1
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Peng C, Cheng Y, Ma M, Chen Q, Duan Y, Liu S, Cheng H, Yang H, Huang J, Bu W, Shi C, Wu X, Chen J, Zheng R, Liu Z, Ji Z, Wang J, Huang X, Wang P, Sha W, Ge B, Wang L. Mycobacterium tuberculosis suppresses host antimicrobial peptides by dehydrogenating L-alanine. Nat Commun 2024; 15:4216. [PMID: 38760394 PMCID: PMC11101664 DOI: 10.1038/s41467-024-48588-4] [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: 09/18/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
Antimicrobial peptides (AMPs), ancient scavengers of bacteria, are very poorly induced in macrophages infected by Mycobacterium tuberculosis (M. tuberculosis), but the underlying mechanism remains unknown. Here, we report that L-alanine interacts with PRSS1 and unfreezes the inhibitory effect of PRSS1 on the activation of NF-κB pathway to induce the expression of AMPs, but mycobacterial alanine dehydrogenase (Ald) Rv2780 hydrolyzes L-alanine and reduces the level of L-alanine in macrophages, thereby suppressing the expression of AMPs to facilitate survival of mycobacteria. Mechanistically, PRSS1 associates with TAK1 and disruptes the formation of TAK1/TAB1 complex to inhibit TAK1-mediated activation of NF-κB pathway, but interaction of L-alanine with PRSS1, disables PRSS1-mediated impairment on TAK1/TAB1 complex formation, thereby triggering the activation of NF-κB pathway to induce expression of AMPs. Moreover, deletion of antimicrobial peptide gene β-defensin 4 (Defb4) impairs the virulence by Rv2780 during infection in mice. Both L-alanine and the Rv2780 inhibitor, GWP-042, exhibits excellent inhibitory activity against M. tuberculosis infection in vivo. Our findings identify a previously unrecognized mechanism that M. tuberculosis uses its own alanine dehydrogenase to suppress host immunity, and provide insights relevant to the development of effective immunomodulators that target M. tuberculosis.
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Affiliation(s)
- Cheng Peng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Yuanna Cheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Mingtong Ma
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Qiu Chen
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Yongjia Duan
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Shanshan Liu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Hongyu Cheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Hua Yang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jingping Huang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Wenyi Bu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Chenyue Shi
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Xiangyang Wu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianxia Chen
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhonghua Liu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhe Ji
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Jie Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaochen Huang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Peng Wang
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Sha
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China.
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Lin Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China.
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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2
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Krieger IV, Yalamanchili S, Dickson P, Engelhart CA, Zimmerman MD, Wood J, Clary E, Nguyen J, Thornton N, Centrella PA, Chan B, Cuozzo JW, Gengenbacher M, Guié MA, Guilinger JP, Bienstock C, Hartl H, Hupp CD, Jetson R, Satoh T, Yeoman JTS, Zhang Y, Dartois V, Schnappinger D, Keefe AD, Sacchettini JC. Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening. ACS Infect Dis 2024; 10:1561-1575. [PMID: 38577994 PMCID: PMC11091879 DOI: 10.1021/acsinfecdis.3c00592] [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: 11/02/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
DNA-encoded chemical library (DEL) technology provides a time- and cost-efficient method to simultaneously screen billions of compounds for their affinity to a protein target of interest. Here we report its use to identify a novel chemical series of inhibitors of the thioesterase activity of polyketide synthase 13 (Pks13) from Mycobacterium tuberculosis (Mtb). We present three chemically distinct series of inhibitors along with their enzymatic and Mtb whole cell potency, the measure of on-target activity in cells, and the crystal structures of inhibitor-enzyme complexes illuminating their interactions with the active site of the enzyme. One of these inhibitors showed a favorable pharmacokinetic profile and demonstrated efficacy in an acute mouse model of tuberculosis (TB) infection. These findings and assay developments will aid in the advancement of TB drug discovery.
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Affiliation(s)
- Inna V. Krieger
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | | | - Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Matthew D Zimmerman
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
| | - Jeremy Wood
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Ethan Clary
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Jasmine Nguyen
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Natalie Thornton
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Paolo A. Centrella
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Betty Chan
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Auron
Therapeutics, 55 Chapel
Street, Newton, Massachusetts 02458, United States
| | - John W Cuozzo
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Relay
Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Martin Gengenbacher
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
| | - Marie-Aude Guié
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John P Guilinger
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Corey Bienstock
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Hajnalka Hartl
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Orogen
Therapeutics, 12 Gill
Street, Woburn, Massachusetts 01801, United States
| | - Christopher D. Hupp
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Ipsen Bioscience
Inc., 1 Main Street, Cambridge, Massachusetts 02142, United States
| | - Rachael Jetson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Valo
Health, 75 Hayden Avenue, Lexington, Massachusetts 02141, United States
| | - Takashi Satoh
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- EXO
Therapeutics, 150 Cambridgepark
Drive, suite 300, Cambridge, Massachusetts 02140, United States
| | - John T. S. Yeoman
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Recludix
Pharmaceuticals, 222
Third Street, Cambridge, Massachusetts 02142, United States
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Veronique Dartois
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
- Hackensack
Meridian School of Medicine, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Anthony D. Keefe
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - James C. Sacchettini
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
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3
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Canales CSC, Pavan AR, Dos Santos JL, Pavan FR. In silico drug design strategies for discovering novel tuberculosis therapeutics. Expert Opin Drug Discov 2024; 19:471-491. [PMID: 38374606 DOI: 10.1080/17460441.2024.2319042] [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: 11/08/2023] [Accepted: 02/12/2024] [Indexed: 02/21/2024]
Abstract
INTRODUCTION Tuberculosis remains a significant concern in global public health due to its intricate biology and propensity for developing antibiotic resistance. Discovering new drugs is a protracted and expensive endeavor, often spanning over a decade and incurring costs in the billions. However, computer-aided drug design (CADD) has surfaced as a nimbler and more cost-effective alternative. CADD tools enable us to decipher the interactions between therapeutic targets and novel drugs, making them invaluable in the quest for new tuberculosis treatments. AREAS COVERED In this review, the authors explore recent advancements in tuberculosis drug discovery enabled by in silico tools. The main objectives of this review article are to highlight emerging drug candidates identified through in silico methods and to provide an update on the therapeutic targets associated with Mycobacterium tuberculosis. EXPERT OPINION These in silico methods have not only streamlined the drug discovery process but also opened up new horizons for finding novel drug candidates and repositioning existing ones. The continued advancements in these fields hold great promise for more efficient, ethical, and successful drug development in the future.
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Affiliation(s)
- Christian S Carnero Canales
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
- School of Pharmacy, biochemistry and biotechnology, Santa Maria Catholic University, Arequipa, Perú
| | - Aline Renata Pavan
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
| | | | - Fernando Rogério Pavan
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
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4
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Xia F, Zhang H, Yang H, Zheng M, Min W, Sun C, Yuan K, Yang P. Targeting polyketide synthase 13 for the treatment of tuberculosis. Eur J Med Chem 2023; 259:115702. [PMID: 37544185 DOI: 10.1016/j.ejmech.2023.115702] [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: 06/17/2023] [Revised: 07/15/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023]
Abstract
Tuberculosis (TB) is one of the most threatening diseases for humans, however, the drug treatment strategy for TB has been stagnant and inadequate, which could not meet current treatment needs. TB is caused by Mycobacterial tuberculosis, which has a unique cell wall that plays a crucial role in its growth, virulence, and drug resistance. Polyketide synthase 13 (Pks13) is an essential enzyme that catalyzes the biosynthesis of the cell wall and its critical role is only found in Mycobacteria. Therefore, Pks13 is a promising target for developing novel anti-TB drugs. In this review, we first introduced the mechanism of targeting Pks13 for TB treatment. Subsequently, we focused on summarizing the recent advance of Pks13 inhibitors, including the challenges encountered during their discovery and the rational design strategies employed to overcome these obstacles, which could be helpful for the development of novel Pks13 inhibitors in the future.
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Affiliation(s)
- Fei Xia
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Haoling Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Huanaoyu Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Mingming Zheng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wenjian Min
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Chengliang Sun
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China.
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5
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Wang S, Luan J, Chen L, Liu H, Li W, Wang J. Computational characteristics of the structure-activity relationship of inhibitors targeting Pks13-TE domain. Comput Biol Chem 2023; 104:107864. [PMID: 37028177 DOI: 10.1016/j.compbiolchem.2023.107864] [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: 02/11/2023] [Revised: 03/22/2023] [Accepted: 04/01/2023] [Indexed: 04/09/2023]
Abstract
Multiple studies have established the Pks13-TE domain as a promising target for anti-tuberculosis drug development. However, recent findings have revealed that the lead compound currently in the pipeline for Pks13-TE has significant cardiotoxicity issues. Given the pressing need for new chemical structures for Pks13-TE inhibitors, this study aims to provide a detailed understanding of the Pks13-TE domain binding site through the application of computational chemical biology techniques. Our results highlight the size and shape of the Pks13-TE domain binding pocket, key residues including Asp1644, Asn1640, Phe1670, and Tyr1674 within the pocket, and inhibitor pharmacophore characteristics such as aromatic ring sites, positively charged sites, and hydrogen bond donors. To our knowledge, these simulation results are novel and contribute to the discovery of next-generation Pks13-TE inhibitors without similar prior studies.
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Affiliation(s)
- Shizun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jiasi Luan
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lu Chen
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Haihan Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Weixia Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
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6
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Naidu A, Nayak SS, Lulu S S, Sundararajan V. Advances in computational frameworks in the fight against TB: The way forward. Front Pharmacol 2023; 14:1152915. [PMID: 37077815 PMCID: PMC10106641 DOI: 10.3389/fphar.2023.1152915] [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: 01/28/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Around 1.6 million people lost their life to Tuberculosis in 2021 according to WHO estimates. Although an intensive treatment plan exists against the causal agent, Mycobacterium Tuberculosis, evolution of multi-drug resistant strains of the pathogen puts a large number of global populations at risk. Vaccine which can induce long-term protection is still in the making with many candidates currently in different phases of clinical trials. The COVID-19 pandemic has further aggravated the adversities by affecting early TB diagnosis and treatment. Yet, WHO remains adamant on its "End TB" strategy and aims to substantially reduce TB incidence and deaths by the year 2035. Such an ambitious goal would require a multi-sectoral approach which would greatly benefit from the latest computational advancements. To highlight the progress of these tools against TB, through this review, we summarize recent studies which have used advanced computational tools and algorithms for-early TB diagnosis, anti-mycobacterium drug discovery and in the designing of the next-generation of TB vaccines. At the end, we give an insight on other computational tools and Machine Learning approaches which have successfully been applied in biomedical research and discuss their prospects and applications against TB.
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Affiliation(s)
| | | | | | - Vino Sundararajan
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
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7
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Zhang W, Lun S, Wang SS, Cai YP, Yang F, Tang J, Bishai WR, Yu LF. Structure-Based Optimization of Coumestan Derivatives as Polyketide Synthase 13-Thioesterase(Pks13-TE) Inhibitors with Improved hERG Profiles for Mycobacterium tuberculosis Treatment. J Med Chem 2022; 65:13240-13252. [PMID: 36174223 DOI: 10.1021/acs.jmedchem.2c01064] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pks13 was identified as a key enzyme involved in the final step of mycolic acid biosynthesis. We previously identified antitubercular coumestans that targeted Pks13-TE, and these compounds exhibited high potency both in vitro and in vivo. However, lead compound 8 presented potential safety concerns because it inhibits the hERG potassium channel in electrophysiology patch-clamp assays (IC50 = 0.52 μM). By comparing the Pks13-TE-compound 8 complex and the ligand-binding pocket of the hERG ion channel, fluoro-substituted and oxazine-containing coumestans were designed and synthesized. Fluoro-substituted compound 23 and oxazine-containing coumestan 32 showed excellent antitubercular activity against both drug-susceptible and drug-resistant Mtb strains (MIC = 0.0039-0.0078 μg/mL) and exhibited limited hERG inhibition (IC50 ≥ 25 μM). Moreover, 32 exhibited improved metabolic stability relative to parent compound 8 while showing favorable bioavailability in mouse models via serum inhibition titration assays.
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Affiliation(s)
- Wei Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Shichun Lun
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, Maryland 21231-1044, United States
| | - Shuang-Shuang Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Yan-Peng Cai
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Fan Yang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Jie Tang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - William R Bishai
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, Maryland 21231-1044, United States
| | - Li-Fang Yu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
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8
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Fernandes GFS, Thompson AM, Castagnolo D, Denny WA, Dos Santos JL. Tuberculosis Drug Discovery: Challenges and New Horizons. J Med Chem 2022; 65:7489-7531. [PMID: 35612311 DOI: 10.1021/acs.jmedchem.2c00227] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the past 2000 years, tuberculosis (TB) has claimed more lives than any other infectious disease. In 2020 alone, TB was responsible for 1.5 million deaths worldwide, comparable to the 1.8 million deaths caused by COVID-19. The World Health Organization has stated that new TB drugs must be developed to end this pandemic. After decades of neglect in this field, a renaissance era of TB drug discovery has arrived, in which many novel candidates have entered clinical trials. However, while hundreds of molecules are reported annually as promising anti-TB agents, very few successfully progress to clinical development. In this Perspective, we critically review those anti-TB compounds published in the last 6 years that demonstrate good in vivo efficacy against Mycobacterium tuberculosis. Additionally, we highlight the main challenges and strategies for developing new TB drugs and the current global pipeline of drug candidates in clinical studies to foment fresh research perspectives.
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Affiliation(s)
- Guilherme F S Fernandes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Andrew M Thompson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Daniele Castagnolo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - William A Denny
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jean L Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800903, Brazil
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9
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Dhameliya TM, Devani AA, Patel KA, Shah KC. Comprehensive Coverage on Anti‐mycobacterial Endeavour Reported in 2021. ChemistrySelect 2022. [DOI: 10.1002/slct.202200921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Aanal A. Devani
- L. M. College of Pharmacy, Navrangpura Ahmedabad 380 009 Gujarat India
| | - Krupa A. Patel
- L. M. College of Pharmacy, Navrangpura Ahmedabad 380 009 Gujarat India
| | - Kashvi C. Shah
- L. M. College of Pharmacy, Navrangpura Ahmedabad 380 009 Gujarat India
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Wilson C, Ray P, Zuccotto F, Hernandez J, Aggarwal A, Mackenzie C, Caldwell N, Taylor M, Huggett M, Mathieson M, Murugesan D, Smith A, Davis S, Cocco M, Parai MK, Acharya A, Tamaki F, Scullion P, Epemolu O, Riley J, Stojanovski L, Lopez-Román EM, Torres-Gómez PA, Toledo AM, Guijarro-Lopez L, Camino I, Engelhart CA, Schnappinger D, Massoudi LM, Lenaerts A, Robertson GT, Walpole C, Matthews D, Floyd D, Sacchettini JC, Read KD, Encinas L, Bates RH, Green SR, Wyatt PG. Optimization of TAM16, a Benzofuran That Inhibits the Thioesterase Activity of Pks13; Evaluation toward a Preclinical Candidate for a Novel Antituberculosis Clinical Target. J Med Chem 2022; 65:409-423. [PMID: 34910486 PMCID: PMC8762665 DOI: 10.1021/acs.jmedchem.1c01586] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Indexed: 11/28/2022]
Abstract
With increasing drug resistance in tuberculosis (TB) patient populations, there is an urgent need for new drugs. Ideally, new agents should work through novel targets so that they are unencumbered by preexisting clinical resistance to current treatments. Benzofuran 1 was identified as a potential lead for TB inhibiting a novel target, the thioesterase domain of Pks13. Although, having promising activity against Mycobacterium tuberculosis, its main liability was inhibition of the hERG cardiac ion channel. This article describes the optimization of the series toward a preclinical candidate. Despite improvements in the hERG liability in vitro, when new compounds were assessed in ex vivo cardiotoxicity models, they still induced cardiac irregularities. Further series development was stopped because of concerns around an insufficient safety window. However, the demonstration of in vivo activity for multiple series members further validates Pks13 as an attractive novel target for antitubercular drugs and supports development of alternative chemotypes.
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Affiliation(s)
- Caroline Wilson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Peter Ray
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jorge Hernandez
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Anup Aggarwal
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Claire Mackenzie
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Malcolm Taylor
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Margaret Huggett
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Michael Mathieson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Dinakaran Murugesan
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Alasdair Smith
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Susan Davis
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Mattia Cocco
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Maloy K. Parai
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Arjun Acharya
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Fabio Tamaki
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul Scullion
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jennifer Riley
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laste Stojanovski
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Eva Maria Lopez-Román
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | | | - Ana Maria Toledo
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Laura Guijarro-Lopez
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Isabel Camino
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Lisa M. Massoudi
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Anne Lenaerts
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gregory T. Robertson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Chris Walpole
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - David Matthews
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - David Floyd
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - James C. Sacchettini
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Lourdes Encinas
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Robert H. Bates
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
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