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Kassem AF, Sabt A, Korycka-Machala M, Shaldam MA, Kawka M, Dziadek B, Kuzioła M, Dziadek J, Batran RZ. New coumarin linked thiazole derivatives as antimycobacterial agents: Design, synthesis, enoyl acyl carrier protein reductase (InhA) inhibition and molecular modeling. Bioorg Chem 2024; 150:107511. [PMID: 38870705 DOI: 10.1016/j.bioorg.2024.107511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/15/2024]
Abstract
Tuberculosis is a global serious problem that imposes major health, economic and social challenges worldwide. The search for new antitubercular drugs is extremely important which could be achieved via inhibition of different druggable targets. Mycobacterium tuberculosis enoyl acyl carrier protein reductase (InhA) enzyme is essential for the survival of M. tuberculosis. In this investigation, a series of coumarin based thiazole derivatives was synthesized relying on a molecular hybridization approach and was assessed against thewild typeMtb H37Rv and its mutant strain (ΔkatG) via inhibiting InhA enzyme. Among the synthesized derivatives, compounds 2b, 3i and 3j were the most potent against wild type M. tuberculosis with MIC values ranging from 6 to 8 μg/ mL and displayed low cytotoxicity towards mouse fibroblasts at concentrations 8-13 times higher than the MIC values. The three hybrids could also inhibit the growth of ΔkatGmutant strain which is resistant to isoniazid (INH). Compounds 2b and 3j were able to inhibit the growth of mycobacteria inside human macrophages, indicating their ability to penetrate human professional phagocytes. The two derivatives significantly suppress mycobacterial biofilm formation by 10-15 %. The promising target compounds were also assessed for their inhibitory effect against InhA and showed potent effectiveness with IC50 values of 0.737 and 1.494 µM, respectively. Molecular docking studies revealed that the tested compounds occupied the active site of InhA in contact with the NAD+ molecule. The 4-phenylcoumarin aromatic system showed binding interactions within the hydrophobic pocket of the active site. Furthermore, H-bond formation and π -π stacking interactions were also recorded for the promising derivatives.
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Affiliation(s)
- Asmaa F Kassem
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Małgorzata Korycka-Machala
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | - Moataz A Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Malwina Kawka
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Bożena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Magdalena Kuzioła
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland.
| | - Rasha Z Batran
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt.
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2
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MacLelland V, Kravitz M, Gupta A. Therapeutic and diagnostic applications of antisense peptide nucleic acids. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102086. [PMID: 38204913 PMCID: PMC10777018 DOI: 10.1016/j.omtn.2023.102086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Peptide nucleic acids (PNAs) are synthetic nucleic acid analogs with a neutral N-(2-aminoethyl) glycine backbone. PNAs possess unique physicochemical characteristics such as increased resistance to enzymatic degradation, ionic strength and stability over a wide range of temperatures and pH, and low intrinsic electrostatic repulsion against complementary target oligonucleotides. PNA has been widely used as an antisense oligonucleotide (ASO). Despite the favorable characteristics of PNA, in comparison with other ASO technologies, the use of antisense PNA for novel therapeutics has lagged. This review provides a brief overview of PNA, its antisense mechanisms of action, delivery strategies, and highlights successful applications of PNA, focusing on anti-pathogenic, anti-neurodegenerative disease, anti-cancer, and diagnostic agents. For each application, several studies are discussed focusing on the different target sites of the PNA, design of different PNAs and the therapeutic outcome in different cell lines and animal models. Thereafter, persisting limitations slowing the successful integration of antisense PNA therapeutics are discussed in order to highlight actionable next steps in the development and optimization of PNA as an ASO.
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Affiliation(s)
- Victoria MacLelland
- Department of Pharmaceutical Sciences, University of Saint Joseph, West Hartford, CT 06117, USA
| | - Madeline Kravitz
- Department of Pharmaceutical Sciences, University of Saint Joseph, West Hartford, CT 06117, USA
| | - Anisha Gupta
- Department of Pharmaceutical Sciences, University of Saint Joseph, West Hartford, CT 06117, USA
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3
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Kuralt V, Frlan R. Navigating the Chemical Space of ENR Inhibitors: A Comprehensive Analysis. Antibiotics (Basel) 2024; 13:252. [PMID: 38534687 DOI: 10.3390/antibiotics13030252] [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: 01/31/2024] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Antimicrobial resistance is a global health threat that requires innovative strategies against drug-resistant bacteria. Our study focuses on enoyl-acyl carrier protein reductases (ENRs), in particular FabI, FabK, FabV, and InhA, as potential antimicrobial agents. Despite their promising potential, the lack of clinical approvals for inhibitors such as triclosan and isoniazid underscores the challenges in achieving preclinical success. In our study, we curated and analyzed a dataset of 1412 small molecules recognized as ENR inhibitors, investigating different structural variants. Using advanced cheminformatic tools, we mapped the physicochemical landscape and identified specific structural features as key determinants of bioactivity. Furthermore, we investigated whether the compounds conform to Lipinski rules, PAINS, and Brenk filters, which are crucial for the advancement of compounds in development pipelines. Furthermore, we investigated structural diversity using four different representations: Chemotype diversity, molecular similarity, t-SNE visualization, molecular complexity, and cluster analysis. By using advanced bioinformatics tools such as matched molecular pairs (MMP) analysis, machine learning, and SHAP analysis, we were able to improve our understanding of the activity cliques and the precise effects of the functional groups. In summary, this chemoinformatic investigation has unraveled the FAB inhibitors and provided insights into rational antimicrobial design, seamlessly integrating computation into the discovery of new antimicrobial agents.
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Affiliation(s)
- Vid Kuralt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Rok Frlan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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Amr K, Elissawy AM, Ibrahim N, Elnaggar MS, Fawzy IM, Singab ANB. Unveiling the Antimicrobial and Larvicidal Potential of Butyrolactones and Orsellinic Acid Derivatives from the Morus alba-derived Fungus Aspergillus terreus via Integrated In vitro and In silico Approaches. Chem Biodivers 2024; 21:e202301900. [PMID: 38282171 DOI: 10.1002/cbdv.202301900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 01/30/2024]
Abstract
The emergence of multi-drug-resistant microbial strains spurred the search for antimicrobial agents; as a result, two distinct approaches were combined: four in vitro studies and four corresponding molecular docking investigations. Antituberculosis, anti-methicillin-resistant Staphylococcus aureus (anti-MRSA), antifungal, and larvicidal activities of the crude extract, two fractions, and seven isolated compounds from Aspergillus terreus derived from Morus alba roots were explored. The isolated compounds (5 butyrolactones and 2 orsellinic acid derivatives) showed potent to moderate antitubercular activity with MIC values ranging from 1.95 to 62.5 μg/mL (compared to isoniazid, 0.24 μg/mL) and promising anti-MRSA potential with inhibition zone diameters ranging from 8 to 25 mm. Additionally, the in silico study proved that the isolated compounds bind to the two corresponding proteins' active sites with high to moderate -(C-Docker interaction energies) and stable interactions. The isolated compounds displayed antifungal activities against different fungal strains at diverse degrees of activity, among them compound (8"S,9")-dihydroxy-dihydrobutyrolactone I eliciting the best antifungal activity. Meanwhile, all isolated compounds, fractions, and the crude extract demonstrated extremely selective potent to moderate activity against Cryptococcus neoformans. The isolated five butyrolactone derivatives could develop potential mosquito larvicidal agents as a result of promising docking outcomes in the larval enzyme carboxylesterase.
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Affiliation(s)
- Khadiga Amr
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Organization of African Unity Street 1, 11566, Cairo, Egypt
| | - Ahmed M Elissawy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Organization of African Unity Street 1, 11566, Cairo, Egypt
- Center of Drug Discovery Research and Development, Ain-Shams University, Organization of African Unity Street 1, 11566, Cairo, Egypt
| | - Nehal Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Organization of African Unity Street 1, 11566, Cairo, Egypt
| | - Mohamed S Elnaggar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Organization of African Unity Street 1, 11566, Cairo, Egypt
| | - Iten M Fawzy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt, Cairo, 12311, Egypt
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Organization of African Unity Street 1, 11566, Cairo, Egypt
- Center of Drug Discovery Research and Development, Ain-Shams University, Organization of African Unity Street 1, 11566, Cairo, Egypt
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5
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Reddyrajula R, Etikyala U, Manga V, Kumar Dalimba U. Discovery of 1,2,3-triazole incorporated indole-piperazines as potent antitubercular agents: Design, synthesis, in vitro biological evaluation, molecular docking and ADME studies. Bioorg Med Chem 2024; 98:117562. [PMID: 38184947 DOI: 10.1016/j.bmc.2023.117562] [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: 10/19/2023] [Revised: 12/07/2023] [Accepted: 12/17/2023] [Indexed: 01/09/2024]
Abstract
In this report, a library consisting of three sets of indole-piperazine derivatives was designed through the molecular hybridization approach. In total, fifty new hybrid compounds (T1-T50) were synthesized and screened for antitubercular activity against Mycobacterium tuberculosis H37Rv strain (ATCC-27294). Five (T36, T43, T44, T48 and T49) among fifty compounds exhibited significant inhibitory potency with the MIC of 1.6 µg/mL, which is twofold more potent than the standard first-line TB drug Pyrazinamide and equipotent with Isoniazid. N-1,2,3-triazolyl indole-piperazine derivatives displayed improved inhibition activity as compared to the simple and N-benzyl indole-piperazine derivatives. In addition, the observed activity profile of indole-piperazines was similar to standard anti-TB drugs (isoniazid and pyrazinamide) against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa strains, demonstrating the compounds' selectivity towards the Mycobacterium tuberculosis H37Rv strain. All the active anti-TB compounds are proved to be non-toxic (with IC50 > 300 μg/mL) as verified through the toxicity evaluation against VERO cell lines. Additionally, molecular docking studies against two target enzymes (Inh A and CYP121) were performed to validate the activity profile of indole-piperazine derivatives. Further, in silico-ADME prediction and pharmacokinetic parameters indicated that these compounds have good oral bioavailability.
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Affiliation(s)
- Rajkumar Reddyrajula
- Central Research facility, National Institute of Technology Karnataka, Surathkal, Mangalore 575025, India
| | - Umadevi Etikyala
- Medicinal Chemistry Laboratory, Department of Chemistry, Osmania University, Hyderabad 500076, India
| | - Vijjulatha Manga
- Medicinal Chemistry Laboratory, Department of Chemistry, Osmania University, Hyderabad 500076, India
| | - Udaya Kumar Dalimba
- Organic and Materials Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Surathkal, Mangalore 575025, India.
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Zhang Q, Han J, Zhu Y, Yu F, Hu X, Tong HHY, Liu H. Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays. J Comput Aided Mol Des 2023; 37:695-706. [PMID: 37642861 DOI: 10.1007/s10822-023-00530-4] [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: 05/09/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Multidrug-resistant tuberculosis (MDR-TB) continues to spread worldwide and remains one of the leading causes of death among infectious diseases. The enoyl-acyl carrier protein reductase (InhA) belongs to FAS-II family and is essential for the formation of the Mycobacterium tuberculosis cell wall. Recent years, InhA direct inhibitors have been extensively studied to overcome MDR-TB. However, there are still no inhibitors that have entered clinical research. Here, the ensemble docking-based virtual screening along with biological assay were used to identify potent InhA direct inhibitors from Chembridge, Chemdiv, and Specs. Ultimately, 34 compounds were purchased and first assayed for the binding affinity, of which four compounds can bind InhA well with KD values ranging from 48.4 to 56.2 µM. Among them, compound 9,222,034 has the best inhibitory activity against InhA enzyme with an IC50 value of 18.05 µM. In addition, the molecular dynamic simulation and binding free energy calculation indicate that the identified compounds bind to InhA with "extended" conformation. Residue energy decomposition shows that residues such as Tyr158, Met161, and Met191 have higher energy contributions in the binding of compounds. By analyzing the binding modes, we found that these compounds can bind to a hydrophobic sub-pocket formed by residues Tyr158, Phe149, Ile215, Leu218, etc., resulting in extensive van der Waals interactions. In summary, this study proposed an efficient strategy for discovering InhA direct inhibitors through ensemble docking-based virtual screening, and finally identified four active compounds with new skeletons, which can provide valuable information for the discovery and optimization of InhA direct inhibitors.
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Affiliation(s)
- Qianqian Zhang
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Jianting Han
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Yongchang Zhu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Xiaopeng Hu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Henry H Y Tong
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China.
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7
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Medha, Joshi H, Sharma S, Sharma M. Elucidating the function of hypothetical PE_PGRS45 protein of Mycobacterium tuberculosis as an oxido-reductase: a potential target for drug repurposing for the treatment of tuberculosis. J Biomol Struct Dyn 2023; 41:10009-10025. [PMID: 36448553 DOI: 10.1080/07391102.2022.2151514] [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: 04/06/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
Mycobacterium tuberculosis (Mtb) encodes a total of 67 PE_PGRS proteins and definite functions of many of them are still unknown. This study reports PE_PGRS45 (Rv2615c) protein from Mtb as NADPH dependent oxido-reductase having substrate specificity for fatty acyl Coenzyme A. Computational studies predicted PE_PGRS45 to be an integral membrane protein of Mtb. Expression of PE_PGRS45 in non-pathogenic Mycobacterium smegmatis, which does not possess PE_PGRS genes, confirmed its membrane localization. This protein was observed to have NADPH binding motif. Experimental validation confirmed its NADPH dependent oxido-reductase activity (Km value = 34.85 ± 9.478 μM, Vmax = 96.77 ± 7.184 nmol/min/mg of protein). Therefore, its potential to be targeted by first line anti-tubercular drug Isoniazid (INH) was investigated. INH was predicted to bind within the active site of PE_PGRS45 protein and experiments validated its inhibitory effect on the oxido-reductase activity of PE_PGRS45 with IC50/Ki values of 5.66 μM. Mtb is resistant to first line drugs including INH. Therefore, to address the problem of drug resistant TB, docking and Molecular Dynamics (MD) simulation studies between PE_PGRS45 and three drugs (Entacapone, Tolcapone and Verapamil) which are being used in Parkinson's and hypertension treatment were performed. PE_PGRS45 bound the three drugs with similar or better affinity in comparison to INH. Additionally, INH and these drugs bound within the same active site of PE_PGRS45. This study discovered Mtb's PE_PGRS45 protein to have an oxido-reductase activity and could be targeted by drugs that can be repurposed for TB treatment. Furthermore, in-vitro and in-vivo validation will aid in drug-resistant TB treatment. HIGHLIGHTSIn-silico and in-vitro studies of hypothetical protein PE_PGRS45 (Rv2615c) of Mycobacterium tuberculosis (Mtb) reveals it to be an integral membrane proteinPE_PGRS45 protein has substrate specificity for fatty acyl Coenzyme A (fatty acyl CoA) and possess NADPH dependent oxido-reductase activityDocking and simulation studies revealed that first line anti-tubercular drug Isoniazid (INH) and other drugs with anti-TB property have strong affinity for PE_PGRS45 proteinOxido-reductase activity of PE_PGRS45 protein is inhibited by INHPE_PGRS45 protein could be targeted by drugs that can be repurposed for TB treatmentCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Medha
- DSKC Bio Discovery Lab and Department of Zoology, Miranda House, University of Delhi, New Delhi, India
| | - Hemant Joshi
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Sadhna Sharma
- DSKC Bio Discovery Lab and Department of Zoology, Miranda House, University of Delhi, New Delhi, India
| | - Monika Sharma
- DSKC Bio Discovery Lab and Department of Zoology, Miranda House, University of Delhi, New Delhi, India
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Khalifa A, Khalil A, Abdel-Aziz MM, Albohy A, Mohamady S. Isatin-pyrimidine hybrid derivatives as enoyl acyl carrier protein reductase (InhA) inhibitors against Mycobacterium tuberculosis. Bioorg Chem 2023; 138:106591. [PMID: 37201321 DOI: 10.1016/j.bioorg.2023.106591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/20/2023] [Accepted: 05/02/2023] [Indexed: 05/20/2023]
Abstract
Tuberculosis is a worldwide problem that impose a burden on the economy due to continuous development of resistant strains. The development of new antitubercular drugs is a need and can be achieved through inhibition of druggable targets. Mycobacterium tuberculosis enoyl acyl carrier protein (ACP) reductase (InhA) is an important enzyme for Mycobacterium tuberculosis survival. In this study, we report the synthesis of isatin derivatives that could treat TB through inhibition of this enzyme. Compound 4l showed IC50 value (0.6 ± 0.94 µM) similar to isoniazid but is also effective against MDR and XDR Mycobacterium tuberculosis strains (MIC of 0.48 and 3.9 µg/mL, respectively). Molecular docking studies suggest that this compound binds through the use of relatively unexplored hydrophobic pocket in the active site. Molecular dynamics was used to investigate and support the stability of 4l complex with the target enzyme. This study paves the way for the design and synthesis of novel antitubercular drugs.
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Affiliation(s)
- Abdalrahman Khalifa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Amira Khalil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt
| | - Marwa M Abdel-Aziz
- The Regional Center for Mycology & Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Amgad Albohy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt.
| | - Samy Mohamady
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt.
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Modi P, Patel S, Chhabria M. Discovery of newer pyrazole derivatives with potential anti-tubercular activity via 3D-QSAR based pharmacophore modelling, virtual screening, molecular docking and molecular dynamics simulation studies. Mol Divers 2023; 27:1547-1566. [PMID: 35969333 DOI: 10.1007/s11030-022-10511-8] [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: 05/10/2022] [Accepted: 07/30/2022] [Indexed: 11/28/2022]
Abstract
Tuberculosis is one of the leading causes of death of at least one million people annually. The deadliest infectious disease has caused more than 120 million deaths in humans since 1882. The cell wall structure of Mycobacterium tuberculosis is important for survival in the host environment. InhA is the foremost target for the development of novel anti-tubercular agents. Therefore, we report pharmacophore-based virtual screening (ZINC and ASINEX databases) and molecular docking study (PDB Code: 4TZK) to identify and design potent inhibitors targeting to InhA. A five-point pharmacophore model AADHR_1 (with R2 = 0.97 and Q2 = 0.77) was developed by using 47 compounds with its reported MIC values. Further, to identify and design potent hit molecules based on lead identification and modification, generated hypothesis employed for virtual screening using ZINC and ASINEX databases. Predicted pyrazole derivatives further gauged for drug likeliness and docked against enoyl acyl carrier protein reductase to categorize the essential amino acid interactions to the active site of the enzyme. Structure elucidation of these synthesized compounds was carried out using IR, MS, 1H-NMR and 13C-NMR spectroscopy. Amongst all the synthesized compounds, some of the compounds 5a, 5c, 5d and 5e were found to be potent with their MIC ranging from 2.23 to 4.61 µM. Based on preliminary anti-tubercular activity synthesized potent molecules were further assessed for MDR-TB, XDR-TB and cytotoxic study.
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Affiliation(s)
- Palmi Modi
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India
- L. J. Institute of Pharmacy, L J University, Ahmedabad, Gujarat, 382 210, India
| | - Shivani Patel
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India
- Division of Biological and Life Sciences, Ahmedabad University, Ahmedabad, Gujarat, 380009, India
| | - Mahesh Chhabria
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India.
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Sulistyowaty MI, Putra GS, Ekowati J, Widiandani T, Matsunami K. <em>In silico</em> study of phytochemicals contained in brucea javanica in inhibiting the InhA enzyme as antituberculosis. J Public Health Afr 2023. [PMID: 37492543 PMCID: PMC10365667 DOI: 10.4081/jphia.2023.2518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Background: Currently Mycobacterium tuberculosis is found to be resistant to the treatment of tuberculosis with rifampin and isoniazid (INH) and often stated as multi-drug resistance (MDR). Knowledge and determination of biological properties of plant extracts is a source of drug candidates in various health fields. Therefore, natural products are important in the discovery of new drugs, especially in disease therapy, particularly for tropical dis- eases, tuberculosis. Brucea javanica, known as Buah Makasar, is found in many Asian countries including Indonesia. This plant fruit has a very bitter taste so it cannot be directly consumed and is often used as a traditional medicine to prevent some diseases, especially malaria. There has been no research on the effectiveness of Buah Makasar in tuberculosis.
Objective: This study aims to identify compounds contained in Brucea javanica, namely bruceines, bruceosides and yadanzio-sides in inhibiting the InhA enzyme found in the wall of Mycobacterium tuberculosis.
Methods: This in-silico study is using Molegro Virtual Docker (MVD) Ver. 5.5. We compared it to the native ligand, namely N-(4- Methylbenzoyl)-4-Benzylpiperidine (code: 4PI) and the reference drug standard, INH.
Results: In-silico results show that yadanziosides found in Brucea javanica have the potential to inhibit the InhA enzyme. Bruceoside F (-190.76 Kcal/mol) has the lowest MolDock score among the 27 other compounds. It is also having lower MolDock score than the native ligand 4PI (-120.61 Kcal/mol) and INH (- 54.44 Kcal/mol).
Conclusions: Brucea javanica can be considered as source of drug development for againts tuberculosis.
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Kuppuswamy U, Rajan RK, Kumar A, Ramanathan M. In-silico and in-vitro analysis of novel substituted benzimidazolyl derivatives for antimycobacterial potentials targeting enoyl acyl carrier protein reductase (InhA). FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2022. [DOI: 10.1186/s43094-022-00449-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abstract
Background
The emergence of mutated drug-resistant strains of Mycobacterium tuberculosis has reinvigorated the development of effective chemotherapy for MDR-TB (multidrug-resistant resistance tuberculosis). Enoyl acyl carrier protein reductase (InhA) involved in the mycobacterial fatty acid elongation system has been chosen as a potential target.
Result
All of the lead compounds had a definite Rf value and a sharp melting point, confirming that no tautomeric forms exist and that the keto (CO) group is apparent in the IR and 13C NMR spectrum data. Structure-based drug design revealed the presence of amino acid residues like TYR 158, ILE 194, and PHE 149 which are crucial for InhA inhibitory activity and were considered favorable interactions. Among all, compounds 4, 5a, and 5c showed better docking and binding free energy owing to favorable interactions. Interestingly, there was a strong correlation between the binding free energy and the antimycobacterial susceptibility assay, where compounds 4, 5a, and 5c had greater activity. All the lead compounds also had good oral absorption and gut permeability. The presence of a carboxylic linker (–COOH–) between benzimidazole and the rest of the structure of the lead compounds was found to be crucial for activity as the oxygen atom and hydroxyl group of the linker formed most of the favorable interactions. The presence of chlorophenyl showed a favorable effect on InhA inhibition which might be owing to its hydrophobic interaction with PHE 149.
Conclusion
Three of the seven lead compounds synthesized had an IC value of approximately 0.5 μg/ml in the in-vitro Alamar blue assay against the Mycobacterium tuberculosis H37Rv strain, which is roughly comparable to the standard marketed drug, Isoniazid (INH). This manifestation of promising activity that resulted from combining in-silico and wet lab experimentation could be a great starting point for developing potent antimycobacterial agents to combat multidrug-resistant tuberculosis.
Graphical abstract
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12
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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13
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Xu X, Dong B, Peng L, Gao C, He Z, Wang C, Zeng J. Anti-tuberculosis drug development via targeting the cell envelope of Mycobacterium tuberculosis. Front Microbiol 2022; 13:1056608. [PMID: 36620019 PMCID: PMC9810820 DOI: 10.3389/fmicb.2022.1056608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis possesses a dynamic cell envelope, which consists of a peptidoglycan layer, a mycolic acid layer, and an arabinogalactan polysaccharide. This envelope possesses a highly complex and unique structure representing a barrier that protects and assists the growth of M. tuberculosis and allows its adaptation to the host. It regulates the immune response of the host cells, causing their damage. Therefore, the cell envelope of M. tuberculosis is an attractive target for vaccine and drug development. The emergence of multidrug-resistant as well as extensively drug resistant tuberculosis and co-infection with HIV prevented an effective control of this disease. Thus, the discovery and development of new drugs is a major keystone for TB treatment and control. This review mainly summarizes the development of drug enzymes involved in the biosynthesis of the cell wall in M. tuberculosis, and other potential drug targets in this pathway, to provide more effective strategies for the development of new drugs.
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Affiliation(s)
- Xinyue Xu
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Baoyu Dong
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Lijun Peng
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chao Gao
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.,Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiqun He
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chuan Wang
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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14
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Novel 1,2,3-Triazole-Based Benzothiazole Derivatives: Efficient Synthesis, DFT, Molecular Docking, and ADMET Studies. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238555. [PMID: 36500647 PMCID: PMC9740823 DOI: 10.3390/molecules27238555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
A new series of 1,2,3-triazole derivatives 5a-f based on benzothiazole were synthesized by the 1,3-dipolar cycloaddition reaction of S-propargyl mercaptobenzothiazole and α-halo ester/amide in moderate to good yields (47-75%). The structure of all products was characterized by 1H NMR, 13C NMR, and CHN elemental data. This protocol is easy and green and proceeds under mild and green reaction conditions with available starting materials. The structural and electronic analysis and 1H and 13C chemical shifts of the characterized structure of 5e were also calculated by applying the B3LYP/6-31 + G(d, p) level of density functional theory (DFT) method. In the final section, all the synthesized compounds were evaluated for their anti-inflammatory activity by biochemical COX-2 inhibition, antifungal inhibition with CYP51, anti-tuberculosis target protein ENR, DPRE1, pks13, and Thymidylate kinase by molecular docking studies. The ADMET analysis of the molecules 5a-f revealed that 5d and 5a are the most-promising drug-like molecules out of the six synthesized molecules.
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15
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Binding Thermodynamics and Dissociation Kinetics Analysis Uncover the Key Structural Motifs of Phenoxyphenol Derivatives as the Direct InhA Inhibitors and the Hotspot Residues of InhA. Int J Mol Sci 2022; 23:ijms231710102. [PMID: 36077494 PMCID: PMC9456180 DOI: 10.3390/ijms231710102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Given the current epidemic of multidrug-resistant tuberculosis, there is an urgent need to develop new drugs to combat drug-resistant tuberculosis. Direct inhibitors of the InhA target do not require activation and thus can overcome drug resistance caused by mutations in drug-activating enzymes. In this work, the binding thermodynamic and kinetic information of InhA to its direct inhibitors, phenoxyphenol derivatives, were explored through multiple computer-aided drug design (CADD) strategies. The results show that the van der Waals interactions were the main driving force for protein–ligand binding, among which hydrophobic residues such as Tyr158, Phe149, Met199 and Ile202 have high energy contribution. The AHRR pharmacophore model generated by multiple ligands demonstrated that phenoxyphenol derivatives inhibitors can form pi–pi stacking and hydrophobic interactions with InhA target. In addition, the order of residence time predicted by random acceleration molecular dynamics was consistent with the experimental values. The intermediate states of these inhibitors could form hydrogen bonds and van der Waals interactions with surrounding residues during dissociation. Overall, the binding and dissociation mechanisms at the atomic level obtained in this work can provide important theoretical guidance for the development of InhA direct inhibitors with higher activity and proper residence time.
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16
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Dutta A, Trivedi P, Gehlot PS, Gogoi D, Hazarika R, Chetia P, Kumar A, Chaliha AK, Chaturvedi V, Sarma D. Design and Synthesis of Quinazolinone-Triazole Hybrids as Potent Anti-Tubercular Agents. ACS APPLIED BIO MATERIALS 2022; 5:4413-4424. [PMID: 36053225 DOI: 10.1021/acsabm.2c00562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A straightforward and convenient methodology has been developed for the reaction of 2-aminobenzamide and carbonyls affording 2,3-dihydroquinazolin-4(1H)-ones using aqueous solution of [C12Py][FeCl3Br]. The developed methodology was applied for the synthesis of 25 quinazolinone-triazole hybrids followed by evaluation of their in vitro anti-tubercular (TB) activity. The results revealed that 8 quinazolinone-triazole hybrids displayed promising activity having MIC values of 0.78-12.5 μg/mL. The compound 3if with MIC 0.78 μg/mL was found to be the lead nominee among the series, better than Ethambutol, a first line anti-TB drug and comparable with Rifampicin. The active compounds with MIC values ≤ 6.25 μg/mL were subjected to in vitro cytotoxicity and found nontoxic. In drug-drug interaction, compounds 3ia and 3ii interacted synergistically with all the three anti-TB drugs, INH, RFM, and EMB. Other 3 compounds interacted either in synergistic or additive manners. Important information on the binding interaction of the target compounds with the active sites of 1DQY Antigen 85C from Mycobacterium tuberculosis and Enoyl acyl carrier protein reductase (InhA) enzymes was obtained from molecular docking studies. Screening of the drug-likeness properties and bioactivity score indicates that synthesized molecules could be projected as potential drug candidates. Based on the current study, quinazolinone-triazole hybrids framework can be useful in drug development for TB.
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Affiliation(s)
- Apurba Dutta
- Department of Chemistry, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Priyanka Trivedi
- Biochemistry Division, Central Drug Research Institute, CSIR, Lucknow 226001, India
| | - Praveen Singh Gehlot
- AcSIR, Salt and Marine Chemicals Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Dipshikha Gogoi
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Roktopol Hazarika
- Department of Chemistry, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Pankaj Chetia
- Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Arvind Kumar
- AcSIR, Salt and Marine Chemicals Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Amrita Kashyap Chaliha
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Vinita Chaturvedi
- Biochemistry Division, Central Drug Research Institute, CSIR, Lucknow 226001, India
| | - Diganta Sarma
- Department of Chemistry, Dibrugarh University, Dibrugarh, Assam 786004, India
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17
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Dhivya LS, Sarvesh S, S AS. Inhibition of Mycobacterium tuberculosis InhA (Enoyl-acyl carrier protein reductase) by synthetic Chalcones: a molecular modelling analysis and in-vitro evidence. J Biomol Struct Dyn 2022:1-19. [PMID: 35751128 DOI: 10.1080/07391102.2022.2086922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Tuberculosis (TB) is a serious infectious disease caused by the bacillus Mycobacterium tuberculosis (Mtb). The World Health Organization (WHO) estimates that 1.8 million people die each year from TB, with 10 million new cases being registered each year. In this study, 50 Chalcones were developed, five of which were synthesized, and their inhibitory effects against Mtb were studied. The discovery of new powerful inhibitors with IC50 values in the sub-micro molar range resulted from the development of structure-activity relationships (SAR). The goal of the molecular modelling studies was to uncover the most important structural criteria underpinning the binding affinity and selectivity of this class of inhibitors as possible anti-TB drugs. Because of their great efficacy and selectivity, our developed nitro and benzyloxy substituted Chalcones compounds appear to be promising anti-TB therapies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- L S Dhivya
- Dr. APJ Kalam Research Lab, Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Kancheepuram, Tamil Nadu, India
| | - Sabarathinam Sarvesh
- Drug Testing Laboratory, Interdisciplinary Institute of Indian System of Medicine (IIISM), SRM Institute of Science and Technology, Kancheepuram, Tamil Nadu, India
| | - Ankul Singh S
- Department of Pharmacology, SRM College of Pharmacy, SRM Institute of Science and Technology, Kancheepuram, Tamil Nadu, India
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18
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Hebade MJ, Dhumal ST, Kamble SS, Deshmukh TR, Khedkar VM, Hese SV, Gacche RN, Dawane BS. DTP/SiO 2 Assisted Synthesis of New Benzimidazole-Thiazole Conjugates Targeting Antitubercular and Antioxidant Activities. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2056210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Madhav J. Hebade
- Department of Chemistry, Badrinarayan Barwale Mahavidyalaya, Jalna, Maharashtra, India
| | - Sambhaji T. Dhumal
- Department of Chemistry, Ramkrishna Paramhansa Mahavidyalaya, Osmanabad, Maharashtra, India
| | - Sonali S. Kamble
- Department of Biochemistry, Gramin Science (Vocational) College, Nanded, Maharashtra, India
| | - Tejshri R. Deshmukh
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Vijay M. Khedkar
- Department of Pharmaceutical Chemistry, School of Pharmacy, Vishwakarma University, Pune, Maharashtra, India
| | - Shrikant V. Hese
- Department of Chemistry, D. D. Bhoyar College of Arts and Science Mouda, Nagpur, India
| | - Rajesh N. Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Bhaskar S. Dawane
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, India
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19
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Crystal structures, DFT calculations and Hirshfeld surface analysis of two (E)-3-(aryl)-1-(naphthalen-1-yl)prop-2-en-1-one chalcone derivatives, potential Mycobacterium tuberculosis Enoyl ACP reductase (InhA) inhibitors and optical materials: conformational differences within the prop-2-en-1-one unit. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Girase PS, Dhawan S, Kumar V, Shinde SR, Palkar MB, Karpoormath R. An appraisal of anti-mycobacterial activity with structure-activity relationship of piperazine and its analogues: A review. Eur J Med Chem 2020; 210:112967. [PMID: 33190957 DOI: 10.1016/j.ejmech.2020.112967] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023]
Abstract
Piperazine, is privileged six membered nitrogen containing heterocyclic ring also known as 1,4-Diazacyclohexane. Consequently, piperazine is a versatile medicinally important scaffold and is an essential core in numerous marketed drugs with diverse pharmacological activities. In recent years several potent molecules containing piperazine as an essential subunit of the structural frame have been reported, especially against Mycobacterium tuberculosis (MTB). Remarkably, a good number of these reported molecules also displayed potential activity against multidrug-resistant (MDR), and extremely drug-resistant (XDR) strains of MTB. In this review, we have made a concerted effort to retrace anti-mycobacterial compounds for the past five decades (1971-2019) specifically where piperazine has been used as a vital building block. This review will benefit medicinal chemists as it elaborates on the design, rationale and structure-activity relationship (SAR) of the reported potent piperazine based anti-TB molecules, which in turn will assist them in addressing the gaps, exploiting the reported strategies and developing safer, selective, and cost-effective anti-mycobacterial agents.
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Affiliation(s)
- Pankaj S Girase
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Sanjeev Dhawan
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Vishal Kumar
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Suraj R Shinde
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Mahesh B Palkar
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa; Department of Pharmaceutical Chemistry, K.L.E. College of Pharmacy (Constituent Unit of KAHER), Vidyanagar, Hubballi, 580031, Karnataka, India
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa.
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21
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Armstrong T, Lamont M, Lanne A, Alderwick LJ, Thomas NR. Inhibition of Mycobacterium tuberculosis InhA: Design, synthesis and evaluation of new di-triclosan derivatives. Bioorg Med Chem 2020; 28:115744. [PMID: 33007556 DOI: 10.1016/j.bmc.2020.115744] [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: 07/10/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 11/25/2022]
Abstract
Multi-drug resistant tuberculosis (MDR-TB) represents a growing problem for global healthcare systems. In addition to 1.3 million deaths in 2018, the World Health Organisation reported 484,000 new cases of MDR-TB. Isoniazid is a key anti-TB drug that inhibits InhA, a crucial enzyme in the cell wall biosynthesis pathway and identical in Mycobacterium tuberculosis and M. bovis. Isoniazid is a pro-drug which requires activation by the enzyme KatG, mutations in KatG prevent activation and confer INH-resistance. 'Direct inhibitors' of InhA are attractive as they would circumvent the main clinically observed resistance mechanisms. A library of new 1,5-triazoles, designed to mimic the structures of both triclosan molecules uniquely bound to InhA have been synthesised. The inhibitory activity of these compounds was evaluated using isolated enzyme assays with 2 (5-chloro-2-(4-(5-(((4-(4-chloro-2-hydroxyphenoxy)benzyl)oxy)methyl)-1H-1,2,3-triazol-1-yl)phenoxy)phenol) exhibiting an IC50 of 5.6 µM. Whole-cell evaluation was also performed, with 11 (5-chloro-2-(4-(5-(((4-(cyclopropylmethoxy)benzyl)oxy)methyl)-1H-1,2,3-triazol-1-yl)phenoxy)phenol) showing the greatest potency, with an MIC99 of 12.9 µM against M. bovis.
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Affiliation(s)
- Tom Armstrong
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Malcolm Lamont
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Alice Lanne
- Institute of Microbiology and Infection, School of Bioscience, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Luke J Alderwick
- Institute of Microbiology and Infection, School of Bioscience, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Neil R Thomas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.
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22
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Ghiano DG, Recio-Balsells A, Bortolotti A, Defelipe LA, Turjanski A, Morbidoni HR, Labadie GR. New one-pot synthesis of anti-tuberculosis compounds inspired on isoniazid. Eur J Med Chem 2020; 208:112699. [PMID: 32927391 DOI: 10.1016/j.ejmech.2020.112699] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/22/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022]
Abstract
A library of thirty N-substituted tosyl N'-acryl-hydrazones was prepared with p-toluenesulfonyl hydrazide, methyl propiolate and different aldehydes in a one-pot synthesis via an aza-Michael reaction. The scope of the reaction was studied, including aliphatic, isoprenylic, aromatic and carbocyclic aldehydes. The prepared collection was tested against Mycobacterium tuberculosis H37Rv. Nine analogs of the collection showed Minimum Inhibitory Concentration ≤10 μM, of which the most active members (MIC of 1.25 μM) were exclusively E isomers. In order to validate the mechanism of action of the most active acrylates, we tested their activity on a M. tuberculosis InhA over-expressing strain obtaining MIC that consistently doubled those obtained on the wild type strain. Additionally, the binding mode of those analogs on M. tuberculosis InhA was investigated by docking simulations. The results displayed a hydrogen bond interaction between the sulfonamide and Ile194 and the carbonyl of the methyl ester with Tyr 158 (both critical residues in the interaction with the fatty acyl chain substrate), where the main differences on the binding mode relays on the hydrophobicity of the nitrogen substituent. Additionally, chemoinformatic analysis was performed to evaluate in silico possible cytotoxicity risk and ADME-Tox profile. Based on their simple preparation and interesting antimycobacterial activity profile, the newly prepared aza-acrylates are promising candidates for antitubercular drug development.
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Affiliation(s)
- Diego G Ghiano
- Instituto de Química Rosario, UNR, CONICET, Suipacha 531, S2002LRK, Rosario, Argentina
| | | | - Ana Bortolotti
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Santa Fe 3100, S2002KTR, Rosario, Argentina
| | - Lucas A Defelipe
- IQUIBICEN-CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Adrián Turjanski
- IQUIBICEN-CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Héctor R Morbidoni
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Santa Fe 3100, S2002KTR, Rosario, Argentina; Consejo de Investigaciones Científicas, Universidad Nacional de Rosario, Argentina
| | - Guillermo R Labadie
- Instituto de Química Rosario, UNR, CONICET, Suipacha 531, S2002LRK, Rosario, Argentina; Departamento de Química Orgánica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina.
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23
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Ramesh D, Joji A, Vijayakumar BG, Sethumadhavan A, Mani M, Kannan T. Indole chalcones: Design, synthesis, in vitro and in silico evaluation against Mycobacterium tuberculosis. Eur J Med Chem 2020; 198:112358. [DOI: 10.1016/j.ejmech.2020.112358] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/04/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022]
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24
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Faïon L, Djaout K, Frita R, Pintiala C, Cantrelle FX, Moune M, Vandeputte A, Bourbiaux K, Piveteau C, Herledan A, Biela A, Leroux F, Kremer L, Blaise M, Tanina A, Wintjens R, Hanoulle X, Déprez B, Willand N, Baulard AR, Flipo M. Discovery of the first Mycobacterium tuberculosis MabA (FabG1) inhibitors through a fragment-based screening. Eur J Med Chem 2020; 200:112440. [PMID: 32505086 DOI: 10.1016/j.ejmech.2020.112440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis (M.tb), the etiologic agent of tuberculosis, remains the leading cause of death from a single infectious agent worldwide. The emergence of drug-resistant M.tb strains stresses the need for drugs acting on new targets. Mycolic acids are very long chain fatty acids playing an essential role in the architecture and permeability of the mycobacterial cell wall. Their biosynthesis involves two fatty acid synthase (FAS) systems. Among the four enzymes (MabA, HadAB/BC, InhA and KasA/B) of the FAS-II cycle, MabA (FabG1) remains the only one for which specific inhibitors have not been reported yet. The development of a new LC-MS/MS based enzymatic assay allowed the screening of a 1280 fragment-library and led to the discovery of the first small molecules that inhibit MabA activity. A fragment from the anthranilic acid series was optimized into more potent inhibitors and their binding to MabA was confirmed by 19F ligand-observed NMR experiments.
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Affiliation(s)
- Léo Faïon
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Kamel Djaout
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Rosangela Frita
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Catalin Pintiala
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Francois-Xavier Cantrelle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France; CNRS, ERL9002 - Integrative Structural Biology, F-59000, Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Alexandre Vandeputte
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Kevin Bourbiaux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Alexandre Biela
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293, Montpellier, France; INSERM, Institut de Recherche en Infectiologie de Montpellier, Montpellier, France
| | - Mickael Blaise
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293, Montpellier, France
| | - Abdalkarim Tanina
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire (CP206/04), Département RD3, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - René Wintjens
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire (CP206/04), Département RD3, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Xavier Hanoulle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France; CNRS, ERL9002 - Integrative Structural Biology, F-59000, Lille, France
| | - Benoit Déprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.
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Kienle M, Eisenring P, Stoessel B, Horlacher OP, Hasler S, van Colen G, Hartkoorn RC, Vocat A, Cole ST, Altmann KH. Synthesis and Structure–Activity Relationship Studies of C2-Modified Analogs of the Antimycobacterial Natural Product Pyridomycin. J Med Chem 2020; 63:1105-1131. [DOI: 10.1021/acs.jmedchem.9b01457] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Maryline Kienle
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Patrick Eisenring
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Barbara Stoessel
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Oliver P. Horlacher
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Samuel Hasler
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Gwénaëlle van Colen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Ruben C. Hartkoorn
- Global Health Institute, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anthony Vocat
- Global Health Institute, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Stewart T. Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
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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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A platform for target prediction of phenotypic screening hit molecules. J Mol Graph Model 2019; 95:107485. [PMID: 31836397 PMCID: PMC6983931 DOI: 10.1016/j.jmgm.2019.107485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 09/25/2019] [Accepted: 10/21/2019] [Indexed: 01/09/2023]
Abstract
Many drug discovery programmes, particularly for infectious diseases, are conducted phenotypically. Identifying the targets of phenotypic screening hits experimentally can be complex, time-consuming, and expensive. However, it would be valuable to know what the molecular target(s) is, as knowledge of the binding pose of the hit molecule in the binding site can facilitate the compound optimisation. Furthermore, knowing the target would allow de-prioritisation of less attractive chemical series or molecular targets. To generate target-hypotheses for phenotypic active compounds, an in silico platform was developed that utilises both ligand and protein-structure information to generate a ranked set of predicted molecular targets. As a result of the web-based workflow the user obtains a set of 3D structures of the predicted targets with the active molecule bound. The platform was exemplified using Mycobacterium tuberculosis, the causative organism of tuberculosis. In a test that we performed, the platform was able to predict the targets of 60% of compounds investigated, where there was some similarity to a ligand in the protein database. An algorithm to predict the molecular target(s) of phenotypic hits against TB. Uses information based on the ligand and protein structure. Allow visualisation of proposed binding pose. Web interface developed.
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Kouman KC, Keita M, Kre N’Guessan R, Owono Owono LC, Megnassan E, Frecer V, Miertus S. Structure-Based Design and in Silico Screening of Virtual Combinatorial Library of Benzamides Inhibiting 2-trans Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis with Favorable Predicted Pharmacokinetic Profiles. Int J Mol Sci 2019; 20:ijms20194730. [PMID: 31554227 PMCID: PMC6802012 DOI: 10.3390/ijms20194730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 01/24/2023] Open
Abstract
Background: During the previous decade a new class of benzamide-based inhibitors of 2-trans enoyl-acyl carrier protein reductase (InhA) of Mycobacterium tuberculosis (Mt) with unusual binding mode have emerged. Here we report in silico design and evaluation of novel benzamide InhA-Mt inhibitors with favorable predicted pharmacokinetic profiles. Methods: By using in situ modifications of the crystal structure of N-benzyl-4-((heteroaryl)methyl) benzamide (BHMB)-InhA complex (PDB entry 4QXM), 3D models of InhA-BHMBx complexes were prepared for a training set of 19 BHMBs with experimentally determined inhibitory potencies (half-maximal inhibitory concentrations IC50exp). In the search for active conformation of the BHMB1-19, linear QSAR model was prepared, which correlated computed gas phase enthalpies of formation (∆∆HMM) of InhA-BHMBx complexes with the IC50exp. Further, taking into account the solvent effect and entropy changes upon ligand, binding resulted in a superior QSAR model correlating computed complexation Gibbs free energies (∆∆Gcom). The successive pharmacophore model (PH4) generated from the active conformations of BHMBs served as a virtual screening tool of novel analogs included in a virtual combinatorial library (VCL) of compounds containing benzamide scaffolds. The VCL filtered by Lipinski’s rule-of-five was screened by the PH4 model to identify new BHMB analogs. Results: Gas phase QSAR model: −log10(IC50exp) = pIC50exp = −0.2465 × ∆∆HMM + 7.95503, R2 = 0.94; superior aqueous phase QSAR model: pIC50exp = −0.2370 × ∆∆Gcom + 7.8783, R2 = 0.97 and PH4 pharmacophore model: pIC50exp = 1.0013 × pIC50exp − 0.0085, R2 = 0.95. The VCL of more than 114 thousand BHMBs was filtered down to 73,565 analogs Lipinski’s rule. The five-point PH4 screening retained 90 new and potent BHMBs with predicted inhibitory potencies IC50pre up to 65 times lower than that of BHMB1 (IC50exp = 20 nM). Predicted pharmacokinetic profile of the new analogs showed enhanced cell membrane permeability and high human oral absorption compared to current anti-tuberculotics. Conclusions: Combined use of QSAR models that considered binding of the BHMBs to InhA, pharmacophore model, and ADME properties helped to recognize bound active conformation of the benzamide inhibitors, permitted in silico screening of VCL of compounds sharing benzamide scaffold and identification of new analogs with predicted high inhibitory potencies and favorable pharmacokinetic profiles.
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Affiliation(s)
- Koffi Charles Kouman
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Melalie Keita
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Raymond Kre N’Guessan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Luc Calvin Owono Owono
- International Centre for Theoretical Physics, ICTP-UNESCO, Strada Costiera 11, I-34151 Trieste, Italy;
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, P.O. Box 47, Yaoundé 1, Cameroon
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
| | - Eugene Megnassan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
- International Centre for Theoretical Physics, ICTP-UNESCO, Strada Costiera 11, I-34151 Trieste, Italy;
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Laboratoire de Cristallographie—Physique Moléculaire, University of Cocody (now Felix Houphouët-Boigny), Abidjan 22, Côte d’Ivoire
- Laboratoire de Chimie Organique Structurale et Théorique, University of Cocody (now Felix Houphouët-Boigny), Abidjan 22, Côte d’Ivoire
- Correspondence: ; Tel.: +225-02-36-30-08
| | - Vladimir Frecer
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, SK-83232 Bratislava, Slovakia
| | - Stanislav Miertus
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
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In Silico Repositioning of Cannabigerol as a Novel Inhibitor of the Enoyl Acyl Carrier Protein (ACP) Reductase (InhA). Molecules 2019; 24:molecules24142567. [PMID: 31311157 PMCID: PMC6680637 DOI: 10.3390/molecules24142567] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/08/2019] [Accepted: 07/13/2019] [Indexed: 12/22/2022] Open
Abstract
Cannabigerol (CBG) and cannabichromene (CBC) are non-psychoactive cannabinoids that have raised increasing interest in recent years. These compounds exhibit good tolerability and low toxicity, representing promising candidates for drug repositioning. To identify novel potential therapeutic targets for CBG and CBC, an integrated ligand-based and structure-based study was performed. The results of the analysis led to the identification of CBG as a low micromolar inhibitor of the Enoyl acyl carrier protein (ACP) reductase (InhA) enzyme.
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Vasava MS, Bhoi MN, Rathwa SK, Shetty SS, Patel RD, Rajani DP, Rajani SD, Patel A, Pandya HA, Patel HD. Novel 1,4-dihydropyrano[2,3-c]pyrazole derivatives: Synthesis, characterization, biological evaluation and in silico study. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Modi P, Patel S, Chhabria M. Structure-based design, synthesis and biological evaluation of a newer series of pyrazolo[1,5-a]pyrimidine analogues as potential anti-tubercular agents. Bioorg Chem 2019; 87:240-251. [PMID: 30908967 DOI: 10.1016/j.bioorg.2019.02.044] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/23/2019] [Accepted: 02/20/2019] [Indexed: 11/16/2022]
Abstract
In-depth study of structure-based drug designing can provide vital leads for the development of novel, clinically active molecules. In this present study, twenty six novel pyrazolo[1,5-a]pyrimidine analogues (6a-6z) were designed using molecular docking studies. The designed molecules were synthesized in good yields. Structural elucidation of the synthesized molecules was carried out using IR, MS, 1H NMR and 13C NMR spectroscopy. All the synthesized compounds were evaluated for their in-vitro anti-tubercular activity against H37Rv strain by Alamar Blue assay method. Most of the synthesized compounds displayed potent anti-tubercular activities. Amongst all the tested compounds 6p, 6g, 6n and 6h exhibited promising anti-tubercular activity. Further, these potent compounds were gauged for MDR-TB, XDR-TB and cytotoxic study. None of these compounds exhibited potent cytotoxicity. Stability of protein ligand complex was further evaluated by molecular dynamics simulation for 10 ns. All these results indicate that the synthesized compounds could be potential leads for further development of new potent anti-tubercular agents.
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Affiliation(s)
- Palmi Modi
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009 Gujarat, India; Department of Pharmacy, Dharmsinh Desai University, Nadiad, 387001 Gujarat, India; Department of Pharmaceutical Chemistry, L. J. Institute of Pharmacy, Ahmedabad, 382210 Gujarat, India
| | - Shivani Patel
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009 Gujarat, India; Division of Biological and Life Sciences, Ahmedabad University, Ahmedabad, 380009 Gujarat, India
| | - Mahesh Chhabria
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009 Gujarat, India.
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Duca G, Pogrebnoi S, Boldescu V, Aksakal F, Uncu A, Valica V, Uncu L, Negres S, Nicolescu F, Macaev F. Tryptanthrin Analogues as Inhibitors of Enoyl-acyl Carrier Protein Reductase: Activity against Mycobacterium tuberculosis, Toxicity, Modeling of Enzyme Binding. Curr Top Med Chem 2019; 19:609-619. [PMID: 30834838 DOI: 10.2174/1568026619666190304125740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 10/01/2018] [Accepted: 11/01/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND High numbers of infection with resistant forms of Micobacterium tuberculosis (Mtb) contribute to a constant growing demand in new highly active and effective therapeutics. Current drug discovery efforts directed towards new antituberculosis agents include the development of new inhibitors of enoyl-acyl carrier protein reductase (InhA) that do not require activation by the specific enzymes. Tryptanthrin is a known inhibitor of Mtb InhA and its analogues are investigated as potential agents with antimycobacterial efficiency. OBJECTIVE The main objective of the presented research was to develop a new group of tryptanthrin analogues with good inhibition properties against Mtb. METHODS Synthesis of new derivatives of 5H-[1,3,4]thiadiazolo[2,3- b]quinazolin-5-one and evaluation of their activity against Mtb, as well as acute and chronic toxicity studies were carried out. Molecular modeling studies were performed to investigate the binding mechanisms of the synthesized ligands with InhA. Binding energies and non-covalent interactions stabilizing the ligand-receptor complexes were obtained from the results of molecular docking. RESULTS The most active compound in the obtained series, 2-(propylthio)-5H-[1,3,4]thiadiazolo[2,3- b]quinazolin-5-one, exhibited the superior inhibition activity (up to 100%) against mycobacterial growth at MIC 6.5 µg/mL, showed good affinity to the InhA enzyme in docking studies and demonstrated a very low per oral toxicity in animals falling under the category 5 according to GHS classification. CONCLUSION 2-(propylthio)-5H-[1,3,4]thiadiazolo[2,3-b]quinazolin-5-one can be further explored for the development of a new series of compounds active against Mtb.
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Affiliation(s)
- Gheorghe Duca
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry, Chisinau, Moldova, Republic of
| | - Serghei Pogrebnoi
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry, Chisinau, Moldova, Republic of
| | - Veaceslav Boldescu
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry, Chisinau, Moldova, Republic of
| | - Fatma Aksakal
- Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Andrei Uncu
- Scientific Center for Drug Research, "Nicolae Testemitanu" State University of Medicine and Pharmacy, Chisinau, Moldova, Republic of
| | - Vladimir Valica
- Scientific Center for Drug Research, "Nicolae Testemitanu" State University of Medicine and Pharmacy, Chisinau, Moldova, Republic of
| | - Livia Uncu
- Scientific Center for Drug Research, "Nicolae Testemitanu" State University of Medicine and Pharmacy, Chisinau, Moldova, Republic of
| | - Simona Negres
- Department of Pharmacology and Clinical Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Florica Nicolescu
- Department of Pharmacology and Clinical Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Fliur Macaev
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry, Chisinau, Moldova, Republic of.,Scientific Center for Drug Research, "Nicolae Testemitanu" State University of Medicine and Pharmacy, Chisinau, Moldova, Republic of
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Structure-based design of some isonicotinic acid hydrazide analogues as potential antitubercular agents. Bioorg Chem 2018; 80:721-732. [DOI: 10.1016/j.bioorg.2018.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/22/2018] [Accepted: 07/26/2018] [Indexed: 11/18/2022]
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Swatko-Ossor M, Klimek K, Belcarz A, Kaczor AA, Pitucha M, Ginalska G. Do new N-substituted 3-amino-4-phenyl-5-oxo-pyrazolinecarboxamide derivatives exhibit antitubercular potential? Eur J Pharm Sci 2018; 121:155-165. [PMID: 29802898 DOI: 10.1016/j.ejps.2018.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 04/20/2018] [Accepted: 05/23/2018] [Indexed: 11/27/2022]
Abstract
As a continuation of previous tests concerning new N-substituted 3-amino-4-phenyl-5-oxo-pyrazolinecarboxamide derivatives (R3, R4 and R8) of notable antibacterial activity, their antitubercular potential against different mycobacterial strains was estimated. Tests performed on virulent (reference and clinical) strains of Mycobacterium bovis and Mycobacterium tuberculosis revealed the highest therapeutic potential of R8 derivative: MIC within the range 7.8-15.6 μg/ml and TI (therapeutic index) within the range 46.5-93. Moreover, the synergistic interaction was found between R3, R4 and R8 derivatives and rifampicin, one of the front-line antitubercular drugs. R8/rifampicin mixture in concentrations effective in inhibition of Mycobacterium tuberculosis strain was non-cytotoxic against GMK cells, displaying cell viability approximately 88-97% when compared to control. Molecular docking study enabled to conclude that enoyl acyl carrier protein reductase (InhA) can be considered as a potential molecular target of tested pyrazole derivatives. Although further modifications of chemical structure of the investigated pyrazole derivatives is required, in order to increase their antitubercular efficacy and therapeutic safety, these compounds, in particular R8 compound, can be promising for the treatment of human and bovine tuberculosis.
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Affiliation(s)
- Marta Swatko-Ossor
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland
| | - Katarzyna Klimek
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland
| | - Anna Belcarz
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland.
| | - Agnieszka Anna Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; University of Eastern Finland, School of Pharmacy, Department of Pharmaceutical Chemistry, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Monika Pitucha
- Independent Radiopharmacy Unit Department of Organic Chemistry, Medical University of Lublin, Chodzki 4A, 20-093 Lublin, Poland
| | - Grazyna Ginalska
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland
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Modi P, Patel S, Chhabria MT. Identification of some novel pyrazolo[1,5-a]pyrimidine derivatives as InhA inhibitors through pharmacophore-based virtual screening and molecular docking. J Biomol Struct Dyn 2018; 37:1736-1749. [PMID: 29663870 DOI: 10.1080/07391102.2018.1465852] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The InhA inhibitors play key role in mycolic acid synthesis by preventing the fatty acid biosynthesis pathway. In this present article, Pharmacophore modelling and molecular docking study followed by in silico virtual screening could be considered as effective strategy to identify newer enoyl-ACP reductase inhibitors. Pyrrolidine carboxamide derivatives were opted to generate pharmacophore models using HypoGen algorithm in Discovery studio 2.1. Further it was employed to screen Zinc and Minimaybridge databases to identify and design newer potent hit molecules. The retrieved newer hits were further evaluated for their drug likeliness and docked against enoyl acyl carrier protein reductase. Here, novel pyrazolo[1,5-a]pyrimidine analogues were designed and synthesized with good yields. Structural elucidation of synthesized final molecules was perform through IR, MASS, 1H-NMR, 13C-NMR spectroscopy and further tested for its in vitro anti-tubercular activity against H37Rv strain using Microplate Alamar blue assay (MABA) method. Most of the synthesized compounds displayed strong anti-tubercular activities. Further, these potent compounds were gauged for MDR-TB, XDR-TB and cytotoxic study.
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Affiliation(s)
- Palmi Modi
- a Department of Pharmaceutical Chemistry , L. M. College of Pharmacy , Ahmedabad 380009 , Gujarat , India.,b Department of Pharmacy , Dharmsinh Desai University , Nadiad 387001 , Gujarat , India
| | - Shivani Patel
- a Department of Pharmaceutical Chemistry , L. M. College of Pharmacy , Ahmedabad 380009 , Gujarat , India.,c Division of Biological and Life Sciences , Ahmedabad University , Ahmedabad 380009 , Gujarat , India
| | - Mahesh T Chhabria
- a Department of Pharmaceutical Chemistry , L. M. College of Pharmacy , Ahmedabad 380009 , Gujarat , India
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AlMatar M, Makky EA, Var I, Kayar B, Köksal F. Novel compounds targeting InhA for TB therapy. Pharmacol Rep 2018; 70:217-226. [DOI: 10.1016/j.pharep.2017.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/26/2017] [Accepted: 09/12/2017] [Indexed: 02/07/2023]
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Campaniço A, Moreira R, Lopes F. Drug discovery in tuberculosis. New drug targets and antimycobacterial agents. Eur J Med Chem 2018; 150:525-545. [DOI: 10.1016/j.ejmech.2018.03.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 01/24/2023]
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Synthesis, biological evaluation and molecular modeling studies of phenyl-/benzhydrylpiperazine derivatives as potential MAO inhibitors. Bioorg Chem 2018; 77:252-262. [DOI: 10.1016/j.bioorg.2018.01.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/07/2018] [Accepted: 01/12/2018] [Indexed: 11/21/2022]
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Suresh A, Srinivasarao S, Agnieszka N, Ewa AK, Alvala M, Lherbet C, Chandra Sekhar KVG. Design and synthesis of 9H-fluorenone based 1,2,3-triazole analogues asMycobacterium tuberculosisInhA inhibitors. Chem Biol Drug Des 2018; 91:1078-1086. [DOI: 10.1111/cbdd.13127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/17/2017] [Accepted: 08/24/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Amaroju Suresh
- Department of Chemistry; Birla Institute of Technology and Science; Hyderabad Telangana India
| | - Singireddi Srinivasarao
- Department of Chemistry; Birla Institute of Technology and Science; Hyderabad Telangana India
| | - Napiórkowska Agnieszka
- Microbiology Department; National Tuberculosis and Lung Diseases Research Institute; Warsaw Poland
| | - Augustynowicz-Kopeć Ewa
- Microbiology Department; National Tuberculosis and Lung Diseases Research Institute; Warsaw Poland
| | - Mallika Alvala
- National Institute of Pharmaceutical Education and Research-Hyderabad; Hyderabad Telangana India
| | - Christian Lherbet
- Laboratoire SPCMIB (UMR CNRS 5068); Université Paul Sabatier; Université de Toulouse; Toulouse Cedex France
- ITAV-USR3505, CNRS, UPS; Université de Toulouse; Toulouse France
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Srivastava S, Bimal D, Bohra K, Singh B, Ponnan P, Jain R, Varma-Basil M, Maity J, Thirumal M, Prasad AK. Synthesis and antimycobacterial activity of 1-(β-d-Ribofuranosyl)-4-coumarinyloxymethyl- / -coumarinyl-1,2,3-triazole. Eur J Med Chem 2018. [PMID: 29529504 DOI: 10.1016/j.ejmech.2018.02.067] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A series of β-d-ribofuranosyl coumarinyl-1,2,3-triazoles have been synthesized by Cu-catalyzed cycloaddition reaction between azidosugar and 7-O-/7-alkynylated coumarins in 62-70% overall yields. The in vitro antimycobacterial activity evaluation of the synthesized triazolo-conjugates against Mycobacterium tuberculosis revealed that compounds were bactericidal in nature and some of them were found to be more active than one of the first line antimycobacterial drug ethambutol against sensitive reference strain H37Rv, and 7 to 420 times more active than all four first line antimycobacterial drugs (isoniazid, rifampicin, ethambutol and streptomycin) against multidrug resistant clinical isolate 591. Study of in silico pharmacokinetic profile indicated the drug like characters for the test molecules. Further, transmission electron microscopic experiments revealed that these compounds interfere with the constitution of bacterial cell wall possibly by targeting mycobacterial InhA and DNA gyrase enzymes. Study conducted on the activities of the test compounds on bacterial InhA and DNA gyrase revealed that the most bactericidal test compound, N1-(β-d-ribofuranosyl)-C4-(4-methylcoumarin-7-oxymethyl)-1,2,3-triazole (6b) and its corresponding directly linked conjugate N1-(β-d-ribofuranosyl)-C4-(4-methylcoumarin-7-yl)-1,2,3-triazole (11b) significantly inhibited the activity of both the enzymes. The results were further supported by molecular docking studies of the compound 6b and 11b with bacterial InhA and DNA gyrase B enzymes. Further, the cytotoxicity study of some of the better active compounds on THP-1 macrophage cell line using MTT assay showed that the synthesized compounds were non-cytotoxic.
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Affiliation(s)
| | - Devla Bimal
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Kapil Bohra
- Department of Chemistry, University of Delhi, Delhi-110007, India; Department of Chemistry, Deen Dayal Upadhyaya College, University of Delhi, Delhi-110078, India
| | - Balram Singh
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Prija Ponnan
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Ruchi Jain
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Mandira Varma-Basil
- Department of Microbiology, VP Chest Institute, University of Delhi, Delhi-110007, India
| | - Jyotirmoy Maity
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - M Thirumal
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Ashok K Prasad
- Department of Chemistry, University of Delhi, Delhi-110007, India.
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An overview on crystal structures of InhA protein: Apo-form, in complex with its natural ligands and inhibitors. Eur J Med Chem 2018; 146:318-343. [PMID: 29407960 DOI: 10.1016/j.ejmech.2018.01.047] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 11/23/2022]
Abstract
The enoyl-ACP reductase InhA from the mycobacterial fatty acid biosynthesis pathway has become a target of interest for the development of new anti-tubercular drugs. This protein has been identified as essential for the survival of Mycobacterium tuberculosis, the causative agent of tuberculosis, and as the main target of two pro-drugs: isoniazid, the frontline anti-tubercular drug, and ethionamide, a second-line medicine. Since most cases of resistance to isoniazid and ethionamide result from mutations in the mycobacterial activating enzyme (KatG for isoniazid and EthA for ethionamide), research of direct InhA inhibitors, avoiding the activation step, has emerged as a promising strategy for combating tuberculosis. Thereby, InhA is drawing much attention and its three-dimensional structure has been particularly studied. A better understanding of key sites of interactions responsible for InhA inhibition arises thus as an essential tool for the rational design of new potent inhibitors. In this paper, we propose an overview of the 80 available crystal structures of wild-type and mutant InhA, in its apo form, in complex with its cofactor, with an analogue of its natural ligands (C16 fatty acid and/or NADH) or with inhibitors. We will first discuss structural and mechanistic aspects in order to highlight key features of the protein before delivering thorough inventory of structures of InhA in the presence of synthetic ligands to underline the key interactions implicated in high affinity inhibition.
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43
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Evaluation of heteroatom-rich derivatives as antitubercular agents with InhA inhibition properties. Med Chem Res 2018. [DOI: 10.1007/s00044-017-2064-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Molecular modeling of drug-pathophysiological Mtb protein targets: Synthesis of some 2-thioxo-1, 3-thiazolidin-4-one derivatives as anti-tubercular agents. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Kumar V, Jhamb SS, Sobhia ME. Cell wall permeability assisted virtual screening to identify potential direct InhA inhibitors of Mycobacterium tuberculosis and their biological evaluation. J Biomol Struct Dyn 2017; 36:3274-3290. [PMID: 28974157 DOI: 10.1080/07391102.2017.1387176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The arising cases of isoniazid-resistance have motivated research interests toward new class of molecules known as direct InhA inhibitors. Here, a combine approach of shape-based pharmacophore and descriptor-based 2D QSAR was used to identify the potential direct InhA inhibitors. The approach is duly assisted with in vitro testing and molecular dynamics simulations. A combination of empirical parameters was derived to use as a filter for cell wall permeability while 2D QSAR was used as another filter to predict the biological activity. Both filters were applied to prioritize the molecules for biological evaluation against anti-TB activity. It led to 6 potential molecules which showed > 90% inhibition of H37Rv strain of Mycobacterium tuberculosis in BACTEC assay. Further, MMGBSA binding free energy of identified molecules was compared with available highly potent molecule, 5-hexyl-2-(2-methylphenoxy) phenol (IC50 = 5nM) using molecular dynamics simulations. It showed two molecules with comparatively higher affinity toward InhA as compared to potent molecule. It indicated the candidature of identified molecules to be further considered in anti-TB drug development pipeline.
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Affiliation(s)
- Vivek Kumar
- a Department of Pharmacoinformatics , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| | - Sarbjit Singh Jhamb
- b Common Biological Testing Lab (CBTL), Department of Pharmaceuticals , National Institute of Pharmaceutical Education and Research (NIPER) , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| | - M Elizabeth Sobhia
- a Department of Pharmacoinformatics , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
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46
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Lone MY, Manhas A, Athar M, Jha PC. Identification of InhA inhibitors: A combination of virtual screening, molecular dynamics simulations and quantum chemical studies. J Biomol Struct Dyn 2017; 36:2951-2965. [DOI: 10.1080/07391102.2017.1372313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Mohsin Y. Lone
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - Anu Manhas
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - Mohd. Athar
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - Prakash C. Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
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48
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Štular T, Lešnik S, Rožman K, Schink J, Zdouc M, Ghysels A, Liu F, Aldrich CC, Haupt VJ, Salentin S, Daminelli S, Schroeder M, Langer T, Gobec S, Janežič D, Konc J. Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction. J Med Chem 2016; 59:11069-11078. [PMID: 27936766 DOI: 10.1021/acs.jmedchem.6b01277] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Drug discovery is usually focused on a single protein target; in this process, existing compounds that bind to related proteins are often ignored. We describe ProBiS plugin, extension of our earlier ProBiS-ligands approach, which for a given protein structure allows prediction of its binding sites and, for each binding site, the ligands from similar binding sites in the Protein Data Bank. We developed a new database of precalculated binding site comparisons of about 290000 proteins to allow fast prediction of binding sites in existing proteins. The plugin enables advanced viewing of predicted binding sites, ligands' poses, and their interactions in three-dimensional graphics. Using the InhA query protein, an enoyl reductase enzyme in the Mycobacterium tuberculosis fatty acid biosynthesis pathway, we predicted its possible ligands and assessed their inhibitory activity experimentally. This resulted in three previously unrecognized inhibitors with novel scaffolds, demonstrating the plugin's utility in the early drug discovery process.
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Affiliation(s)
- Tanja Štular
- National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Samo Lešnik
- National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Kaja Rožman
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Julia Schink
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska , Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Mitja Zdouc
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska , Glagoljaška 8, SI-6000 Koper, Slovenia
| | - An Ghysels
- Center for Molecular Modeling, Ghent University , Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Feng Liu
- AAT Bioquest, Inc. , 520 Mercury Drive, Sunnyvale, California 94085, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
| | - V Joachim Haupt
- Biotechnology Center (BIOTEC), Technische Universität Dresden , 01307 Dresden, Germany
| | - Sebastian Salentin
- Biotechnology Center (BIOTEC), Technische Universität Dresden , 01307 Dresden, Germany
| | - Simone Daminelli
- Biotechnology Center (BIOTEC), Technische Universität Dresden , 01307 Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden , 01307 Dresden, Germany
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna , Althanstrasse 14, A-1090 Vienna, Austria
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Dušanka Janežič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska , Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Janez Konc
- National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska , Glagoljaška 8, SI-6000 Koper, Slovenia
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49
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Recent advancements in the development of anti-tuberculosis drugs. Bioorg Med Chem Lett 2016; 27:370-386. [PMID: 28017531 DOI: 10.1016/j.bmcl.2016.11.084] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/16/2016] [Accepted: 11/27/2016] [Indexed: 01/09/2023]
Abstract
Modern chemotherapy has significantly improved patient outcomes against drug-sensitive tuberculosis. However, the rapid emergence of drug-resistant tuberculosis, together with the bacterium's ability to persist and remain latent present a major public health challenge. To overcome this problem, research into novel anti-tuberculosis targets and drug candidates is thus of paramount importance. This review article provides an overview of tuberculosis highlighting the recent advances and tools that are employed in the field of anti-tuberculosis drug discovery. The predominant focus is on anti-tuberculosis agents that are currently in the pipeline, i.e. clinical trials.
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50
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Matviiuk T, Madacki J, Mori G, Orena BS, Menendez C, Kysil A, André-Barrès C, Rodriguez F, Korduláková J, Mallet-Ladeira S, Voitenko Z, Pasca MR, Lherbet C, Baltas M. Pyrrolidinone and pyrrolidine derivatives: Evaluation as inhibitors of InhA and Mycobacterium tuberculosis. Eur J Med Chem 2016; 123:462-475. [DOI: 10.1016/j.ejmech.2016.07.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 01/04/2023]
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