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Ahmed S, Prabahar AE, Saxena AK. Molecular docking-based interaction studies on imidazo[1,2-a] pyridine ethers and squaramides as anti-tubercular agents. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023:1-23. [PMID: 37365919 DOI: 10.1080/1062936x.2023.2225872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023]
Abstract
Development of new anti-tubercular agents is required in the wake of resistance to the existing and newly approved drugs through novel-validated targets like ATP synthase, etc. The major limitation of poor correlation between docking scores and biological activity by SBDD was overcome by a novel approach of quantitatively correlating the interactions of different amino acid residues present in the target protein structure with the activity. This approach well predicted the ATP synthase inhibitory activity of imidazo[1,2-a] pyridine ethers and squaramides (r = 0.84) in terms of Glu65b interactions. Hence, the models were developed on combined (r = 0.78), and training (r = 0.82) sets of 52, and 27 molecules, respectively. The training set model well predicted the diverse dataset (r = 0.84), test set (r = 0.755), and, external dataset (rext = 0.76). This model predicted three compounds from a focused library generated by incorporating the essential features of the ATP synthase inhibition with the pIC50 values in the range of 0.0508-0.1494 µM. Molecular dynamics simulation studies ascertain the stability of the protein structure and the docked poses of the ligands. The developed model(s) may be useful in the identification and optimization of novel compounds against TB.
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Affiliation(s)
- S Ahmed
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research, Kashipur, India
- Department of Pharmaceutical Chemistry, Teerthanker Mahaveer College of Pharmacy, Moradabad, India
| | - A E Prabahar
- Department of Pharmaceutical Chemistry, Teerthanker Mahaveer College of Pharmacy, Moradabad, India
| | - A K Saxena
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research, Kashipur, India
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Kelam LM, Wani MA, Dhaked DK. An update on ATP synthase inhibitors: A unique target for drug development in M. tuberculosis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:87-104. [PMID: 37105260 DOI: 10.1016/j.pbiomolbio.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 04/29/2023]
Abstract
ATP synthase is a key protein in the oxidative phosphorylation process, as it aids in the effective production of ATP (Adenosine triphosphate) in all life's of kingdoms. ATP synthases have distinctive properties that contribute to efficient ATP synthesis. The ATP synthase of mycobacterium is of special relevance since it has been identified as a target for potential anti-TB molecules, especially Bedaquiline (BDQ). Better knowledge of how mycobacterial ATP synthase functions and its peculiar characteristics will aid in our understanding of bacterial energy metabolism adaptations. Furthermore, identifying and understanding the important distinctions between human ATP synthase and bacterial ATP synthase may provide insight into the design and development of inhibitors that target specific ATP synthase. In recent years, many potential candidates targeting the ATP synthase of mycobacterium have been developed. In this review, we discuss the druggable targets of the Electron transport chain (ETC) and recently identified potent inhibitors (including clinical molecules) from 2015 to 2022 of diverse classes that target ATP synthase of M. tuberculosis.
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Affiliation(s)
- Lakshmi Mounika Kelam
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, 700054, West Bengal, India
| | - Mushtaq Ahmad Wani
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, 700054, West Bengal, India
| | - Devendra K Dhaked
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, 700054, West Bengal, India.
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Kumar G, Kapoor S. Targeting mycobacterial membranes and membrane proteins: Progress and limitations. Bioorg Med Chem 2023; 81:117212. [PMID: 36804747 DOI: 10.1016/j.bmc.2023.117212] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Among the various bacterial infections, tuberculosis continues to hold center stage. Its causative agent, Mycobacterium tuberculosis, possesses robust defense mechanisms against most front-line antibiotic drugs and host responses due to their complex cell membranes with unique lipid molecules. It is now well-established that bacteria change their membrane composition to optimize their environment to survive and elude drug action. Thus targeting membrane or membrane components is a promising avenue for exploiting the chemical space focussed on developing novel membrane-centric anti-bacterial small molecules. These approaches are more effective, non-toxic, and can attenuate resistance phenotype. We present the relevance of targeting the mycobacterial membrane as a practical therapeutic approach. The review highlights the direct and indirect targeting of membrane structure and function. Direct membrane targeting agents cause perturbation in the membrane potential and can cause leakage of the cytoplasmic contents. In contrast, indirect membrane targeting agents disrupt the function of membrane-associated proteins involved in cell wall biosynthesis or energy production. We discuss the chronological chemical improvements in various scaffolds targeting specific membrane-associated protein targets, their clinical evaluation, and up-to-date account of their ''mechanisms of action, potency, selectivity'' and limitations. The sources of anti-TB drugs/inhibitors discussed in this work have emerged from target-based identification, cell-based phenotypic screening, drug repurposing, and natural products. We believe this review will inspire the exploration of uncharted chemical space for informing the development of new scaffolds that can inhibit novel mycobacterial membrane targets.
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Affiliation(s)
- Gautam Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Departemnt of Natural Products, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad 500037, India.
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan.
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Dasmahapatra U, Chanda K. Synthetic approaches to potent heterocyclic inhibitors of tuberculosis: A decade review. Front Pharmacol 2022; 13:1021216. [DOI: 10.3389/fphar.2022.1021216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) continues to be a significant global health concern with about 1.5 million deaths annually. Despite efforts to develop more efficient vaccines, reliable diagnostics, and chemotherapeutics, tuberculosis has become a concern to world health due to HIV, the rapid growth of bacteria that are resistant to treatment, and the recently introduced COVID-19 pandemic. As is well known, advances in synthetic organic chemistry have historically enabled the production of important life-saving medications that have had a tremendous impact on patients’ lives and health all over the world. Small-molecule research as a novel chemical entity for a specific disease target offers in-depth knowledge and potential therapeutic targets. In this viewpoint, we concentrated on the synthesis of a number of heterocycles reported in the previous decade and the screening of their inhibitory action against diverse strains of Mycobacterium tuberculosis. These findings offer specific details on the structure-based activity of several heterocyclic scaffolds backed by their in vitro tests as a promising class of antitubercular medicines, which will be further useful to build effective treatments to prevent this terrible illness.
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5
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Asymmetric synthesis of bedaquiline based on bimetallic activation and non-covalent interaction promotion strategies. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1387-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Ahmed S, Prabahar AE, Saxena AK. Molecular docking-based interactions in QSAR studies on Mycobacterium tuberculosis ATP synthase inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:289-305. [PMID: 35532308 DOI: 10.1080/1062936x.2022.2066175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/09/2022] [Indexed: 05/19/2023]
Abstract
Tuberculosis (TB) is a global threat with a large burden across the continents in terms of mortality, morbidity, and financial losses. The disease has evolved into multi-drug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) tuberculosis owing to numerous factors ranging from patients' non-compliance to demographical implications. There have been very few new drugs for resistant TB. Resistance has already been reported even for the newly introduced drug bedaquiline. An attempt has been made to integrate both structure-based and QSAR drug design techniques (QSAR-SBDD) for the identification of novel leads. The docking scores normally do not correlate with the activity. Hence, the docking results have been analysed in terms of the number of interactions rather than docking scores. The parameters derived from interactions have been used in developing the QSAR models. The best model shows a good correlation (r = 0.908) between the activity and interaction parameter 'C' describing the sum of all the interactions with each amino acid residue. This model also predicts external dataset with a good correlation (rext = 0.851) and can be used for the identification of novel chemical entities (NCEs) and repurposed drugs for TB therapeutics.
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Affiliation(s)
- S Ahmed
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research, Kashipur, India
- Department of Pharmaceutical Chemistry, Teerthanker Mahaveer College of Pharmacy, Moradabad, India
| | - A E Prabahar
- Department of Pharmaceutical Chemistry, Teerthanker Mahaveer College of Pharmacy, Moradabad, India
| | - A K Saxena
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research, Kashipur, India
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Kumar A, Karkara BB, Panda G. Novel candidates in the clinical development pipeline for TB drug development and their Synthetic Approaches. Chem Biol Drug Des 2021; 98:787-827. [PMID: 34397161 DOI: 10.1111/cbdd.13934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/03/2021] [Accepted: 08/07/2021] [Indexed: 11/29/2022]
Abstract
Tuberculosis (TB) is an infection caused by Mycobacterium tuberculosis (Mtb) and one of the deadliest infectious diseases in the world. Mtb has the ability to become dormant within the host and to develop resistance. Hence, new antitubercular agents are required to overcome problems in the treatment of multidrug resistant-Tb (MDR-Tb) and extensively drug resistant-Tb (XDR-Tb) along with shortening the treatment time. Several efforts are being made to develop very effective new drugs for Tb, within the pharmaceutical industry, the academia, and through public private partnerships. This review will address the anti-tubercular activities, biological target, mode of action, synthetic approaches and thoughtful concept for the development of several new drugs currently in the clinical trial pipeline (up to October 2019) for tuberculosis. The aim of this review may be very useful in scheming new chemical entities (NCEs) for Mtb.
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Affiliation(s)
- Amit Kumar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, UP, India
| | - Bidhu Bhusan Karkara
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, UP, India.,Department of Pharmaceutical Science, Vignan's Foundation for Science, Technology and Research University, Guntur, 522213, AP, India
| | - Gautam Panda
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, UP, India
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Inhibitors of F 1F 0-ATP synthase enzymes for the treatment of tuberculosis and cancer. Future Med Chem 2021; 13:911-926. [PMID: 33845594 DOI: 10.4155/fmc-2021-0010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The spectacular success of the mycobacterial F1F0-ATP synthase inhibitor bedaquiline for the treatment of drug-resistant tuberculosis has generated wide interest in the development of other inhibitors of this enzyme. Work in this realm has included close analogues of bedaquiline with better safety profiles and 'bedaquiline-like' compounds, some of which show potent antibacterial activity in vitro although none have yet progressed to clinical trials. The search has lately extended to a range of new scaffolds as potential inhibitors, including squaramides, diaminoquinazolines, chloroquinolines, dihydropyrazolo[1,5-a]pyrazin-4-ones, thiazolidinediones, diaminopyrimidines and tetrahydroquinolines. Because of the ubiquitous expression of ATP synthase enzymes, there has also been interest in inhibitors of other bacterial ATP synthases, as well as inhibitors of human mitochondrial ATP synthase for cancer therapy. The latter encompass both complex natural products and simpler small molecules. The review seeks to demonstrate the breadth of the structural types of molecules able to effectively inhibit the function of variants of this intriguing enzyme.
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Calvert MB, Furkert DP, Cooper CB, Brimble MA. Synthetic approaches towards bedaquiline and its derivatives. Bioorg Med Chem Lett 2020; 30:127172. [PMID: 32291133 DOI: 10.1016/j.bmcl.2020.127172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 01/11/2023]
Abstract
Bedaquiline is a diarylquinoline drug that demonstrates potent and selective inhibition of mycobacterial ATP synthase, and is clinically administered for the treatment of multi-drug resistant tuberculosis. Due to its excellent activity and novel mechanism of action, bedaquiline has been the focus of a number of synthetic studies. This review will discuss these synthetic approaches, as well as the synthesis and bioactivity of the numerous derivatives and molecular probes inspired by bedaquiline.
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Affiliation(s)
- Matthew B Calvert
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand
| | - Daniel P Furkert
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Symonds Street, Auckland 1010, New Zealand
| | - Christopher B Cooper
- Global Alliance for TB Drug Development, 40 Wall Street, New York, NY 10005, USA
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Symonds Street, Auckland 1010, New Zealand.
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Karkara BB, Mishra SS, Singh BN, Panda G. Synthesis of 2-methoxy-3-(thiophen-2-ylmethyl)quinoline containing amino carbinols as antitubercular agents. Bioorg Chem 2020; 99:103775. [PMID: 32222618 DOI: 10.1016/j.bioorg.2020.103775] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/13/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022]
Abstract
We have designed and synthesized 2-methoxy-3-(thiophen-2-ylmethyl)quinoline containing amino carbinols as possible anti-tubercular agents to combat the disease. These molecules were synthesized by tethering amino ether linkage with hydroxyl group to diarylquinoline skeleton; hydroxyl and amine chains were engrafted on diaryl ring. They were evaluated against strain (H37Ra) of Mycobacterium tuberculosis and most of compounds showed in vitro antitubercular activity. Two compounds having diaryl quinoline hydroxyl amino ether scaffold and three compounds having diaryl amino alkyl carbinol core showed activities at 6.25 μg/mL. This study explores diaryl carbinol prototype as inhibitor against Mycobacterium tuberculosis.
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Affiliation(s)
- Bidhu Bhusan Karkara
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute BS, 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Shashank Shekhar Mishra
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute BS, 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Bhupendra N Singh
- Microbiology Division, CSIR-Central Drug Research Institute BS 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India; Academiy of Scientific and Innovative Research, New Delhi 110001, India
| | - Gautam Panda
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute BS, 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India; Academiy of Scientific and Innovative Research, New Delhi 110001, India.
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Tan Z, Ci C, Yang J, Wu Y, Cao L, Jiang H, Zhang M. Catalytic Conversion of N-Heteroaromatics to Functionalized Arylamines by Merging Hydrogen Transfer and Selective Coupling. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00394] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Zhenda Tan
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, People’s Republic of China
| | - Chenggang Ci
- Key Laboratory of Computational Catalytic Chemistry of Guizhou Province, Department of Chemistry and Chemical Engineering, Qiannan Normal University for Nationalities, Duyun 558000, People’s Republic of China
| | - Jian Yang
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, People’s Republic of China
| | - Yang Wu
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, People’s Republic of China
| | - Liang Cao
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, People’s Republic of China
| | - Huanfeng Jiang
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, People’s Republic of China
| | - Min Zhang
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, People’s Republic of China
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Narang R, Kumar R, Kalra S, Nayak SK, Khatik GL, Kumar GN, Sudhakar K, Singh SK. Recent advancements in mechanistic studies and structure activity relationship of FoF1 ATP synthase inhibitor as antimicrobial agent. Eur J Med Chem 2019; 182:111644. [DOI: 10.1016/j.ejmech.2019.111644] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 12/17/2022]
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13
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Dorababu A, Kamble RR, Shaikh SKJ, Somagond SM, Bayannavar PK, Joshi SD. Synthesis, Docking, and Pharmacological Evaluation of Derivatives of α‐Aminoketones Appended to Sydnones as Potent Antitubercular and Antifungal Scaffolds. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Atukuri Dorababu
- Department of ChemistryKarnatak University Dharwad Pavate Nagar Dharwad Karnataka 580003 India
| | - Ravindra R. Kamble
- Department of ChemistryKarnatak University Dharwad Pavate Nagar Dharwad Karnataka 580003 India
| | - Saba Kauser J. Shaikh
- Department of ChemistryKarnatak University Dharwad Pavate Nagar Dharwad Karnataka 580003 India
| | - Shilpa M. Somagond
- Department of ChemistryKarnatak University Dharwad Pavate Nagar Dharwad Karnataka 580003 India
| | - Praveen K. Bayannavar
- Department of ChemistryKarnatak University Dharwad Pavate Nagar Dharwad Karnataka 580003 India
| | - Shrinivas D. Joshi
- Department of Pharmaceutical Chemistry, SET's College of PharmacyNovel Drug Design and Discovery Laboratory Sangolli Rayanna Nagar Dharwad Karnataka 580002 India
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Quinoline and quinolone dimers and their biological activities: An overview. Eur J Med Chem 2019; 161:101-117. [DOI: 10.1016/j.ejmech.2018.10.035] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 01/28/2023]
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