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Unni S, Kommu P, Aouti S, Nalli Y, Bharath MMS, Ali A, Padmanabhan B. Structural insights into the modulation Of SOD1 aggregation By a fungal metabolite Phialomustin-B: Therapeutic potential in ALS. PLoS One 2024; 19:e0298196. [PMID: 38446760 PMCID: PMC10917278 DOI: 10.1371/journal.pone.0298196] [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] [Received: 07/18/2023] [Accepted: 01/19/2024] [Indexed: 03/08/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal human motor neuron disease leading to muscle atrophy and paralysis. Mutations in superoxide dismutase 1 (SOD1) are associated with familial ALS (fALS). The SOD1 mutants in ALS have a toxic-gain of function by destabilizing the functional SOD1 homodimer, consequently inducing fibril-like aggregation with a cytotoxic non-native trimer intermediate. Therefore, reducing SOD1 oligomerization via chemical modulators is an optimal therapy in ALS. Here, we report the discovery of Phialomustin-B, an unsaturated secondary metabolite from the endophytic fungus Phialophora mustea, as a modulator of SOD1 aggregation. The crystal structure of the SOD1-Phialomustin complex refined to 1.90 Å resolution demonstrated for the first time that the ligand binds to the dimer interface and the lateral region near the electrostatic loop. The aggregation analyses of SOD1WT and the disease mutant SOD1A4V revealed that Phialomustin-B reduces cytotoxic trimerization. We propose that Phialomustin-B is a potent lead molecule with therapeutic potential in fALS.
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Affiliation(s)
- Sruthi Unni
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Padmini Kommu
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Snehal Aouti
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Yedukondalu Nalli
- CSIR-Indian Institute of Integrative Medicine, Natural Product Division, Jammu, India
| | - M. M. Srinivas Bharath
- Department of Clinical Psychopharmacology and Neurotoxicology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Asif Ali
- CSIR-Indian Institute of Integrative Medicine, Natural Product Division, Jammu, India
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, India
| | - Balasundaram Padmanabhan
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, India
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Cho I, Yoon S, Park S, Hong SW, Cho E, Kim E, Kim HY, Kim Y. Immobilized Amyloid Hexamer Fragments to Map Active Sites of Amyloid-Targeting Chemicals. ACS Chem Neurosci 2023; 14:9-18. [PMID: 36445044 DOI: 10.1021/acschemneuro.2c00449] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
As amyloid-β (Aβ) peptide is considered a biomarker and pathological culprit of Alzheimer's disease, Aβ-targeting compounds have been investigated for diagnostics development and drug discovery of the disorder. Unlike amyloid plaque targeting agents, such as clinically available amyloid radiotracers intercalating into the β-sheet structures of the aggregates, monomer and oligomer targeting chemicals are difficult to develop, as the transient and polymorphic nature of these peptides impedes their structural understanding. Here, we report a mapping approach to explore targeting residues of Aβ-imaging probes and Aβ-regulating drug candidates by utilizing a set of fragmented Aβ hexamers immobilized on a 96-well microplate in combination with fluorescent full-length Aβ for on-plate aggregation. To evaluate the mapping potential of the peptide plate, we tested previously reported fluorescent imaging agents (CRANAD-28, bis-ANS), aggregation inhibitors (curcumin, scyllo-inositol), and aggregate dissociators (necrostatin-1, sunitinib) targeting Aβ. Our approach enabled mechanistic understanding of compounds targeting nonfibrillar Aβ on an interacting sequence level.
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Affiliation(s)
- Illhwan Cho
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea
| | - Soljee Yoon
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Department of Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon21983, Republic of Korea
| | - Sunghyun Park
- Department of Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon21983, Republic of Korea
| | - Seung Woo Hong
- Department of Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon21983, Republic of Korea
| | - Eunjung Cho
- Department of Medical Science, Yonsei University College of Medicine, Seoul03722, Republic of Korea.,Department of Psychiatry, Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul03722, Republic of Korea.,Brain Korea 21 Four Project for Medical Science, Yonsei University College of Medicine, Seoul03722, Republic of Korea
| | - Eosu Kim
- Department of Medical Science, Yonsei University College of Medicine, Seoul03722, Republic of Korea.,Department of Psychiatry, Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul03722, Republic of Korea
| | - Hye Yun Kim
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea
| | - YoungSoo Kim
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Department of Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon21983, Republic of Korea.,Integrated Science and Engineering Division, Yonsei University, Incheon21983, Republic of Korea.,POSTECH-Yonsei Campus, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk37673, Republic of Korea.,Amyloid Solution, Seongnam, Gyeonggi13486, Republic of Korea
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Sedov I, Khaibrakhmanova D. Molecular Mechanisms of Inhibition of Protein Amyloid Fibril Formation: Evidence and Perspectives Based on Kinetic Models. Int J Mol Sci 2022; 23:ijms232113428. [PMID: 36362217 PMCID: PMC9657184 DOI: 10.3390/ijms232113428] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Inhibition of fibril formation is considered a possible treatment strategy for amyloid-related diseases. Understanding the molecular nature of inhibitor action is crucial for the design of drug candidates. In the present review, we describe the common kinetic models of fibril formation and classify known inhibitors by the mechanism of their interactions with the aggregating protein and its oligomers. This mechanism determines the step or steps of the aggregation process that become inhibited and the observed changes in kinetics and equilibrium of fibril formation. The results of numerous studies indicate that possible approaches to antiamyloid inhibitor discovery include the search for the strong binders of protein monomers, cappers blocking the ends of the growing fibril, or the species absorbing on the surface of oligomers preventing nucleation. Strongly binding inhibitors stabilizing the native state can be promising for the structured proteins while designing the drug candidates targeting disordered proteins is challenging.
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Affiliation(s)
- Igor Sedov
- Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Correspondence: ; Tel.: +7-9600503916
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Study of Inducing Factors on Resveratrol and Antioxidant Content in Germinated Peanuts. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27175700. [PMID: 36080467 PMCID: PMC9458182 DOI: 10.3390/molecules27175700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022]
Abstract
When peanuts germinate, bioactive compounds such as resveratrol (RES), γ-aminobutyric acid (GABA), isoflavones, and polyphenol compounds are generated. Peanut kernels were germinated in the dark for two days, and stimuli including soaking liquid, rice koji, high-pressure processing (HPP), and ultrasonic treatment were tested for their ability to activate the defense mechanisms of peanut kernels, thus increasing their bioactive compound content. The results of this study indicate that no RES was detected in ungerminated peanuts, and only 5.58 μg/g of GABA was present, while unstimulated germinated peanuts contained 4.03 µg/g of RES and 258.83 μg/g of GABA. The RES content of the germinated peanuts increased to 13.64 μg/g after soaking in 0.2% phenylalanine solution, whereas a higher GABA content of 651.51 μg/g was observed after the peanuts were soaked in 0.2% glutamate. Soaking peanuts in 5% rice koji produced the highest RES and GABA contents (28.83 µg/g and 506.34 μg/g, respectively). Meanwhile, the RES and GABA contents of HPP-treated germinated peanuts (i.e., treated with HPP at 100 MPa for 10 min) increased to 7.66 μg/g and 497.09 μg/g, respectively, whereas those of ultrasonic-treated germinated peanuts (for 20 min) increased to 13.02 μg/g and 318.71 μg/g, respectively. After soaking peanuts in 0.5% rice koji, followed by HPP treatment at 100 MPa for 10 min, the RES and GABA contents of the germinated peanuts increased to 37.78 μg/g and 1196.98 μg/g, while the RES and GABA contents of the germinated peanuts treated with rice koji followed by ultrasonic treatment for 20 min increased to 46.53 μg/g and 974.52 μg/g, respectively. The flavonoid and polyphenol contents of the germinated peanuts also increased after exposure to various external stimuli, improving their DPPH free radical-scavenging ability and showing the good potential of germinated peanuts as functional products.
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Khurshid B, Rehman AU, Muhammad S, Wadood A, Anwar J. Toward the Noninvasive Diagnosis of Alzheimer's Disease: Molecular Basis for the Specificity of Curcumin for Fibrillar Amyloid-β. ACS OMEGA 2022; 7:22032-22038. [PMID: 35785332 PMCID: PMC9245119 DOI: 10.1021/acsomega.2c02995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Recent studies show that curcumin, a naturally fluorescent dye, can be used for the noninvasive optical imaging of retinal amyloid-β (Aβ) plaques. We investigated the molecular basis for curcumin's specificity for hierarchical Aβ structures using molecular dynamics simulations, with a focus on how curcumin is able to detect and discriminate different amyloid morphologies. Curcumin inhibits and breaks up β-sheet formation in Aβ monomers. With disordered Aβ structures, curcumin forms a coarse-grained composite structure. With an ordered fibril, curcumin's interaction is highly specific, and the curcumin molecules are deposited in the fibril groove. Curcumin tends to self-aggregate, which is finely balanced with its affinity for Aβ. This tendency concentrates curcumin molecules at Aβ deposition sites, potentially increasing the fluorescence signal. This is probably why curcumin is such an effective amyloid imaging agent.
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Affiliation(s)
- Beenish Khurshid
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
- Department
of Chemistry, University of Lancaster, Lancaster LA1 4YB, United Kingdom
| | - Ashfaq Ur Rehman
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697, United States
| | - Shabbir Muhammad
- Department
of Chemistry, College of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Abdul Wadood
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Jamshed Anwar
- Department
of Chemistry, University of Lancaster, Lancaster LA1 4YB, United Kingdom
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