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Dow LF, Case AM, Paustian MP, Pinkerton BR, Simeon P, Trippier PC. The evolution of small molecule enzyme activators. RSC Med Chem 2023; 14:2206-2230. [PMID: 37974956 PMCID: PMC10650962 DOI: 10.1039/d3md00399j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
There is a myriad of enzymes within the body responsible for maintaining homeostasis by providing the means to convert substrates to products as and when required. Physiological enzymes are tightly controlled by many signaling pathways and their products subsequently control other pathways. Traditionally, most drug discovery efforts focus on identifying enzyme inhibitors, due to upregulation being prevalent in many diseases and the existence of endogenous substrates that can be modified to afford inhibitor compounds. As enzyme downregulation and reduction of endogenous activators are observed in multiple diseases, the identification of small molecules with the ability to activate enzymes has recently entered the medicinal chemistry toolbox to afford chemical probes and potential therapeutics as an alternative means to intervene in diseases. In this review we highlight the progress made in the identification and advancement of non-kinase enzyme activators and their potential in treating various disease states.
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Affiliation(s)
- Louise F Dow
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Alfie M Case
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Megan P Paustian
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Braeden R Pinkerton
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Princess Simeon
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Paul C Trippier
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center Omaha NE 68106 USA
- UNMC Center for Drug Discovery, University of Nebraska Medical Center Omaha NE 68106 USA
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2
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Yuan X, Wu X, Xiong J, Yan B, Gao R, Liu S, Zong M, Ge J, Lou W. Hydrolase mimic via second coordination sphere engineering in metal-organic frameworks for environmental remediation. Nat Commun 2023; 14:5974. [PMID: 37749093 PMCID: PMC10520056 DOI: 10.1038/s41467-023-41716-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023] Open
Abstract
Enzymes achieve high catalytic activity with their elaborate arrangements of amino acid residues in confined optimized spaces. Nevertheless, when exposed to complicated environmental implementation scenarios, including high acidity, organic solvent and high ionic strength, enzymes exhibit low operational stability and poor activity. Here, we report a metal-organic frameworks (MOFs)-based artificial enzyme system via second coordination sphere engineering to achieve high hydrolytic activity under mild conditions. Experiments and theoretical calculations reveal that amide cleavage catalyzed by MOFs follows two distinct catalytic mechanisms, Lewis acid- and hydrogen bonding-mediated hydrolytic processes. The hydrogen bond formed in the secondary coordination sphere exhibits 11-fold higher hydrolytic activity than the Lewis acidic zinc ions. The MOFs exhibit satisfactory degradation performance of toxins and high stability under extreme working conditions, including complicated fermentation broth and high ethanol environments, and display broad substrate specificity. These findings hold great promise for designing artificial enzymes for environmental remediation.
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Affiliation(s)
- Xin Yuan
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China
| | - Xiaoling Wu
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China.
| | - Jun Xiong
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China
| | - Binhang Yan
- Department of Chemical Engineering, Tsinghua University, 100084, Beijing, China
| | - Ruichen Gao
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China
| | - Shuli Liu
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China
| | - Minhua Zong
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China
| | - Jun Ge
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, 100084, Beijing, China.
| | - Wenyong Lou
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China.
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Somin S, Kulasiri D, Samarasinghe S. Alleviating the unwanted effects of oxidative stress on Aβ clearance: a review of related concepts and strategies for the development of computational modelling. Transl Neurodegener 2023; 12:11. [PMID: 36907887 PMCID: PMC10009979 DOI: 10.1186/s40035-023-00344-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/21/2023] [Indexed: 03/14/2023] Open
Abstract
Treatment for Alzheimer's disease (AD) can be more effective in the early stages. Although we do not completely understand the aetiology of the early stages of AD, potential pathological factors (amyloid beta [Aβ] and tau) and other co-factors have been identified as causes of AD, which may indicate some of the mechanism at work in the early stages of AD. Today, one of the primary techniques used to help delay or prevent AD in the early stages involves alleviating the unwanted effects of oxidative stress on Aβ clearance. 4-Hydroxynonenal (HNE), a product of lipid peroxidation caused by oxidative stress, plays a key role in the adduction of the degrading proteases. This HNE employs a mechanism which decreases catalytic activity. This process ultimately impairs Aβ clearance. The degradation of HNE-modified proteins helps to alleviate the unwanted effects of oxidative stress. Having a clear understanding of the mechanisms associated with the degradation of the HNE-modified proteins is essential for the development of strategies and for alleviating the unwanted effects of oxidative stress. The strategies which could be employed to decrease the effects of oxidative stress include enhancing antioxidant activity, as well as the use of nanozymes and/or specific inhibitors. One area which shows promise in reducing oxidative stress is protein design. However, more research is needed to improve the effectiveness and accuracy of this technique. This paper discusses the interplay of potential pathological factors and AD. In particular, it focuses on the effect of oxidative stress on the expression of the Aβ-degrading proteases through adduction of the degrading proteases caused by HNE. The paper also elucidates other strategies that can be used to alleviate the unwanted effects of oxidative stress on Aβ clearance. To improve the effectiveness and accuracy of protein design, we explain the application of quantum mechanical/molecular mechanical approach.
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Affiliation(s)
- Sarawoot Somin
- Centre for Advanced Computational Solutions (C-fACS), Lincoln University, Christchurch, 7647, New Zealand.,Department of Wine, Food and Molecular Biosciences, Lincoln University, Christchurch, 7647, New Zealand
| | - Don Kulasiri
- Centre for Advanced Computational Solutions (C-fACS), Lincoln University, Christchurch, 7647, New Zealand. .,Department of Wine, Food and Molecular Biosciences, Lincoln University, Christchurch, 7647, New Zealand.
| | - Sandhya Samarasinghe
- Centre for Advanced Computational Solutions (C-fACS), Lincoln University, Christchurch, 7647, New Zealand
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4
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Wilson Alphonse CR, Rajesh Kannan R, Nagarajan N. PITRM1 interaction studies with amyloidogenic nonapeptide mutants of familial Alzheimer's disease. J Biomol Struct Dyn 2022:1-12. [PMID: 35751131 DOI: 10.1080/07391102.2022.2092554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Amyloid β-protein (ABP) is found to be the major cause for the development of neurodegeneration which leads to Alzheimer's. The Aβ nonapeptide segment, QKLVFFAED (amino acids 15-23) is the highly amyloidogenic central region of Aβ. Familial mutation in Aβ increases the aggregation property of the peptide compared to the Native (Wild) amyloid-beta (Aβ) and these mutations fall on the Aβ nonapeptide segment. The catalytic activity of pitrilysin metallopeptidase 1(PITRM1) with familial mutant Aβ (Flemish, Arctic, Dutch, Italian and Iowa) during interaction is examined using molecular dynamic simulation. The molecular dynamics simulation of PITRM1 and the Aβ nonapeptide segment showed similar RMSD with respect to stability. The active site amino acid (AA) H108, hydrophobic pocket AA residues L111, F123, F124, and L127 and the basic pocket AA residues R888 and H896 showed similar interactions with both wild and familial Aβ. The molecular level interaction between amyloid beta and PITRM1 were similar in the wild and familial mutants except for the Arctic mutant. The hydrophobic interaction was commonly observed between the S1 hydrophobic pocket and the LVFF region, the Arctic mutant showed less hydrogen bond formation consistently when compared to other complexes. This molecular information on catalytic activity suggests that modulating inactive PITRM1 or an increase in expression of PITRM1 can help in eliminating different kinds of familial mutant Aβ in neurodegenerative cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carlton Ranjith Wilson Alphonse
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Rajaretinam Rajesh Kannan
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Nagasundaram Nagarajan
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India.,School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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5
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Prabhakar R. Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. J Chem Inf Model 2022; 62:2466-2480. [PMID: 35451306 DOI: 10.1021/acs.jcim.2c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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6
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Tetrahydroxy Stilbene Glucoside Ameliorates Cognitive Impairments and Pathology in APP/PS1 Transgenic Mice. Curr Med Sci 2021; 41:279-286. [PMID: 33877543 DOI: 10.1007/s11596-021-2344-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/26/2020] [Indexed: 10/21/2022]
Abstract
Cognitive impairment is the main clinical manifestation of Alzheimer's disease (AD), and amyloid-β (Aβ) deposition and senile plaques are the characteristic neuropathological hallmarks in AD brains. This study aimed to explore the effect and mechanism of tetrahydroxy stilbene glucoside (TSG) on cognitive function in APP/PS1 mice during long-term administration. Here, we treated APP/PS1 model mice of AD with different doses of TSG (50 mg/kg and 100 mg/kg) for 5 to 17 months by gavage, and we further observed whether TSG could ameliorate the cognitive decline in APP/PS1 mice using behavioral tests, and investigated the possible mechanisms by immunohistochemistry and Western blotting. Our results showed that TSG treatment rescued the spatial and non-spatial learning and memory impairments of APP/PS1 mice at Morris water maze test and novel object recognition test. Furthermore, Aβ40/42 deposition in the cortex and hippocampus of APP/PS1 mice treated with TSG was significantly reduced compared to the wild type mice using the immunohistochemical technique. Finally, Western blotting showed that TSG primarily decreased the APP expression to avoid the Aβ plaque deposition in the cortex and hippocampus of mice. These results reveal the beneficial effects of TSG in APP/PS1-AD mice, which may be associated with the reduction of Aβ deposits in the brain.
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7
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Portelinha J, Duay SS, Yu SI, Heilemann K, Libardo MDJ, Juliano SA, Klassen JL, Angeles-Boza AM. Antimicrobial Peptides and Copper(II) Ions: Novel Therapeutic Opportunities. Chem Rev 2021; 121:2648-2712. [PMID: 33524257 DOI: 10.1021/acs.chemrev.0c00921] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The emergence of new pathogens and multidrug resistant bacteria is an important public health issue that requires the development of novel classes of antibiotics. Antimicrobial peptides (AMPs) are a promising platform with great potential for the identification of new lead compounds that can combat the aforementioned pathogens due to their broad-spectrum antimicrobial activity and relatively low rate of resistance emergence. AMPs of multicellular organisms made their debut four decades ago thanks to ingenious researchers who asked simple questions about the resistance to bacterial infections of insects. Questions such as "Do fruit flies ever get sick?", combined with pioneering studies, have led to an understanding of AMPs as universal weapons of the immune system. This review focuses on a subclass of AMPs that feature a metal binding motif known as the amino terminal copper and nickel (ATCUN) motif. One of the metal-based strategies of hosts facing a pathogen, it includes wielding the inherent toxicity of copper and deliberately trafficking this metal ion into sites of infection. The sudden increase in the concentration of copper ions in the presence of ATCUN-containing AMPs (ATCUN-AMPs) likely results in a synergistic interaction. Herein, we examine common structural features in ATCUN-AMPs that exist across species, and we highlight unique features that deserve additional attention. We also present the current state of knowledge about the molecular mechanisms behind their antimicrobial activity and the methods available to study this promising class of AMPs.
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Affiliation(s)
- Jasmin Portelinha
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Searle S Duay
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States.,Chemistry Department, Adamson University, 900 San Marcelino Street, Ermita, Manila 1000, Philippines
| | - Seung I Yu
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Kara Heilemann
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - M Daben J Libardo
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Samuel A Juliano
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Alfredo M Angeles-Boza
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States.,Institute of Material Science, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
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Liang J, Pitsillou E, Man AYL, Madzima S, Bresnehan SM, Nakai ME, Hung A, Karagiannis TC. Utilisation of the OliveNet™ Library to investigate phenolic compounds using molecular modelling studies in the context of Alzheimer's disease. Comput Biol Chem 2020; 87:107271. [PMID: 32521495 DOI: 10.1016/j.compbiolchem.2020.107271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 01/05/2023]
Abstract
Alzheimer's disease (AD) is a debilitating neurodegenerative disease that affects over 47 million people worldwide, and is the most common form of dementia. There is a vast body of literature demonstrating that the disease is caused by an accumulation of toxic extracellular amyloid-β (Aβ) peptides and intracellular neurofibrillary tangles that consist of hyperphosphorylated tau. Adherence to the Mediterranean diet has been shown to reduce the incidence of AD and the phenolic compounds in extra virgin olive oil, including oleocanthal, have gained a significant amount of attention. A large number of these ligands have been described in the pre-existing literature and 222 of these compounds have been characterised in the OliveNet™ database. In this study, molecular docking was used to screen the 222 phenolic compounds from the OliveNet™ database and assess their ability to bind to various forms of the Aβ and tau proteins. The phenolic ligands were found to be binding strongly to the hairpin-turn of the Aβ1-40 and Aβ1-42 monomers, and binding sites were also identified in the tau fibril protein structures. Luteolin-4'-O-rutinoside, oleuricine A, isorhoifolin, luteolin-7-O-rutinoside, cyanidin-3-O-rutinoside and luteolin-7,4-O-diglucoside were predicted to be novel lead compounds. Molecular dynamics (MD) simulations performed using well-known olive ligands bound to Aβ1-42 oligomers highlighted that future work may examine potential anti-aggregating properties of novel compounds in the OliveNet™ database. This may lead to the development and evaluation of new compounds that may have efficacy against Alzheimer's disease.
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Affiliation(s)
- Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; School of Science, RMIT University, VIC 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Abella Y L Man
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Sibonginkosi Madzima
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Sarah M Bresnehan
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Michael E Nakai
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Andrew Hung
- School of Science, RMIT University, VIC 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia.
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Active Sites in Heterogeneous Catalytic Reaction on Metal and Metal Oxide: Theory and Practice. Catalysts 2018. [DOI: 10.3390/catal8100478] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Active sites play an essential role in heterogeneous catalysis and largely determine the reaction properties. Yet identification and study of the active sites remain challenging owing to their dynamic behaviors during catalysis process and issues with current characterization techniques. This article provides a short review of research progresses in active sites of metal and metal oxide catalysts, which covers the past achievements, current research status, and perspectives in this research field. In particular, the concepts and theories of active sites are introduced. Major experimental and computational approaches that are used in active site study are summarized, with their applications and limitations being discussed. An outlook of future research direction in both experimental and computational catalysis research is provided.
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