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Khenifi ML, Serseg T, Migas P, Krauze-Baranowska M, Özdemir S, Bensouici C, Alghonaim MI, Al-Khafaji K, Alsalamah SA, Boudjeniba M, Yousfi M, Boufahja F, Bendif H, Mahdid M. HPLC-DAD-MS Characterization, Antioxidant Activity, α-amylase Inhibition, Molecular Docking, and ADMET of Flavonoids from Fenugreek Seeds. Molecules 2023; 28:7798. [PMID: 38067527 PMCID: PMC10708475 DOI: 10.3390/molecules28237798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Fenugreek (Trigonella foenum-graecum) has a great beneficial health effect; it has been used in traditional medicine by many cultures. Likewise, the α-amylase inhibitors are potential compounds in the development of drugs for the treatment of diabetes. The beneficial health effects of fenugreek lead us to explore the chemical composition of the seeds and their antioxidant and α-amylase inhibition activities. The flavonoid extraction from fenugreek seeds was achieved with methanol through a Soxhlet apparatus. Then, the flavonoid glycosides were characterized using HPLC-DAD-ESI-MS analysis. The antioxidant capacity of fenugreek seed was measured using DPPH, FRAP, ABTS, and CUPRAC assays. Finally, the α-amylase inhibition activity was carried out using in vitro and in silico methods. The methanolic extract was found to contain high amounts of total phenolics (154.68 ± 1.50 μg GAE/mg E), flavonoids (37.69 ± 0.73 μg QE/mg E). The highest radical-scavenging ability was recorded for the methanolic extract against DPPH (IC50 = 556.6 ± 9.87 μg/mL), ABTS (IC50 = 593.62 ± 9.35 μg/mL). The ME had the best reducing power according to the CUPRAC (A 0.5 = 451.90 ± 9.07 μg/mL). The results indicate that the methanolic extracts of fenugreek seed best α-amylase inhibition activities IC50 = 653.52 ± 3.24 μg/mL. Twenty-seven flavonoids were detected, and all studied flavonoids selected have good affinity and stabilize very well in the pocket of α-amylase. The interactions between the studied flavonoids with α-amylase were investigated. The flavonoids from fenugreek seed present a good inhibitory effect against α-amylase, which is beneficial for the prevention of diabetes and its complications.
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Affiliation(s)
- Mohammed Lamine Khenifi
- Laboratoire d’Ethnobotanique et Substances Naturelles, Departement of Biology, Ecole Normale Supérieure de Kouba, B.P 92, Kouba 16308, Algeria; (M.L.K.); (M.B.); (H.B.); (M.M.)
- Laboratoire des Sciences Appliquées et Didactiques, Ecole Normale Supérieure de Laghouat, B.P 4033 la gare routière, Laghouat 03000, Algeria;
| | - Talia Serseg
- Laboratoire des Sciences Appliquées et Didactiques, Ecole Normale Supérieure de Laghouat, B.P 4033 la gare routière, Laghouat 03000, Algeria;
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat 03000, Algeria;
| | - Piotr Migas
- Pharmacognosy with Medicinal Plants Garden, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (P.M.); (M.K.-B.)
| | - Mirosława Krauze-Baranowska
- Pharmacognosy with Medicinal Plants Garden, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (P.M.); (M.K.-B.)
| | - Sadin Özdemir
- Food Processing Programme, Technical Science Vocational School Mersin University, Mersin TR-33343, Turkey;
| | - Chawki Bensouici
- Biotechnology Research Center (CRBT), Ali Mendjli New Town UV 03, B.P E73, Constantine 25016, Algeria;
| | - Mohammed I. Alghonaim
- Biology Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (M.I.A.); (S.A.A.)
| | - Khattab Al-Khafaji
- Department of Environmental Science, College of Energy and Environmental Science, Al-Karkh University of Science, Baghdad 10081, Iraq;
| | - Sulaiman A. Alsalamah
- Biology Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (M.I.A.); (S.A.A.)
| | - Messaoud Boudjeniba
- Laboratoire d’Ethnobotanique et Substances Naturelles, Departement of Biology, Ecole Normale Supérieure de Kouba, B.P 92, Kouba 16308, Algeria; (M.L.K.); (M.B.); (H.B.); (M.M.)
| | - Mohamed Yousfi
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat 03000, Algeria;
| | - Fehmi Boufahja
- Biology Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (M.I.A.); (S.A.A.)
| | - Hamdi Bendif
- Laboratoire d’Ethnobotanique et Substances Naturelles, Departement of Biology, Ecole Normale Supérieure de Kouba, B.P 92, Kouba 16308, Algeria; (M.L.K.); (M.B.); (H.B.); (M.M.)
- Department of Natural and life Sciences, Faculty of Sciences, University of Msila, Msila 28000, Algeria
| | - Mohamed Mahdid
- Laboratoire d’Ethnobotanique et Substances Naturelles, Departement of Biology, Ecole Normale Supérieure de Kouba, B.P 92, Kouba 16308, Algeria; (M.L.K.); (M.B.); (H.B.); (M.M.)
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2
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Kaur G, Mankoo OK, Goyal D, Goyal B. Unveiling How Hydroxytyrosol Destabilizes α-Syn Oligomers Using Molecular Simulations. J Phys Chem B 2023. [PMID: 37319389 DOI: 10.1021/acs.jpcb.3c02434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The etiology of Parkinson's disease (PD) is mainly linked to the α-synuclein (α-Syn) fibrillogenesis. Hydroxytyrosol (HT), also known as 3,4-dihydroxyphenylethanol, is a naturally occurring polyphenol, found in extra virgin olive oil, and has been shown to have cardioprotective, anticancer, antiobesity, and antidiabetic properties. HT has neuroprotective benefits in neurodegenerative diseases and lessens the severity of PD by reducing the aggregation of α-Syn and destabilizing the preformed toxic α-Syn oligomers. However, the molecular mechanism by which HT destabilizes α-Syn oligomers and alleviates the accompanying cytotoxicity remains unexplored. The impact of HT on the α-Syn oligomer structure and its potential binding mechanism was examined in this work by employing molecular dynamics (MD) simulations. The secondary structure analysis depicted that HT significantly reduces the β-sheet and concomitantly increases the coil content of α-Syn trimer. Visualization of representative conformations from the clustering analysis depicted the hydrogen bond interactions of the hydroxyl groups in HT with the N-terminal and nonamyloid-β component (NAC) region residues of α-Syn trimer, which, in turn, leads to the weakening of interchain interactions in α-Syn trimer and resulted in the disruption of the α-Syn oligomer. The binding free energy calculations depict that HT binds favorably to α-Syn trimer (ΔGbinding = -23.25 ± 7.86 kcal/mol) and a notable reduction in the interchain binding affinity of α-Syn trimer on the incorporation of HT, which, in turn, highlights its potential to disrupt α-Syn oligomers. The current research provided mechanistic insights into the destabilization of α-Syn trimer by HT, which, in turn, will provide new clues for developing therapeutics against PD.
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Affiliation(s)
- Gagandeep Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Opinder Kaur Mankoo
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, DAV College, Sector 10, Chandigarh-160011, India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147004, Punjab, India
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3
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Kato K, Nakayoshi T, Nagura A, Hishinuma E, Hiratsuka M, Kurimoto E, Oda A. Structural investigation of pathogenic variants in dihydropyrimidinase using molecular dynamics simulations. J Mol Graph Model 2022; 117:108288. [PMID: 35961217 DOI: 10.1016/j.jmgm.2022.108288] [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: 11/29/2021] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 01/14/2023]
Abstract
Dihydropyrimidinase (DHP) is an enzyme that catabolizes the degradation of pyrimidine and fluoropyrimidine drugs such as 5-fluorouracil. DHP deficiency triggers various clinical symptoms and increases the risk of fluoropyrimidine drug toxicity. Various pathogenic variants of DHP cause DHP deficiency, and their catalytic activities have been well studied. However, the three-dimensional structures of DHP variants have not been clarified. In this study, we investigated the effects of mutations on DHP structures using the molecular dynamics simulations. Simulations of the wild type and 10 variants were performed and compared. In the T68R, D81G, G278D, and L337P variants, the flexibilities of structures related to the interaction for oligomer formation increased in comparison with those of the wild type. W117R, T343A, and R412 M mutations affected the structures of stereochemistry gate loops or the substrate-binding pocket. The three-dimensional structures of W360R and G435R variants were suggested to collapse. On the other hand, only slight structural changes were observed in the R181W variant, whose experimentally observed activity was similar to that of the wild type. The computational results are expected to clarify the relationship between clinical mutations and structural effects of drug-metabolizing enzymes.
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Affiliation(s)
- Koichi Kato
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi, 468-8503, Japan; Faculty of Pharmaceutical Sciences, Shonan University of Medical Sciences, 16-48 Kamishinano, Totsu-ka-ku, Yokohama, Kanagawa, 244-0806, Japan; College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi, 463-8521, Japan
| | - Tomoki Nakayoshi
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi, 468-8503, Japan; Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigasi, Asaminami-ku, Hiroshima, Hiroshima, 731-3194, Japan
| | - Ayuka Nagura
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi, 468-8503, Japan
| | - Eiji Hishinuma
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, 980-8573, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi, 980-8573, Japan
| | - Masahiro Hiratsuka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, 980-8573, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi, 980-8573, Japan; Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Miyagi, 980-8574, Japan
| | - Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi, 468-8503, Japan
| | - Akifumi Oda
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi, 468-8503, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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4
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Yao Y, Tang Y, Zhou Y, Yang Z, Wei G. Baicalein exhibits differential effects and mechanisms towards disruption of α-synuclein fibrils with different polymorphs. Int J Biol Macromol 2022; 220:316-325. [PMID: 35981677 DOI: 10.1016/j.ijbiomac.2022.08.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/30/2022] [Accepted: 08/11/2022] [Indexed: 11/05/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative diseases with no cure yet and its major hallmark is α-synuclein fibrillary aggregates. The crucial role of α-synuclein aggregation in PD makes it an attractive target for potential disease-modifying therapies. Disaggregation of α-synuclein fibrils is considered as one of the promising therapeutic strategies to treat PD. The wild type (WT) and mutant α-synuclein fibrils exhibit different polymorphs and provide therapeutic targets for PD. Recent experiments reported that a flavonoid baicalein can disrupt WT α-synuclein fibrils. However, the underlying disruptive mechanism remains largely elusive, and whether BAC is capable of disrupting mutant α-synuclein fibrils is also unknown. Herein, we performed microsecond molecular dynamics simulations on cryo-EM-determined WT and two familial PD-associated mutant (E46K and H50Q) α-synuclein fibrils with and without baicalein. We find that baicalein destructs WT fibril by disrupting E46-K80 salt-bridge and β-sheets, and by remodeling the inter-protofilament interface. And baicalein can also damage E46K and H50Q mutant fibrils, but to different extents and via different mechanisms. The E46K fibril disruption is initiated from E61-K80 salt-bridge and N-terminal β-sheet, while the H50Q fibril disruption starts from the inter-protofilament interface and N-terminal β-sheet. These results reveal that disruptive effects and modes of baicalein on α-synuclein fibrils are polymorphism-dependent. This study suggests that baicalein may be a potential drug candidate to disrupt both WT and E46K/H50Q mutant α-synuclein fibrils and alleviate the pathological process of PD.
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Affiliation(s)
- Yifei Yao
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Yun Zhou
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Zhongyuan Yang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
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5
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Mohanty L, Mishra C, Pradhan SK, Mishra SR, Nayak G. Identification of novel polymorphism and in silico analysis of caprine DNAJB3 gene. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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6
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Deciphering Structural Alterations Associated with Activity Reductions of Genetic Polymorphisms in Cytochrome P450 2A6 Using Molecular Dynamics Simulations. Int J Mol Sci 2021; 22:ijms221810119. [PMID: 34576282 PMCID: PMC8469730 DOI: 10.3390/ijms221810119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/04/2022] Open
Abstract
Cytochrome P450 (CYP) 2A6 is a monooxygenase involved in the metabolism of various endogenous and exogenous chemicals, such as nicotine and therapeutic drugs. The genetic polymorphisms in CYP2A6 are a cause of individual variation in smoking behavior and drug toxicities. The enzymatic activities of the allelic variants of CYP2A6 were analyzed in previous studies. However, the three-dimensional structures of the mutants were not investigated, and the mechanisms underlying activity reduction remain unknown. In this study, to investigate the structural changes involved in the reduction in enzymatic activities, we performed molecular dynamics simulations for ten allelic mutants of CYP2A6. For the calculated wild type structure, no significant structural changes were observed in comparison with the experimental structure. On the other hand, the mutations affected the interaction with heme, substrates, and the redox partner. In CYP2A6.44, a structural change in the substrate access channel was also observed. Those structural effects could explain the alteration of enzymatic activity caused by the mutations. The results of simulations provide useful information regarding the relationship between genotype and phenotype.
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7
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Mizuno H, Hoshino J, So M, Kogure Y, Fujii T, Ubara Y, Takaichi K, Nakaniwa T, Tanaka H, Kurisu G, Kametani F, Nakagawa M, Yoshinaga T, Sekijima Y, Higuchi K, Goto Y, Yazaki M. Dialysis-related amyloidosis associated with a novel β 2-microglobulin variant. Amyloid 2021; 28:42-49. [PMID: 32875920 DOI: 10.1080/13506129.2020.1813097] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Till date, there had been no reported case of dialysis-related amyloidosis (DRA) associated with a β2-microglobulin variant. We report here a 41-year-old haemodialysis patient with systemic amyloidosis, exhibiting macroglossia and swelling salivary glands, uncommon clinical manifestations for DRA. Molecular analysis showed that the patient had a new variant of β2-microglobulin (V27M). Extracted amyloid protein was predominantly composed of variant β2-microglobulin. In vitro analysis revealed that this variant β2-microglobulin had a strong amyloidogenic propensity, probably owing to the decreased stability caused by a bulky methionine residue. Our data clearly show that V27M variant is amyloidogenic and this mutation results in unusual clinical manifestations. To date, only one amyloidogenic β2-microglobulin variant (D76N) has been reported in non-dialysis patients. It is noteworthy that the V27M and D76N variants show substantial differences in both clinical phenotypes and pathomechanical features. This is the first case of DRA associated with a naturally occurring β2-microglobulin variant.
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Affiliation(s)
| | - Junichi Hoshino
- Nephrology Center, Toranomon Hospital, Tokyo, Japan.,Okinaka Memorial Institute for Medical Sciences, Tokyo, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yuta Kogure
- Nephrology Center, Toranomon Hospital, Tokyo, Japan.,Department of Nephrology & Hypertension, Saitama Medical Center, Kawagoe, Japan
| | - Takeshi Fujii
- Department of Pathology, Toranomon Hospital, Tokyo, Japan
| | - Yoshifumi Ubara
- Nephrology Center, Toranomon Hospital, Tokyo, Japan.,Okinaka Memorial Institute for Medical Sciences, Tokyo, Japan
| | - Kenmei Takaichi
- Nephrology Center, Toranomon Hospital, Tokyo, Japan.,Okinaka Memorial Institute for Medical Sciences, Tokyo, Japan
| | | | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Fuyuki Kametani
- Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Mayuko Nakagawa
- Institute for Biomedical Sciences, Shinshu University, Matsumoto, Japan.,Clinical Laboratory Sciences Division, Shinshu University Graduate of School of Medicine, Matsumoto, Japan
| | - Tsuneaki Yoshinaga
- Institute for Biomedical Sciences, Shinshu University, Matsumoto, Japan.,Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Matsumoto, Japan
| | - Yoshiki Sekijima
- Institute for Biomedical Sciences, Shinshu University, Matsumoto, Japan.,Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Matsumoto, Japan
| | - Keiichi Higuchi
- Institute for Biomedical Sciences, Shinshu University, Matsumoto, Japan.,Department of Aging Biology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Masahide Yazaki
- Institute for Biomedical Sciences, Shinshu University, Matsumoto, Japan.,Clinical Laboratory Sciences Division, Shinshu University Graduate of School of Medicine, Matsumoto, Japan
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8
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Ezaj MMA, Junaid M, Akter Y, Nahrin A, Siddika A, Afrose SS, Nayeem SMA, Haque MS, Moni MA, Hosen SMZ. Whole proteome screening and identification of potential epitopes of SARS-CoV-2 for vaccine design-an immunoinformatic, molecular docking and molecular dynamics simulation accelerated robust strategy. J Biomol Struct Dyn 2021; 40:6477-6502. [PMID: 33586620 DOI: 10.1080/07391102.2021.1886171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the most cryptic pandemic outbreak of the 21st century, has gripped more than 1.8 million people to death and infected almost eighty six million. As it is a new variant of SARS, there is no approved drug or vaccine available against this virus. This study aims to predict some promising cytotoxic T lymphocyte epitopes in the SARS-CoV-2 proteome utilizing immunoinformatic approaches. Firstly, we identified 21 epitopes from 7 different proteins of SARS-CoV-2 inducing immune response and checked for allergenicity and conservancy. Based on these factors, we selected the top three epitopes, namely KAYNVTQAF, ATSRTLSYY, and LTALRLCAY showing functional interactions with the maximum number of MHC alleles and no allergenicity. Secondly, the 3D model of selected epitopes and HLA-A*29:02 were built and Molecular Docking simulation was performed. Most interestingly, the best two epitopes predicted by docking are part of two different structural proteins of SARS-CoV-2, namely Membrane Glycoprotein (ATSRTLSYY) and Nucleocapsid Phosphoprotein (KAYNVTQAF), which are generally target of choice for vaccine designing. Upon Molecular Docking, interactions between selected epitopes and HLA-A*29:02 were further validated by 50 ns Molecular Dynamics (MD) simulation. Analysis of RMSD, Rg, SASA, number of hydrogen bonds, RMSF, MM-PBSA, PCA, and DCCM from MD suggested that ATSRTLSYY is the most stable and promising epitope than KAYNVTQAF epitope. Moreover, we also identified B-cell epitopes for each of the antigenic proteins of SARS CoV-2. Findings of our work will be a good resource for wet lab experiments and will lessen the timeline for vaccine construction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Muzahid Ahmed Ezaj
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.,Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh
| | - Md Junaid
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh
| | - Yeasmin Akter
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Biotechnology & Genetic Engineering, Noakhali Science & Technology University, Noakhali, Bangladesh
| | - Afsana Nahrin
- Department of Pharmacy, University of Science and Technology Chittagong, Chattogram, Bangladesh
| | - Aysha Siddika
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Syeda Samira Afrose
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - S M Abdul Nayeem
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Md Sajedul Haque
- Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - S M Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh.,Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for Applied Medical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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9
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Childers MC, Daggett V. Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions. Biophys J 2020; 119:1995-2009. [PMID: 33091379 DOI: 10.1016/j.bpj.2020.08.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/09/2020] [Accepted: 08/31/2020] [Indexed: 01/18/2023] Open
Abstract
During amyloidogenesis, proteins undergo conformational changes that allow them to aggregate and assemble into insoluble, fibrillar structures. Soluble oligomers that form during this process typically contain 2-24 monomeric subunits and are cytotoxic. Before the formation of these soluble oligomers, monomeric species first adopt aggregation-competent conformations. Knowledge of the structures of these intermediate states is invaluable to the development of molecular strategies to arrest pathological amyloid aggregation. However, the highly dynamic and interconverting nature of amyloidogenic species limits biophysical characterization of their structures during amyloidogenesis. Here, we use molecular dynamics simulations to probe conformations sampled by monomeric transthyretin under amyloidogenic conditions. We show that certain β-strands in transthyretin tend to unfold and sample nonnative conformations and that the edge strands in one β-sheet (the DAGH sheet) are particularly susceptible to conformational changes in the monomeric state. We also find that changes in the tertiary structure of transthyretin can be associated with disruptions to the secondary structure. We evaluated the conformations produced by molecular dynamics by calculating how well molecular-dynamics-derived structures reproduced NMR-derived interatomic distances. Finally, we leverage our computational results to produce experimentally testable hypotheses that may aid experimental explorations of pathological conformations of transthyretin.
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Affiliation(s)
- Matthew C Childers
- Department of Bioengineering, University of Washington, Seattle, Washington.
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, Washington
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10
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Loureiro RJS, Faísca PFN. The Early Phase of β2-Microglobulin Aggregation: Perspectives From Molecular Simulations. Front Mol Biosci 2020; 7:578433. [PMID: 33134317 PMCID: PMC7550760 DOI: 10.3389/fmolb.2020.578433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/08/2020] [Indexed: 11/24/2022] Open
Abstract
Protein β2-microglobulin is the causing agent of two amyloidosis, dialysis related amyloidosis (DRA), affecting the bones and cartilages of individuals with chronic renal failure undergoing long-term hemodialysis, and a systemic amyloidosis, found in one French family, which impairs visceral organs. The protein’s small size and its biomedical significance attracted the attention of theoretical scientists, and there are now several studies addressing its aggregation mechanism in the context of molecular simulations. Here, we review the early phase of β2-microglobulin aggregation, by focusing on the identification and structural characterization of monomers with the ability to trigger aggregation, and initial small oligomers (dimers, tetramers, hexamers etc.) formed in the so-called nucleation phase. We focus our analysis on results from molecular simulations and integrate our views with those coming from in vitro experiments to provide a broader perspective of this interesting field of research. We also outline directions for future computer simulation studies.
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Affiliation(s)
- Rui J S Loureiro
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Patrícia F N Faísca
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal.,Department of Physics, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
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11
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Kato K, Nakayoshi T, Sato M, Kurimoto E, Oda A. Molecular Dynamics Simulations for Three-Dimensional Structures of Orotate Phosphoribosyltransferases Constructed from a Simplified Amino Acid Set. ACS OMEGA 2020; 5:13069-13076. [PMID: 32548492 PMCID: PMC7288596 DOI: 10.1021/acsomega.0c01012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/19/2020] [Indexed: 05/08/2023]
Abstract
Proteins of modern terrestrial organisms are composed of nearly 20 amino acids; however, the amino acid sets of primitive organisms may have contained fewer than 20 amino acids. Furthermore, the full set of 20 amino acids is not required by some proteins to encode their function. Indeed, simplified variants of Escherichia coli (E. coli) orotate phosphoribosyltransferase (OPRTase) constructed by Akanuma et al. and composed of a limited amino acid set exhibit significant catalytic activity for the growth of E. coli. However, its structural details are currently unclear. Here, we predict the structures of simplified variants of OPRTase using molecular dynamics (MD) simulations and evaluate the accuracy of the MD simulations for simplified proteins. The three-dimensional structure of the wild-type was largely maintained in the simplified variants, but differences in the catalyst loop and C-terminal helix were observed. These results are considered sufficient to elucidate the differences in catalytic activity between the wild-type and simplified OPRTase variants. Thus, using MD simulations to make structural predictions appears to be a useful strategy when investigating non-wild-type proteins composed of reduced amino acid sets.
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Affiliation(s)
- Koichi Kato
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Department
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Tomoki Nakayoshi
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Mizuha Sato
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Eiji Kurimoto
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- .
Phone: +81-52-832-1151
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12
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Akın-Balı DF, Al-Khafaji K, Aktas SH, Taskin-Tok T. Bioinformatic and computational analysis for predominant mutations of the Nrf2/Keap1 complex in pediatric leukemia. J Biomol Struct Dyn 2020; 39:4290-4303. [PMID: 32469262 DOI: 10.1080/07391102.2020.1775702] [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] [Indexed: 12/19/2022]
Abstract
The levels of reactive oxygen species (ROS) are tightly controlled and regulated by Nuclear Factor Erythroid-2-Like 2 (Nrf2) transcription factor, which is the main regulator of antioxidant responses and its suppressor protein Kelch-like ECH-associated protein 1 (Keap1). Our previous study has identified six novel changes in Nrf2/Keap1 pathway in pediatric ALL, which were described for the first time. These changes in the pathway are likely to alter the evolutionary process of amino acids and cause structural changes in the final products of genes. In this study, we aimed to compare the pathogenicity of eight determined mutations reported in our previous study by utilizing different programs with different algorithms and molecular dynamics simulation. Since it is too difficult to handle each existing mutation in a wet laboratory, in silico methods may give suggestion to choose the important mutations for further analysis and to establish the appropriate patient population and conduct wet laboratory studies. For this purpose, four different algorithms were used to evaluate the effects of single amino acid mutation. In addition, root-mean-square deviation, root-mean-square fluctuation and free-energy landscape analyses were performed to observe stability, flexibility and energetically favorable conformations, respectively, for each amino acid mutation. As a result, our study emphasizes the importance of Keap1 mutations in pediatric ALL Nrf2/Keap1 pathway, a total of eight mutations, two of which were shown for the first time in our study. Especially the mutations in the Keap1 Broad-Complex, Tramtrack and Bric-à-brac domain are worthy of attention.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dilara Fatma Akın-Balı
- Faculty of Medicine, Department of Medical Biology, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
| | - Sedef Hande Aktas
- Vocational School of Health Services, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Tugba Taskin-Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey.,Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
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13
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Houndonougbo Y, Pugh B, VanWormer K, April C, Burgis N. Structural dynamics of inosine triphosphate pyrophosphatase (ITPA) protein and two clinically relevant mutants: molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:1236-1247. [PMID: 32129147 DOI: 10.1080/07391102.2020.1727363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The inosine triphosphate pyrophosphatase (ITPA) protein is responsible for removing noncanonical purine nucleoside triphosphates from intracellular nucleotide pools. Absence of ITPA results in genomic instability and increased levels of inosine in DNA and RNA. The proline to threonine substitution at position 32 (P32T) affects roughly 15% of the global population and can modulate treatment outcomes for cancer, lupus, and hepatitis C patients. The substitution of arginine with cysteine at position 178 (R178C) is extremely uncommon and has only been reported in a small cohort of early infantile encephalopathy patients suggesting that a functional ITPA protein is required for life in humans. Here we present molecular dynamic simulations that describe the structure and dynamics of the wild-type ITPA homodimer and two of its clinically relevant mutants, P32T and R178C. The simulation results indicate that both the P32T and R178C mutations alter the structure and dynamic properties of the protein and provide a possible explanation of the experimentally observed effect of the mutations on ITPA activity. Specifically, the mutations increased the overall flexibility of the protein and changed the dominant collective motions of the top lobe as well as the helix 2 of the lower lobe. Moreover, we have identified key active-site residues that are classified as essential or intermediate for inosine triphosphate (ITP) hydrolyzing activity based on their hydrogen bond occupancy. Here we also present biochemical data indicating that the R178C mutant has very low ITP hydrolyzing activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yao Houndonougbo
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Bethany Pugh
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Kandise VanWormer
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Caitlin April
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Nicholas Burgis
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
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14
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Lin B, Zhang H, Zheng Q. How do mutations affect the structural characteristics and substrate binding of CYP21A2? An investigation by molecular dynamics simulations. Phys Chem Chem Phys 2020; 22:8870-8877. [DOI: 10.1039/d0cp00763c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
CYP21A2 mutations affect the activity of the protein leading to CAH disease.
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Affiliation(s)
- Baihui Lin
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
| | - Hongxing Zhang
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
| | - Qingchuan Zheng
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
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15
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J S Loureiro R, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, F N Faísca P. The Early Phase of β2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ΔN6 Variant. Biomolecules 2019; 9:biom9080366. [PMID: 31416179 PMCID: PMC6722664 DOI: 10.3390/biom9080366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 08/08/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
Human β2-microglobulin (b2m) protein is classically associated with dialysis-related amyloidosis (DRA). Recently, the single point mutant D76N was identified as the causative agent of a hereditary systemic amyloidosis affecting visceral organs. To get insight into the early stage of the β2m aggregation mechanism, we used molecular simulations to perform an in depth comparative analysis of the dimerization phase of the D76N mutant and the ΔN6 variant, a cleaved form lacking the first six N-terminal residues, which is a major component of ex vivo amyloid plaques from DRA patients. We also provide first glimpses into the tetramerization phase of D76N at physiological pH. Results from extensive protein–protein docking simulations predict an essential role of the C- and N-terminal regions (both variants), as well as of the BC-loop (ΔN6 variant), DE-loop (both variants) and EF-loop (D76N mutant) in dimerization. The terminal regions are more relevant under acidic conditions while the BC-, DE- and EF-loops gain importance at physiological pH. Our results recapitulate experimental evidence according to which Tyr10 (A-strand), Phe30 and His31 (BC-loop), Trp60 and Phe62 (DE-loop) and Arg97 (C-terminus) act as dimerization hot-spots, and further predict the occurrence of novel residues with the ability to nucleate dimerization, namely Lys-75 (EF-loop) and Trp-95 (C-terminus). We propose that D76N tetramerization is mainly driven by the self-association of dimers via the N-terminus and DE-loop, and identify Arg3 (N-terminus), Tyr10, Phe56 (D-strand) and Trp60 as potential tetramerization hot-spots.
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Affiliation(s)
- Rui J S Loureiro
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Patrícia F N Faísca
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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16
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Liu WS, Wang RR, Li WY, Rong M, Liu CL, Ma Y, Wang RL. Investigating the reason for loss-of-function of Src homology 2 domain-containing protein tyrosine phosphatase 2 (SHP2) caused by Y279C mutation through molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:2509-2520. [DOI: 10.1080/07391102.2019.1634641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Wen-Shan Liu
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Mei Rong
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Chi-Lu Liu
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Ying Ma
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
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17
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Niu RJ, Zheng QC, Zhang HX. Molecular dynamics simulations study of influence of Tyr422Ala mutation on transcriptional enhancer activation domain 4 (TEAD4) and transcription co-activators complexes. J Theor Biol 2019; 472:27-35. [DOI: 10.1016/j.jtbi.2019.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/28/2019] [Accepted: 04/09/2019] [Indexed: 01/08/2023]
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18
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Dongmo Foumthuim CJ, Corazza A, Esposito G, Fogolari F. Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces. MOLECULAR BIOSYSTEMS 2018; 13:2625-2637. [PMID: 29051937 DOI: 10.1039/c7mb00464h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Most proteins adsorb on the walls of the box without major distortions in local geometry, whereas free molecules maintain proper structures and fluctuations as observed in explicit solvent molecular dynamics simulations. The major conclusions from the simulations are as follows: (i) the adopted implicit solvent model is adequate to describe protein dynamics and thermodynamics; (ii) adsorption occurs readily and is irreversible on the simulated timescale; (iii) the regions most involved in molecular encounters and stable interactions with the walls are the same as those that are important in protein-protein and protein-nanoparticle interactions; (iv) unfolding following adsorption occurs at regions found to be flexible by both experiments and simulations; (v) thermodynamic analysis suggests a very large contribution from van der Waals interactions, whereas unfavorable electrostatic interactions are not found to contribute much to adsorption energy. Surfaces with different degrees of hydrophobicity may occur in vivo. Our simulations show that adsorption is a fast and irreversible process which is accompanied by partial unfolding. The results and the thermodynamic analysis presented here are consistent with and rationalize previous experimental work.
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19
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Zhan JY, Ma K, Zheng QC, Yang GH, Zhang HX. Exploring the interactional details between aldose reductase (AKR1B1) and 3-Mercapto-5H-1,2,4-triazino[5,6-b]indole-5-acetic acid through molecular dynamics simulations. J Biomol Struct Dyn 2018; 37:1724-1735. [PMID: 29671687 DOI: 10.1080/07391102.2018.1465851] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aldose reductase (AKR1B1) has been considered as a significant target for designing drugs to counteract the development of diabetic complications. In the present study, molecular dynamics (MD) simulations and molecular mechanics generalized Born surface area (MM-GB/SA) calculations were performed to make sure which tautomer is the preferred one among three tautomeric forms (Mtia1, Mtia2, and Mtia3) of 3-Mercapto-5H-1,2,4-triazino[5,6-b]indole-5-acetic acid (Mtia) for binding to AKR1B1. The overall structural features and the results of calculated binding free energies indicate that Mtia1 and Mtia2 have more superiority than Mtia3 in terms of binding to AKR1B1. Furtherly, the local active site conformational characteristics and non-covalent interaction analysis were identified. The results indicate that the combination of Mtia2 and AKR1B1 is more stable than that of Mtia1. Furthermore, two extra hydrogen bonds between AKR1B1 and Mtia2 are found with respect to Mtia1. In addition, Mtia2 makes slightly stronger electrostatic interaction with the positively charged nicotinamide group of NADP+ than Mtia1. Based on the results above, Mtia2 is the preferred tautomeric form among the three tautomers. Our study can provide an insight into the details of the interaction between AKR1B1 and Mtia at the atomic level, and will be helpful for the further design of AKR1B1 inhibitors.
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Key Words
- AKR1B1, Aldose Reductase
- ARI, aldose reductase inhibitor
- FEL, free energy landscape
- MD, molecular dynamics
- MM-GB/SA calculation
- MM-GB/SA, molecular mechanics generalized Born surface area
- Mtia, 3-Mercapto-5H-1,2,4-triazino[5,6-b]indole-5-acetic acid
- PCA, principal component analysis
- Three AKR1B1-Mtia complex systems: AKR1B1-Mtia1, AKR1B1-Mtia2, and AKR1B1-Mtia3
- Three tautomeric forms of Mtia: Mtia1, Mtia2, and Mtia3
- aldose reductase
- inhibitor
- molecular dynamics
- tautomer
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Affiliation(s)
- Jiu-Yu Zhan
- b International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Ke Ma
- c Department of Pediatric Outpatient , The First Hospital of Jilin University , Changchun 130021 , People's Republic of China
| | - Qing-Chuan Zheng
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education , Jilin University , Changchun 130023 , People's Republic of China.,b International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Guang-Hui Yang
- d Jilin Provincial Institute of Education , Changchun 130022 , People's Republic of China
| | - Hong-Xing Zhang
- b International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
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20
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Cheng B, Li Y, Ma L, Wang Z, Petersen RB, Zheng L, Chen Y, Huang K. Interaction between amyloidogenic proteins and biomembranes in protein misfolding diseases: Mechanisms, contributors, and therapy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1876-1888. [PMID: 29466701 DOI: 10.1016/j.bbamem.2018.02.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 12/14/2022]
Abstract
The toxic deposition of misfolded amyloidogenic proteins is associated with more than fifty protein misfolding diseases (PMDs), including Alzheimer's disease, Parkinson's disease and type 2 diabetes mellitus. Protein deposition is a multi-step process modulated by a variety of factors, in particular by membrane-protein interaction. The interaction results in permeabilization of biomembranes contributing to the cytotoxicity that leads to PMDs. Different biological and physiochemical factors, such as protein sequence, lipid composition, and chaperones, are known to affect the membrane-protein interaction. Here, we provide a comprehensive review of the mechanisms and contributing factors of the interaction between biomembranes and amyloidogenic proteins, and a summary of the therapeutic approaches to PMDs that target this interaction. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Biao Cheng
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430023, China; Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430023, China
| | - Yang Li
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liang Ma
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhuoyi Wang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mt. Pleasant, MI 48858, USA
| | - Ling Zheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan 430072, China
| | - Yuchen Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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