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Dash S, Rathi E, Kumar A, Chawla K, Joseph A, Kini SG. Structure-activity relationship mediated molecular insights of DprE1 inhibitors: A Comprehensive Review. J Biomol Struct Dyn 2024; 42:6472-6522. [PMID: 37395797 DOI: 10.1080/07391102.2023.2230312] [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: 04/03/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023]
Abstract
Emerging threats of multi-drug resistant (MDR), extensively drug-resistant (XDR), and totally drug-resistant (TDR) tuberculosis led to the discovery of a novel target which was entitled Decaprenylphosphoryl-β-D-ribose 2'-epimerase (DprE1) enzyme. DprE1 is composed of two isoforms, decaprenylphosphoryl-β-D-ribose oxidase (DprE1) and decaprenylphosphoryl-D-2-keto erythro pentose reductase (DprE2). The enzymes, DprE1 and DprE2, regulate the two-step epimerization process to form DPA (Decaprenylphosphoryl arabinose) from DPX (Decaprenylphosphoryl-D-ribose), which is the sole precursor in the cell wall synthesis of arabinogalactan (AG) and lipoarabinomannan (LAM). Target-based and whole-cell-based screening played an imperative role in the identification of the druggable target, DprE1, whereas the druggability of the DprE2 enzyme is not proved yet. To date, diverse scaffolds of heterocyclic and aromatic ring systems have been reported as DprE1 inhibitors based on their interaction mode, i.e. covalent, and non-covalent inhibitors. This review describes the structure-activity relationship (SAR) of reported covalent and non-covalent inhibitors to enlighten about the crucial pharmacophoric features required for DprE1 inhibition, along with in-silico studies which characterize the amino acid residues responsible for covalent and non-covalent interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Swagatika Dash
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ekta Rathi
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Avinash Kumar
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Suvarna G Kini
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Manipal Mc Gill Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, Karnataka, India
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Delgado T, Pais JP, Pires D, Estrada FGA, Guedes RC, Anes E, Constantino L. Development of New Drugs to Treat Tuberculosis Based on the Dinitrobenzamide Scaffold. Pharmaceuticals (Basel) 2024; 17:559. [PMID: 38794129 PMCID: PMC11124350 DOI: 10.3390/ph17050559] [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: 03/12/2024] [Revised: 04/14/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Tuberculosis (TB) continues to be a major global health challenge and a leading cause of death from infectious diseases. Inspired by the results from a previous work by our group on antimycobacterial N-alkylnitrobenzamides, which are structurally related to the nitrobenzamide family of decaprenylphosphoryl-β-d-ribose oxidase (DprE1) inhibitors, the present study explored a broad array of substituted benzamides. We particularly focused on previously unexplored 3,5-dinitrobenzamide derivatives. Starting with 3,5-dinitrobenzoic acid, we synthesized a diverse library of amides, incorporating both linear and cyclic amine moieties and also assessed the impact of terminal aromatic groups connected through ether, ester, or amide bonds on the bioactivity of the compounds. The synthesis primarily utilized nucleophilic addition/elimination, SN2, and Mitsunobu reactions. The activity was impacted mainly by two structural features, the addition of an aromatic moiety as a terminal group and the type of linker. The most interesting compounds (c2, d1, and d2, MIC = 0.031 μg/mL) exhibited activities against Mycobacterium Tuberculosis (Mtb) H37Rv comparable to isoniazid. Complementary computational studies helped elucidate potential interactions with DprE1, enhancing our understanding of the molecular basis of their action. Our findings suggest that the most active compounds provide a promising foundation for the continued development of new antimycobacterial agents.
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Affiliation(s)
- Tiago Delgado
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - João P. Pais
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - David Pires
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Filipe G. A. Estrada
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Elsa Anes
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Luis Constantino
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
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Nandikolla A, Khetmalis YM, Venkata Siva Kumar B, Chandu A, Karan Kumar B, Shetye G, Ma R, Murugesan S, Franzblau SG, Chandra Sekhar KVG. Design, synthesis and biological evaluation of phenanthridine amide and 1,2,3-triazole analogues against Mycobacterium tuberculosis. RSC Med Chem 2023; 14:1549-1561. [PMID: 37593576 PMCID: PMC10429663 DOI: 10.1039/d3md00115f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/29/2023] [Indexed: 08/19/2023] Open
Abstract
The phenanthridine core exhibits antitubercular activity, according to reports from the literature. Several 1,2,3-triazole-based heterocyclic compounds are well-known antitubercular agents. A series of twenty-five phenanthridine amide and 1,2,3-triazole derivatives are synthesized and analyzed using ESI-MS, 1HNMR, and 13CNMR on the basis of our earlier findings that phenanthridine and 1,2,3-triazoles shown good antitubercular activity. The synthesized phenanthridine amide and 1,2,3-triazole analogues were tested in vitro against Mycobacterium tuberculosis H37Rv and minimum inhibitory concentration (MIC) values were determined utilizing non-replicating and replicating low-oxygen recovery assay (LORA) and microplate Alamar Blue assay (MABA) methodologies. The phenanthridine amide derivative PA-01 had an MIC of 61.31 μM in MABA and 62.09 μM in the LORA technique, showing intense anti-TB activity. Amongst the phenanthridine triazole derivatives, PT-09, with MICs of 41.47 and 78.75 μM against the tested strain of Mtb in both MABA and LORA was the most active one. The final analogues' drug-likeness is predicted using absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies. The most active compounds PA-01 and PT-09 were further subjected to in silico docking studies. Using the Glide module of Schrodinger, molecular docking analysis was carried out to estimate the plausible binding pattern of PA-01 and PT-09 at the active site of Mycobacterial DNA topoisomerase II (PDB code: 5BS8). Further, molecular dynamics studies of PA-01 and PT-09 were also carried out.
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Affiliation(s)
- Adinarayana Nandikolla
- Department of Chemistry, Birla Institute of Technology and Science, Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal Hyderabad - 500078 Telangana India +91 40 66303527
| | - Yogesh Mahadu Khetmalis
- Department of Chemistry, Birla Institute of Technology and Science, Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal Hyderabad - 500078 Telangana India +91 40 66303527
| | - Boddupalli Venkata Siva Kumar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal Hyderabad - 500078 Telangana India +91 40 66303527
| | - Ala Chandu
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani Pilani Campus Pilani-333031 Rajasthan India
| | - Banoth Karan Kumar
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani Pilani Campus Pilani-333031 Rajasthan India
| | - Gauri Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago 833 South Wood Street Chicago IL 60612 USA
| | - Rui Ma
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago 833 South Wood Street Chicago IL 60612 USA
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani Pilani Campus Pilani-333031 Rajasthan India
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago 833 South Wood Street Chicago IL 60612 USA
| | - Kondapalli Venkata Gowri Chandra Sekhar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal Hyderabad - 500078 Telangana India +91 40 66303527
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Pais JP, Antoniuk O, Freire R, Pires D, Valente E, Anes E, Constantino L. Nitrobenzoates and Nitrothiobenzoates with Activity against M. tuberculosis. Microorganisms 2023; 11:microorganisms11040969. [PMID: 37110393 PMCID: PMC10142844 DOI: 10.3390/microorganisms11040969] [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: 02/27/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Esters of weak acids have shown improved antimycobacterial activity over the corresponding free acids and nitro benzoates in particular have previously shown to have a very intriguing activity. To expand the potential of nitro-derivatives of benzoic acid as antimycobacterial drugs and explore the effects of various structural features on the activity of these compounds, we have obtained a library of 64 derivatives containing esters and thioesters of benzoates and studied their activity against M. tuberculosis, the stability of the compounds, their activation by mycobacterial enzymes and the potential cytotoxicity against human monocytic THP-1 cell line. Our results showed that the most active compounds are those with an aromatic nitro substitution, with the 3,5-dinitro esters series being the most active. Also, the greater antitubercular activity for the nitro derivatives was shown to be unrelated to their pKa values or hydrolysis rates. Given the conventional relationship between nitro-containing substances and toxicity, one might anticipate that the great antimicrobial activity of nitro compounds would be associated with high toxicity; yet, we have not found such a relationship. The nitrobenzoate scaffold, particularly the 3,5-dinitrobenzoate scaffold, merits further investigation, because it has the potential to generate future antimycobacterial agents with improved activity.
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Affiliation(s)
- João P Pais
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Olha Antoniuk
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Raquel Freire
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - David Pires
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Center for Interdisciplinary Research in Health, Católica Medical School, Universidade Católica Portuguesa, Estrada Octávio Pato, 2635-631 Rio de Mouro, Portugal
| | - Emília Valente
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Elsa Anes
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Luis Constantino
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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Amado PM, Woodley C, Cristiano MLS, O’Neill PM. Recent Advances of DprE1 Inhibitors against Mycobacterium tuberculosis: Computational Analysis of Physicochemical and ADMET Properties. ACS OMEGA 2022; 7:40659-40681. [PMID: 36406587 PMCID: PMC9670723 DOI: 10.1021/acsomega.2c05307] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/21/2022] [Indexed: 05/14/2023]
Abstract
Decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1) is a critical flavoenzyme in Mycobacterium tuberculosis, catalyzing a vital step in the production of lipoarabinomannan and arabinogalactan, both of which are essential for cell wall biosynthesis. Due to its periplasmic localization, DprE1 is a susceptible target, and several compounds with diverse scaffolds have been discovered that inhibit this enzyme, covalently or noncovalently. We evaluated a total of ∼1519 DprE1 inhibitors disclosed in the literature from 2009 to April 2022 by performing an in-depth analysis of physicochemical descriptors and absorption, distribution, metabolism, excretion, and toxicity (ADMET), to gain new insights into these properties in DprE1 inhibitors. Several molecular properties that should facilitate the design and optimization of future DprE1 inhibitors are described, allowing for the development of improved analogues targeting M. tuberculosis.
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Affiliation(s)
- Patrícia
S. M. Amado
- Center
of Marine Sciences - CCMAR, University of
Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry and Pharmacy, FCT, University
of Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Christopher Woodley
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Maria L. S. Cristiano
- Center
of Marine Sciences - CCMAR, University of
Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry and Pharmacy, FCT, University
of Algarve, P-8005-039 Faro, Portugal
- Email
for M.L.S.C.:
| | - Paul M. O’Neill
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
- Email for P.M.O.:
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3,5-Dinitrobenzoate and 3,5-Dinitrobenzamide Derivatives: Mechanistic, Antifungal, and In Silico Studies. J CHEM-NY 2022. [DOI: 10.1155/2022/2336175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fungal infections, including those caused by Candida spp., are recognized in immunocompromised individuals for their high rates of morbidity and mortality. Microorganism resistance to conventional drugs compromises treatment effectiveness and yet also reveals the need to develop new drugs. In many compounds, nitro groups contribute to antimicrobial activity; thus, the inhibitory activity of a collection of twenty esters and amides (derived from 3,5-dinitrobenzoic acid) against Candida spp. was elucidated using microdilution methods to determine the Minimum Inhibitory Concentration (MIC) and Minimum Fungicide Concentration (MFC), as well as probable mechanisms of action. The structures of the synthesized compounds were characterized by FTIR spectroscopy, 1H-NMR, 13C NMR, and HRMS. Of the tested derivatives, ten presented fungicidal activity against at least one of the tested strains. Ethyl 3,5-dinitrobenzoate (2) exhibited the most potent antifungal activity against Candida albicans (MIC = 125 µg/mL; 0.52 mM), Candida krusei (MIC = 100 µg/mL; 4.16 mM), and Candida tropicalis (MIC = 500 µg/ml; 2.08 mM). The structure of the second most potent derivative (propyl 3,5-dinitrobenzoate (3) reveals that esters with short alkyl side chains exhibit better biological activity profiles. Compounds 2 and 3 presented a mechanism of action involving the fungal cell membrane. Though compound 2 modeling against C. albicans revealed a multitarget antifungal mechanism of action, involving various cellular processes, interference in the synthesis of ergosterol was observed. Our results demonstrate that certain ester derivatives containing aromatic ring nitro groups may be useful in the search for new antifungal drugs.
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Facile synthesis of C1-substituted β-carbolines as CDK4 inhibitors for the treatment of cancer. Bioorg Chem 2022; 121:105659. [DOI: 10.1016/j.bioorg.2022.105659] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/05/2022] [Accepted: 02/05/2022] [Indexed: 01/04/2023]
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Verma H, Choudhary S, Kumar M, Silakari O. In silico guided design of non-covalent inhibitors of DprE1: synthesis and biological evaluation. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:333-352. [PMID: 33784906 DOI: 10.1080/1062936x.2021.1900390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
DprE1 is a potential target of resistant tuberculosis (TB), especially multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. 2-benzoxazolinone is a closely related bioisostere of some scaffolds such as benzoxazoles, benzimidazole, benzothiazolinone, and benzothiazoles that have been previously explored against DprE1. Thus, a ligand-based quantitative pharmacophore model (AHRR.8) of DprE1 was developed and this pharmacophore model was utilized in activity profiling of some 2-benzoxazolinones from an in-house database using virtual screening. Obtained hits were subject to molecular docking, molecular dynamics (MD), and MM/GBSA calculations, which resulted in benzoyl-substituted derivatives of 2-benzoxazolinone showing strong interactions with the key amino acid residues in the active site of DprE1. Based on in silico results, the top five hits were duly synthesized and evaluated against the XDR-TB strain. This study is an initial effort to explore 2-benzoxazolinones against XDR-TB, which can be submitted further to lead optimization for refining the results.
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Affiliation(s)
- H Verma
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - S Choudhary
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - M Kumar
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - O Silakari
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
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Li L, Wang A, Wang B, Liu M, Lv K, Tao Z, Ma C, Ma X, Han B, Wang A, Lu Y. N-(2-Phenoxy)ethyl imidazo[1,2-a]pyridine-3-carboxamides containing various amine moieties: Design, synthesis and antitubercular activity. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.07.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Khaligh NG, Abbo H, Titinchi SJ, Johan MR. An Overview of Recent Advances in Biological and Pharmaceutical Developments of Fluoro-containing Drugs. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824666191213123930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
:
This review article provides a brief assessment of the biological and pharmaceutical
developments of fluorinated drugs. It also discusses possible impacts on the further
development of new fluoro-containing pharmaceuticals. Structural aspects of new
drug-candidates currently under development and their biological properties, therapeutic
potential and syntheses are critically evaluated
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Affiliation(s)
- Nader G. Khaligh
- Nanotechnology and Catalysis Research Center, Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hanna Abbo
- Department of Chemistry, College of Science, University of Basrah, Basrah, Iraq
| | - Salam J.J. Titinchi
- Department of Chemistry, University of the Western Cape, Cape Town, South Africa
| | - Mohd R. Johan
- Nanotechnology and Catalysis Research Center, Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
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