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El-Sayed SM, Ahmed SA, Gulia K, Lenhard JR, Hassan AHE, Farahat AA. Small Molecules Incorporating Privileged Amidine Moiety as Potential Hits Combating Antibiotic-Resistant Bacteria. Pharmaceuticals (Basel) 2023; 16:1040. [PMID: 37513951 PMCID: PMC10384254 DOI: 10.3390/ph16071040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The continuing need for the discovery of potent antibacterial agents against antibiotic-resistant pathogens is the driving force for many researchers to design and develop such agents. Herein, we report the design, synthesis, and biological evaluation of amidine derivatives as new antibacterial agents. Compound 13d was the most active in this study against a wide range of antibiotic-resistant, and susceptible, Gram-positive, and Gram-negative bacterial strains. Time-kill assay experiments indicated that compound 13d was an effective bactericidal compound against the tested organisms at the log-phase of bacterial growth. Docking simulations were performed to assess in silico its mode of action regarding UPPS, KARI, and DNA as potential bacterial targets. Results unveiled the importance of structural features of compound 13d in its biological activity including central thiophene ring equipped with left and right pyrrolo[2,3-b]pyridine and phenyl moieties and two terminal amidines cyclized into 4,5-dihydro-1H-imidazol-2-yl functionalities. Collectively, compound 13d represents a possible hit for future development of potent antibacterial agents.
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Affiliation(s)
- Selwan M El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 35712, Egypt
| | - Samar A Ahmed
- Department of Clinical and Administrative Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA
| | - Kanika Gulia
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
| | - Justin R Lenhard
- Department of Clinical and Administrative Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA
| | - Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Medicinal Chemistry Laboratory, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Abdelbasset A Farahat
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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2
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Bayaraa T, Gaete J, Sutiono S, Kurz J, Lonhienne T, Harmer JR, Bernhardt PV, Sieber V, Guddat L, Schenk G. Dihydroxy‐Acid Dehydratases From Pathogenic Bacteria: Emerging Drug Targets to Combat Antibiotic Resistance. Chemistry 2022; 28:e202200927. [PMID: 35535733 PMCID: PMC9543379 DOI: 10.1002/chem.202200927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 11/30/2022]
Abstract
There is an urgent global need for the development of novel therapeutics to combat the rise of various antibiotic‐resistant superbugs. Enzymes of the branched‐chain amino acid (BCAA) biosynthesis pathway are an attractive target for novel anti‐microbial drug development. Dihydroxy‐acid dehydratase (DHAD) is the third enzyme in the BCAA biosynthesis pathway. It relies on an Fe−S cluster for catalytic activity and has recently also gained attention as a catalyst in cell‐free enzyme cascades. Two types of Fe−S clusters have been identified in DHADs, i.e. [2Fe−2S] and [4Fe−4S], with the latter being more prone to degradation in the presence of oxygen. Here, we characterise two DHADs from bacterial human pathogens, Staphylococcus aureus and Campylobacter jejuni (SaDHAD and CjDHAD). Purified SaDHAD and CjDHAD are virtually inactive, but activity could be reversibly reconstituted in vitro (up to ∼19,000‐fold increase with kcat as high as ∼6.7 s−1). Inductively‐coupled plasma‐optical emission spectroscopy (ICP‐OES) measurements are consistent with the presence of [4Fe−4S] clusters in both enzymes. N‐isopropyloxalyl hydroxamate (IpOHA) and aspterric acid are both potent inhibitors for both SaDHAD (Ki=7.8 and 51.6 μM, respectively) and CjDHAD (Ki=32.9 and 35.1 μM, respectively). These compounds thus present suitable starting points for the development of novel anti‐microbial chemotherapeutics.
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Affiliation(s)
- Tenuun Bayaraa
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Jose Gaete
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic resources Campus Straubing for Biotechnology and Sustainability Technical University of Munich Schulgasse 16 94315 Straubing Germany
| | - Julia Kurz
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Thierry Lonhienne
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Jeffrey R. Harmer
- Centre for Advanced Imaging The University of Queensland Brisbane 4072 Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Volker Sieber
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
- Chair of Chemistry of Biogenic resources Campus Straubing for Biotechnology and Sustainability Technical University of Munich Schulgasse 16 94315 Straubing Germany
| | - Luke Guddat
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
- Sustainable Minerals Institute The University of Queensland Brisbane 4072 Australia
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane 4072 Australia
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3
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Valera A, Wang S, Carr R, Trembleau L, Deng H. Characterization of a class II ketol-acid reductoisomerase from Mycobacterium tuberculosis. RSC Adv 2022; 12:10540-10544. [PMID: 35425013 PMCID: PMC8985424 DOI: 10.1039/d1ra08876a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/30/2022] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium tuberculosis ketol-acid reductoisomerases have been widely studied due to their metabolic importance towards development of drug-resistant bacteria treatment. We here report the biochemical characterization of a new KARI (MtKARI-II) from a Mycobacterium tuberculosis variant with a similar kinetic profile to class I KARIs. Phylogenetic analysis suggested that MtKARI-II is clustered into a class II KARI superfamily. Biochemical characterization of an unusual class II KARI (MtKARI-II) from a Mycobacterium tuberculosis variant.![]()
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Affiliation(s)
- Ane Valera
- Department of Chemistry, University of Aberdeen Aberdeen AB24 3UE Scotland UK
| | - Shan Wang
- Department of Chemistry, University of Aberdeen Aberdeen AB24 3UE Scotland UK
| | | | - Laurent Trembleau
- Department of Chemistry, University of Aberdeen Aberdeen AB24 3UE Scotland UK
| | - Hai Deng
- Department of Chemistry, University of Aberdeen Aberdeen AB24 3UE Scotland UK
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4
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Liang YF, Long ZX, Zhang YJ, Luo CY, Yan LT, Gao WY, Li H. The chemical mechanisms of the enzymes in the branched-chain amino acids biosynthetic pathway and their applications. Biochimie 2021; 184:72-87. [PMID: 33607240 DOI: 10.1016/j.biochi.2021.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/27/2022]
Abstract
l-Valine, l-isoleucine, and l-leucine are three key proteinogenic amino acids, and they are also the essential amino acids required for mammalian growth, possessing important and to some extent, special physiological and biological functions. Because of the branched structures in their carbon chains, they are also named as branched-chain amino acids (BCAAs). This review will highlight the advance in studies of the enzymes involved in the biosynthetic pathway of BCAAs, concentrating on their chemical mechanisms and applications in screening herbicides and antibacterial agents. The uses of some of these enzymes in lab scale organic synthesis are also discussed.
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Affiliation(s)
- Yan-Fei Liang
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Zi-Xian Long
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Ya-Jian Zhang
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Cai-Yun Luo
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Le-Tian Yan
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Wen-Yun Gao
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China.
| | - Heng Li
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China.
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5
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Kandale A, Patel K, Hussein WM, Wun SJ, Zheng S, Tan L, West NP, Schenk G, Guddat LW, McGeary RP. Analogues of the Herbicide, N-Hydroxy- N-isopropyloxamate, Inhibit Mycobacterium tuberculosis Ketol-Acid Reductoisomerase and Their Prodrugs Are Promising Anti-TB Drug Leads. J Med Chem 2021; 64:1670-1684. [PMID: 33512163 DOI: 10.1021/acs.jmedchem.0c01919] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New drugs to treat tuberculosis (TB) are urgently needed to combat the increase in resistance observed among the current first-line and second-line treatments. Here, we propose ketol-acid reductoisomerase (KARI) as a target for anti-TB drug discovery. Twenty-two analogues of IpOHA, an inhibitor of plant KARI, were evaluated as antimycobacterial agents. The strongest inhibitor of Mycobacterium tuberculosis (Mt) KARI has a Ki value of 19.7 nM, fivefold more potent than IpOHA (Ki = 97.7 nM). This and four other potent analogues are slow- and tight-binding inhibitors of MtKARI. Three compounds were cocrystallized with Staphylococcus aureus KARI and yielded crystals that diffracted to 1.6-2.0 Å resolution. Prodrugs of these compounds possess antimycobacterial activity against H37Rv, a virulent strain of human TB, with the most active compound having an MIC90 of 2.32 ± 0.04 μM. This compound demonstrates a very favorable selectivity window and represents a highly promising lead as an anti-TB agent.
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Affiliation(s)
- Ajit Kandale
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Khushboo Patel
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Shun Jie Wun
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Shan Zheng
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia.,Sustainable Minerals Institute, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia.,Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
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6
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Lin X, Kurz JL, Patel KM, Wun SJ, Hussein WM, Lonhienne T, West NP, McGeary RP, Schenk G, Guddat LW. Discovery of a Pyrimidinedione Derivative with Potent Inhibitory Activity against Mycobacterium tuberculosis Ketol-Acid Reductoisomerase. Chemistry 2021; 27:3130-3141. [PMID: 33215746 DOI: 10.1002/chem.202004665] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Indexed: 12/26/2022]
Abstract
New drugs aimed at novel targets are urgently needed to combat the increasing rate of drug-resistant tuberculosis (TB). Herein, the National Cancer Institute Developmental Therapeutic Program (NCI-DTP) chemical library was screened against a promising new target, ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid (BCAA) biosynthesis pathway. From this library, 6-hydroxy-2-methylthiazolo[4,5-d]pyrimidine-5,7(4H,6H)-dione (NSC116565) was identified as a potent time-dependent inhibitor of Mycobacterium tuberculosis (Mt) KARI with a Ki of 95.4 nm. Isothermal titration calorimetry studies showed that this inhibitor bound to MtKARI in the presence and absence of the cofactor, nicotinamide adenine dinucleotide phosphate (NADPH), which was confirmed by crystal structures of the compound in complex with closely related Staphylococcus aureus KARI. It is also shown that NSC116565 inhibits the growth of H37Ra and H37Rv strains of Mt with MIC50 values of 2.93 and 6.06 μm, respectively. These results further validate KARI as a TB drug target and show that NSC116565 is a promising lead for anti-TB drug development.
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Affiliation(s)
- Xin Lin
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Julia L Kurz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Khushboo M Patel
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Shun Jie Wun
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia.,Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan University, Helwan, Egypt
| | - Thierry Lonhienne
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
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