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Khan O, Jones G, Lazou M, Joseph-McCarthy D, Kozakov D, Beglov D, Vajda S. Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. J Chem Inf Model 2024; 64:2084-2100. [PMID: 38456842 DOI: 10.1021/acs.jcim.3c01969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The knowledge of ligand binding hot spots and of the important interactions within such hot spots is crucial for the design of lead compounds in the early stages of structure-based drug discovery. The computational solvent mapping server FTMap can reliably identify binding hot spots as consensus clusters, free energy minima that bind a variety of organic probe molecules. However, in its current implementation, FTMap provides limited information on regions within the hot spots that tend to interact with specific pharmacophoric features of potential ligands. E-FTMap is a new server that expands on the original FTMap protocol. E-FTMap uses 119 organic probes, rather than the 16 in the original FTMap, to exhaustively map binding sites, and identifies pharmacophore features as atomic consensus sites where similar chemical groups bind. We validate E-FTMap against a set of 109 experimentally derived structures of fragment-lead pairs, finding that highly ranked pharmacophore features overlap with the corresponding atoms in both fragments and lead compounds. Additionally, comparisons of mapping results to ensembles of bound ligands reveal that pharmacophores generated with E-FTMap tend to sample highly conserved protein-ligand interactions. E-FTMap is available as a web server at https://eftmap.bu.edu.
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Affiliation(s)
- Omeir Khan
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - George Jones
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Maria Lazou
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Diane Joseph-McCarthy
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Acpharis Inc., Holliston, Massachusetts 01746, United States
| | - Sandor Vajda
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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2
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Howieson VM, Zeng J, Kloehn J, Spry C, Marchetti C, Lunghi M, Varesio E, Soper A, Coyne AG, Abell C, van Dooren GG, Saliba KJ. Pantothenate biosynthesis in Toxoplasma gondii tachyzoites is not a drug target. INTERNATIONAL JOURNAL FOR PARASITOLOGY: DRUGS AND DRUG RESISTANCE 2023; 22:1-8. [PMID: 37004488 PMCID: PMC10102396 DOI: 10.1016/j.ijpddr.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/08/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023]
Abstract
Toxoplasma gondii is a pervasive apicomplexan parasite that can cause severe disease and death in immunocompromised individuals and the developing foetus. The treatment of toxoplasmosis often leads to serious side effects and novel drugs and drug targets are therefore actively sought. In 2014, Mageed and colleagues suggested that the T. gondii pantothenate synthetase, the enzyme responsible for the synthesis of the vitamin B5 (pantothenate), the precursor of the important cofactor, coenzyme A, is a good drug target. Their conclusion was based on the ability of potent inhibitors of the M. tuberculosis pantothenate synthetase to inhibit the proliferation of T. gondii tachyzoites. They also reported that the inhibitory effect of the compounds could be antagonised by supplementing the medium with pantothenate, supporting their conclusion that the compounds were acting on the intended target. Contrary to these observations, we find that compound SW314, one of the compounds used in the Mageed et al. study and previously shown to be active against M. tuberculosis pantothenate synthetase in vitro, is inactive against the T. gondii pantothenate synthetase and does not inhibit tachyzoite proliferation, despite gaining access into the parasite in situ. Furthermore, we validate the recent observation that the pantothenate synthetase gene in T. gondii can be disrupted without detrimental effect to the survival of the tachyzoite-stage parasite in the presence or absence of extracellular pantothenate. We conclude that the T. gondii pantothenate synthetase is not essential during the tachyzoite stage of the parasite and it is therefore not a target for drug discovery against T. gondii tachyzoites.
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:life12091438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying “magic bullets” amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand–target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural–energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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Shulga DA, Ivanov NN, Palyulin VA. In Silico Structure-Based Approach for Group Efficiency Estimation in Fragment-Based Drug Design Using Evaluation of Fragment Contributions. Molecules 2022; 27:molecules27061985. [PMID: 35335347 PMCID: PMC8951103 DOI: 10.3390/molecules27061985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 12/10/2022] Open
Abstract
The notion of a contribution of a specific group in an organic molecule’s property and/or activity is both common in our thinking and is still not strictly correct due to the inherent non-additivity of free energy with respect to molecular fragments composing a molecule. The fragment- based drug discovery (FBDD) approach has proven to be fruitful in addressing the above notions. The main difficulty of the FBDD, however, is in its reliance on the low throughput and expensive experimental means of determining the fragment-sized molecules binding. In this article we propose a way to enhance the throughput and availability of the FBDD methods by judiciously using an in silico means of assessing the contribution to ligand-receptor binding energy of fragments of a molecule under question using a previously developed in silico Reverse Fragment Based Drug Discovery (R-FBDD) approach. It has been shown that the proposed structure-based drug discovery (SBDD) type of approach fills in the vacant niche among the existing in silico approaches, which mainly stem from the ligand-based drug discovery (LBDD) counterparts. In order to illustrate the applicability of the approach, our work retrospectively repeats the findings of the use case of an FBDD hit-to-lead project devoted to the experimentally based determination of additive group efficiency (GE)—an analog of ligand efficiency (LE) for a group in the molecule—using the Free-Wilson (FW) decomposition. It is shown that in using our in silico approach to evaluate fragment contributions of a ligand and to estimate GE one can arrive at similar decisions as those made using the experimentally determined activity-based FW decomposition. It is also shown that the approach is rather robust to the choice of the scoring function, provided the latter demonstrates a decent scoring power. We argue that the proposed approach of in silico assessment of GE has a wider applicability domain and expect that it will be widely applicable to enhance the net throughput of drug discovery based on the FBDD paradigm.
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Chitti S, Van Calster K, Cappoen D, Nandikolla A, Khetmalis YM, Cos P, Kumar BK, Murugesan S, Gowri Chandra Sekhar KV. Design, synthesis and biological evaluation of benzo-[ d]-imidazo-[2,1- b]-thiazole and imidazo-[2,1- b]-thiazole carboxamide triazole derivatives as antimycobacterial agents. RSC Adv 2022; 12:22385-22401. [PMID: 36105967 PMCID: PMC9364363 DOI: 10.1039/d2ra03318f] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/03/2022] [Indexed: 11/21/2022] Open
Abstract
In the search for new anti-mycobacterial agents, we revealed the importance of imidazo-[2,1-b]-thiazole and benzo-[d]-imidazo-[2,1-b]-thiazole carboxamide derivatives. We designed, in silico ADMET predicted and synthesized four series of novel imidazo-[2,1-b]-thiazole and benzo-[d]-imidazo-[2,1-b]-thiazole carboxamide analogues in combination with piperazine and various 1,2,3 triazoles. All the synthesized derivatives were characterized by 1H NMR, 13C NMR, HPLC and MS spectral analysis and evaluated for in vitro antitubercular activity. The most active benzo-[d]-imidazo-[2,1-b]-thiazole derivative IT10, carrying a 4-nitro phenyl moiety, displayed IC90 of 7.05 μM and IC50 of 2.32 μM against Mycobacterium tuberculosis (Mtb) H37Ra, while no acute cellular toxicity was observed (>128 μM) towards the MRC-5 lung fibroblast cell line. Another benzo-[d]-imidazo-[2,1-b]-thiazole compound, IT06, which possesses a 2,4-dichloro phenyl moiety, also showed significant activity with IC50 2.03 μM and IC90 15.22 μM against the tested strain of Mtb. Furthermore, the selected hits showed no activity towards a panel of non-tuberculous mycobacteria (NTM), thus suggesting a selective inhibition of Mtb by the tested imidazo-[2,1-b]-thiazole derivatives over the selected panel of NTM. Molecular docking and dynamics studies were also carried out for the most active compounds IT06 and IT10 in order to understand the putative binding pattern, as well as stability of the protein–ligand complex, against the selected target Pantothenate synthetase of Mtb. In the search for new anti-mycobacterial agents, we revealed the importance of imidazo-[2,1-b]-thiazole and benzo-[d]-imidazo-[2,1-b]-thiazole carboxamide derivatives.![]()
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Affiliation(s)
- Surendar Chitti
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad-500 078, Telangana, India
| | - Kevin Van Calster
- Laboratory of Microbiology, Parasitology and Hygiene, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Adinarayana Nandikolla
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad-500 078, Telangana, India
| | - Yogesh Mahadu Khetmalis
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad-500 078, Telangana, India
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Banoth Karan Kumar
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani-333031, Rajasthan, India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani-333031, Rajasthan, India
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Kollár L, Gobec M, Proj M, Smrdel L, Knez D, Imre T, Gömöry Á, Petri L, Ábrányi-Balogh P, Csányi D, Ferenczy GG, Gobec S, Sosič I, Keserű GM. Fragment-Sized and Bidentate (Immuno)Proteasome Inhibitors Derived from Cysteine and Threonine Targeting Warheads. Cells 2021; 10:3431. [PMID: 34943940 PMCID: PMC8700061 DOI: 10.3390/cells10123431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
Constitutive- and immunoproteasomes are part of the ubiquitin-proteasome system (UPS), which is responsible for the protein homeostasis. Selective inhibition of the immunoproteasome offers opportunities for the treatment of numerous diseases, including inflammation, autoimmune diseases, and hematologic malignancies. Although several inhibitors have been reported, selective nonpeptidic inhibitors are sparse. Here, we describe two series of compounds that target both proteasomes. First, benzoxazole-2-carbonitriles as fragment-sized covalent immunoproteasome inhibitors are reported. Systematic substituent scans around the fragment core of benzoxazole-2-carbonitrile led to compounds with single digit micromolar inhibition of the β5i subunit. Experimental and computational reactivity studies revealed that the substituents do not affect the covalent reactivity of the carbonitrile warhead, but mainly influence the non-covalent recognition. Considering the small size of the inhibitors, this finding emphasizes the importance of the non-covalent recognition step in the covalent mechanism of action. As a follow-up series, bidentate inhibitors are disclosed, in which electrophilic heterocyclic fragments, i.e., 2-vinylthiazole, benzoxazole-2-carbonitrile, and benzimidazole-2-carbonitrile were linked to threonine-targeting (R)-boroleucine moieties. These compounds were designed to bind both the Thr1 and β5i-subunit-specific residue Cys48. However, inhibitory activities against (immuno)proteasome subunits showed that bidentate compounds inhibit the β5, β5i, β1, and β1i subunits with submicromolar to low-micromolar IC50 values. Inhibitory assays against unrelated enzymes showed that compounds from both series are selective for proteasomes. The presented nonpeptidic and covalent derivatives are suitable hit compounds for the development of either β5i-selective immunoproteasome inhibitors or compounds targeting multiple subunits of both proteasomes.
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Affiliation(s)
- Levente Kollár
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, H-1117 Budapest, Hungary; (L.K.); (L.P.); (P.Á.-B.); (D.C.); (G.G.F.)
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (M.G.); (M.P.); (L.S.); (D.K.); (S.G.)
| | - Matic Proj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (M.G.); (M.P.); (L.S.); (D.K.); (S.G.)
| | - Lara Smrdel
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (M.G.); (M.P.); (L.S.); (D.K.); (S.G.)
| | - Damijan Knez
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (M.G.); (M.P.); (L.S.); (D.K.); (S.G.)
| | - Tímea Imre
- MS Metabolomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, H-1117 Budapest, Hungary;
| | - Ágnes Gömöry
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, H-1117 Budapest, Hungary;
| | - László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, H-1117 Budapest, Hungary; (L.K.); (L.P.); (P.Á.-B.); (D.C.); (G.G.F.)
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, H-1117 Budapest, Hungary; (L.K.); (L.P.); (P.Á.-B.); (D.C.); (G.G.F.)
| | - Dorottya Csányi
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, H-1117 Budapest, Hungary; (L.K.); (L.P.); (P.Á.-B.); (D.C.); (G.G.F.)
| | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, H-1117 Budapest, Hungary; (L.K.); (L.P.); (P.Á.-B.); (D.C.); (G.G.F.)
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (M.G.); (M.P.); (L.S.); (D.K.); (S.G.)
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (M.G.); (M.P.); (L.S.); (D.K.); (S.G.)
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, H-1117 Budapest, Hungary; (L.K.); (L.P.); (P.Á.-B.); (D.C.); (G.G.F.)
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8
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Synthesis, structural elucidation, pharmacological and molecular docking studies of terpolymer transition metal complexes. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Butman HS, Kotzé TJ, Dowd CS, Strauss E. Vitamin in the Crosshairs: Targeting Pantothenate and Coenzyme A Biosynthesis for New Antituberculosis Agents. Front Cell Infect Microbiol 2020; 10:605662. [PMID: 33384970 PMCID: PMC7770189 DOI: 10.3389/fcimb.2020.605662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Despite decades of dedicated research, there remains a dire need for new drugs against tuberculosis (TB). Current therapies are generations old and problematic. Resistance to these existing therapies results in an ever-increasing burden of patients with disease that is difficult or impossible to treat. Novel chemical entities with new mechanisms of action are therefore earnestly required. The biosynthesis of coenzyme A (CoA) has long been known to be essential in Mycobacterium tuberculosis (Mtb), the causative agent of TB. The pathway has been genetically validated by seminal studies in vitro and in vivo. In Mtb, the CoA biosynthetic pathway is comprised of nine enzymes: four to synthesize pantothenate (Pan) from l-aspartate and α-ketoisovalerate; five to synthesize CoA from Pan and pantetheine (PantSH). This review gathers literature reports on the structure/mechanism, inhibitors, and vulnerability of each enzyme in the CoA pathway. In addition to traditional inhibition of a single enzyme, the CoA pathway offers an antimetabolite strategy as a promising alternative. In this review, we provide our assessment of what appear to be the best targets, and, thus, which CoA pathway enzymes present the best opportunities for antitubercular drug discovery moving forward.
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Affiliation(s)
- Hailey S. Butman
- Department of Chemistry, George Washington University, Washington, DC, United States
| | - Timothy J. Kotzé
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington, DC, United States
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
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Garg A, Kumari B, Singhal N, Kumar M. Using molecular-mimicry-inducing pathways of pathogens as novel drug targets. Drug Discov Today 2019; 24:1943-1952. [DOI: 10.1016/j.drudis.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/04/2018] [Accepted: 10/16/2018] [Indexed: 01/27/2023]
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11
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Liyanage SI, Gupta M, Wu F, Taylor M, Carter MD, Weaver DF. Inhibition of Pantothenate Synthetase by Analogs of β-Alanine Precursor Ineffective as an Antibacterial Strategy. Chemotherapy 2019; 64:22-27. [PMID: 31167192 DOI: 10.1159/000499899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/24/2019] [Indexed: 11/19/2022]
Abstract
BACKGROUND Pantothenate, the fundamental precursor to coenzyme A, is required for optimal growth and virulence of microbial pathogens. It is synthesized by the enzyme-catalyzed condensation of β-alanine and pantoate, which has shown susceptibility to inhibition by analogs of its molecular constituents. Accordingly, analogs of β-alanine are gaining inquiry as potential antimicrobial chemotherapeutics. METHODS We synthesized and evaluated 35 derivatives of β-alanine, substituted at the α, β, amine, and carboxyl sites, derived from in silico, dynamic molecular modeling to be potential competitive inhibitors of pantothenate synthetase. Employing the Clinical Laboratory Standards M7-A6 broth microdilution method, we tested these for inhibition of growth in Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. RESULTS All compounds proved entirely ineffective in all species tested, with no inhibition of growth being observed up to 200 µM/mL. CONCLUSIONS Upon revision of the literature, we conclude that high enzyme selectivity or external salvage mechanisms may render this strategy futile against most bacteria.
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Affiliation(s)
- S Imindu Liyanage
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Mayuri Gupta
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Fan Wu
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Marcy Taylor
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Michael D Carter
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada, .,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada, .,Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, .,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada,
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12
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Waman VP, Vedithi SC, Thomas SE, Bannerman BP, Munir A, Skwark MJ, Malhotra S, Blundell TL. Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery. Emerg Microbes Infect 2019; 8:109-118. [PMID: 30866765 PMCID: PMC6334779 DOI: 10.1080/22221751.2018.1561158] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/03/2018] [Accepted: 12/09/2018] [Indexed: 01/08/2023]
Abstract
Of the more than 190 distinct species of Mycobacterium genus, many are economically and clinically important pathogens of humans or animals. Among those mycobacteria that infect humans, three species namely Mycobacterium tuberculosis (causative agent of tuberculosis), Mycobacterium leprae (causative agent of leprosy) and Mycobacterium abscessus (causative agent of chronic pulmonary infections) pose concern to global public health. Although antibiotics have been successfully developed to combat each of these, the emergence of drug-resistant strains is an increasing challenge for treatment and drug discovery. Here we describe the impact of the rapid expansion of genome sequencing and genome/pathway annotations that have greatly improved the progress of structure-guided drug discovery. We focus on the applications of comparative genomics, metabolomics, evolutionary bioinformatics and structural proteomics to identify potential drug targets. The opportunities and challenges for the design of drugs for M. tuberculosis, M. leprae and M. abscessus to combat resistance are discussed.
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Affiliation(s)
| | | | | | | | - Asma Munir
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Marcin J. Skwark
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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13
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Kwiatkowski J, Liu B, Tee DHY, Chen G, Ahmad NHB, Wong YX, Poh ZY, Ang SH, Tan ESW, Ong EH, Nurul Dinie, Poulsen A, Pendharkar V, Sangthongpitag K, Lee MA, Sepramaniam S, Ho SY, Cherian J, Hill J, Keller TH, Hung AW. Fragment-Based Drug Discovery of Potent Protein Kinase C Iota Inhibitors. J Med Chem 2018; 61:4386-4396. [PMID: 29688013 DOI: 10.1021/acs.jmedchem.8b00060] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein kinase C iota (PKC-ι) is an atypical kinase implicated in the promotion of different cancer types. A biochemical screen of a fragment library has identified several hits from which an azaindole-based scaffold was chosen for optimization. Driven by a structure-activity relationship and supported by molecular modeling, a weakly bound fragment was systematically grown into a potent and selective inhibitor against PKC-ι.
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Affiliation(s)
- Jacek Kwiatkowski
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Boping Liu
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Doris Hui Ying Tee
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Guoying Chen
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Nur Huda Binte Ahmad
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Yun Xuan Wong
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Zhi Ying Poh
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Shi Hua Ang
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Eldwin Sum Wai Tan
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Esther Hq Ong
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Nurul Dinie
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Anders Poulsen
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Vishal Pendharkar
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Kanda Sangthongpitag
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - May Ann Lee
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Sugunavathi Sepramaniam
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Soo Yei Ho
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Joseph Cherian
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
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14
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Szabó G, Túrós GI, Kolok S, Vastag M, Sánta Z, Dékány M, Lévay GI, Greiner I, Natsumi M, Tatsuya W, Keserű GM. Fragment Based Optimization of Metabotropic Glutamate Receptor 2 (mGluR2) Positive Allosteric Modulators in the Absence of Structural Information. J Med Chem 2018; 62:234-246. [PMID: 29505715 DOI: 10.1021/acs.jmedchem.8b00161] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Metabotropic glutamate receptor 2 (mGluR2) positive allosteric modulators (PAMs) have been implicated as potential pharmacotherapy for psychiatric conditions. Screening our corporate compound deck, we identified a benzotriazole fragment (4) that was rapidly optimized to a potent and metabolically stable early lead (16). The highly lipophilic character of 16, together with its limited solubility, permeability, and high protein binding, however, did not allow reaching of the proof of concept in vivo. Since further attempts on the optimization of druglike properties were unsuccessful, the original hit 4 has been revisited and was optimized following the principles of fragment based drug discovery (FBDD). Lacking structural information on the receptor-ligand complex, we implemented a group efficiency (GE) based strategy and identified a new fragment like lead (60) with more balanced profile. Significant improvement achieved on the druglike properties nominated the compound for in vivo proof of concept studies that revealed the chemotype being a promising PAM lead targeting mGluR2 receptors.
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Affiliation(s)
- György Szabó
- Gedeon Richter Plc. , 19-21 Gyömrői út , Budapest 1103 , Hungary
| | - György I Túrós
- Gedeon Richter Plc. , 19-21 Gyömrői út , Budapest 1103 , Hungary
| | - Sándor Kolok
- Gedeon Richter Plc. , 19-21 Gyömrői út , Budapest 1103 , Hungary
| | - Mónika Vastag
- Gedeon Richter Plc. , 19-21 Gyömrői út , Budapest 1103 , Hungary
| | - Zsuzsanna Sánta
- Gedeon Richter Plc. , 19-21 Gyömrői út , Budapest 1103 , Hungary
| | - Miklós Dékány
- Gedeon Richter Plc. , 19-21 Gyömrői út , Budapest 1103 , Hungary
| | - György I Lévay
- Gedeon Richter Plc. , 19-21 Gyömrői út , Budapest 1103 , Hungary
| | - István Greiner
- Gedeon Richter Plc. , 19-21 Gyömrői út , Budapest 1103 , Hungary
| | - Minami Natsumi
- Mitsubishi Tanabe Pharma Corporation , 1000, Kamoshida-cho , Aoba-ku, Yokohama 227-0033 , Japan
| | - Watanabe Tatsuya
- Mitsubishi Tanabe Pharma Corporation , 1000, Kamoshida-cho , Aoba-ku, Yokohama 227-0033 , Japan
| | - György M Keserű
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences, Hungarian Academy of Sciences , 2 Magyar Tudósok Körútja , Budapest 1117 , Hungary
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15
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Dietl AM, Meir Z, Shadkchan Y, Osherov N, Haas H. Riboflavin and pantothenic acid biosynthesis are crucial for iron homeostasis and virulence in the pathogenic mold Aspergillus fumigatus. Virulence 2018; 9:1036-1049. [PMID: 30052132 PMCID: PMC6068542 DOI: 10.1080/21505594.2018.1482181] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Aspergillus fumigatus is the most prevalent airborne fungal pathogen, causing invasive fungal infections mainly in immunosuppressed individuals. Death rates from invasive aspergillosis remain high because of limited treatment options and increasing antifungal resistance. The aim of this study was to identify key fungal-specific genes participating in vitamin B biosynthesis in A. fumigatus. Because these genes are absent in humans they can serve as possible novel targets for antifungal drug development. METHODS By sequence homology we identified, deleted and analysed four key A. fumigatus genes (riboB, panA, pyroA, thiB) involved respectively in the biosynthesis of riboflavin (vitamin B2), pantothenic acid (vitamin B5), pyridoxine (vitamin B6) and thiamine (vitamin B1). RESULTS Deletion of riboB, panA, pyroA or thiB resulted in respective vitamin auxotrophy. Lack of riboflavin and pantothenic acid biosynthesis perturbed many cellular processes including iron homeostasis. Virulence in murine pulmonary and systemic models of infection was severely attenuated following deletion of riboB and panA, strongly reduced after pyroA deletion and weakly attenuated after thiB deletion. CONCLUSIONS This study reveals the biosynthetic pathways of the vitamins riboflavin and pantothenic acid as attractive targets for novel antifungal therapy. Moreover, the virulence studies with auxotrophic mutants serve to identify the availability of nutrients to pathogens in host niches. ABBREVIATIONS BPS: bathophenanthrolinedisulfonate; BSA: bovine serum albumin; CFU: colony forming unit; -Fe: iron starvation; +Fe: iron sufficiency; hFe: high iron; NRPSs: nonribosomal peptide synthetases; PKSs: polyketide synthaseses; wt: wild type.
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Affiliation(s)
- Anna-Maria Dietl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Zohar Meir
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
| | - Yona Shadkchan
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
| | - Hubertus Haas
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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16
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Cavalluzzi MM, Mangiatordi GF, Nicolotti O, Lentini G. Ligand efficiency metrics in drug discovery: the pros and cons from a practical perspective. Expert Opin Drug Discov 2017; 12:1087-1104. [PMID: 28814111 DOI: 10.1080/17460441.2017.1365056] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Ligand efficiency metrics are almost universally accepted as a valuable indicator of compound quality and an aid to reduce attrition. Areas covered: In this review, the authors describe ligand efficiency metrics giving a balanced overview on their merits and points of weakness in order to enable the readers to gain an informed opinion. Relevant theoretical breakthroughs and drug-like properties are also illustrated. Several recent exemplary case studies are discussed in order to illustrate the main fields of application of ligand efficiency metrics. Expert opinion: As a medicinal chemist guide, ligand efficiency metrics perform in a context- and chemotype-dependent manner; thus, they should not be used as a magic box. Since the 'big bang' of efficiency metrics occurred more or less ten years ago and the average time to develop a new drug is over the same period, the next few years will give a clearer outlook on the increased rate of success, if any, gained by means of these new intriguing tools.
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Affiliation(s)
| | | | - Orazio Nicolotti
- a Department of Pharmacy - Drug Sciences , University of Bari Aldo Moro , Bari , Italy
| | - Giovanni Lentini
- a Department of Pharmacy - Drug Sciences , University of Bari Aldo Moro , Bari , Italy
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17
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Ellis CK, Rice S, Maurer D, Stahl R, Waters WR, Palmer MV, Nol P, Rhyan JC, VerCauteren KC, Koziel JA. Use of fecal volatile organic compound analysis to discriminate between non-vaccinated and BCG-Vaccinated cattle prior to and after Mycobacterium bovis challenge. PLoS One 2017; 12:e0179914. [PMID: 28686691 PMCID: PMC5501492 DOI: 10.1371/journal.pone.0179914] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 06/06/2017] [Indexed: 11/18/2022] Open
Abstract
Bovine tuberculosis is a zoonotic disease of global public health concern. Development of diagnostic tools to improve test accuracy and efficiency in domestic livestock and enable surveillance of wildlife reservoirs would improve disease management and eradication efforts. Use of volatile organic compound analysis in breath and fecal samples is being developed and optimized as a means to detect disease in humans and animals. In this study we demonstrate that VOCs present in fecal samples can be used to discriminate between non-vaccinated and BCG-vaccinated cattle prior to and after Mycobacterium bovis challenge.
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Affiliation(s)
- Christine K. Ellis
- United States Department of Agriculture, Animal Plant and Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, United States of America
| | - Somchai Rice
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Devin Maurer
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Randal Stahl
- United States Department of Agriculture, Animal Plant and Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, United States of America
| | - W. Ray Waters
- United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Ames, Iowa, United States of America
| | - Mitchell V. Palmer
- United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Ames, Iowa, United States of America
| | - Pauline Nol
- United States Department of Agriculture, Animal Plant and Health Inspection Service, Veterinary Services, Wildlife Livestock Disease Investigations Team, Fort Collins, Colorado, United States of America
| | - Jack C. Rhyan
- United States Department of Agriculture, Animal Plant and Health Inspection Service, Veterinary Services, Wildlife Livestock Disease Investigations Team, Fort Collins, Colorado, United States of America
| | - Kurt C. VerCauteren
- United States Department of Agriculture, Animal Plant and Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, United States of America
| | - Jacek A. Koziel
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
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18
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Ryan A, Polycarpou E, Lack NA, Evangelopoulos D, Sieg C, Halman A, Bhakta S, Eleftheriadou O, McHugh TD, Keany S, Lowe ED, Ballet R, Abuhammad A, Jacobs WR, Ciulli A, Sim E. Investigation of the mycobacterial enzyme HsaD as a potential novel target for anti-tubercular agents using a fragment-based drug design approach. Br J Pharmacol 2017; 174:2209-2224. [PMID: 28380256 PMCID: PMC5481647 DOI: 10.1111/bph.13810] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 03/22/2017] [Accepted: 03/24/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND AND PURPOSE With the emergence of extensively drug-resistant tuberculosis, there is a need for new anti-tubercular drugs that work through novel mechanisms of action. The meta cleavage product hydrolase, HsaD, has been demonstrated to be critical for the survival of Mycobacterium tuberculosis in macrophages and is encoded in an operon involved in cholesterol catabolism, which is identical in M. tuberculosis and M. bovis BCG. EXPERIMENTAL APPROACH We generated a mutant strain of M. bovis BCG with a deletion of hsaD and tested its growth on cholesterol. Using a fragment based approach, over 1000 compounds were screened by a combination of differential scanning fluorimetry, NMR spectroscopy and enzymatic assay with pure recombinant HsaD to identify potential inhibitors. We used enzymological and structural studies to investigate derivatives of the inhibitors identified and to test their effects on growth of M. bovis BCG and M. tuberculosis. KEY RESULTS The hsaD deleted strain was unable to grow on cholesterol as sole carbon source but did grow on glucose. Of seven chemically distinct 'hits' from the library, two chemical classes of fragments were found to bind in the vicinity of the active site of HsaD by X-ray crystallography. The compounds also inhibited growth of M. tuberculosis on cholesterol. The most potent inhibitor of HsaD was also found to be the best inhibitor of mycobacterial growth on cholesterol-supplemented minimal medium. CONCLUSIONS AND IMPLICATIONS We propose that HsaD is a novel therapeutic target, which should be fully exploited in order to design and discover new anti-tubercular drugs. LINKED ARTICLES This article is part of a themed section on Drug Metabolism and Antibiotic Resistance in Micro-organisms. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.14/issuetoc.
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Affiliation(s)
- Ali Ryan
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
| | - Elena Polycarpou
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
| | - Nathan A Lack
- Department of PharmacologyUniversity of OxfordOxfordUK
- School of MedicineKoç UniversityIstanbulTurkey
| | - Dimitrios Evangelopoulos
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological SciencesBirkbeck, University of LondonLondonUK
- Centre for Clinical MicrobiologyUniversity College London, Royal Free CampusLondonUK
- Mycobacterial Metabolism and Antibiotic Research LaboratoryThe Francis Crick Institute, Mill Hill LaboratoryLondonUK
| | - Christian Sieg
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
| | - Alice Halman
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological SciencesBirkbeck, University of LondonLondonUK
| | - Olga Eleftheriadou
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
| | - Timothy D McHugh
- Centre for Clinical MicrobiologyUniversity College London, Royal Free CampusLondonUK
| | | | - Edward D Lowe
- Department of BiochemistryUniversity of OxfordOxfordUK
| | - Romain Ballet
- Department of PharmacologyUniversity of OxfordOxfordUK
| | | | - William R Jacobs
- Department of Microbiology and ImmunologyHoward Hughes Medical Institute, Albert Einstein College of MedicineBronxNew YorkUSA
| | - Alessio Ciulli
- Department of ChemistryUniversity of CambridgeCambridgeUK
- Division of Biological Chemistry & Drug Discovery, School of Life SciencesUniversity of Dundee, James Black CentreDundeeUK
| | - Edith Sim
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
- Department of PharmacologyUniversity of OxfordOxfordUK
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19
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20
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Abstract
Tuberculosis is an infectious disease associated with significant mortality and morbidity worldwide, particularly in developing countries. The rise of antibiotic resistance in Mycobacterium tuberculosis (Mtb) urgently demands the development of new drug leads to tackle resistant strains. Fragment-based methods have recently emerged at the forefront of pharmaceutical development as a means to generate more effective lead structures, via the identification of fragment molecules that form weak but high quality interactions with the target biomolecule and subsequent fragment optimization. This review highlights a number of novel inhibitors of Mtb targets that have been developed through fragment-based approaches in recent years.
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21
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Mendes V, Blundell TL. Targeting tuberculosis using structure-guided fragment-based drug design. Drug Discov Today 2016; 22:546-554. [PMID: 27742535 DOI: 10.1016/j.drudis.2016.10.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 01/20/2023]
Abstract
Fragment-based drug discovery is now widely used in academia and industry to obtain small molecule inhibitors for a given target and is established for many fields of research including antimicrobials and oncology. Many molecules derived from fragment-based approaches are already in clinical trials and two - vemurafenib and venetoclax - are on the market, but the approach has been used sparsely in the tuberculosis field. Here, we describe the progress of our group and others, and examine the most recent successes and challenges in developing compounds with antimycobacterial activity.
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Affiliation(s)
- Vitor Mendes
- Department of Biochemistry, University of Cambridge, Cambridge CB21GA, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge CB21GA, UK.
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22
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Wang Y, Wach JY, Sheehan P, Zhong C, Zhan C, Harris R, Almo SC, Bishop J, Haggarty SJ, Ramek A, Berry KN, O’Herin C, Koehler AN, Hung AW, Young DW. Diversity-Oriented Synthesis as a Strategy for Fragment Evolution against GSK3β. ACS Med Chem Lett 2016; 7:852-6. [PMID: 27660690 DOI: 10.1021/acsmedchemlett.6b00230] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/14/2016] [Indexed: 11/30/2022] Open
Abstract
Traditional fragment-based drug discovery (FBDD) relies heavily on structural analysis of the hits bound to their targets. Herein, we present a complementary approach based on diversity-oriented synthesis (DOS). A DOS-based fragment collection was able to produce initial hit compounds against the target GSK3β, allow the systematic synthesis of related fragment analogues to explore fragment-level structure-activity relationship, and finally lead to the synthesis of a more potent compound.
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Affiliation(s)
- Yikai Wang
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Jean-Yves Wach
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Patrick Sheehan
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Cheng Zhong
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Chenyang Zhan
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Richard Harris
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Steven C. Almo
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Joshua Bishop
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
- Department of Neurology & Psychiatry, Harvard Medical School and Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Stephen J. Haggarty
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
- Department of Neurology & Psychiatry, Harvard Medical School and Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Alexander Ramek
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Kayla N. Berry
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Conor O’Herin
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Angela N. Koehler
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Alvin W. Hung
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Damian W. Young
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
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23
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Neue Mitglieder der Royal Society: C. Abell, E. Kumacheva, R. E. Morris / Präsident der Chemical Society of Japan: H. Yamamoto. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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New Fellows of the Royal Society: C. Abell, E. Kumacheva, and R. E. Morris / President of the Chemical Society of Japan: H. Yamamoto. Angew Chem Int Ed Engl 2016; 55:7031. [DOI: 10.1002/anie.201604256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Keserű GM, Erlanson DA, Ferenczy GG, Hann MM, Murray CW, Pickett SD. Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia. J Med Chem 2016; 59:8189-206. [DOI: 10.1021/acs.jmedchem.6b00197] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- György M. Keserű
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Daniel A. Erlanson
- Carmot Therapeutics, Inc. 409 Illinois Street, San Francisco, California 94158, United States
| | - György G. Ferenczy
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Michael M. Hann
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Stephen D. Pickett
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
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26
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Radoux CJ, Olsson TSG, Pitt WR, Groom CR, Blundell TL. Identifying Interactions that Determine Fragment Binding at Protein Hotspots. J Med Chem 2016; 59:4314-25. [PMID: 27043011 DOI: 10.1021/acs.jmedchem.5b01980] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods do little to suggest which interactions within a pocket are the most important for binding. Here we illustrate a method that samples atomic hotspots with simple molecular probes to produce fragment hotspot maps. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores. For ligand-bound structures, they provide an intuitive visual guide within the binding site, directing medicinal chemists where to grow the molecule and alerting them to suboptimal interactions within the original hit. The fragment hotspot map calculation is validated using experimental binding positions of 21 fragments and subsequent lead molecules. The ligands are found in high scoring areas of the fragment hotspot maps, with fragment atoms having a median percentage rank of 97%. Protein kinase B and pantothenate synthetase are examined in detail. In each case, the fragment hotspot maps are able to rationalize a Free-Wilson analysis of SAR data from a fragment-based drug design project.
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Affiliation(s)
- Chris J Radoux
- Cambridge Crystallographic Data Centre , 12 Union Road, Cambridge, CB2 1EZ, United Kingdom.,Department of Biochemistry, University of Cambridge , Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Tjelvar S G Olsson
- Cambridge Crystallographic Data Centre , 12 Union Road, Cambridge, CB2 1EZ, United Kingdom.,John Innes Centre, Norwich Research Park , Colney Lane, Norwich, Norfolk NR4 7UH, United Kingdom
| | - Will R Pitt
- UCB , 208 Bath Road, Slough, West Berkshire SL1 3WE, United Kingdom
| | - Colin R Groom
- Cambridge Crystallographic Data Centre , 12 Union Road, Cambridge, CB2 1EZ, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge , Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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Hung AW, Silvestre HL, Wen S, George GPC, Boland J, Blundell TL, Ciulli A, Abell C. Optimization of Inhibitors of Mycobacterium tuberculosis Pantothenate Synthetase Based on Group Efficiency Analysis. ChemMedChem 2015; 11:38-42. [PMID: 26486566 PMCID: PMC4949533 DOI: 10.1002/cmdc.201500414] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Indexed: 11/06/2022]
Abstract
Ligand efficiency has proven to be a valuable concept for optimization of leads in the early stages of drug design. Taking this one step further, group efficiency (GE) evaluates the binding efficiency of each appendage of a molecule, further fine‐tuning the drug design process. Here, GE analysis is used to systematically improve the potency of inhibitors of Mycobacterium tuberculosis pantothenate synthetase, an important target in tuberculosis therapy. Binding efficiencies were found to be distributed unevenly within a lead molecule derived using a fragment‐based approach. Substitution of the less efficient parts of the molecule allowed systematic development of more potent compounds. This method of dissecting and analyzing different groups within a molecule offers a rational and general way of carrying out lead optimization, with potential broad application within drug discovery.
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Affiliation(s)
- Alvin W Hung
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.,Experimental Therapeutic Centre, A-STAR, 11 Biopolis Way, Singapore, 138667, Singapore
| | - H Leonardo Silvestre
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, CB2 1GA, UK
| | - Shijun Wen
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Guillaume P C George
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Jennifer Boland
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, CB2 1GA, UK
| | - Alessio Ciulli
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.,Division of Biological Chemistry & Drug Discovery, College of Life Sciences, James Black Centre, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.
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