1
|
Kumar A, Vashisth H. Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface. J Chem Inf Model 2024; 64:2068-2076. [PMID: 38460144 PMCID: PMC10966652 DOI: 10.1021/acs.jcim.3c01933] [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: 12/04/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/11/2024]
Abstract
The highly conserved protease enzyme from SARS-CoV-2 (MPro) is crucial for viral replication and is an attractive target for the design of novel inhibitory compounds. MPro is known to be conformationally flexible and has been stabilized in an extended conformation in a complex with a novel nanobody (NB2B4), which inhibits the dimerization of the enzyme via binding to an allosteric site. However, the energetic contributions of the nanobody residues stabilizing the MPro/nanobody interface remain unresolved. We probed these residues using all-atom MD simulations in combination with alchemical free energy calculations by studying the physical residue-residue interactions and discovered the role of hydrophobic and electrostatic interactions in stabilizing the complex. Specifically, we found via mutational analysis that three interfacial nanobody residues (Y59, R106, and L109) contributed significantly, two residues (L107 and P110) contributed moderately, and two residues (H112 and T113) contributed minimally to the overall binding affinity of the nanobody. We also discovered that the nanobody affinity could be enhanced via a charge-reversal mutation (D62R) that alters the local interfacial electrostatic environment of this residue in the complex. These findings are potentially useful in designing novel synthetic nanobodies as allosteric inhibitors of MPro.
Collapse
Affiliation(s)
- Amit Kumar
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Harish Vashisth
- Department
of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, New Hampshire 03824, United States
| |
Collapse
|
2
|
Ryan SK, Ugalde CL, Rolland AS, Skidmore J, Devos D, Hammond TR. Therapeutic inhibition of ferroptosis in neurodegenerative disease. Trends Pharmacol Sci 2023; 44:674-688. [PMID: 37657967 DOI: 10.1016/j.tips.2023.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 09/03/2023]
Abstract
Iron accumulation has been associated with the etiology and progression of multiple neurodegenerative diseases (NDDs). The exact role of iron in these diseases is not fully understood, but an iron-dependent form of regulated cell death called ferroptosis could be key. Although there is substantial preclinical and clinical evidence that ferroptosis plays a role in NDD, there are still questions regarding how to target ferroptosis therapeutically, including which proteins to target, identification of clinically relevant biomarkers, and which patients might benefit most. Clinical trials of iron- and ferroptosis-targeted therapies are beginning to provide some answers, but there is growing interest in developing new ferroptosis inhibitors. We describe newly identified ferroptosis targets, opportunities, and challenges in NDD, as well as key considerations for progressing new therapeutics to the clinic.
Collapse
Affiliation(s)
- Sean K Ryan
- Sanofi, Rare and Neurologic Diseases, Cambridge, MA, USA
| | - Cathryn L Ugalde
- The ALBORADA Drug Discovery Institute, University of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, UK
| | - Anne-Sophie Rolland
- Department of Medical Pharmacology, Expert Center of Parkinson's Disease, ALS, and Neurogenetics, University of Lille, LilNCog, Lille Neuroscience and Cognition, INSERM UMR S1172, CHU de Lille, LICEND, COEN, Center, NS-PARK Network, France
| | - John Skidmore
- The ALBORADA Drug Discovery Institute, University of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, UK
| | - David Devos
- Department of Medical Pharmacology, Expert Center of Parkinson's Disease, ALS, and Neurogenetics, University of Lille, LilNCog, Lille Neuroscience and Cognition, INSERM UMR S1172, CHU de Lille, LICEND, COEN, Center, NS-PARK Network, France
| | | |
Collapse
|
3
|
Uceda S, Echeverry-Alzate V, Reiriz-Rojas M, Martínez-Miguel E, Pérez-Curiel A, Gómez-Senent S, Beltrán-Velasco AI. Gut Microbial Metabolome and Dysbiosis in Neurodegenerative Diseases: Psychobiotics and Fecal Microbiota Transplantation as a Therapeutic Approach-A Comprehensive Narrative Review. Int J Mol Sci 2023; 24:13294. [PMID: 37686104 PMCID: PMC10487945 DOI: 10.3390/ijms241713294] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The comprehensive narrative review conducted in this study delves into the mechanisms of communication and action at the molecular level in the human organism. The review addresses the complex mechanism involved in the microbiota-gut-brain axis as well as the implications of alterations in the microbial composition of patients with neurodegenerative diseases. The pathophysiology of neurodegenerative diseases with neuronal loss or death is analyzed, as well as the mechanisms of action of the main metabolites involved in the bidirectional communication through the microbiota-gut-brain axis. In addition, interventions targeting gut microbiota restructuring through fecal microbiota transplantation and the use of psychobiotics-pre- and pro-biotics-are evaluated as an opportunity to reduce the symptomatology associated with neurodegeneration in these pathologies. This review provides valuable information and facilitates a better understanding of the neurobiological mechanisms to be addressed in the treatment of neurodegenerative diseases.
Collapse
Affiliation(s)
- Sara Uceda
- BRABE Group, Psychology Department, School of Life and Nature Sciences, Nebrija University, 28240 Madrid, Spain
| | - Víctor Echeverry-Alzate
- BRABE Group, Psychology Department, School of Life and Nature Sciences, Nebrija University, 28240 Madrid, Spain
| | - Manuel Reiriz-Rojas
- BRABE Group, Psychology Department, School of Life and Nature Sciences, Nebrija University, 28240 Madrid, Spain
| | - Esther Martínez-Miguel
- Health Department, School of Life and Nature Sciences, Nebrija University, 28240 Madrid, Spain
| | - Ana Pérez-Curiel
- Health Department, School of Life and Nature Sciences, Nebrija University, 28240 Madrid, Spain
| | - Silvia Gómez-Senent
- Health Department, School of Life and Nature Sciences, Nebrija University, 28240 Madrid, Spain
| | | |
Collapse
|
4
|
A novel splicing variant of DJ-1 in Parkinson's disease induces mitochondrial dysfunction. Heliyon 2023; 9:e14039. [PMID: 36915530 PMCID: PMC10006478 DOI: 10.1016/j.heliyon.2023.e14039] [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: 12/12/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
Several studies have identified mutations in neuroprotective genes in a few cases of Parkinson's disease (PD); however, the role of alternative splicing changes in PD remains unelucidated. Based on the transcriptome analysis of substantia nigra (SN) tissues obtained from PD cases and age-matched healthy controls, we identified a novel alternative splicing variant of DJ-1, lacking exon 6 (DJ-1 ΔE6), frequently detected in the SN of patients with PD. We found that the exon 6 skipping of DJ-1 induces mitochondrial dysfunction and impaired antioxidant capability. According to an in silico modeling study, the exon 6 skipping of DJ-1 disrupts the structural state suitable for the oxidation of the cysteine 106 residue that is a prerequisite for activating its neuroprotective roles. Our results suggest that change in DJ-1 alternative splicing may contribute to PD progression and provide an insight for studying PD etiology and its potential therapeutic targets.
Collapse
|
5
|
Naren P, Cholkar A, Kamble S, Khan SS, Srivastava S, Madan J, Mehra N, Tiwari V, Singh SB, Khatri DK. Pathological and Therapeutic Advances in Parkinson's Disease: Mitochondria in the Interplay. J Alzheimers Dis 2023; 94:S399-S428. [PMID: 36093711 PMCID: PMC10473111 DOI: 10.3233/jad-220682] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2022] [Indexed: 11/15/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative illness majorly affecting the population between the ages of 55 to 65 years. Progressive dopaminergic neuronal loss and the collective assemblage of misfolded alpha-synuclein in the substantia nigra, remain notable neuro-pathological hallmarks of the disease. Multitudes of mechanistic pathways have been proposed in attempts to unravel the pathogenesis of PD but still, it remains elusive. The convergence of PD pathology is found in organelle dysfunction where mitochondria remain a major contributor. Mitochondrial processes like bioenergetics, mitochondrial dynamics, and mitophagy are under strict regulation by the mitochondrial genome and nuclear genome. These processes aggravate neurodegenerative activities upon alteration through neuroinflammation, oxidative damage, apoptosis, and proteostatic stress. Therefore, the mitochondria have grabbed a central position in the patho-mechanistic exploration of neurodegenerative diseases like PD. The management of PD remains a challenge to physicians to date, due to the variable therapeutic response of patients and the limitation of conventional chemical agents which only offer symptomatic relief with minimal to no disease-modifying effect. This review describes the patho-mechanistic pathways involved in PD not only limited to protein dyshomeostasis and oxidative stress, but explicit attention has been drawn to exploring mechanisms like organelle dysfunction, primarily mitochondria and mitochondrial genome influence, while delineating the newer exploratory targets such as GBA1, GLP, LRRK2, and miRNAs and therapeutic agents targeting them.
Collapse
Affiliation(s)
- Padmashri Naren
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Anjali Cholkar
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Suchita Kamble
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Sabiya Samim Khan
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Saurabh Srivastava
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana, India
| | - Jitender Madan
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana, India
| | - Neelesh Mehra
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana, India
| | - Vinod Tiwari
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.) Varanasi (U.P.), India
| | - Shashi Bala Singh
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Dharmendra Kumar Khatri
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| |
Collapse
|
6
|
Persulfidation of DJ-1: Mechanism and Consequences. Biomolecules 2022; 13:biom13010027. [PMID: 36671412 PMCID: PMC9856005 DOI: 10.3390/biom13010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
DJ-1 (also called PARK7) is a ubiquitously expressed protein involved in the etiology of Parkinson disease and cancers. At least one of its three cysteine residues is functionally essential, and its oxidation state determines the specific function of the enzyme. DJ-1 was recently reported to be persulfidated in mammalian cell lines, but the implications of this post-translational modification have not yet been analyzed. Here, we report that recombinant DJ-1 is reversibly persulfidated at cysteine 106 by reaction with various sulfane donors and subsequently inhibited. Strikingly, this reaction is orders of magnitude faster than C106 oxidation by H2O2, and persulfidated DJ-1 behaves differently than sulfinylated DJ-1. Both these PTMs most likely play a dedicated role in DJ-1 signaling or protective pathways.
Collapse
|
7
|
Kumar A, Vashisth H. Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides. J Chem Inf Model 2022; 62:3381-3390. [PMID: 35833626 PMCID: PMC10129845 DOI: 10.1021/acs.jcim.2c00376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conserved noncoding RNA elements in viral genomes interact with proteins to regulate various events during viral replication. We report studies on the recognition mechanisms of two helical peptides, namely, a native (Rev) peptide and a lab-evolved (RSG1.2) peptide, by a highly conserved viral RNA element from the human immunodeficiency virus 1 genome. Specifically, we investigated the physical interactions between the viral RNA molecule and helical peptides by computing free energy changes on mutating key amino acid residues involved in recognition of an internal loop in the viral RNA molecule.
Collapse
Affiliation(s)
- Amit Kumar
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
| |
Collapse
|
8
|
Ali MZ, Dholaniya PS. Oxidative phosphorylation mediated pathogenesis of Parkinson's disease and its implication via Akt signaling. Neurochem Int 2022; 157:105344. [PMID: 35483538 DOI: 10.1016/j.neuint.2022.105344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 12/21/2022]
Abstract
Substantia Nigra Pars-compacta (SNpc), in the basal ganglion region, is a primary source of dopamine release. These dopaminergic neurons require more energy than other neurons, as they are highly arborized and redundant. Neurons meet most of their energy demand (∼90%) from mitochondria. Oxidative phosphorylation (OxPhos) is the primary pathway for energy production. Many genes involved in Parkinson's disease (PD) have been associated with OxPhos, especially complex I. Abrogation in complex I leads to reduced ATP formation in these neurons, succumbing to death by inducing apoptosis. This review discusses the interconnection between complex I-associated PD genes and specific mitochondrial metabolic factors (MMFs) of OxPhos. Interestingly, all the complex I-associated PD genes discussed here have been linked to the Akt signaling pathway; thus, neuron survival is promoted and smooth mitochondrial function is ensured. Any changes in these genes disrupt the Akt pathway, which hampers the opening of the permeability transition pore (PTP) via GSK3β dephosphorylation; promotes destabilization of OxPhos; and triggers the release of pro-apoptotic factors.
Collapse
Affiliation(s)
- Md Zainul Ali
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500 046, India
| | - Pankaj Singh Dholaniya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500 046, India.
| |
Collapse
|
9
|
Kumar A, Vashisth H. Conformational dynamics and energetics of viral RNA recognition by lab-evolved proteins. Phys Chem Chem Phys 2021; 23:24773-24779. [PMID: 34714308 PMCID: PMC8579469 DOI: 10.1039/d1cp03822b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/14/2021] [Indexed: 12/01/2022]
Abstract
The conserved and structured elements in viral RNA genomes interact with proteins to regulate various events in the viral life cycle and have become key targets for developing novel therapeutic approaches. We probe physical interactions between lab-evolved proteins and a viral RNA element from the HIV-1 genome. Specifically, we study the role of an arginine-rich loop in recognition of designed proteins by the viral RNA element. We report free energy calculations to quantitatively estimate the protein/RNA binding energetics, focusing on the mutations of arginine residues involved in recognition of the major groove of RNA by proteins.
Collapse
Affiliation(s)
- Amit Kumar
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, USA.
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, USA.
| |
Collapse
|
10
|
Li W, Fu Y, Halliday GM, Sue CM. PARK Genes Link Mitochondrial Dysfunction and Alpha-Synuclein Pathology in Sporadic Parkinson's Disease. Front Cell Dev Biol 2021; 9:612476. [PMID: 34295884 PMCID: PMC8291125 DOI: 10.3389/fcell.2021.612476] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/10/2021] [Indexed: 11/28/2022] Open
Abstract
Parkinson’s disease (PD) is an age-related neurodegenerative disorder affecting millions of people worldwide. The disease is characterized by the progressive loss of dopaminergic neurons and spread of Lewy pathology (α-synuclein aggregates) in the brain but the pathogenesis remains elusive. PD presents substantial clinical and genetic variability. Although its complex etiology and pathogenesis has hampered the breakthrough in targeting disease modification, recent genetic tools advanced our approaches. As such, mitochondrial dysfunction has been identified as a major pathogenic hub for both familial and sporadic PD. In this review, we summarize the effect of mutations in 11 PARK genes (SNCA, PRKN, PINK1, DJ-1, LRRK2, ATP13A2, PLA2G6, FBXO7, VPS35, CHCHD2, and VPS13C) on mitochondrial function as well as their relevance in the formation of Lewy pathology. Overall, these genes play key roles in mitochondrial homeostatic control (biogenesis and mitophagy) and functions (e.g., energy production and oxidative stress), which may crosstalk with the autophagy pathway, induce proinflammatory immune responses, and increase oxidative stress that facilitate the aggregation of α-synuclein. Thus, rectifying mitochondrial dysregulation represents a promising therapeutic approach for neuroprotection in PD.
Collapse
Affiliation(s)
- Wen Li
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia.,Kolling Institute of Medical Research, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - YuHong Fu
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia.,School of Medical Science, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Glenda M Halliday
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia.,School of Medical Science, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Carolyn M Sue
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia.,Kolling Institute of Medical Research, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, NSW, Australia
| |
Collapse
|
11
|
Huang M, Chen S. DJ-1 in neurodegenerative diseases: Pathogenesis and clinical application. Prog Neurobiol 2021; 204:102114. [PMID: 34174373 DOI: 10.1016/j.pneurobio.2021.102114] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/22/2021] [Accepted: 06/21/2021] [Indexed: 12/23/2022]
Abstract
Neurodegenerative diseases (NDs) are one of the major health threats to human characterized by selective and progressive neuronal loss. The mechanisms of NDs are still not fully understood. The study of genetic defects and disease-related proteins offers us a window into the mystery of it, and the extension of knowledge indicates that different NDs share similar features, mechanisms, and even genetic or protein abnormalities. Among these findings, PARK7 and its production DJ-1 protein, which was initially found implicated in PD, have also been found altered in other NDs. PARK7 mutations, altered expression and posttranslational modification (PTM) cause DJ-1 abnormalities, which in turn lead to downstream mechanisms shared by most NDs, such as mitochondrial dysfunction, oxidative stress, protein aggregation, autophagy defects, and so on. The knowledge of DJ-1 derived from PD researches might apply to other NDs in both basic research and clinical application, and might yield novel insights into and alternative approaches for dealing with NDs.
Collapse
Affiliation(s)
- Maoxin Huang
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Shengdi Chen
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China; Lab for Translational Research of Neurodegenerative Diseases, Institute of Immunochemistry, Shanghai Tech University, 201210, Shanghai, China.
| |
Collapse
|