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Amandy FV, Neri GLL, Manzano JAH, Go AD, Macabeo APG. Polypharmacology-Driven Discovery and Design of Highly Selective, Dual and Multitargeting Inhibitors of Mycobacterium tuberculosis - A Review. Curr Drug Targets 2024; 25:620-634. [PMID: 38859782 DOI: 10.2174/0113894501306302240526160804] [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: 01/24/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024]
Abstract
The increasing demand for novel antitubercular agents has been the main 'force' of many TB research efforts due to the uncontrolled growing number of drug-resistant strains of M. tuberculosis in the clinical setting. Many strategies have been employed to address the drug-resistant issue, including a trend that is gaining attention, which is the design and discovery of Mtb inhibitors that are either dual- or multitargeting. The multiple-target design concept is not new in medicinal chemistry. With a growing number of newly discovered Mtb proteins, numerous targets are now available for developing new biochemical/cell-based assays and computer-aided drug design (CADD) protocols. To describe the achievements and overarching picture of this field in anti- infective drug discovery, we provide in this review small molecules that exhibit profound inhibitory activity against the tubercle bacilli and are identified to trace two or more Mtb targets. This review also presents emerging design methodologies for developing new anti-TB agents, particularly tailored to structure-based CADD.
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Affiliation(s)
- Franklin V Amandy
- The Graduate School, University of Santo Tomas, España Blvd., Manila 1015, Philippines
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
- Department of Chemistry, College of Science, Adamson University, San Marcelino St., Ermita, Manila 1000, Philippines
| | - Gabriel L L Neri
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
| | - Joe A H Manzano
- The Graduate School, University of Santo Tomas, España Blvd., Manila 1015, Philippines
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
| | - Adrian D Go
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
- Department of Chemistry, College of Science, Adamson University, San Marcelino St., Ermita, Manila 1000, Philippines
| | - Allan P G Macabeo
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
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Stevens M, Howe C, Ray AM, Washburn A, Chitre S, Sivinski J, Park Y, Hoang QQ, Chapman E, Johnson SM. Analogs of nitrofuran antibiotics are potent GroEL/ES inhibitor pro-drugs. Bioorg Med Chem 2020; 28:115710. [PMID: 33007545 DOI: 10.1016/j.bmc.2020.115710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 01/14/2023]
Abstract
In two previous studies, we identified compound 1 as a moderate GroEL/ES inhibitor with weak to moderate antibacterial activity against Gram-positive and Gram-negative bacteria including Bacillus subtilis, methicillin-resistant Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, and SM101 Escherichia coli (which has a compromised lipopolysaccharide biosynthetic pathway making bacteria more permeable to drugs). Extending from those studies, we developed two series of analogs with key substructures resembling those of known antibacterials, nitroxoline (hydroxyquinoline moiety) and nifuroxazide/nitrofurantoin (bis-cyclic-N-acylhydrazone scaffolds). Through biochemical and cell-based assays, we identified potent GroEL/ES inhibitors that selectively blocked E. faecium, S. aureus, and E. coli proliferation with low cytotoxicity to human colon and intestine cells in vitro. Initially, only the hydroxyquinoline-bearing analogs were found to be potent inhibitors in our GroEL/ES-mediated substrate refolding assays; however, subsequent testing in the presence of an E. coli nitroreductase (NfsB) in situ indicated that metabolites of the nitrofuran-bearing analogs were potent GroEL/ES inhibitor pro-drugs. Consequently, this study has identified a new target of nitrofuran-containing drugs, and is the first reported instance of such a unique class of GroEL/ES chaperonin inhibitors. The intriguing results presented herein provide impetus for expanded studies to validate inhibitor mechanisms and optimize this antibacterial class using the respective GroEL/ES chaperonin systems and nitroreductases from E. coli and the ESKAPE bacteria.
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Affiliation(s)
- Mckayla Stevens
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Chris Howe
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Anne-Marie Ray
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Alex Washburn
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Siddhi Chitre
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Jared Sivinski
- The University of Arizona, College of Pharmacy, Department of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ 85721, United States
| | - Yangshin Park
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States; Stark Neurosciences Research Institute, Indiana University School of Medicine. 320 W. 15th Street, Suite 414, Indianapolis, IN 46202, United States; Department of Neurology, Indiana University School of Medicine. 635 Barnhill Drive, Indianapolis, IN 46202, United States
| | - Quyen Q Hoang
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States; Stark Neurosciences Research Institute, Indiana University School of Medicine. 320 W. 15th Street, Suite 414, Indianapolis, IN 46202, United States; Department of Neurology, Indiana University School of Medicine. 635 Barnhill Drive, Indianapolis, IN 46202, United States
| | - Eli Chapman
- The University of Arizona, College of Pharmacy, Department of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ 85721, United States
| | - Steven M Johnson
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States.
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Riffo-Vasquez Y, Kanabar V, Keir SD, E-Lacerda RR, Man F, Jackson DJ, Corrigall V, Coates ARM, Page CP. Modulation of allergic inflammation in the lung by a peptide derived from Mycobacteria tuberculosis chaperonin 60.1. Clin Exp Allergy 2020; 50:508-519. [PMID: 31845415 DOI: 10.1111/cea.13550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/25/2019] [Accepted: 12/01/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND We have previously demonstrated that Mycobacteria tuberculosis chaperonin 60.1 inhibits leucocyte diapedesis and bronchial hyperresponsiveness in a murine model of allergic lung inflammation. METHODS In the present study, we have investigated the effect of a shorter peptide sequence derived from Cpn 60.1, named IRL201104, on allergic lung inflammation induced by ovalbumin (OVA) in mice and by house dust mite (HDM) in guinea pigs, as well as investigating the action of IRL201104 on human cells in vitro. RESULTS Pre-treatment of mice or guinea pigs with IRL201104 inhibits the infiltration of eosinophils to the lung, cytokine release, and in guinea pig skin, inhibits allergen-induced vascular permeability. The protective effect of intranasal IRL201104 against OVA-induced eosinophilia persisted for up to 20 days post-treatment. Moreover, OVA-sensitized mice treated intranasally with 20 ng/kg of IRL201104 show a significant increase in the expression of the anti-inflammatory molecule ubiquitin A20 and significant inhibition of the activation of NF-κB in lung tissue. Our results also show that A20 expression was significantly reduced in blood leucocytes and ASM obtained from patients with asthma compared to cells obtained from healthy subjects which were restored after incubation with IRL201104 in vitro, when added alone, or in combination with LPS or TNF-α in ASM. CONCLUSIONS Our results suggest that a peptide derived from mycobacterial Cpn60.1 has a long-lasting anti-inflammatory and immunomodulatory activity which may help explain some of the protective effects of TB against allergic diseases.
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Affiliation(s)
- Yanira Riffo-Vasquez
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Sciences, King's College London, London, UK
| | - Varsha Kanabar
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Sciences, King's College London, London, UK
| | - Sandra D Keir
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Sciences, King's College London, London, UK
| | - Rodrigo R E-Lacerda
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Sciences, King's College London, London, UK
| | - Francis Man
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Sciences, King's College London, London, UK
| | - David J Jackson
- Asthma Care Guy's & St Thomas' NHS Trust, London, UK.,Faculty of Life Sciences and Medicine, MRC & Asthma UK Centre, Guy's Hospital, King's College London, London, UK
| | - Valerie Corrigall
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Sciences, King's College London, London, UK
| | - Anthony R M Coates
- Medical Microbiology, Institute of Infection and Immunity, St George's, University of London, London, UK
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Sciences, King's College London, London, UK
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Washburn A, Abdeen S, Ovechkina Y, Ray AM, Stevens M, Chitre S, Sivinski J, Park Y, Johnson J, Hoang QQ, Chapman E, Parish T, Johnson SM. Dual-targeting GroEL/ES chaperonin and protein tyrosine phosphatase B (PtpB) inhibitors: A polypharmacology strategy for treating Mycobacterium tuberculosis infections. Bioorg Med Chem Lett 2019; 29:1665-1672. [PMID: 31047750 DOI: 10.1016/j.bmcl.2019.04.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/20/2019] [Accepted: 04/23/2019] [Indexed: 12/13/2022]
Abstract
Current treatments for Mycobacterium tuberculosis infections require long and complicated regimens that can lead to patient non-compliance, increasing incidences of antibiotic-resistant strains, and lack of efficacy against latent stages of disease. Thus, new therapeutics are needed to improve tuberculosis standard of care. One strategy is to target protein homeostasis pathways by inhibiting molecular chaperones such as GroEL/ES (HSP60/10) chaperonin systems. M. tuberculosis has two GroEL homologs: GroEL1 is not essential but is important for cytokine-dependent granuloma formation, while GroEL2 is essential for survival and likely functions as the canonical housekeeping chaperonin for folding proteins. Another strategy is to target the protein tyrosine phosphatase B (PtpB) virulence factor that M. tuberculosis secretes into host cells to help evade immune responses. In the present study, we have identified a series of GroEL/ES inhibitors that inhibit M. tuberculosis growth in liquid culture and biochemical function of PtpB in vitro. With further optimization, such dual-targeting GroEL/ES and PtpB inhibitors could be effective against all stages of tuberculosis - actively replicating bacteria, bacteria evading host cell immune responses, and granuloma formation in latent disease - which would be a significant advance to augment current therapeutics that primarily target actively replicating bacteria.
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Affiliation(s)
- Alex Washburn
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Sanofar Abdeen
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Yulia Ovechkina
- Infectious Disease Research Institute, 1616 Eastlake Ave E, Seattle, WA 98102, United States
| | - Anne-Marie Ray
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Mckayla Stevens
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Siddhi Chitre
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Jared Sivinski
- The University of Arizona, College of Pharmacy, Department of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ 85721, United States
| | - Yangshin Park
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States; Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 W. 15th Street, Suite 414, Indianapolis, IN 46202, United States; Department of Neurology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, United States
| | - James Johnson
- Infectious Disease Research Institute, 1616 Eastlake Ave E, Seattle, WA 98102, United States
| | - Quyen Q Hoang
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States; Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 W. 15th Street, Suite 414, Indianapolis, IN 46202, United States; Department of Neurology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, United States
| | - Eli Chapman
- The University of Arizona, College of Pharmacy, Department of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ 85721, United States
| | - Tanya Parish
- Infectious Disease Research Institute, 1616 Eastlake Ave E, Seattle, WA 98102, United States
| | - Steven M Johnson
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States.
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Masoudi-Sobhanzadeh Y, Motieghader H. World Competitive Contests (WCC) algorithm: A novel intelligent optimization algorithm for biological and non-biological problems. INFORMATICS IN MEDICINE UNLOCKED 2016; 3:15-28. [PMID: 32363231 PMCID: PMC7185599 DOI: 10.1016/j.imu.2016.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/29/2016] [Accepted: 06/27/2016] [Indexed: 02/02/2023] Open
Abstract
Since different sciences face lots of problems which cannot be solved in reasonable time order, we need new methods and algorithms for getting acceptable answers in proper time order. In the present study, a novel intelligent optimization algorithm, known as WCC (World Competitive Contests), has been proposed and applied to find the transcriptional factor binding sites (TFBS) and eight benchmark functions discovery processes. We recognize the need to introduce an intelligent optimization algorithm because the TFBS discovery is a biological and an NP-Hard problem. Although there are some intelligent algorithms for the purpose of solving the above-mentioned problems, an optimization algorithm with good and acceptable performance, which is based on the real parameters, is essential. Like the other optimization algorithms, the proposed algorithm starts with the first population of teams. After teams are put into different groups, they will begin competing against their rival teams. The highly qualified teams will ascend to the elimination stage and will play each other in the next rounds. The other teams will wait for a new season to start. In this paper, we’re going to implement our proposed algorithm and compare it with five famous optimization algorithms from the perspective of the following: the obtained results, stability, convergence, standard deviation and elapsed time, which are applied to the real and randomly created datasets with different motif sizes. According to our obtained results, in many cases, the WCC׳s performance is better than the other algorithms’. A new optimization algorithm which is named as WCC (World Competitive Contests) and is inspired by human sport rules is introduced. WCC is applied to TFBS (transcriptional factor binding sites) problem and eight benchmark functions. WCC is compared with the five known optimization algorithms. Experimental results show WCC’s remarkable performance relative to other optimization algorithms on eight benchmark functions and TFBS problem. WCC is implementable on the problems which can’t be solved in reasonable time order (NP problems).
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Affiliation(s)
- Yosef Masoudi-Sobhanzadeh
- Department of Computer Engineering, Payam Noor University, Tabriz, Iran.,Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Habib Motieghader
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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The evolution of protein moonlighting: adaptive traps and promiscuity in the chaperonins. Biochem Soc Trans 2015; 42:1709-14. [PMID: 25399594 DOI: 10.1042/bst20140225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Moonlighting proteins exhibit functions that are alternative to their main role in the cell. Heat-shock proteins, also known as molecular chaperones, are now recognized for their wide range of activities in and/or outside the cell, being prominent examples of moonlighting proteins. Chaperonins are highly conserved molecular chaperones that fold other proteins into their native conformation allowing them to carry out essential functions in the cell. Activities alternative to folding have been reported for the chaperonin (Cpn) 60 protein. Preservation of various alternative functions in one protein conflicts with the optimization of each of the functions. What evolutionary mechanisms have allowed the persistence of moonlighting proteins, and in particular the chaperonins, remains a mystery. In the present article, I argue that mechanisms that increase the resistance of phenotypes to genetic and environmental perturbations enable the persistence of a reservoir of genetic variants, each potentially codifying for a distinct function. Gene duplication is one such mechanism that has characterized the expansion and has been concomitant with the emergence of novel functions in these protein families. Indeed, Cpn60 performs a large list of folding-independent functions, including roles in the transmission of viruses from insects to plants and stimulation of the immune system, among others. In addition to the innovation promoted by gene duplication, I discuss that the Cpn60 protein comprises a hidden amino acid combinatorial code that may well be responsible for its ability to develop novel functions while maintaining an optimized folding ability. The present review points to a complex model of evolution of protein moonlighting.
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Kumar CMS, Mande SC, Mahajan G. Multiple chaperonins in bacteria--novel functions and non-canonical behaviors. Cell Stress Chaperones 2015; 20:555-74. [PMID: 25986150 PMCID: PMC4463927 DOI: 10.1007/s12192-015-0598-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 01/05/2023] Open
Abstract
Chaperonins are a class of molecular chaperones that assemble into a large double ring architecture with each ring constituting seven to nine subunits and enclosing a cavity for substrate encapsulation. The well-studied Escherichia coli chaperonin GroEL binds non-native substrates and encapsulates them in the cavity thereby sequestering the substrates from unfavorable conditions and allowing the substrates to fold. Using this mechanism, GroEL assists folding of about 10-15 % of cellular proteins. Surprisingly, about 30 % of the bacteria express multiple chaperonin genes. The presence of multiple chaperonins raises questions on whether they increase general chaperoning ability in the cell or have developed specific novel cellular roles. Although the latter view is widely supported, evidence for the former is beginning to appear. Some of these chaperonins can functionally replace GroEL in E. coli and are generally indispensable, while others are ineffective and likewise are dispensable. Additionally, moonlighting functions for several chaperonins have been demonstrated, indicating a functional diversity among the chaperonins. Furthermore, proteomic studies have identified diverse substrate pools for multiple chaperonins. We review the current perception on multiple chaperonins and their physiological and functional specificities.
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Affiliation(s)
- C M Santosh Kumar
- Laboratory of Structural Biology, National Centre for Cell Science, Pune, 411007, India,
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