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Irfan A, Faisal S, Ahmad S, Saif MJ, Zahoor AF, Khan SG, Javid J, Al-Hussain SA, Muhammed MT, Zaki MEA. An Exploration of the Inhibitory Mechanism of Rationally Screened Benzofuran-1,3,4-Oxadiazoles and-1,2,4-Triazoles as Inhibitors of NS5B RdRp Hepatitis C Virus through Pharmacoinformatic Approaches. Biomedicines 2023; 11:3085. [PMID: 38002085 PMCID: PMC10669698 DOI: 10.3390/biomedicines11113085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Benzofuran, 1,3,4-oxadiazole, and 1,2,4-triazole are privileged heterocyclic moieties that display the most promising and wide spectrum of biological activities against a wide variety of diseases. In the current study, benzofuran-1,3,4-oxadiazole BF1-BF7 and benzofuran-1,2,4-triazole compounds BF8-BF15 were tested against HCV NS5B RNA-dependent RNA polymerase (RdRp) utilizing structure-based screening via a computer-aided drug design (CADD) approach. A molecular docking approach was applied to evaluate the binding potential of benzofuran-appended 1,3,4-oxadiazole and 1,2,4-triazole BF1-BF15 molecules. Benzofuran-1,3,4-oxadiazole scaffolds BF1-BF7 showed lesser binding affinities (-12.63 to -14.04 Kcal/mol) than benzofuran-1,2,4-triazole scaffolds BF8-BF15 (-14.11 to -16.09 Kcal/mol) against the HCV NS5B enzyme. Molecular docking studies revealed the excellent binding affinity scores exhibited by benzofuran-1,2,4-triazole structural motifs BF-9 (-16.09 Kcal/mol), BF-12 (-15.75 Kcal/mol), and BF-13 (-15.82 Kcal/mol), respectively, which were comparatively better than benzofuran-based HCV NS5B inhibitors' standard reference drug Nesbuvir (-15.42 Kcal/mol). A molecular dynamics simulation assay was also conducted to obtain valuable insights about the enzyme-compounds interaction profile and structural stability, which indicated the strong intermolecular energies of the BF-9+NS5B complex and the BF-12+NS5B complex as per the MM-PBSA method, while the BF-12+NS5B complex was the most stable system as per the MM-GBSA calculation. The drug-likeness and ADMET studies of all the benzofuran-1,2,4-triazole derivatives BF8-BF15 revealed that these compounds possessed good medicinal chemistry profiles in agreement with all the evaluated parameters for being drugs. The molecular docking affinity scores, MM-PBSA/MM-GBSA and MD-simulation stability analysis, drug-likeness profiling, and ADMET study assessment indicated that N-4-fluorophenyl-S-linked benzofuran-1,2,4-triazole BF-12 could be a future promising anti-HCV NS5B RdRp inhibitor therapeutic drug candidate that has a structural agreement with the Nesbuvir standard reference drug.
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Affiliation(s)
- Ali Irfan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.I.); (A.F.Z.)
| | - Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar 25000, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36, Lebanon
- Department of Natural Sciences, Lebanese American University, Beirut P.O. Box 36, Lebanon
| | - Muhammad Jawwad Saif
- Department of Applied Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.I.); (A.F.Z.)
| | - Samreen Gul Khan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.I.); (A.F.Z.)
| | - Jamila Javid
- Department of Chemistry, University of Sialkot, Sialkot 51040, Pakistan
| | - Sami A. Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13623, Saudi Arabia
| | - Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Suleyman Demirel University, Isparta 32260, Turkey
| | - Magdi E. A. Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13623, Saudi Arabia
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Singh A, Singh K, Sharma A, Kaur K, Chadha R, Bedi PMS. Recent advances in antifungal drug development targeting lanosterol 14α-demethylase (CYP51): A comprehensive review with structural and molecular insights. Chem Biol Drug Des 2023; 102:606-639. [PMID: 37220949 DOI: 10.1111/cbdd.14266] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 05/25/2023]
Abstract
Fungal infections are posing serious threat to healthcare system due to emerging resistance among available antifungal agents. Among available antifungal agents in clinical practice, azoles (diazole, 1,2,4-triazole and tetrazole) remained most effective and widely prescribed antifungal agents. Now their associated side effects and emerging resistance pattern raised a need of new and potent antifungal agents. Lanosterol 14α-demethylase (CYP51) is responsible for the oxidative removal of 14α-methyl group of sterol precursors lanosterol and 24(28)-methylene-24,25-dihydrolanosterol in ergosterol biosynthesis hence an essential component of fungal life cycle and prominent target for antifungal drug development. This review will shed light on various azole- as well as non-azoles-based derivatives as potential antifungal agents that target fungal CYP51. Review will provide deep insight about structure activity relationship, pharmacological outcomes, and interactions of derivatives with CYP51 at molecular level. It will help medicinal chemists working on antifungal development in designing more rational, potent, and safer antifungal agents by targeting fungal CYP51 for tackling emerging antifungal drug resistance.
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Affiliation(s)
- Atamjit Singh
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Karanvir Singh
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Aman Sharma
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Kirandeep Kaur
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Renu Chadha
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Preet Mohinder Singh Bedi
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
- Drug and Pollution testing Laboratory, Guru Nanak Dev University, Amritsar, Punjab, India
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3
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Zhou Z, Zhang J, Zhou E, Ren C, Wang J, Wang Y. Small molecule NS5B RdRp non-nucleoside inhibitors for the treatment of HCV infection: A medicinal chemistry perspective. Eur J Med Chem 2022; 240:114595. [PMID: 35868125 DOI: 10.1016/j.ejmech.2022.114595] [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: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) infection has become a global health problem with enormous risks. Nonstructural protein 5B (NS5B) RNA-dependent RNA polymerase (RdRp) is a component of HCV, which can promote the formation of the viral RNA replication complex and is also an essential part of the replication complex itself. It plays a vital role in the synthesis of the positive and negative strands of HCV RNA. Therefore, the development of small-molecule inhibitors targeting NS5B RdRp is of great value for treating HCV infection-related diseases. Compared with NS5B RdRp nucleoside inhibitors, non-nucleoside inhibitors have more flexible structures, simpler mechanisms of action, and more predictable efficacy and safety of drugs in humans. Technological advances over the past decade have led to remarkable achievements in developing NS5B RdRp inhibitors. This review will summarize the non-nucleoside inhibitors targeting NS5B RdRp developed in the past decade and describe their structure optimization process and structure-activity relationship.
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Affiliation(s)
- Zhilan Zhou
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China
| | - Enda Zhou
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu, Sichuan, 611130, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China.
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Jian-Bo T, Xing Z, Shuai B, Ding L, Tian-Hao W. Topomer CoMFA and HQSAR Study on Benzimidazole Derivative as NS5B Polymerase Inhibitor. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210804125607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
In recent years, the number of people infected with the hepatitis C virus
(HCV) is increasing rapidly. This has become a major threat to global health, therefore, new anti-
HCV drugs are urgently needed. HCV NS5B polymerase is an RNA-dependent RNA polymerase
(RdRp), which plays an important role in virus replication, and can effectively prevent the replication
of HCV sub-genomic RNA in daughter cells. It is considered a very promising HCV therapeutic
target for the design of anti-HCV drugs.
Methods:
In order to explore the relationship between the structure of benzimidazole derivative and
its inhibitory activity on NS5B polymerase, holographic quantitative structure-activity relationship
(HQSAR) and Topomer comparative molecular field analysis (CoMFA) were used to establish benzimidazole
QSAR model of derivative inhibitors.
Results:
The results show that for the Topomer CoMFA model, the cross-validation coefficient q2
value is 0.883, and the non-cross-validation coefficient r2 value is 0.975. The model is reasonable,
reliable, and has a good predictive ability. For the HQSAR model, the cross-validated q2 value is
0.922, and the uncross-validated r2 value is 0.971, indicating that the model data fit well and has a
high predictive ability. Through the analysis of the contour map and color code diagram, 40 new
benzimidazole inhibitor molecules were designed, and all of them have higher activity than template
molecules, and the new molecules have significant interaction sites with protein 3SKE.
Conclusion:
The 3D-QSAR model established by Topomer CoMFA and HQSAR has good prediction
results and the statistical verification is valid. The newly designed molecules and docking results
provide theoretical guidance for the synthesis of new NS5B polymerase inhibitors and for the identification
of key residues that the inhibitors bind to NS5B, which helps to better understand their inhibitory
mechanism. These findings are helpful for the development of new anti-HCV drugs.
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Affiliation(s)
- Tong Jian-Bo
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Zhang Xing
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Bian Shuai
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Luo Ding
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Wang Tian-Hao
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
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5
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Pan G, Lu L, Zhuang W, Huang Q. Synthesis of Indole-Fused Six-, Seven-, or Eight-Membered N,O-Heterocycles via Rhodium-Catalyzed NH-Indole-Directed C-H Acetoxylation/Hydrolysis/Annulation. J Org Chem 2021; 86:16753-16763. [PMID: 34756052 DOI: 10.1021/acs.joc.1c01982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report herein the facile synthesis of indole-fused six-, seven-, or eight-membered N,O-heterocycles through rhodium-catalyzed C-H acetoxylation/hydrolysis/annulation. The notable features of this method include C-H acetoxylation using NH-indole as the intrinsic directing group, high functional group compatibility, and construction of indole-fused medium-sized rings.
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Affiliation(s)
- Guoshuai Pan
- Fujian Key Laboratory of Polymer Materials, College of Chemistry & Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, P. R. China
| | - Leipeng Lu
- Fujian Key Laboratory of Polymer Materials, College of Chemistry & Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, P. R. China
| | - Weihui Zhuang
- Fujian Key Laboratory of Polymer Materials, College of Chemistry & Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, P. R. China
| | - Qiufeng Huang
- Fujian Key Laboratory of Polymer Materials, College of Chemistry & Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fuzhou, Fujian 35007, P.R. China
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6
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Deb B, Debnath S, Chakraborty A, Majumdar S. Bis-indolylation of aldehydes and ketones using silica-supported FeCl 3: molecular docking studies of bisindoles by targeting SARS-CoV-2 main protease binding sites. RSC Adv 2021; 11:30827-30839. [PMID: 35498942 PMCID: PMC9041420 DOI: 10.1039/d1ra05679d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
We report herein an operationally simple, efficient and versatile procedure for the synthesis of bis-indolylmethanes via the reaction of indoles with aldehydes or ketones in the presence of silica-supported ferric chloride under grindstone conditions. The prepared supported catalyst was characterized by SEM and EDX spectroscopy. The present protocol has several advantages such as shorter reaction time, high yield, avoidance of using harmful organic solvents during the reaction and tolerance of a wide range of functional groups. Molecular docking studies targeted toward the binding site of SARS-CoV-2 main protease (3CLpro or Mpro) enzymes were investigated with the synthesized bis-indoles. Our study revealed that some of the synthesized compounds have potentiality to inhibit the SARS-CoV-2 Mpro enzyme by interacting with key amino acid residues of the active sites via hydrophobic as well as hydrogen bonding interactions. Silica supported FeCl3 catalyzed simple protocol for the synthesis of bis-indolylmethanes was explored via grindstone chemistry. Synthesized compounds were screened virtually as inhibitor by targeting the binding site of SARS-CoV-2 main protease enzyme.![]()
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Affiliation(s)
- Barnali Deb
- Department of Chemistry, Tripura University Suryamaninagar 799 022 India +91-381-237-4802 +91-381-237-9070
| | - Sudhan Debnath
- Department of Chemistry, Netaji Subhash Mahavidalaya Tripura 799114 India
| | - Ankita Chakraborty
- Department of Chemistry, Tripura University Suryamaninagar 799 022 India +91-381-237-4802 +91-381-237-9070
| | - Swapan Majumdar
- Department of Chemistry, Tripura University Suryamaninagar 799 022 India +91-381-237-4802 +91-381-237-9070
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7
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Elghoneimy LK, Ismail MI, Boeckler FM, Azzazy HME, Ibrahim TM. Facilitating SARS CoV-2 RNA-Dependent RNA polymerase (RdRp) drug discovery by the aid of HCV NS5B palm subdomain binders: In silico approaches and benchmarking. Comput Biol Med 2021; 134:104468. [PMID: 34015671 PMCID: PMC8111889 DOI: 10.1016/j.compbiomed.2021.104468] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/25/2021] [Accepted: 04/30/2021] [Indexed: 01/18/2023]
Abstract
Corona Virus 2019 Disease (COVID-19) is a rapidly emerging pandemic caused by a newly discovered beta coronavirus, called Sever Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2). SARS CoV-2 is an enveloped, single stranded RNA virus that depends on RNA-dependent RNA polymerase (RdRp) to replicate. Therefore, SARS CoV-2 RdRp is considered as a promising target to cease virus replication. SARS CoV-2 polymerase shows high structural similarity to Hepatitis C Virus-1b genotype (HCV-1b) polymerase. Arising from the high similarity between SARS CoV-2 RdRp and HCV NS5B, we utilized the reported small-molecule binders to the palm subdomain of HCV NS5B (genotype 1b) to generate a high-quality DEKOIS 2.0 benchmark set and conducted a benchmarking analysis against HCV NS5B. The three highly cited and publicly available docking tools AutoDock Vina, FRED and PLANTS were benchmarked. Based on the benchmarking results and analysis via pROC-Chemotype plot, PLANTS showed the best screening performance and can recognize potent binders at the early enrichment. Accordingly, we used PLANTS in a prospective virtual screening to repurpose both the FDA-approved drugs (DrugBank) and the HCV-NS5B palm subdomain binders (BindingDB) for SARS CoV-2 RdRp palm subdomain. Further assessment by molecular dynamics simulations for 50 ns recommended diosmin (from DrugBank) and compound 3 (from BindingDB) to be the best potential binders to SARS CoV-2 RdRp palm subdomain. The best predicted compounds are recommended to be biologically investigated against COVID-19. In conclusion, this work provides in-silico analysis to propose possible SARS CoV-2 RdRp palm subdomain binders recommended as a remedy for COVID-19. Up-to-our knowledge, this study is the first to propose binders at the palm subdomain of SARS CoV2 RdRp. Furthermore, this study delivers an example of how to make use of a high quality custom-made DEKOIS 2.0 benchmark set as a procedure to elevate the virtual screening success rate against a vital target of the rapidly emerging pandemic.
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Affiliation(s)
- Laila K Elghoneimy
- Department of Chemistry, School of Sciences and Engineering, American University in Cairo, AUC Avenue, SSE # 1184, P.O. Box 74, New Cairo, 11835, Egypt
| | - Muhammad I Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, Al-Sherouk City, Cairo-Suez Desert Road, 11837, Cairo, Egypt
| | - Frank M Boeckler
- Department of Pharmacy, Eberhard-Karls University, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Hassan M E Azzazy
- Department of Chemistry, School of Sciences and Engineering, American University in Cairo, AUC Avenue, SSE # 1184, P.O. Box 74, New Cairo, 11835, Egypt
| | - Tamer M Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt.
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Dorababu A. Indole - a promising pharmacophore in recent antiviral drug discovery. RSC Med Chem 2020; 11:1335-1353. [PMID: 34095843 PMCID: PMC8126882 DOI: 10.1039/d0md00288g] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/04/2020] [Indexed: 12/17/2022] Open
Abstract
The bicyclic molecule indole has been in the limelight because of its numerous pharmacological potencies. It is used as an excellent scaffold in drug discovery of medicinal drugs such as antimicrobials, anticancer agents, antihypertensives, anti-proliferative agents and anti-inflammatory agents. In spite of its diverse therapeutic activity, it is used as a key pharmacophore in synthesizing the most potent biological agents. Besides, viral infections are ubiquitous and their prevention and cure have become a great challenge. In this regard, the design of indole-containing antiviral drugs is accomplished to combat viral infections. A lot of research is being carried out towards antiviral drug discovery by many researchers round the clock. Herein, the antiviral activity of recently discovered indole scaffolds is compiled and critically evaluated to give a meaningful summary. In addition, the structure-activity relationship of remarkable antiviral agents is discussed. Also, the structural motifs attributed to noteworthy antiviral properties are highlighted to guide future antiviral research.
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Affiliation(s)
- Atukuri Dorababu
- Department of Chemistry, SRMPP Govt. First Grade College Huvinahadagali-583219 Karnataka India
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9
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Ban K, Yamamoto Y, Sajiki H, Sawama Y. Arylation of indoles using cyclohexanones dually-catalyzed by niobic acid and palladium-on-carbons. Org Biomol Chem 2020; 18:3898-3902. [PMID: 32400844 DOI: 10.1039/d0ob00702a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
3-Arylindoles were easily constructed from indoles and cyclohexanone derivatives using a combination of catalytic niobic acid-on-carbon (Nb2O5/C) and palladium-on-carbon (Pd/C) under heating conditions without any oxidants. The Lewis acidic Nb2O5/C promoted the nucleophilic addition of indoles to the cyclohexanones, and the subsequent dehydration and Pd/C-catalyzed dehydrogenation produced the 3-arylindoles. The additive 2,3-dimethyl-1,3-butadiene worked as a hydrogen acceptor to facilitate the dehydrogenation step.
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Affiliation(s)
- Kazuho Ban
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigakunishi, Gifu 501-1196, Japan.
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10
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Wang M, Wu Y, Xu C, Zhao R, Huang Y, Zeng X, Chen T. Design and Synthesis of 2-(5-Phenylindol-3-yl)benzimidazole Derivatives with Antiproliferative Effects towards Triple-Negative Breast Cancer Cells by Activation of ROS-Mediated Mitochondria Dysfunction. Chem Asian J 2019; 14:2648-2655. [PMID: 31144429 DOI: 10.1002/asia.201900468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/10/2019] [Indexed: 12/31/2022]
Abstract
Benzimidazole derivatives are widely studied because of their broad-spectrum biological activity, such as antitumor properties and excellent fluorescence performance. Herein, two types of 2-(5-phenylindol-3-yl)benzimidazole derivatives (1 a-1 h and 2 a-2 e) were rationally designed and synthesized. When these compounds were investigated in vitro anti-screening assays, we found that all of them possessed antitumor effect, in particular compound 1 b, which showed an outstanding antiproliferative effect on MDA-MB-231 cells (IC50 ≈2.6 μm). A study of the drug action mechanisms in cells showed that the antitumor activity of the compounds is proportional to their lipophilicity and cellular uptake; the tested compounds all entered the lysosome of MDA-MB-231 cells and caused changes in the levels of reactive oxygen species (ROS), and then caused mitochondrial damage. Apparent differences in the ROS levels for each compound suggest that the lethality of these compounds towards MDA-MB-231 cells is closely related to the ROS levels. Taken together, this study not only provides a theoretical basis for 2-(5-phenylindol-3-yl)benzimidazole anticarcinogens but also offers new thinking on the rational design of next-generation antitumor benzimidazole derivatives.
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Affiliation(s)
- Mengying Wang
- Department of Chemistry, Jinan University, Guangzhou, 510632, China
| | - Yusheng Wu
- Department of Chemistry, Jinan University, Guangzhou, 510632, China
| | - Cuifang Xu
- Department of Chemistry, Jinan University, Guangzhou, 510632, China
| | - Rucheng Zhao
- Department of Chemistry, Jinan University, Guangzhou, 510632, China
| | - Yanyu Huang
- Department of Chemistry, Jinan University, Guangzhou, 510632, China
| | - Xiangchao Zeng
- Department of Chemistry, Jinan University, Guangzhou, 510632, China
| | - Tianfeng Chen
- Department of Chemistry, Jinan University, Guangzhou, 510632, China
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11
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Yuan W, Yu Z, Song W, Li Y, Fang Z, Zhu B, Li X, Wang H, Hong W, Sun N. Indole-core-based novel antibacterial agent targeting FtsZ. Infect Drug Resist 2019; 12:2283-2296. [PMID: 31413605 PMCID: PMC6662167 DOI: 10.2147/idr.s208757] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/03/2019] [Indexed: 12/23/2022] Open
Abstract
Background The prevalence of drug-resistant bacterial infections urges the development of new antibacterial agents that possess a mechanism of action different from traditional antibiotics. FtsZ has been recognized as a key functional protein in bacterial cell division and it is currently believed to be a potential target for the development of novel antibacterial agents. Purpose The primary aim of the study is to screen out an inhibitor targeting at FtsZ and followed to investigate its antibacterial activity and mode of action. Methods Cell-based cell division inhibitory screening assay, antimicrobial susceptibility test, minimum bactericidal concentration assay, time-killing curve determination, FtsZ polymerization assay, GTPase activity assay, and molecular modeling were performed in the present study. Results The screening study from a small library consisting of benzimidazole and indole derivatives discovered a compound (CZ74) with an indole-core structure. The compound exhibited strong cell division inhibitory effect. In addition, CZ74 shows high antibacterial potency against a number of tested Gram-positive bacteria, such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus. The minimum inhibitory concentration values obtained were within the range of 2–4 µg/mL. The results of biological study revealed that CZ74 at 2 µg/mL is able to disrupt FtsZ polymerization and inhibit GTPase activity and cell division. From molecular modeling study, CZ74 is found possibly binding into the interdomain cleft of FtsZ protein and then leads to inhibitory effects. Conclusion This indole-cored molecule CZ74 could be a potential lead compound and could be further developed as a new generation of antibacterial agents targeting FtsZ to combat against multidrug-resistant bacteria.
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Affiliation(s)
- Wenchang Yuan
- The Fifth Affiliated Hospital of Guangzhou Medical University , Guangzhou 510700, People's Republic of China
| | - Zhiwu Yu
- Division of Laboratory Science, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, People's Republic of China
| | - Weiqi Song
- School of Public Health, Guangzhou Medical University, Guangzhou 511436, People's Republic of China
| | - Yanan Li
- Department of Pharmacy, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, People's Republic of China
| | - Zhiyuan Fang
- The Fifth Affiliated Hospital of Guangzhou Medical University , Guangzhou 510700, People's Republic of China
| | - Baizhen Zhu
- The Fifth Affiliated Hospital of Guangzhou Medical University , Guangzhou 510700, People's Republic of China
| | - Xiaomei Li
- The Fifth Affiliated Hospital of Guangzhou Medical University , Guangzhou 510700, People's Republic of China
| | - Hao Wang
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, People's Republic of China
| | - Wei Hong
- School of Chemistry and Chemical Engineering, North Minzu University, Yinchuan 750021, People's Republic of China
| | - Ning Sun
- The Fifth Affiliated Hospital of Guangzhou Medical University , Guangzhou 510700, People's Republic of China.,State Key Laboratory of Chemical Biology and Drug Discovery, and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, People's Republic of China
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12
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Wang Z, Chen Z, Li J, Huang J, Zheng C, Liu JP. Combined 3D-QSAR, molecular docking and molecular dynamics study on the benzimidazole inhibitors targeting HCV NS5B polymerase. J Biomol Struct Dyn 2019; 38:1071-1082. [PMID: 30915896 DOI: 10.1080/07391102.2019.1593244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The hepatitis C virus (HCV)-infected population has continued to grow during recent years, and novel HCV antiviral agents are urgently needed. In this work, a combined theoretical study was performed on the HCV non-structural 5B (NS5B) polymerase and 53 benzimidazole inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were carried out with ligand-based and receptor-based alignments. Ligand-based QSAR models (cross-validated q2 of 0.918 for CoMFA and 0.825 for CoMSIA) were found to be superior to receptor-based approaches (cross-validated q2 of 0.765 for CoMFA and 0.740 for CoMSIA). Based on the most predictive CoMFA and CoMSIA models, the structural features that were essential for the inhibitory activity of benzimidazoles were characterized. A molecular dynamics study revealed that the induced fit effect between NS5B and its substrate may be responsible for the inferiority of the receptor-based CoMFA and CoMSIA models. The binding-free energy calculated using the MM/PBSA method correlated well with the experimental results and revealed that the van der Waals and electrostatic interactions most contributed to the binding. In addition, energetically favorable NS5B residues were identified by the per-residue decomposition of binding-free energy. The results presented in this work provide meaningful information for the design of novel benzimidazole inhibitors targeting the NS5B polymerase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Zhenming Chen
- Laboratory of Biocatalysis, College of Life & Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jianfeng Li
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jing Huang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Chenni Zheng
- Laboratory of Biocatalysis, College of Life & Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jun-Ping Liu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,Department of Immunology, Central Eastern Clinical School, Monash University, Melbourne, Vitoria, Australia.,Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
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13
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Kim D, Goo JI, Kim MI, Lee SJ, Choi M, Than TT, Nguyen PH, Windisch MP, Lee K, Choi Y, Lee C. Suppression of Hepatitis C Virus Genome Replication and Particle Production by a Novel Diacylglycerol Acyltransferases Inhibitor. Molecules 2018; 23:molecules23082083. [PMID: 30127285 PMCID: PMC6222871 DOI: 10.3390/molecules23082083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/01/2018] [Accepted: 08/11/2018] [Indexed: 11/23/2022] Open
Abstract
Diacylglycerol acyltransferases (DGATs) play a critical role in the biosynthesis of endogenous triglycerides (TGs) and formation of lipid droplets (LDs) in the liver. In particular, one member of DGATs, DGAT-1 was reported to be an essential host factor for the efficient production of hepatitis C virus (HCV) particles. By utilizing our previously characterized three different groups of twelve DGAT inhibitors, we found that one of the DGAT inhibitors, a 2-((4-adamantylphenoxy) methyl)-N-(furan-2-ylmethyl)-1H-benzo[d]imidazole-5-carboxam (10j) is a potent suppressor of both HCV genome replication and particle production. 10j was able to induce inhibition of these two critical viral functions in a mutually separate manner. Abrogation of the viral genome replication by 10j led to a significant reduction in the viral protein expression as well. Interestingly, we found that its antiviral effect did not depend on the reduction of TG biosynthesis by 10j. This suggests that the inhibitory activity of 10j against DGATs may not be directly related with its antiviral action.
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Affiliation(s)
- Dahee Kim
- College of Pharmacy, Dongguk University, Goyang 10326, Korea.
| | - Ja-Il Goo
- School of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea.
| | - Mi Il Kim
- College of Pharmacy, Dongguk University, Goyang 10326, Korea.
| | - Sung-Jin Lee
- College of Pharmacy, Dongguk University, Goyang 10326, Korea.
| | - Moonju Choi
- College of Pharmacy, Dongguk University, Goyang 10326, Korea.
| | - Thoa Thi Than
- Hepatitis Research Laboratory, Department of Applied Molecular Virology, Institut Pasteur Korea, 696, Seongnam 13488, Korea.
| | - Phuong Hong Nguyen
- Hepatitis Research Laboratory, Department of Applied Molecular Virology, Institut Pasteur Korea, 696, Seongnam 13488, Korea.
| | - Marc P Windisch
- Hepatitis Research Laboratory, Department of Applied Molecular Virology, Institut Pasteur Korea, 696, Seongnam 13488, Korea.
| | - Kyeong Lee
- College of Pharmacy, Dongguk University, Goyang 10326, Korea.
| | - Yongseok Choi
- School of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea.
| | - Choongho Lee
- College of Pharmacy, Dongguk University, Goyang 10326, Korea.
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14
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15
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Polák P, Tobrman T. The synthesis of polysubstituted indoles from 3-bromo-2-indolyl phosphates. Org Biomol Chem 2018; 15:6233-6241. [PMID: 28702629 DOI: 10.1039/c7ob01127j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel methodology for the synthesis of functionalised indoles based on the cross-coupling reactions of 3-bromo-2-indolyl phosphates is described. The preparation involves the conversion of easily available 2-oxindoles to 3,3-dibromo-2-oxindoles followed by the Perkow reaction affording 3-bromo-2-indolyl phosphates. Then bromine atom is substituted regioselectively by the Suzuki coupling reaction. We observed that aluminum chloride promoted the reaction of 3-substituted-2-indolyl phosphates with organozinc reagents furnishing 2,3-disubstituted indoles as final products. The overall diversity and efficiency of the methodology was demonstrated by the synthesis of bioactive molecule from easily available substances.
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Affiliation(s)
- Peter Polák
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic.
| | - Tomáš Tobrman
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic.
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16
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Li E, Wang Y, Yu W, Lv Z, Peng Y, Liu B, Li S, Ho W, Wang Q, Li H, Chang J. Synthesis and biological evaluation of a novel β-D-2'-deoxy-2'-α-fluoro-2'-β-C-(fluoromethyl)uridine phosphoramidate prodrug for the treatment of hepatitis C virus infection. Eur J Med Chem 2017; 143:107-113. [PMID: 29172078 DOI: 10.1016/j.ejmech.2017.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/01/2017] [Accepted: 11/08/2017] [Indexed: 12/15/2022]
Abstract
A novel β-D-2'-deoxy-2'-α-fluoro-2'-β-C-(fluoromethyl)uridine phosphoramidate prodrug (1) has been synthesized. This compound exhibits submicromolar-level antiviral activity in vitro against HCV genotypes 1b, 1a, 2a, and S282T replicons (EC50 = 0.18-1.13 μM) with low cytotoxicity (CC50 > 1000 μM). Administered orally, prodrug 1 is well tolerated at doses of up to 4 g/kg in mice, and produces a high level of the corresponding triphosphate in rat liver.
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Affiliation(s)
- Ertong Li
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Yafeng Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China; Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Wenquan Yu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Zhigang Lv
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Youmei Peng
- Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Bingjie Liu
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wenzhe Ho
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Qingduan Wang
- Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Junbiao Chang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China.
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17
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Yu W, Li E, Lv Z, Liu K, Guo X, Liu Y, Chang J. Synthesis and Anti-HCV Activity of a Novel 2',3'-Dideoxy-2'-α-fluoro-2'-β- C-methyl Guanosine Phosphoramidate Prodrug. ACS Med Chem Lett 2017. [PMID: 28626533 DOI: 10.1021/acsmedchemlett.7b00174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A novel 2',3'-dideoxy-2'-α-fluoro-2'-β-C-methyl-6-methoxy guanosine (8) and its phosphoramidate prodrug (1) have been designed and synthesized. Their biological activity was evaluated in both cytotoxicity and cell-based HCV replicon assays. Neither compounds exhibited cytotoxicity up to the highest concentration tested (100 μM) in the Huh-7 cell line. The prodrug (1) displayed nanomolar level antiviral activity (EC50 = 0.39-1.1 μM) against the HCV genotype (GT) 1a, 1b, 2a, and 1b S282T replicons.
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Affiliation(s)
- Wenquan Yu
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Ertong Li
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Zhigang Lv
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Ke Liu
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Xiaohe Guo
- High & New Technology Research Center of Henan Academy of Sciences, Zhengzhou, Henan 450002, P. R. China
| | - Yuan Liu
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Junbiao Chang
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
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18
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Synthesis and biological evaluation of indole core-based derivatives with potent antibacterial activity against resistant bacterial pathogens. J Antibiot (Tokyo) 2017; 70:832-844. [PMID: 28465626 DOI: 10.1038/ja.2017.55] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/12/2017] [Accepted: 03/20/2017] [Indexed: 01/17/2023]
Abstract
The emergence of drug resistance in bacterial pathogens is a growing clinical problem that poses difficult challenges in patient management. To exacerbate this problem, there is currently a serious lack of antibacterial agents that are designed to target extremely drug-resistant bacterial strains. Here we describe the design, synthesis and antibacterial testing of a series of 40 novel indole core derivatives, which are predicated by molecular modeling to be potential glycosyltransferase inhibitors. Twenty of these derivatives were found to show in vitro inhibition of Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. Four of these strains showed additional activity against Gram-negative bacteria, including extended-spectrum beta-lactamase producing Enterobacteriaceae, imipenem-resistant Klebsiella pneumoniae and multidrug-resistant Acinetobacter baumanii, and against Mycobacterium tuberculosis H37Ra. These four compounds are candidates for developing into broad-spectrum anti-infective agents.
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19
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The discovery of indole derivatives as novel hepatitis C virus inhibitors. Eur J Med Chem 2016; 116:147-155. [DOI: 10.1016/j.ejmech.2016.03.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/16/2022]
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