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Naik B, Gupta N, Godara P, Srivastava V, Kumar P, Giri R, Prajapati VK, Pandey KC, Prusty D. Structure-based virtual screening approach reveals natural multi-target compounds for the development of antimalarial drugs to combat drug resistance. J Biomol Struct Dyn 2024; 42:7384-7408. [PMID: 37528665 DOI: 10.1080/07391102.2023.2240415] [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: 01/19/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
Compared to the previous year, there has been an increase of nearly 2 million malaria cases in 2021. The emergence of drug-resistant strains of Plasmodium falciparum, the most deadly malaria parasite, has led to a decline in the effectiveness of existing antimalarial drugs. To address this problem, the present study aimed to identify natural compounds with the potential to inhibit multiple validated antimalarial drug targets. The natural compounds from the Natural Product Activity and Species Source (NPASS) database were screened against ten validated drug targets of Plasmodium falciparum using a structure-based molecular docking method. Twenty compounds, with targets ranging from three to five, were determined as the top hits. The molecular dynamics simulations of the top six complexes (NPC246162 in complex with PfAdSS, PfGDH, and PfNMT; NPC271270 in complex with PfCK, PfGDH, and PfdUTPase) confirmed their stable binding affinity in the dynamic environment. The Tanimoto coefficient and distance matrix score analysis show the structural divergence of all the hit compounds from known antimalarials, indicating minimum chances of cross-resistance. Thus, we propose further investigating these compounds in biochemical and parasite inhibition studies to reveal the real therapeutic potential. If found successful, these compounds may be a new avenue for future drug discovery efforts to combat existing antimalarial drug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Biswajit Naik
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Nidhi Gupta
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Priya Godara
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Varshita Srivastava
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Kailash C Pandey
- Icmr-National Institute of Malaria Research, And Academy of Scientific and Innovative Research (AcSIR-ICMR), India
| | - Dhaneswar Prusty
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
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2
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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] [MESH Headings] [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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Sabt A, Abdulla MH, Ebaid MS, Pawełczyk J, Abd El Salam HA, Son NT, Ha NX, Vaali Mohammed MA, Traiki T, Elsawi AE, Dziadek B, Dziadek J, Eldehna WM. Identification of 2-( N-aryl-1,2,3-triazol-4-yl) quinoline derivatives as antitubercular agents endowed with InhA inhibitory activity. Front Chem 2024; 12:1424017. [PMID: 39170867 PMCID: PMC11337105 DOI: 10.3389/fchem.2024.1424017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/12/2024] [Indexed: 08/23/2024] Open
Abstract
The spread of drug-resistant tuberculosis strains has become a significant economic burden globally. To tackle this challenge, there is a need to develop new drugs that target specific mycobacterial enzymes. Among these enzymes, InhA, which is crucial for the survival of Mycobacterium tuberculosis, is a key target for drug development. Herein, 24 compounds were synthesized by merging 4-carboxyquinoline with triazole motifs. These molecules were then tested for their effectiveness against different strains of tuberculosis, including M. bovis BCG, M. tuberculosis, and M. abscessus. Additionally, their ability to inhibit the InhA enzyme was also evaluated. Several molecules showed potential as inhibitors of M. tuberculosis. Compound 5n displayed the highest efficacy with a MIC value of 12.5 μg/mL. Compounds 5g, 5i, and 5n exhibited inhibitory effects on InhA. Notably, 5n showed significant activity compared to the reference drug Isoniazid. Molecular docking analysis revealed interactions between these molecules and their target enzyme. Additionally, the molecular dynamic simulations confirmed the stability of the complexes formed by quinoline-triazole conjugate 5n with the InhA. Finally, 5n underwent in silico analysis to predict its ADME characteristics. These findings provide promising insights for developing novel small compounds that are safe and effective for the global fight against tuberculosis.
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Affiliation(s)
- Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Center, Dokki, Egypt
| | - Maha-Hamadien Abdulla
- Colorectal Research Chair, Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Manal S. Ebaid
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Center, Dokki, Egypt
- Department of Chemistry, College of Science, Northern Border University, Arar, Saudi Arabia
| | - Jakub Pawełczyk
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | | | - Ninh The Son
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Department of Chemistry, Graduate University of Science and Technology, Hanoi, Vietnam
| | - Nguyen Xuan Ha
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Mansoor-Ali Vaali Mohammed
- Colorectal Research Chair, Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Thamer Traiki
- Colorectal Research Chair, Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed E. Elsawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Bozena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jaroslaw Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt
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4
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Moreno-Ceballos A, Caballero NA, Castro ME, Perez-Aguilar JM, Mammino L, Melendez FJ. In Silico Approach: Anti-Tuberculosis Activity of Caespitate in the H37Rv Strain. Curr Issues Mol Biol 2024; 46:6489-6507. [PMID: 39057029 PMCID: PMC11275643 DOI: 10.3390/cimb46070387] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 07/28/2024] Open
Abstract
Tuberculosis is a highly lethal bacterial disease worldwide caused by Mycobacterium tuberculosis (Mtb). Caespitate is a phytochemical isolated from Helichrysum caespititium, a plant used in African traditional medicine that shows anti-tubercular activity, but its mode of action remains unknown. It is suggested that there are four potential targets in Mtb, specifically in the H37Rv strain: InhA, MabA, and UGM, enzymes involved in the formation of Mtb's cell wall, and PanK, which plays a role in cell growth. Two caespitate conformational structures from DFT conformational analysis in the gas phase (GC) and in solution with DMSO (CS) were selected. Molecular docking calculations, MM/GBSA analysis, and ADME parameter evaluations were performed. The docking results suggest that CS is the preferred caespitate conformation when interacting with PanK and UGM. In both cases, the two intramolecular hydrogen bonds characteristic of caespitate's molecular structure were maintained to achieve the most stable complexes. The MM/GBSA study confirmed that PanK/caespitate and UGM/caespitate were the most stable complexes. Caespitate showed favorable pharmacokinetic characteristics, suggesting rapid absorption, permeability, and high bioavailability. Additionally, it is proposed that caespitate may exhibit antibacterial and antimonial activity. This research lays the foundation for the design of anti-tuberculosis drugs from natural sources, especially by identifying potential drug targets in Mtb.
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Affiliation(s)
- Andrea Moreno-Ceballos
- Laboratorio de Química Teórica, Centro de Investigación, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Edif. FCQ10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico; (A.M.-C.); (J.M.P.-A.)
| | - Norma A. Caballero
- Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Edif. BIO1, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico
| | - María Eugenia Castro
- Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Complejo de Ciencias, ICUAP, Edif. IC10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico;
| | - Jose Manuel Perez-Aguilar
- Laboratorio de Química Teórica, Centro de Investigación, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Edif. FCQ10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico; (A.M.-C.); (J.M.P.-A.)
| | - Liliana Mammino
- School of Mathematical and Natural Science, University of Venda, Thohoyandou 0950, South Africa;
| | - Francisco J. Melendez
- Laboratorio de Química Teórica, Centro de Investigación, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Edif. FCQ10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico; (A.M.-C.); (J.M.P.-A.)
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5
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Harrison GA, Wang ER, Cho K, Mreyoud Y, Sarkar S, Almqvist F, Patti GJ, Stallings CL. Inducing vulnerability to InhA inhibition restores isoniazid susceptibility in drug-resistant Mycobacterium tuberculosis. mBio 2024; 15:e0296823. [PMID: 38294237 PMCID: PMC10936210 DOI: 10.1128/mbio.02968-23] [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: 11/13/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024] Open
Abstract
Of the approximately 10 million cases of Mycobacterium tuberculosis (Mtb) infections each year, over 10% are resistant to the frontline antibiotic isoniazid (INH). INH resistance is predominantly caused by mutations that decrease the activity of the bacterial enzyme KatG, which mediates the conversion of the pro-drug INH to its active form INH-NAD. We previously discovered an inhibitor of Mtb respiration, C10, that enhances the bactericidal activity of INH, prevents the emergence of INH-resistant mutants, and re-sensitizes a collection of INH-resistant mutants to INH through an unknown mechanism. To investigate the mechanism of action of C10, we exploited the toxicity of high concentrations of C10 to select for resistant mutants. We discovered two mutations that confer resistance to the disruption of energy metabolism and allow for the growth of Mtb in high C10 concentrations, indicating that growth inhibition by C10 is associated with inhibition of respiration. Using these mutants as well as direct inhibitors of the Mtb electron transport chain, we provide evidence that inhibition of energy metabolism by C10 is neither sufficient nor necessary to potentiate killing by INH. Instead, we find that C10 acts downstream of INH-NAD synthesis, causing Mtb to become particularly sensitive to inhibition of the INH-NAD target, InhA, without changing the concentration of INH-NAD or the activity of InhA, the two predominant mechanisms of potentiating INH. Our studies revealed that there exists a vulnerability in Mtb that can be exploited to render Mtb sensitive to otherwise subinhibitory concentrations of InhA inhibitor.IMPORTANCEIsoniazid (INH) is a critical frontline antibiotic to treat Mycobacterium tuberculosis (Mtb) infections. INH efficacy is limited by its suboptimal penetration of the Mtb-containing lesion and by the prevalence of clinical INH resistance. We previously discovered a compound, C10, that enhances the bactericidal activity of INH, prevents the emergence of INH-resistant mutants, and re-sensitizes a set of INH-resistant mutants to INH. Resistance is typically mediated by katG mutations that decrease the activation of INH, which is required for INH to inhibit the essential enzyme InhA. Our current work demonstrates that C10 re-sensitizes INH-resistant katG-hypomorphs without enhancing the activation of INH. We furthermore show that C10 causes Mtb to become particularly vulnerable to InhA inhibition without compromising InhA activity on its own. Therefore, C10 represents a novel strategy to curtail the development of INH resistance and to sensitize Mtb to sub-lethal doses of INH, such as those achieved at the infection site.
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Affiliation(s)
- Gregory A. Harrison
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erin R. Wang
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yassin Mreyoud
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Souvik Sarkar
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Fredrik Almqvist
- Department of Chemistry, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, UCMR, Umeå University, Umeå, Sweden
| | - Gary J. Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Christina L. Stallings
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
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Khaleel EF, Sabt A, Korycka-Machala M, Badi RM, Son NT, Ha NX, Hamissa MF, Elsawi AE, Elkaeed EB, Dziadek B, Eldehna WM, Dziadek J. Identification of new anti-mycobacterial agents based on quinoline-isatin hybrids targeting enoyl acyl carrier protein reductase (InhA). Bioorg Chem 2024; 144:107138. [PMID: 38262087 DOI: 10.1016/j.bioorg.2024.107138] [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: 10/22/2023] [Revised: 01/07/2024] [Accepted: 01/14/2024] [Indexed: 01/25/2024]
Abstract
Tuberculosis (TB) is a global issue that poses a significant economic burden as a result of the ongoing emergence of drug-resistant strains. The urgent requirement for the development of novel antitubercular drugs can be addressed by targeting specific enzymes. One such enzyme, Mycobacterium tuberculosis (MTB) enoyl-acyl carrier protein (enoyl-ACP) reductase (InhA), plays a crucial role in the survival of the MTB bacterium. In this research study, a series of hybrid compounds combining quinolone and isatin were synthesized and assessed for their effectiveness against MTB, as well as their ability to inhibit the activity of the InhA enzyme in this bacterium. Among the compounds tested, 7a and 5g exhibited the most potent inhibitory activity against MTB, with minimum inhibitory concentration (MIC) values of 55 and 62.5 µg/mL, respectively. These compounds were further evaluated for their inhibitory effects on InhA and demonstrated significant activity compared to the reference drug Isoniazid (INH), with IC50 values of 0.35 ± 0.01 and 1.56 ± 0.06 µM, respectively. Molecular docking studies investigated the interactions between compounds 7a and 5g and the target enzyme, revealing hydrophobic contacts with important amino acid residues in the active site. To further confirm the stability of the complexes formed by 5g and 7a with the target enzyme, molecular dynamic simulations were employed, which demonstrated that both compounds 7a and 5g undergo minor structural changes and remain nearly stable throughout the simulated process, as assessed through RMSD, RMSF, and Rg values.
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Affiliation(s)
- Eman F Khaleel
- Department of Medical Physiology, College of Medicine, King Khalid University, Asir 61421, Saudi Arabia
| | - Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Center, Dokki, Cairo 12622, Egypt
| | - Malgorzata Korycka-Machala
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | - Rehab Mustafa Badi
- Department of Medical Physiology, College of Medicine, King Khalid University, Asir 61421, Saudi Arabia
| | - Ninh The Son
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi 10000, Viet Nam
| | - Nguyen Xuan Ha
- Institute of Natural Products Chemistry, VAST, 18 Hoang Quoc Viet, Caugiay, Hanoi 10000, Viet Nam
| | - Mohamed Farouk Hamissa
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic
| | - Ahmed E Elsawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33516, Egypt
| | - Eslam B Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh 13713, Saudi Arabia.
| | - Bozena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33516, Egypt.
| | - Jaroslaw Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland.
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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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8
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Zawal AG, Abdel-Aziz MM, Elbatreek MH, El-Shanawani AA, Abdel-Aziz LM, Elbaramawi SS. Design, synthesis, in vitro and in silico evaluation of novel substituted 1,2,4-triazole analogues as dual human VEGFR-2 and TB-InhA inhibitors. Bioorg Chem 2023; 141:106883. [PMID: 37774433 DOI: 10.1016/j.bioorg.2023.106883] [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: 08/01/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
Cancer is a leading cause of death globally and has been associated with Mycobacterium tuberculosis (Mtb). The angiogenesis-related VEGFR-2 is a common target between cancer and Mtb. Here, we aimed to synthesize and validate potent dual human VEGFR-2 inhibitors as anticancer and anti-mycobacterial agents. Two series of 1,2,4-triazole-based compounds (6a-l and 11a-e) were designed and synthesized through a molecular hybridization approach. Activities of all synthesized compounds were evaluated against human VEGFR-2 in addition to drug-sensitive, multidrug-resistant and extensive-drug resistant Mtb. Compounds 6a, 6c, 6e, 6f, 6h, 6l, 11a, 11d and 11e showed promising inhibitory effect on VEGFR-2 (IC50 = 0.15 - 0.39 µM), anti-proliferative activities against cancerous cells and low cytotoxicity against normal cells. The most potent compounds (6e and 11a) increased apoptosis percentage. Additionally, compounds 6h, 6i, 6l and 11c showed the highest activities against all Mtb strains, and thus were evaluated against enoyl-acyl carrier protein reductase (InhA) which is essential for Mtb cell wall synthesis. Interestingly, the compounds showed excellent InhA inhibition activities with IC50 range of 1.3 - 4.7 µM. Docking study revealed high binding affinities toward targeted enzymes; human VEGFR-2 and Mtb InhA. In conclusion, 1,2,4-triazole analogues are suggested as potent anticancer and antimycobacterial agents via inhibition of human VEGFR-2 and Mtb InhA.
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Affiliation(s)
- Amira G Zawal
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Marwa M Abdel-Aziz
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Mahmoud H Elbatreek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Abdalla A El-Shanawani
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Lobna M Abdel-Aziz
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Samar S Elbaramawi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt.
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9
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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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10
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Kumar G, C A. Natural products and their analogues acting against Mycobacterium tuberculosis: A recent update. Drug Dev Res 2023; 84:779-804. [PMID: 37086027 DOI: 10.1002/ddr.22063] [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: 11/25/2022] [Revised: 02/28/2023] [Accepted: 04/01/2023] [Indexed: 04/23/2023]
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases caused by Mycobacterium tuberculosis (M.tb). It is responsible for significant causes of mortality and morbidity worldwide. M.tb possesses robust defense mechanisms against most antibiotic drugs and host responses due to their complex cell membranes with unique lipid molecules. Thus, the efficacy of existing front-line drugs is diminishing, and new and recurring cases of TB arising from multidrug-resistant M.tb are increasing. TB begs the scientific community to explore novel therapeutic avenues. A precise knowledge of the compounds with their mode of action could aid in developing new anti-TB agents that can kill latent and actively multiplying M.tb. This can help in the shortening of the anti-TB regimen and can improve the outcome of treatment strategies. Natural products have contributed several antibiotics for TB treatment. The sources of anti-TB drugs/inhibitors discussed in this work are target-based identification/cell-based and phenotypic screening from natural products. Some of the recently identified natural products derived leads have reached clinical stages of TB drug development, which include rifapentine, CPZEN-45, spectinamide-1599 and 1810. We believe these anti-TB agents could emerge as superior therapeutic compounds to treat TB over known Food and Drug Administration drugs.
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Affiliation(s)
- Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Telangana, India
| | - Amrutha C
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Telangana, India
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11
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Teneva Y, Simeonova R, Valcheva V, Angelova VT. Recent Advances in Anti-Tuberculosis Drug Discovery Based on Hydrazide-Hydrazone and Thiadiazole Derivatives Targeting InhA. Pharmaceuticals (Basel) 2023; 16:ph16040484. [PMID: 37111241 PMCID: PMC10140854 DOI: 10.3390/ph16040484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Tuberculosis is an extremely serious problem of global public health. Its incidence is worsened by the presence of multidrug-resistant (MDR) strains of Mycobacterium tuberculosis. More serious forms of drug resistance have been observed in recent years. Therefore, the discovery and/or synthesis of new potent and less toxic anti-tubercular compounds is very critical, especially having in mind the consequences and the delays in treatment caused by the COVID-19 pandemic. Enoyl-acyl carrier protein reductase (InhA) is an important enzyme involved in the biosynthesis of mycolic acid, a major component of the M. tuberculosis cell wall. At the same time, it is a key enzyme in the development of drug resistance, making it an important target for the discovery of new antimycobacterial agents. Many different chemical scaffolds, including hydrazide hydrazones and thiadiazoles, have been evaluated for their InhA inhibitory activity. The aim of this review is to evaluate recently described hydrazide-hydrazone- and thiadiazole-containing derivatives that inhibit InhA activity, resulting in antimycobacterial effects. In addition, a brief review of the mechanisms of action of currently available anti-tuberculosis drugs is provided, including recently approved agents and molecules in clinical trials.
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Affiliation(s)
- Yoanna Teneva
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
| | - Rumyana Simeonova
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
| | - Violeta Valcheva
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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12
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Harrison GA, Cho K, Wang ER, Sarkar S, Almqvist F, Patti GJ, Stallings CL. Inducing vulnerability to InhA inhibition restores isoniazid susceptibility in drug resistant Mycobacterium tuberculosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527416. [PMID: 36798348 PMCID: PMC9934558 DOI: 10.1101/2023.02.06.527416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Of the approximately 10 million cases of Mycobacterium tuberculosis (Mtb) infections each year, over 10% are resistant to the frontline antibiotic isoniazid (INH). INH resistance is predominantly caused by mutations that decrease the activity of the bacterial enzyme KatG, which mediates conversion of the pro-drug INH to its active form INH-NAD. We previously discovered an inhibitor of Mtb respiration, C10, that enhances the bactericidal activity of INH, prevents the emergence of INH-resistant mutants, and re-sensitizes a collection of INH-resistant mutants to INH through an unknown mechanism. To investigate the mechanism of action of C10, we exploited the toxicity of high concentrations of C10 to select for resistant mutants. We discovered two mutations that confer resistance to the disruption of energy metabolism and allow for growth of Mtb in high C10 concentrations, indicating that growth inhibition by C10 is associated with inhibition of respiration. Using these mutants as well as direct inhibitors of the Mtb electron transport chain, we provide evidence that inhibition of energy metabolism by C10 is neither sufficient nor necessary to potentiate killing by INH. Instead, we find that C10 acts downstream of INH-NAD synthesis, causing Mtb to become particularly sensitive to inhibition of the INH-NAD target, InhA, without changing the concentration of INH-NAD or the activity of InhA, the two predominant mechanisms of potentiating INH. Our studies revealed that there exists a vulnerability in Mtb that can be exploited to render Mtb sensitive to otherwise subinhibitory concentrations of InhA inhibitor.
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Affiliation(s)
- Gregory A. Harrison
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, MO, USA
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO USA
| | - Erin R. Wang
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, MO, USA
| | - Souvik Sarkar
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
| | - Fredrik Almqvist
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
- Umeå Centre for Microbial Research, UCMR, Umeå University, SE-90187 Umeå, Sweden
| | - Gary J. Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO USA
| | - Christina L. Stallings
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, MO, USA
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Rossini NDO, Dias MVB. Mutations and insights into the molecular mechanisms of resistance of Mycobacterium tuberculosis to first-line. Genet Mol Biol 2023; 46:e20220261. [PMID: 36718771 PMCID: PMC9887390 DOI: 10.1590/1678-4685-gmb-2022-0261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/18/2022] [Indexed: 01/28/2023] Open
Abstract
Genetically antimicrobial resistance in Mycobacterium tuberculosis is currently one of the most important aspects of tuberculosis, considering that there are emerging resistant strains for almost every known drug used for its treatment. There are multiple antimicrobials used for tuberculosis treatment, and the most effective ones are the first-line drugs, which include isoniazid, pyrazinamide, rifampicin, and ethambutol. In this context, understanding the mechanisms of action and resistance of these molecules is essential for proposing new therapies and strategies of treatment. Additionally, understanding how and where mutations arise conferring a resistance profile to the bacteria and their effect on bacterial metabolism is an important requisite to be taken in producing safer and less susceptible drugs to the emergence of resistance. In this review, we summarize the most recent literature regarding novel mutations reported between 2017 and 2022 and the advances in the molecular mechanisms of action and resistance against first-line drugs used in tuberculosis treatment, highlighting recent findings in pyrazinamide resistance involving PanD and, additionally, resistance-conferring mutations for novel drugs such as bedaquiline, pretomanid, delamanid and linezolid.
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Affiliation(s)
- Nicolas de Oliveira Rossini
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil. Universidade de São PauloInstituto de Ciências BiomédicasDepartamento de MicrobiologiaSão PauloSPBrazil
| | - Marcio Vinicius Bertacine Dias
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil. Universidade de São PauloInstituto de Ciências BiomédicasDepartamento de MicrobiologiaSão PauloSPBrazil,University of Warwick, Department of Chemistry, Coventry, United Kingdom. University of WarwickDepartment of ChemistryCoventryUnited Kingdom
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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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15
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Developing New Treatments for COVID-19 through Dual-Action Antiviral/Anti-Inflammatory Small Molecules and Physiologically Based Pharmacokinetic Modeling. Int J Mol Sci 2022; 23:ijms23148006. [PMID: 35887353 PMCID: PMC9325261 DOI: 10.3390/ijms23148006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 01/27/2023] Open
Abstract
Broad-spectrum antiviral agents that are effective against many viruses are difficult to develop, as the key molecules, as well as the biochemical pathways by which they cause infection, differ largely from one virus to another. This was more strongly highlighted by the COVID-19 pandemic, which found health systems all over the world largely unprepared and proved that the existing armamentarium of antiviral agents is not sufficient to address viral threats with pandemic potential. The clinical protocols for the treatment of COVID-19 are currently based on the use of inhibitors of the inflammatory cascade (dexamethasone, baricitinib), or inhibitors of the cytopathic effect of the virus (monoclonal antibodies, molnupiravir or nirmatrelvir/ritonavir), using different agents. There is a critical need for an expanded armamentarium of orally bioavailable small-molecular medicinal agents, including those that possess dual antiviral and anti-inflammatory (AAI) activity that would be readily available for the early treatment of mild to moderate COVID-19 in high-risk patients. A multidisciplinary approach that involves the use of in silico screening tools to identify potential drug targets of an emerging pathogen, as well as in vitro and in vivo models for the determination of a candidate drug’s efficacy and safety, are necessary for the rapid and successful development of antiviral agents with potentially dual AAI activity. Characterization of candidate AAI molecules with physiologically based pharmacokinetics (PBPK) modeling would provide critical data for the accurate dosing of new therapeutic agents against COVID-19. This review analyzes the dual mechanisms of AAI agents with potential anti-SARS-CoV-2 activity and discusses the principles of PBPK modeling as a conceptual guide to develop new pharmacological modalities for the treatment of COVID-19.
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16
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Keleş Atıcı R, Doğan ŞD, Gündüz MG, Krishna VS, Chebaiki M, Homberset H, Lherbet C, Mourey L, Tønjum T. Urea derivatives carrying a thiophenylthiazole moiety: Design, synthesis, and evaluation of antitubercular and InhA inhibitory activities. Drug Dev Res 2022; 83:1292-1304. [PMID: 35769019 DOI: 10.1002/ddr.21958] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/05/2022]
Abstract
The recent emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) has complicated and significantly slowed efforts to eradicate and/or reduce the worldwide incidence of life-threatening acute and chronic cases of tuberculosis. To overcome this setback, researchers have increased the intensity of their work to identify new small-molecule compounds that are expected to remain efficacious antimicrobials against Mtb. Here, we describe our effort to apply the principles of molecular hybridization to synthesize 16 compounds carrying thiophene and thiazole rings beside the core urea functionality (TTU1-TTU16). Following extensive structural characterization, the obtained compounds were initially evaluated for their antimycobacterial activity against Mtb H37Rv. Subsequently, three derivatives standing out with their anti-Mtb activity profiles and low cytotoxicity (TTU5, TTU6, and TTU12) were tested on isoniazid-resistant clinical isolates carrying katG and inhA mutations. Additionally, due to their pharmacophore similarities to the well-known InhA inhibitors, the molecules were screened for their enoyl acyl carrier protein reductase (InhA) inhibitory potentials. Molecular docking studies were performed to support the experimental enzyme inhibition data. Finally, drug-likeness of the selected compounds was established by theoretical calculations of physicochemical descriptors.
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Affiliation(s)
- Rüveyde Keleş Atıcı
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Şengül Dilem Doğan
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Miyase Gözde Gündüz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Vagolu Siva Krishna
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Melina Chebaiki
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, Toulouse, France
| | - Håvard Homberset
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Christian Lherbet
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway.,Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, Oslo, Norway
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17
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Potentiating the Anti-Tuberculosis Efficacy of Peptide Nucleic Acids through Combinations with Permeabilizing Drugs. Microbiol Spectr 2022; 10:e0126221. [PMID: 35171048 PMCID: PMC8849056 DOI: 10.1128/spectrum.01262-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The emergence of antimicrobial resistance warrants for the development of improved treatment approaches. In this regard, peptide nucleic acids (PNAs) have shown great promise, exhibiting antibiotic properties through the targeting of cellular nucleic acids. We aimed to study the efficacy of PNA as an anti-tuberculosis agent. Since the efficacy of PNA is limited by its low penetration into the cell, we also investigated combinatorial treatments using permeabilizing drugs to improve PNA efficacy. Various concentrations of anti-inhA PNA, permeabilizing drugs, and their combinations were screened against extracellular and intracellular mycobacteria.0.625 to 5 μM anti-inhA PNA was observed to merely inhibit the growth of extracellular M. smegmatis, while low intracellular bacterial load was reduced by 2 or 2.5 log-fold when treated with 2.5 or 5 μM PNA, respectively. Anti-inhA PNA against M. tuberculosis H37Ra exhibited bactericidal properties at 2.5 and 5 μM and enabled a slight reduction in intracellular M. tuberculosis at concentrations from 2.5 to 20 μM. Of the permeabilizing drugs tested, ethambutol showed the most permeabilizing potential and ultimately potentiated anti-inhA PNA to the greatest extent, reducing its efficacious concentration to 1.25 μM against both M. smegmatis and M. tuberculosis. Furthermore, an enhanced clearance of 1.3 log-fold was observed for ethambutol-anti-inhA PNA combinations against intracellular M. tuberculosis. Thus, permeabilizing drug-PNA combinations indeed exhibit improved efficacies. We therefore propose that anti-inhA PNA could improve therapy even when applied in minute doses as an addition to the current anti-tuberculosis drug regimen. IMPORTANCE Peptide nucleic acids have great potential in therapeutics as anti-gene/anti-sense agents. However, their limited uptake in cells has curtailed their widespread application. Through this study, we explore a PNA-drug combinatorial strategy to improve the efficacy of PNAs and reduce their effective concentrations. This work also focuses on improving tuberculosis treatment, which is hindered by the emergence of antimicrobial-resistant strains of Mycobacterium tuberculosis. It is observed that the antibacterial efficacy of anti-inhA PNA is enhanced when it is combined with permeabilizing drugs, particularly ethambutol. This indicates that the addition of even small concentrations of anti-inhA PNA to the current TB regimen could potentiate their therapeutic efficiency. We hypothesize that this system would also overcome isoniazid resistance, since the resistance mutations lie outside the designed anti-inhA PNA target site.
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18
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Moorey AR, Cabanillas A, Batt SM, Ghidelli-Disse S, Urones B, Sanz O, Lelievre J, Bantscheff M, Cox LR, Besra GS. The multi-target aspect of an MmpL3 inhibitor: The BM212 series of compounds bind EthR2, a transcriptional regulator of ethionamide activation. Cell Surf 2021; 7:100068. [PMID: 34888432 PMCID: PMC8634040 DOI: 10.1016/j.tcsw.2021.100068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) ensures that drug discovery efforts remain at the forefront of TB research. There are multiple different experimental approaches that can be employed in the discovery of anti-TB agents. Notably, inhibitors of MmpL3 are numerous and structurally diverse in Mtb and have been discovered through the generation of spontaneous resistant mutants and subsequent whole genome sequencing studies. However, this approach is not always reliable and can lead to incorrect target assignment and requires orthogonal confirmatory approaches. In fact, many of these inhibitors have also been shown to act as multi-target agents, with secondary targets in Mtb, as well as in other non-MmpL3-containing pathogens. Herein, we have investigated further the cellular targets of the MmpL3-inhibitor BM212 and a number of BM212 analogues. To determine the alternative targets of BM212, which may have been masked by MmpL3 mutations, we have applied a combination of chemo-proteomic profiling using bead-immobilised BM212 derivatives and protein extracts, along with whole-cell and biochemical assays. The study identified EthR2 (Rv0078) as a protein that binds BM212 analogues. We further demonstrated binding of BM212 to EthR2 through an in vitro tryptophan fluorescence assay, which showed significant quenching of tryptophan fluorescence upon addition of BM212. Our studies have demonstrated the value of revisiting drugs with ambiguous targets, such as MmpL3, in an attempt to find alternative targets and the study of off-target effects to understand more precisely target engagement of new hits emerging from drug screening campaigns.
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Affiliation(s)
- Alice R Moorey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Alejandro Cabanillas
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Sarah M Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | | | - Beatriz Urones
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Olalla Sanz
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Joel Lelievre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Marcus Bantscheff
- Cellzome - a GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Liam R Cox
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
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19
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Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach. Int J Mol Sci 2021; 22:ijms222413259. [PMID: 34948055 PMCID: PMC8703488 DOI: 10.3390/ijms222413259] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/09/2021] [Accepted: 11/14/2021] [Indexed: 12/12/2022] Open
Abstract
Developing new, more effective antibiotics against resistant Mycobacterium tuberculosis that inhibit its essential proteins is an appealing strategy for combating the global tuberculosis (TB) epidemic. Finding a compound that can target a particular cavity in a protein and interrupt its enzymatic activity is the crucial objective of drug design and discovery. Such a compound is then subjected to different tests, including clinical trials, to study its effectiveness against the pathogen in the host. In recent times, new techniques, which involve computational and analytical methods, enhanced the chances of drug development, as opposed to traditional drug design methods, which are laborious and time-consuming. The computational techniques in drug design have been improved with a new generation of software used to develop and optimize active compounds that can be used in future chemotherapeutic development to combat global tuberculosis resistance. This review provides an overview of the evolution of tuberculosis resistance, existing drug management, and the design of new anti-tuberculosis drugs developed based on the contributions of computational techniques. Also, we show an appraisal of available software and databases on computational drug design with an insight into the application of this software and databases in the development of anti-tubercular drugs. The review features a perspective involving machine learning, artificial intelligence, quantum computing, and CRISPR combination with available computational techniques as a prospective pathway to design new anti-tubercular drugs to combat resistant tuberculosis.
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Kisten K, Kumalo HM, Machaba KE, Ndagi U, Mhlongo NN. Drug repurposing approach against Mycobacterium tuberculosis Enoyl-[acyl-carrier-protein] reductase: insight from molecular dynamics simulations. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1968390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kimona Kisten
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M. Kumalo
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kgothatso E. Machaba
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Umar Ndagi
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Minna, Nigeria
| | - Ndumiso N. Mhlongo
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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21
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Prasad MS, Bhole RP, Khedekar PB, Chikhale RV. Mycobacterium enoyl acyl carrier protein reductase (InhA): A key target for antitubercular drug discovery. Bioorg Chem 2021; 115:105242. [PMID: 34392175 DOI: 10.1016/j.bioorg.2021.105242] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/16/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Enoyl acyl carrier protein reductase (InhA) is a key enzyme involved in fatty acid synthesis mainly mycolic acid biosynthesis that is a part of NADH dependent acyl carrier protein reductase family. The aim of the present literature is to underline the different scaffolds or enzyme inhibitors that inhibit mycolic acid biosynthesis mainly cell wall synthesis by inhibiting enzyme InhA. Various scaffolds were identified based on the screening technologies like high throughput screening, encoded library technology, fragment-based screening. The compounds studied include indirect inhibitors (Isoniazid, Ethionamide, Prothionamide) and direct inhibitors (Triclosan/Diphenyl ethers, Pyrrolidine Carboxamides, Pyrroles, Acetamides, Thiadiazoles, Triazoles) with better efficacy against drug resistance. Out of the several scaffolds studied, pyrrolidine carboxamides were found to be the best molecules targeting InhA having good bioavailability properties and better MIC. This review provides with a detailed information, analysis, structure activity relationship and useful insight on various scaffolds as InhA inhibitors.
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Affiliation(s)
- Mayuri S Prasad
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MS, India
| | - Ritesh P Bhole
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune 411018, Maharashtra, India
| | - Pramod B Khedekar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MS, India.
| | - Rupesh V Chikhale
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom.
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22
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Rosa TLSA, Marques MAM, DeBoard Z, Hutchins K, Silva CAA, Montague CR, Yuan T, Amaral JJ, Atella GC, Rosa PS, Mattos KA, VanderVen BC, Lahiri R, Sampson NS, Brennan PJ, Belisle JT, Pessolani MCV, Berrêdo-Pinho M. Reductive Power Generated by Mycobacterium leprae Through Cholesterol Oxidation Contributes to Lipid and ATP Synthesis. Front Cell Infect Microbiol 2021; 11:709972. [PMID: 34395315 PMCID: PMC8355898 DOI: 10.3389/fcimb.2021.709972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/13/2021] [Indexed: 12/21/2022] Open
Abstract
Upon infection, Mycobacterium leprae, an obligate intracellular bacillus, induces accumulation of cholesterol-enriched lipid droplets (LDs) in Schwann cells (SCs). LDs are promptly recruited to M. leprae-containing phagosomes, and inhibition of this process decreases bacterial survival, suggesting that LD recruitment constitutes a mechanism by which host-derived lipids are delivered to intracellular M. leprae. We previously demonstrated that M. leprae has preserved only the capacity to oxidize cholesterol to cholestenone, the first step of the normal cholesterol catabolic pathway. In this study we investigated the biochemical relevance of cholesterol oxidation on bacterial pathogenesis in SCs. Firstly, we showed that M. leprae increases the uptake of LDL-cholesterol by infected SCs. Moreover, fluorescence microscopy analysis revealed a close association between M. leprae and the internalized LDL-cholesterol within the host cell. By using Mycobacterium smegmatis mutant strains complemented with M. leprae genes, we demonstrated that ml1942 coding for 3β-hydroxysteroid dehydrogenase (3β-HSD), but not ml0389 originally annotated as cholesterol oxidase (ChoD), was responsible for the cholesterol oxidation activity detected in M. leprae. The 3β-HSD activity generates the electron donors NADH and NADPH that, respectively, fuel the M. leprae respiratory chain and provide reductive power for the biosynthesis of the dominant bacterial cell wall lipids phthiocerol dimycocerosate (PDIM) and phenolic glycolipid (PGL)-I. Inhibition of M. leprae 3β-HSD activity with the 17β-[N-(2,5-di-t-butylphenyl)carbamoyl]-6-azaandrost-4-en-3one (compound 1), decreased bacterial intracellular survival in SCs. In conclusion, our findings confirm the accumulation of cholesterol in infected SCs and its potential delivery to the intracellular bacterium. Furthermore, we provide strong evidence that cholesterol oxidation is an essential catabolic pathway for M. leprae pathogenicity and point to 3β-HSD as a prime drug target that may be used in combination with current multidrug regimens to shorten leprosy treatment and ameliorate nerve damage.
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Affiliation(s)
- Thabatta L S A Rosa
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Maria Angela M Marques
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Zachary DeBoard
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Kelly Hutchins
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Carlos Adriano A Silva
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Christine R Montague
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Tianao Yuan
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States
| | - Julio J Amaral
- Laboratório de Química Biológica, Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia, Rio de Janeiro, Brazil
| | - Georgia C Atella
- Laboratório de Bioquímica de Lipídeos e Lipoproteínas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patrícia S Rosa
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil
| | - Katherine A Mattos
- Departmento de Controle de Qualidade, Instituto de Tecnologia em Imunobiológicos, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Brian C VanderVen
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Ramanuj Lahiri
- Department of Health and Human Services, Health Resources and Services Administration, Healthcare Systems Bureau, National Hansen's Disease Programs, Baton Rouge, LA, United States
| | - Nicole S Sampson
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States
| | - Patrick J Brennan
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - John T Belisle
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Maria Cristina V Pessolani
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcia Berrêdo-Pinho
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8853056. [PMID: 34258282 PMCID: PMC8241505 DOI: 10.1155/2021/8853056] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 12/23/2022]
Abstract
The recent outbreak of the deadly coronavirus disease 19 (COVID-19) pandemic poses serious health concerns around the world. The lack of approved drugs or vaccines continues to be a challenge and further necessitates the discovery of new therapeutic molecules. Computer-aided drug design has helped to expedite the drug discovery and development process by minimizing the cost and time. In this review article, we highlight two important categories of computer-aided drug design (CADD), viz., the ligand-based as well as structured-based drug discovery. Various molecular modeling techniques involved in structure-based drug design are molecular docking and molecular dynamic simulation, whereas ligand-based drug design includes pharmacophore modeling, quantitative structure-activity relationship (QSARs), and artificial intelligence (AI). We have briefly discussed the significance of computer-aided drug design in the context of COVID-19 and how the researchers continue to rely on these computational techniques in the rapid identification of promising drug candidate molecules against various drug targets implicated in the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The structural elucidation of pharmacological drug targets and the discovery of preclinical drug candidate molecules have accelerated both structure-based as well as ligand-based drug design. This review article will help the clinicians and researchers to exploit the immense potential of computer-aided drug design in designing and identification of drug molecules and thereby helping in the management of fatal disease.
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Docking-Based Virtual Screening and Molecular Dynamics Simulations of Quercetin Analogs as Enoyl-Acyl Carrier Protein Reductase (InhA) Inhibitors of Mycobacterium tuberculosis. Sci Pharm 2021. [DOI: 10.3390/scipharm89020020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The emergence of multidrug-resistant Mycobacterium tuberculosis (MTB) has become a major problem in treating tuberculosis (TB) and shows the need to develop new and efficient drugs for better TB control. This study aimed to use in silico techniques to discover potential inhibitors to the Enoyl-[acyl-carrier-protein] reductase (InhA), which controls mycobacterial cell wall construction. Initially, 391 quercetin analogs present in the KNApSAck_3D database were selected, filters were sequentially applied by docking-based virtual screening. After recategorizing the variables (bond energy prediction and molecular interaction, including hydrogen bond and hydrophobic bond), compounds C00013874, C00006532, and C00013887 were selected as hit ligands. These compounds showed great hydrophobic contributions, and for each hit ligand, 100 ns of molecular dynamic simulations were performed, and the binding free energy was calculated. C00013874 demonstrated the greatest capacity for the InhA enzyme inhibition with ΔGbind = −148.651 kcal/mol compare to NAD (native ligand) presented a ΔGbind = −87.570 kcal/mol. These data are preliminary studies and might be a suitable candidate for further experimental analysis.
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25
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Remodelling structure-based drug design using machine learning. Emerg Top Life Sci 2021; 5:13-27. [PMID: 33825834 DOI: 10.1042/etls20200253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022]
Abstract
To keep up with the pace of rapid discoveries in biomedicine, a plethora of research endeavors had been directed toward Rational Drug Development that slowly gave way to Structure-Based Drug Design (SBDD). In the past few decades, SBDD played a stupendous role in identification of novel drug-like molecules that are capable of altering the structures and/or functions of the target macromolecules involved in different disease pathways and networks. Unfortunately, post-delivery drug failures due to adverse drug interactions have constrained the use of SBDD in biomedical applications. However, recent technological advancements, along with parallel surge in clinical research have led to the concomitant establishment of other powerful computational techniques such as Artificial Intelligence (AI) and Machine Learning (ML). These leading-edge tools with the ability to successfully predict side-effects of a wide range of drugs have eventually taken over the field of drug design. ML, a subset of AI, is a robust computational tool that is capable of data analysis and analytical model building with minimal human intervention. It is based on powerful algorithms that use huge sets of 'training data' as inputs to predict new output values, which improve iteratively through experience. In this review, along with a brief discussion on the evolution of the drug discovery process, we have focused on the methodologies pertaining to the technological advancements of machine learning. This review, with specific examples, also emphasises the tremendous contributions of ML in the field of biomedicine, while exploring possibilities for future developments.
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26
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Targeting NAD-dependent dehydrogenases in drug discovery against infectious diseases and cancer. Biochem Soc Trans 2021; 48:693-707. [PMID: 32311017 DOI: 10.1042/bst20191261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 12/24/2022]
Abstract
Dehydrogenases are oxidoreductase enzymes that play a variety of fundamental functions in the living organisms and have primary roles in pathogen survival and infection processes as well as in cancer development. We review here a sub-set of NAD-dependent dehydrogenases involved in human diseases and the recent advancements in drug development targeting pathogen-associated NAD-dependent dehydrogenases. We focus also on the molecular aspects of the inhibition process listing the structures of the most relevant molecules targeting this enzyme family. Our aim is to review the most impacting findings regarding the discovery of novel inhibitory compounds targeting the selected NAD-dependent dehydrogenases involved in cancer and infectious diseases.
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27
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Phosphorylation on PstP Regulates Cell Wall Metabolism and Antibiotic Tolerance in Mycobacterium smegmatis. J Bacteriol 2021; 203:JB.00563-20. [PMID: 33257524 DOI: 10.1128/jb.00563-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/18/2020] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium tuberculosis and its relatives, like many bacteria, have dynamic cell walls that respond to environmental stresses. Modulation of cell wall metabolism in stress is thought to be responsible for decreased permeability and increased tolerance to antibiotics. The signaling systems that control cell wall metabolism under stress, however, are poorly understood. Here, we examine the cell wall regulatory function of a key cell wall regulator, the serine/threonine phosphatase PstP, in the model organism Mycobacterium smegmatis We show that the peptidoglycan regulator CwlM is a substrate of PstP. We find that a phosphomimetic mutation, pstP T171E, slows growth, misregulates both mycolic acid and peptidoglycan metabolism in different conditions, and interferes with antibiotic tolerance. These data suggest that phosphorylation on PstP affects its activity against various substrates and is important in the transition between growth and stasis.IMPORTANCE Regulation of cell wall assembly is essential for bacterial survival and contributes to pathogenesis and antibiotic tolerance in mycobacteria, including pathogens such as Mycobacterium tuberculosis However, little is known about how the cell wall is regulated in stress. We describe a pathway of cell wall modulation in Mycobacterium smegmatis through the only essential Ser/Thr phosphatase, PstP. We showed that phosphorylation on PstP is important in regulating peptidoglycan metabolism in the transition to stasis and mycolic acid metabolism in growth. This regulation also affects antibiotic tolerance in growth and stasis. This work helps us to better understand the phosphorylation-mediated cell wall regulation circuitry in Mycobacteria.
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28
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Kumar G, Narayan R, Kapoor S. Chemical Tools for Illumination of Tuberculosis Biology, Virulence Mechanisms, and Diagnosis. J Med Chem 2020; 63:15308-15332. [PMID: 33307693 DOI: 10.1021/acs.jmedchem.0c01337] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases and begs the scientific community to up the ante for research and exploration of completely novel therapeutic avenues. Chemical biology-inspired design of tunable chemical tools has aided in clinical diagnosis, facilitated discovery of therapeutics, and begun to enable investigation of virulence mechanisms at the host-pathogen interface of Mycobacterium tuberculosis. This Perspective highlights chemical tools specific to mycobacterial proteins and the cell lipid envelope that have furnished rapid and selective diagnostic strategies and provided unprecedented insights into the function of the mycobacterial proteome and lipidome. We discuss chemical tools that have enabled elucidating otherwise intractable biological processes by leveraging the unique lipid and metabolite repertoire of mycobacterial species. Some of these probes represent exciting starting points with the potential to illuminate poorly understood aspects of mycobacterial pathogenesis, particularly the host membrane-pathogen interactions.
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Affiliation(s)
- Gautam Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India
| | - Rishikesh Narayan
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Ponda 403 401, Goa, India
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India.,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India
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29
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Jayaraman M, Ramadas K. An integrated computational investigation to unveil the structural impacts of mutation on the InhA structural gene of Mycobacterium tuberculosis. J Mol Graph Model 2020; 101:107768. [DOI: 10.1016/j.jmgm.2020.107768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 10/23/2022]
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30
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Kuldeep J, Sharma SK, Sharma T, Singh BN, Siddiqi MI. Targeting Mycobacterium Tuberculosis Enoyl-Acyl Carrier Protein Reductase Using Computational Tools for Identification of Potential Inhibitor and their Biological Activity. Mol Inform 2020; 40:e2000211. [PMID: 33283460 DOI: 10.1002/minf.202000211] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/18/2020] [Indexed: 01/07/2023]
Abstract
Enoyl-acyl carrier protein reductase (InhA) of type II fatty acid synthase system is involved in the synthesis of mycolic acids which is a major component of the bacterial cell wall. Since they are the key enzymes playing a very significant role in the FASII pathway of the bacterium. In this study, we have developed a workflow for identification of InhA inhibitors by utilizing in silico virtual screening approaches based on various machine learning algorithms followed by pharmacophore based virtual screening. The hits screened from the models were further subjected to molecular docking. Further, based on the XP docking score best twenty compounds were subjected to molecular dynamics study. Finally, nine compounds were shortlisted on the basis of best stable ligand RMSD, c-alpha RMSD, and RMSF plot for biological evaluation studies. Experimental validation of the shortlisted compounds identified one compound JFD01724 having potent inhibitory activity and was able to inhibit the growth of mycobacterium tuberculosis. Further medicinal chemistry efforts may help to improve the inhibitory potency of the identified compound.
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Affiliation(s)
- Jitendra Kuldeep
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India, 226031
| | - Sandeep K Sharma
- Microbiology Division, CSIR-Central Drug Research Institute, Lucknow, India, 226031
| | - Tanuj Sharma
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India, 226031
| | - Bhupendra N Singh
- Microbiology Division, CSIR-Central Drug Research Institute, Lucknow, India, 226031
| | - Mohammad Imran Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India, 226031
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31
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Ishibashi D, Ishikawa T, Mizuta S, Tange H, Nakagaki T, Hamada T, Nishida N. Novel Compounds Identified by Structure-Based Prion Disease Drug Discovery Using In Silico Screening Delay the Progression of an Illness in Prion-Infected Mice. Neurotherapeutics 2020; 17:1836-1849. [PMID: 32767031 PMCID: PMC7851219 DOI: 10.1007/s13311-020-00903-9] [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] [Indexed: 11/26/2022] Open
Abstract
The accumulation of abnormal prion protein (PrPSc) produced by the structure conversion of PrP (PrPC) in the brain induces prion disease. Although the conversion process of the protein is still not fully elucidated, it has been known that the intramolecular chemical bridging in the most fragile pocket of PrP, known as the "hot spot," stabilizes the structure of PrPC and inhibits the conversion process. Using our original structure-based drug discovery algorithm, we identified the low molecular weight compounds that predicted binding to the hot spot. NPR-130 and NPR-162 strongly bound to recombinant PrP in vitro, and fragment molecular orbital (FMO) analysis indicated that the high affinity of those candidates to the PrP is largely dependent on nonpolar interactions, such as van der Waals interactions. Those NPRs showed not only significant reduction of the PrPSc levels but also remarkable decrease of the number of aggresomes in persistently prion-infected cells. Intriguingly, treatment with those candidate compounds significantly prolonged the survival period of prion-infected mice and suppressed prion disease-specific pathological damage, such as vacuole degeneration, PrPSc accumulation, microgliosis, and astrogliosis in the brain, suggesting their possible clinical use. Our results indicate that in silico drug discovery using NUDE/DEGIMA may be widely useful to identify candidate compounds that effectively stabilize the protein.
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Affiliation(s)
- Daisuke Ishibashi
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
- Department of Immunological and Molecular Pharmacology, Faculty of Pharmaceutical Science, Fukuoka University, 8-19-1 Nanakuma Jonan-ku, Fukuoka, 814-0180, Japan.
| | - Takeshi Ishikawa
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
- Department of Chemistry, Biotechnology, and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima, 890-0065, Japan
| | - Satoshi Mizuta
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Hiroya Tange
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Takehiro Nakagaki
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Tsuyoshi Hamada
- Nagasaki Advanced Computing Center, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
- Nagasaki Advanced Computing Center, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan
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32
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Rani A, Johansen MD, Roquet-Banères F, Kremer L, Awolade P, Ebenezer O, Singh P, Sumanjit, Kumar V. Design and synthesis of 4-Aminoquinoline-isoindoline-dione-isoniazid triads as potential anti-mycobacterials. Bioorg Med Chem Lett 2020; 30:127576. [PMID: 32980514 DOI: 10.1016/j.bmcl.2020.127576] [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: 07/28/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022]
Abstract
A series of 4-aminoquinoline-isoindoline-dione-isoniazid triads were synthesized and assessed for their anti-mycobacterial activities and cytotoxicity. Most of the synthesized compounds exhibited promising activities against the mc26230 strain of M. tuberculosis with MIC in the range of 5.1-11.9 µM and were non-cytotoxic against Vero cells. The conjugates lacking either isoniazid or quinoline core in their structural framework failed to inhibit the growth of M. tuberculosis; thus, further strengthening the proposed design of triads in the present study.
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Affiliation(s)
- Anu Rani
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Matt D Johansen
- Institut de Recherche en Infectiologie (IRIM) de Montpellier, CNRS, UMR 9004 Université de Montpellier, France
| | - Françoise Roquet-Banères
- Institut de Recherche en Infectiologie (IRIM) de Montpellier, CNRS, UMR 9004 Université de Montpellier, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie (IRIM) de Montpellier, CNRS, UMR 9004 Université de Montpellier, France; INSERM, IRIM, 34293 Montpellier, France
| | - Paul Awolade
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Oluwakemi Ebenezer
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Parvesh Singh
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Sumanjit
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Vipan Kumar
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
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33
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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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34
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Saikia S, Bordoloi M. Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective. Curr Drug Targets 2020; 20:501-521. [PMID: 30360733 DOI: 10.2174/1389450119666181022153016] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/08/2018] [Accepted: 08/28/2018] [Indexed: 01/21/2023]
Abstract
Molecular docking is a process through which small molecules are docked into the macromolecular structures for scoring its complementary values at the binding sites. It is a vibrant research area with dynamic utility in structure-based drug-designing, lead optimization, biochemical pathway and for drug designing being the most attractive tools. Two pillars for a successful docking experiment are correct pose and affinity prediction. Each program has its own advantages and drawbacks with respect to their docking accuracy, ranking accuracy and time consumption so a general conclusion cannot be drawn. Moreover, users don't always consider sufficient diversity in their test sets which results in certain programs to outperform others. In this review, the prime focus has been laid on the challenges of docking and troubleshooters in existing programs, underlying algorithmic background of docking, preferences regarding the use of docking programs for best results illustrated with examples, comparison of performance for existing tools and algorithms, state of art in docking, recent trends of diseases and current drug industries, evidence from clinical trials and post-marketing surveillance are discussed. These aspects of the molecular drug designing paradigm are quite controversial and challenging and this review would be an asset to the bioinformatics and drug designing communities.
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Affiliation(s)
- Surovi Saikia
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
| | - Manobjyoti Bordoloi
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
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Molecular Docking and Chemical Analysis of Alcohol Compounds (C16-C20) Bound to InhA Receptors as Mycobactericidal Candidates. JURNAL KIMIA SAINS DAN APLIKASI 2020. [DOI: 10.14710/jksa.23.5.135-141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by a bacterium called Mycobacterium tuberculosis. TB infection spreads through the air and is more likely when using inappropriate disinfectants in medical and laboratory equipment related to TB research. Appropriate disinfectants used for laboratory equipment can reduce the risk of TB disease transmission. Alcohol compound is a common disinfectant with broad-spectrum activity against microbes, viruses, and fungi. Molecular Docking can be applied to support virtual receptor-ligand screening in finding the right mycobactericidal agent as a disinfectant candidate from the alcohol group. Based on docking analysis, octadecanol (C18) has potential as a mycobactericidal agent with InhA as its specific receptor. Gibbs (ΔG) free energy obtained by octadecanol (C18) and InhA is -4.9 kcal/mol.
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Naik B, Gupta N, Ojha R, Singh S, Prajapati VK, Prusty D. High throughput virtual screening reveals SARS-CoV-2 multi-target binding natural compounds to lead instant therapy for COVID-19 treatment. Int J Biol Macromol 2020; 160:1-17. [PMID: 32470577 PMCID: PMC7250083 DOI: 10.1016/j.ijbiomac.2020.05.184] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/21/2022]
Abstract
The present-day world is severely suffering from the recently emerged SARS-CoV-2. The lack of prescribed drugs for the deadly virus has stressed the likely need to identify novel inhibitors to alleviate and stop the pandemic. In the present high throughput virtual screening study, we used in silico techniques like receptor-ligand docking, Molecular dynamic (MD), and ADME properties to screen natural compounds. It has been documented that many natural compounds display antiviral activities, including anti–SARS-CoV effect. The present study deals with compounds of Natural Product Activity and Species Source (NPASS) database with known biological activity that probably impedes the activity of six essential enzymes of the virus. Promising drug-like compounds were identified, demonstrating better docking score and binding energy for each druggable targets. After an extensive screening analysis, three novel multi-target natural compounds were predicted to subdue the activity of three/more major drug targets simultaneously. Concerning the utility of natural compounds in the formulation of many therapies, we propose these compounds as excellent lead candidates for the development of therapeutic drugs against SARS-CoV-2.
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Affiliation(s)
- Biswajit Naik
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Nidhi Gupta
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Rupal Ojha
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Dhaneswar Prusty
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India.
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Berdigaliyev N, Aljofan M. An overview of drug discovery and development. Future Med Chem 2020; 12:939-947. [PMID: 32270704 DOI: 10.4155/fmc-2019-0307] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/18/2020] [Indexed: 01/01/2023] Open
Abstract
A new medicine will take an average of 10-15 years and more than US$2 billion before it can reach the pharmacy shelf. Traditionally, drug discovery relied on natural products as the main source of new drug entities, but was later shifted toward high-throughput synthesis and combinatorial chemistry-based development. New technologies such as ultra-high-throughput drug screening and artificial intelligence are being heavily employed to reduce the cost and the time of early drug discovery, but they remain relatively unchanged. However, are there other potentially faster and cheaper means of drug discovery? Is drug repurposing a viable alternative? In this review, we discuss the different means of drug discovery including their advantages and disadvantages.
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Affiliation(s)
- Nurken Berdigaliyev
- Department of biomedical Science, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan
| | - Mohamad Aljofan
- Department of biomedical Science, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan
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Mycobacterial Cell Wall: A Source of Successful Targets for Old and New Drugs. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Eighty years after the introduction of the first antituberculosis (TB) drug, the treatment of drug-susceptible TB remains very cumbersome, requiring the use of four drugs (isoniazid, rifampicin, ethambutol and pyrazinamide) for two months followed by four months on isoniazid and rifampicin. Two of the drugs used in this “short”-course, six-month chemotherapy, isoniazid and ethambutol, target the mycobacterial cell wall. Disruption of the cell wall structure can enhance the entry of other TB drugs, resulting in a more potent chemotherapy. More importantly, inhibition of cell wall components can lead to mycobacterial cell death. The complexity of the mycobacterial cell wall offers numerous opportunities to develop drugs to eradicate Mycobacterium tuberculosis, the causative agent of TB. In the past 20 years, researchers from industrial and academic laboratories have tested new molecules to find the best candidates that will change the face of TB treatment: drugs that will shorten TB treatment and be efficacious against active and latent, as well as drug-resistant TB. Two of these new TB drugs block components of the mycobacterial cell wall and have reached phase 3 clinical trial. This article reviews TB drugs targeting the mycobacterial cell wall in use clinically and those in clinical development.
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AlMatar M, Var I, Kayar B, Köksal F. Differential Expression of Resistant and Efflux Pump Genes in MDR-TB Isolates. Endocr Metab Immune Disord Drug Targets 2020; 20:271-287. [DOI: 10.2174/1871530319666191009153834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/21/2019] [Accepted: 07/22/2019] [Indexed: 12/20/2022]
Abstract
Background:Numerous investigations demonstrate efflux as a worldwide bacterial mode of action which contributes to the resistance of drugs. The activity of antibiotics, which subjects to efflux, can be improved by the combined usage of efflux inhibitors. However, the efflux role to the overall levels of antibiotic resistance of clinical M. tuberculosis isolates is inadequately comprehended and is still disregarded by many.Method:Here, we assessed the contribution of resistant genes associated with isoniazid (INH) and rifampin (R) resistance to the levels of drug resistance in the (27) clinical isolates of MDR-TB. Additionally, the role of the resistance for six putative drug efflux pump genes to the antibiotics was investigated. The level of katG expression was down-regulated in 24/27 (88.88%) of MDR-TB isolates. Of the 27 MDR-TB isolates, inhA, oxyR-ahpC, and rpoB showed either overexpression or up-regulation in 8 (29.62%), 4 (14.81 %), and 24 (88.88%), respectively. Moreover, the efflux pump genes drrA, drrB, efpA, Rv2459, Rv1634, and Rv1250 were overexpressed under INH/RIF plus fresh pomegranate juice (FPJ) stress signifying the efflux pumps contribution to the overall levels of the resistance of MDR-TB isolates.Conclusion:These results displayed that the levels of drug resistance of MDR-TB clinical isolates are due to combination among drug efflux pump and the presence of mutations in target genes, a truth which is often ignored by the specialists of tuberculosis in favour of the almost undoubted significance of drug target- gene mutations for the resistance in M. tuberculosis.
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Affiliation(s)
- Manaf AlMatar
- Department of Biotechnology, Institute of Natural and Applied Sciences (Fen Bilimleri Enstitusu), Cukurova University, Adana, Turkey
| | - Işıl Var
- Department of Food Engineering, Agricultural Faculty, Cukurova University, Adana, Turkey
| | - Begüm Kayar
- Department of Medical Microbiology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Fatih Köksal
- Department of Medical Microbiology, Faculty of Medicine, Cukurova University, Adana, Turkey
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Das N, Jena PK, Pradhan SK. Arabinosyltransferase C enzyme of Mycobacterium tuberculosis, a potential drug target: An insight from molecular docking study. Heliyon 2020; 6:e02693. [PMID: 32090179 PMCID: PMC7026281 DOI: 10.1016/j.heliyon.2019.e02693] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 08/22/2019] [Accepted: 10/16/2019] [Indexed: 11/29/2022] Open
Abstract
Multi-drug resistant in Mycobacterium tuberculosis (M.tb) is considered as major bottleneck in the treatment and cure of tuberculosis (TB). Several anti-tubercular drugs fail in its efficacy due to drug-resistant M.tb developed mechanism for resistance. So, research across globe has been carried out to develop effective anti-TB drugs to improve the treatment of these strains. Traditional drug development methods have been proved unsuccessful as it fails to develop a broad-spectrum drug due to lack of structure based approach. Several studies have been conducted in this regard and identified several drug target sites that influence drug-resistant M.tb strains. In this study, the attempt was to study the interaction between the protein Arabinosyltransferase C with the two existing drugs (Ethambutol and Isoniazid) and five modified molecules derived from Ethambutol by calculating their binding affinity and mode of binding through molecular docking study using AutoDock 4. From the comparison study of the existing drug (EMB and INH) and the five proposed modified molecules (Emb1, Emb2, Emb3, Emb4 and Emb5), it is analysed that Emb1 and Emb3 with binding affinities -5.77 kcal/mol and -5.13 kcal/mol respectively can be considered as potential inhibitors of Arabinosyltransferase C in Mycobacterium tuberculosis which is responsible for cell wall synthesis. The facts provided may be further verified experimentally for future drug discovery process to make a stand against tuberculosis and contribute an advance research for worthy antimycobacterial strategies.
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Affiliation(s)
- Nisha Das
- Department of Chemistry, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India
| | - Pradip Kumar Jena
- Department of Chemistry, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India
| | - Sukanta Kumar Pradhan
- BIF Centre, Department of Bioinformatics, Centre for Post Graduate Studies, Odisha University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India
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Gandhi K, Patel M. Collocating Novel Targets for Tuberculosis (TB) Drug Discovery. Curr Drug Discov Technol 2020; 18:307-316. [PMID: 31987022 DOI: 10.2174/1570163817666200121143036] [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: 08/13/2019] [Revised: 11/23/2019] [Accepted: 01/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mycobacterium tuberculosis, being a resistive species is an incessant threat to the world population for the treatment of Tuberculosis (TB). An advanced genetic or a molecular level approach is mandatory for both diagnosis and therapy as the prevalence of multi drug-resistant (MDR) and extensively drug- resistant (XDR) TB. METHODS A literature review was conducted, focusing essentially on the development of biomarkers and targets to extrapolate the Tuberculosis Drug Discovery process. RESULTS AND DISCUSSION In this article, we have discussed several substantial targets and genetic mutations occurring in a diseased or treatment condition of TB patients. It includes expressions in Bhlhe40, natural resistance associated macrophage protein 1 (NRAMP1) and vitamin D receptor (VDR) with its mechanistic actions that have made a significant impact on TB. Moreover, recently identified compounds; imidazopyridine amine derivative (Q203), biphenyl amide derivative (DG70), azetidine, thioquinazole, tetrahydroindazole and 2- mercapto- quinazoline scaffolds for several targets such as adenosine triphosphate (ATP), amino acid and fatty acid have been briefed for their confirmed hits and therapeutic activity.
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Affiliation(s)
- Karan Gandhi
- Faculty of Pharmacy, Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, Charusat campus, Changa, Gujarat, India
| | - Mehul Patel
- Department of Pharmaceutical Chemistry, Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, Charusat Campus, Changa, Gujarat, India
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Bagchi A. Latest trends in structure based drug design with protein targets. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:1-23. [PMID: 32312418 DOI: 10.1016/bs.apcsb.2019.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structure based drug designing is an important endeavor in the field of structural bioinformatics. Previously the entire process was dependent on the wet-lab experiments to build libraries of ligand molecules. And the molecules used to be tested to determine their binding efficacies with protein target. However, the entire process is very lengthy and above all highly expensive. With the advent of supercomputers and increasing computational powers, the search process for finding suitable ligand molecules against target proteins have become more streamlined and cost-effective. Now the entire ligand search process is performed in-silico with the help of the techniques of virtual screening, molecular docking simulations and molecular dynamics studies. In the present chapter, a brief overview of the computational techniques involved in structure based drug designing is presented with a special emphasis on the thermodynamic principles behind the molecular interactions.
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Affiliation(s)
- Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, India
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Synthesis, characterization, crystal structure biological activity of 4-{2-[5-(4-fluoro-phenyl)- [1,3,4]oxadiazol-2-ylsulfanyl]-ethyl}-morpholine. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Madhavaram M, Nampally V, Gangadhari S, Palnati MK, Tigulla P. High-throughput virtual screening, ADME analysis, and estimation of MM/GBSA binding-free energies of azoles as potential inhibitors of Mycobacterium tuberculosis H37Rv. J Recept Signal Transduct Res 2019; 39:312-320. [DOI: 10.1080/10799893.2019.1660895] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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46
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Vilchèze C, Jacobs WR. The Isoniazid Paradigm of Killing, Resistance, and Persistence in Mycobacterium tuberculosis. J Mol Biol 2019; 431:3450-3461. [PMID: 30797860 PMCID: PMC6703971 DOI: 10.1016/j.jmb.2019.02.016] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/05/2019] [Accepted: 02/11/2019] [Indexed: 12/20/2022]
Abstract
Isoniazid (INH) was the first synthesized drug that mediated bactericidal killing of the bacterium Mycobacterium tuberculosis, a major clinical breakthrough. To this day, INH remains a cornerstone of modern tuberculosis (TB) chemotherapy. This review describes the serendipitous discovery of INH, its effectiveness on TB patients, and early studies to discover its mechanisms of bacteriocidal activity. Forty years after its introduction as a TB drug, the development of gene transfer in mycobacteria enabled the discovery of the genes encoding INH resistance, namely, the activator (katG) and the target (inhA) of INH. Further biochemical and x-ray crystallography studies on KatG and InhA proteins and mutants provided comprehensive understanding of INH mode of action and resistance mechanisms. Bacterial cultures can harbor subpopulations that are genetically or phenotypically resistant cells, the latter known as persisters. Treatment of exponentially growing cultures of M. tuberculosis with INH reproducibly kills 99% to 99.9% of cells in 3 days. Importantly, the surviving cells are slowly replicating or non-replicating cells expressing a unique stress response signature: these are the persisters. These persisters can be visualized using dual-reporter mycobacteriophages and their formation prevented using reducing compounds, such as N-acetylcysteine or vitamin C, that enhance M. tuberculosis' respiration. Altogether, this review portrays a detailed molecular analysis of INH killing and resistance mechanisms including persistence. The phenomenon of persistence is clearly the single greatest impediment to TB control, and research aimed at understanding persistence will provide new strategies to improve TB chemotherapy.
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Affiliation(s)
- Catherine Vilchèze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.
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Li G, Zhang J, Jiang Y, Zhao LL, Liu H, Li M, Zhao X, Wan K. Cross-resistance of isoniazid, para-aminosalicylic acid and pasiniazid against isoniazid-resistant Mycobacterium tuberculosis isolates in China. J Glob Antimicrob Resist 2019; 20:275-281. [PMID: 31425771 DOI: 10.1016/j.jgar.2019.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/25/2019] [Accepted: 08/06/2019] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES Pasiniazid is a chemical complex of isoniazid (INH) and para-aminosalicylic acid (PAS). The aim of this study was to explore the cross-resistance of INH, PAS and pasiniazid against INH-resistant Mycobacterium tuberculosis isolates in China. METHODS A Microplate alamarBlue® Assay was performed to determine the minimum inhibitory concentrations (MICs) of INH, PAS and pasiniazid against 109 INH-resistant M. tuberculosis isolates. A statistical analysis of the relationship between different genotypes, gene mutations, and INH, PAS or pasiniazid susceptibility was then performed. RESULTS Among the 109 INH-resistant isolates, 13 (11.9%) and 21 (19.3%) showed resistance to PAS and pasiniazid, respectively. Among the 13 PAS-resistant M. tuberculosis isolates, 11 remained susceptible to pasiniazid. Of 63 INH-resistant isolates harbouring mutations in katG, the inhA promoter or the oxyR-ahpC intergenic region, 52 remained susceptible to pasiniazid. Moreover, 11 of 13 pasiniazid-resistant isolates carried mutations in katG, the inhA promoter or the oxyR-ahpC intergenic region. CONCLUSION Taken together, these results demonstrate that PAS resistance and mutations in thekatG gene, inhA promoter or oxyR-ahpC intergenic region in INH-resistant M. tuberculosis have little effect on pasiniazid susceptibility.
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Affiliation(s)
- Guilian Li
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jingrui Zhang
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Laboratory, Shijiazhuang Obstetrics and Gynecology Hospital, the Fourth Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, China
| | - Yi Jiang
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Li-Li Zhao
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Haican Liu
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Machao Li
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiuqin Zhao
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Kanglin Wan
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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Batool M, Ahmad B, Choi S. A Structure-Based Drug Discovery Paradigm. Int J Mol Sci 2019; 20:ijms20112783. [PMID: 31174387 PMCID: PMC6601033 DOI: 10.3390/ijms20112783] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 12/14/2022] Open
Abstract
Structure-based drug design is becoming an essential tool for faster and more cost-efficient lead discovery relative to the traditional method. Genomic, proteomic, and structural studies have provided hundreds of new targets and opportunities for future drug discovery. This situation poses a major problem: the necessity to handle the “big data” generated by combinatorial chemistry. Artificial intelligence (AI) and deep learning play a pivotal role in the analysis and systemization of larger data sets by statistical machine learning methods. Advanced AI-based sophisticated machine learning tools have a significant impact on the drug discovery process including medicinal chemistry. In this review, we focus on the currently available methods and algorithms for structure-based drug design including virtual screening and de novo drug design, with a special emphasis on AI- and deep-learning-based methods used for drug discovery.
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Affiliation(s)
- Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea.
| | - Bilal Ahmad
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea.
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea.
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O'Neill EC, Schorn M, Larson CB, Millán-Aguiñaga N. Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining. Crit Rev Microbiol 2019; 45:255-277. [PMID: 30985219 DOI: 10.1080/1040841x.2019.1590307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Intense competition between microbes in the environment has directed the evolution of antibiotic production in bacteria. Humans have harnessed these natural molecules for medicinal purposes, magnifying them from environmental concentrations to industrial scale. This increased exposure to antibiotics has amplified antibiotic resistance across bacteria, spurring a global antimicrobial crisis and a search for antibiotics with new modes of action. Genetic insights into these antibiotic-producing microbes reveal that they have evolved several resistance strategies to avoid self-toxicity, including product modification, substrate transport and binding, and target duplication or modification. Of these mechanisms, target duplication or modification will be highlighted in this review, as it uniquely links an antibiotic to its mode of action. We will further discuss and propose a strategy to mine microbial genomes for these genes and their associated biosynthetic gene clusters to discover novel antibiotics using target directed genome mining.
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Affiliation(s)
- Ellis C O'Neill
- a Department of Plant Sciences, University of Oxford , Oxford , Oxfordshire , UK
| | - Michelle Schorn
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Charles B Larson
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Natalie Millán-Aguiñaga
- c Universidad Autónoma de Baja California, Facultad de Ciencias Marinas , Ensenada , Baja California , México
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50
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Discovery and development of novel rhodanine derivatives targeting enoyl-acyl carrier protein reductase. Bioorg Med Chem 2019; 27:1509-1516. [DOI: 10.1016/j.bmc.2019.02.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/12/2022]
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