1
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Sabarathinam S, Ganamurali N, Satheesh S, Dhanasekaran D, Raja A. Pharmacokinetic correlation of structurally modified chalcone derivatives as promising leads to treat tuberculosis. Future Med Chem 2023; 15:1903-1913. [PMID: 37877262 DOI: 10.4155/fmc-2023-0161] [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: 10/26/2023] Open
Abstract
In this study, we evaluated the potential of curated structurally modified chalcone derivatives as anti-tuberculosis (TB) agents through computer-aided drug design. Compounds from the flavonoid family known as chalcones were identified by the chemical group 1,3-diaryl-2-propen-1-one. After a search of the literature, 14 outstanding structurally modified chalcones were selected and evaluated for inhibitory activity against Mycobacterium tuberculosis H37Rv targets. The therapeutic potential of the chalcones was directly based on the drug-likeness and pharmacokinetic properties of the synthesized compounds. Prompt drug selection and personalized therapy are required to prevent TB from progressing and spreading to others. Pharmacokinetic parameters helps in the identification of lead molecule, at the earlier stages of drug development.
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Affiliation(s)
- Sarvesh Sabarathinam
- Drug Testing Laboratory, Interdisciplinary Institute of Indian System of Medicine, SRM Institute of Science & Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
- Clinical Trial Unit, Metabolic Ward, Interdisciplinary Institute of Indian System of Medicine, SRM Institute of Science & Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
- Certificate Program-Analytical Techniques in Herbal Drug Industry, Interdisciplinary Institute of Indian System of Medicine, SRM Institute of Science & Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Nila Ganamurali
- Certificate Program-Analytical Techniques in Herbal Drug Industry, Interdisciplinary Institute of Indian System of Medicine, SRM Institute of Science & Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Sanjana Satheesh
- Department of Biotechnology, Birla Institute of Technology & Science, Dubai Campus, Dubai International Academic City, PO Box 345055, Dubai, United Arab Emirates
| | - Dhivya Dhanasekaran
- Certificate Program-Analytical Techniques in Herbal Drug Industry, Interdisciplinary Institute of Indian System of Medicine, SRM Institute of Science & Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Arun Raja
- Department of Community Medicine, Sree Balaji Medical College & Hospital, Chrompet, Chennai, Tamil Nadu, 600044, India
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2
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Yadav S, Soni A, Tanwar O, Bhadane R, Besra GS, Kawathekar N. DprE1 Inhibitors: Enduring Aspirations for Future Antituberculosis Drug Discovery. ChemMedChem 2023; 18:e202300099. [PMID: 37246503 DOI: 10.1002/cmdc.202300099] [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: 02/19/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 05/30/2023]
Abstract
DprE1 is a crucial enzyme involved in the cell wall synthesis of Mycobacterium tuberculosis and a promising target for antituberculosis drug development. However, its unique structural characteristics for ligand binding and association with DprE2 make developing new clinical compounds challenging. This review provides an in-depth analysis of the structural requirements for both covalent and non-covalent inhibitors, their 2D and 3D binding patterns, as well as their biological activity data in vitro and in vivo, including pharmacokinetic information. We also introduce a protein quality score (PQS) and an active-site map of the DprE1 enzyme to help medicinal chemists better understand DprE1 inhibition and develop new and effective anti-TB drugs. Furthermore, we examine the resistance mechanisms associated with DprE1 inhibitors to understand future developments due to resistance emergence. This comprehensive review offers insight into the DprE1 active site, including protein-binding maps, PQS, and graphical representations of known inhibitors, making it a valuable resource for medicinal chemists working on future antitubercular compounds.
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Affiliation(s)
- Saloni Yadav
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
| | - Aastha Soni
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
| | - Omprakash Tanwar
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
| | - Rajendra Bhadane
- Turku Cellular Microbiology Laboratory (TCML), Åbo Akademi University, 20014, Turku, Finland
- Institute of Biomedicine, University of Turku, 20520, Turku, Finland
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Neha Kawathekar
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
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3
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Young RJ. Today's drug discovery and the shadow of the rule of 5. Expert Opin Drug Discov 2023; 18:965-972. [PMID: 37378429 DOI: 10.1080/17460441.2023.2228199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION The rule of 5 developed by Lipinski et al., a landmark and prescient piece of scholarship, focused the minds of drug hunters by systematically characterizing the physical make-up of drug molecules for the first time, noting many sub-optimal compounds identified by high-throughput screening practices. Its profound influence on thinking and practices, whilst providing benefit, perhaps etched the guidelines too strongly in the minds of some drug hunters who applied the bounds too literally without understanding the implications of the underlying statistics. AREAS COVERED This opinion is based on recent key developments that take thinking, measurements, and standards beyond those first set out, particularly the influences of molecular weight and the understanding, measurement, and calculation of lipophilicity. EXPERT OPINION Techniques and technologies for physicochemical estimations set new standards. It is timely to celebrate the significance and influence of the rule of 5, whilst taking thinking to new levels with better characterizations. The shadow of the rule of 5 may be long, but it is not dark, as new measurements, predictions and principles emerge as guiding lights in the design and prioritization of higher-quality molecules redefining the meaning of beyond the rule of 5.
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Affiliation(s)
- Robert J Young
- Blue Burgundy (Drug Discovery Consultancy) Ltd, Bedford, UK
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4
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Stegemann S, Moreton C, Svanbäck S, Box K, Motte G, Paudel A. Trends in oral small-molecule drug discovery and product development based on product launches before and after the Rule of Five. Drug Discov Today 2023; 28:103344. [PMID: 36442594 DOI: 10.1016/j.drudis.2022.103344] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/28/2022] [Accepted: 09/01/2022] [Indexed: 11/26/2022]
Abstract
In 1997, the 'Rule of Five' (Ro5) suggested physicochemical limitations for orally administered drugs, based on the analysis of chemical libraries from the early 1990s. In this review, we report on the trends in oral drug product development by analyzing products launched between 1994 and 1997 and between 2013 and 2019. Our analysis confirmed that most new oral drugs are within the Ro5 descriptors; however, the number of new drug products of drugs with molecular weight (MW) and calculated partition coefficient (clogP) beyond the Ro5 has slightly increased. Analysis revealed that there is no single scientific or technological reason for this trend, but that it likely results from incremental advances are being made in molecular biology, target diversity, drug design, medicinal chemistry, predictive modeling, drug metabolism and pharmacokinetics, and drug delivery.
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Affiliation(s)
- Sven Stegemann
- Institute for Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria.
| | | | - Sami Svanbäck
- The Solubility Company Ltd, Viikinkaari 4, 00790 Helsinki, Finland
| | - Karl Box
- Pion Inc. (UK) Ltd, Forest Row, UK
| | - Geneviève Motte
- JEN Pharma Consulting, 182 Rue Henri Latour, 1450 Chastre, Belgium
| | - Amrit Paudel
- Institute for Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria; Research Center Pharmaceutical Engineering GmbH, Inffeldgasse 13, 8010 Graz, Austria
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5
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Supramolecular organization and dynamics of mannosylated phosphatidylinositol lipids in the mycobacterial plasma membrane. Proc Natl Acad Sci U S A 2023; 120:e2212755120. [PMID: 36693100 PMCID: PMC9945971 DOI: 10.1073/pnas.2212755120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), a disease that claims ~1.6 million lives annually. The current treatment regime is long and expensive, and missed doses contribute to drug resistance. Therefore, development of new anti-TB drugs remains one of the highest public health priorities. Mtb has evolved a complex cell envelope that represents a formidable barrier to antibiotics. The Mtb cell envelop consists of four distinct layers enriched for Mtb specific lipids and glycans. Although the outer membrane, comprised of mycolic acid esters, has been extensively studied, less is known about the plasma membrane, which also plays a critical role in impacting antibiotic efficacy. The Mtb plasma membrane has a unique lipid composition, with mannosylated phosphatidylinositol lipids (phosphatidyl-myoinositol mannosides, PIMs) comprising more than 50% of the lipids. However, the role of PIMs in the structure and function of the membrane remains elusive. Here, we used multiscale molecular dynamics (MD) simulations to understand the structure-function relationship of the PIM lipid family and decipher how they self-organize to shape the biophysical properties of mycobacterial plasma membranes. We assess both symmetric and asymmetric assemblies of the Mtb plasma membrane and compare this with residue distributions of Mtb integral membrane protein structures. To further validate the model, we tested known anti-TB drugs and demonstrated that our models agree with experimental results. Thus, our work sheds new light on the organization of the mycobacterial plasma membrane. This paves the way for future studies on antibiotic development and understanding Mtb membrane protein function.
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6
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Machine Learning Prediction of Mycobacterial Cell Wall Permeability of Drugs and Drug-like Compounds. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020633. [PMID: 36677691 PMCID: PMC9863426 DOI: 10.3390/molecules28020633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023]
Abstract
The cell wall of Mycobacterium tuberculosis and related organisms has a very complex and unusual organization that makes it much less permeable to nutrients and antibiotics, leading to the low activity of many potential antimycobacterial drugs against whole-cell mycobacteria compared to their isolated molecular biotargets. The ability to predict and optimize the cell wall permeability could greatly enhance the development of novel antitubercular agents. Using an extensive structure-permeability dataset for organic compounds derived from published experimental big data (5371 compounds including 2671 penetrating and 2700 non-penetrating compounds), we have created a predictive classification model based on fragmental descriptors and an artificial neural network of a novel architecture that provides better accuracy (cross-validated balanced accuracy 0.768, sensitivity 0.768, specificity 0.769, area under ROC curve 0.911) and applicability domain compared with the previously published results.
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7
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Young RJ, Flitsch SL, Grigalunas M, Leeson PD, Quinn RJ, Turner NJ, Waldmann H. The Time and Place for Nature in Drug Discovery. JACS AU 2022; 2:2400-2416. [PMID: 36465532 PMCID: PMC9709949 DOI: 10.1021/jacsau.2c00415] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 05/31/2023]
Abstract
The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.
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Affiliation(s)
| | - Sabine L. Flitsch
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Grigalunas
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Paul D. Leeson
- Paul
Leeson Consulting Limited, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K.
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
- Faculty of
Chemistry and Chemical Biology, Technical
University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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8
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Radhakrishnan A, Brown CM, Guy CS, Cooper C, Pacheco-Gomez R, Stansfeld PJ, Fullam E. Interrogation of the Pathogen Box reveals small molecule ligands against the mycobacterial trehalose transporter LpqY-SugABC. RSC Med Chem 2022; 13:1225-1233. [PMID: 36320433 PMCID: PMC9579956 DOI: 10.1039/d2md00104g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/01/2022] [Indexed: 12/04/2022] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, claims ∼1.5 million lives annually. Effective chemotherapy is essential to control TB, however the emergence of drug-resistant strains of TB have seriously threatened global attempts to control and eradicate this deadly pathogen. Trehalose recycling via the LpqY-SugABC importer is essential for the virulence and survival of Mtb and inhibiting or hijacking this transport system is an attractive approach for the development of novel anti-tubercular and diagnostic agents. Therefore, we interrogated the drug-like compounds in the open-source Medicines for Malaria Pathogen Box and successfully identified seven compounds from the TB, kinetoplastids and reference compound disease sets that recognise LpqY. The molecules have diverse chemical scaffolds, are not specific trehalose analogues, and may be used as novel templates to facilitate the development of therapeutics that kill Mtb with a novel mechanism of action via the mycobacterial trehalose LpqY-SugABC transport system.
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Affiliation(s)
- Anjana Radhakrishnan
- School of Life Sciences, University of Warwick Coventry CV4 7AL UK +44 (0)2476 574239
| | - Chelsea M Brown
- School of Life Sciences, University of Warwick Coventry CV4 7AL UK +44 (0)2476 574239
| | - Collette S Guy
- School of Life Sciences, University of Warwick Coventry CV4 7AL UK +44 (0)2476 574239
| | - Charlotte Cooper
- School of Life Sciences, University of Warwick Coventry CV4 7AL UK +44 (0)2476 574239
| | - Raul Pacheco-Gomez
- Malvern Panalytical Ltd, Enigma Business Park Grovewood Road Malvern WR14 1XZ UK
| | - Phillip J Stansfeld
- School of Life Sciences, University of Warwick Coventry CV4 7AL UK +44 (0)2476 574239
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Elizabeth Fullam
- School of Life Sciences, University of Warwick Coventry CV4 7AL UK +44 (0)2476 574239
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9
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Guy CS, Tomás RMF, Tang Q, Gibson MI, Fullam E. Imaging of antitubercular dimeric boronic acids at the mycobacterial cell surface by click-probe capture. Chem Commun (Camb) 2022; 58:9361-9364. [PMID: 35917119 PMCID: PMC9387567 DOI: 10.1039/d2cc02407a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Dimeric boronic acids kill Mycobacterium tuberculosis (Mtb) by targeting mycobacterial specific extracellular glycans, removing the requirement for a therapeutic agent to permeate the complex cell envelope. Here we report the successful development and use of new ‘clickable’ boronic acid probes as a powerful method to enable the direct detection and visualisation of this unique class of cell-surface targeting antitubercular agents. Antitubercular ‘clickable’ diboronic acid agents are directly incorporated into the mycobacterial cell envelope through glycan-targeting.![]()
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Affiliation(s)
- Collette S Guy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Ruben M F Tomás
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Qiao Tang
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Elizabeth Fullam
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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10
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Karlikowska M, Singh A, Bhatt A, Ott S, Bottrill AR, Besra GS, Fullam E. Biochemical and phenotypic characterisation of the Mycobacterium smegmatis transporter UspABC. Cell Surf 2021; 7:100052. [PMID: 34296047 PMCID: PMC8281650 DOI: 10.1016/j.tcsw.2021.100052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 11/08/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is an intracellular human pathogen that has evolved to survive in a nutrient limited environment within the host for decades. Accordingly, Mtb has developed strategies to acquire scarce nutrients and the mycobacterial transporter systems provide an important route for the import of key energy sources. However, the physiological role of the Mtb transporters and their substrate preference(s) are poorly characterised. Previous studies have established that the Mtb UspC solute-binding domain recognises amino- and phosphorylated-sugars, indicating that the mycobacterial UspABC transporter plays a key role in the import of peptidoglycan precursors. Herein, we have used a wide array of approaches to investigate the role of UspABC in Mycobacterium smegmatis by analysis of mutant strains that either lack the solute binding domain: ΔuspC or the entire transport complex: ΔuspABC. Analysis of mycobacterial transcripts shows that the uspABC system is functionally expressed in mycobacteria as a contiguous reading frame. Topology mapping confirms an Nin-Cin orientation of the UspAB integral membrane spanning domains. Phenotypic microarray profiling of commercially available sugars suggests, unexpectedly, that the uspC and ΔuspABC mutants had different carbon utilisation profiles and that neither strain utilised glucose-1-phosphate. Furthermore, proteomics analysis showed an alteration in the abundance of proteins involved in sugar and lipid metabolism, crucial for cell envelope synthesis, and we propose that UspABC has an important role in determining the interplay between these pathways.
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Affiliation(s)
| | - Albel Singh
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Apoorva Bhatt
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Sascha Ott
- Warwick Medical School, University of Warwick, CV4 7AL, UK
- Bioinformatics Research Technology Platform, University of Warwick, Coventry CV4 7AL, UK
| | | | - Gurdyal S. Besra
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Elizabeth Fullam
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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11
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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12
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A Fine-Tuned Lipophilicity/Hydrophilicity Ratio Governs Antibacterial Potency and Selectivity of Bifurcated Halogen Bond-Forming NBTIs. Antibiotics (Basel) 2021; 10:antibiotics10070862. [PMID: 34356782 PMCID: PMC8300687 DOI: 10.3390/antibiotics10070862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022] Open
Abstract
Herein, we report the design of a focused library of novel bacterial topoisomerase inhibitors (NBTIs) based on innovative mainly monocyclic right-hand side fragments active against DNA gyrase and Topo IV. They exhibit a very potent and wide range of antibacterial activity, even against some of the most concerning hard-to-treat pathogens for which new antibacterials are urgently needed, as reported by the WHO and CDC. NBTIs enzyme activity and whole cell potency seems to depend on the fine-tuned lipophilicity/hydrophilicity ratio that governs the permeability of those compounds through the bacterial membranes. Lipophilicity of NBTIs is apparently optimal for passing through the membrane of Gram-positive bacteria, but the higher, although not excessive lipophilicity and suitable hydrophilicity seems to determine the passage through Gram-negative bacterial membranes. However, due to the considerable hERG inhibition, which is still at least two orders of magnitude away from MICs, continued optimization is required to realize their full potential.
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13
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Kingdon ADH, Alderwick LJ. Structure-based in silico approaches for drug discovery against Mycobacterium tuberculosis. Comput Struct Biotechnol J 2021; 19:3708-3719. [PMID: 34285773 PMCID: PMC8258792 DOI: 10.1016/j.csbj.2021.06.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis is the causative agent of TB and was estimated to cause 1.4 million death in 2019, alongside 10 million new infections. Drug resistance is a growing issue, with multi-drug resistant infections representing 3.3% of all new infections, hence novel antimycobacterial drugs are urgently required to combat this growing health emergency. Alongside this, increased knowledge of gene essentiality in the pathogenic organism and larger compound databases can aid in the discovery of new drug compounds. The number of protein structures, X-ray based and modelled, is increasing and now accounts for greater than > 80% of all predicted M. tuberculosis proteins; allowing novel targets to be investigated. This review will focus on structure-based in silico approaches for drug discovery, covering a range of complexities and computational demands, with associated antimycobacterial examples. This includes molecular docking, molecular dynamic simulations, ensemble docking and free energy calculations. Applications of machine learning onto each of these approaches will be discussed. The need for experimental validation of computational hits is an essential component, which is unfortunately missing from many current studies. The future outlooks of these approaches will also be discussed.
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Key Words
- CV, collective variable
- Docking
- Drug discovery
- In silico
- LIE, Linear Interaction Energy
- MD, Molecular Dynamic
- MDR, multi-drug resistant
- MMPB(GB)SA, Molecular Mechanics with Poisson Boltzmann (or generalised Born) and Surface Area solvation
- Machine learning
- Mt, Mycobacterium tuberculosis
- Mycobacterium tuberculosis
- PTC, peptidyl transferase centre
- RMSD, root-mean square-deviation
- Tuberculosis, TB
- cMD, Classical Molecular Dynamic
- cryo-EM, cryogenic electron microscopy
- ns, nanosecond
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Affiliation(s)
- Alexander D H Kingdon
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Luke J Alderwick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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14
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Pflégr V, Horváth L, Stolaříková J, Pál A, Korduláková J, Bősze S, Vinšová J, Krátký M. Design and synthesis of 2-(2-isonicotinoylhydrazineylidene)propanamides as InhA inhibitors with high antitubercular activity. Eur J Med Chem 2021; 223:113668. [PMID: 34198149 DOI: 10.1016/j.ejmech.2021.113668] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/17/2022]
Abstract
Based on successful antitubercular isoniazid scaffold we have designed its "mee-too" analogues by a combination of this drug linked with substituted anilines through pyruvic acid as a bridge. Lipophilicity important for passive diffusion through impenetrable mycobacterial cell wall was increased by halogen substitution on the aniline. We prepared twenty new 2-(2-isonicotinoylhydrazineylidene)propanamides that were assayed against susceptible Mycobacterium tuberculosis H37Rv, nontuberculous mycobacteria, and also multidrug-resistant tuberculous strains (MDR-TB). All the compounds showed excellent activity not only against Mtb. (minimum inhibitory concentrations, MIC, from ≤0.03 μM), but also against M. kansasii (MIC ≥2 μM). The most active molecules have CF3 and OCF3 substituent in the position 4 on the aniline ring. MIC against MDR-TB were from 8 μM. The most effective derivatives were used for the mechanism of action investigation. The treatment of Mtb. H37Ra with tested compounds led to decreased production of mycolic acids and the strains overproducing InhA were more resistant to them. These results confirm that studied compounds inhibit the enoyl-acyl carrier protein reductase (InhA) in mycobacteria. The compounds did not show any cytotoxic and cytostatic activity for HepG2 cells. The amides can be considered as a promising scaffold for antitubercular drug discovery having better antimicrobial properties than original isoniazid together with a significantly improved pharmaco-toxicological profile.
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Affiliation(s)
- Václav Pflégr
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Lilla Horváth
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Institute of Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, Budapest, H-1117, P.O. Box 32, 1518, Budapest 112, Hungary
| | - Jiřina Stolaříková
- Laboratory for Mycobacterial Diagnostics and Tuberculosis, Regional Institute of Public Health in Ostrava, Partyzánské náměstí 7, 702 00, Ostrava, Czech Republic
| | - Adrián Pál
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina CH-1, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina CH-1, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Szilvia Bősze
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Institute of Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, Budapest, H-1117, P.O. Box 32, 1518, Budapest 112, Hungary
| | - Jarmila Vinšová
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05, Hradec Králové, Czech Republic.
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15
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Bhanot A, Sundriyal S. Physicochemical Profiling and Comparison of Research Antiplasmodials and Advanced Stage Antimalarials with Oral Drugs. ACS OMEGA 2021; 6:6424-6437. [PMID: 33718733 PMCID: PMC7948433 DOI: 10.1021/acsomega.1c00104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
To understand the property space of antimalarials, we collated a large dataset of research antiplasmodial (RAP) molecules with known in vitro potencies and advanced stage antimalarials (ASAMs) with established oral bioavailability. While RAP molecules are "non-druglike", ASAM molecules display properties closer to Lipinski's and Veber's thresholds. Comparison within the different potency groups of RAP molecules indicates that the in vitro potency is positively correlated to the molecular weight, the calculated octanol-water partition coefficient (clog P), aromatic ring counts (#Ar), and hydrogen bond acceptors. Despite both categories being bioavailable, the ASAM molecules are relatively larger and more lipophilic, have a lower polar surface area, and possess a higher count of heteroaromatic rings than oral drugs. Also, antimalarials are found to have a higher proportion of aromatic (#ArN) and basic nitrogen (#BaN) counts, features implicitly used in the design of antimalarial molecules but not well studied hitherto. We also propose using descriptors scaled by the sum of #ArN and #BaN (SBAN) to define an antimalarial property space. Together, these results may have important applications in the identification and optimization of future antimalarials.
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Affiliation(s)
- Amritansh Bhanot
- Department of Pharmacy, Birla
Institute of Technology and Science Pilani, Pilani Campus,
Vidya Vihar, Pilani, Rajasthan 333 031, India
| | - Sandeep Sundriyal
- Department of Pharmacy, Birla
Institute of Technology and Science Pilani, Pilani Campus,
Vidya Vihar, Pilani, Rajasthan 333 031, India
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Malík I, Čižmárik J, Kováč G, Pecháčová M, Hudecova L. Telacebec (Q203): Is there a novel effective and safe anti-tuberculosis drug on the horizon? CESKA A SLOVENSKA FARMACIE : CASOPIS CESKE FARMACEUTICKE SPOLECNOSTI A SLOVENSKE FARMACEUTICKE SPOLECNOSTI 2021; 70:164–171. [PMID: 34875838 DOI: 10.5817/csf2021-5-164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High prevalence and stronger emergency of various forms of drug-resistant tuberculosis (DR-TB), including the multidrug-resistant (MDR-TB) as well as extensively drug-resistant (XDR-TB) ones, caused by variously resistant Mycobacterium tuberculosis pathogens, make first-line anti-tuberculosis (anti-TB) agents therapeutically more and more ineffective. Therefore, there is an imperative to develop novel highly efficient (synthetic) agents against both drug-sensitive-TB and DR-TB. The exploration of various heterocycles as prospective core scaffolds for the discovery, development and optimization of anti-TB drugs remains an intriguing scientific endeavour. Telacebec (Q203; TCB), a molecule containing an imidazo[1,2-a]pyridine-3-carboxamide (IPA) structural motif, is considered a novel very promising anti-TB agent showing a unique mechanism of action. The compound blocks oxidative phosphorylation by inhibiting a mycobacterial respiratory chain due to interference with a specific cytochrome b subunit (QcrB) of transmembrane bc1 menaquinol-cytochrome c oxidoreductase as an essential component for transporting electrons across the membrane from menaquinol to other specific subunit, cytochrome c (QcrC). Thus, the ability of mycobacteria to synthesize adenosine-5´-triphosphate is limited and energy generating machinery is disabled. The TCB molecule effectively fights drug-susceptible, MDR as well as XDR M. tuberculosis strains. The article briefly explains a mechanism of an anti-TB action related to the compounds containing a variously substituted IPA scaffold and is focused on their fundamental structure-anti-TB activity relationships as well. Special consideration is paid to TCB indicating the importance of particular structural fragments for maintaining (or even improving) favourable pharmacodynamic, pharmacokinetic and/or toxicological properties. High lipophilicity of TCB might be regarded as one of the key physicochemical properties with positive impact on anti-TB effect of the drug. In January 2021, the TCB molecule was also involved in phase-II clinical trials focused on the treatment of Coronavirus Disease-19 caused by Severe Acute Respiratory Syndrome Coronavirus 2.
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