1765792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Chaitanya K. Jaladanki
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Anuj Gahlawat
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Gajanan Rathod
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Hardeep Sandhu
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Kousar Jahan
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
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14
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Önal HT, Yuzer A, Ince M, Ayaz F. Photo induced anti-inflammatory activities of a Thiophene substituted subphthalocyanine derivative. Photodiagnosis Photodyn Ther 2020; 30:101701. [PMID: 32184175 DOI: 10.1016/j.pdpdt.2020.101701] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/29/2020] [Accepted: 02/28/2020] [Indexed: 10/24/2022]
Abstract
Materials that possess photo induced biological activities present opportunities for more localized, targeted and efficient treatment options that may also reduce side effects. There have been studies supporting photo induced effects of photosensitizers as anti-cancer, anti-inflammatory and anti-microbial agents. In this study, we tested photo activated anti-inflammatory effects of a Thiophene substituted subphthalocyanine (SubPc) derivative. Thiophene and its derivatives are well known for their anti-inflammatory and anti-microbial effects. There are unwanted side effects associated with Thiophene derivatives. By substituting this biologically active molecule to SubPc structure we acquired control over its activation. Upon light treatment this derivative exerted anti-inflammatory activity on the mammalian macrophages in vitro based on the substantial decrease in extracellular inflammatory cytokine levels. Our results suggest that Thiophene substituted SubPc derivative has photo induced anti-inflammatory activities. This material can be used for the treatment of patients suffering from chronic inflammation that are not associated with a bacterial burden such as autoimmune diseases and inflammatory or allergic reactions.
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Affiliation(s)
- Harika Topal Önal
- Department of Biotechnology, Faculty of Arts and Science, Mersin University, Mersin, 33110, Turkey
| | - Abdulcelil Yuzer
- Advanced Technology Research & Application Center, Mersin University, Mersin, 33110, Turkey
| | - Mine Ince
- Advanced Technology Research & Application Center, Mersin University, Mersin, 33110, Turkey; Department of Energy Systems Engineering, Faculty of Technology, Tarsus University, 33400 Tarsus, Turkey.
| | - Furkan Ayaz
- Department of Biotechnology, Faculty of Arts and Science, Mersin University, Mersin, 33110, Turkey.
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15
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target Validation. Angew Chem Int Ed Engl 2019; 58:17930-17952. [DOI: 10.1002/anie.201812164] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/08/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
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16
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Abstract
The stilbenoid combretastatin and its derivatives are potent inhibitors of angiogenesis and cell proliferation and induce apoptosis. They disrupt cytoskeletal dynamics and modulate cell morphology, motility, and invasion. Hence they have been viewed as potential as anticancer agents. The impediments of poor solubility and bioavailability and the spontaneous geometric isomerisation of combretastatin into an inactive form have led to intensive efforts towards evolving novel analogues to provide more efficacious biological outcome. Importantly, isomerically stable and biologically active cis-restricted analogues have been synthesised and tested. However, very few analogues have been tested in preclinical models to assess their effects on processes relevant to cancer development and progression. Hence the accent here is on the signalling systems operated by the new derivatives and their biological effects with reference to cancer progression. Combretastatins modulate an extensive network of signalling emphasising their varied versatility. Harnessing these systems and accentuating or counteracting aberrant signalling could open potential avenues of approach to the designing of novel derivatives with enhanced performance. The import of mammalian target of rapamycin pathway, which co-ordinates growth factor receptor signalling, epithelial-mesenchymal transition activation and angiogenic signalling, is emphasised. It may be viewed as a prime target for allosteric inhibition in combination with combretastatin analogues to ascertain their potential in cancer control.
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Affiliation(s)
- Gajanan V Sherbet
- School of Engineering, University of Newcastle Upon Tyne, Newcastle Upon Tyne, UK.,The Institute for Molecular Medicine, Huntington Beach, California
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17
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemische Epigenetik: der Einfluss chemischer und chemo‐biologischer Techniken auf die Zielstruktur‐Validierung von Bromodomänen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
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18
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A Molecular Dynamics Study of Vasoactive Intestinal Peptide Receptor 1 and the Basis of Its Therapeutic Antagonism. Int J Mol Sci 2019; 20:ijms20184348. [PMID: 31491880 PMCID: PMC6770453 DOI: 10.3390/ijms20184348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/30/2019] [Accepted: 08/20/2019] [Indexed: 12/21/2022] Open
Abstract
Vasoactive intestinal peptide receptor 1 (VPAC1) is a member of a secretin-like subfamily of G protein-coupled receptors. Its endogenous neuropeptide (VIP), secreted by neurons and immune cells, modulates various physiological functions such as exocrine and endocrine secretions, immune response, smooth muscles relaxation, vasodilation, and fetal development. As a drug target, VPAC1 has been selected for therapy of inflammatory diseases but drug discovery is still hampered by lack of its crystal structure. In this study we presented the homology model of this receptor constructed with the well-known web service GPCRM. The VPAC1 model is composed of extracellular and transmembrane domains that form a complex with an endogenous hormone VIP. Using the homology model of VPAC1 the mechanism of action of potential drug candidates for VPAC1 was described. Only two series of small-molecule antagonists of confirmed biological activity for VPAC1 have been described thus far. Molecular docking and a series of molecular dynamics simulations were performed to elucidate their binding to VPAC1 and resulting antagonist effect. The presented work provides the basis for the possible binding mode of VPAC1 antagonists and determinants of their molecular recognition in the context of other class B GPCRs. Until the crystal structure of VPAC1 will be released, the presented homology model of VPAC1 can serve as a scaffold for drug discovery studies and is available from the author upon request.
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19
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Spura J, Farhati A, Romanovs V, Borodulin A, Belakovs S, Popelis J, Shestakova I, Dammak M, Jouikov V. Novel R3M (M = Si, Ge) substituted furan and thiophene-derived aldimines: Synthesis, electrochemistry, and biological activity. CR CHIM 2019. [DOI: 10.1016/j.crci.2019.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Synthesis of carbohydrazides and carboxamides as anti-tubercular agents. Eur J Med Chem 2018; 156:871-884. [DOI: 10.1016/j.ejmech.2018.07.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/15/2018] [Accepted: 07/17/2018] [Indexed: 11/23/2022]
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21
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HC2091 Kills Mycobacterium tuberculosis by Targeting the MmpL3 Mycolic Acid Transporter. Antimicrob Agents Chemother 2018; 62:AAC.02459-17. [PMID: 29661875 DOI: 10.1128/aac.02459-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/09/2018] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis, caused by the intracellular pathogen Mycobacterium tuberculosis, is a deadly disease that requires a long course of treatment. The emergence of drug-resistant strains has driven efforts to discover new small molecules that can kill the bacterium. Here, we report characterizations of the compound HC2091, which kills M. tuberculosis in a time- and dose-dependent manner in vitro and inhibits M. tuberculosis growth in macrophages. Whole-genome sequencing of spontaneous HC2091-resistant mutants identified single-nucleotide variants in the mmpL3 mycolic acid transporter gene. HC2091-resistant mutants do not exhibit cross-resistance with the well-characterized Mycobacterium membrane protein large 3 (MmpL3) inhibitor SQ109, suggesting a distinct mechanism of interaction with MmpL3. Additionally, HC2091 does not modulate bacterial membrane potential or kill nonreplicating M. tuberculosis, thus acting differently from other known MmpL3 inhibitors. RNA sequencing (RNA-seq) transcriptional profiling and lipid profiling of M. tuberculosis treated with HC2091 or SQ109 show that the two compounds target a similar pathway. HC2091 has a chemical structure dissimilar to those of previously described MmpL3 inhibitors, supporting the notion that HC2091 is a new class of MmpL3 inhibitor.
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22
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Abu-Laban M, Kumal RR, Casey J, Becca J, LaMaster D, Pacheco CN, Sykes DG, Jensen L, Haber LH, Hayes DJ. Comparison of thermally actuated retro-diels-alder release groups for nanoparticle based nucleic acid delivery. J Colloid Interface Sci 2018; 526:312-321. [PMID: 29751265 DOI: 10.1016/j.jcis.2018.04.085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/03/2018] [Accepted: 04/23/2018] [Indexed: 12/18/2022]
Abstract
The present study explores alternate pericyclic chemistries for tethering amine-terminal biomolecules onto silver nanoparticles. Employing the versatile tool of the retro-Diels-Alder (rDA) reaction, three thermally-labile cycloadducts are constructed that cleave at variable temperature ranges. While the reaction between furan and maleimide has widely been reported, the current study also evaluates the reverse reaction kinetics between thiophene-maleimide, and pyrrole-maleimide cycloadducts. Density Functional Theorem (DFT) calculations used to model and plan the experiments, predict energy barriers for the thiophene-maleimide reverse reaction to be greatest, and the pyrrole-maleimide barriers the lowest. Based on the computational analyses, it is projected that the cycloreversion rate would occur slowest with the thiophene, followed by furan, and finally pyrrole would yield the promptest release. These thermally-responsive linkers, characterized by Electrospray Ionization Mass Spectrometry, 1H and 13C NMR, are thiol-linked to silver nanoparticles and conjugate single stranded siRNA mimics with 5' fluorescein tag. Second harmonic generation spectroscopy (SHG) and fluorescence spectroscopy are used to measure release and rate of release. The SHG decay constants and fluorescence release profiles obtained for the three rDA reactions confirm the trends obtained from the DFT computations.
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Affiliation(s)
- Mohammad Abu-Laban
- The Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Raju R Kumal
- The Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - Jonathan Casey
- The Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Jeff Becca
- The Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Daniel LaMaster
- The Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - Carlos N Pacheco
- The Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States; The NMR Facility, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Dan G Sykes
- The Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Lasse Jensen
- The Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Louis H Haber
- The Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - Daniel J Hayes
- The Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, United States; Materials Research Institute, Materials Characterization Lab, Millennium Science Complex, The Pennsylvania State University, University Park, PA 16802, United States; The Huck Institute of the Life Sciences, Millennium Science Complex, The Pennsylvania State University, University Park, PA 16802, United States.
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23
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Sadiq F, Zhao J, Hussain M, Wang Z. Effect of thiophene substitution on the intersystem crossing of arene photosensitizers. Photochem Photobiol Sci 2018; 17:1794-1803. [DOI: 10.1039/c8pp00230d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Thiophene substitution gives energy level-matched S1/T2 states and the ISC is enhanced, which was not observed with phenyl substitution.
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Affiliation(s)
- Farhan Sadiq
- State Key Laboratory of Fine Chemicals
- School of Chemical Engineering
- Dalian University of Technology
- Dalian 116024
- P. R. China
| | - Jianzhang Zhao
- State Key Laboratory of Fine Chemicals
- School of Chemical Engineering
- Dalian University of Technology
- Dalian 116024
- P. R. China
| | - Mushraf Hussain
- State Key Laboratory of Fine Chemicals
- School of Chemical Engineering
- Dalian University of Technology
- Dalian 116024
- P. R. China
| | - Zhijia Wang
- State Key Laboratory of Fine Chemicals
- School of Chemical Engineering
- Dalian University of Technology
- Dalian 116024
- P. R. China
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24
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Jaladanki CK, Shaikh A, Bharatam PV. Biotransformation of Isoniazid by Cytochromes P450: Analyzing the Molecular Mechanism using Density Functional Theory. Chem Res Toxicol 2017; 30:2060-2073. [DOI: 10.1021/acs.chemrestox.7b00129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chaitanya K. Jaladanki
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar, Mohali, 160 062 Punjab, India
| | - Akbar Shaikh
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar, Mohali, 160 062 Punjab, India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar, Mohali, 160 062 Punjab, India
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25
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Rudik AV, Dmitriev AV, Bezhentsev VM, Lagunin AA, Filimonov DA, Poroikov VV. Prediction of metabolites of epoxidation reaction in MetaTox. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:833-842. [PMID: 29157013 DOI: 10.1080/1062936x.2017.1399165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Biotransformation is a process of the chemical modifications which may lead to the reactive metabolites, in particular the epoxides. Epoxide reactive metabolites may cause the toxic effects. The prediction of such metabolites is important for drug development and ecotoxicology studies. Epoxides are formed by some oxidation reactions, usually catalysed by cytochromes P450, and represent a large class of three-membered cyclic ethers. Identification of molecules, which may be epoxidized, and indication of the specific location of epoxide functional group (which is called SOE - site of epoxidation) are important for prediction of epoxide metabolites. Datasets from 355 molecules and 615 reactions were created for training and validation. The prediction of SOE is based on a combination of LMNA (Labelled Multilevel Neighbourhood of Atom) descriptors and Bayesian-like algorithm implemented in PASS software and MetaTox web-service. The average invariant accuracy of prediction (AUC) calculated in leave-one-out and 20-fold cross-validation procedures is 0.9. Prediction of epoxide formation based on the created SAR model is included as the component of MetaTox web-service ( http://www.way2drug.com/mg ).
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Affiliation(s)
- A V Rudik
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
| | - A V Dmitriev
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
| | - V M Bezhentsev
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
| | - A A Lagunin
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
- b Medico-biological Faculty , Pirogov Russian National Research Medical University , Moscow , Russia
| | - D A Filimonov
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
| | - V V Poroikov
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
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26
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Dang NL, Hughes TB, Miller GP, Swamidass SJ. Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and Thiophenes. Chem Res Toxicol 2017; 30:1046-1059. [PMID: 28256829 DOI: 10.1021/acs.chemrestox.6b00336] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Structural alerts are commonly used in drug discovery to identify molecules likely to form reactive metabolites and thereby become toxic. Unfortunately, as useful as structural alerts are, they do not effectively model if, when, and why metabolism renders safe molecules toxic. Toxicity due to a specific structural alert is highly conditional, depending on the metabolism of the alert, the reactivity of its metabolites, dosage, and competing detoxification pathways. A systems approach, which explicitly models these pathways, could more effectively assess the toxicity risk of drug candidates. In this study, we demonstrated that mathematical models of P450 metabolism can predict the context-specific probability that a structural alert will be bioactivated in a given molecule. This study focuses on the furan, phenol, nitroaromatic, and thiophene alerts. Each of these structural alerts can produce reactive metabolites through certain metabolic pathways but not always. We tested whether our metabolism modeling approach, XenoSite, can predict when a given molecule's alerts will be bioactivated. Specifically, we used models of epoxidation, quinone formation, reduction, and sulfur-oxidation to predict the bioactivation of furan-, phenol-, nitroaromatic-, and thiophene-containing drugs. Our models separated bioactivated and not-bioactivated furan-, phenol-, nitroaromatic-, and thiophene-containing drugs with AUC performances of 100%, 73%, 93%, and 88%, respectively. Metabolism models accurately predict whether alerts are bioactivated and thus serve as a practical approach to improve the interpretability and usefulness of structural alerts. We expect that this same computational approach can be extended to most other structural alerts and later integrated into toxicity risk models. This advance is one necessary step toward our long-term goal of building comprehensive metabolic models of bioactivation and detoxification to guide assessment and design of new therapeutic molecules.
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Affiliation(s)
- Na Le Dang
- Department of Pathology and Immunology, Washington University School of Medicine , Campus Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Tyler B Hughes
- Department of Pathology and Immunology, Washington University School of Medicine , Campus Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Grover P Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205, United States
| | - S Joshua Swamidass
- Department of Pathology and Immunology, Washington University School of Medicine , Campus Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, United States
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27
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Hu J, Li G, Huang ZB, Zhang J, Shi DQ, Zhao Y. Pd-Catalyzed thiophene directed regioselective functionalization of arenes: a direct approach to multiply-substituted benzyl amines. Org Chem Front 2017. [DOI: 10.1039/c7qo00236j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A thiophene directed ortho-C–H functionalization via a palladium catalyst in the synthesis of multiply-substituted benzyl amines has been developed.
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Affiliation(s)
- Jundie Hu
- Key Laboratory of Organic Synthesis of Jiangsu Province
- College of Chemistry
- Chemical Engineering and Materials Science Soochow University
- Suzhou 215123
- China
| | - Guobao Li
- Key Laboratory of Organic Synthesis of Jiangsu Province
- College of Chemistry
- Chemical Engineering and Materials Science Soochow University
- Suzhou 215123
- China
| | - Zhi-Bin Huang
- Key Laboratory of Organic Synthesis of Jiangsu Province
- College of Chemistry
- Chemical Engineering and Materials Science Soochow University
- Suzhou 215123
- China
| | - Jingyu Zhang
- College of Physics
- Optoelectronics and Energy & Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou 215006
- China
| | - Da-Qing Shi
- Key Laboratory of Organic Synthesis of Jiangsu Province
- College of Chemistry
- Chemical Engineering and Materials Science Soochow University
- Suzhou 215123
- China
| | - Yingsheng Zhao
- Key Laboratory of Organic Synthesis of Jiangsu Province
- College of Chemistry
- Chemical Engineering and Materials Science Soochow University
- Suzhou 215123
- China
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28
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Dixit VA, Deshpande S. Advances in Computational Prediction of Regioselective and Isoform-Specific Drug Metabolism Catalyzed by CYP450s. ChemistrySelect 2016. [DOI: 10.1002/slct.201601051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
| | - Shirish Deshpande
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
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Herrera-Martínez M, Hernández-Ramírez VI, Hernández-Carlos B, Chávez-Munguía B, Calderón-Oropeza MA, Talamás-Rohana P. Antiamoebic Activity of Adenophyllum aurantium (L.) Strother and Its Effect on the Actin Cytoskeleton of Entamoeba histolytica. Front Pharmacol 2016; 7:169. [PMID: 27445810 PMCID: PMC4922267 DOI: 10.3389/fphar.2016.00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/03/2016] [Indexed: 11/13/2022] Open
Abstract
In Mexico, the Adenophyllum aurantium (L.) Strother plant is consumed as an infusion to treat intestinal diseases such as amoebiasis, which is an endemic health problem in Mexico and other countries. However, the effect of A. aurantium on Entamoeba histolytica, the causative agent of amoebiasis, is unknown. An aerial part methanolic extract (AaMeA), a root methanolic extract (AaMeR) and a root ethyl acetate extract (AaEaR) were tested on E. histolytica trophozoites. AaMeA and AaMeR did not show antiproliferative activity; however, AaEaR exhibited an in vitro GI50 of 230 μg/ml, and it was able to inhibit the differentiation of Entamoeba invadens trophozoites into cysts. The intraperitoneal administration of AaEaR (2.5 or 5 mg) to hamsters that were infected with E. histolytica inhibited the development of amoebic liver abscesses in 48.5 or 89.0% of the animals, respectively. Adhesion to fibronectin and erythrophagocytosis were 28.7 and 37.5% inhibited by AaEaR, respectively. An ultrastructure analysis of AaEaR-treated trophozoites shows a decrease in the number of vacuoles but no apparent cell damage. Moreover, this extract affected the actin cytoskeleton structuration, and it prevented the formation of contractile rings by mechanism(s) that were independent of reactive oxygen species and RhoA activation pathways. (13)C NMR data showed that the major compounds in the AaEaR extract are thiophenes. Our results suggest that AaEaR may be effective in treatments against amoebiasis, nevertheless, detailed toxicity studies on thiophenes, contained in AaEaR, are required to avoid misuse of this vegetal species.
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Affiliation(s)
- Mayra Herrera-Martínez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalCiudad de México, Mexico
| | - Verónica I. Hernández-Ramírez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalCiudad de México, Mexico
| | | | - Bibiana Chávez-Munguía
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalCiudad de México, Mexico
| | | | - Patricia Talamás-Rohana
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalCiudad de México, Mexico
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