1
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Chikhale RV, Choudhary R, Malhotra J, Eldesoky GE, Mangal P, Patil PC. Identification of novel hit molecules targeting M. tuberculosis polyketide synthase 13 by combining generative AI and physics-based methods. Comput Biol Med 2024; 176:108573. [PMID: 38723396 DOI: 10.1016/j.compbiomed.2024.108573] [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: 02/21/2024] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024]
Abstract
In this work we investigated the Pks13-TE domain, which plays a critical role in the viability of the mycobacteria. In this report, we have used a series of AI and Physics-based tools to identify Pks13-TE inhibitors. The Reinvent 4, pKCSM, KDeep, and SwissADME are AI-ML-based tools. AutoDock Vina, PLANTS, MDS, and MM-GBSA are physics-based methods. A combination of these methods yields powerful support in the drug discovery cycle. Known inhibitors of Pks13-TE were collected, curated, and used as input for the AI-based tools, and Mol2Mol molecular optimisation methods generated novel inhibitors. These ligands were filtered based on physics-based methods like molecular docking and molecular dynamics using multiple tools for consensus generation. Rigorous analysis was performed on the selected compounds to reduce the chemical space while retaining the most promising compounds. The molecule interactions, stability of the protein-ligand complexes and the comparable binding energies with the native ligand were essential factors for narrowing the ligands set. The filtered ligands from docking, MDS, and binding energy colocations were further tested for their ADMET properties since they are among the essential criteria for this series of molecules. It was found that ligands Mt1 to Mt6 have excellent predicted pharmacokinetic, pharmacodynamic and toxicity profiles and good synthesisability.
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Affiliation(s)
- Rupesh V Chikhale
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, UK.
| | - Rinku Choudhary
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 5600413, India; Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed to Be University, Pune-Satara Road, Pune, India
| | - Jagriti Malhotra
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 5600413, India; Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed to Be University, Pune-Satara Road, Pune, India
| | - Gaber E Eldesoky
- Chemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Parth Mangal
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 5600413, India; Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed to Be University, Pune-Satara Road, Pune, India
| | - Pritee Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed to Be University, Pune-Satara Road, Pune, India
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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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Shyam M, Kumar S, Singh V. Unlocking Opportunities for Mycobacterium leprae and Mycobacterium ulcerans. ACS Infect Dis 2024; 10:251-269. [PMID: 38295025 PMCID: PMC10862552 DOI: 10.1021/acsinfecdis.3c00371] [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: 07/31/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
In the recent decade, scientific communities have toiled to tackle the emerging burden of drug-resistant tuberculosis (DR-TB) and rapidly growing opportunistic nontuberculous mycobacteria (NTM). Among these, two neglected mycobacteria species of the Acinetobacter family, Mycobacterium leprae and Mycobacterium ulcerans, are the etiological agents of leprosy and Buruli ulcer infections, respectively, and fall under the broad umbrella of neglected tropical diseases (NTDs). Unfortunately, lackluster drug discovery efforts have been made against these pathogenic bacteria in the recent decade, resulting in the discovery of only a few countable hits and majorly repurposing anti-TB drug candidates such as telacebec (Q203), P218, and TB47 for current therapeutic interventions. Major ignorance in drug candidate identification might aggravate the dramatic consequences of rapidly spreading mycobacterial NTDs in the coming days. Therefore, this Review focuses on an up-to-date account of drug discovery efforts targeting selected druggable targets from both bacilli, including the accompanying challenges that have been identified and are responsible for the slow drug discovery. Furthermore, a succinct discussion of the all-new possibilities that could be alternative solutions to mitigate the neglected mycobacterial NTD burden and subsequently accelerate the drug discovery effort is also included. We anticipate that the state-of-the-art strategies discussed here may attract major attention from the scientific community to navigate and expand the roadmap for the discovery of next-generation therapeutics against these NTDs.
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Affiliation(s)
- Mousumi Shyam
- Department
of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mersa, Ranchi, Jharkhand 835215, India
| | - Sumit Kumar
- Holistic
Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
| | - Vinayak Singh
- Holistic
Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, University of Cape Town, Rondebosch 7701, South Africa
- Institute
of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Observatory 7925, Cape Town, South Africa
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4
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Verma A, Naik B, Kumar V, Mishra S, Choudhary M, Khan JM, Gupta AK, Pandey P, Rustagi S, Kakati B, Gupta S. Revolutionizing Tuberculosis Treatment: Uncovering New Drugs and Breakthrough Inhibitors to Combat Drug-Resistant Mycobacterium tuberculosis. ACS Infect Dis 2023; 9:2369-2385. [PMID: 37944023 DOI: 10.1021/acsinfecdis.3c00436] [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] [Indexed: 11/12/2023]
Abstract
Tuberculosis (TB) is a global health threat that causes significant mortality. This review explores chemotherapeutics that target essential processes in Mycobacterium tuberculosis, such as DNA replication, protein synthesis, cell wall formation, energy metabolism, and proteolysis. We emphasize the need for new drugs to treat drug-resistant strains and shorten the treatment duration. Emerging targets and promising inhibitors were identified by examining the intricate biology of TB. This review provides an overview of recent developments in the search for anti-TB drugs with a focus on newly validated targets and inhibitors. We aimed to contribute to efforts to combat TB and improve therapeutic outcomes.
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Affiliation(s)
- Ankit Verma
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Bindu Naik
- Department of Food Science and Technology, Graphic Era Deemed to be University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Sadhna Mishra
- Faculty of Agricultural Sciences, GLA University, Mathura 281406, UP, India
| | - Megha Choudhary
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Arun Kumar Gupta
- Department of Food Science and Technology, Graphic Era Deemed to be University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchur 788011, Assam, India
| | - Sarvesh Rustagi
- Department of Food Technology, UCALS, Uttaranchal University, Dehradun 248007, Uttarakhand, India
| | - Barnali Kakati
- Department of Microbiology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, U.K., India
| | - Sanjay Gupta
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
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5
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Altharawi A, Alossaimi MA, Alanazi MM, Alqahatani SM, Tahir Ul Qamar M. An integrated computational approach towards novel drugs discovery against polyketide synthase 13 thioesterase domain of Mycobacterium tuberculosis. Sci Rep 2023; 13:7014. [PMID: 37117557 PMCID: PMC10147368 DOI: 10.1038/s41598-023-34222-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/26/2023] [Indexed: 04/30/2023] Open
Abstract
The acquired drug resistance by Mycobacterium tuberculosis (M. tuberculosis) to antibiotics urges the need for developing novel anti-M. tuberculosis drugs that possess novel mechanism of action. Since traditional drug discovery is a labor-intensive and costly process, computer aided drug design is highly appreciated tool as it speeds up and lower the cost of drug development process. Herein, Asinex antibacterial compounds were virtually screened against thioesterase domain of Polyketide synthase 13, a unique enzyme that forms α-alkyl β-ketoesters as a direct precursor of mycolic acids which are essential components of the lipid-rich cell wall of M. tuberculosis. The study identified three drug-like compounds as the most promising leads; BBB_26582140, BBD_30878599 and BBC_29956160 with binding energy value of - 11.25 kcal/mol, - 9.87 kcal/mol and - 9.33 kcal/mol, respectively. The control molecule binding energy score is -9.25 kcal/mol. Also, the docked complexes were dynamically stable with maximum root mean square deviation (RMSD) value of 3 Å. Similarly, the MM-GB\PBSA method revealed highly stable complexes with mean energy values < - 75 kcal/mol for all three systems. The net binding energy scores are validated by WaterSwap and entropy energy analysis. Furthermore, The in silico druglike and pharmacokinetic investigation revealed that the compounds could be suitable candidates for additional experimentations. In summary, the study findings are significant, and the compounds may be used in experimental validation pipeline to develop potential drugs against drug-resistant tuberculosis.
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Affiliation(s)
- Ali Altharawi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Manal A Alossaimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Safar M Alqahatani
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Muhammad Tahir Ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, 38000, Pakistan.
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6
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Alsayed SSR, Gunosewoyo H. Tuberculosis: Pathogenesis, Current Treatment Regimens and New Drug Targets. Int J Mol Sci 2023; 24:ijms24065202. [PMID: 36982277 PMCID: PMC10049048 DOI: 10.3390/ijms24065202] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/03/2023] [Accepted: 03/05/2023] [Indexed: 03/30/2023] Open
Abstract
Mycobacterium tuberculosis (M. tb), the causative agent of TB, is a recalcitrant pathogen that is rife around the world, latently infecting approximately a quarter of the worldwide population. The asymptomatic status of the dormant bacteria escalates to the transmissible, active form when the host's immune system becomes debilitated. The current front-line treatment regimen for drug-sensitive (DS) M. tb strains is a 6-month protocol involving four different drugs that requires stringent adherence to avoid relapse and resistance. Poverty, difficulty to access proper treatment, and lack of patient compliance contributed to the emergence of more sinister drug-resistant (DR) strains, which demand a longer duration of treatment with more toxic and more expensive drugs compared to the first-line regimen. Only three new drugs, bedaquiline (BDQ) and the two nitroimidazole derivatives delamanid (DLM) and pretomanid (PMD) were approved in the last decade for treatment of TB-the first anti-TB drugs with novel mode of actions to be introduced to the market in more than 50 years-reflecting the attrition rates in the development and approval of new anti-TB drugs. Herein, we will discuss the M. tb pathogenesis, current treatment protocols and challenges to the TB control efforts. This review also aims to highlight several small molecules that have recently been identified as promising preclinical and clinical anti-TB drug candidates that inhibit new protein targets in M. tb.
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Affiliation(s)
- Shahinda S R Alsayed
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
| | - Hendra Gunosewoyo
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
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7
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Kumar G, Kapoor S. Targeting mycobacterial membranes and membrane proteins: Progress and limitations. Bioorg Med Chem 2023; 81:117212. [PMID: 36804747 DOI: 10.1016/j.bmc.2023.117212] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Among the various bacterial infections, tuberculosis continues to hold center stage. Its causative agent, Mycobacterium tuberculosis, possesses robust defense mechanisms against most front-line antibiotic drugs and host responses due to their complex cell membranes with unique lipid molecules. It is now well-established that bacteria change their membrane composition to optimize their environment to survive and elude drug action. Thus targeting membrane or membrane components is a promising avenue for exploiting the chemical space focussed on developing novel membrane-centric anti-bacterial small molecules. These approaches are more effective, non-toxic, and can attenuate resistance phenotype. We present the relevance of targeting the mycobacterial membrane as a practical therapeutic approach. The review highlights the direct and indirect targeting of membrane structure and function. Direct membrane targeting agents cause perturbation in the membrane potential and can cause leakage of the cytoplasmic contents. In contrast, indirect membrane targeting agents disrupt the function of membrane-associated proteins involved in cell wall biosynthesis or energy production. We discuss the chronological chemical improvements in various scaffolds targeting specific membrane-associated protein targets, their clinical evaluation, and up-to-date account of their ''mechanisms of action, potency, selectivity'' and limitations. The sources of anti-TB drugs/inhibitors discussed in this work have emerged from target-based identification, cell-based phenotypic screening, drug repurposing, and natural products. We believe this review will inspire the exploration of uncharted chemical space for informing the development of new scaffolds that can inhibit novel mycobacterial membrane targets.
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Affiliation(s)
- Gautam Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Departemnt of Natural Products, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad 500037, India.
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan.
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8
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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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9
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Identification of novel inhibitors for mycobacterial polyketide synthase 13 via in silico drug screening assisted by the parallel compound screening with genetic algorithm-based programs. J Antibiot (Tokyo) 2022; 75:552-558. [PMID: 35941150 DOI: 10.1038/s41429-022-00549-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/05/2022] [Accepted: 07/19/2022] [Indexed: 11/08/2022]
Abstract
Identifying small compounds capable of inhibiting Mycobacterium tuberculosis polyketide synthase 13 (Pks13), in charge of final step of mycolic acid biosynthesis, could lead to the development of a novel antituberculosis drug. This study screened for lead compounds capable of targeting M. tuberculosis Pks13 from a chemical library comprising 154,118 compounds through multiple in silico docking simulations. The parallel compound screening (PCS), conducted via two genetic algorithm-based programs was applied in the screening strategy. Out of seven experimentally validated compounds, four compounds showed inhibitory effects on the growth of the model mycobacteria (Mycobacterium smegmatis). Subsequent docking simulation of analogs of the promising leads with the assistance of PCS resulted in the identification of three additional compounds with potent antimycobacterial effects (compounds A1, A2, and A5). Further, molecular dynamics simulation predicted stable interaction between M. tuberculosis Pks13 active site and compound A2, which showed potent antimycobacterial activity comparable to that of isoniazid. The present study demonstrated the efficacy of in silico structure-based drug screening through PCS in antituberculosis drug discovery.
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10
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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: 46] [Impact Index Per Article: 23.0] [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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11
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Kuang W, Zhang H, Wang X, Yang P. Overcoming Mycobacterium tuberculosis through small molecule inhibitors to break down cell wall synthesis. Acta Pharm Sin B 2022; 12:3201-3214. [PMID: 35967276 PMCID: PMC9366312 DOI: 10.1016/j.apsb.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/08/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) utilizes multiple mechanisms to obtain antibiotic resistance during the treatment of infections. In addition, the biofilms, secreted by MTB, can further protect the latter from the contact with drug molecules and immune cells. These self-defending mechanisms lay a formidable challenge to develop effective therapeutic agents against chronic and recurring antibiotic-tolerant MTB infections. Although several inexpensive and effective drugs (isoniazid, rifampicin, pyrazinamide and ethambutol) have been discovered for the treatment regimen, MTB continues to cause considerable morbidity and mortality worldwide. Antibiotic resistance and tolerance remain major global issues, and innovative therapeutic strategies are urgently needed to address the challenges associated with pathogenic bacteria. Gratifyingly, the cell wall synthesis of tubercle bacilli requires the participation of many enzymes which exclusively exist in prokaryotic organisms. These enzymes, absent in human hepatocytes, are recognized as promising targets to develop anti-tuberculosis drug. In this paper, we discussed the critical roles of potential drug targets in regulating cell wall synthesis of MTB. And also, we systematically reviewed the advanced development of novel bioactive compounds or drug leads for inhibition of cell wall synthesis, including their discovery, chemical modification, in vitro and in vivo evaluation.
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Affiliation(s)
- Wenbin Kuang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haolin Zhang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Corresponding author.
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12
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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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13
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Cazzaniga G, Mori M, Chiarelli LR, Gelain A, Meneghetti F, Villa S. Natural products against key Mycobacterium tuberculosis enzymatic targets: Emerging opportunities for drug discovery. Eur J Med Chem 2021; 224:113732. [PMID: 34399099 DOI: 10.1016/j.ejmech.2021.113732] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/15/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
For centuries, natural products (NPs) have served as powerful therapeutics against a variety of human ailments. Nowadays, they still represent invaluable resources for the treatment of many diseases, including bacterial infections. After nearly three decades since the World Health Organization's (WHO) declaration of tuberculosis (TB) as a global health emergency, Mycobacterium tuberculosis (Mtb) continues to claim millions of lives, remaining among the leading causes of death worldwide. In the last years, several efforts have been devoted to shortening and improving treatment outcomes, and to overcoming the increasing resistance phenomenon. Nature has always provided a virtually unlimited source of bioactive molecules, which have inspired the development of new drugs. NPs are characterized by an exceptional chemical and structural diversity, the result of millennia of evolutionary responses to various stimuli. Thanks to their favorable structural features and their enzymatic origin, they are naturally prone to bind proteins and exhibit bioactivities. Furthermore, their worldwide distribution and ease of accessibility has contributed to promote investigations on their activity. Overall, these characteristics make NPs excellent models for the design of novel therapeutics. This review offers a critical and comprehensive overview of the most promising NPs, isolated from plants, fungi, marine species, and bacteria, endowed with inhibitory properties against traditional and emerging mycobacterial enzymatic targets. A selection of 86 compounds is here discussed, with a special emphasis on their biological activity, structure-activity relationships, and mechanism of action. Our study corroborates the antimycobacterial potential of NPs, substantiating their relevance in future drug discovery and development efforts.
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Affiliation(s)
- Giulia Cazzaniga
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Laurent Roberto Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, via A. Ferrata 9, 27100, Pavia, Italy
| | - Arianna Gelain
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy.
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
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